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

Example 11 with DonorWithSpecimens

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

the class DonorServiceTest method testCreateDonorAlreadyExists.

@Test
public void testCreateDonorAlreadyExists() {
    val studyId = DEFAULT_STUDY_ID;
    val randomGender = randomGenerator.randomElement(newArrayList(DONOR_GENDER));
    val randomDonorSubmitterId = randomGenerator.generateRandomUUIDAsString();
    val expectedId = idService.generateDonorId(randomDonorSubmitterId, studyId);
    val donorWithSpecimens = new DonorWithSpecimens();
    donorWithSpecimens.setStudyId(studyId);
    donorWithSpecimens.setDonorSubmitterId(randomDonorSubmitterId);
    donorWithSpecimens.setDonorGender(randomGender);
    donorWithSpecimens.setInfo("someKey", "someValue");
    val donorId = service.create(donorWithSpecimens);
    assertThat(donorId).isEqualTo(expectedId);
    donorWithSpecimens.setDonorId("DO123");
    assertSongError(() -> service.create(donorWithSpecimens), DONOR_ID_IS_CORRUPTED);
    donorWithSpecimens.setDonorId(expectedId);
    assertSongError(() -> service.create(donorWithSpecimens), DONOR_ALREADY_EXISTS);
    donorWithSpecimens.setDonorId("");
    assertSongError(() -> service.create(donorWithSpecimens), DONOR_ALREADY_EXISTS);
    donorWithSpecimens.setDonorId(null);
    assertSongError(() -> service.create(donorWithSpecimens), DONOR_ALREADY_EXISTS);
}

Example 12 with DonorWithSpecimens

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

the class EntityTest method testStudyWithDonors.

@Test
public void testStudyWithDonors() {
    val study1 = Study.create("d1", "b1", "c1", "a1");
    val study2 = Study.create("d2", "b2", "c2", "a2");
    val s1 = new StudyWithDonors();
    s1.setStudy(study1);
    val s1_same = new StudyWithDonors();
    s1_same.setName(study1.getName());
    s1_same.setOrganization(study1.getOrganization());
    s1_same.setStudyId(study1.getStudyId());
    s1_same.setDescription(study1.getDescription());
    assertEntitiesEqual(s1, s1_same, true);
    val s2 = new StudyWithDonors();
    s2.setStudy(study2);
    assertEntitiesNotEqual(s1, s2);
    // ---------------
    val specimen1 = Specimen.create("mySpecimen1", "mySpecimenSubmitter1", "myDonor1", SPECIMEN_CLASSES.get(2), SPECIMEN_TYPES.get(2));
    val specimen2 = Specimen.create("mySpecimen2", "mySpecimenSubmitter2", "myDonor2", SPECIMEN_CLASSES.get(1), SPECIMEN_TYPES.get(1));
    val sample11 = Sample.create("mySample11", "mySubmitterSample11", "mySpecimen11", SAMPLE_TYPES.get(2));
    val sample12 = Sample.create("mySample12", "mySubmitterSample12", "mySpecimen12", SAMPLE_TYPES.get(2));
    val sampleGroup1 = newArrayList(sample11, sample12);
    val sample21 = Sample.create("mySample21", "mySubmitterSample21", "mySpecimen21", SAMPLE_TYPES.get(3));
    val sample22 = Sample.create("mySample22", "mySubmitterSample22", "mySpecimen22", SAMPLE_TYPES.get(3));
    val sampleGroup2 = newArrayList(sample21, sample22);
    val specimenWithSample1 = new SpecimenWithSamples();
    specimenWithSample1.setSpecimen(specimen1);
    specimenWithSample1.setSamples(sampleGroup1);
    val specimenWithSample2 = new SpecimenWithSamples();
    specimenWithSample2.setSpecimen(specimen2);
    specimenWithSample2.setSamples(sampleGroup2);
    val specimenWSampleGroup1 = newArrayList(specimenWithSample1, specimenWithSample2);
    val specimenWSampleGroup2 = newArrayList(specimenWithSample1);
    val donor1 = Donor.create("myDonor1", "myDonorSubmitter1", DEFAULT_STUDY_ID, "male");
    val donor2 = Donor.create("myDonor2", "myDonorSubmitter2", DEFAULT_STUDY_ID, "female");
    val d1 = new DonorWithSpecimens();
    d1.setDonor(donor1);
    d1.setSpecimens(specimenWSampleGroup1);
    val d2 = new DonorWithSpecimens();
    d2.setDonor(donor2);
    d2.setSpecimens(specimenWSampleGroup2);
    // 00 -- matchingDonorGroup=0    matchingStudy=0
    s1.setStudy(study1);
    s1.setDonors(newArrayList(d1));
    s2.setStudy(study2);
    s2.setDonors(newArrayList(d2));
    assertEntitiesNotEqual(s1, s2);
    // 01 -- matchingDonorGroup=0    matchingStudy=1
    s1.setStudy(study1);
    s1.setDonors(newArrayList(d1));
    s2.setStudy(study1);
    s2.setDonors(newArrayList(d2));
    assertEntitiesNotEqual(s1, s2);
    // 10 -- matchingDonorGroup=1    matchingStudy=0
    s1.setStudy(study1);
    s1.setDonors(newArrayList(d1));
    s2.setStudy(study2);
    s2.setDonors(newArrayList(d1));
    assertEntitiesNotEqual(s1, s2);
    // 11 -- matchingDonorGroup=1    matchingStudy=1
    s1.setStudy(study1);
    s1.setDonors(newArrayList(d1));
    s2.setStudy(study1);
    s2.setDonors(newArrayList(d1));
    assertEntitiesEqual(s1, s2, true);
    s1.setInfo("key1", "f5c9381090a53c54358feb2ba5b7a3d7");
    s2.setInfo("key2", "6329334b-dcd5-53c8-98fd-9812ac386d30");
    assertInfoKVPair(s1, "key1", "f5c9381090a53c54358feb2ba5b7a3d7");
    assertEntitiesNotEqual(s1, s2);
    s1.setInfo("key1", "f5c9381090a53c54358feb2ba5b7a3d7");
    s2.setInfo("key1", "6329334b-dcd5-53c8-98fd-9812ac386d30");
    assertEntitiesNotEqual(s1, s2);
    // Test getters
    assertThat(s1.getDescription()).isEqualTo(study1.getDescription());
    assertThat(s1.getName()).isEqualTo(study1.getName());
    assertThat(s1.getOrganization()).isEqualTo(study1.getOrganization());
    assertThat(s1.getStudyId()).isEqualTo(study1.getStudyId());
    assertThat(s1.getStudy()).isNotSameAs(study1);
    assertThat(s1.getDonors()).containsExactlyInAnyOrder(d1);
    assertInfoKVPair(s1, "key1", "f5c9381090a53c54358feb2ba5b7a3d7");
    // Assert addDonor
    val sLeft = new StudyWithDonors();
    sLeft.setStudy(study1);
    sLeft.setDonors(newArrayList(d1, d2));
    val sRight = new StudyWithDonors();
    sRight.setStudy(study1);
    sRight.addDonor(d1);
    sRight.addDonor(d2);
    assertThat(sLeft).isEqualTo(sRight);
}

