Examples with Study org.icgc.dcc.song.server.model.entity.Study used on opensource projects

Example 1 with Study

use of org.icgc.dcc.song.server.model.entity.Study in project SONG by overture-stack.

the class EntityTest method testStudy.

@Test
public void testStudy() {
    val study1 = new Study();
    study1.setDescription("a");
    study1.setName("b");
    study1.setOrganization("c");
    study1.setStudyId("d");
    val study1_same = Study.create("d", "b", "c", "a");
    assertEntitiesEqual(study1, study1_same, true);
    val study2 = Study.create("a1", "b1", "c1", "d1");
    assertEntitiesNotEqual(study1, study2);
    study1.setInfo("key1", "f5c9381090a53c54358feb2ba5b7a3d7");
    study1_same.setInfo("key2", "6329334b-dcd5-53c8-98fd-9812ac386d30");
    assertEntitiesNotEqual(study1, study1_same);
    // Test getters
    assertThat(study1.getDescription()).isEqualTo("a");
    assertThat(study1.getName()).isEqualTo("b");
    assertThat(study1.getOrganization()).isEqualTo("c");
    assertThat(study1.getStudyId()).isEqualTo("d");
    assertInfoKVPair(study1, "key1", "f5c9381090a53c54358feb2ba5b7a3d7");
}

Example 2 with Study

use of org.icgc.dcc.song.server.model.entity.Study in project SONG by overture-stack.

the class AnalysisServiceTest method testGetAnalysisAndIdSearch.

@Test
public void testGetAnalysisAndIdSearch() {
    val studyGenerator = createStudyGenerator(studyService, randomGenerator);
    val studyId = studyGenerator.createRandomStudy();
    val analysisGenerator = createAnalysisGenerator(studyId, service, payloadGenerator);
    val numAnalysis = 10;
    val sraMap = Maps.<String, SequencingReadAnalysis>newHashMap();
    val vcaMap = Maps.<String, VariantCallAnalysis>newHashMap();
    val expectedAnalyses = Sets.<Analysis>newHashSet();
    for (int i = 1; i <= numAnalysis; i++) {
        if (i % 2 == 0) {
            val sra = analysisGenerator.createDefaultRandomSequencingReadAnalysis();
            assertThat(sraMap.containsKey(sra.getAnalysisId())).isFalse();
            sraMap.put(sra.getAnalysisId(), sra);
            expectedAnalyses.add(sra);
        } else {
            val vca = analysisGenerator.createDefaultRandomVariantCallAnalysis();
            assertThat(sraMap.containsKey(vca.getAnalysisId())).isFalse();
            vcaMap.put(vca.getAnalysisId(), vca);
            expectedAnalyses.add(vca);
        }
    }
    assertThat(expectedAnalyses).hasSize(numAnalysis);
    assertThat(sraMap.keySet().size() + vcaMap.keySet().size()).isEqualTo(numAnalysis);
    val expectedVCAs = newHashSet(vcaMap.values());
    val expectedSRAs = newHashSet(sraMap.values());
    assertThat(expectedSRAs).hasSize(sraMap.keySet().size());
    assertThat(expectedVCAs).hasSize(vcaMap.keySet().size());
    val actualAnalyses = service.getAnalysis(studyId);
    val actualSRAs = actualAnalyses.stream().filter(x -> resolveAnalysisType(x.getAnalysisType()) == SEQUENCING_READ).collect(toSet());
    val actualVCAs = actualAnalyses.stream().filter(x -> resolveAnalysisType(x.getAnalysisType()) == VARIANT_CALL).collect(toSet());
    assertThat(actualSRAs).hasSize(sraMap.keySet().size());
    assertThat(actualVCAs).hasSize(vcaMap.keySet().size());
    assertThat(actualSRAs).containsAll(expectedSRAs);
    assertThat(actualVCAs).containsAll(expectedVCAs);
    // Do a study-wide idSearch and verify the response effectively has the same
    // number of results as the getAnalysis method
    val searchedAnalyses = service.idSearch(studyId, createIdSearchRequest(null, null, null, null));
    assertThat(searchedAnalyses).hasSameSizeAs(expectedAnalyses);
    assertThat(searchedAnalyses).containsOnlyElementsOf(expectedAnalyses);
}