Examples with Resource org.alfresco.event.sdk.model.v1.model.Resource used on opensource projects

Example 96 with Resource

use of org.alfresco.event.sdk.model.v1.model.Resource in project cqf-ruler by DBCG.

the class CqlExecutionProvider method resolveResult.

@SuppressWarnings("unchecked")
private void resolveResult(RequestDetails theRequestDetails, EvaluationResult evalResult, Parameters result) {
    try {
        Object res = evalResult.forExpression("return");
        if (res == null) {
            result.addParameter().setName("value").setValue(new StringType("null"));
        } else if (res instanceof List<?>) {
            if (!((List<?>) res).isEmpty() && ((List<?>) res).get(0) instanceof Resource) {
                result.addParameter().setName("value").setResource(bundler.bundle((Iterable<Resource>) res, theRequestDetails.getFhirServerBase()));
            } else {
                result.addParameter().setName("value").setValue(new StringType(res.toString()));
            }
        } else if (res instanceof Iterable) {
            result.addParameter().setName("value").setResource(bundler.bundle((Iterable<Resource>) res, theRequestDetails.getFhirServerBase()));
        } else if (res instanceof Resource) {
            result.addParameter().setName("value").setResource((Resource) res);
        } else if (res instanceof Type) {
            result.addParameter().setName("value").setValue((Type) res);
        } else {
            result.addParameter().setName("value").setValue(new StringType(res.toString()));
        }
        result.addParameter().setName("resultType").setValue(new StringType(resolveType(res)));
    } catch (RuntimeException re) {
        re.printStackTrace();
        String message = re.getMessage() != null ? re.getMessage() : re.getClass().getName();
        result.addParameter().setName("error").setValue(new StringType(message));
    }
}

Example 97 with Resource

use of org.alfresco.event.sdk.model.v1.model.Resource in project cqf-ruler by DBCG.

the class LibraryEvaluationProvider method evaluate.

