-
Notifications
You must be signed in to change notification settings - Fork 12
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #1029 from aehrc/issue/1020
Fix comparison and arithmetic operations for instants
- Loading branch information
Showing
19 changed files
with
454 additions
and
45 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
195 changes: 195 additions & 0 deletions
195
...rver/src/test/java/au/csiro/pathling/fhirpath/operator/ComparisonOperatorInstantTest.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,195 @@ | ||
| /* | ||
| * Copyright 2022 Commonwealth Scientific and Industrial Research | ||
| * Organisation (CSIRO) ABN 41 687 119 230. | ||
| * | ||
| * Licensed under the Apache License, Version 2.0 (the "License"); | ||
| * you may not use this file except in compliance with the License. | ||
| * You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| */ | ||
|
|
||
| package au.csiro.pathling.fhirpath.operator; | ||
|
|
||
| import static au.csiro.pathling.test.assertions.Assertions.assertThat; | ||
| import static org.junit.jupiter.api.Assertions.assertEquals; | ||
| import static org.junit.jupiter.api.Assertions.assertTrue; | ||
|
|
||
| import au.csiro.pathling.fhirpath.FhirPath; | ||
| import au.csiro.pathling.fhirpath.element.ElementDefinition; | ||
| import au.csiro.pathling.fhirpath.element.ElementPath; | ||
| import au.csiro.pathling.fhirpath.parser.ParserContext; | ||
| import au.csiro.pathling.test.builders.DatasetBuilder; | ||
| import au.csiro.pathling.test.builders.ElementPathBuilder; | ||
| import au.csiro.pathling.test.builders.ParserContextBuilder; | ||
| import au.csiro.pathling.test.helpers.FhirHelpers; | ||
| import ca.uhn.fhir.context.FhirContext; | ||
| import java.time.Instant; | ||
| import java.util.Collections; | ||
| import java.util.Optional; | ||
| import org.apache.spark.sql.Dataset; | ||
| import org.apache.spark.sql.Row; | ||
| import org.apache.spark.sql.RowFactory; | ||
| import org.apache.spark.sql.SparkSession; | ||
| import org.apache.spark.sql.types.DataTypes; | ||
| import org.hl7.fhir.r4.model.Enumerations.FHIRDefinedType; | ||
| import org.junit.jupiter.api.BeforeEach; | ||
| import org.junit.jupiter.api.Tag; | ||
| import org.junit.jupiter.api.Test; | ||
| import org.springframework.beans.factory.annotation.Autowired; | ||
| import org.springframework.boot.test.context.SpringBootTest; | ||
|
|
||
| /** | ||
| * @author John Grimes | ||
| */ | ||
| @SpringBootTest | ||
| @Tag("UnitTest") | ||
| class ComparisonOperatorInstantTest { | ||
|
|
||
| @Autowired | ||
| SparkSession spark; | ||
|
|
||
| @Autowired | ||
| FhirContext fhirContext; | ||
|
|
||
| static final String ID_ALIAS = "_abc123"; | ||
| private ElementPath left; | ||
| private ElementPath right; | ||
| private ParserContext parserContext; | ||
|
|
||
| @BeforeEach | ||
| void setUp() { | ||
| final Optional<ElementDefinition> optionalLeftDefinition = FhirHelpers | ||
| .getChildOfResource(fhirContext, "Observation", "issued"); | ||
| assertTrue(optionalLeftDefinition.isPresent()); | ||
| final ElementDefinition leftDefinition = optionalLeftDefinition.get(); | ||
| assertTrue(leftDefinition.getFhirType().isPresent()); | ||
| assertEquals(FHIRDefinedType.INSTANT, leftDefinition.getFhirType().get()); | ||
|
|
||
| final Dataset<Row> leftDataset = new DatasetBuilder(spark) | ||
| .withIdColumn(ID_ALIAS) | ||
| .withColumn(DataTypes.TimestampType) | ||
| .withRow("patient-1", Instant.ofEpochMilli(1667690454622L)) // Equal, exact | ||
| .withRow("patient-2", Instant.ofEpochMilli(1667690454621L)) // Less than | ||
| .withRow("patient-3", Instant.ofEpochMilli(1667690454623L)) // Greater than | ||
| .build(); | ||
| left = new ElementPathBuilder(spark) | ||
| .dataset(leftDataset) | ||
| .idAndValueColumns() | ||
| .expression("authoredOn") | ||
| .singular(true) | ||
| .definition(leftDefinition) | ||
| .buildDefined(); | ||
|
|
||
| final Optional<ElementDefinition> optionalRightDefinition = FhirHelpers | ||
| .getChildOfResource(fhirContext, "Condition", "onsetDateTime"); | ||
| assertTrue(optionalRightDefinition.isPresent()); | ||
| final ElementDefinition rightDefinition = optionalRightDefinition.get(); | ||
