diff --git a/pom.xml b/pom.xml index 0e940cd..49eb257 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ edu.gatech vrdr - 4.0.6 + 4.0.7 jar VRDR diff --git a/src/main/java/edu/gatech/chai/VRDR/model/util/CommonUtil.java b/src/main/java/edu/gatech/chai/VRDR/model/util/CommonUtil.java index fdeaa39..fbe9ecd 100644 --- a/src/main/java/edu/gatech/chai/VRDR/model/util/CommonUtil.java +++ b/src/main/java/edu/gatech/chai/VRDR/model/util/CommonUtil.java @@ -63,10 +63,10 @@ public class CommonUtil { public static List deathReportingIdentifierTypeCodes = new ArrayList(Arrays.asList(deathCertificateIdCode,deathCertificateFileNumberCode,deathCertificateLicenseNumberCode, nationalProviderIdentifierCode,stateRegistryIdCode,SocialSecurityNumberCode)); public static final HashSet certifierTypeSet = new HashSet<>(Arrays.asList( - new CodeableConcept().addCoding(new Coding(CommonUtil.snomedSystemUrl,"455381000124109","Medical Examiner/Coroner")), + new CodeableConcept().addCoding(new Coding(CommonUtil.snomedSystemUrl,"455381000124109","Death certification by medical examiner or coroner (procedure)")), new CodeableConcept().addCoding(new Coding(CommonUtil.snomedSystemUrl,"434641000124105","Death certification and verification by physician (procedure)")), - new CodeableConcept().addCoding(new Coding(CommonUtil.snomedSystemUrl,"434651000124107","Physician certified death certificate")), - new CodeableConcept().addCoding(new Coding(CommonUtil.nullFlavorHL7System,"OTH","Other")) + new CodeableConcept().addCoding(new Coding(CommonUtil.snomedSystemUrl,"434651000124107","Death certification by physician (procedure)")), + new CodeableConcept().addCoding(new Coding(CommonUtil.nullFlavorHL7System,"OTH","Other (Specify)")) )); public static final HashSet yesNoUnknownSet = new HashSet<>(Arrays.asList(yesCode,noCode,unknownCode)); public static final HashSet yesNoNASet = new HashSet<>(Arrays.asList(yesCode,noCode,notApplicableCode)); diff --git a/src/main/java/edu/gatech/chai/VRDR/model/util/DeathCertificateUtil.java b/src/main/java/edu/gatech/chai/VRDR/model/util/DeathCertificateUtil.java index 00dedd8..9f42ffc 100644 --- a/src/main/java/edu/gatech/chai/VRDR/model/util/DeathCertificateUtil.java +++ b/src/main/java/edu/gatech/chai/VRDR/model/util/DeathCertificateUtil.java @@ -3,8 +3,8 @@ import org.hl7.fhir.r4.model.CodeableConcept; import org.hl7.fhir.r4.model.Coding; import org.hl7.fhir.r4.model.Composition; -import org.hl7.fhir.r4.model.Extension; -import org.hl7.fhir.r4.model.StringType; +import org.hl7.fhir.r4.model.Extension; +import org.hl7.fhir.r4.model.StringType; import org.hl7.fhir.r4.model.Composition.CompositionStatus; import edu.gatech.chai.VRDR.model.ActivityAtTimeOfDeath; @@ -44,25 +44,25 @@ import edu.gatech.chai.VRDR.model.TobaccoUseContributedToDeath; public class DeathCertificateUtil { - public static final CompositionStatus status = CompositionStatus.FINAL; - public static final String title = "Death Certificate"; + public static final CompositionStatus status = CompositionStatus.FINAL; + public static final String title = "Death Certificate"; public static final CodeableConcept typeFixedValue = new CodeableConcept() .addCoding(new Coding(CommonUtil.loincSystemUrl,"64297-5","Death