@SuppressWarnings({ "unchecked" })
@Operation(name = "$evaluate", idempotent = true, type = Library.class)
public Bundle evaluate(@IdParam IdType theId, @OperationParam(name = "patientId") String patientId, @OperationParam(name = "periodStart") String periodStart, @OperationParam(name = "periodEnd") String periodEnd, @OperationParam(name = "productLine") String productLine, @OperationParam(name = "terminologyEndpoint") Endpoint terminologyEndpoint, @OperationParam(name = "dataEndpoint") Endpoint dataEndpoint, @OperationParam(name = "context") String contextParam, @OperationParam(name = "executionResults") String executionResults, @OperationParam(name = "parameters") Parameters parameters, @OperationParam(name = "additionalData") Bundle additionalData, RequestDetails theRequestDetails) {
    log.info("Library evaluation started..");
    if (patientId == null && contextParam != null && contextParam.equals("Patient")) {
        log.error("Patient id null");
        throw new IllegalArgumentException("Must specify a patientId when executing in Patient context.");
    }
    Bundle libraryBundle = new Bundle();
    Library theResource = null;
    if (additionalData != null) {
        for (Bundle.BundleEntryComponent entry : additionalData.getEntry()) {
            if (entry.getResource().fhirType().equals("Library")) {
                libraryBundle.addEntry(entry);
                if (entry.getResource().getIdElement().equals(theId)) {
                    theResource = (Library) entry.getResource();
                }
            }
        }
    }
    if (theResource == null) {
        theResource = read(theId, theRequestDetails);
    }
    VersionedIdentifier libraryIdentifier = new VersionedIdentifier().withId(theResource.getName()).withVersion(theResource.getVersion());
    TerminologyProvider terminologyProvider;
    if (terminologyEndpoint != null) {
        IGenericClient client = Clients.forEndpoint(getFhirContext(), terminologyEndpoint);
        terminologyProvider = new R4FhirTerminologyProvider(client);
    } else {
        terminologyProvider = myJpaTerminologyProviderFactory.create(new SystemRequestDetails());
    }
    DataProvider dataProvider;
    if (dataEndpoint != null) {
        List<RetrieveProvider> retrieveProviderList = new ArrayList<>();
        IGenericClient client = Clients.forEndpoint(dataEndpoint);
        RestFhirRetrieveProvider retriever = new RestFhirRetrieveProvider(new SearchParameterResolver(getFhirContext()), client);
        retriever.setTerminologyProvider(terminologyProvider);
        if (terminologyEndpoint == null || (terminologyEndpoint != null && !terminologyEndpoint.getAddress().equals(dataEndpoint.getAddress()))) {
            retriever.setExpandValueSets(true);
        }
        retrieveProviderList.add(retriever);
        if (additionalData != null) {
            BundleRetrieveProvider bundleProvider = new BundleRetrieveProvider(getFhirContext(), additionalData);
            bundleProvider.setTerminologyProvider(terminologyProvider);
            retrieveProviderList.add(bundleProvider);
            PriorityRetrieveProvider priorityProvider = new PriorityRetrieveProvider(retrieveProviderList);
            dataProvider = new CompositeDataProvider(myModelResolver, priorityProvider);
        } else {
            dataProvider = new CompositeDataProvider(myModelResolver, retriever);
        }
    } else {
        List<RetrieveProvider> retrieveProviderList = new ArrayList<>();
        JpaFhirRetrieveProvider retriever = new JpaFhirRetrieveProvider(getDaoRegistry(), new SearchParameterResolver(getFhirContext()));
        retriever.setTerminologyProvider(terminologyProvider);
        // Assume it's a different server, therefore need to expand.
        if (terminologyEndpoint != null) {
            retriever.setExpandValueSets(true);
        }
        retrieveProviderList.add(retriever);
        if (additionalData != null) {
            BundleRetrieveProvider bundleProvider = new BundleRetrieveProvider(getFhirContext(), additionalData);
            bundleProvider.setTerminologyProvider(terminologyProvider);
            retrieveProviderList.add(bundleProvider);
            PriorityRetrieveProvider priorityProvider = new PriorityRetrieveProvider(retrieveProviderList);
            dataProvider = new CompositeDataProvider(myModelResolver, priorityProvider);
        } else {
            dataProvider = new CompositeDataProvider(myModelResolver, retriever);
        }
    }
    LibraryContentProvider bundleLibraryProvider = new BundleFhirLibraryContentProvider(this.getFhirContext(), libraryBundle, adapterFactory, libraryVersionSelector);
    LibraryContentProvider jpaLibraryContentProvider = this.myJpaLibraryContentProviderFactory.create(theRequestDetails);
    List<LibraryContentProvider> sourceProviders = new ArrayList<LibraryContentProvider>(Arrays.asList(bundleLibraryProvider, jpaLibraryContentProvider));
    LibraryLoader libraryLoader = this.myLibraryLoaderFactory.create(sourceProviders);
    CqlEngine engine = new CqlEngine(libraryLoader, Collections.singletonMap("http://hl7.org/fhir", dataProvider), terminologyProvider);
    Map<String, Object> resolvedParameters = new HashMap<>();
    if (parameters != null) {
        for (Parameters.ParametersParameterComponent pc : parameters.getParameter()) {
            resolvedParameters.put(pc.getName(), pc.getValue());
        }
    }
    if (periodStart != null && periodEnd != null) {
        // resolve the measurement period
        Interval measurementPeriod = new Interval(Operations.resolveRequestDate(periodStart, true), true, Operations.resolveRequestDate(periodEnd, false), true);
        resolvedParameters.put("Measurement Period", new Interval(DateTime.fromJavaDate((Date) measurementPeriod.getStart()), true, DateTime.fromJavaDate((Date) measurementPeriod.getEnd()), true));
    }
    if (productLine != null) {
        resolvedParameters.put("Product Line", productLine);
    }
    EvaluationResult evalResult = engine.evaluate(libraryIdentifier, null, Pair.of(contextParam != null ? contextParam : "Unspecified", patientId == null ? "null" : patientId), resolvedParameters, this.getDebugMap());
    List<Resource> results = new ArrayList<>();
    FhirMeasureBundler bundler = new FhirMeasureBundler();
    if (evalResult != null && evalResult.expressionResults != null) {
        for (Map.Entry<String, Object> def : evalResult.expressionResults.entrySet()) {
            Parameters result = new Parameters();
            try {
                result.setId(def.getKey());
                Object res = def.getValue();
                if (res == null) {
                    result.addParameter().setName("value").setValue(new StringType("null"));
                } else if (res instanceof List<?>) {
                    if (((List<?>) res).size() > 0 && ((List<?>) res).get(0) instanceof Resource) {
                        if (executionResults != null && executionResults.equals("Summary")) {
                            result.addParameter().setName("value").setValue(new StringType(((Resource) ((List<?>) res).get(0)).getIdElement().getResourceType() + "/" + ((Resource) ((List<?>) res).get(0)).getIdElement().getIdPart()));
                        } else {
                            result.addParameter().setName("value").setResource(bundler.bundle((Iterable<Resource>) res, theRequestDetails.getFhirServerBase()));
                        }
                    } else {
                        result.addParameter().setName("value").setValue(new StringType(res.toString()));
                    }
                } else if (res instanceof Iterable) {
                    result.addParameter().setName("value").setResource(bundler.bundle((Iterable<Resource>) res, theRequestDetails.getFhirServerBase()));
                } else if (res instanceof Resource) {
                    if (executionResults != null && executionResults.equals("Summary")) {
                        result.addParameter().setName("value").setValue(new StringType(((Resource) res).getIdElement().getResourceType() + "/" + ((Resource) res).getIdElement().getIdPart()));
                    } else {
                        result.addParameter().setName("value").setResource((Resource) res);
                    }
                } else if (res instanceof Type) {
                    result.addParameter().setName("value").setValue((Type) res);
                } else {
                    result.addParameter().setName("value").setValue(new StringType(res.toString()));
                }
                result.addParameter().setName("resultType").setValue(new StringType(resolveType(res)));
            } catch (RuntimeException re) {
                re.printStackTrace();
                String message = re.getMessage() != null ? re.getMessage() : re.getClass().getName();
                result.addParameter().setName("error").setValue(new StringType(message));
            }
            results.add(result);
        }
    }
    return bundler.bundle(results, theRequestDetails.getFhirServerBase());
}

