Examples with ModelInfo org.hl7.elm_modelinfo.r1.ModelInfo used on opensource projects

Example 26 with ModelInfo

use of org.hl7.elm_modelinfo.r1.ModelInfo in project clinical_quality_language by cqframework.

the class TypeBuilder method dataTypeToQName.

public QName dataTypeToQName(DataType type) {
    if (type instanceof NamedType) {
        NamedType namedType = (NamedType) type;
        ModelInfo modelInfo = mr.getModel(namedType.getNamespace()).getModelInfo();
        return new QName(modelInfo.getTargetUrl() != null ? modelInfo.getTargetUrl() : modelInfo.getUrl(), namedType.getTarget() != null ? namedType.getTarget() : namedType.getSimpleName());
    }
    // ERROR:
    throw new IllegalArgumentException("A named type is required in this context.");
}

Example 27 with ModelInfo

use of org.hl7.elm_modelinfo.r1.ModelInfo in project clinical_quality_language by cqframework.

the class DataRequirementsProcessorTest method TestDataRequirementsProcessorOpioidIssueLibrary.

@Test
public void TestDataRequirementsProcessorOpioidIssueLibrary() {
    CqlTranslatorOptions cqlTranslatorOptions = new CqlTranslatorOptions();
    cqlTranslatorOptions.getFormats().add(CqlTranslator.Format.JSON);
    cqlTranslatorOptions.setCollapseDataRequirements(true);
    cqlTranslatorOptions.setAnalyzeDataRequirements(true);
    try {
        NamespaceInfo ni = new NamespaceInfo("fhir.cdc.opioid-cds", "http://fhir.org/guides/cdc/opioid-cds");
        CqlTranslator translator = createTranslator(ni, "OpioidCDSSTU3/cql/OpioidCDSREC10_bug_repo.cql", cqlTranslatorOptions);
        translator.toELM();
        assertTrue(translator.getErrors().isEmpty());
        libraryManager.cacheLibrary(translator.getTranslatedLibrary());
        DataRequirementsProcessor dqReqTrans = new DataRequirementsProcessor();
        org.hl7.fhir.r5.model.Library moduleDefinitionLibrary = dqReqTrans.gatherDataRequirements(libraryManager, translator.getTranslatedLibrary(), cqlTranslatorOptions, null, false);
        assertNotNull(moduleDefinitionLibrary);
        RelatedArtifact ra = null;
        // FHIR-ModelInfo
        ra = getDependency(moduleDefinitionLibrary, "http://fhir.org/guides/cqf/common/Library/FHIR-ModelInfo|3.0.0");
        assertNotNull(ra, "Expected depends-on http://fhir.org/guides/cqf/common/Library/FHIR-ModelInfo|3.0.0");
        // FHIRHelpers
        ra = getDependency(moduleDefinitionLibrary, "http://hl7.org/fhir/Library/FHIRHelpers|3.0.0");
        assertNotNull(ra, "Expected depends-on http://hl7.org/fhir/Library/FHIRHelpers|3.0.0");
        // OpioidCDSCommon
        ra = getDependency(moduleDefinitionLibrary, "http://fhir.org/guides/cdc/opioid-cds/Library/OpioidCDSCommon|1.2.3");
        assertNotNull(ra, "Expected depends-on http://fhir.org/guides/cdc/opioid-cds/Library/OpioidCDSCommon|1.2.3");
        // OpioidCDSRoutines
        ra = getDependency(moduleDefinitionLibrary, "http://fhir.org/guides/cdc/opioid-cds/Library/OpioidCDSRoutines|1.2.3");
        assertNotNull(ra, "Expected depends-on http://fhir.org/guides/cdc/opioid-cds/Library/OpioidCDSRoutines|1.2.3");
        // OpioidCDSCommonConfig
        ra = getDependency(moduleDefinitionLibrary, "http://fhir.org/guides/cdc/opioid-cds/Library/OpioidCDSCommonConfig|1.2.3");
        assertNotNull(ra, "Expected depends-on http://fhir.org/guides/cdc/opioid-cds/Library/OpioidCDSCommonConfig|1.2.3");
        // depends-on http://fhir.org/guides/cdc/opioid-cds/ValueSet/observation-category-laboratory
