use of com.ibm.cloud.cloudant.v1.model.Attachment in project cqf-ruler by DBCG.
the class ActivityDefinitionApplyProvider method resolveDiagnosticReport.
private DiagnosticReport resolveDiagnosticReport(ActivityDefinition activityDefinition, String patientId) {
DiagnosticReport diagnosticReport = new DiagnosticReport();
diagnosticReport.setStatus(DiagnosticReport.DiagnosticReportStatus.UNKNOWN);
diagnosticReport.setSubject(new Reference(patientId));
if (activityDefinition.hasCode()) {
diagnosticReport.setCode(activityDefinition.getCode());
} else {
throw new ActivityDefinitionApplyException("Missing required ActivityDefinition.code property for DiagnosticReport");
}
if (activityDefinition.hasRelatedArtifact()) {
List<Attachment> presentedFormAttachments = new ArrayList<>();
for (RelatedArtifact artifact : activityDefinition.getRelatedArtifact()) {
Attachment attachment = new Attachment();
if (artifact.hasUrl()) {
attachment.setUrl(artifact.getUrl());
}
if (artifact.hasDisplay()) {
attachment.setTitle(artifact.getDisplay());
}
presentedFormAttachments.add(attachment);
}
diagnosticReport.setPresentedForm(presentedFormAttachments);
}
return diagnosticReport;
}
use of com.ibm.cloud.cloudant.v1.model.Attachment in project cqf-ruler by DBCG.
the class ActivityDefinitionApplyProvider method resolveCommunicationRequest.
private CommunicationRequest resolveCommunicationRequest(ActivityDefinition activityDefinition, String patientId) {
CommunicationRequest communicationRequest = new CommunicationRequest();
communicationRequest.setStatus(CommunicationRequest.CommunicationRequestStatus.UNKNOWN);
communicationRequest.setSubject(new Reference(patientId));
// Unsure if this is correct - this is the way Motive is doing it...
if (activityDefinition.hasCode()) {
if (activityDefinition.getCode().hasText()) {
communicationRequest.addPayload().setContent(new StringType(activityDefinition.getCode().getText()));
}
}
if (activityDefinition.hasRelatedArtifact()) {
for (RelatedArtifact artifact : activityDefinition.getRelatedArtifact()) {
if (artifact.hasUrl()) {
Attachment attachment = new Attachment().setUrl(artifact.getUrl());
if (artifact.hasDisplay()) {
attachment.setTitle(artifact.getDisplay());
}
CommunicationRequest.CommunicationRequestPayloadComponent payload = new CommunicationRequest.CommunicationRequestPayloadComponent();
payload.setContent(artifact.hasDisplay() ? attachment.setTitle(artifact.getDisplay()) : attachment);
communicationRequest.setPayload(Collections.singletonList(payload));
}
// TODO - other relatedArtifact types
}
}
return communicationRequest;
}
use of com.ibm.cloud.cloudant.v1.model.Attachment in project cqf-ruler by DBCG.
the class ActivityDefinitionApplyProvider method resolveTask.
private Task resolveTask(ActivityDefinition activityDefinition, String patientId) {
Task task = new Task();
task.setStatus(Task.TaskStatus.DRAFT);
task.setIntent(Task.TaskIntent.PROPOSAL);
task.setFor(new Reference(patientId));
Task.ParameterComponent input = new Task.ParameterComponent();
if (activityDefinition.hasCode()) {
task.setCode(activityDefinition.getCode());
input.setType(activityDefinition.getCode());
}
// Extension defined by CPG-on-FHIR for Questionnaire canonical URI
Extension collectsWith = activityDefinition.getExtensionByUrl("http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-collectWith");
if (collectsWith != null && collectsWith.getValueAsPrimitive().toString() != null) {
CanonicalType uri = new CanonicalType(collectsWith.getValueAsPrimitive().toString());
input.setValue(uri);
}
if (activityDefinition.hasRelatedArtifact()) {
for (RelatedArtifact artifact : activityDefinition.getRelatedArtifact()) {
if (artifact.hasUrl()) {
Attachment attachment = new Attachment().setUrl(artifact.getUrl());
if (artifact.hasDisplay()) {
attachment.setTitle(artifact.getDisplay());
}
input.setValue(artifact.hasDisplay() ? attachment.setTitle(artifact.getDisplay()) : attachment);
}
// TODO - other relatedArtifact types
}
}
// If input has been populated, then add it to the Task.
if (input.getType() != null || input.getValue() != null) {
task.addInput(input);
}
return task;
}
use of com.ibm.cloud.cloudant.v1.model.Attachment in project cqf-ruler by DBCG.
the class STU3CarePlanToCdsCard 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.DSTU3).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.hasLabel()) {
suggestions.setLabel(action.getLabel());
hasSuggestions = true;
if (action.hasDescription()) {
actions.setDescription(action.getDescription());
}
if (action.hasType() && !action.getType().getCode().equals("fire-event")) {
String code = action.getType().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;
}
use of com.ibm.cloud.cloudant.v1.model.Attachment in project hl7v2-fhir-converter by LinuxForHealth.
the class Hl7ORUMessageTest method test_oru_multipleOBXofDifferentTypes.
