Examples with Retrieve org.hl7.elm.r1.Retrieve used on opensource projects

Example 1 with Retrieve

use of org.hl7.elm.r1.Retrieve in project beneficiary-fhir-data by CMSgov.

the class AbstractR4ResourceProvider method createBundleFor.

/**
 * Creates a Bundle of resources for the given data using the given {@link ResourceTypeV2}.
 *
 * @param resourceTypes The {@link ResourceTypeV2} data to retrieve.
 * @param mbi The mbi to look up associated data for.
 * @param isHashed Denotes if the given mbi is hashed.
 * @param lastUpdated Date range of desired lastUpdate values to retrieve data for.
 * @param serviceDate Date range of the desired service date to retrieve data for.
 * @return A Bundle with data found using the provided parameters.
 */
@VisibleForTesting
Bundle createBundleFor(Set<ResourceTypeV2<T>> resourceTypes, String mbi, boolean isHashed, boolean excludeSamhsa, DateRangeParam lastUpdated, DateRangeParam serviceDate) {
    List<T> resources = new ArrayList<>();
    for (ResourceTypeV2<T> type : resourceTypes) {
        List<?> entities;
        entities = claimDao.findAllByMbiAttribute(type.getEntityClass(), type.getEntityMbiRecordAttribute(), mbi, isHashed, lastUpdated, serviceDate, type.getEntityEndDateAttribute());
        resources.addAll(entities.stream().filter(e -> !excludeSamhsa || hasNoSamhsaData(metricRegistry, e)).map(e -> type.getTransformer().transform(metricRegistry, e)).collect(Collectors.toList()));
    }
    Bundle bundle = new Bundle();
    resources.forEach(c -> {
        Bundle.BundleEntryComponent entry = bundle.addEntry();
        entry.setResource((Resource) c);
    });
    return bundle;
}

Example 2 with Retrieve

use of org.hl7.elm.r1.Retrieve in project kindling by HL7.

the class PageProcessor method getSnomedCTConcept.

public void getSnomedCTConcept(Map<String, SnomedConceptUsage> concepts, ValueSet vs, ConceptSetFilterComponent c) throws Exception {
    ConceptDefinitionComponent def = workerContext.getCodeDefinition("http://snomed.info/sct", c.getValue());
    if (def == null) {
        throw new Exception("Unable to retrieve definition for SNOMED code: " + c.getValue());
    }
    String d = def.getDisplay();
    if (concepts.containsKey(c.getValue()))
        concepts.get(c.getValue()).update(d, vs);
    else
        concepts.put(c.getValue(), new SnomedConceptUsage(c.getValue(), d, vs));
}

Example 3 with Retrieve

use of org.hl7.elm.r1.Retrieve in project kindling by HL7.

the class SourceParser method ftpFetch.

private byte[] ftpFetch(String n) throws Exception {
    URI url = new URI(n);
    String server = url.getHost();
    int port = 21;
    FTPClient ftpClient = new FTPClient();
    ftpClient.connect(server, port);
    ftpClient.login("anonymous", "anonymous");
    ftpClient.enterLocalPassiveMode();
    ftpClient.setFileType(FTP.BINARY_FILE_TYPE);
    // APPROACH #1: using retrieveFile(String, OutputStream)
    String remoteFile1 = url.getPath();
    ByteArrayOutputStream bytes = new ByteArrayOutputStream();
    boolean success = ftpClient.retrieveFile(remoteFile1, bytes);
    bytes.close();
    if (!success)
        throw new Exception("Unable to retrieve " + n);
    return bytes.toByteArray();
}

Example 4 with Retrieve

use of org.hl7.elm.r1.Retrieve in project cqf-ruler by DBCG.

the class CqlExecutionProvider method evaluate.