certificate")); public static final Composition.CompositionAttestationMode attesterMode = Composition.CompositionAttestationMode.LEGAL; public static final CodeableConcept eventCodeFixedValue = new CodeableConcept() - .addCoding(new Coding(CommonUtil.snomedSystemUrl,"103693007","Diagnostic procedure (procedure)")); + .addCoding(new Coding(CommonUtil.snomedSystemUrl,"103693007",null)); public static final String vrdrDocumentSectionUrl = "http://hl7.org/fhir/us/vrdr/CodeSystem/vrdr-document-section-cs"; public static final CodeableConcept decendentDemographicsSectionCode = new CodeableConcept() .addCoding(new Coding(vrdrDocumentSectionUrl,"DecedentDemographics","")); public static final CodeableConcept deathInvestigationSectionCode = new CodeableConcept() .addCoding(new Coding(vrdrDocumentSectionUrl,"DeathInvestigation","")); public static final CodeableConcept deathCertificationSectionCode = new CodeableConcept() - .addCoding(new Coding(vrdrDocumentSectionUrl,"DeathCertification","")); + .addCoding(new Coding(vrdrDocumentSectionUrl,"DeathCertification","")); public static final CodeableConcept decedentDispositionSectionCode = new CodeableConcept() .addCoding(new Coding(vrdrDocumentSectionUrl,"DecedentDisposition","")); public static final CodeableConcept codedContentSectionCode = new CodeableConcept() .addCoding(new Coding(vrdrDocumentSectionUrl,"CodedContent","")); - + public static final Class[] decedentDemographicResources = {Decedent.class, DecedentFather.class, DecedentMother.class, DecedentSpouse.class, DecedentAge.class, BirthRecordIdentifier.class, DecedentEducationLevel.class, DecedentMilitaryService.class, DecedentUsualWork.class, EmergingIssues.class, InputRaceAndEthnicity.class}; @@ -76,13 +76,13 @@ public class DeathCertificateUtil { public static final Class[] codedContentResources = {ActivityAtTimeOfDeath.class, AutomatedUnderlyingCauseOfDeath.class, CodedRaceAndEthnicity.class,EntityAxisCauseOfDeath.class,RecordAxisCauseOfDeath.class,PlaceOfInjury.class, CodingStatusValues.class}; - - public static final String filingFormatExtensionUrl = "http://hl7.org/fhir/us/vrdr/StructureDefinition/FilingFormat"; - public static final String filingFormatExtensionCodeSystem = "http://hl7.org/fhir/us/vrdr/CodeSystem/vrdr-filing-format-cs"; - public static final CodeableConcept electronicFilingFormat = new CodeableConcept() - .addCoding(new Coding().setSystem(filingFormatExtensionCodeSystem).setCode("electronic").setDisplay("Electronic")); - public static final CodeableConcept mixedFilingFormat = new CodeableConcept() - .addCoding(new Coding().setSystem(filingFormatExtensionCodeSystem).setCode("mixed").setDisplay("Mixed")); - public static final CodeableConcept paperFilingFormat = new CodeableConcept() - .addCoding(new Coding().setSystem(filingFormatExtensionCodeSystem).setCode("paper").setDisplay("Paper")); + + public static final String filingFormatExtensionUrl = "http://hl7.org/fhir/us/vrdr/StructureDefinition/FilingFormat"; + public static final String filingFormatExtensionCodeSystem = "http://hl7.org/fhir/us/vrdr/CodeSystem/vrdr-filing-format-cs"; + public static final CodeableConcept electronicFilingFormat = new CodeableConcept() + .addCoding(new