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

Example 26 with Library

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

the class ExpressionEvaluation method setupContext.

private Context setupContext(DomainResource instance, String cql, String patientId, Boolean aliasedExpression, RequestDetails theRequest) {
    JpaFhirDal jpaFhirDal = jpaFhirDalFactory.create(theRequest);
    List<CanonicalType> libraries = getLibraryReferences(instance, theRequest);
    String fhirVersion = this.fhirContext.getVersion().getVersion().getFhirVersionString();
    // Remove LocalLibrary from cache first...
    VersionedIdentifier localLibraryIdentifier = new VersionedIdentifier().withId("LocalLibrary");
    globalLibraryCache.remove(localLibraryIdentifier);
    // temporary LibraryLoader to resolve library dependencies when building
    // includes
    LibraryLoader tempLibraryLoader = libraryLoaderFactory.create(new ArrayList<LibraryContentProvider>(Arrays.asList(jpaLibraryContentProviderFactory.create(theRequest))));
    String source = "";
    if (aliasedExpression) {
        if (libraries.size() != 1) {
            throw new RuntimeException("If an aliased expression is provided, there must be exactly one primary Library");
        }
        VersionedIdentifier vi = getVersionedIdentifierFromCanonical(libraries.get(0));
        // Still not the best way to build include, but at least checks dal for an
        // existing library
        // Check if id works for LibraryRetrieval
        org.cqframework.cql.elm.execution.Library executionLibrary = null;
        try {
            executionLibrary = tempLibraryLoader.load(vi);
        } catch (Exception e) {
        // log error
        }
        if (executionLibrary == null) {
            Library library = (Library) jpaFhirDal.read(new IdType("Library", Canonicals.getIdPart(libraries.get(0))));
            vi.setId(library.getName());
            if (library.getVersion() != null) {
                vi.setVersion(library.getVersion());
            }
        }
        source = String.format("library LocalLibrary using FHIR version '" + fhirVersion + "' include FHIRHelpers version '" + fhirVersion + "' called FHIRHelpers %s parameter %s %s parameter \"%%context\" %s define Expression: %s", buildIncludes(tempLibraryLoader, jpaFhirDal, libraries, theRequest), instance.fhirType(), instance.fhirType(), instance.fhirType(), vi.getId() + ".\"" + cql + "\"");
    } else {
        source = String.format("library LocalLibrary using FHIR version '" + fhirVersion + "' include FHIRHelpers version '" + fhirVersion + "' called FHIRHelpers %s parameter %s %s parameter \"%%context\" %s define Expression: %s", buildIncludes(tempLibraryLoader, jpaFhirDal, libraries, theRequest), instance.fhirType(), instance.fhirType(), instance.fhirType(), cql);
    }
    LibraryLoader libraryLoader = libraryLoaderFactory.create(new ArrayList<LibraryContentProvider>(Arrays.asList(jpaLibraryContentProviderFactory.create(theRequest), new InMemoryLibraryContentProvider(Arrays.asList(source)))));
    // resolve execution context
    return setupContext(instance, patientId, libraryLoader, theRequest);
}

Example 27 with Library

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

the class DataOperationProviderIT method testDstu3MeasureDataRequirementsOperation.

@Disabled("Erroring because could not convert r5 Library to dstu3")
@Test
public void testDstu3MeasureDataRequirementsOperation() throws IOException {
    String bundleAsText = stringFromResource("Exm105Dstu3MeasureBundle.json");
    Bundle bundle = (Bundle) getFhirContext().newJsonParser().parseResource(bundleAsText);
    getClient().transaction().withBundle(bundle).execute();
    Parameters params = new Parameters();
    params.addParameter().setName("startPeriod").setValue(new StringType("2019-01-01"));
    params.addParameter().setName("endPeriod").setValue(new StringType("2020-01-01"));
    Library returnLibrary = getClient().operation().onInstance(new IdType("Measure", "measure-EXM105-FHIR3-8.0.000")).named("$data-requirements").withParameters(params).returnResourceType(Library.class).execute();
    assertNotNull(returnLibrary);
}

Example 28 with Library

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

the class ElmCacheResourceChangeListener method invalidateCacheById.

private void invalidateCacheById(IIdType theId) {
    if (!theId.getResourceType().equals("Library")) {
        return;
    }
    try {
        IBaseResource library = this.myLibraryDao.read(theId);
        String name = this.myNameFunction.apply(library);
        String version = this.myVersionFunction.apply(library);
        this.myGlobalLibraryCache.remove(new VersionedIdentifier().withId(name).withVersion(version));
    }// name and version.
     catch (Exception e) {
        // TODO: This needs to be smarter... the issue is that ELM is cached with
        // library name and version as the key since
        // that's the access path the CQL engine uses, but change notifications occur
        // with the resource Id, which is not
        // necessarily tied to the resource name. In any event, if a unknown resource is
        // deleted, clear all libraries as a workaround.
        // One option is to maintain a cache with multiple indices.
        ourLog.debug("Failed to locate resource {} to look up name and version. Clearing all libraries from cache.", theId.getValueAsString());
        this.myGlobalLibraryCache.clear();
    }
}

Example 29 with Library

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

the class ActivityDefinitionApplyProvider method resolveActivityDefinition.

