Examples with FhirPath au.csiro.pathling.fhirpath.FhirPath used on opensource projects

Example 1 with FhirPath

use of au.csiro.pathling.fhirpath.FhirPath 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;
}

Example 2 with FhirPath

use of au.csiro.pathling.fhirpath.FhirPath in project pathling by aehrc.

the class WhereFunction method invoke.

@Nonnull
@Override
public FhirPath invoke(@Nonnull final NamedFunctionInput input) {
    checkUserInput(input.getArguments().size() == 1, "where function accepts one argument");
    final NonLiteralPath inputPath = input.getInput();
    checkUserInput(input.getArguments().get(0) instanceof NonLiteralPath, "Argument to where function cannot be a literal: " + input.getArguments().get(0).getExpression());
    final NonLiteralPath argumentPath = (NonLiteralPath) input.getArguments().get(0);
    checkUserInput(argumentPath instanceof BooleanPath && argumentPath.isSingular(), "Argument to where function must be a singular Boolean: " + argumentPath.getExpression());
    checkUserInput(argumentPath.getThisColumn().isPresent(), "Argument to where function must be navigable from collection item (use $this): " + argumentPath.getExpression());
    final Column argumentValue = argumentPath.getValueColumn();
    // The result is the input value if it is equal to true, or null otherwise (signifying the
    // absence of a value).
    final Column idColumn = argumentPath.getIdColumn();
    final Column thisValue = checkPresent(argumentPath.getThisValueColumn());
    final Column thisEid = checkPresent(argumentPath.getThisOrderingColumn());
    final Column valueColumn = when(argumentValue.equalTo(true), thisValue).otherwise(lit(null));
    final String expression = expressionFromInput(input, NAME);
    return inputPath.copy(expression, argumentPath.getDataset(), idColumn, inputPath.getEidColumn().map(c -> thisEid), valueColumn, inputPath.isSingular(), inputPath.getThisColumn());
}

Example 3 with FhirPath

use of au.csiro.pathling.fhirpath.FhirPath 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 4 with FhirPath

use of au.csiro.pathling.fhirpath.FhirPath 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 5 with FhirPath

use of au.csiro.pathling.fhirpath.FhirPath in project pathling by aehrc.

the class SearchExecutor method initializeDataset.

@Nonnull
private Dataset<Row> initializeDataset() {
    final ResourcePath resourcePath = ResourcePath.build(getFhirContext(), getDatabase(), subjectResource, subjectResource.toCode(), true, true);
    final Dataset<Row> subjectDataset = resourcePath.getDataset();
    final Column subjectIdColumn = resourcePath.getIdColumn();
    final Dataset<Row> dataset;
    if (filters.isEmpty() || filters.get().getValuesAsQueryTokens().isEmpty()) {
        // If there are no filters, return all resources.
        dataset = subjectDataset;
    } else {
        final Collection<FhirPath> fhirPaths = new ArrayList<>();
        @Nullable Column filterIdColumn = null;
        @Nullable Column filterColumn = null;
        ResourcePath currentContext = ResourcePath.build(getFhirContext(), getDatabase(), subjectResource, subjectResource.toCode(), true);
        // https://hl7.org/fhir/R4/search.html#combining.
        for (final StringOrListParam orParam : filters.get().getValuesAsQueryTokens()) {
            @Nullable Column orColumn = null;
            for (final StringParam param : orParam.getValuesAsQueryTokens()) {
                final ParserContext parserContext = buildParserContext(currentContext, Collections.singletonList(currentContext.getIdColumn()));
                final Parser parser = new Parser(parserContext);
                final String expression = param.getValue();
                checkUserInput(!expression.isBlank(), "Filter expression cannot be blank");
                final FhirPath fhirPath = parser.parse(expression);
                checkUserInput(fhirPath instanceof BooleanPath || fhirPath instanceof BooleanLiteralPath, "Filter expression must be of Boolean type: " + fhirPath.getExpression());
                final Column filterValue = fhirPath.getValueColumn();
                // Add each expression to a list that will later be joined.
                fhirPaths.add(fhirPath);
                // Combine all the OR columns with OR logic.
                orColumn = orColumn == null ? filterValue : orColumn.or(filterValue);
                // subject resource dataset with the joined filter datasets.
                if (filterIdColumn == null) {
                    filterIdColumn = fhirPath.getIdColumn();
                }
                // Update the context to build the next expression from the same dataset.
                currentContext = currentContext.copy(currentContext.getExpression(), fhirPath.getDataset(), fhirPath.getIdColumn(), currentContext.getEidColumn(), fhirPath.getValueColumn(), currentContext.isSingular(), currentContext.getThisColumn());
            }
            // Combine all the columns at this level with AND logic.
            filterColumn = filterColumn == null ? orColumn : filterColumn.and(orColumn);
        }
        checkNotNull(filterIdColumn);
        checkNotNull(filterColumn);
        check(!fhirPaths.isEmpty());
        // Get the full resources which are present in the filtered dataset.
        final String filterIdAlias = randomAlias();
        final Dataset<Row> filteredIds = currentContext.getDataset().select(filterIdColumn.alias(filterIdAlias)).filter(filterColumn);
        dataset = subjectDataset.join(filteredIds, subjectIdColumn.equalTo(col(filterIdAlias)), "left_semi");
    }
    if (getConfiguration().getSpark().getCacheDatasets()) {
        // We cache the dataset because we know it will be accessed for both the total and the record
        // retrieval.
        log.debug("Caching search dataset");
        dataset.cache();
    }
    return dataset;
}