use of org.hl7.fhir.dstu3.formats.JsonParser in project cqf-ruler by DBCG.
the class CdsHooksServlet method doPost.
@Override
@SuppressWarnings("deprecation")
protected void doPost(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
logger.info(request.getRequestURI());
try {
// validate that we are dealing with JSON
if (request.getContentType() == null || !request.getContentType().startsWith("application/json")) {
throw new ServletException(String.format("Invalid content type %s. Please use application/json.", request.getContentType()));
}
String baseUrl = this.myAppProperties.getServer_address();
String service = request.getPathInfo().replace("/", "");
JsonParser parser = new JsonParser();
Request cdsHooksRequest = new Request(service, parser.parse(request.getReader()).getAsJsonObject(), JsonHelper.getObjectRequired(getService(service), "prefetch"));
logger.info(cdsHooksRequest.getRequestJson().toString());
Hook hook = HookFactory.createHook(cdsHooksRequest);
String hookName = hook.getRequest().getHook();
logger.info("cds-hooks hook: {}", hookName);
logger.info("cds-hooks hook instance: {}", hook.getRequest().getHookInstance());
logger.info("cds-hooks maxCodesPerQuery: {}", this.getProviderConfiguration().getMaxCodesPerQuery());
logger.info("cds-hooks expandValueSets: {}", this.getProviderConfiguration().getExpandValueSets());
logger.info("cds-hooks searchStyle: {}", this.getProviderConfiguration().getSearchStyle());
logger.info("cds-hooks prefetch maxUriLength: {}", this.getProviderConfiguration().getMaxUriLength());
logger.info("cds-hooks local server address: {}", baseUrl);
logger.info("cds-hooks fhir server address: {}", hook.getRequest().getFhirServerUrl());
logger.info("cds-hooks cql_logging_enabled: {}", this.getProviderConfiguration().getCqlLoggingEnabled());
PlanDefinition planDefinition = read(Ids.newId(PlanDefinition.class, hook.getRequest().getServiceName()));
AtomicBoolean planDefinitionHookMatchesRequestHook = new AtomicBoolean(false);
planDefinition.getAction().forEach(action -> {
action.getTrigger().forEach(trigger -> {
if (hookName.equals(trigger.getName())) {
planDefinitionHookMatchesRequestHook.set(true);
return;
}
});
if (planDefinitionHookMatchesRequestHook.get()) {
return;
}
});
if (!planDefinitionHookMatchesRequestHook.get()) {
throw new ServletException("ERROR: Request hook does not match the service called.");
}
// No tenant information available, so create local system request
RequestDetails requestDetails = new SystemRequestDetails();
LibraryLoader libraryLoader = libraryLoaderFactory.create(Lists.newArrayList(jpaLibraryContentProviderFactory.create(requestDetails)));
CanonicalType canonical = planDefinition.getLibrary().get(0);
Library library = search(Library.class, Searches.byCanonical(canonical)).single();
org.cqframework.cql.elm.execution.Library elm = libraryLoader.load(new VersionedIdentifier().withId(library.getName()).withVersion(library.getVersion()));
Context context = new Context(elm);
context.setDebugMap(this.getDebugMap());
// provider case
// No tenant information available for cds-hooks
TerminologyProvider serverTerminologyProvider = myJpaTerminologyProviderFactory.create(requestDetails);
context.registerDataProvider("http://hl7.org/fhir", // TODO make sure tooling
fhirRetrieveProviderFactory.create(requestDetails, serverTerminologyProvider));
// handles remote
context.registerTerminologyProvider(serverTerminologyProvider);
context.registerLibraryLoader(libraryLoader);
context.setContextValue("Patient", hook.getRequest().getContext().getPatientId().replace("Patient/", ""));
context.setExpressionCaching(true);
EvaluationContext<PlanDefinition> evaluationContext = new R4EvaluationContext(hook, FhirContext.forCached(FhirVersionEnum.R4).newRestfulGenericClient(baseUrl), context, elm, planDefinition, this.getProviderConfiguration(), this.modelResolver);
this.setAccessControlHeaders(response);
response.setHeader("Content-Type", ContentType.APPLICATION_JSON.getMimeType());
R4HookEvaluator evaluator = new R4HookEvaluator(this.modelResolver);
String jsonResponse = toJsonResponse(evaluator.evaluate(evaluationContext));
logger.info(jsonResponse);
response.getWriter().println(jsonResponse);
} catch (BaseServerResponseException e) {
this.setAccessControlHeaders(response);
// This will be overwritten with the correct status code downstream if needed.
response.setStatus(500);
response.getWriter().println("ERROR: Exception connecting to remote server.");
this.printMessageAndCause(e, response);
this.handleServerResponseException(e, response);
this.printStackTrack(e, response);
logger.error(e.toString());
} catch (DataProviderException e) {
this.setAccessControlHeaders(response);
// This will be overwritten with the correct status code downstream if needed.
response.setStatus(500);
response.getWriter().println("ERROR: Exception in DataProvider.");
this.printMessageAndCause(e, response);
if (e.getCause() != null && (e.getCause() instanceof BaseServerResponseException)) {
this.handleServerResponseException((BaseServerResponseException) e.getCause(), response);
}
this.printStackTrack(e, response);
logger.error(e.toString());
} catch (CqlException e) {
this.setAccessControlHeaders(response);
// This will be overwritten with the correct status code downstream if needed.
response.setStatus(500);
response.getWriter().println("ERROR: Exception in CQL Execution.");
this.printMessageAndCause(e, response);
if (e.getCause() != null && (e.getCause() instanceof BaseServerResponseException)) {
this.handleServerResponseException((BaseServerResponseException) e.getCause(), response);
}
this.printStackTrack(e, response);
logger.error(e.toString());
} catch (Exception e) {
logger.error(e.toString());
throw new ServletException("ERROR: Exception in cds-hooks processing.", e);
}
}
use of org.hl7.fhir.dstu3.formats.JsonParser 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;
}
use of org.hl7.fhir.dstu3.formats.JsonParser in project Gravity-SDOH-Exchange-RI by FHIR.
the class TaskPollingService method demoRunQRThroughStructureMap.
