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

Example 1 with Donor

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

the class DonorServiceTest method testUpdateDonor.

@Test
public void testUpdateDonor() {
    val studyId = DEFAULT_STUDY_ID;
    val info = JsonUtils.fromSingleQuoted("{'test': 'new json'}");
    val d = new DonorWithSpecimens();
    d.setDonorId("");
    d.setDonorSubmitterId("Triangle-Arrow-S");
    d.setStudyId(studyId);
    d.setDonorGender("male");
    val id = service.create(d);
    assertThat(id).isEqualTo(d.getDonorId());
    val d2 = new Donor();
    d2.setDonorId(id);
    d2.setDonorSubmitterId("X21-Beta-17");
    d2.setStudyId(studyId);
    d2.setDonorGender("female");
    d2.setInfo(info);
    val response = service.update(d2);
    assertThat(response).isEqualTo("OK");
    val d3 = service.read(id);
    assertThat(d3).isEqualToComparingFieldByField(d2);
}

Example 2 with Donor

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

the class SerializationTest method testDonorToJson.

@Test
public void testDonorToJson() {
    val donor = new Donor();
    val json = JsonUtils.toJson(donor);
    val expected = "{'donorId':'','donorSubmitterId':'','studyId':'','donorGender':''," + "'info':{}}";
    val expectedJson = JsonUtils.fromSingleQuoted(expected);
    assertThat(json).isEqualTo(expectedJson);
}

Example 3 with Donor

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

the class StudyWithDonorsServiceTest method testReadWithChildren.

@Test
public void testReadWithChildren() {
    // Create random isolated study
    val studyId = studyGenerator.createRandomStudy();
    // Generate Random SequencingRead analyses
    val analysisGenerator = createAnalysisGenerator(studyId, analysisService, randomGenerator);
    val numAnalysis = 11;
    val analysisMap = Maps.<String, SequencingReadAnalysis>newHashMap();
    for (int i = 0; i < numAnalysis; i++) {
        val sequencingReadAnalysis = analysisGenerator.createDefaultRandomSequencingReadAnalysis();
        analysisMap.put(sequencingReadAnalysis.getAnalysisId(), sequencingReadAnalysis);
    }
    // Extract expected donors and verify
    val expectedDonors = analysisMap.values().stream().flatMap(x -> x.getSample().stream()).map(CompositeEntity::getDonor).collect(toSet());
    assertThat(expectedDonors).hasSize(numAnalysis);
    assertThat(expectedDonors.stream().map(Donor::getDonorSubmitterId).distinct().count()).isEqualTo(numAnalysis);
    assertThat(expectedDonors.stream().filter(x -> x.getStudyId().equals(studyId)).count()).isEqualTo(numAnalysis);
    // Extract expected specimens and verify
    val expectedSpecimens = analysisMap.values().stream().flatMap(x -> x.getSample().stream()).map(CompositeEntity::getSpecimen).collect(toSet());
    assertThat(expectedSpecimens).hasSize(numAnalysis);
    assertThat(expectedSpecimens.stream().map(Specimen::getSpecimenSubmitterId).distinct().count()).isEqualTo(numAnalysis);
    // Extract expected samples and verify
    val expectedSamples = analysisMap.values().stream().flatMap(x -> x.getSample().stream()).collect(toSet());
    val expectedSampleSubmitterIds = expectedSamples.stream().map(Sample::getSampleSubmitterId).collect(toSet());
    assertThat(expectedSamples).hasSize(numAnalysis);
    assertThat(expectedSampleSubmitterIds).hasSize(numAnalysis);
    // Run the target method to test, readWithChildren
    val studyWithDonors = studyWithDonorsService.readWithChildren(studyId);
    // Extract actual donors
    val actualDonors = studyWithDonors.getDonors().stream().map(DonorWithSpecimens::createDonor).collect(toSet());
    // Extract actual specimens
    val actualSpecimens = studyWithDonors.getDonors().stream().map(DonorWithSpecimens::getSpecimens).flatMap(Collection::stream).map(SpecimenWithSamples::getSpecimen).collect(toSet());
    // Extract actual samples
    val actualSamples = studyWithDonors.getDonors().stream().map(DonorWithSpecimens::getSpecimens).flatMap(Collection::stream).map(SpecimenWithSamples::getSamples).flatMap(Collection::stream).collect(toSet());
    val actualSampleSubmitterIds = actualSamples.stream().map(Sample::getSampleSubmitterId).collect(toSet());
    // Verify expected donors and actual donors match
    assertSetsMatch(expectedDonors, actualDonors);
    // Verify expected specimens and actual specimens match
    assertSetsMatch(expectedSpecimens, actualSpecimens);
    // Verify expected sampleSubmitterIds and actual sampleSubmitterIds match
    assertSetsMatch(expectedSampleSubmitterIds, actualSampleSubmitterIds);
}

Example 4 with Donor

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

the class EntityTest method testDonor.

@Test
public void testDonor() {
    val donor1 = new Donor();
    donor1.setDonorGender("male");
    donor1.setDonorSubmitterId("donorSubmitter1");
    donor1.setDonorId("donor1");
    donor1.setStudyId("study1");
    val donor1_same = Donor.create("donor1", "donorSubmitter1", "study1", "male");
    assertEntitiesEqual(donor1, donor1_same, true);
    val donor2 = Donor.create("donor2", "donorSubmitter2", "study2", "female");
    assertEntitiesNotEqual(donor1, donor2);
    donor1.setInfo("key1", "f5c9381090a53c54358feb2ba5b7a3d7");
    donor1_same.setInfo("key2", "6329334b-dcd5-53c8-98fd-9812ac386d30");
    assertEntitiesNotEqual(donor1, donor1_same);
    // Test getters
    assertThat(donor1.getStudyId()).isEqualTo("study1");
    assertThat(donor1.getDonorGender()).isEqualTo("male");
    assertThat(donor1.getDonorSubmitterId()).isEqualTo("donorSubmitter1");
    assertThat(donor1.getDonorId()).isEqualTo("donor1");
    assertInfoKVPair(donor1, "key1", "f5c9381090a53c54358feb2ba5b7a3d7");
}

Example 5 with Donor

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

the class SerializationTest method testDonorSettings.

@Test
public void testDonorSettings() {
    val donor = new Donor();
    donor.setDonorId(null);
    val json = JsonUtils.toJson(donor);
    System.err.printf("json='%s'\n", json);
    val expected = "{'donorId':null,'donorSubmitterId':'','studyId':'','donorGender':''," + "'info':{}}";
    val expectedJson = JsonUtils.fromSingleQuoted(expected);
    assertThat(json).isEqualTo(expectedJson);
}