use of org.hl7.fhir.dstu2016may.model.Attachment in project hl7v2-fhir-converter by LinuxForHealth.
the class Hl7DocumentReferenceFHIRConversionTest method doc_ref_content_test.
@ParameterizedTest
@ValueSource(strings = { "MDM^T02", "MDM^T06" })
void doc_ref_content_test(String segment) {
String documentReferenceMessage = "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|" + segment + "^MDM_T02|64322|P|2.6|123|456|ER|AL|USA|ASCII|en|2.6|56789^NID^UID|MCM||||\n" + "PID|1||000054321^^^MRN|||||||||||||M|CAT|||||N\n" + "PV1|1|I||||||||||||||||||||||||||||||||||||||||||\n" + "ORC|NW|||PGN001|SC|D|1|||MS|MS|||||\n" + "OBR|1||||||20170825010500|||||||||||||002|||||F||||||||\n" + "TXA|1||TEXT||||201801180346||<PHYSID1>||||||||||AV|||<PHYSID2>||\n" + // Next three lines create an attachment
"OBX|1|TX|||ECHOCARDIOGRAPHIC REPORT||||||F|||202101010000|||\n" + "OBX|2|TX|||NORMAL LV CHAMBER SIZE WITH MILD CONCENTRIC LVH||||||F|||202101010000|||\n" + "OBX|3|TX|||HYPERDYNAMIC LV SYSTOLIC FUNCTION, VISUAL EF 80%||||||F|||202101010000|||\n";
DocumentReference report = ResourceUtils.getDocumentReference(ftv, documentReferenceMessage);
DocumentReference.DocumentReferenceContentComponent content = report.getContentFirstRep();
// Future TXA.3, currently always defaults to text/plain
assertThat(content.getAttachment().getContentType()).isEqualTo("text/plain");
// TXA.7 date
assertThat(content.getAttachment().getCreationElement().toString()).containsPattern("2018-01-18T03:46:00");
assertThat(content.getAttachment().hasData()).isTrue();
String decodedData = new String(Base64.getDecoder().decode(content.getAttachment().getDataElement().getValueAsString()));
assertThat(decodedData).isEqualTo("ECHOCARDIOGRAPHIC REPORT\nNORMAL LV CHAMBER SIZE WITH MILD CONCENTRIC LVH\nHYPERDYNAMIC LV SYSTOLIC FUNCTION, VISUAL EF 80%");
// TODO: Determine if we need to look at anything other than OBX.2 when it is TX
// Leave this test in place as a reminder
documentReferenceMessage = "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|" + segment + "^MDM_T02|64322|P|2.6|123|456|ER|AL|USA|ASCII|en|2.6|56789^NID^UID|MCM||||\n" + "PID|1||000054321^^^MRN|||||||||||||M|CAT|||||N\n" + "PV1|1|I||||||||||||||||||||||||||||||||||||||||||\n" + "ORC|NW|||PGN001|SC|D|1|||MS|MS|||||\n" + "OBR|1||||||20170825010500|||||||||||||002|||||F||||||||\n" + "TXA|1||||||201801180346||<PHYSID1>||||||||||AV|||<PHYSID2>||\n" + // TODO: find better code for this test which is to see that OBX.2 is the fallback.
"OBX|1|SN|||||||||F";
report = ResourceUtils.getDocumentReference(ftv, documentReferenceMessage);
content = report.getContentFirstRep();
// Because the OBX is not TX, the content is put in an Observation
// FHIR requires a Content element, so only a minimal one is created.
