Examples with BundleEntryComponent org.hl7.fhir.dstu2016may.model.Bundle.BundleEntryComponent used on opensource projects

Example 91 with BundleEntryComponent

use of org.hl7.fhir.dstu2016may.model.Bundle.BundleEntryComponent in project hl7v2-fhir-converter by LinuxForHealth.

the class HL7MessageModel method deduplicate.

// General deduplication utility. Currently only Organizations.
// Bundle is passed by reference and may be modified
private void deduplicate(Bundle bundle) {
    List<BundleEntryComponent> entries = bundle.getEntry();
    Iterator<BundleEntryComponent> i = entries.iterator();
    while (i.hasNext()) {
        // Safe traversal for removal
        BundleEntryComponent entry = i.next();
        // Currently only looking for duplicate Organizations, because their Urls and Id's are created from org data.
        if (entry.getFullUrl().startsWith("Organization/") && duplicateFound(entry, entries)) {
            // Safe removal
            i.remove();
        }
    }
}

Example 92 with BundleEntryComponent

use of org.hl7.fhir.dstu2016may.model.Bundle.BundleEntryComponent in project cqf-ruler by DBCG.

the class ProcessMessageProvider method processMessageBundle.

@Operation(name = "$process-message-bundle", idempotent = false)
public Bundle processMessageBundle(HttpServletRequest theServletRequest, RequestDetails theRequestDetails, @OperationParam(name = "content", min = 1, max = 1) @Description(formalDefinition = "The message to process (or, if using asynchronous messaging, it may be a response message to accept)") Bundle theMessageToProcess) {
    logger.info("Validating the Bundle");
    Bundle bundle = theMessageToProcess;
    Boolean errorExists = false;
    OperationOutcome outcome = validateBundle(errorExists, bundle);
    if (!errorExists) {
        IVersionSpecificBundleFactory bundleFactory = this.getFhirContext().newBundleFactory();
        bundle.setId(getUUID());
        bundleFactory.initializeWithBundleResource(bundle);
        Bundle dafBundle = (Bundle) bundleFactory.getResourceBundle();
        dafBundle.setTimestamp(new Date());
        this.getDaoRegistry().getResourceDao(Bundle.class).create(dafBundle);
        MessageHeader messageHeader = null;
        String patientId = null;
        String commId = null;
        List<MessageHeader> headers = BundleUtil.toListOfResourcesOfType(this.getFhirContext(), bundle, MessageHeader.class);
        for (MessageHeader mh : headers) {
            messageHeader = mh;
            messageHeader.setId(getUUID());
            Meta meta = messageHeader.getMeta();
            meta.setLastUpdated(new Date());
            messageHeader.setMeta(meta);
        }
        List<IBaseResource> resources = new ArrayList<>();
        List<Patient> patients = BundleUtil.toListOfResourcesOfType(this.getFhirContext(), bundle, Patient.class);
        for (Patient p : patients) {
            patientId = p.getId();
            p.setId(p.getIdElement().toVersionless());
            resources.add(p);
        }
        List<Bundle> bundles = BundleUtil.toListOfResourcesOfType(this.getFhirContext(), bundle, Bundle.class);
        for (Bundle b : bundles) {
            patientId = this.processBundle(b, theRequestDetails);
            b.setId(b.getIdElement().toVersionless());
            resources.add(b);
        }
        for (BundleEntryComponent e : bundle.getEntry()) {
            Resource r = e.getResource();
            if (r == null) {
                continue;
            }
            if (r.fhirType().equals("Bundle") || r.fhirType().equals("MessageHeader") || r.fhirType().equals("Patient")) {
                continue;
            }
            r.setId(r.getIdElement().toVersionless());
            resources.add(r);
        }
        if (patientId != null) {
            commId = constructAndSaveCommunication(patientId);
        }
        if (messageHeader == null) {
            messageHeader = constructMessageHeaderResource();
            BundleEntryComponent entryComp = new BundleEntryComponent();
            entryComp.setResource(messageHeader);
            dafBundle.addEntry(entryComp);
        }
        if (commId != null) {
            List<Reference> referenceList = new ArrayList<>();
            Reference commRef = new Reference();
            commRef.setReference("Communication/" + commId);
            referenceList.add(commRef);
            messageHeader.setFocus(referenceList);
        }
        IVersionSpecificBundleFactory newBundleFactory = this.getFhirContext().newBundleFactory();
        newBundleFactory.addResourcesToBundle(resources, BundleTypeEnum.TRANSACTION, theRequestDetails.getFhirServerBase(), null, null);
        Bundle transactionBundle = (Bundle) newBundleFactory.getResourceBundle();
        for (BundleEntryComponent entry : transactionBundle.getEntry()) {
            UriType uri = new UriType(theRequestDetails.getFhirServerBase() + "/" + entry.getResource().fhirType() + "/" + entry.getResource().getIdElement().getIdPart());
            Enumeration<HTTPVerb> method = new Enumeration<>(new HTTPVerbEnumFactory());
            method.setValue(HTTPVerb.PUT);
            entry.setRequest(new BundleEntryRequestComponent(method, uri));
        }
        @SuppressWarnings("unchecked") IFhirSystemDao<Bundle, Meta> fhirSystemDao = this.getDaoRegistry().getSystemDao();
        fhirSystemDao.transaction(theRequestDetails, transactionBundle);
        return dafBundle;
    } else {
        BundleEntryComponent entryComp = new BundleEntryComponent();
        entryComp.setResource(outcome);
        bundle.addEntry(entryComp);
        return bundle;
    }
}

