Tags: kbase/catalog
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v2.3.0 release (develop -> master) (#129) * Update controller.py * Create pr_build.yml * Create release-main.yml * Create manual-build.yml * Update db.py * Update controller.py * Update db.py * Update pr_build.yml * Update controller.py * Update controller.py * add GHA test.yml, codeql, and dependabot.yml (#136) * mongo7 upgrade * upgrade pymongo to 4.7.2 * update python to 3.9.19 * update Makefile and run_tests.sh scripts * update submodules * fix gradle not found * start nms service with docker-compose * update nms submodule to the latest * install docker-compose in GHA * switch catalog mongo7 port to 27018 * fix mongo port * fix mongo port mapping * set admin_users * check admin users * shut down NMS service properly * fix nms curl * update mock_auth service * update the commit * Update test.cfg.example * Update test.cfg.example * Update core_registration_test.py * update message * test method_spec_admin_users * test simple_good_repo old commit * test register hack * remove jars nms submodules * update Dockerfile * remove kbapi_common submodule * fix deprecated mongo auth * remove all submodules in catalog * create MongoClient through passing in params * add a comment for mock_auth server.py * simplify code * adjust params in MongoClient * add debug log messages in list_user_favorites func * try reinitiate mongoclient * update __init__ in db.py file * fix typo * add check_db_schema * add boolean flag for schema check * collection direct call * remove debugging message * display catalog version * fix failed unit test in startup_test.py * trigger lazy load collection * clean up files * remove comments from Makefile * validate Install Docker Compose step in ci * use docker compose * map NMS to the local port 27018 * Add a clearer comment for the environment variable in test.yml * move env to jobs level * add more comments in server.py * add more comments in db.py * remove check_db_schema related functions * revert back changes * move self._db_schema_checked flag outside function * refactor _create_indexes function * encapsulate create_indexes in the DBIndexes class * add comment at the top of server.py file * refactor db.py file * add flag for mongo client * update wrapper function * add initialize_mongo_client function manually * add _close_mongo_client function * try run tests without a lock * revert self.lock changes * Recreate the database and collection handles after reinitializing the client * revert back tests * remove decorator related code * add comment why need to manually close mongoclient * update comments * refactor the db.py and add comments for docker-compose file * add a comment for _ensure_mongo_connection function * Clarify the comments in the db.py and docker-compose.yml files * remove NarrativeMethodStore section and update the test instructions in the test/test.cfg.example file * expound on the explanation * fix c&p error * fix typos and clarify comments * make sure NMS is clean after each test * remove uwsgi from dockerfile * add Pipenv and Pipenv.lock files * upload Pipfiles * add missing lib pyyaml * move semantic_version to packages * fix mongo_authMechanism name * add retrywrites param * move release notes from README.md to RELEASE_NOTES.md * removed mongodb-retrywrites from test.cfg.example * add tests for retryWrites * fix format * add print meesage to verify retryWrites setting * remove print * fix typo in README.md * uncomment trivy-scan --------- Co-authored-by: Boris <[email protected]> Co-authored-by: Sijie Xiang <[email protected]>