        ra = getDependency(moduleDefinitionLibrary, "http://fhir.org/guides/cdc/opioid-cds/ValueSet/observation-category-laboratory");
        assertNotNull(ra, "Expected depends-on http://fhir.org/guides/cdc/opioid-cds/ValueSet/observation-category-laboratory");
        // depends-on http://fhir.org/guides/cdc/opioid-cds/ValueSet/pcp-medications
        ra = getDependency(moduleDefinitionLibrary, "http://fhir.org/guides/cdc/opioid-cds/ValueSet/pcp-medications");
        assertNotNull(ra, "Expected depends-on http://fhir.org/guides/cdc/opioid-cds/ValueSet/pcp-medications");
        // depends-on http://fhir.org/guides/cdc/opioid-cds/ValueSet/cocaine-medications
        ra = getDependency(moduleDefinitionLibrary, "http://fhir.org/guides/cdc/opioid-cds/ValueSet/cocaine-medications");
        assertNotNull(ra, "Expected depends-on http://fhir.org/guides/cdc/opioid-cds/ValueSet/cocaine-medications");
        // parameter "Negative PCP Screenings Count Since Last POS": integer
        ParameterDefinition pd = null;
        pd = getParameter(moduleDefinitionLibrary, "ContextPrescriptions");
        assertNotNull(pd, "Expected parameter ContextPrescriptions");
        assertEquals(pd.getType(), Enumerations.FHIRAllTypes.MEDICATIONREQUEST);
        assertEquals(pd.getUse(), Enumerations.OperationParameterUse.IN);
        assertEquals(pd.getMax(), "*");
        pd = getParameter(moduleDefinitionLibrary, "Patient");
        assertNotNull(pd, "Expected parameter Patient");
        assertEquals(pd.getType(), Enumerations.FHIRAllTypes.PATIENT);
        assertEquals(pd.getUse(), Enumerations.OperationParameterUse.OUT);
        assertEquals(pd.getMax(), "1");
        pd = getParameter(moduleDefinitionLibrary, "Lookback Year");
        assertNotNull(pd, "Expected parameter Lookback Year");
        assertEquals(pd.getType(), Enumerations.FHIRAllTypes.PERIOD);
        assertEquals(pd.getUse(), Enumerations.OperationParameterUse.OUT);
        assertEquals(pd.getMax(), "1");
        pd = getParameter(moduleDefinitionLibrary, "PCP Screenings");
        assertNotNull(pd, "Expected parameter PCP Screenings");
        assertEquals(pd.getType(), Enumerations.FHIRAllTypes.OBSERVATION);
        assertEquals(pd.getUse(), Enumerations.OperationParameterUse.OUT);
        assertEquals(pd.getMax(), "*");
        pd = getParameter(moduleDefinitionLibrary, "Positive PCP Screenings");
        assertNotNull(pd, "Expected parameter Positive PCP Screenings");
        assertEquals(pd.getType(), Enumerations.FHIRAllTypes.OBSERVATION);
        assertEquals(pd.getUse(), Enumerations.OperationParameterUse.OUT);
        assertEquals(pd.getMax(), "*");
        pd = getParameter(moduleDefinitionLibrary, "Negative PCP Screenings");
        assertNotNull(pd, "Expected parameter Negative PCP Screenings");
        assertEquals(pd.getType(), Enumerations.FHIRAllTypes.OBSERVATION);
        assertEquals(pd.getUse(), Enumerations.OperationParameterUse.OUT);
        assertEquals(pd.getMax(), "*");
        pd = getParameter(moduleDefinitionLibrary, "Negative PCP Screenings Count Since Last POS");
        assertNotNull(pd, "Expected parameter Negative PCP Screenings Count Since Last POS");
        assertEquals(pd.getType(), Enumerations.FHIRAllTypes.INTEGER);
        assertEquals(pd.getUse(), Enumerations.OperationParameterUse.OUT);
        assertEquals(pd.getMax(), "1");
        pd = getParameter(moduleDefinitionLibrary, "Positive PCP Dates in Lookback Period");