Example 93 with BundleEntryComponent

use of org.hl7.fhir.dstu2016may.model.Bundle.BundleEntryComponent in project cqf-ruler by DBCG.

the class CacheValueSetsProviderIT method testCacheValueSetsAlreadyExpanded.

// Get help with this....
// @Test
// public void testCacheValueSetsExpandAndAddConcepts() throws Exception {
// Endpoint endpoint = uploadLocalServerEndpoint();
// RequestDetails details = Mockito.mock(RequestDetails.class);
// ValueSet vs =
// uploadValueSet("valueset/valueset-buprenorphine-and-methadone-medications.json");
// vs.getCompose().getInclude().forEach(include -> {
// assertTrue(!include.hasConcept());
// });
// StringAndListParam stringAndListParam =
// getStringAndListParamFromValueSet(vs);
// IGenericClient localClient = createClient(ourCtx, endpoint);
// //
// localClient.operation().onServer().named("updateCodeSystems").withNoParameters(Parameters.class).execute();
// Resource outcomeResource = cacheValueSetsProvider.cacheValuesets(details,
// endpoint.getIdElement(), stringAndListParam, null, null);
// assertTrue(outcomeResource instanceof Bundle);
// Bundle resultBundle = (Bundle) outcomeResource;
// assertTrue(resultBundle.getEntry().size() == 1);
// BundleEntryComponent entry = resultBundle.getEntry().get(0);
// assertTrue(entry.getResponse().getLocation().startsWith("ValueSet/" +
// vs.getIdElement().getIdPart()));
// assertTrue(entry.getResponse().getStatus().equals("200 OK"));
// ValueSet resultingValueSet =
// localClient.read().resource(ValueSet.class).withId(vs.getIdElement()).execute();
// resultingValueSet.getCompose().getInclude().forEach(include -> {
// assertTrue(include.hasConcept());
// });
// }
@Test
public void testCacheValueSetsAlreadyExpanded() throws Exception {
    Endpoint endpoint = uploadLocalServerEndpoint();
    RequestDetails details = Mockito.mock(RequestDetails.class);
    ValueSet vs = uploadValueSet("valueset/valueset-benzodiazepine-medications.json");
    StringAndListParam stringAndListParam = getStringAndListParamFromValueSet(vs);
    Resource outcomeResource = cacheValueSetsProvider.cacheValuesets(details, endpoint.getIdElement(), stringAndListParam, null, null);
    assertTrue(outcomeResource instanceof Bundle);
    Bundle resultBundle = (Bundle) outcomeResource;
    assertEquals(1, resultBundle.getEntry().size());
    BundleEntryComponent entry = resultBundle.getEntry().get(0);
    assertTrue(entry.getResponse().getLocation().startsWith("ValueSet/" + vs.getIdElement().getIdPart()));
    assertEquals("200 OK", entry.getResponse().getStatus());
}

Example 94 with BundleEntryComponent

use of org.hl7.fhir.dstu2016may.model.Bundle.BundleEntryComponent in project cqf-ruler by DBCG.

the class CacheValueSetsProviderIT method testCacheValueSetsNoCompose.