// Future OBX.2 is the backup for content type, but currently always defaults to text/plain
assertThat(content.getAttachment().hasContentType()).isTrue();
// Currently always defaults to text/plain
assertThat(content.getAttachment().getContentType()).isEqualTo("text/plain");
// TXA.7 date
assertThat(content.getAttachment().getCreationElement().toString()).containsPattern("2018-01-18T03:46:00");
assertThat(content.getAttachment().hasData()).isFalse();
// Test that content is created even if TXA.7 is empty
documentReferenceMessage = "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|" + segment + "^MDM_T02|64322|P|2.6|123|456|ER|AL|USA|ASCII|en|2.6|56789^NID^UID|MCM||||\n" + "PID|1||000054321^^^MRN|||||||||||||M|CAT|||||N\n" + "PV1|1|I||||||||||||||||||||||||||||||||||||||||||\n" + "ORC|NW|||PGN001|SC|D|1|||MS|MS|||||\n" + "OBR|1||||||20170825010500|||||||||||||002|||||F||||||||\n" + // Ensure that empty TXA.7 still works
"TXA|1||||||||<PHYSID1>||||||||||AV|||<PHYSID2>||\n" + "OBX|1|SN|||||||||F";
report = ResourceUtils.getDocumentReference(ftv, documentReferenceMessage);
content = report.getContentFirstRep();
// Because the OBX is not TX, the content is put in an Observation
// FHIR requires a Content element, so only a minimal one is created.
// Currently always defaults to text/plain
assertThat(content.getAttachment().hasContentType()).isTrue();
// Currently always defaults to text/plain, even if not data for content
assertThat(content.getAttachment().getContentType()).isEqualTo("text/plain");
// No TXA.7 date
assertThat(content.getAttachment().hasCreationElement()).isFalse();
assertThat(content.getAttachment().hasData()).isFalse();
}
use of org.hl7.fhir.dstu2016may.model.Attachment in project hl7v2-fhir-converter by LinuxForHealth.
the class Hl7ORUMessageTest method test_oru_with_specimen.
// Suppress warnings about too many assertions in a test. Justification: creating a FHIR message is very costly; we need to check many asserts per creation for efficiency.
@java.lang.SuppressWarnings("squid:S5961")
@Test
void test_oru_with_specimen() throws IOException {
String hl7message = "MSH|^~\\\\&|SendTest1|Sendfac1|Receiveapp1|Receivefac1|200603081747|security|ORU^R01|MSGID000005|T|2.6\r" + "PID||45483|45483||SMITH^SUZIE^||20160813|M|||123 MAIN STREET^^SCHENECTADY^NY^12345||(123)456-7890|||||^^^T||||||||||||\r" + "OBR|1||986^IA PHIMS Stage^2.16.840.1.114222.4.3.3.5.1.2^ISO|1051-2^New Born Screening^LN|||20151009173644|||||||||||||002|||||F|||2740^Tsadok^Janetary~2913^Merrit^Darren^F~3065^Mahoney^Paul^J~4723^Loh^Robert^L~9052^Winter^Oscar^||||3065^Mahoney^Paul^J|\r" + "OBX|1|ST|TS-F-01-002^Endocrine Disorders^L||obs report||||||F\r" + "SPM|1|SpecimenID||BLD|||||||P||||||201410060535|201410060821||Y||||||1\r";
List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
// Verify that the right resources are created
List<Resource> patientResource = ResourceUtils.getResourceList(e, ResourceType.Patient);
assertThat(patientResource).hasSize(1);
List<Resource> diagnosticReport = ResourceUtils.getResourceList(e, ResourceType.DiagnosticReport);
assertThat(diagnosticReport).hasSize(1);
List<Resource> servReqResource = ResourceUtils.getResourceList(e, ResourceType.ServiceRequest);
assertThat(servReqResource).hasSize(1);
List<Resource> obsResource = ResourceUtils.getResourceList(e, ResourceType.Observation);
assertThat(obsResource).hasSize(1);
List<Resource> practitionerResource = ResourceUtils.getResourceList(e, ResourceType.Practitioner);
assertThat(practitionerResource).hasSize(1);
List<Resource> specimenResource = ResourceUtils.getResourceList(e, ResourceType.Specimen);
assertThat(specimenResource).hasSize(1);
// Expecting only the above resources, no extras!
