Examples with Parameters org.hl7.fhir.r5.model.Parameters used on opensource projects

Example 11 with Parameters

use of org.hl7.fhir.r5.model.Parameters in project kindling by HL7.

the class OldSpreadsheetParser method readOperations.

private void readOperations(List<Operation> oplist, Sheet sheet) throws Exception {
    Map<String, Operation> ops = new HashMap<String, Operation>();
    Map<String, OperationParameter> params = new HashMap<String, OperationParameter>();
    if (sheet != null) {
        for (int row = 0; row < sheet.rows.size(); row++) {
            String name = sheet.getColumn(row, "Name");
            String use = sheet.getColumn(row, "Use");
            String doco = sheet.getColumn(row, "Documentation");
            String type = sheet.getColumn(row, "Type");
            List<OperationExample> examples = loadOperationExamples(sheet.getColumn(row, "Example.Request"), sheet.getColumn(row, "Example.Response"));
            List<OperationExample> examples2 = loadOperationExamples(sheet.getColumn(row, "Example2.Request"), sheet.getColumn(row, "Example2.Response"));
            if (name != null && !name.equals("") && !name.startsWith("!")) {
                if (!name.contains(".")) {
                    if (!type.equals("operation"))
                        throw new Exception("Invalid type on operation " + type + " at " + getLocation(row));
                    if (!name.toLowerCase().equals(name))
                        throw new Exception("Invalid name on operation " + name + " - must be all lower case (use dashes) at " + getLocation(row));
                    params.clear();
                    boolean system = false;
                    boolean istype = false;
                    boolean instance = false;
                    for (String c : use.split("\\|")) {
                        c = c.trim();
                        if ("system".equalsIgnoreCase(c))
                            system = true;
                        else if ("resource".equalsIgnoreCase(c))
                            istype = true;
                        else if ("instance".equalsIgnoreCase(c))
                            instance = true;
                        else
                            throw new Exception("unknown operation use code " + c + " at " + getLocation(row));
                    }
                    Operation op = new Operation(name, system, istype, instance, sheet.getColumn(row, "Type"), sheet.getColumn(row, "Title"), doco, sheet.getColumn(row, "Footer"), examples, parseBoolean(sheet.getColumn(row, "Idempotent"), row, false));
                    op.setStandardsStatus(StandardsStatus.fromCode(sheet.getColumn(row, "Standards-Status")));
                    op.setNormativeVersion(sheet.getColumn(row, "Normative-Version"));
                    op.setFooter2(sheet.getColumn(row, "Footer2"));
                    op.setFmm(sheet.getColumn(row, "fmm"));
                    op.getExamples2().addAll(examples2);
                    oplist.add(op);
                    ops.put(name, op);
                } else {
                    String context = name.substring(0, name.lastIndexOf('.'));
                    String pname = name.substring(name.lastIndexOf('.') + 1);
                    Operation operation;
                    List<OperationParameter> plist;
                    if (context.contains(".")) {
                        String opname = name.substring(0, name.indexOf('.'));
                        // inside of a tuple
                        if (!Utilities.noString(use))
                            throw new Exception("Tuple parameters: use must be blank at " + getLocation(row));
                        operation = ops.get(opname);
                        if (operation == null)
                            throw new Exception("Unknown Operation '" + opname + "' at " + getLocation(row));
                        OperationParameter param = params.get(context);
                        if (param == null)
                            throw new Exception("Tuple parameter '" + context + "' not found at " + getLocation(row));
                        if (!param.getFhirType().equals("Tuple"))
                            throw new Exception("Tuple parameter '" + context + "' type must be Tuple at " + getLocation(row));
                        plist = param.getParts();
                    } else {
                        if (!use.equals("in") && !use.equals("out"))
                            throw new Exception("Only allowed use is 'in' or 'out' at " + getLocation(row));
                        operation = ops.get(context);
                        if (operation == null)
                            throw new Exception("Unknown Operation '" + context + "' at " + getLocation(row));
                        plist = operation.getParameters();
                    }
                    String profile = sheet.getColumn(row, "Profile");
                    String min = sheet.getColumn(row, "Min");
                    String max = sheet.getColumn(row, "Max");
                    OperationParameter p = new OperationParameter(pname, use, doco, Integer.parseInt(min), max, type, sheet.getColumn(row, "Search Type"), profile);
                    String bs = sheet.getColumn(row, "Binding");
                    if (!Utilities.noString(bs))
                        p.setBs(bindings.get(bs));
                    plist.add(p);
                    params.put(name, p);
                }
            }
        }
    }
}

