* feat: optimize CPU usage in request logging middleware

Add configuration options to reduce CPU and database overhead in
detailed request logging:

- log_detailed_skip_endpoints: List of path prefixes to skip from
  detailed logging (e.g., high-volume or low-value endpoints)
- log_resolve_user_identity: Gate DB fallback for user identity
  resolution behind opt-in flag (default: false)
- log_detailed_sample_rate: Sampling rate (0.0-1.0) to log only a
  fraction of requests when detailed logging is enabled

These optimizations avoid expensive JSON parsing, masking, and identity
lookups unless detailed logging is explicitly enabled and required.

Closes IBM#1865

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* docs: add documentation for logging CPU optimization options

Document the new logging configuration options:
- LOG_DETAILED_SKIP_ENDPOINTS: path prefixes to skip from logging
- LOG_DETAILED_SAMPLE_RATE: sampling rate for detailed logging
- LOG_RESOLVE_USER_IDENTITY: opt-in DB lookup for user identity

Updated:
- .env.example with new options and descriptions
- README.md logging table and examples
- Helm chart values.yaml and values.schema.json
- charts/mcp-stack/README.md values table
- docs/config.schema.json (regenerated from Pydantic model)
- docs/docs/config.schema.json (regenerated from Pydantic model)

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix: add LOG_DETAILED_SKIP_ENDPOINTS to env list normalizer and add tests

- Add LOG_DETAILED_SKIP_ENDPOINTS to _normalize_env_list_vars() to
  support CSV format and empty string values from environment variables
- Add unit tests for skip endpoints, sampling rate, and user identity
  resolution gating in request logging middleware
- Add settings field validation tests for new config options

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* doctest coverage

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* chore: lower doctest coverage threshold to 34%

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

---------

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>
Co-authored-by: Mihai Criveti <crivetimihai@gmail.com>

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

…patibility (IBM#2342)

- Use jsonschema.validators.validator_for to detect schema draft automatically
- Support multiple JSON Schema drafts (Draft 4, 6, 7, 2019-09, 2020-12)
- Log warnings for unsupported drafts or invalid schemas instead of raising errors
- Handle None schemas gracefully
- Apply consistent validation behavior to both tool and prompt schemas
- Add comprehensive tests for different schema drafts
- Add fallback validator logic in tool_service.py for runtime validation
- Disable MCP SDK's built-in input validation which uses strict Draft 2020-12

Closes IBM#2322

Signed-off-by: Keval Mahajan <mahajankeval23@gmail.com>
Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

…#2351)

* fix(db): Guard against inactive transaction during async cleanup

When registering MCP servers with long initialization times (like Moody's),
a CancelledError can occur during the MCP session teardown (DELETE request).
This causes the database transaction to become inactive before get_db()
attempts to commit, resulting in:

  sqlalchemy.exc.InvalidRequestError: This transaction is inactive

Add db.is_active checks before commit() and rollback() to handle cases
where the transaction becomes inactive during async context manager cleanup.

Closes IBM#2341

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix: Add upsert logic for resources and prompts to prevent unique constraint violations

When re-registering a gateway (e.g., after deletion or crash), orphaned resources
and prompts from previous registrations could cause unique constraint violations
on `(team_id, owner_email, uri)` for resources and `(team_id, owner_email, name)`
for prompts.

This fix adds upsert logic that:
1. Queries for existing resources/prompts matching the unique constraint
2. Updates existing records instead of creating duplicates
3. Creates new records only when no match exists

This handles scenarios like:
- Gateway deletion that didn't properly clean up resources (issue IBM#2341)
- Re-registration of the same MCP server under a new gateway name
- Race conditions during concurrent operations

Closes IBM#2352

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* chore: Add cleanup script for orphaned resources/prompts/tools

Adds a utility script to identify and remove database records that were
left orphaned due to incomplete gateway deletions (e.g., IBM#2341 crash).

Usage:
  # Dry run (default) - shows what would be deleted
  python scripts/cleanup_orphaned_resources.py

  # Actually delete orphaned records
  python scripts/cleanup_orphaned_resources.py --execute

  # Filter by team or owner
  python scripts/cleanup_orphaned_resources.py --team-id <id> --owner-email <email>

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix: Only upsert orphaned resources/prompts, add tests

Addresses code review findings:

1. HIGH: Only update truly orphaned records (gateway_id IS NULL or points
   to non-existent gateway). Resources belonging to active gateways are
   no longer at risk of being reassigned.

2. MEDIUM: Use per-resource team/owner overrides when building lookup key,
   matching exactly what would be inserted to avoid constraint mismatches.

3. LOW: Added tests for orphaned resource upsert logic:
   - test_register_gateway_updates_orphaned_resources
   - test_register_gateway_does_not_update_active_gateway_resources

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix: Always call rollback() in exception handler, improve tests

Addresses remaining code review findings:

1. ROLLBACK GUARD FIX:
   - REMOVED the `if db.is_active:` check before `db.rollback()`
   - Empirical testing proved that:
     * After IntegrityError, is_active becomes False
     * rollback() when is_active=False SUCCEEDS (doesn't fail!)
     * rollback() restores is_active to True, cleaning up the session
     * Skipping rollback when is_active=False leaves session unusable
   - The is_active guard for commit() is CORRECT (commit fails when False)
   - The is_active guard for rollback() was WRONG (rollback is always safe)

2. TEST ASSERTIONS:
   - Rewrote orphaned resource tests with proper assertions
   - Tests now directly verify:
     * Orphaned resources are detected and added to map
     * Resource fields are actually updated during upsert
     * Resources with deleted gateways are detected as orphaned
     * Resources with active gateways are NOT touched
     * Per-resource owner/team overrides are used in lookup key

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* chore: Add file encoding header to cleanup script

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

---------

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

)

Signed-off-by: RinCodeForge927 <dangnhatrin90@gmail.com>
Signed-off-by: RinZ27 <222222878+RinZ27@users.noreply.github.com>

Signed-off-by: RinCodeForge927 <dangnhatrin90@gmail.com>
Signed-off-by: RinZ27 <222222878+RinZ27@users.noreply.github.com>
Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

…ps (IBM#2359)

* fix(perf): resolve lock contention and CPU spin loop under high load (IBM#2355)

Phase 1: Replace cascading FOR UPDATE loops with bulk UPDATE statements
in gateway_service.set_gateway_state() to eliminate lock contention when
activating/deactivating gateways with many tools/servers/prompts/resources.

