Examples with FhirComponents org.hl7.davinci.r4.FhirComponents used on opensource projects

Example 1 with FhirComponents

use of org.hl7.davinci.r4.FhirComponents in project CRD by HL7-DaVinci.

the class CardBuilder method createSuggestionWithNote.

public static Suggestion createSuggestionWithNote(Card card, IBaseResource request, FhirComponentsT fhirComponents, String label, String description, boolean isRecommended, CoverageGuidance coverageGuidance) {
    Date now = new Date();
    Suggestion requestWithNoteSuggestion = new Suggestion();
    requestWithNoteSuggestion.setLabel(label);
    requestWithNoteSuggestion.setIsRecommended(isRecommended);
    List<Action> actionList = new ArrayList<>();
    // build the Annotation
    Annotation annotation = new Annotation();
    StringType author = new StringType();
    author.setValue(card.getSource().getLabel());
    annotation.setAuthor(author);
    String text = card.getSummary() + ": " + card.getDetail();
    annotation.setText(text);
    // set the date and time to now
    annotation.setTime(now);
    IBaseResource resource = FhirRequestProcessor.addNoteToRequest(request, annotation);
    try {
        // build the Extension with the coverage information
        Extension extension = new Extension();
        extension.setUrl("http://hl7.org/fhir/us/davinci-crd/StructureDefinition/ext-coverage-information");
        Extension coverageInfo = new Extension();
        coverageInfo.setUrl("coverageInfo").setValue(coverageGuidance.getCoding());
        extension.addExtension(coverageInfo);
        Extension coverageExtension = new Extension();
        Reference coverageReference = new Reference();
        // TODO: get the coverage from the prefetch and pass it into here instead of retrieving it from the request
        coverageReference.setReference(FhirRequestProcessor.getCoverageFromRequest(request).getReference());
        coverageExtension.setUrl("coverage").setValue(coverageReference);
        extension.addExtension(coverageExtension);
        Extension date = new Extension();
        date.setUrl("date").setValue(new DateType().setValue(now));
        extension.addExtension(date);
        Extension identifier = new Extension();
        String id = UUID.randomUUID().toString();
        identifier.setUrl("identifier").setValue(new StringType(id));
        extension.addExtension(identifier);
        resource = FhirRequestProcessor.addExtensionToRequest(resource, extension);
    } catch (NoCoverageException e) {
        logger.warn("No Coverage, discrete coverage extension will not be included: " + e.getMessage());
    }
    Action updateAction = new Action(fhirComponents);
    updateAction.setType(Action.TypeEnum.update);
    updateAction.setDescription(description);
    updateAction.setResource(resource);
    actionList.add(updateAction);
    requestWithNoteSuggestion.setActions(actionList);
    return requestWithNoteSuggestion;
}

Example 2 with FhirComponents

use of org.hl7.davinci.r4.FhirComponents in project CRD by HL7-DaVinci.

the class JacksonBundleDeserializer method deserialize.

@Override
public Bundle deserialize(JsonParser p, DeserializationContext ctxt) throws IOException, JsonProcessingException {
    FhirComponents fhirComponents = new FhirComponents();
    ObjectMapper mapper = (ObjectMapper) p.getCodec();
    JsonNode node = mapper.readTree(p);
    IBaseResource parsedResource = fhirComponents.getJsonParser().parseResource(mapper.writeValueAsString(node));
    return (Bundle) parsedResource;
}

Example 3 with FhirComponents

use of org.hl7.davinci.r4.FhirComponents in project CRD by HL7-DaVinci.

the class CdsConnectFileStore method processFhirFiles.

private void processFhirFiles(List<CdsConnectFile> files, String topic) {
    // process the fhir resource files
    // setup the proper FHIR Context for the version of FHIR we are dealing with
    FhirContext r4ctx = new org.hl7.davinci.r4.FhirComponents().getFhirContext();
    IParser r4parser = r4ctx.newJsonParser();
    // suppress the unknown element warnings
    r4parser.setParserErrorHandler(new SuppressParserErrorHandler());
    // process all of the files found within the topic/artifact
    for (CdsConnectFile file : files) {
        String path = file.getPath();
        String filename = file.getFilename();
        if (filename.endsWith(".json")) {
            logger.info("        process: FHIR Resource: " + filename);
            String[] parts = filename.split("-");
            if (parts.length > 2) {
                // String resourceType = parts[0];
                String fhirVersion = parts[1];
                String name = parts[2];
                IBaseResource baseResource = null;
                byte[] fileContents = file.getCqlBundle();
                if (fhirVersion.equalsIgnoreCase("R4")) {
                    baseResource = r4parser.parseResource(new ByteArrayInputStream(fileContents));
                }
                processFhirResource(baseResource, path, filename, fhirVersion, topic);
            }
        }
    }
}

