Examples with FINAL org.hl7.fhir.r4.model.Observation.ObservationStatus.FINAL used on opensource projects

Example 56 with FINAL

use of org.hl7.fhir.r4.model.Observation.ObservationStatus.FINAL in project geoprism-registry by terraframe.

the class FhirExportSynchronizationManager method writeToFile.

public File writeToFile() throws IOException {
    final FhirExternalSystem system = (FhirExternalSystem) this.config.getSystem();
    try (FhirConnection connection = FhirConnectionFactory.get(system)) {
        String name = SessionPredicate.generateId();
        File root = new File(new File(VaultProperties.getPath("vault.default"), "files"), name);
        root.mkdirs();
        Bundle bundle = this.generateBundle(connection);
        FhirContext ctx = FhirContext.forR4();
        IParser parser = ctx.newJsonParser();
        try {
            parser.encodeResourceToWriter(bundle, new FileWriter(new File(root, "bundle.json")));
        } catch (DataFormatException | IOException e) {
            throw new ProgrammingErrorException(e);
        }
        return root;
    } catch (Exception e) {
        throw new HttpError(e);
    }
}

Example 57 with FINAL

use of org.hl7.fhir.r4.model.Observation.ObservationStatus.FINAL 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 58 with FINAL

use of org.hl7.fhir.r4.model.Observation.ObservationStatus.FINAL 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);
}

Example 59 with FINAL

use of org.hl7.fhir.r4.model.Observation.ObservationStatus.FINAL 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);
    }
}

Example 60 with FINAL

use of org.hl7.fhir.r4.model.Observation.ObservationStatus.FINAL in project pathling by aehrc.

the class ManifestConverter method populateScope.

void populateScope(@Nonnull final PassportScope passportScope, @Nonnull final VisaManifest manifest) {
    // Create a filter for the Patient resource.
    final String patientIdCollection = manifest.getPatientIds().stream().map(id -> "'" + id + "'").collect(Collectors.joining(" combine "));
    final String patientIdFilter = "identifier.where(system = '" + StringLiteralPath.escapeFhirPathString(patientIdSystem) + "').where(value in (" + patientIdCollection + "))" + ".empty().not()";
    final Set<String> patientFilters = passportScope.get(ResourceType.PATIENT);
    if (patientFilters == null) {
        passportScope.put(ResourceType.PATIENT, new HashSet<>(List.of(patientIdFilter)));
    } else {
        patientFilters.add(patientIdFilter);
    }
    // See: https://www.hl7.org/fhir/r4/compartmentdefinition-patient.html
    for (final ResourceType resourceType : ResourceType.values()) {
        if (resourceType.equals(ResourceType.DOMAINRESOURCE) || resourceType.equals(ResourceType.RESOURCE) || resourceType.equals(ResourceType.NULL)) {
            continue;
        }
        final RuntimeResourceDefinition definition = fhirContext.getResourceDefinition(resourceType.toCode());
        final List<RuntimeSearchParam> searchParams = definition.getSearchParamsForCompartmentName("Patient");
        for (final RuntimeSearchParam searchParam : searchParams) {
            final String path = searchParam.getPath();
            // Remove the leading "[resource type]." from the path.
            final String pathTrimmed = path.replaceFirst("^" + resourceType.toCode() + "\\.", "");
            // Paths that end with this resolve pattern are polymorphic references, and will need
            // to be resolved using `ofType()` within our implementation.
            final String resolvePattern = ".where(resolve() is Patient)";
            final String filter;
            if (pathTrimmed.endsWith(resolvePattern)) {
                filter = pathTrimmed.replace(resolvePattern, ".resolve().ofType(Patient)." + patientIdFilter);
            } else {
                final Set<String> targets = searchParam.getTargets();
                if (targets.size() > 0 && !targets.contains("Patient")) {
                    // Patient, we need to skip it altogether.
                    continue;
                } else if (targets.size() == 1) {
                    // If the search parameter is monomorphic, we can resolve it without `ofType`.
                    filter = pathTrimmed + ".resolve()." + patientIdFilter;
                } else {
                    // If the search parameter is polymorphic, we also need to resolve it to Patient. Note
                    // that polymorphic references with an "Any" type have zero targets.
                    filter = pathTrimmed + ".resolve().ofType(Patient)." + patientIdFilter;
                }
            }
            // Add the filter to the map.
            final Set<String> filters = passportScope.get(resourceType);
            if (filters == null) {
                passportScope.put(resourceType, new HashSet<>(List.of(filter)));
            } else {
                filters.add(filter);
            }
        }
    }
}