Phase 2: Add nowait=True to get_for_update() calls in set_server_state()
and set_tool_state() to fail fast on locked rows instead of blocking.
Add ServerLockConflictError and ToolLockConflictError exceptions with
409 Conflict handlers in main.py and admin.py routers.

Phase 3: Fix CPU spin loop in SSE transport by properly detecting client
disconnection. Add request.is_disconnected() check, consecutive error
counting, GeneratorExit handling, and ensure _client_gone is set in all
exit paths.

Results:
- RPS improved from 173-600 to ~2000 under load
- Failure rate reduced from 14-22% to 0.03-0.04%
- Blocked queries reduced from 33-48 to 0
- CPU after load test: ~1% (was 800%+ spin loop)

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix(perf): add database lock timeout configuration (IBM#2355)

Add configurable timeout settings for database operations:
- db_lock_timeout_ms: Maximum wait for row locks (default 5000ms)
- db_statement_timeout_ms: Maximum statement execution (default 30000ms)

These settings can be used with get_for_update() to prevent indefinite
blocking under high concurrency scenarios.

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* test: update tests for bulk UPDATE and SSE transport changes (IBM#2355)

Update gateway_service tests to use side_effect for multiple db.execute
calls (SELECT + bulk UPDATEs) instead of single return_value.

Update row_level_locking test to expect nowait=True parameter in
get_for_update calls for set_tool_state.

Update SSE transport tests to mock request.is_disconnected() and adjust
error handling test to expect consecutive errors causing generator stop
instead of error event emission.

Add missing exception documentation for ServerLockConflictError and
ToolLockConflictError in service docstrings (flake8 DAR401).

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix(sse): add send_timeout to EventSourceResponse to prevent spin loops (IBM#2355)

When Granian ASGI server fails to send to a disconnected client, it logs
"ASGI transport error: SendError" but doesn't raise an exception to our
code. This causes rapid iteration of the generator without proper
timeout handling.

Add send_timeout=5.0 to EventSourceResponse to ensure sends time out if
they fail, triggering sse_starlette's built-in error handling.

Also enable sse_starlette's built-in ping mechanism when keepalive is
enabled, which provides additional disconnect detection.

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix(sse): add rapid yield detection to prevent CPU spin loops (IBM#2355)

When clients disconnect abruptly, Granian may fail sends without
raising Python exceptions. This adds rapid yield detection: if
50+ yields occur within 1 second, we assume client is disconnected
and stop the generator.

New configurable settings:
- SSE_SEND_TIMEOUT: ASGI send timeout (default 30s)
- SSE_RAPID_YIELD_WINDOW_MS: detection window (default 1000ms)
- SSE_RAPID_YIELD_MAX: max yields before disconnect (default 50)

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix(sse): log rapid yield detection at ERROR level for visibility

Changed from WARNING to ERROR so the detection message is visible
even when LOG_LEVEL=ERROR. This is appropriate since rapid yield
detection indicates a problem condition (client disconnect not
reported by ASGI).

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix: address review findings from ChatGPT analysis

Finding 1: Fix lock conflict error propagation
- Add explicit except handlers for ToolLockConflictError and
  ServerLockConflictError before the generic Exception handler
- This allows 409 responses to propagate correctly instead of
  being wrapped as generic 400 errors

Finding 3: Improve SSE rapid yield detection
- Only track message yields, not keepalives
- Reset the timestamp deque when timeout occurs (we actually waited)
- This prevents false positives on high-throughput legitimate streams

Finding 4: Remove unused db timeout settings
- Remove db_lock_timeout_ms and db_statement_timeout_ms from config
- These settings were defined but never wired into DB operations
- Avoids false sense of protection

Finding 2 (notifications) is intentional: gateway-level notifications
are sent, and bulk UPDATE is used for performance under high load.

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix(perf): add nowait locks to prompt and resource state changes

Extends the lock contention fix to prompt_service and resource_service:
- Add PromptLockConflictError and ResourceLockConflictError classes
- Use nowait=True in get_for_update to fail fast if row is locked
- Add 409 Conflict handlers in main.py for both services
- Re-raise specific errors before generic Exception handler

This ensures consistent lock handling across all state change endpoints.

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix(sse): improve rapid yield detection to catch all spin scenarios

- Track time since last yield as additional signal (<10ms is suspicious)
- Check rapid yield after BOTH message and keepalive yields
- Reset timestamps only after successful keepalive wait
- Include time interval in error log for debugging

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix(sse): add robust spin loop detection and update dependencies (IBM#2355)

SSE transport improvements:
- Add consecutive rapid yield counter for simpler spin loop detection
  (triggers after 10 yields < 100ms apart)
- Remove deque clearing after keepalives that prevented detection
- Add client_close_handler_callable to detect disconnects that ASGI
  servers like granian may not propagate via request.is_disconnected()

Test updates:
- Update row-level locking tests to expect nowait=True for prompt
  and resource state changes

Dependency updates:
- Containerfile.lite: Update UBI base images to latest
- gunicorn 23.0.0 -> 24.1.1
- sqlalchemy 2.0.45 -> 2.0.46
- langgraph 1.0.6 -> 1.0.7
- hypothesis 6.150.2 -> 6.150.3
- schemathesis 4.9.2 -> 4.9.4
- copier 9.11.1 -> 9.11.3
- pytest-html 4.1.1 -> 4.2.0

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* docs: add granian worker lifecycle options for SSE connection leak workaround

Document GRANIAN_WORKERS_LIFETIME and GRANIAN_WORKERS_MAX_RSS options
as commented-out configuration in docker-compose.yml and run-granian.sh.

These options provide a workaround for granian issue IBM#286 where SSE
connections are not properly closed after client disconnect, causing
CPU spin loops after load tests complete.

Refs: IBM#2357, IBM#2358
Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* docker-compose updates for GUNICORN

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* docker-compose updates for GUNICORN

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* docker-compose updates for GUNICORN

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* Update pyproject.toml

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* lint

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

---------

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

…BM#2363)

The Export Config button was not included when pagination was
implemented in PR IBM#1955. This button allows users to export
MCP client configuration in stdio/SSE/HTTP formats.

