Examples with EntityView org.sagebionetworks.repo.model.table.EntityView used on opensource projects

Example 1 with EntityView

use of org.sagebionetworks.repo.model.table.EntityView in project BridgeServer2 by Sage-Bionetworks.

the class Exporter3ServiceTest method initExporter3.

@Test
public void initExporter3() throws Exception {
    // App has no exporter3config.
    app.setExporter3Configuration(null);
    app.setExporter3Enabled(false);
    // Mock SynapseHelper.
    Team createdTeam = new Team();
    createdTeam.setId(String.valueOf(DATA_ACCESS_TEAM_ID));
    when(mockSynapseHelper.createTeamWithRetry(any())).thenReturn(createdTeam);
    Project createdProject = new Project();
    createdProject.setId(PROJECT_ID);
    when(mockSynapseHelper.createEntityWithRetry(any(Project.class))).thenReturn(createdProject);
    EntityView trackingView = new EntityView();
    trackingView.setScopeIds(new ArrayList<>());
    when(mockSynapseHelper.getEntityWithRetry(SYNAPSE_TRACKING_VIEW_ID, EntityView.class)).thenReturn(trackingView);
    TableEntity createdTable = new TableEntity();
    createdTable.setId(PARTICIPANT_VERSION_TABLE_ID);
    when(mockSynapseHelper.createTableWithColumnsAndAcls(anyList(), anySet(), anySet(), anyString(), anyString())).thenReturn(PARTICIPANT_VERSION_TABLE_ID);
    Folder createdFolder = new Folder();
    createdFolder.setId(RAW_FOLDER_ID);
    when(mockSynapseHelper.createEntityWithRetry(any(Folder.class))).thenReturn(createdFolder);
    ExternalS3StorageLocationSetting createdStorageLocation = new ExternalS3StorageLocationSetting();
    createdStorageLocation.setStorageLocationId(STORAGE_LOCATION_ID);
    when(mockSynapseHelper.createStorageLocationForEntity(eq(RAW_FOLDER_ID), any(ExternalS3StorageLocationSetting.class))).thenReturn(createdStorageLocation);
    // Execute and verify output.
    Exporter3Configuration returnedEx3Config = exporter3Service.initExporter3(TestConstants.TEST_APP_ID);
    assertEquals(returnedEx3Config.getDataAccessTeamId().longValue(), DATA_ACCESS_TEAM_ID);
    assertEquals(returnedEx3Config.getParticipantVersionTableId(), PARTICIPANT_VERSION_TABLE_ID);
    assertEquals(returnedEx3Config.getProjectId(), PROJECT_ID);
    assertEquals(returnedEx3Config.getRawDataFolderId(), RAW_FOLDER_ID);
    assertEquals(returnedEx3Config.getStorageLocationId().longValue(), STORAGE_LOCATION_ID);
    // Verify created team.
    ArgumentCaptor<Team> teamToCreateCaptor = ArgumentCaptor.forClass(Team.class);
    verify(mockSynapseHelper).createTeamWithRetry(teamToCreateCaptor.capture());
    Team teamToCreate = teamToCreateCaptor.getValue();
    assertEquals(teamToCreate.getName(), EXPECTED_TEAM_NAME);
    // Verify created project. Note that we call this method again later, which is why we verify it twice now.
    ArgumentCaptor<Entity> entitiesToCreateCaptor = ArgumentCaptor.forClass(Project.class);
    verify(mockSynapseHelper, times(2)).createEntityWithRetry(entitiesToCreateCaptor.capture());
    List<Entity> entitiesToCreateList = entitiesToCreateCaptor.getAllValues();
    Project projectToCreate = (Project) entitiesToCreateList.get(0);
    assertEquals(projectToCreate.getName(), EXPECTED_PROJECT_NAME);
    // Verify project ACLs.
    verify(mockSynapseHelper).createAclWithRetry(PROJECT_ID, ADMIN_PRINCIPAL_ID_SET, READ_ONLY_PRINCIPAL_ID_SET);
    // Verify project added to tracking view. For whatever reason, view scope IDs don't include the "syn" prefix.
    ArgumentCaptor<EntityView> viewToUpdateCaptor = ArgumentCaptor.forClass(EntityView.class);
    verify(mockSynapseHelper).updateEntityWithRetry(viewToUpdateCaptor.capture());
    EntityView viewToUpdate = viewToUpdateCaptor.getValue();
    assertTrue(viewToUpdate.getScopeIds().contains(PROJECT_ID_WITHOUT_PREFIX));
    // Verify created participant version table.
    verify(mockSynapseHelper).createTableWithColumnsAndAcls(Exporter3Service.PARTICIPANT_VERSION_COLUMN_MODELS, READ_ONLY_PRINCIPAL_ID_SET, ADMIN_PRINCIPAL_ID_SET, PROJECT_ID, Exporter3Service.TABLE_NAME_PARTICIPANT_VERSIONS);
    // Verify created folder.
    Folder folderToCreate = (Folder) entitiesToCreateList.get(1);
    assertEquals(folderToCreate.getName(), Exporter3Service.FOLDER_NAME_BRIDGE_RAW_DATA);
    assertEquals(folderToCreate.getParentId(), PROJECT_ID);
    // Verify folder ACLs.
    verify(mockSynapseHelper).createAclWithRetry(RAW_FOLDER_ID, ADMIN_PRINCIPAL_ID_SET, READ_ONLY_PRINCIPAL_ID_SET);
    // Verify we write to S3 for the storage location.
    verify(mockS3Helper).writeLinesToS3(RAW_HEALTH_DATA_BUCKET, TestConstants.TEST_APP_ID + "/owner.txt", ImmutableList.of(EXPORTER_SYNAPSE_USER));
    // Verify created storage location.
    ArgumentCaptor<ExternalS3StorageLocationSetting> storageLocationToCreateCaptor = ArgumentCaptor.forClass(ExternalS3StorageLocationSetting.class);
    verify(mockSynapseHelper).createStorageLocationForEntity(eq(RAW_FOLDER_ID), storageLocationToCreateCaptor.capture());
    ExternalS3StorageLocationSetting storageLocationToCreate = storageLocationToCreateCaptor.getValue();
    assertEquals(storageLocationToCreate.getBaseKey(), TestConstants.TEST_APP_ID);
    assertEquals(storageLocationToCreate.getBucket(), RAW_HEALTH_DATA_BUCKET);
    assertTrue(storageLocationToCreate.getStsEnabled());
    // Verify updated app.
    ArgumentCaptor<App> appToUpdateCaptor = ArgumentCaptor.forClass(App.class);
    verify(mockAppService).updateApp(appToUpdateCaptor.capture(), eq((true)));
    App appToUpdate = appToUpdateCaptor.getValue();
    assertTrue(appToUpdate.isExporter3Enabled());
    Exporter3Configuration ex3ConfigToCreate = appToUpdate.getExporter3Configuration();
    assertEquals(ex3ConfigToCreate, returnedEx3Config);
}

