From e582c72d8d2c93e9240ffff6ab309421c34e1e82 Mon Sep 17 00:00:00 2001 From: Asaf Levi Date: Thu, 9 Mar 2023 18:42:05 +0200 Subject: [PATCH 01/25] health insights sdk for java --- .vscode/cspell.json | 3 + .../CHANGELOG.md | 13 + .../README.md | 131 + .../package.json | 5 + .../pom.xml | 110 + .../AzureHealthInsightsServiceVersion.java | 34 + .../CancerProfilingAsyncClient.java | 185 + .../CancerProfilingClient.java | 182 + .../CancerProfilingClientBuilder.java | 290 + .../CancerProfilingClientImpl.java | 839 + .../implementation/package-info.java | 10 + .../models/ClinicalCodedElement.java | 109 + .../models/ClinicalDocumentType.java | 64 + .../models/ClinicalNoteEvidence.java | 90 + .../models/DocumentContent.java | 60 + .../models/DocumentContentSourceType.java | 49 + .../cancerprofiling/models/DocumentType.java | 52 + .../models/InferenceEvidence.java | 62 + .../cancerprofiling/models/JobStatus.java | 55 + .../models/OncoPhenotypeData.java | 65 + .../models/OncoPhenotypeInference.java | 119 + .../models/OncoPhenotypeInferenceType.java | 64 + .../OncoPhenotypeModelConfiguration.java | 131 + .../models/OncoPhenotypePatientResult.java | 58 + .../models/OncoPhenotypeResult.java | 123 + .../models/OncoPhenotypeResults.java | 58 + .../models/PatientDocument.java | 156 + .../cancerprofiling/models/PatientInfo.java | 95 + .../models/PatientInfoSex.java | 49 + .../cancerprofiling/models/PatientRecord.java | 94 + .../cancerprofiling/models/package-info.java | 9 + .../cancerprofiling/package-info.java | 9 + .../src/main/java/module-info.java | 14 + ...health-insights-cancerprofiling.properties | 2 + .../src/samples/README.md | 57 + .../SampleInferCancerProfile.java | 172 + .../insights/cancerprofiling/AllSamples.java | 25 + .../CancerProfilingClientTest.java | 56 + .../CancerProfilingClientTestBase.java | 70 + .../CancerProfilingClientTest.request.json | 25 + .../CancerProfilingClientTest.test.json | 79 + .../tests.yml | 10 + .../CHANGELOG.md | 13 + .../README.md | 139 + .../package.json | 5 + .../pom.xml | 110 + .../AzureHealthInsightsServiceVersion.java | 34 + .../ClinicalMatchingAsyncClient.java | 319 + .../ClinicalMatchingClient.java | 317 + .../ClinicalMatchingClientBuilder.java | 290 + .../ClinicalMatchingClientImpl.java | 1519 + .../implementation/package-info.java | 10 + .../clinicalmatching/models/AcceptedAge.java | 57 + .../models/AcceptedAgeRange.java | 67 + .../clinicalmatching/models/AgeUnit.java | 49 + .../clinicalmatching/models/AreaGeometry.java | 60 + .../models/AreaProperties.java | 57 + .../models/ClinicalCodedElement.java | 109 + .../models/ClinicalDocumentType.java | 64 + .../models/ClinicalNoteEvidence.java | 90 + .../models/ClinicalTrialAcceptedSex.java | 52 + .../models/ClinicalTrialDemographics.java | 69 + .../models/ClinicalTrialDetails.java | 112 + .../models/ClinicalTrialMetadata.java | 201 + .../models/ClinicalTrialPhase.java | 58 + .../models/ClinicalTrialPurpose.java | 70 + .../ClinicalTrialRecruitmentStatus.java | 52 + .../models/ClinicalTrialRegistryFilter.java | 353 + .../models/ClinicalTrialResearchFacility.java | 109 + .../models/ClinicalTrialSource.java | 46 + .../models/ClinicalTrialStudyType.java | 52 + .../models/ClinicalTrials.java | 75 + .../models/ContactDetails.java | 93 + .../models/DocumentContent.java | 60 + .../models/DocumentContentSourceType.java | 49 + .../clinicalmatching/models/DocumentType.java | 52 + .../models/ExtendedClinicalCodedElement.java | 122 + .../models/GeoJsonGeometryType.java | 43 + .../models/GeoJsonPropertiesSubType.java | 43 + .../clinicalmatching/models/GeoJsonType.java | 43 + .../models/GeographicArea.java | 78 + .../models/GeographicLocation.java | 94 + .../clinicalmatching/models/JobStatus.java | 55 + .../models/PatientDocument.java | 156 + .../clinicalmatching/models/PatientInfo.java | 95 + .../models/PatientInfoSex.java | 49 + .../models/PatientRecord.java | 94 + .../models/TrialMatcherData.java | 65 + .../models/TrialMatcherInference.java | 148 + .../models/TrialMatcherInferenceEvidence.java | 78 + .../models/TrialMatcherInferenceType.java | 43 + .../TrialMatcherModelConfiguration.java | 98 + .../models/TrialMatcherPatientResult.java | 74 + .../models/TrialMatcherResult.java | 123 + .../models/TrialMatcherResults.java | 75 + .../clinicalmatching/models/package-info.java | 9 + .../clinicalmatching/package-info.java | 9 + .../src/main/java/module-info.java | 14 + ...ealth-insights-clinicalmatching.properties | 2 + .../src/samples/README.md | 68 + .../SampleMatchTrialAsync.java | 117 + .../insights/clinicalmatching/AllSamples.java | 51 + .../ClinicalMatchingClientTest.java | 58 + .../ClinicalMatchingClientTestBase.java | 70 + .../Sample_MatchTrial_PatientFhir.json | 37509 ++++++++++++++++ .../ClinicalMatchingClientTest.request.json | 50 + .../ClinicalMatchingClientTest.test.json | 79 + .../tests.yml | 10 + sdk/healthinsights/ci.yml | 43 + sdk/healthinsights/pom.xml | 14 + 110 files 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sdk/healthinsights/azure-health-insights-clinicalmatching/src/test/resources/session-records/ClinicalMatchingClientTest.test.json create mode 100644 sdk/healthinsights/azure-health-insights-clinicalmatching/tests.yml create mode 100644 sdk/healthinsights/ci.yml create mode 100644 sdk/healthinsights/pom.xml diff --git a/.vscode/cspell.json b/.vscode/cspell.json index 95f7cdb4d5e24..479374dd3a044 100644 --- a/.vscode/cspell.json +++ b/.vscode/cspell.json @@ -245,6 +245,7 @@ "Deserialization", "destfile", "Dgenerate", + "dicom", "doclint", "doclinting", "doctitle", @@ -258,6 +259,7 @@ "eventhub", "eventhubs", "failondeprecatedstatus", + "FHIR", "filereports", "gapra", "gltf", @@ -311,6 +313,7 @@ "okhttp", "OLTP", "onboarded", + "Onco", "onenote", "pwsh", "protonj", diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/CHANGELOG.md b/sdk/healthinsights/azure-health-insights-cancerprofiling/CHANGELOG.md new file mode 100644 index 0000000000000..f887f194c985e --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/CHANGELOG.md @@ -0,0 +1,13 @@ +# Release History + +## 1.0.0-beta.1 (Unreleased) + +- Azure AzureHealthInsights client library for Java. This package contains Microsoft Azure AzureHealthInsights client library. + +### Features Added + +### Breaking Changes + +### Bugs Fixed + +### Other Changes diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md b/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md new file mode 100644 index 0000000000000..50860f2469044 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md @@ -0,0 +1,131 @@ +# Azure Azure Health Insights Cancer Profiling client library for Java + + +## Getting started + +### Prerequisites + +- A [Java Development Kit (JDK)][jdk] with version 8 or above +- [Azure Subscription][azure_subscription] +- An existing Cognitive Services Health Insights instance. + +For more information about creating the resource or how to get the location and sku information see [here][cognitive_resource_cli]. + +### Include the Package + +[//]: # ({x-version-update-start;com.azure:azure-health-insights-cancerprofiling;current}) + +```xml + + com.azure + azure-health-insights-cancerprofiling + 1.0.0-beta.1 + +``` + +[//]: # ({x-version-update-end}) + +### Authenticate the client + +In order to interact with the Health Insighs Cancer Profiling service, you'll need to create an instance of the [`CancerProfilingClient`][cancer_profiling_client_class] class. You will need an **endpoint** and an **API key** to instantiate a client object. + +#### Get API Key + +You can obtain the endpoint and API key from the resource information in the [Azure Portal][azure_portal]. + +Alternatively, you can use the [Azure CLI][azure_cli] snippet below to get the API key from the Health Insights resource. + +```bash +az cognitiveservices account keys list --resource-group --name +``` + +#### Create a CancerProfilingClient with an API Key Credential + +Once you have the value for the API key, you can pass it as a string into an instance of **AzureKeyCredential**. Use the key as the credential parameter +to authenticate the client: + +```Java Snippet: +String endpoint = "endpoint"; +String apiKey = "apiKey"; +OncoPhenotypeAsyncClient asyncClient = new CancerProfilingClientBuilder() + .endpoint(endpoint) + .serviceVersion(AzureHealthInsightsServiceVersion.getLatest()) + .credential(new AzureKeyCredential(apiKey)) + .buildAsyncClient(); +``` + +## Key concepts + +The Cancer Profiling model allows you to infer cancer attributes such as tumor site, histology, clinical stage TNM categories and pathologic stage TNM categories from unstructured clinical documents. + +## Examples + +Infer key cancer attributes such as tumor site, histology, clinical stage TNM categories and pathologic stage TNM categories from a patient's unstructured clinical documents. + + +```Java readme-sample-InferCancerProfile +CancerProfilingAsyncClient asyncClient = new CancerProfilingClientBuilder() + .endpoint(endpoint) + .serviceVersion(AzureHealthInsightsServiceVersion.getLatest()) + .credential(new AzureKeyCredential(apiKey)) + .buildAsyncClient(); + + PollerFlux asyncPoller = asyncClient.beginInferCancerProfile(oncoPhenotypeData); + OncoPhenotypeResult result = asyncPoller.blockLast().getValue(); + + OncoPhenotypeResults oncoResults = result.getResults(); + oncoResults.getPatients().forEach(patient_result -> { + System.out.println("\n==== Inferences of Patient " + patient_result.getId() + " ===="); + patient_result.getInferences().forEach(onco_inference -> { + System.out.println("\n=== Clinical Type: " + onco_inference.getType() + " Value: " + onco_inference.getValue() + " ConfidenceScore: " + onco_inference.getConfidenceScore() + " ==="); + onco_inference.getEvidence().forEach(evidence -> { + if (evidence.getPatientDataEvidence() != null) { + ClinicalNoteEvidence dataEvidence = evidence.getPatientDataEvidence(); + System.out.println("Evidence " + dataEvidence.getId() + " " + dataEvidence.getOffset() + " " + dataEvidence.getLength() + " " + dataEvidence.getText()); + } + if (evidence.getPatientInfoEvidence() != null) { + ClinicalCodedElement infoEvidence = evidence.getPatientInfoEvidence(); + System.out.println("Evidence " + infoEvidence.getSystem() + " " + infoEvidence.getCode() + " " + infoEvidence.getName() + " " + infoEvidence.getValue()); + } + }); + }); + }); + + +``` + +## Troubleshooting + +## Next steps + +### Additional documentation + +## Contributing + +This project welcomes contributions and suggestions. Most contributions require you to agree to a Contributor License Agreement (CLA) declaring that you have the right to, and actually do, grant us the rights to use your contribution. For details, visit [cla.microsoft.com][cla]. + +When you submit a pull request, a CLA-bot will automatically determine whether you need to provide a CLA and decorate the PR appropriately (e.g., label, comment). Simply follow the instructions provided by the bot. You will only need to do this once across all repos using our CLA. + +This project has adopted the [Microsoft Open Source Code of Conduct][code_of_conduct]. For more information see the [Code of Conduct FAQ][coc_faq] or contact [opencode@microsoft.com][coc_contact] with any additional questions or comments. + + +[cla]: https://cla.microsoft.com +[code_of_conduct]: https://opensource.microsoft.com/codeofconduct/ +[coc_faq]: https://opensource.microsoft.com/codeofconduct/faq/ +[coc_contact]: mailto:opencode@microsoft.com +[azure_subscription]: https://azure.microsoft.com/free/ +[cognitive_resource_cli]: https://docs.microsoft.com/azure/cognitive-services/cognitive-services-apis-create-account-cli + +[azure_cli]: https://docs.microsoft.com/cli/azure +[azure_portal]: https://portal.azure.com diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/package.json b/sdk/healthinsights/azure-health-insights-cancerprofiling/package.json new file mode 100644 index 0000000000000..ded9535dc3f1e --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/package.json @@ -0,0 +1,5 @@ +{ + "dependencies": { + "mvn": "^3.5.0" + } +} diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/pom.xml b/sdk/healthinsights/azure-health-insights-cancerprofiling/pom.xml new file mode 100644 index 0000000000000..a45d54e44757e --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/pom.xml @@ -0,0 +1,110 @@ + + + 4.0.0 + + com.azure + azure-client-sdk-parent + 1.7.0 + ../../parents/azure-client-sdk-parent + + + com.azure + azure-health-insights-cancerprofiling + 1.0.0-beta.1 + jar + + Microsoft Azure SDK for HealthInsights Management + This package contains Microsoft Azure HealthInsights client library. + https://github.com/Azure/azure-sdk-for-java + + + + The MIT License (MIT) + http://opensource.org/licenses/MIT + repo + + + + + https://github.com/Azure/azure-sdk-for-java + scm:git:git@github.com:Azure/azure-sdk-for-java.git + scm:git:git@github.com:Azure/azure-sdk-for-java.git + HEAD + + + + microsoft + Microsoft + + + + UTF-8 + true + + + + com.azure + azure-core + 1.35.0 + + + com.azure + azure-core-http-netty + 1.12.8 + + + org.junit.jupiter + junit-jupiter-api + 5.9.1 + test + + + org.junit.jupiter + junit-jupiter-engine + 5.9.1 + test + + + org.mockito + mockito-core + 4.5.1 + test + + + com.azure + azure-core-test + 1.14.0 + test + + + com.azure + azure-identity + 1.7.3 + test + + + + + + + com.azure.tools + codesnippet-maven-plugin + 1.0.0-beta.8 + + **/src/samples/java/**/*.java + ${project.basedir}/src/samples/java + **/src/main/java/**/*.java + ${project.basedir}/src/main/java + true + ${project.basedir}/README.md + true + 120 + false + + + + + diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/AzureHealthInsightsServiceVersion.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/AzureHealthInsightsServiceVersion.java new file mode 100644 index 0000000000000..e2d51c4e1ca63 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/AzureHealthInsightsServiceVersion.java @@ -0,0 +1,34 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.cancerprofiling; + +import com.azure.core.util.ServiceVersion; + +/** Service version of CancerProfilingClient. */ +public enum AzureHealthInsightsServiceVersion implements ServiceVersion { + /** Enum value 2023-03-01-preview. */ + V2023_03_01_PREVIEW("2023-03-01-preview"); + + private final String version; + + AzureHealthInsightsServiceVersion(String version) { + this.version = version; + } + + /** {@inheritDoc} */ + @Override + public String getVersion() { + return this.version; + } + + /** + * Gets the latest service version supported by this client library. + * + * @return The latest {@link AzureHealthInsightsServiceVersion}. + */ + public static AzureHealthInsightsServiceVersion getLatest() { + return V2023_03_01_PREVIEW; + } +} diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/CancerProfilingAsyncClient.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/CancerProfilingAsyncClient.java new file mode 100644 index 0000000000000..fff32b4684280 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/CancerProfilingAsyncClient.java @@ -0,0 +1,185 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.cancerprofiling; + +import com.azure.core.annotation.Generated; +import com.azure.core.annotation.ReturnType; +import com.azure.core.annotation.ServiceClient; +import com.azure.core.annotation.ServiceMethod; +import com.azure.core.exception.ClientAuthenticationException; +import com.azure.core.exception.HttpResponseException; +import com.azure.core.exception.ResourceModifiedException; +import com.azure.core.exception.ResourceNotFoundException; +import com.azure.core.http.rest.RequestOptions; +import com.azure.core.util.BinaryData; +import com.azure.core.util.polling.PollerFlux; +import com.azure.health.insights.cancerprofiling.implementation.CancerProfilingClientImpl; +import com.azure.health.insights.cancerprofiling.models.OncoPhenotypeData; +import com.azure.health.insights.cancerprofiling.models.OncoPhenotypeResult; + +/** Initializes a new instance of the asynchronous CancerProfilingClient type. */ +@ServiceClient(builder = CancerProfilingClientBuilder.class, isAsync = true) +public final class CancerProfilingAsyncClient { + @Generated private final CancerProfilingClientImpl serviceClient; + + /** + * Initializes an instance of CancerProfilingAsyncClient class. + * + * @param serviceClient the service client implementation. + */ + @Generated + CancerProfilingAsyncClient(CancerProfilingClientImpl serviceClient) { + this.serviceClient = serviceClient; + } + + /** + * Create Onco Phenotype job + * + *

Creates an Onco Phenotype job with the given request body. + * + *

Header Parameters + * + * + * + * + * + * + *
Header Parameters
NameTypeRequiredDescription
repeatability-request-idStringNoRepeatability request ID header
repeatability-first-sentStringNoRepeatability first sent header as HTTP-date
+ * + * You can add these to a request with {@link RequestOptions#addHeader} + * + *

Request Body Schema + * + * 

{@code
+     * {
+     *     patients (Required): [
+     *          (Required){
+     *             id: String (Required)
+     *             info (Optional): {
+     *                 sex: String(female/male/unspecified) (Optional)
+     *                 birthDate: LocalDate (Optional)
+     *                 clinicalInfo (Optional): [
+     *                      (Optional){
+     *                         system: String (Required)
+     *                         code: String (Required)
+     *                         name: String (Optional)
+     *                         value: String (Optional)
+     *                     }
+     *                 ]
+     *             }
+     *             data (Optional): [
+     *                  (Optional){
+     *                     type: String(note/fhirBundle/dicom/genomicSequencing) (Required)
+     *                     clinicalType: String(consultation/dischargeSummary/historyAndPhysical/procedure/progress/imaging/laboratory/pathology) (Optional)
+     *                     id: String (Required)
+     *                     language: String (Optional)
+     *                     createdDateTime: OffsetDateTime (Optional)
+     *                     content (Required): {
+     *                         sourceType: String(inline/reference) (Required)
+     *                         value: String (Required)
+     *                     }
+     *                 }
+     *             ]
+     *         }
+     *     ]
+     *     configuration (Optional): {
+     *         verbose: Boolean (Optional)
+     *         includeEvidence: Boolean (Optional)
+     *         inferenceTypes (Optional): [
+     *             String(tumorSite/histology/clinicalStageT/clinicalStageN/clinicalStageM/pathologicStageT/pathologicStageN/pathologicStageM) (Optional)
+     *         ]
+     *         checkForCancerCase: Boolean (Optional)
+     *     }
+     * }
+     * }
+ * + *

Response Body Schema + * + * 

{@code
+     * {
+     *     jobId: String (Required)
+     *     createdDateTime: OffsetDateTime (Required)
+     *     expirationDateTime: OffsetDateTime (Required)
+     *     lastUpdateDateTime: OffsetDateTime (Required)
+     *     status: String(notStarted/running/succeeded/failed/partiallyCompleted) (Required)
+     *     errors (Optional): [
+     *         ResponseError (Optional)
+     *     ]
+     *     results (Optional): {
+     *         patients (Required): [
+     *              (Required){
+     *                 id: String (Required)
+     *                 inferences (Required): [
+     *                      (Required){
+     *                         type: String(tumorSite/histology/clinicalStageT/clinicalStageN/clinicalStageM/pathologicStageT/pathologicStageN/pathologicStageM) (Required)
+     *                         value: String (Required)
+     *                         description: String (Optional)
+     *                         confidenceScore: Double (Optional)
+     *                         evidence (Optional): [
+     *                              (Optional){
+     *                                 patientDataEvidence (Optional): {
+     *                                     id: String (Required)
+     *                                     text: String (Optional)
+     *                                     offset: int (Required)
+     *                                     length: int (Required)
+     *                                 }
+     *                                 patientInfoEvidence (Optional): {
+     *                                     system: String (Required)
+     *                                     code: String (Required)
+     *                                     name: String (Optional)
+     *                                     value: String (Optional)
+     *                                 }
+     *                                 importance: Double (Optional)
+     *                             }
+     *                         ]
+     *                         caseId: String (Optional)
+     *                     }
+     *                 ]
+     *             }
+     *         ]
+     *         modelVersion: String (Required)
+     *     }
+     * }
+     * }
+ * + * @param oncoPhenotypeData The body of the Onco Phenotype request. + * @param requestOptions The options to configure the HTTP request before HTTP client sends it. + * @throws HttpResponseException thrown if the request is rejected by server. + * @throws ClientAuthenticationException thrown if the request is rejected by server on status code 401. + * @throws ResourceNotFoundException thrown if the request is rejected by server on status code 404. + * @throws ResourceModifiedException thrown if the request is rejected by server on status code 409. + * @return the {@link PollerFlux} for polling of the response for the Onco Phenotype request. + */ + @Generated + @ServiceMethod(returns = ReturnType.LONG_RUNNING_OPERATION) + public PollerFlux beginInferCancerProfile( + BinaryData oncoPhenotypeData, RequestOptions requestOptions) { + return this.serviceClient.beginInferCancerProfileAsync(oncoPhenotypeData, requestOptions); + } + + /** + * Create Onco Phenotype job + * + *

Creates an Onco Phenotype job with the given request body. + * + * @param oncoPhenotypeData The body of the Onco Phenotype request. + * @throws IllegalArgumentException thrown if parameters fail the validation. + * @throws com.azure.core.exception.HttpResponseException thrown if the request is rejected by server. + * @throws ClientAuthenticationException thrown if the request is rejected by server on status code 401. + * @throws ResourceNotFoundException thrown if the request is rejected by server on status code 404. + * @throws ResourceModifiedException thrown if the request is rejected by server on status code 409. + * @throws RuntimeException all other wrapped checked exceptions if the request fails to be sent. + * @return the {@link PollerFlux} for polling of the response for the Onco Phenotype request. + */ + @Generated + @ServiceMethod(returns = ReturnType.LONG_RUNNING_OPERATION) + public PollerFlux beginInferCancerProfile( + OncoPhenotypeData oncoPhenotypeData) { + // Generated convenience method for beginInferCancerProfileWithModel + RequestOptions requestOptions = new RequestOptions(); + return serviceClient.beginInferCancerProfileWithModelAsync( + BinaryData.fromObject(oncoPhenotypeData), requestOptions); + } +} diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/CancerProfilingClient.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/CancerProfilingClient.java new file mode 100644 index 0000000000000..743850249f012 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/CancerProfilingClient.java @@ -0,0 +1,182 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.cancerprofiling; + +import com.azure.core.annotation.Generated; +import com.azure.core.annotation.ReturnType; +import com.azure.core.annotation.ServiceClient; +import com.azure.core.annotation.ServiceMethod; +import com.azure.core.exception.ClientAuthenticationException; +import com.azure.core.exception.HttpResponseException; +import com.azure.core.exception.ResourceModifiedException; +import com.azure.core.exception.ResourceNotFoundException; +import com.azure.core.http.rest.RequestOptions; +import com.azure.core.util.BinaryData; +import com.azure.core.util.polling.SyncPoller; +import com.azure.health.insights.cancerprofiling.models.OncoPhenotypeData; +import com.azure.health.insights.cancerprofiling.models.OncoPhenotypeResult; + +/** Initializes a new instance of the synchronous CancerProfilingClient type. */ +@ServiceClient(builder = CancerProfilingClientBuilder.class) +public final class CancerProfilingClient { + @Generated private final CancerProfilingAsyncClient client; + + /** + * Initializes an instance of CancerProfilingClient class. + * + * @param client the async client. + */ + @Generated + CancerProfilingClient(CancerProfilingAsyncClient client) { + this.client = client; + } + + /** + * Create Onco Phenotype job + * + *

Creates an Onco Phenotype job with the given request body. + * + *

Header Parameters + * + * + * + * + * + * + *
Header Parameters
NameTypeRequiredDescription
repeatability-request-idStringNoRepeatability request ID header
repeatability-first-sentStringNoRepeatability first sent header as HTTP-date
+ * + * You can add these to a request with {@link RequestOptions#addHeader} + * + *

Request Body Schema + * + * 

{@code
+     * {
+     *     patients (Required): [
+     *          (Required){
+     *             id: String (Required)
+     *             info (Optional): {
+     *                 sex: String(female/male/unspecified) (Optional)
+     *                 birthDate: LocalDate (Optional)
+     *                 clinicalInfo (Optional): [
+     *                      (Optional){
+     *                         system: String (Required)
+     *                         code: String (Required)
+     *                         name: String (Optional)
+     *                         value: String (Optional)
+     *                     }
+     *                 ]
+     *             }
+     *             data (Optional): [
+     *                  (Optional){
+     *                     type: String(note/fhirBundle/dicom/genomicSequencing) (Required)
+     *                     clinicalType: String(consultation/dischargeSummary/historyAndPhysical/procedure/progress/imaging/laboratory/pathology) (Optional)
+     *                     id: String (Required)
+     *                     language: String (Optional)
+     *                     createdDateTime: OffsetDateTime (Optional)
+     *                     content (Required): {
+     *                         sourceType: String(inline/reference) (Required)
+     *                         value: String (Required)
+     *                     }
+     *                 }
+     *             ]
+     *         }
+     *     ]
+     *     configuration (Optional): {
+     *         verbose: Boolean (Optional)
+     *         includeEvidence: Boolean (Optional)
+     *         inferenceTypes (Optional): [
+     *             String(tumorSite/histology/clinicalStageT/clinicalStageN/clinicalStageM/pathologicStageT/pathologicStageN/pathologicStageM) (Optional)
+     *         ]
+     *         checkForCancerCase: Boolean (Optional)
+     *     }
+     * }
+     * }
+ * + *

Response Body Schema + * + * 

{@code
+     * {
+     *     jobId: String (Required)
+     *     createdDateTime: OffsetDateTime (Required)
+     *     expirationDateTime: OffsetDateTime (Required)
+     *     lastUpdateDateTime: OffsetDateTime (Required)
+     *     status: String(notStarted/running/succeeded/failed/partiallyCompleted) (Required)
+     *     errors (Optional): [
+     *         ResponseError (Optional)
+     *     ]
+     *     results (Optional): {
+     *         patients (Required): [
+     *              (Required){
+     *                 id: String (Required)
+     *                 inferences (Required): [
+     *                      (Required){
+     *                         type: String(tumorSite/histology/clinicalStageT/clinicalStageN/clinicalStageM/pathologicStageT/pathologicStageN/pathologicStageM) (Required)
+     *                         value: String (Required)
+     *                         description: String (Optional)
+     *                         confidenceScore: Double (Optional)
+     *                         evidence (Optional): [
+     *                              (Optional){
+     *                                 patientDataEvidence (Optional): {
+     *                                     id: String (Required)
+     *                                     text: String (Optional)
+     *                                     offset: int (Required)
+     *                                     length: int (Required)
+     *                                 }
+     *                                 patientInfoEvidence (Optional): {
+     *                                     system: String (Required)
+     *                                     code: String (Required)
+     *                                     name: String (Optional)
+     *                                     value: String (Optional)
+     *                                 }
+     *                                 importance: Double (Optional)
+     *                             }
+     *                         ]
+     *                         caseId: String (Optional)
+     *                     }
+     *                 ]
+     *             }
+     *         ]
+     *         modelVersion: String (Required)
+     *     }
+     * }
+     * }
+ * + * @param oncoPhenotypeData The body of the Onco Phenotype request. + * @param requestOptions The options to configure the HTTP request before HTTP client sends it. + * @throws HttpResponseException thrown if the request is rejected by server. + * @throws ClientAuthenticationException thrown if the request is rejected by server on status code 401. + * @throws ResourceNotFoundException thrown if the request is rejected by server on status code 404. + * @throws ResourceModifiedException thrown if the request is rejected by server on status code 409. + * @return the {@link SyncPoller} for polling of the response for the Onco Phenotype request. + */ + @Generated + @ServiceMethod(returns = ReturnType.LONG_RUNNING_OPERATION) + public SyncPoller beginInferCancerProfile( + BinaryData oncoPhenotypeData, RequestOptions requestOptions) { + return this.client.beginInferCancerProfile(oncoPhenotypeData, requestOptions).getSyncPoller(); + } + + /** + * Create Onco Phenotype job + * + *

Creates an Onco Phenotype job with the given request body. + * + * @param oncoPhenotypeData The body of the Onco Phenotype request. + * @throws IllegalArgumentException thrown if parameters fail the validation. + * @throws com.azure.core.exception.HttpResponseException thrown if the request is rejected by server. + * @throws ClientAuthenticationException thrown if the request is rejected by server on status code 401. + * @throws ResourceNotFoundException thrown if the request is rejected by server on status code 404. + * @throws ResourceModifiedException thrown if the request is rejected by server on status code 409. + * @throws RuntimeException all other wrapped checked exceptions if the request fails to be sent. + * @return the {@link SyncPoller} for polling of the response for the Onco Phenotype request. + */ + @Generated + @ServiceMethod(returns = ReturnType.LONG_RUNNING_OPERATION) + public SyncPoller beginInferCancerProfile( + OncoPhenotypeData oncoPhenotypeData) { + // Generated convenience method for beginInferCancerProfileWithModel + return client.beginInferCancerProfile(oncoPhenotypeData).getSyncPoller(); + } +} diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/CancerProfilingClientBuilder.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/CancerProfilingClientBuilder.java new file mode 100644 index 0000000000000..6f375a4011424 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/CancerProfilingClientBuilder.java @@ -0,0 +1,290 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.cancerprofiling; + +import com.azure.core.annotation.Generated; +import com.azure.core.annotation.ServiceClientBuilder; +import com.azure.core.client.traits.AzureKeyCredentialTrait; +import com.azure.core.client.traits.ConfigurationTrait; +import com.azure.core.client.traits.EndpointTrait; +import com.azure.core.client.traits.HttpTrait; +import com.azure.core.credential.AzureKeyCredential; +import com.azure.core.http.HttpClient; +import com.azure.core.http.HttpHeaders; +import com.azure.core.http.HttpPipeline; +import com.azure.core.http.HttpPipelineBuilder; +import com.azure.core.http.HttpPipelinePosition; +import com.azure.core.http.policy.AddDatePolicy; +import com.azure.core.http.policy.AddHeadersFromContextPolicy; +import com.azure.core.http.policy.AddHeadersPolicy; +import com.azure.core.http.policy.AzureKeyCredentialPolicy; +import com.azure.core.http.policy.CookiePolicy; +import com.azure.core.http.policy.HttpLogOptions; +import com.azure.core.http.policy.HttpLoggingPolicy; +import com.azure.core.http.policy.HttpPipelinePolicy; +import com.azure.core.http.policy.HttpPolicyProviders; +import com.azure.core.http.policy.RequestIdPolicy; +import com.azure.core.http.policy.RetryOptions; +import com.azure.core.http.policy.RetryPolicy; +import com.azure.core.http.policy.UserAgentPolicy; +import com.azure.core.util.ClientOptions; +import com.azure.core.util.Configuration; +import com.azure.core.util.CoreUtils; +import com.azure.core.util.builder.ClientBuilderUtil; +import com.azure.core.util.serializer.JacksonAdapter; +import com.azure.health.insights.cancerprofiling.implementation.CancerProfilingClientImpl; +import java.util.ArrayList; +import java.util.List; +import java.util.Map; +import java.util.Objects; + +/** A builder for creating a new instance of the CancerProfilingClient type. */ +@ServiceClientBuilder(serviceClients = {CancerProfilingClient.class, CancerProfilingAsyncClient.class}) +public final class CancerProfilingClientBuilder + implements HttpTrait, + ConfigurationTrait, + AzureKeyCredentialTrait, + EndpointTrait { + @Generated private static final String SDK_NAME = "name"; + + @Generated private static final String SDK_VERSION = "version"; + + @Generated + private static final Map PROPERTIES = + CoreUtils.getProperties("azure-health-insights-cancerprofiling.properties"); + + @Generated private final List pipelinePolicies; + + /** Create an instance of the CancerProfilingClientBuilder. */ + @Generated + public CancerProfilingClientBuilder() { + this.pipelinePolicies = new ArrayList<>(); + } + + /* + * The HTTP pipeline to send requests through. + */ + @Generated private HttpPipeline pipeline; + + /** {@inheritDoc}. */ + @Generated + @Override + public CancerProfilingClientBuilder pipeline(HttpPipeline pipeline) { + this.pipeline = pipeline; + return this; + } + + /* + * The HTTP client used to send the request. + */ + @Generated private HttpClient httpClient; + + /** {@inheritDoc}. */ + @Generated + @Override + public CancerProfilingClientBuilder httpClient(HttpClient httpClient) { + this.httpClient = httpClient; + return this; + } + + /* + * The logging configuration for HTTP requests and responses. + */ + @Generated private HttpLogOptions httpLogOptions; + + /** {@inheritDoc}. */ + @Generated + @Override + public CancerProfilingClientBuilder httpLogOptions(HttpLogOptions httpLogOptions) { + this.httpLogOptions = httpLogOptions; + return this; + } + + /* + * The client options such as application ID and custom headers to set on a request. + */ + @Generated private ClientOptions clientOptions; + + /** {@inheritDoc}. */ + @Generated + @Override + public CancerProfilingClientBuilder clientOptions(ClientOptions clientOptions) { + this.clientOptions = clientOptions; + return this; + } + + /* + * The retry options to configure retry policy for failed requests. + */ + @Generated private RetryOptions retryOptions; + + /** {@inheritDoc}. */ + @Generated + @Override + public CancerProfilingClientBuilder retryOptions(RetryOptions retryOptions) { + this.retryOptions = retryOptions; + return this; + } + + /** {@inheritDoc}. */ + @Generated + @Override + public CancerProfilingClientBuilder addPolicy(HttpPipelinePolicy customPolicy) { + Objects.requireNonNull(customPolicy, "'customPolicy' cannot be null."); + pipelinePolicies.add(customPolicy); + return this; + } + + /* + * The configuration store that is used during construction of the service client. + */ + @Generated private Configuration configuration; + + /** {@inheritDoc}. */ + @Generated + @Override + public CancerProfilingClientBuilder configuration(Configuration configuration) { + this.configuration = configuration; + return this; + } + + /* + * The AzureKeyCredential used for authentication. + */ + @Generated private AzureKeyCredential azureKeyCredential; + + /** {@inheritDoc}. */ + @Generated + @Override + public CancerProfilingClientBuilder credential(AzureKeyCredential azureKeyCredential) { + this.azureKeyCredential = azureKeyCredential; + return this; + } + + /* + * The service endpoint + */ + @Generated private String endpoint; + + /** {@inheritDoc}. */ + @Generated + @Override + public CancerProfilingClientBuilder endpoint(String endpoint) { + this.endpoint = endpoint; + return this; + } + + /* + * Service version + */ + @Generated private AzureHealthInsightsServiceVersion serviceVersion; + + /** + * Sets Service version. + * + * @param serviceVersion the serviceVersion value. + * @return the CancerProfilingClientBuilder. + */ + @Generated + public CancerProfilingClientBuilder serviceVersion(AzureHealthInsightsServiceVersion serviceVersion) { + this.serviceVersion = serviceVersion; + return this; + } + + /* + * The retry policy that will attempt to retry failed requests, if applicable. + */ + @Generated private RetryPolicy retryPolicy; + + /** + * Sets The retry policy that will attempt to retry failed requests, if applicable. + * + * @param retryPolicy the retryPolicy value. + * @return the CancerProfilingClientBuilder. + */ + @Generated + public CancerProfilingClientBuilder retryPolicy(RetryPolicy retryPolicy) { + this.retryPolicy = retryPolicy; + return this; + } + + /** + * Builds an instance of CancerProfilingClientImpl with the provided parameters. + * + * @return an instance of CancerProfilingClientImpl. + */ + @Generated + private CancerProfilingClientImpl buildInnerClient() { + HttpPipeline localPipeline = (pipeline != null) ? pipeline : createHttpPipeline(); + AzureHealthInsightsServiceVersion localServiceVersion = + (serviceVersion != null) ? serviceVersion : AzureHealthInsightsServiceVersion.getLatest(); + CancerProfilingClientImpl client = + new CancerProfilingClientImpl( + localPipeline, JacksonAdapter.createDefaultSerializerAdapter(), endpoint, localServiceVersion); + return client; + } + + @Generated + private HttpPipeline createHttpPipeline() { + Configuration buildConfiguration = + (configuration == null) ? Configuration.getGlobalConfiguration() : configuration; + HttpLogOptions localHttpLogOptions = this.httpLogOptions == null ? new HttpLogOptions() : this.httpLogOptions; + ClientOptions localClientOptions = this.clientOptions == null ? new ClientOptions() : this.clientOptions; + List policies = new ArrayList<>(); + String clientName = PROPERTIES.getOrDefault(SDK_NAME, "UnknownName"); + String clientVersion = PROPERTIES.getOrDefault(SDK_VERSION, "UnknownVersion"); + String applicationId = CoreUtils.getApplicationId(localClientOptions, localHttpLogOptions); + policies.add(new UserAgentPolicy(applicationId, clientName, clientVersion, buildConfiguration)); + policies.add(new RequestIdPolicy()); + policies.add(new AddHeadersFromContextPolicy()); + HttpHeaders headers = new HttpHeaders(); + localClientOptions.getHeaders().forEach(header -> headers.set(header.getName(), header.getValue())); + if (headers.getSize() > 0) { + policies.add(new AddHeadersPolicy(headers)); + } + this.pipelinePolicies.stream() + .filter(p -> p.getPipelinePosition() == HttpPipelinePosition.PER_CALL) + .forEach(p -> policies.add(p)); + HttpPolicyProviders.addBeforeRetryPolicies(policies); + policies.add(ClientBuilderUtil.validateAndGetRetryPolicy(retryPolicy, retryOptions, new RetryPolicy())); + policies.add(new AddDatePolicy()); + policies.add(new CookiePolicy()); + if (azureKeyCredential != null) { + policies.add(new AzureKeyCredentialPolicy("Ocp-Apim-Subscription-Key", azureKeyCredential)); + } + this.pipelinePolicies.stream() + .filter(p -> p.getPipelinePosition() == HttpPipelinePosition.PER_RETRY) + .forEach(p -> policies.add(p)); + HttpPolicyProviders.addAfterRetryPolicies(policies); + policies.add(new HttpLoggingPolicy(httpLogOptions)); + HttpPipeline httpPipeline = + new HttpPipelineBuilder() + .policies(policies.toArray(new HttpPipelinePolicy[0])) + .httpClient(httpClient) + .clientOptions(localClientOptions) + .build(); + return httpPipeline; + } + + /** + * Builds an instance of CancerProfilingAsyncClient class. + * + * @return an instance of CancerProfilingAsyncClient. + */ + @Generated + public CancerProfilingAsyncClient buildAsyncClient() { + return new CancerProfilingAsyncClient(buildInnerClient()); + } + + /** + * Builds an instance of CancerProfilingClient class. + * + * @return an instance of CancerProfilingClient. + */ + @Generated + public CancerProfilingClient buildClient() { + return new CancerProfilingClient(new CancerProfilingAsyncClient(buildInnerClient())); + } +} diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/implementation/CancerProfilingClientImpl.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/implementation/CancerProfilingClientImpl.java new file mode 100644 index 0000000000000..6734576e5032c --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/implementation/CancerProfilingClientImpl.java @@ -0,0 +1,839 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.cancerprofiling.implementation; + +import com.azure.core.annotation.BodyParam; +import com.azure.core.annotation.ExpectedResponses; +import com.azure.core.annotation.HeaderParam; +import com.azure.core.annotation.Host; +import com.azure.core.annotation.HostParam; +import com.azure.core.annotation.Post; +import com.azure.core.annotation.QueryParam; +import com.azure.core.annotation.ReturnType; +import com.azure.core.annotation.ServiceInterface; +import com.azure.core.annotation.ServiceMethod; +import com.azure.core.annotation.UnexpectedResponseExceptionType; +import com.azure.core.exception.ClientAuthenticationException; +import com.azure.core.exception.HttpResponseException; +import com.azure.core.exception.ResourceModifiedException; +import com.azure.core.exception.ResourceNotFoundException; +import com.azure.core.http.HttpPipeline; +import com.azure.core.http.HttpPipelineBuilder; +import com.azure.core.http.policy.CookiePolicy; +import com.azure.core.http.policy.RetryPolicy; +import com.azure.core.http.policy.UserAgentPolicy; +import com.azure.core.http.rest.RequestOptions; +import com.azure.core.http.rest.Response; +import com.azure.core.http.rest.RestProxy; +import com.azure.core.util.BinaryData; +import com.azure.core.util.Context; +import com.azure.core.util.DateTimeRfc1123; +import com.azure.core.util.FluxUtil; +import com.azure.core.util.polling.DefaultPollingStrategy; +import com.azure.core.util.polling.PollerFlux; +import com.azure.core.util.polling.SyncPoller; +import com.azure.core.util.serializer.JacksonAdapter; +import com.azure.core.util.serializer.SerializerAdapter; +import com.azure.core.util.serializer.TypeReference; +import com.azure.health.insights.cancerprofiling.AzureHealthInsightsServiceVersion; +import com.azure.health.insights.cancerprofiling.models.OncoPhenotypeResult; +import java.time.Duration; +import java.time.OffsetDateTime; +import java.util.UUID; +import reactor.core.publisher.Mono; + +/** Initializes a new instance of the CancerProfilingClient type. */ +public final class CancerProfilingClientImpl { + /** The proxy service used to perform REST calls. */ + private final CancerProfilingClientService service; + + /** + * Supported Cognitive Services endpoints (protocol and hostname, for example: + * https://westus2.api.cognitive.microsoft.com). + */ + private final String endpoint; + + /** + * Gets Supported Cognitive Services endpoints (protocol and hostname, for example: + * https://westus2.api.cognitive.microsoft.com). + * + * @return the endpoint value. + */ + public String getEndpoint() { + return this.endpoint; + } + + /** Service version. */ + private final AzureHealthInsightsServiceVersion serviceVersion; + + /** + * Gets Service version. + * + * @return the serviceVersion value. + */ + public AzureHealthInsightsServiceVersion getServiceVersion() { + return this.serviceVersion; + } + + /** The HTTP pipeline to send requests through. */ + private final HttpPipeline httpPipeline; + + /** + * Gets The HTTP pipeline to send requests through. + * + * @return the httpPipeline value. + */ + public HttpPipeline getHttpPipeline() { + return this.httpPipeline; + } + + /** The serializer to serialize an object into a string. */ + private final SerializerAdapter serializerAdapter; + + /** + * Gets The serializer to serialize an object into a string. + * + * @return the serializerAdapter value. + */ + public SerializerAdapter getSerializerAdapter() { + return this.serializerAdapter; + } + + /** + * Initializes an instance of CancerProfilingClient client. + * + * @param endpoint Supported Cognitive Services endpoints (protocol and hostname, for example: + * https://westus2.api.cognitive.microsoft.com). + * @param serviceVersion Service version. + */ + public CancerProfilingClientImpl(String endpoint, AzureHealthInsightsServiceVersion serviceVersion) { + this( + new HttpPipelineBuilder() + .policies(new UserAgentPolicy(), new RetryPolicy(), new CookiePolicy()) + .build(), + JacksonAdapter.createDefaultSerializerAdapter(), + endpoint, + serviceVersion); + } + + /** + * Initializes an instance of CancerProfilingClient client. + * + * @param httpPipeline The HTTP pipeline to send requests through. + * @param endpoint Supported Cognitive Services endpoints (protocol and hostname, for example: + * https://westus2.api.cognitive.microsoft.com). + * @param serviceVersion Service version. + */ + public CancerProfilingClientImpl( + HttpPipeline httpPipeline, String endpoint, AzureHealthInsightsServiceVersion serviceVersion) { + this(httpPipeline, JacksonAdapter.createDefaultSerializerAdapter(), endpoint, serviceVersion); + } + + /** + * Initializes an instance of CancerProfilingClient client. + * + * @param httpPipeline The HTTP pipeline to send requests through. + * @param serializerAdapter The serializer to serialize an object into a string. + * @param endpoint Supported Cognitive Services endpoints (protocol and hostname, for example: + * https://westus2.api.cognitive.microsoft.com). + * @param serviceVersion Service version. + */ + public CancerProfilingClientImpl( + HttpPipeline httpPipeline, + SerializerAdapter serializerAdapter, + String endpoint, + AzureHealthInsightsServiceVersion serviceVersion) { + this.httpPipeline = httpPipeline; + this.serializerAdapter = serializerAdapter; + this.endpoint = endpoint; + this.serviceVersion = serviceVersion; + this.service = + RestProxy.create(CancerProfilingClientService.class, this.httpPipeline, this.getSerializerAdapter()); + } + + /** + * The interface defining all the services for CancerProfilingClient to be used by the proxy service to perform REST + * calls. + */ + @Host("{endpoint}/healthinsights") + @ServiceInterface(name = "CancerProfilingClien") + public interface CancerProfilingClientService { + @Post("/oncophenotype/jobs") + @ExpectedResponses({200, 202}) + @UnexpectedResponseExceptionType( + value = ClientAuthenticationException.class, + code = {401}) + @UnexpectedResponseExceptionType( + value = ResourceNotFoundException.class, + code = {404}) + @UnexpectedResponseExceptionType( + value = ResourceModifiedException.class, + code = {409}) + @UnexpectedResponseExceptionType(HttpResponseException.class) + Mono> inferCancerProfile( + @HostParam("endpoint") String endpoint, + @QueryParam("api-version") String apiVersion, + @HeaderParam("accept") String accept, + @BodyParam("application/json") BinaryData oncoPhenotypeData, + RequestOptions requestOptions, + Context context); + } + + /** + * Create Onco Phenotype job + * + *

Creates an Onco Phenotype job with the given request body. + * + *

Header Parameters + * + * + * + * + * + * + *
Header Parameters
NameTypeRequiredDescription
repeatability-request-idStringNoRepeatability request ID header
repeatability-first-sentStringNoRepeatability first sent header as HTTP-date
+ * + * You can add these to a request with {@link RequestOptions#addHeader} + * + *

Request Body Schema + * + * 

{@code
+     * {
+     *     patients (Required): [
+     *          (Required){
+     *             id: String (Required)
+     *             info (Optional): {
+     *                 sex: String(female/male/unspecified) (Optional)
+     *                 birthDate: LocalDate (Optional)
+     *                 clinicalInfo (Optional): [
+     *                      (Optional){
+     *                         system: String (Required)
+     *                         code: String (Required)
+     *                         name: String (Optional)
+     *                         value: String (Optional)
+     *                     }
+     *                 ]
+     *             }
+     *             data (Optional): [
+     *                  (Optional){
+     *                     type: String(note/fhirBundle/dicom/genomicSequencing) (Required)
+     *                     clinicalType: String(consultation/dischargeSummary/historyAndPhysical/procedure/progress/imaging/laboratory/pathology) (Optional)
+     *                     id: String (Required)
+     *                     language: String (Optional)
+     *                     createdDateTime: OffsetDateTime (Optional)
+     *                     content (Required): {
+     *                         sourceType: String(inline/reference) (Required)
+     *                         value: String (Required)
+     *                     }
+     *                 }
+     *             ]
+     *         }
+     *     ]
+     *     configuration (Optional): {
+     *         verbose: Boolean (Optional)
+     *         includeEvidence: Boolean (Optional)
+     *         inferenceTypes (Optional): [
+     *             String(tumorSite/histology/clinicalStageT/clinicalStageN/clinicalStageM/pathologicStageT/pathologicStageN/pathologicStageM) (Optional)
+     *         ]
+     *         checkForCancerCase: Boolean (Optional)
+     *     }
+     * }
+     * }
+ * + *

Response Body Schema + * + * 

{@code
+     * {
+     *     jobId: String (Required)
+     *     createdDateTime: OffsetDateTime (Required)
+     *     expirationDateTime: OffsetDateTime (Required)
+     *     lastUpdateDateTime: OffsetDateTime (Required)
+     *     status: String(notStarted/running/succeeded/failed/partiallyCompleted) (Required)
+     *     errors (Optional): [
+     *         ResponseError (Optional)
+     *     ]
+     *     results (Optional): {
+     *         patients (Required): [
+     *              (Required){
+     *                 id: String (Required)
+     *                 inferences (Required): [
+     *                      (Required){
+     *                         type: String(tumorSite/histology/clinicalStageT/clinicalStageN/clinicalStageM/pathologicStageT/pathologicStageN/pathologicStageM) (Required)
+     *                         value: String (Required)
+     *                         description: String (Optional)
+     *                         confidenceScore: Double (Optional)
+     *                         evidence (Optional): [
+     *                              (Optional){
+     *                                 patientDataEvidence (Optional): {
+     *                                     id: String (Required)
+     *                                     text: String (Optional)
+     *                                     offset: int (Required)
+     *                                     length: int (Required)
+     *                                 }
+     *                                 patientInfoEvidence (Optional): {
+     *                                     system: String (Required)
+     *                                     code: String (Required)
+     *                                     name: String (Optional)
+     *                                     value: String (Optional)
+     *                                 }
+     *                                 importance: Double (Optional)
+     *                             }
+     *                         ]
+     *                         caseId: String (Optional)
+     *                     }
+     *                 ]
+     *             }
+     *         ]
+     *         modelVersion: String (Required)
+     *     }
+     * }
+     * }
+ * + * @param oncoPhenotypeData The body of the Onco Phenotype request. + * @param requestOptions The options to configure the HTTP request before HTTP client sends it. + * @throws HttpResponseException thrown if the request is rejected by server. + * @throws ClientAuthenticationException thrown if the request is rejected by server on status code 401. + * @throws ResourceNotFoundException thrown if the request is rejected by server on status code 404. + * @throws ResourceModifiedException thrown if the request is rejected by server on status code 409. + * @return the response for the Onco Phenotype request along with {@link Response} on successful completion of + * {@link Mono}. + */ + @ServiceMethod(returns = ReturnType.SINGLE) + private Mono> inferCancerProfileWithResponseAsync( + BinaryData oncoPhenotypeData, RequestOptions requestOptions) { + final String accept = "application/json"; + RequestOptions requestOptionsLocal = requestOptions == null ? new RequestOptions() : requestOptions; + requestOptionsLocal.setHeader("repeatability-request-id", UUID.randomUUID().toString()); + requestOptionsLocal.setHeader( + "repeatability-first-sent", DateTimeRfc1123.toRfc1123String(OffsetDateTime.now())); + return FluxUtil.withContext( + context -> + service.inferCancerProfile( + this.getEndpoint(), + this.getServiceVersion().getVersion(), + accept, + oncoPhenotypeData, + requestOptionsLocal, + context)); + } + + /** + * Create Onco Phenotype job + * + *

Creates an Onco Phenotype job with the given request body. + * + *

Header Parameters + * + * + * + * + * + * + *
Header Parameters
NameTypeRequiredDescription
repeatability-request-idStringNoRepeatability request ID header
repeatability-first-sentStringNoRepeatability first sent header as HTTP-date
+ * + * You can add these to a request with {@link RequestOptions#addHeader} + * + *

Request Body Schema + * + * 

{@code
+     * {
+     *     patients (Required): [
+     *          (Required){
+     *             id: String (Required)
+     *             info (Optional): {
+     *                 sex: String(female/male/unspecified) (Optional)
+     *                 birthDate: LocalDate (Optional)
+     *                 clinicalInfo (Optional): [
+     *                      (Optional){
+     *                         system: String (Required)
+     *                         code: String (Required)
+     *                         name: String (Optional)
+     *                         value: String (Optional)
+     *                     }
+     *                 ]
+     *             }
+     *             data (Optional): [
+     *                  (Optional){
+     *                     type: String(note/fhirBundle/dicom/genomicSequencing) (Required)
+     *                     clinicalType: String(consultation/dischargeSummary/historyAndPhysical/procedure/progress/imaging/laboratory/pathology) (Optional)
+     *                     id: String (Required)
+     *                     language: String (Optional)
+     *                     createdDateTime: OffsetDateTime (Optional)
+     *                     content (Required): {
+     *                         sourceType: String(inline/reference) (Required)
+     *                         value: String (Required)
+     *                     }
+     *                 }
+     *             ]
+     *         }
+     *     ]
+     *     configuration (Optional): {
+     *         verbose: Boolean (Optional)
+     *         includeEvidence: Boolean (Optional)
+     *         inferenceTypes (Optional): [
+     *             String(tumorSite/histology/clinicalStageT/clinicalStageN/clinicalStageM/pathologicStageT/pathologicStageN/pathologicStageM) (Optional)
+     *         ]
+     *         checkForCancerCase: Boolean (Optional)
+     *     }
+     * }
+     * }
+ * + *

Response Body Schema + * + * 

{@code
+     * {
+     *     jobId: String (Required)
+     *     createdDateTime: OffsetDateTime (Required)
+     *     expirationDateTime: OffsetDateTime (Required)
+     *     lastUpdateDateTime: OffsetDateTime (Required)
+     *     status: String(notStarted/running/succeeded/failed/partiallyCompleted) (Required)
+     *     errors (Optional): [
+     *         ResponseError (Optional)
+     *     ]
+     *     results (Optional): {
+     *         patients (Required): [
+     *              (Required){
+     *                 id: String (Required)
+     *                 inferences (Required): [
+     *                      (Required){
+     *                         type: String(tumorSite/histology/clinicalStageT/clinicalStageN/clinicalStageM/pathologicStageT/pathologicStageN/pathologicStageM) (Required)
+     *                         value: String (Required)
+     *                         description: String (Optional)
+     *                         confidenceScore: Double (Optional)
+     *                         evidence (Optional): [
+     *                              (Optional){
+     *                                 patientDataEvidence (Optional): {
+     *                                     id: String (Required)
+     *                                     text: String (Optional)
+     *                                     offset: int (Required)
+     *                                     length: int (Required)
+     *                                 }
+     *                                 patientInfoEvidence (Optional): {
+     *                                     system: String (Required)
+     *                                     code: String (Required)
+     *                                     name: String (Optional)
+     *                                     value: String (Optional)
+     *                                 }
+     *                                 importance: Double (Optional)
+     *                             }
+     *                         ]
+     *                         caseId: String (Optional)
+     *                     }
+     *                 ]
+     *             }
+     *         ]
+     *         modelVersion: String (Required)
+     *     }
+     * }
+     * }
+ * + * @param oncoPhenotypeData The body of the Onco Phenotype request. + * @param requestOptions The options to configure the HTTP request before HTTP client sends it. + * @throws HttpResponseException thrown if the request is rejected by server. + * @throws ClientAuthenticationException thrown if the request is rejected by server on status code 401. + * @throws ResourceNotFoundException thrown if the request is rejected by server on status code 404. + * @throws ResourceModifiedException thrown if the request is rejected by server on status code 409. + * @return the {@link PollerFlux} for polling of the response for the Onco Phenotype request. + */ + @ServiceMethod(returns = ReturnType.LONG_RUNNING_OPERATION) + public PollerFlux beginInferCancerProfileAsync( + BinaryData oncoPhenotypeData, RequestOptions requestOptions) { + return PollerFlux.create( + Duration.ofSeconds(1), + () -> this.inferCancerProfileWithResponseAsync(oncoPhenotypeData, requestOptions), + new DefaultPollingStrategy<>( + this.getHttpPipeline(), + "{endpoint}/healthinsights".replace("{endpoint}", this.getEndpoint()), + null, + requestOptions != null && requestOptions.getContext() != null + ? requestOptions.getContext() + : Context.NONE), + TypeReference.createInstance(BinaryData.class), + TypeReference.createInstance(BinaryData.class)); + } + + /** + * Create Onco Phenotype job + * + *

Creates an Onco Phenotype job with the given request body. + * + *

Header Parameters + * + * + * + * + * + * + *
Header Parameters
NameTypeRequiredDescription
repeatability-request-idStringNoRepeatability request ID header
repeatability-first-sentStringNoRepeatability first sent header as HTTP-date
+ * + * You can add these to a request with {@link RequestOptions#addHeader} + * + *

Request Body Schema + * + * 

{@code
+     * {
+     *     patients (Required): [
+     *          (Required){
+     *             id: String (Required)
+     *             info (Optional): {
+     *                 sex: String(female/male/unspecified) (Optional)
+     *                 birthDate: LocalDate (Optional)
+     *                 clinicalInfo (Optional): [
+     *                      (Optional){
+     *                         system: String (Required)
+     *                         code: String (Required)
+     *                         name: String (Optional)
+     *                         value: String (Optional)
+     *                     }
+     *                 ]
+     *             }
+     *             data (Optional): [
+     *                  (Optional){
+     *                     type: String(note/fhirBundle/dicom/genomicSequencing) (Required)
+     *                     clinicalType: String(consultation/dischargeSummary/historyAndPhysical/procedure/progress/imaging/laboratory/pathology) (Optional)
+     *                     id: String (Required)
+     *                     language: String (Optional)
+     *                     createdDateTime: OffsetDateTime (Optional)
+     *                     content (Required): {
+     *                         sourceType: String(inline/reference) (Required)
+     *                         value: String (Required)
+     *                     }
+     *                 }
+     *             ]
+     *         }
+     *     ]
+     *     configuration (Optional): {
+     *         verbose: Boolean (Optional)
+     *         includeEvidence: Boolean (Optional)
+     *         inferenceTypes (Optional): [
+     *             String(tumorSite/histology/clinicalStageT/clinicalStageN/clinicalStageM/pathologicStageT/pathologicStageN/pathologicStageM) (Optional)
+     *         ]
+     *         checkForCancerCase: Boolean (Optional)
+     *     }
+     * }
+     * }
+ * + *