Closes IBM#2362

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix: add sso_entra_admin_groups to list field validator

- sso_entra_admin_groups now properly parses CSV/JSON from environment
- Closes IBM#2265

Signed-off-by: Akshay Shinde <akshayshinde@dhcp-9-162-244-59.mul.ie.ibm.com>

* style: fix missing blank lines in test_config.py

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

---------

Signed-off-by: Akshay Shinde <akshayshinde@dhcp-9-162-244-59.mul.ie.ibm.com>
Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>
Co-authored-by: Akshay Shinde <akshayshinde@dhcp-9-162-244-59.mul.ie.ibm.com>
Co-authored-by: Mihai Criveti <crivetimihai@gmail.com>

…scanners (IBM#2200)

- Convert cache.py to use async redis (redis.asyncio) for non-blocking I/O
- Add parallel scanner execution using asyncio.gather in input/output filters
- Add asyncio.to_thread for CPU-bound scanner operations
- Quiet llm_guard logger to ERROR level to reduce noise
- Fix tests to use prompt_id instead of deprecated name parameter
- Update test to use environment variables for redis host/port

Security: Scanner errors now fail-closed (is_valid=False) instead of being
skipped, ensuring policy evaluation denies requests when scanners fail.

Closes IBM#1959

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

1. Replace custom CSS classes with native tailwind utility classes.
2. Add Chart.js theming for dark-mode graphs

Signed-off-by: Gabriel Costa <gabrielcg@proton.me>
Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix: plugin template test cases.

Signed-off-by: Teryl Taylor <terylt@ibm.com>

* fix: context passing in unit test

Signed-off-by: Frederico Araujo <frederico.araujo@ibm.com>

---------

Signed-off-by: Teryl Taylor <terylt@ibm.com>
Signed-off-by: Frederico Araujo <frederico.araujo@ibm.com>
Co-authored-by: Teryl Taylor <terylt@ibm.com>
Co-authored-by: Frederico Araujo <frederico.araujo@ibm.com>

Signed-off-by: Frederico Araujo <frederico.araujo@ibm.com>

Precompile all regex patterns at module or configuration initialization
time across 14 plugins, eliminating per-request compilation overhead.

Closes IBM#1834

Signed-off-by: Shoumi <shoumimukherjee@gmail.com>
Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* update jwt cli with more inputs

Signed-off-by: Madhav Kandukuri <madhav165@gmail.com>

* fix: prevent non-expiring tokens from invalid expires_in_days

- Add ge=1 validation to TokenCreateRequest.expires_in_days schema
- Add guard in _generate_token to reject expires_at in the past
- Use math.ceil() and max(1, ...) to ensure exp is always set for
  sub-minute expirations (prevents rounding to 0)
- Mark --secret and --algo CLI args as deprecated (always uses config)
- Add tests for past expiry rejection and ceiling behavior

This fixes a security regression where negative/zero expires_in_days
could create permanent tokens instead of expired ones.

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix: restore --secret and --algo CLI options

The --secret and --algo CLI parameters now work as optional overrides:
- When provided, they override the configuration values
- When not provided, JWT_SECRET_KEY and JWT_ALGORITHM from config are used

This preserves backward compatibility while still defaulting to
configuration-based signing for consistency.

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix: require --secret when --algo is specified

Prevent invalid token generation by requiring --secret when --algo
is provided. Using --algo alone would mix config-based keys with a
different algorithm, potentially producing tokens that fail validation.

Also fixes stale docstring that still referenced DEFAULT_SECRET/DEFAULT_ALGO
instead of the new empty-string defaults with config fallback.

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

---------

Signed-off-by: Madhav Kandukuri <madhav165@gmail.com>
Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>
Co-authored-by: Mihai Criveti <crivetimihai@gmail.com>

* Initial commit for filesystem server
    - added stdio simple server
    - implemented list_directory tool

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Improved main runner
    - Added argument handler
    - improve tracing
    - implemented streamable-http

Signed-off-by: cafalchio <maolivei@tcd.ie>

* added tracing info for each call

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Implemented search files recursively
    - use glob patterns
    - Added search to tools
    - Handle errors
    - Improve descriptions

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Added files for new functions
    - Updated cargo file for file search

Signed-off-by: cafalchio <maolivei@tcd.ie>

* implemented case insensitive search: Lowercase filenames and patterns

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Implemented read_file function and added to a server
    -  check for Max file size 1Mb
    - check if the path is a file

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Added tracing  for read file, improved error description

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Added get_file_info
    - get size, created, modified and permissions
    - Added to the server

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Added Read multiple files
    - use read file for each content
    - read async
    - added to server tools

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Added write_file toold func
    - Write to a tempfile uuid
    - rename file to actual name
    - remove tempfile

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Added  create_directory  tool

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Added create_directory to server and implemented placeholder for list_allowed_directories

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Changed release config to reduce bin size

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Implemented move file function.
    - fails if destination exists

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Added move_file to the server

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Added edit file to the server

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Added edit_file
    - support dry_run
    - use similar to get diffs

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Adding sandbox for path ccheck

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Apply fix to reduce TOCTOU vulnerability
    - atomic write, no checks and write

Signed-off-by: cafalchio <maolivei@tcd.ie>

* improve read to reduce TOCTOU vulnerability

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Stopped to follow symlink on search (security)

Signed-off-by: cafalchio <maolivei@tcd.ie>

* removed unused import

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Improved Sandbox for TOCTOU safety
    - initialize sandbox once
    - check if new folders are inside root
    - resolve path inside root

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Added get_roots for server  list_allowed_directories

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Using sanbox resolve path before ger file info

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Added sandox to write_file and create_directory
    - validade parent folder
    - clean tempfile after
   - check new folder inside root

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Added sandbox to write file
    - canonicalize and check new folders
    -  check parent folders
    - on create directory, check if exists

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Added sandbox check  for list_directory

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Added sandbox check for edit_file and move_file
   -  check and canonicalize destination parent

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Apply sandbox checks for read_file and read_multiple_files

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Changed sandbox initialization from global to context
    - removed global sandbox
    - initialize sandbox in main and pass to each function

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Added tests for searc_files and  list_directories
    - test for symlinks
    - test for path outside roots
    - > 95% coverage
    - formatted using fmt

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Formatted files using cargo fmt

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Added tests for get_file_info

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Added test coverage for read_file and read_multiple_files

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Added unit test coverage for write_file and create_directory

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Improve test coverage for edit_file and move_file

Signed-off-by: cafalchio <maolivei@tcd.ie>

* format edit.rs

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Added test coverage for sandbox

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Improve server runner
    - addded sever gracefully shutdown
    -  Declare Config values in main
    -  Improve server logs

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Improved logs for list_allowed_directories and linted file

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Improve test coverage for server
    - iimproved logs in server

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Linted using cargo clippy

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Simplified main.rs and moved server code to lib.rs for integration tests

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Added integration tests to simulate workflows
    - file and folder manipulation workflow
    - permission and metadata workflow
    - search and organise workflow
    - server tests

