From bbf7b928abe477586a3c057828da4d64bb22515e Mon Sep 17 00:00:00 2001 From: Gordon Farrell Date: Wed, 30 Oct 2024 13:59:10 -0600 Subject: [PATCH 01/23] update parsing schemas to properly grab RR info --- .../app/default_schemas/ecr.json | 31 ++++++++++++++ .../default_schemas/ecr_viewer_metadata.json | 41 +++++++++++++------ .../default_schemas/ecr_with_metadata.json | 31 ++++++++++++++ .../app/default_schemas/philly_ecr.json | 8 ++-- 4 files changed, 94 insertions(+), 17 deletions(-) diff --git a/containers/message-parser/app/default_schemas/ecr.json b/containers/message-parser/app/default_schemas/ecr.json index 843a65d7cb..2dc4e0ae65 100644 --- a/containers/message-parser/app/default_schemas/ecr.json +++ b/containers/message-parser/app/default_schemas/ecr.json @@ -332,5 +332,36 @@ "fhir_path": "Bundle.entry.resource.where(resourceType='Observation').where(meta.profile='http: //hl7.org/fhir/us/ecr/StructureDefinition/us-ph-pregnancy-status-observation').value.coding.display", "data_type": "string", "nullable": true + }, + "rr": { + "fhir_path": "Bundle.entry.resource.where(resourceType='Observation').where(meta.profile = 'http://hl7.org/fhir/us/ecr/StructureDefinition/rr-reportability-information-observation')", + "data_type": "array", + "nullable": true, + "secondary_schema": { + "uuid": { + "fhir_path": "Observation.id", + "data_type": "string", + "nullable": true, + "metadata": { + "category": "RR Reportability Information" + } + }, + "condition": { + "fhir_path": "Observation.valueCodeableConcept.coding.display", + "data_type": "string", + "nullable": true, + "metadata": { + "category": "RR Reportability Information" + } + }, + "rule_summaries": { + "fhir_path": "Observation.extension.where(url = 'http://hl7.org/fhir/us/ecr/StructureDefinition/us-ph-determination-of-reportability-rule-extension').valueString", + "data_type": "string", + "nullable": true, + "metadata": { + "category": "RR Reportability Information" + } + } + } } } diff --git a/containers/message-parser/app/default_schemas/ecr_viewer_metadata.json b/containers/message-parser/app/default_schemas/ecr_viewer_metadata.json index d4316bd247..ed5e15f069 100644 --- a/containers/message-parser/app/default_schemas/ecr_viewer_metadata.json +++ b/containers/message-parser/app/default_schemas/ecr_viewer_metadata.json @@ -28,20 +28,35 @@ "category": "Personal info" } }, - "reportable_condition": { - "fhir_path": "Bundle.entry.resource.where(meta.profile = 'http://hl7.org/fhir/us/ecr/StructureDefinition/rr-reportability-information-observation').valueCodeableConcept.coding.display", - "data_type": "string", + "rr": { + "fhir_path": "Bundle.entry.resource.where(resourceType='Observation').where(meta.profile = 'http://hl7.org/fhir/us/ecr/StructureDefinition/rr-reportability-information-observation')", + "data_type": "array", "nullable": true, - "metadata": { - "category": "RR Reportability Information" - } - }, - "rule_summary": { - "fhir_path": "Bundle.entry.resource.where(meta.profile = 'http://hl7.org/fhir/us/ecr/StructureDefinition/rr-reportability-information-observation').extension.where(url = 'http://hl7.org/fhir/us/ecr/StructureDefinition/us-ph-determination-of-reportability-rule-extension').valueString", - "data_type": "string", - "nullable": true, - "metadata": { - "category": "RR Reportability Information" + "secondary_schema": { + "uuid": { + "fhir_path": "Observation.id", + "data_type": "string", + "nullable": true, + "metadata": { + "category": "RR Reportability Information" + } + }, + "condition": { + "fhir_path": "Observation.valueCodeableConcept.coding.display", + "data_type": "string", + "nullable": true, + "metadata": { + "category": "RR Reportability Information" + } + }, + "rule_summaries": { + "fhir_path": "Observation.extension.where(url = 'http://hl7.org/fhir/us/ecr/StructureDefinition/us-ph-determination-of-reportability-rule-extension').valueString", + "data_type": "string", + "nullable": true, + "metadata": { + "category": "RR Reportability Information" + } + } } }, "report_date": { diff --git a/containers/message-parser/app/default_schemas/ecr_with_metadata.json b/containers/message-parser/app/default_schemas/ecr_with_metadata.json index 2e1dedab45..5dcac09e18 100644 --- a/containers/message-parser/app/default_schemas/ecr_with_metadata.json +++ b/containers/message-parser/app/default_schemas/ecr_with_metadata.json @@ -104,6 +104,37 @@ "data_type": "string", "nullable": true }, + "rr": { + "fhir_path": "Bundle.entry.resource.where(resourceType='Observation').where(meta.profile = 'http://hl7.org/fhir/us/ecr/StructureDefinition/rr-reportability-information-observation')", + "data_type": "array", + "nullable": true, + "secondary_schema": { + "uuid": { + "fhir_path": "Observation.id", + "data_type": "string", + "nullable": true, + "metadata": { + "category": "RR Reportability Information" + } + }, + "condition": { + "fhir_path": "Observation.valueCodeableConcept.coding.display", + "data_type": "string", + "nullable": true, + "metadata": { + "category": "RR Reportability Information" + } + }, + "rule_summaries": { + "fhir_path": "Observation.extension.where(url = 'http://hl7.org/fhir/us/ecr/StructureDefinition/us-ph-determination-of-reportability-rule-extension').valueString", + "data_type": "string", + "nullable": true, + "metadata": { + "category": "RR Reportability Information" + } + } + } + }, "status": { "fhir_path": "Bundle.entry.resource.where(resourceType='Composition').section.where(title = 'Reportability Response Information Section').extension.where(url='http://hl7.org/fhir/us/ecr/StructureDefinition/rr-eicr-processing-status-extension').valueCodeableConcept.coding.where(system='urn:oid:2.16.840.1.114222.4.5.274').code", "data_type": "string", diff --git a/containers/message-parser/app/default_schemas/philly_ecr.json b/containers/message-parser/app/default_schemas/philly_ecr.json index d6e58877c3..2f44be8413 100644 --- a/containers/message-parser/app/default_schemas/philly_ecr.json +++ b/containers/message-parser/app/default_schemas/philly_ecr.json @@ -336,12 +336,12 @@ } }, "rr": { - "fhir_path": "Bundle.entry.resource.where(meta.profile = 'http://hl7.org/fhir/us/ecr/StructureDefinition/rr-reportability-information-observation')", + "fhir_path": "Bundle.entry.resource.where(resourceType='Observation').where(meta.profile = 'http://hl7.org/fhir/us/ecr/StructureDefinition/rr-reportability-information-observation')", "data_type": "array", "nullable": true, "secondary_schema": { "uuid": { - "fhir_path": "(meta.profile = 'http://hl7.org/fhir/us/ecr/StructureDefinition/rr-reportability-information-observation').id", + "fhir_path": "Observation.id", "data_type": "string", "nullable": true, "metadata": { @@ -349,7 +349,7 @@ } }, "condition": { - "fhir_path": "(meta.profile = 'http://hl7.org/fhir/us/ecr/StructureDefinition/rr-reportability-information-observation').valueCodeableConcept.coding.display", + "fhir_path": "Observation.valueCodeableConcept.coding.display", "data_type": "string", "nullable": true, "metadata": { @@ -357,7 +357,7 @@ } }, "rule_summaries": { - "fhir_path": "(meta.profile = 'http://hl7.org/fhir/us/ecr/StructureDefinition/rr-reportability-information-observation').extension.where(url = 'http://hl7.org/fhir/us/ecr/StructureDefinition/us-ph-determination-of-reportability-rule-extension').valueString", + "fhir_path": "Observation.extension.where(url = 'http://hl7.org/fhir/us/ecr/StructureDefinition/us-ph-determination-of-reportability-rule-extension').valueString", "data_type": "string", "nullable": true, "metadata": { From 50ec0df3d587a1caa78fd3ffdc779cf356c1310c Mon Sep 17 00:00:00 2001 From: Gordon Farrell Date: Thu, 31 Oct 2024 13:49:00 -0600 Subject: [PATCH 02/23] save loop for conditions and rule summaries working in postgres --- .../save-fhir-data/save-fhir-data-service.ts | 70 ++++++++++--------- .../src/app/api/save-fhir-data/types.ts | 1 + 2 files changed, 39 insertions(+), 32 deletions(-) diff --git a/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts b/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts index 715b8adb49..3921223956 100644 --- a/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts +++ b/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts @@ -435,43 +435,49 @@ export const saveMetadataToPostgres = async ( ) => { const { ParameterizedQuery: PQ } = pgPromise; - if (process.env.METADATA_DATABASE_SCHEMA == "extended") { - return NextResponse.json( - { - message: - "Only the default metadata schema is implemented for Postgres.", - }, - { status: 501 }, - ); - } - const saveToEcrData = new PQ({ - text: "INSERT INTO ecr_data (eICR_ID,patient_name_last,patient_name_first,patient_birth_date,data_source,report_date) VALUES ($1, $2, $3, $4, $5, $6) RETURNING eICR_ID", - values: [ - ecrId, - metadata.last_name, - metadata.first_name, - metadata.birth_date, - "DB", - metadata.report_date, - ], - }); + try { + // Start transaction + const saveECR = await database.tx(async (t) => { + // Insert main ECR data + const saveToEcrData = new PQ({ + text: "INSERT INTO ecr_data (eICR_ID, patient_name_last, patient_name_first, patient_birth_date, data_source, report_date) VALUES ($1, $2, $3, $4, $5, $6) RETURNING eICR_ID", + values: [ + ecrId, + metadata.last_name, + metadata.first_name, + metadata.birth_date, + "DB", + metadata.report_date, + ], + }); - const saveRRConditions = new PQ({ - text: "INSERT INTO ecr_rr_conditions (uuid, eICR_ID, condition) VALUES (uuid_generate_v4(), $1, $2) RETURNING uuid", - values: [ecrId, metadata.reportable_condition], - }); + const ecrData = await t.one(saveToEcrData); - try { - const saveECR = await database.one(saveToEcrData); - const savedRRCondition = await database.one(saveRRConditions); + // Loop through each condition in rr array + if (metadata.rr && metadata.rr.length > 0) { + for (const rrItem of metadata.rr) { + // Insert into ecr_rr_conditions + const saveRRConditions = new PQ({ + text: "INSERT INTO ecr_rr_conditions (uuid, eICR_ID, condition) VALUES (uuid_generate_v4(), $1, $2) RETURNING uuid", + values: [ecrId, rrItem.condition], + }); - const saveRRSummary = new PQ({ - text: "INSERT INTO ecr_rr_rule_summaries (uuid, ecr_rr_conditions_id,rule_summary) VALUES (uuid_generate_v4(), $1, $2)", - values: [savedRRCondition.uuid, metadata.rule_summary], - }); + const savedRRCondition = await t.one(saveRRConditions); + + // Insert into ecr_rr_rule_summaries + const saveRRSummary = new PQ({ + text: "INSERT INTO ecr_rr_rule_summaries (uuid, ecr_rr_conditions_id, rule_summary) VALUES (uuid_generate_v4(), $1, $2)", + values: [savedRRCondition.uuid, rrItem.rule_summaries], + }); - await database.none(saveRRSummary); + await t.none(saveRRSummary); + } + + return ecrData; + } + }); + // On successful transaction, return response return NextResponse.json( { message: "Success. Saved metadata to database: " + saveECR.eICR_ID }, { status: 200 }, diff --git a/containers/ecr-viewer/src/app/api/save-fhir-data/types.ts b/containers/ecr-viewer/src/app/api/save-fhir-data/types.ts index 2f3b819aa7..cd7dab09d2 100644 --- a/containers/ecr-viewer/src/app/api/save-fhir-data/types.ts +++ b/containers/ecr-viewer/src/app/api/save-fhir-data/types.ts @@ -80,5 +80,6 @@ export interface BundleMetadata { data_source: string; reportable_condition: string; rule_summary: string; + rr: RR[] | undefined; report_date: string; } From d6930c990375fbfe7d36231c368e859b0c5f2fc5 Mon Sep 17 00:00:00 2001 From: Gordon Farrell Date: Thu, 31 Oct 2024 13:52:14 -0600 Subject: [PATCH 03/23] update comments --- .../src/app/api/save-fhir-data/save-fhir-data-service.ts | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts b/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts index 3921223956..1a2fc354bd 100644 --- a/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts +++ b/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts @@ -438,7 +438,7 @@ export const saveMetadataToPostgres = async ( try { // Start transaction const saveECR = await database.tx(async (t) => { - // Insert main ECR data + // Insert main ECR metadata const saveToEcrData = new PQ({ text: "INSERT INTO ecr_data (eICR_ID, patient_name_last, patient_name_first, patient_birth_date, data_source, report_date) VALUES ($1, $2, $3, $4, $5, $6) RETURNING eICR_ID", values: [ @@ -453,10 +453,10 @@ export const saveMetadataToPostgres = async ( const ecrData = await t.one(saveToEcrData); - // Loop through each condition in rr array + // Loop through each condition/rule object in rr array if (metadata.rr && metadata.rr.length > 0) { for (const rrItem of metadata.rr) { - // Insert into ecr_rr_conditions + // Insert condition into ecr_rr_conditions const saveRRConditions = new PQ({ text: "INSERT INTO ecr_rr_conditions (uuid, eICR_ID, condition) VALUES (uuid_generate_v4(), $1, $2) RETURNING uuid", values: [ecrId, rrItem.condition], @@ -464,7 +464,7 @@ export const saveMetadataToPostgres = async ( const savedRRCondition = await t.one(saveRRConditions); - // Insert into ecr_rr_rule_summaries + // Insert associated rule summary into ecr_rr_rule_summaries const saveRRSummary = new PQ({ text: "INSERT INTO ecr_rr_rule_summaries (uuid, ecr_rr_conditions_id, rule_summary) VALUES (uuid_generate_v4(), $1, $2)", values: [savedRRCondition.uuid, rrItem.rule_summaries], From ae7b6874f9c28516cf0691197f5df07f0ebecb2d Mon Sep 17 00:00:00 2001 From: Gordon Farrell Date: Tue, 5 Nov 2024 12:29:17 -0700 Subject: [PATCH 04/23] update listEcrDataService and tests to retrieve conditions and summaries as arrays --- .../app/api/services/listEcrDataService.ts | 15 +++--- .../app/api/tests/listEcrDataService.test.tsx | 46 +++++++++---------- 2 files changed, 31 insertions(+), 30 deletions(-) diff --git a/containers/ecr-viewer/src/app/api/services/listEcrDataService.ts b/containers/ecr-viewer/src/app/api/services/listEcrDataService.ts index 96fa94d14f..41b0f7ac95 100644 --- a/containers/ecr-viewer/src/app/api/services/listEcrDataService.ts +++ b/containers/ecr-viewer/src/app/api/services/listEcrDataService.ts @@ -12,8 +12,8 @@ export type EcrMetadataModel = { patient_name_first: string; patient_name_last: string; patient_birth_date: Date; - condition: string; - rule_summary: string; + conditions: []; + rule_summaries: []; report_date: Date; date_created: Date; }; @@ -23,8 +23,8 @@ export type EcrDisplay = { patient_first_name: string; patient_last_name: string; patient_date_of_birth: string | undefined; - reportable_condition: string; - rule_summary: string; + reportable_conditions: []; + rule_summaries: []; patient_report_date: string; date_created: string; }; @@ -41,8 +41,9 @@ export async function listEcrData( searchTerm?: string, ): Promise { let whereClause = generateSearchStatement(searchTerm); - const ecrDataQuery = `SELECT ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date, erc.condition, ers.rule_summary, ed.report_date FROM ecr_data ed LEFT JOIN ecr_rr_conditions erc ON ed.eICR_ID = erc.eICR_ID LEFT JOIN ecr_rr_rule_summaries ers ON erc.uuid = ers.ecr_rr_conditions_id ${whereClause}order by ed.report_date DESC OFFSET ${startIndex} ROWS FETCH NEXT ${itemsPerPage} ROWS ONLY`; + const ecrDataQuery = `SELECT ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date, ARRAY_AGG(DISTINCT erc.condition) AS conditions, ARRAY_AGG(DISTINCT ers.rule_summary) AS rule_summaries FROM ecr_data ed LEFT JOIN ecr_rr_conditions erc ON ed.eICR_ID = erc.eICR_ID LEFT JOIN ecr_rr_rule_summaries ers ON erc.uuid = ers.ecr_rr_conditions_id ${whereClause} GROUP BY ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date ORDER BY ed.report_date DESC OFFSET ${startIndex} ROWS FETCH NEXT ${itemsPerPage} ROWS ONLY;`; const list = await database.manyOrNone(ecrDataQuery); + return processMetadata(list); } @@ -62,8 +63,8 @@ export const processMetadata = ( patient_date_of_birth: object.patient_birth_date ? formatDate(new Date(object.patient_birth_date!).toISOString()) : "", - reportable_condition: object.condition || "", - rule_summary: object.rule_summary || "", + reportable_conditions: object.conditions || [], + rule_summaries: object.rule_summaries || [], date_created: object.date_created ? convertUTCToLocalString( formatDateTime(new Date(object.date_created!).toISOString()), diff --git a/containers/ecr-viewer/src/app/api/tests/listEcrDataService.test.tsx b/containers/ecr-viewer/src/app/api/tests/listEcrDataService.test.tsx index fea5568aee..b7e47e6232 100644 --- a/containers/ecr-viewer/src/app/api/tests/listEcrDataService.test.tsx +++ b/containers/ecr-viewer/src/app/api/tests/listEcrDataService.test.tsx @@ -26,8 +26,8 @@ describe("listEcrDataService", () => { patient_name_last: "Person", patient_birth_date: new Date(), report_date: new Date(), - condition: "Long", - rule_summary: "Longer", + conditions: ["Long"], + rule_summaries: ["Longer"], data_source: "DB", data: "", data_link: "", @@ -39,8 +39,8 @@ describe("listEcrDataService", () => { patient_name_last: "Test", patient_birth_date: new Date(), report_date: new Date(), - condition: "Stuff", - rule_summary: "Other stuff", + conditions: ["Stuff"], + rule_summaries: ["Other stuff", "Even more stuff"], data_source: "DB", data: "", data_link: "", @@ -60,11 +60,11 @@ describe("listEcrDataService", () => { patient_first_name: any; } | { - rule_summary: string; + rule_summaries: []; ecrId: string; patient_report_date: string; date_created: any; - reportable_condition: string; + reportable_conditions: []; patient_last_name: string; patient_date_of_birth: string; patient_first_name: string; @@ -77,8 +77,8 @@ describe("listEcrDataService", () => { patient_last_name: expect.any(String), patient_date_of_birth: expect.any(String), patient_report_date: expect.any(String), - reportable_condition: expect.any(String), - rule_summary: expect.any(String), + reportable_conditions: expect.any(Array), + rule_summaries: expect.any(Array), }, { ecrId: "ecr2", @@ -87,8 +87,8 @@ describe("listEcrDataService", () => { patient_last_name: expect.any(String), patient_date_of_birth: expect.any(String), patient_report_date: expect.any(String), - reportable_condition: expect.any(String), - rule_summary: expect.any(String), + reportable_conditions: expect.any(Array), + rule_summaries: expect.any(Array), }, ]; const result = processMetadata(responseBody); @@ -104,7 +104,7 @@ describe("listEcrDataService", () => { database.manyOrNone = jest.fn(() => Promise.resolve([])); const actual = await listEcrData(startIndex, itemsPerPage); expect(database.manyOrNone).toHaveBeenCalledExactlyOnceWith( - "SELECT ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date, erc.condition, ers.rule_summary, ed.report_date FROM ecr_data ed LEFT JOIN ecr_rr_conditions erc ON ed.eICR_ID = erc.eICR_ID LEFT JOIN ecr_rr_rule_summaries ers ON erc.uuid = ers.ecr_rr_conditions_id order by ed.report_date DESC OFFSET 0 ROWS FETCH NEXT 25 ROWS ONLY", + "SELECT ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date, ARRAY_AGG(DISTINCT erc.condition) AS conditions, ARRAY_AGG(DISTINCT ers.rule_summary) AS rule_summaries FROM ecr_data ed LEFT JOIN ecr_rr_conditions erc ON ed.eICR_ID = erc.eICR_ID LEFT JOIN ecr_rr_rule_summaries ers ON erc.uuid = ers.ecr_rr_conditions_id GROUP BY ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date ORDER BY ed.report_date DESC OFFSET 0 ROWS FETCH NEXT 25 ROWS ONLY;", ); expect(actual).toBeEmpty(); }); @@ -119,8 +119,8 @@ describe("listEcrDataService", () => { patient_name_first: "Billy", patient_name_last: "Bob", report_date: new Date("06/21/2024 8:00 AM EDT"), - condition: "stuff", - rule_summary: "yup", + conditions: ["super ebola", "double ebola"], + rule_summaries: ["watch out for super ebola"], data: "", data_link: "", data_source: "DB", @@ -133,7 +133,7 @@ describe("listEcrDataService", () => { const actual: EcrDisplay[] = await listEcrData(startIndex, itemsPerPage); expect(database.manyOrNone).toHaveBeenCalledExactlyOnceWith( - "SELECT ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date, erc.condition, ers.rule_summary, ed.report_date FROM ecr_data ed LEFT JOIN ecr_rr_conditions erc ON ed.eICR_ID = erc.eICR_ID LEFT JOIN ecr_rr_rule_summaries ers ON erc.uuid = ers.ecr_rr_conditions_id order by ed.report_date DESC OFFSET 0 ROWS FETCH NEXT 25 ROWS ONLY", + "SELECT ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date, ARRAY_AGG(DISTINCT erc.condition) AS conditions, ARRAY_AGG(DISTINCT ers.rule_summary) AS rule_summaries FROM ecr_data ed LEFT JOIN ecr_rr_conditions erc ON ed.eICR_ID = erc.eICR_ID LEFT JOIN ecr_rr_rule_summaries ers ON erc.uuid = ers.ecr_rr_conditions_id GROUP BY ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date ORDER BY ed.report_date DESC OFFSET 0 ROWS FETCH NEXT 25 ROWS ONLY;", ); expect(actual).toEqual([ { @@ -143,13 +143,13 @@ describe("listEcrDataService", () => { patient_first_name: "Billy", patient_last_name: "Bob", patient_report_date: "06/21/2024 8:00 AM EDT", - reportable_condition: "stuff", - rule_summary: "yup", + reportable_conditions: ["super ebola", "double ebola"], + rule_summaries: ["watch out for super ebola"], }, ]); }); - it("should get data from the fhir_metadata table", async () => { + it("should get data from the ecr_data, conditions, and rule summaries tables", async () => { database.manyOrNone<{ EcrMetadataModel }> = jest.fn(() => Promise.resolve([ { @@ -159,8 +159,8 @@ describe("listEcrDataService", () => { patient_name_last: "lnam", patient_birth_date: new Date("1990-01-01T05:00:00.000Z"), report_date: new Date("2024-06-20T04:00:00.000Z"), - condition: "sick", - rule_summary: "stuff", + conditions: ["sick", "tired"], + rule_summaries: ["stuff", "disease discovered"], data: "", data_link: "", data_source: "DB", @@ -172,7 +172,7 @@ describe("listEcrDataService", () => { let itemsPerPage = 25; const actual: EcrDisplay[] = await listEcrData(startIndex, itemsPerPage); expect(database.manyOrNone).toHaveBeenCalledExactlyOnceWith( - "SELECT ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date, erc.condition, ers.rule_summary, ed.report_date FROM ecr_data ed LEFT JOIN ecr_rr_conditions erc ON ed.eICR_ID = erc.eICR_ID LEFT JOIN ecr_rr_rule_summaries ers ON erc.uuid = ers.ecr_rr_conditions_id order by ed.report_date DESC OFFSET 0 ROWS FETCH NEXT 25 ROWS ONLY", + "SELECT ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date, ARRAY_AGG(DISTINCT erc.condition) AS conditions, ARRAY_AGG(DISTINCT ers.rule_summary) AS rule_summaries FROM ecr_data ed LEFT JOIN ecr_rr_conditions erc ON ed.eICR_ID = erc.eICR_ID LEFT JOIN ecr_rr_rule_summaries ers ON erc.uuid = ers.ecr_rr_conditions_id GROUP BY ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date ORDER BY ed.report_date DESC OFFSET 0 ROWS FETCH NEXT 25 ROWS ONLY;", ); expect(actual).toEqual([ { @@ -182,8 +182,8 @@ describe("listEcrDataService", () => { patient_first_name: "boy", patient_last_name: "lnam", patient_report_date: "06/20/2024 12:00 AM EDT", - reportable_condition: "sick", - rule_summary: "stuff", + reportable_conditions: ["sick", "tired"], + rule_summaries: ["stuff", "disease discovered"], }, ]); }); @@ -195,7 +195,7 @@ describe("listEcrDataService", () => { let searchTerm = "abc"; await listEcrData(startIndex, itemsPerPage, searchTerm); expect(database.manyOrNone).toHaveBeenCalledExactlyOnceWith( - "SELECT ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date, erc.condition, ers.rule_summary, ed.report_date FROM ecr_data ed LEFT JOIN ecr_rr_conditions erc ON ed.eICR_ID = erc.eICR_ID LEFT JOIN ecr_rr_rule_summaries ers ON erc.uuid = ers.ecr_rr_conditions_id WHERE ed.patient_name_first ILIKE '%abc%' OR ed.patient_name_last ILIKE '%abc%' order by ed.report_date DESC OFFSET 0 ROWS FETCH NEXT 25 ROWS ONLY", + "SELECT ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date, ARRAY_AGG(DISTINCT erc.condition) AS conditions, ARRAY_AGG(DISTINCT ers.rule_summary) AS rule_summaries FROM ecr_data ed LEFT JOIN ecr_rr_conditions erc ON ed.eICR_ID = erc.eICR_ID LEFT JOIN ecr_rr_rule_summaries ers ON erc.uuid = ers.ecr_rr_conditions_id WHERE ed.patient_name_first ILIKE '%abc%' OR ed.patient_name_last ILIKE '%abc%' GROUP BY ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date ORDER BY ed.report_date DESC OFFSET 0 ROWS FETCH NEXT 25 ROWS ONLY;", ); }); }); From 7ee88cda8a116db9809cd9e3b9f0e7091d081b36 Mon Sep 17 00:00:00 2001 From: Gordon Farrell Date: Tue, 5 Nov 2024 13:05:12 -0700 Subject: [PATCH 05/23] wip --- .../src/app/components/EcrTable.tsx | 41 ++++++++++++++----- 1 file changed, 31 insertions(+), 10 deletions(-) diff --git a/containers/ecr-viewer/src/app/components/EcrTable.tsx b/containers/ecr-viewer/src/app/components/EcrTable.tsx index 17c1834d9d..927d60e37d 100644 --- a/containers/ecr-viewer/src/app/components/EcrTable.tsx +++ b/containers/ecr-viewer/src/app/components/EcrTable.tsx @@ -76,6 +76,22 @@ const renderListEcrTableData = (listFhirData: EcrDisplay[]) => { }); }; +/** + * Concatenates an array of strings and adds a blank line between each (Used for conditions and rule summaries) + * @param stringArray - An array of strings to be concatenated + * @returns - The array items as a string separated by two newlines + */ +const concatenateAndAddNewlines = (stringArray: [string]) => { + let concatenatedString = ""; + + for (const item in stringArray) { + concatenatedString += stringArray[item]; + concatenatedString += "\n\n\n\n"; + } + + return concatenatedString; +}; + /** * Formats a single row of the eCR table. * @param item - The eCR data to be formatted. @@ -83,14 +99,19 @@ const renderListEcrTableData = (listFhirData: EcrDisplay[]) => { * @returns A JSX table row element representing the eCR data. */ const formatRow = (item: EcrDisplay, index: number) => { - let patient_first_name = toSentenceCase(item.patient_first_name); - let patient_last_name = toSentenceCase(item.patient_last_name); - let createDateObj = new Date(item.date_created); - let createDateDate = formatDate(createDateObj); - let createDateTime = formatTime(createDateObj); - let patientReportDateObj = new Date(item.patient_report_date); - let patientReportDate = formatDate(patientReportDateObj); - let patientReportTime = formatTime(patientReportDateObj); + const patient_first_name = toSentenceCase(item.patient_first_name); + const patient_last_name = toSentenceCase(item.patient_last_name); + const createDateObj = new Date(item.date_created); + const createDateDate = formatDate(createDateObj); + const createDateTime = formatTime(createDateObj); + const patientReportDateObj = new Date(item.patient_report_date); + const patientReportDate = formatDate(patientReportDateObj); + const patientReportTime = formatTime(patientReportDateObj); + + const conditionsString = concatenateAndAddNewlines( + item.reportable_conditions, + ); + const summariesString = concatenateAndAddNewlines(item.rule_summaries); return ( @@ -111,8 +132,8 @@ const formatRow = (item: EcrDisplay, index: number) => {