Response Body Schema + * + * 

{@code
+     * {
+     *     jobId: String (Required)
+     *     createdDateTime: OffsetDateTime (Required)
+     *     expirationDateTime: OffsetDateTime (Required)
+     *     lastUpdateDateTime: OffsetDateTime (Required)
+     *     status: String(notStarted/running/succeeded/failed/partiallyCompleted) (Required)
+     *     errors (Optional): [
+     *         ResponseError (Optional)
+     *     ]
+     *     results (Optional): {
+     *         patients (Required): [
+     *              (Required){
+     *                 id: String (Required)
+     *                 inferences (Required): [
+     *                      (Required){
+     *                         type: String(tumorSite/histology/clinicalStageT/clinicalStageN/clinicalStageM/pathologicStageT/pathologicStageN/pathologicStageM) (Required)
+     *                         value: String (Required)
+     *                         description: String (Optional)
+     *                         confidenceScore: Double (Optional)
+     *                         evidence (Optional): [
+     *                              (Optional){
+     *                                 patientDataEvidence (Optional): {
+     *                                     id: String (Required)
+     *                                     text: String (Optional)
+     *                                     offset: int (Required)
+     *                                     length: int (Required)
+     *                                 }
+     *                                 patientInfoEvidence (Optional): {
+     *                                     system: String (Required)
+     *                                     code: String (Required)
+     *                                     name: String (Optional)
+     *                                     value: String (Optional)
+     *                                 }
+     *                                 importance: Double (Optional)
+     *                             }
+     *                         ]
+     *                         caseId: String (Optional)
+     *                     }
+     *                 ]
+     *             }
+     *         ]
+     *         modelVersion: String (Required)
+     *     }
+     * }
+     * }
+ * + * @param oncoPhenotypeData The body of the Onco Phenotype request. + * @param requestOptions The options to configure the HTTP request before HTTP client sends it. + * @throws HttpResponseException thrown if the request is rejected by server. + * @throws ClientAuthenticationException thrown if the request is rejected by server on status code 401. + * @throws ResourceNotFoundException thrown if the request is rejected by server on status code 404. + * @throws ResourceModifiedException thrown if the request is rejected by server on status code 409. + * @return the {@link SyncPoller} for polling of the response for the Onco Phenotype request. + */ + @ServiceMethod(returns = ReturnType.LONG_RUNNING_OPERATION) + public SyncPoller beginInferCancerProfile( + BinaryData oncoPhenotypeData, RequestOptions requestOptions) { + return this.beginInferCancerProfileAsync(oncoPhenotypeData, requestOptions).getSyncPoller(); + } + + /** + * Create Onco Phenotype job + * + *

Creates an Onco Phenotype job with the given request body. + * + *

Header Parameters + * + * + * + * + * + * + *
Header Parameters
NameTypeRequiredDescription
repeatability-request-idStringNoRepeatability request ID header
repeatability-first-sentStringNoRepeatability first sent header as HTTP-date
+ * + * You can add these to a request with {@link RequestOptions#addHeader} + * + *

Request Body Schema + * + * 

{@code
+     * {
+     *     patients (Required): [
+     *          (Required){
+     *             id: String (Required)
+     *             info (Optional): {
+     *                 sex: String(female/male/unspecified) (Optional)
+     *                 birthDate: LocalDate (Optional)
+     *                 clinicalInfo (Optional): [
+     *                      (Optional){
+     *                         system: String (Required)
+     *                         code: String (Required)
+     *                         name: String (Optional)
+     *                         value: String (Optional)
+     *                     }
+     *                 ]
+     *             }
+     *             data (Optional): [
+     *                  (Optional){
+     *                     type: String(note/fhirBundle/dicom/genomicSequencing) (Required)
+     *                     clinicalType: String(consultation/dischargeSummary/historyAndPhysical/procedure/progress/imaging/laboratory/pathology) (Optional)
+     *                     id: String (Required)
+     *                     language: String (Optional)
+     *                     createdDateTime: OffsetDateTime (Optional)
+     *                     content (Required): {
+     *                         sourceType: String(inline/reference) (Required)
+     *                         value: String (Required)
+     *                     }
+     *                 }
+     *             ]
+     *         }
+     *     ]
+     *     configuration (Optional): {
+     *         verbose: Boolean (Optional)
+     *         includeEvidence: Boolean (Optional)
+     *         inferenceTypes (Optional): [
+     *             String(tumorSite/histology/clinicalStageT/clinicalStageN/clinicalStageM/pathologicStageT/pathologicStageN/pathologicStageM) (Optional)
+     *         ]
+     *         checkForCancerCase: Boolean (Optional)
+     *     }
+     * }
+     * }
+ * + *

Response Body Schema + * + * 

{@code
+     * {
+     *     jobId: String (Required)
+     *     createdDateTime: OffsetDateTime (Required)
+     *     expirationDateTime: OffsetDateTime (Required)
+     *     lastUpdateDateTime: OffsetDateTime (Required)
+     *     status: String(notStarted/running/succeeded/failed/partiallyCompleted) (Required)
+     *     errors (Optional): [
+     *         ResponseError (Optional)
+     *     ]
+     *     results (Optional): {
+     *         patients (Required): [
+     *              (Required){
+     *                 id: String (Required)
+     *                 inferences (Required): [
+     *                      (Required){
+     *                         type: String(tumorSite/histology/clinicalStageT/clinicalStageN/clinicalStageM/pathologicStageT/pathologicStageN/pathologicStageM) (Required)
+     *                         value: String (Required)
+     *                         description: String (Optional)
+     *                         confidenceScore: Double (Optional)
+     *                         evidence (Optional): [
+     *                              (Optional){
+     *                                 patientDataEvidence (Optional): {
+     *                                     id: String (Required)
+     *                                     text: String (Optional)
+     *                                     offset: int (Required)
+     *                                     length: int (Required)
+     *                                 }
+     *                                 patientInfoEvidence (Optional): {
+     *                                     system: String (Required)
+     *                                     code: String (Required)
+     *                                     name: String (Optional)
+     *                                     value: String (Optional)
+     *                                 }
+     *                                 importance: Double (Optional)
+     *                             }
+     *                         ]
+     *                         caseId: String (Optional)
+     *                     }
+     *                 ]
+     *             }
+     *         ]
+     *         modelVersion: String (Required)
+     *     }
+     * }
+     * }
+ * + * @param oncoPhenotypeData The body of the Onco Phenotype request. + * @param requestOptions The options to configure the HTTP request before HTTP client sends it. + * @throws HttpResponseException thrown if the request is rejected by server. + * @throws ClientAuthenticationException thrown if the request is rejected by server on status code 401. + * @throws ResourceNotFoundException thrown if the request is rejected by server on status code 404. + * @throws ResourceModifiedException thrown if the request is rejected by server on status code 409. + * @return the {@link PollerFlux} for polling of the response for the Onco Phenotype request. + */ + @ServiceMethod(returns = ReturnType.LONG_RUNNING_OPERATION) + public PollerFlux beginInferCancerProfileWithModelAsync( + BinaryData oncoPhenotypeData, RequestOptions requestOptions) { + return PollerFlux.create( + Duration.ofSeconds(1), + () -> this.inferCancerProfileWithResponseAsync(oncoPhenotypeData, requestOptions), + new DefaultPollingStrategy<>( + this.getHttpPipeline(), + "{endpoint}/healthinsights".replace("{endpoint}", this.getEndpoint()), + null, + requestOptions != null && requestOptions.getContext() != null + ? requestOptions.getContext() + : Context.NONE), + TypeReference.createInstance(OncoPhenotypeResult.class), + TypeReference.createInstance(OncoPhenotypeResult.class)); + } + + /** + * Create Onco Phenotype job + * + *

Creates an Onco Phenotype job with the given request body. + * + *

Header Parameters + * + * + * + * + * + * + *
Header Parameters
NameTypeRequiredDescription
repeatability-request-idStringNoRepeatability request ID header
repeatability-first-sentStringNoRepeatability first sent header as HTTP-date
+ * + * You can add these to a request with {@link RequestOptions#addHeader} + * + *

Request Body Schema + * + * 

{@code
+     * {
+     *     patients (Required): [
+     *          (Required){
+     *             id: String (Required)
+     *             info (Optional): {
+     *                 sex: String(female/male/unspecified) (Optional)
+     *                 birthDate: LocalDate (Optional)
+     *                 clinicalInfo (Optional): [
+     *                      (Optional){
+     *                         system: String (Required)
+     *                         code: String (Required)
+     *                         name: String (Optional)
+     *                         value: String (Optional)
+     *                     }
+     *                 ]
+     *             }
+     *             data (Optional): [
+     *                  (Optional){
+     *                     type: String(note/fhirBundle/dicom/genomicSequencing) (Required)
+     *                     clinicalType: String(consultation/dischargeSummary/historyAndPhysical/procedure/progress/imaging/laboratory/pathology) (Optional)
+     *                     id: String (Required)
+     *                     language: String (Optional)
+     *                     createdDateTime: OffsetDateTime (Optional)
+     *                     content (Required): {
+     *                         sourceType: String(inline/reference) (Required)
+     *                         value: String (Required)
+     *                     }
+     *                 }
+     *             ]
+     *         }
+     *     ]
+     *     configuration (Optional): {
+     *         verbose: Boolean (Optional)
+     *         includeEvidence: Boolean (Optional)
+     *         inferenceTypes (Optional): [
+     *             String(tumorSite/histology/clinicalStageT/clinicalStageN/clinicalStageM/pathologicStageT/pathologicStageN/pathologicStageM) (Optional)
+     *         ]
+     *         checkForCancerCase: Boolean (Optional)
+     *     }
+     * }
+     * }
+ * + *

Response Body Schema + * + * 

{@code
+     * {
+     *     jobId: String (Required)
+     *     createdDateTime: OffsetDateTime (Required)
+     *     expirationDateTime: OffsetDateTime (Required)
+     *     lastUpdateDateTime: OffsetDateTime (Required)
+     *     status: String(notStarted/running/succeeded/failed/partiallyCompleted) (Required)
+     *     errors (Optional): [
+     *         ResponseError (Optional)
+     *     ]
+     *     results (Optional): {
+     *         patients (Required): [
+     *              (Required){
+     *                 id: String (Required)
+     *                 inferences (Required): [
+     *                      (Required){
+     *                         type: String(tumorSite/histology/clinicalStageT/clinicalStageN/clinicalStageM/pathologicStageT/pathologicStageN/pathologicStageM) (Required)
+     *                         value: String (Required)
+     *                         description: String (Optional)
+     *                         confidenceScore: Double (Optional)
+     *                         evidence (Optional): [
+     *                              (Optional){
+     *                                 patientDataEvidence (Optional): {
+     *                                     id: String (Required)
+     *                                     text: String (Optional)
+     *                                     offset: int (Required)
+     *                                     length: int (Required)
+     *                                 }
+     *                                 patientInfoEvidence (Optional): {
+     *                                     system: String (Required)
+     *                                     code: String (Required)
+     *                                     name: String (Optional)
+     *                                     value: String (Optional)
+     *                                 }
+     *                                 importance: Double (Optional)
+     *                             }
+     *                         ]
+     *                         caseId: String (Optional)
+     *                     }
+     *                 ]
+     *             }
+     *         ]
+     *         modelVersion: String (Required)
+     *     }
+     * }
+     * }
+ * + * @param oncoPhenotypeData The body of the Onco Phenotype request. + * @param requestOptions The options to configure the HTTP request before HTTP client sends it. + * @throws HttpResponseException thrown if the request is rejected by server. + * @throws ClientAuthenticationException thrown if the request is rejected by server on status code 401. + * @throws ResourceNotFoundException thrown if the request is rejected by server on status code 404. + * @throws ResourceModifiedException thrown if the request is rejected by server on status code 409. + * @return the {@link SyncPoller} for polling of the response for the Onco Phenotype request. + */ + @ServiceMethod(returns = ReturnType.LONG_RUNNING_OPERATION) + public SyncPoller beginInferCancerProfileWithModel( + BinaryData oncoPhenotypeData, RequestOptions requestOptions) { + return this.beginInferCancerProfileWithModelAsync(oncoPhenotypeData, requestOptions).getSyncPoller(); + } +} diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/implementation/package-info.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/implementation/package-info.java new file mode 100644 index 0000000000000..0bd37018b715f --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/implementation/package-info.java @@ -0,0 +1,10 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +/** + * Package containing the implementations for AzureHealthInsights. Azure Health Insights provides an API that serves + * insight models, specific for Health & Life Sciences, that perform analysis and provide inferences to be used by a + * human. + */ +package com.azure.health.insights.cancerprofiling.implementation; diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/ClinicalCodedElement.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/ClinicalCodedElement.java new file mode 100644 index 0000000000000..adcace4280b1c --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/ClinicalCodedElement.java @@ -0,0 +1,109 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.cancerprofiling.models; + +import com.azure.core.annotation.Fluent; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; + +/** A piece of clinical information, expressed as a code in a clinical coding system. */ +@Fluent +public final class ClinicalCodedElement { + /* + * The clinical coding system, e.g. ICD-10, SNOMED-CT, UMLS. + */ + @JsonProperty(value = "system", required = true) + private String system; + + /* + * The code within the given clinical coding system. + */ + @JsonProperty(value = "code", required = true) + private String code; + + /* + * The name of this coded concept in the coding system. + */ + @JsonProperty(value = "name") + private String name; + + /* + * A value associated with the code within the given clinical coding system. + */ + @JsonProperty(value = "value") + private String value; + + /** + * Creates an instance of ClinicalCodedElement class. + * + * @param system the system value to set. + * @param code the code value to set. + */ + @JsonCreator + public ClinicalCodedElement( + @JsonProperty(value = "system", required = true) String system, + @JsonProperty(value = "code", required = true) String code) { + this.system = system; + this.code = code; + } + + /** + * Get the system property: The clinical coding system, e.g. ICD-10, SNOMED-CT, UMLS. + * + * @return the system value. + */ + public String getSystem() { + return this.system; + } + + /** + * Get the code property: The code within the given clinical coding system. + * + * @return the code value. + */ + public String getCode() { + return this.code; + } + + /** + * Get the name property: The name of this coded concept in the coding system. + * + * @return the name value. + */ + public String getName() { + return this.name; + } + + /** + * Set the name property: The name of this coded concept in the coding system. + * + * @param name the name value to set. + * @return the ClinicalCodedElement object itself. + */ + public ClinicalCodedElement setName(String name) { + this.name = name; + return this; + } + + /** + * Get the value property: A value associated with the code within the given clinical coding system. + * + * @return the value value. + */ + public String getValue() { + return this.value; + } + + /** + * Set the value property: A value associated with the code within the given clinical coding system. + * + * @param value the value value to set. + * @return the ClinicalCodedElement object itself. + */ + public ClinicalCodedElement setValue(String value) { + this.value = value; + return this; + } +} diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/ClinicalDocumentType.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/ClinicalDocumentType.java new file mode 100644 index 0000000000000..06780e9704a1d --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/ClinicalDocumentType.java @@ -0,0 +1,64 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.cancerprofiling.models; + +import com.azure.core.util.ExpandableStringEnum; +import com.fasterxml.jackson.annotation.JsonCreator; +import java.util.Collection; + +/** The type of the clinical document. */ +public final class ClinicalDocumentType extends ExpandableStringEnum { + /** Static value consultation for ClinicalDocumentType. */ + public static final ClinicalDocumentType CONSULTATION = fromString("consultation"); + + /** Static value dischargeSummary for ClinicalDocumentType. */ + public static final ClinicalDocumentType DISCHARGE_SUMMARY = fromString("dischargeSummary"); + + /** Static value historyAndPhysical for ClinicalDocumentType. */ + public static final ClinicalDocumentType HISTORY_AND_PHYSICAL = fromString("historyAndPhysical"); + + /** Static value procedure for ClinicalDocumentType. */ + public static final ClinicalDocumentType PROCEDURE = fromString("procedure"); + + /** Static value progress for ClinicalDocumentType. */ + public static final ClinicalDocumentType PROGRESS = fromString("progress"); + + /** Static value imaging for ClinicalDocumentType. */ + public static final ClinicalDocumentType IMAGING = fromString("imaging"); + + /** Static value laboratory for ClinicalDocumentType. */ + public static final ClinicalDocumentType LABORATORY = fromString("laboratory"); + + /** Static value pathology for ClinicalDocumentType. */ + public static final ClinicalDocumentType PATHOLOGY = fromString("pathology"); + + /** + * Creates a new instance of ClinicalDocumentType value. + * + * @deprecated Use the {@link #fromString(String)} factory method. + */ + @Deprecated + public ClinicalDocumentType() {} + + /** + * Creates or finds a ClinicalDocumentType from its string representation. + * + * @param name a name to look for. + * @return the corresponding ClinicalDocumentType. + */ + @JsonCreator + public static ClinicalDocumentType fromString(String name) { + return fromString(name, ClinicalDocumentType.class); + } + + /** + * Gets known ClinicalDocumentType values. + * + * @return known ClinicalDocumentType values. + */ + public static Collection values() { + return values(ClinicalDocumentType.class); + } +} diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/ClinicalNoteEvidence.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/ClinicalNoteEvidence.java new file mode 100644 index 0000000000000..4445d1e692d99 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/ClinicalNoteEvidence.java @@ -0,0 +1,90 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.cancerprofiling.models; + +import com.azure.core.annotation.Immutable; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; + +/** A piece of evidence from a clinical note (text document). */ +@Immutable +public final class ClinicalNoteEvidence { + /* + * The identifier of the document containing the evidence. + */ + @JsonProperty(value = "id", required = true) + private String id; + + /* + * The actual text span which is evidence for the inference. + */ + @JsonProperty(value = "text") + private String text; + + /* + * The start index of the evidence text span in the document (0 based). + */ + @JsonProperty(value = "offset", required = true) + private int offset; + + /* + * The length of the evidence text span. + */ + @JsonProperty(value = "length", required = true) + private int length; + + /** + * Creates an instance of ClinicalNoteEvidence class. + * + * @param id the id value to set. + * @param offset the offset value to set. + * @param length the length value to set. + */ + @JsonCreator + private ClinicalNoteEvidence( + @JsonProperty(value = "id", required = true) String id, + @JsonProperty(value = "offset", required = true) int offset, + @JsonProperty(value = "length", required = true) int length) { + this.id = id; + this.offset = offset; + this.length = length; + } + + /** + * Get the id property: The identifier of the document containing the evidence. + * + * @return the id value. + */ + public String getId() { + return this.id; + } + + /** + * Get the text property: The actual text span which is evidence for the inference. + * + * @return the text value. + */ + public String getText() { + return this.text; + } + + /** + * Get the offset property: The start index of the evidence text span in the document (0 based). + * + * @return the offset value. + */ + public int getOffset() { + return this.offset; + } + + /** + * Get the length property: The length of the evidence text span. + * + * @return the length value. + */ + public int getLength() { + return this.length; + } +} diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/DocumentContent.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/DocumentContent.java new file mode 100644 index 0000000000000..fdb2d6a84e05c --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/DocumentContent.java @@ -0,0 +1,60 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.cancerprofiling.models; + +import com.azure.core.annotation.Immutable; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; + +/** The content of the patient document. */ +@Immutable +public final class DocumentContent { + /* + * The type of the content's source. + * In case the source type is 'inline', the content is given as a string (for instance, text). + * In case the source type is 'reference', the content is given as a URI. + */ + @JsonProperty(value = "sourceType", required = true) + private DocumentContentSourceType sourceType; + + /* + * The content of the document, given either inline (as a string) or as a reference (URI). + */ + @JsonProperty(value = "value", required = true) + private String value; + + /** + * Creates an instance of DocumentContent class. + * + * @param sourceType the sourceType value to set. + * @param value the value value to set. + */ + @JsonCreator + public DocumentContent( + @JsonProperty(value = "sourceType", required = true) DocumentContentSourceType sourceType, + @JsonProperty(value = "value", required = true) String value) { + this.sourceType = sourceType; + this.value = value; + } + + /** + * Get the sourceType property: The type of the content's source. In case the source type is 'inline', the content + * is given as a string (for instance, text). In case the source type is 'reference', the content is given as a URI. + * + * @return the sourceType value. + */ + public DocumentContentSourceType getSourceType() { + return this.sourceType; + } + + /** + * Get the value property: The content of the document, given either inline (as a string) or as a reference (URI). + * + * @return the value value. + */ + public String getValue() { + return this.value; + } +} diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/DocumentContentSourceType.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/DocumentContentSourceType.java new file mode 100644 index 0000000000000..8e9b064cccf25 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/DocumentContentSourceType.java @@ -0,0 +1,49 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.cancerprofiling.models; + +import com.azure.core.util.ExpandableStringEnum; +import com.fasterxml.jackson.annotation.JsonCreator; +import java.util.Collection; + +/** + * The type of the content's source. In case the source type is 'inline', the content is given as a string (for + * instance, text). In case the source type is 'reference', the content is given as a URI. + */ +public final class DocumentContentSourceType extends ExpandableStringEnum { + /** Static value inline for DocumentContentSourceType. */ + public static final DocumentContentSourceType INLINE = fromString("inline"); + + /** Static value reference for DocumentContentSourceType. */ + public static final DocumentContentSourceType REFERENCE = fromString("reference"); + + /** + * Creates a new instance of DocumentContentSourceType value. + * + * @deprecated Use the {@link #fromString(String)} factory method. + */ + @Deprecated + public DocumentContentSourceType() {} + + /** + * Creates or finds a DocumentContentSourceType from its string representation. + * + * @param name a name to look for. + * @return the corresponding DocumentContentSourceType. + */ + @JsonCreator + public static DocumentContentSourceType fromString(String name) { + return fromString(name, DocumentContentSourceType.class); + } + + /** + * Gets known DocumentContentSourceType values. + * + * @return known DocumentContentSourceType values. + */ + public static Collection values() { + return values(DocumentContentSourceType.class); + } +} diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/DocumentType.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/DocumentType.java new file mode 100644 index 0000000000000..8a7fe417617be --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/DocumentType.java @@ -0,0 +1,52 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.cancerprofiling.models; + +import com.azure.core.util.ExpandableStringEnum; +import com.fasterxml.jackson.annotation.JsonCreator; +import java.util.Collection; + +/** The type of the patient document, such as 'note' (text document) or 'fhirBundle' (FHIR JSON document). */ +public final class DocumentType extends ExpandableStringEnum { + /** Static value note for DocumentType. */ + public static final DocumentType NOTE = fromString("note"); + + /** Static value fhirBundle for DocumentType. */ + public static final DocumentType FHIR_BUNDLE = fromString("fhirBundle"); + + /** Static value dicom for DocumentType. */ + public static final DocumentType DICOM = fromString("dicom"); + + /** Static value genomicSequencing for DocumentType. */ + public static final DocumentType GENOMIC_SEQUENCING = fromString("genomicSequencing"); + + /** + * Creates a new instance of DocumentType value. + * + * @deprecated Use the {@link #fromString(String)} factory method. + */ + @Deprecated + public DocumentType() {} + + /** + * Creates or finds a DocumentType from its string representation. + * + * @param name a name to look for. + * @return the corresponding DocumentType. + */ + @JsonCreator + public static DocumentType fromString(String name) { + return fromString(name, DocumentType.class); + } + + /** + * Gets known DocumentType values. + * + * @return known DocumentType values. + */ + public static Collection values() { + return values(DocumentType.class); + } +} diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/InferenceEvidence.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/InferenceEvidence.java new file mode 100644 index 0000000000000..cfb2a452af0b5 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/InferenceEvidence.java @@ -0,0 +1,62 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.cancerprofiling.models; + +import com.azure.core.annotation.Immutable; +import com.fasterxml.jackson.annotation.JsonProperty; + +/** A piece of evidence corresponding to an inference. */ +@Immutable +public final class InferenceEvidence { + /* + * A piece of evidence from a clinical note (text document). + */ + @JsonProperty(value = "patientDataEvidence") + private ClinicalNoteEvidence patientDataEvidence; + + /* + * A piece of clinical information, expressed as a code in a clinical coding + * system. + */ + @JsonProperty(value = "patientInfoEvidence") + private ClinicalCodedElement patientInfoEvidence; + + /* + * A value indicating how important this piece of evidence is for the inference. + */ + @JsonProperty(value = "importance") + private Double importance; + + /** Creates an instance of InferenceEvidence class. */ + private InferenceEvidence() {} + + /** + * Get the patientDataEvidence property: A piece of evidence from a clinical note (text document). + * + * @return the patientDataEvidence value. + */ + public ClinicalNoteEvidence getPatientDataEvidence() { + return this.patientDataEvidence; + } + + /** + * Get the patientInfoEvidence property: A piece of clinical information, expressed as a code in a clinical coding + * system. + * + * @return the patientInfoEvidence value. + */ + public ClinicalCodedElement getPatientInfoEvidence() { + return this.patientInfoEvidence; + } + + /** + * Get the importance property: A value indicating how important this piece of evidence is for the inference. + * + * @return the importance value. + */ + public Double getImportance() { + return this.importance; + } +} diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/JobStatus.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/JobStatus.java new file mode 100644 index 0000000000000..0ba97158b2238 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/JobStatus.java @@ -0,0 +1,55 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.cancerprofiling.models; + +import com.azure.core.util.ExpandableStringEnum; +import com.fasterxml.jackson.annotation.JsonCreator; +import java.util.Collection; + +/** The status of the processing job. */ +public final class JobStatus extends ExpandableStringEnum { + /** Static value notStarted for JobStatus. */ + public static final JobStatus NOT_STARTED = fromString("notStarted"); + + /** Static value running for JobStatus. */ + public static final JobStatus RUNNING = fromString("running"); + + /** Static value succeeded for JobStatus. */ + public static final JobStatus SUCCEEDED = fromString("succeeded"); + + /** Static value failed for JobStatus. */ + public static final JobStatus FAILED = fromString("failed"); + + /** Static value partiallyCompleted for JobStatus. */ + public static final JobStatus PARTIALLY_COMPLETED = fromString("partiallyCompleted"); + + /** + * Creates a new instance of JobStatus value. + * + * @deprecated Use the {@link #fromString(String)} factory method. + */ + @Deprecated + public JobStatus() {} + + /** + * Creates or finds a JobStatus from its string representation. + * + * @param name a name to look for. + * @return the corresponding JobStatus. + */ + @JsonCreator + public static JobStatus fromString(String name) { + return fromString(name, JobStatus.class); + } + + /** + * Gets known JobStatus values. + * + * @return known JobStatus values. + */ + public static Collection values() { + return values(JobStatus.class); + } +} diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/OncoPhenotypeData.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/OncoPhenotypeData.java new file mode 100644 index 0000000000000..34683a558141e --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/OncoPhenotypeData.java @@ -0,0 +1,65 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.cancerprofiling.models; + +import com.azure.core.annotation.Fluent; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import java.util.List; + +/** The body of the Onco Phenotype request. */ +@Fluent +public final class OncoPhenotypeData { + /* + * The list of patients, including their clinical information and data. + */ + @JsonProperty(value = "patients", required = true) + private List patients; + + /* + * Configuration affecting the Onco Phenotype model's inference. + */ + @JsonProperty(value = "configuration") + private OncoPhenotypeModelConfiguration configuration; + + /** + * Creates an instance of OncoPhenotypeData class. + * + * @param patients the patients value to set. + */ + @JsonCreator + public OncoPhenotypeData(@JsonProperty(value = "patients", required = true) List patients) { + this.patients = patients; + } + + /** + * Get the patients property: The list of patients, including their clinical information and data. + * + * @return the patients value. + */ + public List getPatients() { + return this.patients; + } + + /** + * Get the configuration property: Configuration affecting the Onco Phenotype model's inference. + * + * @return the configuration value. + */ + public OncoPhenotypeModelConfiguration getConfiguration() { + return this.configuration; + } + + /** + * Set the configuration property: Configuration affecting the Onco Phenotype model's inference. + * + * @param configuration the configuration value to set. + * @return the OncoPhenotypeData object itself. + */ + public OncoPhenotypeData setConfiguration(OncoPhenotypeModelConfiguration configuration) { + this.configuration = configuration; + return this; + } +} diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/OncoPhenotypeInference.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/OncoPhenotypeInference.java new file mode 100644 index 0000000000000..10c2bd1ebf79a --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/OncoPhenotypeInference.java @@ -0,0 +1,119 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.cancerprofiling.models; + +import com.azure.core.annotation.Immutable; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import java.util.List; + +/** An inference made by the Onco Phenotype model regarding a patient. */ +@Immutable +public final class OncoPhenotypeInference { + /* + * The type of the Onco Phenotype inference + */ + @JsonProperty(value = "type", required = true) + private OncoPhenotypeInferenceType type; + + /* + * The value of the inference, as relevant for the given inference type. + */ + @JsonProperty(value = "value", required = true) + private String value; + + /* + * The description corresponding to the inference value. + */ + @JsonProperty(value = "description") + private String description; + + /* + * Confidence score for this inference. + */ + @JsonProperty(value = "confidenceScore") + private Double confidenceScore; + + /* + * The evidence corresponding to the inference value. + */ + @JsonProperty(value = "evidence") + private List evidence; + + /* + * An identifier for a clinical case, if there are multiple clinical cases regarding the same patient. + */ + @JsonProperty(value = "caseId") + private String caseId; + + /** + * Creates an instance of OncoPhenotypeInference class. + * + * @param type the type value to set. + * @param value the value value to set. + */ + @JsonCreator + private OncoPhenotypeInference( + @JsonProperty(value = "type", required = true) OncoPhenotypeInferenceType type, + @JsonProperty(value = "value", required = true) String value) { + this.type = type; + this.value = value; + } + + /** + * Get the type property: The type of the Onco Phenotype inference. + * + * @return the type value. + */ + public OncoPhenotypeInferenceType getType() { + return this.type; + } + + /** + * Get the value property: The value of the inference, as relevant for the given inference type. + * + * @return the value value. + */ + public String getValue() { + return this.value; + } + + /** + * Get the description property: The description corresponding to the inference value. + * + * @return the description value. + */ + public String getDescription() { + return this.description; + } + + /** + * Get the confidenceScore property: Confidence score for this inference. + * + * @return the confidenceScore value. + */ + public Double getConfidenceScore() { + return this.confidenceScore; + } + + /** + * Get the evidence property: The evidence corresponding to the inference value. + * + * @return the evidence value. + */ + public List getEvidence() { + return this.evidence; + } + + /** + * Get the caseId property: An identifier for a clinical case, if there are multiple clinical cases regarding the + * same patient. + * + * @return the caseId value. + */ + public String getCaseId() { + return this.caseId; + } +} diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/OncoPhenotypeInferenceType.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/OncoPhenotypeInferenceType.java new file mode 100644 index 0000000000000..a20cd237d07ed --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/OncoPhenotypeInferenceType.java @@ -0,0 +1,64 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.cancerprofiling.models; + +import com.azure.core.util.ExpandableStringEnum; +import com.fasterxml.jackson.annotation.JsonCreator; +import java.util.Collection; + +/** The type of the Onco Phenotype inference. */ +public final class OncoPhenotypeInferenceType extends ExpandableStringEnum { + /** Static value tumorSite for OncoPhenotypeInferenceType. */ + public static final OncoPhenotypeInferenceType TUMOR_SITE = fromString("tumorSite"); + + /** Static value histology for OncoPhenotypeInferenceType. */ + public static final OncoPhenotypeInferenceType HISTOLOGY = fromString("histology"); + + /** Static value clinicalStageT for OncoPhenotypeInferenceType. */ + public static final OncoPhenotypeInferenceType CLINICAL_STAGET = fromString("clinicalStageT"); + + /** Static value clinicalStageN for OncoPhenotypeInferenceType. */ + public static final OncoPhenotypeInferenceType CLINICAL_STAGEN = fromString("clinicalStageN"); + + /** Static value clinicalStageM for OncoPhenotypeInferenceType. */ + public static final OncoPhenotypeInferenceType CLINICAL_STAGEM = fromString("clinicalStageM"); + + /** Static value pathologicStageT for OncoPhenotypeInferenceType. */ + public static final OncoPhenotypeInferenceType PATHOLOGIC_STAGET = fromString("pathologicStageT"); + + /** Static value pathologicStageN for OncoPhenotypeInferenceType. */ + public static final OncoPhenotypeInferenceType PATHOLOGIC_STAGEN = fromString("pathologicStageN"); + + /** Static value pathologicStageM for OncoPhenotypeInferenceType. */ + public static final OncoPhenotypeInferenceType PATHOLOGIC_STAGEM = fromString("pathologicStageM"); + + /** + * Creates a new instance of OncoPhenotypeInferenceType value. + * + * @deprecated Use the {@link #fromString(String)} factory method. + */ + @Deprecated + public OncoPhenotypeInferenceType() {} + + /** + * Creates or finds a OncoPhenotypeInferenceType from its string representation. + * + * @param name a name to look for. + * @return the corresponding OncoPhenotypeInferenceType. + */ + @JsonCreator + public static OncoPhenotypeInferenceType fromString(String name) { + return fromString(name, OncoPhenotypeInferenceType.class); + } + + /** + * Gets known OncoPhenotypeInferenceType values. + * + * @return known OncoPhenotypeInferenceType values. + */ + public static Collection values() { + return values(OncoPhenotypeInferenceType.class); + } +} diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/OncoPhenotypeModelConfiguration.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/OncoPhenotypeModelConfiguration.java new file mode 100644 index 0000000000000..6b633087c50be --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/OncoPhenotypeModelConfiguration.java @@ -0,0 +1,131 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.cancerprofiling.models; + +import com.azure.core.annotation.Fluent; +import com.fasterxml.jackson.annotation.JsonProperty; +import java.util.List; + +/** Configuration affecting the Onco Phenotype model's inference. */ +@Fluent +public final class OncoPhenotypeModelConfiguration { + /* + * An indication whether the model should produce verbose output. + */ + @JsonProperty(value = "verbose") + private Boolean verbose; + + /* + * An indication whether the model's output should include evidence for the inferences. + */ + @JsonProperty(value = "includeEvidence") + private Boolean includeEvidence; + + /* + * A list of inference types to be inferred for the current request. + * This could be used if only part of the Onco Phenotype inferences are required. + * If this list is omitted or empty, the model will return all the inference types. + */ + @JsonProperty(value = "inferenceTypes") + private List inferenceTypes; + + /* + * An indication whether to perform a preliminary step on the patient's documents to determine whether they relate + * to a Cancer case. + */ + @JsonProperty(value = "checkForCancerCase") + private Boolean checkForCancerCase; + + /** Creates an instance of OncoPhenotypeModelConfiguration class. */ + public OncoPhenotypeModelConfiguration() {} + + /** + * Get the verbose property: An indication whether the model should produce verbose output. + * + * @return the verbose value. + */ + public Boolean isVerbose() { + return this.verbose; + } + + /** + * Set the verbose property: An indication whether the model should produce verbose output. + * + * @param verbose the verbose value to set. + * @return the OncoPhenotypeModelConfiguration object itself. + */ + public OncoPhenotypeModelConfiguration setVerbose(Boolean verbose) { + this.verbose = verbose; + return this; + } + + /** + * Get the includeEvidence property: An indication whether the model's output should include evidence for the + * inferences. + * + * @return the includeEvidence value. + */ + public Boolean isIncludeEvidence() { + return this.includeEvidence; + } + + /** + * Set the includeEvidence property: An indication whether the model's output should include evidence for the + * inferences. + * + * @param includeEvidence the includeEvidence value to set. + * @return the OncoPhenotypeModelConfiguration object itself. + */ + public OncoPhenotypeModelConfiguration setIncludeEvidence(Boolean includeEvidence) { + this.includeEvidence = includeEvidence; + return this; + } + + /** + * Get the inferenceTypes property: A list of inference types to be inferred for the current request. This could be + * used if only part of the Onco Phenotype inferences are required. If this list is omitted or empty, the model will + * return all the inference types. + * + * @return the inferenceTypes value. + */ + public List getInferenceTypes() { + return this.inferenceTypes; + } + + /** + * Set the inferenceTypes property: A list of inference types to be inferred for the current request. This could be + * used if only part of the Onco Phenotype inferences are required. If this list is omitted or empty, the model will + * return all the inference types. + * + * @param inferenceTypes the inferenceTypes value to set. + * @return the OncoPhenotypeModelConfiguration object itself. + */ + public OncoPhenotypeModelConfiguration setInferenceTypes(List inferenceTypes) { + this.inferenceTypes = inferenceTypes; + return this; + } + + /** + * Get the checkForCancerCase property: An indication whether to perform a preliminary step on the patient's + * documents to determine whether they relate to a Cancer case. + * + * @return the checkForCancerCase value. + */ + public Boolean isCheckForCancerCase() { + return this.checkForCancerCase; + } + + /** + * Set the checkForCancerCase property: An indication whether to perform a preliminary step on the patient's + * documents to determine whether they relate to a Cancer case. + * + * @param checkForCancerCase the checkForCancerCase value to set. + * @return the OncoPhenotypeModelConfiguration object itself. + */ + public OncoPhenotypeModelConfiguration setCheckForCancerCase(Boolean checkForCancerCase) { + this.checkForCancerCase = checkForCancerCase; + return this; + } +} diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/OncoPhenotypePatientResult.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/OncoPhenotypePatientResult.java new file mode 100644 index 0000000000000..f80c7c286f772 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/OncoPhenotypePatientResult.java @@ -0,0 +1,58 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.cancerprofiling.models; + +import com.azure.core.annotation.Immutable; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import java.util.List; + +/** The results of the model's work for a single patient. */ +@Immutable +public final class OncoPhenotypePatientResult { + /* + * The identifier given for the patient in the request. + */ + @JsonProperty(value = "id", required = true) + private String id; + + /* + * The model's inferences for the given patient. + */ + @JsonProperty(value = "inferences", required = true) + private List inferences; + + /** + * Creates an instance of OncoPhenotypePatientResult class. + * + * @param id the id value to set. + * @param inferences the inferences value to set. + */ + @JsonCreator + private OncoPhenotypePatientResult( + @JsonProperty(value = "id", required = true) String id, + @JsonProperty(value = "inferences", required = true) List inferences) { + this.id = id; + this.inferences = inferences; + } + + /** + * Get the id property: The identifier given for the patient in the request. + * + * @return the id value. + */ + public String getId() { + return this.id; + } + + /** + * Get the inferences property: The model's inferences for the given patient. + * + * @return the inferences value. + */ + public List getInferences() { + return this.inferences; + } +} diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/OncoPhenotypeResult.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/OncoPhenotypeResult.java new file mode 100644 index 0000000000000..c2361f8a5c782 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/OncoPhenotypeResult.java @@ -0,0 +1,123 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.cancerprofiling.models; + +import com.azure.core.annotation.Immutable; +import com.azure.core.models.ResponseError; +import com.fasterxml.jackson.annotation.JsonProperty; +import java.time.OffsetDateTime; +import java.util.List; + +/** The response for the Onco Phenotype request. */ +@Immutable +public final class OncoPhenotypeResult { + /* + * A processing job identifier. + */ + @JsonProperty(value = "jobId", required = true, access = JsonProperty.Access.WRITE_ONLY) + private String jobId; + + /* + * The date and time when the processing job was created. + */ + @JsonProperty(value = "createdDateTime", required = true, access = JsonProperty.Access.WRITE_ONLY) + private OffsetDateTime createdDateTime; + + /* + * The date and time when the processing job is set to expire. + */ + @JsonProperty(value = "expirationDateTime", required = true, access = JsonProperty.Access.WRITE_ONLY) + private OffsetDateTime expirationDateTime; + + /* + * The date and time when the processing job was last updated. + */ + @JsonProperty(value = "lastUpdateDateTime", required = true, access = JsonProperty.Access.WRITE_ONLY) + private OffsetDateTime lastUpdateDateTime; + + /* + * The status of the processing job. + */ + @JsonProperty(value = "status", required = true, access = JsonProperty.Access.WRITE_ONLY) + private JobStatus status; + + /* + * An array of errors, if any errors occurred during the processing job. + */ + @JsonProperty(value = "errors", access = JsonProperty.Access.WRITE_ONLY) + private List errors; + + /* + * The inference results for the Onco Phenotype request. + */ + @JsonProperty(value = "results", access = JsonProperty.Access.WRITE_ONLY) + private OncoPhenotypeResults results; + + /** Creates an instance of OncoPhenotypeResult class. */ + private OncoPhenotypeResult() {} + + /** + * Get the jobId property: A processing job identifier. + * + * @return the jobId value. + */ + public String getJobId() { + return this.jobId; + } + + /** + * Get the createdDateTime property: The date and time when the processing job was created. + * + * @return the createdDateTime value. + */ + public OffsetDateTime getCreatedDateTime() { + return this.createdDateTime; + } + + /** + * Get the expirationDateTime property: The date and time when the processing job is set to expire. + * + * @return the expirationDateTime value. + */ + public OffsetDateTime getExpirationDateTime() { + return this.expirationDateTime; + } + + /** + * Get the lastUpdateDateTime property: The date and time when the processing job was last updated. + * + * @return the lastUpdateDateTime value. + */ + public OffsetDateTime getLastUpdateDateTime() { + return this.lastUpdateDateTime; + } + + /** + * Get the status property: The status of the processing job. + * + * @return the status value. + */ + public JobStatus getStatus() { + return this.status; + } + + /** + * Get the errors property: An array of errors, if any errors occurred during the processing job. + * + * @return the errors value. + */ + public List getErrors() { + return this.errors; + } + + /** + * Get the results property: The inference results for the Onco Phenotype request. + * + * @return the results value. + */ + public OncoPhenotypeResults getResults() { + return this.results; + } +} diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/OncoPhenotypeResults.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/OncoPhenotypeResults.java new file mode 100644 index 0000000000000..70bf0da19e7aa --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/OncoPhenotypeResults.java @@ -0,0 +1,58 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.cancerprofiling.models; + +import com.azure.core.annotation.Immutable; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import java.util.List; + +/** The inference results for the Onco Phenotype request. */ +@Immutable +public final class OncoPhenotypeResults { + /* + * Results for the patients given in the request. + */ + @JsonProperty(value = "patients", required = true) + private List patients; + + /* + * The version of the model used for inference, expressed as the model date. + */ + @JsonProperty(value = "modelVersion", required = true) + private String modelVersion; + + /** + * Creates an instance of OncoPhenotypeResults class. + * + * @param patients the patients value to set. + * @param modelVersion the modelVersion value to set. + */ + @JsonCreator + private OncoPhenotypeResults( + @JsonProperty(value = "patients", required = true) List patients, + @JsonProperty(value = "modelVersion", required = true) String modelVersion) { + this.patients = patients; + this.modelVersion = modelVersion; + } + + /** + * Get the patients property: Results for the patients given in the request. + * + * @return the patients value. + */ + public List getPatients() { + return this.patients; + } + + /** + * Get the modelVersion property: The version of the model used for inference, expressed as the model date. + * + * @return the modelVersion value. + */ + public String getModelVersion() { + return this.modelVersion; + } +} diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/PatientDocument.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/PatientDocument.java new file mode 100644 index 0000000000000..6bd3e0220f0e9 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/PatientDocument.java @@ -0,0 +1,156 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.cancerprofiling.models; + +import com.azure.core.annotation.Fluent; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import java.time.OffsetDateTime; + +/** A clinical document related to a patient. Document here is in the wide sense - not just a text document (note). */ +@Fluent +public final class PatientDocument { + /* + * The type of the patient document, such as 'note' (text document) or 'fhirBundle' (FHIR JSON document). + */ + @JsonProperty(value = "type", required = true) + private DocumentType type; + + /* + * The type of the clinical document. + */ + @JsonProperty(value = "clinicalType") + private ClinicalDocumentType clinicalType; + + /* + * A given identifier for the document. Has to be unique across all documents for a single patient. + */ + @JsonProperty(value = "id", required = true) + private String id; + + /* + * A 2 letter ISO 639-1 representation of the language of the document. + */ + @JsonProperty(value = "language") + private String language; + + /* + * The date and time when the document was created. + */ + @JsonProperty(value = "createdDateTime") + private OffsetDateTime createdDateTime; + + /* + * The content of the patient document. + */ + @JsonProperty(value = "content", required = true) + private DocumentContent content; + + /** + * Creates an instance of PatientDocument class. + * + * @param type the type value to set. + * @param id the id value to set. + * @param content the content value to set. + */ + @JsonCreator + public PatientDocument( + @JsonProperty(value = "type", required = true) DocumentType type, + @JsonProperty(value = "id", required = true) String id, + @JsonProperty(value = "content", required = true) DocumentContent content) { + this.type = type; + this.id = id; + this.content = content; + } + + /** + * Get the type property: The type of the patient document, such as 'note' (text document) or 'fhirBundle' (FHIR + * JSON document). + * + * @return the type value. + */ + public DocumentType getType() { + return this.type; + } + + /** + * Get the clinicalType property: The type of the clinical document. + * + * @return the clinicalType value. + */ + public ClinicalDocumentType getClinicalType() { + return this.clinicalType; + } + + /** + * Set the clinicalType property: The type of the clinical document. + * + * @param clinicalType the clinicalType value to set. + * @return the PatientDocument object itself. + */ + public PatientDocument setClinicalType(ClinicalDocumentType clinicalType) { + this.clinicalType = clinicalType; + return this; + } + + /** + * Get the id property: A given identifier for the document. Has to be unique across all documents for a single + * patient. + * + * @return the id value. + */ + public String getId() { + return this.id; + } + + /** + * Get the language property: A 2 letter ISO 639-1 representation of the language of the document. + * + * @return the language value. + */ + public String getLanguage() { + return this.language; + } + + /** + * Set the language property: A 2 letter ISO 639-1 representation of the language of the document. + * + * @param language the language value to set. + * @return the PatientDocument object itself. + */ + public PatientDocument setLanguage(String language) { + this.language = language; + return this; + } + + /** + * Get the createdDateTime property: The date and time when the document was created. + * + * @return the createdDateTime value. + */ + public OffsetDateTime getCreatedDateTime() { + return this.createdDateTime; + } + + /** + * Set the createdDateTime property: The date and time when the document was created. + * + * @param createdDateTime the createdDateTime value to set. + * @return the PatientDocument object itself. + */ + public PatientDocument setCreatedDateTime(OffsetDateTime createdDateTime) { + this.createdDateTime = createdDateTime; + return this; + } + + /** + * Get the content property: The content of the patient document. + * + * @return the content value. + */ + public DocumentContent getContent() { + return this.content; + } +} diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/PatientInfo.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/PatientInfo.java new file mode 100644 index 0000000000000..89d04f05c3321 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/PatientInfo.java @@ -0,0 +1,95 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.cancerprofiling.models; + +import com.azure.core.annotation.Fluent; +import com.fasterxml.jackson.annotation.JsonProperty; +import java.time.LocalDate; +import java.util.List; + +/** Patient structured information, including demographics and known structured clinical information. */ +@Fluent +public final class PatientInfo { + /* + * The patient's sex. + */ + @JsonProperty(value = "sex") + private PatientInfoSex sex; + + /* + * The patient's date of birth. + */ + @JsonProperty(value = "birthDate") + private LocalDate birthDate; + + /* + * Known clinical information for the patient, structured. + */ + @JsonProperty(value = "clinicalInfo") + private List clinicalInfo; + + /** Creates an instance of PatientInfo class. */ + public PatientInfo() {} + + /** + * Get the sex property: The patient's sex. + * + * @return the sex value. + */ + public PatientInfoSex getSex() { + return this.sex; + } + + /** + * Set the sex property: The patient's sex. + * + * @param sex the sex value to set. + * @return the PatientInfo object itself. + */ + public PatientInfo setSex(PatientInfoSex sex) { + this.sex = sex; + return this; + } + + /** + * Get the birthDate property: The patient's date of birth. + * + * @return the birthDate value. + */ + public LocalDate getBirthDate() { + return this.birthDate; + } + + /** + * Set the birthDate property: The patient's date of birth. + * + * @param birthDate the birthDate value to set. + * @return the PatientInfo object itself. + */ + public PatientInfo setBirthDate(LocalDate birthDate) { + this.birthDate = birthDate; + return this; + } + + /** + * Get the clinicalInfo property: Known clinical information for the patient, structured. + * + * @return the clinicalInfo value. + */ + public List getClinicalInfo() { + return this.clinicalInfo; + } + + /** + * Set the clinicalInfo property: Known clinical information for the patient, structured. + * + * @param clinicalInfo the clinicalInfo value to set. + * @return the PatientInfo object itself. + */ + public PatientInfo setClinicalInfo(List clinicalInfo) { + this.clinicalInfo = clinicalInfo; + return this; + } +} diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/PatientInfoSex.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/PatientInfoSex.java new file mode 100644 index 0000000000000..9d2ffa0e1d8b3 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/PatientInfoSex.java @@ -0,0 +1,49 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.cancerprofiling.models; + +import com.azure.core.util.ExpandableStringEnum; +import com.fasterxml.jackson.annotation.JsonCreator; +import java.util.Collection; + +/** The patient's sex. */ +public final class PatientInfoSex extends ExpandableStringEnum { + /** Static value female for PatientInfoSex. */ + public static final PatientInfoSex FEMALE = fromString("female"); + + /** Static value male for PatientInfoSex. */ + public static final PatientInfoSex MALE = fromString("male"); + + /** Static value unspecified for PatientInfoSex. */ + public static final PatientInfoSex UNSPECIFIED = fromString("unspecified"); + + /** + * Creates a new instance of PatientInfoSex value. + * + * @deprecated Use the {@link #fromString(String)} factory method. + */ + @Deprecated + public PatientInfoSex() {} + + /** + * Creates or finds a PatientInfoSex from its string representation. + * + * @param name a name to look for. + * @return the corresponding PatientInfoSex. + */ + @JsonCreator + public static PatientInfoSex fromString(String name) { + return fromString(name, PatientInfoSex.class); + } + + /** + * Gets known PatientInfoSex values. + * + * @return known PatientInfoSex values. + */ + public static Collection values() { + return values(PatientInfoSex.class); + } +} diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/PatientRecord.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/PatientRecord.java new file mode 100644 index 0000000000000..71a069487f7b1 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/PatientRecord.java @@ -0,0 +1,94 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.cancerprofiling.models; + +import com.azure.core.annotation.Fluent; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import java.util.List; + +/** A patient record, including their clinical information and data. */ +@Fluent +public final class PatientRecord { + /* + * A given identifier for the patient. Has to be unique across all patients in a single request. + */ + @JsonProperty(value = "id", required = true) + private String id; + + /* + * Patient structured information, including demographics and known structured clinical information. + */ + @JsonProperty(value = "info") + private PatientInfo info; + + /* + * Patient unstructured clinical data, given as documents. + */ + @JsonProperty(value = "data") + private List data; + + /** + * Creates an instance of PatientRecord class. + * + * @param id the id value to set. + */ + @JsonCreator + public PatientRecord(@JsonProperty(value = "id", required = true) String id) { + this.id = id; + } + + /** + * Get the id property: A given identifier for the patient. Has to be unique across all patients in a single + * request. + * + * @return the id value. + */ + public String getId() { + return this.id; + } + + /** + * Get the info property: Patient structured information, including demographics and known structured clinical + * information. + * + * @return the info value. + */ + public PatientInfo getInfo() { + return this.info; + } + + /** + * Set the info property: Patient structured information, including demographics and known structured clinical + * information. + * + * @param info the info value to set. + * @return the PatientRecord object itself. + */ + public PatientRecord setInfo(PatientInfo info) { + this.info = info; + return this; + } + + /** + * Get the data property: Patient unstructured clinical data, given as documents. + * + * @return the data value. + */ + public List getData() { + return this.data; + } + + /** + * Set the data property: Patient unstructured clinical data, given as documents. + * + * @param data the data value to set. + * @return the PatientRecord object itself. + */ + public PatientRecord setData(List data) { + this.data = data; + return this; + } +} diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/package-info.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/package-info.java new file mode 100644 index 0000000000000..69bf37e5296aa --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/package-info.java @@ -0,0 +1,9 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +/** + * Package containing the data models for AzureHealthInsights. Azure Health Insights provides an API that serves insight + * models, specific for Health & Life Sciences, that perform analysis and provide inferences to be used by a human. + */ +package com.azure.health.insights.cancerprofiling.models; diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/package-info.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/package-info.java new file mode 100644 index 0000000000000..443b2cc5f7515 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/package-info.java @@ -0,0 +1,9 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +/** + * Package containing the classes for AzureHealthInsights. Azure Health Insights provides an API that serves insight + * models, specific for Health & Life Sciences, that perform analysis and provide inferences to be used by a human. + */ +package com.azure.health.insights.cancerprofiling; diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/module-info.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/module-info.java new file mode 100644 index 0000000000000..04ec3f09d9b76 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/module-info.java @@ -0,0 +1,14 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +module com.azure.health.insights.cancerprofiling { + requires transitive com.azure.core; + + exports com.azure.health.insights.cancerprofiling; + exports com.azure.health.insights.cancerprofiling.models; + + opens com.azure.health.insights.cancerprofiling.models to + com.azure.core, + com.fasterxml.jackson.databind; +} diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/resources/azure-health-insights-cancerprofiling.properties b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/resources/azure-health-insights-cancerprofiling.properties new file mode 100644 index 0000000000000..ca812989b4f27 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/resources/azure-health-insights-cancerprofiling.properties @@ -0,0 +1,2 @@ +name=${project.artifactId} +version=${project.version} diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/samples/README.md b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/samples/README.md new file mode 100644 index 0000000000000..3f4bbc8f2a46c --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/samples/README.md @@ -0,0 +1,57 @@ +--- +page_type: sample +languages: + - java +products: + - azure + - azure-cognitive-services + - azure-health-insights-cancerprofiling +urlFragment: healthinsights-java-samples +--- + +# Azure Health Insights client library samples for Java + +Azure Health Insights Cancer Profiling samples are a set of self-contained Java programs that demonstrate interacting with Azure self-contained service using the client library. Each sample focuses on a specific scenario and can be executed independently. + +## Key concepts + + +Key concepts are explained in detail [here] +## Getting started + + +Getting started explained in detail [here] + +## Examples + +The following sections provide code samples covering common scenario operations with the Azure Health Insights CancerProfiling client library. + +All of these samples need the endpoint to your Health Insights resource, and your Health Insights API key. + +|**File Name**|**Description**| +|----------------|-------------| +|[SampleInferCancerProfile.java][infer_cancer_profiling]|Get the inferred cancer staging| + +## Troubleshooting + + +Troubleshooting steps can be found [here]. + +## Next steps + + +See [Next steps]. + +## Contributing + +If you would like to become an active contributor to this project please refer to our [Contribution +Guidelines][SDK_README_CONTRIBUTING] for more information. + + diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/samples/java/com/azure/health/insights/cancerprofiling/SampleInferCancerProfile.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/samples/java/com/azure/health/insights/cancerprofiling/SampleInferCancerProfile.java new file mode 100644 index 0000000000000..0c92fbabf869c --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/samples/java/com/azure/health/insights/cancerprofiling/SampleInferCancerProfile.java @@ -0,0 +1,172 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. + +package com.azure.health.insights.cancerprofiling; + +import java.io.IOException; +import java.time.LocalDate; +import java.time.OffsetDateTime; +import java.util.Arrays; +import java.util.LinkedList; + +import com.azure.core.credential.AzureKeyCredential; +import com.azure.core.util.polling.PollerFlux; +import com.azure.health.insights.cancerprofiling.models.PatientInfoSex; +import com.azure.health.insights.cancerprofiling.models.ClinicalCodedElement; +import com.azure.health.insights.cancerprofiling.models.PatientInfo; +import com.azure.health.insights.cancerprofiling.models.PatientRecord; +import com.azure.health.insights.cancerprofiling.models.PatientDocument; +import com.azure.health.insights.cancerprofiling.models.ClinicalDocumentType; +import com.azure.health.insights.cancerprofiling.models.DocumentType; +import com.azure.health.insights.cancerprofiling.models.DocumentContentSourceType; +import com.azure.health.insights.cancerprofiling.models.DocumentContent; +import com.azure.health.insights.cancerprofiling.models.OncoPhenotypeResults; +import com.azure.health.insights.cancerprofiling.models.OncoPhenotypeModelConfiguration; +import com.azure.health.insights.cancerprofiling.models.OncoPhenotypeData; +import com.azure.health.insights.cancerprofiling.models.OncoPhenotypeResult; +import com.azure.health.insights.cancerprofiling.models.ClinicalNoteEvidence; + +public class SampleInferCancerProfile { + public static void runSample(String endpoint, String apiKey) throws InterruptedException, IOException { + CancerProfilingAsyncClient asyncClient = new CancerProfilingClientBuilder() + .endpoint(endpoint) + .serviceVersion(AzureHealthInsightsServiceVersion.getLatest()) + .credential(new AzureKeyCredential(apiKey)) + .buildAsyncClient(); + + // construct Patient + PatientRecord patient1 = new PatientRecord("patient_id"); + PatientInfo patientInfo = new PatientInfo(); + patientInfo.setBirthDate(LocalDate.parse("1965-12-26")); + patientInfo.setSex(PatientInfoSex.FEMALE); + patient1.setInfo(patientInfo); + LinkedList patientDocuments = new LinkedList<>(); + patient1.setData(patientDocuments); + + // Add imaging document + final String docContent1 = String.join(System.getProperty("line.separator"), + "15.8.2021", + "Jane Doe 091175-8967", + "42 year old female, married with 3 children, works as a nurse. ", + "Healthy, no medications taken on a regular basis.", + "PMHx is significant for migraines with aura, uses Mirena for contraception.", + "Smoking history of 10 pack years (has stopped and relapsed several times).", + "She is in c/o 2 weeks of productive cough and shortness of breath.", + "She has a fever of 37.8 and general weakness. ", + "Denies night sweats and rash. She denies symptoms of rhinosinusitis, asthma, and heartburn. ", + "On PE:", + "GENERAL: mild pallor, no cyanosis. Regular breathing rate. ", + "LUNGS: decreased breath sounds on the base of the right lung. Vesicular breathing.", + " No crackles, rales, and wheezes. Resonant percussion. ", + "PLAN: ", + "Will be referred for a chest x-ray. ", + "======================================", + "CXR showed mild nonspecific opacities in right lung base. ", + "PLAN:", + "Findings are suggestive of a working diagnosis of pneumonia. The patient is referred to a follow-up CXR in 2 weeks."); + + PatientDocument patientDocument1 = new PatientDocument( + DocumentType.NOTE, + "doc1", + new DocumentContent(DocumentContentSourceType.INLINE, docContent1)); + + patientDocument1.setClinicalType(ClinicalDocumentType.IMAGING); + patientDocument1.setLanguage("en"); + patientDocument1.setCreatedDateTime(OffsetDateTime.parse("2021-08-15T10:15:30+01:00")); + patient1.getData().add(patientDocument1); + + // Add Pathology documents + String docContent2 = String.join(System.getProperty("line.separator"), + "Oncology Clinic ", + "20.10.2021", + "Jane Doe 091175-8967", + "42-year-old healthy female who works as a nurse in the ER of this hospital. ", + "First menstruation at 11 years old. First delivery- 27 years old. She has 3 children.", + "Didn’t breastfeed. ", + "Contraception- Mirena.", + "Smoking- 10 pack years. ", + "Mother- Belarusian. Father- Georgian. ", + "About 3 months prior to admission, she stated she had SOB and was febrile. ", + "She did a CXR as an outpatient which showed a finding in the base of the right lung- possibly an infiltrate.", + "She was treated with antibiotics with partial response. ", + "6 weeks later a repeat CXR was performed- a few solid dense findings in the right lung. ", + "Therefore, she was referred for a PET-CT which demonstrated increased uptake in the right breast, lymph nodes on the right a few areas in the lungs and liver. ", + "On biopsy from the lesion in the right breast- triple negative adenocarcinoma. Genetic testing has not been done thus far. ", + "Genetic counseling- the patient denies a family history of breast, ovary, uterus, and prostate cancer. Her mother has chronic lymphocytic leukemia (CLL). ", + "She is planned to undergo genetic tests because the aggressive course of the disease, and her young age. ", + "Impression:", + "Stage 4 triple negative breast adenocarcinoma. ", + "Could benefit from biological therapy. ", + "Different treatment options were explained- the patient wants to get a second opinion."); + + PatientDocument patientDocument2 = new PatientDocument(DocumentType.NOTE, + "doc2", + new DocumentContent(DocumentContentSourceType.INLINE, docContent2)); + patientDocument2.setClinicalType(ClinicalDocumentType.PATHOLOGY); + patientDocument2.setLanguage("en"); + patientDocument2.setCreatedDateTime(OffsetDateTime.parse("2021-10-20T22:00:00.00Z")); + patient1.getData().add(patientDocument2); + + String docContent3 = String.join(System.getProperty("line.separator"), + "PATHOLOGY REPORT", + " Clinical Information", + "Ultrasound-guided biopsy; A. 18 mm mass; most likely diagnosis based on imaging: IDC", + " Diagnosis", + " A. BREAST, LEFT AT 2:00 4 CM FN; ULTRASOUND-GUIDED NEEDLE CORE BIOPSIES:", + " - Invasive carcinoma of no special type (invasive ductal carcinoma), grade 1", + " Nottingham histologic grade: 1/3 (tubules 2; nuclear grade 2; mitotic rate 1; total score; 5/9)", + " Fragments involved by invasive carcinoma: 2", + " Largest measurement of invasive carcinoma on a single fragment: 7 mm", + " Ductal carcinoma in situ (DCIS): Present", + " Architectural pattern: Cribriform", + " Nuclear grade: 2-", + " -intermediate", + " Necrosis: Not identified", + " Fragments involved by DCIS: 1", + " Largest measurement of DCIS on a single fragment: Span 2 mm", + " Microcalcifications: Present in benign breast tissue and invasive carcinoma", + " Blocks with invasive carcinoma: A1", + " Special studies: Pending"); + + PatientDocument patientDocument3 = new PatientDocument(DocumentType.NOTE, + "doc3", + new DocumentContent(DocumentContentSourceType.INLINE, docContent3)); + patientDocument3.setClinicalType(ClinicalDocumentType.PATHOLOGY); + patientDocument3.setLanguage("en"); + patientDocument3.setCreatedDateTime(OffsetDateTime.parse("2022-01-01T10:15:30+01:00")); + + patient1.getData().add(patientDocument3); + + // Set configuration to include evidence for the cancer staging inferences + OncoPhenotypeModelConfiguration configuration = new OncoPhenotypeModelConfiguration(); + configuration.setIncludeEvidence(true); + + // Construct the request with the patient and configration + OncoPhenotypeData oncoPhenotypeData = new OncoPhenotypeData(Arrays.asList(patient1)); + oncoPhenotypeData.setConfiguration(configuration); + + PollerFlux asyncPoller = asyncClient.beginInferCancerProfile(oncoPhenotypeData); + OncoPhenotypeResult result = asyncPoller.blockLast().getValue(); + printResults(result); + } + + private static void printResults(OncoPhenotypeResult result) { + OncoPhenotypeResults oncoResults = result.getResults(); + oncoResults.getPatients().forEach(patient_result -> { + System.out.println("\n==== Inferences of Patient " + patient_result.getId() + " ===="); + patient_result.getInferences().forEach(onco_inference -> { + System.out.println("\n=== Clinical Type: " + onco_inference.getType() + " Value: " + onco_inference.getValue() + " ConfidenceScore: " + onco_inference.getConfidenceScore() + " ==="); + onco_inference.getEvidence().forEach(evidence -> { + if (evidence.getPatientDataEvidence() != null) { + ClinicalNoteEvidence dataEvidence = evidence.getPatientDataEvidence(); + System.out.println("Evidence " + dataEvidence.getId() + " " + dataEvidence.getOffset() + " " + dataEvidence.getLength() + " " + dataEvidence.getText()); + } + if (evidence.getPatientInfoEvidence() != null) { + ClinicalCodedElement infoEvidence = evidence.getPatientInfoEvidence(); + System.out.println("Evidence " + infoEvidence.getSystem() + " " + infoEvidence.getCode() + " " + infoEvidence.getName() + " " + infoEvidence.getValue()); + } + }); + }); + }); + } +} diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/java/com/azure/health/insights/cancerprofiling/AllSamples.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/java/com/azure/health/insights/cancerprofiling/AllSamples.java new file mode 100644 index 0000000000000..3e200206b4464 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/java/com/azure/health/insights/cancerprofiling/AllSamples.java @@ -0,0 +1,25 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. + +package com.azure.health.insights.cancerprofiling; + +import java.io.IOException; + +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; + +public class AllSamples { + String endpoint; + String apiKey; + + @BeforeEach + public void init() { + endpoint = System.getenv("SDK_JAVA_HDS_ENDPOINT"); + apiKey = System.getenv("SDK_JAVA_HDS_APIKEY"); + } + + @Test + public void inferCancerProfile() throws InterruptedException, IOException { + SampleInferCancerProfile.runSample(endpoint, apiKey); + } +} diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/java/com/azure/health/insights/cancerprofiling/CancerProfilingClientTest.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/java/com/azure/health/insights/cancerprofiling/CancerProfilingClientTest.java new file mode 100644 index 0000000000000..a36cdd97eb248 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/java/com/azure/health/insights/cancerprofiling/CancerProfilingClientTest.java @@ -0,0 +1,56 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. + +package com.azure.health.insights.cancerprofiling; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import com.azure.health.insights.cancerprofiling.models.OncoPhenotypePatientResult; +import com.azure.health.insights.cancerprofiling.models.OncoPhenotypeResult; +import com.azure.health.insights.cancerprofiling.models.OncoPhenotypeInference; + +import com.azure.core.util.serializer.TypeReference; + +import com.azure.core.http.rest.RequestOptions; +import com.azure.core.util.BinaryData; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; + +import java.util.Arrays; +import java.util.List; + +/** + * Unit tests for {@link CancerProfilingClient}. + */ +public class CancerProfilingClientTest extends CancerProfilingClientTestBase { + + private CancerProfilingClient getClient() { + return getClientBuilder().buildClient(); + } + + @Test + public void test() { + try { + testCancerProfilingWithResponse(request -> { + BinaryData responseValue = getClient().beginInferCancerProfile(request, new RequestOptions()).waitForCompletion().getValue(); + OncoPhenotypeResult respone = responseValue.toObject(TypeReference.createInstance(OncoPhenotypeResult.class)); + + List patients = respone.getResults().getPatients(); + assertEquals(1, patients.size()); + OncoPhenotypePatientResult patient = patients.get(0); + assertEquals(8, patient.getInferences().size()); + OncoPhenotypeInference inference = patient.getInferences().get(0); + assertEquals("BREAST", inference.getDescription()); + assertEquals(0.5563, inference.getEvidence().get(0).getImportance()); + }); + + } catch (Throwable t) { + String message = t.toString() + "\n" + Arrays.toString(t.getStackTrace()); + t.printStackTrace(); + Assertions.fail(message); + return; + } + + System.out.println("Success"); + } +} diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/java/com/azure/health/insights/cancerprofiling/CancerProfilingClientTestBase.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/java/com/azure/health/insights/cancerprofiling/CancerProfilingClientTestBase.java new file mode 100644 index 0000000000000..a7df9fd5f10e8 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/java/com/azure/health/insights/cancerprofiling/CancerProfilingClientTestBase.java @@ -0,0 +1,70 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. + +package com.azure.health.insights.cancerprofiling; + +import com.azure.core.credential.AzureKeyCredential; +import com.azure.core.http.HttpClient; +import com.azure.core.http.HttpPipeline; +import com.azure.core.http.HttpPipelineBuilder; +import com.azure.core.http.policy.AzureKeyCredentialPolicy; +import com.azure.core.http.policy.HttpPipelinePolicy; +import com.azure.core.test.TestBase; +import com.azure.core.test.TestMode; +import com.azure.core.util.BinaryData; +import com.azure.core.util.Configuration; + +import java.nio.file.Paths; +import java.util.function.Consumer; + + +/** + * Base class for OncoPhenotype clients test. + */ +public class CancerProfilingClientTestBase extends TestBase { + private static final String FAKE_API_KEY = "fakeKeyPlaceholder"; + private static final String OCP_APIM_SUBSCRIPTION_KEY = "Ocp-Apim-Subscription-Key"; + + void testCancerProfilingWithResponse(Consumer testRunner) { + testRunner.accept(getOncoPhenotypeRequest()); + } + + CancerProfilingClientBuilder getClientBuilder() { + String endpoint = getEndpoint(); + + HttpPipelinePolicy authPolicy = new AzureKeyCredentialPolicy(OCP_APIM_SUBSCRIPTION_KEY, + new AzureKeyCredential(getKey())); + HttpClient httpClient; + if (getTestMode() == TestMode.RECORD || getTestMode() == TestMode.LIVE) { + httpClient = HttpClient.createDefault(); + } else { + httpClient = interceptorManager.getPlaybackClient(); + } + HttpPipeline httpPipeline = new HttpPipelineBuilder() + .httpClient(httpClient) + .policies(authPolicy, interceptorManager.getRecordPolicy()).build(); + + return new CancerProfilingClientBuilder() + .pipeline(httpPipeline) + .endpoint(endpoint); + } + + private String getKey() { + if (getTestMode() == TestMode.PLAYBACK) { + return FAKE_API_KEY; + } else { + return Configuration.getGlobalConfiguration().get("AZURE_HEALTHINSIGHTS_API_KEY"); + } + } + + String getEndpoint() { + return interceptorManager.isPlaybackMode() + ? "https://localhost:8080" + : Configuration.getGlobalConfiguration().get("AZURE_HEALTHINSIGHTS_ENDPOINT"); + } + + private BinaryData getOncoPhenotypeRequest() { + BinaryData requestBody = BinaryData.fromFile(Paths.get("target/test-classes/session-records/CancerProfilingClientTest.request.json")); + return requestBody; + } +} diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/resources/session-records/CancerProfilingClientTest.request.json b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/resources/session-records/CancerProfilingClientTest.request.json new file mode 100644 index 0000000000000..1144d64c1c3a6 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/resources/session-records/CancerProfilingClientTest.request.json @@ -0,0 +1,25 @@ +{ + "configuration": { + "checkForCancerCase": true, + "verbose": false, + "includeEvidence": true + }, + "patients": [ + { + "id": "patient1", + "data": [ + { + "kind": "note", + "clinicalType": "pathology", + "id": "document1", + "language": "en", + "createdDateTime": "2022-01-01T10:15:30+01:00", + "content": { + "sourceType": "inline", + "value": "Laterality: Left \n Tumor type present: Invasive duct carcinoma; duct carcinoma in situ \n Tumor site: Upper inner quadrant \n Invasive carcinoma \n Histologic type: Ductal \n Size of invasive component: 0.9 cm \n Histologic Grade - Nottingham combined histologic score: 1 out of 3 \n In situ carcinoma (DCIS) \n Histologic type of DCIS: Cribriform and solid \n Necrosis in DCIS: Yes \n DCIS component of invasive carcinoma: Extensive \n" + } + } + ] + } + ] +} diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/resources/session-records/CancerProfilingClientTest.test.json b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/resources/session-records/CancerProfilingClientTest.test.json new file mode 100644 index 0000000000000..ff9e6d3d39153 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/resources/session-records/CancerProfilingClientTest.test.json @@ -0,0 +1,79 @@ +{ + "networkCallRecords" : [ + { + "Method" : "POST", + "Uri" : "https://REDACTED.cognitiveservices.azure.com/healthinsights/oncophenotype/jobs?api-version=2023-03-01-preview", + "Headers" : { + "Accept": "*/*", + "Accept-Encoding": "gzip, deflate", + "Connection": "keep-alive", + "Content-Length": "776", + "Content-Type": "application/json", + "Ocp-Apim-Subscription-Key": "00000000000000000000000000000000" + }, + "Response" : { + "apim-request-id": "6fe9d49e-abb0-4d34-9b3b-bb1ae44eef3a", + "Content-Length": "0", + "Date": "Sun, 29 Jan 2023 09:11:47 GMT", + "operation-location": "https://fake_ad_resource.cognitiveservices.azure.com//healthinsights/oncophenotype/jobs/7b4841b5-e7d4-4202-a300-6455ff4148de?api-version=2023-03-01-preview", + "Strict-Transport-Security": "max-age=31536000; includeSubDomains; preload", + "X-Content-Type-Options": "nosniff", + "x-envoy-upstream-service-time": "101", + "x-ms-region": "West Europe", + "StatusCode" : "202", + "Body" : null, + "Content-Type" : "application/json", + "Retry-After": "1" + }, + "Exception" : null + }, + { + "Method" : "GET", + "Uri" : "https://REDACTED.cognitiveservices.azure.com/healthinsights/oncophenotype/jobs/7b4841b5-e7d4-4202-a300-6455ff4148de?api-version=2023-03-01-preview", + "Headers" : { + "Accept": "*/*", + "Accept-Encoding": "gzip, deflate", + "Connection": "keep-alive", + "Ocp-Apim-Subscription-Key": "00000000000000000000000000000000" + }, + "Response" : { + "apim-request-id": "1012b87e-f033-479d-829f-c74f6077060e", + "Content-Length": "196", + "Content-Type": "application/json; charset=utf-8", + "Date": "Sun, 29 Jan 2023 09:11:48 GMT", + "Strict-Transport-Security": "max-age=31536000; includeSubDomains; preload", + "X-Content-Type-Options": "nosniff", + "x-envoy-upstream-service-time": "63", + "x-ms-region": "West Europe", + "StatusCode" : "200", + "Body" : "{\n\"jobId\": \"7b4841b5-e7d4-4202-a300-6455ff4148de\",\n\"createdDateTime\": \"2023-01-29T09:16:35Z\",\n\"expirationDateTime\": \"2023-01-30T09:16:35Z\",\n\"lastUpdateDateTime\": \"2023-01-29T09:16:35Z\",\n\"status\": \"running\"\n}", + "Exception" : null + } + }, + { + "Method" : "GET", + "Uri" : "https://REDACTED.cognitiveservices.azure.com/healthinsights/oncophenotype/jobs/7b4841b5-e7d4-4202-a300-6455ff4148de?api-version=2023-03-01-preview", + "Headers" : { + "Accept": "*/*", + "Accept-Encoding": "gzip, deflate", + "Connection": "keep-alive", + "Ocp-Apim-Subscription-Key": "00000000000000000000000000000000" + }, + "Response" : { + "apim-request-id": "8fc0d436-b092-42ab-bdf9-bc75af5a7a5a", + "Content-Length": "4462", + "Content-Type": "application/json; charset=utf-8", + "Date": "Sun, 29 Jan 2023 09:11:48 GMT", + "Strict-Transport-Security": "max-age=31536000; includeSubDomains; preload", + "X-Content-Type-Options": "nosniff", + "x-envoy-upstream-service-time": "63", + "x-ms-region": "West Europe", + "StatusCode" : "200", + "Body" : "{\n\"results\": {\n\"patients\": [\n{\n\"id\": \"patient1\",\n\"inferences\": [\n{\n\"type\": \"tumorSite\",\n\"evidence\": [\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Upper inner\",\n\"offset\": 108,\n\"length\": 11\n},\n\"importance\": 0.5563\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"duct\",\n\"offset\": 68,\n\"length\": 4\n},\n\"importance\": 0.0156\n}\n],\n\"value\": \"C50.2\",\n\"description\": \"BREAST\",\n\"confidenceScore\": 0.9214\n},\n{\n\"type\": \"histology\",\n\"evidence\": [\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Ductal\",\n\"offset\": 174,\n\"length\": 6\n},\n\"importance\": 0.2937\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Invasive duct\",\n\"offset\": 43,\n\"length\": 13\n},\n\"importance\": 0.2439\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"invasive\",\n\"offset\": 193,\n\"length\": 8\n},\n\"importance\": 0.1588\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"duct\",\n\"offset\": 68,\n\"length\": 4\n},\n\"importance\": 0.1483\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"solid\",\n\"offset\": 368,\n\"length\": 5\n},\n\"importance\": 0.0694\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Cribriform\",\n\"offset\": 353,\n\"length\": 10\n},\n\"importance\": 0.043\n}\n],\n\"value\": \"8500\",\n\"confidenceScore\": 0.9973\n},\n{\n\"type\": \"clinicalStageT\",\n\"evidence\": [\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Invasive duct carcinoma; duct\",\n\"offset\": 43,\n\"length\": 29\n},\n\"importance\": 0.2613\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"invasive\",\n\"offset\": 193,\n\"length\": 8\n},\n\"importance\": 0.1341\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Laterality: Left\",\n\"offset\": 0,\n\"length\": 17\n},\n\"importance\": 0.0874\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Invasive\",\n\"offset\": 133,\n\"length\": 8\n},\n\"importance\": 0.0722\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"situ\",\n\"offset\": 86,\n\"length\": 4\n},\n\"importance\": 0.0651\n}\n],\n\"value\": \"T1\",\n\"confidenceScore\": 0.9956\n},\n{\n\"type\": \"clinicalStageN\",\n\"evidence\": [\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Invasive duct carcinoma; duct carcinoma in situ\",\n\"offset\": 43,\n\"length\": 47\n},\n\"importance\": 0.1529\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"invasive carcinoma: Extensive\",\n\"offset\": 423,\n\"length\": 30\n},\n\"importance\": 0.0782\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Invasive\",\n\"offset\": 133,\n\"length\": 8\n},\n\"importance\": 0.0715\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Tumor\",\n\"offset\": 95,\n\"length\": 5\n},\n\"importance\": 0.0513\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Left\",\n\"offset\": 13,\n\"length\": 4\n},\n\"importance\": 0.0325\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Tumor\",\n\"offset\": 22,\n\"length\": 5\n},\n\"importance\": 0.0174\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Histologic\",\n\"offset\": 156,\n\"length\": 10\n},\n\"importance\": 0.0066\n}\n],\n\"value\": \"N0\",\n\"confidenceScore\": 0.9931\n},\n{\n\"type\": \"clinicalStageM\",\n\"evidence\": [\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Laterality: Left\",\n\"offset\": 0,\n\"length\": 17\n},\n\"importance\": 0.1579\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Invasive duct\",\n\"offset\": 43,\n\"length\": 13\n},\n\"importance\": 0.1493\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Histologic Grade - Nottingham\",\n\"offset\": 225,\n\"length\": 29\n},\n\"importance\": 0.1038\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Invasive\",\n\"offset\": 133,\n\"length\": 8\n},\n\"importance\": 0.089\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"duct carcinoma\",\n\"offset\": 68,\n\"length\": 14\n},\n\"importance\": 0.0807\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"invasive\",\n\"offset\": 423,\n\"length\": 8\n},\n\"importance\": 0.057\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Extensive\",\n\"offset\": 444,\n\"length\": 9\n},\n\"importance\": 0.0494\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Tumor\",\n\"offset\": 22,\n\"length\": 5\n},\n\"importance\": 0.0311\n}\n],\n\"value\": \"None\",\n\"confidenceScore\": 0.5217\n},\n{\n\"type\": \"pathologicStageT\",\n\"evidence\": [\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Invasive duct\",\n\"offset\": 43,\n\"length\": 13\n},\n\"importance\": 0.3125\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Left\",\n\"offset\": 13,\n\"length\": 4\n},\n\"importance\": 0.201\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"invasive\",\n\"offset\": 193,\n\"length\": 8\n},\n\"importance\": 0.1244\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"invasive\",\n\"offset\": 423,\n\"length\": 8\n},\n\"importance\": 0.0961\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Invasive\",\n\"offset\": 133,\n\"length\": 8\n},\n\"importance\": 0.0623\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Tumor\",\n\"offset\": 22,\n\"length\": 5\n},\n\"importance\": 0.0583\n}\n],\n\"value\": \"T1\",\n\"confidenceScore\": 0.9477\n},\n{\n\"type\": \"pathologicStageN\",\n\"evidence\": [\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"invasive component:\",\n\"offset\": 193,\n\"length\": 19\n},\n\"importance\": 0.1402\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Nottingham combined histologic score:\",\n\"offset\": 244,\n\"length\": 37\n},\n\"importance\": 0.1096\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Invasive carcinoma\",\n\"offset\": 133,\n\"length\": 18\n},\n\"importance\": 0.1067\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Ductal\",\n\"offset\": 174,\n\"length\": 6\n},\n\"importance\": 0.0896\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Invasive duct carcinoma;\",\n\"offset\": 43,\n\"length\": 24\n},\n\"importance\": 0.0831\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Histologic\",\n\"offset\": 156,\n\"length\": 10\n},\n\"importance\": 0.0447\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"in situ\",\n\"offset\": 83,\n\"length\": 7\n},\n\"importance\": 0.042\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Tumor\",\n\"offset\": 22,\n\"length\": 5\n},\n\"importance\": 0.0092\n}\n],\n\"value\": \"N0\",\n\"confidenceScore\": 0.7927\n},\n{\n\"type\": \"pathologicStageM\",\n\"evidence\": [\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"In situ carcinoma (DCIS)\",\n\"offset\": 298,\n\"length\": 24\n},\n\"importance\": 0.1111\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Nottingham combined histologic\",\n\"offset\": 244,\n\"length\": 30\n},\n\"importance\": 0.0999\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"invasive carcinoma:\",\n\"offset\": 423,\n\"length\": 19\n},\n\"importance\": 0.0787\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"invasive\",\n\"offset\": 193,\n\"length\": 8\n},\n\"importance\": 0.0617\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Invasive duct carcinoma;\",\n\"offset\": 43,\n\"length\": 24\n},\n\"importance\": 0.0594\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Tumor\",\n\"offset\": 22,\n\"length\": 5\n},\n\"importance\": 0.0579\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"of DCIS:\",\n\"offset\": 343,\n\"length\": 8\n},\n\"importance\": 0.0483\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Laterality:\",\n\"offset\": 0,\n\"length\": 11\n},\n\"importance\": 0.0324\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Invasive carcinoma\",\n\"offset\": 133,\n\"length\": 18\n},\n\"importance\": 0.0269\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"carcinoma in\",\n\"offset\": 73,\n\"length\": 12\n},\n\"importance\": 0.0202\n},\n{\n\"patientDataEvidence\": {\n\"id\": \"document1\",\n\"text\": \"Tumor\",\n\"offset\": 95,\n\"length\": 5\n},\n\"importance\": 0.0112\n}\n],\n\"value\": \"M0\",\n\"confidenceScore\": 0.9208\n}\n]\n}\n],\n\"modelVersion\": \"2023-03-01-preview\"\n},\n\"jobId\": \"7b4841b5-e7d4-4202-a300-6455ff4148de\",\n\"createdDateTime\": \"2023-01-29T09:16:35Z\",\n\"expirationDateTime\": \"2023-01-30T09:16:35Z\",\n\"lastUpdateDateTime\": \"2023-01-29T09:16:36Z\",\n\"status\": \"succeeded\"\n}", + "Exception" : null + } + } + + ], + "variables" : [ ] +} diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/tests.yml b/sdk/healthinsights/azure-health-insights-cancerprofiling/tests.yml new file mode 100644 index 0000000000000..d79fef966e6d2 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/tests.yml @@ -0,0 +1,10 @@ +trigger: none + +stages: + - template: /eng/pipelines/templates/stages/archetype-sdk-tests.yml + parameters: + ServiceDirectory: healthinsights + Artifacts: + - name: azure-health-insights-cancerprofiling + groupId: com.azure + safeName: azurehealthinsightscancerprofiling diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/CHANGELOG.md b/sdk/healthinsights/azure-health-insights-clinicalmatching/CHANGELOG.md new file mode 100644 index 0000000000000..f887f194c985e --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/CHANGELOG.md @@ -0,0 +1,13 @@ +# Release History + +## 1.0.0-beta.1 (Unreleased) + +- Azure AzureHealthInsights client library for Java. This package contains Microsoft Azure AzureHealthInsights client library. + +### Features Added + +### Breaking Changes + +### Bugs Fixed + +### Other Changes diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/README.md b/sdk/healthinsights/azure-health-insights-clinicalmatching/README.md new file mode 100644 index 0000000000000..1695d82c359f6 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/README.md @@ -0,0 +1,139 @@ +# Azure Azure Health Insights Clinical Matching client library for Java + +## Getting started + +### Prerequisites + +- A [Java Development Kit (JDK)][jdk] with version 8 or above +- [Azure Subscription][azure_subscription] +- An existing Cognitive Services Health Insights instance. + +For more information about creating the resource or how to get the location and sku information see [here][cognitive_resource_cli]. + +### Include the Package + +[//]: # ({x-version-update-start;com.azure:azure-health-insights-clinicalmatching;current}) + +```xml + + com.azure + azure-health-insights-clinicalmatching + 1.0.0-beta.1 + +``` + +[//]: # ({x-version-update-end}) + +### Authenticate the client + +In order to interact with the Health Insighs Clinical Matching service, you'll need to create an instance of the [`ClinicalMatchingClient`][clinical_matching_client_class] class. You will need an **endpoint** and an **API key** to instantiate a client object. + +#### Get API Key + +You can obtain the endpoint and API key from the resource information in the [Azure Portal][azure_portal]. + +Alternatively, you can use the [Azure CLI][azure_cli] snippet below to get the API key from the Health Insights resource. + +```bash +az cognitiveservices account keys list --resource-group --name +``` + +#### Create a ClinicalMatchingClient with an API Key Credential + +Once you have the value for the API key, you can pass it as a string into an instance of **AzureKeyCredential**. Use the key as the credential parameter +to authenticate the client: + +```Java Snippet: +String endpoint = "endpoint"; +String apiKey = "apiKey"; +ClinicalMatchingAsyncClient asyncClient = new ClinicalMatchingClientBuilder() + .endpoint(endpoint) + .serviceVersion(AzureHealthInsightsServiceVersion.getLatest()) + .httpClient(HttpClient.createDefault(new HttpClientOptions())) + .credential(new AzureKeyCredential(apiKey)) + .buildAsyncClient(); + +``` + +## Key concepts + +Trial Matcher provides the user of the services two main modes of operation: patients centric and clinical trial centric. +- On patient centric mode, the Trial Matcher model bases the patient matching on the clinical condition, location, priorities, eligibility criteria, and other criteria that the patient and/or service users may choose to prioritize. The model helps narrow down and prioritize the set of relevant clinical trials to a smaller set of trials to start with, that the specific patient appears to be qualified for. +- On clinical trial centric, the Trial Matcher is finding a group of patients potentially eligible to a clinical trial. The Trial Matcher narrows down the patients, first filtered on clinical condition and selected clinical observations, and then focuses on those patients who met the baseline criteria, to find the group of patients that appears to be eligible patients to a trial. + +## Examples + +Finding potential eligible trials for a patient. + +```Java readme-sample-MatchTrialsSync +ClinicalMatchingClient syncClient = new ClinicalMatchingClientBuilder() + .endpoint(endpoint) + .serviceVersion(AzureHealthInsightsServiceVersion.getLatest()) + .httpClient(HttpClient.createDefault(new HttpClientOptions())) + .credential(new AzureKeyCredential(apiKey)) + .buildClient(); + +SyncPoller syncPoller = syncClient.beginMatchTrials(BinaryData.fromObject(trialMatcherOptions), null); +PollResponse pollerResponse = syncPoller.waitForCompletion(); + +LongRunningOperationStatus status = pollerResponse.getStatus(); +System.out.println("Status " + status); +TrialMatcherResult tmRespone = pollerResponse.getValue().toObject(TypeReference.createInstance(TrialMatcherResult.class)); +if (status == LongRunningOperationStatus.SUCCESSFULLY_COMPLETED) { + TrialMatcherResults tmResults = tmRespone.getResults(); + tmResults.getPatients().forEach(patientResult -> { + System.out.println("Inferences of Patient " + patientResult.getId()); + patientResult.getInferences().forEach(inference -> { + System.out.println("Trial Id " + inference.getId()); + System.out.println("Type: " + inference.getType() + " Value: " + inference.getValue()); + System.out.println("Description " + inference.getDescription()); + }); + }); +} else if (status == LongRunningOperationStatus.FAILED) { + List errors = tmRespone.getErrors(); + errors.forEach(error -> { + System.out.println(error.getCode() + " : " + error.getMessage()); + }); +} + +``` + +## Troubleshooting + +## Next steps + +To see the full example source files, see: + + +### Additional documentation + + +## Contributing + +This project welcomes contributions and suggestions. Most contributions require you to agree to a Contributor License Agreement (CLA) declaring that you have the right to, and actually do, grant us the rights to use your contribution. For details, visit [cla.microsoft.com][cla]. + +When you submit a pull request, a CLA-bot will automatically determine whether you need to provide a CLA and decorate the PR appropriately (e.g., label, comment). Simply follow the instructions provided by the bot. You will only need to do this once across all repos using our CLA. + +This project has adopted the [Microsoft Open Source Code of Conduct][code_of_conduct]. For more information see the [Code of Conduct FAQ][coc_faq] or contact [opencode@microsoft.com][coc_contact] with any additional questions or comments. + + +[cla]: https://cla.microsoft.com +[code_of_conduct]: https://opensource.microsoft.com/codeofconduct/ +[coc_faq]: https://opensource.microsoft.com/codeofconduct/faq/ +[coc_contact]: mailto:opencode@microsoft.com +[azure_subscription]: https://azure.microsoft.com/free/ +[cognitive_resource_cli]: https://docs.microsoft.com/azure/cognitive-services/cognitive-services-apis-create-account-cli + +[azure_cli]: https://docs.microsoft.com/cli/azure +[azure_portal]: https://portal.azure.com \ No newline at end of file diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/package.json b/sdk/healthinsights/azure-health-insights-clinicalmatching/package.json new file mode 100644 index 0000000000000..ded9535dc3f1e --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/package.json @@ -0,0 +1,5 @@ +{ + "dependencies": { + "mvn": "^3.5.0" + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/pom.xml b/sdk/healthinsights/azure-health-insights-clinicalmatching/pom.xml new file mode 100644 index 0000000000000..651c68874999a --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/pom.xml @@ -0,0 +1,110 @@ + + + 4.0.0 + + com.azure + azure-client-sdk-parent + 1.7.0 + ../../parents/azure-client-sdk-parent + + + com.azure + azure-health-insights-clinicalmatching + 1.0.0-beta.1 + jar + + Microsoft Azure SDK for HealthInsights Management + This package contains Microsoft Azure HealthInsights client library. + https://github.com/Azure/azure-sdk-for-java + + + + The MIT License (MIT) + http://opensource.org/licenses/MIT + repo + + + + + https://github.com/Azure/azure-sdk-for-java + scm:git:git@github.com:Azure/azure-sdk-for-java.git + scm:git:git@github.com:Azure/azure-sdk-for-java.git + HEAD + + + + microsoft + Microsoft + + + + UTF-8 + true + + + + com.azure + azure-core + 1.35.0 + + + com.azure + azure-core-http-netty + 1.12.8 + + + org.junit.jupiter + junit-jupiter-api + 5.9.1 + test + + + org.junit.jupiter + junit-jupiter-engine + 5.9.1 + test + + + org.mockito + mockito-core + 4.5.1 + test + + + com.azure + azure-core-test + 1.14.0 + test + + + com.azure + azure-identity + 1.7.3 + test + + + + + + + com.azure.tools + codesnippet-maven-plugin + 1.0.0-beta.8 + + **/src/samples/java/**/*.java + ${project.basedir}/src/samples/java + **/src/main/java/**/*.java + ${project.basedir}/src/main/java + true + ${project.basedir}/README.md + true + 120 + true + + + + + diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/AzureHealthInsightsServiceVersion.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/AzureHealthInsightsServiceVersion.java new file mode 100644 index 0000000000000..1abf2e3361517 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/AzureHealthInsightsServiceVersion.java @@ -0,0 +1,34 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching; + +import com.azure.core.util.ServiceVersion; + +/** Service version of ClinicalMatchingClient. */ +public enum AzureHealthInsightsServiceVersion implements ServiceVersion { + /** Enum value 2023-03-01-preview. */ + V2023_03_01_PREVIEW("2023-03-01-preview"); + + private final String version; + + AzureHealthInsightsServiceVersion(String version) { + this.version = version; + } + + /** {@inheritDoc} */ + @Override + public String getVersion() { + return this.version; + } + + /** + * Gets the latest service version supported by this client library. + * + * @return The latest {@link AzureHealthInsightsServiceVersion}. + */ + public static AzureHealthInsightsServiceVersion getLatest() { + return V2023_03_01_PREVIEW; + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingAsyncClient.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingAsyncClient.java new file mode 100644 index 0000000000000..3f114f4efe0d4 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingAsyncClient.java @@ -0,0 +1,319 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching; + +import com.azure.core.annotation.Generated; +import com.azure.core.annotation.ReturnType; +import com.azure.core.annotation.ServiceClient; +import com.azure.core.annotation.ServiceMethod; +import com.azure.core.exception.ClientAuthenticationException; +import com.azure.core.exception.HttpResponseException; +import com.azure.core.exception.ResourceModifiedException; +import com.azure.core.exception.ResourceNotFoundException; +import com.azure.core.http.rest.RequestOptions; +import com.azure.core.util.BinaryData; +import com.azure.core.util.polling.PollerFlux; +import com.azure.health.insights.clinicalmatching.implementation.ClinicalMatchingClientImpl; +import com.azure.health.insights.clinicalmatching.models.TrialMatcherData; +import com.azure.health.insights.clinicalmatching.models.TrialMatcherResult; + +/** Initializes a new instance of the asynchronous ClinicalMatchingClient type. */ +@ServiceClient(builder = ClinicalMatchingClientBuilder.class, isAsync = true) +public final class ClinicalMatchingAsyncClient { + @Generated private final ClinicalMatchingClientImpl serviceClient; + + /** + * Initializes an instance of ClinicalMatchingAsyncClient class. + * + * @param serviceClient the service client implementation. + */ + @Generated + ClinicalMatchingAsyncClient(ClinicalMatchingClientImpl serviceClient) { + this.serviceClient = serviceClient; + } + + /** + * Create Trial Matcher job + * + *