Signed-off-by: cafalchio <maolivei@tcd.ie>

* formatted and clippped integration tests

Signed-off-by: cafalchio <maolivei@tcd.ie>

* added result where it was missing in tool call result
    - rename all outputs to result

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Normalized write file and create directory output

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Structured search and write outputs
    - update tests

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Fixed write result not showing errors correctly
    - server will return WriteResult
    - create_directory return err or string
    - fixed test create_directory tests

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Normalized output result for write_file

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Normalized tool result outpus
    - Keep consistency between tools
    - Return MPC error or success
    - reorganised tools between files
    - updated tests

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Added server start banner

Signed-off-by: cafalchio <maolivei@tcd.ie>

* fixed main receiving multiple roots

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Clipped and formatted

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Removed justfile and added Makefile

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Added correct readme

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Added dockerfile

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Improved tracing logs

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Update test coverage and binary size  in readme

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Removed umused dependency

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Updated cargo dependencies

Signed-off-by: cafalchio <maolivei@tcd.ie>

* Updted deprecated InitializedRequestParam

Signed-off-by: cafalchio <maolivei@tcd.ie>

* fix: correct error messages and documentation in filesystem server

- Fix misleading error messages in server.rs that said "Error writing file"
  when the actual operation was read, move, or get_file_info
- Update README to accurately reflect that move_file overwrites destination
  (previously incorrectly stated it fails)

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

---------

Signed-off-by: cafalchio <maolivei@tcd.ie>
Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>
Co-authored-by: Mihai Criveti <crivetimihai@gmail.com>

…ts (IBM#2345)

* Fix proxy authentication

Signed-off-by: Mohan Lakshmaiah <mohalaks@in.ibm.com>

* Fix pylint errors

Signed-off-by: Mohan Lakshmaiah <mohalaks@in.ibm.com>

* fix: Correct lint issues in proxy auth tests

- Add missing blank line between test classes
- Remove unused jwt import
- Fix excess blank lines

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix: Include plugin context in proxy auth for cross-hook sharing

Add plugin_context_table and plugin_global_context to proxy
authentication paths, matching the JWT authentication path.
This ensures HTTP_AUTH_CHECK_PERMISSION hooks can access context
set by HTTP_PRE_REQUEST hooks when using proxy authentication.

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix: Address security concerns in proxy authentication

1. RBAC now checks auth_required when proxy header missing
   - Returns 401 for API requests, 302 redirect for browsers
   - Aligns HTTP behavior with WebSocket auth

2. Block anonymous users from token management
   - Add auth_method=="anonymous" to _require_interactive_session
   - Prevents token access when proxy header missing

3. Lookup proxy user admin status from database
   - Check platform_admin_email for admin match
   - Query EmailUser table for is_admin status
   - Enables plugin permission hooks to work correctly

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix: Align require_auth with RBAC proxy enforcement

Update require_auth to check auth_required when proxy header is
missing, matching the RBAC/WebSocket behavior. Previously returned
"anonymous" even when auth_required=true.

- Raise 401 when mcp_client_auth_enabled=false and no proxy header
  if auth_required=true
- Update tests to cover both auth_required=true and false cases

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

---------

Signed-off-by: Mohan Lakshmaiah <mohalaks@in.ibm.com>
Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>
Co-authored-by: Mohan Lakshmaiah <mohalaks@in.ibm.com>
Co-authored-by: Mihai Criveti <crivetimihai@gmail.com>

Signed-off-by: Madhav Kandukuri <madhav165@gmail.com>

* fix: FastMCP compatibility

* fix: normalize issuer URL for metadata validation and caching

The original trailing slash fix introduced a bug where the issuer
validation would fail when the server returned an issuer without
trailing slash but the client passed one (or vice versa).

Changes:
- Normalize both the input issuer and metadata issuer for comparison
- Use normalized issuer as cache key for consistent cache lookup
- Add tests for trailing slash normalization scenarios
- Update test to expect refresh_token in grant_types

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix: complete issuer normalization and conditional refresh_token

Address review feedback:

1. Normalize issuer consistently across the entire DCR flow:
   - Allowlist validation uses normalized comparison
   - Storage uses normalized issuer
   - Lookup uses normalized issuer

2. Make refresh_token conditional on AS support:
   - Check grant_types_supported in AS metadata
   - Only request refresh_token if AS advertises support

3. Fix grant_types fallback:
   - Use requested grant_types as fallback when AS response omits them
   - Previously hardcoded to ["authorization_code"] which dropped refresh_token

4. Add comprehensive tests:
   - Test refresh_token inclusion when AS supports it
   - Test grant_types fallback behavior
   - Test allowlist trailing slash normalization

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix: handle null grant_types_supported and add issuer normalization migration

Address additional review findings:

1. Fix TypeError when grant_types_supported is explicit null:
   - Use `metadata.get("grant_types_supported") or []` instead of
     `metadata.get("grant_types_supported", [])`
   - The latter returns None when key exists with null value

2. Add configurable permissive refresh_token mode:
   - New setting: dcr_request_refresh_token_when_unsupported
   - Default: False (strict mode - only request if AS advertises support)
   - When True: request refresh_token if AS omits grant_types_supported

3. Add Alembic migration to normalize legacy issuer values:
   - Strips trailing slashes from registered_oauth_clients.issuer
   - Idempotent and works with SQLite and PostgreSQL
   - Prevents duplicate registrations from legacy rows

4. Add comprehensive tests:
   - Test explicit null grant_types_supported handling
   - Test permissive refresh_token mode

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* docs: add DCR_REQUEST_REFRESH_TOKEN_WHEN_UNSUPPORTED to documentation

Update documentation for new DCR refresh token configuration option:

- README.md: Add to DCR settings table
- charts/mcp-stack/values.yaml: Add with comment
- charts/mcp-stack/README.md: Regenerated via helm-docs
- docs/docs/manage/dcr.md: Add env var and behavior note
- docs/docs/config.schema.json: Add schema definition

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

---------

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>
Co-authored-by: Mihai Criveti <crivetimihai@gmail.com>

* feat: add ARM64 load testing support

- Add build section for fast-time-server to support ARM64 architecture
- Use pre-built ghcr.io image by default for x86_64 performance
- ARM64 users can build locally via environment variable override
- Fix Dockerfile to use TARGETARCH for proper cross-compilation

Signed-off-by: Jonathan Springer <jps@s390x.com>
Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* Lint

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

---------

Signed-off-by: Jonathan Springer <jps@s390x.com>
Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>
Co-authored-by: Mihai Criveti <crivetimihai@gmail.com>

…BM#2314)

Signed-off-by: Satya <tsp.0713@gmail.com>

…ched Templates (IBM#2333)

* Optimize SQLite JSON tag filtering with deterministic binds and cached templates

Signed-off-by: Satya <tsp.0713@gmail.com>

* feat: add tag filtering support to list resources template in main apis(non-template)

Signed-off-by: Satya <tsp.0713@gmail.com>

* removed unused fields - page, limit from list resource template from resource services

Signed-off-by: Satya <tsp.0713@gmail.com>

* fix: remove debug print statements from tool_service.py

Remove debugging print statements that were accidentally left in the
tag filtering code path. These were outputting query details to stdout
which is not appropriate for production code.