/**
* ORU messages with an OBR and multiple OBX segments create records only for non TX type OBX
* The OBX type TX are added to the presentedForm as an attachment for the diagnostic
* @throws IOException
*/
// 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_multipleOBXofDifferentTypes() throws IOException {
String json = ftv.convert(new File("src/test/resources/ORU-multiline-short.hl7"), OPTIONS_PRETTYPRINT);
assertThat(json).isNotBlank();
LOGGER.debug("FHIR json result:\n" + json);
// Verify conversion
FHIRContext context = new FHIRContext();
IBaseResource bundleResource = context.getParser().parseResource(json);
assertThat(bundleResource).isNotNull();
Bundle b = (Bundle) bundleResource;
Assertions.assertSame(BundleType.COLLECTION, b.getType(), "Bundle type not expected");
List<BundleEntryComponent> e = b.getEntry();
// Verify that the right resources have been created
List<Resource> patientResource = ResourceUtils.getResourceList(e, ResourceType.Patient);
assertThat(patientResource).hasSize(1);
List<Resource> encounterResource = ResourceUtils.getResourceList(e, ResourceType.Encounter);
assertThat(encounterResource).hasSize(1);
List<Resource> organizationResource = ResourceUtils.getResourceList(e, ResourceType.Organization);
// We expect an organization created from an Encounter.serviceProvider reference
assertThat(organizationResource).hasSize(1);
List<Resource> practitionerResource = ResourceUtils.getResourceList(e, ResourceType.Practitioner);
assertThat(practitionerResource).hasSize(4);
List<Resource> messageHeader = ResourceUtils.getResourceList(e, ResourceType.MessageHeader);
assertThat(messageHeader).hasSize(1);
// Verify Diagnostic Report is created as expected
List<Resource> reportResource = ResourceUtils.getResourceList(e, ResourceType.DiagnosticReport);
assertThat(reportResource).hasSize(1);
List<Resource> servReqResource = ResourceUtils.getResourceList(e, ResourceType.ServiceRequest);
assertThat(servReqResource).hasSize(1);
// Verify there are no extra resources created
assertThat(e).hasSize(10);
// Verify no observations are created
List<Resource> obsResource = ResourceUtils.getResourceList(e, ResourceType.Observation);
// TODO: When NTE is implemented, then update this to one.
assertThat(obsResource).isEmpty();
// /////////////////////////////////////////
// Now confirm content of the diagnosticReport because we don't have separate tests for DiagnosticReport
// /////////////////////////////////////////
DiagnosticReport diag = ResourceUtils.getResourceDiagnosticReport(reportResource.get(0), context);
// Verify status from OBR.25
assertThat(diag.getStatus().toCode()).isEqualTo("final");
// Verify category from OBR.24
assertThat(diag.getCategory()).hasSize(1);
DatatypeUtils.checkCommonCodeableConceptAssertions(diag.getCategoryFirstRep(), "CT", "CAT Scan", "http://terminology.hl7.org/CodeSystem/v2-0074", "CT");
// Verify code from OBR.4; This tests scenario of the code not being in the default loinc system.
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("ECHO CARDIOGRAM COMPLETE");
assertThat(coding.hasCode()).isTrue();
assertThat(coding.getCode()).hasToString("1487");
assertThat(coding.hasSystem()).isFalse();
// Verify encounter reference
assertThat(diag.getEncounter().isEmpty()).isFalse();
// 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("2020-08-02T12:44:55+08:00");
// Verify issued from OBR.22
assertThat(diag.getIssued()).isNull();
// Verify resultsInterpreter from OBR.32
assertThat(diag.getResultsInterpreter()).isEmpty();
// 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).isEmpty();
// Verify result reference
List<Reference> obsRef = diag.getResult();
assertThat(obsRef).isEmpty();
// Verify attachment to diagnostic report
List<Attachment> attachments = diag.getPresentedForm();
Assertions.assertEquals(1, attachments.size(), "Unexpected number of attachments");
Attachment a = attachments.get(0);
Assertions.assertTrue(a.getContentType().equalsIgnoreCase("text/plain"), "Incorrect content type");
Assertions.assertTrue(a.getLanguage().equalsIgnoreCase("en"), "Incorrect language");
// Verify data attachment after decoding
String decoded = new String(Base64.getDecoder().decode(a.getDataElement().getValueAsString()));
System.out.println("Decoded: '" + decoded + "'");
Assertions.assertEquals("\n[PII] Emergency Department\nED Encounter Arrival Date: [ADDRESS] [PERSONALNAME]:", decoded, "Incorrect data");
Assertions.assertTrue(a.getTitle().equalsIgnoreCase("ECHO CARDIOGRAM COMPLETE"), "Incorrect title");
// Verify creation data is persisted correctly - 2020-08-02T12:44:55+08:00
Calendar c = Calendar.getInstance();
// needed to completely clear out calendar object
c.clear();
c.set(2020, 7, 2, 12, 44, 55);
c.setTimeZone(TimeZone.getTimeZone(ZoneId.of("+08:00")));
Date d = c.getTime();
Assertions.assertEquals(d, a.getCreation(), "Incorrect creation date");
// //////////////////////////////////
for (Resource res : obsResource) {
// Verify encounter reference exists
Observation obs = (Observation) res;
assertThat(obs.getEncounter().isEmpty()).isFalse();
assertThat(obs.getEncounter().getReference().substring(0, 10)).isEqualTo("Encounter/");
// Verify subject reference to Patient exists
assertThat(obs.getSubject().isEmpty()).isFalse();
assertThat(obs.getSubject().getReference().substring(0, 8)).isEqualTo("Patient/");
}
}
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