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

Example 11 with JsonParser

use of org.hl7.fhir.r5.elementmodel.JsonParser in project kindling by HL7.

the class PageProcessor method r2Json.

private String r2Json(ValueSet vs) throws Exception {
    ByteArrayOutputStream bytes = new ByteArrayOutputStream();
    IParser json = new JsonParser().setOutputStyle(OutputStyle.PRETTY);
    json.setSuppressXhtml("Snipped for Brevity");
    json.compose(bytes, vs);
    return new String(bytes.toByteArray());
}

Example 12 with JsonParser

use of org.hl7.fhir.r5.elementmodel.JsonParser in project kindling by HL7.

the class BindingsParser method loadValueSet.

private ValueSet loadValueSet(String ref, String committee) throws Exception {
    String folder = new File(filename).getParent();
    String srcName;
    IParser p;
    if (new File(Utilities.path(folder, ref + ".xml")).exists()) {
        p = new XmlParser();
        srcName = Utilities.path(folder, ref + ".xml");
    } else if (new File(Utilities.path(folder, ref + ".json")).exists()) {
        p = new JsonParser();
        srcName = Utilities.path(folder, ref + ".json");
    } else
        throw new Exception("Unable to find source for " + ref + " in " + filename + " (" + Utilities.path(folder, ref + ".xml/json)"));
    FileInputStream input = new FileInputStream(srcName);
    try {
        ValueSet result = ValueSetUtilities.makeShareable((ValueSet) p.parse(input));
        result.setId(ref.substring(9));
        if (!result.hasExperimental())
            result.setExperimental(false);
        // if (!result.hasUrl())
        result.setUrl("http://hl7.org/fhir/ValueSet/" + ref.substring(9));
        if (!result.hasVersion() || result.getUrl().startsWith("http://hl7.org/fhir"))
            result.setVersion(version);
        if (!Utilities.noString(committee)) {
            if (!result.hasExtension(ToolingExtensions.EXT_WORKGROUP)) {
                result.addExtension().setUrl(ToolingExtensions.EXT_WORKGROUP).setValue(new CodeType(committee));
            } else {
                String ec = ToolingExtensions.readStringExtension(result, ToolingExtensions.EXT_WORKGROUP);
                if (!ec.equals(committee))
                    System.out.println("ValueSet " + result.getUrl() + " WG mismatch 1: is " + ec + ", want to set to " + committee);
            }
        }
        result.setUserData("filename", "valueset-" + ref.substring(9));
        result.setUserData("path", "valueset-" + ref.substring(9) + ".html");
        new CodeSystemConvertor(codeSystems).convert(p, result, srcName, packageInfo);
        return result;
    } finally {
        IOUtils.closeQuietly(input);
    }
}

Example 13 with JsonParser

use of org.hl7.fhir.r5.elementmodel.JsonParser in project kindling by HL7.

the class Publisher method buildLoincExample.

private String buildLoincExample(String filename) throws FileNotFoundException, Exception {
    LoincToDEConvertor conv = new LoincToDEConvertor();
    conv.setDefinitions(Utilities.path(page.getFolders().srcDir, "loinc", "loincS.xml"));
    conv.process();
    IParser xml = new XmlParser().setOutputStyle(OutputStyle.PRETTY);
    FileOutputStream s = new FileOutputStream(Utilities.path(page.getFolders().dstDir, filename + ".xml"));
    xml.compose(s, conv.getBundle());
    s.close();
    IParser json = new JsonParser().setOutputStyle(OutputStyle.PRETTY);
    s = new FileOutputStream(Utilities.path(page.getFolders().dstDir, filename + ".json"));
    json.compose(s, conv.getBundle());
    s.close();
    return "Loinc Narrative";
}

Example 14 with JsonParser

use of org.hl7.fhir.r5.elementmodel.JsonParser in project kindling by HL7.

the class Publisher method produceTypeProfile.

