Skip to content

Commit

Permalink
re-enable internal jobs controller
Browse files Browse the repository at this point in the history
  • Loading branch information
@Foxcapades
Foxcapades committed Sep 25, 2024
1 parent afe8277 commit 154a354
Showing 1 changed file with 85 additions and 73 deletions.
158 changes: 85 additions & 73 deletions src/main/java/org/veupathdb/service/eda/Resources.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@
import org.veupathdb.service.eda.access.repo.RestrictionLevelRepo;
import org.veupathdb.service.eda.compute.controller.ComputeController;
import org.veupathdb.service.eda.compute.controller.ExpirationController;
import org.veupathdb.service.eda.compute.controller.InternalJobsController;
import org.veupathdb.service.eda.compute.service.JobsController;
import org.veupathdb.service.eda.data.service.AppsService;
import org.veupathdb.service.eda.data.service.FilterAwareMetadataService;
Expand Down Expand Up @@ -61,43 +62,47 @@

/**
* Service Resource Registration.
*
* <p>
* This is where all the individual service specific resources and middleware
* should be registered.
*/
public class Resources extends ContainerResources {
private static final Logger LOG = LogManager.getLogger(Resources.class);

// Subsetting Config
private static final EnvironmentVars SUBSET_ENV = new EnvironmentVars();
private static final CountDownLatch APP_DB_INIT_SIGNAL = new CountDownLatch(1);
private static final BinaryFilesManager BINARY_FILES_MANAGER = new BinaryFilesManager(
new SimpleStudyFinder(Resources.getBinaryFilesDirectory().toString()));
private static final MetadataCache METADATA_CACHE = new MetadataCache(BINARY_FILES_MANAGER, APP_DB_INIT_SIGNAL);
private static final ExecutorService FILE_READ_THREAD_POOL = Executors.newCachedThreadPool();
private static final ExecutorService DESERIALIZER_THREAD_POOL = Executors.newFixedThreadPool(16);
private static final EnvironmentVars SUBSET_ENV = new EnvironmentVars();
private static final CountDownLatch APP_DB_INIT_SIGNAL = new CountDownLatch(1);
private static final BinaryFilesManager BINARY_FILES_MANAGER = new BinaryFilesManager(
new SimpleStudyFinder(Resources.getBinaryFilesDirectory().toString()));
private static final MetadataCache METADATA_CACHE = new MetadataCache(
BINARY_FILES_MANAGER,
APP_DB_INIT_SIGNAL
);
private static final ExecutorService FILE_READ_THREAD_POOL = Executors.newCachedThreadPool();
private static final ExecutorService DESERIALIZER_THREAD_POOL = Executors.newFixedThreadPool(16);

// use in-memory test DB unless "real" application DB is configured
private static boolean USE_IN_MEMORY_TEST_DATABASE = true;

// Download Files Config
public static final Path DOWNLOAD_FILES_MOUNT_PATH = getReadableDir(Paths.get(Environment.getRequiredVar("DOWNLOAD_FILES_MOUNT_PATH")));
private static final String USER_SCHEMA_PROP = "USER_SCHEMA";
public static final Path DOWNLOAD_FILES_MOUNT_PATH = getReadableDir(Paths.get(Environment.getRequiredVar(
"DOWNLOAD_FILES_MOUNT_PATH")));
private static final String USER_SCHEMA_PROP = "USER_SCHEMA";

// Project-specific config
private static Map<String,String> SCHEMA_MAP;
private static final String RAW_FILES_DIR_PROP = "RAW_FILES_DIR";
private static Map<String,String> PROJECT_DIR_MAP;
private static Map<String, String> SCHEMA_MAP;
private static final String RAW_FILES_DIR_PROP = "RAW_FILES_DIR";
private static Map<String, String> PROJECT_DIR_MAP;

private static final String SERVER_PORT = getRequiredVar("SERVER_PORT");
private static final String SERVER_PORT = getRequiredVar("SERVER_PORT");
private static final String CONSOLIDATED_SERVICE_URL = "http://localhost:" + SERVER_PORT;


