Examples with ConceptMapEquivalence org.hl7.fhir.dstu3.model.Enumerations.ConceptMapEquivalence used on opensource projects

Example 1 with ConceptMapEquivalence

use of org.hl7.fhir.dstu3.model.Enumerations.ConceptMapEquivalence in project org.hl7.fhir.core by hapifhir.

the class StructureMapUtilities method parseConceptMap.

private void parseConceptMap(StructureMap result, FHIRLexer lexer) throws FHIRLexerException {
    lexer.token("conceptmap");
    ConceptMap map = new ConceptMap();
    String id = lexer.readConstant("map id");
    if (!id.startsWith("#"))
        lexer.error("Concept Map identifier must start with #");
    map.setId(id);
    // todo: how to add this to the text format
    map.setStatus(PublicationStatus.DRAFT);
    result.getContained().add(map);
    lexer.token("{");
    lexer.skipComments();
    // lexer.token("source");
    // map.setSource(new UriType(lexer.readConstant("source")));
    // lexer.token("target");
    // map.setSource(new UriType(lexer.readConstant("target")));
    Map<String, String> prefixes = new HashMap<String, String>();
    while (lexer.hasToken("prefix")) {
        lexer.token("prefix");
        String n = lexer.take();
        lexer.token("=");
        String v = lexer.readConstant("prefix url");
        prefixes.put(n, v);
    }
    while (lexer.hasToken("unmapped")) {
        lexer.token("unmapped");
        lexer.token("for");
        String n = readPrefix(prefixes, lexer);
        ConceptMapGroupComponent g = getGroup(map, n, null);
        lexer.token("=");
        String v = lexer.take();
        if (v.equals("provided")) {
            g.getUnmapped().setMode(ConceptMapGroupUnmappedMode.PROVIDED);
        } else
            lexer.error("Only unmapped mode PROVIDED is supported at this time");
    }
    while (!lexer.hasToken("}")) {
        String srcs = readPrefix(prefixes, lexer);
        lexer.token(":");
        String sc = lexer.getCurrent().startsWith("\"") ? lexer.readConstant("code") : lexer.take();
        ConceptMapEquivalence eq = readEquivalence(lexer);
        String tgts = (eq != ConceptMapEquivalence.UNMATCHED) ? readPrefix(prefixes, lexer) : "";
        ConceptMapGroupComponent g = getGroup(map, srcs, tgts);
        SourceElementComponent e = g.addElement();
        e.setCode(sc);
        if (e.getCode().startsWith("\""))
            e.setCode(lexer.processConstant(e.getCode()));
        TargetElementComponent tgt = e.addTarget();
        if (eq != ConceptMapEquivalence.EQUIVALENT)
            tgt.setEquivalence(eq);
        if (tgt.getEquivalence() != ConceptMapEquivalence.UNMATCHED) {
            lexer.token(":");
            tgt.setCode(lexer.take());
            if (tgt.getCode().startsWith("\""))
                tgt.setCode(lexer.processConstant(tgt.getCode()));
        }
        if (lexer.hasComment())
            tgt.setComment(lexer.take().substring(2).trim());
    }
    lexer.token("}");
}

Example 2 with ConceptMapEquivalence

use of org.hl7.fhir.dstu3.model.Enumerations.ConceptMapEquivalence in project org.hl7.fhir.core by hapifhir.

the class StructureMapUtilities method parseConceptMap.

