From c8f175b8abba1661db94420277a005f9b9b37a13 Mon Sep 17 00:00:00 2001 From: Luis Pabon Date: Sat, 28 Sep 2024 13:53:40 -0400 Subject: [PATCH] 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 Co-authored-by: Sylvie Co-authored-by: jcrichlake <145698165+jcrichlake@users.noreply.github.com> Co-authored-by: saquino0827 * Add control id test, update test name * Fix order of mockLogger registration and injection * Fixed prod prefix mapping Co-Authored-By: halprin * 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 Co-authored-by: jorge Lopez Co-authored-by: Tiffini Johnson 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 Co-authored-by: Sylvie Co-authored-by: jcrichlake <145698165+jcrichlake@users.noreply.github.com> Co-authored-by: saquino0827 Co-authored-by: James Herr Co-authored-by: halprin Co-authored-by: Jorge Lopez <49923512+jorg3lopez@users.noreply.github.com> --- .../etor/messages/IdentifierCode.java | 9 + .../custom/MapLocalObservationCodes.java | 188 + .../resources/transformation_definitions.json | 15 + .../MapLocalObservationCodesTest.groovy | 322 + ...01_CDPH_OBX_to_LOINC_0_initial_message.hl7 | 138 + ...1_CDPH_OBX_to_LOINC_1_hl7_translation.fhir | 14698 ++++++++++++++++ ...PH_OBX_to_LOINC_2_fhir_transformation.fhir | 11926 +++++++++++++ ...H_OBX_to_LOINC_3_hl7_translation_final.hl7 | 119 + .../external/hapi/HapiHelper.java | 38 + .../external/hapi/HapiHelperTest.groovy | 59 + 10 files changed, 27512 insertions(+) create mode 100644 etor/src/main/java/gov/hhs/cdc/trustedintermediary/etor/messages/IdentifierCode.java create mode 100644 etor/src/main/java/gov/hhs/cdc/trustedintermediary/etor/ruleengine/transformation/custom/MapLocalObservationCodes.java create mode 100644 etor/src/test/groovy/gov/hhs/cdc/trustedintermediary/etor/ruleengine/transformation/custom/MapLocalObservationCodesTest.groovy create mode 100644 examples/CA/020_CA_ORU_R01_CDPH_OBX_to_LOINC_0_initial_message.hl7 create mode 100644 examples/CA/020_CA_ORU_R01_CDPH_OBX_to_LOINC_1_hl7_translation.fhir create mode 100644 examples/CA/020_CA_ORU_R01_CDPH_OBX_to_LOINC_2_fhir_transformation.fhir create mode 100644 examples/CA/020_CA_ORU_R01_CDPH_OBX_to_LOINC_3_hl7_translation_final.hl7 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 new file mode 100644 index 000000000..e3309825c --- /dev/null +++ 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: + */ +public record IdentifierCode(String code, String display, String codingSystem) {} diff --git a/etor/src/main/java/gov/hhs/cdc/trustedintermediary/etor/ruleengine/transformation/custom/MapLocalObservationCodes.java b/etor/src/main/java/gov/hhs/cdc/trustedintermediary/etor/ruleengine/transformation/custom/MapLocalObservationCodes.java new file mode 100644 index 000000000..da9a09f74 --- /dev/null +++ b/etor/src/main/java/gov/hhs/cdc/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 codingMap; + + public MapLocalObservationCodes() { + initMap(); + } + + @Override + public void transform(FhirResource resource, Map 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 index 0f90d5922..0daf8a52d 100644 --- 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", diff --git a/etor/src/test/groovy/gov/hhs/cdc/trustedintermediary/etor/ruleengine/transformation/custom/MapLocalObservationCodesTest.groovy b/etor/src/test/groovy/gov/hhs/cdc/trustedintermediary/etor/ruleengine/transformation/custom/MapLocalObservationCodesTest.groovy new file mode 100644 index 000000000..0fc7f9341 --- /dev/null +++ b/etor/src/test/groovy/gov/hhs/cdc/trustedintermediary/etor/ruleengine/transformation/custom/MapLocalObservationCodesTest.groovy @@ -0,0 +1,322 @@ +package gov.hhs.cdc.trustedintermediary.etor.ruleengine.transformation.custom + +import gov.hhs.cdc.trustedintermediary.ExamplesHelper +import gov.hhs.cdc.trustedintermediary.context.TestApplicationContext +import gov.hhs.cdc.trustedintermediary.external.hapi.HapiFhirHelper +import gov.hhs.cdc.trustedintermediary.external.hapi.HapiFhirResource +import gov.hhs.cdc.trustedintermediary.external.hapi.HapiHelper +import gov.hhs.cdc.trustedintermediary.wrappers.Logger +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 +import spock.lang.Specification + +class MapLocalObservationCodesTest extends Specification { + def transformClass + def mockLogger = Mock(Logger) + + def setup() { + TestApplicationContext.reset() + TestApplicationContext.init() + TestApplicationContext.register(Logger, mockLogger) + TestApplicationContext.injectRegisteredImplementations() + + transformClass = new MapLocalObservationCodes() + } + + def "When message has a mappable local observation code in OBX-3.4/5/6, should add the mapped code to OBX-3.1/2/3"() { + given: + def bundle = HapiFhirHelper.createMessageBundle(messageTypeCode: 'ORU_R01') + + def observation = new Observation() + observation.code.addCoding(getCoding(initialCode, initialDisplay, true, "alt-coding" )) + bundle.addEntry(new Bundle.BundleEntryComponent().setResource(observation)) + + when: + transformClass.transform(new HapiFhirResource(bundle), null) + + then: + def transformedObservation = HapiHelper.resourceInBundle(bundle, Observation.class) + def transformedCodingList = transformedObservation.getCode().getCoding() + transformedCodingList.size() == 2 + + // Mapped code should be added as the primary coding + evaluateCoding( + transformedCodingList[0], + expectedCode, + expectedDisplay, + expectedCodingSystem, + "coding", + expectedExtensionSystem) + + // Local code should remain as the alternate coding + evaluateCoding( + transformedCodingList[1], + initialCode, + initialDisplay, + HapiHelper.LOCAL_CODE_URL, + "alt-coding", + HapiHelper.LOCAL_CODE) + + where: + initialCode | initialDisplay || expectedCode | expectedDisplay | expectedCodingSystem | expectedExtensionSystem + "99717-32" | "Adrenoleukodystrophy deficiency newborn screening interpretation" || "85269-9" | "X-linked Adrenoleukodystrophy (X- ALD) newborn screen interpretation" | HapiHelper.LOINC_URL | HapiHelper.LOINC_CODE + "99717-34" | "Adrenoleukodystrophy Mutation comments/discussion" || "PLT325" | "ABCD1 gene mutation found [Identifier] in DBS by Sequencing" | null | HapiHelper.PLT_CODE + } + + def "When message has an unmapped local observation code in OBX-3.4/5/6, no mapping should occur and a warning should be logged"() { + given: + final String LOCAL_CODE = "UNMAPPED" + final String LOCAL_DISPLAY = "An unmapped local code" + def bundle = HapiFhirHelper.createMessageBundle(messageTypeCode: 'ORU_R01') + + def observation = new Observation() + observation.code.addCoding(getCoding(LOCAL_CODE, LOCAL_DISPLAY, true, "alt-coding" )) + bundle.addEntry(new