Coding().setSystem(filingFormatExtensionCodeSystem).setCode("electronic").setDisplay("Electronic")); + public static final CodeableConcept mixedFilingFormat = new CodeableConcept() + .addCoding(new Coding().setSystem(filingFormatExtensionCodeSystem).setCode("mixed").setDisplay("Mixed")); + public static final CodeableConcept paperFilingFormat = new CodeableConcept() + .addCoding(new Coding().setSystem(filingFormatExtensionCodeSystem).setCode("paper").setDisplay("Paper")); } \ No newline at end of file diff --git a/src/main/java/edu/gatech/chai/VRDR/model/util/DeathCertificationProcedureUtil.java b/src/main/java/edu/gatech/chai/VRDR/model/util/DeathCertificationProcedureUtil.java index 815ce7d..d2916ee 100644 --- a/src/main/java/edu/gatech/chai/VRDR/model/util/DeathCertificationProcedureUtil.java +++ b/src/main/java/edu/gatech/chai/VRDR/model/util/DeathCertificationProcedureUtil.java @@ -5,7 +5,7 @@ public class DeathCertificationProcedureUtil { public static final CodeableConcept categoryFixedValue = new CodeableConcept() - .addCoding(new Coding(CommonUtil.snomedSystemUrl,"103693007","Diagnostic procedure")); + .addCoding(new Coding(CommonUtil.snomedSystemUrl,"103693007",null)); public static final CodeableConcept codeFixedValue = new CodeableConcept() .addCoding(new Coding(CommonUtil.snomedSystemUrl,"308646001","Death certification")); diff --git a/src/main/java/edu/gatech/chai/VRDR/model/util/DeathLocationUtil.java b/src/main/java/edu/gatech/chai/VRDR/model/util/DeathLocationUtil.java index d1b733b..1997aee 100644 --- a/src/main/java/edu/gatech/chai/VRDR/model/util/DeathLocationUtil.java +++ b/src/main/java/edu/gatech/chai/VRDR/model/util/DeathLocationUtil.java @@ -8,13 +8,13 @@ public class DeathLocationUtil { public static final CodeableConcept VALUE_HOSPITAL = new CodeableConcept().addCoding(new Coding(CommonUtil.snomedSystemUrl,"16983000","Death in hospital")); - public static final CodeableConcept VALUE_EMERGENCY_OUTPATIENT = new CodeableConcept().addCoding(new Coding(CommonUtil.snomedSystemUrl,"450391000124102","Death in hospital-based emergency department or outpatient department (event)")); + public static final CodeableConcept VALUE_EMERGENCY_OUTPATIENT = new CodeableConcept().addCoding(new Coding(CommonUtil.snomedSystemUrl,"450391000124102","Death in hospital-based emergency department or outpatient department")); public static final CodeableConcept VALUE_HOME = new CodeableConcept().addCoding(new Coding(CommonUtil.snomedSystemUrl,"440081000124100","Death in home")); public static final CodeableConcept VALUE_HOSPICE = new CodeableConcept().addCoding(new Coding(CommonUtil.snomedSystemUrl,"440071000124103","Death in hospice")); public static final CodeableConcept VALUE_ARRIVAL = new CodeableConcept().addCoding(new Coding(CommonUtil.snomedSystemUrl,"63238001","Dead on arrival at hospital")); - public static final CodeableConcept VALUE_NURSINGHOME = new CodeableConcept().addCoding(new Coding(CommonUtil.snomedSystemUrl,"450381000124100","Death in nursing home or long term care facility (event)")); - public static final CodeableConcept VALUE_UNKNOWN = new CodeableConcept().addCoding(new Coding(CommonUtil.snomedSystemUrl,"UNK","Unknown")); - public static final CodeableConcept VALUE_OTHER = new CodeableConcept().addCoding(new