{patientReportTime} - {item.reportable_condition} - {item.rule_summary} + {conditionsString} + {summariesString} ); }; From c81b62ec3810d3c69ed10d0c1a6ecd0c024a92b8 Mon Sep 17 00:00:00 2001 From: Gordon Farrell Date: Wed, 6 Nov 2024 11:17:16 -0700 Subject: [PATCH 06/23] wip --- .../src/app/api/services/listEcrDataService.ts | 5 +++-- .../src/app/components/EcrTableClient.tsx | 18 ++++++++++++++++++ 2 files changed, 21 insertions(+), 2 deletions(-) diff --git a/containers/ecr-viewer/src/app/api/services/listEcrDataService.ts b/containers/ecr-viewer/src/app/api/services/listEcrDataService.ts index 23b4fde004..b1cc9e7ce6 100644 --- a/containers/ecr-viewer/src/app/api/services/listEcrDataService.ts +++ b/containers/ecr-viewer/src/app/api/services/listEcrDataService.ts @@ -46,7 +46,7 @@ export async function listEcrData( searchTerm?: string, ): Promise { const list = await database.manyOrNone( - "SELECT ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date, ed.report_date, ARRAY_AGG(DISTINCT erc.condition) AS conditions, ARRAY_AGG(DISTINCT ers.rule_summary) AS rule_summaries FROM ecr_data ed LEFT JOIN ecr_rr_conditions erc ON ed.eICR_ID = erc.eICR_ID LEFT JOIN ecr_rr_rule_summaries ers ON erc.uuid = ers.ecr_rr_conditions_id where $[whereClause] $[sortStatement] OFFSET $[startIndex] ROWS FETCH NEXT $[itemsPerPage] ROWS ONLY", + "SELECT ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date, ed.report_date, ARRAY_AGG(DISTINCT erc.condition) AS conditions, ARRAY_AGG(DISTINCT ers.rule_summary) AS rule_summaries FROM ecr_data ed LEFT JOIN ecr_rr_conditions erc ON ed.eICR_ID = erc.eICR_ID LEFT JOIN ecr_rr_rule_summaries ers ON erc.uuid = ers.ecr_rr_conditions_id where $[whereClause] GROUP BY ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date $[sortStatement] OFFSET $[startIndex] ROWS FETCH NEXT $[itemsPerPage] ROWS ONLY", { whereClause: generateSearchStatement(searchTerm), startIndex, @@ -54,6 +54,7 @@ export async function listEcrData( sortStatement: generateSortStatement(sortColumn, sortDirection), }, ); + return processMetadata(list); } @@ -106,7 +107,7 @@ export const getTotalEcrCount = async ( /** * A custom type format for search statement - * @param searchTerm - Optiaonl search term used to filter + * @param searchTerm - Optional search term used to filter * @returns custom type format object for use by pg-promise */ export const generateSearchStatement = (searchTerm?: string) => ({ diff --git a/containers/ecr-viewer/src/app/components/EcrTableClient.tsx b/containers/ecr-viewer/src/app/components/EcrTableClient.tsx index 88f4233e8a..113e609083 100644 --- a/containers/ecr-viewer/src/app/components/EcrTableClient.tsx +++ b/containers/ecr-viewer/src/app/components/EcrTableClient.tsx @@ -233,6 +233,8 @@ const getAriaSortValue = (sortDirection: string): AriaSortType => { * @returns An array of JSX table row elements representing the list of eCRs. */ const renderListEcrTableData = (listFhirData: EcrDisplay[]) => { + console.log("Whats coming down", listFhirData); + return listFhirData.map((item, index) => { return formatRow(item, index); }); @@ -305,3 +307,19 @@ const formatTime = (date: Date) => { return `${hours}:${minutesStr} ${ampm}`; }; + +/** + * Concatenates an array of strings and adds a blank line between each (Used for conditions and rule summaries) + * @param stringArray - An array of strings to be concatenated + * @returns - The array items as a string separated by two newlines + */ +const concatenateAndAddNewlines = (stringArray: [string]) => { + let concatenatedString = ""; + + for (const item in stringArray) { + concatenatedString += stringArray[item]; + concatenatedString += "\n\n\n\n"; + } + + return concatenatedString; +}; From 6810888fe3021c7bbaad887205c18cfdc7a53a04 Mon Sep 17 00:00:00 2001 From: Gordon Farrell Date: Thu, 7 Nov 2024 10:56:18 -0700 Subject: [PATCH 07/23] concatenate string arrays with newlines for ecr library display --- .../src/app/components/EcrTableClient.tsx | 30 +++++++++++-------- .../ecr-viewer/src/styles/custom-styles.scss | 4 +++ 2 files changed, 21 insertions(+), 13 deletions(-) diff --git a/containers/ecr-viewer/src/app/components/EcrTableClient.tsx b/containers/ecr-viewer/src/app/components/EcrTableClient.tsx index 113e609083..c08caee55e 100644 --- a/containers/ecr-viewer/src/app/components/EcrTableClient.tsx +++ b/containers/ecr-viewer/src/app/components/EcrTableClient.tsx @@ -233,8 +233,6 @@ const getAriaSortValue = (sortDirection: string): AriaSortType => { * @returns An array of JSX table row elements representing the list of eCRs. */ const renderListEcrTableData = (listFhirData: EcrDisplay[]) => { - console.log("Whats coming down", listFhirData); - return listFhirData.map((item, index) => { return formatRow(item, index); }); @@ -247,14 +245,19 @@ const renderListEcrTableData = (listFhirData: EcrDisplay[]) => { * @returns A JSX table row element representing the eCR data. */ const formatRow = (item: EcrDisplay, index: number) => { - let patient_first_name = toSentenceCase(item.patient_first_name); - let patient_last_name = toSentenceCase(item.patient_last_name); - let createDateObj = new Date(item.date_created); - let createDateDate = formatDate(createDateObj); - let createDateTime = formatTime(createDateObj); - let patientReportDateObj = new Date(item.patient_report_date); - let patientReportDate = formatDate(patientReportDateObj); - let patientReportTime = formatTime(patientReportDateObj); + const patient_first_name = toSentenceCase(item.patient_first_name); + const patient_last_name = toSentenceCase(item.patient_last_name); + const createDateObj = new Date(item.date_created); + const createDateDate = formatDate(createDateObj); + const createDateTime = formatTime(createDateObj); + const patientReportDateObj = new Date(item.patient_report_date); + const patientReportDate = formatDate(patientReportDateObj); + const patientReportTime = formatTime(patientReportDateObj); + + const conditionsString = concatenateAndAddNewlines( + item.reportable_conditions, + ); + const ruleSummariesString = concatenateAndAddNewlines(item.rule_summaries); return ( @@ -275,8 +278,8 @@ const formatRow = (item: EcrDisplay, index: number) => {
{patientReportTime} - {item.reportable_condition} - {item.rule_summary} + {conditionsString} + {ruleSummariesString} ); }; @@ -318,7 +321,8 @@ const concatenateAndAddNewlines = (stringArray: [string]) => { for (const item in stringArray) { concatenatedString += stringArray[item]; - concatenatedString += "\n\n\n\n"; + + if (item < stringArray.length - 1) concatenatedString += "\n\n"; } return concatenatedString; diff --git a/containers/ecr-viewer/src/styles/custom-styles.scss b/containers/ecr-viewer/src/styles/custom-styles.scss index 86c19b8f8c..ceb8b0e16b 100644 --- a/containers/ecr-viewer/src/styles/custom-styles.scss +++ b/containers/ecr-viewer/src/styles/custom-styles.scss @@ -7,6 +7,10 @@ $nav-wrapper-width: 15.625rem; $main-container-padding: 1rem; $main-min-width: $ecr-viewer-container-min-width + $ecr-viewer-gap + $nav-wrapper-width + $main-container-padding * 2; +.allow-newline{ + white-space: break-spaces; +} + .library-patient-column{ min-width: 16.3rem; width: 18%; From e1fee1570e54522b9d788411a2805130d4e3ab15 Mon Sep 17 00:00:00 2001 From: Gordon Farrell Date: Thu, 7 Nov 2024 10:58:35 -0700 Subject: [PATCH 08/23] update snapshot test --- .../__snapshots__/EcrTable.test.tsx.snap | 300 +++++++++--------- 1 file changed, 150 insertions(+), 150 deletions(-) diff --git a/containers/ecr-viewer/src/app/tests/components/__snapshots__/EcrTable.test.tsx.snap b/containers/ecr-viewer/src/app/tests/components/__snapshots__/EcrTable.test.tsx.snap index d1c47ed597..84f3ed45af 100644 --- a/containers/ecr-viewer/src/app/tests/components/__snapshots__/EcrTable.test.tsx.snap +++ b/containers/ecr-viewer/src/app/tests/components/__snapshots__/EcrTable.test.tsx.snap @@ -126,12 +126,12 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - reportable-condition-1 - - - rule-summary-1 - + + @@ -157,12 +157,12 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - reportable-condition-2 - - - rule-summary-2 - + + @@ -188,12 +188,12 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - reportable-condition-3 - - - rule-summary-3 - + + @@ -219,12 +219,12 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - reportable-condition-4 - - - rule-summary-4 - + + @@ -250,12 +250,12 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - reportable-condition-5 - - - rule-summary-5 - + + @@ -281,12 +281,12 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - reportable-condition-6 - - - rule-summary-6 - + + @@ -312,12 +312,12 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - reportable-condition-7 - - - rule-summary-7 - + + @@ -343,12 +343,12 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - reportable-condition-8 - - - rule-summary-8 - + + @@ -374,12 +374,12 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - reportable-condition-9 - - - rule-summary-9 - + + @@ -405,12 +405,12 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - reportable-condition-10 - - - rule-summary-10 - + + @@ -436,12 +436,12 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - reportable-condition-11 - - - rule-summary-11 - + + @@ -467,12 +467,12 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - reportable-condition-12 - - - rule-summary-12 - + + @@ -498,12 +498,12 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - reportable-condition-13 - - - rule-summary-13 - + + @@ -529,12 +529,12 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - reportable-condition-14 - - - rule-summary-14 - + + @@ -560,12 +560,12 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - reportable-condition-15 - - - rule-summary-15 - + + @@ -591,12 +591,12 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - reportable-condition-16 - - - rule-summary-16 - + + @@ -622,12 +622,12 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - reportable-condition-17 - - - rule-summary-17 - + + @@ -653,12 +653,12 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - reportable-condition-18 - - - rule-summary-18 - + + @@ -684,12 +684,12 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - reportable-condition-19 - - - rule-summary-19 - + + @@ -715,12 +715,12 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - reportable-condition-20 - - - rule-summary-20 - + + @@ -746,12 +746,12 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - reportable-condition-21 - - - rule-summary-21 - + + @@ -777,12 +777,12 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - reportable-condition-22 - - - rule-summary-22 - + + @@ -808,12 +808,12 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - reportable-condition-23 - - - rule-summary-23 - + + @@ -839,12 +839,12 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - reportable-condition-24 - - - rule-summary-24 - + + @@ -870,12 +870,12 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - reportable-condition-25 - - - rule-summary-25 - + + From b8174bb5a8e1cafb26fef891030eb264779b1d49 Mon Sep 17 00:00:00 2001 From: Gordon Farrell Date: Thu, 7 Nov 2024 13:12:49 -0700 Subject: [PATCH 09/23] update tests with new qeury --- .../src/app/api/tests/listEcrDataService.test.tsx | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/containers/ecr-viewer/src/app/api/tests/listEcrDataService.test.tsx b/containers/ecr-viewer/src/app/api/tests/listEcrDataService.test.tsx index 9d91d4ab5d..67f2c0cc55 100644 --- a/containers/ecr-viewer/src/app/api/tests/listEcrDataService.test.tsx +++ b/containers/ecr-viewer/src/app/api/tests/listEcrDataService.test.tsx @@ -113,7 +113,7 @@ describe("listEcrDataService", () => { ); expect(database.manyOrNone).toHaveBeenCalledOnce(); expect(database.manyOrNone).toHaveBeenCalledWith( - "SELECT ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date, erc.condition, ers.rule_summary, ed.report_date FROM ecr_data ed LEFT JOIN ecr_rr_conditions erc ON ed.eICR_ID = erc.eICR_ID LEFT JOIN ecr_rr_rule_summaries ers ON erc.uuid = ers.ecr_rr_conditions_id where $[whereClause] $[sortStatement] OFFSET $[startIndex] ROWS FETCH NEXT $[itemsPerPage] ROWS ONLY", + "SELECT ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date, ed.report_date, ARRAY_AGG(DISTINCT erc.condition) AS conditions, ARRAY_AGG(DISTINCT ers.rule_summary) AS rule_summaries FROM ecr_data ed LEFT JOIN ecr_rr_conditions erc ON ed.eICR_ID = erc.eICR_ID LEFT JOIN ecr_rr_rule_summaries ers ON erc.uuid = ers.ecr_rr_conditions_id where $[whereClause] GROUP BY ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date $[sortStatement] OFFSET $[startIndex] ROWS FETCH NEXT $[itemsPerPage] ROWS ONLY", { whereClause: expect.any(Object), startIndex, @@ -156,7 +156,7 @@ describe("listEcrDataService", () => { expect(database.manyOrNone).toHaveBeenCalledOnce(); expect(database.manyOrNone).toHaveBeenCalledWith( - "SELECT ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date, erc.condition, ers.rule_summary, ed.report_date FROM ecr_data ed LEFT JOIN ecr_rr_conditions erc ON ed.eICR_ID = erc.eICR_ID LEFT JOIN ecr_rr_rule_summaries ers ON erc.uuid = ers.ecr_rr_conditions_id where $[whereClause] $[sortStatement] OFFSET $[startIndex] ROWS FETCH NEXT $[itemsPerPage] ROWS ONLY", + "SELECT ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date, ed.report_date, ARRAY_AGG(DISTINCT erc.condition) AS conditions, ARRAY_AGG(DISTINCT ers.rule_summary) AS rule_summaries FROM ecr_data ed LEFT JOIN ecr_rr_conditions erc ON ed.eICR_ID = erc.eICR_ID LEFT JOIN ecr_rr_rule_summaries ers ON erc.uuid = ers.ecr_rr_conditions_id where $[whereClause] GROUP BY ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date $[sortStatement] OFFSET $[startIndex] ROWS FETCH NEXT $[itemsPerPage] ROWS ONLY", { whereClause: expect.any(Object), startIndex, @@ -209,7 +209,7 @@ describe("listEcrDataService", () => { ); expect(database.manyOrNone).toHaveBeenCalledOnce(); expect(database.manyOrNone).toHaveBeenCalledWith( - "SELECT ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date, erc.condition, ers.rule_summary, ed.report_date FROM ecr_data ed LEFT JOIN ecr_rr_conditions erc ON ed.eICR_ID = erc.eICR_ID LEFT JOIN ecr_rr_rule_summaries ers ON erc.uuid = ers.ecr_rr_conditions_id where $[whereClause] $[sortStatement] OFFSET $[startIndex] ROWS FETCH NEXT $[itemsPerPage] ROWS ONLY", + "SELECT ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date, ed.report_date, ARRAY_AGG(DISTINCT erc.condition) AS conditions, ARRAY_AGG(DISTINCT ers.rule_summary) AS rule_summaries FROM ecr_data ed LEFT JOIN ecr_rr_conditions erc ON ed.eICR_ID = erc.eICR_ID LEFT JOIN ecr_rr_rule_summaries ers ON erc.uuid = ers.ecr_rr_conditions_id where $[whereClause] GROUP BY ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date $[sortStatement] OFFSET $[startIndex] ROWS FETCH NEXT $[itemsPerPage] ROWS ONLY", { whereClause: expect.any(Object), startIndex, @@ -247,7 +247,7 @@ describe("listEcrDataService", () => { ); expect(database.manyOrNone).toHaveBeenCalledOnce(); expect(database.manyOrNone).toHaveBeenCalledWith( - "SELECT ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date, erc.condition, ers.rule_summary, ed.report_date FROM ecr_data ed LEFT JOIN ecr_rr_conditions erc ON ed.eICR_ID = erc.eICR_ID LEFT JOIN ecr_rr_rule_summaries ers ON erc.uuid = ers.ecr_rr_conditions_id where $[whereClause] $[sortStatement] OFFSET $[startIndex] ROWS FETCH NEXT $[itemsPerPage] ROWS ONLY", + "SELECT ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date, ed.report_date, ARRAY_AGG(DISTINCT erc.condition) AS conditions, ARRAY_AGG(DISTINCT ers.rule_summary) AS rule_summaries FROM ecr_data ed LEFT JOIN ecr_rr_conditions erc ON ed.eICR_ID = erc.eICR_ID LEFT JOIN ecr_rr_rule_summaries ers ON erc.uuid = ers.ecr_rr_conditions_id where $[whereClause] GROUP BY ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date $[sortStatement] OFFSET $[startIndex] ROWS FETCH NEXT $[itemsPerPage] ROWS ONLY", { whereClause: expect.any(Object), startIndex, @@ -273,7 +273,7 @@ describe("listEcrDataService", () => { ); expect(database.manyOrNone).toHaveBeenCalledOnce(); expect(database.manyOrNone).toHaveBeenCalledWith( - "SELECT ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date, erc.condition, ers.rule_summary, ed.report_date FROM ecr_data ed LEFT JOIN ecr_rr_conditions erc ON ed.eICR_ID = erc.eICR_ID LEFT JOIN ecr_rr_rule_summaries ers ON erc.uuid = ers.ecr_rr_conditions_id where $[whereClause] $[sortStatement] OFFSET $[startIndex] ROWS FETCH NEXT $[itemsPerPage] ROWS ONLY", + "SELECT ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date, ed.report_date, ARRAY_AGG(DISTINCT erc.condition) AS conditions, ARRAY_AGG(DISTINCT ers.rule_summary) AS rule_summaries FROM ecr_data ed LEFT JOIN ecr_rr_conditions erc ON ed.eICR_ID = erc.eICR_ID LEFT JOIN ecr_rr_rule_summaries ers ON erc.uuid = ers.ecr_rr_conditions_id where $[whereClause] GROUP BY ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date $[sortStatement] OFFSET $[startIndex] ROWS FETCH NEXT $[itemsPerPage] ROWS ONLY", { whereClause: expect.any(Object), startIndex, From 682350d21fc5c47c3f4d1a78ceeea74c4910e7a2 Mon Sep 17 00:00:00 2001 From: Gordon Farrell Date: Thu, 7 Nov 2024 13:18:09 -0700 Subject: [PATCH 10/23] remove extra fields from BundleMetadata type --- containers/ecr-viewer/src/app/api/save-fhir-data/types.ts | 2 -- 1 file changed, 2 deletions(-) diff --git a/containers/ecr-viewer/src/app/api/save-fhir-data/types.ts b/containers/ecr-viewer/src/app/api/save-fhir-data/types.ts index cd7dab09d2..83701cad8e 100644 --- a/containers/ecr-viewer/src/app/api/save-fhir-data/types.ts +++ b/containers/ecr-viewer/src/app/api/save-fhir-data/types.ts @@ -78,8 +78,6 @@ export interface BundleMetadata { first_name: string; birth_date: string; data_source: string; - reportable_condition: string; - rule_summary: string; rr: RR[] | undefined; report_date: string; } From 822b38795f9d39c32883b6b7a2e841932337191d Mon Sep 17 00:00:00 2001 From: Gordon Farrell Date: Thu, 7 Nov 2024 13:43:17 -0700 Subject: [PATCH 11/23] change parameter type --- containers/ecr-viewer/src/app/components/EcrTableClient.tsx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/containers/ecr-viewer/src/app/components/EcrTableClient.tsx b/containers/ecr-viewer/src/app/components/EcrTableClient.tsx index c08caee55e..fb548af1ba 100644 --- a/containers/ecr-viewer/src/app/components/EcrTableClient.tsx +++ b/containers/ecr-viewer/src/app/components/EcrTableClient.tsx @@ -316,7 +316,7 @@ const formatTime = (date: Date) => { * @param stringArray - An array of strings to be concatenated * @returns - The array items as a string separated by two newlines */ -const concatenateAndAddNewlines = (stringArray: [string]) => { +const concatenateAndAddNewlines = (stringArray: []) => { let concatenatedString = ""; for (const item in stringArray) { From 2112db381ece777cbb4c462fd7bd23f2d1a703d2 Mon Sep 17 00:00:00 2001 From: Gordon Farrell Date: Thu, 7 Nov 2024 13:56:43 -0700 Subject: [PATCH 12/23] play with typing to make turbo build happy --- containers/ecr-viewer/src/app/components/EcrTableClient.tsx | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/containers/ecr-viewer/src/app/components/EcrTableClient.tsx b/containers/ecr-viewer/src/app/components/EcrTableClient.tsx index fb548af1ba..35e510795b 100644 --- a/containers/ecr-viewer/src/app/components/EcrTableClient.tsx +++ b/containers/ecr-viewer/src/app/components/EcrTableClient.tsx @@ -320,7 +320,8 @@ const concatenateAndAddNewlines = (stringArray: []) => { let concatenatedString = ""; for (const item in stringArray) { - concatenatedString += stringArray[item]; + console.log("Item: ", item); + concatenatedString += stringArray[item as number]; if (item < stringArray.length - 1) concatenatedString += "\n\n"; } From c5ccec042d346a837ecc0249d86ff92b19af76ea Mon Sep 17 00:00:00 2001 From: Gordon Farrell Date: Thu, 7 Nov 2024 13:58:11 -0700 Subject: [PATCH 13/23] play with typing to make turbo build happy --- containers/ecr-viewer/src/app/components/EcrTableClient.tsx | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/containers/ecr-viewer/src/app/components/EcrTableClient.tsx b/containers/ecr-viewer/src/app/components/EcrTableClient.tsx index 35e510795b..506c495885 100644 --- a/containers/ecr-viewer/src/app/components/EcrTableClient.tsx +++ b/containers/ecr-viewer/src/app/components/EcrTableClient.tsx @@ -320,10 +320,10 @@ const concatenateAndAddNewlines = (stringArray: []) => { let concatenatedString = ""; for (const item in stringArray) { - console.log("Item: ", item); - concatenatedString += stringArray[item as number]; + const itemAsNumber = item as number; + concatenatedString += stringArray[itemAsNumber]; - if (item < stringArray.length - 1) concatenatedString += "\n\n"; + if (itemAsNumber < stringArray.length - 1) concatenatedString += "\n\n"; } return concatenatedString; From 1d213e2e7b57b1eed04897c7c88dfcdc724e03fa Mon Sep 17 00:00:00 2001 From: Gordon Farrell Date: Thu, 7 Nov 2024 14:06:40 -0700 Subject: [PATCH 14/23] play with typing to make turbo build happy --- containers/ecr-viewer/src/app/components/EcrTableClient.tsx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/containers/ecr-viewer/src/app/components/EcrTableClient.tsx b/containers/ecr-viewer/src/app/components/EcrTableClient.tsx index 506c495885..968d94356f 100644 --- a/containers/ecr-viewer/src/app/components/EcrTableClient.tsx +++ b/containers/ecr-viewer/src/app/components/EcrTableClient.tsx @@ -320,7 +320,7 @@ const concatenateAndAddNewlines = (stringArray: []) => { let concatenatedString = ""; for (const item in stringArray) { - const itemAsNumber = item as number; + const itemAsNumber = Number(item); concatenatedString += stringArray[itemAsNumber]; if (itemAsNumber < stringArray.length - 1) concatenatedString += "\n\n"; From 0f5439d0809afa65baaf00989e5167cfd8446ca3 Mon Sep 17 00:00:00 2001 From: Gordon Farrell Date: Tue, 12 Nov 2024 09:57:58 -0700 Subject: [PATCH 15/23] fix scoping issue with variable --- containers/ecr-viewer/cypress/assets/data.sql | 18 +----------------- .../save-fhir-data/save-fhir-data-service.ts | 2 +- 2 files changed, 2 insertions(+), 18 deletions(-) diff --git a/containers/ecr-viewer/cypress/assets/data.sql b/containers/ecr-viewer/cypress/assets/data.sql index f57481a23d..830e74d76c 100644 --- a/containers/ecr-viewer/cypress/assets/data.sql +++ b/containers/ecr-viewer/cypress/assets/data.sql @@ -1,17 +1 @@ -INSERT INTO fhir (ecr_id, data) VALUES ('1.2.840.114350.1.13.478.3.7.8.688883.230886', '{"resourceType": "Bundle", "type": "batch", "entry": [{"fullUrl": "urn:uuid:1.2.840.114350.1.13.478.3.7.8.688883.230886", "resource": {"resourceType": "Composition", "id": "1.2.840.114350.1.13.478.3.7.8.688883.230886", "meta": {"profile": ["http://hl7.org/fhir/us/ecr/StructureDefinition/eicr-composition"], "source": "ecr"}, "identifier": [{"use": "official", "type": {"coding": [{"code": "55751-2", "display": "Initial Public Health Case Report", "system": "http://loinc.org"}]}, "value": "59086a94-a174-11ec-a982-0050561597b4", "assigner": {"display": "EPC"}}], "extension": [{"url": "http://hl7.org/fhir/StructureDefinition/composition-clinicaldocument-versionNumber", "valueString": "2"}, {"url": "https://www.hl7.org/implement/standards/product_brief.cfm?product_id=436", "valueString": "2016-12-01"}], "status": "final", "type": {"coding": [{"code": "55751-2", "display": "Initial Public Health Case Report", "system": "http://loinc.org"}]}, "date": "2022-07-28T09:01:22-05:00", "title": "Initial Public Health Case Report", "confidentiality": "N", "section": [{"id": "b7a7ed08-af88-4a31-cc4e-8dddd58b7fc8", "title": "Miscellaneous Notes", "text": {"status": "generated", "div": "Not on file documented in this encounter"}, "code": {"coding": [{"code": "10164-2", "display": "HISTORY OF PRESENT ILLNESS", "system": "http://loinc.org"}]}, "mode": "snapshot"}, {"id": "C353C60C-0E7D-11ED-B8BA-0050561597B4", "title": "Immunizations", "text": {"status": "generated", "div": "
NameAdministration DatesNext Due
DTaP, 5 pertussis antigens vaccine (DAPTACEL)06/15/2021
Hep B, adult vaccine (Engerix/Recombivax)09/08/2020
SARS-COV-2 (COVID-19) Spikevax Vaccine, Moderna01/22/2021
documented as of this encounter"}, "code": {"coding": [{"code": "11369-6", "display": "History of Immunization Narrative", "system": "http://loinc.org"}]}, "mode": "snapshot"}, {"id": "C35D1446-0E7D-11ED-B8BA-0050561597B4", "title": "Administered Medications", "text": {"status": "generated", "div": "Not on file documented in this encounter"}, "code": {"coding": [{"code": "29549-3", "display": "MEDICATIONS ADMINISTERED", "system": "http://loinc.org"}]}, "mode": "snapshot"}, {"id": "60fcb933-b9b4-9c30-95c7-0f5959ed7d19", "title": "Plan of Treatment", "text": {"status": "generated", "div": "
Pending Results
NameTypePriorityAssociated DiagnosesDate/Time
PCR SARS-CoV-2 and Influenza A/BLabRoutine07/27/2022 3:49 PM CDT
PCR SARS-CoV-2 and Influenza A/BLabRoutine07/27/2022 3:49 PM CDT
PCR SARS-CoV-2 and Influenza A/BLabRoutine07/27/2022 3:49 PM CDT
PCR SARS-CoV-2 and Influenza A/BLabRoutine07/27/2022 3:49 PM CDT
PCR SARS-CoV-2 and Influenza A/BLabRoutine07/27/2022 3:49 PM CDT
Scheduled Orders
NameTypePriorityAssociated DiagnosesOrder Schedule
PCR Hepatitis C Virus QtLabRoutineOrdered: 5/12/22
documented as of this encounter"}, "code": {"coding": [{"code": "18776-5", "display": "Plan of care note", "system": "http://loinc.org"}]}, "mode": "snapshot", "entry": [{"reference": "CarePlan/af1c1713-7fbd-ea81-9302-95cc4b8538e0"}]}, {"id": "C3659A58-0E7D-11ED-B8BA-0050561597B4", "title": "Problems", "text": {"status": "generated", "div": "
Active ProblemsNoted Date
COVID toes7/13/22
Chest pain on breathing5/26/22
Type 1 diabetes2/28/22
Overview:Formatting of this note might be different from the original.
08/30/21 28.69 kg/m\u00b2BMI Readings from Last 1 Encounters:
Plague pneumonia6/16/21
Absence of menstruation6/12/18
Foot callus8/11/17
Overview:Formatting of this note might be different from the original.
Ouch.
documented as of this encounter (statuses as of 07/28/2022)"}, "code": {"coding": [{"code": "11450-4", "display": "Problem list - Reported", "system": "http://loinc.org"}]}, "mode": "snapshot", "entry": [{"display": "Problem - Foot callus", "reference": "Condition/b3261c72-c3b2-1090-e228-e4b29bafe642"}, {"display": "Problem - Absence of menstruation", "reference": "Condition/d091a7b5-acc3-3900-cd65-6a6893c7a421"}, {"display": "Problem - Plague pneumonia", "reference": "Condition/94a7a6cb-50bc-54fd-2be2-b2f1be515676"}, {"display": "Problem - Type 1 diabetes", "reference": "Condition/02e5d344-16d4-3bb4-6a4d-05ed5d68c5db"}, {"display": "Problem - Chest pain on breathing", "reference": "Condition/3bcdaef9-d201-2f29-cd86-88f93479710f"}, {"display": "Problem - COVID toes", "reference": "Condition/38e833d1-1001-9e83-4167-2684381498ac"}]}, {"id": "76c78cbd-1c55-fd84-d8df-54e0750d9eab", "title": "Reason for Visit", "text": {"status": "generated", "div": "Not on file"}, "code": {"coding": [{"code": "29299-5", "display": "REASON FOR VISIT", "system": "http://loinc.org"}]}, "mode": "snapshot", "extension": [{"url": "http://hl7.org/fhir/cda/ccda/StructureDefinition/2.16.840.1.113883.10.20.22.2.12", "valueString": "Not on file"}]}, {"id": "C38436E8-0E7D-11ED-B8BA-0050561597B4", "title": "Results", "text": {"status": "generated", "div": "
  • (ABNORMAL) SARS-CoV-2 PCR (07/27/2022 3:49 PM CDT)