Bundle.BundleEntryComponent().setResource(observation)) + + when: + transformClass.transform(new HapiFhirResource(bundle), null) + + then: + 1 * mockLogger.logWarning(*_) + + def transformedObservation = HapiHelper.resourceInBundle(bundle, Observation.class) + def transformedCodingList = transformedObservation.getCode().getCoding() + transformedCodingList.size() == 1 + + observation.code.coding == transformedCodingList + } + + def "When message has a mappable local observation code in OBX-3.4/5/6 and other content in OBX3-1/2/3, no mapping should occur"() { + given: + def bundle = HapiFhirHelper.createMessageBundle(messageTypeCode: 'ORU_R01') + + def observation = new Observation() + observation.code.addCoding(getCoding(obx31code, obx32display, false, "coding" )) + observation.code.addCoding(getCoding("99717-32", "Adrenoleukodystrophy deficiency newborn screening interpretation", true, "alt-coding" )) + + bundle.addEntry(new Bundle.BundleEntryComponent().setResource(observation)) + + when: + transformClass.transform(new HapiFhirResource(bundle), null) + + then: + def transformedObservation = HapiHelper.resourceInBundle(bundle, Observation.class) + def transformedCodingList = transformedObservation.getCode().getCoding() + transformedCodingList.size() == 2 + + observation.code.coding == transformedCodingList + + where: + obx31code | obx32display + "some_code" | "Some display" + "some_code" | null + null | "Some display" + } + + def "When message has a LOINC code, no mapping should occur"() { + given: + final String CODE = "A_LOINC_CODE" + final String DISPLAY = "Some display" + + def bundle = HapiFhirHelper.createMessageBundle(messageTypeCode: 'ORU_R01') + + def observation = new Observation() + observation.code.addCoding(getCoding(CODE, DISPLAY, false, codingSystem )) + bundle.addEntry(new Bundle.BundleEntryComponent().setResource(observation)) + + when: + transformClass.transform(new HapiFhirResource(bundle), null) + + then: + def transformedObservation = HapiHelper.resourceInBundle(bundle, Observation.class) + def transformedCodingList = transformedObservation.getCode().getCoding() + transformedCodingList.size() == 1 + + observation.code.coding == transformedCodingList + + where: + codingSystem << ["coding", "alt-coding"] + } + + def "When no coding system, no mapping should occur"() { + given: + final String LOCAL_CODE = "A_LOCAL_CODE" + final String LOCAL_DISPLAY = "The local code description" + def bundle = HapiFhirHelper.createMessageBundle(messageTypeCode: 'ORU_R01') + + def observation = new Observation() + def coding = new Coding() + coding.code = LOCAL_CODE + coding.display = LOCAL_DISPLAY + coding.addExtension(HapiHelper.EXTENSION_CWE_CODING, new StringType("alt-coding")) + coding.addExtension(HapiHelper.EXTENSION_CODING_SYSTEM, new StringType(HapiHelper.LOCAL_CODE)) + observation.code.addCoding(coding) + + bundle.addEntry(new Bundle.BundleEntryComponent().setResource(observation)) + + when: + transformClass.transform(new HapiFhirResource(bundle), null) + + then: + def transformedObservation = HapiHelper.resourceInBundle(bundle, Observation.class) + def transformedCodingList = transformedObservation.getCode().getCoding() + transformedCodingList.size() == 1 + + observation.code.coding == transformedCodingList + } + + def "When no coding extension, no mapping should occur"() { + given: + final String LOCAL_CODE = "A_LOCAL_CODE" + final String LOCAL_DISPLAY = "The local code description" + def bundle = HapiFhirHelper.createMessageBundle(messageTypeCode: 'ORU_R01') + + def observation = new Observation() + def coding = new Coding() + coding.system = HapiHelper.LOCAL_CODE_URL + coding.code = LOCAL_CODE + coding.display = LOCAL_DISPLAY + observation.code.addCoding(coding) + + bundle.addEntry(new Bundle.BundleEntryComponent().setResource(observation)) + + when: + transformClass.transform(new HapiFhirResource(bundle), null) + + then: + def transformedObservation = HapiHelper.resourceInBundle(bundle, Observation.class) + def transformedCodingList = transformedObservation.getCode().getCoding() + transformedCodingList.size() == 1 + + observation.code.coding == transformedCodingList + } + + def "When no observation identifier, the observation does not change"() { + given: + def bundle = HapiFhirHelper.createMessageBundle(messageTypeCode: 'ORU_R01') + + // Add an observation with an observation value and a status, but no observation identifier + def observation = new Observation() + observation.status = Observation.ObservationStatus.FINAL + def valueCoding = new Coding() + valueCoding.code = "123456" + observation.valueCodeableConcept.coding.add(valueCoding) + bundle.addEntry(new Bundle.BundleEntryComponent().setResource(observation)) + + when: + transformClass.transform(new HapiFhirResource(bundle), null) + + then: + def transformedObservation = HapiHelper.resourceInBundle(bundle, Observation.class) + + observation == transformedObservation + } + + def "When message has multiple observations, local and non-local codes are handled appropriately"() { + given: + final String FHIR_ORU_PATH = "../CA/020_CA_ORU_R01_CDPH_OBX_to_LOINC_1_hl7_translation.fhir" + def fhirResource = ExamplesHelper.getExampleFhirResource(FHIR_ORU_PATH) + def bundle = fhirResource.getUnderlyingResource() as Bundle + def initialObservations = HapiHelper.resourcesInBundle(bundle, Observation.class).toList() + + expect: + initialObservations.size() == 114 + + when: + transformClass.transform(new HapiFhirResource(bundle), null) + + then: + def transformedObservations = HapiHelper.resourcesInBundle(bundle, Observation.class).toList() + transformedObservations.size() == 114 + + // Assortment of LOINC codes - ensure they are left as-is + def initialLoinc1 = getObservationByCode(initialObservations, "57721-3") + def transformedLoinc1 = getObservationByCode(transformedObservations, "57721-3") + initialLoinc1 == transformedLoinc1 + + def initialLoinc2 = getObservationByCode(initialObservations, "8339-4") + def transformedLoinc2 = getObservationByCode(transformedObservations, "8339-4") + initialLoinc2 == transformedLoinc2 + + def initialLoinc3 = getObservationByCode(initialObservations, "54104-5") + def transformedLoinc3 = getObservationByCode(transformedObservations, "54104-5") + initialLoinc3 == transformedLoinc3 + + // Mappable local code to LOINC - should have mapped code added + def mappedLoinc = getObservationByCode(transformedObservations, "99717-33") + mappedLoinc.code.coding.size() == 2 + + evaluateCoding( + mappedLoinc.code.coding[0], + "85268-1", + "X-linked Adrenoleukodystrophy (X- ALD) newborn screening comment-discussion", + HapiHelper.LOINC_URL, + "coding", + HapiHelper.LOINC_CODE) + + evaluateCoding( + mappedLoinc.code.coding[1], + "99717-33", + "Adrenoleukodystrophy