Examples with SnapshotRequestModel bio.terra.model.SnapshotRequestModel used on opensource projects

Example 11 with SnapshotRequestModel

use of bio.terra.model.SnapshotRequestModel in project jade-data-repo by DataBiosphere.

the class SnapshotConnectedTest method testMinimal.

@Test
public void testMinimal() throws Exception {
    DatasetSummaryModel datasetMinimalSummary = setupMinimalDataset();
    String datasetName = PDAO_PREFIX + datasetMinimalSummary.getName();
    BigQueryProject bigQueryProject = TestUtils.bigQueryProjectForDatasetName(datasetDao, dataLocationService, datasetMinimalSummary.getName());
    long datasetParticipants = queryForCount(datasetName, "participant", bigQueryProject);
    assertThat("dataset participants loaded properly", datasetParticipants, equalTo(2L));
    long datasetSamples = queryForCount(datasetName, "sample", bigQueryProject);
    assertThat("dataset samples loaded properly", datasetSamples, equalTo(5L));
    SnapshotRequestModel snapshotRequest = makeSnapshotTestRequest(datasetMinimalSummary, "dataset-minimal-snapshot.json");
    MockHttpServletResponse response = performCreateSnapshot(snapshotRequest, "");
    SnapshotSummaryModel summaryModel = validateSnapshotCreated(snapshotRequest, response);
    SnapshotModel snapshotModel = getTestSnapshot(summaryModel.getId(), snapshotRequest, datasetMinimalSummary);
    List<TableModel> tables = snapshotModel.getTables();
    Optional<TableModel> participantTable = tables.stream().filter(t -> t.getName().equals("participant")).findFirst();
    Optional<TableModel> sampleTable = tables.stream().filter(t -> t.getName().equals("sample")).findFirst();
    assertThat("participant table exists", participantTable.isPresent(), equalTo(true));
    assertThat("sample table exists", sampleTable.isPresent(), equalTo(true));
    long snapshotParticipants = queryForCount(summaryModel.getName(), "participant", bigQueryProject);
    assertThat("dataset participants loaded properly", snapshotParticipants, equalTo(1L));
    assertThat("participant row count matches expectation", participantTable.get().getRowCount(), equalTo(1));
    long snapshotSamples = queryForCount(summaryModel.getName(), "sample", bigQueryProject);
    assertThat("dataset samples loaded properly", snapshotSamples, equalTo(2L));
    assertThat("sample row count matches expectation", sampleTable.get().getRowCount(), equalTo(2));
    List<RelationshipModel> relationships = snapshotModel.getRelationships();
    assertThat("a relationship comes back", relationships.size(), equalTo(1));
    RelationshipModel relationshipModel = relationships.get(0);
    assertThat("relationship name is right", relationshipModel.getName(), equalTo("participant_sample"));
    assertThat("from table is right", relationshipModel.getFrom().getTable(), equalTo("participant"));
    assertThat("from column is right", relationshipModel.getFrom().getColumn(), equalTo("id"));
    assertThat("to table is right", relationshipModel.getTo().getTable(), equalTo("sample"));
    assertThat("to column is right", relationshipModel.getTo().getColumn(), equalTo("participant_id"));
}

Example 12 with SnapshotRequestModel

use of bio.terra.model.SnapshotRequestModel in project jade-data-repo by DataBiosphere.

the class SnapshotConnectedTest method testArrayStruct.

@Test
public void testArrayStruct() throws Exception {
    DatasetSummaryModel datasetArraySummary = setupArrayStructDataset();
    String datasetName = PDAO_PREFIX + datasetArraySummary.getName();
    BigQueryProject bigQueryProject = TestUtils.bigQueryProjectForDatasetName(datasetDao, dataLocationService, datasetArraySummary.getName());
    long datasetParticipants = queryForCount(datasetName, "participant", bigQueryProject);
    assertThat("dataset participants loaded properly", datasetParticipants, equalTo(2L));
    long datasetSamples = queryForCount(datasetName, "sample", bigQueryProject);
    assertThat("dataset samples loaded properly", datasetSamples, equalTo(5L));
    SnapshotRequestModel snapshotRequest = makeSnapshotTestRequest(datasetArraySummary, "snapshot-array-struct.json");
    MockHttpServletResponse response = performCreateSnapshot(snapshotRequest, "");
    SnapshotSummaryModel summaryModel = validateSnapshotCreated(snapshotRequest, response);
    getTestSnapshot(summaryModel.getId(), snapshotRequest, datasetArraySummary);
    long snapshotParticipants = queryForCount(summaryModel.getName(), "participant", bigQueryProject);
    assertThat("dataset participants loaded properly", snapshotParticipants, equalTo(2L));
    long snapshotSamples = queryForCount(summaryModel.getName(), "sample", bigQueryProject);
    assertThat("dataset samples loaded properly", snapshotSamples, equalTo(3L));
}