Creates a Trial Matcher job with the given request body. + * + *

Header Parameters + * + * + * + * + * + * + *
Header Parameters
NameTypeRequiredDescription
repeatability-request-idStringNoRepeatability request ID header
repeatability-first-sentStringNoRepeatability first sent header as HTTP-date
+ * + * You can add these to a request with {@link RequestOptions#addHeader} + * + *

Request Body Schema + * + * 

{@code
+     * {
+     *     patients (Required): [
+     *          (Required){
+     *             id: String (Required)
+     *             info (Optional): {
+     *                 sex: String(female/male/unspecified) (Optional)
+     *                 birthDate: LocalDate (Optional)
+     *                 clinicalInfo (Optional): [
+     *                      (Optional){
+     *                         system: String (Required)
+     *                         code: String (Required)
+     *                         name: String (Optional)
+     *                         value: String (Optional)
+     *                     }
+     *                 ]
+     *             }
+     *             data (Optional): [
+     *                  (Optional){
+     *                     type: String(note/fhirBundle/dicom/genomicSequencing) (Required)
+     *                     clinicalType: String(consultation/dischargeSummary/historyAndPhysical/procedure/progress/imaging/laboratory/pathology) (Optional)
+     *                     id: String (Required)
+     *                     language: String (Optional)
+     *                     createdDateTime: OffsetDateTime (Optional)
+     *                     content (Required): {
+     *                         sourceType: String(inline/reference) (Required)
+     *                         value: String (Required)
+     *                     }
+     *                 }
+     *             ]
+     *         }
+     *     ]
+     *     configuration (Optional): {
+     *         verbose: Boolean (Optional)
+     *         includeEvidence: Boolean (Optional)
+     *         clinicalTrials (Required): {
+     *             customTrials (Optional): [
+     *                  (Optional){
+     *                     id: String (Required)
+     *                     eligibilityCriteriaText: String (Optional)
+     *                     demographics (Optional): {
+     *                         acceptedSex: String(all/female/male) (Optional)
+     *                         acceptedAgeRange (Optional): {
+     *                             minimumAge (Optional): {
+     *                                 unit: String(years/months/days) (Required)
+     *                                 value: double (Required)
+     *                             }
+     *                             maximumAge (Optional): (recursive schema, see maximumAge above)
+     *                         }
+     *                     }
+     *                     metadata (Required): {
+     *                         phases (Optional): [
+     *                             String(notApplicable/earlyPhase1/phase1/phase2/phase3/phase4) (Optional)
+     *                         ]
+     *                         studyType: String(interventional/observational/expandedAccess/patientRegistries) (Optional)
+     *                         recruitmentStatus: String(unknownStatus/notYetRecruiting/recruiting/enrollingByInvitation) (Optional)
+     *                         conditions (Required): [
+     *                             String (Required)
+     *                         ]
+     *                         sponsors (Optional): [
+     *                             String (Optional)
+     *                         ]
+     *                         contacts (Optional): [
+     *                              (Optional){
+     *                                 name: String (Optional)
+     *                                 email: String (Optional)
+     *                                 phone: String (Optional)
+     *                             }
+     *                         ]
+     *                         facilities (Optional): [
+     *                              (Optional){
+     *                                 name: String (Required)
+     *                                 city: String (Optional)
+     *                                 state: String (Optional)
+     *                                 country: String (Required)
+     *                             }
+     *                         ]
+     *                     }
+     *                 }
+     *             ]
+     *             registryFilters (Optional): [
+     *                  (Optional){
+     *                     conditions (Optional): [
+     *                         String (Optional)
+     *                     ]
+     *                     studyTypes (Optional): [
+     *                         String(interventional/observational/expandedAccess/patientRegistries) (Optional)
+     *                     ]
+     *                     recruitmentStatuses (Optional): [
+     *                         String(unknownStatus/notYetRecruiting/recruiting/enrollingByInvitation) (Optional)
+     *                     ]
+     *                     sponsors (Optional): [
+     *                         String (Optional)
+     *                     ]
+     *                     phases (Optional): [
+     *                         String(notApplicable/earlyPhase1/phase1/phase2/phase3/phase4) (Optional)
+     *                     ]
+     *                     purposes (Optional): [
+     *                         String(notApplicable/screening/diagnostic/prevention/healthServicesResearch/treatment/deviceFeasibility/supportiveCare/basicScience/other) (Optional)
+     *                     ]
+     *                     ids (Optional): [
+     *                         String (Optional)
+     *                     ]
+     *                     sources (Optional): [
+     *                         String(custom/clinicaltrials.gov) (Optional)
+     *                     ]
+     *                     facilityNames (Optional): [
+     *                         String (Optional)
+     *                     ]
+     *                     facilityLocations (Optional): [
+     *                          (Optional){
+     *                             city: String (Optional)
+     *                             state: String (Optional)
+     *                             country: String (Required)
+     *                         }
+     *                     ]
+     *                     facilityAreas (Optional): [
+     *                          (Optional){
+     *                             type: String(Feature) (Required)
+     *                             geometry (Required): {
+     *                                 type: String(Point) (Required)
+     *                                 coordinates (Required): [
+     *                                     double (Required)
+     *                                 ]
+     *                             }
+     *                             properties (Required): {
+     *                                 subType: String(Circle) (Required)
+     *                                 radius: double (Required)
+     *                             }
+     *                         }
+     *                     ]
+     *                 }
+     *             ]
+     *         }
+     *     }
+     * }
+     * }
+ * + *

Response Body Schema + * + * 

{@code
+     * {
+     *     jobId: String (Required)
+     *     createdDateTime: OffsetDateTime (Required)
+     *     expirationDateTime: OffsetDateTime (Required)
+     *     lastUpdateDateTime: OffsetDateTime (Required)
+     *     status: String(notStarted/running/succeeded/failed/partiallyCompleted) (Required)
+     *     errors (Optional): [
+     *         ResponseError (Optional)
+     *     ]
+     *     results (Optional): {
+     *         patients (Required): [
+     *              (Required){
+     *                 id: String (Required)
+     *                 inferences (Required): [
+     *                      (Required){
+     *                         type: String(trialEligibility) (Required)
+     *                         value: String (Required)
+     *                         description: String (Optional)
+     *                         confidenceScore: Double (Optional)
+     *                         evidence (Optional): [
+     *                              (Optional){
+     *                                 eligibilityCriteriaEvidence: String (Optional)
+     *                                 patientDataEvidence (Optional): {
+     *                                     id: String (Required)
+     *                                     text: String (Optional)
+     *                                     offset: int (Required)
+     *                                     length: int (Required)
+     *                                 }
+     *                                 patientInfoEvidence (Optional): {
+     *                                     system: String (Required)
+     *                                     code: String (Required)
+     *                                     name: String (Optional)
+     *                                     value: String (Optional)
+     *                                 }
+     *                                 importance: Double (Optional)
+     *                             }
+     *                         ]
+     *                         id: String (Optional)
+     *                         source: String(custom/clinicaltrials.gov) (Optional)
+     *                         metadata (Optional): {
+     *                             phases (Optional): [
+     *                                 String(notApplicable/earlyPhase1/phase1/phase2/phase3/phase4) (Optional)
+     *                             ]
+     *                             studyType: String(interventional/observational/expandedAccess/patientRegistries) (Optional)
+     *                             recruitmentStatus: String(unknownStatus/notYetRecruiting/recruiting/enrollingByInvitation) (Optional)
+     *                             conditions (Required): [
+     *                                 String (Required)
+     *                             ]
+     *                             sponsors (Optional): [
+     *                                 String (Optional)
+     *                             ]
+     *                             contacts (Optional): [
+     *                                  (Optional){
+     *                                     name: String (Optional)
+     *                                     email: String (Optional)
+     *                                     phone: String (Optional)
+     *                                 }
+     *                             ]
+     *                             facilities (Optional): [
+     *                                  (Optional){
+     *                                     name: String (Required)
+     *                                     city: String (Optional)
+     *                                     state: String (Optional)
+     *                                     country: String (Required)
+     *                                 }
+     *                             ]
+     *                         }
+     *                     }
+     *                 ]
+     *                 neededClinicalInfo (Optional): [
+     *                      (Optional){
+     *                         system: String (Required)
+     *                         code: String (Required)
+     *                         name: String (Optional)
+     *                         value: String (Optional)
+     *                         semanticType: String (Optional)
+     *                         category: String (Optional)
+     *                     }
+     *                 ]
+     *             }
+     *         ]
+     *         modelVersion: String (Required)
+     *         knowledgeGraphLastUpdateDate: LocalDate (Optional)
+     *     }
+     * }
+     * }
+ * + * @param trialMatcherData The body of the Trial Matcher request. + * @param requestOptions The options to configure the HTTP request before HTTP client sends it. + * @throws HttpResponseException thrown if the request is rejected by server. + * @throws ClientAuthenticationException thrown if the request is rejected by server on status code 401. + * @throws ResourceNotFoundException thrown if the request is rejected by server on status code 404. + * @throws ResourceModifiedException thrown if the request is rejected by server on status code 409. + * @return the {@link PollerFlux} for polling of the response for the Trial Matcher request. + */ + @Generated + @ServiceMethod(returns = ReturnType.LONG_RUNNING_OPERATION) + public PollerFlux beginMatchTrials( + BinaryData trialMatcherData, RequestOptions requestOptions) { + return this.serviceClient.beginMatchTrialsAsync(trialMatcherData, requestOptions); + } + + /** + * Create Trial Matcher job + * + *

Creates a Trial Matcher job with the given request body. + * + * @param trialMatcherData The body of the Trial Matcher request. + * @throws IllegalArgumentException thrown if parameters fail the validation. + * @throws com.azure.core.exception.HttpResponseException thrown if the request is rejected by server. + * @throws ClientAuthenticationException thrown if the request is rejected by server on status code 401. + * @throws ResourceNotFoundException thrown if the request is rejected by server on status code 404. + * @throws ResourceModifiedException thrown if the request is rejected by server on status code 409. + * @throws RuntimeException all other wrapped checked exceptions if the request fails to be sent. + * @return the {@link PollerFlux} for polling of the response for the Trial Matcher request. + */ + @Generated + @ServiceMethod(returns = ReturnType.LONG_RUNNING_OPERATION) + public PollerFlux beginMatchTrials(TrialMatcherData trialMatcherData) { + // Generated convenience method for beginMatchTrialsWithModel + RequestOptions requestOptions = new RequestOptions(); + return serviceClient.beginMatchTrialsWithModelAsync(BinaryData.fromObject(trialMatcherData), requestOptions); + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingClient.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingClient.java new file mode 100644 index 0000000000000..84409ccc394c1 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingClient.java @@ -0,0 +1,317 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching; + +import com.azure.core.annotation.Generated; +import com.azure.core.annotation.ReturnType; +import com.azure.core.annotation.ServiceClient; +import com.azure.core.annotation.ServiceMethod; +import com.azure.core.exception.ClientAuthenticationException; +import com.azure.core.exception.HttpResponseException; +import com.azure.core.exception.ResourceModifiedException; +import com.azure.core.exception.ResourceNotFoundException; +import com.azure.core.http.rest.RequestOptions; +import com.azure.core.util.BinaryData; +import com.azure.core.util.polling.SyncPoller; +import com.azure.health.insights.clinicalmatching.models.TrialMatcherData; +import com.azure.health.insights.clinicalmatching.models.TrialMatcherResult; + +/** Initializes a new instance of the synchronous ClinicalMatchingClient type. */ +@ServiceClient(builder = ClinicalMatchingClientBuilder.class) +public final class ClinicalMatchingClient { + @Generated private final ClinicalMatchingAsyncClient client; + + /** + * Initializes an instance of ClinicalMatchingClient class. + * + * @param client the async client. + */ + @Generated + ClinicalMatchingClient(ClinicalMatchingAsyncClient client) { + this.client = client; + } + + /** + * Create Trial Matcher job + * + *

Creates a Trial Matcher job with the given request body. + * + *

Header Parameters + * + * + * + * + * + * + *
Header Parameters
NameTypeRequiredDescription
repeatability-request-idStringNoRepeatability request ID header
repeatability-first-sentStringNoRepeatability first sent header as HTTP-date
+ * + * You can add these to a request with {@link RequestOptions#addHeader} + * + *

Request Body Schema + * + * 

{@code
+     * {
+     *     patients (Required): [
+     *          (Required){
+     *             id: String (Required)
+     *             info (Optional): {
+     *                 sex: String(female/male/unspecified) (Optional)
+     *                 birthDate: LocalDate (Optional)
+     *                 clinicalInfo (Optional): [
+     *                      (Optional){
+     *                         system: String (Required)
+     *                         code: String (Required)
+     *                         name: String (Optional)
+     *                         value: String (Optional)
+     *                     }
+     *                 ]
+     *             }
+     *             data (Optional): [
+     *                  (Optional){
+     *                     type: String(note/fhirBundle/dicom/genomicSequencing) (Required)
+     *                     clinicalType: String(consultation/dischargeSummary/historyAndPhysical/procedure/progress/imaging/laboratory/pathology) (Optional)
+     *                     id: String (Required)
+     *                     language: String (Optional)
+     *                     createdDateTime: OffsetDateTime (Optional)
+     *                     content (Required): {
+     *                         sourceType: String(inline/reference) (Required)
+     *                         value: String (Required)
+     *                     }
+     *                 }
+     *             ]
+     *         }
+     *     ]
+     *     configuration (Optional): {
+     *         verbose: Boolean (Optional)
+     *         includeEvidence: Boolean (Optional)
+     *         clinicalTrials (Required): {
+     *             customTrials (Optional): [
+     *                  (Optional){
+     *                     id: String (Required)
+     *                     eligibilityCriteriaText: String (Optional)
+     *                     demographics (Optional): {
+     *                         acceptedSex: String(all/female/male) (Optional)
+     *                         acceptedAgeRange (Optional): {
+     *                             minimumAge (Optional): {
+     *                                 unit: String(years/months/days) (Required)
+     *                                 value: double (Required)
+     *                             }
+     *                             maximumAge (Optional): (recursive schema, see maximumAge above)
+     *                         }
+     *                     }
+     *                     metadata (Required): {
+     *                         phases (Optional): [
+     *                             String(notApplicable/earlyPhase1/phase1/phase2/phase3/phase4) (Optional)
+     *                         ]
+     *                         studyType: String(interventional/observational/expandedAccess/patientRegistries) (Optional)
+     *                         recruitmentStatus: String(unknownStatus/notYetRecruiting/recruiting/enrollingByInvitation) (Optional)
+     *                         conditions (Required): [
+     *                             String (Required)
+     *                         ]
+     *                         sponsors (Optional): [
+     *                             String (Optional)
+     *                         ]
+     *                         contacts (Optional): [
+     *                              (Optional){
+     *                                 name: String (Optional)
+     *                                 email: String (Optional)
+     *                                 phone: String (Optional)
+     *                             }
+     *                         ]
+     *                         facilities (Optional): [
+     *                              (Optional){
+     *                                 name: String (Required)
+     *                                 city: String (Optional)
+     *                                 state: String (Optional)
+     *                                 country: String (Required)
+     *                             }
+     *                         ]
+     *                     }
+     *                 }
+     *             ]
+     *             registryFilters (Optional): [
+     *                  (Optional){
+     *                     conditions (Optional): [
+     *                         String (Optional)
+     *                     ]
+     *                     studyTypes (Optional): [
+     *                         String(interventional/observational/expandedAccess/patientRegistries) (Optional)
+     *                     ]
+     *                     recruitmentStatuses (Optional): [
+     *                         String(unknownStatus/notYetRecruiting/recruiting/enrollingByInvitation) (Optional)
+     *                     ]
+     *                     sponsors (Optional): [
+     *                         String (Optional)
+     *                     ]
+     *                     phases (Optional): [
+     *                         String(notApplicable/earlyPhase1/phase1/phase2/phase3/phase4) (Optional)
+     *                     ]
+     *                     purposes (Optional): [
+     *                         String(notApplicable/screening/diagnostic/prevention/healthServicesResearch/treatment/deviceFeasibility/supportiveCare/basicScience/other) (Optional)
+     *                     ]
+     *                     ids (Optional): [
+     *                         String (Optional)
+     *                     ]
+     *                     sources (Optional): [
+     *                         String(custom/clinicaltrials.gov) (Optional)
+     *                     ]
+     *                     facilityNames (Optional): [
+     *                         String (Optional)
+     *                     ]
+     *                     facilityLocations (Optional): [
+     *                          (Optional){
+     *                             city: String (Optional)
+     *                             state: String (Optional)
+     *                             country: String (Required)
+     *                         }
+     *                     ]
+     *                     facilityAreas (Optional): [
+     *                          (Optional){
+     *                             type: String(Feature) (Required)
+     *                             geometry (Required): {
+     *                                 type: String(Point) (Required)
+     *                                 coordinates (Required): [
+     *                                     double (Required)
+     *                                 ]
+     *                             }
+     *                             properties (Required): {
+     *                                 subType: String(Circle) (Required)
+     *                                 radius: double (Required)
+     *                             }
+     *                         }
+     *                     ]
+     *                 }
+     *             ]
+     *         }
+     *     }
+     * }
+     * }
+ * + *

Response Body Schema + * + * 

{@code
+     * {
+     *     jobId: String (Required)
+     *     createdDateTime: OffsetDateTime (Required)
+     *     expirationDateTime: OffsetDateTime (Required)
+     *     lastUpdateDateTime: OffsetDateTime (Required)
+     *     status: String(notStarted/running/succeeded/failed/partiallyCompleted) (Required)
+     *     errors (Optional): [
+     *         ResponseError (Optional)
+     *     ]
+     *     results (Optional): {
+     *         patients (Required): [
+     *              (Required){
+     *                 id: String (Required)
+     *                 inferences (Required): [
+     *                      (Required){
+     *                         type: String(trialEligibility) (Required)
+     *                         value: String (Required)
+     *                         description: String (Optional)
+     *                         confidenceScore: Double (Optional)
+     *                         evidence (Optional): [
+     *                              (Optional){
+     *                                 eligibilityCriteriaEvidence: String (Optional)
+     *                                 patientDataEvidence (Optional): {
+     *                                     id: String (Required)
+     *                                     text: String (Optional)
+     *                                     offset: int (Required)
+     *                                     length: int (Required)
+     *                                 }
+     *                                 patientInfoEvidence (Optional): {
+     *                                     system: String (Required)
+     *                                     code: String (Required)
+     *                                     name: String (Optional)
+     *                                     value: String (Optional)
+     *                                 }
+     *                                 importance: Double (Optional)
+     *                             }
+     *                         ]
+     *                         id: String (Optional)
+     *                         source: String(custom/clinicaltrials.gov) (Optional)
+     *                         metadata (Optional): {
+     *                             phases (Optional): [
+     *                                 String(notApplicable/earlyPhase1/phase1/phase2/phase3/phase4) (Optional)
+     *                             ]
+     *                             studyType: String(interventional/observational/expandedAccess/patientRegistries) (Optional)
+     *                             recruitmentStatus: String(unknownStatus/notYetRecruiting/recruiting/enrollingByInvitation) (Optional)
+     *                             conditions (Required): [
+     *                                 String (Required)
+     *                             ]
+     *                             sponsors (Optional): [
+     *                                 String (Optional)
+     *                             ]
+     *                             contacts (Optional): [
+     *                                  (Optional){
+     *                                     name: String (Optional)
+     *                                     email: String (Optional)
+     *                                     phone: String (Optional)
+     *                                 }
+     *                             ]
+     *                             facilities (Optional): [
+     *                                  (Optional){
+     *                                     name: String (Required)
+     *                                     city: String (Optional)
+     *                                     state: String (Optional)
+     *                                     country: String (Required)
+     *                                 }
+     *                             ]
+     *                         }
+     *                     }
+     *                 ]
+     *                 neededClinicalInfo (Optional): [
+     *                      (Optional){
+     *                         system: String (Required)
+     *                         code: String (Required)
+     *                         name: String (Optional)
+     *                         value: String (Optional)
+     *                         semanticType: String (Optional)
+     *                         category: String (Optional)
+     *                     }
+     *                 ]
+     *             }
+     *         ]
+     *         modelVersion: String (Required)
+     *         knowledgeGraphLastUpdateDate: LocalDate (Optional)
+     *     }
+     * }
+     * }
+ * + * @param trialMatcherData The body of the Trial Matcher request. + * @param requestOptions The options to configure the HTTP request before HTTP client sends it. + * @throws HttpResponseException thrown if the request is rejected by server. + * @throws ClientAuthenticationException thrown if the request is rejected by server on status code 401. + * @throws ResourceNotFoundException thrown if the request is rejected by server on status code 404. + * @throws ResourceModifiedException thrown if the request is rejected by server on status code 409. + * @return the {@link SyncPoller} for polling of the response for the Trial Matcher request. + */ + @Generated + @ServiceMethod(returns = ReturnType.LONG_RUNNING_OPERATION) + public SyncPoller beginMatchTrials( + BinaryData trialMatcherData, RequestOptions requestOptions) { + return this.client.beginMatchTrials(trialMatcherData, requestOptions).getSyncPoller(); + } + + /** + * Create Trial Matcher job + * + *