assertThat(e).hasSize(6);
// /////////////////////////////////////////
// Now confirm content of the diagnosticReport because we don't have separate tests for DiagnosticReport
// /////////////////////////////////////////
DiagnosticReport diag = ResourceUtils.getResourceDiagnosticReport(diagnosticReport.get(0), context);
// Verify status from OBR.25
assertThat(diag.getStatus().toCode()).isEqualTo("final");
// Verify category from OBR.24
assertThat(diag.getCategory()).isEmpty();
// Verify code from OBR.4
assertThat(diag.hasCode()).isTrue();
List<Coding> codings = diag.getCode().getCoding();
assertThat(codings).hasSize(1);
Coding coding = codings.get(0);
assertThat(coding.hasDisplay()).isTrue();
assertThat(coding.getDisplay()).hasToString("New Born Screening");
assertThat(coding.hasCode()).isTrue();
assertThat(coding.getCode()).hasToString("1051-2");
assertThat(coding.hasSystem()).isTrue();
assertThat(coding.getSystem()).hasToString("http://loinc.org");
// Verify encounter reference
assertThat(diag.getEncounter().isEmpty()).isTrue();
// Verify subject reference
assertThat(diag.getSubject().isEmpty()).isFalse();
// Verify effectiveDateTime from OBR.7 and OBR.8
// This also verifies the type, confirming effectiveDateTime was set rather than effectivePeriod
assertThat(diag.getEffectiveDateTimeType().asStringValue()).isEqualTo("2015-10-09T17:36:44+08:00");
// Verify issued from OBR.22
assertThat(diag.getIssued()).isNull();
// Verify resultsInterpreter from OBR.32
assertThat(diag.getResultsInterpreter()).hasSize(1);
// Verify basedOn is ref to the ServiceRequest created for ORC or OBR
assertThat(diag.getBasedOn()).hasSize(1);
assertThat(diag.getBasedOn().get(0).getReference().substring(0, 15)).isEqualTo("ServiceRequest/");
// Verify specimen reference
List<Reference> spmRef = diag.getSpecimen();
assertThat(spmRef).hasSize(1);
assertThat(spmRef.get(0).isEmpty()).isFalse();
// Verify result reference
List<Reference> obsRef = diag.getResult();
assertThat(obsRef).hasSize(1);
assertThat(obsRef.get(0).isEmpty()).isFalse();
// Verify presentedForm from OBX of type ST - No attachments expected because OBX of type not TX creates an Observation.
List<Attachment> attachments = diag.getPresentedForm();
Assertions.assertEquals(0, attachments.size(), "Unexpected number of attachments");
// //////////////////////////////////
for (Resource res : obsResource) {
// Verify encounter reference
Observation obs = (Observation) res;
assertThat(obs.getEncounter().isEmpty()).isTrue();
// Verify subject reference to Patient exists
assertThat(obs.getSubject().isEmpty()).isFalse();
assertThat(obs.getSubject().getReference().substring(0, 8)).isEqualTo("Patient/");
}
}
use of org.hl7.fhir.dstu2016may.model.Attachment in project hl7v2-fhir-converter by LinuxForHealth.
the class Hl7ORUMessageTest method test_oru_with_multiple_reports.
// Suppress warnings about too many assertions in a test. Justification: creating a FHIR message is very costly; we need to check many asserts per creation for efficiency.