Coding(CommonUtil.snomedSystemUrl,"OTH","Other")); + public static final CodeableConcept VALUE_NURSINGHOME = new CodeableConcept().addCoding(new Coding(CommonUtil.snomedSystemUrl,"450381000124100","Death in nursing home or long term care facility")); + public static final CodeableConcept VALUE_UNKNOWN = new CodeableConcept().addCoding(new Coding(CommonUtil.nullFlavorHL7System,"UNK","UNK")); + public static final CodeableConcept VALUE_OTHER = new CodeableConcept().addCoding(new Coding(CommonUtil.nullFlavorHL7System,"OTH","Other")); public static final HashSet placeOfDeathTypeSet = new HashSet<>(Arrays.asList( VALUE_HOSPITAL, VALUE_EMERGENCY_OUTPATIENT, @@ -22,8 +22,8 @@ public class DeathLocationUtil { VALUE_HOSPICE, VALUE_ARRIVAL, VALUE_NURSINGHOME, - VALUE_OTHER, - VALUE_UNKNOWN + VALUE_UNKNOWN, + VALUE_OTHER )); public static CodeableConcept typeCode = new CodeableConcept(new Coding().setSystem("http://hl7.org/fhir/us/vrdr/CodeSystem/vrdr-location-type-cs").setCode("death").setDisplay("death location")); } diff --git a/src/main/java/edu/gatech/chai/VRDR/model/util/DecedentDispositionMethodUtil.java b/src/main/java/edu/gatech/chai/VRDR/model/util/DecedentDispositionMethodUtil.java index 6a38599..c07a079 100644 --- a/src/main/java/edu/gatech/chai/VRDR/model/util/DecedentDispositionMethodUtil.java +++ b/src/main/java/edu/gatech/chai/VRDR/model/util/DecedentDispositionMethodUtil.java @@ -18,6 +18,5 @@ public class DecedentDispositionMethodUtil { public static final CodeableConcept VALUE_CREMATIONCODE = new CodeableConcept().addCoding(new Coding().setCode("449961000124104").setSystem(CommonUtil.snomedSystemUrl).setDisplay("Cremation")); public static final CodeableConcept VALUE_ENTOMBEDCODE = new CodeableConcept().addCoding(new Coding().setCode("449931000124108").setSystem(CommonUtil.snomedSystemUrl).setDisplay("Entombment")); public static final CodeableConcept VALUE_REMOVALFROMSTATECODE = new CodeableConcept().addCoding(new Coding().setCode("449941000124103").setSystem(CommonUtil.snomedSystemUrl).setDisplay("Removal from state")); - public static final CodeableConcept VALUE_HOSPITALDISPOSITIONCODE = new CodeableConcept().addCoding(new Coding().setCode("373066001").setSystem(CommonUtil.snomedSystemUrl).setDisplay("Hospital Disposition")); - public static List valueCodesetList = new ArrayList(Arrays.asList(VALUE_DONATEDCODE,VALUE_BURIALCODE,VALUE_CREMATIONCODE,VALUE_ENTOMBEDCODE,VALUE_REMOVALFROMSTATECODE,VALUE_HOSPITALDISPOSITIONCODE)); + public static List valueCodesetList = new ArrayList(Arrays.asList(VALUE_DONATEDCODE,VALUE_BURIALCODE,VALUE_CREMATIONCODE,VALUE_ENTOMBEDCODE,VALUE_REMOVALFROMSTATECODE)); } \ No newline at end of file diff --git a/src/main/java/edu/gatech/chai/VRDR/model/util/DecedentTransportationRoleUtil.java b/src/main/java/edu/gatech/chai/VRDR/model/util/DecedentTransportationRoleUtil.java index f5c310e..32a4f5c 100644 --- a/src/main/java/edu/gatech/chai/VRDR/model/util/DecedentTransportationRoleUtil.java +++ b/src/main/java/edu/gatech/chai/VRDR/model/util/DecedentTransportationRoleUtil.java @@ -14,8 +14,8 @@ public class DecedentTransportationRoleUtil { public static final CodeableConcept code = new CodeableConcept() .addCoding(new