Creates a Trial Matcher job with the given request body. + * + * @param trialMatcherData The body of the Trial Matcher request. + * @throws IllegalArgumentException thrown if parameters fail the validation. + * @throws com.azure.core.exception.HttpResponseException thrown if the request is rejected by server. + * @throws ClientAuthenticationException thrown if the request is rejected by server on status code 401. + * @throws ResourceNotFoundException thrown if the request is rejected by server on status code 404. + * @throws ResourceModifiedException thrown if the request is rejected by server on status code 409. + * @throws RuntimeException all other wrapped checked exceptions if the request fails to be sent. + * @return the {@link SyncPoller} for polling of the response for the Trial Matcher request. + */ + @Generated + @ServiceMethod(returns = ReturnType.LONG_RUNNING_OPERATION) + public SyncPoller beginMatchTrials(TrialMatcherData trialMatcherData) { + // Generated convenience method for beginMatchTrialsWithModel + return client.beginMatchTrials(trialMatcherData).getSyncPoller(); + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingClientBuilder.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingClientBuilder.java new file mode 100644 index 0000000000000..d94f2f6ee68ff --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingClientBuilder.java @@ -0,0 +1,290 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching; + +import com.azure.core.annotation.Generated; +import com.azure.core.annotation.ServiceClientBuilder; +import com.azure.core.client.traits.AzureKeyCredentialTrait; +import com.azure.core.client.traits.ConfigurationTrait; +import com.azure.core.client.traits.EndpointTrait; +import com.azure.core.client.traits.HttpTrait; +import com.azure.core.credential.AzureKeyCredential; +import com.azure.core.http.HttpClient; +import com.azure.core.http.HttpHeaders; +import com.azure.core.http.HttpPipeline; +import com.azure.core.http.HttpPipelineBuilder; +import com.azure.core.http.HttpPipelinePosition; +import com.azure.core.http.policy.AddDatePolicy; +import com.azure.core.http.policy.AddHeadersFromContextPolicy; +import com.azure.core.http.policy.AddHeadersPolicy; +import com.azure.core.http.policy.AzureKeyCredentialPolicy; +import com.azure.core.http.policy.CookiePolicy; +import com.azure.core.http.policy.HttpLogOptions; +import com.azure.core.http.policy.HttpLoggingPolicy; +import com.azure.core.http.policy.HttpPipelinePolicy; +import com.azure.core.http.policy.HttpPolicyProviders; +import com.azure.core.http.policy.RequestIdPolicy; +import com.azure.core.http.policy.RetryOptions; +import com.azure.core.http.policy.RetryPolicy; +import com.azure.core.http.policy.UserAgentPolicy; +import com.azure.core.util.ClientOptions; +import com.azure.core.util.Configuration; +import com.azure.core.util.CoreUtils; +import com.azure.core.util.builder.ClientBuilderUtil; +import com.azure.core.util.serializer.JacksonAdapter; +import com.azure.health.insights.clinicalmatching.implementation.ClinicalMatchingClientImpl; +import java.util.ArrayList; +import java.util.List; +import java.util.Map; +import java.util.Objects; + +/** A builder for creating a new instance of the ClinicalMatchingClient type. */ +@ServiceClientBuilder(serviceClients = {ClinicalMatchingClient.class, ClinicalMatchingAsyncClient.class}) +public final class ClinicalMatchingClientBuilder + implements HttpTrait, + ConfigurationTrait, + AzureKeyCredentialTrait, + EndpointTrait { + @Generated private static final String SDK_NAME = "name"; + + @Generated private static final String SDK_VERSION = "version"; + + @Generated + private static final Map PROPERTIES = + CoreUtils.getProperties("azure-health-insights-clinicalmatching.properties"); + + @Generated private final List pipelinePolicies; + + /** Create an instance of the ClinicalMatchingClientBuilder. */ + @Generated + public ClinicalMatchingClientBuilder() { + this.pipelinePolicies = new ArrayList<>(); + } + + /* + * The HTTP pipeline to send requests through. + */ + @Generated private HttpPipeline pipeline; + + /** {@inheritDoc}. */ + @Generated + @Override + public ClinicalMatchingClientBuilder pipeline(HttpPipeline pipeline) { + this.pipeline = pipeline; + return this; + } + + /* + * The HTTP client used to send the request. + */ + @Generated private HttpClient httpClient; + + /** {@inheritDoc}. */ + @Generated + @Override + public ClinicalMatchingClientBuilder httpClient(HttpClient httpClient) { + this.httpClient = httpClient; + return this; + } + + /* + * The logging configuration for HTTP requests and responses. + */ + @Generated private HttpLogOptions httpLogOptions; + + /** {@inheritDoc}. */ + @Generated + @Override + public ClinicalMatchingClientBuilder httpLogOptions(HttpLogOptions httpLogOptions) { + this.httpLogOptions = httpLogOptions; + return this; + } + + /* + * The client options such as application ID and custom headers to set on a request. + */ + @Generated private ClientOptions clientOptions; + + /** {@inheritDoc}. */ + @Generated + @Override + public ClinicalMatchingClientBuilder clientOptions(ClientOptions clientOptions) { + this.clientOptions = clientOptions; + return this; + } + + /* + * The retry options to configure retry policy for failed requests. + */ + @Generated private RetryOptions retryOptions; + + /** {@inheritDoc}. */ + @Generated + @Override + public ClinicalMatchingClientBuilder retryOptions(RetryOptions retryOptions) { + this.retryOptions = retryOptions; + return this; + } + + /** {@inheritDoc}. */ + @Generated + @Override + public ClinicalMatchingClientBuilder addPolicy(HttpPipelinePolicy customPolicy) { + Objects.requireNonNull(customPolicy, "'customPolicy' cannot be null."); + pipelinePolicies.add(customPolicy); + return this; + } + + /* + * The configuration store that is used during construction of the service client. + */ + @Generated private Configuration configuration; + + /** {@inheritDoc}. */ + @Generated + @Override + public ClinicalMatchingClientBuilder configuration(Configuration configuration) { + this.configuration = configuration; + return this; + } + + /* + * The AzureKeyCredential used for authentication. + */ + @Generated private AzureKeyCredential azureKeyCredential; + + /** {@inheritDoc}. */ + @Generated + @Override + public ClinicalMatchingClientBuilder credential(AzureKeyCredential azureKeyCredential) { + this.azureKeyCredential = azureKeyCredential; + return this; + } + + /* + * The service endpoint + */ + @Generated private String endpoint; + + /** {@inheritDoc}. */ + @Generated + @Override + public ClinicalMatchingClientBuilder endpoint(String endpoint) { + this.endpoint = endpoint; + return this; + } + + /* + * Service version + */ + @Generated private AzureHealthInsightsServiceVersion serviceVersion; + + /** + * Sets Service version. + * + * @param serviceVersion the serviceVersion value. + * @return the ClinicalMatchingClientBuilder. + */ + @Generated + public ClinicalMatchingClientBuilder serviceVersion(AzureHealthInsightsServiceVersion serviceVersion) { + this.serviceVersion = serviceVersion; + return this; + } + + /* + * The retry policy that will attempt to retry failed requests, if applicable. + */ + @Generated private RetryPolicy retryPolicy; + + /** + * Sets The retry policy that will attempt to retry failed requests, if applicable. + * + * @param retryPolicy the retryPolicy value. + * @return the ClinicalMatchingClientBuilder. + */ + @Generated + public ClinicalMatchingClientBuilder retryPolicy(RetryPolicy retryPolicy) { + this.retryPolicy = retryPolicy; + return this; + } + + /** + * Builds an instance of ClinicalMatchingClientImpl with the provided parameters. + * + * @return an instance of ClinicalMatchingClientImpl. + */ + @Generated + private ClinicalMatchingClientImpl buildInnerClient() { + HttpPipeline localPipeline = (pipeline != null) ? pipeline : createHttpPipeline(); + AzureHealthInsightsServiceVersion localServiceVersion = + (serviceVersion != null) ? serviceVersion : AzureHealthInsightsServiceVersion.getLatest(); + ClinicalMatchingClientImpl client = + new ClinicalMatchingClientImpl( + localPipeline, JacksonAdapter.createDefaultSerializerAdapter(), endpoint, localServiceVersion); + return client; + } + + @Generated + private HttpPipeline createHttpPipeline() { + Configuration buildConfiguration = + (configuration == null) ? Configuration.getGlobalConfiguration() : configuration; + HttpLogOptions localHttpLogOptions = this.httpLogOptions == null ? new HttpLogOptions() : this.httpLogOptions; + ClientOptions localClientOptions = this.clientOptions == null ? new ClientOptions() : this.clientOptions; + List policies = new ArrayList<>(); + String clientName = PROPERTIES.getOrDefault(SDK_NAME, "UnknownName"); + String clientVersion = PROPERTIES.getOrDefault(SDK_VERSION, "UnknownVersion"); + String applicationId = CoreUtils.getApplicationId(localClientOptions, localHttpLogOptions); + policies.add(new UserAgentPolicy(applicationId, clientName, clientVersion, buildConfiguration)); + policies.add(new RequestIdPolicy()); + policies.add(new AddHeadersFromContextPolicy()); + HttpHeaders headers = new HttpHeaders(); + localClientOptions.getHeaders().forEach(header -> headers.set(header.getName(), header.getValue())); + if (headers.getSize() > 0) { + policies.add(new AddHeadersPolicy(headers)); + } + this.pipelinePolicies.stream() + .filter(p -> p.getPipelinePosition() == HttpPipelinePosition.PER_CALL) + .forEach(p -> policies.add(p)); + HttpPolicyProviders.addBeforeRetryPolicies(policies); + policies.add(ClientBuilderUtil.validateAndGetRetryPolicy(retryPolicy, retryOptions, new RetryPolicy())); + policies.add(new AddDatePolicy()); + policies.add(new CookiePolicy()); + if (azureKeyCredential != null) { + policies.add(new AzureKeyCredentialPolicy("Ocp-Apim-Subscription-Key", azureKeyCredential)); + } + this.pipelinePolicies.stream() + .filter(p -> p.getPipelinePosition() == HttpPipelinePosition.PER_RETRY) + .forEach(p -> policies.add(p)); + HttpPolicyProviders.addAfterRetryPolicies(policies); + policies.add(new HttpLoggingPolicy(httpLogOptions)); + HttpPipeline httpPipeline = + new HttpPipelineBuilder() + .policies(policies.toArray(new HttpPipelinePolicy[0])) + .httpClient(httpClient) + .clientOptions(localClientOptions) + .build(); + return httpPipeline; + } + + /** + * Builds an instance of ClinicalMatchingAsyncClient class. + * + * @return an instance of ClinicalMatchingAsyncClient. + */ + @Generated + public ClinicalMatchingAsyncClient buildAsyncClient() { + return new ClinicalMatchingAsyncClient(buildInnerClient()); + } + + /** + * Builds an instance of ClinicalMatchingClient class. + * + * @return an instance of ClinicalMatchingClient. + */ + @Generated + public ClinicalMatchingClient buildClient() { + return new ClinicalMatchingClient(new ClinicalMatchingAsyncClient(buildInnerClient())); + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/implementation/ClinicalMatchingClientImpl.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/implementation/ClinicalMatchingClientImpl.java new file mode 100644 index 0000000000000..8d1c768d75560 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/implementation/ClinicalMatchingClientImpl.java @@ -0,0 +1,1519 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.implementation; + +import com.azure.core.annotation.BodyParam; +import com.azure.core.annotation.ExpectedResponses; +import com.azure.core.annotation.HeaderParam; +import com.azure.core.annotation.Host; +import com.azure.core.annotation.HostParam; +import com.azure.core.annotation.Post; +import com.azure.core.annotation.QueryParam; +import com.azure.core.annotation.ReturnType; +import com.azure.core.annotation.ServiceInterface; +import com.azure.core.annotation.ServiceMethod; +import com.azure.core.annotation.UnexpectedResponseExceptionType; +import com.azure.core.exception.ClientAuthenticationException; +import com.azure.core.exception.HttpResponseException; +import com.azure.core.exception.ResourceModifiedException; +import com.azure.core.exception.ResourceNotFoundException; +import com.azure.core.http.HttpPipeline; +import com.azure.core.http.HttpPipelineBuilder; +import com.azure.core.http.policy.CookiePolicy; +import com.azure.core.http.policy.RetryPolicy; +import com.azure.core.http.policy.UserAgentPolicy; +import com.azure.core.http.rest.RequestOptions; +import com.azure.core.http.rest.Response; +import com.azure.core.http.rest.RestProxy; +import com.azure.core.util.BinaryData; +import com.azure.core.util.Context; +import com.azure.core.util.DateTimeRfc1123; +import com.azure.core.util.FluxUtil; +import com.azure.core.util.polling.DefaultPollingStrategy; +import com.azure.core.util.polling.PollerFlux; +import com.azure.core.util.polling.SyncPoller; +import com.azure.core.util.serializer.JacksonAdapter; +import com.azure.core.util.serializer.SerializerAdapter; +import com.azure.core.util.serializer.TypeReference; +import com.azure.health.insights.clinicalmatching.AzureHealthInsightsServiceVersion; +import com.azure.health.insights.clinicalmatching.models.TrialMatcherResult; +import java.time.Duration; +import java.time.OffsetDateTime; +import java.util.UUID; +import reactor.core.publisher.Mono; + +/** Initializes a new instance of the ClinicalMatchingClient type. */ +public final class ClinicalMatchingClientImpl { + /** The proxy service used to perform REST calls. */ + private final ClinicalMatchingClientService service; + + /** + * Supported Cognitive Services endpoints (protocol and hostname, for example: + * https://westus2.api.cognitive.microsoft.com). + */ + private final String endpoint; + + /** + * Gets Supported Cognitive Services endpoints (protocol and hostname, for example: + * https://westus2.api.cognitive.microsoft.com). + * + * @return the endpoint value. + */ + public String getEndpoint() { + return this.endpoint; + } + + /** Service version. */ + private final AzureHealthInsightsServiceVersion serviceVersion; + + /** + * Gets Service version. + * + * @return the serviceVersion value. + */ + public AzureHealthInsightsServiceVersion getServiceVersion() { + return this.serviceVersion; + } + + /** The HTTP pipeline to send requests through. */ + private final HttpPipeline httpPipeline; + + /** + * Gets The HTTP pipeline to send requests through. + * + * @return the httpPipeline value. + */ + public HttpPipeline getHttpPipeline() { + return this.httpPipeline; + } + + /** The serializer to serialize an object into a string. */ + private final SerializerAdapter serializerAdapter; + + /** + * Gets The serializer to serialize an object into a string. + * + * @return the serializerAdapter value. + */ + public SerializerAdapter getSerializerAdapter() { + return this.serializerAdapter; + } + + /** + * Initializes an instance of ClinicalMatchingClient client. + * + * @param endpoint Supported Cognitive Services endpoints (protocol and hostname, for example: + * https://westus2.api.cognitive.microsoft.com). + * @param serviceVersion Service version. + */ + public ClinicalMatchingClientImpl(String endpoint, AzureHealthInsightsServiceVersion serviceVersion) { + this( + new HttpPipelineBuilder() + .policies(new UserAgentPolicy(), new RetryPolicy(), new CookiePolicy()) + .build(), + JacksonAdapter.createDefaultSerializerAdapter(), + endpoint, + serviceVersion); + } + + /** + * Initializes an instance of ClinicalMatchingClient client. + * + * @param httpPipeline The HTTP pipeline to send requests through. + * @param endpoint Supported Cognitive Services endpoints (protocol and hostname, for example: + * https://westus2.api.cognitive.microsoft.com). + * @param serviceVersion Service version. + */ + public ClinicalMatchingClientImpl( + HttpPipeline httpPipeline, String endpoint, AzureHealthInsightsServiceVersion serviceVersion) { + this(httpPipeline, JacksonAdapter.createDefaultSerializerAdapter(), endpoint, serviceVersion); + } + + /** + * Initializes an instance of ClinicalMatchingClient client. + * + * @param httpPipeline The HTTP pipeline to send requests through. + * @param serializerAdapter The serializer to serialize an object into a string. + * @param endpoint Supported Cognitive Services endpoints (protocol and hostname, for example: + * https://westus2.api.cognitive.microsoft.com). + * @param serviceVersion Service version. + */ + public ClinicalMatchingClientImpl( + HttpPipeline httpPipeline, + SerializerAdapter serializerAdapter, + String endpoint, + AzureHealthInsightsServiceVersion serviceVersion) { + this.httpPipeline = httpPipeline; + this.serializerAdapter = serializerAdapter; + this.endpoint = endpoint; + this.serviceVersion = serviceVersion; + this.service = + RestProxy.create(ClinicalMatchingClientService.class, this.httpPipeline, this.getSerializerAdapter()); + } + + /** + * The interface defining all the services for ClinicalMatchingClient to be used by the proxy service to perform + * REST calls. + */ + @Host("{endpoint}/healthinsights") + @ServiceInterface(name = "ClinicalMatchingClie") + public interface ClinicalMatchingClientService { + @Post("/trialmatcher/jobs") + @ExpectedResponses({200, 202}) + @UnexpectedResponseExceptionType( + value = ClientAuthenticationException.class, + code = {401}) + @UnexpectedResponseExceptionType( + value = ResourceNotFoundException.class, + code = {404}) + @UnexpectedResponseExceptionType( + value = ResourceModifiedException.class, + code = {409}) + @UnexpectedResponseExceptionType(HttpResponseException.class) + Mono> matchTrials( + @HostParam("endpoint") String endpoint, + @QueryParam("api-version") String apiVersion, + @HeaderParam("accept") String accept, + @BodyParam("application/json") BinaryData trialMatcherData, + RequestOptions requestOptions, + Context context); + } + + /** + * Create Trial Matcher job + * + *

Creates a Trial Matcher job with the given request body. + * + *

Header Parameters + * + * + * + * + * + * + *
Header Parameters
NameTypeRequiredDescription
repeatability-request-idStringNoRepeatability request ID header
repeatability-first-sentStringNoRepeatability first sent header as HTTP-date
+ * + * You can add these to a request with {@link RequestOptions#addHeader} + * + *

Request Body Schema + * + * 

{@code
+     * {
+     *     patients (Required): [
+     *          (Required){
+     *             id: String (Required)
+     *             info (Optional): {
+     *                 sex: String(female/male/unspecified) (Optional)
+     *                 birthDate: LocalDate (Optional)
+     *                 clinicalInfo (Optional): [
+     *                      (Optional){
+     *                         system: String (Required)
+     *                         code: String (Required)
+     *                         name: String (Optional)
+     *                         value: String (Optional)
+     *                     }
+     *                 ]
+     *             }
+     *             data (Optional): [
+     *                  (Optional){
+     *                     type: String(note/fhirBundle/dicom/genomicSequencing) (Required)
+     *                     clinicalType: String(consultation/dischargeSummary/historyAndPhysical/procedure/progress/imaging/laboratory/pathology) (Optional)
+     *                     id: String (Required)
+     *                     language: String (Optional)
+     *                     createdDateTime: OffsetDateTime (Optional)
+     *                     content (Required): {
+     *                         sourceType: String(inline/reference) (Required)
+     *                         value: String (Required)
+     *                     }
+     *                 }
+     *             ]
+     *         }
+     *     ]
+     *     configuration (Optional): {
+     *         verbose: Boolean (Optional)
+     *         includeEvidence: Boolean (Optional)
+     *         clinicalTrials (Required): {
+     *             customTrials (Optional): [
+     *                  (Optional){
+     *                     id: String (Required)
+     *                     eligibilityCriteriaText: String (Optional)
+     *                     demographics (Optional): {
+     *                         acceptedSex: String(all/female/male) (Optional)
+     *                         acceptedAgeRange (Optional): {
+     *                             minimumAge (Optional): {
+     *                                 unit: String(years/months/days) (Required)
+     *                                 value: double (Required)
+     *                             }
+     *                             maximumAge (Optional): (recursive schema, see maximumAge above)
+     *                         }
+     *                     }
+     *                     metadata (Required): {
+     *                         phases (Optional): [
+     *                             String(notApplicable/earlyPhase1/phase1/phase2/phase3/phase4) (Optional)
+     *                         ]
+     *                         studyType: String(interventional/observational/expandedAccess/patientRegistries) (Optional)
+     *                         recruitmentStatus: String(unknownStatus/notYetRecruiting/recruiting/enrollingByInvitation) (Optional)
+     *                         conditions (Required): [
+     *                             String (Required)
+     *                         ]
+     *                         sponsors (Optional): [
+     *                             String (Optional)
+     *                         ]
+     *                         contacts (Optional): [
+     *                              (Optional){
+     *                                 name: String (Optional)
+     *                                 email: String (Optional)
+     *                                 phone: String (Optional)
+     *                             }
+     *                         ]
+     *                         facilities (Optional): [
+     *                              (Optional){
+     *                                 name: String (Required)
+     *                                 city: String (Optional)
+     *                                 state: String (Optional)
+     *                                 country: String (Required)
+     *                             }
+     *                         ]
+     *                     }
+     *                 }
+     *             ]
+     *             registryFilters (Optional): [
+     *                  (Optional){
+     *                     conditions (Optional): [
+     *                         String (Optional)
+     *                     ]
+     *                     studyTypes (Optional): [
+     *                         String(interventional/observational/expandedAccess/patientRegistries) (Optional)
+     *                     ]
+     *                     recruitmentStatuses (Optional): [
+     *                         String(unknownStatus/notYetRecruiting/recruiting/enrollingByInvitation) (Optional)
+     *                     ]
+     *                     sponsors (Optional): [
+     *                         String (Optional)
+     *                     ]
+     *                     phases (Optional): [
+     *                         String(notApplicable/earlyPhase1/phase1/phase2/phase3/phase4) (Optional)
+     *                     ]
+     *                     purposes (Optional): [
+     *                         String(notApplicable/screening/diagnostic/prevention/healthServicesResearch/treatment/deviceFeasibility/supportiveCare/basicScience/other) (Optional)
+     *                     ]
+     *                     ids (Optional): [
+     *                         String (Optional)
+     *                     ]
+     *                     sources (Optional): [
+     *                         String(custom/clinicaltrials.gov) (Optional)
+     *                     ]
+     *                     facilityNames (Optional): [
+     *                         String (Optional)
+     *                     ]
+     *                     facilityLocations (Optional): [
+     *                          (Optional){
+     *                             city: String (Optional)
+     *                             state: String (Optional)
+     *                             country: String (Required)
+     *                         }
+     *                     ]
+     *                     facilityAreas (Optional): [
+     *                          (Optional){
+     *                             type: String(Feature) (Required)
+     *                             geometry (Required): {
+     *                                 type: String(Point) (Required)
+     *                                 coordinates (Required): [
+     *                                     double (Required)
+     *                                 ]
+     *                             }
+     *                             properties (Required): {
+     *                                 subType: String(Circle) (Required)
+     *                                 radius: double (Required)
+     *                             }
+     *                         }
+     *                     ]
+     *                 }
+     *             ]
+     *         }
+     *     }
+     * }
+     * }
+ * + *

Response Body Schema + * + * 

{@code
+     * {
+     *     jobId: String (Required)
+     *     createdDateTime: OffsetDateTime (Required)
+     *     expirationDateTime: OffsetDateTime (Required)
+     *     lastUpdateDateTime: OffsetDateTime (Required)
+     *     status: String(notStarted/running/succeeded/failed/partiallyCompleted) (Required)
+     *     errors (Optional): [
+     *         ResponseError (Optional)
+     *     ]
+     *     results (Optional): {
+     *         patients (Required): [
+     *              (Required){
+     *                 id: String (Required)
+     *                 inferences (Required): [
+     *                      (Required){
+     *                         type: String(trialEligibility) (Required)
+     *                         value: String (Required)
+     *                         description: String (Optional)
+     *                         confidenceScore: Double (Optional)
+     *                         evidence (Optional): [
+     *                              (Optional){
+     *                                 eligibilityCriteriaEvidence: String (Optional)
+     *                                 patientDataEvidence (Optional): {
+     *                                     id: String (Required)
+     *                                     text: String (Optional)
+     *                                     offset: int (Required)
+     *                                     length: int (Required)
+     *                                 }
+     *                                 patientInfoEvidence (Optional): {
+     *                                     system: String (Required)
+     *                                     code: String (Required)
+     *                                     name: String (Optional)
+     *                                     value: String (Optional)
+     *                                 }
+     *                                 importance: Double (Optional)
+     *                             }
+     *                         ]
+     *                         id: String (Optional)
+     *                         source: String(custom/clinicaltrials.gov) (Optional)
+     *                         metadata (Optional): {
+     *                             phases (Optional): [
+     *                                 String(notApplicable/earlyPhase1/phase1/phase2/phase3/phase4) (Optional)
+     *                             ]
+     *                             studyType: String(interventional/observational/expandedAccess/patientRegistries) (Optional)
+     *                             recruitmentStatus: String(unknownStatus/notYetRecruiting/recruiting/enrollingByInvitation) (Optional)
+     *                             conditions (Required): [
+     *                                 String (Required)
+     *                             ]
+     *                             sponsors (Optional): [
+     *                                 String (Optional)
+     *                             ]
+     *                             contacts (Optional): [
+     *                                  (Optional){
+     *                                     name: String (Optional)
+     *                                     email: String (Optional)
+     *                                     phone: String (Optional)
+     *                                 }
+     *                             ]
+     *                             facilities (Optional): [
+     *                                  (Optional){
+     *                                     name: String (Required)
+     *                                     city: String (Optional)
+     *                                     state: String (Optional)
+     *                                     country: String (Required)
+     *                                 }
+     *                             ]
+     *                         }
+     *                     }
+     *                 ]
+     *                 neededClinicalInfo (Optional): [
+     *                      (Optional){
+     *                         system: String (Required)
+     *                         code: String (Required)
+     *                         name: String (Optional)
+     *                         value: String (Optional)
+     *                         semanticType: String (Optional)
+     *                         category: String (Optional)
+     *                     }
+     *                 ]
+     *             }
+     *         ]
+     *         modelVersion: String (Required)
+     *         knowledgeGraphLastUpdateDate: LocalDate (Optional)
+     *     }
+     * }
+     * }
+ * + * @param trialMatcherData The body of the Trial Matcher request. + * @param requestOptions The options to configure the HTTP request before HTTP client sends it. + * @throws HttpResponseException thrown if the request is rejected by server. + * @throws ClientAuthenticationException thrown if the request is rejected by server on status code 401. + * @throws ResourceNotFoundException thrown if the request is rejected by server on status code 404. + * @throws ResourceModifiedException thrown if the request is rejected by server on status code 409. + * @return the response for the Trial Matcher request along with {@link Response} on successful completion of {@link + * Mono}. + */ + @ServiceMethod(returns = ReturnType.SINGLE) + private Mono> matchTrialsWithResponseAsync( + BinaryData trialMatcherData, RequestOptions requestOptions) { + final String accept = "application/json"; + RequestOptions requestOptionsLocal = requestOptions == null ? new RequestOptions() : requestOptions; + requestOptionsLocal.setHeader("repeatability-request-id", UUID.randomUUID().toString()); + requestOptionsLocal.setHeader( + "repeatability-first-sent", DateTimeRfc1123.toRfc1123String(OffsetDateTime.now())); + return FluxUtil.withContext( + context -> + service.matchTrials( + this.getEndpoint(), + this.getServiceVersion().getVersion(), + accept, + trialMatcherData, + requestOptionsLocal, + context)); + } + + /** + * Create Trial Matcher job + * + *

Creates a Trial Matcher job with the given request body. + * + *

Header Parameters + * + * + * + * + * + * + *
Header Parameters
NameTypeRequiredDescription
repeatability-request-idStringNoRepeatability request ID header
repeatability-first-sentStringNoRepeatability first sent header as HTTP-date
+ * + * You can add these to a request with {@link RequestOptions#addHeader} + * + *

Request Body Schema + * + * 

{@code
+     * {
+     *     patients (Required): [
+     *          (Required){
+     *             id: String (Required)
+     *             info (Optional): {
+     *                 sex: String(female/male/unspecified) (Optional)
+     *                 birthDate: LocalDate (Optional)
+     *                 clinicalInfo (Optional): [
+     *                      (Optional){
+     *                         system: String (Required)
+     *                         code: String (Required)
+     *                         name: String (Optional)
+     *                         value: String (Optional)
+     *                     }
+     *                 ]
+     *             }
+     *             data (Optional): [
+     *                  (Optional){
+     *                     type: String(note/fhirBundle/dicom/genomicSequencing) (Required)
+     *                     clinicalType: String(consultation/dischargeSummary/historyAndPhysical/procedure/progress/imaging/laboratory/pathology) (Optional)
+     *                     id: String (Required)
+     *                     language: String (Optional)
+     *                     createdDateTime: OffsetDateTime (Optional)
+     *                     content (Required): {
+     *                         sourceType: String(inline/reference) (Required)
+     *                         value: String (Required)
+     *                     }
+     *                 }
+     *             ]
+     *         }
+     *     ]
+     *     configuration (Optional): {
+     *         verbose: Boolean (Optional)
+     *         includeEvidence: Boolean (Optional)
+     *         clinicalTrials (Required): {
+     *             customTrials (Optional): [
+     *                  (Optional){
+     *                     id: String (Required)
+     *                     eligibilityCriteriaText: String (Optional)
+     *                     demographics (Optional): {
+     *                         acceptedSex: String(all/female/male) (Optional)
+     *                         acceptedAgeRange (Optional): {
+     *                             minimumAge (Optional): {
+     *                                 unit: String(years/months/days) (Required)
+     *                                 value: double (Required)
+     *                             }
+     *                             maximumAge (Optional): (recursive schema, see maximumAge above)
+     *                         }
+     *                     }
+     *                     metadata (Required): {
+     *                         phases (Optional): [
+     *                             String(notApplicable/earlyPhase1/phase1/phase2/phase3/phase4) (Optional)
+     *                         ]
+     *                         studyType: String(interventional/observational/expandedAccess/patientRegistries) (Optional)
+     *                         recruitmentStatus: String(unknownStatus/notYetRecruiting/recruiting/enrollingByInvitation) (Optional)
+     *                         conditions (Required): [
+     *                             String (Required)
+     *                         ]
+     *                         sponsors (Optional): [
+     *                             String (Optional)
+     *                         ]
+     *                         contacts (Optional): [
+     *                              (Optional){
+     *                                 name: String (Optional)
+     *                                 email: String (Optional)
+     *                                 phone: String (Optional)
+     *                             }
+     *                         ]
+     *                         facilities (Optional): [
+     *                              (Optional){
+     *                                 name: String (Required)
+     *                                 city: String (Optional)
+     *                                 state: String (Optional)
+     *                                 country: String (Required)
+     *                             }
+     *                         ]
+     *                     }
+     *                 }
+     *             ]
+     *             registryFilters (Optional): [
+     *                  (Optional){
+     *                     conditions (Optional): [
+     *                         String (Optional)
+     *                     ]
+     *                     studyTypes (Optional): [
+     *                         String(interventional/observational/expandedAccess/patientRegistries) (Optional)
+     *                     ]
+     *                     recruitmentStatuses (Optional): [
+     *                         String(unknownStatus/notYetRecruiting/recruiting/enrollingByInvitation) (Optional)
+     *                     ]
+     *                     sponsors (Optional): [
+     *                         String (Optional)
+     *                     ]
+     *                     phases (Optional): [
+     *                         String(notApplicable/earlyPhase1/phase1/phase2/phase3/phase4) (Optional)
+     *                     ]
+     *                     purposes (Optional): [
+     *                         String(notApplicable/screening/diagnostic/prevention/healthServicesResearch/treatment/deviceFeasibility/supportiveCare/basicScience/other) (Optional)
+     *                     ]
+     *                     ids (Optional): [
+     *                         String (Optional)
+     *                     ]
+     *                     sources (Optional): [
+     *                         String(custom/clinicaltrials.gov) (Optional)
+     *                     ]
+     *                     facilityNames (Optional): [
+     *                         String (Optional)
+     *                     ]
+     *                     facilityLocations (Optional): [
+     *                          (Optional){
+     *                             city: String (Optional)
+     *                             state: String (Optional)
+     *                             country: String (Required)
+     *                         }
+     *                     ]
+     *                     facilityAreas (Optional): [
+     *                          (Optional){
+     *                             type: String(Feature) (Required)
+     *                             geometry (Required): {
+     *                                 type: String(Point) (Required)
+     *                                 coordinates (Required): [
+     *                                     double (Required)
+     *                                 ]
+     *                             }
+     *                             properties (Required): {
+     *                                 subType: String(Circle) (Required)
+     *                                 radius: double (Required)
+     *                             }
+     *                         }
+     *                     ]
+     *                 }
+     *             ]
+     *         }
+     *     }
+     * }
+     * }
+ * + *

Response Body Schema + * + * 

{@code
+     * {
+     *     jobId: String (Required)
+     *     createdDateTime: OffsetDateTime (Required)
+     *     expirationDateTime: OffsetDateTime (Required)
+     *     lastUpdateDateTime: OffsetDateTime (Required)
+     *     status: String(notStarted/running/succeeded/failed/partiallyCompleted) (Required)
+     *     errors (Optional): [
+     *         ResponseError (Optional)
+     *     ]
+     *     results (Optional): {
+     *         patients (Required): [
+     *              (Required){
+     *                 id: String (Required)
+     *                 inferences (Required): [
+     *                      (Required){
+     *                         type: String(trialEligibility) (Required)
+     *                         value: String (Required)
+     *                         description: String (Optional)
+     *                         confidenceScore: Double (Optional)
+     *                         evidence (Optional): [
+     *                              (Optional){
+     *                                 eligibilityCriteriaEvidence: String (Optional)
+     *                                 patientDataEvidence (Optional): {
+     *                                     id: String (Required)
+     *                                     text: String (Optional)
+     *                                     offset: int (Required)
+     *                                     length: int (Required)
+     *                                 }
+     *                                 patientInfoEvidence (Optional): {
+     *                                     system: String (Required)
+     *                                     code: String (Required)
+     *                                     name: String (Optional)
+     *                                     value: String (Optional)
+     *                                 }
+     *                                 importance: Double (Optional)
+     *                             }
+     *                         ]
+     *                         id: String (Optional)
+     *                         source: String(custom/clinicaltrials.gov) (Optional)
+     *                         metadata (Optional): {
+     *                             phases (Optional): [
+     *                                 String(notApplicable/earlyPhase1/phase1/phase2/phase3/phase4) (Optional)
+     *                             ]
+     *                             studyType: String(interventional/observational/expandedAccess/patientRegistries) (Optional)
+     *                             recruitmentStatus: String(unknownStatus/notYetRecruiting/recruiting/enrollingByInvitation) (Optional)
+     *                             conditions (Required): [
+     *                                 String (Required)
+     *                             ]
+     *                             sponsors (Optional): [
+     *                                 String (Optional)
+     *                             ]
+     *                             contacts (Optional): [
+     *                                  (Optional){
+     *                                     name: String (Optional)
+     *                                     email: String (Optional)
+     *                                     phone: String (Optional)
+     *                                 }
+     *                             ]
+     *                             facilities (Optional): [
+     *                                  (Optional){
+     *                                     name: String (Required)
+     *                                     city: String (Optional)
+     *                                     state: String (Optional)
+     *                                     country: String (Required)
+     *                                 }
+     *                             ]
+     *                         }
+     *                     }
+     *                 ]
+     *                 neededClinicalInfo (Optional): [
+     *                      (Optional){
+     *                         system: String (Required)
+     *                         code: String (Required)
+     *                         name: String (Optional)
+     *                         value: String (Optional)
+     *                         semanticType: String (Optional)
+     *                         category: String (Optional)
+     *                     }
+     *                 ]
+     *             }
+     *         ]
+     *         modelVersion: String (Required)
+     *         knowledgeGraphLastUpdateDate: LocalDate (Optional)
+     *     }
+     * }
+     * }
+ * + * @param trialMatcherData The body of the Trial Matcher request. + * @param requestOptions The options to configure the HTTP request before HTTP client sends it. + * @throws HttpResponseException thrown if the request is rejected by server. + * @throws ClientAuthenticationException thrown if the request is rejected by server on status code 401. + * @throws ResourceNotFoundException thrown if the request is rejected by server on status code 404. + * @throws ResourceModifiedException thrown if the request is rejected by server on status code 409. + * @return the {@link PollerFlux} for polling of the response for the Trial Matcher request. + */ + @ServiceMethod(returns = ReturnType.LONG_RUNNING_OPERATION) + public PollerFlux beginMatchTrialsAsync( + BinaryData trialMatcherData, RequestOptions requestOptions) { + return PollerFlux.create( + Duration.ofSeconds(1), + () -> this.matchTrialsWithResponseAsync(trialMatcherData, requestOptions), + new DefaultPollingStrategy<>( + this.getHttpPipeline(), + "{endpoint}/healthinsights".replace("{endpoint}", this.getEndpoint()), + null, + requestOptions != null && requestOptions.getContext() != null + ? requestOptions.getContext() + : Context.NONE), + TypeReference.createInstance(BinaryData.class), + TypeReference.createInstance(BinaryData.class)); + } + + /** + * Create Trial Matcher job + * + *

Creates a Trial Matcher job with the given request body. + * + *

Header Parameters + * + * + * + * + * + * + *
Header Parameters
NameTypeRequiredDescription
repeatability-request-idStringNoRepeatability request ID header
repeatability-first-sentStringNoRepeatability first sent header as HTTP-date
+ * + * You can add these to a request with {@link RequestOptions#addHeader} + * + *

Request Body Schema + * + * 

{@code
+     * {
+     *     patients (Required): [
+     *          (Required){
+     *             id: String (Required)
+     *             info (Optional): {
+     *                 sex: String(female/male/unspecified) (Optional)
+     *                 birthDate: LocalDate (Optional)
+     *                 clinicalInfo (Optional): [
+     *                      (Optional){
+     *                         system: String (Required)
+     *                         code: String (Required)
+     *                         name: String (Optional)
+     *                         value: String (Optional)
+     *                     }
+     *                 ]
+     *             }
+     *             data (Optional): [
+     *                  (Optional){
+     *                     type: String(note/fhirBundle/dicom/genomicSequencing) (Required)
+     *                     clinicalType: String(consultation/dischargeSummary/historyAndPhysical/procedure/progress/imaging/laboratory/pathology) (Optional)
+     *                     id: String (Required)
+     *                     language: String (Optional)
+     *                     createdDateTime: OffsetDateTime (Optional)
+     *                     content (Required): {
+     *                         sourceType: String(inline/reference) (Required)
+     *                         value: String (Required)
+     *                     }
+     *                 }
+     *             ]
+     *         }
+     *     ]
+     *     configuration (Optional): {
+     *         verbose: Boolean (Optional)
+     *         includeEvidence: Boolean (Optional)
+     *         clinicalTrials (Required): {
+     *             customTrials (Optional): [
+     *                  (Optional){
+     *                     id: String (Required)
+     *                     eligibilityCriteriaText: String (Optional)
+     *                     demographics (Optional): {
+     *                         acceptedSex: String(all/female/male) (Optional)
+     *                         acceptedAgeRange (Optional): {
+     *                             minimumAge (Optional): {
+     *                                 unit: String(years/months/days) (Required)
+     *                                 value: double (Required)
+     *                             }
+     *                             maximumAge (Optional): (recursive schema, see maximumAge above)
+     *                         }
+     *                     }
+     *                     metadata (Required): {
+     *                         phases (Optional): [
+     *                             String(notApplicable/earlyPhase1/phase1/phase2/phase3/phase4) (Optional)
+     *                         ]
+     *                         studyType: String(interventional/observational/expandedAccess/patientRegistries) (Optional)
+     *                         recruitmentStatus: String(unknownStatus/notYetRecruiting/recruiting/enrollingByInvitation) (Optional)
+     *                         conditions (Required): [
+     *                             String (Required)
+     *                         ]
+     *                         sponsors (Optional): [
+     *                             String (Optional)
+     *                         ]
+     *                         contacts (Optional): [
+     *                              (Optional){
+     *                                 name: String (Optional)
+     *                                 email: String (Optional)
+     *                                 phone: String (Optional)
+     *                             }
+     *                         ]
+     *                         facilities (Optional): [
+     *                              (Optional){
+     *                                 name: String (Required)
+     *                                 city: String (Optional)
+     *                                 state: String (Optional)
+     *                                 country: String (Required)
+     *                             }
+     *                         ]
+     *                     }
+     *                 }
+     *             ]
+     *             registryFilters (Optional): [
+     *                  (Optional){
+     *                     conditions (Optional): [
+     *                         String (Optional)
+     *                     ]
+     *                     studyTypes (Optional): [
+     *                         String(interventional/observational/expandedAccess/patientRegistries) (Optional)
+     *                     ]
+     *                     recruitmentStatuses (Optional): [
+     *                         String(unknownStatus/notYetRecruiting/recruiting/enrollingByInvitation) (Optional)
+     *                     ]
+     *                     sponsors (Optional): [
+     *                         String (Optional)
+     *                     ]
+     *                     phases (Optional): [
+     *                         String(notApplicable/earlyPhase1/phase1/phase2/phase3/phase4) (Optional)
+     *                     ]
+     *                     purposes (Optional): [
+     *                         String(notApplicable/screening/diagnostic/prevention/healthServicesResearch/treatment/deviceFeasibility/supportiveCare/basicScience/other) (Optional)
+     *                     ]
+     *                     ids (Optional): [
+     *                         String (Optional)
+     *                     ]
+     *                     sources (Optional): [
+     *                         String(custom/clinicaltrials.gov) (Optional)
+     *                     ]
+     *                     facilityNames (Optional): [
+     *                         String (Optional)
+     *                     ]
+     *                     facilityLocations (Optional): [
+     *                          (Optional){
+     *                             city: String (Optional)
+     *                             state: String (Optional)
+     *                             country: String (Required)
+     *                         }
+     *                     ]
+     *                     facilityAreas (Optional): [
+     *                          (Optional){
+     *                             type: String(Feature) (Required)
+     *                             geometry (Required): {
+     *                                 type: String(Point) (Required)
+     *                                 coordinates (Required): [
+     *                                     double (Required)
+     *                                 ]
+     *                             }
+     *                             properties (Required): {
+     *                                 subType: String(Circle) (Required)
+     *                                 radius: double (Required)
+     *                             }
+     *                         }
+     *                     ]
+     *                 }
+     *             ]
+     *         }
+     *     }
+     * }
+     * }
+ * + *

Response Body Schema + * + * 

{@code
+     * {
+     *     jobId: String (Required)
+     *     createdDateTime: OffsetDateTime (Required)
+     *     expirationDateTime: OffsetDateTime (Required)
+     *     lastUpdateDateTime: OffsetDateTime (Required)
+     *     status: String(notStarted/running/succeeded/failed/partiallyCompleted) (Required)
+     *     errors (Optional): [
+     *         ResponseError (Optional)
+     *     ]
+     *     results (Optional): {
+     *         patients (Required): [
+     *              (Required){
+     *                 id: String (Required)
+     *                 inferences (Required): [
+     *                      (Required){
+     *                         type: String(trialEligibility) (Required)
+     *                         value: String (Required)
+     *                         description: String (Optional)
+     *                         confidenceScore: Double (Optional)
+     *                         evidence (Optional): [
+     *                              (Optional){
+     *                                 eligibilityCriteriaEvidence: String (Optional)
+     *                                 patientDataEvidence (Optional): {
+     *                                     id: String (Required)
+     *                                     text: String (Optional)
+     *                                     offset: int (Required)
+     *                                     length: int (Required)
+     *                                 }
+     *                                 patientInfoEvidence (Optional): {
+     *                                     system: String (Required)
+     *                                     code: String (Required)
+     *                                     name: String (Optional)
+     *                                     value: String (Optional)
+     *                                 }
+     *                                 importance: Double (Optional)
+     *                             }
+     *                         ]
+     *                         id: String (Optional)
+     *                         source: String(custom/clinicaltrials.gov) (Optional)
+     *                         metadata (Optional): {
+     *                             phases (Optional): [
+     *                                 String(notApplicable/earlyPhase1/phase1/phase2/phase3/phase4) (Optional)
+     *                             ]
+     *                             studyType: String(interventional/observational/expandedAccess/patientRegistries) (Optional)
+     *                             recruitmentStatus: String(unknownStatus/notYetRecruiting/recruiting/enrollingByInvitation) (Optional)
+     *                             conditions (Required): [
+     *                                 String (Required)
+     *                             ]
+     *                             sponsors (Optional): [
+     *                                 String (Optional)
+     *                             ]
+     *                             contacts (Optional): [
+     *                                  (Optional){
+     *                                     name: String (Optional)
+     *                                     email: String (Optional)
+     *                                     phone: String (Optional)
+     *                                 }
+     *                             ]
+     *                             facilities (Optional): [
+     *                                  (Optional){
+     *                                     name: String (Required)
+     *                                     city: String (Optional)
+     *                                     state: String (Optional)
+     *                                     country: String (Required)
+     *                                 }
+     *                             ]
+     *                         }
+     *                     }
+     *                 ]
+     *                 neededClinicalInfo (Optional): [
+     *                      (Optional){
+     *                         system: String (Required)
+     *                         code: String (Required)
+     *                         name: String (Optional)
+     *                         value: String (Optional)
+     *                         semanticType: String (Optional)
+     *                         category: String (Optional)
+     *                     }
+     *                 ]
+     *             }
+     *         ]
+     *         modelVersion: String (Required)
+     *         knowledgeGraphLastUpdateDate: LocalDate (Optional)
+     *     }
+     * }
+     * }
+ * + * @param trialMatcherData The body of the Trial Matcher request. + * @param requestOptions The options to configure the HTTP request before HTTP client sends it. + * @throws HttpResponseException thrown if the request is rejected by server. + * @throws ClientAuthenticationException thrown if the request is rejected by server on status code 401. + * @throws ResourceNotFoundException thrown if the request is rejected by server on status code 404. + * @throws ResourceModifiedException thrown if the request is rejected by server on status code 409. + * @return the {@link SyncPoller} for polling of the response for the Trial Matcher request. + */ + @ServiceMethod(returns = ReturnType.LONG_RUNNING_OPERATION) + public SyncPoller beginMatchTrials( + BinaryData trialMatcherData, RequestOptions requestOptions) { + return this.beginMatchTrialsAsync(trialMatcherData, requestOptions).getSyncPoller(); + } + + /** + * Create Trial Matcher job + * + *

Creates a Trial Matcher job with the given request body. + * + *

Header Parameters + * + * + * + * + * + * + *
Header Parameters
NameTypeRequiredDescription
repeatability-request-idStringNoRepeatability request ID header
repeatability-first-sentStringNoRepeatability first sent header as HTTP-date
+ * + * You can add these to a request with {@link RequestOptions#addHeader} + * + *

Request Body Schema + * + * 

{@code
+     * {
+     *     patients (Required): [
+     *          (Required){
+     *             id: String (Required)
+     *             info (Optional): {
+     *                 sex: String(female/male/unspecified) (Optional)
+     *                 birthDate: LocalDate (Optional)
+     *                 clinicalInfo (Optional): [
+     *                      (Optional){
+     *                         system: String (Required)
+     *                         code: String (Required)
+     *                         name: String (Optional)
+     *                         value: String (Optional)
+     *                     }
+     *                 ]
+     *             }
+     *             data (Optional): [
+     *                  (Optional){
+     *                     type: String(note/fhirBundle/dicom/genomicSequencing) (Required)
+     *                     clinicalType: String(consultation/dischargeSummary/historyAndPhysical/procedure/progress/imaging/laboratory/pathology) (Optional)
+     *                     id: String (Required)
+     *                     language: String (Optional)
+     *                     createdDateTime: OffsetDateTime (Optional)
+     *                     content (Required): {
+     *                         sourceType: String(inline/reference) (Required)
+     *                         value: String (Required)
+     *                     }
+     *                 }
+     *             ]
+     *         }
+     *     ]
+     *     configuration (Optional): {
+     *         verbose: Boolean (Optional)
+     *         includeEvidence: Boolean (Optional)
+     *         clinicalTrials (Required): {
+     *             customTrials (Optional): [
+     *                  (Optional){
+     *                     id: String (Required)
+     *                     eligibilityCriteriaText: String (Optional)
+     *                     demographics (Optional): {
+     *                         acceptedSex: String(all/female/male) (Optional)
+     *                         acceptedAgeRange (Optional): {
+     *                             minimumAge (Optional): {
+     *                                 unit: String(years/months/days) (Required)
+     *                                 value: double (Required)
+     *                             }
+     *                             maximumAge (Optional): (recursive schema, see maximumAge above)
+     *                         }
+     *                     }
+     *                     metadata (Required): {
+     *                         phases (Optional): [
+     *                             String(notApplicable/earlyPhase1/phase1/phase2/phase3/phase4) (Optional)
+     *                         ]
+     *                         studyType: String(interventional/observational/expandedAccess/patientRegistries) (Optional)
+     *                         recruitmentStatus: String(unknownStatus/notYetRecruiting/recruiting/enrollingByInvitation) (Optional)
+     *                         conditions (Required): [
+     *                             String (Required)
+     *                         ]
+     *                         sponsors (Optional): [
+     *                             String (Optional)
+     *                         ]
+     *                         contacts (Optional): [
+     *                              (Optional){
+     *                                 name: String (Optional)
+     *                                 email: String (Optional)
+     *                                 phone: String (Optional)
+     *                             }
+     *                         ]
+     *                         facilities (Optional): [
+     *                              (Optional){
+     *                                 name: String (Required)
+     *                                 city: String (Optional)
+     *                                 state: String (Optional)
+     *                                 country: String (Required)
+     *                             }
+     *                         ]
+     *                     }
+     *                 }
+     *             ]
+     *             registryFilters (Optional): [
+     *                  (Optional){
+     *                     conditions (Optional): [
+     *                         String (Optional)
+     *                     ]
+     *                     studyTypes (Optional): [
+     *                         String(interventional/observational/expandedAccess/patientRegistries) (Optional)
+     *                     ]
+     *                     recruitmentStatuses (Optional): [
+     *                         String(unknownStatus/notYetRecruiting/recruiting/enrollingByInvitation) (Optional)
+     *                     ]
+     *                     sponsors (Optional): [
+     *                         String (Optional)
+     *                     ]
+     *                     phases (Optional): [
+     *                         String(notApplicable/earlyPhase1/phase1/phase2/phase3/phase4) (Optional)
+     *                     ]
+     *                     purposes (Optional): [
+     *                         String(notApplicable/screening/diagnostic/prevention/healthServicesResearch/treatment/deviceFeasibility/supportiveCare/basicScience/other) (Optional)
+     *                     ]
+     *                     ids (Optional): [
+     *                         String (Optional)
+     *                     ]
+     *                     sources (Optional): [
+     *                         String(custom/clinicaltrials.gov) (Optional)
+     *                     ]
+     *                     facilityNames (Optional): [
+     *                         String (Optional)
+     *                     ]
+     *                     facilityLocations (Optional): [
+     *                          (Optional){
+     *                             city: String (Optional)
+     *                             state: String (Optional)
+     *                             country: String (Required)
+     *                         }
+     *                     ]
+     *                     facilityAreas (Optional): [
+     *                          (Optional){
+     *                             type: String(Feature) (Required)
+     *                             geometry (Required): {
+     *                                 type: String(Point) (Required)
+     *                                 coordinates (Required): [
+     *                                     double (Required)
+     *                                 ]
+     *                             }
+     *                             properties (Required): {
+     *                                 subType: String(Circle) (Required)
+     *                                 radius: double (Required)
+     *                             }
+     *                         }
+     *                     ]
+     *                 }
+     *             ]
+     *         }
+     *     }
+     * }
+     * }
+ * + *

Response Body Schema + * + * 

{@code
+     * {
+     *     jobId: String (Required)
+     *     createdDateTime: OffsetDateTime (Required)
+     *     expirationDateTime: OffsetDateTime (Required)
+     *     lastUpdateDateTime: OffsetDateTime (Required)
+     *     status: String(notStarted/running/succeeded/failed/partiallyCompleted) (Required)
+     *     errors (Optional): [
+     *         ResponseError (Optional)
+     *     ]
+     *     results (Optional): {
+     *         patients (Required): [
+     *              (Required){
+     *                 id: String (Required)
+     *                 inferences (Required): [
+     *                      (Required){
+     *                         type: String(trialEligibility) (Required)
+     *                         value: String (Required)
+     *                         description: String (Optional)
+     *                         confidenceScore: Double (Optional)
+     *                         evidence (Optional): [
+     *                              (Optional){
+     *                                 eligibilityCriteriaEvidence: String (Optional)
+     *                                 patientDataEvidence (Optional): {
+     *                                     id: String (Required)
+     *                                     text: String (Optional)
+     *                                     offset: int (Required)
+     *                                     length: int (Required)
+     *                                 }
+     *                                 patientInfoEvidence (Optional): {
+     *                                     system: String (Required)
+     *                                     code: String (Required)
+     *                                     name: String (Optional)
+     *                                     value: String (Optional)
+     *                                 }
+     *                                 importance: Double (Optional)
+     *                             }
+     *                         ]
+     *                         id: String (Optional)
+     *                         source: String(custom/clinicaltrials.gov) (Optional)
+     *                         metadata (Optional): {
+     *                             phases (Optional): [
+     *                                 String(notApplicable/earlyPhase1/phase1/phase2/phase3/phase4) (Optional)
+     *                             ]
+     *                             studyType: String(interventional/observational/expandedAccess/patientRegistries) (Optional)
+     *                             recruitmentStatus: String(unknownStatus/notYetRecruiting/recruiting/enrollingByInvitation) (Optional)
+     *                             conditions (Required): [
+     *                                 String (Required)
+     *                             ]
+     *                             sponsors (Optional): [
+     *                                 String (Optional)
+     *                             ]
+     *                             contacts (Optional): [
+     *                                  (Optional){
+     *                                     name: String (Optional)
+     *                                     email: String (Optional)
+     *                                     phone: String (Optional)
+     *                                 }
+     *                             ]
+     *                             facilities (Optional): [
+     *                                  (Optional){
+     *                                     name: String (Required)
+     *                                     city: String (Optional)
+     *                                     state: String (Optional)
+     *                                     country: String (Required)
+     *                                 }
+     *                             ]
+     *                         }
+     *                     }
+     *                 ]
+     *                 neededClinicalInfo (Optional): [
+     *                      (Optional){
+     *                         system: String (Required)
+     *                         code: String (Required)
+     *                         name: String (Optional)
+     *                         value: String (Optional)
+     *                         semanticType: String (Optional)
+     *                         category: String (Optional)
+     *                     }
+     *                 ]
+     *             }
+     *         ]
+     *         modelVersion: String (Required)
+     *         knowledgeGraphLastUpdateDate: LocalDate (Optional)
+     *     }
+     * }
+     * }
+ * + * @param trialMatcherData The body of the Trial Matcher request. + * @param requestOptions The options to configure the HTTP request before HTTP client sends it. + * @throws HttpResponseException thrown if the request is rejected by server. + * @throws ClientAuthenticationException thrown if the request is rejected by server on status code 401. + * @throws ResourceNotFoundException thrown if the request is rejected by server on status code 404. + * @throws ResourceModifiedException thrown if the request is rejected by server on status code 409. + * @return the {@link PollerFlux} for polling of the response for the Trial Matcher request. + */ + @ServiceMethod(returns = ReturnType.LONG_RUNNING_OPERATION) + public PollerFlux beginMatchTrialsWithModelAsync( + BinaryData trialMatcherData, RequestOptions requestOptions) { + return PollerFlux.create( + Duration.ofSeconds(1), + () -> this.matchTrialsWithResponseAsync(trialMatcherData, requestOptions), + new DefaultPollingStrategy<>( + this.getHttpPipeline(), + "{endpoint}/healthinsights".replace("{endpoint}", this.getEndpoint()), + null, + requestOptions != null && requestOptions.getContext() != null + ? requestOptions.getContext() + : Context.NONE), + TypeReference.createInstance(TrialMatcherResult.class), + TypeReference.createInstance(TrialMatcherResult.class)); + } + + /** + * Create Trial Matcher job + * + *

Creates a Trial Matcher job with the given request body. + * + *

Header Parameters + * + * + * + * + * + * + *
Header Parameters
NameTypeRequiredDescription
repeatability-request-idStringNoRepeatability request ID header
repeatability-first-sentStringNoRepeatability first sent header as HTTP-date
+ * + * You can add these to a request with {@link RequestOptions#addHeader} + * + *

Request Body Schema + * + * 

{@code
+     * {
+     *     patients (Required): [
+     *          (Required){
+     *             id: String (Required)
+     *             info (Optional): {
+     *                 sex: String(female/male/unspecified) (Optional)
+     *                 birthDate: LocalDate (Optional)
+     *                 clinicalInfo (Optional): [
+     *                      (Optional){
+     *                         system: String (Required)
+     *                         code: String (Required)
+     *                         name: String (Optional)
+     *                         value: String (Optional)
+     *                     }
+     *                 ]
+     *             }
+     *             data (Optional): [
+     *                  (Optional){
+     *                     type: String(note/fhirBundle/dicom/genomicSequencing) (Required)
+     *                     clinicalType: String(consultation/dischargeSummary/historyAndPhysical/procedure/progress/imaging/laboratory/pathology) (Optional)
+     *                     id: String (Required)
+     *                     language: String (Optional)
+     *                     createdDateTime: OffsetDateTime (Optional)
+     *                     content (Required): {
+     *                         sourceType: String(inline/reference) (Required)
+     *                         value: String (Required)
+     *                     }
+     *                 }
+     *             ]
+     *         }
+     *     ]
+     *     configuration (Optional): {
+     *         verbose: Boolean (Optional)
+     *         includeEvidence: Boolean (Optional)
+     *         clinicalTrials (Required): {
+     *             customTrials (Optional): [
+     *                  (Optional){
+     *                     id: String (Required)
+     *                     eligibilityCriteriaText: String (Optional)
+     *                     demographics (Optional): {
+     *                         acceptedSex: String(all/female/male) (Optional)
+     *                         acceptedAgeRange (Optional): {
+     *                             minimumAge (Optional): {
+     *                                 unit: String(years/months/days) (Required)
+     *                                 value: double (Required)
+     *                             }
+     *                             maximumAge (Optional): (recursive schema, see maximumAge above)
+     *                         }
+     *                     }
+     *                     metadata (Required): {
+     *                         phases (Optional): [
+     *                             String(notApplicable/earlyPhase1/phase1/phase2/phase3/phase4) (Optional)
+     *                         ]
+     *                         studyType: String(interventional/observational/expandedAccess/patientRegistries) (Optional)
+     *                         recruitmentStatus: String(unknownStatus/notYetRecruiting/recruiting/enrollingByInvitation) (Optional)
+     *                         conditions (Required): [
+     *                             String (Required)
+     *                         ]
+     *                         sponsors (Optional): [
+     *                             String (Optional)
+     *                         ]
+     *                         contacts (Optional): [
+     *                              (Optional){
+     *                                 name: String (Optional)
+     *                                 email: String (Optional)
+     *                                 phone: String (Optional)
+     *                             }
+     *                         ]
+     *                         facilities (Optional): [
+     *                              (Optional){
+     *                                 name: String (Required)
+     *                                 city: String (Optional)
+     *                                 state: String (Optional)
+     *                                 country: String (Required)
+     *                             }
+     *                         ]
+     *                     }
+     *                 }
+     *             ]
+     *             registryFilters (Optional): [
+     *                  (Optional){
+     *                     conditions (Optional): [
+     *                         String (Optional)
+     *                     ]
+     *                     studyTypes (Optional): [
+     *                         String(interventional/observational/expandedAccess/patientRegistries) (Optional)
+     *                     ]
+     *                     recruitmentStatuses (Optional): [
+     *                         String(unknownStatus/notYetRecruiting/recruiting/enrollingByInvitation) (Optional)
+     *                     ]
+     *                     sponsors (Optional): [
+     *                         String (Optional)
+     *                     ]
+     *                     phases (Optional): [
+     *                         String(notApplicable/earlyPhase1/phase1/phase2/phase3/phase4) (Optional)
+     *                     ]
+     *                     purposes (Optional): [
+     *                         String(notApplicable/screening/diagnostic/prevention/healthServicesResearch/treatment/deviceFeasibility/supportiveCare/basicScience/other) (Optional)
+     *                     ]
+     *                     ids (Optional): [
+     *                         String (Optional)
+     *                     ]
+     *                     sources (Optional): [
+     *                         String(custom/clinicaltrials.gov) (Optional)
+     *                     ]
+     *                     facilityNames (Optional): [
+     *                         String (Optional)
+     *                     ]
+     *                     facilityLocations (Optional): [
+     *                          (Optional){
+     *                             city: String (Optional)
+     *                             state: String (Optional)
+     *                             country: String (Required)
+     *                         }
+     *                     ]
+     *                     facilityAreas (Optional): [
+     *                          (Optional){
+     *                             type: String(Feature) (Required)
+     *                             geometry (Required): {
+     *                                 type: String(Point) (Required)
+     *                                 coordinates (Required): [
+     *                                     double (Required)
+     *                                 ]
+     *                             }
+     *                             properties (Required): {
+     *                                 subType: String(Circle) (Required)
+     *                                 radius: double (Required)
+     *                             }
+     *                         }
+     *                     ]
+     *                 }
+     *             ]
+     *         }
+     *     }
+     * }
+     * }
+ * + *