// Service URLs -- these can be removed once inter-component communication is done in-memory.
// For ease of transition in EDA consolidation, communication between these components is still done via http.
public static final String SUBSETTING_SERVICE_URL = CONSOLIDATED_SERVICE_URL;
public static final String MERGING_SERVICE_URL = CONSOLIDATED_SERVICE_URL;
public static final String COMPUTE_SERVICE_URL = CONSOLIDATED_SERVICE_URL;
public static final String SUBSETTING_SERVICE_URL = CONSOLIDATED_SERVICE_URL;
public static final String MERGING_SERVICE_URL = CONSOLIDATED_SERVICE_URL;
public static final String COMPUTE_SERVICE_URL = CONSOLIDATED_SERVICE_URL;
public static final String DATASET_ACCESS_SERVICE_URL = CONSOLIDATED_SERVICE_URL;

public static final String RSERVE_URL = getRequiredVar("RSERVE_URL");
Expand All @@ -112,33 +117,33 @@ public Resources(Options opts) {

// Project-specific user schemas.
SCHEMA_MAP = new ProjectSpecificProperties<>(
new ProjectSpecificProperties.PropertySpec[] { required(USER_SCHEMA_PROP) },
map -> {
// add trailing '.' to schema names for convenience later
String rawSchemaName = map.get(USER_SCHEMA_PROP);
return rawSchemaName + (rawSchemaName.endsWith(".") ? "" : ".");
}
new ProjectSpecificProperties.PropertySpec[]{required(USER_SCHEMA_PROP)},
map -> {
// add trailing '.' to schema names for convenience later
String rawSchemaName = map.get(USER_SCHEMA_PROP);
return rawSchemaName + (rawSchemaName.endsWith(".") ? "" : ".");
}
).toMap();

// Project-specific download directories. Study download files have a project-aware directory structure.
PROJECT_DIR_MAP = new ProjectSpecificProperties<>(
new ProjectSpecificProperties.PropertySpec[] { required(RAW_FILES_DIR_PROP) },
map -> map.get(RAW_FILES_DIR_PROP)
new ProjectSpecificProperties.PropertySpec[]{required(RAW_FILES_DIR_PROP)},
map -> map.get(RAW_FILES_DIR_PROP)
).toMap();

if (opts.getAppDbOpts().name().isPresent() || opts.getAppDbOpts().tnsName().isPresent()) {
// application database configured; use it
USE_IN_MEMORY_TEST_DATABASE = false;
} else {
LOG.warn("No application database configured! Using in-memory database. This should only appear in test environments.");
LOG.warn(
"No application database configured! Using in-memory database. This should only appear in test environments.");
}

// load cached permissions data.
try {
ApprovalStatusRepo.Select.populateApprovalStatusCache();
RestrictionLevelRepo.Select.populateRestrictionLevelCache();
}
catch (Exception e) {
} catch (Exception e) {
throw new RuntimeException(e);
}

Expand All @@ -150,7 +155,7 @@ public Resources(Options opts) {
if (!USE_IN_MEMORY_TEST_DATABASE) {
DbManager.initApplicationDatabase(opts);
LOG.info("Using application DB connection URL: " +
DbManager.getInstance().getApplicationDatabase().getConfig().getConnectionUrl());
DbManager.getInstance().getApplicationDatabase().getConfig().getConnectionUrl());
APP_DB_INIT_SIGNAL.countDown();
}
}
Expand All @@ -160,20 +165,23 @@ public static MetadataCache getMetadataCache() {
}

