Examples with Argument org.hl7.fhir.utilities.graphql.Argument used on opensource projects

Example 31 with Argument

use of org.hl7.fhir.utilities.graphql.Argument in project pathling by aehrc.

the class SubsumesFunctionTest method createNullCodingArg.

CodingPath createNullCodingArg() {
    final Dataset<Row> dataset = new DatasetBuilder(spark).withIdColumn().withStructTypeColumns(codingStructType()).withIdValueRows(ALL_RES_IDS, id -> null).buildWithStructValue();
    final ElementPath argument = new ElementPathBuilder(spark).fhirType(FHIRDefinedType.CODING).dataset(dataset).idAndValueColumns().build();
    return (CodingPath) argument;
}

Example 32 with Argument

use of org.hl7.fhir.utilities.graphql.Argument in project pathling by aehrc.

the class SubsumesFunctionTest method createCodingArg.

CodingPath createCodingArg() {
    final Dataset<Row> dataset = new DatasetBuilder(spark).withIdColumn().withStructTypeColumns(codingStructType()).withIdValueRows(ALL_RES_IDS, id -> rowFromCoding(CODING_MEDIUM)).withIdValueRows(ALL_RES_IDS, id -> rowFromCoding(CODING_OTHER3)).buildWithStructValue();
    final ElementPath argument = new ElementPathBuilder(spark).fhirType(FHIRDefinedType.CODING).dataset(dataset).idAndValueColumns().build();
    return (CodingPath) argument;
}

Example 33 with Argument

use of org.hl7.fhir.utilities.graphql.Argument in project pathling by aehrc.

the class ValueSetMapping method toIntersection.

/**
 * Constructs a {@link ValueSet} representing the intersection of a set of codings and a server
 *
 * @param valueSetUri the server defined value set.
 * @param codings the set of codings to intersect.
 * @return the intersection value set.
 */
@Nonnull
public static ValueSet toIntersection(@Nonnull final String valueSetUri, @Nonnull final Collection<SimpleCoding> codings) {
    final Set<CodeSystemReference> validCodeSystems = codings.stream().filter(SimpleCoding::isDefined).map(coding -> new CodeSystemReference(Optional.ofNullable(coding.getSystem()), Optional.ofNullable(coding.getVersion()))).collect(Collectors.toUnmodifiableSet());
    // Create a ValueSet to represent the intersection of the input codings and the ValueSet
    // described by the URI in the argument.
    final ValueSet intersection = new ValueSet();
    final ValueSetComposeComponent compose = new ValueSetComposeComponent();
    final List<ConceptSetComponent> includes = new ArrayList<>();
    // Create an include section for each unique code system present within the input codings.
    for (final CodeSystemReference codeSystem : validCodeSystems) {
        final ConceptSetComponent include = new ConceptSetComponent();
        include.setValueSet(Collections.singletonList(new CanonicalType(valueSetUri)));
        // noinspection OptionalGetWithoutIsPresent
        include.setSystem(codeSystem.getSystem().get());
        codeSystem.getVersion().ifPresent(include::setVersion);
        // Add the codings that match the current code system.
        final List<ConceptReferenceComponent> concepts = codings.stream().filter(codeSystem::matchesCoding).map(SimpleCoding::getCode).filter(Objects::nonNull).distinct().map(code -> {
            final ConceptReferenceComponent concept = new ConceptReferenceComponent();
            concept.setCode(code);
            return concept;
        }).collect(Collectors.toList());
        if (!concepts.isEmpty()) {
            include.setConcept(concepts);
            includes.add(include);
        }
    }
    compose.setInclude(includes);
    intersection.setCompose(compose);
    return intersection;
}

Example 34 with Argument

use of org.hl7.fhir.utilities.graphql.Argument 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;
        CqlCompilerException 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 ? CqlCompilerException.ErrorSeverity.Error : CqlCompilerException.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 ? CqlCompilerException.ErrorSeverity.Error : CqlCompilerException.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 ? CqlCompilerException.ErrorSeverity.Error : CqlCompilerException.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 ? CqlCompilerException.ErrorSeverity.Error : CqlCompilerException.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", CqlCompilerException.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 ? CqlCompilerException.ErrorSeverity.Error : CqlCompilerException.ErrorSeverity.Warning, getTrackBack(ctx), e));
        }
    }
    retrieves.add(retrieve);
    retrieve.setResultType(new ListType((DataType) namedType));
    return retrieve;
}

Example 35 with Argument

use of org.hl7.fhir.utilities.graphql.Argument in project quality-measure-and-cohort-service by Alvearie.

the class AnyColumnVisitor method visitFunctionRef.

@Override
public Object visitFunctionRef(FunctionRef elm, AnyColumnContext context) {
    if (AnyColumnFunctions.FUNCTION_NAMES.contains(elm.getName())) {
        if (elm.getOperand().size() == 2) {
            QName dataType = ((As) elm.getOperand().get(0)).getOperand().getResultTypeName();
            // TODO - validate that the first operand is a model object. We really should be doing that at the
            // method declaration level instead of Choice<Any>, but that will require the model
            // to have a base class that everything extends from.
            String columnMatchLogic = null;
            if (elm.getOperand().get(1) instanceof Literal) {
                columnMatchLogic = ((Literal) elm.getOperand().get(1)).getValue();
            } else {
                throw new IllegalArgumentException(String.format("Second argument to %s function at %s must be a literal", elm.getName(), elm.getLocator()));
            }
            StringMatcher matcher = null;
            if (elm.getName().equals(AnyColumnFunctions.FUNC_ANY_COLUMN)) {
                matcher = new PrefixStringMatcher(columnMatchLogic);
            } else if (elm.getName().equals(AnyColumnFunctions.FUNC_ANY_COLUMN_REGEX)) {
                matcher = new RegexStringMatcher(columnMatchLogic);
            } else {
                throw new IllegalArgumentException(String.format("Found declared, but unsupported AnyColumn function %s at %s", elm.getName(), elm.getLocator()));
            }
            context.reportAnyColumn(dataType, matcher);
        } else {
            throw new IllegalArgumentException(String.format("%s function at %s should have exactly two arguments", elm.getName(), elm.getLocator()));
        }
    }
    return super.visitFunctionRef(elm, context);
}