    ComponentValueRef RangeTest MethodAnalysis TimePerformed AtPathologist Signature
    SARS-CoV-2 Nucleic Acid (Result)Detected (A)Not DetectedVUMC CERNER LAB
    Comment:
    This test was performed using a multiplexed nucleic acid amplification test that is labeled Emergence Use Only by the U.S. FDA. Results of this test should not be used as the sole basis for diagnosis, treatment, or other management decisions.A detected result is positive and indicates the presence of the virus in the sample. A not detected result indicates that the test did not detect the virus in the sample.
    SARS-CoV-2 Nucleic Acid Method (Comment)
    This test was performed using the Roche 6800 COVID-19 test. This test is currently approved for clinical diagnostic testing under Emergency Use Authorization of the FDA; the result should not be considered experimental or for research purposes.Other    		VUMC CERNER LAB
    Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
    Other07/27/2022 3:49 PM CDT07/27/2022 3:58 PM CDT
    Resulting Agency Comment
    Ordered by Romney H Humphries
    Authorizing ProviderResult Type
    No PcpLAB BODY FLUIDS AND STOOLS ORDERABLES
    Performing OrganizationAddressCity/State/ZIP CodePhone Number
    VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
  • (ABNORMAL) SARS-CoV-2 PCR (07/27/2022 3:49 PM CDT)
    ComponentValueRef RangeTest MethodAnalysis TimePerformed AtPathologist Signature
    SARS-CoV-2 Nucleic Acid (Result)Detected (A)Not DetectedVUMC CERNER LAB
    Comment:
    This test was performed using a multiplexed nucleic acid amplification test that is labeled Emergence Use Only by the U.S. FDA. Results of this test should not be used as the sole basis for diagnosis, treatment, or other management decisions.A detected result is positive and indicates the presence of the virus in the sample. A not detected result indicates that the test did not detect the virus in the sample.
    SARS-CoV-2 Nucleic Acid Method (Comment)
    This test was performed using the Roche 6800 COVID-19 test. This test is currently approved for clinical diagnostic testing under Emergency Use Authorization of the FDA; the result should not be considered experimental or for research purposes.Oropharynx    		VUMC CERNER LAB
    Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
    Oropharynx07/27/2022 3:49 PM CDT07/27/2022 3:58 PM CDT
    Resulting Agency Comment
    Ordered by Romney H Humphries
    Authorizing ProviderResult Type
    No PcpLAB BODY FLUIDS AND STOOLS ORDERABLES
    Performing OrganizationAddressCity/State/ZIP CodePhone Number
    VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
  • SARS-CoV-2 PCR (07/27/2022 3:49 PM CDT)
    ComponentValueRef RangeTest MethodAnalysis TimePerformed AtPathologist Signature
    SARS-CoV-2 Nucleic Acid (Result)Not DetectedNot DetectedVUMC CERNER LAB
    Comment:
    This test was performed using a multiplexed nucleic acid amplification test that is labeled Emergence Use Only by the U.S. FDA. Results of this test should not be used as the sole basis for diagnosis, treatment, or other management decisions.A detected result is positive and indicates the presence of the virus in the sample. A not detected result indicates that the test did not detect the virus in the sample.
    SARS-CoV-2 Nucleic Acid Method (Comment)
    This test was performed using the Roche 6800 COVID-19 test. This test is currently approved for clinical diagnostic testing under Emergency Use Authorization of the FDA; the result should not be considered experimental or for research purposes.Nasopharynx    		VUMC CERNER LAB
    Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
    Nasopharynx07/27/2022 3:49 PM CDT07/27/2022 3:58 PM CDT
    Resulting Agency Comment
    Ordered by Romney H Humphries
    Authorizing ProviderResult Type
    No PcpLAB BODY FLUIDS AND STOOLS ORDERABLES
    Performing OrganizationAddressCity/State/ZIP CodePhone Number
    VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
  • SARS-CoV-2 PCR (07/27/2022 3:49 PM CDT)
    ComponentValueRef RangeTest MethodAnalysis TimePerformed AtPathologist Signature
    SARS-CoV-2 Nucleic Acid (Result)Not DetectedNot DetectedVUMC CERNER LAB
    Comment:
    This test was performed using a multiplexed nucleic acid amplification test that is labeled Emergence Use Only by the U.S. FDA. Results of this test should not be used as the sole basis for diagnosis, treatment, or other management decisions.A detected result is positive and indicates the presence of the virus in the sample. A not detected result indicates that the test did not detect the virus in the sample.
    SARS-CoV-2 Nucleic Acid Method (Comment)
    This test was performed using the Roche 6800 COVID-19 test. This test is currently approved for clinical diagnostic testing under Emergency Use Authorization of the FDA; the result should not be considered experimental or for research purposes.Nares    		VUMC CERNER LAB
    Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
    Nares07/27/2022 3:49 PM CDT07/27/2022 3:58 PM CDT
    Resulting Agency Comment
    Ordered by Romney H Humphries
    Authorizing ProviderResult Type
    No PcpLAB BODY FLUIDS AND STOOLS ORDERABLES
    Performing OrganizationAddressCity/State/ZIP CodePhone Number
    VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
  • SARS-CoV-2 PCR (07/27/2022 3:49 PM CDT)
    ComponentValueRef RangeTest MethodAnalysis TimePerformed AtPathologist Signature
    SARS-CoV-2 Nucleic Acid (Result)Not DetectedNot DetectedVUMC CERNER LAB
    Comment:
    This test was performed using a multiplexed nucleic acid amplification test that is labeled Emergence Use Only by the U.S. FDA. Results of this test should not be used as the sole basis for diagnosis, treatment, or other management decisions.A detected result is positive and indicates the presence of the virus in the sample. A not detected result indicates that the test did not detect the virus in the sample.
    SARS-CoV-2 Nucleic Acid Method (Comment)
    This test was performed using the Roche 6800 COVID-19 test. This test is currently approved for clinical diagnostic testing under Emergency Use Authorization of the FDA; the result should not be considered experimental or for research purposes.BAL    		VUMC CERNER LAB
    Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
    BAL07/27/2022 3:49 PM CDT07/27/2022 3:58 PM CDT
    Resulting Agency Comment
    Ordered by Romney H Humphries
    Authorizing ProviderResult Type
    No PcpLAB BODY FLUIDS AND STOOLS ORDERABLES
    Performing OrganizationAddressCity/State/ZIP CodePhone Number
    VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
  • (ABNORMAL) Hepatitis C IgG w/Rfx PCR (05/12/2022 6:00 AM CDT)
    ComponentValueRef RangeTest MethodAnalysis TimePerformed AtPathologist Signature
    Hepatitis C AntibodyPositive (A)NegativeVUMC CERNER LAB
    Comment:
    Negative: Antibodies to HCV not detected; does not exclude possibility of infection with HCV.Equivocal: Antibodies to HCV may or may not be present; repeat serologic testing in approximately 8 weeks or nucleic acid testing is recommended to assess possible infection. Positive: Presumptive history of HCV infection; nucleic acid testing recommended to document viral replication.
    Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
    Blood05/12/2022 6:00 AM CDT05/12/2022 11:30 AM CDT
    Authorizing ProviderResult Type
    Charles W Stratton MDLAB BLOOD ORDERABLES
    Performing OrganizationAddressCity/State/ZIP CodePhone Number
    VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
  • Cytogenomic SNP microarray (04/04/2022 11:55 AM CDT)
    Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
    Blood04/04/2022 11:55 AM CDT04/18/2022 2:46 PM CDT
    Narrative
    VUMC CERNER LAB - 04/18/2022 2:57 PM CDTMICROARRAY REPORT- Corrected Request#: CG-22-0000006 Service date: 4/4/2022 11:55 Microarray Result: Normal female Microarray Interpretation: SNP chromosomal microarray analysis (CMA) of a blood sample from this patient demonstrated no copy number changes of known clinical significance. No large regions of homozygosity (ROH) were detected. The ISCN nomenclature describing this result is: arr(X,1-22)x2. Electronically signed out by: Benfield, Luis A on 04/18/2022 ___________________________________________________________________ Clinical indication: Specimen List: Blood Date in Lab: 4/18/2022 14:46 Date Collected: 4/4/2022 11:55 ___________________________________________________________________ Disclaimer: Copy number gains less than 400 kb in size and copy number losses less than 200 kb in size will not be reported unless they represent a known or suspected clinically relevant imbalance. The reporting of copy number variants less than 100 kb in size is at the discretion of the laboratory and some clinically relevant copy number changes under 50 kb may not be reported due to limitations in probe coverage in certain genomic regions. Copy number changes of any size with no apparent clinical significance (likely benign or benign) have not been discussed in this report but may be available upon request. Regions of homozygosity (ROH) less than 10 Mb in size will not be reported unless the ROH is clinically relevant for potential uniparental disomy. Genome-wide ROH under 2% will not be reported. Copy number variants less than 200 kb associated with a carrier status for autosomal recessive conditions will not be reported unless specifically indicated in the reason for referral. This microarray was designed and manufactured by Affymetrix for the sole purpose of identifying DNA copy number gains and losses associated with chromosomal imbalances and regions of homozygosity (ROH) associated with uniparental isodisomy (isoUPD).This microarray will detect aneuploidy, deletions and duplications of loci represented on the microarray. \u00a0It will not detect balanced alterations including: reciprocal translocations, inversions and balanced insertions. It will not detect point mutations and imbalances less than 10 kb. \u00a0Failure to detect an alteration at any locus does not exclude the diagnosis of any of the disorders represented on the microarray. This assay is not designed to detect mosaic gains and losses and its performance in detecting mosaicism has not been established. This test was developed and its performance characteristics determined by Affymetrix as required by CLIA \u00c2\u201988 regulations. This test is used for clinical purposes and the accuracy and precision has been established and verified by this laboratory. This test has not been cleared or approved by the U.S. Food and Drug Administration. Interpretation of copy number variants is performed using VUMC-laboratory maintained databases as well as the following resources: Database of Genomic Variants (http://dgv.tcag.ca/dgv/app/home) Online Mendelian Inheritance in Man (http://www.omim.org/) UCSC Genome Bioinformatics (http://genome.ucsc.edu/cgi-bin/hgGateway) ClinGen Clinical Genome Resource (http://www.ncbi.nlm.nih.gov/projects/dbvar/clingen) DECIPHER Database (https://decipher.sanger.ac.uk/browser) PubMed-NCBI (http://www.ncbi.nlm.nih.gov/pubmed) Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen). PMID: 31690835 Method: Microarray platform: ThermoFisher Scientific CytoScanTM HD Cytogenetics Solution Version: 1.1 (Based on UCSC hg19 assembly) Number of loci analyzed: 2,696,550 Mean probe spacing: <700 bp Testing performed at Vanderbilt Cytogenetics One Hundred Oaks Laboratory, Suite 21100, 719 Thompson Ln, Nashville, TN 37204 \u00a0phone 615-875-0228, fax 615-875-0234
    Resulting Agency Comment
    testing comment
    Authorizing ProviderResult Type
    Carda Testprovqa MDLAB GENETIC TESTING
    Performing OrganizationAddressCity/State/ZIP CodePhone Number
    VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
  • Pharmacogenomics (03/31/2022 5:36 PM CDT)
    Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
    DNA03/31/2022 5:36 PM CDT03/31/2022 5:44 PM CDT
    Narrative
    VUMC CERNER LAB - 03/31/2022 5:51 PM CDTPharmacogenomics: Final Report Request #: MD-22-0000041 Service Date: 3/31/2022 17:36 Reason for Request: Genotyping for Determination of Drug Efficacy, Dosage and Safety Type of Specimen: DNA Date Received: 3/31/2022 17:44 Date Reported: 3/31/2022 17:51 Interpretation: Results from this assay may indicate dosage adjustments or medication alternatives that should be considered for this patient. Additional information regarding the implications of these results is available at www.mydruggenome.org. For VUMC patients, clinical decision support regarding the management of this patient with respect to specific drugs based upon the patient''s genotype as listed below is available in the patient''s electronic medical record under Genomic Indicators. Clinical decision support may also be provided for some drugs through order entry and medication prescribing tools utilized within the VUMC system. Comments: Results: CYP2C19 - \u00a0Cancelled CYP2C9 - \u00a0 Cancelled CYP2D6 - \u00a0 Cancelled CYP3A5 - \u00a0 Cancelled CYP4F2 - \u00a0 Cancelled DPYD - \u00a0 \u00a0 Cancelled NUDT15 - \u00a0 Cancelled SLCO1B1 - \u00a0Cancelled TPMT - \u00a0 \u00a0 Cancelled VKORC1 - \u00a0 Cancelled These results should be correlated with other laboratory and clinical findings and additional testing should be considered if clinically indicated. Methodology: DNA was extracted from this specimen and screened for 37 variants in 10 genes that are associated with drug absorption, distribution, metabolism, excretion or response. The reported genotypes were determined using PCR amplification and oligonucleotide primers specific for each interrogated region of the genes listed within this panel. Fluorophore labeled probes were used to identify each variant. Variants analyzed in this assay include: CYP2C19 *2, *3, *4, *6, *8, *17; CYP2C9 *2, *3, *6, *8; CYP3A5 *3, *6, *7; CYP4F2 *3; DPYD *2A, *13, c.557A>G, c.1236G>A (HapB3), c.2846A>T; \u00a0NUDT15 *2 or *3; SLCO1B1 *5; TPMT *2, *3B, *3C, *4; VKORC1 promoter variant c.-1639G>A; and CYP2D6 copy number and variants *2, *2A, *3, *4, *6, *7, *9, *10, *17, *29 and *41. A *1 allele is considered the reference (normal) sequence and is reported if none of the variants analyzed for a particular gene is detected. This assay is specific for the variants listed above and cannot exclude the presence of other variants within these genes that may affect the pharmacologic function of the protein product encoded by these genes. In most cases, variants for a particular gene exist on separate alleles; however, for individuals in which multiple variants in the same gene are detected, this assay cannot determine if the variants are on the same allele or on different alleles. Further, due to the highly polymorphic nature of these regions, rare variants may exist that could affect the sensitivity or specificity of this assay and lead to a false-negative or a false-positive result. Electronically signed out by: Barba, Elizabeth on 03/31/2022 This assay has not been cleared or approved by the US Food and Drug Administration. The performance of this assay was tested and validated prior to use for patient testing. This test is used for clinical purposes and should not be regarded as investigational or research. This laboratory is regulated by the Clinical Laboratory Improvement Act of 1988.
    Authorizing ProviderResult Type
    Carda Testprovqa MDLAB GENETIC TESTING
    Performing OrganizationAddressCity/State/ZIP CodePhone Number
    VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
  • Drug Toxicology Monitoring Base Pnl w/Conf, Oral Fl-QSTD (03/29/2022 1:53 PM CDT)
    ComponentValueRef RangeTest MethodAnalysis TimePerformed AtPathologist Signature
    Drug Toxicology Monitoring Base Pnl w/Conf, Oral Fl
    VPLS clients: \u00a0 See separate report sent to client.VUMC patients: \u00a0Results faxed to Vanderbilt Medical Record.    		VUMC CERNER LAB
    Comment: This test was performed at: Quest Laboratory,Location Varies,,,,,,
    Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
    Oral03/29/2022 1:53 PM CDT03/29/2022 2:07 PM CDT
    Authorizing ProviderResult Type
    Carda Testprovqa MDLAB BODY FLUIDS AND STOOLS ORDERABLES
    Performing OrganizationAddressCity/State/ZIP CodePhone Number
    VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
  • Results Called (03/22/2022 1:27 PM CDT)
    ComponentValueRef RangeTest MethodAnalysis TimePerformed AtPathologist Signature
    Test CalledkVUMC CERNER LAB
    Reason CalledQNSVUMC CERNER LAB
    Called TotestVUMC CERNER LAB
    Read BackYesVUMC CERNER LAB
    Collector IDtest123VUMC CERNER LAB
    Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
    Blood03/22/2022 1:27 PM CDT03/22/2022 1:29 PM CDT
    Authorizing ProviderResult Type
    E Mark Watts MDLAB BLOOD ORDERABLES
    Performing OrganizationAddressCity/State/ZIP CodePhone Number
    VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
  • (ABNORMAL) Culture Bact CSF (03/17/2022 1:34 PM CDT)
    ComponentValueRef RangeTest MethodAnalysis TimePerformed AtPathologist Signature
    Final ReportModerate growth Neisseria meningitidisVUMC CERNER LAB
    Organism IDNeisseria meningitidis (POSITIVE)VUMC CERNER LAB
    Gram Stain Report
    1+ White Blood Cells3+ Gram negative diplococci; restreak for isolation    		VUMC CERNER LAB
    Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
    CSF03/17/2022 1:34 PM CDT03/17/2022 1:34 PM CDT
    Authorizing ProviderResult Type
    Adam Clark Seegmiller MDLAB MICROBIOLOGY - GENERAL ORDERABLES
    Performing OrganizationAddressCity/State/ZIP CodePhone Number
    VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
  • (ABNORMAL) Culture Bact CSF (03/17/2022 1:11 PM CDT)
    ComponentValueRef RangeTest MethodAnalysis TimePerformed AtPathologist Signature
    Final ReportLight growth Acinetobacter baumanniiVUMC CERNER LAB
    Organism IDAcinetobacter baumannii (POSITIVE)VUMC CERNER LAB
    Gram Stain Report1+ Gram negative rodVUMC CERNER LAB
    Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
    CSF03/17/2022 1:11 PM CDT03/17/2022 1:11 PM CDT
    OrganismAntibioticMethodSusceptibility
    Acinetobacter baumanniiAmikacinMIC0.25: Susceptible
    Acinetobacter baumanniiAvycaz (Ceftazidime/Avibactam)MIC0.05: Intermediate
    Acinetobacter baumanniiLevofloxacinMIC0.75: Resistant
    Authorizing ProviderResult Type
    Adam Clark Seegmiller MDLAB MICROBIOLOGY - GENERAL ORDERABLES
    Performing OrganizationAddressCity/State/ZIP CodePhone Number
    VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
  • SARS-CoV-2 PCR (03/11/2022 1:05 PM CST)
    ComponentValueRef RangeTest MethodAnalysis TimePerformed AtPathologist Signature
    SARS-CoV-2 Nucleic Acid (Result)Not DetectedNot DetectedVUMC CERNER LAB
    Comment:
    This test was performed using a multiplexed nucleic acid amplification test that is labeled Emergence Use Only by the U.S. FDA. Results of this test should not be used as the sole basis for diagnosis, treatment, or other management decisions.A detected result is positive and indicates the presence of the virus in the sample. A not detected result indicates that the test did not detect the virus in the sample.
    SARS-CoV-2 Nucleic Acid Method (Comment)
    This test was performed using the Hologic Panther COVID-19 test. This test is currently approved for clinical diagnostic testing under Emergency Use Authorization of the FDA; the result should not be considered experimental or for research purposes.Nares    		VUMC CERNER LAB
    Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
    Nares03/11/2022 1:05 PM CST03/11/2022 1:46 PM CST
    Authorizing ProviderResult Type
    Adam Clark Seegmiller MDLAB BODY FLUIDS AND STOOLS ORDERABLES
    Performing OrganizationAddressCity/State/ZIP CodePhone Number
    VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
  • FISH ALL Pnl (03/11/2022 1:05 PM CST)
    Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
    Blood03/11/2022 1:05 PM CST03/11/2022 1:09 PM CST
    Narrative
    VUMC CERNER LAB - 03/11/2022 1:27 PM CSTFISH REPORT Request#:CG-22-0000003 Service date:3/11/2022 13:05 FISH IMPRESSION: Abnormal for homozygous deletion of CDKN2A locus at 9p21 in __% of cells. FISH KARYOTYPE: nuc ish (DXZ1x1,DYZ3x1,D18Z1x2)[200] COMMENTS: Results of the FISH studies with the 21 DNA probes described above were analyzed in at least 200 cells per probe and no abnormal signal patterns were detected for the target regions of chromosomes 1, 4, 7, 9, 10, 11, 12, 14, 17, 19, 21, and 22. Normal cut off values for probes: 1.0% for t(1;19) PBX1/TCF3 1.0% for t(9;22) BCR/ABL1 1.0% for KMT2A (11q23) 1.0% for t(12;21) ETV6/RUNX1 1.0% for IKZF1/CEP7 3.0% for CEP 4 2.0% for CEP 10 2.0% for CEP 17 1.0% for CDKN2A/CEP9 (9p21) 1.0% for IGH breakapart 1.0% for ABL2 breakapart 1.0% for ABL1 breakapart These probes were developed by Vysis and their performance characteristics determined by VUMC as required by the CLIA ''88 regulations. \u00a0These probes have not been cleared or approved by the U.S. Food and Drug administration. Ferrin Courtney Wheeler, PhD, FACMG reviewed and approved Electronically signed out by: Mavrak, Geoffrey A on 03/11/2022 Clinical History: \u00a0ALL Specimen List: Blood Date In Lab: 3/11/2022 13:09 Date Collected: 3/11/2022 13:05 Testing performed at Vanderbilt Cytogenetics One Hundred Oaks Laboratory, Suite 21100, 719 Thompson Ln, Nashville, TN 37204 \u00a0phone 615-875-0228, fax 615-875-0234
    Authorizing ProviderResult Type
    Adam Clark Seegmiller MDLAB GENETIC TESTING
    Performing OrganizationAddressCity/State/ZIP CodePhone Number
    VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
  • (ABNORMAL) Culture Bact Bld Adult (03/11/2022 8:51 AM CST)
    ComponentValueRef RangeTest MethodAnalysis TimePerformed AtPathologist Signature
    Final Report
    Gram positive cocci; restreak for isolation Isolated from Aerobic bottleStaphylococcus aureus    		VUMC CERNER LAB
    Organism IDStaphylococcus aureus (POSITIVE)VUMC CERNER LAB
    Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
    Blood (Antecub)03/11/2022 8:51 AM CST03/11/2022 8:51 AM CST
    OrganismAntibioticMethodSusceptibility
    Staphylococcus aureusAmpicillinMIC0.25: Susceptible
    Staphylococcus aureusRifampinMIC0.75: Resistant
    Staphylococcus aureusVancomycinMIC0.05: Susceptible
    Authorizing ProviderResult Type
    Adam Clark Seegmiller MDLAB MICROBIOLOGY - GENERAL ORDERABLES
    Performing OrganizationAddressCity/State/ZIP CodePhone Number
    VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
  • (ABNORMAL) Culture Bact Urine (03/10/2022 2:30 PM CST)
    ComponentValueRef RangeTest MethodAnalysis TimePerformed AtPathologist Signature
    Final Report>100,000 cfu/ml Proteus mirabilisVUMC CERNER LAB
    Organism IDProteus mirabilis (POSITIVE)VUMC CERNER LAB
    Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
    Urine03/10/2022 2:30 PM CST03/10/2022 2:49 PM CST
    OrganismAntibioticMethodSusceptibility
    Proteus mirabilisAztreonamMIC0.75: Resistant
    Proteus mirabilisCefoxitinMIC0.25: Intermediate
    Proteus mirabilisLevofloxacinMIC0.05: Susceptible
    Authorizing ProviderResult Type
    Adam Clark Seegmiller MDLAB MICROBIOLOGY - GENERAL ORDERABLES
    Performing OrganizationAddressCity/State/ZIP CodePhone Number
    VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
  • (ABNORMAL) Culture Bact Bld Adult (03/10/2022 10:00 AM CST)
    ComponentValueRef RangeTest MethodAnalysis TimePerformed AtPathologist Signature
    Final Report
    Gram Positive Cocci Restreak for isolation Isolated from Aerobic bottleStaphylococcus aureus    		VUMC CERNER LAB
    Organism IDStaphylococcus aureus (POSITIVE)VUMC CERNER LAB
    Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
    Blood (Antecub)03/10/2022 10:00 AM CST03/10/2022 2:08 PM CST
    OrganismAntibioticMethodSusceptibility
    Staphylococcus aureusAmpicillinMIC3: Resistant
    Staphylococcus aureusVancomycinMIC0.03: Susceptible
    Staphylococcus aureusLevofloxacinMIC2: Intermediate
    Authorizing ProviderResult Type
    Katelyn Kennedy Atwater MDLAB MICROBIOLOGY - GENERAL ORDERABLES
    Performing OrganizationAddressCity/State/ZIP CodePhone Number
    VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
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Tobacco UseTypesPacks/DayYears UsedDate
Smoking Tobacco: Never Assessed
Sex Assigned at BirthDate Recorded
Not on file
documented as of this encounter"}, "code": {"coding": [{"code": "29762-2", "display": "Social history Narrative", "system": "http://loinc.org"}]}, "mode": "snapshot"}, {"id": "cb659e44-f9d5-aef2-d594-41967f8e33cb", "title": "Encounter Details", "text": {"status": "generated", "div": "
DateTypeDepartmentCare TeamDescription
2/18/22Transcribe OrdersVanderbilt University Adult Hospital1211 Medical Center DrNashville, TN 37232615-322-5000Tech, Lab, MLT
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Reportability Response Information Section
"}, "extension": [{"url": "http://hl7.org/fhir/us/ecr/StructureDefinition/eicr-initiation-type-extension", "valueCodeableConcept": {"text": "official", "coding": [{"code": "88085-6", "display": "Reportability response report Document Public health", "system": "http://loinc.org"}]}}, {"url": "http://hl7.org/fhir/us/ecr/StructureDefinition/rr-eicr-processing-status-extension", "valueCodeableConcept": {"coding": [{"code": "RRVS19", "display": "eICR processed", "system": "urn:oid:2.16.840.1.114222.4.5.274"}]}}], "code": {"coding": [{"code": "88085-6", "display": "Reportability response report Document Public health", "system": "http://loinc.org"}]}, "entry": [{"display": "Relevant Reportable Condition Observation - Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder)", "reference": "Observation/b41712c4-2a89-4acc-ac69-84e5bdbe9ebe"}, {"display": "Relevant Reportable Condition Observation - Viral hepatitis type C (disorder)", "reference": "Observation/58500c6e-8dfc-4534-8e9c-be1db7256bd6"}, {"display": "Relevant Reportable Condition Observation - Viral hepatitis type C (disorder)", "reference": "Observation/bd5e96b0-05da-4003-ac0c-eb4cc02a98cd"}, {"display": "Relevant Reportable Condition Observation - Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder)", "reference": "Observation/f7106df9-08a6-4708-8511-388e59ea9a4d"}, {"display": "Relevant Reportable Condition Observation - Plague (disorder)", "reference": "Observation/b468a4bc-516e-4a68-b2d3-e1304ff92784"}, {"display": "Relevant Reportable Condition Observation - Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder)", "reference": "Observation/cae6f2e7-5d8c-45c0-b38f-4e402fc5a850"}]}], "subject": {"reference": "Patient/8f17ebaf-226e-4565-a8e4-1fd09cc4f25a"}, "relatesTo": [{"code": "replaces", "targetReference": {"reference": "Composition/1.2.840.114350.1.13.478.3.7.8.688883.212673"}, "extension": [{"url": 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Request#:CG-22-0000003
Service date:3/11/2022 13:05


