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

Example 1 with SnapshotRequestModel

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

the class SnapshotValidationTest method makeSnapshotRowIdsRequest.

// Generate a valid snapshot-by-rowId request, we will tweak individual pieces to test validation below
public SnapshotRequestModel makeSnapshotRowIdsRequest() {
    SnapshotRequestRowIdTableModel snapshotRequestTableModel = new SnapshotRequestRowIdTableModel().tableName("snapshot").columns(Arrays.asList("col1", "col2", "col3")).rowIds(Arrays.asList("row1", "row2", "row3"));
    SnapshotRequestRowIdModel rowIdSpec = new SnapshotRequestRowIdModel().tables(Collections.singletonList(snapshotRequestTableModel));
    SnapshotRequestContentsModel snapshotRequestContentsModel = new SnapshotRequestContentsModel().datasetName("dataset").mode(SnapshotRequestContentsModel.ModeEnum.BYROWID).rowIdSpec(rowIdSpec);
    return new SnapshotRequestModel().contents(Collections.singletonList(snapshotRequestContentsModel));
}

Example 2 with SnapshotRequestModel

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

the class SnapshotValidationTest method makeSnapshotByQueryRequest.

// Generate a valid snapshot-by-query request, we will tweak individual pieces to test validation below
public SnapshotRequestModel makeSnapshotByQueryRequest() {
    SnapshotRequestQueryModel querySpec = new SnapshotRequestQueryModel().assetName("asset").query("SELECT * FROM dataset");
    SnapshotRequestContentsModel snapshotRequestContentsModel = new SnapshotRequestContentsModel().datasetName("dataset").mode(SnapshotRequestContentsModel.ModeEnum.BYQUERY).querySpec(querySpec);
    return new SnapshotRequestModel().contents(Collections.singletonList(snapshotRequestContentsModel));
}

Example 3 with SnapshotRequestModel

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

the class SnapshotValidationTest method testSnapshotByQuery.

@Test
public void testSnapshotByQuery() throws Exception {
    SnapshotRequestModel querySpec = this.snapshotByQueryRequestModel;
    querySpec.getContents().get(0).getQuerySpec().setQuery(null);
    expectBadSnapshotCreateRequest(snapshotByQueryRequestModel);
}

Example 4 with SnapshotRequestModel

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

the class SnapshotTest method snapshotRowIdsHappyPathTest.

@Test
public void snapshotRowIdsHappyPathTest() throws Exception {
    // fetch rowIds from the ingested dataset by querying the participant table
    DatasetModel dataset = dataRepoFixtures.getDataset(steward(), datasetId);
    String datasetProject = dataset.getDataProject();
    String bqDatasetName = PdaoConstant.PDAO_PREFIX + dataset.getName();
    String participantTable = "participant";
    String sampleTable = "sample";
    BigQuery bigQuery = BigQueryFixtures.getBigQuery(dataset.getDataProject(), stewardToken);
    String sql = String.format("SELECT %s FROM `%s.%s.%s`", PdaoConstant.PDAO_ROW_ID_COLUMN, datasetProject, bqDatasetName, participantTable);
    TableResult participantIds = BigQueryFixtures.query(sql, bigQuery);
    List<String> participantIdList = StreamSupport.stream(participantIds.getValues().spliterator(), false).map(v -> v.get(0).getStringValue()).collect(Collectors.toList());
    sql = String.format("SELECT %s FROM `%s.%s.%s`", PdaoConstant.PDAO_ROW_ID_COLUMN, datasetProject, bqDatasetName, sampleTable);
    TableResult sampleIds = BigQueryFixtures.query(sql, bigQuery);
    List<String> sampleIdList = StreamSupport.stream(sampleIds.getValues().spliterator(), false).map(v -> v.get(0).getStringValue()).collect(Collectors.toList());
    // swap in these row ids in the request
    SnapshotRequestModel requestModel = jsonLoader.loadObject("ingest-test-snapshot-row-ids-test.json", SnapshotRequestModel.class);
    requestModel.getContents().get(0).getRowIdSpec().getTables().get(0).setRowIds(participantIdList);
    requestModel.getContents().get(0).getRowIdSpec().getTables().get(1).setRowIds(sampleIdList);
    SnapshotSummaryModel snapshotSummary = dataRepoFixtures.createSnapshotWithRequest(steward(), dataset.getName(), 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("new snapshot has the correct number of tables", requestModel.getContents().get(0).getRowIdSpec().getTables().size(), snapshot.getTables().size());
    // TODO: get the snapshot and make sure the number of rows matches with the row ids input
    assertThat("one relationship comes through", snapshot.getRelationships().size(), equalTo(1));
    assertThat("the right relationship comes through", snapshot.getRelationships().get(0).getName(), equalTo("sample_participants"));
}

Example 5 with SnapshotRequestModel

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

the class SnapshotTest method snapshotByQueryHappyPathTest.

@Test
public void snapshotByQueryHappyPathTest() throws Exception {
    DatasetModel dataset = dataRepoFixtures.getDataset(steward(), datasetId);
    String datasetName = dataset.getName();
    SnapshotRequestModel requestModel = jsonLoader.loadObject("ingest-test-snapshot-query.json", SnapshotRequestModel.class);
    // swap in the correct dataset name (with the id at the end)
    requestModel.getContents().get(0).setDatasetName(datasetName);
    requestModel.getContents().get(0).getQuerySpec().setQuery("SELECT " + datasetName + ".sample.datarepo_row_id FROM " + datasetName + ".sample WHERE " + datasetName + ".sample.id ='sample6'");
    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());
}