deficiency newborn screening comments-discussion", + HapiHelper.LOCAL_CODE_URL, + "alt-coding", + HapiHelper.LOCAL_CODE) + + // Mappable local code to PLT - should have mapped code added + def mappedPlt = getObservationByCode(transformedObservations, "99717-48") + mappedPlt.code.coding.size() == 2 + + evaluateCoding( + mappedPlt.code.coding[0], + "PLT3258", + "IDUA gene mutations found [Identifier] in DBS by Sequencing", + null, + "coding", + HapiHelper.PLT_CODE) + + evaluateCoding( + mappedPlt.code.coding[1], + "99717-48", + "MPS I IDUA Gene Sequence Mutation Information", + HapiHelper.LOCAL_CODE_URL, + "alt-coding", + HapiHelper.LOCAL_CODE) + + // Unmapped local code - ensure it is left as-is + def initialAccession = getObservationByCode(initialObservations, "99717-5") + def transformedAccession = getObservationByCode(transformedObservations, "99717-5") + initialAccession == transformedAccession + } + + Observation getObservationByCode(List observationList, String code) { + return observationList.find {observation -> observation.code?.coding?.find { coding -> coding.code == code}} + } + + Coding getCoding(String code, String display, boolean localCoding, String cweCoding) { + def coding = new Coding() + coding.system = localCoding ? HapiHelper.LOCAL_CODE_URL : HapiHelper.LOINC_URL + coding.code = code + coding.display = display + + coding.addExtension(HapiHelper.EXTENSION_CWE_CODING, new StringType(cweCoding)) + coding.addExtension(HapiHelper.EXTENSION_CODING_SYSTEM, new StringType(localCoding ? HapiHelper.LOCAL_CODE : HapiHelper.LOINC_CODE)) + return coding + } + + void evaluateCoding( + Coding coding, + String expectedCode, + String expectedDisplay, + String expectedSystem, + String expectedExtensionCoding, + String expectedExtensionSystem) { + assert coding.code == expectedCode + assert coding.display == expectedDisplay + assert coding.system == expectedSystem + assert coding.extension.size() == 2 + assert coding.getExtensionString(HapiHelper.EXTENSION_CWE_CODING) == expectedExtensionCoding + assert coding.getExtensionString(HapiHelper.EXTENSION_CODING_SYSTEM) == expectedExtensionSystem + } +} diff --git a/examples/CA/020_CA_ORU_R01_CDPH_OBX_to_LOINC_0_initial_message.hl7 b/examples/CA/020_CA_ORU_R01_CDPH_OBX_to_LOINC_0_initial_message.hl7 new file mode 100644 index 000000000..2d3d0867a --- /dev/null +++ b/examples/CA/020_CA_ORU_R01_CDPH_OBX_to_LOINC_0_initial_message.hl7 @@ -0,0 +1,138 @@ +MSH|^~\&|SISGDSP|SISGDSP|SISHIERECEIVER^11903029^L,M,N|^^L,M,N|20240711034913||ORU^R01^ORU_R01|243747623|T|2.5.1 +PID|1||80009197^^^&NPI^MR||NICUABG^TESTONE^^^^^B||20240607|M||2076-8^Native Hawaiian or Other Pacific Islander||||||||||||2186-5^Not Hispanic or Latino||N|1 +NK1|1|NICUABG|MTH^Mother +ORC|RE|7241234515^FormNumber||189609160^HospOrdNumber|||||||||||||||||^^^^^^^^^R797| N 054TS ARALC, TS102 E^^SAN DIEGO^CA^99999-9999 +OBR|1|7241234515^FormNumber||54089-8^NB Screen Panel Patient AHIC|||202407111346|||||||||||||||20240711034913|||F +OBR|2|7241234515^FormNumber||57128-1^Newborn Screening Report summary panel|||202407111346|||||||||||||||20240711034913|||F +OBX|1|CE|57721-3^Reason for lab test in Dried blood spot^LN|1|LA12421-6^Initial screen^LN|||N|||F|||20240711034913 +OBX|2|CE|57718-9^Sample quality of Dried blood spot^LN|1|LA12432-3^Acceptable^LN|||N|||F|||20240711034913 +OBX|3|CE|57130-7^Newborn screening report - overall interpretation^LN|1|LA18944-1^Screen is out of range for at least one condition^LN|||N|||F|||20240711034913 +OBX|4|CE|57131-5^Newborn conditions with positive markers [Identifier] in Dried blood spot^LN|1|LA12532-0^BIO^LN|||N|||F|||20240711034913 +OBX|5|CE|57720-5^Newborn conditions with equivocal markers [Identifier] in Dried blood spot^LN|1|LA137-2^None^LN|||N|||F|||20240711034913 +OBX|6|TX|57724-7^Newborn screening short narrative summary^LN|1|ACTION REQUIRED\.br\\.br\NBS Testing Lab - COMMUNITY REG MEDICAL CENTER LAB \R\EG 4389EVA EESEN, TS054 E, FRESNO, CA 99999\.br\\.br\Genetic Disease Laboratory - GDL W 057DR HCLE, TS016 E, RICHMOND, CA 99999-9999\.br\\.br\Lab Director - Genetic Disease Laboratory, (510) 231-1790\.br\\.br\Duplicate\.br\\.br\Follow-up:\.br\\.br\Acyl Carnitine Panel: Reference Ranges for acylcarnitines are based on specimens collected on newborns who are less than 10 days old. \.br\\.br\Biotinidase Deficiency: This screen for Biotinidase Deficiency was positive. Another specimen MUST be collected on this infant. \.br\\.br\If you have any questions regarding these screening outcomes, please contact the Newborn Screening Staff at at . \.br\\.br\Methods and Limitations:\.br\\.br\Assays for ALD Tier-1, BD, CAH, CF, GAL, MS/MS Acylcarnitine and Amino Acid Panels, PCH, hemoglobinopathies, and SCID were performed at the testing laboratory specified on the front of this report. Assays for ALD Tier-2, CAH Tier-2, Pompe Disease Tier-1, MPS I Tier-1, and SMA were developed and/or optimized by the Genetic Disease Laboratory (GDL), and performed at GDL. Performance characteristics of these assays are determined by GDL. The SMA assay is designed to identify 95% of SMA patients who have homozygous deletions of the SMN1 gene on chromosome 5q. These assays have not been cleared or approved by the U.S. Food and Drug Administration (FDA). The FDA has determined that such clearance or approval is not necessary. The assays are used for clinical purposes. They should not be regarded as investigational or for research. GDL is certified under the Clinical Laboratory Improvement Amendments of 1988 (CLIA-88) to perform high complexity genetic disease screening. \.br\Attention Healthcare Provider:\.br\\.br\\.br\|||N|||F|||20240711034913 +OBX|7|TX|57129-9^Full newborn screening summary report for display or printing^LN|1||||N|||F|||20240711034913 +OBR|3|7241234515^FormNumber||57717-1^Newborn screen card data panel|||202407111346|||||||||||||||20240711034913|||F +OBX|1|ST|57716-3^State printed on filter paper card [Identifier] in NBS card^LN|1|CA|||N|||F|||20240711034913 +OBX|2|NM|8339-4^Birthweight^LN|1|3500|grams||N|||F|||20240711034913 +OBX|3|CE|57722-1^Birth plurality of Pregnancy^LN|1|LA12411-7^Singleton^LN|||N|||F|||20240711034913 +OBX|4|NM|73806-2^Newborn age in hours^LN|1|34|day(s)||N|||F|||20240711034913 +OBX|5|CE|57713-0^Infant NICU factors that affect newborn screening interpretation^LN|1|LA137-2^None^LN|||N|||F|||20240711034913 +OBX|6|CE|67704-7^Feeding types^LN|1|LA16914-6^Breast milk^LN|||N|||F|||20240711034913 +OBX|7|TX|^^^99717-5^Accession Number^L|1|193-08-269/21-2024-21|||N|||F|||20240711034913 +OBX|8|TX|62324-9^Post-discharge provider name^LN|1|EUSTRATIA