Examples with JsonParser org.hl7.fhir.r5.elementmodel.JsonParser used on opensource projects

Example 16 with JsonParser

use of org.hl7.fhir.r5.elementmodel.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);
    }
}

Example 17 with JsonParser

use of org.hl7.fhir.r5.elementmodel.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;
}

Example 18 with JsonParser

use of org.hl7.fhir.r5.elementmodel.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.");
}

Example 19 with JsonParser

use of org.hl7.fhir.r5.elementmodel.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());
    }
}

Example 20 with JsonParser

use of org.hl7.fhir.r5.elementmodel.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);
}