/**
 * Evaluates a CQL expression and returns the results as a Parameters resource.
 *
 * @param theRequestDetails   the {@link RequestDetails RequestDetails}
 * @param subject             ***Only Patient is supported as of now*** Subject
 *                            for which the expression will be
 *                            evaluated. This corresponds to the context in
 *                            which the expression will be evaluated and is
 *                            represented as a relative FHIR id (e.g.
 *                            Patient/123), which establishes both the context
 *                            and context value for the evaluation
 * @param expression          Expression to be evaluated. Note that this is an
 *                            expression of CQL, not the text of a library with
 *                            definition statements.
 * @param parameters          Any input parameters for the expression.
 *                            {@link Parameters} Parameters defined in this
 *                            input will be made available by name to the CQL
 *                            expression. Parameter types are mapped to CQL as
 *                            specified in the Using CQL section of the CPG
 *                            Implementation guide. If a parameter appears more
 *                            than once in the input Parameters resource, it is
 *                            represented with a List in the input CQL. If a
 *                            parameter has parts, it is represented as a Tuple
 *                            in the input CQL.
 * @param library             A library to be included. The {@link Library}
 *                            library is resolved by url and made available by
 *                            name within the expression to be evaluated.
 * @param useServerData       Whether to use data from the server performing the
 *                            evaluation. If this parameter is true (the
 *                            default), then the operation will use data first
 *                            from any bundles provided as parameters (through
 *                            the data and prefetch parameters), second data
 *                            from the server performing the operation, and
 *                            third, data from the dataEndpoint parameter (if
 *                            provided). If this parameter is false, the
 *                            operation will use data first from the bundles
 *                            provided in the data or prefetch parameters, and
 *                            second from the dataEndpoint parameter (if
 *                            provided).
 * @param data                Data to be made available to the library
 *                            evaluation. This parameter is exclusive with the
 *                            prefetchData parameter (i.e. either provide all
 *                            data as a single bundle, or provide data using
 *                            multiple bundles with prefetch descriptions).
 * @param prefetchData        ***Not Yet Implemented***
 * @param dataEndpoint        An {@link Endpoint} endpoint to use to access data
 *                            referenced by retrieve operations in the library.
 *                            If provided, this endpoint is used after the data
 *                            or prefetchData bundles, and the server, if the
 *                            useServerData parameter is true.
 * @param contentEndpoint     An {@link Endpoint} endpoint to use to access
 *                            content (i.e. libraries) referenced by the
 *                            library. If no content endpoint is supplied, the
 *                            evaluation will attempt to retrieve content from
 *                            the server on which the operation is being
 *                            performed.
 * @param terminologyEndpoint An {@link Endpoint} endpoint to use to access
 *                            terminology (i.e. valuesets, codesystems, and
 *                            membership testing) referenced by the library. If
 *                            no terminology endpoint is supplied, the
 *                            evaluation will attempt to use the server on which
 *                            the operation is being performed as the
 *                            terminology server.
 * @return The result of evaluating the given expression, returned as a FHIR
 *         type, either a {@link Resource} resource, or a FHIR-defined type
 *         corresponding to the CQL return type, as defined in the Using CQL
 *         section of the CPG Implementation guide. If the result is a List of
 *         resources, the result will be a {@link Bundle} Bundle . If the result
 *         is a CQL system-defined or FHIR-defined type, the result is returned
 *         as a {@link Parameters} Parameters resource
 */
@Operation(name = "$cql")
@Description(shortDefinition = "$cql", value = "Evaluates a CQL expression and returns the results as a Parameters resource. Defined: http://build.fhir.org/ig/HL7/cqf-recommendations/OperationDefinition-cpg-cql.html", example = "$cql?expression=5*5")
public Parameters evaluate(RequestDetails theRequestDetails, @OperationParam(name = "subject", max = 1) String subject, @OperationParam(name = "expression", min = 1, max = 1) String expression, @OperationParam(name = "parameters", max = 1) Parameters parameters, @OperationParam(name = "library") List<Parameters> library, @OperationParam(name = "useServerData", max = 1) BooleanType useServerData, @OperationParam(name = "data", max = 1) Bundle data, @OperationParam(name = "prefetchData") List<Parameters> prefetchData, @OperationParam(name = "dataEndpoint", max = 1) Endpoint dataEndpoint, @OperationParam(name = "contentEndpoint", max = 1) Endpoint contentEndpoint, @OperationParam(name = "terminologyEndpoint", max = 1) Endpoint terminologyEndpoint) {
    if (prefetchData != null) {
        throw new NotImplementedException("prefetchData is not yet supported.");
    }
    if (useServerData == null) {
        useServerData = new BooleanType(true);
    }
    List<LibraryParameter> libraryParameters = new ArrayList<>();
    if (library != null) {
        for (Parameters libraryParameter : library) {
            String url = null;
            String name = null;
            for (ParametersParameterComponent param : libraryParameter.getParameter()) {
                switch(param.getName()) {
                    case "url":
                        url = ((StringType) param.getValue()).asStringValue();
                        break;
                    case "name":
                        name = ((StringType) param.getValue()).asStringValue();
                        break;
                    default:
                        throw new IllegalArgumentException("Only url and name parts are allowed for Parameter: library");
                }
            }
            if (url == null) {
                throw new IllegalArgumentException("If library parameter must provide a url parameter part.");
            }
            libraryParameters.add(new LibraryParameter().withUrl(url).withName(name));
        }
    // Remove LocalLibrary from cache first...
    }
    VersionedIdentifier localLibraryIdentifier = new VersionedIdentifier().withId("LocalLibrary").withVersion("1.0.0");
    globalLibraryCache.remove(localLibraryIdentifier);
    CqlEngine engine = setupEngine(localLibraryIdentifier, expression, libraryParameters, subject, parameters, contentEndpoint, dataEndpoint, terminologyEndpoint, data, useServerData.booleanValue(), theRequestDetails);
    Map<String, Object> resolvedParameters = new HashMap<String, Object>();
    if (parameters != null) {
        for (Parameters.ParametersParameterComponent pc : parameters.getParameter()) {
            resolvedParameters.put(pc.getName(), pc.getValue());
        }
    }
    String contextType = subject != null ? subject.substring(0, subject.lastIndexOf("/") - 1) : null;
    String subjectId = subject != null ? subject.substring(0, subject.lastIndexOf("/") - 1) : null;
    EvaluationResult evalResult = engine.evaluate(localLibraryIdentifier, null, Pair.of(contextType != null ? contextType : "Unspecified", subjectId == null ? "null" : subject), resolvedParameters, this.getDebugMap());
    if (evalResult != null && evalResult.expressionResults != null) {
        if (evalResult.expressionResults.size() > 1) {
            logger.debug("Evaluation resulted in more than one expression result.  ");
        }
        Parameters result = new Parameters();
        resolveResult(theRequestDetails, evalResult, result);
        return result;
    }
    return null;
}