Response Body Schema + * + * 

{@code
+     * {
+     *     jobId: String (Required)
+     *     createdDateTime: OffsetDateTime (Required)
+     *     expirationDateTime: OffsetDateTime (Required)
+     *     lastUpdateDateTime: OffsetDateTime (Required)
+     *     status: String(notStarted/running/succeeded/failed/partiallyCompleted) (Required)
+     *     errors (Optional): [
+     *         ResponseError (Optional)
+     *     ]
+     *     results (Optional): {
+     *         patients (Required): [
+     *              (Required){
+     *                 id: String (Required)
+     *                 inferences (Required): [
+     *                      (Required){
+     *                         type: String(trialEligibility) (Required)
+     *                         value: String (Required)
+     *                         description: String (Optional)
+     *                         confidenceScore: Double (Optional)
+     *                         evidence (Optional): [
+     *                              (Optional){
+     *                                 eligibilityCriteriaEvidence: String (Optional)
+     *                                 patientDataEvidence (Optional): {
+     *                                     id: String (Required)
+     *                                     text: String (Optional)
+     *                                     offset: int (Required)
+     *                                     length: int (Required)
+     *                                 }
+     *                                 patientInfoEvidence (Optional): {
+     *                                     system: String (Required)
+     *                                     code: String (Required)
+     *                                     name: String (Optional)
+     *                                     value: String (Optional)
+     *                                 }
+     *                                 importance: Double (Optional)
+     *                             }
+     *                         ]
+     *                         id: String (Optional)
+     *                         source: String(custom/clinicaltrials.gov) (Optional)
+     *                         metadata (Optional): {
+     *                             phases (Optional): [
+     *                                 String(notApplicable/earlyPhase1/phase1/phase2/phase3/phase4) (Optional)
+     *                             ]
+     *                             studyType: String(interventional/observational/expandedAccess/patientRegistries) (Optional)
+     *                             recruitmentStatus: String(unknownStatus/notYetRecruiting/recruiting/enrollingByInvitation) (Optional)
+     *                             conditions (Required): [
+     *                                 String (Required)
+     *                             ]
+     *                             sponsors (Optional): [
+     *                                 String (Optional)
+     *                             ]
+     *                             contacts (Optional): [
+     *                                  (Optional){
+     *                                     name: String (Optional)
+     *                                     email: String (Optional)
+     *                                     phone: String (Optional)
+     *                                 }
+     *                             ]
+     *                             facilities (Optional): [
+     *                                  (Optional){
+     *                                     name: String (Required)
+     *                                     city: String (Optional)
+     *                                     state: String (Optional)
+     *                                     country: String (Required)
+     *                                 }
+     *                             ]
+     *                         }
+     *                     }
+     *                 ]
+     *                 neededClinicalInfo (Optional): [
+     *                      (Optional){
+     *                         system: String (Required)
+     *                         code: String (Required)
+     *                         name: String (Optional)
+     *                         value: String (Optional)
+     *                         semanticType: String (Optional)
+     *                         category: String (Optional)
+     *                     }
+     *                 ]
+     *             }
+     *         ]
+     *         modelVersion: String (Required)
+     *         knowledgeGraphLastUpdateDate: LocalDate (Optional)
+     *     }
+     * }
+     * }
+ * + * @param trialMatcherData The body of the Trial Matcher request. + * @param requestOptions The options to configure the HTTP request before HTTP client sends it. + * @throws HttpResponseException thrown if the request is rejected by server. + * @throws ClientAuthenticationException thrown if the request is rejected by server on status code 401. + * @throws ResourceNotFoundException thrown if the request is rejected by server on status code 404. + * @throws ResourceModifiedException thrown if the request is rejected by server on status code 409. + * @return the {@link SyncPoller} for polling of the response for the Trial Matcher request. + */ + @ServiceMethod(returns = ReturnType.LONG_RUNNING_OPERATION) + public SyncPoller beginMatchTrialsWithModel( + BinaryData trialMatcherData, RequestOptions requestOptions) { + return this.beginMatchTrialsWithModelAsync(trialMatcherData, requestOptions).getSyncPoller(); + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/implementation/package-info.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/implementation/package-info.java new file mode 100644 index 0000000000000..d4bea9038803b --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/implementation/package-info.java @@ -0,0 +1,10 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +/** + * Package containing the implementations for AzureHealthInsights. Azure Health Insights provides an API that serves + * insight models, specific for Health & Life Sciences, that perform analysis and provide inferences to be used by a + * human. + */ +package com.azure.health.insights.clinicalmatching.implementation; diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/AcceptedAge.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/AcceptedAge.java new file mode 100644 index 0000000000000..d077c6d5be573 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/AcceptedAge.java @@ -0,0 +1,57 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.annotation.Immutable; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; + +/** A person's age, given as a number (value) and a unit (e.g. years, months). */ +@Immutable +public final class AcceptedAge { + /* + * Possible units for a person's age. + */ + @JsonProperty(value = "unit", required = true) + private AgeUnit unit; + + /* + * The number of years/months/days that represents the person's age. + */ + @JsonProperty(value = "value", required = true) + private double value; + + /** + * Creates an instance of AcceptedAge class. + * + * @param unit the unit value to set. + * @param value the value value to set. + */ + @JsonCreator + public AcceptedAge( + @JsonProperty(value = "unit", required = true) AgeUnit unit, + @JsonProperty(value = "value", required = true) double value) { + this.unit = unit; + this.value = value; + } + + /** + * Get the unit property: Possible units for a person's age. + * + * @return the unit value. + */ + public AgeUnit getUnit() { + return this.unit; + } + + /** + * Get the value property: The number of years/months/days that represents the person's age. + * + * @return the value value. + */ + public double getValue() { + return this.value; + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/AcceptedAgeRange.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/AcceptedAgeRange.java new file mode 100644 index 0000000000000..f524e1aea2509 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/AcceptedAgeRange.java @@ -0,0 +1,67 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.annotation.Fluent; +import com.fasterxml.jackson.annotation.JsonProperty; + +/** A definition of the range of ages accepted by a clinical trial. Contains a minimum age and/or a maximum age. */ +@Fluent +public final class AcceptedAgeRange { + /* + * A person's age, given as a number (value) and a unit (e.g. years, months) + */ + @JsonProperty(value = "minimumAge") + private AcceptedAge minimumAge; + + /* + * A person's age, given as a number (value) and a unit (e.g. years, months) + */ + @JsonProperty(value = "maximumAge") + private AcceptedAge maximumAge; + + /** Creates an instance of AcceptedAgeRange class. */ + public AcceptedAgeRange() {} + + /** + * Get the minimumAge property: A person's age, given as a number (value) and a unit (e.g. years, months). + * + * @return the minimumAge value. + */ + public AcceptedAge getMinimumAge() { + return this.minimumAge; + } + + /** + * Set the minimumAge property: A person's age, given as a number (value) and a unit (e.g. years, months). + * + * @param minimumAge the minimumAge value to set. + * @return the AcceptedAgeRange object itself. + */ + public AcceptedAgeRange setMinimumAge(AcceptedAge minimumAge) { + this.minimumAge = minimumAge; + return this; + } + + /** + * Get the maximumAge property: A person's age, given as a number (value) and a unit (e.g. years, months). + * + * @return the maximumAge value. + */ + public AcceptedAge getMaximumAge() { + return this.maximumAge; + } + + /** + * Set the maximumAge property: A person's age, given as a number (value) and a unit (e.g. years, months). + * + * @param maximumAge the maximumAge value to set. + * @return the AcceptedAgeRange object itself. + */ + public AcceptedAgeRange setMaximumAge(AcceptedAge maximumAge) { + this.maximumAge = maximumAge; + return this; + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/AgeUnit.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/AgeUnit.java new file mode 100644 index 0000000000000..4e56d838ebc16 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/AgeUnit.java @@ -0,0 +1,49 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.util.ExpandableStringEnum; +import com.fasterxml.jackson.annotation.JsonCreator; +import java.util.Collection; + +/** Possible units for a person's age. */ +public final class AgeUnit extends ExpandableStringEnum { + /** Static value years for AgeUnit. */ + public static final AgeUnit YEARS = fromString("years"); + + /** Static value months for AgeUnit. */ + public static final AgeUnit MONTHS = fromString("months"); + + /** Static value days for AgeUnit. */ + public static final AgeUnit DAYS = fromString("days"); + + /** + * Creates a new instance of AgeUnit value. + * + * @deprecated Use the {@link #fromString(String)} factory method. + */ + @Deprecated + public AgeUnit() {} + + /** + * Creates or finds a AgeUnit from its string representation. + * + * @param name a name to look for. + * @return the corresponding AgeUnit. + */ + @JsonCreator + public static AgeUnit fromString(String name) { + return fromString(name, AgeUnit.class); + } + + /** + * Gets known AgeUnit values. + * + * @return known AgeUnit values. + */ + public static Collection values() { + return values(AgeUnit.class); + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/AreaGeometry.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/AreaGeometry.java new file mode 100644 index 0000000000000..4f789cc09f030 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/AreaGeometry.java @@ -0,0 +1,60 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.annotation.Immutable; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import java.util.List; + +/** `GeoJSON` geometry, representing the area circle's center. */ +@Immutable +public final class AreaGeometry { + /* + * `GeoJSON` geometry type. + */ + @JsonProperty(value = "type", required = true) + private GeoJsonGeometryType type; + + /* + * Coordinates of the area circle's center, represented according to the `GeoJSON` standard. + * This is an array of 2 decimal numbers, longitude and latitude (precisely in this order). + */ + @JsonProperty(value = "coordinates", required = true) + private List coordinates; + + /** + * Creates an instance of AreaGeometry class. + * + * @param type the type value to set. + * @param coordinates the coordinates value to set. + */ + @JsonCreator + public AreaGeometry( + @JsonProperty(value = "type", required = true) GeoJsonGeometryType type, + @JsonProperty(value = "coordinates", required = true) List coordinates) { + this.type = type; + this.coordinates = coordinates; + } + + /** + * Get the type property: `GeoJSON` geometry type. + * + * @return the type value. + */ + public GeoJsonGeometryType getType() { + return this.type; + } + + /** + * Get the coordinates property: Coordinates of the area circle's center, represented according to the `GeoJSON` + * standard. This is an array of 2 decimal numbers, longitude and latitude (precisely in this order). + * + * @return the coordinates value. + */ + public List getCoordinates() { + return this.coordinates; + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/AreaProperties.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/AreaProperties.java new file mode 100644 index 0000000000000..61932f79d7897 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/AreaProperties.java @@ -0,0 +1,57 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.annotation.Immutable; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; + +/** `GeoJSON` object properties. */ +@Immutable +public final class AreaProperties { + /* + * `GeoJSON` object sub-type. + */ + @JsonProperty(value = "subType", required = true) + private GeoJsonPropertiesSubType subType; + + /* + * The radius of the area's circle, in meters. + */ + @JsonProperty(value = "radius", required = true) + private double radius; + + /** + * Creates an instance of AreaProperties class. + * + * @param subType the subType value to set. + * @param radius the radius value to set. + */ + @JsonCreator + public AreaProperties( + @JsonProperty(value = "subType", required = true) GeoJsonPropertiesSubType subType, + @JsonProperty(value = "radius", required = true) double radius) { + this.subType = subType; + this.radius = radius; + } + + /** + * Get the subType property: `GeoJSON` object sub-type. + * + * @return the subType value. + */ + public GeoJsonPropertiesSubType getSubType() { + return this.subType; + } + + /** + * Get the radius property: The radius of the area's circle, in meters. + * + * @return the radius value. + */ + public double getRadius() { + return this.radius; + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalCodedElement.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalCodedElement.java new file mode 100644 index 0000000000000..79b7008a65226 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalCodedElement.java @@ -0,0 +1,109 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.annotation.Fluent; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; + +/** A piece of clinical information, expressed as a code in a clinical coding system. */ +@Fluent +public final class ClinicalCodedElement { + /* + * The clinical coding system, e.g. ICD-10, SNOMED-CT, UMLS. + */ + @JsonProperty(value = "system", required = true) + private String system; + + /* + * The code within the given clinical coding system. + */ + @JsonProperty(value = "code", required = true) + private String code; + + /* + * The name of this coded concept in the coding system. + */ + @JsonProperty(value = "name") + private String name; + + /* + * A value associated with the code within the given clinical coding system. + */ + @JsonProperty(value = "value") + private String value; + + /** + * Creates an instance of ClinicalCodedElement class. + * + * @param system the system value to set. + * @param code the code value to set. + */ + @JsonCreator + public ClinicalCodedElement( + @JsonProperty(value = "system", required = true) String system, + @JsonProperty(value = "code", required = true) String code) { + this.system = system; + this.code = code; + } + + /** + * Get the system property: The clinical coding system, e.g. ICD-10, SNOMED-CT, UMLS. + * + * @return the system value. + */ + public String getSystem() { + return this.system; + } + + /** + * Get the code property: The code within the given clinical coding system. + * + * @return the code value. + */ + public String getCode() { + return this.code; + } + + /** + * Get the name property: The name of this coded concept in the coding system. + * + * @return the name value. + */ + public String getName() { + return this.name; + } + + /** + * Set the name property: The name of this coded concept in the coding system. + * + * @param name the name value to set. + * @return the ClinicalCodedElement object itself. + */ + public ClinicalCodedElement setName(String name) { + this.name = name; + return this; + } + + /** + * Get the value property: A value associated with the code within the given clinical coding system. + * + * @return the value value. + */ + public String getValue() { + return this.value; + } + + /** + * Set the value property: A value associated with the code within the given clinical coding system. + * + * @param value the value value to set. + * @return the ClinicalCodedElement object itself. + */ + public ClinicalCodedElement setValue(String value) { + this.value = value; + return this; + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalDocumentType.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalDocumentType.java new file mode 100644 index 0000000000000..d0ad8ed1dc955 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalDocumentType.java @@ -0,0 +1,64 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.util.ExpandableStringEnum; +import com.fasterxml.jackson.annotation.JsonCreator; +import java.util.Collection; + +/** The type of the clinical document. */ +public final class ClinicalDocumentType extends ExpandableStringEnum { + /** Static value consultation for ClinicalDocumentType. */ + public static final ClinicalDocumentType CONSULTATION = fromString("consultation"); + + /** Static value dischargeSummary for ClinicalDocumentType. */ + public static final ClinicalDocumentType DISCHARGE_SUMMARY = fromString("dischargeSummary"); + + /** Static value historyAndPhysical for ClinicalDocumentType. */ + public static final ClinicalDocumentType HISTORY_AND_PHYSICAL = fromString("historyAndPhysical"); + + /** Static value procedure for ClinicalDocumentType. */ + public static final ClinicalDocumentType PROCEDURE = fromString("procedure"); + + /** Static value progress for ClinicalDocumentType. */ + public static final ClinicalDocumentType PROGRESS = fromString("progress"); + + /** Static value imaging for ClinicalDocumentType. */ + public static final ClinicalDocumentType IMAGING = fromString("imaging"); + + /** Static value laboratory for ClinicalDocumentType. */ + public static final ClinicalDocumentType LABORATORY = fromString("laboratory"); + + /** Static value pathology for ClinicalDocumentType. */ + public static final ClinicalDocumentType PATHOLOGY = fromString("pathology"); + + /** + * Creates a new instance of ClinicalDocumentType value. + * + * @deprecated Use the {@link #fromString(String)} factory method. + */ + @Deprecated + public ClinicalDocumentType() {} + + /** + * Creates or finds a ClinicalDocumentType from its string representation. + * + * @param name a name to look for. + * @return the corresponding ClinicalDocumentType. + */ + @JsonCreator + public static ClinicalDocumentType fromString(String name) { + return fromString(name, ClinicalDocumentType.class); + } + + /** + * Gets known ClinicalDocumentType values. + * + * @return known ClinicalDocumentType values. + */ + public static Collection values() { + return values(ClinicalDocumentType.class); + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalNoteEvidence.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalNoteEvidence.java new file mode 100644 index 0000000000000..567c6025e9556 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalNoteEvidence.java @@ -0,0 +1,90 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.annotation.Immutable; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; + +/** A piece of evidence from a clinical note (text document). */ +@Immutable +public final class ClinicalNoteEvidence { + /* + * The identifier of the document containing the evidence. + */ + @JsonProperty(value = "id", required = true) + private String id; + + /* + * The actual text span which is evidence for the inference. + */ + @JsonProperty(value = "text") + private String text; + + /* + * The start index of the evidence text span in the document (0 based). + */ + @JsonProperty(value = "offset", required = true) + private int offset; + + /* + * The length of the evidence text span. + */ + @JsonProperty(value = "length", required = true) + private int length; + + /** + * Creates an instance of ClinicalNoteEvidence class. + * + * @param id the id value to set. + * @param offset the offset value to set. + * @param length the length value to set. + */ + @JsonCreator + private ClinicalNoteEvidence( + @JsonProperty(value = "id", required = true) String id, + @JsonProperty(value = "offset", required = true) int offset, + @JsonProperty(value = "length", required = true) int length) { + this.id = id; + this.offset = offset; + this.length = length; + } + + /** + * Get the id property: The identifier of the document containing the evidence. + * + * @return the id value. + */ + public String getId() { + return this.id; + } + + /** + * Get the text property: The actual text span which is evidence for the inference. + * + * @return the text value. + */ + public String getText() { + return this.text; + } + + /** + * Get the offset property: The start index of the evidence text span in the document (0 based). + * + * @return the offset value. + */ + public int getOffset() { + return this.offset; + } + + /** + * Get the length property: The length of the evidence text span. + * + * @return the length value. + */ + public int getLength() { + return this.length; + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialAcceptedSex.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialAcceptedSex.java new file mode 100644 index 0000000000000..eda0f5c084e2e --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialAcceptedSex.java @@ -0,0 +1,52 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.util.ExpandableStringEnum; +import com.fasterxml.jackson.annotation.JsonCreator; +import java.util.Collection; + +/** + * Possible values for the Sex eligibility criterion as accepted by clinical trials, which indicates the sex of people + * who may participate in a clinical study. + */ +public final class ClinicalTrialAcceptedSex extends ExpandableStringEnum { + /** Static value all for ClinicalTrialAcceptedSex. */ + public static final ClinicalTrialAcceptedSex ALL = fromString("all"); + + /** Static value female for ClinicalTrialAcceptedSex. */ + public static final ClinicalTrialAcceptedSex FEMALE = fromString("female"); + + /** Static value male for ClinicalTrialAcceptedSex. */ + public static final ClinicalTrialAcceptedSex MALE = fromString("male"); + + /** + * Creates a new instance of ClinicalTrialAcceptedSex value. + * + * @deprecated Use the {@link #fromString(String)} factory method. + */ + @Deprecated + public ClinicalTrialAcceptedSex() {} + + /** + * Creates or finds a ClinicalTrialAcceptedSex from its string representation. + * + * @param name a name to look for. + * @return the corresponding ClinicalTrialAcceptedSex. + */ + @JsonCreator + public static ClinicalTrialAcceptedSex fromString(String name) { + return fromString(name, ClinicalTrialAcceptedSex.class); + } + + /** + * Gets known ClinicalTrialAcceptedSex values. + * + * @return known ClinicalTrialAcceptedSex values. + */ + public static Collection values() { + return values(ClinicalTrialAcceptedSex.class); + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialDemographics.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialDemographics.java new file mode 100644 index 0000000000000..d83c5c94cdb2a --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialDemographics.java @@ -0,0 +1,69 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.annotation.Fluent; +import com.fasterxml.jackson.annotation.JsonProperty; + +/** Demographic criteria for a clinical trial. */ +@Fluent +public final class ClinicalTrialDemographics { + /* + * Indication of the sex of people who may participate in the clinical trial. + */ + @JsonProperty(value = "acceptedSex") + private ClinicalTrialAcceptedSex acceptedSex; + + /* + * A definition of the range of ages accepted by a clinical trial. Contains a minimum age and/or a maximum age. + */ + @JsonProperty(value = "acceptedAgeRange") + private AcceptedAgeRange acceptedAgeRange; + + /** Creates an instance of ClinicalTrialDemographics class. */ + public ClinicalTrialDemographics() {} + + /** + * Get the acceptedSex property: Indication of the sex of people who may participate in the clinical trial. + * + * @return the acceptedSex value. + */ + public ClinicalTrialAcceptedSex getAcceptedSex() { + return this.acceptedSex; + } + + /** + * Set the acceptedSex property: Indication of the sex of people who may participate in the clinical trial. + * + * @param acceptedSex the acceptedSex value to set. + * @return the ClinicalTrialDemographics object itself. + */ + public ClinicalTrialDemographics setAcceptedSex(ClinicalTrialAcceptedSex acceptedSex) { + this.acceptedSex = acceptedSex; + return this; + } + + /** + * Get the acceptedAgeRange property: A definition of the range of ages accepted by a clinical trial. Contains a + * minimum age and/or a maximum age. + * + * @return the acceptedAgeRange value. + */ + public AcceptedAgeRange getAcceptedAgeRange() { + return this.acceptedAgeRange; + } + + /** + * Set the acceptedAgeRange property: A definition of the range of ages accepted by a clinical trial. Contains a + * minimum age and/or a maximum age. + * + * @param acceptedAgeRange the acceptedAgeRange value to set. + * @return the ClinicalTrialDemographics object itself. + */ + public ClinicalTrialDemographics setAcceptedAgeRange(AcceptedAgeRange acceptedAgeRange) { + this.acceptedAgeRange = acceptedAgeRange; + return this; + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialDetails.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialDetails.java new file mode 100644 index 0000000000000..dc657ae468945 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialDetails.java @@ -0,0 +1,112 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.annotation.Fluent; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; + +/** A description of a clinical trial. */ +@Fluent +public final class ClinicalTrialDetails { + /* + * A given identifier for the clinical trial. Has to be unique within a list of clinical trials. + */ + @JsonProperty(value = "id", required = true) + private String id; + + /* + * The eligibility criteria of the clinical trial (inclusion and exclusion), given as text. + */ + @JsonProperty(value = "eligibilityCriteriaText") + private String eligibilityCriteriaText; + + /* + * Demographic criteria for a clinical trial. + */ + @JsonProperty(value = "demographics") + private ClinicalTrialDemographics demographics; + + /* + * Trial data which is of interest to the potential participant. + */ + @JsonProperty(value = "metadata", required = true) + private ClinicalTrialMetadata metadata; + + /** + * Creates an instance of ClinicalTrialDetails class. + * + * @param id the id value to set. + * @param metadata the metadata value to set. + */ + @JsonCreator + public ClinicalTrialDetails( + @JsonProperty(value = "id", required = true) String id, + @JsonProperty(value = "metadata", required = true) ClinicalTrialMetadata metadata) { + this.id = id; + this.metadata = metadata; + } + + /** + * Get the id property: A given identifier for the clinical trial. Has to be unique within a list of clinical + * trials. + * + * @return the id value. + */ + public String getId() { + return this.id; + } + + /** + * Get the eligibilityCriteriaText property: The eligibility criteria of the clinical trial (inclusion and + * exclusion), given as text. + * + * @return the eligibilityCriteriaText value. + */ + public String getEligibilityCriteriaText() { + return this.eligibilityCriteriaText; + } + + /** + * Set the eligibilityCriteriaText property: The eligibility criteria of the clinical trial (inclusion and + * exclusion), given as text. + * + * @param eligibilityCriteriaText the eligibilityCriteriaText value to set. + * @return the ClinicalTrialDetails object itself. + */ + public ClinicalTrialDetails setEligibilityCriteriaText(String eligibilityCriteriaText) { + this.eligibilityCriteriaText = eligibilityCriteriaText; + return this; + } + + /** + * Get the demographics property: Demographic criteria for a clinical trial. + * + * @return the demographics value. + */ + public ClinicalTrialDemographics getDemographics() { + return this.demographics; + } + + /** + * Set the demographics property: Demographic criteria for a clinical trial. + * + * @param demographics the demographics value to set. + * @return the ClinicalTrialDetails object itself. + */ + public ClinicalTrialDetails setDemographics(ClinicalTrialDemographics demographics) { + this.demographics = demographics; + return this; + } + + /** + * Get the metadata property: Trial data which is of interest to the potential participant. + * + * @return the metadata value. + */ + public ClinicalTrialMetadata getMetadata() { + return this.metadata; + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialMetadata.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialMetadata.java new file mode 100644 index 0000000000000..1914368e010a9 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialMetadata.java @@ -0,0 +1,201 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.annotation.Fluent; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import java.util.List; + +/** Trial data which is of interest to the potential participant. */ +@Fluent +public final class ClinicalTrialMetadata { + /* + * Phases which are relevant for the clinical trial. + * Each clinical trial can be in a certain phase or in multiple phases. + */ + @JsonProperty(value = "phases") + private List phases; + + /* + * Possible study types of a clinical trial. + */ + @JsonProperty(value = "studyType") + private ClinicalTrialStudyType studyType; + + /* + * Possible recruitment status of a clinical trial. + */ + @JsonProperty(value = "recruitmentStatus") + private ClinicalTrialRecruitmentStatus recruitmentStatus; + + /* + * Medical conditions and their synonyms which are relevant for the clinical trial, given as strings. + */ + @JsonProperty(value = "conditions", required = true) + private List conditions; + + /* + * Sponsors/collaborators involved with the trial. + */ + @JsonProperty(value = "sponsors") + private List sponsors; + + /* + * Contact details of the trial administrators, for patients that want to participate in the trial. + */ + @JsonProperty(value = "contacts") + private List contacts; + + /* + * Research facilities where the clinical trial is conducted. + */ + @JsonProperty(value = "facilities") + private List facilities; + + /** + * Creates an instance of ClinicalTrialMetadata class. + * + * @param conditions the conditions value to set. + */ + @JsonCreator + public ClinicalTrialMetadata(@JsonProperty(value = "conditions", required = true) List conditions) { + this.conditions = conditions; + } + + /** + * Get the phases property: Phases which are relevant for the clinical trial. Each clinical trial can be in a + * certain phase or in multiple phases. + * + * @return the phases value. + */ + public List getPhases() { + return this.phases; + } + + /** + * Set the phases property: Phases which are relevant for the clinical trial. Each clinical trial can be in a + * certain phase or in multiple phases. + * + * @param phases the phases value to set. + * @return the ClinicalTrialMetadata object itself. + */ + public ClinicalTrialMetadata setPhases(List phases) { + this.phases = phases; + return this; + } + + /** + * Get the studyType property: Possible study types of a clinical trial. + * + * @return the studyType value. + */ + public ClinicalTrialStudyType getStudyType() { + return this.studyType; + } + + /** + * Set the studyType property: Possible study types of a clinical trial. + * + * @param studyType the studyType value to set. + * @return the ClinicalTrialMetadata object itself. + */ + public ClinicalTrialMetadata setStudyType(ClinicalTrialStudyType studyType) { + this.studyType = studyType; + return this; + } + + /** + * Get the recruitmentStatus property: Possible recruitment status of a clinical trial. + * + * @return the recruitmentStatus value. + */ + public ClinicalTrialRecruitmentStatus getRecruitmentStatus() { + return this.recruitmentStatus; + } + + /** + * Set the recruitmentStatus property: Possible recruitment status of a clinical trial. + * + * @param recruitmentStatus the recruitmentStatus value to set. + * @return the ClinicalTrialMetadata object itself. + */ + public ClinicalTrialMetadata setRecruitmentStatus(ClinicalTrialRecruitmentStatus recruitmentStatus) { + this.recruitmentStatus = recruitmentStatus; + return this; + } + + /** + * Get the conditions property: Medical conditions and their synonyms which are relevant for the clinical trial, + * given as strings. + * + * @return the conditions value. + */ + public List getConditions() { + return this.conditions; + } + + /** + * Get the sponsors property: Sponsors/collaborators involved with the trial. + * + * @return the sponsors value. + */ + public List getSponsors() { + return this.sponsors; + } + + /** + * Set the sponsors property: Sponsors/collaborators involved with the trial. + * + * @param sponsors the sponsors value to set. + * @return the ClinicalTrialMetadata object itself. + */ + public ClinicalTrialMetadata setSponsors(List sponsors) { + this.sponsors = sponsors; + return this; + } + + /** + * Get the contacts property: Contact details of the trial administrators, for patients that want to participate in + * the trial. + * + * @return the contacts value. + */ + public List getContacts() { + return this.contacts; + } + + /** + * Set the contacts property: Contact details of the trial administrators, for patients that want to participate in + * the trial. + * + * @param contacts the contacts value to set. + * @return the ClinicalTrialMetadata object itself. + */ + public ClinicalTrialMetadata setContacts(List contacts) { + this.contacts = contacts; + return this; + } + + /** + * Get the facilities property: Research facilities where the clinical trial is conducted. + * + * @return the facilities value. + */ + public List getFacilities() { + return this.facilities; + } + + /** + * Set the facilities property: Research facilities where the clinical trial is conducted. + * + * @param facilities the facilities value to set. + * @return the ClinicalTrialMetadata object itself. + */ + public ClinicalTrialMetadata setFacilities(List facilities) { + this.facilities = facilities; + return this; + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialPhase.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialPhase.java new file mode 100644 index 0000000000000..e8593e819f9b1 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialPhase.java @@ -0,0 +1,58 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.util.ExpandableStringEnum; +import com.fasterxml.jackson.annotation.JsonCreator; +import java.util.Collection; + +/** Possible phases of a clinical trial. */ +public final class ClinicalTrialPhase extends ExpandableStringEnum { + /** Static value notApplicable for ClinicalTrialPhase. */ + public static final ClinicalTrialPhase NOT_APPLICABLE = fromString("notApplicable"); + + /** Static value earlyPhase1 for ClinicalTrialPhase. */ + public static final ClinicalTrialPhase EARLY_PHASE1 = fromString("earlyPhase1"); + + /** Static value phase1 for ClinicalTrialPhase. */ + public static final ClinicalTrialPhase PHASE1 = fromString("phase1"); + + /** Static value phase2 for ClinicalTrialPhase. */ + public static final ClinicalTrialPhase PHASE2 = fromString("phase2"); + + /** Static value phase3 for ClinicalTrialPhase. */ + public static final ClinicalTrialPhase PHASE3 = fromString("phase3"); + + /** Static value phase4 for ClinicalTrialPhase. */ + public static final ClinicalTrialPhase PHASE4 = fromString("phase4"); + + /** + * Creates a new instance of ClinicalTrialPhase value. + * + * @deprecated Use the {@link #fromString(String)} factory method. + */ + @Deprecated + public ClinicalTrialPhase() {} + + /** + * Creates or finds a ClinicalTrialPhase from its string representation. + * + * @param name a name to look for. + * @return the corresponding ClinicalTrialPhase. + */ + @JsonCreator + public static ClinicalTrialPhase fromString(String name) { + return fromString(name, ClinicalTrialPhase.class); + } + + /** + * Gets known ClinicalTrialPhase values. + * + * @return known ClinicalTrialPhase values. + */ + public static Collection values() { + return values(ClinicalTrialPhase.class); + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialPurpose.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialPurpose.java new file mode 100644 index 0000000000000..6934d763ecc9f --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialPurpose.java @@ -0,0 +1,70 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.util.ExpandableStringEnum; +import com.fasterxml.jackson.annotation.JsonCreator; +import java.util.Collection; + +/** Possible purposes of a clinical trial. */ +public final class ClinicalTrialPurpose extends ExpandableStringEnum { + /** Static value notApplicable for ClinicalTrialPurpose. */ + public static final ClinicalTrialPurpose NOT_APPLICABLE = fromString("notApplicable"); + + /** Static value screening for ClinicalTrialPurpose. */ + public static final ClinicalTrialPurpose SCREENING = fromString("screening"); + + /** Static value diagnostic for ClinicalTrialPurpose. */ + public static final ClinicalTrialPurpose DIAGNOSTIC = fromString("diagnostic"); + + /** Static value prevention for ClinicalTrialPurpose. */ + public static final ClinicalTrialPurpose PREVENTION = fromString("prevention"); + + /** Static value healthServicesResearch for ClinicalTrialPurpose. */ + public static final ClinicalTrialPurpose HEALTH_SERVICES_RESEARCH = fromString("healthServicesResearch"); + + /** Static value treatment for ClinicalTrialPurpose. */ + public static final ClinicalTrialPurpose TREATMENT = fromString("treatment"); + + /** Static value deviceFeasibility for ClinicalTrialPurpose. */ + public static final ClinicalTrialPurpose DEVICE_FEASIBILITY = fromString("deviceFeasibility"); + + /** Static value supportiveCare for ClinicalTrialPurpose. */ + public static final ClinicalTrialPurpose SUPPORTIVE_CARE = fromString("supportiveCare"); + + /** Static value basicScience for ClinicalTrialPurpose. */ + public static final ClinicalTrialPurpose BASIC_SCIENCE = fromString("basicScience"); + + /** Static value other for ClinicalTrialPurpose. */ + public static final ClinicalTrialPurpose OTHER = fromString("other"); + + /** + * Creates a new instance of ClinicalTrialPurpose value. + * + * @deprecated Use the {@link #fromString(String)} factory method. + */ + @Deprecated + public ClinicalTrialPurpose() {} + + /** + * Creates or finds a ClinicalTrialPurpose from its string representation. + * + * @param name a name to look for. + * @return the corresponding ClinicalTrialPurpose. + */ + @JsonCreator + public static ClinicalTrialPurpose fromString(String name) { + return fromString(name, ClinicalTrialPurpose.class); + } + + /** + * Gets known ClinicalTrialPurpose values. + * + * @return known ClinicalTrialPurpose values. + */ + public static Collection values() { + return values(ClinicalTrialPurpose.class); + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialRecruitmentStatus.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialRecruitmentStatus.java new file mode 100644 index 0000000000000..c75612c177bcc --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialRecruitmentStatus.java @@ -0,0 +1,52 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.util.ExpandableStringEnum; +import com.fasterxml.jackson.annotation.JsonCreator; +import java.util.Collection; + +/** Possible recruitment status of a clinical trial. */ +public final class ClinicalTrialRecruitmentStatus extends ExpandableStringEnum { + /** Static value unknownStatus for ClinicalTrialRecruitmentStatus. */ + public static final ClinicalTrialRecruitmentStatus UNKNOWN_STATUS = fromString("unknownStatus"); + + /** Static value notYetRecruiting for ClinicalTrialRecruitmentStatus. */ + public static final ClinicalTrialRecruitmentStatus NOT_YET_RECRUITING = fromString("notYetRecruiting"); + + /** Static value recruiting for ClinicalTrialRecruitmentStatus. */ + public static final ClinicalTrialRecruitmentStatus RECRUITING = fromString("recruiting"); + + /** Static value enrollingByInvitation for ClinicalTrialRecruitmentStatus. */ + public static final ClinicalTrialRecruitmentStatus ENROLLING_BY_INVITATION = fromString("enrollingByInvitation"); + + /** + * Creates a new instance of ClinicalTrialRecruitmentStatus value. + * + * @deprecated Use the {@link #fromString(String)} factory method. + */ + @Deprecated + public ClinicalTrialRecruitmentStatus() {} + + /** + * Creates or finds a ClinicalTrialRecruitmentStatus from its string representation. + * + * @param name a name to look for. + * @return the corresponding ClinicalTrialRecruitmentStatus. + */ + @JsonCreator + public static ClinicalTrialRecruitmentStatus fromString(String name) { + return fromString(name, ClinicalTrialRecruitmentStatus.class); + } + + /** + * Gets known ClinicalTrialRecruitmentStatus values. + * + * @return known ClinicalTrialRecruitmentStatus values. + */ + public static Collection values() { + return values(ClinicalTrialRecruitmentStatus.class); + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialRegistryFilter.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialRegistryFilter.java new file mode 100644 index 0000000000000..d218381a4f5ea --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialRegistryFilter.java @@ -0,0 +1,353 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.annotation.Fluent; +import com.fasterxml.jackson.annotation.JsonProperty; +import java.util.List; + +/** A filter defining a subset of clinical trials from a given clinical trial registry (e.g. clinicaltrials.gov). */ +@Fluent +public final class ClinicalTrialRegistryFilter { + /* + * Trials with any of the given medical conditions will be included in the selection (provided that other + * limitations are satisfied). + * Leaving this list empty will not limit the medical conditions. + */ + @JsonProperty(value = "conditions") + private List conditions; + + /* + * Trials with any of the given study types will be included in the selection (provided that other limitations are + * satisfied). + * Leaving this list empty will not limit the study types. + */ + @JsonProperty(value = "studyTypes") + private List studyTypes; + + /* + * Trials with any of the given recruitment statuses will be included in the selection (provided that other + * limitations are satisfied). + * Leaving this list empty will not limit the recruitment statuses. + */ + @JsonProperty(value = "recruitmentStatuses") + private List recruitmentStatuses; + + /* + * Trials with any of the given sponsors will be included in the selection (provided that other limitations are + * satisfied). + * Leaving this list empty will not limit the sponsors. + */ + @JsonProperty(value = "sponsors") + private List sponsors; + + /* + * Trials with any of the given phases will be included in the selection (provided that other limitations are + * satisfied). + * Leaving this list empty will not limit the phases. + */ + @JsonProperty(value = "phases") + private List phases; + + /* + * Trials with any of the given purposes will be included in the selection (provided that other limitations are + * satisfied). + * Leaving this list empty will not limit the purposes. + */ + @JsonProperty(value = "purposes") + private List purposes; + + /* + * Trials with any of the given identifiers will be included in the selection (provided that other limitations are + * satisfied). + * Leaving this list empty will not limit the trial identifiers. + */ + @JsonProperty(value = "ids") + private List ids; + + /* + * Trials with any of the given sources will be included in the selection (provided that other limitations are + * satisfied). + * Leaving this list empty will not limit the sources. + */ + @JsonProperty(value = "sources") + private List sources; + + /* + * Trials with any of the given facility names will be included in the selection (provided that other limitations + * are satisfied). + * Leaving this list empty will not limit the trial facility names. + */ + @JsonProperty(value = "facilityNames") + private List facilityNames; + + /* + * Trials with any of the given facility locations will be included in the selection (provided that other + * limitations are satisfied). + * Leaving this list empty will not limit the trial facility locations. + */ + @JsonProperty(value = "facilityLocations") + private List facilityLocations; + + /* + * Trials with any of the given facility area boundaries will be included in the selection (provided that other + * limitations are satisfied). + * Leaving this list empty will not limit the trial facility area boundaries. + */ + @JsonProperty(value = "facilityAreas") + private List facilityAreas; + + /** Creates an instance of ClinicalTrialRegistryFilter class. */ + public ClinicalTrialRegistryFilter() {} + + /** + * Get the conditions property: Trials with any of the given medical conditions will be included in the selection + * (provided that other limitations are satisfied). Leaving this list empty will not limit the medical conditions. + * + * @return the conditions value. + */ + public List getConditions() { + return this.conditions; + } + + /** + * Set the conditions property: Trials with any of the given medical conditions will be included in the selection + * (provided that other limitations are satisfied). Leaving this list empty will not limit the medical conditions. + * + * @param conditions the conditions value to set. + * @return the ClinicalTrialRegistryFilter object itself. + */ + public ClinicalTrialRegistryFilter setConditions(List conditions) { + this.conditions = conditions; + return this; + } + + /** + * Get the studyTypes property: Trials with any of the given study types will be included in the selection (provided + * that other limitations are satisfied). Leaving this list empty will not limit the study types. + * + * @return the studyTypes value. + */ + public List getStudyTypes() { + return this.studyTypes; + } + + /** + * Set the studyTypes property: Trials with any of the given study types will be included in the selection (provided + * that other limitations are satisfied). Leaving this list empty will not limit the study types. + * + * @param studyTypes the studyTypes value to set. + * @return the ClinicalTrialRegistryFilter object itself. + */ + public ClinicalTrialRegistryFilter setStudyTypes(List studyTypes) { + this.studyTypes = studyTypes; + return this; + } + + /** + * Get the recruitmentStatuses property: Trials with any of the given recruitment statuses will be included in the + * selection (provided that other limitations are satisfied). Leaving this list empty will not limit the recruitment + * statuses. + * + * @return the recruitmentStatuses value. + */ + public List getRecruitmentStatuses() { + return this.recruitmentStatuses; + } + + /** + * Set the recruitmentStatuses property: Trials with any of the given recruitment statuses will be included in the + * selection (provided that other limitations are satisfied). Leaving this list empty will not limit the recruitment + * statuses. + * + * @param recruitmentStatuses the recruitmentStatuses value to set. + * @return the ClinicalTrialRegistryFilter object itself. + */ + public ClinicalTrialRegistryFilter setRecruitmentStatuses( + List recruitmentStatuses) { + this.recruitmentStatuses = recruitmentStatuses; + return this; + } + + /** + * Get the sponsors property: Trials with any of the given sponsors will be included in the selection (provided that + * other limitations are satisfied). Leaving this list empty will not limit the sponsors. + * + * @return the sponsors value. + */ + public List getSponsors() { + return this.sponsors; + } + + /** + * Set the sponsors property: Trials with any of the given sponsors will be included in the selection (provided that + * other limitations are satisfied). Leaving this list empty will not limit the sponsors. + * + * @param sponsors the sponsors value to set. + * @return the ClinicalTrialRegistryFilter object itself. + */ + public ClinicalTrialRegistryFilter setSponsors(List sponsors) { + this.sponsors = sponsors; + return this; + } + + /** + * Get the phases property: Trials with any of the given phases will be included in the selection (provided that + * other limitations are satisfied). Leaving this list empty will not limit the phases. + * + * @return the phases value. + */ + public List getPhases() { + return this.phases; + } + + /** + * Set the phases property: Trials with any of the given phases will be included in the selection (provided that + * other limitations are satisfied). Leaving this list empty will not limit the phases. + * + * @param phases the phases value to set. + * @return the ClinicalTrialRegistryFilter object itself. + */ + public ClinicalTrialRegistryFilter setPhases(List phases) { + this.phases = phases; + return this; + } + + /** + * Get the purposes property: Trials with any of the given purposes will be included in the selection (provided that + * other limitations are satisfied). Leaving this list empty will not limit the purposes. + * + * @return the purposes value. + */ + public List getPurposes() { + return this.purposes; + } + + /** + * Set the purposes property: Trials with any of the given purposes will be included in the selection (provided that + * other limitations are satisfied). Leaving this list empty will not limit the purposes. + * + * @param purposes the purposes value to set. + * @return the ClinicalTrialRegistryFilter object itself. + */ + public ClinicalTrialRegistryFilter setPurposes(List purposes) { + this.purposes = purposes; + return this; + } + + /** + * Get the ids property: Trials with any of the given identifiers will be included in the selection (provided that + * other limitations are satisfied). Leaving this list empty will not limit the trial identifiers. + * + * @return the ids value. + */ + public List getIds() { + return this.ids; + } + + /** + * Set the ids property: Trials with any of the given identifiers will be included in the selection (provided that + * other limitations are satisfied). Leaving this list empty will not limit the trial identifiers. + * + * @param ids the ids value to set. + * @return the ClinicalTrialRegistryFilter object itself. + */ + public ClinicalTrialRegistryFilter setIds(List ids) { + this.ids = ids; + return this; + } + + /** + * Get the sources property: Trials with any of the given sources will be included in the selection (provided that + * other limitations are satisfied). Leaving this list empty will not limit the sources. + * + * @return the sources value. + */ + public List getSources() { + return this.sources; + } + + /** + * Set the sources property: Trials with any of the given sources will be included in the selection (provided that + * other limitations are satisfied). Leaving this list empty will not limit the sources. + * + * @param sources the sources value to set. + * @return the ClinicalTrialRegistryFilter object itself. + */ + public ClinicalTrialRegistryFilter setSources(List sources) { + this.sources = sources; + return this; + } + + /** + * Get the facilityNames property: Trials with any of the given facility names will be included in the selection + * (provided that other limitations are satisfied). Leaving this list empty will not limit the trial facility names. + * + * @return the facilityNames value. + */ + public List getFacilityNames() { + return this.facilityNames; + } + + /** + * Set the facilityNames property: Trials with any of the given facility names will be included in the selection + * (provided that other limitations are satisfied). Leaving this list empty will not limit the trial facility names. + * + * @param facilityNames the facilityNames value to set. + * @return the ClinicalTrialRegistryFilter object itself. + */ + public ClinicalTrialRegistryFilter setFacilityNames(List facilityNames) { + this.facilityNames = facilityNames; + return this; + } + + /** + * Get the facilityLocations property: Trials with any of the given facility locations will be included in the + * selection (provided that other limitations are satisfied). Leaving this list empty will not limit the trial + * facility locations. + * + * @return the facilityLocations value. + */ + public List getFacilityLocations() { + return this.facilityLocations; + } + + /** + * Set the facilityLocations property: Trials with any of the given facility locations will be included in the + * selection (provided that other limitations are satisfied). Leaving this list empty will not limit the trial + * facility locations. + * + * @param facilityLocations the facilityLocations value to set. + * @return the ClinicalTrialRegistryFilter object itself. + */ + public ClinicalTrialRegistryFilter setFacilityLocations(List facilityLocations) { + this.facilityLocations = facilityLocations; + return this; + } + + /** + * Get the facilityAreas property: Trials with any of the given facility area boundaries will be included in the + * selection (provided that other limitations are satisfied). Leaving this list empty will not limit the trial + * facility area boundaries. + * + * @return the facilityAreas value. + */ + public List getFacilityAreas() { + return this.facilityAreas; + } + + /** + * Set the facilityAreas property: Trials with any of the given facility area boundaries will be included in the + * selection (provided that other limitations are satisfied). Leaving this list empty will not limit the trial + * facility area boundaries. + * + * @param facilityAreas the facilityAreas value to set. + * @return the ClinicalTrialRegistryFilter object itself. + */ + public ClinicalTrialRegistryFilter setFacilityAreas(List facilityAreas) { + this.facilityAreas = facilityAreas; + return this; + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialResearchFacility.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialResearchFacility.java new file mode 100644 index 0000000000000..627b9ef2234fc --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialResearchFacility.java @@ -0,0 +1,109 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.annotation.Fluent; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; + +/** Details of a research facility where a clinical trial is conducted. */ +@Fluent +public final class ClinicalTrialResearchFacility { + /* + * The facility's name. + */ + @JsonProperty(value = "name", required = true) + private String name; + + /* + * City name. + */ + @JsonProperty(value = "city") + private String city; + + /* + * State name. + */ + @JsonProperty(value = "state") + private String state; + + /* + * Country name. + */ + @JsonProperty(value = "country", required = true) + private String country; + + /** + * Creates an instance of ClinicalTrialResearchFacility class. + * + * @param name the name value to set. + * @param country the country value to set. + */ + @JsonCreator + public ClinicalTrialResearchFacility( + @JsonProperty(value = "name", required = true) String name, + @JsonProperty(value = "country", required = true) String country) { + this.name = name; + this.country = country; + } + + /** + * Get the name property: The facility's name. + * + * @return the name value. + */ + public String getName() { + return this.name; + } + + /** + * Get the city property: City name. + * + * @return the city value. + */ + public String getCity() { + return this.city; + } + + /** + * Set the city property: City name. + * + * @param city the city value to set. + * @return the ClinicalTrialResearchFacility object itself. + */ + public ClinicalTrialResearchFacility setCity(String city) { + this.city = city; + return this; + } + + /** + * Get the state property: State name. + * + * @return the state value. + */ + public String getState() { + return this.state; + } + + /** + * Set the state property: State name. + * + * @param state the state value to set. + * @return the ClinicalTrialResearchFacility object itself. + */ + public ClinicalTrialResearchFacility setState(String state) { + this.state = state; + return this; + } + + /** + * Get the country property: Country name. + * + * @return the country value. + */ + public String getCountry() { + return this.country; + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialSource.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialSource.java new file mode 100644 index 0000000000000..36497c06fc146 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialSource.java @@ -0,0 +1,46 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.util.ExpandableStringEnum; +import com.fasterxml.jackson.annotation.JsonCreator; +import java.util.Collection; + +/** Possible sources of a clinical trial. */ +public final class ClinicalTrialSource extends ExpandableStringEnum { + /** Static value custom for ClinicalTrialSource. */ + public static final ClinicalTrialSource CUSTOM = fromString("custom"); + + /** Static value clinicaltrials.gov for ClinicalTrialSource. */ + public static final ClinicalTrialSource CLINICALTRIALS_GOV = fromString("clinicaltrials.gov"); + + /** + * Creates a new instance of ClinicalTrialSource value. + * + * @deprecated Use the {@link #fromString(String)} factory method. + */ + @Deprecated + public ClinicalTrialSource() {} + + /** + * Creates or finds a ClinicalTrialSource from its string representation. + * + * @param name a name to look for. + * @return the corresponding ClinicalTrialSource. + */ + @JsonCreator + public static ClinicalTrialSource fromString(String name) { + return fromString(name, ClinicalTrialSource.class); + } + + /** + * Gets known ClinicalTrialSource values. + * + * @return known ClinicalTrialSource values. + */ + public static Collection values() { + return values(ClinicalTrialSource.class); + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialStudyType.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialStudyType.java new file mode 100644 index 0000000000000..f1bd739b9f819 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialStudyType.java @@ -0,0 +1,52 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.util.ExpandableStringEnum; +import com.fasterxml.jackson.annotation.JsonCreator; +import java.util.Collection; + +/** Possible study types of a clinical trial. */ +public final class ClinicalTrialStudyType extends ExpandableStringEnum { + /** Static value interventional for ClinicalTrialStudyType. */ + public static final ClinicalTrialStudyType INTERVENTIONAL = fromString("interventional"); + + /** Static value observational for ClinicalTrialStudyType. */ + public static final ClinicalTrialStudyType OBSERVATIONAL = fromString("observational"); + + /** Static value expandedAccess for ClinicalTrialStudyType. */ + public static final ClinicalTrialStudyType EXPANDED_ACCESS = fromString("expandedAccess"); + + /** Static value patientRegistries for ClinicalTrialStudyType. */ + public static final ClinicalTrialStudyType PATIENT_REGISTRIES = fromString("patientRegistries"); + + /** + * Creates a new instance of ClinicalTrialStudyType value. + * + * @deprecated Use the {@link #fromString(String)} factory method. + */ + @Deprecated + public ClinicalTrialStudyType() {} + + /** + * Creates or finds a ClinicalTrialStudyType from its string representation. + * + * @param name a name to look for. + * @return the corresponding ClinicalTrialStudyType. + */ + @JsonCreator + public static ClinicalTrialStudyType fromString(String name) { + return fromString(name, ClinicalTrialStudyType.class); + } + + /** + * Gets known ClinicalTrialStudyType values. + * + * @return known ClinicalTrialStudyType values. + */ + public static Collection values() { + return values(ClinicalTrialStudyType.class); + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrials.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrials.java new file mode 100644 index 0000000000000..ea9d0bc2778ef --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrials.java @@ -0,0 +1,75 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.annotation.Fluent; +import com.fasterxml.jackson.annotation.JsonProperty; +import java.util.List; + +/** + * The clinical trials that the patient(s) should be matched to. The trial selection can be given as a list of custom + * clinical trials and/or a list of filters to known clinical trial registries. In case both are given, the resulting + * trial set is a union of the two sets. + */ +@Fluent +public final class ClinicalTrials { + /* + * A list of clinical trials. + */ + @JsonProperty(value = "customTrials") + private List customTrials; + + /* + * A list of filters, each one creating a selection of trials from a given + * clinical trial registry. + */ + @JsonProperty(value = "registryFilters") + private List registryFilters; + + /** Creates an instance of ClinicalTrials class. */ + public ClinicalTrials() {} + + /** + * Get the customTrials property: A list of clinical trials. + * + * @return the customTrials value. + */ + public List getCustomTrials() { + return this.customTrials; + } + + /** + * Set the customTrials property: A list of clinical trials. + * + * @param customTrials the customTrials value to set. + * @return the ClinicalTrials object itself. + */ + public ClinicalTrials setCustomTrials(List customTrials) { + this.customTrials = customTrials; + return this; + } + + /** + * Get the registryFilters property: A list of filters, each one creating a selection of trials from a given + * clinical trial registry. + * + * @return the registryFilters value. + */ + public List getRegistryFilters() { + return this.registryFilters; + } + + /** + * Set the registryFilters property: A list of filters, each one creating a selection of trials from a given + * clinical trial registry. + * + * @param registryFilters the registryFilters value to set. + * @return the ClinicalTrials object itself. + */ + public ClinicalTrials setRegistryFilters(List registryFilters) { + this.registryFilters = registryFilters; + return this; + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ContactDetails.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ContactDetails.java new file mode 100644 index 0000000000000..bb9d0acac9a12 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ContactDetails.java @@ -0,0 +1,93 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.annotation.Fluent; +import com.fasterxml.jackson.annotation.JsonProperty; + +/** A person's contact details. */ +@Fluent +public final class ContactDetails { + /* + * The person's name. + */ + @JsonProperty(value = "name") + private String name; + + /* + * The person's email. + */ + @JsonProperty(value = "email") + private String email; + + /* + * A person's phone number. + */ + @JsonProperty(value = "phone") + private String phone; + + /** Creates an instance of ContactDetails class. */ + public ContactDetails() {} + + /** + * Get the name property: The person's name. + * + * @return the name value. + */ + public String getName() { + return this.name; + } + + /** + * Set the name property: The person's name. + * + * @param name the name value to set. + * @return the ContactDetails object itself. + */ + public ContactDetails setName(String name) { + this.name = name; + return this; + } + + /** + * Get the email property: The person's email. + * + * @return the email value. + */ + public String getEmail() { + return this.email; + } + + /** + * Set the email property: The person's email. + * + * @param email the email value to set. + * @return the ContactDetails object itself. + */ + public ContactDetails setEmail(String email) { + this.email = email; + return this; + } + + /** + * Get the phone property: A person's phone number. + * + * @return the phone value. + */ + public String getPhone() { + return this.phone; + } + + /** + * Set the phone property: A person's phone number. + * + * @param phone the phone value to set. + * @return the ContactDetails object itself. + */ + public ContactDetails setPhone(String phone) { + this.phone = phone; + return this; + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/DocumentContent.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/DocumentContent.java new file mode 100644 index 0000000000000..fd0d84d288155 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/DocumentContent.java @@ -0,0 +1,60 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.annotation.Immutable; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; + +/** The content of the patient document. */ +@Immutable +public final class DocumentContent { + /* + * The type of the content's source. + * In case the source type is 'inline', the content is given as a string (for instance, text). + * In case the source type is 'reference', the content is given as a URI. + */ + @JsonProperty(value = "sourceType", required = true) + private DocumentContentSourceType sourceType; + + /* + * The content of the document, given either inline (as a string) or as a reference (URI). + */ + @JsonProperty(value = "value", required = true) + private String value; + + /** + * Creates an instance of DocumentContent class. + * + * @param sourceType the sourceType value to set. + * @param value the value value to set. + */ + @JsonCreator + public DocumentContent( + @JsonProperty(value = "sourceType", required = true) DocumentContentSourceType sourceType, + @JsonProperty(value = "value", required = true) String value) { + this.sourceType = sourceType; + this.value = value; + } + + /** + * Get the sourceType property: The type of the content's source. In case the source type is 'inline', the content + * is given as a string (for instance, text). In case the source type is 'reference', the content is given as a URI. + * + * @return the sourceType value. + */ + public DocumentContentSourceType getSourceType() { + return this.sourceType; + } + + /** + * Get the value property: The content of the document, given either inline (as a string) or as a reference (URI). + * + * @return the value value. + */ + public String getValue() { + return this.value; + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/DocumentContentSourceType.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/DocumentContentSourceType.java new file mode 100644 index 0000000000000..42f1aff66fb20 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/DocumentContentSourceType.java @@ -0,0 +1,49 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.util.ExpandableStringEnum; +import com.fasterxml.jackson.annotation.JsonCreator; +import java.util.Collection; + +/** + * The type of the content's source. In case the source type is 'inline', the content is given as a string (for + * instance, text). In case the source type is 'reference', the content is given as a URI. + */ +public final class DocumentContentSourceType extends ExpandableStringEnum { + /** Static value inline for DocumentContentSourceType. */ + public static final DocumentContentSourceType INLINE = fromString("inline"); + + /** Static value reference for DocumentContentSourceType. */ + public static final DocumentContentSourceType REFERENCE = fromString("reference"); + + /** + * Creates a new instance of DocumentContentSourceType value. + * + * @deprecated Use the {@link #fromString(String)} factory method. + */ + @Deprecated + public DocumentContentSourceType() {} + + /** + * Creates or finds a DocumentContentSourceType from its string representation. + * + * @param name a name to look for. + * @return the corresponding DocumentContentSourceType. + */ + @JsonCreator + public static DocumentContentSourceType fromString(String name) { + return fromString(name, DocumentContentSourceType.class); + } + + /** + * Gets known DocumentContentSourceType values. + * + * @return known DocumentContentSourceType values. + */ + public static Collection values() { + return values(DocumentContentSourceType.class); + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/DocumentType.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/DocumentType.java new file mode 100644 index 0000000000000..591b3a4416d51 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/DocumentType.java @@ -0,0 +1,52 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.util.ExpandableStringEnum; +import com.fasterxml.jackson.annotation.JsonCreator; +import java.util.Collection; + +/** The type of the patient document, such as 'note' (text document) or 'fhirBundle' (FHIR JSON document). */ +public final class DocumentType extends ExpandableStringEnum { + /** Static value note for DocumentType. */ + public static final DocumentType NOTE = fromString("note"); + + /** Static value fhirBundle for DocumentType. */ + public static final DocumentType FHIR_BUNDLE = fromString("fhirBundle"); + + /** Static value dicom for DocumentType. */ + public static final DocumentType DICOM = fromString("dicom"); + + /** Static value genomicSequencing for DocumentType. */ + public static final DocumentType GENOMIC_SEQUENCING = fromString("genomicSequencing"); + + /** + * Creates a new instance of DocumentType value. + * + * @deprecated Use the {@link #fromString(String)} factory method. + */ + @Deprecated + public DocumentType() {} + + /** + * Creates or finds a DocumentType from its string representation. + * + * @param name a name to look for. + * @return the corresponding DocumentType. + */ + @JsonCreator + public static DocumentType fromString(String name) { + return fromString(name, DocumentType.class); + } + + /** + * Gets known DocumentType values. + * + * @return known DocumentType values. + */ + public static Collection values() { + return values(DocumentType.class); + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ExtendedClinicalCodedElement.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ExtendedClinicalCodedElement.java new file mode 100644 index 0000000000000..9ca2af7285615 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ExtendedClinicalCodedElement.java @@ -0,0 +1,122 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.annotation.Immutable; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; + +/** + * A piece of clinical information, expressed as a code in a clinical coding system, extended by semantic information. + */ +@Immutable +public final class ExtendedClinicalCodedElement { + /* + * The clinical coding system, e.g. ICD-10, SNOMED-CT, UMLS. + */ + @JsonProperty(value = "system", required = true) + private String system; + + /* + * The code within the given clinical coding system. + */ + @JsonProperty(value = "code", required = true) + private String code; + + /* + * The name of this coded concept in the coding system. + */ + @JsonProperty(value = "name") + private String name; + + /* + * A value associated with the code within the given clinical coding system. + */ + @JsonProperty(value = "value") + private String value; + + /* + * The [UMLS semantic type](https://www.nlm.nih.gov/research/umls/META3_current_semantic_types.html) associated + * with the coded concept. + */ + @JsonProperty(value = "semanticType") + private String semanticType; + + /* + * The bio-medical category related to the coded concept, e.g. Diagnosis, Symptom, Medication, Examination. + */ + @JsonProperty(value = "category") + private String category; + + /** + * Creates an instance of ExtendedClinicalCodedElement class. + * + * @param system the system value to set. + * @param code the code value to set. + */ + @JsonCreator + private ExtendedClinicalCodedElement( + @JsonProperty(value = "system", required = true) String system, + @JsonProperty(value = "code", required = true) String code) { + this.system = system; + this.code = code; + } + + /** + * Get the system property: The clinical coding system, e.g. ICD-10, SNOMED-CT, UMLS. + * + * @return the system value. + */ + public String getSystem() { + return this.system; + } + + /** + * Get the code property: The code within the given clinical coding system. + * + * @return the code value. + */ + public String getCode() { + return this.code; + } + + /** + * Get the name property: The name of this coded concept in the coding system. + * + * @return the name value. + */ + public String getName() { + return this.name; + } + + /** + * Get the value property: A value associated with the code within the given clinical coding system. + * + * @return the value value. + */ + public String getValue() { + return this.value; + } + + /** + * Get the semanticType property: The [UMLS semantic + * type](https://www.nlm.nih.gov/research/umls/META3_current_semantic_types.html) associated with the coded concept. + * + * @return the semanticType value. + */ + public String getSemanticType() { + return this.semanticType; + } + + /** + * Get the category property: The bio-medical category related to the coded concept, e.g. Diagnosis, Symptom, + * Medication, Examination. + * + * @return the category value. + */ + public String getCategory() { + return this.category; + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/GeoJsonGeometryType.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/GeoJsonGeometryType.java new file mode 100644 index 0000000000000..e450453618974 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/GeoJsonGeometryType.java @@ -0,0 +1,43 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.util.ExpandableStringEnum; +import com.fasterxml.jackson.annotation.JsonCreator; +import java.util.Collection; + +/** `GeoJSON` geometry type. */ +public final class GeoJsonGeometryType extends ExpandableStringEnum { + /** Static value Point for GeoJsonGeometryType. */ + public static final GeoJsonGeometryType POINT = fromString("Point"); + + /** + * Creates a new instance of GeoJsonGeometryType value. + * + * @deprecated Use the {@link #fromString(String)} factory method. + */ + @Deprecated + public GeoJsonGeometryType() {} + + /** + * Creates or finds a GeoJsonGeometryType from its string representation. + * + * @param name a name to look for. + * @return the corresponding GeoJsonGeometryType. + */ + @JsonCreator + public static GeoJsonGeometryType fromString(String name) { + return fromString(name, GeoJsonGeometryType.class); + } + + /** + * Gets known GeoJsonGeometryType values. + * + * @return known GeoJsonGeometryType values. + */ + public static Collection values() { + return values(GeoJsonGeometryType.class); + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/GeoJsonPropertiesSubType.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/GeoJsonPropertiesSubType.java new file mode 100644 index 0000000000000..24474c20caa43 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/GeoJsonPropertiesSubType.java @@ -0,0 +1,43 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.util.ExpandableStringEnum; +import com.fasterxml.jackson.annotation.JsonCreator; +import java.util.Collection; + +/** `GeoJSON` object sub-type. */ +public final class GeoJsonPropertiesSubType extends ExpandableStringEnum { + /** Static value Circle for GeoJsonPropertiesSubType. */ + public static final GeoJsonPropertiesSubType CIRCLE = fromString("Circle"); + + /** + * Creates a new instance of GeoJsonPropertiesSubType value. + * + * @deprecated Use the {@link #fromString(String)} factory method. + */ + @Deprecated + public GeoJsonPropertiesSubType() {} + + /** + * Creates or finds a GeoJsonPropertiesSubType from its string representation. + * + * @param name a name to look for. + * @return the corresponding GeoJsonPropertiesSubType. + */ + @JsonCreator + public static GeoJsonPropertiesSubType fromString(String name) { + return fromString(name, GeoJsonPropertiesSubType.class); + } + + /** + * Gets known GeoJsonPropertiesSubType values. + * + * @return known GeoJsonPropertiesSubType values. + */ + public static Collection values() { + return values(GeoJsonPropertiesSubType.class); + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/GeoJsonType.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/GeoJsonType.java new file mode 100644 index 0000000000000..e5e204ac3272b --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/GeoJsonType.java @@ -0,0 +1,43 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.util.ExpandableStringEnum; +import com.fasterxml.jackson.annotation.JsonCreator; +import java.util.Collection; + +/** `GeoJSON` type. */ +public final class GeoJsonType extends ExpandableStringEnum { + /** Static value Feature for GeoJsonType. */ + public static final GeoJsonType FEATURE = fromString("Feature"); + + /** + * Creates a new instance of GeoJsonType value. + * + * @deprecated Use the {@link #fromString(String)} factory method. + */ + @Deprecated + public GeoJsonType() {} + + /** + * Creates or finds a GeoJsonType from its string representation. + * + * @param name a name to look for. + * @return the corresponding GeoJsonType. + */ + @JsonCreator + public static GeoJsonType fromString(String name) { + return fromString(name, GeoJsonType.class); + } + + /** + * Gets known GeoJsonType values. + * + * @return known GeoJsonType values. + */ + public static Collection values() { + return values(GeoJsonType.class); + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/GeographicArea.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/GeographicArea.java new file mode 100644 index 0000000000000..cc54a3c9b393c --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/GeographicArea.java @@ -0,0 +1,78 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.annotation.Immutable; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; + +/** + * A geographic area, expressed as a `Circle` geometry represented using a `GeoJSON Feature` (see [GeoJSON + * spec](https://tools.ietf.org/html/rfc7946)). + */ +@Immutable +public final class GeographicArea { + /* + * `GeoJSON` type. + */ + @JsonProperty(value = "type", required = true) + private GeoJsonType type; + + /* + * `GeoJSON` geometry, representing the area circle's center. + */ + @JsonProperty(value = "geometry", required = true) + private AreaGeometry geometry; + + /* + * `GeoJSON` object properties. + */ + @JsonProperty(value = "properties", required = true) + private AreaProperties properties; + + /** + * Creates an instance of GeographicArea class. + * + * @param type the type value to set. + * @param geometry the geometry value to set. + * @param properties the properties value to set. + */ + @JsonCreator + public GeographicArea( + @JsonProperty(value = "type", required = true) GeoJsonType type, + @JsonProperty(value = "geometry", required = true) AreaGeometry geometry, + @JsonProperty(value = "properties", required = true) AreaProperties properties) { + this.type = type; + this.geometry = geometry; + this.properties = properties; + } + + /** + * Get the type property: `GeoJSON` type. + * + * @return the type value. + */ + public GeoJsonType getType() { + return this.type; + } + + /** + * Get the geometry property: `GeoJSON` geometry, representing the area circle's center. + * + * @return the geometry value. + */ + public AreaGeometry getGeometry() { + return this.geometry; + } + + /** + * Get the properties property: `GeoJSON` object properties. + * + * @return the properties value. + */ + public AreaProperties getProperties() { + return this.properties; + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/GeographicLocation.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/GeographicLocation.java new file mode 100644 index 0000000000000..8f400447a6bf1 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/GeographicLocation.java @@ -0,0 +1,94 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.annotation.Fluent; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; + +/** + * A location given as a combination of city/state/country. It could specify a city, a state or a country.<br />In + * case a city is specified, either state + country or country (for countries where there are no states) should be + * added. In case a state is specified (without a city), country should be added. + */ +@Fluent +public final class GeographicLocation { + /* + * City name. + */ + @JsonProperty(value = "city") + private String city; + + /* + * State name. + */ + @JsonProperty(value = "state") + private String state; + + /* + * Country name. + */ + @JsonProperty(value = "country", required = true) + private String country; + + /** + * Creates an instance of GeographicLocation class. + * + * @param country the country value to set. + */ + @JsonCreator + public GeographicLocation(@JsonProperty(value = "country", required = true) String country) { + this.country = country; + } + + /** + * Get the city property: City name. + * + * @return the city value. + */ + public String getCity() { + return this.city; + } + + /** + * Set the city property: City name. + * + * @param city the city value to set. + * @return the GeographicLocation object itself. + */ + public GeographicLocation setCity(String city) { + this.city = city; + return this; + } + + /** + * Get the state property: State name. + * + * @return the state value. + */ + public String getState() { + return this.state; + } + + /** + * Set the state property: State name. + * + * @param state the state value to set. + * @return the GeographicLocation object itself. + */ + public GeographicLocation setState(String state) { + this.state = state; + return this; + } + + /** + * Get the country property: Country name. + * + * @return the country value. + */ + public String getCountry() { + return this.country; + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/JobStatus.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/JobStatus.java new file mode 100644 index 0000000000000..dc898cf4caa9d --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/JobStatus.java @@ -0,0 +1,55 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.util.ExpandableStringEnum; +import com.fasterxml.jackson.annotation.JsonCreator; +import java.util.Collection; + +/** The status of the processing job. */ +public final class JobStatus extends ExpandableStringEnum { + /** Static value notStarted for JobStatus. */ + public static final JobStatus NOT_STARTED = fromString("notStarted"); + + /** Static value running for JobStatus. */ + public static final JobStatus RUNNING = fromString("running"); + + /** Static value succeeded for JobStatus. */ + public static final JobStatus SUCCEEDED = fromString("succeeded"); + + /** Static value failed for JobStatus. */ + public static final JobStatus FAILED = fromString("failed"); + + /** Static value partiallyCompleted for JobStatus. */ + public static final JobStatus PARTIALLY_COMPLETED = fromString("partiallyCompleted"); + + /** + * Creates a new instance of JobStatus value. + * + * @deprecated Use the {@link #fromString(String)} factory method. + */ + @Deprecated + public JobStatus() {} + + /** + * Creates or finds a JobStatus from its string representation. + * + * @param name a name to look for. + * @return the corresponding JobStatus. + */ + @JsonCreator + public static JobStatus fromString(String name) { + return fromString(name, JobStatus.class); + } + + /** + * Gets known JobStatus values. + * + * @return known JobStatus values. + */ + public static Collection values() { + return values(JobStatus.class); + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/PatientDocument.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/PatientDocument.java new file mode 100644 index 0000000000000..152f5e33973af --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/PatientDocument.java @@ -0,0 +1,156 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.annotation.Fluent; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import java.time.OffsetDateTime; + +/** A clinical document related to a patient. Document here is in the wide sense - not just a text document (note). */ +@Fluent +public final class PatientDocument { + /* + * The type of the patient document, such as 'note' (text document) or 'fhirBundle' (FHIR JSON document). + */ + @JsonProperty(value = "type", required = true) + private DocumentType type; + + /* + * The type of the clinical document. + */ + @JsonProperty(value = "clinicalType") + private ClinicalDocumentType clinicalType; + + /* + * A given identifier for the document. Has to be unique across all documents for a single patient. + */ + @JsonProperty(value = "id", required = true) + private String id; + + /* + * A 2 letter ISO 639-1 representation of the language of the document. + */ + @JsonProperty(value = "language") + private String language; + + /* + * The date and time when the document was created. + */ + @JsonProperty(value = "createdDateTime") + private OffsetDateTime createdDateTime; + + /* + * The content of the patient document. + */ + @JsonProperty(value = "content", required = true) + private DocumentContent content; + + /** + * Creates an instance of PatientDocument class. + * + * @param type the type value to set. + * @param id the id value to set. + * @param content the content value to set. + */ + @JsonCreator + public PatientDocument( + @JsonProperty(value = "type", required = true) DocumentType type, + @JsonProperty(value = "id", required = true) String id, + @JsonProperty(value = "content", required = true) DocumentContent content) { + this.type = type; + this.id = id; + this.content = content; + } + + /** + * Get the type property: The type of the patient document, such as 'note' (text document) or 'fhirBundle' (FHIR + * JSON document). + * + * @return the type value. + */ + public DocumentType getType() { + return this.type; + } + + /** + * Get the clinicalType property: The type of the clinical document. + * + * @return the clinicalType value. + */ + public ClinicalDocumentType getClinicalType() { + return this.clinicalType; + } + + /** + * Set the clinicalType property: The type of the clinical document. + * + * @param clinicalType the clinicalType value to set. + * @return the PatientDocument object itself. + */ + public PatientDocument setClinicalType(ClinicalDocumentType clinicalType) { + this.clinicalType = clinicalType; + return this; + } + + /** + * Get the id property: A given identifier for the document. Has to be unique across all documents for a single + * patient. + * + * @return the id value. + */ + public String getId() { + return this.id; + } + + /** + * Get the language property: A 2 letter ISO 639-1 representation of the language of the document. + * + * @return the language value. + */ + public String getLanguage() { + return this.language; + } + + /** + * Set the language property: A 2 letter ISO 639-1 representation of the language of the document. + * + * @param language the language value to set. + * @return the PatientDocument object itself. + */ + public PatientDocument setLanguage(String language) { + this.language = language; + return this; + } + + /** + * Get the createdDateTime property: The date and time when the document was created. + * + * @return the createdDateTime value. + */ + public OffsetDateTime getCreatedDateTime() { + return this.createdDateTime; + } + + /** + * Set the createdDateTime property: The date and time when the document was created. + * + * @param createdDateTime the createdDateTime value to set. + * @return the PatientDocument object itself. + */ + public PatientDocument setCreatedDateTime(OffsetDateTime createdDateTime) { + this.createdDateTime = createdDateTime; + return this; + } + + /** + * Get the content property: The content of the patient document. + * + * @return the content value. + */ + public DocumentContent getContent() { + return this.content; + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/PatientInfo.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/PatientInfo.java new file mode 100644 index 0000000000000..e0b7dad72969d --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/PatientInfo.java @@ -0,0 +1,95 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.annotation.Fluent; +import com.fasterxml.jackson.annotation.JsonProperty; +import java.time.LocalDate; +import java.util.List; + +/** Patient structured information, including demographics and known structured clinical information. */ +@Fluent +public final class PatientInfo { + /* + * The patient's sex. + */ + @JsonProperty(value = "sex") + private PatientInfoSex sex; + + /* + * The patient's date of birth. + */ + @JsonProperty(value = "birthDate") + private LocalDate birthDate; + + /* + * Known clinical information for the patient, structured. + */ + @JsonProperty(value = "clinicalInfo") + private List clinicalInfo; + + /** Creates an instance of PatientInfo class. */ + public PatientInfo() {} + + /** + * Get the sex property: The patient's sex. + * + * @return the sex value. + */ + public PatientInfoSex getSex() { + return this.sex; + } + + /** + * Set the sex property: The patient's sex. + * + * @param sex the sex value to set. + * @return the PatientInfo object itself. + */ + public PatientInfo setSex(PatientInfoSex sex) { + this.sex = sex; + return this; + } + + /** + * Get the birthDate property: The patient's date of birth. + * + * @return the birthDate value. + */ + public LocalDate getBirthDate() { + return this.birthDate; + } + + /** + * Set the birthDate property: The patient's date of birth. + * + * @param birthDate the birthDate value to set. + * @return the PatientInfo object itself. + */ + public PatientInfo setBirthDate(LocalDate birthDate) { + this.birthDate = birthDate; + return this; + } + + /** + * Get the clinicalInfo property: Known clinical information for the patient, structured. + * + * @return the clinicalInfo value. + */ + public List getClinicalInfo() { + return this.clinicalInfo; + } + + /** + * Set the clinicalInfo property: Known clinical information for the patient, structured. + * + * @param clinicalInfo the clinicalInfo value to set. + * @return the PatientInfo object itself. + */ + public PatientInfo setClinicalInfo(List clinicalInfo) { + this.clinicalInfo = clinicalInfo; + return this; + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/PatientInfoSex.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/PatientInfoSex.java new file mode 100644 index 0000000000000..623a9f7edb4b6 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/PatientInfoSex.java @@ -0,0 +1,49 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.util.ExpandableStringEnum; +import com.fasterxml.jackson.annotation.JsonCreator; +import java.util.Collection; + +/** The patient's sex. */ +public final class PatientInfoSex extends ExpandableStringEnum { + /** Static value female for PatientInfoSex. */ + public static final PatientInfoSex FEMALE = fromString("female"); + + /** Static value male for PatientInfoSex. */ + public static final PatientInfoSex MALE = fromString("male"); + + /** Static value unspecified for PatientInfoSex. */ + public static final PatientInfoSex UNSPECIFIED = fromString("unspecified"); + + /** + * Creates a new instance of PatientInfoSex value. + * + * @deprecated Use the {@link #fromString(String)} factory method. + */ + @Deprecated + public PatientInfoSex() {} + + /** + * Creates or finds a PatientInfoSex from its string representation. + * + * @param name a name to look for. + * @return the corresponding PatientInfoSex. + */ + @JsonCreator + public static PatientInfoSex fromString(String name) { + return fromString(name, PatientInfoSex.class); + } + + /** + * Gets known PatientInfoSex values. + * + * @return known PatientInfoSex values. + */ + public static Collection values() { + return values(PatientInfoSex.class); + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/PatientRecord.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/PatientRecord.java new file mode 100644 index 0000000000000..3565397624e19 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/PatientRecord.java @@ -0,0 +1,94 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.annotation.Fluent; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import java.util.List; + +/** A patient record, including their clinical information and data. */ +@Fluent +public final class PatientRecord { + /* + * A given identifier for the patient. Has to be unique across all patients in a single request. + */ + @JsonProperty(value = "id", required = true) + private String id; + + /* + * Patient structured information, including demographics and known structured clinical information. + */ + @JsonProperty(value = "info") + private PatientInfo info; + + /* + * Patient unstructured clinical data, given as documents. + */ + @JsonProperty(value = "data") + private List data; + + /** + * Creates an instance of PatientRecord class. + * + * @param id the id value to set. + */ + @JsonCreator + public PatientRecord(@JsonProperty(value = "id", required = true) String id) { + this.id = id; + } + + /** + * Get the id property: A given identifier for the patient. Has to be unique across all patients in a single + * request. + * + * @return the id value. + */ + public String getId() { + return this.id; + } + + /** + * Get the info property: Patient structured information, including demographics and known structured clinical + * information. + * + * @return the info value. + */ + public PatientInfo getInfo() { + return this.info; + } + + /** + * Set the info property: Patient structured information, including demographics and known structured clinical + * information. + * + * @param info the info value to set. + * @return the PatientRecord object itself. + */ + public PatientRecord setInfo(PatientInfo info) { + this.info = info; + return this; + } + + /** + * Get the data property: Patient unstructured clinical data, given as documents. + * + * @return the data value. + */ + public List getData() { + return this.data; + } + + /** + * Set the data property: Patient unstructured clinical data, given as documents. + * + * @param data the data value to set. + * @return the PatientRecord object itself. + */ + public PatientRecord setData(List data) { + this.data = data; + return this; + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/TrialMatcherData.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/TrialMatcherData.java new file mode 100644 index 0000000000000..c4103726a0e02 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/TrialMatcherData.java @@ -0,0 +1,65 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.annotation.Fluent; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import java.util.List; + +/** The body of the Trial Matcher request. */ +@Fluent +public final class TrialMatcherData { + /* + * The list of patients, including their clinical information and data. + */ + @JsonProperty(value = "patients", required = true) + private List patients; + + /* + * Configuration affecting the Trial Matcher model's inference. + */ + @JsonProperty(value = "configuration") + private TrialMatcherModelConfiguration configuration; + + /** + * Creates an instance of TrialMatcherData class. + * + * @param patients the patients value to set. + */ + @JsonCreator + public TrialMatcherData(@JsonProperty(value = "patients", required = true) List patients) { + this.patients = patients; + } + + /** + * Get the patients property: The list of patients, including their clinical information and data. + * + * @return the patients value. + */ + public List getPatients() { + return this.patients; + } + + /** + * Get the configuration property: Configuration affecting the Trial Matcher model's inference. + * + * @return the configuration value. + */ + public TrialMatcherModelConfiguration getConfiguration() { + return this.configuration; + } + + /** + * Set the configuration property: Configuration affecting the Trial Matcher model's inference. + * + * @param configuration the configuration value to set. + * @return the TrialMatcherData object itself. + */ + public TrialMatcherData setConfiguration(TrialMatcherModelConfiguration configuration) { + this.configuration = configuration; + return this; + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/TrialMatcherInference.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/TrialMatcherInference.java new file mode 100644 index 0000000000000..2b029458e5b1a --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/TrialMatcherInference.java @@ -0,0 +1,148 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.annotation.Immutable; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import java.util.List; + +/** An inference made by the Trial Matcher model regarding a patient. */ +@Immutable +public final class TrialMatcherInference { + /* + * The type of the Trial Matcher inference. + */ + @JsonProperty(value = "type", required = true) + private TrialMatcherInferenceType type; + + /* + * The value of the inference, as relevant for the given inference type. + */ + @JsonProperty(value = "value", required = true) + private String value; + + /* + * The description corresponding to the inference value. + */ + @JsonProperty(value = "description") + private String description; + + /* + * Confidence score for this inference. + */ + @JsonProperty(value = "confidenceScore") + private Double confidenceScore; + + /* + * The evidence corresponding to the inference value. + */ + @JsonProperty(value = "evidence") + private List evidence; + + /* + * The identifier of the clinical trial. + */ + @JsonProperty(value = "id") + private String id; + + /* + * Possible sources of a clinical trial. + */ + @JsonProperty(value = "source") + private ClinicalTrialSource source; + + /* + * Trial data which is of interest to the potential participant. + */ + @JsonProperty(value = "metadata") + private ClinicalTrialMetadata metadata; + + /** + * Creates an instance of TrialMatcherInference class. + * + * @param type the type value to set. + * @param value the value value to set. + */ + @JsonCreator + private TrialMatcherInference( + @JsonProperty(value = "type", required = true) TrialMatcherInferenceType type, + @JsonProperty(value = "value", required = true) String value) { + this.type = type; + this.value = value; + } + + /** + * Get the type property: The type of the Trial Matcher inference. + * + * @return the type value. + */ + public TrialMatcherInferenceType getType() { + return this.type; + } + + /** + * Get the value property: The value of the inference, as relevant for the given inference type. + * + * @return the value value. + */ + public String getValue() { + return this.value; + } + + /** + * Get the description property: The description corresponding to the inference value. + * + * @return the description value. + */ + public String getDescription() { + return this.description; + } + + /** + * Get the confidenceScore property: Confidence score for this inference. + * + * @return the confidenceScore value. + */ + public Double getConfidenceScore() { + return this.confidenceScore; + } + + /** + * Get the evidence property: The evidence corresponding to the inference value. + * + * @return the evidence value. + */ + public List getEvidence() { + return this.evidence; + } + + /** + * Get the id property: The identifier of the clinical trial. + * + * @return the id value. + */ + public String getId() { + return this.id; + } + + /** + * Get the source property: Possible sources of a clinical trial. + * + * @return the source value. + */ + public ClinicalTrialSource getSource() { + return this.source; + } + + /** + * Get the metadata property: Trial data which is of interest to the potential participant. + * + * @return the metadata value. + */ + public ClinicalTrialMetadata getMetadata() { + return this.metadata; + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/TrialMatcherInferenceEvidence.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/TrialMatcherInferenceEvidence.java new file mode 100644 index 0000000000000..6a54c200e7588 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/TrialMatcherInferenceEvidence.java @@ -0,0 +1,78 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.annotation.Immutable; +import com.fasterxml.jackson.annotation.JsonProperty; + +/** A piece of evidence corresponding to a Trial Matcher inference. */ +@Immutable +public final class TrialMatcherInferenceEvidence { + /* + * A piece of evidence from the eligibility criteria text of a clinical trial. + */ + @JsonProperty(value = "eligibilityCriteriaEvidence") + private String eligibilityCriteriaEvidence; + + /* + * A piece of evidence from a clinical note (text document). + */ + @JsonProperty(value = "patientDataEvidence") + private ClinicalNoteEvidence patientDataEvidence; + + /* + * A piece of clinical information, expressed as a code in a clinical coding + * system. + */ + @JsonProperty(value = "patientInfoEvidence") + private ClinicalCodedElement patientInfoEvidence; + + /* + * A value indicating how important this piece of evidence is for the inference. + */ + @JsonProperty(value = "importance") + private Double importance; + + /** Creates an instance of TrialMatcherInferenceEvidence class. */ + private TrialMatcherInferenceEvidence() {} + + /** + * Get the eligibilityCriteriaEvidence property: A piece of evidence from the eligibility criteria text of a + * clinical trial. + * + * @return the eligibilityCriteriaEvidence value. + */ + public String getEligibilityCriteriaEvidence() { + return this.eligibilityCriteriaEvidence; + } + + /** + * Get the patientDataEvidence property: A piece of evidence from a clinical note (text document). + * + * @return the patientDataEvidence value. + */ + public ClinicalNoteEvidence getPatientDataEvidence() { + return this.patientDataEvidence; + } + + /** + * Get the patientInfoEvidence property: A piece of clinical information, expressed as a code in a clinical coding + * system. + * + * @return the patientInfoEvidence value. + */ + public ClinicalCodedElement getPatientInfoEvidence() { + return this.patientInfoEvidence; + } + + /** + * Get the importance property: A value indicating how important this piece of evidence is for the inference. + * + * @return the importance value. + */ + public Double getImportance() { + return this.importance; + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/TrialMatcherInferenceType.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/TrialMatcherInferenceType.java new file mode 100644 index 0000000000000..a18eec386cddf --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/TrialMatcherInferenceType.java @@ -0,0 +1,43 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.util.ExpandableStringEnum; +import com.fasterxml.jackson.annotation.JsonCreator; +import java.util.Collection; + +/** The type of the Trial Matcher inference. */ +public final class TrialMatcherInferenceType extends ExpandableStringEnum { + /** Static value trialEligibility for TrialMatcherInferenceType. */ + public static final TrialMatcherInferenceType TRIAL_ELIGIBILITY = fromString("trialEligibility"); + + /** + * Creates a new instance of TrialMatcherInferenceType value. + * + * @deprecated Use the {@link #fromString(String)} factory method. + */ + @Deprecated + public TrialMatcherInferenceType() {} + + /** + * Creates or finds a TrialMatcherInferenceType from its string representation. + * + * @param name a name to look for. + * @return the corresponding TrialMatcherInferenceType. + */ + @JsonCreator + public static TrialMatcherInferenceType fromString(String name) { + return fromString(name, TrialMatcherInferenceType.class); + } + + /** + * Gets known TrialMatcherInferenceType values. + * + * @return known TrialMatcherInferenceType values. + */ + public static Collection values() { + return values(TrialMatcherInferenceType.class); + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/TrialMatcherModelConfiguration.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/TrialMatcherModelConfiguration.java new file mode 100644 index 0000000000000..9c289067e2fa7 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/TrialMatcherModelConfiguration.java @@ -0,0 +1,98 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.annotation.Fluent; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; + +/** Configuration affecting the Trial Matcher model's inference. */ +@Fluent +public final class TrialMatcherModelConfiguration { + /* + * An indication whether the model should produce verbose output. + */ + @JsonProperty(value = "verbose") + private Boolean verbose; + + /* + * An indication whether the model's output should include evidence for the inferences. + */ + @JsonProperty(value = "includeEvidence") + private Boolean includeEvidence; + + /* + * The clinical trials that the patient(s) should be matched to.
The trial + * selection can be given as a list of custom clinical trials and/or a list of + * filters to known clinical trial registries. In case both are given, the + * resulting trial set is a union of the two sets. + */ + @JsonProperty(value = "clinicalTrials", required = true) + private ClinicalTrials clinicalTrials; + + /** + * Creates an instance of TrialMatcherModelConfiguration class. + * + * @param clinicalTrials the clinicalTrials value to set. + */ + @JsonCreator + public TrialMatcherModelConfiguration( + @JsonProperty(value = "clinicalTrials", required = true) ClinicalTrials clinicalTrials) { + this.clinicalTrials = clinicalTrials; + } + + /** + * Get the verbose property: An indication whether the model should produce verbose output. + * + * @return the verbose value. + */ + public Boolean isVerbose() { + return this.verbose; + } + + /** + * Set the verbose property: An indication whether the model should produce verbose output. + * + * @param verbose the verbose value to set. + * @return the TrialMatcherModelConfiguration object itself. + */ + public TrialMatcherModelConfiguration setVerbose(Boolean verbose) { + this.verbose = verbose; + return this; + } + + /** + * Get the includeEvidence property: An indication whether the model's output should include evidence for the + * inferences. + * + * @return the includeEvidence value. + */ + public Boolean isIncludeEvidence() { + return this.includeEvidence; + } + + /** + * Set the includeEvidence property: An indication whether the model's output should include evidence for the + * inferences. + * + * @param includeEvidence the includeEvidence value to set. + * @return the TrialMatcherModelConfiguration object itself. + */ + public TrialMatcherModelConfiguration setIncludeEvidence(Boolean includeEvidence) { + this.includeEvidence = includeEvidence; + return this; + } + + /** + * Get the clinicalTrials property: The clinical trials that the patient(s) should be matched to. <br />The + * trial selection can be given as a list of custom clinical trials and/or a list of filters to known clinical trial + * registries. In case both are given, the resulting trial set is a union of the two sets. + * + * @return the clinicalTrials value. + */ + public ClinicalTrials getClinicalTrials() { + return this.clinicalTrials; + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/TrialMatcherPatientResult.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/TrialMatcherPatientResult.java new file mode 100644 index 0000000000000..24c645590170f --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/TrialMatcherPatientResult.java @@ -0,0 +1,74 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.annotation.Immutable; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import java.util.List; + +/** The results of the model's work for a single patient. */ +@Immutable +public final class TrialMatcherPatientResult { + /* + * The identifier given for the patient in the request. + */ + @JsonProperty(value = "id", required = true) + private String id; + + /* + * The model's inferences for the given patient. + */ + @JsonProperty(value = "inferences", required = true) + private List inferences; + + /* + * Clinical information which is needed to provide better trial matching results for the patient. + */ + @JsonProperty(value = "neededClinicalInfo") + private List neededClinicalInfo; + + /** + * Creates an instance of TrialMatcherPatientResult class. + * + * @param id the id value to set. + * @param inferences the inferences value to set. + */ + @JsonCreator + private TrialMatcherPatientResult( + @JsonProperty(value = "id", required = true) String id, + @JsonProperty(value = "inferences", required = true) List inferences) { + this.id = id; + this.inferences = inferences; + } + + /** + * Get the id property: The identifier given for the patient in the request. + * + * @return the id value. + */ + public String getId() { + return this.id; + } + + /** + * Get the inferences property: The model's inferences for the given patient. + * + * @return the inferences value. + */ + public List getInferences() { + return this.inferences; + } + + /** + * Get the neededClinicalInfo property: Clinical information which is needed to provide better trial matching + * results for the patient. + * + * @return the neededClinicalInfo value. + */ + public List getNeededClinicalInfo() { + return this.neededClinicalInfo; + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/TrialMatcherResult.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/TrialMatcherResult.java new file mode 100644 index 0000000000000..8f40e378f2d8f --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/TrialMatcherResult.java @@ -0,0 +1,123 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.annotation.Immutable; +import com.azure.core.models.ResponseError; +import com.fasterxml.jackson.annotation.JsonProperty; +import java.time.OffsetDateTime; +import java.util.List; + +/** The response for the Trial Matcher request. */ +@Immutable +public final class TrialMatcherResult { + /* + * A processing job identifier. + */ + @JsonProperty(value = "jobId", required = true, access = JsonProperty.Access.WRITE_ONLY) + private String jobId; + + /* + * The date and time when the processing job was created. + */ + @JsonProperty(value = "createdDateTime", required = true, access = JsonProperty.Access.WRITE_ONLY) + private OffsetDateTime createdDateTime; + + /* + * The date and time when the processing job is set to expire. + */ + @JsonProperty(value = "expirationDateTime", required = true, access = JsonProperty.Access.WRITE_ONLY) + private OffsetDateTime expirationDateTime; + + /* + * The date and time when the processing job was last updated. + */ + @JsonProperty(value = "lastUpdateDateTime", required = true, access = JsonProperty.Access.WRITE_ONLY) + private OffsetDateTime lastUpdateDateTime; + + /* + * The status of the processing job. + */ + @JsonProperty(value = "status", required = true, access = JsonProperty.Access.WRITE_ONLY) + private JobStatus status; + + /* + * An array of errors, if any errors occurred during the processing job. + */ + @JsonProperty(value = "errors", access = JsonProperty.Access.WRITE_ONLY) + private List errors; + + /* + * The inference results for the Trial Matcher request. + */ + @JsonProperty(value = "results", access = JsonProperty.Access.WRITE_ONLY) + private TrialMatcherResults results; + + /** Creates an instance of TrialMatcherResult class. */ + private TrialMatcherResult() {} + + /** + * Get the jobId property: A processing job identifier. + * + * @return the jobId value. + */ + public String getJobId() { + return this.jobId; + } + + /** + * Get the createdDateTime property: The date and time when the processing job was created. + * + * @return the createdDateTime value. + */ + public OffsetDateTime getCreatedDateTime() { + return this.createdDateTime; + } + + /** + * Get the expirationDateTime property: The date and time when the processing job is set to expire. + * + * @return the expirationDateTime value. + */ + public OffsetDateTime getExpirationDateTime() { + return this.expirationDateTime; + } + + /** + * Get the lastUpdateDateTime property: The date and time when the processing job was last updated. + * + * @return the lastUpdateDateTime value. + */ + public OffsetDateTime getLastUpdateDateTime() { + return this.lastUpdateDateTime; + } + + /** + * Get the status property: The status of the processing job. + * + * @return the status value. + */ + public JobStatus getStatus() { + return this.status; + } + + /** + * Get the errors property: An array of errors, if any errors occurred during the processing job. + * + * @return the errors value. + */ + public List getErrors() { + return this.errors; + } + + /** + * Get the results property: The inference results for the Trial Matcher request. + * + * @return the results value. + */ + public TrialMatcherResults getResults() { + return this.results; + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/TrialMatcherResults.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/TrialMatcherResults.java new file mode 100644 index 0000000000000..151b7cadbc078 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/TrialMatcherResults.java @@ -0,0 +1,75 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +package com.azure.health.insights.clinicalmatching.models; + +import com.azure.core.annotation.Immutable; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import java.time.LocalDate; +import java.util.List; + +/** The inference results for the Trial Matcher request. */ +@Immutable +public final class TrialMatcherResults { + /* + * Results for the patients given in the request. + */ + @JsonProperty(value = "patients", required = true) + private List patients; + + /* + * The version of the model used for inference, expressed as the model date. + */ + @JsonProperty(value = "modelVersion", required = true) + private String modelVersion; + + /* + * The date when the clinical trials knowledge graph was last updated. + */ + @JsonProperty(value = "knowledgeGraphLastUpdateDate") + private LocalDate knowledgeGraphLastUpdateDate; + + /** + * Creates an instance of TrialMatcherResults class. + * + * @param patients the patients value to set. + * @param modelVersion the modelVersion value to set. + */ + @JsonCreator + private TrialMatcherResults( + @JsonProperty(value = "patients", required = true) List patients, + @JsonProperty(value = "modelVersion", required = true) String modelVersion) { + this.patients = patients; + this.modelVersion = modelVersion; + } + + /** + * Get the patients property: Results for the patients given in the request. + * + * @return the patients value. + */ + public List getPatients() { + return this.patients; + } + + /** + * Get the modelVersion property: The version of the model used for inference, expressed as the model date. + * + * @return the modelVersion value. + */ + public String getModelVersion() { + return this.modelVersion; + } + + /** + * Get the knowledgeGraphLastUpdateDate property: The date when the clinical trials knowledge graph was last + * updated. + * + * @return the knowledgeGraphLastUpdateDate value. + */ + public LocalDate getKnowledgeGraphLastUpdateDate() { + return this.knowledgeGraphLastUpdateDate; + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/package-info.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/package-info.java new file mode 100644 index 0000000000000..f40be2cc64470 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/package-info.java @@ -0,0 +1,9 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +/** + * Package containing the data models for AzureHealthInsights. Azure Health Insights provides an API that serves insight + * models, specific for Health & Life Sciences, that perform analysis and provide inferences to be used by a human. + */ +package com.azure.health.insights.clinicalmatching.models; diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/package-info.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/package-info.java new file mode 100644 index 0000000000000..b6d8a6dea6a4e --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/package-info.java @@ -0,0 +1,9 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +/** + * Package containing the classes for AzureHealthInsights. Azure Health Insights provides an API that serves insight + * models, specific for Health & Life Sciences, that perform analysis and provide inferences to be used by a human. + */ +package com.azure.health.insights.clinicalmatching; diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/module-info.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/module-info.java new file mode 100644 index 0000000000000..943a11dfab9be --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/module-info.java @@ -0,0 +1,14 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. +// Code generated by Microsoft (R) AutoRest Code Generator. + +module com.azure.health.insights.clinicalmatching { + requires transitive com.azure.core; + + exports com.azure.health.insights.clinicalmatching; + exports com.azure.health.insights.clinicalmatching.models; + + opens com.azure.health.insights.clinicalmatching.models to + com.azure.core, + com.fasterxml.jackson.databind; +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/resources/azure-health-insights-clinicalmatching.properties b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/resources/azure-health-insights-clinicalmatching.properties new file mode 100644 index 0000000000000..ca812989b4f27 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/resources/azure-health-insights-clinicalmatching.properties @@ -0,0 +1,2 @@ +name=${project.artifactId} +version=${project.version} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/README.md b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/README.md new file mode 100644 index 0000000000000..dc54c217b0b2c --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/README.md @@ -0,0 +1,68 @@ +--- +page_type: sample +languages: + - java +products: + - azure + - azure-cognitive-services + - azure-health-insights-clinicalmatching +urlFragment: healthinsights-java-samples +--- + +# Azure Health Insights client library samples for Java + +Azure Health Insights Clinical Matching samples are a set of self-contained Java programs that demonstrate interacting with Azure self-contained service using the client library. Each sample focuses on a specific scenario and can be executed independently. + +## Key concepts + + +Key concepts are explained in detail [here] +## Getting started + + +Getting started explained in detail [here] + +## Examples + +The following sections provide code samples covering common scenario operations with the Azure Health Insights ClinicalMatching client library. + +All of these samples need the endpoint to your Health Insights resource, and your Health Insights API key. + +|**File Name**|**Description**| +|----------------|-------------| + + +## Troubleshooting + + +Troubleshooting steps can be found [here]. + +## Next steps + + +See [Next steps]. + +## Contributing + +If you would like to become an active contributor to this project please refer to our [Contribution +Guidelines][SDK_README_CONTRIBUTING] for more information. + + diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/java/com/azure/health/insights/clinicalmatching/SampleMatchTrialAsync.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/java/com/azure/health/insights/clinicalmatching/SampleMatchTrialAsync.java new file mode 100644 index 0000000000000..4edffd98ffd0e --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/java/com/azure/health/insights/clinicalmatching/SampleMatchTrialAsync.java @@ -0,0 +1,117 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. + +package com.azure.health.insights.clinicalmatching; + +import java.io.IOException; +import java.time.LocalDate; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; + +import com.azure.core.credential.AzureKeyCredential; +import com.azure.core.http.HttpClient; +import com.azure.core.util.HttpClientOptions; +import com.azure.core.util.polling.PollerFlux; +import com.azure.health.insights.clinicalmatching.models.TrialMatcherData; +import com.azure.health.insights.clinicalmatching.models.GeographicLocation; +import com.azure.health.insights.clinicalmatching.models.ClinicalTrials; +import com.azure.health.insights.clinicalmatching.models.ClinicalTrialSource; +import com.azure.health.insights.clinicalmatching.models.ClinicalTrialRegistryFilter; +import com.azure.health.insights.clinicalmatching.models.PatientInfoSex; +import com.azure.health.insights.clinicalmatching.models.ClinicalCodedElement; +import com.azure.health.insights.clinicalmatching.models.PatientInfo; +import com.azure.health.insights.clinicalmatching.models.PatientRecord; +import com.azure.health.insights.clinicalmatching.models.TrialMatcherModelConfiguration; +import com.azure.health.insights.clinicalmatching.models.TrialMatcherResults; +import com.azure.health.insights.clinicalmatching.models.TrialMatcherResult; +import com.azure.health.insights.clinicalmatching.models.ClinicalTrialStudyType; +import com.azure.health.insights.clinicalmatching.models.ClinicalTrialPhase; + +/* + * This example demonstrates Finding potential eligible trials for a patient, + * based on patient’s structured medical information. + * + * It looks for structured clinical trials that were taken from ClinicalTrials.gov + * Trial Matcher model matches a single patient to a set of relevant clinical trials, + * that this patient appears to be qualified for. This use case will demonstrate: + * a. How to use the trial matcher when patient clinical health information is provided to the + * Trial Matcher in a key-value structure with coded elements. + * b. How to use the clinical trial configuration to narrow down the trial condition, + * recruitment status, location and other criteria that the service users may choose to prioritize. + */ +public class SampleMatchTrialAsync { + public static void runSample(String endpoint, String apiKey) throws InterruptedException, IOException { + + ClinicalMatchingAsyncClient asyncClient = new ClinicalMatchingClientBuilder() + .endpoint(endpoint) + .serviceVersion(AzureHealthInsightsServiceVersion.getLatest()) + .httpClient(HttpClient.createDefault(new HttpClientOptions())) + .credential(new AzureKeyCredential(apiKey)) + .buildAsyncClient(); + + // construct Patient + PatientRecord patient1 = new PatientRecord("patient_1"); + PatientInfo patientInfo = new PatientInfo(); + patientInfo.setBirthDate(LocalDate.parse("1965-12-26")); + patientInfo.setSex(PatientInfoSex.MALE); + final List clinicalInfo = new ArrayList(); + patientInfo.setClinicalInfo(clinicalInfo); + patient1.setInfo(patientInfo); + + final String system = "http://www.nlm.nih.gov/research/umls"; + // Attach clinical info to the patient + clinicalInfo.add(createClinicalCodedElement(system, "C0006826", "Malignant Neoplasms", "true")); + clinicalInfo.add(createClinicalCodedElement(system, "C1522449", "Therapeutic radiology procedure", "true")); + clinicalInfo.add(createClinicalCodedElement(system, "C1512162", "Eastern Cooperative Oncology Group", "1")); + clinicalInfo.add(createClinicalCodedElement(system, "C0019693", "HIV Infections", "false")); + clinicalInfo.add(createClinicalCodedElement(system, "C1300072", "Tumor stage", "2")); + + // Create registry filter + ClinicalTrialRegistryFilter registryFilters = new ClinicalTrialRegistryFilter(); + // Limit the trial to a specific patient condition ("Non-small cell lung cancer") + registryFilters.setConditions(Arrays.asList("Non-small cell lung cancer")); + // Limit the clinical trial to a certain phase, phase 1 + registryFilters.setPhases(Arrays.asList(ClinicalTrialPhase.PHASE1)); + // Specify the clinical trial registry source as ClinicalTrials.Gov + registryFilters.setSources(Arrays.asList(ClinicalTrialSource.CLINICALTRIALS_GOV)); + // Limit the clinical trial to a certain location, in this case California, USA + registryFilters.setFacilityLocations(Arrays.asList(new GeographicLocation("United States"))); + // Limit the trial to a specific study type, interventional + registryFilters.setStudyTypes(Arrays.asList(ClinicalTrialStudyType.INTERVENTIONAL)); + + // Construct ClinicalTrial instance and attach the registry filter to it. + ClinicalTrials clinicalTrials = new ClinicalTrials(); + clinicalTrials.setRegistryFilters(Arrays.asList(registryFilters)); + + // Create TrialMatcherData + TrialMatcherModelConfiguration configuration = new TrialMatcherModelConfiguration(clinicalTrials); + TrialMatcherData trialMatcherData = new TrialMatcherData(Arrays.asList(patient1)); + trialMatcherData.setConfiguration(configuration); + + PollerFlux asyncPoller = asyncClient.beginMatchTrials(trialMatcherData); + + TrialMatcherResult response = asyncPoller.blockLast().getValue(); + printResults(response); + } + + private static void printResults(TrialMatcherResult tmRespone) { + TrialMatcherResults tmResults = tmRespone.getResults(); + + tmResults.getPatients().forEach(patientResult -> { + System.out.println("Inferences of Patient " + patientResult.getId()); + patientResult.getInferences().forEach(inference -> { + System.out.println("Trial Id " + inference.getId()); + System.out.println("Type: " + inference.getType() + " Value: " + inference.getValue()); + System.out.println("Description " + inference.getDescription()); + }); + }); + } + + private static ClinicalCodedElement createClinicalCodedElement(String system, String code, String name, String value) { + ClinicalCodedElement element = new ClinicalCodedElement(system, code); + element.setName(name); + element.setValue(value); + return element; + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/test/java/com/azure/health/insights/clinicalmatching/AllSamples.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/test/java/com/azure/health/insights/clinicalmatching/AllSamples.java new file mode 100644 index 0000000000000..6a13f23c5d44a --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/test/java/com/azure/health/insights/clinicalmatching/AllSamples.java @@ -0,0 +1,51 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. + +package com.azure.health.insights.clinicalmatching; + +import java.io.IOException; + +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; + +public class AllSamples { + String endpoint; + String apiKey; + + @BeforeEach + public void init() { + endpoint = System.getenv("SDK_JAVA_HDS_ENDPOINT"); + apiKey = System.getenv("SDK_JAVA_HDS_APIKEY"); + } + + @Test + public void matchTrialCustomTrial() throws InterruptedException, IOException { + SampleMatchTrialCustomTrial.runSample(endpoint, apiKey); + } + + // @Test + public void matchTrialGradualMatching() throws InterruptedException, IOException { + SampleMatchTrialGradualMatching.runSample(endpoint, apiKey); + } + + // @Test + public void matchTrialPatientFhir() throws InterruptedException, IOException { + SampleMatchTrialPatientFhir.runSample(endpoint, apiKey); + } + + // @Test + public void matchTrialsSync() throws InterruptedException, IOException { + SampleMatchTrialSync.runSample(endpoint, apiKey); + } + + // @Test + public void matchTrialAsync() throws InterruptedException, IOException { + SampleMatchTrialAsync.runSample(endpoint, apiKey); + } + + // @Test + public void matchTrialUnstructuredClinicalNote() throws InterruptedException, IOException { + SampleMatchTrialUnstructuredClinicalNote.runSample(endpoint, apiKey); + } + +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/test/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingClientTest.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/test/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingClientTest.java new file mode 100644 index 0000000000000..c07e78683854b --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/test/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingClientTest.java @@ -0,0 +1,58 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. + +package com.azure.health.insights.clinicalmatching; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import com.azure.health.insights.clinicalmatching.models.TrialMatcherResult; +import com.azure.health.insights.clinicalmatching.models.TrialMatcherInference; +import com.azure.health.insights.clinicalmatching.models.TrialMatcherPatientResult; +import com.azure.core.util.serializer.TypeReference; + +import com.azure.core.http.rest.RequestOptions; +import com.azure.core.util.BinaryData; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; + +import java.util.Arrays; +import java.util.List; + +/** + * Unit tests for {@link ClinicalMatchingClient}. + */ +public class ClinicalMatchingClientTest extends ClinicalMatchingClientTestBase { + + private ClinicalMatchingClient getClient() { + return getClientBuilder().buildClient(); + } + + @Test + public void test() { + // playback + try { + testTMWithResponse(request -> { + + BinaryData responseValue = getClient().beginMatchTrials(request, new RequestOptions()).waitForCompletion().getValue(); + + TrialMatcherResult tmRespone = responseValue.toObject(TypeReference.createInstance(TrialMatcherResult.class)); + List patients = tmRespone.getResults().getPatients(); + assertEquals(1, patients.size()); + TrialMatcherPatientResult patient = patients.get(0); + assertEquals(17, patient.getInferences().size()); + TrialMatcherInference inference = patient.getInferences().get(0); + assertEquals("NCT05428943", inference.getId()); + assertEquals(0.0, inference.getConfidenceScore()); + assertEquals("C0006826", inference.getEvidence().get(0).getPatientInfoEvidence().getCode()); + }); + + } catch (Throwable t) { + String message = t.toString() + "\n" + Arrays.toString(t.getStackTrace()); + t.printStackTrace(); + Assertions.fail(message); + return; + } + + System.out.println("Success"); + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/test/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingClientTestBase.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/test/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingClientTestBase.java new file mode 100644 index 0000000000000..e2bebcaaaad72 --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/test/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingClientTestBase.java @@ -0,0 +1,70 @@ +// Copyright (c) Microsoft Corporation. All rights reserved. +// Licensed under the MIT License. + +package com.azure.health.insights.clinicalmatching; + +import com.azure.core.credential.AzureKeyCredential; +import com.azure.core.http.HttpClient; +import com.azure.core.http.HttpPipeline; +import com.azure.core.http.HttpPipelineBuilder; +import com.azure.core.http.policy.AzureKeyCredentialPolicy; +import com.azure.core.http.policy.HttpPipelinePolicy; +import com.azure.core.test.TestBase; +import com.azure.core.test.TestMode; +import com.azure.core.util.BinaryData; +import com.azure.core.util.Configuration; + +import java.nio.file.Paths; +import java.util.function.Consumer; + + +/** + * Base class for TM clients test. + */ +public class ClinicalMatchingClientTestBase extends TestBase { + private static final String FAKE_API_KEY = "fakeKeyPlaceholder"; + private static final String OCP_APIM_SUBSCRIPTION_KEY = "Ocp-Apim-Subscription-Key"; + + void testTMWithResponse(Consumer testRunner) { + testRunner.accept(getTMRequest()); + } + + ClinicalMatchingClientBuilder getClientBuilder() { + String endpoint = getEndpoint(); + + HttpPipelinePolicy authPolicy = new AzureKeyCredentialPolicy(OCP_APIM_SUBSCRIPTION_KEY, + new AzureKeyCredential(getKey())); + HttpClient httpClient; + if (getTestMode() == TestMode.RECORD || getTestMode() == TestMode.LIVE) { + httpClient = HttpClient.createDefault(); + } else { + httpClient = interceptorManager.getPlaybackClient(); + } + HttpPipeline httpPipeline = new HttpPipelineBuilder() + .httpClient(httpClient) + .policies(authPolicy, interceptorManager.getRecordPolicy()).build(); + + return new ClinicalMatchingClientBuilder() + .pipeline(httpPipeline) + .endpoint(endpoint); + } + + private String getKey() { + if (getTestMode() == TestMode.PLAYBACK) { + return FAKE_API_KEY; + } else { + return Configuration.getGlobalConfiguration().get("AZURE_HEALTHINSIGHTS_API_KEY"); + } + } + + String getEndpoint() { + return interceptorManager.isPlaybackMode() + ? "https://localhost:8080" + : Configuration.getGlobalConfiguration().get("AZURE_HEALTHINSIGHTS_ENDPOINT"); + } + + private BinaryData getTMRequest() { + BinaryData requestBody = BinaryData.fromFile(Paths.get("target/test-classes/session-records/ClinicalMatchingClientTest.request.json")); + return requestBody; + } +} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/test/resources/Sample_MatchTrial_PatientFhir.json b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/test/resources/Sample_MatchTrial_PatientFhir.json new file mode 100644 index 0000000000000..9623f459c83ab --- /dev/null +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/test/resources/Sample_MatchTrial_PatientFhir.json @@ -0,0 +1,37509 @@ +{ + "resourceType": "Bundle", + "id": "1ca45d61-eb04-4c7d-9784-05e31e03e3c6", + "meta": { + "profile": [ + "http://hl7.org/fhir/4.0.1/StructureDefinition/Bundle" + ] + }, + "identifier": { + "system": "urn:ietf:rfc:3986", + "value": "urn:uuid:1ca45d61-eb04-4c7d-9784-05e31e03e3c6" + }, + "type": "document", + "entry": [ + { + "fullUrl": "Composition/baff5da4-0b29-4a57-906d-0e23d6d49eea", + "resource": { + "resourceType": "Composition", + "id": "baff5da4-0b29-4a57-906d-0e23d6d49eea", + "status": "final", + "type": { + "coding": [ + { + "system": "http://loinc.org", + "code": "11488-4", + "display": "Consult note" + } + ], + "text": "Consult note" + }, + "subject": { + "reference": "Patient/894a042e-625c-48b3-a710-759e09454897", + "type": "Patient" + }, + "encounter": { + "reference": "Encounter/d6535404-17da-4282-82c2-2eb7b9b86a47", + "type": "Encounter", + "display": "unknown" + }, + "date": "2022-08-16", + "author": [ + { + "reference": "Practitioner/082e9fc4-7483-4ef8-b83d-ea0733859cdc", + "type": "Practitioner", + "display": "Unknown" + } + ], + "title": "Consult note", + "section": [ + { + "title": "Chief Complaint", + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "46239-0", + "display": "Reason for visit and chief complaint" + } + ], + "text": "Chief Complaint" + }, + "text": { + "div": "
\r\n\t\t\t\t\t\t\t