Example 12 with Parameters

use of org.hl7.fhir.r5.model.Parameters in project kindling by HL7.

the class JsonLDDefinitionsGenerator method generate.

// private String genDate;
// private String version;
// private BuildWorkerContext workerContext;
public void generate(Definitions definitions, IniFile ini, String tmpResDir, String dstDir, String srcDir, FHIRVersion version, String genDate, BuildWorkerContext workerContext) throws Exception {
    // this.genDate = genDate;
    // this.version = version;
    // this.workerContext = workerContext;
    JsonObject defn = new JsonObject();
    JsonObject context = new JsonObject();
    defn.add("@context", context);
    defn.addProperty("@id", "http://hl7.org/fhir/");
    context.addProperty("fhir", "http://hl7.org/fhir/");
    context.addProperty("xsd", "http://www.w3.org/2001/XMLSchema#");
    // properties for primitives, helpers, format features
    addProperty(context, "value", "fhir:value", "xsd:string");
    addProperty(context, "decimal", "fhir:value", "xsd:decimal");
    addProperty(context, "integer", "fhir:value", "xsd:integer");
    if (!version.isR4B()) {
        addProperty(context, "integer64", "fhir:value", "xsd:string");
    }
    addProperty(context, "boolean", "fhir:value", "xsd:boolean");
    addProperty(context, "binary", "fhir:value", "xsd:base64Binary");
    addProperty(context, "date", "fhir:value", "xsd:date");
    addProperty(context, "dateTime", "fhir:value", "xsd:dateTime");
    addProperty(context, "gYearMonth", "fhir:value", "xsd:gYearMonth");
    addProperty(context, "gYear", "fhir:value", "xsd:gYear");
    addProperty(context, "link", "fhir:link", "@id");
    addProperty(context, "concept", "fhir:concept", "@id");
    addProperty(context, "index", "fhir:index", "xsd:integer");
    addProperty(context, "role", "fhir:nodeRole", "@id");
    // elements defined in FHIR:
    for (TypeRef tr : definitions.getKnownTypes()) {
        if (!definitions.hasPrimitiveType(tr.getName()) && !tr.getName().equals("SimpleQuantity") && !tr.getName().equals("MoneyQuantity")) {
            TypeDefn root = definitions.getElementDefn(tr.getName());
            new JsonLDGenerator(definitions, workerContext, definitions.getKnownTypes()).generate(context, root, version, genDate);
        }
    }
    List<String> names = new ArrayList<String>();
    names.addAll(definitions.getResources().keySet());
    names.addAll(definitions.getBaseResources().keySet());
    names.add("Parameters");
    Collections.sort(names);
    for (String name : names) {
        ResourceDefn root = definitions.getResourceByName(name);
        new JsonLDGenerator(definitions, workerContext, definitions.getKnownTypes()).generate(context, root.getRoot(), version, genDate);
    }
    save(defn, dstDir + "fhir.jsonld");
}

Example 13 with Parameters

use of org.hl7.fhir.r5.model.Parameters in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7DocumentReferenceFHIRConversionTest method doc_ref_has_all_fields_in_yaml.