Example 5 with Retrieve

use of org.hl7.elm.r1.Retrieve in project cqf-ruler by DBCG.

the class CqlExecutionProvider method evaluate.

/**
 * Evaluates a CQL expression and returns the results as a Parameters resource.
 *
 * @param theRequestDetails   the {@link RequestDetails RequestDetails}
 * @param subject             Subject for which the expression will be
 *                            evaluated. This corresponds to the context in
 *                            which the expression will be evaluated and is
 *                            represented as a relative FHIR id (e.g.
 *                            Patient/123), which establishes both the context
 *                            and context value for the evaluation
 * @param expression          Expression to be evaluated. Note that this is an
 *                            expression of CQL, not the text of a library with
 *                            definition statements.
 * @param parameters          Any input parameters for the expression.
 *                            {@link Parameters} Parameters defined in this
 *                            input will be made available by name to the CQL
 *                            expression. Parameter types are mapped to CQL as
 *                            specified in the Using CQL section of the CPG
 *                            Implementation guide. If a parameter appears more
 *                            than once in the input Parameters resource, it is
 *                            represented with a List in the input CQL. If a
 *                            parameter has parts, it is represented as a Tuple
 *                            in the input CQL.
 * @param library             A library to be included. The {@link Library}
 *                            library is resolved by url and made available by
 *                            name within the expression to be evaluated.
 * @param useServerData       Whether to use data from the server performing the
 *                            evaluation. If this parameter is true (the
 *                            default), then the operation will use data first
 *                            from any bundles provided as parameters (through
 *                            the data and prefetch parameters), second data
 *                            from the server performing the operation, and
 *                            third, data from the dataEndpoint parameter (if
 *                            provided). If this parameter is false, the
 *                            operation will use data first from the bundles
 *                            provided in the data or prefetch parameters, and
 *                            second from the dataEndpoint parameter (if
 *                            provided).
 * @param data                Data to be made available to the library
 *                            evaluation. This parameter is exclusive with the
 *                            prefetchData parameter (i.e. either provide all
 *                            data as a single bundle, or provide data using
 *                            multiple bundles with prefetch descriptions).
 * @param prefetchData        ***Not Yet Implemented***
 * @param dataEndpoint        An {@link Endpoint} endpoint to use to access data
 *                            referenced by retrieve operations in the library.
 *                            If provided, this endpoint is used after the data
 *                            or prefetchData bundles, and the server, if the
 *                            useServerData parameter is true.
 * @param contentEndpoint     An {@link Endpoint} endpoint to use to access
 *                            content (i.e. libraries) referenced by the
 *                            library. If no content endpoint is supplied, the
 *                            evaluation will attempt to retrieve content from
 *                            the server on which the operation is being
 *                            performed.
 * @param terminologyEndpoint An {@link Endpoint} endpoint to use to access
 *                            terminology (i.e. valuesets, codesystems, and
 *                            membership testing) referenced by the library. If
 *                            no terminology endpoint is supplied, the
 *                            evaluation will attempt to use the server on which