HUBBARD|||N|||F|||20240711034913 +OBX|9|TX|62327-2^Post-discharge provider practice address^LN|1|N 054TS ARALC, TS102 E SAN DIEGO CA 99999-9999 USA|||N|||F|||20240711034913 +OBR|4|7241234515^FormNumber||57794-0^Newborn screening test results panel in Dried blood spot|||202407111346|||||||||||||||20240711034913|||F +OBR|5|7241234515^FormNumber||53261-4^Amino acid newborn screen panel|||202407111346|||||||||||||||20240711034913|||F +OBX|1|NM|47633-3^Glycine [Moles/volume] in Dried blood spot^LN|1|0.5|µmol/L||N|||F|||20240711034913 +OBX|2|NM|53150-9^Alanine+Beta Alanine+Sarcosine [Moles/volume] in Dried blood spot^LN|1|500|µmol/L|<1000|N|||F|||20240711034913 +OBX|3|NM|47799-2^Valine [Moles/volume] in Dried blood spot^LN|1|0.5|µmol/L||N|||F|||20240711034913 +OBX|4|NM|53151-7^Valine/Phenylalanine [Molar ratio] in Dried blood spot^LN|1|0.00645|{Ratio}|<4.3|N|||F|||20240711034913 +OBX|5|NM|53152-5^Alloisoleucine+Isoleucine+Leucine+Hydroxyproline^LN|1|125|µmol/L|<230|N|||F|||20240711034913 +OBX|6|NM|53154-1^Alloisoleucine+Isoleucine+Leucine+Hydroxyproline/Alanine [Molar ratio] in Dried blood spot^LN|1|0.65|{Ratio}|<1.35|N|||F|||20240711034913 +OBX|7|NM|29573-3^Phenylalanine [Moles/volume] in Dried blood spot^LN|1|77.5|µmol/L|<175|N|||F|||20240711034913 +OBX|8|NM|35572-7^Phenylalanine/Tyrosine [Molar ratio] in Dried blood spot^LN|1|0.75|{Ratio}|<2.6|N|||F|||20240711034913 +OBX|9|NM|35571-9^Tyrosine [Moles/volume] in Dried blood spot^LN|1|425|µmol/L|<680|N|||F|||20240711034913 +OBX|10|NM|53231-7^Succinylacetone [Moles/volume] in Dried blood spot^LN|1|2.25|µmol/L|<6.1|N|||F|||20240711034913 +OBX|11|NM|47700-0^Methionine [Moles/volume] in Dried blood spot^LN|1|27|µmol/L|6.3-100|N|||F|||20240711034913 +OBX|12|NM|42892-0^Citrulline [Moles/volume] in Dried blood spot^LN|1|16.25|µmol/L|5-49|N|||F|||20240711034913 +OBX|13|NM|54092-2^Citrulline/Arginine [Molar ratio] in Dried blood spot^LN|1|3|{Ratio}|<4.8|N|||F|||20240711034913 +OBX|14|NM|53155-8^Asparagine+Ornithine [Moles/volume] in Dried blood spot^LN|1|400|µmol/L|<800|N|||F|||20240711034913 +OBX|15|NM|75215-4^Ornithine/Citrulline [Molar ratio] in Dried blood spot^LN|1|0.5|{Ratio}||N|||F|||20240711034913 +OBX|16|NM|47562-4^Arginine [Moles/volume] in Dried blood spot^LN|1|25|µmol/L|<63|N|||F|||20240711034913 +OBX|17|NM|75214-7^Arginine/Ornithine [Molar ratio] in Dried blood spot^LN|1|0.7|{Ratio}|<1.9|N|||F|||20240711034913 +OBX|18|NM|47732-3^Proline [Moles/volume] in Dried blood spot^LN|1|750|µmol/L|<1500|N|||F|||20240711034913 +OBX|19|TX|57710-6^Amino acidemias newborn screening comment/discussion^LN|1|Negative|||N|||F|||20240711034913 +OBR|6|7241234515^FormNumber||58092-8^Acylcarnitine newborn screen panel|||202407111346|||||||||||||||20240711034913|||F +OBX|1|CE|58088-6^Acylcarnitine newborn screen interpretation^LN|1|LA18592-8^In range^LN|||N|||F|||20240711034913 +OBX|2|TX|58093-6^Acylcarnitine newborn screening comment/discussion^LN|1|Negative|||N|||F|||20240711034913 +OBR|7|7241234515^FormNumber||57084-6^Fatty acid oxidation newborn screen panel|||202407111346|||||||||||||||20240711034913|||F +OBX|1|NM|38481-8^Carnitine.free (C0)^LN|1|33|µmol/L|6.4-125|N|||F|||20240711034913 +OBX|2|NM|53235-8^Carnitine.free (C0)/Palmitoylcarnitine (C16)+Stearoylcarnitine (C18)^LN|1|37.5|{Ratio}|<70|N|||F|||20240711034913 +OBX|3|NM|50157-7^Acetylcarnitine (C2)^LN|1|20.38|µmol/L|10-80|N|||F|||20240711034913 +OBX|4|NM|75212-1^Malonylcarnitine (C3-DC)/Decanoylcarnitine (C10) [Molar ratio] in Dried blood spot^LN|1|0.62500|{Ratio}|<7.6|N|||F|||20240711034913 +OBX|5|NM|45211-0^Hexanoylcarnitine (C6)^LN|1|0.48|µmol/L|<0.95|N|||F|||20240711034913 +OBX|6|NM|53175-6^Octanoylcarnitine (C8)^LN|1|0.3|µmol/L|<0.45|N|||F|||20240711034913 +OBX|7|NM|53177-2^Octanoylcarnitine (C8)/Decanoylcarnitine (C10)^LN|1|0.5|{Ratio}||N|||F|||20240711034913 +OBX|8|NM|53174-9^Octenoylcarnitine (C8:1)^LN|1|0.35|µmol/L|<0.65|N|||F|||20240711034913 +OBX|9|NM|45197-1^Decanoylcarnitine (C10)^LN|1|0.32|µmol/L|<0.65|N|||F|||20240711034913 +OBX|10|NM|45198-9^Decenoylcarnitine (C10:1)^LN|1|0.22|µmol/L|<0.45|N|||F|||20240711034913 +OBX|11|NM|45199-7^Dodecanoylcarnitine (C12)^LN|1|1|µmol/L|<2|N|||F|||20240711034913 +OBX|12|NM|45200-3^Dodecenoylcarnitine (C12:1)^LN|1|0.5|µmol/L||N|||F|||20240711034913 +OBX|13|NM|53192-1^Tetradecanoylcarnitine (C14)^LN|1|0.6|µmol/L|<1.2|N|||F|||20240711034913 +OBX|14|NM|53191-3^Tetradecenoylcarnitine (C14:1)^LN|1|0.4|µmol/L|<0.9|N|||F|||20240711034913 +OBX|15|NM|53194-7^Tetradecenoylcarnitine (C14:1)/Dodecenoylcarnitine (C12:1)^LN|1|0.5|{Ratio}||N|||F|||20240711034913 +OBX|16|NM|53190-5^Tetradecadienoylcarnitine (C14:2)^LN|1|0.5|µmol/L||N|||F|||20240711034913 +OBX|17|NM|50281-5^3-Hydroxytetradecanoylcarnitine (C14-OH)^LN|1|0.1|µmol/L|<0.2|N|||F|||20240711034913 +OBX|18|NM|53199-6^Palmitoylcarnitine (C16)^LN|1|5|µmol/L|<12|N|||F|||20240711034913 +OBX|19|NM|53198-8^Palmitoleylcarnitine (C16:1)^LN|1|0.7|µmol/L|<1.4|N|||F|||20240711034913 +OBX|20|NM|50125-4^3-Hydroxypalmitoylcarnitine (C16-OH)^LN|1|0.05|µmol/L|<0.1|N|||F|||20240711034913 +OBX|21|NM|53201-0^3-Hydroxypalmitoylcarnitine (C16-OH)/Palmitoylcarnitine (C16)^LN|1|0.01000|{Ratio}|<0.07|N|||F|||20240711034913 +OBX|22|NM|53241-6^Stearoylcarnitine (C18)^LN|1|2|µmol/L|<3.5|N|||F|||20240711034913 +OBX|23|NM|53202-8^Oleoylcarnitine (C18:1)^LN|1|3.5|µmol/L|<7|N|||F|||20240711034913 +OBX|24|NM|45217-7^Linoleoylcarnitine (C18:2)^LN|1|0.5|µmol/L||N|||F|||20240711034913 +OBX|25|NM|50132-0^3-Hydroxystearoylcarnitine (C18-OH)^LN|1|0.05|µmol/L|<0.1|N|||F|||20240711034913 +OBX|26|NM|50113-0^3-Hydroxyoleoylcarnitine (C18:1-OH)^LN|1|0.05|µmol/L|<0.1|N|||F|||20240711034913 +OBR|8|7241234515^FormNumber||57085-3^Organic acid newborn screen panel|||202407111346|||||||||||||||20240711034913|||F +OBX|1|NM|53160-8^Propionylcarnitine (C3)^LN|1|3.15|µmol/L|<7.9|N|||F|||20240711034913 +OBX|2|NM|53163-2^Propionylcarnitine (C3)/Acetylcarnitine (C2)^LN|1|0.15|{Ratio}|<0.42|N|||F|||20240711034913 +OBX|3|NM|67708-8^Malonylcarnitine (C3-DC)+3-Hydroxybutyrylcarnitine (C4-OH)^LN|1|0.2|µmol/L|<0.48|N|||F|||20240711034913 +OBX|4|NM|53166-5^Butyrylcarnitine+Isobutyrylcarnitine (C4)^LN|1|0.85|µmol/L|<1.7|N|||F|||20240711034913 +OBX|5|NM|45216-9^Isovalerylcarnitine+Methylbutyrylcarnitine (C5)^LN|1|0.5|µmol/L|<0.95|N|||F|||20240711034913 +OBX|6|NM|53240-8^Isovalerylcarnitine+Methylbutyrylcarnitine (C5)/Propionylcarnitine (C3)^LN|1|0.15873|{Ratio}|<0.38|N|||F|||20240711034913 +OBX|7|NM|53170-7^Tiglylcarnitine (C5:1)^LN|1|0.3|µmol/L|<0.5|N|||F|||20240711034913 +OBX|8|NM|50106-4^3-Hydroxyisovalerylcarnitine (C5-OH)^LN|1|0.45|µmol/L|<1.15|N|||F|||20240711034913 +OBX|9|NM|67710-4^Glutarylcarnitine (C5-DC)+3-Hydroxyhexanoylcarnitine (C6-OH)^LN|1|0.3|µmol/L|<0.38|N|||F|||20240711034913 +OBX|10|NM|75216-2^Glutarylcarnitine (C5-DC)/Malonylcarnitine (C3-DC) [Molar ratio] in Dried blood spot^LN|1|1.50000|{Ratio}|>0.1|N|||F|||20240711034913 +OBR|9|7241234515^FormNumber||54078-1^Cystic fibrosis newborn screening panel|||202407111346|||||||||||||||20240711034913|||F +OBX|1|NM|48633-2^Trypsinogen I.free^LN|1|31.00|ng/mL|<69|N|||F|||20240711034913 +OBX|2|CE|46769-6^Cystic fibrosis newborn screen interpretation^LN|1|LA18592-8^In range^LN|||N|||F|||20240711034913 +OBX|3|TX|57707-2^Cystic fibrosis newborn screening comment/discussion^LN|1|Negative|||N|||F|||20240711034913 +OBR|10|7241234515^FormNumber||57086-1^Congenital adrenal hyperplasia newborn screening panel|||202407111346|||||||||||||||20240711034913|||F +OBX|1|NM|38473-5^17-Hydroxyprogesterone^LN|1|35|nmol/L|<85|N|||F|||20240711034913 +OBX|2|CE|46758-9^Congenital adrenal hyperplasia newborn screen interpretation^LN|1|LA18592-8^In range^LN|||N|||F|||20240711034913 +OBX|3|TX|57706-4^Congenital adrenal hyperplasia newborn screening comment-discussion^LN|1|Negative|||N|||F|||20240711034913 +OBR|11|7241234515^FormNumber||54090-6^Thyroid newborn screening panel|||202407111346|||||||||||||||20240711034913|||F +OBX|1|NM|29575-8^Thyrotropin^LN|1|14.50|mIU/L|<29|N|||F|||20240711034913 +OBX|2|CE|46762-1^Congenital hypothyroidism newborn screen interpretation^LN|1|LA18592-8^In range^LN|||N|||F|||20240711034913 +OBX|3|TX|57705-6^Congenital hypothyroidism newborn screening comment-discussion^LN|1|Negative|||N|||F|||20240711034913 +OBR|12|7241234515^FormNumber||54079-9^Galactosemia newborn screening panel|||202407111346|||||||||||||||20240711034913|||F +OBX|1|NM|42906-8^Galactose 1 phosphate uridyl transferase^LN|1|55.00|enzyme units|>50|N|||F|||20240711034913 +OBX|2|CE|46737-3^Galactosemias newborn screen interpretation^LN|1|LA18592-8^In range^LN|||N|||F|||20240711034913 +OBX|3|TX|57704-9^Galactosemias newborn screening comment-discussion^LN|1|Negative|||N|||F|||20240711034913 +OBR|13|7241234515^FormNumber||54081-5^Hemoglobinopathies newborn screening panel|||202407111346|||||||||||||||20240711034913|||F +OBX|1|TX|54104-5^Hemoglobin pattern^LN|1|FA||||||F|||20240711034913 +OBX|2|TX|57703-1^Hemoglobin disorders newborn screening comment/discussion^LN|1|Usual hemoglobin pattern. These results assume no transfusion prior to testing and do not rule out the possibility of a thalassemia trait or rare hemoglobin variants.||||||F|||20240711034913 +OBR|14|7241234515^FormNumber||57087-9^Biotinidase newborn screening panel|||202407111346|||||||||||||||20240711034913|||F +OBX|1|NM|75217-0^Biotinidase [Enzymatic activity/volume] in Dried blood spot^LN|1|8.00|ERU|>10|L|||F|||20240711034913 +OBX|2|CE|46761-3^Biotinidase deficiency newborn screen interpretation^LN|1|LA18593-6^Out of range^LN|||A|||F|||20240711034913 +OBX|3|TX|57699-1^Biotinidase deficiency newborn screening comment-discussion^LN|1|Positive|||A|||F|||20240711034913 +OBR|15|7241234515^FormNumber||62333-0^Severe combined immunodeficiency (SCID) newborn screening panel|||202407111346|||||||||||||||20240711034913|||F +OBX|1|NM|62320-7^T-cell receptor excision circle [#/volume] in Dried blood spot by Probe and target amplification method^LN|1|33|copies/µL|>18|N|||F|||20240711034913 +OBX|2|CE|62321-5^Severe combined immunodeficiency newborn screen interpretation^LN|1|LA18592-8^In range^LN|||N|||F|||20240711034913 +OBX|3|TX|62322-3^Severe combined immunodeficiency newborn screening comment-discussion^LN|1|Negative|||N|||F|||20240711034913 +OBR|16|7241234515^FormNumber||63414-7^Pompe Disease newborn screening panel|||202407111346|||||||||||||||20240711034913|||F +OBX|1|NM|55827-0^Acid alpha glucosidase [Enzymatic activity/volume] in DBS^LN|1|12.923|µmol/L/h|>=2.079|N|||F|||20240711034913 +OBX|2|CE|63415-4^Pompe Disease deficiency newborn screen interpretation^LN|1|LA18592-8^In range^LN|||N|||F|||20240711034913 +OBX|3|TX|63416-2^Pompe Disease deficiency newborn screening comments-discussion^LN|1|Negative|||N|||F|||20240711034913 +OBR|17|7241234515^FormNumber||79563-3^Mucopolysaccharidosis type I newborn screening panel|||202407111346|||||||||||||||20240711034913|||F +OBX|1|NM|55909-6^Alpha-L-iduronidase [Enzymatic activity/volume] in DBS^LN|1|3.117|µmol/L/h|>=1.2204|N|||F|||20240711034913 +OBX|2|CE|79564-1^Mucopolysaccharidosis type I newborn screen interpretation^LN|1|LA18592-8^In range^LN|||N|||F|||20240711034913 +OBX|3|TX|79565-8^Mucopolysaccharidosis type I newborn screening comment-discussion^LN|1|Negative|||N|||F|||20240711034913 +OBR|18|7241234515^FormNumber||92005-8^Spinal muscular atrophy newborn screening panel|||202407111346|||||||||||||||20240711034913|||F +OBX|1|TX|^^^99717-60^SMN1 Homozygous Deletion Analysis^L|1|Exon 7 Present||Exon 7 Present|N|||F|||20240711034913 +OBX|2|CE|92004-1^Spinal muscular atrophy newborn screen interpretation^LN|1|LA18592-8^In range^LN|||N|||F|||20240711034913 +OBX|3|TX|92003-3^Spinal muscular atrophy newborn screening comment-discussion^LN|1|SMA Negative|||N|||F|||20240711034913 +OBR|19|7241234515^FormNumber||^^^99717-28^Adrenoleukodystrophy newborn screening panel^L|||202407111346|||||||||||||||20240711034913|||F +OBX|1|CE|^^^99717-32^Adrenoleukodystrophy deficiency newborn screening interpretation^L|1|LA18592-8^In range^LN|||N|||F|||20240711034913 +OBX|2|TX|^^^99717-33^Adrenoleukodystrophy deficiency newborn screening comments-discussion^L|1|Negative|||N|||F|||20240711034913 +OBX|3|TX|^^^99717-34^Adrenoleukodystrophy Mutation comments/discussion^L|1|Negative|||N|||F|||20240711034913 +OBX|4|TX|^^^99717-6^17-Hydroxyprogesterone (CAH II)^L|1|Negative|||N|||F|||20240711034913 +OBX|5|TX|^^^99717-35^Cystic fibrosis Sequencing newborn screening interpretation^L|1|Negative|||N|||F|||20240711034913 +OBX|6|TX|^^^99717-36^Cystic fibrosis Sequencing newborn screening 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+MSH|^~\&|SISGDSP|CDPH|EPIC|R797|20240711034913||ORU^R01|243747623|T|2.5.1 +PID|1||80009197||NICUABG^TESTONE||20240607|M||2076-8^Native Hawaiian or Other Pacific Islander||||||||||||2186-5^Not Hispanic or Latino||N|1 +NK1|1|NICUABG|MTH^Mother +ORC|RE|189609160^HospOrdNumber||7241234515^FormNumber|||||||||||||||||^^^^^^^^^R797|N 054TS ARALC, TS102 E^^SAN DIEGO^CA^99999-9999 +OBR|1|189609160^HospOrdNumber||54089-8^NB Screen Panel Patient AHIC^CDPHGSPEAP|||202407111346|||||||||||||||20240711034913|||F +OBX|1|CE|57721-3^Reason for lab test in Dried blood spot^LN|1|LA12421-6^Initial screen^LN|||N|||F|||20240711034913 +OBX|2|CE|57718-9^Sample quality of Dried blood spot^LN|1|LA12432-3^Acceptable^LN|||N|||F|||20240711034913 +OBX|3|CE|57130-7^Newborn