Example 98 with Resource

use of org.alfresco.event.sdk.model.v1.model.Resource 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 99 with Resource

use of org.alfresco.event.sdk.model.v1.model.Resource in project cqf-ruler by DBCG.

the class Stu3EvaluationContext method applyCqlToResources.

@Override
List<Object> applyCqlToResources(List<Object> resources) {
    if (resources == null || resources.isEmpty()) {
        return new ArrayList<>();
    }
    Bundle bundle = new Bundle();
    for (Object res : resources) {
        bundle.addEntry(new Bundle.BundleEntryComponent().setResource((Resource) res));
    }
    Parameters parameters = new Parameters();
    parameters.addParameter().setName("resourceBundle").setResource(bundle);
    Parameters ret = this.getSystemFhirClient().operation().onType(Bundle.class).named("$apply-cql").withParameters(parameters).execute();
    Bundle appliedResources = (Bundle) ret.getParameter().get(0).getResource();
    return appliedResources.getEntry().stream().map(Bundle.BundleEntryComponent::getResource).collect(Collectors.toList());
}

Example 100 with Resource

use of org.alfresco.event.sdk.model.v1.model.Resource in project cqf-ruler by DBCG.

the class CacheValueSetsProvider method cacheValuesets.

/**
 * Using basic authentication this {@link Operation Operation} will update
 * any {@link ValueSet Valueset} listed given the {@link Endpoint Endpoint}
 * provided.
 * Any Valuesets that require expansion will be expanded.
 *
 * @param details    the {@link RequestDetails RequestDetails}
 * @param endpointId the {@link Endpoint Endpoint} id
 * @param valuesets  the {@link StringAndListParam list} of {@link ValueSet
 *                   Valueset} ids
 * @param userName   the userName
 * @param password   the password
 * @return the {@link OperationOutcome OperationOutcome} or the resulting
 *         {@link Bundle Bundle}
 */
@Description(shortDefinition = "$cache-valuesets", value = "Using basic authentication this Operation will update any Valueset listed given the Endpoint provided. Any Valuesets that require expansion will be expanded.", example = "Endpoint/example-id/$cache-valuesets?valuesets=valuesetId1&valuesets=valuesetId2&user=user&password=password")
@Operation(name = "$cache-valuesets", idempotent = true, type = Endpoint.class)
public Resource cacheValuesets(RequestDetails details, @IdParam IdType endpointId, @OperationParam(name = "valuesets") StringAndListParam valuesets, @OperationParam(name = "user") String userName, @OperationParam(name = "pass") String password) {
    Endpoint endpoint = null;
    try {
        endpoint = this.endpointDao.read(endpointId);
        if (endpoint == null) {
            return createErrorOutcome("Could not find Endpoint/" + endpointId);
        }
    } catch (Exception e) {
        return createErrorOutcome("Could not find Endpoint/" + endpointId + "\n" + e);
    }
    IGenericClient client = Clients.forEndpoint(ourCtx, endpoint);
    if (userName != null || password != null) {
        if (userName == null) {
            return createErrorOutcome("Password was provided, but not a user name.");
        } else if (password == null) {
            return createErrorOutcome("User name was provided, but not a password.");
        }
        BasicAuthInterceptor basicAuth = new BasicAuthInterceptor(userName, password);
        client.registerInterceptor(basicAuth);
    // TODO - more advanced security like bearer tokens, etc...
    }
    try {
        Bundle bundleToPost = new Bundle();
        for (StringOrListParam params : valuesets.getValuesAsQueryTokens()) {
            for (StringParam valuesetId : params.getValuesAsQueryTokens()) {
                bundleToPost.addEntry().setRequest(new Bundle.BundleEntryRequestComponent().setMethod(Bundle.HTTPVerb.PUT).setUrl("ValueSet/" + valuesetId.getValue())).setResource(resolveValueSet(client, valuesetId.getValue()));
            }
        }
        return (Resource) systemDao.transaction(details, bundleToPost);
    } catch (Exception e) {
        return createErrorOutcome(e.getMessage());
    }
}