// For library use
public Resource resolveActivityDefinition(ActivityDefinition activityDefinition, String patientId, String practitionerId, String organizationId, RequestDetails theRequest) throws FHIRException {
    Resource result = newResource(activityDefinition.getKind().toCode());
    switch(result.fhirType()) {
        case "ServiceRequest":
            result = resolveServiceRequest(activityDefinition, patientId, practitionerId, organizationId);
            break;
        case "MedicationRequest":
            result = resolveMedicationRequest(activityDefinition, patientId);
            break;
        case "SupplyRequest":
            result = resolveSupplyRequest(activityDefinition, practitionerId, organizationId);
            break;
        case "Procedure":
            result = resolveProcedure(activityDefinition, patientId);
            break;
        case "DiagnosticReport":
            result = resolveDiagnosticReport(activityDefinition, patientId);
            break;
        case "Communication":
            result = resolveCommunication(activityDefinition, patientId);
            break;
        case "CommunicationRequest":
            result = resolveCommunicationRequest(activityDefinition, patientId);
            break;
        case "Task":
            result = resolveTask(activityDefinition, patientId);
            break;
    }
    for (ActivityDefinition.ActivityDefinitionDynamicValueComponent dynamicValue : activityDefinition.getDynamicValue()) {
        // ActivityDefinition apply operation does not fail.
        try {
            if (dynamicValue.getExpression() != null) {
                // Special case for setting a Patient reference
                if ("Patient".equals(dynamicValue.getExpression().getExpression())) {
                    this.modelResolver.setValue(result, dynamicValue.getPath(), new Reference(patientId));
                } else {
                    /*
						 * TODO: Passing the activityDefinition as context here because that's what will
						 * have the libraries, but perhaps the "context" here should be the result
						 * resource?
						 */
                    Object value = expressionEvaluation.evaluateInContext(activityDefinition, dynamicValue.getExpression().getExpression(), patientId, theRequest);
                    if (value != null) {
                        logger.debug("dynamicValue value: {}", value);
                        if (value instanceof Boolean) {
                            value = new BooleanType((Boolean) value);
                        } else if (value instanceof DateTime) {
                            value = Date.from(((DateTime) value).getDateTime().toInstant());
                        } else if (value instanceof String) {
                            value = new StringType((String) value);
                        }
                        this.modelResolver.setValue(result, dynamicValue.getPath(), value);
                    } else {
                        logger.warn("WARNING: ActivityDefinition has null value for path: {}", dynamicValue.getPath());
                    }
                }
            }
        } catch (Exception e) {
            logger.error("ERROR: ActivityDefinition dynamicValue {} could not be applied and threw exception {}", dynamicValue.getPath(), e.toString());
            logger.error(e.toString());
        }
    }
    return result;
}

Example 30 with Library

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

the class CqlExecutionProviderIT method testDataBundleCqlExecutionProviderWithSubject.

@Test
public void testDataBundleCqlExecutionProviderWithSubject() throws Exception {
    Parameters params = new Parameters();
    Parameters libraryParameter = new Parameters();
    params.addParameter().setName("subject").setValue(new StringType("Patient/SimplePatient"));
    libraryParameter.addParameter().setName("url").setValue(new StringType(this.getClient().getServerBase() + "Library/SimpleDstu3Library"));
    libraryParameter.addParameter().setName("name").setValue(new StringType("SimpleDstu3Library"));
    params.addParameter().setName("library").setResource(libraryParameter);
    params.addParameter().setName("expression").setValue(new StringType("SimpleDstu3Library.\"observationRetrieve\""));
    String packagePrefix = "org/opencds/cqf/ruler/cpg/dstu3/provider/";
    loadResource(packagePrefix + "SimpleDstu3Library.json");
    loadResource(packagePrefix + "SimplePatient.json");
    Bundle data = (Bundle) loadResource(packagePrefix + "SimpleDataBundle.json");
    params.addParameter().setName("data").setResource(data);
    params.addParameter().setName("useServerData").setValue(new BooleanType(false));
    Parameters results = getClient().operation().onServer().named("$cql").withParameters(params).execute();
    assertTrue(results.getParameter().get(0).getResource() instanceof Bundle);
    assertTrue(((Bundle) results.getParameter().get(0).getResource()).getEntry().get(0).getResource() instanceof Observation);
    assertTrue(results.getParameter().get(1).getValue() instanceof StringType);
    assertTrue(((StringType) results.getParameter().get(1).getValue()).asStringValue().equals("List"));
    logger.debug("Results: ", results);
}