Example 4 with FhirComponents

use of org.hl7.davinci.r4.FhirComponents in project CRD by HL7-DaVinci.

the class GitHubFileStore method processFhirFolder.

private void processFhirFolder(String topic, String fhirVersion, String fhirPath) {
    fhirVersion = fhirVersion.toUpperCase();
    logger.info("      GitHubFileStore::processFhirFolder(): " + fhirVersion + ": " + fhirPath);
    // setup the proper FHIR Context for the version of FHIR we are dealing with
    FhirContext ctx = null;
    if (fhirVersion.equalsIgnoreCase("R4")) {
        ctx = new org.hl7.davinci.r4.FhirComponents().getFhirContext();
    } else {
        logger.warn("unsupported FHIR version: " + fhirVersion + ", skipping folder");
        return;
    }
    IParser parser = ctx.newJsonParser();
    // suppress the unknown element warnings
    parser.setParserErrorHandler(new SuppressParserErrorHandler());
    for (String folder : connection.getDirectory(fhirPath)) {
        if (folder.equalsIgnoreCase("resources")) {
            String fullFolderPath = fhirPath + "/" + folder;
            for (String resource : connection.getDirectory(fullFolderPath)) {
                String filename = resource;
                String fullFilePath = fullFolderPath + "/" + filename;
                logger.info("        process: FHIR Resource: " + filename);
                String[] parts = filename.split("-");
                if (parts.length > 2) {
                    // = parts[0];
                    String resourceType;
                    if (!parts[1].equalsIgnoreCase(fhirVersion)) {
                        logger.warn("GitHubFileStore::processFhirFolder() warning: FhirVersion doesn't match!");
                        continue;
                    }
                    InputStream inputStream = connection.getFile(fullFilePath);
                    if (inputStream != null) {
                        IBaseResource baseResource = parser.parseResource(inputStream);
                        processFhirResource(baseResource, filename, filename, fhirVersion, topic);
                    } else {
                        logger.warn("could not find file: " + fullFilePath);
                        continue;
                    }
                }
            }
        }
    }
}

Example 5 with FhirComponents

use of org.hl7.davinci.r4.FhirComponents in project CRD by HL7-DaVinci.

the class CdsService method handleRequest.