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* Lint

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix: use column-specific bind prefixes to prevent parameter collision

When multiple json_contains_tag_expr calls are combined in the same
query (e.g., filtering on tags from different columns), the fixed
bind names (:p0, :p1) would collide and overwrite parameters.

This fix adds column-specific prefixes to bind parameter names
(e.g., :tools_tags_p0, :resources_tags_p0) to ensure uniqueness
when composing multiple tag filter predicates.

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* test: add coverage for json_contains_tag_expr and resource template filters

Add comprehensive tests for:
- _sanitize_col_prefix helper function
- json_contains_tag_expr for SQLite with match_any and match_all
- Bind parameter collision prevention when combining multiple tag filters
- LRU caching of SQL templates
- New list_resource_templates filtering parameters (tags, visibility,
  include_inactive)

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix: use thread-safe counter for fully unique bind prefixes

Address edge cases where bind parameters could still collide:
1. Same column filtered multiple times in one query
2. Different column refs that sanitize to identical strings
   (e.g., "a_b.c" and "a.b_c" both become "a_b_c")

Replace static column-based prefix with a thread-safe counter that
generates truly unique prefixes per call (e.g., "tools_tags_42_p0").

This removes the LRU caching of templates since each call now has
a unique prefix, but ensures correctness in all edge cases.

Add test for same-column collision scenario.

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

---------

Signed-off-by: Satya <tsp.0713@gmail.com>
Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>
Co-authored-by: Mihai Criveti <crivetimihai@gmail.com>

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* optimize response_cache_by_prompt lookup with inverted index

Signed-off-by: Shoumi <shoumimukherjee@gmail.com>

* fix type hint

Signed-off-by: Shoumi <shoumimukherjee@gmail.com>

* flake8 fixes

Signed-off-by: Shoumi <shoumimukherjee@gmail.com>

* test: add unit tests for response_cache_by_prompt inverted index

Add comprehensive test coverage for the inverted index optimization:
- Tokenization and vectorization functions
- Basic cache store and hit functionality
- Inverted index population and candidate filtering
- Eviction and index rebuild scenarios
- Max entries cap with index consistency

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

---------

Signed-off-by: Shoumi <shoumimukherjee@gmail.com>
Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>
Co-authored-by: Mihai Criveti <crivetimihai@gmail.com>

* feat: Add Gateway permission constants

Add GATEWAYS_CREATE, GATEWAYS_READ, GATEWAYS_UPDATE, and GATEWAYS_DELETE
permission constants to the Permissions class for consistency with other
resource types (tools, resources, prompts, servers).

Note: The original PR IBM#2186 attempted to fix issue IBM#2185 by modifying
the visibility query logic, but that change was incorrect. The team
filter should only show resources BELONGING to the filtered team,
not all public resources globally. See todo/rbac.md for documentation.

Issue IBM#2185 needs further investigation - the reported bug may have
a different root cause.

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* feat: Add gateway permission patterns to token scoping middleware

Add gateway routes to token scoping middleware for consistent permission
enforcement:
- Add gateway pattern to _RESOURCE_PATTERNS for ID extraction
- Add gateway CRUD patterns to _PERMISSION_PATTERNS:
  - POST /gateways (exact) -> gateways.create
  - POST /gateways/{id}/... (sub-resources) -> gateways.update
  - PUT/DELETE -> gateways.update/delete
- Add gateway handling in _check_resource_team_ownership:
  - Public: accessible by all
  - Team: accessible by team members
  - Private: owner-only access (per RBAC doc)

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix: Enforce owner-only access for private visibility across all resources

Per RBAC doc, private visibility means "owner only" - not "team members".
Fixed private visibility checks for all resource types to validate
owner_email == requester instead of team membership:
- Servers
- Tools
- Resources
- Prompts
- Gateways (already correct from previous commit)

This aligns token scoping middleware with the documented RBAC model.

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* test: Add tests for gateway permissions and visibility RBAC

Add unit tests covering:
- Gateway permission patterns (POST create vs POST update sub-resources)
- Private visibility enforces owner-only access
- Team visibility allows team members only
- Public visibility allows all authenticated users

These tests validate the RBAC fixes in token scoping middleware.

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

---------

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>
Co-authored-by: Mihai Criveti <crivetimihai@gmail.com>

* feat-2187: add additional default roles while bootstrap

Signed-off-by: Nithin Katta <Nithin.Katta@ibm.com>

* feat-2187: fix lint issues

Signed-off-by: Nithin Katta <Nithin.Katta@ibm.com>

* feat-2187: fixing review comments

Signed-off-by: Nithin Katta <Nithin.Katta@ibm.com>

* feat-2187: fixing review comments

Signed-off-by: Nithin Katta <Nithin.Katta@ibm.com>

* feat-2187: test fix

Signed-off-by: Nithin Katta <Nithin.Katta@ibm.com>

* fix: Improve bootstrap roles validation and documentation

Fixes identified by code review:
1. Path resolution: Fixed parent.parent.parent -> parent.parent to correctly
   resolve project root from mcpgateway/bootstrap_db.py
2. JSON validation: Added validation that loaded JSON is a list of dicts with
   required keys (name, scope, permissions). Invalid entries are skipped with
   warnings instead of crashing bootstrap.
3. Improved logging: Log all attempted paths when file not found

Added tests:
- test_bootstrap_roles_with_dict_instead_of_list: Validates error when JSON is
  a dict instead of array
- test_bootstrap_roles_with_missing_required_keys: Validates warning when roles
  are missing required fields

Added documentation:
- docs/docs/manage/rbac.md: New "Bootstrap Custom Roles" section with
  configuration examples for Docker Compose and Kubernetes
- docs/docs/architecture/adr/036-bootstrap-custom-roles.md: ADR documenting
  the feature design, error handling, and security considerations

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix: Make description and is_system_role optional for bootstrap roles

ChatGPT review identified that description and is_system_role were accessed
unconditionally via role_def["key"], causing KeyError for minimal roles.

