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Example 1 with DataLocationService

use of bio.terra.service.resourcemanagement.DataLocationService 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"));
}
Also used : BillingProfileModel(bio.terra.model.BillingProfileModel) FieldValue(com.google.cloud.bigquery.FieldValue) CoreMatchers(org.hamcrest.CoreMatchers) SnapshotModel(bio.terra.model.SnapshotModel) Autowired(org.springframework.beans.factory.annotation.Autowired) ActiveProfiles(org.springframework.test.context.ActiveProfiles) StorageOptions(com.google.cloud.storage.StorageOptions) StringUtils(org.apache.commons.lang3.StringUtils) BigQuery(com.google.cloud.bigquery.BigQuery) Assert.assertThat(org.junit.Assert.assertThat) RelationshipModel(bio.terra.model.RelationshipModel) FieldValueList(com.google.cloud.bigquery.FieldValueList) After(org.junit.After) DrsId(bio.terra.service.filedata.DrsId) TableResult(com.google.cloud.bigquery.TableResult) SpringRunner(org.springframework.test.context.junit4.SpringRunner) URI(java.net.URI) DataLocationService(bio.terra.service.resourcemanagement.DataLocationService) MockBean(org.springframework.boot.test.mock.mockito.MockBean) CoreMatchers.containsString(org.hamcrest.CoreMatchers.containsString) PDAO_PREFIX(bio.terra.common.PdaoConstant.PDAO_PREFIX) MediaType(org.springframework.http.MediaType) QueryJobConfiguration(com.google.cloud.bigquery.QueryJobConfiguration) EnumerateSnapshotModel(bio.terra.model.EnumerateSnapshotModel) UUID(java.util.UUID) Category(org.junit.experimental.categories.Category) SnapshotRequestContentsModel(bio.terra.model.SnapshotRequestContentsModel) Collectors(java.util.stream.Collectors) DatasetSummaryModel(bio.terra.model.DatasetSummaryModel) StandardCharsets(java.nio.charset.StandardCharsets) ConfigEnum(bio.terra.service.configuration.ConfigEnum) IOUtils(org.apache.commons.io.IOUtils) List(java.util.List) SpringBootTest(org.springframework.boot.test.context.SpringBootTest) ST(org.stringtemplate.v4.ST) Assert.assertFalse(org.junit.Assert.assertFalse) TestUtils(bio.terra.common.TestUtils) Matchers.equalTo(org.hamcrest.Matchers.equalTo) Optional(java.util.Optional) Storage(com.google.cloud.storage.Storage) ConfigurationService(bio.terra.service.configuration.ConfigurationService) ArgumentMatchers.any(org.mockito.ArgumentMatchers.any) GoogleResourceConfiguration(bio.terra.service.resourcemanagement.google.GoogleResourceConfiguration) ConnectedOperations(bio.terra.common.fixtures.ConnectedOperations) Names(bio.terra.common.fixtures.Names) DRSObject(bio.terra.model.DRSObject) RunWith(org.junit.runner.RunWith) BigQueryProject(bio.terra.service.tabulardata.google.BigQueryProject) DrsIdService(bio.terra.service.filedata.DrsIdService) TableModel(bio.terra.model.TableModel) MockMvcResultMatchers.content(org.springframework.test.web.servlet.result.MockMvcResultMatchers.content) MockHttpServletResponse(org.springframework.mock.web.MockHttpServletResponse) ArrayList(java.util.ArrayList) MockMvc(org.springframework.test.web.servlet.MockMvc) SnapshotRequestModel(bio.terra.model.SnapshotRequestModel) MockMvcRequestBuilders.delete(org.springframework.test.web.servlet.request.MockMvcRequestBuilders.delete) MockMvcRequestBuilders.post(org.springframework.test.web.servlet.request.MockMvcRequestBuilders.post) MvcResult(org.springframework.test.web.servlet.MvcResult) JsonLoader(bio.terra.common.fixtures.JsonLoader) ProfileDao(bio.terra.service.resourcemanagement.ProfileDao) ConnectedTestConfiguration(bio.terra.app.configuration.ConnectedTestConfiguration) StringStartsWith.startsWith(org.hamcrest.core.StringStartsWith.startsWith) Before(org.junit.Before) BlobInfo(com.google.cloud.storage.BlobInfo) FileLoadModel(bio.terra.model.FileLoadModel) FileModel(bio.terra.model.FileModel) Assert.assertNotNull(org.junit.Assert.assertNotNull) ObjectMapper(com.fasterxml.jackson.databind.ObjectMapper) Connected(bio.terra.common.category.Connected) Assert.assertTrue(org.junit.Assert.assertTrue) DeleteResponseModel(bio.terra.model.DeleteResponseModel) Test(org.junit.Test) IamProviderInterface(bio.terra.service.iam.IamProviderInterface) Mockito.when(org.mockito.Mockito.when) SnapshotSourceModel(bio.terra.model.SnapshotSourceModel) DatasetDao(bio.terra.service.dataset.DatasetDao) TimeUnit(java.util.concurrent.TimeUnit) ErrorModel(bio.terra.model.ErrorModel) HttpStatus(org.springframework.http.HttpStatus) IngestRequestModel(bio.terra.model.IngestRequestModel) AutoConfigureMockMvc(org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc) Assert.assertNull(org.junit.Assert.assertNull) SnapshotSummaryModel(bio.terra.model.SnapshotSummaryModel) MockMvcRequestBuilders.get(org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get) Assert.assertEquals(org.junit.Assert.assertEquals) SnapshotSummaryModel(bio.terra.model.SnapshotSummaryModel) RelationshipModel(bio.terra.model.RelationshipModel) CoreMatchers.containsString(org.hamcrest.CoreMatchers.containsString) SnapshotRequestModel(bio.terra.model.SnapshotRequestModel) SnapshotModel(bio.terra.model.SnapshotModel) EnumerateSnapshotModel(bio.terra.model.EnumerateSnapshotModel) BigQueryProject(bio.terra.service.tabulardata.google.BigQueryProject) DatasetSummaryModel(bio.terra.model.DatasetSummaryModel) MockHttpServletResponse(org.springframework.mock.web.MockHttpServletResponse) TableModel(bio.terra.model.TableModel) SpringBootTest(org.springframework.boot.test.context.SpringBootTest) Test(org.junit.Test)