Chief Complaint

\r\n\t\t\t\t\t\t\t

\"swelling of tongue and difficulty breathing and swallowing\"

\r\n\t\t\t\t\t
" + }, + "entry": [ + { + "reference": "List/a7ba1fc8-7544-4f1a-ac4e-c0430159001f", + "type": "List", + "display": "Chief Complaint" + } + ] + }, + { + "title": "History of Present Illness", + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "10164-2", + "display": "History of present illness" + } + ], + "text": "History of Present Illness" + }, + "text": { + "div": "
\r\n\t\t\t\t\t\t\t

History of Present Illness

\r\n\t\t\t\t\t\t\t

77 y o woman in NAD with a h/o CAD, DM2, asthma and HTN on altace for 8 years awoke from sleep around 2:30 am this morning of a sore throat and swelling of tongue. She came immediately to the ED b/c she was having difficulty swallowing and some trouble breathing due to obstruction caused by the swelling. She has never had a similar reaction ever before and she did not have any associated SOB, chest pain, itching, or nausea. She has not noticed any rashes, and has been afebrile. She says that she feels like it is swollen down in her esophagus as well. In the ED she was given 25mg benadryl IV, 125 mg solumedrol IV and pepcid 20 mg IV. This has helped the swelling some but her throat still hurts and it hurts to swallow. Nothing else was able to relieve the pain and nothing make it worse though she has not tried to drink any fluids because of trouble swallowing. She denies any recent travel, recent exposure to unusual plants or animals or other allergens. She has not started any new medications, has not used any new lotions or perfumes and has not eaten any unusual foods. Patient has not taken any of her oral medications today.

\r\n\t\t\t\t\t
" + }, + "entry": [ + { + "reference": "List/c1c10373-6325-4339-b962-c3c114969ccd", + "type": "List", + "display": "History of Present Illness" + } + ] + }, + { + "title": "Surgical History", + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "10164-2", + "display": "History of present illness" + } + ], + "text": "Surgical History" + }, + "text": { + "div": "
\r\n\t\t\t\t\t\t\t

Surgical History

\r\n\t\t\t\t\t\t\t

s/p Cardiac stent in 1999 \r\ns/p hystarectomy in 1970s \r\ns/p kidney stone retrieval 1960s

\r\n\t\t\t\t\t
" + }, + "entry": [ + { + "reference": "List/1d5dcbe4-7206-4a27-b3a8-52e4d30dacfe", + "type": "List", + "display": "Surgical History" + } + ] + }, + { + "title": "Medical History", + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "11348-0", + "display": "Past medical history" + } + ], + "text": "Medical History" + }, + "text": { + "div": "
\r\n\t\t\t\t\t\t\t

Medical History

\r\n\t\t\t\t\t\t\t

+ CAD w/ Left heart cath in 2005 showing 40% LAD, 50% small D2, 40% RCA and 30% large OM; 2006 TTE showing LVEF 60-65% with diastolic dysfunction, LVH, mild LA dilation \r\n+ Hyperlipidemia \r\n+ HTN \r\n+ DM 2, last A1c 6.7 in 9/2005 \r\n+ Asthma/COPD \r\n+ GERD \r\n+ h/o iron deficiency anemia

\r\n\t\t\t\t\t
" + }, + "entry": [ + { + "reference": "List/e0ed81ae-184e-44ce-b45a-2da9cd2eba9c", + "type": "List", + "display": "Medical History" + } + ] + }, + { + "title": "Social History", + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "29762-2", + "display": "Social History" + } + ], + "text": "Social History" + }, + "text": { + "div": "
\r\n\t\t\t\t\t\t\t

Social History

\r\n\t\t\t\t\t\t\t

Patient lives in _______ with daughter _____ (919) _______. Patient does all ADLs and IADLs with no/little assistance. She does own finances and drives. Patient has 4 daughters that all live in the area. Patient does not use tobacco, alcohol, illicit drugs.

\r\n\t\t\t\t\t
" + } + }, + { + "title": "Family History", + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "10157-6", + "display": "Family History" + } + ], + "text": "Family History" + }, + "text": { + "div": "
\r\n\t\t\t\t\t\t\t

Family History

\r\n\t\t\t\t\t\t\t

Patient's Dad died of liver cirrhosis at age 57, mom died of heart attack at age 60. She has 6 siblings who most died of cardiac disease. There is no family history of cancer.