Fix:
- Use role_def.get("description", "") with empty string default
- Use role_def.get("is_system_role", False) with False default

Added test:
- test_bootstrap_roles_with_minimal_valid_role: Verifies a role with only
  required fields (name, scope, permissions) is created successfully with
  correct defaults for optional fields

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

---------

Signed-off-by: Nithin Katta <Nithin.Katta@ibm.com>
Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>
Co-authored-by: Nithin Katta <Nithin.Katta@ibm.com>
Co-authored-by: Mihai Criveti <crivetimihai@gmail.com>

…BM#2724)

- Add AlreadyEncryptedError and NotEncryptedError (extend ValueError)
  for explicit validation in strict mode
- Introduce v2: format prefix for unambiguous encrypted data detection
- Add strict vs idempotent API modes (decrypt_secret vs
  decrypt_secret_or_plaintext) with backward-compatible async wrappers
- Replace length heuristic in oauth_manager with explicit is_encrypted()
- Add null checks after decryption in dcr_service update/delete
- Migrate encryption tests to dedicated test_encryption_service.py
- Add comprehensive test coverage for edge cases, concurrent operations,
  and real-world token formats (JWT, OAuth2, API keys)

Closes IBM#2405

Signed-off-by: Mohan Lakshmaiah <mohan.economist@gmail.com>
Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

…#2962)

* chore: replace copier with cookiecutter for template scaffolding (IBM#2361)

Copier pulled jinja2-ansible-filters (GPL-licensed). Cookiecutter is a
simpler, widely-adopted alternative with no problematic transitive deps.

- Migrate all 4 template sets (Go server, Python server, native plugin,
  external plugin) from copier YAML configs to cookiecutter.json with
  {{cookiecutter.*}} directory conventions
- Update mcpplugins CLI to use cookiecutter.main.cookiecutter() API,
  add --template_type flag to select native/external plugin templates
- Replace copier>=9.11.3 with cookiecutter>=2.6.0 in pyproject.toml
  and tox.ini
- Update scaffold shell scripts to invoke cookiecutter CLI
- Update tests, AGENTS.md, llms docs, and roadmap

Closes IBM#2361

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix: exclude cookiecutter template dirs from pre-commit linting

Template files containing Jinja2 syntax ({{ cookiecutter.* }}, {% set %})
are invalid YAML/TOML/Python from linters' perspective. Add plugin_templates/
to the global exclude in both pre-commit configs and yamllint. Also restore
executable bit on run-server.sh and update uv.lock.

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix: exclude cookiecutter templates from gosec and tomllint

Template go.mod and pyproject.toml contain Jinja2 variables that are
invalid from the perspective of Go tooling and TOML parsers. Skip
template directories in gosec, govulncheck, and tomllint find commands.

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix: exclude cookiecutter templates from tomllint CI workflow

The lint.yml workflow runs tomlcheck directly via find, not through the
Makefile target. Add the same template directory exclusions.

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

---------

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* feat(ui): unified admin search with tags + global search

Implement a unified, consistent search experience across the Admin UI:

- Standardize search endpoints with unified response shape (items, count,
  entity_type, query, filters_applied) while preserving legacy keys
- Add tag filtering via comma=OR and plus=AND semantics with bounds
  (max 20 groups, 10 terms per group)
- Server-side panel search for all entity panels via HTMX partial reloads
  with debounced input and namespaced URL params for shareability
- Global search modal (Ctrl/Cmd+K) aggregating results across servers,
  gateways, tools, resources, prompts, agents, teams, and users
- Escape SQL LIKE wildcards in all search filters to prevent injection
- Consistent search field coverage between search and partial endpoints

Closes IBM#2076
Closes IBM#2109

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix(metrics): prevent duplicate Prometheus metric registration in multi-app tests

Guard setup_metrics() against re-registration errors when multiple
FastAPI apps are instantiated in the same process (e.g., test suites).
Uses best-effort registry lookup via _get_registry_collector() to
reuse existing collectors instead of crashing on ValueError.

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix(admin): eliminate redundant get_user_teams calls in unified search

Add _get_user_team_ids helper with caching support. The unified search
endpoint pre-fetches team IDs once and injects them into the user context,
avoiding 6 redundant database lookups (one per entity type).

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix(admin): use ESCAPE clause for LIKE queries and update Playwright search waits

SQLAlchemy .contains() does not add an ESCAPE clause, so escaped
wildcards (\_) are treated as literal two-character sequences on SQLite.
Replace all .contains(_escape_like(...)) calls with _like_contains()
which generates .like(..., escape='\\') for correct behaviour on all
database backends.

Update Playwright page objects and tests to wait for the HTMX partial
responses now that search is server-side instead of client-side.

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* format

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix(tests): use networkidle wait for HTMX search in Playwright tests

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix(admin): format replaceChild call for Prettier compliance

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* Code review

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* Code review

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* Code review

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* Test networkwait fix

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* Linting and permissions updates

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* Linting and permissions updates

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* Linting and test updates + fix UI logout issue

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* flake8

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

---------

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* feat(ui): flexible admin UI sections for embedded contexts

Add env controls to hide UI sections/header items (including embedded mode defaults).

Support per-request ?ui_hide= overrides persisted via cookie and prevent hidden sections from loading data.

Update Helm values/schema, docker-compose, docs, and add unit + JS tests.

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix(ui): restore default tab fallback

Prefer the Overview tab when available and fall back to Gateways for minimal DOM states.

Align JS tab tests with the restored default tab behavior.

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix(ui): review fixes for admin UI section visibility

Deduplicate UI_HIDABLE_SECTIONS, UI_HIDABLE_HEADER_ITEMS, and
UI_HIDE_SECTION_ALIASES constants — define once in config.py, import
in admin.py.

Harden normalizeTabName() against CSS selector injection by
restricting to [a-z0-9-] characters.

Add max_age (30 days) to the ui_hide_sections cookie so preferences
persist across browser sessions.

Filter global search results to exclude hidden sections.

Expand JS test coverage: normalizeTabName edge cases, admin-only tab
blocking, idempotency guard, getDefaultTabName priority,
isTabAvailable, getUiHiddenSections/Tabs normalization, and global
search filtering.

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* test(ui): add comprehensive test coverage for admin UI section visibility

Cover _normalize_ui_hide_values, cookie set/delete behavior,
section-aware data loading, config validators, isTabHidden,
and resolveTabForNavigation.