private void parseConceptMap(StructureMap result, FHIRLexer lexer) throws FHIRLexerException {
    lexer.token("conceptmap");
    ConceptMap map = new ConceptMap();
    String id = lexer.readConstant("map id");
    if (id.startsWith("#")) {
        throw lexer.error("Concept Map identifier must start with #");
    }
    map.setId(id);
    // todo: how to add this to the text format
    map.setStatus(PublicationStatus.DRAFT);
    result.getContained().add(map);
    lexer.token("{");
    // lexer.token("source");
    // map.setSource(new UriType(lexer.readConstant("source")));
    // lexer.token("target");
    // map.setSource(new UriType(lexer.readConstant("target")));
    Map<String, String> prefixes = new HashMap<String, String>();
    while (lexer.hasToken("prefix")) {
        lexer.token("prefix");
        String n = lexer.take();
        lexer.token("=");
        String v = lexer.readConstant("prefix url");
        prefixes.put(n, v);
    }
    while (lexer.hasToken("unmapped")) {
        lexer.token("unmapped");
        lexer.token("for");
        String n = readPrefix(prefixes, lexer);
        ConceptMapGroupComponent g = getGroup(map, n, null);
        lexer.token("=");
        String v = lexer.take();
        if (v.equals("provided")) {
            g.getUnmapped().setMode(ConceptMapGroupUnmappedMode.PROVIDED);
        } else {
            throw lexer.error("Only unmapped mode PROVIDED is supported at this time");
        }
    }
    while (!lexer.hasToken("}")) {
        String srcs = readPrefix(prefixes, lexer);
        lexer.token(":");
        String sc = lexer.getCurrent().startsWith("\"") ? lexer.readConstant("code") : lexer.take();
        ConceptMapEquivalence eq = readEquivalence(lexer);
        String tgts = (eq != ConceptMapEquivalence.UNMATCHED) ? readPrefix(prefixes, lexer) : "";
        ConceptMapGroupComponent g = getGroup(map, srcs, tgts);
        SourceElementComponent e = g.addElement();
        e.setCode(sc);
        if (e.getCode().startsWith("\"")) {
            e.setCode(lexer.processConstant(e.getCode()));
        }
        TargetElementComponent tgt = e.addTarget();
        tgt.setEquivalence(eq);
        if (tgt.getEquivalence() != ConceptMapEquivalence.UNMATCHED) {
            lexer.token(":");
            tgt.setCode(lexer.take());
            if (tgt.getCode().startsWith("\"")) {
                tgt.setCode(lexer.processConstant(tgt.getCode()));
            }
        }
        tgt.setComment(lexer.getFirstComment());
    }
    lexer.token("}");
}

Example 3 with ConceptMapEquivalence

use of org.hl7.fhir.dstu3.model.Enumerations.ConceptMapEquivalence 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 4 with ConceptMapEquivalence

use of org.hl7.fhir.dstu3.model.Enumerations.ConceptMapEquivalence in project pathling by aehrc.

the class TranslateFunctionTest method translateCodeableConceptWithNonDefaultArguments.

