Examples with RelatedArtifact org.hl7.fhir.r5.model.RelatedArtifact used on opensource projects

Example 26 with RelatedArtifact

use of org.hl7.fhir.r5.model.RelatedArtifact in project clinical_quality_language by cqframework.

the class DataRequirementsProcessorTest method TestLibraryDataRequirements.

@Test
public void TestLibraryDataRequirements() {
    CqlTranslatorOptions cqlTranslatorOptions = new CqlTranslatorOptions();
    cqlTranslatorOptions.getFormats().add(CqlTranslator.Format.JSON);
    try {
        // CqlTranslator translator = createTranslator("/ecqm/resources/library-EXM506-2.2.000.json", cqlTranslatorOptions);
        CqlTranslator translator = createTranslator("CompositeMeasures/cql/BCSComponent.cql", cqlTranslatorOptions);
        translator.toELM();
        assertTrue(translator.getErrors().isEmpty());
        libraryManager.cacheLibrary(translator.getTranslatedLibrary());
        DataRequirementsProcessor dqReqTrans = new DataRequirementsProcessor();
        org.hl7.fhir.r5.model.Library moduleDefinitionLibrary = dqReqTrans.gatherDataRequirements(libraryManager, translator.getTranslatedLibrary(), cqlTranslatorOptions, null, false);
        assertTrue(moduleDefinitionLibrary.getType().getCode("http://terminology.hl7.org/CodeSystem/library-type").equalsIgnoreCase("module-definition"));
        List<Extension> directReferenceCodes = moduleDefinitionLibrary.getExtensionsByUrl("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode");
        assertTrue(directReferenceCodes.size() == 5);
        Extension directReferenceCode = directReferenceCodes.get(0);
        Coding coding = directReferenceCode.getValueCoding();
        assertEquals("http://loinc.org", coding.getSystem());
        assertEquals("21112-8", coding.getCode());
        assertEquals("Birth date", coding.getDisplay());
        assertTrue(moduleDefinitionLibrary.getRelatedArtifact().size() >= 45);
        RelatedArtifact loincCodeSystem = null;
        for (RelatedArtifact relatedArtifact : moduleDefinitionLibrary.getRelatedArtifact()) {
            if (relatedArtifact.getType() == RelatedArtifact.RelatedArtifactType.DEPENDSON && relatedArtifact.getResource() != null && relatedArtifact.getResource().equals("http://loinc.org")) {
                loincCodeSystem = relatedArtifact;
                break;
            }
        }
        assertTrue(loincCodeSystem != null);
        assertTrue(moduleDefinitionLibrary.getParameter().size() >= 16);
        ParameterDefinition measurementPeriod = null;
        for (ParameterDefinition parameter : moduleDefinitionLibrary.getParameter()) {
            if (parameter.getName().equals("Measurement Period")) {
                measurementPeriod = parameter;
                break;
            }
        }
        assertTrue(measurementPeriod != null);
        assertTrue(moduleDefinitionLibrary.getDataRequirement().size() >= 15);
        DataRequirement diagnosisRequirement = null;
        for (DataRequirement requirement : moduleDefinitionLibrary.getDataRequirement()) {
            if (requirement.getType() == Enumerations.FHIRAllTypes.CONDITION && requirement.getCodeFilter().size() == 1) {
                DataRequirement.DataRequirementCodeFilterComponent cfc = requirement.getCodeFilterFirstRep();
                if (cfc.hasPath() && cfc.getPath().equals("code") && cfc.hasValueSet() && cfc.getValueSet().equals("http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.198.12.1071")) {
                    diagnosisRequirement = requirement;
                    break;
                }
            }
        }
        assertTrue(diagnosisRequirement != null);
        FhirContext context = getFhirContext();
        IParser parser = context.newJsonParser();
        String moduleDefString = parser.setPrettyPrint(true).encodeResourceToString(moduleDefinitionLibrary);
        logger.debug(moduleDefString);
    } catch (IOException ioException) {
        ioException.printStackTrace();
    }
}

Example 27 with RelatedArtifact

use of org.hl7.fhir.r5.model.RelatedArtifact in project cqf-ruler by DBCG.

the class DataOperationsProvider method visitLibrary.

private void visitLibrary(Library library, List<Library> queue, Map<String, Library> resources, RequestDetails theRequestDetails) {
    for (RelatedArtifact relatedArtifact : library.getRelatedArtifact()) {
        if (relatedArtifact.getType().equals(RelatedArtifact.RelatedArtifactType.DEPENDSON) && relatedArtifact.hasResource()) {
            IdType id = Ids.newId(Library.class, relatedArtifact.getResource().getReference());
            Library lib = search(Library.class, Searches.byId(id), theRequestDetails).firstOrNull();
            if (lib != null) {
                resources.putIfAbsent(lib.getId(), lib);
                queue.add(lib);
            }
        }
    }
}

Example 28 with RelatedArtifact

use of org.hl7.fhir.r5.model.RelatedArtifact in project cqf-ruler by DBCG.

the class Session method resolveActions.

