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Example 81 with Expression

use of org.hl7.fhir.r4b.model.Expression in project org.hl7.fhir.core by hapifhir.

the class QuestionnaireRenderer method addExpression.

private void addExpression(Piece p, Expression exp, String label, String url) {
    XhtmlNode x = new XhtmlNode(NodeType.Element, "li").style("font-size: 11px");
    p.addHtml(x);
    x.ah(url).tx(label);
    x.tx(": ");
    x.code(exp.getExpression());
}
Also used : XhtmlNode(org.hl7.fhir.utilities.xhtml.XhtmlNode)

Example 82 with Expression

use of org.hl7.fhir.r4b.model.Expression in project pathling by aehrc.

the class ReverseResolveFunction method invoke.

@Nonnull
@Override
public FhirPath invoke(@Nonnull final NamedFunctionInput input) {
    checkUserInput(input.getInput() instanceof ResourcePath, "Input to " + NAME + " function must be a resource: " + input.getInput().getExpression());
    final ResourcePath inputPath = (ResourcePath) input.getInput();
    final String expression = NamedFunction.expressionFromInput(input, NAME);
    checkUserInput(input.getArguments().size() == 1, "reverseResolve function accepts a single argument: " + expression);
    final FhirPath argument = input.getArguments().get(0);
    checkUserInput(argument instanceof ReferencePath, "Argument to reverseResolve function must be a Reference: " + argument.getExpression());
    final ReferencePath referencePath = (ReferencePath) argument;
    // Check that the input type is one of the possible types specified by the argument.
    final Set<ResourceType> argumentTypes = ((ReferencePath) argument).getResourceTypes();
    final ResourceType inputType = inputPath.getResourceType();
    checkUserInput(argumentTypes.contains(inputType), "Reference in argument to reverseResolve does not support input resource type: " + expression);
    // Do a left outer join from the input to the argument dataset using the reference field in the
    // argument.
    final Column joinCondition = referencePath.getResourceEquality(inputPath);
    final Dataset<Row> dataset = join(referencePath.getDataset(), inputPath.getDataset(), joinCondition, JoinType.RIGHT_OUTER);
    // Check the argument for information about the current resource that it originated from - if it
    // is not present, reverse reference resolution will not be possible.
    final NonLiteralPath nonLiteralArgument = (NonLiteralPath) argument;
    checkUserInput(nonLiteralArgument.getCurrentResource().isPresent(), "Argument to reverseResolve must be an element that is navigable from a " + "target resource type: " + expression);
    final ResourcePath currentResource = nonLiteralArgument.getCurrentResource().get();
    final Optional<Column> thisColumn = inputPath.getThisColumn();
    // TODO: Consider removing in the future once we separate ordering from element ID.
    // Create an synthetic element ID column for reverse resolved resources.
    final Column currentResourceValue = currentResource.getValueColumn();
    final WindowSpec windowSpec = Window.partitionBy(inputPath.getIdColumn(), inputPath.getOrderingColumn()).orderBy(currentResourceValue);
    // row_number() is 1-based, and we use 0-based indexes - thus (minus(1)).
    final Column currentResourceIndex = when(currentResourceValue.isNull(), lit(null)).otherwise(row_number().over(windowSpec).minus(lit(1)));
    // We need to add the synthetic EID column to the parser context so that it can be used within
    // joins in certain situations, e.g. extract.
    final Column syntheticEid = inputPath.expandEid(currentResourceIndex);
    final DatasetWithColumn datasetWithEid = QueryHelpers.createColumn(dataset, syntheticEid);
    input.getContext().getNodeIdColumns().putIfAbsent(expression, datasetWithEid.getColumn());
    final ResourcePath result = currentResource.copy(expression, datasetWithEid.getDataset(), inputPath.getIdColumn(), Optional.of(syntheticEid), currentResource.getValueColumn(), false, thisColumn);
    result.setCurrentResource(currentResource);
    return result;
}
Also used : FhirPath(au.csiro.pathling.fhirpath.FhirPath) ResourceType(org.hl7.fhir.r4.model.Enumerations.ResourceType) ResourcePath(au.csiro.pathling.fhirpath.ResourcePath) DatasetWithColumn(au.csiro.pathling.QueryHelpers.DatasetWithColumn) Column(org.apache.spark.sql.Column) DatasetWithColumn(au.csiro.pathling.QueryHelpers.DatasetWithColumn) ReferencePath(au.csiro.pathling.fhirpath.element.ReferencePath) Row(org.apache.spark.sql.Row) NonLiteralPath(au.csiro.pathling.fhirpath.NonLiteralPath) WindowSpec(org.apache.spark.sql.expressions.WindowSpec) Nonnull(javax.annotation.Nonnull)

Example 83 with Expression

use of org.hl7.fhir.r4b.model.Expression in project pathling by aehrc.

the class TranslateFunction method invoke.

