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());
}
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;
}
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);
}
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);
}
}
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);
}
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