@Test
void translateCodeableConceptWithNonDefaultArguments() {
    final Optional<ElementDefinition> optionalDefinition = FhirHelpers.getChildOfResource(fhirContext, "Encounter", "type");
    assertTrue(optionalDefinition.isPresent());
    final ElementDefinition definition = optionalDefinition.get();
    // The translations are
    // {
    // coding1 -> [translated1],
    // coding2 -> [translated1, translated2]
    // coding4 -> [translated2]
    // }
    // Use cases:
    // 1. [ {C2,C3,C1}, {C3}, {C4} ] -> [ [T1, T2],[], [T2]]
    // 2. [ {C3, C5}, {C3} ] -> [ [], [] ]
    // 3. [ {C2} ] -> [[T1, T2]]
    // 4. [ {C3}] -> [[]]
    // 5. [ ]-> []
    // 6. null -> null
    final Dataset<Row> inputDataset = new DatasetBuilder(spark).withIdColumn().withEidColumn().withStructTypeColumns(codeableConceptStructType()).withRow("encounter-1", makeEid(0), rowFromCodeableConcept(new CodeableConcept(CODING_2).addCoding(CODING_3).addCoding(CODING_1))).withRow("encounter-1", makeEid(1), rowFromCodeableConcept(new CodeableConcept(CODING_3).addCoding(CODING_5))).withRow("encounter-1", makeEid(2), rowFromCodeableConcept(new CodeableConcept(CODING_4))).withRow("encounter-2", makeEid(0), rowFromCodeableConcept(new CodeableConcept(CODING_3).addCoding(CODING_5))).withRow("encounter-2", makeEid(1), rowFromCodeableConcept(new CodeableConcept(CODING_3))).withRow("encounter-3", makeEid(0), rowFromCodeableConcept(new CodeableConcept(CODING_2))).withRow("encounter-4", makeEid(0), rowFromCodeableConcept(new CodeableConcept(CODING_3))).withRow("encounter-5", makeEid(0), null).withRow("encounter-6", null, null).buildWithStructValue();
    final ElementPath inputExpression = new ElementPathBuilder(spark).dataset(inputDataset).idAndEidAndValueColumns().expression("Encounter.type").singular(false).definition(definition).buildDefined();
    final ConceptTranslator returnedConceptTranslator = ConceptTranslatorBuilder.toSystem(DEST_SYSTEM_URI).put(new SimpleCoding(CODING_1), TRANSLATED_1).put(new SimpleCoding(CODING_2), TRANSLATED_1, TRANSLATED_2).put(new SimpleCoding(CODING_4), TRANSLATED_2).build();
    // Create a mock terminology client.
    when(terminologyService.translate(any(), any(), anyBoolean(), any())).thenReturn(returnedConceptTranslator);
    // Prepare the inputs to the function.
    final ParserContext parserContext = new ParserContextBuilder(spark, fhirContext).idColumn(inputExpression.getIdColumn()).terminologyClientFactory(terminologyServiceFactory).build();
    final StringLiteralPath conceptMapUrlArgument = StringLiteralPath.fromString("'" + CONCEPT_MAP2_URI + "'", inputExpression);
    final BooleanLiteralPath reverseArgument = BooleanLiteralPath.fromString("true", inputExpression);
    final StringLiteralPath equivalenceArgument = StringLiteralPath.fromString("narrower,equivalent", inputExpression);
    final NamedFunctionInput translateInput = new NamedFunctionInput(parserContext, inputExpression, Arrays.asList(conceptMapUrlArgument, reverseArgument, equivalenceArgument));
    // Invoke the function.
    final FhirPath result = new TranslateFunction().invoke(translateInput);
    final Dataset<Row> expectedResult = new DatasetBuilder(spark).withIdColumn().withEidColumn().withStructTypeColumns(codingStructType()).withRow("encounter-1", makeEid(0, 0), rowFromCoding(TRANSLATED_1)).withRow("encounter-1", makeEid(0, 1), rowFromCoding(TRANSLATED_2)).withRow("encounter-1", makeEid(1, 0), null).withRow("encounter-1", makeEid(2, 0), rowFromCoding(TRANSLATED_2)).withRow("encounter-2", makeEid(0, 0), null).withRow("encounter-2", makeEid(1, 0), null).withRow("encounter-3", makeEid(0, 0), rowFromCoding(TRANSLATED_1)).withRow("encounter-3", makeEid(0, 1), rowFromCoding(TRANSLATED_2)).withRow("encounter-4", makeEid(0, 0), null).withRow("encounter-5", makeEid(0, 0), null).withRow("encounter-6", null, null).buildWithStructValue();
    // Check the result.
    assertThat(result).hasExpression("Encounter.type.translate('" + CONCEPT_MAP2_URI + "', true, 'narrower,equivalent')").isElementPath(CodingPath.class).hasFhirType(FHIRDefinedType.CODING).isNotSingular().selectOrderedResultWithEid().hasRows(expectedResult);
    // Verify mocks
    final Set<SimpleCoding> expectedSourceCodings = ImmutableSet.of(new SimpleCoding(CODING_1), new SimpleCoding(CODING_2), new SimpleCoding(CODING_3), new SimpleCoding(CODING_4), new SimpleCoding(CODING_5));
    final List<ConceptMapEquivalence> expectedEquivalences = Arrays.asList(ConceptMapEquivalence.NARROWER, ConceptMapEquivalence.EQUIVALENT);
    verify(terminologyService).translate(eq(expectedSourceCodings), eq(CONCEPT_MAP2_URI), eq(true), eq(expectedEquivalences));
    verifyNoMoreInteractions(terminologyService);
}

Example 5 with ConceptMapEquivalence

use of org.hl7.fhir.dstu3.model.Enumerations.ConceptMapEquivalence in project pathling by aehrc.

the class TranslateFunctionTest method translateCodingWithDefaultArguments.