private void produceTypeProfile(TypeDefn type) throws Exception {
    // ProfileDefn p = new ProfileDefn();
    // p.putMetadata("id", type.getName());
    // p.putMetadata("name", "Basic StructureDefinition for " + type.getName());
    // p.putMetadata("author.name", "FHIR Specification");
    // p.putMetadata("author.ref", "http://hl7.org/fhir");
    // p.putMetadata("description", "Basic StructureDefinition for " + type.getName() + " for validation support");
    // p.putMetadata("status", "draft");
    // p.putMetadata("date", new SimpleDateFormat("yyyy-MM-dd", new Locale("en", "US")).format(new Date()));
    // p.getElements().add(type);
    // ProfileGenerator pgen = new ProfileGenerator(page.getDefinitions());
    // String fn = "type-" + type.getName() + ".profile.xml";
    // StructureDefinition rp = pgen.generate(p, "type-" + type.getName() + ".profile", "<div>Type definition for " + type.getName() + " from <a href=\"http://hl7.org/fhir/datatypes.html#" + type.getName()
    // + "\">FHIR Specification</a></div>");
    String fn = type.getName().toLowerCase() + ".profile.xml";
    StructureDefinition rp = type.getProfile();
    FileOutputStream s = new FileOutputStream(page.getFolders().dstDir + fn);
    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, rp);
    s.close();
    s = new FileOutputStream(page.getFolders().dstDir + Utilities.changeFileExt(fn, ".canonical.xml"));
    new XmlParser().setOutputStyle(OutputStyle.CANONICAL).compose(s, rp);
    s.close();
    s = new FileOutputStream(page.getFolders().dstDir + Utilities.changeFileExt(fn, ".json"));
    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(s, rp);
    s.close();
    s = new FileOutputStream(page.getFolders().dstDir + Utilities.changeFileExt(fn, ".canonical.json"));
    new JsonParser().setOutputStyle(OutputStyle.CANONICAL).compose(s, rp);
    s.close();
    Utilities.copyFile(new CSFile(page.getFolders().dstDir + fn), new CSFile(Utilities.path(page.getFolders().dstDir, "examples", fn)));
    addToResourceFeed(rp, page.getTypeBundle(), fn);
    // saveAsPureHtml(rp, new FileOutputStream(page.getFolders().dstDir+ "html"
    // + File.separator + "datatypes.html"));
    cloneToXhtml(type.getName().toLowerCase() + ".profile", "StructureDefinition for " + type.getName(), false, "profile-instance:type:" + type.getName(), "Type", null, wg("mnm"));
    jsonToXhtml(type.getName().toLowerCase() + ".profile", "StructureDefinition for " + type.getName(), resource2Json(rp), "profile-instance:type:" + type.getName(), "Type", null, wg("mnm"));
    ttlToXhtml(type.getName().toLowerCase() + ".profile", "StructureDefinition for " + type.getName(), resource2Ttl(rp), "profile-instance:type:" + type.getName(), "Type", null, wg("mnm"));
    String shex = new ShExGenerator(page.getWorkerContext()).generate(HTMLLinkPolicy.NONE, rp);
    TextFile.stringToFile(shex, Utilities.changeFileExt(page.getFolders().dstDir + fn, ".shex"));
    shexToXhtml(type.getName().toLowerCase(), "ShEx statement for " + type.getName(), shex, "profile-instance:type:" + type.getName(), "Type", null, wg("mnm"));
}

Example 15 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();
        JsonObject requestJson = parser.parse(request.getReader()).getAsJsonObject();
        logger.info(requestJson.toString());
        Request cdsHooksRequest = new Request(service, requestJson, JsonHelper.getObjectRequired(getService(service), "prefetch"));
        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.getTriggerDefinition().forEach(triggerDefn -> {
                if (hookName.equals(triggerDefn.getEventName())) {
                    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)));
        Reference reference = planDefinition.getLibrary().get(0);
        Library library = read(reference.getReferenceElement());
        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);
        // TODO make sure tooling handles remote
        context.registerDataProvider("http://hl7.org/fhir", fhirRetrieveProviderFactory.create(requestDetails, serverTerminologyProvider));
        context.registerTerminologyProvider(serverTerminologyProvider);
        context.registerLibraryLoader(libraryLoader);
        context.setContextValue("Patient", hook.getRequest().getContext().getPatientId().replace("Patient/", ""));
        context.setExpressionCaching(true);
        EvaluationContext<PlanDefinition> evaluationContext = new Stu3EvaluationContext(hook, FhirContext.forCached(FhirVersionEnum.DSTU3).newRestfulGenericClient(baseUrl), context, elm, planDefinition, this.getProviderConfiguration(), this.modelResolver);
        this.setAccessControlHeaders(response);
        response.setHeader("Content-Type", ContentType.APPLICATION_JSON.getMimeType());
        Stu3HookEvaluator evaluator = new Stu3HookEvaluator(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);
    }
}