Coding().setSystem(CommonUtil.loincSystemUrl).setCode("69451-3") .setDisplay("Transportation role of decedent")); - public static final CodeableConcept VALUE_DRIVER = new CodeableConcept().addCoding(new Coding(CommonUtil.snomedSystemUrl,"236320001","Driver/Operator")); + public static final CodeableConcept VALUE_DRIVER = new CodeableConcept().addCoding(new Coding(CommonUtil.snomedSystemUrl,"236320001","Vehicle driver")); public static final CodeableConcept VALUE_PASSENGER = new CodeableConcept().addCoding(new Coding(CommonUtil.snomedSystemUrl,"25750003","Passenger")); public static final CodeableConcept VALUE_PEDESTRIAN = new CodeableConcept().addCoding(new Coding(CommonUtil.snomedSystemUrl,"25751800","Pedestrian")); - public static Set valueCodesetList = new HashSet(Arrays.asList(VALUE_DRIVER,VALUE_PASSENGER,VALUE_PEDESTRIAN)); + public static Set valueCodesetList = new HashSet(Arrays.asList(VALUE_DRIVER,VALUE_PASSENGER,VALUE_PEDESTRIAN,CommonUtil.otherCode,CommonUtil.unknownCode,CommonUtil.notApplicableCode)); } \ No newline at end of file diff --git a/src/main/java/edu/gatech/chai/VRDR/model/util/InjuryIncidentUtil.java b/src/main/java/edu/gatech/chai/VRDR/model/util/InjuryIncidentUtil.java index 31c3a67..5ca87b5 100644 --- a/src/main/java/edu/gatech/chai/VRDR/model/util/InjuryIncidentUtil.java +++ b/src/main/java/edu/gatech/chai/VRDR/model/util/InjuryIncidentUtil.java @@ -37,5 +37,5 @@ public class InjuryIncidentUtil { public static final CodeableConcept passengerRoleCode = new CodeableConcept().addCoding(new Coding(CommonUtil.snomedSystemUrl, "257500003", "Passenger")); public static final CodeableConcept pedestrianRoleCode = new CodeableConcept().addCoding(new Coding(CommonUtil.snomedSystemUrl, "257518000", "Pedestrian")); public static Set transportationRoleValueSet = new HashSet(Arrays.asList( - driverRoleCode,passengerRoleCode,pedestrianRoleCode,CommonUtil.otherCode, CommonUtil.unknownCode)); + driverRoleCode,passengerRoleCode,pedestrianRoleCode,CommonUtil.otherCode, CommonUtil.unknownCode, CommonUtil.notApplicableCode)); } \ No newline at end of file diff --git a/src/main/java/edu/gatech/chai/VRDR/model/util/TobaccoUseContributedToDeathUtil.java b/src/main/java/edu/gatech/chai/VRDR/model/util/TobaccoUseContributedToDeathUtil.java index dd83d31..5199d95 100644 --- a/src/main/java/edu/gatech/chai/VRDR/model/util/TobaccoUseContributedToDeathUtil.java +++ b/src/main/java/edu/gatech/chai/VRDR/model/util/TobaccoUseContributedToDeathUtil.java @@ -15,6 +15,6 @@ public class TobaccoUseContributedToDeathUtil { public static final String codeValueSystem = "urn:oid:2.16.840.1.114222.4.5.274"; public static final CodeableConcept VALUE_YESCODE = new CodeableConcept().addCoding(new Coding().setCode("373066001").setSystem(CommonUtil.snomedSystemUrl).setDisplay("Yes")); public static final CodeableConcept VALUE_NOCODE = new CodeableConcept().addCoding(new Coding().setCode("373067005").setSystem(CommonUtil.snomedSystemUrl).setDisplay("No")); - public static final CodeableConcept VALUE_PROBABLECODE = new CodeableConcept().addCoding(new Coding().setCode("2931005").setSystem(CommonUtil.snomedSystemUrl).setDisplay("Probable diagnosis")); + public static final CodeableConcept VALUE_PROBABLECODE = new