CA observation transforms from local code to LOINC or PLT (#1306)

* Create 020_CA_ORU_R01_CDPH_OBX_to_LOINC_0_initial_message.hl7 Copied from the previous set of HL7 test data, with added OBX examples of the new mapping * Update 020_CA_ORU_R01_CDPH_OBX_to_LOINC_0_initial_message.hl7 Fixed typo on some local codes * Adding translated example file #20 * Addin skeleton for transformation * WIP - add initial implementation of MapLocalObservationCode transform * Adding unit test for a single observation * Adding test for local code mappable to a PLT * Update MapLocalObservationCodes.java Add the mapped coding at the beginning of the coding list * Small code cleanup * Add tests for when the initial code is a LOINC code * Refactor tests to remove duplicated code * Add assertion to evaluateCoding * Adding test for when primary code is also populated * Add tests for an unmapped local code and empty observation identifer * Updates to transformation to pass first 2 test cases * WIP - multiple observation test * All curent tests pass, but the code is not pretty and has at least one edge case unnacounted for * Complete the multiple observations test, add the remaining mappings to the lookup * Minor cleanup and refactoring * Replace for() loop with if check for a single coding on the observation * Add MapLocalObservationCodes to transformation_definitions.json * refactor: logging for when local codes not found added method to extract MSH10 to HapiHelper class * Update sender in log warning, restore mock logger in unit tests * Commenting out the PLT codes that haven't been mapped yet so they will cause warnings for now * refactor helper method for msh10 * Minor naming tweaks and comment updates * add null check for cwe extension * Address null check for getSystem method * Missing paren * refactor: added hascodingExtensionWithUrl helper method to HapiHelper added getCodingExtensionByUrl helper method to HapiHelper * refactor: added hasCodingSytem helper method to HapiHelper added getCodingSystem helper method to HapiHelper * Removed comments and empty lines * spotlessApply * WIP: transform refactoring - flatten conditional blocks * Refactor transform into simpler methods * Update minor dependencies to v5.4 (#1339) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Update HapiHelper.java Replace unused assignment with inline return * Update dependency com.azure:azure-storage-blob to v12.28.0 (#1344) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Update Terraform azurerm to v4.3.0 (#1345) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Move urlForCodeType to HapiHelper for future reusability * Adding tests for code coverage and addressing Sonar findings * Adding tests for code coverage and addressing Sonar findings * Adding tests for null and empty bundle for resourcesInBundle * Adding tests for urlForCodeType * HapiHelper: unit test for when bundle is null * Updated RS Hurl Script to Replace MSH Header When Not Toggled (#1342) * Updating hurl scripts * Fixed typo in readme, create temp folder, write scrambled file into temp folder * Fixed directory creation, resolved issue with sed command not copying rest of file * updated readme to include toggle in options, add comments to scramble doing, alerted user to scrambling, removed folder creation for individual file * replaced msh header for oru and orm message types * added msh header replacement for oml message type * switched to msh-9.2 as subfield in conditional * remove temp directory after hurl script runs --------- Co-authored-by: jcrichlake <jeff.crichlake@agile6.com> Co-authored-by: Sylvie <sschuresko@flexion.us> Co-authored-by: jcrichlake <145698165+jcrichlake@users.noreply.github.com> Co-authored-by: saquino0827 <saquino@flexion.us> * Add control id test, update test name * Fix order of mockLogger registration and injection * Fixed prod prefix mapping Co-Authored-By: halprin <halprin@users.noreply.github.com> * Add post-TI and post-RS example files * Update dependency gradle to v8.10.2 (#1347) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Add final 5 PLT mappings; update mapping for 99717-50 * Add comment to clarify behavior of adding the mapped code --------- Co-authored-by: Joel Biskie <jbiskie@flexion.us> Co-authored-by: jorge Lopez <jlopez@flexion.us> Co-authored-by: Tiffini Johnson <tjohnson@flexion.us> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Bella L. Quintero <96704946+pluckyswan@users.noreply.github.com> Co-authored-by: jcrichlake <jeff.crichlake@agile6.com> Co-authored-by: Sylvie <sschuresko@flexion.us> Co-authored-by: jcrichlake <145698165+jcrichlake@users.noreply.github.com> Co-authored-by: saquino0827 <saquino@flexion.us> Co-authored-by: James Herr <jherr@flexion.us> Co-authored-by: halprin <halprin@users.noreply.github.com> Co-authored-by: Jorge Lopez <49923512+jorg3lopez@users.noreply.github.com>
CDCgov · Sep 28, 2024 · c8f175b · c8f175b
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diff --git a/etor/src/main/java/gov/hhs/cdc/trustedintermediary/etor/messages/IdentifierCode.java b/etor/src/main/java/gov/hhs/cdc/trustedintermediary/etor/messages/IdentifierCode.java
@@ -0,0 +1,9 @@
+package gov.hhs.cdc.trustedintermediary.etor.messages;
+
+/**
+ * Represents an identifier triplet, consisting of a code, display value, and coding system.