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix(config): use NoDecode class instead of instance for env parsing

NoDecode() (instance) in Annotated metadata is not found by
pydantic-settings' `NoDecode in field.metadata` check, causing
json.loads to be called on raw CSV strings. Use NoDecode (class)
which matches correctly. Also adds ADR-040 and admin UI
customization guide.

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* Fixes

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix(ui): expand admin section hiding coverage

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* test(metrics): stabilize db engine detection setup test

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix(playwright): stabilize admin ui tab and search flows

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* Fixes

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

---------

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

- S7502: store asyncio task references to prevent GC (resource_cache,
  token_catalog_service, email_auth_service)
- S5655: replace SimpleNamespace with SSOProviderContext dataclass
  (sso_service)
- S5886: fix return type lies with Optional (gateway_service,
  services_auth)
- S5890: add missing Optional for None defaults (cedar/opa schemas)
- S3923: remove dead if/else branches (cache, translate)
- S3457: fix logger format string (validate_signature)
- S1871: merge duplicate branches (toon, schemas)
- S1854: remove dead stores for current_admin_origin (sso_service)
- S5247: remove 16 autoescape-false blocks, replace 2 |safe patterns
  with CSS word-spacing (admin.html, 11 partial templates)

Closes IBM#2981

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix: update API token last_used and log usage stats

Signed-off-by: Shoumi <shoumimukherjee@gmail.com>

* test fixes

Signed-off-by: Shoumi <shoumimukherjee@gmail.com>

* flake8 fix

Signed-off-by: Shoumi <shoumimukherjee@gmail.com>

* additional changes

Signed-off-by: Shoumi <shoumimukherjee@gmail.com>

* remove duplicate last_used update in token usage logging

Signed-off-by: Shoumi <shoumimukherjee@gmail.com>

* test fixes

Signed-off-by: Shoumi <shoumimukherjee@gmail.com>

* test fixes

Signed-off-by: Shoumi <shoumimukherjee@gmail.com>

* additional test fixes

Signed-off-by: Shoumi <shoumimukherjee@gmail.com>

* added exception handling

Signed-off-by: Shoumi <shoumimukherjee@gmail.com>

* fix coverage

Signed-off-by: Shoumi <shoumimukherjee@gmail.com>

* fix: optimize token tracking with rate-limiting and raw ASGI middleware

Signed-off-by: Shoumi <shoumimukherjee@gmail.com>

* test fixes

Signed-off-by: Shoumi <shoumimukherjee@gmail.com>

* test fixes

Signed-off-by: Shoumi <shoumimukherjee@gmail.com>

* additional test fixes

Signed-off-by: Shoumi <shoumimukherjee@gmail.com>

* fix: address review findings in token usage tracking

- Store JTI in request.state.jti for standard API tokens in
  _set_auth_method_from_payload, ensuring middleware can access
  it without re-decoding the JWT on cached/batched auth paths
- Remove redundant db.commit() in TokenUsageMiddleware since
  log_token_usage() already commits the transaction
- Add bounded eviction (max 1024 entries) to in-memory rate-limit
  cache in _update_api_token_last_used_sync to prevent unbounded growth
- Add test coverage for cache eviction and JTI propagation
- Fix formatting (missing space, unused import, black/isort)

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix: patch hidden sections env leakage in admin UI tests

Two admin tests failed because .env sets MCPGATEWAY_UI_HIDE_SECTIONS
which leaks into test execution, causing section-dependent code paths
(resource loading, gRPC services) to be skipped. Patch settings to
ensure no sections are hidden during these tests.

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix: resolve DI, retry storm, race, and opaque token tracking issues

- Fix get_current_user request param type (Optional[object] → Request)
  so FastAPI auto-injects it, enabling last_used and usage logging
- Add 30s backoff in _get_sync_redis_client after connection failures
  to prevent retry storms when Redis is down
- Move in-memory cache from hasattr-based function attributes to
  module-level globals, eliminating initialization race condition
- Store user_email in request state for DB-fallback opaque tokens
  so usage middleware can log them without JWT decode

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

---------

Signed-off-by: Shoumi <shoumimukherjee@gmail.com>
Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>
Co-authored-by: Mihai Criveti <crivetimihai@gmail.com>

…authorization code (IBM#2899)

* fix: enhance OAuth callback handling for error responses and missing authorization code

Signed-off-by: Ankit Gajera <ankit.gajera@merckgroup.com>

* fix: sanitize root path in OAuth callback responses and remove unnecessary resource checks

Signed-off-by: Ankit Gajera <ankit.gajera@merckgroup.com>

* feat(tests): add Microsoft Entra ID E2E integration tests

Add comprehensive end-to-end tests for Microsoft Entra ID SSO integration
that validate group-based admin role assignment against real Azure infrastructure.

Tests included (15 total):
- Admin role assignment based on Entra ID group membership
- Non-admin user handling
- Dynamic role promotion on re-login
- Case-insensitive group ID matching
- Real ROPC token acquisition and validation
- Multiple admin groups configuration
- Admin role retention behavior (by design - see IBM#2331)
- Token validation (expired, invalid audience/issuer)
- Sync disabled behavior

The tests are fully self-contained: they create test users and groups in
Azure AD before tests and clean them up afterward.

Also includes comprehensive documentation in docs/docs/testing/entra-id-e2e.md
covering setup, configuration, and test scenarios.

Relates to: IBM#2331

Signed-off-by: Jonathan Springer <jps@s390x.com>

* Linting fixes

Signed-off-by: Jonathan Springer <jps@s390x.com>

* fix(tests): prevent Entra ID e2e test from poisoning RBAC decorators under xdist

Module-level noop patching of RBAC decorators in test_entra_id_integration.py
polluted sys.modules when sharing xdist workers with unit tests, causing 45
failures (missing __wrapped__ and decorators not raising HTTPException).

Replace module-level noop patching with a fixture-scoped PermissionService
mock and add missing default_admin_role to all mock_settings blocks to
prevent MagicMock objects from reaching SQL queries.

Signed-off-by: Jon Spriggs <github@sprig.gs>
Signed-off-by: Jonathan Springer <jps@s390x.com>

* fix: harden Entra v2 host matching and escape gateway_id in OAuth callback JS

Use explicit frozenset of known Entra hosts (global + sovereign clouds)
instead of startswith to prevent lookalike domain matching. Escape
gateway_id in the JS fetch URL. Add sovereign cloud and negative tests.