FISH IMPRESSION:

Abnormal for homozygous deletion of CDKN2A locus at 9p21 in __% of cells.

FISH KARYOTYPE:



nuc ish (DXZ1x1,DYZ3x1,D18Z1x2)[200]

\u00a0
\u00a0
\u00a0



COMMENTS:



Results of the FISH studies with the 21 DNA probes described above were analyzed in at least 200 cells per probe and no abnormal signal patterns were detected for the target regions of chromosomes 1, 4, 7, 9, 10, 11, 12, 14, 17, 19, 21, and 22.

Normal cut off values for probes:

1.0% for t(1;19) PBX1/TCF3
1.0% for t(9;22) BCR/ABL1
1.0% for KMT2A (11q23)
1.0% for t(12;21) ETV6/RUNX1
1.0% for IKZF1/CEP7
3.0% for CEP 4
2.0% for CEP 10
2.0% for CEP 17
1.0% for CDKN2A/CEP9 (9p21)
1.0% for IGH breakapart
1.0% for ABL2 breakapart
1.0% for ABL1 breakapart

These probes were developed by Vysis and their performance characteristics determined by VUMC as required by the CLIA ''88 regulations. \u00a0These probes have not been cleared or approved by the U.S. Food and Drug administration.


Ferrin Courtney Wheeler, PhD, FACMG
reviewed and approved

Electronically signed out by:
Mavrak, Geoffrey A

on 03/11/2022

Clinical History: \u00a0ALL
Specimen List: Blood
Date In Lab: 3/11/2022 13:09
Date Collected: 3/11/2022 13:05

Testing performed at Vanderbilt Cytogenetics One Hundred Oaks Laboratory, Suite 21100, 719 Thompson Ln,
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VPLS clients: \u00a0 See separate report sent to client.", "note": [{"text": "This test was performed at: Quest Laboratory,Location Varies,,,,,,"}], "extension": [{"url": "http://hl7.org/fhir/R4/specimen.html", "extension": [{"url": "specimen source", "valueString": "Oral"}, {"url": "specimen collection time", "valueDateTime": "2022-03-29T18:53:00Z"}, {"url": "specimen receive time", "valueDateTime": "2022-03-29T19:07:00Z"}, {"url": "observation entry reference value", "valueString": "#Result.1.2.840.114350.1.13.478.3.7.2.798268.2061344.Comp1"}]}], "subject": {"reference": "Patient/8f17ebaf-226e-4565-a8e4-1fd09cc4f25a"}, "performer": [{"display": "VUMC CERNER LAB", "reference": "Organization/e3ece69c-0968-59c9-47dd-f16db731621a"}]}, "request": {"method": "PUT", "url": "Observation/6fc06f11-d0f4-9553-2798-e8dd822678fe"}}, {"fullUrl": "urn:uuid:db8797cb-3129-eff4-9d78-a04b2326f0a2", "resource": {"resourceType": "Observation", "id": "db8797cb-3129-eff4-9d78-a04b2326f0a2", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"], "source": "ecr"}, "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.798268", "value": "2061344"}], "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "laboratory"}]}], "status": "final", "effectiveDateTime": "2022-03-29T20:10:54Z", "valueCodeableConcept": {"coding": [{"code": "16", "system": "urn:oid:1.2.840.114350.1.72.1.5007"}]}, "extension": [{"url": "http://hl7.org/fhir/R4/specimen.html", "extension": [{"url": "specimen source", "valueString": "Oral"}, {"url": "specimen collection time", "valueDateTime": "2022-03-29T18:53:00Z"}, {"url": "specimen receive time", "valueDateTime": "2022-03-29T19:07:00Z"}]}], "subject": {"reference": "Patient/8f17ebaf-226e-4565-a8e4-1fd09cc4f25a"}}, "request": {"method": "PUT", "url": "Observation/db8797cb-3129-eff4-9d78-a04b2326f0a2"}}, {"fullUrl": "urn:uuid:c86958f4-4bd2-7450-15ff-4c490820f58f", "resource": {"resourceType": "DiagnosticReport", "id": "c86958f4-4bd2-7450-15ff-4c490820f58f", "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.798268", "value": "2061345"}], "status": "final", "code": {"coding": [{"code": "201700", "display": "Pharmacogenomics", "system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.696580"}]}, "effectivePeriod": {"start": "2022-03-31T22:36:00Z", "end": "2022-03-31T22:36:00Z"}, "subject": {"reference": "Patient/8f17ebaf-226e-4565-a8e4-1fd09cc4f25a"}, "performer": [{"reference": "Organization/22c6cdd0-bde1-e220-9ba4-2c2802f795ad"}], "result": [{"reference": "Observation/2e9477e8-412b-905c-270f-16ca12bff791"}, {"reference": "Observation/ed66ccf7-584a-1142-b9a4-8fe01b6f21fb"}], "meta": {"source": "ecr"}}, "request": {"method": "PUT", "url": "DiagnosticReport/c86958f4-4bd2-7450-15ff-4c490820f58f"}}, {"fullUrl": "urn:uuid:2e9477e8-412b-905c-270f-16ca12bff791", "resource": {"resourceType": "Observation", "id": "2e9477e8-412b-905c-270f-16ca12bff791", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"], "source": "ecr"}, "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.7.798268.1000", "value": "2061345"}], "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "laboratory"}]}], "status": "final", "code": {"coding": [{"code": "NAR", "system": "urn:oid:1.2.840.114350.1.72.1.5220"}]}, "effectiveDateTime": "2022-03-31T22:51:17Z", "valueString": "Pharmacogenomics: Final Report

Request #: MD-22-0000041

Service Date: 3/31/2022 17:36

Reason for Request: Genotyping for Determination of Drug Efficacy, Dosage and Safety

Type of Specimen: DNA

Date Received: 3/31/2022 17:44

Date Reported: 3/31/2022 17:51

Interpretation:
Results from this assay may indicate dosage adjustments or medication alternatives that should be considered for this patient. Additional information regarding the implications of these results is available at www.mydruggenome.org.

For VUMC patients, clinical decision support regarding the management of this patient with respect to specific drugs based upon the patient''s genotype as listed below is available in the patient''s electronic medical record under Genomic Indicators. Clinical decision support may also be provided for some drugs through order entry and medication prescribing tools utilized within the VUMC system.



Comments:

Results:

CYP2C19 - \u00a0Cancelled

CYP2C9 - \u00a0 Cancelled

CYP2D6 - \u00a0 Cancelled \u00a0

CYP3A5 - \u00a0 Cancelled

CYP4F2 - \u00a0 Cancelled

DPYD - \u00a0 \u00a0 Cancelled

NUDT15 - \u00a0 Cancelled

SLCO1B1 - \u00a0Cancelled \u00a0 \u00a0 \u00a0

TPMT - \u00a0 \u00a0 Cancelled

VKORC1 - \u00a0 Cancelled \u00a0 \u00a0
\u00a0
These results should be correlated with other laboratory and clinical findings and additional testing should be considered if clinically indicated.
\u00a0 \u00a0

Methodology:

DNA was extracted from this specimen and screened for 37 variants in 10 genes that are associated with drug absorption, distribution, metabolism, excretion or response. The reported genotypes were determined using PCR amplification and oligonucleotide primers specific for each interrogated region of the genes listed within this panel. Fluorophore labeled probes were used to identify each variant.

Variants analyzed in this assay include: CYP2C19 *2, *3, *4, *6, *8, *17; CYP2C9 *2, *3, *6, *8; CYP3A5 *3, *6, *7; CYP4F2 *3; DPYD *2A, *13, c.557A>G, c.1236G>A (HapB3), c.2846A>T; \u00a0NUDT15 *2 or *3; SLCO1B1 *5; TPMT *2, *3B, *3C, *4; VKORC1 promoter variant c.-1639G>A; and CYP2D6 copy number and variants *2, *2A, *3, *4, *6, *7, *9, *10, *17, *29 and *41. A *1 allele is considered the reference (normal) sequence and is reported if none of the variants analyzed for a particular gene is detected. This assay is specific for the variants listed above and cannot exclude the presence of other variants within these genes that may affect the pharmacologic function of the protein product encoded by these genes. In most cases, variants for a particular gene exist on separate alleles; however, for individuals in which multiple variants in the same gene are detected, this assay cannot determine if the variants are on the same allele or on different alleles. Further, due to the highly polymorphic
nature of these regions, rare variants may exist that could affect the sensitivity or specificity of this assay and lead to a false-negative or a false-positive result.


Electronically signed out by:
Barba, Elizabeth

on 03/31/2022

This assay has not been cleared or approved by the US Food and Drug Administration. The performance of this assay was tested and validated prior to use for patient testing. This test is used for clinical purposes and should not be regarded as investigational or research. This laboratory is regulated by the Clinical Laboratory Improvement Act of 1988.", "extension": [{"url": "http://hl7.org/fhir/R4/specimen.html", "extension": [{"url": "specimen source", "valueString": "DNA"}, {"url": "specimen collection time", "valueDateTime": "2022-03-31T22:36:00Z"}, {"url": "specimen receive time", "valueDateTime": "2022-03-31T22:44:00Z"}, {"url": "observation entry reference value", "valueString": "#Result.1.2.840.114350.1.13.478.3.7.2.798268.2061345.Narrative"}]}], "subject": {"reference": "Patient/8f17ebaf-226e-4565-a8e4-1fd09cc4f25a"}, "performer": [{"display": "VUMC CERNER LAB", "reference": "Organization/e3ece69c-0968-59c9-47dd-f16db731621a"}]}, "request": {"method": "PUT", "url": "Observation/2e9477e8-412b-905c-270f-16ca12bff791"}}, {"fullUrl": "urn:uuid:ed66ccf7-584a-1142-b9a4-8fe01b6f21fb", "resource": {"resourceType": "Observation", "id": "ed66ccf7-584a-1142-b9a4-8fe01b6f21fb", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"], "source": "ecr"}, "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.798268", "value": "2061345"}], "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "laboratory"}]}], "status": "final", "effectiveDateTime": "2022-03-31T22:51:17Z", "valueCodeableConcept": {"coding": [{"code": "16", "system": "urn:oid:1.2.840.114350.1.72.1.5007"}]}, "extension": [{"url": "http://hl7.org/fhir/R4/specimen.html", "extension": [{"url": "specimen source", "valueString": "DNA"}, {"url": "specimen collection time", "valueDateTime": "2022-03-31T22:36:00Z"}, {"url": "specimen receive time", "valueDateTime": "2022-03-31T22:44:00Z"}]}], "subject": {"reference": "Patient/8f17ebaf-226e-4565-a8e4-1fd09cc4f25a"}}, "request": {"method": "PUT", "url": "Observation/ed66ccf7-584a-1142-b9a4-8fe01b6f21fb"}}, {"fullUrl": "urn:uuid:b0f590a6-4bf5-7add-9716-2bd3ba6defb2", "resource": {"resourceType": "DiagnosticReport", "id": "b0f590a6-4bf5-7add-9716-2bd3ba6defb2", "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.798268", "value": "2061347"}], "status": "final", "code": {"coding": [{"code": "118330", "display": "Cytogenomic SNP microarray", "system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.696580"}]}, "effectivePeriod": {"start": "2022-04-04T16:55:00Z", "end": "2022-04-04T16:55:00Z"}, "subject": {"reference": "Patient/8f17ebaf-226e-4565-a8e4-1fd09cc4f25a"}, "performer": [{"reference": "Organization/22c6cdd0-bde1-e220-9ba4-2c2802f795ad"}], "result": [{"reference": "Observation/2a4f8fb5-f957-3c30-1353-a30aa441a12b"}, {"reference": "Observation/2e70be1d-fa6c-0256-cf67-f695f5bba1ac"}, {"reference": "Observation/97b316f7-bb96-051f-adba-72ddc4ae5825"}], "meta": {"source": "ecr"}}, "request": {"method": "PUT", "url": "DiagnosticReport/b0f590a6-4bf5-7add-9716-2bd3ba6defb2"}}, {"fullUrl": "urn:uuid:2a4f8fb5-f957-3c30-1353-a30aa441a12b", "resource": {"resourceType": "Observation", "id": "2a4f8fb5-f957-3c30-1353-a30aa441a12b", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"], "source": "ecr"}, "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.7.798268.1000", "value": "2061347"}], "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "laboratory"}]}], "status": "final", "code": {"coding": [{"code": "NAR", "system": "urn:oid:1.2.840.114350.1.72.1.5220"}]}, "effectiveDateTime": "2022-04-18T19:57:02Z", "valueString": "MICROARRAY REPORT- Corrected

Request#: CG-22-0000006
Service date: 4/4/2022 11:55

Microarray Result:
Normal female

Microarray Interpretation:
SNP chromosomal microarray analysis (CMA) of a blood sample from this patient demonstrated no copy number changes of known clinical significance. No large regions of homozygosity (ROH) were detected. The ISCN nomenclature describing this result is: arr(X,1-22)x2.
Electronically signed out by:
Benfield, Luis A

on 04/18/2022
___________________________________________________________________

Clinical indication:
Specimen List: Blood
Date in Lab: 4/18/2022 14:46
Date Collected: 4/4/2022 11:55
___________________________________________________________________

Disclaimer:

Copy number gains less than 400 kb in size and copy number losses less than 200 kb in size will not be reported unless they represent a known or suspected clinically relevant imbalance. The reporting of copy number variants less than 100 kb in size is at the discretion of the laboratory and some clinically relevant copy number changes under 50 kb may not be reported due to limitations in probe coverage in certain genomic regions. Copy number changes of any size with no apparent clinical significance (likely benign or benign) have not been discussed in this report but may be available upon request. Regions of homozygosity (ROH) less than 10 Mb in size will not be reported unless the ROH is clinically relevant for potential uniparental disomy. Genome-wide ROH under 2% will not be reported. Copy number variants less than 200 kb associated with a carrier status for autosomal recessive conditions will not be reported unless specifically indicated in the reason for referral.

This microarray was designed and manufactured by Affymetrix for the sole purpose of identifying DNA copy number gains and losses associated with chromosomal imbalances and regions of homozygosity (ROH) associated with uniparental isodisomy (isoUPD).This microarray will detect aneuploidy, deletions and duplications of loci represented on the microarray. \u00a0It will not detect balanced alterations including: reciprocal translocations, inversions and balanced insertions. It will not detect point mutations and imbalances less than 10 kb. \u00a0Failure to detect an alteration at any locus does not exclude the diagnosis of any of the disorders represented on the microarray. This assay is not designed to detect mosaic gains and losses and its performance in detecting mosaicism has not been established. This test was developed and its performance characteristics determined by Affymetrix as required by CLIA \u00c2\u201988 regulations. This test is used for clinical purposes and the accuracy and precision has
been established and verified by this laboratory. This test has not been cleared or approved by the U.S. Food and Drug Administration.

Interpretation of copy number variants is performed using VUMC-laboratory maintained databases as well as the following resources:
Database of Genomic Variants (http://dgv.tcag.ca/dgv/app/home)
Online Mendelian Inheritance in Man (http://www.omim.org/)
UCSC Genome Bioinformatics (http://genome.ucsc.edu/cgi-bin/hgGateway)
ClinGen Clinical Genome Resource (http://www.ncbi.nlm.nih.gov/projects/dbvar/clingen)
DECIPHER Database (https://decipher.sanger.ac.uk/browser)
PubMed-NCBI (http://www.ncbi.nlm.nih.gov/pubmed)
Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen). PMID: 31690835

Method:
Microarray platform: ThermoFisher Scientific CytoScanTM HD Cytogenetics Solution
Version: 1.1 (Based on UCSC hg19 assembly)
Number of loci analyzed: 2,696,550
Mean probe spacing: <700 bp