        assertNotNull(pd, "Expected parameter Positive PCP Dates in Lookback Period");
        assertEquals(pd.getType(), Enumerations.FHIRAllTypes.STRING);
        assertEquals(pd.getUse(), Enumerations.OperationParameterUse.OUT);
        assertEquals(pd.getMax(), "*");
        pd = getParameter(moduleDefinitionLibrary, "Has Positive Screening for PCP in Last 12 Months");
        assertNotNull(pd, "Expected parameter Has Positive Screening for PCP in Last 12 Months");
        assertEquals(pd.getType(), Enumerations.FHIRAllTypes.BOOLEAN);
        assertEquals(pd.getUse(), Enumerations.OperationParameterUse.OUT);
        assertEquals(pd.getMax(), "1");
        pd = getParameter(moduleDefinitionLibrary, "PCP Summary");
        assertNotNull(pd, "Expected parameter PCPSummary");
        assertEquals(pd.getType(), Enumerations.FHIRAllTypes.STRING);
        assertEquals(pd.getUse(), Enumerations.OperationParameterUse.OUT);
        assertEquals(pd.getMax(), "1");
        // dataRequirement Observation {
        // ms: { code, category, value, status, status.value, effective },
        // codeFilter {
        // { category in http://fhir.org/guides/cdc/opioid-cds/ValueSet/observation-category-laboratory },
        // { code in http://fhir.org/guides/cdc/opioid-cds/ValueSet/pcp-medications }
        // }
        // }
        assertTrue(moduleDefinitionLibrary.getDataRequirement().size() == 2);
        DataRequirement dr = null;
        for (DataRequirement r : moduleDefinitionLibrary.getDataRequirement()) {
            if (r.getType() == Enumerations.FHIRAllTypes.OBSERVATION) {
                dr = r;
                break;
            }
        }
        assertNotNull(dr);
        assertEquals(dr.getType(), Enumerations.FHIRAllTypes.OBSERVATION);
        assertTrue(dr.getMustSupport().size() == 6);
        assertTrue(dr.getMustSupport().stream().filter(x -> x.getValue().equals("code")).count() == 1);
        assertTrue(dr.getMustSupport().stream().filter(x -> x.getValue().equals("category")).count() == 1);
        assertTrue(dr.getMustSupport().stream().filter(x -> x.getValue().equals("value")).count() == 1);
        assertTrue(dr.getMustSupport().stream().filter(x -> x.getValue().equals("status")).count() == 1);
        assertTrue(dr.getMustSupport().stream().filter(x -> x.getValue().equals("status.value")).count() == 1);
        assertTrue(dr.getMustSupport().stream().filter(x -> x.getValue().equals("effective")).count() == 1);
        assertTrue(dr.getCodeFilter().size() == 2);
        DataRequirement.DataRequirementCodeFilterComponent cf = null;
        for (DataRequirement.DataRequirementCodeFilterComponent drcf : dr.getCodeFilter()) {
            if (drcf.getPath().equals("category") && drcf.getValueSet().equals("http://fhir.org/guides/cdc/opioid-cds/ValueSet/observation-category-laboratory")) {
                cf = drcf;
                break;
            }
        }
        assertNotNull(cf, "Expected filter on category");
        cf = null;
        for (DataRequirement.DataRequirementCodeFilterComponent drcf : dr.getCodeFilter()) {
            if (drcf.getPath().equals("code") && drcf.getValueSet().equals("http://fhir.org/guides/cdc/opioid-cds/ValueSet/pcp-medications")) {
                cf = drcf;
                break;
            }
        }
        assertNotNull(cf, "Expected filter on code");
    } catch (IOException ioException) {
        ioException.printStackTrace();
    }
}