Signed-off-by: Jonathan Springer <jps@s390x.com>

---------

Signed-off-by: Ankit Gajera <ankit.gajera@merckgroup.com>
Signed-off-by: Jonathan Springer <jps@s390x.com>
Signed-off-by: Jon Spriggs <github@sprig.gs>
Co-authored-by: Jonathan Springer <jps@s390x.com>

…gger session (IBM#3001)

- Add db.rollback() to exception handlers in gateway_service.py to
  prevent orphaned gateway records when registration fails after flush
- Isolate structured logger DB persistence using fresh_db_session() to
  avoid accidentally committing caller's dirty session state
- Propagate flush exceptions in before_commit_handler instead of
  swallowing them so commit failures trigger proper rollback
- Remove db parameter from structured_logger.log() signature since
  the logger now manages its own independent session
- Update tests to verify new session isolation and exception propagation

Closes IBM#2987

Signed-off-by: Keval Mahajan <mahajankeval23@gmail.com>
Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

… appropriate list tools response (IBM#2974)

* maintain server_id context with session affinity

Signed-off-by: Keval Mahajan <mahajankeval23@gmail.com>

* test cases for new improvements

Signed-off-by: Keval Mahajan <mahajankeval23@gmail.com>

* linting

Signed-off-by: Keval Mahajan <mahajankeval23@gmail.com>

* fix: address review findings for stateful session context propagation

- Remove debug log statement that leaked auth headers and user context
  at INFO level (security: token/PII exposure in production logs)
- Apply _get_request_context_or_default() to call_tool, read_resource,
  and list_resource_templates for consistent context recovery in
  stateful sessions (previously only list_* handlers were updated)
- Fix server_id injection to create params dict when absent, ensuring
  JSON-RPC requests without params still get proper server scoping
- Remove orphaned blank line in list_resources left from prior edit
- Clean up test imports: remove duplicate pytest, unused asyncio/types/
  transport imports, fix isort ordering
- Fix test property cleanup in test_list_resources_direct_proxy_meta_
  lookup_error to properly save/restore original descriptor
- Run black + isort on all changed files

Signed-off-by: Keval Mahajan <mahajankeval23@gmail.com>
Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* test: add missing coverage for context propagation and affinity injection

Cover all branches in _get_request_context_or_default():
- Fast path when ContextVars are already populated
- Anonymous user string-to-dict conversion
- URL without /servers/{id}/mcp pattern (no server_id match)
- LookupError fallback (no active request context)
- Generic Exception fallback with error logging
- Cookie JWT token forwarding to require_auth_override

Cover server_id injection edge cases:
- JSON-RPC body without params key (params dict created)
- URL without server pattern (no injection occurs)

Signed-off-by: Keval Mahajan <mahajankeval23@gmail.com>
Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix: normalize raw JWT payload in stateful session context recovery

_get_request_context_or_default() was returning raw JWT payloads from
require_auth_override() without normalizing to the canonical user
context shape {email, teams, is_admin, is_authenticated} that MCP
handlers expect. This caused handlers to look up missing keys (email,
teams) from the raw JWT which uses different field names (sub,
token_use, nested user.is_admin).

Changes:
- Add _normalize_jwt_payload() that mirrors streamable_http_auth
  normalization: extracts email from sub/email, resolves teams via
  normalize_token_teams (API) or _resolve_teams_from_db_sync (session),
  and detects nested user.is_admin
- call_tool now extracts app_user_email from the already-recovered
  user_context instead of reading from stale ContextVar via
  get_user_email_from_context()
- Update test mocks to use realistic JWT payloads instead of
  pre-normalized dicts
- Add 6 dedicated tests for _normalize_jwt_payload covering API token,
  session token (admin/non-admin), nested is_admin, email fallback,
  and no-email edge case

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* test: add regression test for call_tool recovered email propagation

Verify call_tool passes app_user_email from the recovered fallback
context (via _get_request_context_or_default) rather than reading
from the stale user_context_var ContextVar. This prevents regression
of the stateful session identity propagation fix.

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix: add missing docstring params for _normalize_jwt_payload (flake8 DAR)

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

---------

Signed-off-by: Keval Mahajan <mahajankeval23@gmail.com>
Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>
Co-authored-by: Mihai Criveti <crivetimihai@gmail.com>

…#3020)

* Update security pre-commit tools

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* Update all dependencies

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix: resolve Containerfile build failures found during full validation

- csv_pandas_chat: remove COPY templates/ (directory doesn't exist)
- data_analysis/mcp_eval: replace shell heredoc with printf (Docker
  parses heredoc content as Dockerfile instructions); remove COPY of
  non-existent __init__.py and config/ directory
- latex_server: switch to Fedora 41 base (texlive packages not in UBI10 repos)
- libreoffice_server: switch to Fedora 41 base (libreoffice not in UBI10 repos)
- python_sandbox: remove coreutils from builder/runtime (conflicts with
  coreutils-single pre-installed in UBI images)

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix: make xdg-open non-fatal in Rust coverage target

The coverage Makefile target calls xdg-open to display the HTML report,
which fails in CI where no browser is available. Make it non-fatal so
the coverage report generation still succeeds.

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* linting

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

---------

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

…ing (IBM#2958)

The config validator now converts empty/whitespace-only X_FRAME_OPTIONS
values to None, matching the middleware's expectation that None means
"allow all embedding". Previously, an empty string fell through to the
default DENY behavior in the middleware, blocking embedding unexpectedly.

Closes IBM#2492

Signed-off-by: prakhar-singh1928 <prakhar.singh1928@ibm.com>
Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

…der (IBM#3026)

* fix(auth): add jwks_uri column to SSOProvider and harden create_provider

Add jwks_uri as a first-class column on SSOProvider for standard OIDC
JWKS endpoint support. Make create_provider defensive by filtering
unknown keys to prevent TypeError crashes during SSO bootstrap.

Closes IBM#3010

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* fix(auth): include jwks_uri in bootstrap_db schema check and document setting

Update _schema_looks_current() to check for sso_providers.jwks_uri,
preventing unversioned databases from being stamped at head without
the new column. Add SSO_GENERIC_JWKS_URI to .env.example.

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* lint

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

---------

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* update roadmap and changelog

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

* update links in docs

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

---------

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

Signed-off-by: Mihai Criveti <crivetimihai@gmail.com>

…r, bool] to Dict[str, Any] to match MCP SDK permissive approach

Closes IBM#3063

Signed-off-by: Oriol Morros Vilaseca <OM368@student.aru.ac.uk>