+ * Identifiers are used in HL7 fields such as OBR-4 and OBX-3. These fields contain two identifier
+ * triplets, one in subfields 1/2/3, and an alternate in subfields 4/5/6. For reference, see: <a
+ * href="https://hl7-definition.caristix.com/v2/HL7v2.5.1/Fields/OBX.3"</a>
+ */
+public record IdentifierCode(String code, String display, String codingSystem) {}
diff --git a/...c/trustedintermediary/etor/ruleengine/transformation/custom/MapLocalObservationCodes.java b/...c/trustedintermediary/etor/ruleengine/transformation/custom/MapLocalObservationCodes.java
@@ -0,0 +1,188 @@
+package gov.hhs.cdc.trustedintermediary.etor.ruleengine.transformation.custom;
+
+import gov.hhs.cdc.trustedintermediary.context.ApplicationContext;
+import gov.hhs.cdc.trustedintermediary.etor.messages.IdentifierCode;
+import gov.hhs.cdc.trustedintermediary.etor.ruleengine.FhirResource;
+import gov.hhs.cdc.trustedintermediary.etor.ruleengine.transformation.CustomFhirTransformation;
+import gov.hhs.cdc.trustedintermediary.external.hapi.HapiHelper;
+import gov.hhs.cdc.trustedintermediary.wrappers.Logger;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Objects;
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.Coding;
+import org.hl7.fhir.r4.model.Observation;
+import org.hl7.fhir.r4.model.StringType;
+
+/**
+ * Maps local observation codes to LOINC/PLT codes. In order to map a code, the observation must
+ * have a single local code with cwe-coding extension 'alt-coding'. The mapped LOINC or PLT code is
+ * added to the observation as an additional observation coding with cwe-coding extension 'coding'.
+ * When converted to/from HL7, these codings correspond to OBX-3.4/5/6 for the local code, and
+ * OBX-3.1/2/3 for the LOINC/PLT code.
+ */
+public class MapLocalObservationCodes implements CustomFhirTransformation {
+    protected final Logger logger = ApplicationContext.getImplementation(Logger.class);
+
+    private HashMap<String, IdentifierCode> codingMap;
+
+    public MapLocalObservationCodes() {
+        initMap();
+    }
+
+    @Override
+    public void transform(FhirResource<?> resource, Map<String, String> args) {
+        var bundle = (Bundle) resource.getUnderlyingResource();
+        var observations = HapiHelper.resourcesInBundle(bundle, Observation.class);
+
+        for (Observation obv : observations.toList()) {
+            var codingList = obv.getCode().getCoding();
+
+            if (codingList.size() != 1) {
+                continue;
+            }
+
+            var coding = codingList.get(0);
+            if (!hasLocalCodeInAlternateCoding(coding)) {
+                continue;
+            }
+
+            var identifier = codingMap.get(coding.getCode());
+            if (identifier == null) {
+                logUnmappedLocalCode(bundle, coding);
+                continue;
+            }
+
+            var mappedCoding = getMappedCoding(identifier);
+
+            // Add the mapped code as the first in the list, ahead of the existing alternate code
+            codingList.add(0, mappedCoding);
+        }
+    }
+
+    private Boolean hasLocalCodeInAlternateCoding(Coding coding) {
+        if (!HapiHelper.hasCodingExtensionWithUrl(coding, HapiHelper.EXTENSION_CWE_CODING)) {
+            return false;
+        }
+
+        if (!HapiHelper.hasCodingSystem(coding)) {
+            return false;
+        }
+
+        var cwe =
+                HapiHelper.getCodingExtensionByUrl(coding, HapiHelper.EXTENSION_CWE_CODING)
+                        .getValue()
+                        .toString();
+        var codingSystem = HapiHelper.getCodingSystem(coding);
+
+        return Objects.equals(cwe, "alt-coding") && HapiHelper.LOCAL_CODE_URL.equals(codingSystem);
+    }
+
+    private void logUnmappedLocalCode(Bundle bundle, Coding coding) {
+        var msh41Identifier = HapiHelper.getMSH4_1Identifier(bundle);
+        var msh41Value = msh41Identifier != null ? msh41Identifier.getValue() : null;
+
+        logger.logWarning(
+                "Unmapped local code detected: '{}', from sender: '{}', message Id: '{}'",
+                coding.getCode(),
+                msh41Value,
+                HapiHelper.getMessageControlId(bundle));
+    }
+
+    private Coding getMappedCoding(IdentifierCode identifierCode) {
+        var mappedCoding =
+                new Coding(
+                        HapiHelper.urlForCodeType(identifierCode.codingSystem()),
+                        identifierCode.code(),
+                        identifierCode.display());