Testing performed at Vanderbilt Cytogenetics One Hundred Oaks Laboratory, Suite 21100, 719 Thompson Ln,
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"extension": [{"url": "specimen source", "valueString": "Other"}, {"url": "specimen collection time", "valueDateTime": "2022-07-27T20:49:00Z"}, {"url": "specimen receive time", "valueDateTime": "2022-07-27T20:58:00Z"}]}], "subject": {"reference": "Patient/8f17ebaf-226e-4565-a8e4-1fd09cc4f25a"}}, "request": {"method": "PUT", "url": "Observation/01eb7b0c-1ce3-ff8b-cb73-e85b6c8ee41c"}}, {"fullUrl": "urn:uuid:d218e3d4-5585-f9f0-a926-c2740482ac49", "resource": {"resourceType": "Observation", "id": "d218e3d4-5585-f9f0-a926-c2740482ac49", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"], "source": "ecr"}, "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.798268", "value": "2122247"}], "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "laboratory"}]}], "status": "final", "effectiveDateTime": "2022-07-28T14:01:17Z", "valueCodeableConcept": {"coding": [{"code": "16", "system": "urn:oid:1.2.840.114350.1.72.1.5007"}]}, "extension": [{"url": "http://hl7.org/fhir/R4/specimen.html", "extension": [{"url": "specimen source", "valueString": "Other"}, {"url": "specimen collection time", "valueDateTime": "2022-07-27T20:49:00Z"}, {"url": "specimen receive time", "valueDateTime": "2022-07-27T20:58:00Z"}]}], "subject": {"reference": "Patient/8f17ebaf-226e-4565-a8e4-1fd09cc4f25a"}}, "request": {"method": "PUT", "url": "Observation/d218e3d4-5585-f9f0-a926-c2740482ac49"}}, {"fullUrl": "urn:uuid:1cfb73a5-128f-a51c-c396-fb20cd8e2456", "resource": {"resourceType": "Observation", "id": "1cfb73a5-128f-a51c-c396-fb20cd8e2456", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"], "source": "ecr"}, "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.1.1040.1", "value": "Z31828^^72166-2"}], "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "social-history"}]}], "status": "final", "code": {"coding": [{"code": "72166-2", "display": "Tobacco smoking status NHIS", "system": "http://loinc.org"}]}, "valueCodeableConcept": {"coding": [{"code": "266927001", "display": "Tobacco smoking consumption unknown", "system": "http://snomed.info/sct"}]}, "subject": {"reference": "Patient/8f17ebaf-226e-4565-a8e4-1fd09cc4f25a"}}, "request": {"method": "PUT", "url": "Observation/1cfb73a5-128f-a51c-c396-fb20cd8e2456"}}, {"fullUrl": "urn:uuid:", "resource": {"resourceType": "Observation", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"], "source": "ecr"}}, "request": {"method": "PUT", "url": "Observation/"}}, {"fullUrl": "urn:uuid:f5e25af7-945a-cf66-d2d0-8942935165a2", "resource": {"resourceType": "Immunization", "id": "f5e25af7-945a-cf66-d2d0-8942935165a2", "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.768076", "value": "86940"}], "occurrenceDateTime": "2021-01-22", "note": {"text": "SARS-COV-2 (COVID-19) Spikevax Vaccine, Moderna"}, "vaccineCode": {"coding": [{"code": "80777-273-10", "system": "urn:oid:2.16.840.1.113883.6.69"}]}, "lotNumber": "LLSFJK", "manufacturer": {"reference": "Organization/57fcc148-b440-3a80-749b-780325e9680d"}, "status": "completed", "primarySource": true, "patient": {"reference": "Patient/8f17ebaf-226e-4565-a8e4-1fd09cc4f25a"}, "meta": {"source": "ecr"}}, "request": {"method": "PUT", "url": "Immunization/f5e25af7-945a-cf66-d2d0-8942935165a2"}}, {"fullUrl": "urn:uuid:57fcc148-b440-3a80-749b-780325e9680d", "resource": {"resourceType": "Organization", "id": "57fcc148-b440-3a80-749b-780325e9680d", "name": "Moderna US, Inc.", "meta": {"source": "ecr"}}, "request": {"method": "PUT", "url": "Organization/57fcc148-b440-3a80-749b-780325e9680d"}}, {"fullUrl": "urn:uuid:875c24ee-6be0-066b-ca5f-e73b2d914f5b", "resource": {"resourceType": "Immunization", "id": "875c24ee-6be0-066b-ca5f-e73b2d914f5b", "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.768076", "value": "90497"}], "occurrenceDateTime": "2020-09-08", "note": {"text": "Hep B, adult vaccine (Engerix/Recombivax)"}, "vaccineCode": {"coding": [{"display": "Hep B, adult vaccine (Engerix/Recombivax)"}]}, "status": "completed", "primarySource": true, "meta": {"source": "ecr"}}, "request": {"method": "PUT", "url": "Immunization/875c24ee-6be0-066b-ca5f-e73b2d914f5b"}}, {"fullUrl": "urn:uuid:3c8af1dd-2983-5d97-d5f1-f6dd57e9eba1", "resource": {"resourceType": "Immunization", "id": "3c8af1dd-2983-5d97-d5f1-f6dd57e9eba1", "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.768076", "value": "90499"}], "occurrenceDateTime": "2021-06-15", "note": {"text": "DTaP, 5 pertussis antigens vaccine (DAPTACEL)"}, "vaccineCode": {"coding": [{"display": "DTaP, 5 pertussis antigens vaccine (DAPTACEL)"}]}, "status": "completed", "primarySource": true, "meta": {"source": "ecr"}}, "request": {"method": "PUT", "url": "Immunization/3c8af1dd-2983-5d97-d5f1-f6dd57e9eba1"}}]}') ON CONFLICT (ecr_id) DO NOTHING; -WITH inserted_data AS ( - INSERT INTO ecr_data ( - eICR_ID, patient_name_last, patient_name_first, patient_birth_date, data_source, report_date - ) VALUES ( - '1.2.840.114350.1.13.478.3.7.8.688883.230886', 'ZTEST', 'APPLE', '1965-10-05', 'DB', '2022-02-18' - ) - ON CONFLICT (eICR_ID) DO NOTHING - RETURNING eICR_ID -), inserted_condition AS ( - INSERT INTO ecr_rr_conditions (uuid, eICR_ID, condition) - VALUES (uuid_generate_v4(), (SELECT eICR_ID FROM inserted_data), 'Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder),Viral hepatitis type C (disorder),Viral hepatitis type C (disorder),Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder),Plague (disorder),Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder)') - RETURNING uuid -) -INSERT INTO ecr_rr_rule_summaries (uuid, ecr_rr_conditions_id, rule_summary) -VALUES (uuid_generate_v4(), (SELECT uuid FROM inserted_condition), 'Detection of SARS-CoV-2 nucleic acid in a clinical or post-mortem specimen by any method,Detection of Hepatitis C virus antibody in a clinical specimen by any method,Detection of Hepatitis C virus antibody in a clinical specimen by any method,COVID-19 (as a diagnosis or active problem),Detection of SARS-CoV-2 nucleic acid in a clinical or post-mortem specimen by any method,Plague (as a diagnosis or active problem),Detection of SARS-CoV-2 nucleic acid in a clinical or post-mortem specimen by any method') -RETURNING (SELECT eICR_ID FROM inserted_data); \ No newline at end of file +INSERT INTO fhir (ecr_id, data) VALUES ('1.2.840.114350.1.13.478.3.7.8.688883.230886', '{"resourceType": "Bundle", "type": "batch", "entry": [{"fullUrl": "urn:uuid:1.2.840.114350.1.13.478.3.7.8.688883.230886", "resource": {"resourceType": "Composition", "id": "1.2.840.114350.1.13.478.3.7.8.688883.230886", "meta": {"profile": ["http://hl7.org/fhir/us/ecr/StructureDefinition/eicr-composition"], "source": "ecr"}, "identifier": [{"use": "official", "type": {"coding": [{"code": "55751-2", "system": "http://loinc.org", "display": "Initial Public Health Case Report"}]}, "value": "59086a94-a174-11ec-a982-0050561597b4", "assigner": {"display": "EPC"}}], "extension": [{"url": "http://hl7.org/fhir/StructureDefinition/composition-clinicaldocument-versionNumber", "valueString": "2"}, {"url": "https://www.hl7.org/implement/standards/product_brief.cfm?product_id=436", "valueString": "2016-12-01"}], "status": "final", "type": {"coding": [{"code": "55751-2", "system": "http://loinc.org", "display": "Initial Public Health Case Report"}]}, "date": "2022-07-28T09:01:22-05:00", "title": "Initial Public Health Case Report", "confidentiality": "N", "section": [{"id": "b2d80efa-766a-e5f8-e4a4-3581f1871a81", "title": "Miscellaneous Notes", "text": {"status": "generated", "div": "Not on filedocumented in this encounter"}, "code": {"coding": [{"code": "10164-2", "system": "http://loinc.org", "display": "HISTORY OF PRESENT ILLNESS"}]}, "mode": "snapshot"}, {"id": "C353C60C-0E7D-11ED-B8BA-0050561597B4", "title": "Immunizations", "text": {"status": "generated", "div": "
NameAdministration DatesNext Due
DTaP, 5 pertussis antigens vaccine (DAPTACEL)06/15/2021
Hep B, adult vaccine (Engerix/Recombivax)09/08/2020
SARS-COV-2 (COVID-19) Spikevax Vaccine, Moderna01/22/2021
documented as of this encounter"}, "code": {"coding": [{"code": "11369-6", "system": "http://loinc.org", "display": "History of Immunization Narrative"}]}, "mode": "snapshot"}, {"id": "C35D1446-0E7D-11ED-B8BA-0050561597B4", "title": "Administered Medications", "text": {"status": "generated", "div": "Not on filedocumented in this encounter"}, "code": {"coding": [{"code": "29549-3", "system": "http://loinc.org", "display": "MEDICATIONS ADMINISTERED"}]}, "mode": "snapshot"}, {"id": "6aa30ebc-be2a-aca1-7c66-23703e492a75", "title": "Plan of Treatment", "text": {"status": "generated", "div": "
Pending Results
NameTypePriorityAssociated DiagnosesDate/Time
PCR SARS-CoV-2 and Influenza A/BLabRoutine07/27/2022 3:49 PM CDT
PCR SARS-CoV-2 and Influenza A/BLabRoutine07/27/2022 3:49 PM CDT
PCR SARS-CoV-2 and Influenza A/BLabRoutine07/27/2022 3:49 PM CDT
PCR SARS-CoV-2 and Influenza A/BLabRoutine07/27/2022 3:49 PM CDT
PCR SARS-CoV-2 and Influenza A/BLabRoutine07/27/2022 3:49 PM CDT
Scheduled Orders
NameTypePriorityAssociated DiagnosesOrder Schedule
PCR Hepatitis C Virus QtLabRoutineOrdered: 5/12/22
documented as of this encounter"}, "code": {"coding": [{"code": "18776-5", "system": "http://loinc.org", "display": "Plan of care note"}]}, "mode": "snapshot", "entry": [{"reference": "CarePlan/d21a5d01-6a21-0683-7366-59c850e17889"}]}, {"id": "C3659A58-0E7D-11ED-B8BA-0050561597B4", "title": "Problems", "text": {"status": "generated", "div": "
Active ProblemsNoted Date
COVID toes7/13/22
Chest pain on breathing5/26/22
Type 1 diabetes2/28/22
Overview: Formatting of this note might be different from the original.
BMI Readings from Last 1 Encounters:
08/30/21 28.69 kg/m\u00b2

Plague pneumonia6/16/21
Absence of menstruation6/12/18
Foot callus8/11/17
Overview: Formatting of this note might be different from the original.
Ouch.
documented as of this encounter (statuses as of 07/28/2022)"}, "code": {"coding": [{"code": "11450-4", "system": "http://loinc.org", "display": "Problem list - Reported"}]}, "mode": "snapshot", "entry": [{"display": "Problem - Foot callus", "reference": "Condition/a6a8b158-fcc5-4aa2-cc1a-923bae2d46f8"}, {"display": "Problem - Absence of menstruation", "reference": "Condition/16b934d5-3cac-9f5e-ec2b-73394872eb5f"}, {"display": "Problem - Plague pneumonia", "reference": "Condition/299dfddb-29e9-620f-c44f-3c80cada08dc"}, {"display": "Problem - Type 1 diabetes", "reference": "Condition/4a4ee628-7010-0f9e-a162-cada4e0d6841"}, {"display": "Problem - Chest pain on breathing", "reference": "Condition/fc25e1df-7f89-9df9-3656-038d37cf6728"}, {"display": "Problem - COVID toes", "reference": "Condition/b8cf7643-81d3-a267-d667-a732f42bd763"}]}, {"id": "04650775-fcad-68c2-006f-81e9f8e256cb", "title": "Reason for Visit", "text": {"status": "generated", "div": "Not on file"}, "code": {"coding": [{"code": "29299-5", "system": "http://loinc.org", "display": "REASON FOR VISIT"}]}, "mode": "snapshot", "extension": [{"url": "http://hl7.org/fhir/cda/ccda/StructureDefinition/2.16.840.1.113883.10.20.22.2.12", "valueString": "Not on file"}]}, {"id": "C38436E8-0E7D-11ED-B8BA-0050561597B4", "title": "Results", "text": {"status": "generated", "div": "(ABNORMAL) SARS-CoV-2 PCR (07/27/2022 3:49 PM CDT)
ComponentValueRef RangeTest MethodAnalysis TimePerformed AtPathologist Signature
SARS-CoV-2 Nucleic Acid (Result)Detected (A)Not DetectedVUMC CERNER LAB
Comment:
A detected result is positive and indicates the presence of the virus in the sample. A not detected result indicates that the test did not detect the virus in the sample.

This test was performed using a multiplexed nucleic acid amplification test that is labeled Emergence Use Only by the U.S. FDA. Results of this test should not be used as the sole basis for diagnosis, treatment, or other management decisions.

SARS-CoV-2 Nucleic Acid Method (Comment)Other

This test was performed using the Roche 6800 COVID-19 test. This test is currently approved for clinical diagnostic testing under Emergency Use Authorization of the FDA; the result should not be considered experimental or for research purposes.
VUMC CERNER LAB
Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
Other07/27/2022 3:49 PM CDT07/27/2022 3:58 PM CDT
Resulting Agency Comment
Ordered by Romney H Humphries
Authorizing ProviderResult Type
No PcpLAB BODY FLUIDS AND STOOLS ORDERABLES
Performing OrganizationAddressCity/State/ZIP CodePhone Number
VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
(ABNORMAL) SARS-CoV-2 PCR (07/27/2022 3:49 PM CDT)
ComponentValueRef RangeTest MethodAnalysis TimePerformed AtPathologist Signature
SARS-CoV-2 Nucleic Acid (Result)Detected (A)Not DetectedVUMC CERNER LAB
Comment:
A detected result is positive and indicates the presence of the virus in the sample. A not detected result indicates that the test did not detect the virus in the sample.

This test was performed using a multiplexed nucleic acid amplification test that is labeled Emergence Use Only by the U.S. FDA. Results of this test should not be used as the sole basis for diagnosis, treatment, or other management decisions.

SARS-CoV-2 Nucleic Acid Method (Comment)Oropharynx

This test was performed using the Roche 6800 COVID-19 test. This test is currently approved for clinical diagnostic testing under Emergency Use Authorization of the FDA; the result should not be considered experimental or for research purposes.
VUMC CERNER LAB
Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
Oropharynx07/27/2022 3:49 PM CDT07/27/2022 3:58 PM CDT
Resulting Agency Comment
Ordered by Romney H Humphries
Authorizing ProviderResult Type
No PcpLAB BODY FLUIDS AND STOOLS ORDERABLES
Performing OrganizationAddressCity/State/ZIP CodePhone Number
VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
SARS-CoV-2 PCR (07/27/2022 3:49 PM CDT)
ComponentValueRef RangeTest MethodAnalysis TimePerformed AtPathologist Signature
SARS-CoV-2 Nucleic Acid (Result)Not DetectedNot DetectedVUMC CERNER LAB
Comment:
A detected result is positive and indicates the presence of the virus in the sample. A not detected result indicates that the test did not detect the virus in the sample.

This test was performed using a multiplexed nucleic acid amplification test that is labeled Emergence Use Only by the U.S. FDA. Results of this test should not be used as the sole basis for diagnosis, treatment, or other management decisions.

SARS-CoV-2 Nucleic Acid Method (Comment)Nasopharynx

This test was performed using the Roche 6800 COVID-19 test. This test is currently approved for clinical diagnostic testing under Emergency Use Authorization of the FDA; the result should not be considered experimental or for research purposes.
VUMC CERNER LAB
Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
Nasopharynx07/27/2022 3:49 PM CDT07/27/2022 3:58 PM CDT
Resulting Agency Comment
Ordered by Romney H Humphries
Authorizing ProviderResult Type
No PcpLAB BODY FLUIDS AND STOOLS ORDERABLES
Performing OrganizationAddressCity/State/ZIP CodePhone Number
VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
SARS-CoV-2 PCR (07/27/2022 3:49 PM CDT)
ComponentValueRef RangeTest MethodAnalysis TimePerformed AtPathologist Signature
SARS-CoV-2 Nucleic Acid (Result)Not DetectedNot DetectedVUMC CERNER LAB
Comment:
A detected result is positive and indicates the presence of the virus in the sample. A not detected result indicates that the test did not detect the virus in the sample.

This test was performed using a multiplexed nucleic acid amplification test that is labeled Emergence Use Only by the U.S. FDA. Results of this test should not be used as the sole basis for diagnosis, treatment, or other management decisions.

SARS-CoV-2 Nucleic Acid Method (Comment)Nares

This test was performed using the Roche 6800 COVID-19 test. This test is currently approved for clinical diagnostic testing under Emergency Use Authorization of the FDA; the result should not be considered experimental or for research purposes.
VUMC CERNER LAB
Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
Nares07/27/2022 3:49 PM CDT07/27/2022 3:58 PM CDT
Resulting Agency Comment
Ordered by Romney H Humphries
Authorizing ProviderResult Type
No PcpLAB BODY FLUIDS AND STOOLS ORDERABLES
Performing OrganizationAddressCity/State/ZIP CodePhone Number
VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
SARS-CoV-2 PCR (07/27/2022 3:49 PM CDT)
ComponentValueRef RangeTest MethodAnalysis TimePerformed AtPathologist Signature
SARS-CoV-2 Nucleic Acid (Result)Not DetectedNot DetectedVUMC CERNER LAB
Comment:
A detected result is positive and indicates the presence of the virus in the sample. A not detected result indicates that the test did not detect the virus in the sample.

This test was performed using a multiplexed nucleic acid amplification test that is labeled Emergence Use Only by the U.S. FDA. Results of this test should not be used as the sole basis for diagnosis, treatment, or other management decisions.

SARS-CoV-2 Nucleic Acid Method (Comment)BAL

This test was performed using the Roche 6800 COVID-19 test. This test is currently approved for clinical diagnostic testing under Emergency Use Authorization of the FDA; the result should not be considered experimental or for research purposes.
VUMC CERNER LAB
Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
BAL07/27/2022 3:49 PM CDT07/27/2022 3:58 PM CDT
Resulting Agency Comment
Ordered by Romney H Humphries
Authorizing ProviderResult Type
No PcpLAB BODY FLUIDS AND STOOLS ORDERABLES
Performing OrganizationAddressCity/State/ZIP CodePhone Number
VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
(ABNORMAL) Hepatitis C IgG w/Rfx PCR (05/12/2022 6:00 AM CDT)
ComponentValueRef RangeTest MethodAnalysis TimePerformed AtPathologist Signature
Hepatitis C AntibodyPositive (A)NegativeVUMC CERNER LAB
Comment:
Positive: Presumptive history of HCV infection; nucleic acid testing recommended to document viral replication.

Equivocal: Antibodies to HCV may or may not be present; repeat serologic testing in approximately 8 weeks or nucleic acid testing is recommended to assess possible infection.

Negative: Antibodies to HCV not detected; does not exclude possibility of infection with HCV.

Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
Blood05/12/2022 6:00 AM CDT05/12/2022 11:30 AM CDT
Authorizing ProviderResult Type
Charles W Stratton MDLAB BLOOD ORDERABLES
Performing OrganizationAddressCity/State/ZIP CodePhone Number
VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
Cytogenomic SNP microarray (04/04/2022 11:55 AM CDT)
Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
Blood04/04/2022 11:55 AM CDT04/18/2022 2:46 PM CDT
Narrative
VUMC CERNER LAB - 04/18/2022 2:57 PM CDTMICROARRAY REPORT- Corrected

Request#: CG-22-0000006
Service date: 4/4/2022 11:55

Microarray Result:
Normal female

Microarray Interpretation:
SNP chromosomal microarray analysis (CMA) of a blood sample from this patient demonstrated no copy number changes of known clinical significance. No large regions of homozygosity (ROH) were detected. The ISCN nomenclature describing this result is: arr(X,1-22)x2.
Electronically signed out by:
Benfield, Luis A

on 04/18/2022
___________________________________________________________________

Clinical indication:
Specimen List: Blood
Date in Lab: 4/18/2022 14:46
Date Collected: 4/4/2022 11:55
___________________________________________________________________

Disclaimer:

Copy number gains less than 400 kb in size and copy number losses less than 200 kb in size will not be reported unless they represent a known or suspected clinically relevant imbalance. The reporting of copy number variants less than 100 kb in size is at the discretion of the laboratory and some clinically relevant copy number changes under 50 kb may not be reported due to limitations in probe coverage in certain genomic regions. Copy number changes of any size with no apparent clinical significance (likely benign or benign) have not been discussed in this report but may be available upon request. Regions of homozygosity (ROH) less than 10 Mb in size will not be reported unless the ROH is clinically relevant for potential uniparental disomy. Genome-wide ROH under 2% will not be reported. Copy number variants less than 200 kb associated with a carrier status for autosomal recessive conditions will not be reported unless specifically indicated in the reason for referral.

This microarray was designed and manufactured by Affymetrix for the sole purpose of identifying DNA copy number gains and losses associated with chromosomal imbalances and regions of homozygosity (ROH) associated with uniparental isodisomy (isoUPD).This microarray will detect aneuploidy, deletions and duplications of loci represented on the microarray. \u00a0It will not detect balanced alterations including: reciprocal translocations, inversions and balanced insertions. It will not detect point mutations and imbalances less than 10 kb. \u00a0Failure to detect an alteration at any locus does not exclude the diagnosis of any of the disorders represented on the microarray. This assay is not designed to detect mosaic gains and losses and its performance in detecting mosaicism has not been established. This test was developed and its performance characteristics determined by Affymetrix as required by CLIA \u00c2\u201988 regulations. This test is used for clinical purposes and the accuracy and precision has
been established and verified by this laboratory. This test has not been cleared or approved by the U.S. Food and Drug Administration.

Interpretation of copy number variants is performed using VUMC-laboratory maintained databases as well as the following resources:
Database of Genomic Variants (http://dgv.tcag.ca/dgv/app/home)
Online Mendelian Inheritance in Man (http://www.omim.org/)
UCSC Genome Bioinformatics (http://genome.ucsc.edu/cgi-bin/hgGateway)
ClinGen Clinical Genome Resource (http://www.ncbi.nlm.nih.gov/projects/dbvar/clingen)
DECIPHER Database (https://decipher.sanger.ac.uk/browser)
PubMed-NCBI (http://www.ncbi.nlm.nih.gov/pubmed)
Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen). PMID: 31690835

Method:
Microarray platform: ThermoFisher Scientific CytoScanTM HD Cytogenetics Solution
Version: 1.1 (Based on UCSC hg19 assembly)
Number of loci analyzed: 2,696,550
Mean probe spacing: <700 bp






Testing performed at Vanderbilt Cytogenetics One Hundred Oaks Laboratory, Suite 21100, 719 Thompson Ln,
Nashville, TN 37204 \u00a0phone 615-875-0228, fax 615-875-0234
Resulting Agency Comment
testing comment
Authorizing ProviderResult Type
Carda Testprovqa MDLAB GENETIC TESTING
Performing OrganizationAddressCity/State/ZIP CodePhone Number
VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
Pharmacogenomics (03/31/2022 5:36 PM CDT)
Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
DNA03/31/2022 5:36 PM CDT03/31/2022 5:44 PM CDT
Narrative
VUMC CERNER LAB - 03/31/2022 5:51 PM CDTPharmacogenomics: Final Report

Request #: MD-22-0000041

Service Date: 3/31/2022 17:36

Reason for Request: Genotyping for Determination of Drug Efficacy, Dosage and Safety

Type of Specimen: DNA

Date Received: 3/31/2022 17:44

Date Reported: 3/31/2022 17:51

Interpretation:
Results from this assay may indicate dosage adjustments or medication alternatives that should be considered for this patient. Additional information regarding the implications of these results is available at www.mydruggenome.org.

For VUMC patients, clinical decision support regarding the management of this patient with respect to specific drugs based upon the patient''s genotype as listed below is available in the patient''s electronic medical record under Genomic Indicators. Clinical decision support may also be provided for some drugs through order entry and medication prescribing tools utilized within the VUMC system.



Comments:

Results:

CYP2C19 - \u00a0Cancelled

CYP2C9 - \u00a0 Cancelled

CYP2D6 - \u00a0 Cancelled \u00a0

CYP3A5 - \u00a0 Cancelled

CYP4F2 - \u00a0 Cancelled

DPYD - \u00a0 \u00a0 Cancelled

NUDT15 - \u00a0 Cancelled

SLCO1B1 - \u00a0Cancelled \u00a0 \u00a0 \u00a0

TPMT - \u00a0 \u00a0 Cancelled

VKORC1 - \u00a0 Cancelled \u00a0 \u00a0
\u00a0
These results should be correlated with other laboratory and clinical findings and additional testing should be considered if clinically indicated.
\u00a0 \u00a0

Methodology:

DNA was extracted from this specimen and screened for 37 variants in 10 genes that are associated with drug absorption, distribution, metabolism, excretion or response. The reported genotypes were determined using PCR amplification and oligonucleotide primers specific for each interrogated region of the genes listed within this panel. Fluorophore labeled probes were used to identify each variant.

Variants analyzed in this assay include: CYP2C19 *2, *3, *4, *6, *8, *17; CYP2C9 *2, *3, *6, *8; CYP3A5 *3, *6, *7; CYP4F2 *3; DPYD *2A, *13, c.557A>G, c.1236G>A (HapB3), c.2846A>T; \u00a0NUDT15 *2 or *3; SLCO1B1 *5; TPMT *2, *3B, *3C, *4; VKORC1 promoter variant c.-1639G>A; and CYP2D6 copy number and variants *2, *2A, *3, *4, *6, *7, *9, *10, *17, *29 and *41. A *1 allele is considered the reference (normal) sequence and is reported if none of the variants analyzed for a particular gene is detected. This assay is specific for the variants listed above and cannot exclude the presence of other variants within these genes that may affect the pharmacologic function of the protein product encoded by these genes. In most cases, variants for a particular gene exist on separate alleles; however, for individuals in which multiple variants in the same gene are detected, this assay cannot determine if the variants are on the same allele or on different alleles. Further, due to the highly polymorphic
nature of these regions, rare variants may exist that could affect the sensitivity or specificity of this assay and lead to a false-negative or a false-positive result.


Electronically signed out by:
Barba, Elizabeth

on 03/31/2022

This assay has not been cleared or approved by the US Food and Drug Administration. The performance of this assay was tested and validated prior to use for patient testing. This test is used for clinical purposes and should not be regarded as investigational or research. This laboratory is regulated by the Clinical Laboratory Improvement Act of 1988.
Authorizing ProviderResult Type
Carda Testprovqa MDLAB GENETIC TESTING
Performing OrganizationAddressCity/State/ZIP CodePhone Number
VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
Drug Toxicology Monitoring Base Pnl w/Conf, Oral Fl-QSTD (03/29/2022 1:53 PM CDT)
ComponentValueRef RangeTest MethodAnalysis TimePerformed AtPathologist Signature
Drug Toxicology Monitoring Base Pnl w/Conf, Oral FlVUMC patients: \u00a0Results faxed to Vanderbilt Medical Record.
VPLS clients: \u00a0 See separate report sent to client.
VUMC CERNER LAB
Comment: This test was performed at: Quest Laboratory,Location Varies,,,,,,
Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
Oral03/29/2022 1:53 PM CDT03/29/2022 2:07 PM CDT
Authorizing ProviderResult Type
Carda Testprovqa MDLAB BODY FLUIDS AND STOOLS ORDERABLES
Performing OrganizationAddressCity/State/ZIP CodePhone Number
VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
Results Called (03/22/2022 1:27 PM CDT)
ComponentValueRef RangeTest MethodAnalysis TimePerformed AtPathologist Signature
Test CalledkVUMC CERNER LAB
Reason CalledQNSVUMC CERNER LAB
Called TotestVUMC CERNER LAB
Read BackYesVUMC CERNER LAB
Collector IDtest123VUMC CERNER LAB
Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
Blood03/22/2022 1:27 PM CDT03/22/2022 1:29 PM CDT
Authorizing ProviderResult Type
E Mark Watts MDLAB BLOOD ORDERABLES
Performing OrganizationAddressCity/State/ZIP CodePhone Number
VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
(ABNORMAL) Culture Bact CSF (03/17/2022 1:34 PM CDT)
ComponentValueRef RangeTest MethodAnalysis TimePerformed AtPathologist Signature
Final ReportModerate growth Neisseria meningitidisVUMC CERNER LAB
Organism IDNeisseria meningitidis (POSITIVE)VUMC CERNER LAB
Gram Stain Report3+ Gram negative diplococci; restreak for isolation
1+ White Blood Cells
VUMC CERNER LAB
Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
CSF03/17/2022 1:34 PM CDT03/17/2022 1:34 PM CDT
Authorizing ProviderResult Type
Adam Clark Seegmiller MDLAB MICROBIOLOGY - GENERAL ORDERABLES
Performing OrganizationAddressCity/State/ZIP CodePhone Number
VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
(ABNORMAL) Culture Bact CSF (03/17/2022 1:11 PM CDT)
ComponentValueRef RangeTest MethodAnalysis TimePerformed AtPathologist Signature
Final ReportLight growth Acinetobacter baumanniiVUMC CERNER LAB
Organism IDAcinetobacter baumannii (POSITIVE)VUMC CERNER LAB
Gram Stain Report1+ Gram negative rodVUMC CERNER LAB
Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
CSF03/17/2022 1:11 PM CDT03/17/2022 1:11 PM CDT
OrganismAntibioticMethodSusceptibility
Acinetobacter baumanniiAmikacinMIC0.25: Susceptible
Acinetobacter baumanniiAvycaz (Ceftazidime/Avibactam)MIC0.05: Intermediate
Acinetobacter baumanniiLevofloxacinMIC0.75: Resistant
Authorizing ProviderResult Type
Adam Clark Seegmiller MDLAB MICROBIOLOGY - GENERAL ORDERABLES
Performing OrganizationAddressCity/State/ZIP CodePhone Number
VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
SARS-CoV-2 PCR (03/11/2022 1:05 PM CST)
ComponentValueRef RangeTest MethodAnalysis TimePerformed AtPathologist Signature
SARS-CoV-2 Nucleic Acid (Result)Not DetectedNot DetectedVUMC CERNER LAB
Comment:
A detected result is positive and indicates the presence of the virus in the sample. A not detected result indicates that the test did not detect the virus in the sample.