| assertTrue(rightDefinition.getFhirType().isPresent()); | ||
| assertEquals(FHIRDefinedType.DATETIME, rightDefinition.getFhirType().get()); | ||
|
|
||
| final Dataset<Row> rightDataset = new DatasetBuilder(spark) | ||
| .withIdColumn(ID_ALIAS) | ||
| .withColumn(DataTypes.StringType) | ||
| .withRow("patient-1", "2022-11-06T09:20:54.622+10:00") // Equal, exact | ||
| .withRow("patient-2", "2022-11-06T09:20:54.622+10:00") // Less than | ||
| .withRow("patient-3", "2022-11-06T09:20:54.622+10:00") // Greater than | ||
| .build(); | ||
| right = new ElementPathBuilder(spark) | ||
| .dataset(rightDataset) | ||
| .idAndValueColumns() | ||
| .expression("reverseResolve(Condition.subject).onsetDateTime") | ||
| .singular(true) | ||
| .definition(rightDefinition) | ||
| .buildDefined(); | ||
|
|
||
| parserContext = new ParserContextBuilder(spark, fhirContext) | ||
| .groupingColumns(Collections.singletonList(left.getIdColumn())) | ||
| .build(); | ||
| } | ||
|
|
||
| @Test | ||
| void equals() { | ||
| final OperatorInput comparisonInput = new OperatorInput(parserContext, left, right); | ||
| final Operator lessThan = Operator.getInstance("="); | ||
| final FhirPath result = lessThan.invoke(comparisonInput); | ||
|
|
||
| assertThat(result).selectOrderedResult().hasRows( | ||
| RowFactory.create("patient-1", true), // Equal, exact | ||
| RowFactory.create("patient-2", false), // Less than | ||
| RowFactory.create("patient-3", false) // Greater than | ||
| ); | ||
| } | ||
|
|
||
| @Test | ||
| void notEquals() { | ||
| final OperatorInput comparisonInput = new OperatorInput(parserContext, left, right); | ||
| final Operator lessThan = Operator.getInstance("!="); | ||
| final FhirPath result = lessThan.invoke(comparisonInput); | ||
|
|
||
| assertThat(result).selectOrderedResult().hasRows( | ||
| RowFactory.create("patient-1", false), // Equal, exact | ||
| RowFactory.create("patient-2", true), // Less than | ||
| RowFactory.create("patient-3", true) // Greater than | ||
| ); | ||
| } | ||
|
|
||
| @Test | ||
| void lessThan() { | ||
| final OperatorInput comparisonInput = new OperatorInput(parserContext, left, right); | ||
| final Operator lessThan = Operator.getInstance("<"); | ||
| final FhirPath result = lessThan.invoke(comparisonInput); | ||
|
|
||
| assertThat(result).selectOrderedResult().hasRows( | ||
| RowFactory.create("patient-1", false), // Equal, exact | ||
| RowFactory.create("patient-2", true), // Less than | ||
| RowFactory.create("patient-3", false) // Greater than | ||
| ); | ||
| } | ||
|
|
||
| @Test | ||
| void lessThanOrEqualTo() { | ||
| final OperatorInput comparisonInput = new OperatorInput(parserContext, left, right); | ||
| final Operator lessThan = Operator.getInstance("<="); | ||
| final FhirPath result = lessThan.invoke(comparisonInput); | ||
|
|
||
| assertThat(result).selectOrderedResult().hasRows( | ||
| RowFactory.create("patient-1", true), // Equal, exact | ||
| RowFactory.create("patient-2", true), // Less than | ||
| RowFactory.create("patient-3", false) // Greater than | ||
| ); | ||
| } | ||
|
|
||
| @Test | ||
| void greaterThan() { | ||
| final OperatorInput comparisonInput = new OperatorInput(parserContext, left, right); | ||
| final Operator lessThan = Operator.getInstance(">"); | ||
| final FhirPath result = lessThan.invoke(comparisonInput); | ||
|
|
||
| assertThat(result).selectOrderedResult().hasRows( | ||
| RowFactory.create("patient-1", false), // Equal, exact | ||
| RowFactory.create("patient-2", false), // Less than | ||
| RowFactory.create("patient-3", true) // Greater than | ||
| ); | ||
| } | ||
|
|
||
| @Test | ||
| void greaterThanOrEqualTo() { | ||
| final OperatorInput comparisonInput = new OperatorInput(parserContext, left, right); | ||
| final Operator lessThan = Operator.getInstance(">="); | ||
| final FhirPath result = lessThan.invoke(comparisonInput); | ||
|
|
||
| assertThat(result).selectOrderedResult().hasRows( | ||
| RowFactory.create("patient-1", true), // Equal, exact | ||
| RowFactory.create("patient-2", false), // Less than | ||
| RowFactory.create("patient-3", true) // Greater than | ||
| ); | ||
| } | ||
|
|
||
| } |
Oops, something went wrong.