private void resolveActions(RequestDetails theRequest, PlanDefinition planDefinition, List<PlanDefinition.PlanDefinitionActionComponent> actions, Context context, String patientId, RequestGroupBuilder requestGroupBuilder, List<RequestGroup.RequestGroupActionComponent> actionComponents) {
    for (PlanDefinition.PlanDefinitionActionComponent action : actions) {
        boolean conditionsMet = true;
        for (PlanDefinition.PlanDefinitionActionConditionComponent condition : action.getCondition()) {
            if (condition.getKind() == PlanDefinition.ActionConditionKind.APPLICABILITY) {
                if (!condition.hasExpression()) {
                    continue;
                }
                Boolean aliasedExpression = null;
                if (condition.hasLanguage()) {
                    String language = condition.getLanguage();
                    if (language.equals("text/cql.identifier") || language.equals("text/cql-identifier") || language.equals("text/cql.name") || language.equals("text/cql-name")) {
                        aliasedExpression = true;
                    } else {
                        aliasedExpression = false;
                    }
                } else {
                    aliasedExpression = false;
                }
                Object result = expressionEvaluation.evaluateInContext(planDefinition, condition.getExpression(), aliasedExpression, patientId, theRequest);
                if (!(result instanceof Boolean)) {
                    continue;
                }
                if (!(Boolean) result) {
                    conditionsMet = false;
                }
            }
            if (conditionsMet) {
                RequestGroupActionBuilder actionBuilder = new RequestGroupActionBuilder();
                if (action.hasTitle()) {
                    actionBuilder.buildTitle(action.getTitle());
                }
                if (action.hasDescription()) {
                    actionBuilder.buildDescripition(action.getDescription());
                }
                // source
                if (action.hasDocumentation()) {
                    RelatedArtifact artifact = action.getDocumentationFirstRep();
                    RelatedArtifactBuilder artifactBuilder = new RelatedArtifactBuilder();
                    if (artifact.hasDisplay()) {
                        artifactBuilder.buildDisplay(artifact.getDisplay());
                    }
                    if (artifact.hasUrl()) {
                        artifactBuilder.buildUrl(artifact.getUrl());
                    }
                    if (artifact.hasDocument() && artifact.getDocument().hasUrl()) {
                        AttachmentBuilder attachmentBuilder = new AttachmentBuilder();
                        attachmentBuilder.buildUrl(artifact.getDocument().getUrl());
                        artifactBuilder.buildDocument(attachmentBuilder.build());
                    }
                    actionBuilder.buildDocumentation(Collections.singletonList(artifactBuilder.build()));
                }
                // TODO - uuid
                if (action.hasLabel()) {
                    actionBuilder.buildLabel(action.getLabel());
                }
                if (action.hasType()) {
                    actionBuilder.buildType(action.getType());
                }
                if (action.hasDefinition()) {
                    if (action.getDefinition().getReferenceElement().getResourceType().equals("ActivityDefinition")) {
                        if (action.getDefinition().getResource() != null) {
                            ActivityDefinition activityDefinition = (ActivityDefinition) action.getDefinition().getResource();
                            ReferenceBuilder referenceBuilder = new ReferenceBuilder();
                            referenceBuilder.buildDisplay(activityDefinition.getDescription());
                            actionBuilder.buildResource(referenceBuilder.build());
                            if (activityDefinition.hasDescription()) {
                                actionBuilder.buildDescripition(activityDefinition.getDescription());
                            }
                        }
                        ActivityDefinition activityDefinition = this.activityDefinitionDao.read(action.getDefinition().getReferenceElement());
                        if (activityDefinition.hasDescription()) {
                            actionBuilder.buildDescripition(activityDefinition.getDescription());
                        }
                        try {
                            this.activityDefinitionApplyProvider.apply(theRequest, new IdType(action.getDefinition().getReferenceElement().getIdPart()), patientId, null, null, null, null, null, null, null, null).setId(UUID.randomUUID().toString());
                        } catch (FHIRException e) {
                            throw new RuntimeException("Error applying ActivityDefinition " + e.getMessage());
                        }
                        Parameters inParams = new Parameters();
                        inParams.addParameter().setName("patient").setValue(new StringType(patientId));
                        Parameters outParams = this.fhirContext.newRestfulGenericClient(theRequest.getFhirServerBase()).operation().onInstance(new IdDt("ActivityDefinition", action.getDefinition().getId())).named("$apply").withParameters(inParams).useHttpGet().execute();
                        List<Parameters.ParametersParameterComponent> response = outParams.getParameter();
                        Resource resource = response.get(0).getResource().setId(UUID.randomUUID().toString());
                        actionBuilder.buildResourceTarget(resource);
                        actionBuilder.buildResource(new ReferenceBuilder().buildReference(resource.getId()).build());
                    }
                }
                // on here...
                if (action.hasDynamicValue()) {
                    for (PlanDefinition.PlanDefinitionActionDynamicValueComponent dynamicValue : action.getDynamicValue()) {
                        if (dynamicValue.hasPath() && dynamicValue.hasExpression()) {
                            if (dynamicValue.getPath().endsWith("title")) {
                                // summary
                                String title = (String) context.resolveExpressionRef(dynamicValue.getExpression()).evaluate(context);
                                actionBuilder.buildTitle(title);
                            } else if (dynamicValue.getPath().endsWith("description")) {
                                // detail
                                String description = (String) context.resolveExpressionRef(dynamicValue.getExpression()).evaluate(context);
                                actionBuilder.buildDescripition(description);
                            } else if (dynamicValue.getPath().endsWith("extension")) {
                                // indicator
                                String extension = (String) context.resolveExpressionRef(dynamicValue.getExpression()).evaluate(context);
                                actionBuilder.buildExtension(extension);
                            }
                        }
                    }
                }
                if (!actionBuilder.build().isEmpty()) {
                    actionComponents.add(actionBuilder.build());
                }
                if (action.hasAction()) {
                    resolveActions(theRequest, planDefinition, action.getAction(), context, patientId, requestGroupBuilder, actionComponents);
                }
            }
        }
    }
    requestGroupBuilder.buildAction(new ArrayList<>(actionComponents));
}

Example 29 with RelatedArtifact

use of org.hl7.fhir.r5.model.RelatedArtifact 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;
}

Example 30 with RelatedArtifact

use of org.hl7.fhir.r5.model.RelatedArtifact 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;
}