@java.lang.SuppressWarnings("squid:S5961")
@Test
void test_oru_with_multiple_reports() throws IOException {
String hl7message = "MSH|^~\\\\&|SendTest1|Sendfac1|Receiveapp1|Receivefac1|200603081747|security|ORU^R01|MSGID000005|T|2.6\r" + "PID||45483|45483||SMITH^SUZIE^||20160813|M|||123 MAIN STREET^^SCHENECTADY^NY^12345||(123)456-7890|||||^^^T||||||||||||\r" + "OBR|1||986^IA PHIMS Stage^2.16.840.1.114222.4.3.3.5.1.2^ISO|112^Final Echocardiogram Report|||20151009173644|||||||||||||002|||||F|||2740^Tsadok^Janetary~2913^Merrit^Darren^F~3065^Mahoney^Paul^J~4723^Loh^Robert^L~9052^Winter^Oscar^||||3068^JOHN^Paul^J|\r" + "OBX|1|ST|TS-F-01-007^Endocrine Disorders 7^L||obs report||||||F\r" + "OBX|2|ST|TS-F-01-008^Endocrine Disorders 8^L||ECHOCARDIOGRAPHIC REPORT||||||F\r" + "OBR|1||98^IA PHIMS Stage^2.16.840.1.114222.4.3.3.5.1.2^ISO|113^Echocardiogram Report|||20151009173644|||||||||||||002|||||F|||2740^Tsadok^Janetary~2913^Merrit^Darren^F~3065^Mahoney^Paul^J~4723^Loh^Robert^L~9052^Winter^Oscar^||||3065^Mahoney^Paul^J|\r" + "OBX|1|CWE|625-4^Bacteria identified in Stool by Culture^LN^^^^2.33^^result1|1|27268008^Salmonella^SCT^^^^20090731^^Salmonella species|||A^A^HL70078^^^^2.5|||P|||20120301|||^^^^^^^^Bacterial Culture||201203140957||||||\r" + "OBX|2|ST|TS-F-01-002^Endocrine Disorders^L||ECHOCARDIOGRAPHIC REPORT Group 2||||||F\r";
List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
// Verify that the right resources are being created
List<Resource> patientResource = ResourceUtils.getResourceList(e, ResourceType.Patient);
assertThat(patientResource).hasSize(1);
List<Resource> obsResource = ResourceUtils.getResourceList(e, ResourceType.Observation);
assertThat(obsResource).hasSize(4);
List<Resource> practitionerResource = ResourceUtils.getResourceList(e, ResourceType.Practitioner);
assertThat(practitionerResource).hasSize(2);
List<Resource> diagnosticReport = ResourceUtils.getResourceList(e, ResourceType.DiagnosticReport);
assertThat(diagnosticReport).hasSize(2);
List<Resource> servReqResource = ResourceUtils.getResourceList(e, ResourceType.ServiceRequest);
assertThat(servReqResource).hasSize(2);
// Expecting only the above resources, no extras!
assertThat(e).hasSize(11);
// /////////////////////////////////////////
// Now confirm content of the FIRST diagnosticReport because we don't have separate tests for DiagnosticReport
// /////////////////////////////////////////
DiagnosticReport diag = ResourceUtils.getResourceDiagnosticReport(diagnosticReport.get(0), context);
// Verify status from OBR.25
assertThat(diag.getStatus().toCode()).isEqualTo("final");
// Verify category from OBR.24
assertThat(diag.getCategory()).isEmpty();
// Verify code from OBR.4
assertThat(diag.hasCode()).isTrue();
List<Coding> codings = diag.getCode().getCoding();
assertThat(codings).hasSize(1);
Coding coding = codings.get(0);
assertThat(coding.hasDisplay()).isTrue();
assertThat(coding.getDisplay()).hasToString("Final Echocardiogram Report");
assertThat(coding.hasCode()).isTrue();
assertThat(coding.getCode()).hasToString("112");
assertThat(coding.hasSystem()).isFalse();
// Verify encounter reference
assertThat(diag.getEncounter().isEmpty()).isTrue();
// Verify subject reference
assertThat(diag.getSubject().isEmpty()).isFalse();
// Verify effectiveDateTime from OBR.7 and OBR.8
// This also verifies the type, confirming effectiveDateTime was set rather than effectivePeriod
assertThat(diag.getEffectiveDateTimeType().asStringValue()).isEqualTo("2015-10-09T17:36:44+08:00");
// Verify issued from OBR.22
assertThat(diag.getIssued()).isNull();
// Verify resultsInterpreter from OBR.32
assertThat(diag.getResultsInterpreter()).hasSize(1);
// Verify basedOn is ref to the ServiceRequest created for ORC or OBR
assertThat(diag.getBasedOn()).hasSize(1);
assertThat(diag.getBasedOn().get(0).getReference().substring(0, 15)).isEqualTo("ServiceRequest/");
// Verify specimen reference
assertThat(diag.getSpecimen()).isEmpty();
// Verify result reference
List<Reference> obsRef = diag.getResult();
assertThat(obsRef).hasSize(2);
assertThat(obsRef.get(0).isEmpty()).isFalse();
// Verify presentedForm from OBX of type TX - In this case no attachments created because the OBX is not of type TX.
