Examples with StringLiteralPath au.csiro.pathling.fhirpath.literal.StringLiteralPath used on opensource projects

Example 1 with StringLiteralPath

use of au.csiro.pathling.fhirpath.literal.StringLiteralPath in project pathling by aehrc.

the class MemberOfFunction method validateInput.

private void validateInput(@Nonnull final NamedFunctionInput input) {
    final ParserContext context = input.getContext();
    checkUserInput(context.getTerminologyServiceFactory().isPresent(), "Attempt to call terminology function " + NAME + " when terminology service has not been configured");
    final FhirPath inputPath = input.getInput();
    checkUserInput(inputPath instanceof ElementPath && (((ElementPath) inputPath).getFhirType().equals(FHIRDefinedType.CODING) || ((ElementPath) inputPath).getFhirType().equals(FHIRDefinedType.CODEABLECONCEPT)), "Input to memberOf function is of unsupported type: " + inputPath.getExpression());
    checkUserInput(input.getArguments().size() == 1, "memberOf function accepts one argument of type String");
    final FhirPath argument = input.getArguments().get(0);
    checkUserInput(argument instanceof StringLiteralPath, "memberOf function accepts one argument of type String literal");
}

Example 2 with StringLiteralPath

use of au.csiro.pathling.fhirpath.literal.StringLiteralPath in project pathling by aehrc.

the class TranslateFunction method validateInput.

private void validateInput(@Nonnull final NamedFunctionInput input) {
    final ParserContext context = input.getContext();
    checkUserInput(context.getTerminologyServiceFactory().isPresent(), "Attempt to call terminology function " + NAME + " when terminology service has not been configured");
    final FhirPath inputPath = input.getInput();
    checkUserInput(TerminologyUtils.isCodingOrCodeableConcept(inputPath), String.format("Input to %s function is of unsupported type: %s", NAME, inputPath.getExpression()));
    final List<FhirPath> arguments = input.getArguments();
    checkUserInput(arguments.size() >= 1 && arguments.size() <= 3, NAME + " function accepts one required and two optional arguments");
    checkUserInput(arguments.get(0) instanceof StringLiteralPath, String.format("Function `%s` expects `%s` as argument %s", NAME, "String literal", 1));
    checkUserInput(arguments.size() <= 1 || arguments.get(1) instanceof BooleanLiteralPath, String.format("Function `%s` expects `%s` as argument %s", NAME, "Boolean literal", 2));
    checkUserInput(arguments.size() <= 2 || arguments.get(2) instanceof StringLiteralPath, String.format("Function `%s` expects `%s` as argument %s", NAME, "String literal", 3));
}

Example 3 with StringLiteralPath

use of au.csiro.pathling.fhirpath.literal.StringLiteralPath in project pathling by aehrc.

the class ExtensionFunction method invoke.

@Nonnull
@Override
public FhirPath invoke(@Nonnull final NamedFunctionInput input) {
    final String expression = NamedFunction.expressionFromInput(input, NAME);
    checkUserInput(input.getArguments().size() == 1, "extension function must have one argument: " + expression);
    final FhirPath urlArgument = input.getArguments().get(0);
    checkUserInput(urlArgument instanceof StringLiteralPath, "extension function must have argument of type String literal: " + expression);
    final NonLiteralPath inputPath = input.getInput();
    final ElementPath extensionPath = new PathTraversalOperator().invoke(new PathTraversalInput(input.getContext(), inputPath, ExtensionSupport.EXTENSION_ELEMENT_NAME()));
    // Now we need to create a correct argument context for the `where` call.
    final ParserContext argumentContext = input.getContext();
    final FhirPath extensionUrlPath = new PathTraversalOperator().invoke(new PathTraversalInput(argumentContext, extensionPath.toThisPath(), "url"));
    final FhirPath extensionUrCondition = new ComparisonOperator(ComparisonOperation.EQUALS).invoke(new OperatorInput(argumentContext, extensionUrlPath, urlArgument));
    // Override the expression in the function input.
    return new WhereFunction().invoke(new NamedFunctionInput(input.getContext(), extensionPath, Collections.singletonList(extensionUrCondition), expression));
}

Example 4 with StringLiteralPath

use of au.csiro.pathling.fhirpath.literal.StringLiteralPath in project pathling by aehrc.

the class ExtensionFunctionTest method testExtensionOnElements.