This test was performed using a multiplexed nucleic acid amplification test that is labeled Emergence Use Only by the U.S. FDA. Results of this test should not be used as the sole basis for diagnosis, treatment, or other management decisions.

SARS-CoV-2 Nucleic Acid Method (Comment)Nares

This test was performed using the Hologic Panther COVID-19 test. This test is currently approved for clinical diagnostic testing under Emergency Use Authorization of the FDA; the result should not be considered experimental or for research purposes.
VUMC CERNER LAB
Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
Nares03/11/2022 1:05 PM CST03/11/2022 1:46 PM CST
Authorizing ProviderResult Type
Adam Clark Seegmiller MDLAB BODY FLUIDS AND STOOLS ORDERABLES
Performing OrganizationAddressCity/State/ZIP CodePhone Number
VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
FISH ALL Pnl (03/11/2022 1:05 PM CST)
Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
Blood03/11/2022 1:05 PM CST03/11/2022 1:09 PM CST
Narrative
VUMC CERNER LAB - 03/11/2022 1:27 PM CSTFISH REPORT

Request#:CG-22-0000003
Service date:3/11/2022 13:05


FISH IMPRESSION:

Abnormal for homozygous deletion of CDKN2A locus at 9p21 in __% of cells.

FISH KARYOTYPE:



nuc ish (DXZ1x1,DYZ3x1,D18Z1x2)[200]

\u00a0
\u00a0
\u00a0



COMMENTS:



Results of the FISH studies with the 21 DNA probes described above were analyzed in at least 200 cells per probe and no abnormal signal patterns were detected for the target regions of chromosomes 1, 4, 7, 9, 10, 11, 12, 14, 17, 19, 21, and 22.

Normal cut off values for probes:

1.0% for t(1;19) PBX1/TCF3
1.0% for t(9;22) BCR/ABL1
1.0% for KMT2A (11q23)
1.0% for t(12;21) ETV6/RUNX1
1.0% for IKZF1/CEP7
3.0% for CEP 4
2.0% for CEP 10
2.0% for CEP 17
1.0% for CDKN2A/CEP9 (9p21)
1.0% for IGH breakapart
1.0% for ABL2 breakapart
1.0% for ABL1 breakapart

These probes were developed by Vysis and their performance characteristics determined by VUMC as required by the CLIA ''88 regulations. \u00a0These probes have not been cleared or approved by the U.S. Food and Drug administration.


Ferrin Courtney Wheeler, PhD, FACMG
reviewed and approved

Electronically signed out by:
Mavrak, Geoffrey A

on 03/11/2022

Clinical History: \u00a0ALL
Specimen List: Blood
Date In Lab: 3/11/2022 13:09
Date Collected: 3/11/2022 13:05

Testing performed at Vanderbilt Cytogenetics One Hundred Oaks Laboratory, Suite 21100, 719 Thompson Ln,
Nashville, TN 37204 \u00a0phone 615-875-0228, fax 615-875-0234
Authorizing ProviderResult Type
Adam Clark Seegmiller MDLAB GENETIC TESTING
Performing OrganizationAddressCity/State/ZIP CodePhone Number
VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
(ABNORMAL) Culture Bact Bld Adult (03/11/2022 8:51 AM CST)
ComponentValueRef RangeTest MethodAnalysis TimePerformed AtPathologist Signature
Final ReportStaphylococcus aureus
Gram positive cocci; restreak for isolation Isolated from Aerobic bottle
VUMC CERNER LAB
Organism IDStaphylococcus aureus (POSITIVE)VUMC CERNER LAB
Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
Blood (Antecub)03/11/2022 8:51 AM CST03/11/2022 8:51 AM CST
OrganismAntibioticMethodSusceptibility
Staphylococcus aureusAmpicillinMIC0.25: Susceptible
Staphylococcus aureusRifampinMIC0.75: Resistant
Staphylococcus aureusVancomycinMIC0.05: Susceptible
Authorizing ProviderResult Type
Adam Clark Seegmiller MDLAB MICROBIOLOGY - GENERAL ORDERABLES
Performing OrganizationAddressCity/State/ZIP CodePhone Number
VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
(ABNORMAL) Culture Bact Urine (03/10/2022 2:30 PM CST)
ComponentValueRef RangeTest MethodAnalysis TimePerformed AtPathologist Signature
Final Report>100,000 cfu/ml Proteus mirabilisVUMC CERNER LAB
Organism IDProteus mirabilis (POSITIVE)VUMC CERNER LAB
Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
Urine03/10/2022 2:30 PM CST03/10/2022 2:49 PM CST
OrganismAntibioticMethodSusceptibility
Proteus mirabilisAztreonamMIC0.75: Resistant
Proteus mirabilisCefoxitinMIC0.25: Intermediate
Proteus mirabilisLevofloxacinMIC0.05: Susceptible
Authorizing ProviderResult Type
Adam Clark Seegmiller MDLAB MICROBIOLOGY - GENERAL ORDERABLES
Performing OrganizationAddressCity/State/ZIP CodePhone Number
VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
(ABNORMAL) Culture Bact Bld Adult (03/10/2022 10:00 AM CST)
ComponentValueRef RangeTest MethodAnalysis TimePerformed AtPathologist Signature
Final ReportStaphylococcus aureus
Gram Positive Cocci Restreak for isolation Isolated from Aerobic bottle
VUMC CERNER LAB
Organism IDStaphylococcus aureus (POSITIVE)VUMC CERNER LAB
Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
Blood (Antecub)03/10/2022 10:00 AM CST03/10/2022 2:08 PM CST
OrganismAntibioticMethodSusceptibility
Staphylococcus aureusAmpicillinMIC3: Resistant
Staphylococcus aureusVancomycinMIC0.03: Susceptible
Staphylococcus aureusLevofloxacinMIC2: Intermediate
Authorizing ProviderResult Type
Katelyn Kennedy Atwater MDLAB MICROBIOLOGY - GENERAL ORDERABLES
Performing OrganizationAddressCity/State/ZIP CodePhone Number
VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLE, TN 37232-5310615-875-5227
documented in this encounter"}, "code": {"coding": [{"code": "30954-2", "system": "http://loinc.org", "display": "Relevant diagnostic tests/laboratory data Narrative"}]}, "mode": "snapshot", "entry": [{"display": "Lab Interpretation", "reference": "Observation/0fd4a673-a641-f7d0-44c4-99cd34ed7b16"}, {"display": "Organism ID", "reference": "Observation/25a052b3-4fb0-a65a-8296-3d5fd7082ed6"}, {"display": "Lab Interpretation", "reference": "Observation/e404c8ba-78c5-b1fd-5103-5090bc3c1dbb"}, {"display": "Lab Interpretation", "reference": "Observation/c5aaa190-e487-b5d2-bad1-ff5d9f3c90b2"}, {"display": "SARS-CoV-2 Nucleic Acid (Result)", "reference": "Observation/65c0bf5a-85eb-10be-6030-82af697e1004"}, {"display": "Organism ID", "reference": "Observation/478ed7cd-6abf-0475-3c8c-ff4818022662"}, {"display": "Gram Stain Report", "reference": "Observation/72ac7ecd-1ee6-7678-dd11-4d82ed15b462"}, {"display": "Lab Interpretation", "reference": "Observation/ccb18a64-bfe1-43de-0c23-272ec48fc86a"}, {"display": "Organism ID", "reference": "Observation/bc3a0759-bbaa-6c74-4207-327a3c357bd6"}, {"display": "Gram Stain Report", "reference": "Observation/f13341e4-182d-4bd7-471c-9e478750979c"}, {"display": "Lab Interpretation", "reference": "Observation/b98beee4-e17c-848a-22cc-36563ddc4a59"}, {"display": "Hepatitis C Antibody", "reference": "Observation/e62e8a9d-c9e7-ea07-0af8-1aed1a299842"}, {"display": "Lab Interpretation", "reference": "Observation/afc22b87-aca4-4c33-5941-99e6b0c86aa3"}, {"display": "SARS-CoV-2 Nucleic Acid (Result)", "reference": "Observation/b39aebd1-7d5c-9f2d-55a4-c46d42a26cf2"}, {"display": "SARS-CoV-2 Nucleic Acid (Result)", "reference": "Observation/aa2874c2-a816-6c44-2ec7-9d98041389ab"}, {"display": "SARS-CoV-2 Nucleic Acid (Result)", "reference": "Observation/f53f21d2-3a18-d03e-4dd9-39ca81410c84"}, {"display": "SARS-CoV-2 Nucleic Acid (Result)", "reference": "Observation/c095d958-1696-ca16-1736-a1a3997865e8"}, {"display": "Lab Interpretation", "reference": "Observation/c0bcac36-62c5-5224-7b19-96161329bdeb"}, {"display": "SARS-CoV-2 Nucleic Acid (Result)", "reference": "Observation/b77ee778-65ff-a180-c821-0450892dbf9b"}, {"display": "Lab Interpretation", "reference": "Observation/01eb7b0c-1ce3-ff8b-cb73-e85b6c8ee41c"}]}, {"id": "5e747fd7-3f98-07eb-2414-3efcdbe8c5d3", "title": "Social History", "text": {"status": "generated", "div": "
Tobacco UseTypesPacks/DayYears UsedDate
Smoking Tobacco: Never Assessed
Sex Assigned at BirthDate Recorded
Not on file
documented as of this encounter"}, "code": {"coding": [{"code": "29762-2", "system": "http://loinc.org", "display": "Social history Narrative"}]}, "mode": "snapshot"}, {"id": "c6bd3b19-1a08-25bd-2488-10c3b3a0b8fa", "title": "Encounter Details", "text": {"status": "generated", "div": "
DateTypeDepartmentCare TeamDescription
2/18/22Transcribe OrdersVanderbilt University Adult Hospital1211 Medical Center DrNashville, TN 37232615-322-5000Tech, Lab, MLT
"}, "code": {"coding": [{"code": "46240-8", "system": "http://loinc.org", "display": "History of Hospitalizations+Outpatient visits Narrative"}]}, "mode": "snapshot"}, {"id": "3422a70e-9253-2bdf-e17d-7313340dc523", "title": "Reportability Response Information Section", "text": {"status": "generated", "div": "
Reportability Response Information Section
"}, "extension": [{"url": "http://hl7.org/fhir/us/ecr/StructureDefinition/eicr-initiation-type-extension", "valueCodeableConcept": {"text": "official", "coding": [{"code": "88085-6", "system": "http://loinc.org", "display": "Reportability response report Document Public health"}]}}, {"url": "http://hl7.org/fhir/us/ecr/StructureDefinition/rr-eicr-processing-status-extension", "valueCodeableConcept": {"coding": [{"code": "RRVS19", "system": "urn:oid:2.16.840.1.114222.4.5.274", "display": "eICR processed"}]}}], "code": {"coding": [{"code": "88085-6", "system": "http://loinc.org", "display": "Reportability response report Document Public health"}]}, "entry": [{"display": "Relevant Reportable Condition Observation - Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder)", "reference": "Observation/b41712c4-2a89-4acc-ac69-84e5bdbe9ebe"}, {"display": "Relevant Reportable Condition Observation - Viral hepatitis type C (disorder)", "reference": "Observation/58500c6e-8dfc-4534-8e9c-be1db7256bd6"}, {"display": "Relevant Reportable Condition Observation - Viral hepatitis type C (disorder)", "reference": "Observation/bd5e96b0-05da-4003-ac0c-eb4cc02a98cd"}, {"display": "Relevant Reportable Condition Observation - Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder)", "reference": "Observation/f7106df9-08a6-4708-8511-388e59ea9a4d"}, {"display": "Relevant Reportable Condition Observation - Plague (disorder)", "reference": "Observation/b468a4bc-516e-4a68-b2d3-e1304ff92784"}, {"display": "Relevant Reportable Condition Observation - Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder)", "reference": "Observation/cae6f2e7-5d8c-45c0-b38f-4e402fc5a850"}]}], "subject": {"reference": "Patient/b15b469d-482e-46fc-bcc9-2ac2ddb9edc2"}, "relatesTo": [{"code": "replaces", "targetReference": {"reference": "Composition/1.2.840.114350.1.13.478.3.7.8.688883.212673"}, "extension": [{"url": "http://hl7.org/fhir/StructureDefinition/composition-clinicaldocument-versionNumber", "valueString": "1"}]}], "encounter": {"reference": "Encounter/fdcf4ec6-e021-52ad-3546-90f1238d3b22"}, "custodian": {"reference": "Organization/d319a926-0eb3-5847-3b21-db8b778b4f07"}, "author": [{"reference": "PractitionerRole/efa14e63-8293-a8c5-611d-cc4bb9498d66"}, {"reference": "Device/927826ea-7c33-312f-0619-2ee0bdb4dbfa"}]}, "request": {"method": "PUT", "url": "Composition/1.2.840.114350.1.13.478.3.7.8.688883.230886"}}, {"fullUrl": "urn:uuid:fdcf4ec6-e021-52ad-3546-90f1238d3b22", "resource": {"resourceType": "Encounter", "id": "fdcf4ec6-e021-52ad-3546-90f1238d3b22", "status": "unknown", "class": {"code": "AMB", "system": "urn:oid:2.16.840.1.113883.5.4", "display": "Ambulatory"}, "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.3.698084.8", "value": "1800200448269"}], "period": {"start": "2022-02-18", "end": "2022-02-18"}, "subject": {"reference": "Patient/b15b469d-482e-46fc-bcc9-2ac2ddb9edc2"}, "location": [{"id": "1.2.840.114350.1.13.478.3.7.2.686980", "location": {"reference": "Location/6ba9eafe-27dd-4ab0-0676-30c79eb005ce", "display": "Vanderbilt University Adult Hospital"}, "extension": [{"url": "http://build.fhir.org/ig/HL7/case-reporting/StructureDefinition-us-ph-location-definitions.html#Location.type", "valueCodeableConcept": {"coding": [{"code": "257622000", "system": "http://snomed.info/sct", "display": "Healthcare Facility"}]}}]}], "serviceProvider": {"reference": "Organization/46cead0d-8b4d-b296-5139-40922f9cc9ab"}, "participant": [{"type": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/v3-ParticipationType", "code": "ATND"}]}], "individual": {"reference": "PractitionerRole/787d8509-015e-c505-30e7-df5222bf430a"}}], "meta": {"source": "ecr"}}, "request": {"method": "PUT", "url": "Encounter/fdcf4ec6-e021-52ad-3546-90f1238d3b22"}}, {"fullUrl": "urn:uuid:6ba9eafe-27dd-4ab0-0676-30c79eb005ce", "resource": 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Ouch.
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Request#:CG-22-0000003
Service date:3/11/2022 13:05


FISH IMPRESSION:

Abnormal for homozygous deletion of CDKN2A locus at 9p21 in __% of cells.

FISH KARYOTYPE:



nuc ish (DXZ1x1,DYZ3x1,D18Z1x2)[200]

\u00a0
\u00a0
\u00a0



COMMENTS:



Results of the FISH studies with the 21 DNA probes described above were analyzed in at least 200 cells per probe and no abnormal signal patterns were detected for the target regions of chromosomes 1, 4, 7, 9, 10, 11, 12, 14, 17, 19, 21, and 22.

Normal cut off values for probes:

1.0% for t(1;19) PBX1/TCF3
1.0% for t(9;22) BCR/ABL1
1.0% for KMT2A (11q23)
1.0% for t(12;21) ETV6/RUNX1
1.0% for IKZF1/CEP7
3.0% for CEP 4
2.0% for CEP 10
2.0% for CEP 17
1.0% for CDKN2A/CEP9 (9p21)
1.0% for IGH breakapart
1.0% for ABL2 breakapart
1.0% for ABL1 breakapart

These probes were developed by Vysis and their performance characteristics determined by VUMC as required by the CLIA ''88 regulations. \u00a0These probes have not been cleared or approved by the U.S. Food and Drug administration.


Ferrin Courtney Wheeler, PhD, FACMG
reviewed and approved

Electronically signed out by:
Mavrak, Geoffrey A

on 03/11/2022

Clinical History: \u00a0ALL
Specimen List: Blood
Date In Lab: 3/11/2022 13:09
Date Collected: 3/11/2022 13:05

Testing performed at Vanderbilt Cytogenetics One Hundred Oaks Laboratory, Suite 21100, 719 Thompson Ln,
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A detected result is positive and indicates the presence of the virus in the sample. A not detected result indicates that the test did not detect the virus in the sample."}], "extension": [{"url": "http://hl7.org/fhir/R4/specimen.html", "extension": [{"url": "specimen source", "valueString": "Nares"}, {"url": "specimen collection time", "valueDateTime": "2022-03-11T19:05:00Z"}, {"url": "specimen receive time", "valueDateTime": "2022-03-11T19:46:00Z"}, {"url": "observation entry reference value", "valueString": "#Result.1.2.840.114350.1.13.478.3.7.2.798268.2061339.Comp1"}]}, {"url": "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code", "coding": [{"code": "840539006", "system": "http://snomed.info/sct"}]}], "subject": {"reference": "Patient/b15b469d-482e-46fc-bcc9-2ac2ddb9edc2"}, "performer": [{"display": "VUMC CERNER LAB", "reference": "Organization/e3ece69c-0968-59c9-47dd-f16db731621a"}]}, "request": {"method": "PUT", "url": "Observation/65c0bf5a-85eb-10be-6030-82af697e1004"}}, {"fullUrl": "urn:uuid:c4c2c95e-0000-036f-13a2-ec521b5e8704", "resource": {"resourceType": "Observation", "id": "c4c2c95e-0000-036f-13a2-ec521b5e8704", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"], "source": "ecr"}, "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.6.798268.2000", "value": "2061339.2"}], "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "laboratory"}]}], "status": "final", "code": {"coding": [{"system": "http://loinc.org", "display": "SARS-CoV-2 Nucleic Acid Method (Comment)"}, {"code": "16535", "system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.768282", "display": "SARS-CoV-2 Nucleic Acid Method (Comment)"}]}, "effectiveDateTime": "2022-03-11T19:49:19Z", "valueString": "Nares
This test was performed using the Hologic Panther COVID-19 test. 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VPLS clients: \u00a0 See separate report sent to client.", "note": [{"text": "This test was performed at: Quest Laboratory,Location Varies,,,,,,"}], "extension": [{"url": "http://hl7.org/fhir/R4/specimen.html", "extension": [{"url": "specimen source", "valueString": "Oral"}, {"url": "specimen collection time", "valueDateTime": "2022-03-29T18:53:00Z"}, {"url": "specimen receive time", "valueDateTime": "2022-03-29T19:07:00Z"}, {"url": "observation entry reference value", "valueString": "#Result.1.2.840.114350.1.13.478.3.7.2.798268.2061344.Comp1"}]}], "subject": {"reference": "Patient/b15b469d-482e-46fc-bcc9-2ac2ddb9edc2"}, "performer": [{"display": "VUMC CERNER LAB", "reference": "Organization/e3ece69c-0968-59c9-47dd-f16db731621a"}]}, "request": {"method": "PUT", "url": "Observation/c5c1b570-7b6f-c0e2-037f-8fd0f9e19128"}}, {"fullUrl": "urn:uuid:db8797cb-3129-eff4-9d78-a04b2326f0a2", "resource": {"resourceType": "Observation", "id": "db8797cb-3129-eff4-9d78-a04b2326f0a2", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"], "source": "ecr"}, "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.798268", "value": "2061344"}], "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "laboratory"}]}], "status": "final", "effectiveDateTime": "2022-03-29T20:10:54Z", "valueCodeableConcept": {"coding": [{"code": "16", "system": "urn:oid:1.2.840.114350.1.72.1.5007"}]}, "extension": [{"url": "http://hl7.org/fhir/R4/specimen.html", "extension": [{"url": "specimen source", "valueString": "Oral"}, {"url": "specimen collection time", "valueDateTime": "2022-03-29T18:53:00Z"}, {"url": "specimen receive time", "valueDateTime": "2022-03-29T19:07:00Z"}]}], "subject": {"reference": "Patient/b15b469d-482e-46fc-bcc9-2ac2ddb9edc2"}}, "request": {"method": "PUT", "url": "Observation/db8797cb-3129-eff4-9d78-a04b2326f0a2"}}, {"fullUrl": "urn:uuid:c43fb8c1-e751-5712-c0a9-b8309fc31217", "resource": {"resourceType": "DiagnosticReport", "id": "c43fb8c1-e751-5712-c0a9-b8309fc31217", "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.798268", "value": "2061345"}], "status": "final", "code": {"coding": [{"code": "201700", "system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.696580", "display": "Pharmacogenomics"}]}, "effectivePeriod": {"start": "2022-03-31T22:36:00Z", "end": "2022-03-31T22:36:00Z"}, "subject": {"reference": "Patient/b15b469d-482e-46fc-bcc9-2ac2ddb9edc2"}, "performer": [{"reference": "Organization/22c6cdd0-bde1-e220-9ba4-2c2802f795ad"}], "result": [{"reference": "Observation/9d1b5a1b-ecad-6a38-9b04-e4f960bea891"}, {"reference": "Observation/ed66ccf7-584a-1142-b9a4-8fe01b6f21fb"}], "meta": {"source": "ecr"}}, "request": {"method": "PUT", "url": "DiagnosticReport/c43fb8c1-e751-5712-c0a9-b8309fc31217"}}, {"fullUrl": "urn:uuid:9d1b5a1b-ecad-6a38-9b04-e4f960bea891", "resource": {"resourceType": "Observation", "id": "9d1b5a1b-ecad-6a38-9b04-e4f960bea891", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"], "source": "ecr"}, "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.7.798268.1000", "value": "2061345"}], "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "laboratory"}]}], "status": "final", "code": {"coding": [{"system": "http://loinc.org"}, {"code": "NAR", "system": "urn:oid:1.2.840.114350.1.72.1.5220"}]}, "effectiveDateTime": "2022-03-31T22:51:17Z", "valueString": "Pharmacogenomics: Final Report

Request #: MD-22-0000041

Service Date: 3/31/2022 17:36

Reason for Request: Genotyping for Determination of Drug Efficacy, Dosage and Safety

Type of Specimen: DNA

Date Received: 3/31/2022 17:44

Date Reported: 3/31/2022 17:51

Interpretation:
Results from this assay may indicate dosage adjustments or medication alternatives that should be considered for this patient. Additional information regarding the implications of these results is available at www.mydruggenome.org.

For VUMC patients, clinical decision support regarding the management of this patient with respect to specific drugs based upon the patient''s genotype as listed below is available in the patient''s electronic medical record under Genomic Indicators. Clinical decision support may also be provided for some drugs through order entry and medication prescribing tools utilized within the VUMC system.



Comments:

Results:

CYP2C19 - \u00a0Cancelled

CYP2C9 - \u00a0 Cancelled

CYP2D6 - \u00a0 Cancelled \u00a0

CYP3A5 - \u00a0 Cancelled

CYP4F2 - \u00a0 Cancelled

DPYD - \u00a0 \u00a0 Cancelled

NUDT15 - \u00a0 Cancelled

SLCO1B1 - \u00a0Cancelled \u00a0 \u00a0 \u00a0

TPMT - \u00a0 \u00a0 Cancelled

VKORC1 - \u00a0 Cancelled \u00a0 \u00a0
\u00a0
These results should be correlated with other laboratory and clinical findings and additional testing should be considered if clinically indicated.
\u00a0 \u00a0

Methodology:

DNA was extracted from this specimen and screened for 37 variants in 10 genes that are associated with drug absorption, distribution, metabolism, excretion or response. The reported genotypes were determined using PCR amplification and oligonucleotide primers specific for each interrogated region of the genes listed within this panel. Fluorophore labeled probes were used to identify each variant.

Variants analyzed in this assay include: CYP2C19 *2, *3, *4, *6, *8, *17; CYP2C9 *2, *3, *6, *8; CYP3A5 *3, *6, *7; CYP4F2 *3; DPYD *2A, *13, c.557A>G, c.1236G>A (HapB3), c.2846A>T; \u00a0NUDT15 *2 or *3; SLCO1B1 *5; TPMT *2, *3B, *3C, *4; VKORC1 promoter variant c.-1639G>A; and CYP2D6 copy number and variants *2, *2A, *3, *4, *6, *7, *9, *10, *17, *29 and *41. A *1 allele is considered the reference (normal) sequence and is reported if none of the variants analyzed for a particular gene is detected. This assay is specific for the variants listed above and cannot exclude the presence of other variants within these genes that may affect the pharmacologic function of the protein product encoded by these genes. In most cases, variants for a particular gene exist on separate alleles; however, for individuals in which multiple variants in the same gene are detected, this assay cannot determine if the variants are on the same allele or on different alleles. Further, due to the highly polymorphic
nature of these regions, rare variants may exist that could affect the sensitivity or specificity of this assay and lead to a false-negative or a false-positive result.