 *                            the operation is being performed as the
 *                            terminology server.
 * @return The result of evaluating the given expression, returned as a FHIR
 *         type, either a {@link Resource} resource, or a FHIR-defined type
 *         corresponding to the CQL return type, as defined in the Using CQL
 *         section of the CPG Implementation guide. If the result is a List of
 *         resources, the result will be a {@link Bundle} Bundle . If the result
 *         is a CQL system-defined or FHIR-defined type, the result is returned
 *         as a {@link Parameters} Parameters resource
 */
@Operation(name = "$cql")
@Description(shortDefinition = "$cql", value = "Evaluates a CQL expression and returns the results as a Parameters resource. Defined: http://build.fhir.org/ig/HL7/cqf-recommendations/OperationDefinition-cpg-cql.html", example = "$cql?expression=5*5")
public Parameters evaluate(RequestDetails theRequestDetails, @OperationParam(name = "subject", max = 1) String subject, @OperationParam(name = "expression", min = 1, max = 1) String expression, @OperationParam(name = "parameters", max = 1) Parameters parameters, @OperationParam(name = "library") List<Parameters> library, @OperationParam(name = "useServerData", max = 1) BooleanType useServerData, @OperationParam(name = "data", max = 1) Bundle data, @OperationParam(name = "prefetchData") List<Parameters> prefetchData, @OperationParam(name = "dataEndpoint", max = 1) Endpoint dataEndpoint, @OperationParam(name = "contentEndpoint", max = 1) Endpoint contentEndpoint, @OperationParam(name = "terminologyEndpoint", max = 1) Endpoint terminologyEndpoint) {
    if (prefetchData != null) {
        throw new NotImplementedException("prefetchData is not yet supported.");
    }
    if (useServerData == null) {
        useServerData = new BooleanType(true);
    }
    List<LibraryParameter> libraryParameters = new ArrayList<>();
    if (library != null) {
        for (Parameters libraryParameter : library) {
            CanonicalType url = null;
            String name = null;
            for (ParametersParameterComponent param : libraryParameter.getParameter()) {
                switch(param.getName()) {
                    case "url":
                        url = ((CanonicalType) param.getValue());
                        break;
                    case "name":
                        name = ((StringType) param.getValue()).asStringValue();
                        break;
                    default:
                        throw new IllegalArgumentException("Only url and name parts are allowed for Parameter: library");
                }
            }
            if (url == null) {
                throw new IllegalArgumentException("If library parameter must provide a url parameter part.");
            }
            libraryParameters.add(new LibraryParameter().withUrl(url).withName(name));
        }
    // Remove LocalLibrary from cache first...
    }
    VersionedIdentifier localLibraryIdentifier = new VersionedIdentifier().withId("LocalLibrary").withVersion("1.0.0");
    globalLibraryCache.remove(localLibraryIdentifier);
    CqlEngine engine = setupEngine(localLibraryIdentifier, expression, libraryParameters, subject, parameters, contentEndpoint, dataEndpoint, terminologyEndpoint, data, useServerData.booleanValue(), theRequestDetails);
    Map<String, Object> resolvedParameters = new HashMap<>();
    if (parameters != null) {
        for (Parameters.ParametersParameterComponent pc : parameters.getParameter()) {
            resolvedParameters.put(pc.getName(), pc.getValue());
        }
    }
    String contextType = subject != null ? subject.substring(0, subject.lastIndexOf("/") - 1) : null;
    String subjectId = subject != null ? subject.substring(0, subject.lastIndexOf("/") - 1) : null;
    EvaluationResult evalResult = engine.evaluate(localLibraryIdentifier, null, Pair.of(contextType != null ? contextType : "Unspecified", subjectId == null ? "null" : subject), resolvedParameters, this.getDebugMap());
    if (evalResult != null && evalResult.expressionResults != null) {
        if (evalResult.expressionResults.size() > 1) {
            logger.debug("Evaluation resulted in more than one expression result.  ");
        }
        Parameters result = new Parameters();
        resolveResult(theRequestDetails, evalResult, result);
        return result;
    }
    return null;
}