Example 13 with SnapshotRequestModel

use of bio.terra.model.SnapshotRequestModel in project jade-data-repo by DataBiosphere.

the class SnapshotConnectedTest method testDuplicateName.

@Test
public void testDuplicateName() throws Exception {
    // create a snapshot
    SnapshotRequestModel snapshotRequest = makeSnapshotTestRequest(datasetSummary, "snapshot-test-snapshot.json");
    MockHttpServletResponse response = performCreateSnapshot(snapshotRequest, "_dup_");
    SnapshotSummaryModel summaryModel = validateSnapshotCreated(snapshotRequest, response);
    // fetch the snapshot and confirm the metadata matches the request
    SnapshotModel snapshotModel = getTestSnapshot(summaryModel.getId(), snapshotRequest, datasetSummary);
    assertNotNull("fetched snapshot successfully after creation", snapshotModel);
    // check that the snapshot metadata row is unlocked
    String exclusiveLock = snapshotDao.getExclusiveLockState(UUID.fromString(snapshotModel.getId()));
    assertNull("snapshot row is unlocked", exclusiveLock);
    // try to create the same snapshot again and check that it fails
    snapshotRequest.setName(snapshotModel.getName());
    response = performCreateSnapshot(snapshotRequest, null);
    ErrorModel errorModel = handleCreateSnapshotFailureCase(response);
    assertThat(response.getStatus(), equalTo(HttpStatus.BAD_REQUEST.value()));
    assertThat("error message includes name conflict", errorModel.getMessage(), containsString("Snapshot name already exists"));
    // delete and confirm deleted
    connectedOperations.deleteTestSnapshot(snapshotModel.getId());
    connectedOperations.getSnapshotExpectError(snapshotModel.getId(), HttpStatus.NOT_FOUND);
}

Example 14 with SnapshotRequestModel

use of bio.terra.model.SnapshotRequestModel in project jade-data-repo by DataBiosphere.

the class SnapshotTest method snapshotByFullViewHappyPathTest.

@Test
public void snapshotByFullViewHappyPathTest() throws Exception {
    DatasetModel dataset = dataRepoFixtures.getDataset(steward(), datasetId);
    String datasetName = dataset.getName();
    SnapshotRequestModel requestModel = jsonLoader.loadObject("ingest-test-snapshot-fullviews.json", SnapshotRequestModel.class);
    // swap in the correct dataset name (with the id at the end)
    requestModel.getContents().get(0).setDatasetName(datasetName);
    SnapshotSummaryModel snapshotSummary = dataRepoFixtures.createSnapshotWithRequest(steward(), datasetName, requestModel);
    TimeUnit.SECONDS.sleep(10);
    createdSnapshotIds.add(snapshotSummary.getId());
    SnapshotModel snapshot = dataRepoFixtures.getSnapshot(steward(), snapshotSummary.getId());
    assertEquals("new snapshot has been created", snapshot.getName(), requestModel.getName());
    assertEquals("all 5 relationships come through", snapshot.getRelationships().size(), 5);
}

Example 15 with SnapshotRequestModel

use of bio.terra.model.SnapshotRequestModel in project jade-data-repo by DataBiosphere.

the class SnapshotRequestValidator method validate.

@Override
public void validate(@NotNull Object target, Errors errors) {
    if (target != null && target instanceof SnapshotRequestModel) {
        SnapshotRequestModel snapshotRequestModel = (SnapshotRequestModel) target;
        validateSnapshotName(snapshotRequestModel.getName(), errors);
        validateSnapshotProfileId(snapshotRequestModel.getProfileId(), errors);
        validateSnapshotDescription(snapshotRequestModel.getDescription(), errors);
        validateSnapshotContents(snapshotRequestModel.getContents(), errors);
    }
}