TASK-7413 - Implement notifications system

[pfurio]

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[halender]

Task linked: TASK-7413 Implement notifications system

[Copilot]

Pull Request Overview

This PR implements a notifications system in the OpenCGA catalog, adding new managers, database adaptors, API endpoints, CLI commands, and corresponding client support.

• Adds NotificationManager and related methods to CatalogManager and AbstractManager.
• Introduces NotificationDBAdaptor and NotificationConverter, and updates CLI commands and REST client generators to support notifications.
• Extends authorization and permission checks with project administrator functionality, and adjusts CatalogFqn usage in VariantStorageManager.

Reviewed Changes

Copilot reviewed 67 out of 67 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
CatalogManager.java	Added NotificationManager field initialization and a corresponding getter.
AbstractManager.java	Added a new method to get NotificationDBAdaptor and updated query key conversion.
CatalogAuthorizationException.java	Added a new exception method for project administration.
NotificationConverter.java	New converter class for notifications.
UserMongoDBAdaptor.java	Modified query handling for INTERNAL_STATUS_ID, removing conversion logic.
OrganizationMongoDBAdaptorFactory.java	Added NOTIFICATION_COLLECTION support and accessor for NotificationDBAdaptor.
MongoDBAdaptorFactory.java	Added NotificationDBAdaptor accessor method.
UserDBAdaptor.java	Added NOTIFICATIONS query parameter.
NotificationDBAdaptor.java	New interface for Notification database operations.
DBAdaptorFactory.java	Updated with NotificationDBAdaptor method definition.
CatalogAuthorizationManager.java	Extended authorization logic with project admin checks and updated method signature for study administration.
AuthorizationManager.java	Updated interface with new project admin methods and renamed study id parameter.
CLI and REST client files	Added notifications command options, executor, CLI completions, and client generation updates.
VariantStorageManager.java	Updated CatalogFqn method to extract the FQN correctly.

Comments suppressed due to low confidence (3)

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/NotificationsCommandExecutor.java:50

• Since the notifications functionality spans multiple components (manager, adaptor, CLI, etc.), it is important to ensure that comprehensive tests are added to cover these new code paths and edge scenarios.

logger.debug("Executing Notifications command line");

opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/UserMongoDBAdaptor.java:777

• The conversion logic for INTERNAL_STATUS_ID (i.e. converting the status to a positive status) has been removed. Please verify that this change is aligned with the overall behavior expected from the query, as it might affect clients that rely on the transformed status values.

case INTERNAL_STATUS_ID:

opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/manager/VariantStorageManager.java:1083

• The change from using fromProjectFqn to extractFqnFromProjectFqn alters how the FQN is parsed. It is advisable to review that the new method handles all project FQN edge cases consistently with the previous behavior.

CatalogFqn projectFqn = CatalogFqn.extractFqnFromProjectFqn(projectFqnStr);

[Copilot]

Pull Request Overview

This pull request implements a notifications system and integrates it across the catalog, authorization, CLI, and client generator modules. Key changes include:

• Introducing a new NotificationDBAdaptor interface and its corresponding factory methods.
• Adding a notifications query parameter to UserDBAdaptor and updating authorization methods for project-level admin checks.
• Extending CLI options, executors, completers, and client generators to support notifications.

Reviewed Changes

Copilot reviewed 77 out of 77 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
MongoDBAdaptorFactory.java	Adds a new method to obtain the NotificationDBAdaptor for a given organization.
UserDBAdaptor.java	Introduces a new NOTIFICATIONS query parameter for notifications.
NotificationDBAdaptor.java	Defines the NotificationDBAdaptor interface with all relevant notification operations.
DBAdaptorFactory.java	Updates the adaptor factory to include notifications support.
CatalogAuthorizationManager.java	Adds methods for checking project administrator permissions and a helper for retrieving project admins.
AuthorizationManager.java	Updates interface signatures for study and project admin checks.
UsersCommandOptions.java & OrganizationsCommandOptions.java	Updates parameter descriptions for name and email fields.
NotificationsCommandOptions.java	Adds CLI options for notifications commands.
NotificationsCommandExecutor.java	Implements CLI executor methods for aggregation stats, creation, search, info, and visit operations related to notifications.
ExecutorProvider.java, OpencgaCliOptionsParser.java, OpenCgaCompleter.java	Integrates notifications into the command routing and autocompletion.
Client generator files & VariantStorageManager.java	Update code and configuration to account for notifications functionality.