CodeableConcept().addCoding(new Coding().setCode("2931005").setSystem(CommonUtil.snomedSystemUrl).setDisplay("Probably")); public static List valueCodesetList = new ArrayList(Arrays.asList(VALUE_YESCODE,VALUE_NOCODE,VALUE_PROBABLECODE,CommonUtil.unknownCode,CommonUtil.notAskedCode)); } \ No newline at end of file diff --git a/src/test/java/edu/gatech/VRDR/MessagingTest.java b/src/test/java/edu/gatech/VRDR/MessagingTest.java index 9839e85..9345d0d 100644 --- a/src/test/java/edu/gatech/VRDR/MessagingTest.java +++ b/src/test/java/edu/gatech/VRDR/MessagingTest.java @@ -1065,7 +1065,7 @@ public void testCreateBulkUploadPayload() { public void testCodeableConceptPlaceOfDeath() { CodeableConcept codeableConceptPlaceofDeath = CommonUtil.findConceptFromCollectionUsingSimpleString("Death in hospital", DeathDateUtil.placeOfDeathTypeSet); assertEquals("16983000", codeableConceptPlaceofDeath.getCoding().get(0).getCode()); - codeableConceptPlaceofDeath = CommonUtil.findConceptFromCollectionUsingSimpleString("Death in hospital-based emergency department or outpatient department (event)", DeathDateUtil.placeOfDeathTypeSet); + codeableConceptPlaceofDeath = CommonUtil.findConceptFromCollectionUsingSimpleString("Death in hospital-based emergency department or outpatient department", DeathDateUtil.placeOfDeathTypeSet); assertEquals("450391000124102", codeableConceptPlaceofDeath.getCoding().get(0).getCode()); codeableConceptPlaceofDeath = CommonUtil.findConceptFromCollectionUsingSimpleString("Death in home", DeathDateUtil.placeOfDeathTypeSet); assertEquals("440081000124100", codeableConceptPlaceofDeath.getCoding().get(0).getCode()); @@ -1073,12 +1073,14 @@ public void testCodeableConceptPlaceOfDeath() { assertEquals("440071000124103", codeableConceptPlaceofDeath.getCoding().get(0).getCode()); codeableConceptPlaceofDeath = CommonUtil.findConceptFromCollectionUsingSimpleString("Dead on arrival at hospital", DeathDateUtil.placeOfDeathTypeSet); assertEquals("63238001", codeableConceptPlaceofDeath.getCoding().get(0).getCode()); - codeableConceptPlaceofDeath = CommonUtil.findConceptFromCollectionUsingSimpleString("Death in nursing home or long term care facility (event)", DeathDateUtil.placeOfDeathTypeSet); + codeableConceptPlaceofDeath = CommonUtil.findConceptFromCollectionUsingSimpleString("Death in nursing home or long term care facility", DeathDateUtil.placeOfDeathTypeSet); assertEquals("450381000124100", codeableConceptPlaceofDeath.getCoding().get(0).getCode()); - codeableConceptPlaceofDeath = CommonUtil.findConceptFromCollectionUsingSimpleString("Unknown", DeathDateUtil.placeOfDeathTypeSet); + codeableConceptPlaceofDeath = CommonUtil.findConceptFromCollectionUsingSimpleString("UNK", DeathDateUtil.placeOfDeathTypeSet); assertEquals("UNK", codeableConceptPlaceofDeath.getCoding().get(0).getCode()); + assertEquals(CommonUtil.nullFlavorHL7System, codeableConceptPlaceofDeath.getCoding().get(0).getSystem()); codeableConceptPlaceofDeath = CommonUtil.findConceptFromCollectionUsingSimpleString("Other", DeathDateUtil.placeOfDeathTypeSet); assertEquals("OTH", codeableConceptPlaceofDeath.getCoding().get(0).getCode()); + assertEquals(CommonUtil.nullFlavorHL7System, codeableConceptPlaceofDeath.getCoding().get(0).getSystem()); } }