Example 13 with DonorWithSpecimens

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

the class SpecimenServiceTest method testReadAndDeleteByParentId.

@Test
public void testReadAndDeleteByParentId() {
    // Create a donor, and then several specimens, and for each specimen 2 samples
    val studyId = DEFAULT_STUDY_ID;
    val donor = Donor.create("", randomGenerator.generateRandomUUIDAsString(), studyId, randomGenerator.randomElement(newArrayList(DONOR_GENDER)));
    val donorWithSpecimens = new DonorWithSpecimens();
    donorWithSpecimens.setDonor(donor);
    val donorId = donorService.create(donorWithSpecimens);
    val numSpecimens = 5;
    val numSamplesPerSpecimen = 2;
    val expectedSpecimenIds = Sets.<String>newHashSet();
    val expectedSampleIdMap = Maps.<String, Set<String>>newHashMap();
    for (int i = 0; i < numSpecimens; i++) {
        // Create specimen
        val specimen = Specimen.create("", randomGenerator.generateRandomUUIDAsString(), donorId, randomGenerator.randomElement(newArrayList(SPECIMEN_CLASS)), randomGenerator.randomElement(newArrayList(SPECIMEN_TYPE)));
        val specimenId = specimenService.create(studyId, specimen);
        expectedSpecimenIds.add(specimenId);
        // Create samples
        for (int j = 0; j < numSamplesPerSpecimen; j++) {
            val sample = Sample.create("", randomGenerator.generateRandomUUIDAsString(), specimenId, randomGenerator.randomElement(newArrayList(SAMPLE_TYPE)));
            val sampleId = sampleService.create(studyId, sample);
            // Store the expected sampleId
            if (!expectedSampleIdMap.containsKey(specimenId)) {
                expectedSampleIdMap.put(specimenId, newHashSet());
            }
            val sampleIds = expectedSampleIdMap.get(specimenId);
            sampleIds.add(sampleId);
        }
    }
    // ReadByParentId (newly created donorId)
    val specimens = specimenService.readByParentId(donorId);
    assertThat(specimens).hasSize(numSpecimens);
    for (val specimen : specimens) {
        val actualSpecimenId = specimen.getSpecimenId();
        val actualSampleIds = specimen.getSamples().stream().map(Sample::getSampleId).collect(toSet());
        assertThat(expectedSpecimenIds).contains(actualSpecimenId);
        assertThat(actualSampleIds).hasSize(numSamplesPerSpecimen);
        val expectedSampleIds = expectedSampleIdMap.get(actualSpecimenId);
        assertThat(expectedSampleIds).hasSize(numSamplesPerSpecimen);
        assertThat(actualSampleIds).isSubsetOf(expectedSampleIds);
        assertThat(expectedSampleIds).isSubsetOf(actualSampleIds);
    }
    // Assert that reading by a non-existent donorId returns something empty
    val randomDonorId = randomGenerator.generateRandomUUIDAsString();
    assertThat(donorService.isDonorExist(randomDonorId)).isFalse();
    val emptySpecimenList = specimenService.readByParentId(randomDonorId);
    assertThat(emptySpecimenList).isEmpty();
    // Delete by parent id
    val response = specimenService.deleteByParentId(donorId);
    assertThat(response).isEqualTo("OK");
    val emptySpecimenList2 = specimenService.readByParentId(donorId);
    assertThat(emptySpecimenList2).isEmpty();
}

Example 14 with DonorWithSpecimens

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

the class DonorService method readWithSpecimens.

public DonorWithSpecimens readWithSpecimens(@NonNull String id) {
    val donor = new DonorWithSpecimens();
    donor.setDonor(read(id));
    donor.setSpecimens(specimenService.readByParentId(id));
    return donor;
}