// Note: All tests for MDM_T02 and MDM_T06 are the same. Use parameters.
@ParameterizedTest
@ValueSource(strings = { "MDM^T02", "MDM^T06" })
void doc_ref_has_all_fields_in_yaml(String segment) {
    // every field covered in the yaml should be listed here
    String documentReference = "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|" + segment + "^MDM_T02|64322|P|2.6|123|456|ER|AL|USA|ASCII|en|2.6|56789^NID^UID|MCM||||\n" + "PID|1||000054321^^^MRN|||||||||||||M|CAT|||||N\n" + "PV1|1|I||||||||||||||||||||||||||||||||||||||||||\n" + "ORC|NW|||PGN001|SC|D|1|||MS|MS|||||\n" + "OBR|1||||||20170825010500|||||||||||||002|||||F||||||||\n" + "TXA|1|OP|TEXT|20180117144200|5566^PAPLast^PAPFirst^J^^MD|20180117144200|201801180346||<PHYSID>|<PHYSID>|MODL|<MESSAGEID>|4466^TRANSCLast^TRANSCFirst^J||<MESSAGEID>|This segment is for description|PA|R|AV|||||\n" + "OBX|1|SN|||||||||X";
    DocumentReference report = ResourceUtils.getDocumentReference(ftv, documentReference);
    assertThat(report.hasAuthenticator()).isTrue();
    assertThat(report.hasAuthor()).isTrue();
    assertThat(report.hasContent()).isTrue();
    assertThat(report.hasContext()).isTrue();
    assertThat(report.hasDate()).isTrue();
    assertThat(report.hasDescription()).isTrue();
    assertThat(report.hasDocStatus()).isTrue();
    assertThat(report.hasId()).isTrue();
    assertThat(report.hasIdentifier()).isTrue();
    assertThat(report.hasMasterIdentifier()).isTrue();
    assertThat(report.hasSecurityLabel()).isTrue();
    assertThat(report.hasStatus()).isTrue();
    assertThat(report.hasSubject()).isTrue();
    assertThat(report.hasType()).isTrue();
}

Example 14 with Parameters

use of org.hl7.fhir.r5.model.Parameters in project health-patterns by LinuxForHealth.

the class TerminologyService method translateResource.

