psycopg2 issue during startup

[jtdbod]

psycopg2 fails to install during the startup script. Had been previously working fine both for custom Dockerfile and basic container start (docker run -d --privileged --name docker-test -p 8080:80 -p 8021:21 -p 8022:22 quay.io/bgruening/galaxy)

Following errors when starting container:

2025-01-28 13:21:37 WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self-signed certificate in certificate chain (_ssl.c:1007)'))': /simple/psycopg2-binary/
2025-01-28 13:21:37 ERROR: Could not find a version that satisfies the requirement psycopg2-binary==2.9.9 (from versions: none)
2025-01-28 13:21:37 ERROR: No matching distribution found for psycopg2-binary==2.9.9



2025-01-28 13:22:49 Checking if database is up and running
2025-01-28 13:22:53 Traceback (most recent call last):
2025-01-28 13:22:53   File "/usr/local/bin/check_database.py", line 19, in <module>
2025-01-28 13:22:53     mapping = init('/tmp/', db_url)
2025-01-28 13:22:53   File "/galaxy/lib/galaxy/model/mapping.py", line 45, in init
2025-01-28 13:22:53     engine = build_engine(
2025-01-28 13:22:53   File "/galaxy/lib/galaxy/model/orm/engine_factory.py", line 111, in build_engine
2025-01-28 13:22:53     engine = create_engine(url, **engine_options)
2025-01-28 13:22:53   File "<string>", line 2, in create_engine
2025-01-28 13:22:53   File "/galaxy_venv/lib/python3.10/site-packages/sqlalchemy/util/deprecations.py", line 281, in warned
2025-01-28 13:22:53     return fn(*args, **kwargs)  # type: ignore[no-any-return]
2025-01-28 13:22:53   File "/galaxy_venv/lib/python3.10/site-packages/sqlalchemy/engine/create.py", line 599, in create_engine
2025-01-28 13:22:53     dbapi = dbapi_meth(**dbapi_args)
2025-01-28 13:22:53   File "/galaxy_venv/lib/python3.10/site-packages/sqlalchemy/dialects/postgresql/psycopg2.py", line 690, in import_dbapi
2025-01-28 13:22:53     import psycopg2
2025-01-28 13:22:53 ModuleNotFoundError: No module named 'psycopg2'

[bgruening]

Can you please test the new 24.2 image and let me know if you still have problems?

[jtdbod]