Example 2 with EntityView

use of org.sagebionetworks.repo.model.table.EntityView in project BridgeServer2 by Sage-Bionetworks.

the class AppServiceTest method createAppAndUsersDefaultsPasswordPolicy.

@Test
public void createAppAndUsersDefaultsPasswordPolicy() throws SynapseException {
    app.setPasswordPolicy(null);
    app.setExternalIdRequiredOnSignup(false);
    app.setSynapseDataAccessTeamId(null);
    app.setSynapseProjectId(null);
    List<StudyParticipant> participants = ImmutableList.of(new StudyParticipant.Builder().withEmail(TEST_USER_EMAIL).withSynapseUserId(TEST_USER_SYNAPSE_ID).withRoles(ImmutableSet.of(DEVELOPER)).build());
    IdentifierHolder holder = new IdentifierHolder("user-id");
    when(mockParticipantService.createParticipant(any(), any(), anyBoolean())).thenReturn(holder);
    AccessControlList acl = new AccessControlList();
    acl.setResourceAccess(new HashSet<>());
    when(mockSynapseClient.createTeam(any())).thenReturn(team);
    when(mockSynapseClient.createEntity(any())).thenReturn(project);
    when(mockSynapseClient.getACL(any())).thenReturn(acl);
    EntityView view = new EntityView();
    view.setScopeIds(new ArrayList<>());
    when(mockSynapseClient.getEntity(SYNAPSE_TRACKING_VIEW_ID, EntityView.class)).thenReturn(view);
    AppAndUsers mockAppAndUsers = new AppAndUsers(ImmutableList.of("12345678"), app, participants);
    service.createAppAndUsers(mockAppAndUsers);
    verify(mockAppDao).createApp(appCaptor.capture());
    assertNotNull(appCaptor.getValue().getPasswordPolicy());
}

