Examples with Function org.hl7.fhir.r5.model.ExpressionNode.Function used on opensource projects

Example 56 with Function

use of org.hl7.fhir.r5.model.ExpressionNode.Function in project pathling by aehrc.

the class MemberOfFunctionTest method memberOfCodeableConcept.

@Test
void memberOfCodeableConcept() {
    final Coding coding1 = new Coding(LOINC_URL, "10337-4", "Procollagen type I [Mass/volume] in Serum");
    final Coding coding2 = new Coding(LOINC_URL, "10428-1", "Varicella zoster virus immune globulin given [Volume]");
    final Coding coding3 = new Coding(LOINC_URL, "10555-1", null);
    final Coding coding4 = new Coding(LOINC_URL, "10665-8", "Fungus colony count [#/volume] in Unspecified specimen by Environmental culture");
    final Coding coding5 = new Coding(SNOMED_URL, "416399002", "Procollagen type I amino-terminal propeptide level");
    final CodeableConcept codeableConcept1 = new CodeableConcept(coding1);
    codeableConcept1.addCoding(coding5);
    final CodeableConcept codeableConcept2 = new CodeableConcept(coding2);
    final CodeableConcept codeableConcept3 = new CodeableConcept(coding3);
    final CodeableConcept codeableConcept4 = new CodeableConcept(coding3);
    final CodeableConcept codeableConcept5 = new CodeableConcept(coding4);
    final CodeableConcept codeableConcept6 = new CodeableConcept(coding1);
    final Optional<ElementDefinition> optionalDefinition = FhirHelpers.getChildOfResource(fhirContext, "DiagnosticReport", "code");
    assertTrue(optionalDefinition.isPresent());
    final ElementDefinition definition = optionalDefinition.get();
    final Dataset<Row> inputDataset = new DatasetBuilder(spark).withIdColumn().withStructTypeColumns(codeableConceptStructType()).withRow("diagnosticreport-1", rowFromCodeableConcept(codeableConcept1)).withRow("diagnosticreport-2", rowFromCodeableConcept(codeableConcept2)).withRow("diagnosticreport-3", rowFromCodeableConcept(codeableConcept3)).withRow("diagnosticreport-4", rowFromCodeableConcept(codeableConcept4)).withRow("diagnosticreport-5", rowFromCodeableConcept(codeableConcept5)).withRow("diagnosticreport-6", rowFromCodeableConcept(codeableConcept6)).withRow("diagnosticreport-7", null).buildWithStructValue();
    final ElementPath inputExpression = new ElementPathBuilder(spark).dataset(inputDataset).idAndValueColumns().expression("DiagnosticReport.code").singular(true).definition(definition).buildDefined();
    final StringLiteralPath argumentExpression = StringLiteralPath.fromString("'" + MY_VALUE_SET_URL + "'", inputExpression);
    // Setup mocks
    when(terminologyService.intersect(any(), any())).thenReturn(setOfSimpleFrom(codeableConcept1, codeableConcept3, codeableConcept4));
    // Prepare the inputs to the function.
    final ParserContext parserContext = new ParserContextBuilder(spark, fhirContext).terminologyClientFactory(terminologyServiceFactory).build();
    final NamedFunctionInput memberOfInput = new NamedFunctionInput(parserContext, inputExpression, Collections.singletonList(argumentExpression));
    // Invoke the function.
    final FhirPath result = new MemberOfFunction().invoke(memberOfInput);
    final Dataset<Row> expectedResult = new DatasetBuilder(spark).withIdColumn().withColumn(DataTypes.BooleanType).withRow("diagnosticreport-1", true).withRow("diagnosticreport-2", false).withRow("diagnosticreport-3", true).withRow("diagnosticreport-4", true).withRow("diagnosticreport-5", false).withRow("diagnosticreport-6", true).withRow("diagnosticreport-7", null).build();
    // Check the result.
    assertTrue(result instanceof BooleanPath);
    assertThat((BooleanPath) result).hasExpression("DiagnosticReport.code.memberOf('" + MY_VALUE_SET_URL + "')").isSingular().hasFhirType(FHIRDefinedType.BOOLEAN).isElementPath(BooleanPath.class).selectOrderedResult().hasRows(expectedResult);
    verify(terminologyService).intersect(eq(MY_VALUE_SET_URL), eq(setOfSimpleFrom(coding1, coding2, coding3, coding4, coding5)));
    verifyNoMoreInteractions(terminologyService);
}

Example 57 with Function

use of org.hl7.fhir.r5.model.ExpressionNode.Function in project pathling by aehrc.

the class MemberOfFunctionTest method memberOfCoding.

