search

AlexsLemonade / refinebio

Refine.bio harmonizes petabytes of publicly available biological data into ready-to-use datasets for cancer researchers and AI/ML scientists.
https://www.refine.bio/
Other
128 stars 19 forks source link

Fix no_op PostgreSQL version not supported error #3188

Closed arkid15r closed 1 year ago

arkid15r commented 1 year ago

Context

In order to restore staging/prod deploy process CI/CD tests need to be fixed.

Problem or idea

Found 25 test(s).
Creating test database for alias 'default'...
/usr/local/lib/python3.8/dist-packages/django/db/backends/postgresql/base.py:336: RuntimeWarning: Normally Django will use a connection to the 'postgres' database to avoid running initialization queries against the production database when it's not needed (for example, when running tests). Django was unable to create a connection to the 'postgres' database and will use the first PostgreSQL database instead.
  warnings.warn(
Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/django/db/backends/postgresql/base.py", line 331, in _nodb_cursor
    with super()._nodb_cursor() as cursor:
  File "/usr/lib/python3.8/contextlib.py", line 113, in __enter__
    return next(self.gen)
  File "/usr/local/lib/python3.8/dist-packages/django/db/backends/base/base.py", line 711, in _nodb_cursor
    with conn.cursor() as cursor:
  File "/usr/local/lib/python3.8/dist-packages/django/utils/asyncio.py", line 26, in inner
    return func(*args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/django/db/backends/base/base.py", line 323, in cursor
    return self._cursor()
  File "/usr/local/lib/python3.8/dist-packages/django/db/backends/base/base.py", line 299, in _cursor
    self.ensure_connection()
  File "/usr/local/lib/python3.8/dist-packages/django/utils/asyncio.py", line 26, in inner
    return func(*args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/django/db/backends/base/base.py", line 282, in ensure_connection
    self.connect()
  File "/usr/local/lib/python3.8/dist-packages/django/utils/asyncio.py", line 26, in inner
    return func(*args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/django/db/backends/base/base.py", line 265, in connect
    self.init_connection_state()
  File "/usr/local/lib/python3.8/dist-packages/django/db/backends/postgresql/base.py", line 251, in init_connection_state
    super().init_connection_state()
  File "/usr/local/lib/python3.8/dist-packages/django/db/backends/base/base.py", line 232, in init_connection_state
    self.check_database_version_supported()
  File "/usr/local/lib/python3.8/dist-packages/django/db/backends/base/base.py", line 207, in check_database_version_supported
    raise NotSupportedError(
django.db.utils.NotSupportedError: PostgreSQL 11 or later is required (found 9.606).

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/django/db/backends/base/base.py", line 282, in ensure_connection
    self.connect()
  File "/usr/local/lib/python3.8/dist-packages/django/utils/asyncio.py", line 26, in inner
    return func(*args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/django/db/backends/base/base.py", line 263, in connect
    self.connection = self.get_new_connection(conn_params)
  File "/usr/local/lib/python3.8/dist-packages/django/utils/asyncio.py", line 26, in inner
    return func(*args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/django/db/backends/postgresql/base.py", line 215, in get_new_connection
    connection = Database.connect(**conn_params)
  File "/usr/local/lib/python3.8/dist-packages/psycopg2/__init__.py", line 122, in connect
    conn = _connect(dsn, connection_factory=connection_factory, **kwasync)
psycopg2.OperationalError: connection to server at "database" (172.17.0.2), port 5432 failed: FATAL:  database "test_data_refinery" does not exist

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "manage.py", line 22, in <module>
    execute_from_command_line(sys.argv)
  File "/usr/local/lib/python3.8/dist-packages/django/core/management/__init__.py", line 446, in execute_from_command_line
    utility.execute()
  File "/usr/local/lib/python3.8/dist-packages/django/core/management/__init__.py", line 440, in execute
    self.fetch_command(subcommand).run_from_argv(self.argv)
  File "/usr/local/lib/python3.8/dist-packages/django/core/management/commands/test.py", line 24, in run_from_argv
    super().run_from_argv(argv)
  File "/usr/local/lib/python3.8/dist-packages/django/core/management/base.py", line 402, in run_from_argv
    self.execute(*args, **cmd_options)
  File "/usr/local/lib/python3.8/dist-packages/django/core/management/base.py", line 448, in execute
    output = self.handle(*args, **options)
  File "/usr/local/lib/python3.8/dist-packages/django/core/management/commands/test.py", line 68, in handle
    failures = test_runner.run_tests(test_labels)
  File "/usr/local/lib/python3.8/dist-packages/django/test/runner.py", line 1051, in run_tests
    old_config = self.setup_databases(
  File "/usr/local/lib/python3.8/dist-packages/django/test/runner.py", line [947](https://github.com/AlexsLemonade/refinebio/actions/runs/4019855935/jobs/6907173643#step:9:948), in setup_databases
    return _setup_databases(
  File "/usr/local/lib/python3.8/dist-packages/django/test/utils.py", line 220, in setup_databases
    connection.creation.create_test_db(
  File "/usr/local/lib/python3.8/dist-packages/django/db/backends/base/creation.py", line 62, in create_test_db
    self._create_test_db(verbosity, autoclobber, keepdb)
  File "/usr/local/lib/python3.8/dist-packages/django/db/backends/base/creation.py", line 198, in _create_test_db
    with self._nodb_cursor() as cursor:
  File "/usr/lib/python3.8/contextlib.py", line 113, in __enter__
    return next(self.gen)
  File "/usr/local/lib/python3.8/dist-packages/django/db/backends/postgresql/base.py", line 357, in _nodb_cursor
    with conn.cursor() as cursor:
  File "/usr/local/lib/python3.8/dist-packages/django/utils/asyncio.py", line 26, in inner
    return func(*args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/django/db/backends/base/base.py", line 323, in cursor
    return self._cursor()
  File "/usr/local/lib/python3.8/dist-packages/django/db/backends/base/base.py", line 299, in _cursor
    self.ensure_connection()
  File "/usr/local/lib/python3.8/dist-packages/django/utils/asyncio.py", line 26, in inner
    return func(*args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/django/db/backends/base/base.py", line 282, in ensure_connection
    self.connect()
  File "/usr/local/lib/python3.8/dist-packages/django/db/utils.py", line 91, in __exit__
    raise dj_exc_value.with_traceback(traceback) from exc_value
  File "/usr/local/lib/python3.8/dist-packages/django/db/backends/base/base.py", line 282, in ensure_connection
    self.connect()
  File "/usr/local/lib/python3.8/dist-packages/django/utils/asyncio.py", line 26, in inner
    return func(*args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/django/db/backends/base/base.py", line 263, in connect
    self.connection = self.get_new_connection(conn_params)
  File "/usr/local/lib/python3.8/dist-packages/django/utils/asyncio.py", line 26, in inner
    return func(*args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/django/db/backends/postgresql/base.py", line 215, in get_new_connection
    connection = Database.connect(**conn_params)
  File "/usr/local/lib/python3.8/dist-packages/psycopg2/__init__.py", line 122, in connect
    conn = _connect(dsn, connection_factory=connection_factory, **kwasync)
django.db.utils.OperationalError: connection to server at "database" (172.17.0.2), port 5432 failed: FATAL:  database "test_data_refinery" does not exist

Solution or next step

Resolve version requirements problem (upgrade postgres?).

arkid15r commented 1 year ago

Resolved by https://github.com/AlexsLemonade/refinebio/pull/3227