/*
A TEST polling service, implemented during January 2022 Connectathon, that automatically runs questionnaireResponse
resources through a StructureMap. If any exception occurs - just ignore it.
*/
public void demoRunQRThroughStructureMap() {
log.info("Looking for TOP 3 Patient QuestionnaireResponse resources without derived Observations...");
// TODO use repository instead
Bundle tasksBundle = openEhrClient.search().forResource(QuestionnaireResponse.class).where(new StringClientParam(Constants.PARAM_PROFILE).matches().value(SDOHProfiles.QUESTIONNAIRE_RESPONSE)).revInclude(Observation.INCLUDE_DERIVED_FROM.setRecurse(false)).sort().descending(QuestionnaireResponse.AUTHORED).count(3).returnBundle(Bundle.class).execute();
List<QuestionnaireResponse> responses = FhirUtil.getFromBundle(tasksBundle, QuestionnaireResponse.class, Bundle.SearchEntryMode.MATCH);
Set<String> derivedFrom = FhirUtil.getFromBundle(tasksBundle, Observation.class, Bundle.SearchEntryMode.INCLUDE).stream().map(o -> o.getDerivedFromFirstRep().getReferenceElement().getIdPart()).collect(Collectors.toSet());
if (responses.size() != derivedFrom.size()) {
log.info("Found " + (responses.size() - derivedFrom.size()) + " QuestionnaireResponse resources without observations.");
List<QuestionnaireResponse> newResponses = responses.stream().filter(qr -> !derivedFrom.contains(qr.getIdElement().getIdPart())).collect(Collectors.toList());
for (QuestionnaireResponse nr : newResponses) {
log.info("Converting QuestionnaireResponse with id: " + nr.getIdElement().getIdPart());
try {
// TODO move parser logic within the convert service. Use resources instead
JSONParser parser = new JSONParser(JSONParser.MODE_JSON_SIMPLE);
Map<String, Object> result = convertService.convert((JSONObject) parser.parse(fhirContext.newJsonParser().encodeResourceToString(nr)));
Bundle bundle = (Bundle) fhirContext.newJsonParser().parseResource(new JSONObject(result).toJSONString());
bundle.getEntry().forEach(e -> e.setRequest(new Bundle.BundleEntryRequestComponent().setMethod(Bundle.HTTPVerb.POST).setUrl(e.getResource().getClass().getSimpleName())));
openEhrClient.transaction().withBundle(bundle).execute();
} catch (Exception exc) {
// Just ignore this specific resource and go to the next one
log.warn(exc.getMessage(), exc);
}
}
}
log.info("QuestionnaireResponse update process finished.");
}
use of org.hl7.fhir.dstu3.formats.JsonParser in project Gravity-SDOH-Exchange-RI by FHIR.
the class ConvertService method convertToBundle.
private String convertToBundle(JSONObject questionnaireResponse, String mapUri) {
try (ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream()) {
Element element = validationEngine.transform(questionnaireResponse.toString().getBytes(), Manager.FhirFormat.JSON, mapUri);
new JsonParser(validationEngine.getContext()).compose(element, byteArrayOutputStream, org.hl7.fhir.r5.formats.IParser.OutputStyle.PRETTY, null);
return byteArrayOutputStream.toString();
} catch (IOException e) {
throw new IllegalStateException("QuestionnaireResponse with id cannot be parsed.", e.getCause());
}
}
use of org.hl7.fhir.dstu3.formats.JsonParser in project org.hl7.fhir.core by hapifhir.
the class ExtensionDefinitionGenerator method loadResource.
private Resource loadResource(InputStream inputStream, FHIRVersion v) throws IOException, FHIRException {
if (v == FHIRVersion._3_0_1) {
org.hl7.fhir.dstu3.model.Resource res = new org.hl7.fhir.dstu3.formats.JsonParser().parse(inputStream);
return VersionConvertorFactory_30_40.convertResource(res, new BaseAdvisor_30_40(false));
} else if (v == FHIRVersion._1_4_0) {
org.hl7.fhir.dstu2016may.model.Resource res = new org.hl7.fhir.dstu2016may.formats.JsonParser().parse(inputStream);
return VersionConvertorFactory_14_40.convertResource(res);
} else if (v == FHIRVersion._1_0_2) {
org.hl7.fhir.dstu2.model.Resource res = new org.hl7.fhir.dstu2.formats.JsonParser().parse(inputStream);
BaseAdvisor_10_40 advisor = new IGR2ConvertorAdvisor();
return VersionConvertorFactory_10_40.convertResource(res, advisor);
} else if (v == FHIRVersion._4_0_0) {
return new JsonParser().parse(inputStream);
} else
throw new Error("Unsupported version " + v);
}
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