@Test
public void testExtensionOnElements() {
    final ParserContext parserContext = new ParserContextBuilder(spark, fhirContext).build();
    // Construct element dataset from the resource dataset so that the resource path
    // can be used as the current resource for this element path
    // Note: this resource path is not singular as this will be a base for elements.
    final Dataset<Row> resourceLikeDataset = new ResourceDatasetBuilder(spark).withIdColumn().withEidColumn().withStructColumn("name", DataTypes.StringType).withStructColumn("_fid", DataTypes.IntegerType).withStructValueColumn().withExtensionColumn().withRow("observation-1", makeEid(0), RowFactory.create("name1", 0), oneEntryMap(0, MANY_MY_EXTENSIONS)).withRow("observation-2", makeEid(0), RowFactory.create("name2", 1), oneEntryMap(1, ONE_MY_EXTENSION)).withRow("observation-3", makeEid(0), RowFactory.create("name3", 2), oneEntryMap(2, NO_MY_EXTENSIONS)).withRow("observation-4", makeEid(0), RowFactory.create("name4", 3), oneEntryMap(3, ONE_MY_EXTENSION)).withRow("observation-4", makeEid(1), RowFactory.create("name5", 4), oneEntryMap(3, ONE_MY_EXTENSION)).withRow("observation-5", makeEid(0), null, null).withRow("observation-5", makeEid(1), null, null).build();
    when(database.read(ResourceType.OBSERVATION)).thenReturn(resourceLikeDataset);
    final ResourcePath baseResourcePath = ResourcePath.build(fhirContext, database, ResourceType.OBSERVATION, "Observation", false);
    final Dataset<Row> elementDataset = toElementDataset(resourceLikeDataset, baseResourcePath);
    final ElementDefinition codeDefinition = checkPresent(FhirHelpers.getChildOfResource(fhirContext, "Observation", "code"));
    final ElementPath inputPath = new ElementPathBuilder(spark).fhirType(FHIRDefinedType.CODEABLECONCEPT).definition(codeDefinition).dataset(elementDataset).idAndEidAndValueColumns().expression("code").singular(false).currentResource(baseResourcePath).buildDefined();
    final StringLiteralPath argumentExpression = StringLiteralPath.fromString("'" + "uuid:myExtension" + "'", inputPath);
    final NamedFunctionInput extensionInput = new NamedFunctionInput(parserContext, inputPath, Collections.singletonList(argumentExpression));
    final NamedFunction extension = NamedFunction.getInstance("extension");
    final FhirPath result = extension.invoke(extensionInput);
    final Dataset<Row> expectedResult = new DatasetBuilder(spark).withIdColumn().withEidColumn().withStructTypeColumns(DatasetBuilder.SIMPLE_EXTENSION_TYPE).withRow("observation-1", makeEid(0, 0), null).withRow("observation-1", makeEid(0, 1), null).withRow("observation-1", makeEid(0, 2), MANY_EXT_ROW_1).withRow("observation-1", makeEid(0, 3), MANY_EXT_ROW_2).withRow("observation-2", makeEid(0, 0), null).withRow("observation-2", makeEid(0, 1), ONE_EXT_ROW_1).withRow("observation-3", makeEid(0, 0), null).withRow("observation-3", makeEid(0, 1), null).withRow("observation-4", makeEid(0, 0), null).withRow("observation-4", makeEid(0, 1), ONE_EXT_ROW_1).withRow("observation-4", makeEid(1, 0), null).withRow("observation-5", makeEid(0, 0), null).withRow("observation-5", makeEid(1, 0), null).buildWithStructValue();
    assertThat(result).hasExpression("code.extension('uuid:myExtension')").isNotSingular().isElementPath(ElementPath.class).hasFhirType(FHIRDefinedType.EXTENSION).selectOrderedResultWithEid().hasRows(expectedResult);
}

Example 5 with StringLiteralPath

use of au.csiro.pathling.fhirpath.literal.StringLiteralPath in project pathling by aehrc.

the class IifFunctionTest method throwsErrorIfConditionNotBoolean.

@Test
void throwsErrorIfConditionNotBoolean() {
    final ElementPath condition = new ElementPathBuilder(spark).fhirType(FHIRDefinedType.INTEGER).expression("valueInteger").singular(true).build();
    final StringLiteralPath ifTrue = StringLiteralPath.fromString("foo", condition);
    final StringLiteralPath otherwise = StringLiteralPath.fromString("bar", condition);
    final NamedFunctionInput iifInput = new NamedFunctionInput(parserContext, condition, Arrays.asList(condition, ifTrue, otherwise));
    final NamedFunction notFunction = NamedFunction.getInstance("iif");
    final InvalidUserInputError error = assertThrows(InvalidUserInputError.class, () -> notFunction.invoke(iifInput));
    assertEquals("Condition argument to iif must be Boolean: valueInteger", error.getMessage());
}