public static StudyResolver getStudyResolver() {
final BinaryFilesManager binaryFilesManager = Resources.getBinaryFilesManager();
final BinaryFilesManager binaryFilesManager = Resources.getBinaryFilesManager();
final MetadataFileBinaryProvider metadataFileBinaryProvider = new MetadataFileBinaryProvider(binaryFilesManager);
final VariableFactory variableFactory = new VariableFactory(Resources.getApplicationDataSource(),
Resources.getVdiDatasetsSchema() + ".",
metadataFileBinaryProvider,
binaryFilesManager::studyHasFiles);
final VariableFactory variableFactory = new VariableFactory(
Resources.getApplicationDataSource(),
Resources.getVdiDatasetsSchema() + ".",
metadataFileBinaryProvider,
binaryFilesManager::studyHasFiles
);
return new StudyResolver(
METADATA_CACHE,
new StudyFactory(
Resources.getApplicationDataSource(),
Resources.getVdiDatasetsSchema() + ".",
StudyOverview.StudySourceType.USER_SUBMITTED,
variableFactory,
false)
METADATA_CACHE,
new StudyFactory(
Resources.getApplicationDataSource(),
Resources.getVdiDatasetsSchema() + ".",
StudyOverview.StudySourceType.USER_SUBMITTED,
variableFactory,
false
)
);
}

Expand All @@ -196,7 +204,10 @@ public static String getAppDbSchema() {
}

public static Path getBinaryFilesDirectory() {
return Path.of(SUBSET_ENV.getBinaryFilesMount(), SUBSET_ENV.getBinaryFilesDirectory().replace("%DB_BUILD%", SUBSET_ENV.getDbBuild()));
return Path.of(
SUBSET_ENV.getBinaryFilesMount(),
SUBSET_ENV.getBinaryFilesDirectory().replace("%DB_BUILD%", SUBSET_ENV.getDbBuild())
);
}

public static ExecutorService getFileChannelThreadPool() {
Expand All @@ -215,7 +226,7 @@ public static DataSource getUserDataSource() {
return DbManager.userDatabase().getDataSource();
}

public static DataSource getAccountsDataSource() { return DbManager.accountDatabase().getDataSource(); }
public static DataSource getAccountsDataSource() {return DbManager.accountDatabase().getDataSource();}

public static String getUserDbSchema(String projectId) {
if (!SCHEMA_MAP.containsKey(projectId)) {
Expand Down Expand Up @@ -260,40 +271,41 @@ public static BinaryValuesStreamer getBinaryValuesStreamer() {

/**
* Returns an array of JaxRS endpoints, providers, and contexts.
*
* <p>
* Entries in the array can be either classes or instances.
*/
@Override
protected Object[] resources() {
return new Object[]{
// Subsetting
StudiesService.class,
InternalClientsService.class,
ClearMetadataCacheService.class,
// Visualization
AppsService.class,
FilterAwareMetadataService.class,
// Merging
ServiceExternal.class,
ServiceInternal.class,
// Compute
JobsController.class,
ComputeController.class,
ExpirationController.class,
// Access
ApproveEligibleStudiesController.class,
ProviderController.class,
StaffController.class,
EndUserController.class,
PermissionController.class,
HistoryController.class,
// User
UserService.class,
PublicDataService.class,
ImportAnalysisService.class,
MetricsService.class,
// Download
Service.class
// Subsetting
StudiesService.class,
InternalClientsService.class,
ClearMetadataCacheService.class,
// Visualization
AppsService.class,
FilterAwareMetadataService.class,
// Merging
ServiceExternal.class,
ServiceInternal.class,
// Compute
JobsController.class,
ComputeController.class,
ExpirationController.class,
InternalJobsController.class,
// Access
ApproveEligibleStudiesController.class,
ProviderController.class,
StaffController.class,
EndUserController.class,
PermissionController.class,
HistoryController.class,
// User
UserService.class,
PublicDataService.class,
ImportAnalysisService.class,
MetricsService.class,
// Download
Service.class
};
}
}
}

0 comments on commit 154a354

Please sign in to comment.