Example 3 with EntityView

use of org.sagebionetworks.repo.model.table.EntityView in project BridgeServer2 by Sage-Bionetworks.

the class AppServiceTest method addProjectToTrackingView_PutThrows.

@Test
public void addProjectToTrackingView_PutThrows() throws Exception {
    // Set up.
    EntityView view = new EntityView();
    view.setScopeIds(new ArrayList<>());
    when(mockSynapseClient.getEntity(SYNAPSE_TRACKING_VIEW_ID, EntityView.class)).thenReturn(view);
    when(mockSynapseClient.putEntity(view)).thenThrow(SynapseNotFoundException.class);
    // Execute. The exception is swallowed.
    service.addProjectToTrackingView(TEST_PROJECT_ID);
    verify(mockSynapseClient).getEntity(SYNAPSE_TRACKING_VIEW_ID, EntityView.class);
    verify(mockSynapseClient).putEntity(view);
}

Example 4 with EntityView

use of org.sagebionetworks.repo.model.table.EntityView in project BridgeServer2 by Sage-Bionetworks.

the class Exporter3Service method initExporter3.

/**
 * Initializes configs and Synapse resources for Exporter 3.0. Note that if any config already exists, this API
 * will simply ignore them. This allows for two notable scenarios
 * (a) Advanced users can use existing projects or data access teams for Exporter 3.0.
 * (b) If in the future, we add something new (like a notification queue, or a default view), we can re-run this
 * API to create the new stuff without affecting the old stuff.
 */
public Exporter3Configuration initExporter3(String appId) throws BridgeSynapseException, IOException, SynapseException {
    boolean isAppModified = false;
    App app = appService.getApp(appId);
    // Init the Exporter3Config object.
    Exporter3Configuration ex3Config = app.getExporter3Configuration();
    if (ex3Config == null) {
        ex3Config = new Exporter3Configuration();
        app.setExporter3Configuration(ex3Config);
        isAppModified = true;
    }
    // Name in Synapse are globally unique, so we add a random token to the name to ensure it
    // doesn't conflict with an existing name. Also, Synapse names can only contain a certain
    // subset of characters. We've verified this name is acceptable for this transformation.
    String synapseName = BridgeUtils.toSynapseFriendlyName(app.getName());
    String nameScopingToken = getNameScopingToken();
    // Create data access team.
    Long dataAccessTeamId = ex3Config.getDataAccessTeamId();
    if (dataAccessTeamId == null) {
        Team team = new Team();
        team.setName(synapseName + " Access Team " + nameScopingToken);
        team = synapseHelper.createTeamWithRetry(team);
        dataAccessTeamId = Long.parseLong(team.getId());
        LOG.info("Created Synapse team " + dataAccessTeamId);
        ex3Config.setDataAccessTeamId(dataAccessTeamId);
        isAppModified = true;
    }
    Set<Long> adminPrincipalIds = ImmutableSet.of(exporterSynapseId, bridgeAdminTeamId);
    Set<Long> readOnlyPrincipalIds = ImmutableSet.of(bridgeStaffTeamId, dataAccessTeamId);
    // Create project.
    String projectId = ex3Config.getProjectId();
    if (projectId == null) {
        Project project = new Project();
        project.setName(synapseName + " Project " + nameScopingToken);
        project = synapseHelper.createEntityWithRetry(project);
        projectId = project.getId();
        LOG.info("Created Synapse project " + projectId);
        // Create ACLs for project.
        synapseHelper.createAclWithRetry(projectId, adminPrincipalIds, readOnlyPrincipalIds);
        ex3Config.setProjectId(projectId);
        isAppModified = true;
        // We also need to add this project to the tracking view.
        if (StringUtils.isNotBlank(synapseTrackingViewId)) {
            try {
                EntityView view = synapseHelper.getEntityWithRetry(synapseTrackingViewId, EntityView.class);
                if (view != null) {