List<Attachment> attachments = diag.getPresentedForm();
Assertions.assertEquals(0, attachments.size(), "Unexpected number of attachments");
// /////////////////////////////////////////
// Now confirm content of the SECOND diagnosticReport because we don't have separate tests for DiagnosticReport
// /////////////////////////////////////////
DiagnosticReport diag2 = ResourceUtils.getResourceDiagnosticReport(diagnosticReport.get(0), context);
// Verify status from OBR.25
assertThat(diag2.getStatus().toCode()).isEqualTo("final");
// Verify category from OBR.24
assertThat(diag2.getCategory()).isEmpty();
// Verify code from OBR.4
assertThat(diag2.hasCode()).isTrue();
List<Coding> codings2 = diag2.getCode().getCoding();
assertThat(codings2).hasSize(1);
Coding coding2 = codings.get(0);
assertThat(coding2.hasDisplay()).isTrue();
assertThat(coding2.getDisplay()).hasToString("Final Echocardiogram Report");
assertThat(coding2.hasCode()).isTrue();
assertThat(coding2.getCode()).hasToString("112");
assertThat(coding2.hasSystem()).isFalse();
// Verify encounter reference
assertThat(diag2.getEncounter().isEmpty()).isTrue();
// Verify subject reference
assertThat(diag2.getSubject().isEmpty()).isFalse();
// Verify effectiveDateTime from OBR.7 and OBR.8
// This also verifies the type, confirming effectiveDateTime was set rather than effectivePeriod
assertThat(diag2.getEffectiveDateTimeType().asStringValue()).isEqualTo("2015-10-09T17:36:44+08:00");
// Verify issued from OBR.22
assertThat(diag2.getIssued()).isNull();
// Verify resultsInterpreter from OBR.32
assertThat(diag2.getResultsInterpreter()).hasSize(1);
// Verify basedOn is ref to the ServiceRequest created for ORC or OBR
assertThat(diag.getBasedOn()).hasSize(1);
assertThat(diag.getBasedOn().get(0).getReference().substring(0, 15)).isEqualTo("ServiceRequest/");
// Verify specimen reference
assertThat(diag2.getSpecimen()).isEmpty();
// Verify result reference
List<Reference> obsRef2 = diag2.getResult();
assertThat(obsRef2).hasSize(2);
assertThat(obsRef2.get(0).isEmpty()).isFalse();
// Verify presentedForm from OBX of type TX - In this case no attachments created because the OBX is not type TX.
List<Attachment> attachments2 = diag2.getPresentedForm();
Assertions.assertEquals(0, attachments2.size(), "Unexpected number of attachments");
// //////////////////////////////////
for (Resource res : obsResource) {
// Verify encounter reference is not set
Observation obs = (Observation) res;
assertThat(obs.getEncounter().isEmpty()).isTrue();
// Verify subject reference to Patient exists
Base subject = ResourceUtils.getValue(obs, "subject");
assertThat(ResourceUtils.getValueAsString(subject, "reference").substring(0, 8)).isEqualTo("Patient/");
}
}
use of org.hl7.fhir.dstu2016may.model.Attachment in project cqf-ruler by DBCG.
the class Libraries method getFunctions.