@Nonnull
@Override
public FhirPath invoke(@Nonnull final NamedFunctionInput input) {
    validateInput(input);
    final ElementPath inputPath = (ElementPath) input.getInput();
    final ParserContext inputContext = input.getContext();
    final Column idColumn = inputPath.getIdColumn();
    final Column conceptColumn = inputPath.getValueColumn();
    final boolean isCodeableConcept = isCodeableConcept(inputPath);
    final Column codingArrayCol = isCodeableConcept ? conceptColumn.getField("coding") : when(conceptColumn.isNotNull(), array(conceptColumn)).otherwise(lit(null));
    // The definition of the result is always the Coding element.
    @SuppressWarnings("OptionalGetWithoutIsPresent") final ElementDefinition resultDefinition = isCodeableConcept ? inputPath.getChildElement("coding").get() : inputPath.getDefinition().get();
    // Prepare the data which will be used within the map operation. All of these things must be
    // Serializable.
    @SuppressWarnings("OptionalGetWithoutIsPresent") final TerminologyServiceFactory terminologyServiceFactory = inputContext.getTerminologyServiceFactory().get();
    final Arguments arguments = Arguments.of(input);
    final String conceptMapUrl = arguments.getValue(0, String.class);
    final boolean reverse = arguments.getValueOr(1, DEFAULT_REVERSE);
    final String equivalence = arguments.getValueOr(2, DEFAULT_EQUIVALENCE);
    final Dataset<Row> dataset = inputPath.getDataset();
    final MapperWithPreview<List<SimpleCoding>, Row[], ConceptTranslator> mapper = new TranslateMapperWithPreview(MDC.get("requestId"), terminologyServiceFactory, conceptMapUrl, reverse, Strings.parseCsvList(equivalence, wrapInUserInputError(ConceptMapEquivalence::fromCode)));
    final Dataset<Row> translatedDataset = SqlExtensions.mapWithPartitionPreview(dataset, codingArrayCol, SimpleCodingsDecoders::decodeList, mapper, StructField.apply("result", DataTypes.createArrayType(CodingEncoding.DATA_TYPE), true, Metadata.empty()));
    // The result is an array of translations per each input element, which we now
    // need to explode in the same way as for path traversal, creating unique element ids.
    final MutablePair<Column, Column> valueAndEidColumns = new MutablePair<>();
    final Dataset<Row> resultDataset = inputPath.explodeArray(translatedDataset, translatedDataset.col("result"), valueAndEidColumns);
    // Construct a new result expression.
    final String expression = expressionFromInput(input, NAME);
    return ElementPath.build(expression, resultDataset, idColumn, Optional.of(valueAndEidColumns.getRight()), valueAndEidColumns.getLeft(), false, inputPath.getCurrentResource(), inputPath.getThisColumn(), resultDefinition);
}
Also used : TerminologyServiceFactory(au.csiro.pathling.fhir.TerminologyServiceFactory) MutablePair(org.apache.commons.lang3.tuple.MutablePair) ElementPath(au.csiro.pathling.fhirpath.element.ElementPath) Column(org.apache.spark.sql.Column) ConceptTranslator(au.csiro.pathling.terminology.ConceptTranslator) SimpleCodingsDecoders(au.csiro.pathling.fhirpath.encoding.SimpleCodingsDecoders) List(java.util.List) ConceptMapEquivalence(org.hl7.fhir.r4.model.Enumerations.ConceptMapEquivalence) ElementDefinition(au.csiro.pathling.fhirpath.element.ElementDefinition) Row(org.apache.spark.sql.Row) ParserContext(au.csiro.pathling.fhirpath.parser.ParserContext) Nonnull(javax.annotation.Nonnull)

Example 84 with Expression

use of org.hl7.fhir.r4b.model.Expression in project pathling by aehrc.

the class ElementPath method getInstance.