Example 28 with ModelInfo

use of org.hl7.elm_modelinfo.r1.ModelInfo in project clinical_quality_language by cqframework.

the class TestTypes method testModelImporter.

@Test
public void testModelImporter() {
    InputStream is = null;
    try {
        File f = new File(TestTypes.class.getResource("fhir-single.xsd").getFile());
        is = new FileInputStream(f);
        XmlSchemaCollection schemaCol = new XmlSchemaCollection();
        schemaCol.setBaseUri(f.getPath());
        XmlSchema schema = schemaCol.read(new StreamSource(is));
        ModelInfo modelInfo = ModelImporter.fromXsd(schema, new ModelImporterOptions().withModel("QUICK").withElementRedeclarationPolicy(ModelImporterOptions.ElementRedeclarationPolicy.RENAME_INVALID_REDECLARATIONS), null);
        assertThat(modelInfo.getName(), is("QUICK"));
    } catch (FileNotFoundException e) {
        e.printStackTrace();
    }
}

Example 29 with ModelInfo

use of org.hl7.elm_modelinfo.r1.ModelInfo in project clinical_quality_language by cqframework.

the class Cql2ElmVisitor method visitRetrieve.

@Override
@SuppressWarnings("unchecked")
public Retrieve visitRetrieve(cqlParser.RetrieveContext ctx) {
    libraryBuilder.checkLiteralContext();
    List<String> qualifiers = parseQualifiers(ctx.namedTypeSpecifier());
    String model = getModelIdentifier(qualifiers);
    String label = getTypeIdentifier(qualifiers, parseString(ctx.namedTypeSpecifier().referentialOrTypeNameIdentifier()));
    DataType dataType = libraryBuilder.resolveTypeName(model, label);
    if (dataType == null) {
        // ERROR:
        throw new IllegalArgumentException(String.format("Could not resolve type name %s.", label));
    }
    if (!(dataType instanceof ClassType) || !((ClassType) dataType).isRetrievable()) {
        // ERROR:
        throw new IllegalArgumentException(String.format("Specified data type %s does not support retrieval.", label));
    }
    ClassType classType = (ClassType) dataType;
    // BTR -> The original intent of this code was to have the retrieve return the base type, and use the "templateId"
    // element of the retrieve to communicate the "positive" or "negative" profile to the data access layer.
    // However, because this notion of carrying the "profile" through a type is not general, it causes inconsistencies
    // when using retrieve results with functions defined in terms of the same type (see GitHub Issue #131).
    // Based on the discussion there, the retrieve will now return the declared type, whether it is a profile or not.
    // ProfileType profileType = dataType instanceof ProfileType ? (ProfileType)dataType : null;
    // NamedType namedType = profileType == null ? classType : (NamedType)classType.getBaseType();
    NamedType namedType = classType;
    ModelInfo modelInfo = libraryBuilder.getModel(namedType.getNamespace()).getModelInfo();
    boolean useStrictRetrieveTyping = modelInfo.isStrictRetrieveTyping() != null && modelInfo.isStrictRetrieveTyping();
    Retrieve retrieve = of.createRetrieve().withDataType(libraryBuilder.dataTypeToQName((DataType) namedType)).withTemplateId(classType.getIdentifier());
    if (ctx.contextIdentifier() != null) {
        List<String> identifiers = (List<String>) visit(ctx.contextIdentifier());
        Expression contextExpression = resolveQualifiedIdentifier(identifiers);
        retrieve.setContext(contextExpression);
    }
    if (ctx.terminology() != null) {
        if (ctx.codePath() != null) {
            String identifiers = (String) visit(ctx.codePath());
            retrieve.setCodeProperty(identifiers);
        } else if (classType.getPrimaryCodePath() != null) {
            retrieve.setCodeProperty(classType.getPrimaryCodePath());
        }
        Property property = null;
        CqlTranslatorException propertyException = null;
        if (retrieve.getCodeProperty() == null) {
            // ERROR:
            // WARNING:
            propertyException = new CqlSemanticException("Retrieve has a terminology target but does not specify a code path and the type of the retrieve does not have a primary code path defined.", useStrictRetrieveTyping ? CqlTranslatorException.ErrorSeverity.Error : CqlTranslatorException.ErrorSeverity.Warning, getTrackBack(ctx));
            libraryBuilder.recordParsingException(propertyException);
        } else {
            try {
                DataType codeType = libraryBuilder.resolvePath((DataType) namedType, retrieve.getCodeProperty());
                property = of.createProperty().withPath(retrieve.getCodeProperty());
                property.setResultType(codeType);
            } catch (Exception e) {
                // ERROR:
                // WARNING:
                propertyException = new CqlSemanticException(String.format("Could not resolve code path %s for the type of the retrieve %s.", retrieve.getCodeProperty(), namedType.getName()), useStrictRetrieveTyping ? CqlTranslatorException.ErrorSeverity.Error : CqlTranslatorException.ErrorSeverity.Warning, getTrackBack(ctx), e);
                libraryBuilder.recordParsingException(propertyException);
            }
        }
        Expression terminology = null;
        if (ctx.terminology().qualifiedIdentifierExpression() != null) {
            List<String> identifiers = (List<String>) visit(ctx.terminology());
            terminology = resolveQualifiedIdentifier(identifiers);
            track(terminology, ctx.terminology().qualifiedIdentifierExpression());
        } else {
            terminology = parseExpression(ctx.terminology().expression());
        }
        String codeComparator = ctx.codeComparator() != null ? (String) visit(ctx.codeComparator()) : null;
        // Resolve the terminology target using an in or ~ operator
        try {
            if (codeComparator == null) {
                codeComparator = (terminology.getResultType() instanceof ListType || (libraryBuilder.isCompatibleWith("1.5") && terminology.getResultType().isSubTypeOf(libraryBuilder.resolveTypeName("System", "Vocabulary")))) ? "in" : "~";
            }
            if (property == null) {
                throw propertyException;
            }