/**
 * Translates the given single FHIR resource represented as a {@link JsonNode}.
 *
 * @param resource the FHIR resource to translate
 * @returns true if there was something to translate, false otherwise
 * @throws DeIdentifierException if there is an error in the de-identification REST API or parsing the JSON
 * @throws IllegalArgumentException if the given JSON does not have a 'resource' object
 */
private boolean translateResource(JsonNode resource) {
    boolean translatedSomething = false;
    String resourceType = getResourceType(resource);
    boolean isTranslatable = StringUtils.equalsAny(resourceType, TRANSLATABLE_FHIR_TYPES);
    if (!isTranslatable) {
        return translatedSomething;
    }
    ArrayNode extensions = (ArrayNode) resource.get(EXTENSION_OBJECT);
    if (extensions == null) {
        return translatedSomething;
    }
    for (int i = 0; i < extensions.size(); i++) {
        JsonNode extension = extensions.get(i);
        JsonNode urlJson = extension.get(URL_OBJECT);
        JsonNode valueCodeJson = extension.get(VALUE_CODE_OBJECT);
        if (urlJson == null || valueCodeJson == null) {
            // In order to do a translation we need both the url and the valueCode
            continue;
        }
        // The resource's extension URL is the URL for the StructureDefinition, so we resolve a ValueSet if known
        String structureDefinitionURL = urlJson.asText();
        String valueSetURL = valueSetForStructureDefinition.get(structureDefinitionURL);
        // and if known we check the FHIR Server's known ConceptMaps to see if there is a corresponding one
        // http://4603f72b-us-south.lb.appdomain.cloud/fhir-server/api/v4/ConceptMap?_format=json&source-uri=http://hl7.org/fhir/us/core/ValueSet/birthsex
        Bundle bundle = fhirClient.search().forResource(ConceptMap.class).where(ConceptMap.SOURCE_URI.hasId(valueSetURL)).returnBundle(Bundle.class).execute();
        String conceptMapId;
        if (!bundle.getEntry().isEmpty()) {
            Resource conceptMap = bundle.getEntry().get(0).getResource();
            if (bundle.getEntry().size() > 1) {
                System.err.println("Found multiple ConceptMaps that will map " + valueSetURL + " for this StructureDefinition, will use the first one " + conceptMap.getId());
            } else {
                System.out.println("Found ConceptMap for " + valueSetURL + ": " + conceptMap.getId() + " !!");
            }
            conceptMapId = conceptMap.getIdElement().getIdPart();
        } else {
            System.out.println("Did not find ConceptMap for " + valueSetURL + "!!");
            continue;
        }
        // "POST ${FHIR_URL}/${conceptMapID}/$translate?code=${code}&system=${valueSet}&_format=json
        String valueCode = valueCodeJson.asText();
        String url = String.format("%s/ConceptMap/%s/$translate?code=%s&system=%s&_format=json", fhirClient.getServerBase(), conceptMapId, valueCode, valueSetURL);
        Parameters translationResponse = fhirClient.fetchResourceFromUrl(Parameters.class, url);
        // This is what comes back from the server
        // {
        // "resourceType": "Parameters",
        // "parameter": [
        // {
        // "name": "result",
        // "valueBoolean": true
        // },
        // {
        // "name": "match",
        // "part": [
        // {
        // "name": "equivalence",
        // "valueCode": "equivalent"
        // },
        // {
        // "name": "concept",
        // "valueCoding": {
        // "system": "http://ibm.com/fhir/cdm/ValueSet/sex-assigned-at-birth",
        // "code": "male",
        // "display": "Male"
        // }
        // }
        // ]
        // }
        // ]
        // }
        Coding translatedCode = null;
        List<ParametersParameterComponent> parameters = translationResponse.getParameter();
        for (ParametersParameterComponent parameter : parameters) {
            if (parameter.getName().equals(MATCH_VALUE)) {
                List<ParametersParameterComponent> parts = parameter.getPart();
                for (ParametersParameterComponent part : parts) {
                    if (part.getName().equals(CONCEPT_VALUE)) {
                        try {
                            translatedCode = (Coding) part.getValue();
                        } catch (ClassCastException e) {
                            String jsonResponse = fhirClient.getFhirContext().newJsonParser().encodeResourceToString(translationResponse);
                            System.err.println("Found a ConceptMap that will map " + valueSetURL + " for this StructureDefinition, but the FHIR server returned an unknown $translate response (expected a 'valueCoding' part): " + jsonResponse);
                        }
                    }
                }
            }
        }
        if (translatedCode == null) {
            String jsonResponse = fhirClient.getFhirContext().newJsonParser().encodeResourceToString(translationResponse);
            System.err.println("Found a ConceptMap that will map " + valueSetURL + " for this StructureDefinition, but the FHIR server returned an unknown $translate response: " + jsonResponse);
            continue;
        }
        System.out.printf("Found ConceptMap %s which translates (valueCode, system) = (%s, %s) for StructureDefinition %s to (valueCode, system) = (%s, %s) %n", conceptMapId, valueCode, valueSetURL, structureDefinitionURL, translatedCode.getCode(), translatedCode.getSystem());
        String translatedStructuredData = valueSetForStructureDefinition.get(translatedCode.getSystem());
        if (translatedStructuredData == null) {
            System.err.printf("Cannot find the mapping from ValueSet '%s' to its corresponding StructureData for this translation, make sure the corresponding mappings configuration file has it.%n", translatedCode.getSystem());
            continue;
        }
        ((ObjectNode) extension).set(URL_OBJECT, JsonNodeFactory.instance.textNode(translatedStructuredData));
        ((ObjectNode) extension).set(VALUE_CODE_OBJECT, JsonNodeFactory.instance.textNode(translatedCode.getCode()));
        translatedSomething = true;
    }
    return translatedSomething;
}

Example 15 with Parameters

use of org.hl7.fhir.r5.model.Parameters 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;
}