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Enable integration tests #29

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merged 14 commits into from
Apr 8, 2024
Merged

Enable integration tests #29

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6b4dceb
Make import clinical data tests to run
ruslan-forostianov Mar 14, 2024
3e6f92a
Fix testImportClinicalData_WithDuplInMixedAttrFormat
ruslan-forostianov Mar 14, 2024
3632d2b
Enable TestImportProfileData
ruslan-forostianov Mar 14, 2024
0ce5321
Enable the rest of passing script tests
ruslan-forostianov Mar 14, 2024
8b4f29c
Upgrade surefire version to insulate test executions better
ruslan-forostianov Mar 15, 2024
29ab2da
Run db tests at integration-test step
ruslan-forostianov Mar 19, 2024
0de4217
Un-ignore the rest of passing integration tests
ruslan-forostianov Mar 19, 2024
9816ecf
Document how to run integration tests
ruslan-forostianov Mar 19, 2024
49b5f4b
Rename and move int.tests to integerationTest package
ruslan-forostianov Apr 1, 2024
0b48914
Replace wildcard imports in integrationTest folder
ruslan-forostianov Apr 3, 2024
8e49ff5
Move TestImportGenesetData back to own class
ruslan-forostianov Apr 4, 2024
257d2a5
Use static imports for asserts
ruslan-forostianov Apr 5, 2024
b6ca35d
Use asserts from org.junit.Assert class everywhere
ruslan-forostianov Apr 6, 2024
63d58d6
Comment application context configuration that caused tests to fail
ruslan-forostianov Apr 6, 2024
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3 changes: 1 addition & 2 deletions src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoCancerStudy.java
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Expand Up @@ -32,7 +32,6 @@

package org.mskcc.cbio.portal.integrationTest.dao;

import org.junit.Assert;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.mskcc.cbio.portal.dao.DaoCancerStudy;
Expand Down Expand Up @@ -71,7 +70,7 @@ public class TestDaoCancerStudy {
@Test
public void testDaoCancerStudy() throws DaoException, IOException {

Assert.assertEquals("Breast Invasive Carcinoma", DaoTypeOfCancer.getTypeOfCancerById("BRCA").getName());
assertEquals("Breast Invasive Carcinoma", DaoTypeOfCancer.getTypeOfCancerById("BRCA").getName());

CancerStudy cancerStudy = new CancerStudy("GBM", "GBM Description", "gbm", "brca", false);
cancerStudy.setReferenceGenome("hg19");
Expand Down
23 changes: 12 additions & 11 deletions src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoMutation.java
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Expand Up @@ -33,7 +33,6 @@
package org.mskcc.cbio.portal.integrationTest.dao;

import com.fasterxml.jackson.databind.ObjectMapper;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
import org.junit.runner.RunWith;
Expand All @@ -58,7 +57,9 @@
import java.util.Map;
import java.util.Set;

import static org.junit.Assert.assertEquals;
import static org.junit.assertEquals;
import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertTrue;

/**
* JUnit tests for DaoMutation class.
Expand Down Expand Up @@ -223,23 +224,23 @@ private void validateMockAnnotationJson(ExtendedMutation mutation) {
Map<String, Map<String, String>> expectedAnnotationJsonMap = makeMockExpectedAnnotationJsonMap();

// confirm expected sizes
Assert.assertTrue(annotationJsonMap.containsKey("namespace1"));
Assert.assertEquals(expectedAnnotationJsonMap.get("namespace1").size(), annotationJsonMap.get("namespace1").size());
Assert.assertEquals(2, annotationJsonMap.get("namespace1").size());
Assert.assertTrue(annotationJsonMap.containsKey("namespace2"));
Assert.assertEquals(1, annotationJsonMap.get("namespace2").size());
Assert.assertEquals(expectedAnnotationJsonMap.get("namespace2").size(), annotationJsonMap.get("namespace2").size());
assertTrue(annotationJsonMap.containsKey("namespace1"));
assertEquals(expectedAnnotationJsonMap.get("namespace1").size(), annotationJsonMap.get("namespace1").size());
assertEquals(2, annotationJsonMap.get("namespace1").size());
assertTrue(annotationJsonMap.containsKey("namespace2"));
assertEquals(1, annotationJsonMap.get("namespace2").size());
assertEquals(expectedAnnotationJsonMap.get("namespace2").size(), annotationJsonMap.get("namespace2").size());

// compare namespace 1 annotation map values
Map<String, String> namespace1Map = annotationJsonMap.get("namespace1");
Map<String, String> expectedNamespace1Map = expectedAnnotationJsonMap.get("namespace1");
Assert.assertEquals(expectedNamespace1Map.get("header1"), namespace1Map.get("header1"));
Assert.assertEquals(expectedNamespace1Map.get("header2"), namespace1Map.get("header2"));
assertEquals(expectedNamespace1Map.get("header1"), namespace1Map.get("header1"));
assertEquals(expectedNamespace1Map.get("header2"), namespace1Map.get("header2"));

// compare namespace 2 annotation map values
Map<String, String> namespace2Map = annotationJsonMap.get("namespace2");
Map<String, String> expectedNamespace2Map = expectedAnnotationJsonMap.get("namespace2");
Assert.assertEquals(expectedNamespace2Map.get("header1"), namespace2Map.get("header1"));
assertEquals(expectedNamespace2Map.get("header1"), namespace2Map.get("header1"));
}

private String makeMockAnnotationJsonString() {
Expand Down
5 changes: 3 additions & 2 deletions ...est/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportCnaDiscreteLongData.java
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Expand Up @@ -70,6 +70,7 @@
import static org.cbioportal.model.MolecularProfile.DataType.DISCRETE;
import static org.cbioportal.model.MolecularProfile.ImportType.DISCRETE_LONG;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;

@RunWith(SpringJUnit4ClassRunner.class)
Expand Down Expand Up @@ -579,8 +580,8 @@ private void assertSampleExistsInGeneticProfile(String sampleId) throws DaoExcep
geneticProfile.getCancerStudyId(),
sampleStableId
);
Assert.assertNotNull(sample);
Assert.assertTrue(DaoSampleProfile.sampleExistsInGeneticProfile(
assertNotNull(sample);
assertTrue(DaoSampleProfile.sampleExistsInGeneticProfile(
sample.getInternalId(),
geneticProfile.getGeneticProfileId()
));
Expand Down
6 changes: 3 additions & 3 deletions src/test/java/org/mskcc/cbio/portal/scripts/TestCutInvalidCases.java
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Expand Up @@ -33,12 +33,12 @@
package org.mskcc.cbio.portal.scripts;

import org.junit.Test;
import org.mskcc.cbio.portal.scripts.CutInvalidCases;

import static org.junit.Assert.*;

import java.io.File;

import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.fail;

/**
* JUnit test for CutInvalidCases class.
*/
Expand Down
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