@Test
void translateCodingWithDefaultArguments() {
    final Optional<ElementDefinition> optionalDefinition = FhirHelpers.getChildOfResource(fhirContext, "Encounter", "class");
    assertTrue(optionalDefinition.isPresent());
    final ElementDefinition definition = optionalDefinition.get();
    // The translations are
    // {
    // coding1 -> [translated1],
    // coding2 -> [translated1, translated2]
    // }
    // Use cases:
    // 1. [ C2,C3,C1 ] -> [ [T1, T2],[], [T1]]
    // 2. [ C3, C5 ] -> [[],[]]
    // 3. [ C2 ] -> [ [T1, T2] ]
    // 4. [] -> []
    // 5. null -> null
    final Dataset<Row> inputDataset = new DatasetBuilder(spark).withIdColumn().withEidColumn().withStructTypeColumns(codingStructType()).withRow("encounter-1", makeEid(0), rowFromCoding(CODING_2)).withRow("encounter-1", makeEid(1), rowFromCoding(CODING_3)).withRow("encounter-1", makeEid(2), rowFromCoding(CODING_1)).withRow("encounter-2", makeEid(0), rowFromCoding(CODING_3)).withRow("encounter-2", makeEid(1), rowFromCoding(CODING_5)).withRow("encounter-3", makeEid(0), rowFromCoding(CODING_2)).withRow("encounter-4", makeEid(0), null).withRow("encounter-5", null, null).buildWithStructValue();
    final CodingPath inputExpression = (CodingPath) new ElementPathBuilder(spark).dataset(inputDataset).idAndEidAndValueColumns().expression("Encounter.class").singular(false).definition(definition).buildDefined();
    final ConceptTranslator returnedConceptTranslator = ConceptTranslatorBuilder.toSystem(DEST_SYSTEM_URI).put(new SimpleCoding(CODING_1), TRANSLATED_1).put(new SimpleCoding(CODING_2), TRANSLATED_1, TRANSLATED_2).build();
    // Create a mock terminology client.
    when(terminologyService.translate(any(), any(), anyBoolean(), any())).thenReturn(returnedConceptTranslator);
    // Prepare the inputs to the function.
    final ParserContext parserContext = new ParserContextBuilder(spark, fhirContext).idColumn(inputExpression.getIdColumn()).terminologyClientFactory(terminologyServiceFactory).build();
    final StringLiteralPath conceptMapUrlArgument = StringLiteralPath.fromString("'" + CONCEPT_MAP1_URI + "'", inputExpression);
    final NamedFunctionInput translateInput = new NamedFunctionInput(parserContext, inputExpression, Collections.singletonList(conceptMapUrlArgument));
    // Invoke the function.
    final FhirPath result = new TranslateFunction().invoke(translateInput);
    final Dataset<Row> expectedResult = new DatasetBuilder(spark).withIdColumn().withEidColumn().withStructTypeColumns(codingStructType()).withRow("encounter-1", makeEid(0, 0), rowFromCoding(TRANSLATED_1)).withRow("encounter-1", makeEid(0, 1), rowFromCoding(TRANSLATED_2)).withRow("encounter-1", makeEid(1, 0), null).withRow("encounter-1", makeEid(2, 0), rowFromCoding(TRANSLATED_1)).withRow("encounter-2", makeEid(0, 0), null).withRow("encounter-2", makeEid(1, 0), null).withRow("encounter-3", makeEid(0, 0), rowFromCoding(TRANSLATED_1)).withRow("encounter-3", makeEid(0, 1), rowFromCoding(TRANSLATED_2)).withRow("encounter-4", makeEid(0, 0), null).withRow("encounter-5", null, null).buildWithStructValue();
    // Check the result.
    assertThat(result).hasExpression("Encounter.class.translate('" + CONCEPT_MAP1_URI + "')").isElementPath(CodingPath.class).hasFhirType(FHIRDefinedType.CODING).isNotSingular().selectOrderedResultWithEid().hasRows(expectedResult);
    // Verify mocks
    final Set<SimpleCoding> expectedSourceCodings = ImmutableSet.of(new SimpleCoding(CODING_1), new SimpleCoding(CODING_2), new SimpleCoding(CODING_3), new SimpleCoding(CODING_5));
    final List<ConceptMapEquivalence> expectedEquivalences = Collections.singletonList(ConceptMapEquivalence.EQUIVALENT);
    verify(terminologyService).translate(eq(expectedSourceCodings), eq(CONCEPT_MAP1_URI), eq(false), eq(expectedEquivalences));
    verifyNoMoreInteractions(terminologyService);
}