Aggregations

ConnectedTestConfiguration (bio.terra.app.configuration.ConnectedTestConfiguration)1 PDAO_PREFIX (bio.terra.common.PdaoConstant.PDAO_PREFIX)1 TestUtils (bio.terra.common.TestUtils)1 Connected (bio.terra.common.category.Connected)1 ConnectedOperations (bio.terra.common.fixtures.ConnectedOperations)1 JsonLoader (bio.terra.common.fixtures.JsonLoader)1 Names (bio.terra.common.fixtures.Names)1 BillingProfileModel (bio.terra.model.BillingProfileModel)1 DRSObject (bio.terra.model.DRSObject)1 DatasetSummaryModel (bio.terra.model.DatasetSummaryModel)1 DeleteResponseModel (bio.terra.model.DeleteResponseModel)1 EnumerateSnapshotModel (bio.terra.model.EnumerateSnapshotModel)1 ErrorModel (bio.terra.model.ErrorModel)1 FileLoadModel (bio.terra.model.FileLoadModel)1 FileModel (bio.terra.model.FileModel)1 IngestRequestModel (bio.terra.model.IngestRequestModel)1 RelationshipModel (bio.terra.model.RelationshipModel)1 SnapshotModel (bio.terra.model.SnapshotModel)1 SnapshotRequestContentsModel (bio.terra.model.SnapshotRequestContentsModel)1 SnapshotRequestModel (bio.terra.model.SnapshotRequestModel)1