@Test
public void testCacheValueSetsNoCompose() throws Exception {
    Endpoint endpoint = uploadLocalServerEndpoint();
    RequestDetails details = Mockito.mock(RequestDetails.class);
    ValueSet vs = uploadValueSet("valueset/valueset-benzodiazepine-medications.json");
    assertTrue(vs.getCompose().getInclude().isEmpty());
    StringAndListParam stringAndListParam = getStringAndListParamFromValueSet(vs);
    Resource outcomeResource = cacheValueSetsProvider.cacheValuesets(details, endpoint.getIdElement(), stringAndListParam, null, null);
    assertTrue(outcomeResource instanceof Bundle);
    Bundle resultBundle = (Bundle) outcomeResource;
    assertEquals(1, resultBundle.getEntry().size());
    BundleEntryComponent entry = resultBundle.getEntry().get(0);
    assertTrue(entry.getResponse().getLocation().startsWith("ValueSet/" + vs.getIdElement().getIdPart()));
    assertEquals("200 OK", entry.getResponse().getStatus());
// ValueSet resultingValueSet = createClient(ourCtx,
// endpoint).read().resource(ValueSet.class).withId(vs.getIdElement()).execute();
// resultingValueSet not returning with a version
// assertTrue(resultingValueSet.getVersion().endsWith("-cached"));
}

Example 95 with BundleEntryComponent

use of org.hl7.fhir.dstu2016may.model.Bundle.BundleEntryComponent in project cqf-ruler by DBCG.

the class CacheValueSetsProviderIT method testCacheValueSetsAlreadyExpanded.

// Get help with this....
// @Test
// public void testCacheValueSetsExpandAndAddConcepts() throws Exception {
// Endpoint endpoint = uploadLocalServerEndpoint();
// RequestDetails details = Mockito.mock(RequestDetails.class);
// ValueSet vs = uploadValueSet("valueset/valueset-buprenorphine-and-methadone-medications.json");
// vs.getCompose().getInclude().forEach(include -> {
// assertTrue(!include.hasConcept());
// });
// StringAndListParam stringAndListParam = getStringAndListParamFromValueSet(vs);
// IGenericClient localClient = createClient(ourCtx, endpoint);
// // localClient.operation().onServer().named("updateCodeSystems").withNoParameters(Parameters.class).execute();
// Resource outcomeResource = cacheValueSetsProvider.cacheValuesets(details, endpoint.getIdElement(), stringAndListParam, null, null);
// assertTrue(outcomeResource instanceof Bundle);
// Bundle resultBundle = (Bundle) outcomeResource;
// assertTrue(resultBundle.getEntry().size() == 1);
// BundleEntryComponent entry = resultBundle.getEntry().get(0);
// assertTrue(entry.getResponse().getLocation().startsWith("ValueSet/" + vs.getIdElement().getIdPart()));
// assertTrue(entry.getResponse().getStatus().equals("200 OK"));
// ValueSet resultingValueSet = localClient.read().resource(ValueSet.class).withId(vs.getIdElement()).execute();
// resultingValueSet.getCompose().getInclude().forEach(include -> {
// assertTrue(include.hasConcept());
// });
// }
@Test
public void testCacheValueSetsAlreadyExpanded() throws Exception {
    Endpoint endpoint = uploadLocalServerEndpoint();
    RequestDetails details = Mockito.mock(RequestDetails.class);
    ValueSet vs = uploadValueSet("valueset/valueset-benzodiazepine-medications.json");
    StringAndListParam stringAndListParam = getStringAndListParamFromValueSet(vs);
    Resource outcomeResource = cacheValueSetsProvider.cacheValuesets(details, endpoint.getIdElement(), stringAndListParam, null, null);
    assertTrue(outcomeResource instanceof Bundle);
    Bundle resultBundle = (Bundle) outcomeResource;
    assertEquals(1, resultBundle.getEntry().size());
    BundleEntryComponent entry = resultBundle.getEntry().get(0);
    assertTrue(entry.getResponse().getLocation().startsWith("ValueSet/" + vs.getIdElement().getIdPart()));
    assertEquals("200 OK", entry.getResponse().getStatus());
}