@Nonnull
private static ElementPath getInstance(@Nonnull final String expression, @Nonnull final Dataset<Row> dataset, @Nonnull final Column idColumn, @Nonnull final Optional<Column> eidColumn, @Nonnull final Column valueColumn, final boolean singular, @Nonnull final Optional<ResourcePath> currentResource, @Nonnull final Optional<Column> thisColumn, @Nonnull final FHIRDefinedType fhirType) {
    // Look up the class that represents an element with the specified FHIR type.
    final Class<? extends ElementPath> elementPathClass = ElementDefinition.elementClassForType(fhirType).orElse(ElementPath.class);
    final DatasetWithColumnMap datasetWithColumns = eidColumn.map(eidCol -> createColumns(dataset, eidCol, valueColumn)).orElseGet(() -> createColumns(dataset, valueColumn));
    try {
        // Call its constructor and return.
        final Constructor<? extends ElementPath> constructor = elementPathClass.getDeclaredConstructor(String.class, Dataset.class, Column.class, Optional.class, Column.class, boolean.class, Optional.class, Optional.class, FHIRDefinedType.class);
        return constructor.newInstance(expression, datasetWithColumns.getDataset(), idColumn, eidColumn.map(datasetWithColumns::getColumn), datasetWithColumns.getColumn(valueColumn), singular, currentResource, thisColumn, fhirType);
    } catch (final NoSuchMethodException | InstantiationException | IllegalAccessException | InvocationTargetException e) {
        throw new RuntimeException("Problem building an ElementPath class", e);
    }
}
Also used : Getter(lombok.Getter) Dataset(org.apache.spark.sql.Dataset) NonLiteralPath(au.csiro.pathling.fhirpath.NonLiteralPath) FHIRDefinedType(org.hl7.fhir.r4.model.Enumerations.FHIRDefinedType) Column(org.apache.spark.sql.Column) QueryHelpers.createColumns(au.csiro.pathling.QueryHelpers.createColumns) Row(org.apache.spark.sql.Row) Constructor(java.lang.reflect.Constructor) ResourcePath(au.csiro.pathling.fhirpath.ResourcePath) InvocationTargetException(java.lang.reflect.InvocationTargetException) AccessLevel(lombok.AccessLevel) DatasetWithColumnMap(au.csiro.pathling.QueryHelpers.DatasetWithColumnMap) FhirPath(au.csiro.pathling.fhirpath.FhirPath) Optional(java.util.Optional) InvalidUserInputError(au.csiro.pathling.errors.InvalidUserInputError) Nonnull(javax.annotation.Nonnull) DatasetWithColumnMap(au.csiro.pathling.QueryHelpers.DatasetWithColumnMap) InvocationTargetException(java.lang.reflect.InvocationTargetException) Nonnull(javax.annotation.Nonnull)

Example 85 with Expression

use of org.hl7.fhir.r4b.model.Expression in project pathling by aehrc.

the class CodingLiteralPathTest method roundTripWithQuotedComponentWithComma.

@Test
void roundTripWithQuotedComponentWithComma() {
    final String expression = "http://snomed.info/sct|'46,2'|http://snomed.info/sct/32506021000036107/version/20201231";
    final CodingLiteralPath codingLiteralPath = CodingLiteralPath.fromString(expression, inputContext);
    final Coding literalValue = codingLiteralPath.getLiteralValue();
    assertEquals("http://snomed.info/sct", literalValue.getSystem());
    assertEquals("http://snomed.info/sct/32506021000036107/version/20201231", literalValue.getVersion());
    assertEquals("46,2", literalValue.getCode());
    final String actualExpression = codingLiteralPath.getExpression();
    assertEquals(expression, actualExpression);
}
Also used : Coding(org.hl7.fhir.r4.model.Coding) Test(org.junit.jupiter.api.Test) SpringBootTest(org.springframework.boot.test.context.SpringBootTest)

Aggregations

HashMap (java.util.HashMap)33 Test (org.junit.Test)30 Test (org.junit.jupiter.api.Test)30 Patient (org.hl7.fhir.r4.model.Patient)29 CqlEvaluator (com.ibm.cohort.cql.evaluation.CqlEvaluator)28 CqlVersionedIdentifier (com.ibm.cohort.cql.library.CqlVersionedIdentifier)28 ArrayList (java.util.ArrayList)27 Expression (org.hl7.elm.r1.Expression)26 SpringBootTest (org.springframework.boot.test.context.SpringBootTest)25 CqlEvaluationResult (com.ibm.cohort.cql.evaluation.CqlEvaluationResult)24 FHIRException (org.hl7.fhir.exceptions.FHIRException)19 FhirServerConfig (com.ibm.cohort.fhir.client.config.FhirServerConfig)16 Coding (org.hl7.fhir.r4.model.Coding)15 Complex (org.hl7.fhir.r4.utils.formats.Turtle.Complex)14 Row (org.apache.spark.sql.Row)12 List (java.util.List)11 Complex (org.hl7.fhir.dstu3.utils.formats.Turtle.Complex)11 FhirPath (au.csiro.pathling.fhirpath.FhirPath)10 Nonnull (javax.annotation.Nonnull)10 RestIntegrationTest (org.opencds.cqf.ruler.test.RestIntegrationTest)9