\r\n\t\t\t\t\t
" + }, + "entry": [ + { + "reference": "List/22ec7727-c4ca-4477-a42b-51d34a935da6", + "type": "List", + "display": "Family History" + } + ] + }, + { + "title": "Allergies", + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "48765-2", + "display": "Allergies and adverse reactions" + } + ], + "text": "Allergies" + }, + "text": { + "div": "
\r\n\t\t\t\t\t\t\t

Allergies

\r\n\t\t\t\t\t\t\t

Sulfa drugs - rash \r\nCipro - rash \r\nBenadryl – causes mild dystonic reaction

\r\n\t\t\t\t\t
" + }, + "entry": [ + { + "reference": "List/ef6382f6-5089-4eda-9145-d44be736d451", + "type": "List", + "display": "Allergies" + } + ] + }, + { + "title": "Medications", + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "10160-0", + "display": "Medications" + } + ], + "text": "Medications" + }, + "text": { + "div": "
\r\n\t\t\t\t\t\t\t

Medications

\r\n\t\t\t\t\t\t\t

Theophyline (Uniphyl) 600 mg qhs – bronchodilator by increasing cAMP used for \r\ntreating asthma \r\nDiltiazem 300 mg qhs – Ca channel blocker used to control hypertension \r\nSimvistatin (Zocor) 20 mg qhs- HMGCo Reductase inhibitor for hypercholesterolemia \r\nRamipril (Altace) 10 mg BID – ACEI for hypertension and diabetes for renal protective \r\neffect \r\nGlipizide 5 mg BID (diabetes) – sulfonylurea for treatment of diabetes \r\nOmecprazole (Prilosec) 20 mg daily (reflux) – PPI for treatment of ulcers \r\nGabapentin (Neurontin) 100 mg qhs – modulates release of neurotransmitters to treat \r\ndiabetic neuropathy \r\nMetformin 500 mg qam – biguanide used to treat diabetes \r\nAspirin 81 mg qam - prophylaxis for MI and TIA \r\nFluticasone (Flovent) 2 puff bid - corticosteroid to treat airways in asthma/copd \r\nxoperex 1.25mg and Ipratropium 2.5 ml nebulized qam - anticholinergic to treat airways \r\nin COPD

\r\n\t\t\t\t\t
" + }, + "entry": [ + { + "reference": "List/c5490e7d-7447-4f89-8a7d-9871439d55e7", + "type": "List", + "display": "Medications" + } + ] + }, + { + "title": "Review of Systems", + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "10187-3", + "display": "Review of systems" + } + ], + "text": "Review of Systems" + }, + "text": { + "div": "
\r\n\t\t\t\t\t\t\t

Review of Systems

\r\n\t\t\t\t\t\t\t

Constitutional - NAD, has been generally feeling well the last couple of weeks \r\nEyes - no changes in vision, double vision, blurry vision, wears glasses \r\nENT - No congestion, changes in hearing, does not wear hearing aids \r\nSkin/Breast - no rashes \r\nCardiovascular - No SOB, chest pain, heart palpitations \r\nPulmonary - hard to get a breath in but not short of breath, no cough \r\nEndocrine - No changes in appetite \r\nGastro Intestinal - No n/v/d or constipation. Has not eaten because can't swallow solid \r\nfoods. \r\nGenito Urinary - No increased frequency or pain on urination. Some urge incontinence \r\nwith history of prolapse.

\r\n\t\t\t\t\t
" + }, + "entry": [ + { + "reference": "List/cd98589b-54af-4d9f-8fa7-f0ac32bd4df0", + "type": "List", + "display": "Review of Systems" + } + ] + }, + { + "title": "Physical Examination", + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "29545-1", + "display": "Physical findings" + } + ], + "text": "Physical Examination" + }, + "text": { + "div": "
\r\n\t\t\t\t\t\t\t

Physical Examination

\r\n\t\t\t\t\t\t\t

Vitals: \r\nTemp 35.9 \r\nPulse 76 \r\nO2 98% RA \r\nRR 20 \r\nBP 159/111 \r\n\r\nGeneral - NAD, sitting up in bed, well groomed and in nightgown \r\nEyes - PERRLA, EOM intact \r\nENT - Large swollen tounge and cheek on left side, tounge was large and obscured the view of the posterior oropharynx \r\nNeck - No noticeable or palpable swelling, redness or rash around throat or on face \r\nLymph Nodes - No lymphadenopathy \r\nCardiovascular - RRR no m/r/g, no JVD, no carotid bruits \r\nLungs - Clear to auscltation, no use of acessory muscles, no crackles or wheezes. \r\nSkin - No rashes, skin warm and dry, no erythematous areas \r\nAbdomen - Normal bowel sounds, abdomen soft and nontender \r\nExtremeties - No edema, cyanosis or clubbing \r\nMusculo Skeletal - 5/5 strength, normal range of motion, no swollen or erythematous \r\njoints. \r\nNeurological – Alert and oriented x 3, CN 2-12 grossly intact.

\r\n\t\t\t\t\t
" + }, + "entry": [ + { + "reference": "List/4353769c-64cc-4659-a239-efea24311f2e", + "type": "List", + "display": "Physical Examination" + } + ] + }, + { + "title": "Pertinent Diagnostic Tests", + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "22636-5", + "display": "Pathology report relevant history" + } + ], + "text": "Pertinent Diagnostic Tests" + }, + "text": { + "div": "
\r\n\t\t\t\t\t\t\t

Pertinent Diagnostic Tests

\r\n\t\t\t\t\t\t\t

Na 140 \r\nK 4.5 \r\nCl 109 \r\nCo2 23 \r\nBUN 29 \r\nCr 1.0 \r\nCa 9.9 \r\nMg 1.4 \r\nPhos 3.6 \r\n\r\nPTT 26.7 \r\n\r\nWBC 9.9 \r\nHgb 10.0 \r\nHct 30.3 \r\nPlt 373 \r\n\r\nEKG - no signs of ischemia

\r\n\t\t\t\t\t
" + }, + "entry": [ + { + "reference": "List/6bbdb74b-0263-4e3f-9cf0-e3f44dfe1210", + "type": "List", + "display": "Pertinent Diagnostic Tests" + } + ] + }, + { + "title": "Assessment and Plan", + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "51847-2", + "display": "Assessment and Plan" + } + ], + "text": "Assessment and Plan" + }, + "text": { + "div": "
\r\n\t\t\t\t\t\t\t

Assessment and Plan

\r\n\t\t\t\t\t\t\t

77 yo woman presents with significant angioedema in left side of tongue and inner cheek. Possible causes of angioedema include allergic anaphylaxis reaction, drug induced, allergic contact dermatitis, viral infection, drug induced, or a C1 inhibitor deficiency disorder acquired or hereditary. Laryngeal edema can also be caused by tonsillitis, peritonsilar abscess or pharyngeal foreign body.\r\n\r\nIt is unlikely that the patient has edema caused by abscess or tonsillitis since she does not have any associated fever or other signs of infection and the sudden onset of her swelling also argues against this. It is not likely a foreign body since ENT did not find anything when they scoped her.

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++ Swollen tongue: \r\n- Give patient corticosteroid to decrease inflammation and to protect against relapse after initial improvement. 4 days of Dexamethasone 10 mg IV tid. \r\n- Give patient antihistamine to block inflammation as well. 4 days of Diphenhydramine 25 mg bid. \r\n- ENT consult to rule out abscess or foreign object \r\n- Check C1 and C4 levels that would be decreased if the patient had C1 inhibitory complement deficiency \r\n- TSH level to check for hypo/hyper thyroid \r\n- Hold all oral home meds and keep patient NPO until airway swelling is reduced and patient can swallow easily \r\n\r\n++ Asthma/COPD \r\n- continue albuterol and ipratropium nebs prn \r\n- resume theophylline when patient can take oral meds \r\n\r\n++ DM \r\n- Patient is on corticosteroids that increase blood glucose levels, so put patient on sliding scale normal insulin to adjust for high sugars \r\n- Resume neurontin for neuropathy when oral meds can be taken \r\n\r\n++ HTN \r\n- Continue patient’s BP control with Diltiazem drip 5mg/hour \r\n- HOLD altace (ACEI) that is most likely the cause of angioedema \r\n- Consider an alternative HTN medication to replace the ACEI. Can’t use a HCTZ because of sulfa allergy. Also has asthma/COPD picture so beta blocker may not work well either. \r\n\r\n++ CAD s/p PCI in 1999 \r\n- Resume simvastatin and aspirin when patient is able to take oral meds \r\n++ GERD \r\n- famotidine when oral meds are resumed