                    // For whatever reason, view.getScopes() doesn't include the "syn" prefix.
                    view.getScopeIds().add(projectId.substring(3));
                    synapseHelper.updateEntityWithRetry(view);
                }
            } catch (SynapseException ex) {
                LOG.error("Error adding new project " + projectId + " to tracking view " + synapseTrackingViewId + ": " + ex.getMessage(), ex);
            }
        }
    }
    // Create Participant Version Table.
    String participantVersionTableId = ex3Config.getParticipantVersionTableId();
    if (participantVersionTableId == null) {
        participantVersionTableId = synapseHelper.createTableWithColumnsAndAcls(PARTICIPANT_VERSION_COLUMN_MODELS, readOnlyPrincipalIds, adminPrincipalIds, projectId, TABLE_NAME_PARTICIPANT_VERSIONS);
        LOG.info("Created Synapse table " + participantVersionTableId);
        ex3Config.setParticipantVersionTableId(participantVersionTableId);
        isAppModified = true;
    }
    // Create Folder for raw data.
    String rawDataFolderId = ex3Config.getRawDataFolderId();
    if (rawDataFolderId == null) {
        Folder folder = new Folder();
        folder.setName(FOLDER_NAME_BRIDGE_RAW_DATA);
        folder.setParentId(projectId);
        folder = synapseHelper.createEntityWithRetry(folder);
        rawDataFolderId = folder.getId();
        LOG.info("Created Synapse folder " + rawDataFolderId);
        // Create ACLs for folder. This is a separate ACL because we don't want to allow people to modify the
        // raw data.
        synapseHelper.createAclWithRetry(rawDataFolderId, adminPrincipalIds, readOnlyPrincipalIds);
        ex3Config.setRawDataFolderId(rawDataFolderId);
        isAppModified = true;
    }
    // Create storage location.
    Long storageLocationId = ex3Config.getStorageLocationId();
    if (storageLocationId == null) {
        // Create owner.txt so that we can create the storage location.
        s3Helper.writeLinesToS3(rawHealthDataBucket, appId + "/owner.txt", ImmutableList.of(exporterSynapseUser));
        // Create storage location.
        ExternalS3StorageLocationSetting storageLocation = new ExternalS3StorageLocationSetting();
        storageLocation.setBaseKey(appId);
        storageLocation.setBucket(rawHealthDataBucket);
        storageLocation.setStsEnabled(true);
        storageLocation = synapseHelper.createStorageLocationForEntity(rawDataFolderId, storageLocation);
        storageLocationId = storageLocation.getStorageLocationId();
        LOG.info("Created Synapse storage location " + storageLocationId);
        ex3Config.setStorageLocationId(storageLocationId);
        isAppModified = true;
    }
    // Finally, enable Exporter 3.0 if it's not already enabled.
    if (!app.isExporter3Enabled()) {
        app.setExporter3Enabled(true);
        isAppModified = true;
    }
    // exporter3config and exporter3enabled.
    if (isAppModified) {
        appService.updateApp(app, true);
    }
    return ex3Config;
}

Example 5 with EntityView

use of org.sagebionetworks.repo.model.table.EntityView in project BridgeServer2 by Sage-Bionetworks.

the class AppService method addProjectToTrackingView.

// Package-scoped for unit tests.
void addProjectToTrackingView(String projectId) {
    // Add the project to the tracking view, if it exists.
    if (StringUtils.isNotBlank(synapseTrackingViewId)) {
        try {
            EntityView view = synapseClient.getEntity(synapseTrackingViewId, EntityView.class);
            // For whatever reason, view.getScopes() doesn't include the "syn" prefix.
            view.getScopeIds().add(projectId.substring(3));
            synapseClient.putEntity(view);
        } catch (SynapseException ex) {
            LOG.error("Error adding new project " + projectId + " to tracking view " + synapseTrackingViewId + ": " + ex.getMessage(), ex);
        }
    }
}