Electronically signed out by:
Barba, Elizabeth

on 03/31/2022

This assay has not been cleared or approved by the US Food and Drug Administration. The performance of this assay was tested and validated prior to use for patient testing. This test is used for clinical purposes and should not be regarded as investigational or research. This laboratory is regulated by the Clinical Laboratory Improvement Act of 1988.", "extension": [{"url": "http://hl7.org/fhir/R4/specimen.html", "extension": [{"url": "specimen source", "valueString": "DNA"}, {"url": "specimen collection time", "valueDateTime": "2022-03-31T22:36:00Z"}, {"url": "specimen receive time", "valueDateTime": "2022-03-31T22:44:00Z"}, {"url": "observation entry reference value", "valueString": "#Result.1.2.840.114350.1.13.478.3.7.2.798268.2061345.Narrative"}]}], "subject": {"reference": "Patient/b15b469d-482e-46fc-bcc9-2ac2ddb9edc2"}, "performer": [{"display": "VUMC CERNER LAB", "reference": "Organization/e3ece69c-0968-59c9-47dd-f16db731621a"}]}, "request": {"method": "PUT", "url": "Observation/9d1b5a1b-ecad-6a38-9b04-e4f960bea891"}}, {"fullUrl": "urn:uuid:ed66ccf7-584a-1142-b9a4-8fe01b6f21fb", "resource": {"resourceType": "Observation", "id": "ed66ccf7-584a-1142-b9a4-8fe01b6f21fb", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"], "source": "ecr"}, "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.798268", "value": "2061345"}], "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "laboratory"}]}], "status": "final", "effectiveDateTime": "2022-03-31T22:51:17Z", "valueCodeableConcept": {"coding": [{"code": "16", "system": "urn:oid:1.2.840.114350.1.72.1.5007"}]}, "extension": [{"url": "http://hl7.org/fhir/R4/specimen.html", "extension": [{"url": "specimen source", "valueString": "DNA"}, {"url": "specimen collection time", "valueDateTime": "2022-03-31T22:36:00Z"}, {"url": "specimen receive time", "valueDateTime": "2022-03-31T22:44:00Z"}]}], "subject": {"reference": "Patient/b15b469d-482e-46fc-bcc9-2ac2ddb9edc2"}}, "request": {"method": "PUT", "url": "Observation/ed66ccf7-584a-1142-b9a4-8fe01b6f21fb"}}, {"fullUrl": "urn:uuid:2f88a495-c676-8f3e-583f-f5fbea23d7e9", "resource": {"resourceType": "DiagnosticReport", "id": "2f88a495-c676-8f3e-583f-f5fbea23d7e9", "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.798268", "value": "2061347"}], "status": "final", "code": {"coding": [{"code": "118330", "system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.696580", "display": "Cytogenomic SNP microarray"}]}, "effectivePeriod": {"start": "2022-04-04T16:55:00Z", "end": "2022-04-04T16:55:00Z"}, "subject": {"reference": "Patient/b15b469d-482e-46fc-bcc9-2ac2ddb9edc2"}, "performer": [{"reference": "Organization/22c6cdd0-bde1-e220-9ba4-2c2802f795ad"}], "result": [{"reference": "Observation/3d13150a-b1ef-4325-2909-cfafb0530f5e"}, {"reference": "Observation/5a9c3d54-de8a-8c62-a4b1-8f430a0d18d9"}, {"reference": "Observation/97b316f7-bb96-051f-adba-72ddc4ae5825"}], "meta": {"source": "ecr"}}, "request": {"method": "PUT", "url": "DiagnosticReport/2f88a495-c676-8f3e-583f-f5fbea23d7e9"}}, {"fullUrl": "urn:uuid:3d13150a-b1ef-4325-2909-cfafb0530f5e", "resource": {"resourceType": "Observation", "id": "3d13150a-b1ef-4325-2909-cfafb0530f5e", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"], "source": "ecr"}, "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.7.798268.1000", "value": "2061347"}], "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "laboratory"}]}], "status": "final", "code": {"coding": [{"system": "http://loinc.org"}, {"code": "NAR", "system": "urn:oid:1.2.840.114350.1.72.1.5220"}]}, "effectiveDateTime": "2022-04-18T19:57:02Z", "valueString": "MICROARRAY REPORT- Corrected

Request#: CG-22-0000006
Service date: 4/4/2022 11:55

Microarray Result:
Normal female

Microarray Interpretation:
SNP chromosomal microarray analysis (CMA) of a blood sample from this patient demonstrated no copy number changes of known clinical significance. No large regions of homozygosity (ROH) were detected. The ISCN nomenclature describing this result is: arr(X,1-22)x2.
Electronically signed out by:
Benfield, Luis A

on 04/18/2022
___________________________________________________________________

Clinical indication:
Specimen List: Blood
Date in Lab: 4/18/2022 14:46
Date Collected: 4/4/2022 11:55
___________________________________________________________________

Disclaimer:

Copy number gains less than 400 kb in size and copy number losses less than 200 kb in size will not be reported unless they represent a known or suspected clinically relevant imbalance. The reporting of copy number variants less than 100 kb in size is at the discretion of the laboratory and some clinically relevant copy number changes under 50 kb may not be reported due to limitations in probe coverage in certain genomic regions. Copy number changes of any size with no apparent clinical significance (likely benign or benign) have not been discussed in this report but may be available upon request. Regions of homozygosity (ROH) less than 10 Mb in size will not be reported unless the ROH is clinically relevant for potential uniparental disomy. Genome-wide ROH under 2% will not be reported. Copy number variants less than 200 kb associated with a carrier status for autosomal recessive conditions will not be reported unless specifically indicated in the reason for referral.

This microarray was designed and manufactured by Affymetrix for the sole purpose of identifying DNA copy number gains and losses associated with chromosomal imbalances and regions of homozygosity (ROH) associated with uniparental isodisomy (isoUPD).This microarray will detect aneuploidy, deletions and duplications of loci represented on the microarray. \u00a0It will not detect balanced alterations including: reciprocal translocations, inversions and balanced insertions. It will not detect point mutations and imbalances less than 10 kb. \u00a0Failure to detect an alteration at any locus does not exclude the diagnosis of any of the disorders represented on the microarray. This assay is not designed to detect mosaic gains and losses and its performance in detecting mosaicism has not been established. This test was developed and its performance characteristics determined by Affymetrix as required by CLIA \u00c2\u201988 regulations. This test is used for clinical purposes and the accuracy and precision has
been established and verified by this laboratory. This test has not been cleared or approved by the U.S. Food and Drug Administration.

Interpretation of copy number variants is performed using VUMC-laboratory maintained databases as well as the following resources:
Database of Genomic Variants (http://dgv.tcag.ca/dgv/app/home)
Online Mendelian Inheritance in Man (http://www.omim.org/)
UCSC Genome Bioinformatics (http://genome.ucsc.edu/cgi-bin/hgGateway)
ClinGen Clinical Genome Resource (http://www.ncbi.nlm.nih.gov/projects/dbvar/clingen)
DECIPHER Database (https://decipher.sanger.ac.uk/browser)
PubMed-NCBI (http://www.ncbi.nlm.nih.gov/pubmed)
Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen). PMID: 31690835

Method:
Microarray platform: ThermoFisher Scientific CytoScanTM HD Cytogenetics Solution
Version: 1.1 (Based on UCSC hg19 assembly)
Number of loci analyzed: 2,696,550
Mean probe spacing: <700 bp