+        mappedCoding.addExtension(HapiHelper.EXTENSION_CWE_CODING, new StringType("coding"));
+
+        mappedCoding.addExtension(
+                HapiHelper.EXTENSION_CODING_SYSTEM, new StringType(identifierCode.codingSystem()));
+
+        return mappedCoding;
+    }
+
+    private void initMap() {
+        this.codingMap = new HashMap<>();
+        // ALD
+        codingMap.put(
+                "99717-32",
+                new IdentifierCode(
+                        "85269-9",
+                        "X-linked Adrenoleukodystrophy (X- ALD) newborn screen interpretation",
+                        HapiHelper.LOINC_CODE));
+        codingMap.put(
+                "99717-33",
+                new IdentifierCode(
+                        "85268-1",
+                        "X-linked Adrenoleukodystrophy (X- ALD) newborn screening comment-discussion",
+                        HapiHelper.LOINC_CODE));
+        codingMap.put(
+                "99717-34",
+                new IdentifierCode(
+                        "PLT325",
+                        "ABCD1 gene mutation found [Identifier] in DBS by Sequencing",
+                        HapiHelper.PLT_CODE));
+        // CAH
+        codingMap.put(
+                "99717-6",
+                new IdentifierCode(
+                        "53340-6",
+                        "17-Hydroxyprogesterone [Moles/volume] in DBS",
+                        HapiHelper.LOINC_CODE));
+        // CF
+        codingMap.put(
+                "99717-35",
+                new IdentifierCode(
+                        "PLT3289",
+                        "CFTR gene mutation found [Interpretation] in DBS by Sequencing",
+                        HapiHelper.PLT_CODE));
+        codingMap.put(
+                "99717-36",
+                new IdentifierCode(
+                        "PLT3290",
+                        "CFTR gene variant found [Identifier] in DBS by Sequencing comments/discussion",
+                        HapiHelper.PLT_CODE));
+        // MPS I
+        codingMap.put(
+                "99717-48",
+                new IdentifierCode(
+                        "PLT3258",
+                        "IDUA gene mutations found [Identifier] in DBS by Sequencing",
+                        HapiHelper.PLT_CODE));
+        codingMap.put(
+                "99717-44",
+                new IdentifierCode(
+                        "PLT3291",
+                        "IDUA gene variant analysis in DBS by Sequencing comments/discussion",
+                        HapiHelper.PLT_CODE));
+        // MPS II
+        codingMap.put(
+                "99717-50",
+                new IdentifierCode(
+                        "PLT3294",
+                        "IDS gene mutations found [Identifier] in Dried Bloodspot by Molecular genetics method",
+                        HapiHelper.PLT_CODE));
+        // Pompe
+        codingMap.put(
+                "99717-47",
+                new IdentifierCode(
+                        "PLT3252",
+                        "GAA gene mutation found [Identifier] in DBS by Sequencing",
+                        HapiHelper.PLT_CODE));
+        codingMap.put(
+                "99717-46",
+                new IdentifierCode(
+                        "PLT3292",
+                        "GAA gene variant analysis in DBS by Sequencing comments/discussion",
+                        HapiHelper.PLT_CODE));
+        // SMA
+        codingMap.put(
+                "99717-60",
+                new IdentifierCode(
+                        "PLT3293",
+                        "SMN1 exon 7 deletion analysis in DBS by Sequencing",
+                        HapiHelper.PLT_CODE));
+    }
+}
diff --git a/etor/src/main/resources/transformation_definitions.json b/etor/src/main/resources/transformation_definitions.json
@@ -186,6 +186,21 @@
         }
       ]
     },
+    {
+      "name": "ucsdOruMapLocalObservationCodes",
+      "description": "Maps local observation codes in OBX-3.4/5/6 to LOINC/PLT codes in OBX-3.1/2/3",
+      "message": "",
+      "conditions": [
+        "Bundle.entry.resource.ofType(MessageHeader).destination.receiver.resolve().identifier.where(extension.value = 'HD.1').value in ('R797' | 'R508')",
+        "Bundle.entry.resource.ofType(MessageHeader).event.code = 'R01'"
+      ],
+      "rules": [
+        {
+          "name": "MapLocalObservationCodes",
+          "args": {}
+        }
+      ]
+    },
     {
       "name": "ucsdOruCopyOrcOrderProviderToObrOrderProvider",
       "description": "Copies the value from ORC12 and uses this value to replace the value in OBR16",