screening report - overall interpretation^LN|1|LA18944-1^Screen is out of range for at least one condition^LN|||N|||F|||20240711034913 +OBX|4|CE|57131-5^Newborn conditions with positive markers [Identifier] in Dried blood spot^LN|1|LA12532-0^BIO^LN|||N|||F|||20240711034913 +OBX|5|CE|57720-5^Newborn conditions with equivocal markers [Identifier] in Dried blood spot^LN|1|LA137-2^None^LN|||N|||F|||20240711034913 +OBX|6|TX|57724-7^Newborn screening short narrative summary^LN|1|ACTION REQUIRED\.br\\.br\NBS Testing Lab - COMMUNITY REG MEDICAL CENTER LAB \R\EG 4389EVA EESEN, TS054 E, FRESNO, CA 99999\.br\\.br\Genetic Disease Laboratory - GDL W 057DR HCLE, TS016 E, RICHMOND, CA 99999-9999\.br\\.br\Lab Director - Genetic Disease Laboratory, (510) 231-1790\.br\\.br\Duplicate\.br\\.br\Follow-up:\.br\\.br\Acyl Carnitine Panel: Reference Ranges for acylcarnitines are based on specimens collected on newborns who are less than 10 days old. \.br\\.br\Biotinidase Deficiency: This screen for Biotinidase Deficiency was positive. Another specimen MUST be collected on this infant. \.br\\.br\If you have any questions regarding these screening outcomes, please contact the Newborn Screening Staff at at . \.br\\.br\Methods and Limitations:\.br\\.br\Assays for ALD Tier-1, BD, CAH, CF, GAL, MS/MS Acylcarnitine and Amino Acid Panels, PCH, hemoglobinopathies, and SCID were performed at the testing laboratory specified on the front of this report. Assays for ALD Tier-2, CAH Tier-2, Pompe Disease Tier-1, MPS I Tier-1, and SMA were developed and/or optimized by the Genetic Disease Laboratory (GDL), and performed at GDL. Performance characteristics of these assays are determined by GDL. The SMA assay is designed to identify 95% of SMA patients who have homozygous deletions of the SMN1 gene on chromosome 5q. These assays have not been cleared or approved by the U.S. Food and Drug Administration (FDA). The FDA has determined that such clearance or approval is not necessary. The assays are used for clinical purposes. They should not be regarded as investigational or for research. GDL is certified under the Clinical Laboratory Improvement Amendments of 1988 (CLIA-88) to perform high complexity genetic disease screening. \.br\Attention Healthcare Provider:\.br\\.br\\.br\|||N|||F|||20240711034913 +OBX|7|TX|57129-9^Full newborn screening summary report for display or printing^LN|1||||N|||F|||20240711034913 +OBX|8|ST|57716-3^State printed on filter paper card [Identifier] in NBS card^LN|1|CA|||N|||F|||20240711034913 +OBX|9|NM|8339-4^Birthweight^LN|1|3500|grams||N|||F|||20240711034913 +OBX|10|CE|57722-1^Birth plurality of Pregnancy^LN|1|LA12411-7^Singleton^LN|||N|||F|||20240711034913 +OBX|11|NM|73806-2^Newborn age in hours^LN|1|34|day(s)||N|||F|||20240711034913 +OBX|12|CE|57713-0^Infant NICU factors that affect newborn screening interpretation^LN|1|LA137-2^None^LN|||N|||F|||20240711034913 +OBX|13|CE|67704-7^Feeding types^LN|1|LA16914-6^Breast milk^LN|||N|||F|||20240711034913 +OBX|14|TX|^^^99717-5^Accession Number^L|1|193-08-269/21-2024-21|||N|||F|||20240711034913 +OBX|15|TX|62324-9^Post-discharge provider name^LN|1|EUSTRATIA HUBBARD|||N|||F|||20240711034913 +OBX|16|TX|62327-2^Post-discharge provider practice address^LN|1|N 054TS ARALC, TS102 E SAN DIEGO CA 99999-9999 USA|||N|||F|||20240711034913 +OBX|17|NM|47633-3^Glycine [Moles/volume] in Dried blood spot^LN|1|0.5|µmol/L||N|||F|||20240711034913 +OBX|18|NM|53150-9^Alanine+Beta Alanine+Sarcosine [Moles/volume] in Dried blood spot^LN|1|500|µmol/L|<1000|N|||F|||20240711034913 +OBX|19|NM|47799-2^Valine [Moles/volume] in Dried blood spot^LN|1|0.5|µmol/L||N|||F|||20240711034913 +OBX|20|NM|53151-7^Valine/Phenylalanine [Molar ratio] in Dried blood spot^LN|1|0.00645|{Ratio}|<4.3|N|||F|||20240711034913 +OBX|21|NM|53152-5^Alloisoleucine+Isoleucine+Leucine+Hydroxyproline^LN|1|125|µmol/L|<230|N|||F|||20240711034913 +OBX|22|NM|53154-1^Alloisoleucine+Isoleucine+Leucine+Hydroxyproline/Alanine [Molar ratio] in Dried blood spot^LN|1|0.65|{Ratio}|<1.35|N|||F|||20240711034913 +OBX|23|NM|29573-3^Phenylalanine [Moles/volume] in Dried blood spot^LN|1|77.5|µmol/L|<175|N|||F|||20240711034913 +OBX|24|NM|35572-7^Phenylalanine/Tyrosine [Molar ratio] in Dried blood spot^LN|1|0.75|{Ratio}|<2.6|N|||F|||20240711034913 +OBX|25|NM|35571-9^Tyrosine [Moles/volume] in Dried blood spot^LN|1|425|µmol/L|<680|N|||F|||20240711034913 +OBX|26|NM|53231-7^Succinylacetone [Moles/volume] in Dried blood spot^LN|1|2.25|µmol/L|<6.1|N|||F|||20240711034913 +OBX|27|NM|47700-0^Methionine [Moles/volume] in Dried blood spot^LN|1|27|µmol/L|6.3-100|N|||F|||20240711034913 +OBX|28|NM|42892-0^Citrulline [Moles/volume] in Dried blood spot^LN|1|16.25|µmol/L|5-49|N|||F|||20240711034913 +OBX|29|NM|54092-2^Citrulline/Arginine [Molar ratio] in Dried blood spot^LN|1|3|{Ratio}|<4.8|N|||F|||20240711034913 +OBX|30|NM|53155-8^Asparagine+Ornithine [Moles/volume] in Dried blood spot^LN|1|400|µmol/L|<800|N|||F|||20240711034913 +OBX|31|NM|75215-4^Ornithine/Citrulline [Molar ratio] in Dried blood spot^LN|1|0.5|{Ratio}||N|||F|||20240711034913 +OBX|32|NM|47562-4^Arginine [Moles/volume] in Dried blood spot^LN|1|25|µmol/L|<63|N|||F|||20240711034913 +OBX|33|NM|75214-7^Arginine/Ornithine [Molar ratio] in Dried blood spot^LN|1|0.7|{Ratio}|<1.9|N|||F|||20240711034913 +OBX|34|NM|47732-3^Proline [Moles/volume] in Dried blood spot^LN|1|750|µmol/L|<1500|N|||F|||20240711034913 +OBX|35|TX|57710-6^Amino acidemias newborn screening comment/discussion^LN|1|Negative|||N|||F|||20240711034913 +OBX|36|CE|58088-6^Acylcarnitine newborn screen interpretation^LN|1|LA18592-8^In range^LN|||N|||F|||20240711034913 +OBX|37|TX|58093-6^Acylcarnitine newborn screening comment/discussion^LN|1|Negative|||N|||F|||20240711034913 +OBX|38|NM|38481-8^Carnitine.free (C0)^LN|1|33|µmol/L|6.4-125|N|||F|||20240711034913 +OBX|39|NM|53235-8^Carnitine.free (C0)/Palmitoylcarnitine (C16)+Stearoylcarnitine (C18)^LN|1|37.5|{Ratio}|<70|N|||F|||20240711034913 +OBX|40|NM|50157-7^Acetylcarnitine (C2)^LN|1|20.38|µmol/L|10-80|N|||F|||20240711034913 +OBX|41|NM|75212-1^Malonylcarnitine (C3-DC)/Decanoylcarnitine (C10) [Molar ratio] in Dried blood spot^LN|1|0.62500|{Ratio}|<7.6|N|||F|||20240711034913 +OBX|42|NM|45211-0^Hexanoylcarnitine (C6)^LN|1|0.48|µmol/L|<0.95|N|||F|||20240711034913 +OBX|43|NM|53175-6^Octanoylcarnitine (C8)^LN|1|0.3|µmol/L|<0.45|N|||F|||20240711034913 +OBX|44|NM|53177-2^Octanoylcarnitine (C8)/Decanoylcarnitine (C10)^LN|1|0.5|{Ratio}||N|||F|||20240711034913 +OBX|45|NM|53174-9^Octenoylcarnitine (C8:1)^LN|1|0.35|µmol/L|<0.65|N|||F|||20240711034913 +OBX|46|NM|45197-1^Decanoylcarnitine (C10)^LN|1|0.32|µmol/L|<0.65|N|||F|||20240711034913 +OBX|47|NM|45198-9^Decenoylcarnitine (C10:1)^LN|1|0.22|µmol/L|<0.45|N|||F|||20240711034913 +OBX|48|NM|45199-7^Dodecanoylcarnitine (C12)^LN|1|1|µmol/L|<2|N|||F|||20240711034913 +OBX|49|NM|45200-3^Dodecenoylcarnitine (C12:1)^LN|1|0.5|µmol/L||N|||F|||20240711034913 +OBX|50|NM|53192-1^Tetradecanoylcarnitine (C14)^LN|1|0.6|µmol/L|<1.2|N|||F|||20240711034913 +OBX|51|NM|53191-3^Tetradecenoylcarnitine (C14:1)^LN|1|0.4|µmol/L|<0.9|N|||F|||20240711034913 +OBX|52|NM|53194-7^Tetradecenoylcarnitine (C14:1)/Dodecenoylcarnitine (C12:1)^LN|1|0.5|{Ratio}||N|||F|||20240711034913 +OBX|53|NM|53190-5^Tetradecadienoylcarnitine (C14:2)^LN|1|0.5|µmol/L||N|||F|||20240711034913 +OBX|54|NM|50281-5^3-Hydroxytetradecanoylcarnitine (C14-OH)^LN|1|0.1|µmol/L|<0.2|N|||F|||20240711034913 +OBX|55|NM|53199-6^Palmitoylcarnitine (C16)^LN|1|5|µmol/L|<12|N|||F|||20240711034913 +OBX|56|NM|53198-8^Palmitoleylcarnitine (C16:1)^LN|1|0.7|µmol/L|<1.4|N|||F|||20240711034913 +OBX|57|NM|50125-4^3-Hydroxypalmitoylcarnitine (C16-OH)^LN|1|0.05|µmol/L|<0.1|N|||F|||20240711034913 +OBX|58|NM|53201-0^3-Hydroxypalmitoylcarnitine (C16-OH)/Palmitoylcarnitine (C16)^LN|1|0.01000|{Ratio}|<0.07|N|||F|||20240711034913 +OBX|59|NM|53241-6^Stearoylcarnitine (C18)^LN|1|2|µmol/L|<3.5|N|||F|||20240711034913 +OBX|60|NM|53202-8^Oleoylcarnitine (C18:1)^LN|1|3.5|µmol/L|<7|N|||F|||20240711034913 +OBX|61|NM|45217-7^Linoleoylcarnitine (C18:2)^LN|1|0.5|µmol/L||N|||F|||20240711034913 +OBX|62|NM|50132-0^3-Hydroxystearoylcarnitine (C18-OH)^LN|1|0.05|µmol/L|<0.1|N|||F|||20240711034913 +OBX|63|NM|50113-0^3-Hydroxyoleoylcarnitine (C18:1-OH)^LN|1|0.05|µmol/L|<0.1|N|||F|||20240711034913 +OBX|64|NM|53160-8^Propionylcarnitine (C3)^LN|1|3.15|µmol/L|<7.9|N|||F|||20240711034913 +OBX|65|NM|53163-2^Propionylcarnitine (C3)/Acetylcarnitine (C2)^LN|1|0.15|{Ratio}|<0.42|N|||F|||20240711034913 +OBX|66|NM|67708-8^Malonylcarnitine (C3-DC)+3-Hydroxybutyrylcarnitine (C4-OH)^LN|1|0.2|µmol/L|<0.48|N|||F|||20240711034913 +OBX|67|NM|53166-5^Butyrylcarnitine+Isobutyrylcarnitine (C4)^LN|1|0.85|µmol/L|<1.7|N|||F|||20240711034913 +OBX|68|NM|45216-9^Isovalerylcarnitine+Methylbutyrylcarnitine (C5)^LN|1|0.5|µmol/L|<0.95|N|||F|||20240711034913 +OBX|69|NM|53240-8^Isovalerylcarnitine+Methylbutyrylcarnitine (C5)/Propionylcarnitine (C3)^LN|1|0.15873|{Ratio}|<0.38|N|||F|||20240711034913 +OBX|70|NM|53170-7^Tiglylcarnitine (C5:1)^LN|1|0.3|µmol/L|<0.5|N|||F|||20240711034913 +OBX|71|NM|50106-4^3-Hydroxyisovalerylcarnitine (C5-OH)^LN|1|0.45|µmol/L|<1.15|N|||F|||20240711034913 +OBX|72|NM|67710-4^Glutarylcarnitine (C5-DC)+3-Hydroxyhexanoylcarnitine (C6-OH)^LN|1|0.3|µmol/L|<0.38|N|||F|||20240711034913 +OBX|73|NM|75216-2^Glutarylcarnitine (C5-DC)/Malonylcarnitine (C3-DC) [Molar ratio] in Dried blood spot^LN|1|1.50000|{Ratio}|>0.1|N|||F|||20240711034913 +OBX|74|NM|48633-2^Trypsinogen I.free^LN|1|31.00|ng/mL|<69|N|||F|||20240711034913 +OBX|75|CE|46769-6^Cystic fibrosis newborn screen interpretation^LN|1|LA18592-8^In range^LN|||N|||F|||20240711034913 +OBX|76|TX|57707-2^Cystic fibrosis newborn screening comment/discussion^LN|1|Negative|||N|||F|||20240711034913 +OBX|77|NM|38473-5^17-Hydroxyprogesterone^LN|1|35|nmol/L|<85|N|||F|||20240711034913 +OBX|78|CE|46758-9^Congenital adrenal hyperplasia newborn screen interpretation^LN|1|LA18592-8^In range^LN|||N|||F|||20240711034913 +OBX|79|TX|57706-4^Congenital adrenal hyperplasia newborn screening comment-discussion^LN|1|Negative|||N|||F|||20240711034913 +OBX|80|NM|29575-8^Thyrotropin^LN|1|14.50|mIU/L|<29|N|||F|||20240711034913 +OBX|81|CE|46762-1^Congenital hypothyroidism newborn screen interpretation^LN|1|LA18592-8^In range^LN|||N|||F|||20240711034913 +OBX|82|TX|57705-6^Congenital hypothyroidism newborn screening comment-discussion^LN|1|Negative|||N|||F|||20240711034913 +OBX|83|NM|42906-8^Galactose 1 phosphate uridyl transferase^LN|1|55.00|enzyme units|>50|N|||F|||20240711034913 +OBX|84|CE|46737-3^Galactosemias newborn screen interpretation^LN|1|LA18592-8^In range^LN|||N|||F|||20240711034913 +OBX|85|TX|57704-9^Galactosemias newborn screening comment-discussion^LN|1|Negative|||N|||F|||20240711034913 +OBX|86|TX|54104-5^Hemoglobin pattern^LN|1|FA||||||F|||20240711034913 +OBX|87|TX|57703-1^Hemoglobin disorders newborn screening comment/discussion^LN|1|Usual hemoglobin pattern. These results assume no transfusion prior to testing and do not rule out the possibility of a thalassemia trait or rare hemoglobin variants.||||||F|||20240711034913 +OBX|88|NM|75217-0^Biotinidase [Enzymatic activity/volume] in Dried blood spot^LN|1|8.00|ERU|>10|L|||F|||20240711034913 +OBX|89|CE|46761-3^Biotinidase deficiency newborn screen interpretation^LN|1|LA18593-6^Out of range^LN|||A|||F|||20240711034913 +OBX|90|TX|57699-1^Biotinidase deficiency newborn screening comment-discussion^LN|1|Positive|||A|||F|||20240711034913 +OBX|91|NM|62320-7^T-cell receptor excision circle [#/volume] in Dried blood spot by Probe and target amplification method^LN|1|33|copies/µL|>18|N|||F|||20240711034913 +OBX|92|CE|62321-5^Severe combined immunodeficiency newborn screen interpretation^LN|1|LA18592-8^In range^LN|||N|||F|||20240711034913 +OBX|93|TX|62322-3^Severe combined immunodeficiency newborn screening comment-discussion^LN|1|Negative|||N|||F|||20240711034913 +OBX|94|NM|55827-0^Acid alpha glucosidase [Enzymatic activity/volume] in DBS^LN|1|12.923|µmol/L/h|>=2.079|N|||F|||20240711034913 +OBX|95|CE|63415-4^Pompe Disease deficiency newborn screen interpretation^LN|1|LA18592-8^In range^LN|||N|||F|||20240711034913 +OBX|96|TX|63416-2^Pompe Disease deficiency newborn screening comments-discussion^LN|1|Negative|||N|||F|||20240711034913 +OBX|97|NM|55909-6^Alpha-L-iduronidase [Enzymatic activity/volume] in DBS^LN|1|3.117|µmol/L/h|>=1.2204|N|||F|||20240711034913 +OBX|98|CE|79564-1^Mucopolysaccharidosis type I newborn screen interpretation^LN|1|LA18592-8^In range^LN|||N|||F|||20240711034913 +OBX|99|TX|79565-8^Mucopolysaccharidosis type I newborn screening comment-discussion^LN|1|Negative|||N|||F|||20240711034913 +OBX|100|TX|^^^99717-60^SMN1 Homozygous Deletion Analysis^L|1|Exon 7 Present||Exon 7 Present|N|||F|||20240711034913 +OBX|101|CE|92004-1^Spinal muscular atrophy newborn screen interpretation^LN|1|LA18592-8^In range^LN|||N|||F|||20240711034913 +OBX|102|TX|92003-3^Spinal muscular atrophy newborn screening comment-discussion^LN|1|SMA Negative|||N|||F|||20240711034913 +OBX|103|CE|85269-9^X-linked Adrenoleukodystrophy (X- ALD) newborn screen interpretation^LN^99717-32^Adrenoleukodystrophy deficiency newborn screening interpretation^L|1|LA18592-8^In range^LN|||N|||F|||20240711034913 +OBX|104|TX|85268-1^X-linked Adrenoleukodystrophy (X- ALD) newborn screening comment-discussion^LN^99717-33^Adrenoleukodystrophy