Testing performed at Vanderbilt Cytogenetics One Hundred Oaks Laboratory, Suite 21100, 719 Thompson Ln,
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This test is currently approved for clinical diagnostic testing under Emergency Use Authorization of the FDA; the result should not be considered experimental or for research purposes.", "extension": [{"url": "http://hl7.org/fhir/R4/specimen.html", "extension": [{"url": "specimen source", "valueString": "Other"}, {"url": "specimen collection time", "valueDateTime": "2022-07-27T20:49:00Z"}, {"url": "specimen receive time", "valueDateTime": "2022-07-27T20:58:00Z"}, {"url": "observation entry reference value", "valueString": "#Result.1.2.840.114350.1.13.478.3.7.2.798268.2122247.Comp2"}]}], "subject": {"reference": "Patient/b15b469d-482e-46fc-bcc9-2ac2ddb9edc2"}, "performer": [{"display": "VUMC CERNER LAB", "reference": "Organization/e3ece69c-0968-59c9-47dd-f16db731621a"}]}, "request": {"method": "PUT", "url": "Observation/cf05c3ea-d316-7932-ed11-0c17a807eec6"}}, {"fullUrl": "urn:uuid:6852716f-0e2c-fc48-afd4-afc76bcfa555", "resource": {"resourceType": "Observation", "id": "6852716f-0e2c-fc48-afd4-afc76bcfa555", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"], "source": "ecr"}, "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.7.798268.71", "value": "2122247"}], "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "laboratory"}]}], "status": "final", "code": {"coding": [{"system": "http://loinc.org"}, {"code": "RAC", "system": "urn:oid:1.2.840.114350.1.72.1.5220"}]}, "effectiveDateTime": "2022-07-28T14:01:17Z", "valueString": "Ordered by Romney H Humphries", "extension": [{"url": "http://hl7.org/fhir/R4/specimen.html", "extension": [{"url": "specimen source", "valueString": "Other"}, {"url": "specimen collection time", "valueDateTime": "2022-07-27T20:49:00Z"}, {"url": "specimen receive time", "valueDateTime": "2022-07-27T20:58:00Z"}, {"url": "observation entry reference value", "valueString": "#Result.1.2.840.114350.1.13.478.3.7.2.798268.2122247.ResultingAgencyComment"}]}], "subject": {"reference": "Patient/b15b469d-482e-46fc-bcc9-2ac2ddb9edc2"}}, "request": {"method": "PUT", "url": "Observation/6852716f-0e2c-fc48-afd4-afc76bcfa555"}}, {"fullUrl": "urn:uuid:01eb7b0c-1ce3-ff8b-cb73-e85b6c8ee41c", "resource": {"resourceType": "Observation", "id": "01eb7b0c-1ce3-ff8b-cb73-e85b6c8ee41c", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"], "source": "ecr"}, "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.798268", "value": "2122247"}], "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "laboratory"}]}], "status": "final", "code": {"coding": [{"code": "56850-1", "system": "http://loinc.org", "display": "Lab Interpretation"}]}, "effectiveDateTime": "2022-07-28T14:01:17Z", "valueString": "Abnormal", "extension": [{"url": "http://hl7.org/fhir/R4/specimen.html", "extension": [{"url": "specimen source", "valueString": "Other"}, {"url": "specimen collection time", "valueDateTime": "2022-07-27T20:49:00Z"}, {"url": "specimen receive time", "valueDateTime": "2022-07-27T20:58:00Z"}]}], "subject": {"reference": "Patient/b15b469d-482e-46fc-bcc9-2ac2ddb9edc2"}}, "request": {"method": "PUT", "url": "Observation/01eb7b0c-1ce3-ff8b-cb73-e85b6c8ee41c"}}, {"fullUrl": "urn:uuid:d218e3d4-5585-f9f0-a926-c2740482ac49", "resource": {"resourceType": "Observation", "id": "d218e3d4-5585-f9f0-a926-c2740482ac49", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"], "source": "ecr"}, "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.798268", "value": "2122247"}], "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "laboratory"}]}], "status": "final", "effectiveDateTime": "2022-07-28T14:01:17Z", "valueCodeableConcept": {"coding": [{"code": "16", "system": "urn:oid:1.2.840.114350.1.72.1.5007"}]}, "extension": [{"url": "http://hl7.org/fhir/R4/specimen.html", "extension": [{"url": "specimen source", "valueString": "Other"}, {"url": "specimen collection time", "valueDateTime": "2022-07-27T20:49:00Z"}, {"url": "specimen receive time", "valueDateTime": "2022-07-27T20:58:00Z"}]}], "subject": {"reference": "Patient/b15b469d-482e-46fc-bcc9-2ac2ddb9edc2"}}, "request": {"method": "PUT", "url": "Observation/d218e3d4-5585-f9f0-a926-c2740482ac49"}}, {"fullUrl": "urn:uuid:032552b6-005e-b88b-f986-3dc64a5e66ae", "resource": {"resourceType": "Observation", "id": "032552b6-005e-b88b-f986-3dc64a5e66ae", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"], "source": "ecr"}, "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.1.1040.1", "value": "Z31828^^72166-2"}], "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "social-history"}]}], "status": "final", "code": {"coding": [{"code": "72166-2", "system": "http://loinc.org", "display": "Tobacco smoking status NHIS"}]}, "valueCodeableConcept": {"coding": [{"code": "266927001", "system": "http://snomed.info/sct", "display": "Tobacco smoking consumption unknown"}]}, "subject": {"reference": "Patient/b15b469d-482e-46fc-bcc9-2ac2ddb9edc2"}}, "request": {"method": "PUT", "url": "Observation/032552b6-005e-b88b-f986-3dc64a5e66ae"}}, {"fullUrl": "urn:uuid:", "resource": {"resourceType": "Observation", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"], "source": "ecr"}}, "request": {"method": "PUT", "url": "Observation/"}}, {"fullUrl": "urn:uuid:f5e25af7-945a-cf66-d2d0-8942935165a2", "resource": {"resourceType": "Immunization", "id": "f5e25af7-945a-cf66-d2d0-8942935165a2", "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.768076", "value": "86940"}], "occurrenceDateTime": "2021-01-22", "vaccineCode": {"coding": [{"display": "SARS-COV-2 (COVID-19) Spikevax Vaccine, Moderna"}, {"code": "80777-273-10", "system": "urn:oid:2.16.840.1.113883.6.69"}]}, "lotNumber": "LLSFJK", "manufacturer": {"reference": "Organization/57fcc148-b440-3a80-749b-780325e9680d"}, "status": "completed", "primarySource": true, "patient": {"reference": "Patient/b15b469d-482e-46fc-bcc9-2ac2ddb9edc2"}, "meta": {"source": "ecr"}}, "request": {"method": "PUT", "url": "Immunization/f5e25af7-945a-cf66-d2d0-8942935165a2"}}, {"fullUrl": "urn:uuid:57fcc148-b440-3a80-749b-780325e9680d", "resource": {"resourceType": "Organization", "id": "57fcc148-b440-3a80-749b-780325e9680d", "name": "Moderna US, Inc.", "meta": {"source": "ecr"}}, "request": {"method": "PUT", "url": "Organization/57fcc148-b440-3a80-749b-780325e9680d"}}, {"fullUrl": "urn:uuid:875c24ee-6be0-066b-ca5f-e73b2d914f5b", "resource": {"resourceType": "Immunization", "id": "875c24ee-6be0-066b-ca5f-e73b2d914f5b", "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.768076", "value": "90497"}], "occurrenceDateTime": "2020-09-08", "vaccineCode": {"coding": [{"display": "Hep B, adult vaccine (Engerix/Recombivax)"}]}, "status": "completed", "primarySource": true, "meta": {"source": "ecr"}}, "request": {"method": "PUT", "url": "Immunization/875c24ee-6be0-066b-ca5f-e73b2d914f5b"}}, {"fullUrl": "urn:uuid:3c8af1dd-2983-5d97-d5f1-f6dd57e9eba1", "resource": {"resourceType": "Immunization", "id": "3c8af1dd-2983-5d97-d5f1-f6dd57e9eba1", "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.768076", "value": "90499"}], "occurrenceDateTime": "2021-06-15", "vaccineCode": {"coding": [{"display": "DTaP, 5 pertussis antigens vaccine (DAPTACEL)"}]}, "status": "completed", "primarySource": true, "meta": {"source": "ecr"}}, "request": {"method": "PUT", "url": "Immunization/3c8af1dd-2983-5d97-d5f1-f6dd57e9eba1"}}]}') ON CONFLICT (ecr_id) DO NOTHING; diff --git a/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts b/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts index 1a2fc354bd..74308813ff 100644 --- a/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts +++ b/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts @@ -479,7 +479,7 @@ export const saveMetadataToPostgres = async ( // On successful transaction, return response return NextResponse.json( - { message: "Success. Saved metadata to database: " + saveECR.eICR_ID }, + { message: "Success. Saved metadata to database: " + ecrId }, { status: 200 }, ); } catch (error: any) { From 81218c1e1f277b04030a406197306a42f2be1dbf Mon Sep 17 00:00:00 2001 From: Gordon Farrell Date: Tue, 12 Nov 2024 11:51:35 -0700 Subject: [PATCH 16/23] address comments --- .../save-fhir-data/save-fhir-data-service.ts | 2 +- .../app/api/services/listEcrDataService.ts | 8 +- .../app/api/tests/listEcrDataService.test.tsx | 84 +++++++++---------- .../src/app/components/EcrTableClient.tsx | 39 ++++----- .../ecr-viewer/src/styles/custom-styles.scss | 7 +- 5 files changed, 67 insertions(+), 73 deletions(-) diff --git a/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts b/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts index 74308813ff..164af80273 100644 --- a/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts +++ b/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts @@ -437,7 +437,7 @@ export const saveMetadataToPostgres = async ( try { // Start transaction - const saveECR = await database.tx(async (t) => { + await database.tx(async (t) => { // Insert main ECR metadata const saveToEcrData = new PQ({ text: "INSERT INTO ecr_data (eICR_ID, patient_name_last, patient_name_first, patient_birth_date, data_source, report_date) VALUES ($1, $2, $3, $4, $5, $6) RETURNING eICR_ID", diff --git a/containers/ecr-viewer/src/app/api/services/listEcrDataService.ts b/containers/ecr-viewer/src/app/api/services/listEcrDataService.ts index b1cc9e7ce6..b3ca56c76c 100644 --- a/containers/ecr-viewer/src/app/api/services/listEcrDataService.ts +++ b/containers/ecr-viewer/src/app/api/services/listEcrDataService.ts @@ -13,8 +13,8 @@ export type EcrMetadataModel = { patient_name_first: string; patient_name_last: string; patient_birth_date: Date; - conditions: []; - rule_summaries: []; + conditions: string[]; + rule_summaries: string[]; report_date: Date; date_created: Date; }; @@ -24,8 +24,8 @@ export type EcrDisplay = { patient_first_name: string; patient_last_name: string; patient_date_of_birth: string | undefined; - reportable_conditions: []; - rule_summaries: []; + reportable_conditions: string[]; + rule_summaries: string[]; patient_report_date: string; date_created: string; }; diff --git a/containers/ecr-viewer/src/app/api/tests/listEcrDataService.test.tsx b/containers/ecr-viewer/src/app/api/tests/listEcrDataService.test.tsx index 67f2c0cc55..15fbeae823 100644 --- a/containers/ecr-viewer/src/app/api/tests/listEcrDataService.test.tsx +++ b/containers/ecr-viewer/src/app/api/tests/listEcrDataService.test.tsx @@ -10,6 +10,11 @@ import { generateSearchStatement, } from "@/app/api/services/listEcrDataService"; import { database } from "../services/db"; +import { + convertUTCToLocalString, + formatDate, + formatDateTime, +} from "../../services/formatService"; describe("listEcrDataService", () => { describe("process Metadata", () => { @@ -19,14 +24,18 @@ describe("listEcrDataService", () => { }); it("should map each object in responseBody to the correct output structure", () => { + const date1 = new Date(); + const date2 = new Date(); + const date3 = new Date(); + const responseBody: EcrMetadataModel[] = [ { eicr_id: "ecr1", - date_created: new Date(), + date_created: date1, patient_name_first: "Test", patient_name_last: "Person", - patient_birth_date: new Date(), - report_date: new Date(), + patient_birth_date: date2, + report_date: date3, conditions: ["Long"], rule_summaries: ["Longer"], data_source: "DB", @@ -35,11 +44,11 @@ describe("listEcrDataService", () => { }, { eicr_id: "ecr2", - date_created: new Date(), + date_created: date1, patient_name_first: "Another", patient_name_last: "Test", - patient_birth_date: new Date(), - report_date: new Date(), + patient_birth_date: date2, + report_date: date3, conditions: ["Stuff"], rule_summaries: ["Other stuff", "Even more stuff"], data_source: "DB", @@ -48,48 +57,37 @@ describe("listEcrDataService", () => { }, ]; - const expected: ( - | EcrDisplay - | { - rule_summary: any; - ecrId: string; - patient_report_date: any; - date_created: any; - reportable_condition: any; - patient_last_name: any; - patient_date_of_birth: any; - patient_first_name: any; - } - | { - rule_summaries: []; - ecrId: string; - patient_report_date: string; - date_created: any; - reportable_conditions: []; - patient_last_name: string; - patient_date_of_birth: string; - patient_first_name: string; - } - )[] = [ + const expected: EcrDisplay[] = [ { ecrId: "ecr1", - date_created: expect.any(String), - patient_first_name: expect.any(String), - patient_last_name: expect.any(String), - patient_date_of_birth: expect.any(String), - patient_report_date: expect.any(String), - reportable_conditions: expect.any(Array), - rule_summaries: expect.any(Array), + date_created: convertUTCToLocalString( + formatDateTime(date1.toISOString()), + ), + patient_first_name: "Test", + patient_last_name: "Person", + patient_date_of_birth: formatDate(date2.toISOString()), + patient_report_date: convertUTCToLocalString( + formatDateTime(date3.toISOString()), + ), + reportable_conditions: expect.arrayContaining(["Long"]), + rule_summaries: expect.arrayContaining(["Longer"]), }, { ecrId: "ecr2", - date_created: expect.any(String), - patient_first_name: expect.any(String), - patient_last_name: expect.any(String), - patient_date_of_birth: expect.any(String), - patient_report_date: expect.any(String), - reportable_conditions: expect.any(Array), - rule_summaries: expect.any(Array), + date_created: convertUTCToLocalString( + formatDateTime(date1.toISOString()), + ), + patient_first_name: "Another", + patient_last_name: "Test", + patient_date_of_birth: formatDate(date2.toISOString()), + patient_report_date: convertUTCToLocalString( + formatDateTime(date3.toISOString()), + ), + reportable_conditions: expect.arrayContaining(["Stuff"]), + rule_summaries: expect.arrayContaining([ + "Other stuff", + "Even more stuff", + ]), }, ]; const result = processMetadata(responseBody); diff --git a/containers/ecr-viewer/src/app/components/EcrTableClient.tsx b/containers/ecr-viewer/src/app/components/EcrTableClient.tsx index 968d94356f..478738c523 100644 --- a/containers/ecr-viewer/src/app/components/EcrTableClient.tsx +++ b/containers/ecr-viewer/src/app/components/EcrTableClient.tsx @@ -254,10 +254,21 @@ const formatRow = (item: EcrDisplay, index: number) => { const patientReportDate = formatDate(patientReportDateObj); const patientReportTime = formatTime(patientReportDateObj); - const conditionsString = concatenateAndAddNewlines( - item.reportable_conditions, + const conditionsList = ( +
    + {item.reportable_conditions.map((rc, index) => ( +
  • {rc}
    • + ))} +
+ ); + + const summariesList = ( +
    + {item.rule_summaries.map((rs, index) => ( +
  • {rs}
    • + ))} +
); - const ruleSummariesString = concatenateAndAddNewlines(item.rule_summaries); return ( @@ -278,8 +289,8 @@ const formatRow = (item: EcrDisplay, index: number) => {
{patientReportTime} - {conditionsString} - {ruleSummariesString} + {conditionsList} + {summariesList} ); }; @@ -310,21 +321,3 @@ const formatTime = (date: Date) => { return `${hours}:${minutesStr} ${ampm}`; }; - -/** - * Concatenates an array of strings and adds a blank line between each (Used for conditions and rule summaries) - * @param stringArray - An array of strings to be concatenated - * @returns - The array items as a string separated by two newlines - */ -const concatenateAndAddNewlines = (stringArray: []) => { - let concatenatedString = ""; - - for (const item in stringArray) { - const itemAsNumber = Number(item); - concatenatedString += stringArray[itemAsNumber]; - - if (itemAsNumber < stringArray.length - 1) concatenatedString += "\n\n"; - } - - return concatenatedString; -}; diff --git a/containers/ecr-viewer/src/styles/custom-styles.scss b/containers/ecr-viewer/src/styles/custom-styles.scss index d9d048870b..e9a83dd36e 100644 --- a/containers/ecr-viewer/src/styles/custom-styles.scss +++ b/containers/ecr-viewer/src/styles/custom-styles.scss @@ -7,8 +7,11 @@ $nav-wrapper-width: 15.625rem; $main-container-padding: 1rem; $main-min-width: $ecr-viewer-container-min-width + $ecr-viewer-gap + $nav-wrapper-width + $main-container-padding * 2; -.allow-newline{ - white-space: break-spaces; +.ecr-table-list { + @include unstyled-list; + li:not(:first-child) { + margin-top: 1rem; + } } .library-patient-column{ From b02c481e07a9407402c9bba9d8e339a17f32f40d Mon Sep 17 00:00:00 2001 From: Gordon Farrell Date: Tue, 12 Nov 2024 12:51:25 -0700 Subject: [PATCH 17/23] change conditions display to a UL update tests --- .../src/app/components/EcrTableClient.tsx | 4 +- .../app/tests/components/EcrTable.test.tsx | 7 +- .../__snapshots__/EcrTable.test.tsx.snap | 750 ++++++++++++++---- 3 files changed, 607 insertions(+), 154 deletions(-) diff --git a/containers/ecr-viewer/src/app/components/EcrTableClient.tsx b/containers/ecr-viewer/src/app/components/EcrTableClient.tsx index 478738c523..51bf6568e0 100644 --- a/containers/ecr-viewer/src/app/components/EcrTableClient.tsx +++ b/containers/ecr-viewer/src/app/components/EcrTableClient.tsx @@ -256,7 +256,7 @@ const formatRow = (item: EcrDisplay, index: number) => { const conditionsList = (
    - {item.reportable_conditions.map((rc, index) => ( + {item!.reportable_conditions!.map((rc, index) => (
  • {rc}
    • ))}
@@ -264,7 +264,7 @@ const formatRow = (item: EcrDisplay, index: number) => { const summariesList = (
    - {item.rule_summaries.map((rs, index) => ( + {item!.rule_summaries!.map((rs, index) => (
  • {rs}
    • ))}
diff --git a/containers/ecr-viewer/src/app/tests/components/EcrTable.test.tsx b/containers/ecr-viewer/src/app/tests/components/EcrTable.test.tsx index f8e2e1ad24..961d313572 100644 --- a/containers/ecr-viewer/src/app/tests/components/EcrTable.test.tsx +++ b/containers/ecr-viewer/src/app/tests/components/EcrTable.test.tsx @@ -20,8 +20,11 @@ describe("EcrTable", () => { patient_last_name: `last-${i + 1}`, dateModified: `2021-01-0${(i % 9) + 1}`, patient_date_of_birth: `2000-01-0${(i % 9) + 1}`, - reportable_condition: `reportable-condition-${i + 1}`, - rule_summary: `rule-summary-${i + 1}`, + reportable_conditions: [ + `reportable-condition-${i + 1}`, + `second-condition-${i + 1}`, + ], + rule_summaries: [`rule-summary-${i + 1}`, `second-summary-${i + 1}`], patient_report_date: `2021-01-0${(i % 9) + 1}`, date_created: `2021-01-0${(i % 9) + 1}`, })); diff --git a/containers/ecr-viewer/src/app/tests/components/__snapshots__/EcrTable.test.tsx.snap b/containers/ecr-viewer/src/app/tests/components/__snapshots__/EcrTable.test.tsx.snap index 84f3ed45af..8cceb93ca9 100644 --- a/containers/ecr-viewer/src/app/tests/components/__snapshots__/EcrTable.test.tsx.snap +++ b/containers/ecr-viewer/src/app/tests/components/__snapshots__/EcrTable.test.tsx.snap @@ -126,12 +126,30 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - + +
    +
  • + reportable-condition-1 +
    • +
  • + second-condition-1 +
    • +
+ + +
    +
  • + rule-summary-1 +
    • +
  • + second-summary-1 +
    • +
+ @@ -157,12 +175,30 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - + +
    +
  • + reportable-condition-2 +
    • +
  • + second-condition-2 +
    • +
+ + +
    +
  • + rule-summary-2 +
    • +
  • + second-summary-2 +
    • +
+ @@ -188,12 +224,30 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - + +
    +
  • + reportable-condition-3 +
    • +
  • + second-condition-3 +
    • +
+ + +
    +
  • + rule-summary-3 +
    • +
  • + second-summary-3 +
    • +
+ @@ -219,12 +273,30 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - + +
    +
  • + reportable-condition-4 +
    • +
  • + second-condition-4 +
    • +
+ + +
    +
  • + rule-summary-4 +
    • +
  • + second-summary-4 +
    • +
+ @@ -250,12 +322,30 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - + +
    +
  • + reportable-condition-5 +
    • +
  • + second-condition-5 +
    • +
+ + +
    +
  • + rule-summary-5 +
    • +
  • + second-summary-5 +
    • +
+ @@ -281,12 +371,30 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - + +
    +
  • + reportable-condition-6 +
    • +
  • + second-condition-6 +
    • +
+ + +
    +
  • + rule-summary-6 +
    • +
  • + second-summary-6 +
    • +
+ @@ -312,12 +420,30 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - + +
    +
  • + reportable-condition-7 +
    • +
  • + second-condition-7 +
    • +
+ + +
    +
  • + rule-summary-7 +
    • +
  • + second-summary-7 +
    • +
+ @@ -343,12 +469,30 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - + +
    +
  • + reportable-condition-8 +
    • +
  • + second-condition-8 +
    • +
+ + +
    +
  • + rule-summary-8 +
    • +
  • + second-summary-8 +
    • +
+ @@ -374,12 +518,30 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - + +
    +
  • + reportable-condition-9 +
    • +
  • + second-condition-9 +
    • +
+ + +
    +
  • + rule-summary-9 +
    • +
  • + second-summary-9 +
    • +
+ @@ -405,12 +567,30 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - + +
    +
  • + reportable-condition-10 +
    • +
  • + second-condition-10 +
    • +
+ + +
    +
  • + rule-summary-10 +
    • +
  • + second-summary-10 +
    • +
+ @@ -436,12 +616,30 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - + +
    +
  • + reportable-condition-11 +
    • +
  • + second-condition-11 +
    • +
+ + +
    +
  • + rule-summary-11 +
    • +
  • + second-summary-11 +
    • +
+ @@ -467,12 +665,30 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - + +
    +
  • + reportable-condition-12 +
    • +
  • + second-condition-12 +
    • +
+ + +
    +
  • + rule-summary-12 +
    • +
  • + second-summary-12 +
    • +
+ @@ -498,12 +714,30 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - + +
    +
  • + reportable-condition-13 +
    • +
  • + second-condition-13 +
    • +
+ + +
    +
  • + rule-summary-13 +
    • +
  • + second-summary-13 +
    • +
+ @@ -529,12 +763,30 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - + +
    +
  • + reportable-condition-14 +
    • +
  • + second-condition-14 +
    • +
+ + +
    +
  • + rule-summary-14 +
    • +
  • + second-summary-14 +
    • +
+ @@ -560,12 +812,30 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - + +
    +
  • + reportable-condition-15 +
    • +
  • + second-condition-15 +
    • +
+ + +
    +
  • + rule-summary-15 +
    • +
  • + second-summary-15 +
    • +
+ @@ -591,12 +861,30 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - + +
    +
  • + reportable-condition-16 +
    • +
  • + second-condition-16 +
    • +
+ + +
    +
  • + rule-summary-16 +
    • +
  • + second-summary-16 +
    • +
+ @@ -622,12 +910,30 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - + +
    +
  • + reportable-condition-17 +
    • +
  • + second-condition-17 +
    • +
+ + +
    +
  • + rule-summary-17 +
    • +
  • + second-summary-17 +
    • +
+ @@ -653,12 +959,30 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - + +
    +
  • + reportable-condition-18 +
    • +
  • + second-condition-18 +
    • +
+ + +
    +
  • + rule-summary-18 +
    • +
  • + second-summary-18 +
    • +
+ @@ -684,12 +1008,30 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - + +
    +
  • + reportable-condition-19 +
    • +
  • + second-condition-19 +
    • +
+ + +
    +
  • + rule-summary-19 +
    • +
  • + second-summary-19 +
    • +
+ @@ -715,12 +1057,30 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - + +
    +
  • + reportable-condition-20 +
    • +
  • + second-condition-20 +
    • +
+ + +
    +
  • + rule-summary-20 +
    • +
  • + second-summary-20 +
    • +
+ @@ -746,12 +1106,30 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - + +
    +
  • + reportable-condition-21 +
    • +
  • + second-condition-21 +
    • +
+ + +
    +
  • + rule-summary-21 +
    • +
  • + second-summary-21 +
    • +
+ @@ -777,12 +1155,30 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - + +
    +
  • + reportable-condition-22 +
    • +
  • + second-condition-22 +
    • +
+ + +
    +
  • + rule-summary-22 +
    • +
  • + second-summary-22 +
    • +
+ @@ -808,12 +1204,30 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - + +
    +
  • + reportable-condition-23 +
    • +
  • + second-condition-23 +
    • +
+ + +
    +
  • + rule-summary-23 +
    • +
  • + second-summary-23 +
    • +
+ @@ -839,12 +1253,30 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - + +
    +
  • + reportable-condition-24 +
    • +
  • + second-condition-24 +
    • +
+ + +
    +
  • + rule-summary-24 +
    • +
  • + second-summary-24 +
    • +
+ @@ -870,12 +1302,30 @@ exports[`EcrTable should match snapshot 1`] = `
7:00 PM - - + +
    +
  • + reportable-condition-25 +
    • +
  • + second-condition-25 +
    • +
+ + +
    +
  • + rule-summary-25 +
    • +
  • + second-summary-25 +
    • +
+ From 0a6b9322db7a3d3f91a0d71f3c11528d59aa290c Mon Sep 17 00:00:00 2001 From: Gordon Farrell Date: Tue, 12 Nov 2024 13:31:52 -0700 Subject: [PATCH 18/23] cleanup random extras --- containers/ecr-viewer/src/app/components/EcrTableClient.tsx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/containers/ecr-viewer/src/app/components/EcrTableClient.tsx b/containers/ecr-viewer/src/app/components/EcrTableClient.tsx index 51bf6568e0..478738c523 100644 --- a/containers/ecr-viewer/src/app/components/EcrTableClient.tsx +++ b/containers/ecr-viewer/src/app/components/EcrTableClient.tsx @@ -256,7 +256,7 @@ const formatRow = (item: EcrDisplay, index: number) => { const conditionsList = (
    - {item!.reportable_conditions!.map((rc, index) => ( + {item.reportable_conditions.map((rc, index) => (
  • {rc}
    • ))}
@@ -264,7 +264,7 @@ const formatRow = (item: EcrDisplay, index: number) => { const summariesList = (
    - {item!.rule_summaries!.map((rs, index) => ( + {item.rule_summaries.map((rs, index) => (
  • {rs}
    • ))}
From b002c4e37c9594f27d554839683be027336a17a5 Mon Sep 17 00:00:00 2001 From: Gordon Farrell Date: Mon, 18 Nov 2024 09:02:21 -0700 Subject: [PATCH 19/23] updating saving for nested rule summaries --- .../save-fhir-data/save-fhir-data-service.ts | 19 ++++++++++++------- .../src/app/api/save-fhir-data/types.ts | 6 +++++- .../app/default_schemas/ecr.json | 11 +++++++++-- .../default_schemas/ecr_viewer_metadata.json | 11 +++++++++-- .../default_schemas/ecr_with_metadata.json | 11 +++++++++-- .../app/default_schemas/philly_ecr.json | 11 +++++++++-- 6 files changed, 53 insertions(+), 16 deletions(-) diff --git a/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts b/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts index 31a139c68d..1dcb23f625 100644 --- a/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts +++ b/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts @@ -451,13 +451,18 @@ export const saveMetadataToPostgres = async ( const savedRRCondition = await t.one(saveRRConditions); - // Insert associated rule summary into ecr_rr_rule_summaries - const saveRRSummary = new PQ({ - text: "INSERT INTO ecr_rr_rule_summaries (uuid, ecr_rr_conditions_id, rule_summary) VALUES (uuid_generate_v4(), $1, $2)", - values: [savedRRCondition.uuid, rrItem.rule_summaries], - }); - - await t.none(saveRRSummary); + // Loop through the rule summaries array + if (rrItem.rule_summaries && rrItem.rule_summaries.length > 0) { + for (const summaryObj of rrItem.rule_summaries) { + // Insert each associated summary into ecr_rr_rule_summaries + const saveRRSummary = new PQ({ + text: "INSERT INTO ecr_rr_rule_summaries (uuid, ecr_rr_conditions_id, rule_summary) VALUES (uuid_generate_v4(), $1, $2)", + values: [savedRRCondition.uuid, summaryObj.summary], + }); + + await t.none(saveRRSummary); + } + } } return ecrData; diff --git a/containers/ecr-viewer/src/app/api/save-fhir-data/types.ts b/containers/ecr-viewer/src/app/api/save-fhir-data/types.ts index 83701cad8e..f363ddb490 100644 --- a/containers/ecr-viewer/src/app/api/save-fhir-data/types.ts +++ b/containers/ecr-viewer/src/app/api/save-fhir-data/types.ts @@ -19,9 +19,13 @@ interface Lab { specimen_collection_date: Date | undefined; } +interface ruleSummary { + summary: string; +} + interface RR { condition: string; - rule_summaries: string; + rule_summaries: ruleSummary[]; } export interface BundleExtendedMetadata { diff --git a/containers/message-parser/app/default_schemas/ecr.json b/containers/message-parser/app/default_schemas/ecr.json index 2dc4e0ae65..b1cd3473d1 100644 --- a/containers/message-parser/app/default_schemas/ecr.json +++ b/containers/message-parser/app/default_schemas/ecr.json @@ -355,9 +355,16 @@ } }, "rule_summaries": { - "fhir_path": "Observation.extension.where(url = 'http://hl7.org/fhir/us/ecr/StructureDefinition/us-ph-determination-of-reportability-rule-extension').valueString", - "data_type": "string", + "fhir_path": "Observation.extension.where(url = 'http://hl7.org/fhir/us/ecr/StructureDefinition/us-ph-determination-of-reportability-rule-extension')", + "data_type": "array", "nullable": true, + "secondary_schema": { + "summary": { + "fhir_path": "valueString", + "data_type": "string", + "nullable": true + } + }, "metadata": { "category": "RR Reportability Information" } diff --git a/containers/message-parser/app/default_schemas/ecr_viewer_metadata.json b/containers/message-parser/app/default_schemas/ecr_viewer_metadata.json index ed5e15f069..a071c1ff93 100644 --- a/containers/message-parser/app/default_schemas/ecr_viewer_metadata.json +++ b/containers/message-parser/app/default_schemas/ecr_viewer_metadata.json @@ -50,9 +50,16 @@ } }, "rule_summaries": { - "fhir_path": "Observation.extension.where(url = 'http://hl7.org/fhir/us/ecr/StructureDefinition/us-ph-determination-of-reportability-rule-extension').valueString", - "data_type": "string", + "fhir_path": "Observation.extension.where(url = 'http://hl7.org/fhir/us/ecr/StructureDefinition/us-ph-determination-of-reportability-rule-extension')", + "data_type": "array", "nullable": true, + "secondary_schema": { + "summary": { + "fhir_path": "valueString", + "data_type": "string", + "nullable": true + } + }, "metadata": { "category": "RR Reportability Information" } diff --git a/containers/message-parser/app/default_schemas/ecr_with_metadata.json b/containers/message-parser/app/default_schemas/ecr_with_metadata.json index 5dcac09e18..5efed2b05b 100644 --- a/containers/message-parser/app/default_schemas/ecr_with_metadata.json +++ b/containers/message-parser/app/default_schemas/ecr_with_metadata.json @@ -126,9 +126,16 @@ } }, "rule_summaries": { - "fhir_path": "Observation.extension.where(url = 'http://hl7.org/fhir/us/ecr/StructureDefinition/us-ph-determination-of-reportability-rule-extension').valueString", - "data_type": "string", + "fhir_path": "Observation.extension.where(url = 'http://hl7.org/fhir/us/ecr/StructureDefinition/us-ph-determination-of-reportability-rule-extension')", + "data_type": "array", "nullable": true, + "secondary_schema": { + "summary": { + "fhir_path": "valueString", + "data_type": "string", + "nullable": true + } + }, "metadata": { "category": "RR Reportability Information" } diff --git a/containers/message-parser/app/default_schemas/philly_ecr.json b/containers/message-parser/app/default_schemas/philly_ecr.json index 2f44be8413..2619f13a14 100644 --- a/containers/message-parser/app/default_schemas/philly_ecr.json +++ b/containers/message-parser/app/default_schemas/philly_ecr.json @@ -357,9 +357,16 @@ } }, "rule_summaries": { - "fhir_path": "Observation.extension.where(url = 'http://hl7.org/fhir/us/ecr/StructureDefinition/us-ph-determination-of-reportability-rule-extension').valueString", - "data_type": "string", + "fhir_path": "Observation.extension.where(url = 'http://hl7.org/fhir/us/ecr/StructureDefinition/us-ph-determination-of-reportability-rule-extension')", + "data_type": "array", "nullable": true, + "secondary_schema": { + "summary": { + "fhir_path": "valueString", + "data_type": "string", + "nullable": true + } + }, "metadata": { "category": "RR Reportability Information" } From 9b4c0e8434ddcb7e49bd27d9e941e63e8cad1867 Mon Sep 17 00:00:00 2001 From: Gordon Farrell Date: Thu, 21 Nov 2024 09:08:41 -0700 Subject: [PATCH 20/23] get sql server in working order --- containers/ecr-viewer/docker-compose.yml | 9 ++- .../ecr-viewer/seed-scripts/sql/entrypoint.sh | 7 ++ containers/ecr-viewer/sql/extended.sql | 4 +- .../save-fhir-data/save-fhir-data-service.ts | 78 +++++++++++++------ 4 files changed, 70 insertions(+), 28 deletions(-) diff --git a/containers/ecr-viewer/docker-compose.yml b/containers/ecr-viewer/docker-compose.yml index 12a2a7da3b..f4643a30e0 100644 --- a/containers/ecr-viewer/docker-compose.yml +++ b/containers/ecr-viewer/docker-compose.yml @@ -10,6 +10,7 @@ services: environment: - APP_ENV=${APP_ENV:-test} - METADATA_DATABASE_TYPE=${METADATA_DATABASE_TYPE:-postgres} + - METADATA_DATABASE_SCHEMA=${METADATA_DATABASE_SCHEMA} - SOURCE=${SOURCE:-postgres} - DATABASE_URL=postgres://postgres:pw@postgres:5432/ecr_viewer_db - AWS_CUSTOM_ENDPOINT=http://aws-storage:4566 @@ -21,6 +22,9 @@ services: - AZURE_CONTAINER_NAME=${AZURE_CONTAINER_NAME:-ecr-viewer-files} - NEXT_PUBLIC_NON_INTEGRATED_VIEWER=${NEXT_PUBLIC_NON_INTEGRATED_VIEWER:-false} - NEXT_PUBLIC_BASEPATH=${NEXT_PUBLIC_BASEPATH:-/ecr-viewer} + - SQL_SERVER_USER=${SQL_SERVER_USER} + - SQL_SERVER_PASSWORD=${SQL_SERVER_PASSWORD} + - SQL_SERVER_HOST=${SQL_SERVER_HOST:-sqlserver} profiles: - ecr-viewer @@ -54,8 +58,9 @@ services: ports: - "1433:1433" volumes: - - ./seed-scripts/sql:/var/opt/mssql/scripts - entrypoint: /var/opt/mssql/scripts/entrypoint.sh + - ./seed-scripts/sql/entrypoint.sh:/var/opt/mssql/scripts/entrypoint.sh + - ./sql/extended.sql:/var/opt/mssql/scripts/extended.sql + entrypoint: /bin/bash -c "/var/opt/mssql/scripts/entrypoint.sh" healthcheck: test: [ diff --git a/containers/ecr-viewer/seed-scripts/sql/entrypoint.sh b/containers/ecr-viewer/seed-scripts/sql/entrypoint.sh index 5df20d28c1..ff406ba5d4 100755 --- a/containers/ecr-viewer/seed-scripts/sql/entrypoint.sh +++ b/containers/ecr-viewer/seed-scripts/sql/entrypoint.sh @@ -2,6 +2,13 @@ /opt/mssql/bin/sqlservr & +# Wait for SQL Server to start up +until /opt/mssql-tools18/bin/sqlcmd -S localhost -U sa -P $MSSQL_SA_PASSWORD -Q "SELECT 1" -C &>/dev/null; do + echo "Waiting for SQL Server to start..." + sleep 1 +done + +# Run your SQL script /opt/mssql-tools18/bin/sqlcmd -S localhost -U sa -P $MSSQL_SA_PASSWORD -d master -i /var/opt/mssql/scripts/extended.sql -C wait \ No newline at end of file diff --git a/containers/ecr-viewer/sql/extended.sql b/containers/ecr-viewer/sql/extended.sql index bf345d6b59..1d13c5fa43 100644 --- a/containers/ecr-viewer/sql/extended.sql +++ b/containers/ecr-viewer/sql/extended.sql @@ -66,8 +66,8 @@ CREATE TABLE ecr_labs eICR_ID VARCHAR(200) REFERENCES ECR_DATA (eICR_ID), test_type VARCHAR(255), test_type_code VARCHAR(50), - test_type_system VARCHAR(50), - test_result_qualitative VARCHAR(255), + test_type_system VARCHAR(MAX), + test_result_qualitative VARCHAR(MAX), test_result_quantitative FLOAT, test_result_units VARCHAR(50), test_result_code VARCHAR(50), diff --git a/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts b/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts index 1dcb23f625..bc3f9e4cdd 100644 --- a/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts +++ b/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts @@ -175,14 +175,20 @@ export const saveMetadataToSqlServer = async ( metadata: BundleExtendedMetadata, ecrId: string, ) => { - let pool = await sql.connect({ - user: process.env.SQL_SERVER_USER, - password: process.env.SQL_SERVER_PASSWORD, - server: process.env.SQL_SERVER_HOST || "localhost", - options: { - trustServerCertificate: true, - }, - }); + let pool; + + try { + pool = await sql.connect({ + user: process.env.SQL_SERVER_USER, + password: process.env.SQL_SERVER_PASSWORD, + server: process.env.SQL_SERVER_HOST, + options: { + trustServerCertificate: true, + }, + }); + } catch (error) { + console.log("Error connecting to MS SQL Server: ", error); + } const transaction = new sql.Transaction(pool); await transaction.begin(); @@ -191,7 +197,7 @@ export const saveMetadataToSqlServer = async ( try { const ecrDataInsertRequest = new sql.Request(transaction); await ecrDataInsertRequest - .input("eICR_ID", sql.VarChar(200), metadata.eicr_id) + .input("eICR_ID", sql.VarChar(200), ecrId) .input("eicr_set_id", sql.VarChar(255), metadata.eicr_set_id) .input("fhir_reference_link", sql.VarChar(255), null) // Not implemented .input("last_name", sql.VarChar(255), metadata.last_name) @@ -287,13 +293,17 @@ export const saveMetadataToSqlServer = async ( const labInsertRequest = new sql.Request(transaction); await labInsertRequest .input("UUID", sql.VarChar(200), lab.uuid) - .input("eICR_ID", sql.VarChar(200), metadata.eicr_id) + .input("eICR_ID", sql.VarChar(200), ecrId) .input("test_type", sql.VarChar(200), lab.test_type) .input("test_type_code", sql.VarChar(50), lab.test_type_code) - .input("test_type_system", sql.VarChar(50), lab.test_type_system) + .input( + "test_type_system", + sql.VarChar(sql.MAX), + lab.test_type_system, + ) .input( "test_result_qualitative", - sql.VarChar(255), + sql.VarChar(sql.MAX), lab.test_result_qualitative, ) .input( @@ -354,25 +364,39 @@ export const saveMetadataToSqlServer = async ( } if (metadata.rr) { - for (const rule of metadata.rr) { + // Loop through each condition/rule object in rr array + for (const rrItem of metadata.rr) { const rr_conditions_uuid = randomUUID(); const rrConditionsInsertRequest = new sql.Request(transaction); + + // Insert condition into ecr_rr_conditions await rrConditionsInsertRequest .input("UUID", sql.VarChar(200), rr_conditions_uuid) - .input("eICR_ID", sql.VarChar(200), metadata.eicr_id) - .input("condition", sql.VarChar(sql.MAX), rule.condition) + .input("eICR_ID", sql.VarChar(200), ecrId) + .input("condition", sql.VarChar(sql.MAX), rrItem.condition) .query( "INSERT INTO dbo.ecr_rr_conditions VALUES (@UUID, @eICR_ID, @condition)", ); - const ruleSummaryInsertRequest = new sql.Request(transaction); - await ruleSummaryInsertRequest - .input("UUID", sql.VarChar(200), randomUUID()) - .input("ECR_RR_CONDITIONS_ID", sql.VarChar(200), rr_conditions_uuid) - .input("rule_summary", sql.VarChar(sql.MAX), rule.rule_summaries) - .query( - "INSERT INTO dbo.ecr_rr_rule_summaries VALUES (@UUID, @ECR_RR_CONDITIONS_ID, @rule_summary)", - ); + // Loop through the rule summaries array + if (rrItem.rule_summaries && rrItem.rule_summaries.length > 0) { + for (const summary of rrItem.rule_summaries) { + const ruleSummaryInsertRequest = new sql.Request(transaction); + + // Insert each rule summary with reference to the condition + await ruleSummaryInsertRequest + .input("UUID", sql.VarChar(200), randomUUID()) + .input( + "ECR_RR_CONDITIONS_ID", + sql.VarChar(200), + rr_conditions_uuid, + ) + .input("rule_summary", sql.VarChar(sql.MAX), summary.summary) + .query( + "INSERT INTO dbo.ecr_rr_rule_summaries VALUES (@UUID, @ECR_RR_CONDITIONS_ID, @rule_summary)", + ); + } + } } } @@ -394,7 +418,9 @@ export const saveMetadataToSqlServer = async ( ); } finally { // Close the connection pool - pool.close(); + if (pool) { + pool.close(); + } } } else { return NextResponse.json( @@ -502,10 +528,14 @@ export const saveWithMetadata = async ( let fhirDataResult; let metadataResult; const metadataSaveLocation = process.env.METADATA_DATABASE_TYPE; + + console.log("Metadata: ", metadata); + try { fhirDataResult = await saveFhirData(fhirBundle, ecrId, saveSource); if (metadataSaveLocation == "postgres") { + console.log("postgres if case"); metadataResult = await saveMetadataToPostgres( metadata as BundleMetadata, ecrId, From bc1be38c15da857aec3c8bc71c957e6df30a6774 Mon Sep 17 00:00:00 2001 From: Gordon Farrell Date: Thu, 21 Nov 2024 09:12:38 -0700 Subject: [PATCH 21/23] remove console logs --- .../src/app/api/save-fhir-data/save-fhir-data-service.ts | 3 --- 1 file changed, 3 deletions(-) diff --git a/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts b/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts index bc3f9e4cdd..280b55bad6 100644 --- a/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts +++ b/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts @@ -529,13 +529,10 @@ export const saveWithMetadata = async ( let metadataResult; const metadataSaveLocation = process.env.METADATA_DATABASE_TYPE; - console.log("Metadata: ", metadata); - try { fhirDataResult = await saveFhirData(fhirBundle, ecrId, saveSource); if (metadataSaveLocation == "postgres") { - console.log("postgres if case"); metadataResult = await saveMetadataToPostgres( metadata as BundleMetadata, ecrId, From d34d3e4b06b2ad907d491f1c0aa69bf17a72395f Mon Sep 17 00:00:00 2001 From: Gordon Farrell Date: Thu, 21 Nov 2024 09:28:11 -0700 Subject: [PATCH 22/23] Updates to match Josh's sql server changes --- containers/ecr-viewer/sql/extended.sql | 2 +- .../api/save-fhir-data/save-fhir-data-service.ts | 16 +++++++--------- 2 files changed, 8 insertions(+), 10 deletions(-) diff --git a/containers/ecr-viewer/sql/extended.sql b/containers/ecr-viewer/sql/extended.sql index 1d13c5fa43..dd606bd300 100644 --- a/containers/ecr-viewer/sql/extended.sql +++ b/containers/ecr-viewer/sql/extended.sql @@ -66,7 +66,7 @@ CREATE TABLE ecr_labs eICR_ID VARCHAR(200) REFERENCES ECR_DATA (eICR_ID), test_type VARCHAR(255), test_type_code VARCHAR(50), - test_type_system VARCHAR(MAX), + test_type_system VARCHAR(255), test_result_qualitative VARCHAR(MAX), test_result_quantitative FLOAT, test_result_units VARCHAR(50), diff --git a/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts b/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts index 280b55bad6..9e5e749901 100644 --- a/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts +++ b/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts @@ -176,18 +176,20 @@ export const saveMetadataToSqlServer = async ( ecrId: string, ) => { let pool; - try { pool = await sql.connect({ user: process.env.SQL_SERVER_USER, password: process.env.SQL_SERVER_PASSWORD, - server: process.env.SQL_SERVER_HOST, + server: process.env.SQL_SERVER_HOST || "localhost", options: { trustServerCertificate: true, }, }); - } catch (error) { - console.log("Error connecting to MS SQL Server: ", error); + } catch (error: any) { + return NextResponse.json( + { message: "Failed to connect to SQL Server. " + error.message }, + { status: 500 }, + ); } const transaction = new sql.Transaction(pool); @@ -296,11 +298,7 @@ export const saveMetadataToSqlServer = async ( .input("eICR_ID", sql.VarChar(200), ecrId) .input("test_type", sql.VarChar(200), lab.test_type) .input("test_type_code", sql.VarChar(50), lab.test_type_code) - .input( - "test_type_system", - sql.VarChar(sql.MAX), - lab.test_type_system, - ) + .input("test_type_system", sql.VarChar(255), lab.test_type_system) .input( "test_result_qualitative", sql.VarChar(sql.MAX), From ea6e3808bc7dcf632ad03dd55b9c0c5a6d025e3a Mon Sep 17 00:00:00 2001 From: Gordon Farrell Date: Thu, 21 Nov 2024 10:44:19 -0700 Subject: [PATCH 23/23] remove unneeded localhost default --- .../src/app/api/save-fhir-data/save-fhir-data-service.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts b/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts index 9e5e749901..1337ff3fc6 100644 --- a/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts +++ b/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts @@ -180,7 +180,7 @@ export const saveMetadataToSqlServer = async ( pool = await sql.connect({ user: process.env.SQL_SERVER_USER, password: process.env.SQL_SERVER_PASSWORD, - server: process.env.SQL_SERVER_HOST || "localhost", + server: process.env.SQL_SERVER_HOST, options: { trustServerCertificate: true, },