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+trigger: none + +stages: + - template: /eng/pipelines/templates/stages/archetype-sdk-tests.yml + parameters: + ServiceDirectory: healthinsights + Artifacts: + - name: azure-health-insights-clinicalmatching + groupId: com.azure + safeName: azurehealthinsightsclinicalmatching diff --git a/sdk/healthinsights/ci.yml b/sdk/healthinsights/ci.yml new file mode 100644 index 0000000000000..65d7f96f5f098 --- /dev/null +++ b/sdk/healthinsights/ci.yml @@ -0,0 +1,43 @@ +# NOTE: Please refer to https://aka.ms/azsdk/engsys/ci-yaml before editing this file. +trigger: + branches: + include: + - main + - hotfix/* + - release/* + paths: + include: + - sdk/healthinsights/ + exclude: + - sdk/healthinsights/pom.xml + - sdk/healthinsights/azure-health-insights-cancerprofiling/pom.xml + - sdk/healthinsights/azure-health-insights-clinicalmatching/pom.xml + + +pr: + branches: + include: + - main + - feature/* + - hotfix/* + - release/* + paths: + include: + - sdk/healthinsights/ + exclude: + - sdk/healthinsights/pom.xml + - sdk/healthinsights/azure-health-insights-cancerprofiling/pom.xml + - sdk/healthinsights/azure-health-insights-clinicalmatching/pom.xml + +extends: + template: ../../eng/pipelines/templates/stages/archetype-sdk-client.yml + parameters: + ServiceDirectory: healthinsights + Artifacts: + - name: azure-health-insights-clinicalmatching + groupId: com.azure + safeName: azurehealthinsightsclinicalmatching + - name: azure-health-insights-cancerprofiling + groupId: com.azure + safeName: azurehealthinsightscancerprofiling + JavaBuildVersion: 17.0.5 diff --git a/sdk/healthinsights/pom.xml b/sdk/healthinsights/pom.xml new file mode 100644 index 0000000000000..1620d1255c4f1 --- /dev/null +++ b/sdk/healthinsights/pom.xml @@ -0,0 +1,14 @@ + + + 4.0.0 + com.azure + azure-healthinsights-service + pom + 1.0.0 + + azure-health-insights-cancerprofiling + azure-health-insights-clinicalmatching + + From 7ff4a043da5e633ac958f3853ef0abba15083824 Mon Sep 17 00:00:00 2001 From: Asaf Levi Date: Tue, 14 Mar 2023 14:08:09 +0200 Subject: [PATCH 02/25] rename country to countryOrRegion --- .../pom.xml | 4 +-- .../CancerProfilingAsyncClient.java | 2 +- .../CancerProfilingClient.java | 2 +- .../insights/cancerprofiling/AllSamples.java | 2 +- .../pom.xml | 4 +-- .../ClinicalMatchingAsyncClient.java | 8 ++--- .../ClinicalMatchingClient.java | 8 ++--- .../ClinicalMatchingClientImpl.java | 30 +++++++++---------- .../models/ClinicalTrialResearchFacility.java | 20 ++++++------- .../models/GeographicLocation.java | 27 +++++++++-------- .../insights/clinicalmatching/AllSamples.java | 27 ----------------- .../ClinicalMatchingClientTest.request.json | 2 +- 12 files changed, 55 insertions(+), 81 deletions(-) diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/pom.xml b/sdk/healthinsights/azure-health-insights-cancerprofiling/pom.xml index a45d54e44757e..d51deb90707e0 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/pom.xml +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/pom.xml @@ -16,8 +16,8 @@ 1.0.0-beta.1 jar - Microsoft Azure SDK for HealthInsights Management - This package contains Microsoft Azure HealthInsights client library. + Microsoft Azure client library for Health Insights - Cancer Profiling + This package contains Microsoft Azure Health Insights CancerProfiling client library. https://github.com/Azure/azure-sdk-for-java diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/CancerProfilingAsyncClient.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/CancerProfilingAsyncClient.java index fff32b4684280..abdb3473aff46 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/CancerProfilingAsyncClient.java +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/CancerProfilingAsyncClient.java @@ -166,7 +166,7 @@ public PollerFlux beginInferCancerProfile( * * @param oncoPhenotypeData The body of the Onco Phenotype request. * @throws IllegalArgumentException thrown if parameters fail the validation. - * @throws com.azure.core.exception.HttpResponseException thrown if the request is rejected by server. + * @throws HttpResponseException thrown if the request is rejected by server. * @throws ClientAuthenticationException thrown if the request is rejected by server on status code 401. * @throws ResourceNotFoundException thrown if the request is rejected by server on status code 404. * @throws ResourceModifiedException thrown if the request is rejected by server on status code 409. diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/CancerProfilingClient.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/CancerProfilingClient.java index 743850249f012..d00996780a4c7 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/CancerProfilingClient.java +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/CancerProfilingClient.java @@ -165,7 +165,7 @@ public SyncPoller beginInferCancerProfile( * * @param oncoPhenotypeData The body of the Onco Phenotype request. * @throws IllegalArgumentException thrown if parameters fail the validation. - * @throws com.azure.core.exception.HttpResponseException thrown if the request is rejected by server. + * @throws HttpResponseException thrown if the request is rejected by server. * @throws ClientAuthenticationException thrown if the request is rejected by server on status code 401. * @throws ResourceNotFoundException thrown if the request is rejected by server on status code 404. * @throws ResourceModifiedException thrown if the request is rejected by server on status code 409. diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/java/com/azure/health/insights/cancerprofiling/AllSamples.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/java/com/azure/health/insights/cancerprofiling/AllSamples.java index 3e200206b4464..a828670115a2f 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/java/com/azure/health/insights/cancerprofiling/AllSamples.java +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/java/com/azure/health/insights/cancerprofiling/AllSamples.java @@ -18,7 +18,7 @@ public void init() { apiKey = System.getenv("SDK_JAVA_HDS_APIKEY"); } - @Test + // @Test public void inferCancerProfile() throws InterruptedException, IOException { SampleInferCancerProfile.runSample(endpoint, apiKey); } diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/pom.xml b/sdk/healthinsights/azure-health-insights-clinicalmatching/pom.xml index 651c68874999a..c111fbde716ff 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/pom.xml +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/pom.xml @@ -16,8 +16,8 @@ 1.0.0-beta.1 jar - Microsoft Azure SDK for HealthInsights Management - This package contains Microsoft Azure HealthInsights client library. + Microsoft Azure client library for Health Insights - Clinical Matching + This package contains Microsoft Azure Health Insights ClinicalMatching client library. https://github.com/Azure/azure-sdk-for-java diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingAsyncClient.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingAsyncClient.java index 3f114f4efe0d4..f114524146bf2 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingAsyncClient.java +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingAsyncClient.java @@ -126,7 +126,7 @@ public final class ClinicalMatchingAsyncClient { * name: String (Required) * city: String (Optional) * state: String (Optional) - * country: String (Required) + * countryOrRegion: String (Required) * } * ] * } @@ -165,7 +165,7 @@ public final class ClinicalMatchingAsyncClient { * (Optional){ * city: String (Optional) * state: String (Optional) - * country: String (Required) + * countryOrRegion: String (Required) * } * ] * facilityAreas (Optional): [ @@ -256,7 +256,7 @@ public final class ClinicalMatchingAsyncClient { * name: String (Required) * city: String (Optional) * state: String (Optional) - * country: String (Required) + * countryOrRegion: String (Required) * } * ] * } @@ -302,7 +302,7 @@ public PollerFlux beginMatchTrials( * * @param trialMatcherData The body of the Trial Matcher request. * @throws IllegalArgumentException thrown if parameters fail the validation. - * @throws com.azure.core.exception.HttpResponseException thrown if the request is rejected by server. + * @throws HttpResponseException thrown if the request is rejected by server. * @throws ClientAuthenticationException thrown if the request is rejected by server on status code 401. * @throws ResourceNotFoundException thrown if the request is rejected by server on status code 404. * @throws ResourceModifiedException thrown if the request is rejected by server on status code 409. diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingClient.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingClient.java index 84409ccc394c1..567ae684b0a83 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingClient.java +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingClient.java @@ -125,7 +125,7 @@ public final class ClinicalMatchingClient { * name: String (Required) * city: String (Optional) * state: String (Optional) - * country: String (Required) + * countryOrRegion: String (Required) * } * ] * } @@ -164,7 +164,7 @@ public final class ClinicalMatchingClient { * (Optional){ * city: String (Optional) * state: String (Optional) - * country: String (Required) + * countryOrRegion: String (Required) * } * ] * facilityAreas (Optional): [ @@ -255,7 +255,7 @@ public final class ClinicalMatchingClient { * name: String (Required) * city: String (Optional) * state: String (Optional) - * country: String (Required) + * countryOrRegion: String (Required) * } * ] * } @@ -301,7 +301,7 @@ public SyncPoller beginMatchTrials( * * @param trialMatcherData The body of the Trial Matcher request. * @throws IllegalArgumentException thrown if parameters fail the validation. - * @throws com.azure.core.exception.HttpResponseException thrown if the request is rejected by server. + * @throws HttpResponseException thrown if the request is rejected by server. * @throws ClientAuthenticationException thrown if the request is rejected by server on status code 401. * @throws ResourceNotFoundException thrown if the request is rejected by server on status code 404. * @throws ResourceModifiedException thrown if the request is rejected by server on status code 409. diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/implementation/ClinicalMatchingClientImpl.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/implementation/ClinicalMatchingClientImpl.java index 8d1c768d75560..364bcf6c8339d 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/implementation/ClinicalMatchingClientImpl.java +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/implementation/ClinicalMatchingClientImpl.java @@ -273,7 +273,7 @@ Mono> matchTrials( * name: String (Required) * city: String (Optional) * state: String (Optional) - * country: String (Required) + * countryOrRegion: String (Required) * } * ] * } @@ -312,7 +312,7 @@ Mono> matchTrials( * (Optional){ * city: String (Optional) * state: String (Optional) - * country: String (Required) + * countryOrRegion: String (Required) * } * ] * facilityAreas (Optional): [ @@ -403,7 +403,7 @@ Mono> matchTrials( * name: String (Required) * city: String (Optional) * state: String (Optional) - * country: String (Required) + * countryOrRegion: String (Required) * } * ] * } @@ -547,7 +547,7 @@ private Mono> matchTrialsWithResponseAsync( * name: String (Required) * city: String (Optional) * state: String (Optional) - * country: String (Required) + * countryOrRegion: String (Required) * } * ] * } @@ -586,7 +586,7 @@ private Mono> matchTrialsWithResponseAsync( * (Optional){ * city: String (Optional) * state: String (Optional) - * country: String (Required) + * countryOrRegion: String (Required) * } * ] * facilityAreas (Optional): [ @@ -677,7 +677,7 @@ private Mono> matchTrialsWithResponseAsync( * name: String (Required) * city: String (Optional) * state: String (Optional) - * country: String (Required) + * countryOrRegion: String (Required) * } * ] * } @@ -818,7 +818,7 @@ public PollerFlux beginMatchTrialsAsync( * name: String (Required) * city: String (Optional) * state: String (Optional) - * country: String (Required) + * countryOrRegion: String (Required) * } * ] * } @@ -857,7 +857,7 @@ public PollerFlux beginMatchTrialsAsync( * (Optional){ * city: String (Optional) * state: String (Optional) - * country: String (Required) + * countryOrRegion: String (Required) * } * ] * facilityAreas (Optional): [ @@ -948,7 +948,7 @@ public PollerFlux beginMatchTrialsAsync( * name: String (Required) * city: String (Optional) * state: String (Optional) - * country: String (Required) + * countryOrRegion: String (Required) * } * ] * } @@ -1078,7 +1078,7 @@ public SyncPoller beginMatchTrials( * name: String (Required) * city: String (Optional) * state: String (Optional) - * country: String (Required) + * countryOrRegion: String (Required) * } * ] * } @@ -1117,7 +1117,7 @@ public SyncPoller beginMatchTrials( * (Optional){ * city: String (Optional) * state: String (Optional) - * country: String (Required) + * countryOrRegion: String (Required) * } * ] * facilityAreas (Optional): [ @@ -1208,7 +1208,7 @@ public SyncPoller beginMatchTrials( * name: String (Required) * city: String (Optional) * state: String (Optional) - * country: String (Required) + * countryOrRegion: String (Required) * } * ] * } @@ -1349,7 +1349,7 @@ public PollerFlux beginMatchTrialsWithMo * name: String (Required) * city: String (Optional) * state: String (Optional) - * country: String (Required) + * countryOrRegion: String (Required) * } * ] * } @@ -1388,7 +1388,7 @@ public PollerFlux beginMatchTrialsWithMo * (Optional){ * city: String (Optional) * state: String (Optional) - * country: String (Required) + * countryOrRegion: String (Required) * } * ] * facilityAreas (Optional): [ @@ -1479,7 +1479,7 @@ public PollerFlux beginMatchTrialsWithMo * name: String (Required) * city: String (Optional) * state: String (Optional) - * country: String (Required) + * countryOrRegion: String (Required) * } * ] * } diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialResearchFacility.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialResearchFacility.java index 627b9ef2234fc..57e5b293637da 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialResearchFacility.java +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/ClinicalTrialResearchFacility.java @@ -30,23 +30,23 @@ public final class ClinicalTrialResearchFacility { private String state; /* - * Country name. + * Country/region name. */ - @JsonProperty(value = "country", required = true) - private String country; + @JsonProperty(value = "countryOrRegion", required = true) + private String countryOrRegion; /** * Creates an instance of ClinicalTrialResearchFacility class. * * @param name the name value to set. - * @param country the country value to set. + * @param countryOrRegion the countryOrRegion value to set. */ @JsonCreator public ClinicalTrialResearchFacility( @JsonProperty(value = "name", required = true) String name, - @JsonProperty(value = "country", required = true) String country) { + @JsonProperty(value = "countryOrRegion", required = true) String countryOrRegion) { this.name = name; - this.country = country; + this.countryOrRegion = countryOrRegion; } /** @@ -99,11 +99,11 @@ public ClinicalTrialResearchFacility setState(String state) { } /** - * Get the country property: Country name. + * Get the countryOrRegion property: Country/region name. * - * @return the country value. + * @return the countryOrRegion value. */ - public String getCountry() { - return this.country; + public String getCountryOrRegion() { + return this.countryOrRegion; } } diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/GeographicLocation.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/GeographicLocation.java index 8f400447a6bf1..251911aafdc0d 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/GeographicLocation.java +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/GeographicLocation.java @@ -9,9 +9,10 @@ import com.fasterxml.jackson.annotation.JsonProperty; /** - * A location given as a combination of city/state/country. It could specify a city, a state or a country.<br />In - * case a city is specified, either state + country or country (for countries where there are no states) should be - * added. In case a state is specified (without a city), country should be added. + * A location given as a combination of city, state and country/region. It could specify a city, a state or a + * country/region. In case a city is specified, either state +country/region or country/region (for countries/regions + * where there are no states) should be added. In case a state is specified (without a city), country/region should be + * added. */ @Fluent public final class GeographicLocation { @@ -28,19 +29,19 @@ public final class GeographicLocation { private String state; /* - * Country name. + * Country/region name. */ - @JsonProperty(value = "country", required = true) - private String country; + @JsonProperty(value = "countryOrRegion", required = true) + private String countryOrRegion; /** * Creates an instance of GeographicLocation class. * - * @param country the country value to set. + * @param countryOrRegion the countryOrRegion value to set. */ @JsonCreator - public GeographicLocation(@JsonProperty(value = "country", required = true) String country) { - this.country = country; + public GeographicLocation(@JsonProperty(value = "countryOrRegion", required = true) String countryOrRegion) { + this.countryOrRegion = countryOrRegion; } /** @@ -84,11 +85,11 @@ public GeographicLocation setState(String state) { } /** - * Get the country property: Country name. + * Get the countryOrRegion property: Country/region name. * - * @return the country value. + * @return the countryOrRegion value. */ - public String getCountry() { - return this.country; + public String getCountryOrRegion() { + return this.countryOrRegion; } } diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/test/java/com/azure/health/insights/clinicalmatching/AllSamples.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/test/java/com/azure/health/insights/clinicalmatching/AllSamples.java index 6a13f23c5d44a..235aad0e64490 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/test/java/com/azure/health/insights/clinicalmatching/AllSamples.java +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/test/java/com/azure/health/insights/clinicalmatching/AllSamples.java @@ -6,7 +6,6 @@ import java.io.IOException; import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; public class AllSamples { String endpoint; @@ -18,34 +17,8 @@ public void init() { apiKey = System.getenv("SDK_JAVA_HDS_APIKEY"); } - @Test - public void matchTrialCustomTrial() throws InterruptedException, IOException { - SampleMatchTrialCustomTrial.runSample(endpoint, apiKey); - } - - // @Test - public void matchTrialGradualMatching() throws InterruptedException, IOException { - SampleMatchTrialGradualMatching.runSample(endpoint, apiKey); - } - - // @Test - public void matchTrialPatientFhir() throws InterruptedException, IOException { - SampleMatchTrialPatientFhir.runSample(endpoint, apiKey); - } - - // @Test - public void matchTrialsSync() throws InterruptedException, IOException { - SampleMatchTrialSync.runSample(endpoint, apiKey); - } - // @Test public void matchTrialAsync() throws InterruptedException, IOException { SampleMatchTrialAsync.runSample(endpoint, apiKey); } - - // @Test - public void matchTrialUnstructuredClinicalNote() throws InterruptedException, IOException { - SampleMatchTrialUnstructuredClinicalNote.runSample(endpoint, apiKey); - } - } diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/test/resources/session-records/ClinicalMatchingClientTest.request.json b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/test/resources/session-records/ClinicalMatchingClientTest.request.json index 79525574406f3..e296af434d050 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/test/resources/session-records/ClinicalMatchingClientTest.request.json +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/test/resources/session-records/ClinicalMatchingClientTest.request.json @@ -15,7 +15,7 @@ "facilityLocations": [ { "state": "CA", - "country": "United States" + "countryOrRegion": "United States" } ] } From 4c355f0e6509493c7fd49a60130cde02f6af10b4 Mon Sep 17 00:00:00 2001 From: Asaf Levi Date: Wed, 15 Mar 2023 12:19:55 +0200 Subject: [PATCH 03/25] update product name to azure-health-insights --- .../azure-health-insights-cancerprofiling/CHANGELOG.md | 2 +- .../azure-health-insights-cancerprofiling/src/samples/README.md | 2 +- .../azure-health-insights-clinicalmatching/CHANGELOG.md | 2 +- .../src/samples/README.md | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/CHANGELOG.md b/sdk/healthinsights/azure-health-insights-cancerprofiling/CHANGELOG.md index f887f194c985e..42cb75cda259d 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/CHANGELOG.md +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/CHANGELOG.md @@ -2,7 +2,7 @@ ## 1.0.0-beta.1 (Unreleased) -- Azure AzureHealthInsights client library for Java. This package contains Microsoft Azure AzureHealthInsights client library. +- Initial preview of the Azure Health Insights CancerProfiling client library. ### Features Added diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/samples/README.md b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/samples/README.md index 3f4bbc8f2a46c..6cc7b99e71a15 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/samples/README.md +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/samples/README.md @@ -5,7 +5,7 @@ languages: products: - azure - azure-cognitive-services - - azure-health-insights-cancerprofiling + - azure-health-insights urlFragment: healthinsights-java-samples --- diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/CHANGELOG.md b/sdk/healthinsights/azure-health-insights-clinicalmatching/CHANGELOG.md index f887f194c985e..6a5e9392bb830 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/CHANGELOG.md +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/CHANGELOG.md @@ -2,7 +2,7 @@ ## 1.0.0-beta.1 (Unreleased) -- Azure AzureHealthInsights client library for Java. This package contains Microsoft Azure AzureHealthInsights client library. +- Initial preview of the Azure Health Insights ClinicalMatching client library. ### Features Added diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/README.md b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/README.md index dc54c217b0b2c..903f4603d8678 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/README.md +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/README.md @@ -5,7 +5,7 @@ languages: products: - azure - azure-cognitive-services - - azure-health-insights-clinicalmatching + - azure-health-insights urlFragment: healthinsights-java-samples --- From a882ba6e45c69bf458e96765e89d7f859155da49 Mon Sep 17 00:00:00 2001 From: Asaf Levi Date: Wed, 15 Mar 2023 19:21:44 +0200 Subject: [PATCH 04/25] update cspell with missing words --- .vscode/cspell.json | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.vscode/cspell.json b/.vscode/cspell.json index 479374dd3a044..b700ae918d7c3 100644 --- a/.vscode/cspell.json +++ b/.vscode/cspell.json @@ -236,6 +236,7 @@ "creds", "credscan", "curr", + "custom", "databind", "databricks", "DAZURE", @@ -245,7 +246,7 @@ "Deserialization", "destfile", "Dgenerate", - "dicom", + "dicom", "doclint", "doclinting", "doctitle", @@ -273,6 +274,7 @@ "hdinsight", "hvac", "hybridkubernetes", + "insighs", "intellij", "Intellij", "iotcentral", From e3085b8497d37044fd8261192f1c302c89064c05 Mon Sep 17 00:00:00 2001 From: Asaf Levi Date: Wed, 15 Mar 2023 19:57:22 +0200 Subject: [PATCH 05/25] update root pom.xml and version_client.txt --- eng/versioning/version_client.txt | 2 ++ pom.xml | 1 + 2 files changed, 3 insertions(+) diff --git a/eng/versioning/version_client.txt b/eng/versioning/version_client.txt index 1e79a1f494de6..6be00f3ae774e 100644 --- a/eng/versioning/version_client.txt +++ b/eng/versioning/version_client.txt @@ -107,6 +107,8 @@ com.azure:azure-data-tables-perf;1.0.0-beta.1;1.0.0-beta.1 com.azure:azure-digitaltwins-core;1.3.7;1.4.0-beta.1 com.azure:azure-developer-devcenter;1.0.0-beta.2;1.0.0-beta.3 com.azure:azure-e2e;1.0.0-beta.1;1.0.0-beta.1 +com.azure:azure-health-insights-clinicalmatching;1.0.0-beta.1;1.0.0-beta.1 +com.azure:azure-health-insights-cancerprofiling;1.0.0-beta.1;1.0.0-beta.1 com.azure:azure-identity;1.8.1;1.9.0-beta.2 com.azure:azure-identity-perf;1.0.0-beta.1;1.0.0-beta.1 com.azure:azure-iot-deviceupdate;1.0.4;1.1.0-beta.1 diff --git a/pom.xml b/pom.xml index 2c7336bffde95..2466d19a953e2 100644 --- a/pom.xml +++ b/pom.xml @@ -87,6 +87,7 @@ sdk/hdinsight sdk/healthbot sdk/healthcareapis + sdk/healthinsights sdk/hybridcompute sdk/hybridcontainerservice sdk/hybridkubernetes From 00a1e8c9715b35494d178545cf028d8934d3e307 Mon Sep 17 00:00:00 2001 From: Asaf Levi Date: Thu, 16 Mar 2023 09:08:31 +0200 Subject: [PATCH 06/25] update dependency versions --- .../pom.xml | 23 +++++++++++++---- .../pom.xml | 25 ++++++++++++++----- 2 files changed, 37 insertions(+), 11 deletions(-) diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/pom.xml b/sdk/healthinsights/azure-health-insights-cancerprofiling/pom.xml index d51deb90707e0..19528f4e427be 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/pom.xml +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/pom.xml @@ -42,18 +42,19 @@ UTF-8 - true + 0.2 + 0.2 com.azure azure-core - 1.35.0 + 1.37.0 com.azure azure-core-http-netty - 1.12.8 + 1.13.1 org.junit.jupiter @@ -76,13 +77,25 @@ com.azure azure-core-test - 1.14.0 + 1.15.0 test com.azure azure-identity - 1.7.3 + 1.8.1 + test + + + org.mockito + mockito-core + 4.5.1 + test + + + org.slf4j + slf4j-simple + 1.7.36 test diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/pom.xml b/sdk/healthinsights/azure-health-insights-clinicalmatching/pom.xml index c111fbde716ff..fcfddbacee36c 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/pom.xml +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/pom.xml @@ -42,18 +42,19 @@ UTF-8 - true + 0.2 + 0.2 com.azure azure-core - 1.35.0 + 1.37.0 com.azure azure-core-http-netty - 1.12.8 + 1.13.1 org.junit.jupiter @@ -76,13 +77,25 @@ com.azure azure-core-test - 1.14.0 + 1.15.0 test com.azure azure-identity - 1.7.3 + 1.8.1 + test + + + org.mockito + mockito-core + 4.5.1 + test + + + org.slf4j + slf4j-simple + 1.7.36 test @@ -102,7 +115,7 @@ ${project.basedir}/README.md true 120 - true + false From 28815874834e43128f5dcc1909bf159f8ae58e30 Mon Sep 17 00:00:00 2001 From: Asaf Levi <100200009+asaflevi-ms@users.noreply.github.com> Date: Thu, 16 Mar 2023 09:10:57 +0200 Subject: [PATCH 07/25] update dependency versions (#2) --- .../pom.xml | 23 +++++++++++++---- .../pom.xml | 25 ++++++++++++++----- 2 files changed, 37 insertions(+), 11 deletions(-) diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/pom.xml b/sdk/healthinsights/azure-health-insights-cancerprofiling/pom.xml index d51deb90707e0..19528f4e427be 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/pom.xml +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/pom.xml @@ -42,18 +42,19 @@ UTF-8 - true + 0.2 + 0.2 com.azure azure-core - 1.35.0 + 1.37.0 com.azure azure-core-http-netty - 1.12.8 + 1.13.1 org.junit.jupiter @@ -76,13 +77,25 @@ com.azure azure-core-test - 1.14.0 + 1.15.0 test com.azure azure-identity - 1.7.3 + 1.8.1 + test + + + org.mockito + mockito-core + 4.5.1 + test + + + org.slf4j + slf4j-simple + 1.7.36 test diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/pom.xml b/sdk/healthinsights/azure-health-insights-clinicalmatching/pom.xml index c111fbde716ff..fcfddbacee36c 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/pom.xml +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/pom.xml @@ -42,18 +42,19 @@ UTF-8 - true + 0.2 + 0.2 com.azure azure-core - 1.35.0 + 1.37.0 com.azure azure-core-http-netty - 1.12.8 + 1.13.1 org.junit.jupiter @@ -76,13 +77,25 @@ com.azure azure-core-test - 1.14.0 + 1.15.0 test com.azure azure-identity - 1.7.3 + 1.8.1 + test + + + org.mockito + mockito-core + 4.5.1 + test + + + org.slf4j + slf4j-simple + 1.7.36 test @@ -102,7 +115,7 @@ ${project.basedir}/README.md true 120 - true + false From e0f8b9e1b1f4102623a2db4ec77d14272f5fc49b Mon Sep 17 00:00:00 2001 From: Asaf Levi Date: Thu, 16 Mar 2023 10:09:36 +0200 Subject: [PATCH 08/25] skip jacoco --- .../azure-health-insights-cancerprofiling/pom.xml | 3 +-- .../azure-health-insights-clinicalmatching/pom.xml | 3 +-- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/pom.xml b/sdk/healthinsights/azure-health-insights-cancerprofiling/pom.xml index 19528f4e427be..b83a389c2ce01 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/pom.xml +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/pom.xml @@ -42,8 +42,7 @@ UTF-8 - 0.2 - 0.2 + true diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/pom.xml b/sdk/healthinsights/azure-health-insights-clinicalmatching/pom.xml index fcfddbacee36c..aa6c6e44a9ad7 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/pom.xml +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/pom.xml @@ -42,8 +42,7 @@ UTF-8 - 0.2 - 0.2 + true From b81d4b49d4dd5725dd63d20120c9fcd390314e4b Mon Sep 17 00:00:00 2001 From: Asaf Levi Date: Thu, 16 Mar 2023 10:16:01 +0200 Subject: [PATCH 09/25] fix spell checks --- .vscode/cspell.json | 7 +++++-- .../src/samples/README.md | 4 ++-- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/.vscode/cspell.json b/.vscode/cspell.json index 15a2123b35068..2af9266fc2a9d 100644 --- a/.vscode/cspell.json +++ b/.vscode/cspell.json @@ -236,11 +236,11 @@ "creds", "credscan", "curr", - "custom", "databind", "databricks", "DAZURE", - "ddos", + "DAZURE", + "dcis", "deallocate", "decryptor", "Deserialization", @@ -307,6 +307,7 @@ "Lucene", "mgmt", "mibps", + "Mirena", "Mockito", "msal", "msix", @@ -343,6 +344,7 @@ "servicebus", "sftdl", "skus", + "snomed", "sonatype", "Sonatype", "spotbugs", @@ -354,6 +356,7 @@ "timeframe", "tofile", "toFile", + "umls", "undelete", "unmanaged", "unmutated", diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/README.md b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/README.md index 903f4603d8678..a6d303f8edb03 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/README.md +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/README.md @@ -32,7 +32,7 @@ All of these samples need the endpoint to your Health Insights resource, and you |----------------|-------------| @@ -60,7 +60,7 @@ Guidelines][SDK_README_CONTRIBUTING] for more information. [SDK_README_NEXT_STEPS]: [match_trials_async]: [match_trials_sync]: -[sample_cutom_trials]: +[sample_custom_trials]: [sample_gradual_matching]: [sample_match_trials_fhir]: [sample_match_trials_unstructured_clinical_note]: From 75c01ae067c3bc64aa484e9b62390c3afcaa8f36 Mon Sep 17 00:00:00 2001 From: Asaf Levi <100200009+asaflevi-ms@users.noreply.github.com> Date: Thu, 16 Mar 2023 10:19:33 +0200 Subject: [PATCH 10/25] Asaflevi/feature/healthinsights sdk for java (#3) * update dependency versions * skip jacoco * fix spell checks --- .vscode/cspell.json | 7 +++++-- .../src/samples/README.md | 4 ++-- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/.vscode/cspell.json b/.vscode/cspell.json index 15a2123b35068..2af9266fc2a9d 100644 --- a/.vscode/cspell.json +++ b/.vscode/cspell.json @@ -236,11 +236,11 @@ "creds", "credscan", "curr", - "custom", "databind", "databricks", "DAZURE", - "ddos", + "DAZURE", + "dcis", "deallocate", "decryptor", "Deserialization", @@ -307,6 +307,7 @@ "Lucene", "mgmt", "mibps", + "Mirena", "Mockito", "msal", "msix", @@ -343,6 +344,7 @@ "servicebus", "sftdl", "skus", + "snomed", "sonatype", "Sonatype", "spotbugs", @@ -354,6 +356,7 @@ "timeframe", "tofile", "toFile", + "umls", "undelete", "unmanaged", "unmutated", diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/README.md b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/README.md index 903f4603d8678..a6d303f8edb03 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/README.md +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/README.md @@ -32,7 +32,7 @@ All of these samples need the endpoint to your Health Insights resource, and you |----------------|-------------| @@ -60,7 +60,7 @@ Guidelines][SDK_README_CONTRIBUTING] for more information. [SDK_README_NEXT_STEPS]: [match_trials_async]: [match_trials_sync]: -[sample_cutom_trials]: +[sample_custom_trials]: [sample_gradual_matching]: [sample_match_trials_fhir]: [sample_match_trials_unstructured_clinical_note]: From d895b12ac0d00bf1af0896271ca0df63cf004507 Mon Sep 17 00:00:00 2001 From: Asaf Levi Date: Thu, 16 Mar 2023 11:45:09 +0200 Subject: [PATCH 11/25] skip jacoco --- .../azure-health-insights-cancerprofiling/pom.xml | 3 +-- .../azure-health-insights-clinicalmatching/pom.xml | 3 +-- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/pom.xml b/sdk/healthinsights/azure-health-insights-cancerprofiling/pom.xml index 19528f4e427be..b83a389c2ce01 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/pom.xml +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/pom.xml @@ -42,8 +42,7 @@ UTF-8 - 0.2 - 0.2 + true diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/pom.xml b/sdk/healthinsights/azure-health-insights-clinicalmatching/pom.xml index fcfddbacee36c..aa6c6e44a9ad7 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/pom.xml +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/pom.xml @@ -42,8 +42,7 @@ UTF-8 - 0.2 - 0.2 + true From 31ec4c3ddf01455bfd4d97ecd1f69ceec59c0cbc Mon Sep 17 00:00:00 2001 From: Asaf Levi Date: Thu, 16 Mar 2023 11:57:08 +0200 Subject: [PATCH 12/25] linting --- .../com/azure/health/insights/cancerprofiling/AllSamples.java | 1 - 1 file changed, 1 deletion(-) diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/java/com/azure/health/insights/cancerprofiling/AllSamples.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/java/com/azure/health/insights/cancerprofiling/AllSamples.java index a828670115a2f..ac5209ae187a5 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/java/com/azure/health/insights/cancerprofiling/AllSamples.java +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/java/com/azure/health/insights/cancerprofiling/AllSamples.java @@ -6,7 +6,6 @@ import java.io.IOException; import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; public class AllSamples { String endpoint; From b53335b7cb0ffe9d2711433f73925a7be9e1ee01 Mon Sep 17 00:00:00 2001 From: Asaf Levi Date: Wed, 22 Mar 2023 15:48:43 +0200 Subject: [PATCH 13/25] remove redundant plugins --- .../CHANGELOG.md | 8 ------- .../pom.xml | 24 ++----------------- .../CHANGELOG.md | 8 ------- .../pom.xml | 24 ++----------------- 4 files changed, 4 insertions(+), 60 deletions(-) diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/CHANGELOG.md b/sdk/healthinsights/azure-health-insights-cancerprofiling/CHANGELOG.md index 42cb75cda259d..fe2e7e3cef46f 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/CHANGELOG.md +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/CHANGELOG.md @@ -3,11 +3,3 @@ ## 1.0.0-beta.1 (Unreleased) - Initial preview of the Azure Health Insights CancerProfiling client library. - -### Features Added - -### Breaking Changes - -### Bugs Fixed - -### Other Changes diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/pom.xml b/sdk/healthinsights/azure-health-insights-cancerprofiling/pom.xml index b83a389c2ce01..1b588b480e72b 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/pom.xml +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/pom.xml @@ -42,7 +42,8 @@ UTF-8 - true + 0.1 + 0.1 @@ -98,25 +99,4 @@ test - - - - - com.azure.tools - codesnippet-maven-plugin - 1.0.0-beta.8 - - **/src/samples/java/**/*.java - ${project.basedir}/src/samples/java - **/src/main/java/**/*.java - ${project.basedir}/src/main/java - true - ${project.basedir}/README.md - true - 120 - false - - - - diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/CHANGELOG.md b/sdk/healthinsights/azure-health-insights-clinicalmatching/CHANGELOG.md index 6a5e9392bb830..ab3a7cff345e8 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/CHANGELOG.md +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/CHANGELOG.md @@ -3,11 +3,3 @@ ## 1.0.0-beta.1 (Unreleased) - Initial preview of the Azure Health Insights ClinicalMatching client library. - -### Features Added - -### Breaking Changes - -### Bugs Fixed - -### Other Changes diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/pom.xml b/sdk/healthinsights/azure-health-insights-clinicalmatching/pom.xml index aa6c6e44a9ad7..f58a4c1d9c1de 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/pom.xml +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/pom.xml @@ -42,7 +42,8 @@ UTF-8 - true + 0.1 + 0.1 @@ -98,25 +99,4 @@ test - - - - - com.azure.tools - codesnippet-maven-plugin - 1.0.0-beta.8 - - **/src/samples/java/**/*.java - ${project.basedir}/src/samples/java - **/src/main/java/**/*.java - ${project.basedir}/src/main/java - true - ${project.basedir}/README.md - true - 120 - false - - - - From 0a0104d4b7b8a8369049ebd30eeed62f76327346 Mon Sep 17 00:00:00 2001 From: Asaf Levi Date: Wed, 22 Mar 2023 16:12:13 +0200 Subject: [PATCH 14/25] remove test.yaml files --- .../azure-health-insights-cancerprofiling/tests.yml | 10 ---------- .../azure-health-insights-clinicalmatching/tests.yml | 10 ---------- 2 files changed, 20 deletions(-) delete mode 100644 sdk/healthinsights/azure-health-insights-cancerprofiling/tests.yml delete mode 100644 sdk/healthinsights/azure-health-insights-clinicalmatching/tests.yml diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/tests.yml b/sdk/healthinsights/azure-health-insights-cancerprofiling/tests.yml deleted file mode 100644 index d79fef966e6d2..0000000000000 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/tests.yml +++ /dev/null @@ -1,10 +0,0 @@ -trigger: none - -stages: - - template: /eng/pipelines/templates/stages/archetype-sdk-tests.yml - parameters: - ServiceDirectory: healthinsights - Artifacts: - - name: azure-health-insights-cancerprofiling - groupId: com.azure - safeName: azurehealthinsightscancerprofiling diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/tests.yml b/sdk/healthinsights/azure-health-insights-clinicalmatching/tests.yml deleted file mode 100644 index 7f03bdc6ddfb7..0000000000000 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/tests.yml +++ /dev/null @@ -1,10 +0,0 @@ -trigger: none - -stages: - - template: /eng/pipelines/templates/stages/archetype-sdk-tests.yml - parameters: - ServiceDirectory: healthinsights - Artifacts: - - name: azure-health-insights-clinicalmatching - groupId: com.azure - safeName: azurehealthinsightsclinicalmatching From 6167072791853ce0add8e0a943815eb994bd73bd Mon Sep 17 00:00:00 2001 From: Asaf Levi Date: Thu, 23 Mar 2023 11:19:05 +0200 Subject: [PATCH 15/25] remove redundant package.json file --- .../azure-health-insights-cancerprofiling/package.json | 5 ----- .../azure-health-insights-clinicalmatching/package.json | 5 ----- 2 files changed, 10 deletions(-) delete mode 100644 sdk/healthinsights/azure-health-insights-cancerprofiling/package.json delete mode 100644 sdk/healthinsights/azure-health-insights-clinicalmatching/package.json diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/package.json b/sdk/healthinsights/azure-health-insights-cancerprofiling/package.json deleted file mode 100644 index ded9535dc3f1e..0000000000000 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/package.json +++ /dev/null @@ -1,5 +0,0 @@ -{ - "dependencies": { - "mvn": "^3.5.0" - } -} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/package.json b/sdk/healthinsights/azure-health-insights-clinicalmatching/package.json deleted file mode 100644 index ded9535dc3f1e..0000000000000 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/package.json +++ /dev/null @@ -1,5 +0,0 @@ -{ - "dependencies": { - "mvn": "^3.5.0" - } -} From c18a288378f81b0535c480f29b6d444b58c5cd5b Mon Sep 17 00:00:00 2001 From: Asaf Levi Date: Mon, 27 Mar 2023 11:07:56 +0300 Subject: [PATCH 16/25] fix sampes and readmes --- .vscode/cspell.json | 4 +- .../README.md | 169 +++++++++++++----- .../src/samples/README.md | 29 --- .../SampleInferCancerProfile.java | 38 +++- .../insights/cancerprofiling/AllSamples.java | 24 --- .../README.md | 112 +++++++----- .../pom.xml | 8 +- .../src/samples/README.md | 43 +---- .../SampleMatchTrialAsync.java | 49 +++-- .../insights/clinicalmatching/AllSamples.java | 24 --- 10 files changed, 270 insertions(+), 230 deletions(-) delete mode 100644 sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/java/com/azure/health/insights/cancerprofiling/AllSamples.java delete mode 100644 sdk/healthinsights/azure-health-insights-clinicalmatching/src/test/java/com/azure/health/insights/clinicalmatching/AllSamples.java diff --git a/.vscode/cspell.json b/.vscode/cspell.json index 2af9266fc2a9d..cb239a4fdac23 100644 --- a/.vscode/cspell.json +++ b/.vscode/cspell.json @@ -239,7 +239,7 @@ "databind", "databricks", "DAZURE", - "DAZURE", + "ddos", "dcis", "deallocate", "decryptor", @@ -276,7 +276,7 @@ "hdinsight", "hvac", "hybridkubernetes", - "insighs", + "insights", "intellij", "Intellij", "iotcentral", diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md b/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md index 50860f2469044..23640329f5452 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md @@ -1,14 +1,15 @@ # Azure Azure Health Insights Cancer Profiling client library for Java - + +[Health Insights](https://review.learn.microsoft.com/azure/azure-health-insights/?branch=release-azure-health-insights) is an Azure Applied AI Service built with the Azure Cognitive Services Framework, that leverages multiple Cognitive Services, Healthcare API services and other Azure resources. + +The [Cancer Profiling model][cancer_profiling_docs] receives clinical records of oncology patients and outputs cancer staging, such as clinical stage TNM categories and pathologic stage TNM categories as well as tumor site, histology. + ## Getting started ### Prerequisites -- A [Java Development Kit (JDK)][jdk] with version 8 or above +- A [Java Development Kit (JDK)][jdk_link] with version 8 or above - [Azure Subscription][azure_subscription] - An existing Cognitive Services Health Insights instance. @@ -47,10 +48,11 @@ az cognitiveservices account keys list --resource-group -```Java readme-sample-InferCancerProfile -CancerProfilingAsyncClient asyncClient = new CancerProfilingClientBuilder() - .endpoint(endpoint) - .serviceVersion(AzureHealthInsightsServiceVersion.getLatest()) - .credential(new AzureKeyCredential(apiKey)) - .buildAsyncClient(); - - PollerFlux asyncPoller = asyncClient.beginInferCancerProfile(oncoPhenotypeData); - OncoPhenotypeResult result = asyncPoller.blockLast().getValue(); - - OncoPhenotypeResults oncoResults = result.getResults(); - oncoResults.getPatients().forEach(patient_result -> { - System.out.println("\n==== Inferences of Patient " + patient_result.getId() + " ===="); - patient_result.getInferences().forEach(onco_inference -> { - System.out.println("\n=== Clinical Type: " + onco_inference.getType() + " Value: " + onco_inference.getValue() + " ConfidenceScore: " + onco_inference.getConfidenceScore() + " ==="); - onco_inference.getEvidence().forEach(evidence -> { - if (evidence.getPatientDataEvidence() != null) { - ClinicalNoteEvidence dataEvidence = evidence.getPatientDataEvidence(); - System.out.println("Evidence " + dataEvidence.getId() + " " + dataEvidence.getOffset() + " " + dataEvidence.getLength() + " " + dataEvidence.getText()); - } - if (evidence.getPatientInfoEvidence() != null) { - ClinicalCodedElement infoEvidence = evidence.getPatientInfoEvidence(); - System.out.println("Evidence " + infoEvidence.getSystem() + " " + infoEvidence.getCode() + " " + infoEvidence.getName() + " " + infoEvidence.getValue()); - } - }); - }); - }); - - +```Java com.azure.health.insights.cancerprofiling.infercancerprofile +// Construct Patient +PatientRecord patient1 = new PatientRecord("patient_id"); +PatientInfo patientInfo = new PatientInfo(); +patientInfo.setBirthDate(LocalDate.parse("1965-12-26")); +patientInfo.setSex(PatientInfoSex.FEMALE); +patient1.setInfo(patientInfo); +LinkedList patientDocuments = new LinkedList<>(); +patient1.setData(patientDocuments); + +// Add imaging document +final String docContent1 = String.join(System.getProperty("line.separator"), + "15.8.2021", + "Jane Doe 091175-8967", + "42 year old female, married with 3 children, works as a nurse. ", + "Healthy, no medications taken on a regular basis.", + "PMHx is significant for migraines with aura, uses Mirena for contraception.", + "Smoking history of 10 pack years (has stopped and relapsed several times).", + "She is in c/o 2 weeks of productive cough and shortness of breath.", + "She has a fever of 37.8 and general weakness. ", + "Denies night sweats and rash. She denies symptoms of rhinosinusitis, asthma, and heartburn. ", + "On PE:", + "GENERAL: mild pallor, no cyanosis. Regular breathing rate. ", + "LUNGS: decreased breath sounds on the base of the right lung. Vesicular breathing.", + " No crackles, rales, and wheezes. Resonant percussion. ", + "PLAN: ", + "Will be referred for a chest x-ray. ", + "======================================", + "CXR showed mild nonspecific opacities in right lung base. ", + "PLAN:", + "Findings are suggestive of a working diagnosis of pneumonia. The patient is referred to a follow-up CXR in 2 weeks."); + +PatientDocument patientDocument1 = new PatientDocument( + DocumentType.NOTE, + "doc1", + new DocumentContent(DocumentContentSourceType.INLINE, docContent1)); + +patientDocument1.setClinicalType(ClinicalDocumentType.IMAGING); +patientDocument1.setLanguage("en"); +patientDocument1.setCreatedDateTime(OffsetDateTime.parse("2021-08-15T10:15:30+01:00")); +patient1.getData().add(patientDocument1); + +// Add Pathology documents +String docContent2 = String.join(System.getProperty("line.separator"), + "Oncology Clinic ", + "20.10.2021", + "Jane Doe 091175-8967", + "42-year-old healthy female who works as a nurse in the ER of this hospital. ", + "First menstruation at 11 years old. First delivery- 27 years old. She has 3 children.", + "Didn’t breastfeed. ", + "Contraception- Mirena.", + "Smoking- 10 pack years. ", + "Mother- Belarusian. Father- Georgian. ", + "About 3 months prior to admission, she stated she had SOB and was febrile. ", + "She did a CXR as an outpatient which showed a finding in the base of the right lung- possibly an infiltrate.", + "She was treated with antibiotics with partial response. ", + "6 weeks later a repeat CXR was performed- a few solid dense findings in the right lung. ", + "Therefore, she was referred for a PET-CT which demonstrated increased uptake in the right breast, lymph nodes on the right a few areas in the lungs and liver. ", + "On biopsy from the lesion in the right breast- triple negative adenocarcinoma. Genetic testing has not been done thus far. ", + "Genetic counseling- the patient denies a family history of breast, ovary, uterus, and prostate cancer. Her mother has chronic lymphocytic leukemia (CLL). ", + "She is planned to undergo genetic tests because the aggressive course of the disease, and her young age. ", + "Impression:", + "Stage 4 triple negative breast adenocarcinoma. ", + "Could benefit from biological therapy. ", + "Different treatment options were explained- the patient wants to get a second opinion."); + +PatientDocument patientDocument2 = new PatientDocument(DocumentType.NOTE, + "doc2", + new DocumentContent(DocumentContentSourceType.INLINE, docContent2)); +patientDocument2.setClinicalType(ClinicalDocumentType.PATHOLOGY); +patientDocument2.setLanguage("en"); +patientDocument2.setCreatedDateTime(OffsetDateTime.parse("2021-10-20T22:00:00.00Z")); +patient1.getData().add(patientDocument2); + +String docContent3 = String.join(System.getProperty("line.separator"), + "PATHOLOGY REPORT", + " Clinical Information", + "Ultrasound-guided biopsy; A. 18 mm mass; most likely diagnosis based on imaging: IDC", + " Diagnosis", + " A. BREAST, LEFT AT 2:00 4 CM FN; ULTRASOUND-GUIDED NEEDLE CORE BIOPSIES:", + " - Invasive carcinoma of no special type (invasive ductal carcinoma), grade 1", + " Nottingham histologic grade: 1/3 (tubules 2; nuclear grade 2; mitotic rate 1; total score; 5/9)", + " Fragments involved by invasive carcinoma: 2", + " Largest measurement of invasive carcinoma on a single fragment: 7 mm", + " Ductal carcinoma in situ (DCIS): Present", + " Architectural pattern: Cribriform", + " Nuclear grade: 2-", + " -intermediate", + " Necrosis: Not identified", + " Fragments involved by DCIS: 1", + " Largest measurement of DCIS on a single fragment: Span 2 mm", + " Microcalcifications: Present in benign breast tissue and invasive carcinoma", + " Blocks with invasive carcinoma: A1", + " Special studies: Pending"); + +PatientDocument patientDocument3 = new PatientDocument(DocumentType.NOTE, + "doc3", + new DocumentContent(DocumentContentSourceType.INLINE, docContent3)); +patientDocument3.setClinicalType(ClinicalDocumentType.PATHOLOGY); +patientDocument3.setLanguage("en"); +patientDocument3.setCreatedDateTime(OffsetDateTime.parse("2022-01-01T10:15:30+01:00")); + +patient1.getData().add(patientDocument3); + +// Set configuration to include evidence for the cancer staging inferences +OncoPhenotypeModelConfiguration configuration = new OncoPhenotypeModelConfiguration(); +configuration.setIncludeEvidence(true); + +// Construct the request with the patient and configration +OncoPhenotypeData oncoPhenotypeData = new OncoPhenotypeData(Arrays.asList(patient1)); +oncoPhenotypeData.setConfiguration(configuration); + +PollerFlux asyncPoller = asyncClient.beginInferCancerProfile(oncoPhenotypeData); ``` ## Troubleshooting @@ -106,9 +192,7 @@ CancerProfilingAsyncClient asyncClient = new CancerProfilingClientBuilder() This code sample show common scenario operation with the Azure Health Insights Cancer Profiling library. More samples can be found under the [samples](https://github.com/Azure/azure-sdk-for-python/blob/main/sdk/healthinsights/azure-health-insights-cancerprofiling/src/samples/java/com/azure/health/insights/) directory. --> ### Additional documentation - +For more extensive documentation on Azure Health Insights Cancer Profiling, see the [Cancer Profiling documentation][cancer_profiling_docs] on docs.microsoft.com. ## Contributing This project welcomes contributions and suggestions. Most contributions require you to agree to a Contributor License Agreement (CLA) declaring that you have the right to, and actually do, grant us the rights to use your contribution. For details, visit [cla.microsoft.com][cla]. @@ -124,8 +208,11 @@ This project has adopted the [Microsoft Open Source Code of Conduct][code_of_con [coc_contact]: mailto:opencode@microsoft.com [azure_subscription]: https://azure.microsoft.com/free/ [cognitive_resource_cli]: https://docs.microsoft.com/azure/cognitive-services/cognitive-services-apis-create-account-cli +[jdk_link]: https://docs.microsoft.com/java/azure/jdk/?view=azure-java-stable + [azure_cli]: https://docs.microsoft.com/cli/azure [azure_portal]: https://portal.azure.com +[cancer_profiling_docs]: https://review.learn.microsoft.com/azure/cognitive-services/health-decision-support/oncophenotype/overview?branch=main diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/samples/README.md b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/samples/README.md index 6cc7b99e71a15..73b455f1fd9fe 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/samples/README.md +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/samples/README.md @@ -13,15 +13,6 @@ urlFragment: healthinsights-java-samples Azure Health Insights Cancer Profiling samples are a set of self-contained Java programs that demonstrate interacting with Azure self-contained service using the client library. Each sample focuses on a specific scenario and can be executed independently. -## Key concepts - - -Key concepts are explained in detail [here] -## Getting started - - -Getting started explained in detail [here] - ## Examples The following sections provide code samples covering common scenario operations with the Azure Health Insights CancerProfiling client library. @@ -31,27 +22,7 @@ All of these samples need the endpoint to your Health Insights resource, and you |**File Name**|**Description**| |----------------|-------------| |[SampleInferCancerProfile.java][infer_cancer_profiling]|Get the inferred cancer staging| - -## Troubleshooting - - -Troubleshooting steps can be found [here]. - -## Next steps - - -See [Next steps]. - -## Contributing - -If you would like to become an active contributor to this project please refer to our [Contribution -Guidelines][SDK_README_CONTRIBUTING] for more information. diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/samples/java/com/azure/health/insights/cancerprofiling/SampleInferCancerProfile.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/samples/java/com/azure/health/insights/cancerprofiling/SampleInferCancerProfile.java index 0c92fbabf869c..df79b4e74c1e5 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/samples/java/com/azure/health/insights/cancerprofiling/SampleInferCancerProfile.java +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/samples/java/com/azure/health/insights/cancerprofiling/SampleInferCancerProfile.java @@ -3,13 +3,17 @@ package com.azure.health.insights.cancerprofiling; -import java.io.IOException; import java.time.LocalDate; import java.time.OffsetDateTime; import java.util.Arrays; import java.util.LinkedList; +import java.util.concurrent.CountDownLatch; +import java.util.function.Predicate; +import com.azure.core.util.Configuration; import com.azure.core.credential.AzureKeyCredential; +import com.azure.core.util.polling.AsyncPollResponse; +import com.azure.core.util.polling.LongRunningOperationStatus; import com.azure.core.util.polling.PollerFlux; import com.azure.health.insights.cancerprofiling.models.PatientInfoSex; import com.azure.health.insights.cancerprofiling.models.ClinicalCodedElement; @@ -26,15 +30,22 @@ import com.azure.health.insights.cancerprofiling.models.OncoPhenotypeResult; import com.azure.health.insights.cancerprofiling.models.ClinicalNoteEvidence; + public class SampleInferCancerProfile { - public static void runSample(String endpoint, String apiKey) throws InterruptedException, IOException { + public static void main(final String[] args) throws InterruptedException { + // BEGIN: com.azure.health.insights.cancerprofiling.buildasyncclient + String endpoint = Configuration.getGlobalConfiguration().get("AZURE_HEALTH_INSIGHTS_ENDPOINT"); + String apiKey = Configuration.getGlobalConfiguration().get("AZURE_HEALTH_INSIGHTS_API_KEY"); + CancerProfilingAsyncClient asyncClient = new CancerProfilingClientBuilder() .endpoint(endpoint) .serviceVersion(AzureHealthInsightsServiceVersion.getLatest()) .credential(new AzureKeyCredential(apiKey)) .buildAsyncClient(); + // END: com.azure.health.insights.cancerprofiling.buildasyncclient - // construct Patient + // BEGIN: com.azure.health.insights.cancerprofiling.infercancerprofile + // Construct Patient PatientRecord patient1 = new PatientRecord("patient_id"); PatientInfo patientInfo = new PatientInfo(); patientInfo.setBirthDate(LocalDate.parse("1965-12-26")); @@ -146,11 +157,19 @@ public static void runSample(String endpoint, String apiKey) throws InterruptedE oncoPhenotypeData.setConfiguration(configuration); PollerFlux asyncPoller = asyncClient.beginInferCancerProfile(oncoPhenotypeData); - OncoPhenotypeResult result = asyncPoller.blockLast().getValue(); - printResults(result); + // END: com.azure.health.insights.cancerprofiling.infercancerprofile + asyncPoller + .takeUntil(isComplete) + .subscribe(completedResult -> { + System.out.println("Completed poll response, status: " + completedResult.getStatus()); + printResults(completedResult.getValue()); + latch.countDown(); + }); + + latch.await(); } - private static void printResults(OncoPhenotypeResult result) { + private static final void printResults(OncoPhenotypeResult result) { OncoPhenotypeResults oncoResults = result.getResults(); oncoResults.getPatients().forEach(patient_result -> { System.out.println("\n==== Inferences of Patient " + patient_result.getId() + " ===="); @@ -169,4 +188,11 @@ private static void printResults(OncoPhenotypeResult result) { }); }); } + + private static final Predicate> isComplete = response -> { + return response.getStatus() != LongRunningOperationStatus.IN_PROGRESS + && response.getStatus() != LongRunningOperationStatus.NOT_STARTED; + }; + + private static final CountDownLatch latch = new CountDownLatch(1); } diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/java/com/azure/health/insights/cancerprofiling/AllSamples.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/java/com/azure/health/insights/cancerprofiling/AllSamples.java deleted file mode 100644 index ac5209ae187a5..0000000000000 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/java/com/azure/health/insights/cancerprofiling/AllSamples.java +++ /dev/null @@ -1,24 +0,0 @@ -// Copyright (c) Microsoft Corporation. All rights reserved. -// Licensed under the MIT License. - -package com.azure.health.insights.cancerprofiling; - -import java.io.IOException; - -import org.junit.jupiter.api.BeforeEach; - -public class AllSamples { - String endpoint; - String apiKey; - - @BeforeEach - public void init() { - endpoint = System.getenv("SDK_JAVA_HDS_ENDPOINT"); - apiKey = System.getenv("SDK_JAVA_HDS_APIKEY"); - } - - // @Test - public void inferCancerProfile() throws InterruptedException, IOException { - SampleInferCancerProfile.runSample(endpoint, apiKey); - } -} diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/README.md b/sdk/healthinsights/azure-health-insights-clinicalmatching/README.md index 1695d82c359f6..072545f19146d 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/README.md +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/README.md @@ -1,13 +1,14 @@ # Azure Azure Health Insights Clinical Matching client library for Java - + +[Health Insights](https://review.learn.microsoft.com/azure/cognitive-services/health-decision-support/overview?branch=main) is an Azure Applied AI Service built with the Azure Cognitive Services Framework, that leverages multiple Cognitive Services, Healthcare API services and other Azure resources. + +The [Clinical Matching model][clinical_matching_docs] receives patients data and clinical trials protocols, and provides relevant clinical trials based on eligibility criteria. + ## Getting started ### Prerequisites -- A [Java Development Kit (JDK)][jdk] with version 8 or above +- A [Java Development Kit (JDK)][jdk_link] with version 8 or above - [Azure Subscription][azure_subscription] - An existing Cognitive Services Health Insights instance. @@ -46,16 +47,15 @@ az cognitiveservices account keys list --resource-group -```Java readme-sample-MatchTrialsSync -ClinicalMatchingClient syncClient = new ClinicalMatchingClientBuilder() - .endpoint(endpoint) - .serviceVersion(AzureHealthInsightsServiceVersion.getLatest()) - .httpClient(HttpClient.createDefault(new HttpClientOptions())) - .credential(new AzureKeyCredential(apiKey)) - .buildClient(); - -SyncPoller syncPoller = syncClient.beginMatchTrials(BinaryData.fromObject(trialMatcherOptions), null); -PollResponse pollerResponse = syncPoller.waitForCompletion(); - -LongRunningOperationStatus status = pollerResponse.getStatus(); -System.out.println("Status " + status); -TrialMatcherResult tmRespone = pollerResponse.getValue().toObject(TypeReference.createInstance(TrialMatcherResult.class)); -if (status == LongRunningOperationStatus.SUCCESSFULLY_COMPLETED) { - TrialMatcherResults tmResults = tmRespone.getResults(); - tmResults.getPatients().forEach(patientResult -> { - System.out.println("Inferences of Patient " + patientResult.getId()); - patientResult.getInferences().forEach(inference -> { - System.out.println("Trial Id " + inference.getId()); - System.out.println("Type: " + inference.getType() + " Value: " + inference.getValue()); - System.out.println("Description " + inference.getDescription()); - }); - }); -} else if (status == LongRunningOperationStatus.FAILED) { - List errors = tmRespone.getErrors(); - errors.forEach(error -> { - System.out.println(error.getCode() + " : " + error.getMessage()); - }); -} - +```Java com.azure.health.insights.clinicalmatching.findtrials +// Construct Patient +PatientRecord patient1 = new PatientRecord("patient_1"); +PatientInfo patientInfo = new PatientInfo(); +patientInfo.setBirthDate(LocalDate.parse("1965-12-26")); +patientInfo.setSex(PatientInfoSex.MALE); +final List clinicalInfo = new ArrayList(); +patientInfo.setClinicalInfo(clinicalInfo); +patient1.setInfo(patientInfo); + +final String system = "http://www.nlm.nih.gov/research/umls"; +// Attach clinical info to the patient +clinicalInfo.add(createClinicalCodedElement(system, "C0006826", "Malignant Neoplasms", "true")); +clinicalInfo.add(createClinicalCodedElement(system, "C1522449", "Therapeutic radiology procedure", "true")); +clinicalInfo.add(createClinicalCodedElement(system, "C1512162", "Eastern Cooperative Oncology Group", "1")); +clinicalInfo.add(createClinicalCodedElement(system, "C0019693", "HIV Infections", "false")); +clinicalInfo.add(createClinicalCodedElement(system, "C1300072", "Tumor stage", "2")); +clinicalInfo.add(createClinicalCodedElement(system, "METASTATIC", "metastatic", "true")); +clinicalInfo.add(createClinicalCodedElement(system, "C0019163", "Hepatitis B", "false")); +clinicalInfo.add(createClinicalCodedElement(system, "C0018802", "Congestive heart failure", "true")); +clinicalInfo.add(createClinicalCodedElement(system, "C0019196", "Hepatitis C", "false")); +clinicalInfo.add(createClinicalCodedElement(system, "C0220650", "Metastatic malignant neoplasm to brain", "true")); + +// Create registry filter +ClinicalTrialRegistryFilter registryFilters = new ClinicalTrialRegistryFilter(); +// Limit the trial to a specific patient condition ("Non-small cell lung cancer") +registryFilters.setConditions(Arrays.asList("Non-small cell lung cancer")); +// Limit the clinical trial to a certain phase, phase 1 +registryFilters.setPhases(Arrays.asList(ClinicalTrialPhase.PHASE1)); +// Specify the clinical trial registry source as ClinicalTrials.Gov +registryFilters.setSources(Arrays.asList(ClinicalTrialSource.CLINICALTRIALS_GOV)); +// Limit the clinical trial to a certain location, in this case California, USA + +GeographicLocation location = new GeographicLocation("United States"); +location.setCity("Gilbert"); +location.setState("Arizona"); +registryFilters.setFacilityLocations(Arrays.asList(location)); +// Limit the trial to a specific study type, interventional +registryFilters.setStudyTypes(Arrays.asList(ClinicalTrialStudyType.INTERVENTIONAL)); + +// Construct ClinicalTrial instance and attach the registry filter to it. +ClinicalTrials clinicalTrials = new ClinicalTrials(); +clinicalTrials.setRegistryFilters(Arrays.asList(registryFilters)); + +// Create TrialMatcherData +TrialMatcherModelConfiguration configuration = new TrialMatcherModelConfiguration(clinicalTrials); +TrialMatcherData trialMatcherData = new TrialMatcherData(Arrays.asList(patient1)); +trialMatcherData.setConfiguration(configuration); + +PollerFlux asyncPoller = asyncClient.beginMatchTrials(trialMatcherData); ``` ## Troubleshooting @@ -113,9 +132,8 @@ This code sample show common scenario operation with the Azure Health Insights C --> ### Additional documentation - +For more extensive documentation on Azure Health Insights Clinical Matching, see the [Clinical Matching documentation][clinical_matching_docs] on docs.microsoft.com. + ## Contributing @@ -132,8 +150,10 @@ This project has adopted the [Microsoft Open Source Code of Conduct][code_of_con [coc_contact]: mailto:opencode@microsoft.com [azure_subscription]: https://azure.microsoft.com/free/ [cognitive_resource_cli]: https://docs.microsoft.com/azure/cognitive-services/cognitive-services-apis-create-account-cli +[jdk_link]: https://docs.microsoft.com/java/azure/jdk/?view=azure-java-stable +[azure_cli]: https://docs.microsoft.com/cli/azure +[azure_portal]: https://portal.azure.com +[clinical_matching_docs]: https://review.learn.microsoft.com/azure/cognitive-services/health-decision-support/trial-matcher/overview?branch=main -[azure_cli]: https://docs.microsoft.com/cli/azure -[azure_portal]: https://portal.azure.com \ No newline at end of file diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/pom.xml b/sdk/healthinsights/azure-health-insights-clinicalmatching/pom.xml index f58a4c1d9c1de..8f494b7a85568 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/pom.xml +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/pom.xml @@ -43,7 +43,7 @@ UTF-8 0.1 - 0.1 + 0.1 @@ -86,12 +86,6 @@ 1.8.1 test - - org.mockito - mockito-core - 4.5.1 - test - org.slf4j slf4j-simple diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/README.md b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/README.md index a6d303f8edb03..9a2189164d26c 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/README.md +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/README.md @@ -13,14 +13,6 @@ urlFragment: healthinsights-java-samples Azure Health Insights Clinical Matching samples are a set of self-contained Java programs that demonstrate interacting with Azure self-contained service using the client library. Each sample focuses on a specific scenario and can be executed independently. -## Key concepts - - -Key concepts are explained in detail [here] -## Getting started - - -Getting started explained in detail [here] ## Examples @@ -30,39 +22,8 @@ All of these samples need the endpoint to your Health Insights resource, and you |**File Name**|**Description**| |----------------|-------------| - - -## Troubleshooting - - -Troubleshooting steps can be found [here]. - -## Next steps - - -See [Next steps]. - -## Contributing - -If you would like to become an active contributor to this project please refer to our [Contribution -Guidelines][SDK_README_CONTRIBUTING] for more information. + diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/java/com/azure/health/insights/clinicalmatching/SampleMatchTrialAsync.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/java/com/azure/health/insights/clinicalmatching/SampleMatchTrialAsync.java index 4edffd98ffd0e..4d457448ce302 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/java/com/azure/health/insights/clinicalmatching/SampleMatchTrialAsync.java +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/java/com/azure/health/insights/clinicalmatching/SampleMatchTrialAsync.java @@ -3,15 +3,17 @@ package com.azure.health.insights.clinicalmatching; -import java.io.IOException; import java.time.LocalDate; import java.util.ArrayList; import java.util.Arrays; import java.util.List; +import java.util.concurrent.CountDownLatch; +import java.util.function.Predicate; +import com.azure.core.util.Configuration; import com.azure.core.credential.AzureKeyCredential; -import com.azure.core.http.HttpClient; -import com.azure.core.util.HttpClientOptions; +import com.azure.core.util.polling.AsyncPollResponse; +import com.azure.core.util.polling.LongRunningOperationStatus; import com.azure.core.util.polling.PollerFlux; import com.azure.health.insights.clinicalmatching.models.TrialMatcherData; import com.azure.health.insights.clinicalmatching.models.GeographicLocation; @@ -41,16 +43,20 @@ * recruitment status, location and other criteria that the service users may choose to prioritize. */ public class SampleMatchTrialAsync { - public static void runSample(String endpoint, String apiKey) throws InterruptedException, IOException { + public static void main(final String[] args) throws InterruptedException { + // BEGIN: com.azure.health.insights.clinicalmatching.buildasyncclient + String endpoint = Configuration.getGlobalConfiguration().get("AZURE_HEALTH_INSIGHTS_ENDPOINT"); + String apiKey = Configuration.getGlobalConfiguration().get("AZURE_HEALTH_INSIGHTS_API_KEY"); ClinicalMatchingAsyncClient asyncClient = new ClinicalMatchingClientBuilder() .endpoint(endpoint) .serviceVersion(AzureHealthInsightsServiceVersion.getLatest()) - .httpClient(HttpClient.createDefault(new HttpClientOptions())) .credential(new AzureKeyCredential(apiKey)) .buildAsyncClient(); + // END: com.azure.health.insights.clinicalmatching.buildasyncclient - // construct Patient + // BEGIN: com.azure.health.insights.clinicalmatching.findtrials + // Construct Patient PatientRecord patient1 = new PatientRecord("patient_1"); PatientInfo patientInfo = new PatientInfo(); patientInfo.setBirthDate(LocalDate.parse("1965-12-26")); @@ -66,6 +72,11 @@ public static void runSample(String endpoint, String apiKey) throws InterruptedE clinicalInfo.add(createClinicalCodedElement(system, "C1512162", "Eastern Cooperative Oncology Group", "1")); clinicalInfo.add(createClinicalCodedElement(system, "C0019693", "HIV Infections", "false")); clinicalInfo.add(createClinicalCodedElement(system, "C1300072", "Tumor stage", "2")); + clinicalInfo.add(createClinicalCodedElement(system, "METASTATIC", "metastatic", "true")); + clinicalInfo.add(createClinicalCodedElement(system, "C0019163", "Hepatitis B", "false")); + clinicalInfo.add(createClinicalCodedElement(system, "C0018802", "Congestive heart failure", "true")); + clinicalInfo.add(createClinicalCodedElement(system, "C0019196", "Hepatitis C", "false")); + clinicalInfo.add(createClinicalCodedElement(system, "C0220650", "Metastatic malignant neoplasm to brain", "true")); // Create registry filter ClinicalTrialRegistryFilter registryFilters = new ClinicalTrialRegistryFilter(); @@ -76,7 +87,11 @@ public static void runSample(String endpoint, String apiKey) throws InterruptedE // Specify the clinical trial registry source as ClinicalTrials.Gov registryFilters.setSources(Arrays.asList(ClinicalTrialSource.CLINICALTRIALS_GOV)); // Limit the clinical trial to a certain location, in this case California, USA - registryFilters.setFacilityLocations(Arrays.asList(new GeographicLocation("United States"))); + + GeographicLocation location = new GeographicLocation("United States"); + location.setCity("Gilbert"); + location.setState("Arizona"); + registryFilters.setFacilityLocations(Arrays.asList(location)); // Limit the trial to a specific study type, interventional registryFilters.setStudyTypes(Arrays.asList(ClinicalTrialStudyType.INTERVENTIONAL)); @@ -90,9 +105,16 @@ public static void runSample(String endpoint, String apiKey) throws InterruptedE trialMatcherData.setConfiguration(configuration); PollerFlux asyncPoller = asyncClient.beginMatchTrials(trialMatcherData); + // END: com.azure.health.insights.clinicalmatching.findtrials + asyncPoller + .takeUntil(isComplete) + .subscribe(completedResult -> { + System.out.println("Completed poll response, status: " + completedResult.getStatus()); + printResults(completedResult.getValue()); + latch.countDown(); + }); - TrialMatcherResult response = asyncPoller.blockLast().getValue(); - printResults(response); + latch.await(); } private static void printResults(TrialMatcherResult tmRespone) { @@ -108,10 +130,17 @@ private static void printResults(TrialMatcherResult tmRespone) { }); } - private static ClinicalCodedElement createClinicalCodedElement(String system, String code, String name, String value) { + private static final ClinicalCodedElement createClinicalCodedElement(String system, String code, String name, String value) { ClinicalCodedElement element = new ClinicalCodedElement(system, code); element.setName(name); element.setValue(value); return element; } + + private static final Predicate> isComplete = response -> { + return response.getStatus() != LongRunningOperationStatus.IN_PROGRESS + && response.getStatus() != LongRunningOperationStatus.NOT_STARTED; + }; + + private static final CountDownLatch latch = new CountDownLatch(1); } diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/test/java/com/azure/health/insights/clinicalmatching/AllSamples.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/test/java/com/azure/health/insights/clinicalmatching/AllSamples.java deleted file mode 100644 index 235aad0e64490..0000000000000 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/test/java/com/azure/health/insights/clinicalmatching/AllSamples.java +++ /dev/null @@ -1,24 +0,0 @@ -// Copyright (c) Microsoft Corporation. All rights reserved. -// Licensed under the MIT License. - -package com.azure.health.insights.clinicalmatching; - -import java.io.IOException; - -import org.junit.jupiter.api.BeforeEach; - -public class AllSamples { - String endpoint; - String apiKey; - - @BeforeEach - public void init() { - endpoint = System.getenv("SDK_JAVA_HDS_ENDPOINT"); - apiKey = System.getenv("SDK_JAVA_HDS_APIKEY"); - } - - // @Test - public void matchTrialAsync() throws InterruptedException, IOException { - SampleMatchTrialAsync.runSample(endpoint, apiKey); - } -} From 4d32c461b1b25ed1b0d2fbf6bdc63bd9d4375c83 Mon Sep 17 00:00:00 2001 From: Asaf Levi Date: Mon, 27 Mar 2023 11:17:45 +0300 Subject: [PATCH 17/25] spell --- .../azure-health-insights-cancerprofiling/README.md | 2 +- .../azure-health-insights-clinicalmatching/README.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md b/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md index 23640329f5452..d8466639d8b90 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md @@ -31,7 +31,7 @@ For more information about creating the resource or how to get the location and ### Authenticate the client -In order to interact with the Health Insighs Cancer Profiling service, you'll need to create an instance of the [`CancerProfilingClient`][cancer_profiling_client_class] class. You will need an **endpoint** and an **API key** to instantiate a client object. +In order to interact with the Health Insights Cancer Profiling service, you'll need to create an instance of the [`CancerProfilingClient`][cancer_profiling_client_class] class. You will need an **endpoint** and an **API key** to instantiate a client object. #### Get API Key diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/README.md b/sdk/healthinsights/azure-health-insights-clinicalmatching/README.md index 072545f19146d..a9ad4255f1a3a 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/README.md +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/README.md @@ -30,7 +30,7 @@ For more information about creating the resource or how to get the location and ### Authenticate the client -In order to interact with the Health Insighs Clinical Matching service, you'll need to create an instance of the [`ClinicalMatchingClient`][clinical_matching_client_class] class. You will need an **endpoint** and an **API key** to instantiate a client object. +In order to interact with the Health Insights Clinical Matching service, you'll need to create an instance of the [`ClinicalMatchingClient`][clinical_matching_client_class] class. You will need an **endpoint** and an **API key** to instantiate a client object. #### Get API Key From c28c41e39b09b48417dd2339893670c867a5d826 Mon Sep 17 00:00:00 2001 From: Asaf Levi Date: Mon, 27 Mar 2023 11:56:28 +0300 Subject: [PATCH 18/25] fix linting --- .../README.md | 5 ++--- .../SampleInferCancerProfile.java | 20 +++++++++---------- .../CancerProfilingClientTest.java | 2 -- .../SampleMatchTrialAsync.java | 18 ++++++++--------- .../ClinicalMatchingClientTest.java | 2 -- 5 files changed, 21 insertions(+), 26 deletions(-) diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md b/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md index d8466639d8b90..edcffdabccd2a 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md @@ -31,7 +31,7 @@ For more information about creating the resource or how to get the location and ### Authenticate the client -In order to interact with the Health Insights Cancer Profiling service, you'll need to create an instance of the [`CancerProfilingClient`][cancer_profiling_client_class] class. You will need an **endpoint** and an **API key** to instantiate a client object. +In order to interact with the Health Insights Cancer Profiling service, you'll need to create an instance of the [`CancerProfilingClient`][cancer_profiling_client_class] class. You will need an **endpoint** and an **API key** to instantiate a client object. #### Get API Key @@ -45,8 +45,7 @@ az cognitiveservices account keys list --resource-group asyncPoller = asyncClient.beginInferCancerProfile(oncoPhenotypeData); // END: com.azure.health.insights.cancerprofiling.infercancerprofile asyncPoller - .takeUntil(isComplete) - .subscribe(completedResult -> { - System.out.println("Completed poll response, status: " + completedResult.getStatus()); - printResults(completedResult.getValue()); - latch.countDown(); - }); + .takeUntil(isComplete) + .subscribe(completedResult -> { + System.out.println("Completed poll response, status: " + completedResult.getStatus()); + printResults(completedResult.getValue()); + latch.countDown(); + }); latch.await(); } - private static final void printResults(OncoPhenotypeResult result) { + private static void printResults(OncoPhenotypeResult result) { OncoPhenotypeResults oncoResults = result.getResults(); oncoResults.getPatients().forEach(patient_result -> { System.out.println("\n==== Inferences of Patient " + patient_result.getId() + " ===="); @@ -189,10 +189,10 @@ private static final void printResults(OncoPhenotypeResult result) { }); } - private static final Predicate> isComplete = response -> { + private static Predicate> isComplete = response -> { return response.getStatus() != LongRunningOperationStatus.IN_PROGRESS && response.getStatus() != LongRunningOperationStatus.NOT_STARTED; }; - private static final CountDownLatch latch = new CountDownLatch(1); + private static CountDownLatch latch = new CountDownLatch(1); } diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/java/com/azure/health/insights/cancerprofiling/CancerProfilingClientTest.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/java/com/azure/health/insights/cancerprofiling/CancerProfilingClientTest.java index a36cdd97eb248..f21479bf48596 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/java/com/azure/health/insights/cancerprofiling/CancerProfilingClientTest.java +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/java/com/azure/health/insights/cancerprofiling/CancerProfilingClientTest.java @@ -50,7 +50,5 @@ public void test() { Assertions.fail(message); return; } - - System.out.println("Success"); } } diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/java/com/azure/health/insights/clinicalmatching/SampleMatchTrialAsync.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/java/com/azure/health/insights/clinicalmatching/SampleMatchTrialAsync.java index 4d457448ce302..2cfd87cf1e12f 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/java/com/azure/health/insights/clinicalmatching/SampleMatchTrialAsync.java +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/java/com/azure/health/insights/clinicalmatching/SampleMatchTrialAsync.java @@ -107,12 +107,12 @@ public static void main(final String[] args) throws InterruptedException { PollerFlux asyncPoller = asyncClient.beginMatchTrials(trialMatcherData); // END: com.azure.health.insights.clinicalmatching.findtrials asyncPoller - .takeUntil(isComplete) - .subscribe(completedResult -> { - System.out.println("Completed poll response, status: " + completedResult.getStatus()); - printResults(completedResult.getValue()); - latch.countDown(); - }); + .takeUntil(isComplete) + .subscribe(completedResult -> { + System.out.println("Completed poll response, status: " + completedResult.getStatus()); + printResults(completedResult.getValue()); + latch.countDown(); + }); latch.await(); } @@ -130,17 +130,17 @@ private static void printResults(TrialMatcherResult tmRespone) { }); } - private static final ClinicalCodedElement createClinicalCodedElement(String system, String code, String name, String value) { + private static ClinicalCodedElement createClinicalCodedElement(String system, String code, String name, String value) { ClinicalCodedElement element = new ClinicalCodedElement(system, code); element.setName(name); element.setValue(value); return element; } - private static final Predicate> isComplete = response -> { + private static Predicate> isComplete = response -> { return response.getStatus() != LongRunningOperationStatus.IN_PROGRESS && response.getStatus() != LongRunningOperationStatus.NOT_STARTED; }; - private static final CountDownLatch latch = new CountDownLatch(1); + private static CountDownLatch latch = new CountDownLatch(1); } diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/test/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingClientTest.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/test/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingClientTest.java index c07e78683854b..2903ed9ed9400 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/test/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingClientTest.java +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/test/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingClientTest.java @@ -52,7 +52,5 @@ public void test() { Assertions.fail(message); return; } - - System.out.println("Success"); } } From 6ba52e146bccedfa3ff7107a2cdbed7743c0cdd2 Mon Sep 17 00:00:00 2001 From: Asaf Levi Date: Tue, 28 Mar 2023 09:03:54 +0300 Subject: [PATCH 19/25] fix sample repository reference --- .../azure-health-insights-cancerprofiling/README.md | 3 ++- .../azure-health-insights-clinicalmatching/README.md | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md b/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md index edcffdabccd2a..279499ab87b62 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md @@ -188,8 +188,9 @@ PollerFlux asyncPoller = asyncClient.b ## Next steps + ### Additional documentation For more extensive documentation on Azure Health Insights Cancer Profiling, see the [Cancer Profiling documentation][cancer_profiling_docs] on docs.microsoft.com. ## Contributing diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/README.md b/sdk/healthinsights/azure-health-insights-clinicalmatching/README.md index a9ad4255f1a3a..05d345cdb12c0 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/README.md +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/README.md @@ -128,7 +128,7 @@ PollerFlux asyncPoller = asyncClient.beg To see the full example source files, see: ### Additional documentation From b3e6d52d080ce84af7427beb8875ad7b3fcdab2c Mon Sep 17 00:00:00 2001 From: Asaf Levi Date: Tue, 28 Mar 2023 09:12:46 +0300 Subject: [PATCH 20/25] remove duplicate dependency (mockito) --- .../azure-health-insights-cancerprofiling/pom.xml | 6 ------ 1 file changed, 6 deletions(-) diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/pom.xml b/sdk/healthinsights/azure-health-insights-cancerprofiling/pom.xml index 1b588b480e72b..683236ec485db 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/pom.xml +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/pom.xml @@ -86,12 +86,6 @@ 1.8.1 test - - org.mockito - mockito-core - 4.5.1 - test - org.slf4j slf4j-simple From 1f53e87b324333a440d461c209ec05a9d9aff2fa Mon Sep 17 00:00:00 2001 From: Asaf Levi Date: Tue, 28 Mar 2023 09:30:18 +0300 Subject: [PATCH 21/25] alignment (readme) --- .../azure-health-insights-cancerprofiling/README.md | 2 +- .../azure-health-insights-clinicalmatching/README.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md b/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md index 279499ab87b62..b108b7b1ed506 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md @@ -191,7 +191,7 @@ PollerFlux asyncPoller = asyncClient.b This code sample show common scenario operation with the Azure Health Insights Cancer Profiling library. More samples can be found under the [samples](https://github.com/Azure/azure-sdk-for-java/blob/main/sdk/healthinsights/azure-health-insights-cancerprofiling/src/samples/java/com/azure/health/insights/) directory. --> -### Additional documentation +## Additional documentation For more extensive documentation on Azure Health Insights Cancer Profiling, see the [Cancer Profiling documentation][cancer_profiling_docs] on docs.microsoft.com. ## Contributing diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/README.md b/sdk/healthinsights/azure-health-insights-clinicalmatching/README.md index 05d345cdb12c0..88e79fbb480d4 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/README.md +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/README.md @@ -131,7 +131,7 @@ To see the full example source files, see: This code sample show common scenario operation with the Azure Health Insights Clinical Matching library. More samples can be found under the [samples](https://github.com/Azure/azure-sdk-for-java/blob/main/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/java/com/azure/health/insights/) directory. --> -### Additional documentation +## Additional documentation For more extensive documentation on Azure Health Insights Clinical Matching, see the [Clinical Matching documentation][clinical_matching_docs] on docs.microsoft.com. From 3cf67933fd337c3d055c27de3df5a8d6e44078b7 Mon Sep 17 00:00:00 2001 From: Asaf Levi Date: Tue, 28 Mar 2023 14:26:38 +0300 Subject: [PATCH 22/25] fix readme title --- .../azure-health-insights-cancerprofiling/README.md | 2 +- .../azure-health-insights-clinicalmatching/README.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md b/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md index b108b7b1ed506..922efe05707e4 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md @@ -1,4 +1,4 @@ -# Azure Azure Health Insights Cancer Profiling client library for Java +# Azure Cognitive Services Health Insights Cancer Profiling client library for Java [Health Insights](https://review.learn.microsoft.com/azure/azure-health-insights/?branch=release-azure-health-insights) is an Azure Applied AI Service built with the Azure Cognitive Services Framework, that leverages multiple Cognitive Services, Healthcare API services and other Azure resources. diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/README.md b/sdk/healthinsights/azure-health-insights-clinicalmatching/README.md index 88e79fbb480d4..f64ea413e170d 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/README.md +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/README.md @@ -1,4 +1,4 @@ -# Azure Azure Health Insights Clinical Matching client library for Java +# Azure Cognitive Services Health Insights Clinical Matching client library for Java [Health Insights](https://review.learn.microsoft.com/azure/cognitive-services/health-decision-support/overview?branch=main) is an Azure Applied AI Service built with the Azure Cognitive Services Framework, that leverages multiple Cognitive Services, Healthcare API services and other Azure resources. From dbb9d929db5a1741e13839eb329dfe52994b6028 Mon Sep 17 00:00:00 2001 From: Asaf Levi Date: Wed, 29 Mar 2023 10:19:02 +0300 Subject: [PATCH 23/25] setPlaybackSyncPollerPollInterval --- .../azure-health-insights-cancerprofiling/README.md | 1 + .../insights/cancerprofiling/SampleInferCancerProfile.java | 4 ++-- .../insights/cancerprofiling/CancerProfilingClientTest.java | 2 +- .../insights/clinicalmatching/ClinicalMatchingClientTest.java | 3 +-- sdk/healthinsights/ci.yml | 2 +- 5 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md b/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md index 922efe05707e4..68a39d95226b4 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md @@ -216,3 +216,4 @@ This project has adopted the [Microsoft Open Source Code of Conduct][code_of_con [azure_cli]: https://docs.microsoft.com/cli/azure [azure_portal]: https://portal.azure.com [cancer_profiling_docs]: https://review.learn.microsoft.com/azure/cognitive-services/health-decision-support/oncophenotype/overview?branch=main +![Impressions](https://azure-sdk-impressions.azurewebsites.net/api/impressions/azure-sdk-for-java%2Fsdk%2Fdeviceupdate%2Fazure-iot-deviceupdate%2FREADME.png) \ No newline at end of file diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/samples/java/com/azure/health/insights/cancerprofiling/SampleInferCancerProfile.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/samples/java/com/azure/health/insights/cancerprofiling/SampleInferCancerProfile.java index ae715b0a04db6..47da5f142d688 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/samples/java/com/azure/health/insights/cancerprofiling/SampleInferCancerProfile.java +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/samples/java/com/azure/health/insights/cancerprofiling/SampleInferCancerProfile.java @@ -140,8 +140,8 @@ public static void main(final String[] args) throws InterruptedException { " Special studies: Pending"); PatientDocument patientDocument3 = new PatientDocument(DocumentType.NOTE, - "doc3", - new DocumentContent(DocumentContentSourceType.INLINE, docContent3)); + "doc3", + new DocumentContent(DocumentContentSourceType.INLINE, docContent3)); patientDocument3.setClinicalType(ClinicalDocumentType.PATHOLOGY); patientDocument3.setLanguage("en"); patientDocument3.setCreatedDateTime(OffsetDateTime.parse("2022-01-01T10:15:30+01:00")); diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/java/com/azure/health/insights/cancerprofiling/CancerProfilingClientTest.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/java/com/azure/health/insights/cancerprofiling/CancerProfilingClientTest.java index f21479bf48596..c912ec997e262 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/java/com/azure/health/insights/cancerprofiling/CancerProfilingClientTest.java +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/test/java/com/azure/health/insights/cancerprofiling/CancerProfilingClientTest.java @@ -32,7 +32,7 @@ private CancerProfilingClient getClient() { public void test() { try { testCancerProfilingWithResponse(request -> { - BinaryData responseValue = getClient().beginInferCancerProfile(request, new RequestOptions()).waitForCompletion().getValue(); + BinaryData responseValue = setPlaybackSyncPollerPollInterval(getClient().beginInferCancerProfile(request, new RequestOptions())).waitForCompletion().getValue(); OncoPhenotypeResult respone = responseValue.toObject(TypeReference.createInstance(OncoPhenotypeResult.class)); List patients = respone.getResults().getPatients(); diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/test/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingClientTest.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/test/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingClientTest.java index 2903ed9ed9400..6e183fe2bb2d6 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/test/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingClientTest.java +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/test/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingClientTest.java @@ -33,8 +33,7 @@ public void test() { try { testTMWithResponse(request -> { - BinaryData responseValue = getClient().beginMatchTrials(request, new RequestOptions()).waitForCompletion().getValue(); - + BinaryData responseValue = setPlaybackSyncPollerPollInterval(getClient().beginMatchTrials(request, new RequestOptions())).waitForCompletion().getValue(); TrialMatcherResult tmRespone = responseValue.toObject(TypeReference.createInstance(TrialMatcherResult.class)); List patients = tmRespone.getResults().getPatients(); assertEquals(1, patients.size()); diff --git a/sdk/healthinsights/ci.yml b/sdk/healthinsights/ci.yml index 65d7f96f5f098..960570420b498 100644 --- a/sdk/healthinsights/ci.yml +++ b/sdk/healthinsights/ci.yml @@ -40,4 +40,4 @@ extends: - name: azure-health-insights-cancerprofiling groupId: com.azure safeName: azurehealthinsightscancerprofiling - JavaBuildVersion: 17.0.5 + From ea3640e2093de42afd6e509cde11d18bb13b83cc Mon Sep 17 00:00:00 2001 From: Asaf Levi Date: Wed, 29 Mar 2023 10:54:08 +0300 Subject: [PATCH 24/25] update serviceversion class (emitter 0.5.1) --- .../azure-health-insights-cancerprofiling/README.md | 4 ++-- .../CancerProfilingClientBuilder.java | 8 ++++---- ...rsion.java => CancerProfilingServiceVersion.java} | 8 ++++---- .../implementation/CancerProfilingClientImpl.java | 12 ++++++------ .../cancerprofiling/implementation/package-info.java | 5 ++--- .../cancerprofiling/models/package-info.java | 2 +- .../insights/cancerprofiling/package-info.java | 4 ++-- .../cancerprofiling/SampleInferCancerProfile.java | 2 +- .../azure-health-insights-clinicalmatching/README.md | 3 ++- .../ClinicalMatchingClientBuilder.java | 8 ++++---- ...sion.java => ClinicalMatchingServiceVersion.java} | 8 ++++---- .../implementation/ClinicalMatchingClientImpl.java | 12 ++++++------ .../implementation/package-info.java | 2 +- .../clinicalmatching/models/package-info.java | 2 +- .../insights/clinicalmatching/package-info.java | 2 +- .../clinicalmatching/SampleMatchTrialAsync.java | 2 +- 16 files changed, 42 insertions(+), 42 deletions(-) rename sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/{AzureHealthInsightsServiceVersion.java => CancerProfilingServiceVersion.java} (72%) rename sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/{AzureHealthInsightsServiceVersion.java => ClinicalMatchingServiceVersion.java} (72%) diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md b/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md index 68a39d95226b4..815b35ff128a9 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md @@ -53,7 +53,7 @@ String apiKey = Configuration.getGlobalConfiguration().get("AZURE_HEALTH_INSIGHT CancerProfilingAsyncClient asyncClient = new CancerProfilingClientBuilder() .endpoint(endpoint) - .serviceVersion(AzureHealthInsightsServiceVersion.getLatest()) + .serviceVersion(CancerProfilingServiceVersion.getLatest()) .credential(new AzureKeyCredential(apiKey)) .buildAsyncClient(); ``` @@ -216,4 +216,4 @@ This project has adopted the [Microsoft Open Source Code of Conduct][code_of_con [azure_cli]: https://docs.microsoft.com/cli/azure [azure_portal]: https://portal.azure.com [cancer_profiling_docs]: https://review.learn.microsoft.com/azure/cognitive-services/health-decision-support/oncophenotype/overview?branch=main -![Impressions](https://azure-sdk-impressions.azurewebsites.net/api/impressions/azure-sdk-for-java%2Fsdk%2Fdeviceupdate%2Fazure-iot-deviceupdate%2FREADME.png) \ No newline at end of file +![Impressions](https://azure-sdk-impressions.azurewebsites.net/api/impressions/azure-sdk-for-java%2Fsdk%healthinsights%2Fazure-health-insights-cancerprofiling%2FREADME.png) diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/CancerProfilingClientBuilder.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/CancerProfilingClientBuilder.java index 6f375a4011424..34d6afcd437e2 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/CancerProfilingClientBuilder.java +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/CancerProfilingClientBuilder.java @@ -179,7 +179,7 @@ public CancerProfilingClientBuilder endpoint(String endpoint) { /* * Service version */ - @Generated private AzureHealthInsightsServiceVersion serviceVersion; + @Generated private CancerProfilingServiceVersion serviceVersion; /** * Sets Service version. @@ -188,7 +188,7 @@ public CancerProfilingClientBuilder endpoint(String endpoint) { * @return the CancerProfilingClientBuilder. */ @Generated - public CancerProfilingClientBuilder serviceVersion(AzureHealthInsightsServiceVersion serviceVersion) { + public CancerProfilingClientBuilder serviceVersion(CancerProfilingServiceVersion serviceVersion) { this.serviceVersion = serviceVersion; return this; } @@ -218,8 +218,8 @@ public CancerProfilingClientBuilder retryPolicy(RetryPolicy retryPolicy) { @Generated private CancerProfilingClientImpl buildInnerClient() { HttpPipeline localPipeline = (pipeline != null) ? pipeline : createHttpPipeline(); - AzureHealthInsightsServiceVersion localServiceVersion = - (serviceVersion != null) ? serviceVersion : AzureHealthInsightsServiceVersion.getLatest(); + CancerProfilingServiceVersion localServiceVersion = + (serviceVersion != null) ? serviceVersion : CancerProfilingServiceVersion.getLatest(); CancerProfilingClientImpl client = new CancerProfilingClientImpl( localPipeline, JacksonAdapter.createDefaultSerializerAdapter(), endpoint, localServiceVersion); diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/AzureHealthInsightsServiceVersion.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/CancerProfilingServiceVersion.java similarity index 72% rename from sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/AzureHealthInsightsServiceVersion.java rename to sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/CancerProfilingServiceVersion.java index e2d51c4e1ca63..d020a3b853f79 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/AzureHealthInsightsServiceVersion.java +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/CancerProfilingServiceVersion.java @@ -7,13 +7,13 @@ import com.azure.core.util.ServiceVersion; /** Service version of CancerProfilingClient. */ -public enum AzureHealthInsightsServiceVersion implements ServiceVersion { +public enum CancerProfilingServiceVersion implements ServiceVersion { /** Enum value 2023-03-01-preview. */ V2023_03_01_PREVIEW("2023-03-01-preview"); private final String version; - AzureHealthInsightsServiceVersion(String version) { + CancerProfilingServiceVersion(String version) { this.version = version; } @@ -26,9 +26,9 @@ public String getVersion() { /** * Gets the latest service version supported by this client library. * - * @return The latest {@link AzureHealthInsightsServiceVersion}. + * @return The latest {@link CancerProfilingServiceVersion}. */ - public static AzureHealthInsightsServiceVersion getLatest() { + public static CancerProfilingServiceVersion getLatest() { return V2023_03_01_PREVIEW; } } diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/implementation/CancerProfilingClientImpl.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/implementation/CancerProfilingClientImpl.java index 6734576e5032c..fed67e28539ed 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/implementation/CancerProfilingClientImpl.java +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/implementation/CancerProfilingClientImpl.java @@ -37,7 +37,7 @@ import com.azure.core.util.serializer.JacksonAdapter; import com.azure.core.util.serializer.SerializerAdapter; import com.azure.core.util.serializer.TypeReference; -import com.azure.health.insights.cancerprofiling.AzureHealthInsightsServiceVersion; +import com.azure.health.insights.cancerprofiling.CancerProfilingServiceVersion; import com.azure.health.insights.cancerprofiling.models.OncoPhenotypeResult; import java.time.Duration; import java.time.OffsetDateTime; @@ -66,14 +66,14 @@ public String getEndpoint() { } /** Service version. */ - private final AzureHealthInsightsServiceVersion serviceVersion; + private final CancerProfilingServiceVersion serviceVersion; /** * Gets Service version. * * @return the serviceVersion value. */ - public AzureHealthInsightsServiceVersion getServiceVersion() { + public CancerProfilingServiceVersion getServiceVersion() { return this.serviceVersion; } @@ -108,7 +108,7 @@ public SerializerAdapter getSerializerAdapter() { * https://westus2.api.cognitive.microsoft.com). * @param serviceVersion Service version. */ - public CancerProfilingClientImpl(String endpoint, AzureHealthInsightsServiceVersion serviceVersion) { + public CancerProfilingClientImpl(String endpoint, CancerProfilingServiceVersion serviceVersion) { this( new HttpPipelineBuilder() .policies(new UserAgentPolicy(), new RetryPolicy(), new CookiePolicy()) @@ -127,7 +127,7 @@ public CancerProfilingClientImpl(String endpoint, AzureHealthInsightsServiceVers * @param serviceVersion Service version. */ public CancerProfilingClientImpl( - HttpPipeline httpPipeline, String endpoint, AzureHealthInsightsServiceVersion serviceVersion) { + HttpPipeline httpPipeline, String endpoint, CancerProfilingServiceVersion serviceVersion) { this(httpPipeline, JacksonAdapter.createDefaultSerializerAdapter(), endpoint, serviceVersion); } @@ -144,7 +144,7 @@ public CancerProfilingClientImpl( HttpPipeline httpPipeline, SerializerAdapter serializerAdapter, String endpoint, - AzureHealthInsightsServiceVersion serviceVersion) { + CancerProfilingServiceVersion serviceVersion) { this.httpPipeline = httpPipeline; this.serializerAdapter = serializerAdapter; this.endpoint = endpoint; diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/implementation/package-info.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/implementation/package-info.java index 0bd37018b715f..312db8b35faa7 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/implementation/package-info.java +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/implementation/package-info.java @@ -3,8 +3,7 @@ // Code generated by Microsoft (R) AutoRest Code Generator. /** - * Package containing the implementations for AzureHealthInsights. Azure Health Insights provides an API that serves - * insight models, specific for Health & Life Sciences, that perform analysis and provide inferences to be used by a - * human. + * Package containing the implementations for CancerProfiling. Azure Health Insights provides an API that serves insight + * models, specific for Health & Life Sciences, that perform analysis and provide inferences to be used by a human. */ package com.azure.health.insights.cancerprofiling.implementation; diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/package-info.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/package-info.java index 69bf37e5296aa..5b6fbc482f437 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/package-info.java +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/models/package-info.java @@ -3,7 +3,7 @@ // Code generated by Microsoft (R) AutoRest Code Generator. /** - * Package containing the data models for AzureHealthInsights. Azure Health Insights provides an API that serves insight + * Package containing the data models for CancerProfiling. Azure Health Insights provides an API that serves insight * models, specific for Health & Life Sciences, that perform analysis and provide inferences to be used by a human. */ package com.azure.health.insights.cancerprofiling.models; diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/package-info.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/package-info.java index 443b2cc5f7515..a3e51adccf51e 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/package-info.java +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/main/java/com/azure/health/insights/cancerprofiling/package-info.java @@ -3,7 +3,7 @@ // Code generated by Microsoft (R) AutoRest Code Generator. /** - * Package containing the classes for AzureHealthInsights. Azure Health Insights provides an API that serves insight - * models, specific for Health & Life Sciences, that perform analysis and provide inferences to be used by a human. + * Package containing the classes for CancerProfiling. Azure Health Insights provides an API that serves insight models, + * specific for Health & Life Sciences, that perform analysis and provide inferences to be used by a human. */ package com.azure.health.insights.cancerprofiling; diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/samples/java/com/azure/health/insights/cancerprofiling/SampleInferCancerProfile.java b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/samples/java/com/azure/health/insights/cancerprofiling/SampleInferCancerProfile.java index 47da5f142d688..f49a0b4cc09c4 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/src/samples/java/com/azure/health/insights/cancerprofiling/SampleInferCancerProfile.java +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/src/samples/java/com/azure/health/insights/cancerprofiling/SampleInferCancerProfile.java @@ -39,7 +39,7 @@ public static void main(final String[] args) throws InterruptedException { CancerProfilingAsyncClient asyncClient = new CancerProfilingClientBuilder() .endpoint(endpoint) - .serviceVersion(AzureHealthInsightsServiceVersion.getLatest()) + .serviceVersion(CancerProfilingServiceVersion.getLatest()) .credential(new AzureKeyCredential(apiKey)) .buildAsyncClient(); // END: com.azure.health.insights.cancerprofiling.buildasyncclient diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/README.md b/sdk/healthinsights/azure-health-insights-clinicalmatching/README.md index f64ea413e170d..26975c8607e1c 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/README.md +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/README.md @@ -53,7 +53,7 @@ String apiKey = Configuration.getGlobalConfiguration().get("AZURE_HEALTH_INSIGHT ClinicalMatchingAsyncClient asyncClient = new ClinicalMatchingClientBuilder() .endpoint(endpoint) - .serviceVersion(AzureHealthInsightsServiceVersion.getLatest()) + .serviceVersion(ClinicalMatchingServiceVersion.getLatest()) .credential(new AzureKeyCredential(apiKey)) .buildAsyncClient(); ``` @@ -157,3 +157,4 @@ This project has adopted the [Microsoft Open Source Code of Conduct][code_of_con +![Impressions](https://azure-sdk-impressions.azurewebsites.net/api/impressions/azure-sdk-for-java%2Fsdk%healthinsights%2Fazure-health-insights-clinicalmatching%2FREADME.png) diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingClientBuilder.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingClientBuilder.java index d94f2f6ee68ff..6bb761bbfd7e1 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingClientBuilder.java +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingClientBuilder.java @@ -179,7 +179,7 @@ public ClinicalMatchingClientBuilder endpoint(String endpoint) { /* * Service version */ - @Generated private AzureHealthInsightsServiceVersion serviceVersion; + @Generated private ClinicalMatchingServiceVersion serviceVersion; /** * Sets Service version. @@ -188,7 +188,7 @@ public ClinicalMatchingClientBuilder endpoint(String endpoint) { * @return the ClinicalMatchingClientBuilder. */ @Generated - public ClinicalMatchingClientBuilder serviceVersion(AzureHealthInsightsServiceVersion serviceVersion) { + public ClinicalMatchingClientBuilder serviceVersion(ClinicalMatchingServiceVersion serviceVersion) { this.serviceVersion = serviceVersion; return this; } @@ -218,8 +218,8 @@ public ClinicalMatchingClientBuilder retryPolicy(RetryPolicy retryPolicy) { @Generated private ClinicalMatchingClientImpl buildInnerClient() { HttpPipeline localPipeline = (pipeline != null) ? pipeline : createHttpPipeline(); - AzureHealthInsightsServiceVersion localServiceVersion = - (serviceVersion != null) ? serviceVersion : AzureHealthInsightsServiceVersion.getLatest(); + ClinicalMatchingServiceVersion localServiceVersion = + (serviceVersion != null) ? serviceVersion : ClinicalMatchingServiceVersion.getLatest(); ClinicalMatchingClientImpl client = new ClinicalMatchingClientImpl( localPipeline, JacksonAdapter.createDefaultSerializerAdapter(), endpoint, localServiceVersion); diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/AzureHealthInsightsServiceVersion.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingServiceVersion.java similarity index 72% rename from sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/AzureHealthInsightsServiceVersion.java rename to sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingServiceVersion.java index 1abf2e3361517..74c91f584b726 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/AzureHealthInsightsServiceVersion.java +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/ClinicalMatchingServiceVersion.java @@ -7,13 +7,13 @@ import com.azure.core.util.ServiceVersion; /** Service version of ClinicalMatchingClient. */ -public enum AzureHealthInsightsServiceVersion implements ServiceVersion { +public enum ClinicalMatchingServiceVersion implements ServiceVersion { /** Enum value 2023-03-01-preview. */ V2023_03_01_PREVIEW("2023-03-01-preview"); private final String version; - AzureHealthInsightsServiceVersion(String version) { + ClinicalMatchingServiceVersion(String version) { this.version = version; } @@ -26,9 +26,9 @@ public String getVersion() { /** * Gets the latest service version supported by this client library. * - * @return The latest {@link AzureHealthInsightsServiceVersion}. + * @return The latest {@link ClinicalMatchingServiceVersion}. */ - public static AzureHealthInsightsServiceVersion getLatest() { + public static ClinicalMatchingServiceVersion getLatest() { return V2023_03_01_PREVIEW; } } diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/implementation/ClinicalMatchingClientImpl.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/implementation/ClinicalMatchingClientImpl.java index 364bcf6c8339d..adf59b763203a 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/implementation/ClinicalMatchingClientImpl.java +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/implementation/ClinicalMatchingClientImpl.java @@ -37,7 +37,7 @@ import com.azure.core.util.serializer.JacksonAdapter; import com.azure.core.util.serializer.SerializerAdapter; import com.azure.core.util.serializer.TypeReference; -import com.azure.health.insights.clinicalmatching.AzureHealthInsightsServiceVersion; +import com.azure.health.insights.clinicalmatching.ClinicalMatchingServiceVersion; import com.azure.health.insights.clinicalmatching.models.TrialMatcherResult; import java.time.Duration; import java.time.OffsetDateTime; @@ -66,14 +66,14 @@ public String getEndpoint() { } /** Service version. */ - private final AzureHealthInsightsServiceVersion serviceVersion; + private final ClinicalMatchingServiceVersion serviceVersion; /** * Gets Service version. * * @return the serviceVersion value. */ - public AzureHealthInsightsServiceVersion getServiceVersion() { + public ClinicalMatchingServiceVersion getServiceVersion() { return this.serviceVersion; } @@ -108,7 +108,7 @@ public SerializerAdapter getSerializerAdapter() { * https://westus2.api.cognitive.microsoft.com). * @param serviceVersion Service version. */ - public ClinicalMatchingClientImpl(String endpoint, AzureHealthInsightsServiceVersion serviceVersion) { + public ClinicalMatchingClientImpl(String endpoint, ClinicalMatchingServiceVersion serviceVersion) { this( new HttpPipelineBuilder() .policies(new UserAgentPolicy(), new RetryPolicy(), new CookiePolicy()) @@ -127,7 +127,7 @@ public ClinicalMatchingClientImpl(String endpoint, AzureHealthInsightsServiceVer * @param serviceVersion Service version. */ public ClinicalMatchingClientImpl( - HttpPipeline httpPipeline, String endpoint, AzureHealthInsightsServiceVersion serviceVersion) { + HttpPipeline httpPipeline, String endpoint, ClinicalMatchingServiceVersion serviceVersion) { this(httpPipeline, JacksonAdapter.createDefaultSerializerAdapter(), endpoint, serviceVersion); } @@ -144,7 +144,7 @@ public ClinicalMatchingClientImpl( HttpPipeline httpPipeline, SerializerAdapter serializerAdapter, String endpoint, - AzureHealthInsightsServiceVersion serviceVersion) { + ClinicalMatchingServiceVersion serviceVersion) { this.httpPipeline = httpPipeline; this.serializerAdapter = serializerAdapter; this.endpoint = endpoint; diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/implementation/package-info.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/implementation/package-info.java index d4bea9038803b..54a3183a52f9c 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/implementation/package-info.java +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/implementation/package-info.java @@ -3,7 +3,7 @@ // Code generated by Microsoft (R) AutoRest Code Generator. /** - * Package containing the implementations for AzureHealthInsights. Azure Health Insights provides an API that serves + * Package containing the implementations for ClinicalMatching. Azure Health Insights provides an API that serves * insight models, specific for Health & Life Sciences, that perform analysis and provide inferences to be used by a * human. */ diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/package-info.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/package-info.java index f40be2cc64470..93dd62e2759e8 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/package-info.java +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/models/package-info.java @@ -3,7 +3,7 @@ // Code generated by Microsoft (R) AutoRest Code Generator. /** - * Package containing the data models for AzureHealthInsights. Azure Health Insights provides an API that serves insight + * Package containing the data models for ClinicalMatching. Azure Health Insights provides an API that serves insight * models, specific for Health & Life Sciences, that perform analysis and provide inferences to be used by a human. */ package com.azure.health.insights.clinicalmatching.models; diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/package-info.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/package-info.java index b6d8a6dea6a4e..017b5a419b254 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/package-info.java +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/main/java/com/azure/health/insights/clinicalmatching/package-info.java @@ -3,7 +3,7 @@ // Code generated by Microsoft (R) AutoRest Code Generator. /** - * Package containing the classes for AzureHealthInsights. Azure Health Insights provides an API that serves insight + * Package containing the classes for ClinicalMatching. Azure Health Insights provides an API that serves insight * models, specific for Health & Life Sciences, that perform analysis and provide inferences to be used by a human. */ package com.azure.health.insights.clinicalmatching; diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/java/com/azure/health/insights/clinicalmatching/SampleMatchTrialAsync.java b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/java/com/azure/health/insights/clinicalmatching/SampleMatchTrialAsync.java index 2cfd87cf1e12f..36ac6aa57252b 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/java/com/azure/health/insights/clinicalmatching/SampleMatchTrialAsync.java +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/src/samples/java/com/azure/health/insights/clinicalmatching/SampleMatchTrialAsync.java @@ -50,7 +50,7 @@ public static void main(final String[] args) throws InterruptedException { ClinicalMatchingAsyncClient asyncClient = new ClinicalMatchingClientBuilder() .endpoint(endpoint) - .serviceVersion(AzureHealthInsightsServiceVersion.getLatest()) + .serviceVersion(ClinicalMatchingServiceVersion.getLatest()) .credential(new AzureKeyCredential(apiKey)) .buildAsyncClient(); // END: com.azure.health.insights.clinicalmatching.buildasyncclient From b01f33779eac90f60acd97f11f8208a79eeef5d2 Mon Sep 17 00:00:00 2001 From: Asaf Levi Date: Wed, 29 Mar 2023 12:04:36 +0300 Subject: [PATCH 25/25] remove impressions png --- .../azure-health-insights-cancerprofiling/README.md | 6 +++--- .../azure-health-insights-clinicalmatching/README.md | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md b/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md index 815b35ff128a9..6216c18756e76 100644 --- a/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md +++ b/sdk/healthinsights/azure-health-insights-cancerprofiling/README.md @@ -210,10 +210,10 @@ This project has adopted the [Microsoft Open Source Code of Conduct][code_of_con [cognitive_resource_cli]: https://docs.microsoft.com/azure/cognitive-services/cognitive-services-apis-create-account-cli [jdk_link]: https://docs.microsoft.com/java/azure/jdk/?view=azure-java-stable - [azure_cli]: https://docs.microsoft.com/cli/azure [azure_portal]: https://portal.azure.com [cancer_profiling_docs]: https://review.learn.microsoft.com/azure/cognitive-services/health-decision-support/oncophenotype/overview?branch=main + diff --git a/sdk/healthinsights/azure-health-insights-clinicalmatching/README.md b/sdk/healthinsights/azure-health-insights-clinicalmatching/README.md index 26975c8607e1c..2978a55e28827 100644 --- a/sdk/healthinsights/azure-health-insights-clinicalmatching/README.md +++ b/sdk/healthinsights/azure-health-insights-clinicalmatching/README.md @@ -156,5 +156,5 @@ This project has adopted the [Microsoft Open Source Code of Conduct][code_of_con [clinical_matching_docs]: https://review.learn.microsoft.com/azure/cognitive-services/health-decision-support/trial-matcher/overview?branch=main ![Impressions](https://azure-sdk-impressions.azurewebsites.net/api/impressions/azure-sdk-for-java%2Fsdk%healthinsights%2Fazure-health-insights-clinicalmatching%2FREADME.png) +-->