/**
 * Performs generic operations for incoming requests of any type.
 *
 * @param request the generically typed incoming request
 * @return The response from the server
 */
public CdsResponse handleRequest(@Valid @RequestBody requestTypeT request, URL applicationBaseUrl) {
    // create the RequestLog
    RequestLog requestLog = new RequestLog(request, new Date().getTime(), this.fhirComponents.getFhirVersion().toString(), this.id, requestService, 5);
    // Parsed request
    requestLog.advanceTimeline(requestService);
    PrefetchHydrator prefetchHydrator = new PrefetchHydrator(this, request, this.fhirComponents);
    prefetchHydrator.hydrate();
    // hydrated
    requestLog.advanceTimeline(requestService);
    // Attempt a Query Batch Request to backfill missing attributes.
    if (myConfig.isQueryBatchRequest()) {
        QueryBatchRequest qbr = new QueryBatchRequest(this.fhirComponents);
        this.attempQueryBatchRequest(request, qbr);
    }
    logger.info("***** ***** request from requestLog: " + requestLog.toString());
    CdsResponse response = new CdsResponse();
    Gson gson = new Gson();
    final String jsonObject = gson.toJson(request.getPrefetch());
    logger.info("Final populated CRDPrefetch: " + jsonObject);
    // CQL Fetched
    List<CoverageRequirementRuleResult> lookupResults;
    try {
        lookupResults = this.createCqlExecutionContexts(request, fileStore, applicationBaseUrl.toString() + "/");
        requestLog.advanceTimeline(requestService);
    } catch (RequestIncompleteException e) {
        logger.warn("RequestIncompleteException " + request);
        logger.warn(e.getMessage() + "; summary card sent to client");
        response.addCard(CardBuilder.summaryCard(CardTypes.COVERAGE, e.getMessage()));
        requestLog.setCardListFromCards(response.getCards());
        requestLog.setResults(e.getMessage());
        requestService.edit(requestLog);
        return response;
    }
    // process the extension for the configuration
    // load hook configuration with default values
    Configuration hookConfiguration = new Configuration();
    Extension extension = request.getExtension();
    if (extension != null) {
        if (extension.getConfiguration() != null) {
            hookConfiguration = extension.getConfiguration();
        }
    }
    boolean errorCardOnEmpty = !(request instanceof OrderSelectRequest);
    // no error cards on empty when order-select request
    boolean foundApplicableRule = false;
    for (CoverageRequirementRuleResult lookupResult : lookupResults) {
        requestLog.addTopic(requestService, lookupResult.getTopic());
        CqlResultsForCard results = executeCqlAndGetRelevantResults(lookupResult.getContext(), lookupResult.getTopic());
        CoverageRequirements coverageRequirements = results.getCoverageRequirements();
        if (results.ruleApplies()) {
            foundApplicableRule = true;
            if (results.getCoverageRequirements().getApplies()) {
                // if prior auth already approved
                if (coverageRequirements.isPriorAuthApproved()) {
                    response.addCard(CardBuilder.priorAuthCard(results, results.getRequest(), fhirComponents, coverageRequirements.getPriorAuthId(), request.getContext().getPatientId(), lookupResult.getCriteria().getPayorId(), request.getContext().getUserId(), applicationBaseUrl.toString() + "/fhir/" + fhirComponents.getFhirVersion().toString(), fhirResourceRepository));
                } else if (coverageRequirements.isDocumentationRequired() || coverageRequirements.isPriorAuthRequired()) {
                    if (StringUtils.isNotEmpty(coverageRequirements.getQuestionnaireOrderUri()) || StringUtils.isNotEmpty(coverageRequirements.getQuestionnaireFaceToFaceUri()) || StringUtils.isNotEmpty(coverageRequirements.getQuestionnaireLabUri()) || StringUtils.isNotEmpty(coverageRequirements.getQuestionnaireProgressNoteUri()) || StringUtils.isNotEmpty(coverageRequirements.getQuestionnairePARequestUri()) || StringUtils.isNotEmpty(coverageRequirements.getQuestionnairePlanOfCareUri()) || StringUtils.isNotEmpty(coverageRequirements.getQuestionnaireDispenseUri()) || StringUtils.isNotEmpty(coverageRequirements.getQuestionnaireAdditionalUri())) {
                        List<Link> smartAppLinks = createQuestionnaireLinks(request, applicationBaseUrl, lookupResult, results);
                        if (coverageRequirements.isPriorAuthRequired()) {
                            Card card = CardBuilder.transform(CardTypes.PRIOR_AUTH, results, smartAppLinks);
                            card.addSuggestionsItem(CardBuilder.createSuggestionWithNote(card, results.getRequest(), fhirComponents, "Save Update To EHR", "Update original " + results.getRequest().fhirType() + " to add note", true, CoverageGuidance.ADMIN));
                            response.addCard(card);
                        } else if (coverageRequirements.isDocumentationRequired()) {
                            Card card = CardBuilder.transform(CardTypes.DTR_CLIN, results, smartAppLinks);
                            card.addSuggestionsItem(CardBuilder.createSuggestionWithNote(card, results.getRequest(), fhirComponents, "Save Update To EHR", "Update original " + results.getRequest().fhirType() + " to add note", true, CoverageGuidance.CLINICAL));
                            response.addCard(card);
                        }
                        // add a card for an alternative therapy if there is one
                        if (results.getAlternativeTherapy().getApplies() && hookConfiguration.getAlternativeTherapy()) {
                            try {
                                response.addCard(CardBuilder.alternativeTherapyCard(results.getAlternativeTherapy(), results.getRequest(), fhirComponents));
                            } catch (RuntimeException e) {
                                logger.warn("Failed to process alternative therapy: " + e.getMessage());
                            }
                        }
                    } else {
                        logger.warn("Unspecified Questionnaire URI; summary card sent to client");
                        response.addCard(CardBuilder.transform(CardTypes.COVERAGE, results));
                    }
                } else {
                    // no prior auth or documentation required
                    logger.info("Add the no doc or prior auth required card");
                    Card card = CardBuilder.transform(CardTypes.COVERAGE, results);
                    card.addSuggestionsItem(CardBuilder.createSuggestionWithNote(card, results.getRequest(), fhirComponents, "Save Update To EHR", "Update original " + results.getRequest().fhirType() + " to add note", true, CoverageGuidance.COVERED));
                    card.setSelectionBehavior(Card.SelectionBehaviorEnum.ANY);
                    response.addCard(card);
                }
            }
            // apply the DrugInteractions
            if (results.getDrugInteraction().getApplies()) {
                response.addCard(CardBuilder.drugInteractionCard(results.getDrugInteraction(), results.getRequest()));
            }
        }
    }
    // CQL Executed
    requestLog.advanceTimeline(requestService);
    if (errorCardOnEmpty) {
        if (!foundApplicableRule) {
            String msg = "No documentation rules found";
            logger.warn(msg + "; summary card sent to client");
            response.addCard(CardBuilder.summaryCard(CardTypes.COVERAGE, msg));
        }
        CardBuilder.errorCardIfNonePresent(CardTypes.COVERAGE, response);
    }
    // Ading card to requestLog
    requestLog.setCardListFromCards(response.getCards());
    requestService.edit(requestLog);
    return response;
}