deficiency newborn screening comments-discussion^L|1|Negative|||N|||F|||20240711034913 +OBX|105|TX|PLT325^ABCD1 gene mutation found [Identifier] in DBS by Sequencing^PLT^99717-34^Adrenoleukodystrophy Mutation comments/discussion^L|1|Negative|||N|||F|||20240711034913 +OBX|106|TX|53340-6^17-Hydroxyprogesterone [Moles/volume] in DBS^LN^99717-6^17-Hydroxyprogesterone (CAH II)^L|1|Negative|||N|||F|||20240711034913 +OBX|107|TX|^^^99717-35^Cystic fibrosis Sequencing newborn screening interpretation^L|1|Negative|||N|||F|||20240711034913 +OBX|108|TX|^^^99717-36^Cystic fibrosis Sequencing newborn screening comment/discussion^L|1|Negative|||N|||F|||20240711034913 +OBX|109|TX|PLT3258^IDUA gene mutations found [Identifier] in DBS by Sequencing^PLT^99717-48^MPS I IDUA Gene Sequence Mutation Information^L|1|Negative|||N|||F|||20240711034913 +OBX|110|TX|^^^99717-44^MPS I IDUA Gene Sequence Analysis comments/discussion^L|1|Negative|||N|||F|||20240711034913 +OBX|111|TX|PLT3275^IDS gene mutations found [Identifier] in Dried Bloodspot by Molecular genetics method Nominal^PLT^99717-50^MPS II IDS Gene Sequence Mutation Information^L|1|Negative|||N|||F|||20240711034913 +OBX|112|TX|PLT3252^GAA gene mutation found [Identifier] in DBS by Sequencing^PLT^99717-47^Pompe GAA Gene Sequence Analysis Information^L|1|Negative|||N|||F|||20240711034913 +OBX|113|TX|^^^99717-46^Pompe GAA Gene Sequence Analysis comments/discussion^L|1|Negative|||N|||F|||20240711034913 +OBX|114|NM|79321-6^Lysophosphatidylcholine(26:0) [Moles/volume] in Dried blood spot^LN|1|0.2|µmol/L|<0.47|N|||F|||20240711034913 diff --git a/shared/src/main/java/gov/hhs/cdc/trustedintermediary/external/hapi/HapiHelper.java b/shared/src/main/java/gov/hhs/cdc/trustedintermediary/external/hapi/HapiHelper.java index ac57b4d08..8614567c5 100644 --- a/shared/src/main/java/gov/hhs/cdc/trustedintermediary/external/hapi/HapiHelper.java +++ b/shared/src/main/java/gov/hhs/cdc/trustedintermediary/external/hapi/HapiHelper.java @@ -69,6 +69,14 @@ private HapiHelper() {} public static final String EXTENSION_OBR_URL = "https://reportstream.cdc.gov/fhir/StructureDefinition/obr-observation-request"; + public static final String LOCAL_CODE_URL = + "https://terminology.hl7.org/CodeSystem-v2-0396.html#v2-0396-99zzzorL"; + public static final String LOINC_URL = "http://loinc.org"; + + public static final String LOINC_CODE = "LN"; + public static final String PLT_CODE = "PLT"; + public static final String LOCAL_CODE = "L"; + /** * Returns a {@link Stream} of FHIR resources inside the provided {@link Bundle} that match the * given resource type. @@ -93,6 +101,11 @@ public static T resourceInBundle(Bundle bundle, Class re return resourcesInBundle(bundle, resourceType).findFirst().orElse(null); } + // MSH-10 + public static String getMessageControlId(Bundle bundle) { + return bundle.getIdentifier().getValue(); + } + // MSH - Message Header public static MessageHeader getMSHMessageHeader(Bundle bundle) { return resourceInBundle(bundle, MessageHeader.class); @@ -539,6 +552,23 @@ public static void setHD1Identifier(Identifier identifier) { setHl7FieldExtensionValue(identifier, EXTENSION_HD1_DATA_TYPE); } + // Coding resource + public static Extension getCodingExtensionByUrl(Coding coding, String url) { + return coding.getExtensionByUrl(url); + } + + public static boolean hasCodingExtensionWithUrl(Coding coding, String url) { + return coding.getExtensionByUrl(url) != null; + } + + public static boolean hasCodingSystem(Coding coding) { + return coding.getSystem() != null; + } + + public static String getCodingSystem(Coding coding) { + return coding.getSystem(); + } + // CWE - Coded with Exceptions public static String getCWE1Value(Coding coding) { return coding.getCode(); @@ -643,4 +673,12 @@ public static void removeHl7FieldIdentifier(List identifiers, String .getValue() .equalsDeep(dataType)); } + + public static String urlForCodeType(String code) { + return switch (code) { + case HapiHelper.LOINC_CODE -> HapiHelper.LOINC_URL; + case HapiHelper.PLT_CODE -> null; + default -> HapiHelper.LOCAL_CODE_URL; + }; + } } diff --git a/shared/src/test/groovy/gov/hhs/cdc/trustedintermediary/external/hapi/HapiHelperTest.groovy b/shared/src/test/groovy/gov/hhs/cdc/trustedintermediary/external/hapi/HapiHelperTest.groovy index 69ea61d19..e7a6d8dc9 100644 --- a/shared/src/test/groovy/gov/hhs/cdc/trustedintermediary/external/hapi/HapiHelperTest.groovy +++ b/shared/src/test/groovy/gov/hhs/cdc/trustedintermediary/external/hapi/HapiHelperTest.groovy @@ -1,5 +1,6 @@ package gov.hhs.cdc.trustedintermediary.external.hapi +import java.util.stream.Stream import org.hl7.fhir.r4.model.Bundle import org.hl7.fhir.r4.model.Coding import org.hl7.fhir.r4.model.Extension @@ -48,6 +49,33 @@ class HapiHelperTest extends Specification { patientStream.allMatch {patients.contains(it) && it.getResourceType() == ResourceType.Patient } } + def "resourceInBundle returns null when the bundle is null"() { + when: + def result = HapiHelper.resourceInBundle(null, Patient) + + then: + result == null + } + + def "resourcesInBundle returns an empty stream when the bundle is null"() { + when: + def result = HapiHelper.resourcesInBundle(null, Patient) + + then: + result.findAny().isEmpty() + } + + def "resourcesInBundle returns an empty stream when the bundle has no entries"() { + given: + def bundle = new Bundle() + + when: + def result = HapiHelper.resourcesInBundle(bundle, Patient) + + then: + result.findAny().isEmpty() + } + // MSH - Message Header def "getMSHMessageHeader returns the message header from the bundle if it exists"() { given: @@ -313,6 +341,23 @@ class HapiHelperTest extends Specification { convertedMessageHeader.getEventCoding().getDisplay() == expectedDisplay } + // MSH-10 - Message Control Id + def "return the correct value for message identifier"() { + given: + final String EXPECTED_CONTROL_ID = "SomeMessageControlId" + + def bundle = new Bundle() + Identifier identifier = new Identifier() + identifier.setValue(EXPECTED_CONTROL_ID) + bundle.setIdentifier(identifier) + + when: + def actualControlId = HapiHelper.getMessageControlId(bundle) + + then: + actualControlId == EXPECTED_CONTROL_ID + } + def "adds the message type when it doesn't exist"() { given: def expectedSystem = "expectedSystem" @@ -850,4 +895,18 @@ class HapiHelperTest extends Specification { then: ext.getValue() == null } + + def "urlForCodeType should return expected values"() { + when: + def actualResult = HapiHelper.urlForCodeType(inputValue) + + then: + actualResult == expectedResult + + where: + inputValue || expectedResult + "LN" || HapiHelper.LOINC_URL + "L" || HapiHelper.LOCAL_CODE_URL + "PLT" || null + } }