            switch(codeComparator) {
                case "in":
                    {
                        Expression in = libraryBuilder.resolveIn(property, terminology);
                        if (in instanceof In) {
                            retrieve.setCodes(((In) in).getOperand().get(1));
                        } else if (in instanceof InValueSet) {
                            retrieve.setCodes(((InValueSet) in).getValueset());
                        } else if (in instanceof InCodeSystem) {
                            retrieve.setCodes(((InCodeSystem) in).getCodesystem());
                        } else if (in instanceof AnyInValueSet) {
                            retrieve.setCodes(((AnyInValueSet) in).getValueset());
                        } else if (in instanceof AnyInCodeSystem) {
                            retrieve.setCodes(((AnyInCodeSystem) in).getCodesystem());
                        } else {
                            // ERROR:
                            // WARNING:
                            libraryBuilder.recordParsingException(new CqlSemanticException(String.format("Unexpected membership operator %s in retrieve", in.getClass().getSimpleName()), useStrictRetrieveTyping ? CqlTranslatorException.ErrorSeverity.Error : CqlTranslatorException.ErrorSeverity.Warning, getTrackBack(ctx)));
                        }
                    }
                    break;
                case "~":
                    {
                        // Resolve with equivalent to verify the type of the target
                        BinaryExpression equivalent = of.createEquivalent().withOperand(property, terminology);
                        libraryBuilder.resolveBinaryCall("System", "Equivalent", equivalent);
                        // Automatically promote to a list for use in the retrieve target
                        if (!(equivalent.getOperand().get(1).getResultType() instanceof ListType)) {
                            retrieve.setCodes(libraryBuilder.resolveToList(equivalent.getOperand().get(1)));
                        } else {
                            retrieve.setCodes(equivalent.getOperand().get(1));
                        }
                    }
                    break;
                case "=":
                    {
                        // Resolve with equality to verify the type of the source and target
                        BinaryExpression equal = of.createEqual().withOperand(property, terminology);
                        libraryBuilder.resolveBinaryCall("System", "Equal", equal);
                        // Automatically promote to a list for use in the retrieve target
                        if (!(equal.getOperand().get(1).getResultType() instanceof ListType)) {
                            retrieve.setCodes(libraryBuilder.resolveToList(equal.getOperand().get(1)));
                        } else {
                            retrieve.setCodes(equal.getOperand().get(1));
                        }
                    }
                    break;
                default:
                    // ERROR:
                    // WARNING:
                    libraryBuilder.recordParsingException(new CqlSemanticException(String.format("Unknown code comparator % in retrieve", codeComparator), useStrictRetrieveTyping ? CqlTranslatorException.ErrorSeverity.Error : CqlTranslatorException.ErrorSeverity.Warning, getTrackBack(ctx.codeComparator())));
            }
            retrieve.setCodeComparator(codeComparator);
            // In that case, convert to a list of code (Union the Code elements of the Concepts in the list)
            if (retrieve.getCodes() != null && retrieve.getCodes().getResultType() != null && retrieve.getCodes().getResultType() instanceof ListType && ((ListType) retrieve.getCodes().getResultType()).getElementType().equals(libraryBuilder.resolveTypeName("System", "Concept"))) {
                if (retrieve.getCodes() instanceof ToList) {
                    // ToList will always have a single argument
                    ToList toList = (ToList) retrieve.getCodes();
                    // If that argument is a ToConcept, replace the ToList argument with the code (skip the implicit conversion, the data access layer is responsible for it)
                    if (toList.getOperand() instanceof ToConcept) {
                        toList.setOperand(((ToConcept) toList.getOperand()).getOperand());
                    } else {
                        // Otherwise, access the codes property of the resulting Concept
                        Expression codesAccessor = libraryBuilder.buildProperty(toList.getOperand(), "codes", false, toList.getOperand().getResultType());
                        retrieve.setCodes(codesAccessor);
                    }
                } else {
                    // WARNING:
                    libraryBuilder.recordParsingException(new CqlSemanticException("Terminology target is a list of concepts, but expects a list of codes", CqlTranslatorException.ErrorSeverity.Warning, getTrackBack(ctx)));
                }
            }
        } catch (Exception e) {
            // it shouldn't prevent translation unless the modelinfo indicates strict retrieve typing
            if ((libraryBuilder.isCompatibleWith("1.5") && !(terminology.getResultType().isSubTypeOf(libraryBuilder.resolveTypeName("System", "Vocabulary")))) || (!libraryBuilder.isCompatibleWith("1.5") && !(terminology.getResultType() instanceof ListType))) {
                retrieve.setCodes(libraryBuilder.resolveToList(terminology));
            } else {
                retrieve.setCodes(terminology);
            }
            retrieve.setCodeComparator(codeComparator);
            // ERROR:
            // WARNING:
            libraryBuilder.recordParsingException(new CqlSemanticException("Could not resolve membership operator for terminology target of the retrieve.", useStrictRetrieveTyping ? CqlTranslatorException.ErrorSeverity.Error : CqlTranslatorException.ErrorSeverity.Warning, getTrackBack(ctx), e));
        }
    }
    retrieves.add(retrieve);
    retrieve.setResultType(new ListType((DataType) namedType));
    return retrieve;
}