@Test
void memberOfCoding() {
    final Coding coding1 = new Coding(MY_VALUE_SET_URL, "AMB", "ambulatory");
    final Coding coding2 = new Coding(MY_VALUE_SET_URL, "EMER", null);
    final Coding coding3 = new Coding(MY_VALUE_SET_URL, "IMP", "inpatient encounter");
    final Coding coding4 = new Coding(MY_VALUE_SET_URL, "IMP", null);
    final Coding coding5 = new Coding(MY_VALUE_SET_URL, "ACUTE", "inpatient acute");
    final Optional<ElementDefinition> optionalDefinition = FhirHelpers.getChildOfResource(fhirContext, "Encounter", "class");
    assertTrue(optionalDefinition.isPresent());
    final ElementDefinition definition = optionalDefinition.get();
    final Dataset<Row> inputDataset = new DatasetBuilder(spark).withIdColumn().withEidColumn().withStructTypeColumns(codingStructType()).withRow("encounter-1", makeEid(1), rowFromCoding(coding1)).withRow("encounter-1", makeEid(0), rowFromCoding(coding5)).withRow("encounter-2", makeEid(0), rowFromCoding(coding2)).withRow("encounter-3", makeEid(0), rowFromCoding(coding3)).withRow("encounter-4", makeEid(0), rowFromCoding(coding4)).withRow("encounter-5", makeEid(0), rowFromCoding(coding5)).withRow("encounter-6", null, null).buildWithStructValue();
    final CodingPath inputExpression = (CodingPath) new ElementPathBuilder(spark).dataset(inputDataset).idAndEidAndValueColumns().expression("Encounter.class").singular(false).definition(definition).buildDefined();
    final StringLiteralPath argumentExpression = StringLiteralPath.fromString("'" + MY_VALUE_SET_URL + "'", inputExpression);
    // Setup mocks
    when(terminologyService.intersect(any(), any())).thenReturn(setOfSimpleFrom(coding2, coding5));
    // Prepare the inputs to the function.
    final ParserContext parserContext = new ParserContextBuilder(spark, fhirContext).idColumn(inputExpression.getIdColumn()).terminologyClientFactory(terminologyServiceFactory).build();
    final NamedFunctionInput memberOfInput = new NamedFunctionInput(parserContext, inputExpression, Collections.singletonList(argumentExpression));
    // Invoke the function.
    final FhirPath result = new MemberOfFunction().invoke(memberOfInput);
    // The outcome is somehow random with regard to the sequence passed to MemberOfMapperAnswerer.
    final Dataset<Row> expectedResult = new DatasetBuilder(spark).withIdColumn().withEidColumn().withColumn(DataTypes.BooleanType).withRow("encounter-1", makeEid(0), true).withRow("encounter-1", makeEid(1), false).withRow("encounter-2", makeEid(0), true).withRow("encounter-3", makeEid(0), false).withRow("encounter-4", makeEid(0), false).withRow("encounter-5", makeEid(0), true).withRow("encounter-6", null, null).build();
    // Check the result.
    assertThat(result).hasExpression("Encounter.class.memberOf('" + MY_VALUE_SET_URL + "')").isElementPath(BooleanPath.class).hasFhirType(FHIRDefinedType.BOOLEAN).isNotSingular().selectOrderedResultWithEid().hasRows(expectedResult);
    verify(terminologyService).intersect(eq(MY_VALUE_SET_URL), eq(setOfSimpleFrom(coding1, coding2, coding3, coding4, coding5)));
    verifyNoMoreInteractions(terminologyService);
}

Example 58 with Function

use of org.hl7.fhir.r5.model.ExpressionNode.Function 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 59 with Function

use of org.hl7.fhir.r5.model.ExpressionNode.Function 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);
}

Example 60 with Function

use of org.hl7.fhir.r5.model.ExpressionNode.Function in project pathling by aehrc.

the class EmptyFunctionTest method returnsCorrectResults.

@Test
void returnsCorrectResults() {
    final Coding coding1 = new Coding(TestHelpers.SNOMED_URL, "840546002", "Exposure to COVID-19");
    final CodeableConcept concept1 = new CodeableConcept(coding1);
    final Coding coding2 = new Coding(TestHelpers.SNOMED_URL, "248427009", "Fever symptoms");
    final CodeableConcept concept2 = new CodeableConcept(coding2);
    final Dataset<Row> dataset = new DatasetBuilder(spark).withIdColumn().withColumn(codeableConceptStructType()).withRow("observation-1", null).withRow("observation-2", null).withRow("observation-2", null).withRow("observation-3", rowFromCodeableConcept(concept1)).withRow("observation-4", rowFromCodeableConcept(concept1)).withRow("observation-4", null).withRow("observation-5", rowFromCodeableConcept(concept1)).withRow("observation-5", rowFromCodeableConcept(concept2)).build();
    final ElementPath input = new ElementPathBuilder(spark).fhirType(FHIRDefinedType.CODEABLECONCEPT).dataset(dataset).idAndValueColumns().expression("code").build();
    final ParserContext parserContext = new ParserContextBuilder(spark, fhirContext).groupingColumns(Collections.singletonList(input.getIdColumn())).build();
    // Set up the function input.
    final NamedFunctionInput emptyInput = new NamedFunctionInput(parserContext, input, Collections.emptyList());
    // Invoke the function.
    final NamedFunction emptyFunction = NamedFunction.getInstance("empty");
    final FhirPath result = emptyFunction.invoke(emptyInput);
    // Check the result.
    final Dataset<Row> expectedDataset = new DatasetBuilder(spark).withIdColumn().withColumn(DataTypes.BooleanType).withRow("observation-1", true).withRow("observation-2", true).withRow("observation-3", false).withRow("observation-4", false).withRow("observation-5", false).build();
    assertThat(result).hasExpression("code.empty()").isSingular().isElementPath(BooleanPath.class).selectOrderedResult().hasRows(expectedDataset);
}