Examples with DatasetBuilder au.csiro.pathling.test.builders.DatasetBuilder used on opensource projects

Example 1 with DatasetBuilder

use of au.csiro.pathling.test.builders.DatasetBuilder in project pathling by aehrc.

the class CountFunctionTest method doesNotCountNullElements.

@Test
void doesNotCountNullElements() {
    final Dataset<Row> dataset = new DatasetBuilder(spark).withIdColumn().withColumn("gender", DataTypes.StringType).withRow("patient-1", "female").withRow("patient-2", null).withRow("patient-3", "male").build();
    final ElementPath inputPath = new ElementPathBuilder(spark).expression("gender").fhirType(FHIRDefinedType.CODE).dataset(dataset).idAndValueColumns().build();
    final ParserContext parserContext = new ParserContextBuilder(spark, fhirContext).idColumn(inputPath.getIdColumn()).groupingColumns(Collections.emptyList()).build();
    final NamedFunctionInput countInput = new NamedFunctionInput(parserContext, inputPath, Collections.emptyList());
    final NamedFunction count = NamedFunction.getInstance("count");
    final FhirPath result = count.invoke(countInput);
    final Dataset<Row> expectedDataset = new DatasetBuilder(spark).withIdColumn().withColumn(DataTypes.LongType).withRow("patient-1", 2L).build();
    assertThat(result).hasExpression("gender.count()").isSingular().isElementPath(IntegerPath.class).hasFhirType(FHIRDefinedType.UNSIGNEDINT).selectOrderedResult().hasRows(expectedDataset);
}

Example 2 with DatasetBuilder

use of au.csiro.pathling.test.builders.DatasetBuilder in project pathling by aehrc.

the class CountFunctionTest method countsByResourceIdentity.

@Test
void countsByResourceIdentity() {
    final Dataset<Row> patientDataset = new ResourceDatasetBuilder(spark).withIdColumn().withColumn("gender", DataTypes.StringType).withColumn("active", DataTypes.BooleanType).withRow("patient-1", "female", true).withRow("patient-2", "female", false).withRow("patient-3", "male", true).build();
    when(database.read(ResourceType.PATIENT)).thenReturn(patientDataset);
    final ResourcePath inputPath = ResourcePath.build(fhirContext, database, ResourceType.PATIENT, "Patient", false);
    final ParserContext parserContext = new ParserContextBuilder(spark, fhirContext).idColumn(inputPath.getIdColumn()).groupingColumns(Collections.singletonList(inputPath.getIdColumn())).inputExpression("Patient").build();
    final NamedFunctionInput countInput = new NamedFunctionInput(parserContext, inputPath, Collections.emptyList());
    final NamedFunction count = NamedFunction.getInstance("count");
    final FhirPath result = count.invoke(countInput);
    final Dataset<Row> expectedDataset = new DatasetBuilder(spark).withIdColumn().withColumn(DataTypes.LongType).withRow("patient-1", 1L).withRow("patient-2", 1L).withRow("patient-3", 1L).build();
    assertThat(result).hasExpression("count()").isSingular().isElementPath(IntegerPath.class).hasFhirType(FHIRDefinedType.UNSIGNEDINT).selectOrderedResult().hasRows(expectedDataset);
}

Example 3 with DatasetBuilder

use of au.csiro.pathling.test.builders.DatasetBuilder in project pathling by aehrc.

the class CountFunctionTest method countsByGrouping.

@Test
void countsByGrouping() {
    final Dataset<Row> inputDataset = new ResourceDatasetBuilder(spark).withIdColumn().withColumn("gender", DataTypes.StringType).withColumn("active", DataTypes.BooleanType).withRow("patient-1", "female", true).withRow("patient-2", "female", false).withRow("patient-2", "male", true).build();
    when(database.read(ResourceType.PATIENT)).thenReturn(inputDataset);
    final ResourcePath inputPath = new ResourcePathBuilder(spark).database(database).resourceType(ResourceType.PATIENT).expression("Patient").build();
    final Column groupingColumn = inputPath.getElementColumn("gender");
    final ParserContext parserContext = new ParserContextBuilder(spark, fhirContext).groupingColumns(Collections.singletonList(groupingColumn)).inputExpression("Patient").build();
    final NamedFunctionInput countInput = new NamedFunctionInput(parserContext, inputPath, Collections.emptyList());
    final NamedFunction count = NamedFunction.getInstance("count");
    final FhirPath result = count.invoke(countInput);
    final Dataset<Row> expectedDataset = new DatasetBuilder(spark).withColumn(DataTypes.StringType).withColumn(DataTypes.LongType).withRow("female", 2L).withRow("male", 1L).build();
    assertThat(result).hasExpression("count()").isSingular().isElementPath(IntegerPath.class).hasFhirType(FHIRDefinedType.UNSIGNEDINT).selectGroupingResult(Collections.singletonList(groupingColumn)).hasRows(expectedDataset);
}

Example 4 with DatasetBuilder

use of au.csiro.pathling.test.builders.DatasetBuilder 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 DatasetBuilder

use of au.csiro.pathling.test.builders.DatasetBuilder in project pathling by aehrc.

the class FirstFunctionTest method firstOfRootResources.

@Test
void firstOfRootResources() {
    final Dataset<Row> patientDataset = new ResourceDatasetBuilder(spark).withIdColumn().withColumn("gender", DataTypes.StringType).withColumn("active", DataTypes.BooleanType).withRow("patient-1", "female", true).withRow("patient-2", "female", false).withRow("patient-3", "male", true).build();
    when(database.read(ResourceType.PATIENT)).thenReturn(patientDataset);
    final ResourcePath inputPath = ResourcePath.build(fhirContext, database, ResourceType.PATIENT, "Patient", true);
    final ParserContext parserContext = new ParserContextBuilder(spark, fhirContext).groupingColumns(Collections.singletonList(inputPath.getIdColumn())).build();
    final NamedFunctionInput firstInput = new NamedFunctionInput(parserContext, inputPath, Collections.emptyList());
    final NamedFunction firstFunction = NamedFunction.getInstance("first");
    final FhirPath result = firstFunction.invoke(firstInput);
    assertTrue(result instanceof ResourcePath);
    assertThat((ResourcePath) result).hasExpression("Patient.first()").isSingular().hasResourceType(ResourceType.PATIENT);
    final Dataset<Row> expectedDataset = new DatasetBuilder(spark).withIdColumn().withColumn(DataTypes.StringType).withRow("patient-1", "patient-1").withRow("patient-2", "patient-2").withRow("patient-3", "patient-3").build();
    assertThat(result).selectOrderedResult().hasRows(expectedDataset);
}