static LibraryFunctions getFunctions(FhirVersionEnum fhirVersionEnum) {
FhirContext fhirContext = FhirContext.forCached(fhirVersionEnum);
Class<? extends IBaseResource> libraryClass = fhirContext.getResourceDefinition(LIBRARY_RESOURCE_TYPE).getImplementingClass();
Function<IBase, List<IBase>> attachments = Reflections.getFunction(libraryClass, "content");
Function<IBase, String> contentType = Reflections.getPrimitiveFunction(fhirContext.getElementDefinition("Attachment").getImplementingClass(), "contentType");
Function<IBase, byte[]> content = Reflections.getPrimitiveFunction(fhirContext.getElementDefinition("Attachment").getImplementingClass(), "data");
Function<IBase, String> version = Reflections.getVersionFunction(libraryClass);
return new LibraryFunctions(attachments, contentType, content, version);
}
use of org.hl7.fhir.dstu2016may.model.Attachment in project cqf-ruler by DBCG.
the class R4CarePlanToCdsCard method convert.
private static List<CdsCard> convert(RequestGroup requestGroup) {
List<CdsCard> cards = new ArrayList<>();
// links
List<CdsCard.Links> links = new ArrayList<>();
if (requestGroup.hasExtension()) {
for (Extension extension : requestGroup.getExtension()) {
CdsCard.Links link = new CdsCard.Links();
if (extension.getValue() instanceof Attachment) {
Attachment attachment = (Attachment) extension.getValue();
if (attachment.hasUrl()) {
link.setUrl(attachment.getUrl());
}
if (attachment.hasTitle()) {
link.setLabel(attachment.getTitle());
}
if (attachment.hasExtension()) {
link.setType(attachment.getExtensionFirstRep().getValue().primitiveValue());
}
} else {
throw new RuntimeException("Invalid link extension type: " + extension.getValue().fhirType());
}
links.add(link);
}
}
if (requestGroup.hasAction()) {
for (RequestGroup.RequestGroupActionComponent action : requestGroup.getAction()) {
IParser jsonParser = FhirContext.forCached(FhirVersionEnum.R4).newJsonParser().setPrettyPrint(true);
CdsCard card = new CdsCard(jsonParser);
// basic
if (action.hasTitle()) {
card.setSummary(action.getTitle());
}
if (action.hasDescription()) {
card.setDetail(action.getDescription());
}
if (action.hasExtension()) {
card.setIndicator(action.getExtensionFirstRep().getValue().toString());
}
// source
if (action.hasDocumentation()) {
// Assuming first related artifact has everything
RelatedArtifact documentation = action.getDocumentationFirstRep();
CdsCard.Source source = new CdsCard.Source();
if (documentation.hasDisplay()) {
source.setLabel(documentation.getDisplay());
}
if (documentation.hasUrl()) {
source.setUrl(documentation.getUrl());
}
if (documentation.hasDocument() && documentation.getDocument().hasUrl()) {
source.setIcon(documentation.getDocument().getUrl());
}
card.setSource(source);
}
if (action.hasSelectionBehavior()) {
card.setSelectionBehavior(action.getSelectionBehavior().toCode());
}
// suggestions
// TODO - uuid
boolean hasSuggestions = false;
CdsCard.Suggestions suggestions = new CdsCard.Suggestions();
CdsCard.Suggestions.Action actions = new CdsCard.Suggestions.Action();
if (action.hasPrefix()) {
suggestions.setLabel(action.getPrefix());
hasSuggestions = true;
if (action.hasDescription()) {
actions.setDescription(action.getDescription());
}
if (action.hasType() && !action.getType().getCodingFirstRep().getCode().equals("fire-event")) {
String code = action.getType().getCodingFirstRep().getCode();
actions.setType(CdsCard.Suggestions.Action.ActionType.valueOf(code.equals("remove") ? "delete" : code));
}
if (action.hasResource()) {
if (actions.getType().name().equalsIgnoreCase("create")) {
action.getResourceTarget().setId((String) null);
}
actions.setResource(action.getResourceTarget());
}
}
if (hasSuggestions) {
suggestions.addAction(actions);
card.addSuggestion(suggestions);
}
if (!links.isEmpty()) {
card.setLinks(links);
}
cards.add(card);
}
}
return cards;
}
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