Same problem with the 24.2 tag. I'm behind the company firewall. Making new containers used to work but recently I can no longer create new containers. Previously made containers seem to work fine. It seems that psycopg2 pip install is failing during the startup script because of an SSL. I tried using -e USE_HTTPS=True and it gave the same failure mode. If I docker exec -it container_name bash the running container and then python -m pip install pscopg2-binary, it installs and then the startup script continues but then gets hung up trying to make the admin account. 2025-02-25 16:18:31 Checking /export... 2025-02-25 16:18:32 Installing optional dependencies in galaxy virtual environment... 2025-02-25 16:18:32 /galaxy/lib/galaxy/dependencies/__init__.py:72: FutureWarning: The behavior of this method will change in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. 2025-02-25 16:18:32 if plugins_elem: 2025-02-25 16:18:42 WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self-signed certificate in certificate chain (_ssl.c:1000)'))': /simple/psycopg2-binary/ #The above repeats for several attempts before giving up ... 2025-02-25 16:19:57 Checking if database is up and running 2025-02-25 16:20:00 Traceback (most recent call last): 2025-02-25 16:20:00 File "/usr/local/bin/check_database.py", line 19, in <module> 2025-02-25 16:20:00 mapping = init('/tmp/', db_url) 2025-02-25 16:20:00 ^^^^^^^^^^^^^^^^^^^^^ 2025-02-25 16:20:00 File "/galaxy/lib/galaxy/model/mapping.py", line 49, in init 2025-02-25 16:20:00 engine = build_engine( 2025-02-25 16:20:00 ^^^^^^^^^^^^^ 2025-02-25 16:20:00 File "/galaxy/lib/galaxy/model/orm/engine_factory.py", line 111, in build_engine 2025-02-25 16:20:00 engine = create_engine(url, **engine_options) 2025-02-25 16:20:00 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-02-25 16:20:00 File "<string>", line 2, in create_engine 2025-02-25 16:20:00 File "/galaxy_venv/lib/python3.12/site-packages/sqlalchemy/util/deprecations.py", line 281, in warned 2025-02-25 16:20:00 return fn(*args, **kwargs) # type: ignore[no-any-return] 2025-02-25 16:20:00 ^^^^^^^^^^^^^^^^^^^ 2025-02-25 16:20:00 File "/galaxy_venv/lib/python3.12/site-packages/sqlalchemy/engine/create.py", line 599, in create_engine 2025-02-25 16:20:00 dbapi = dbapi_meth(**dbapi_args) 2025-02-25 16:20:00 ^^^^^^^^^^^^^^^^^^^^^^^^ 2025-02-25 16:20:00 File "/galaxy_venv/lib/python3.12/site-packages/sqlalchemy/dialects/postgresql/psycopg2.py", line 690, in import_dbapi 2025-02-25 16:20:00 import psycopg2 2025-02-25 16:20:00 ModuleNotFoundError: No module named 'psycopg2' 2025-02-25 16:32:42 Traceback (most recent call last): 2025-02-25 16:32:42 File "/galaxy_venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 1967, in _exec_single_context 2025-02-25 16:32:42 self.dialect.do_execute( 2025-02-25 16:32:42 File "/galaxy_venv/lib/python3.12/site-packages/sqlalchemy/engine/default.py", line 941, in do_execute 2025-02-25 16:32:42 cursor.execute(statement, parameters) 2025-02-25 16:32:42 psycopg2.errors.UndefinedTable: relation "galaxy_user" does not exist 2025-02-25 16:32:42 LINE 3: FROM galaxy_user 2025-02-25 16:32:42 ^ 2025-02-25 16:32:42 2025-02-25 16:32:42 2025-02-25 16:32:42 The above exception was the direct cause of the following exception: 2025-02-25 16:32:42 2025-02-25 16:32:42 Traceback (most recent call last): 2025-02-25 16:32:42 File "/usr/local/bin/check_database.py", line 25, in <module> 2025-02-25 16:32:42 query.count() 2025-02-25 16:32:42 File "/galaxy_venv/lib/python3.12/site-packages/sqlalchemy/orm/query.py", line 3113, in count 2025-02-25 16:32:42 self._legacy_from_self(col).enable_eagerloads(False).scalar() 2025-02-25 16:32:42 File "/galaxy_venv/lib/python3.12/site-packages/sqlalchemy/orm/query.py", line 2805, in scalar 2025-02-25 16:32:42 ret = self.one() 2025-02-25 16:32:42 ^^^^^^^^^^ 2025-02-25 16:32:42 File "/galaxy_venv/lib/python3.12/site-packages/sqlalchemy/orm/query.py", line 2778, in one 2025-02-25 16:32:42 return self._iter().one() # type: ignore 2025-02-25 16:32:42 ^^^^^^^^^^^^ 2025-02-25 16:32:42 File "/galaxy_venv/lib/python3.12/site-packages/sqlalchemy/orm/query.py", line 2827, in _iter 2025-02-25 16:32:42 result: Union[ScalarResult[_T], Result[_T]] = self.session.execute( 2025-02-25 16:32:42 ^^^^^^^^^^^^^^^^^^^^^ 2025-02-25 16:32:42 File "/galaxy_venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 2362, in execute 2025-02-25 16:32:42 return self._execute_internal( 2025-02-25 16:32:42 ^^^^^^^^^^^^^^^^^^^^^^^ 2025-02-25 16:32:42 File "/galaxy_venv/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 2247, in _execute_internal 2025-02-25 16:32:42 result: Result[Any] = compile_state_cls.orm_execute_statement( 2025-02-25 16:32:42 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-02-25 16:32:42 File "/galaxy_venv/lib/python3.12/site-packages/sqlalchemy/orm/context.py", line 305, in orm_execute_statement 2025-02-25 16:32:42 result = conn.execute( 2025-02-25 16:32:42 ^^^^^^^^^^^^^ 2025-02-25 16:32:42 File "/galaxy_venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 1418, in execute 2025-02-25 16:32:42 return meth( 2025-02-25 16:32:42 ^^^^^ 2025-02-25 16:32:42 File "/galaxy_venv/lib/python3.12/site-packages/sqlalchemy/sql/elements.py", line 515, in _execute_on_connection 2025-02-25 16:32:42 return connection._execute_clauseelement( 2025-02-25 16:32:42 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-02-25 16:32:42 File "/galaxy_venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 1640, in _execute_clauseelement 2025-02-25 16:32:42 ret = self._execute_context( 2025-02-25 16:32:42 ^^^^^^^^^^^^^^^^^^^^^^ 2025-02-25 16:32:42 File "/galaxy_venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 1846, in _execute_context 2025-02-25 16:32:42 return self._exec_single_context( 2025-02-25 16:32:42 ^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-02-25 16:32:42 File "/galaxy_venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 1986, in _exec_single_context 2025-02-25 16:32:42 self._handle_dbapi_exception( 2025-02-25 16:32:42 File "/galaxy_venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 2355, in _handle_dbapi_exception 2025-02-25 16:32:42 raise sqlalchemy_exception.with_traceback(exc_info[2]) from e 2025-02-25 16:32:42 File "/galaxy_venv/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 1967, in _exec_single_context 2025-02-25 16:32:42 self.dialect.do_execute( 2025-02-25 16:32:42 File "/galaxy_venv/lib/python3.12/site-packages/sqlalchemy/engine/default.py", line 941, in do_execute 2025-02-25 16:32:42 cursor.execute(statement, parameters) 2025-02-25 16:32:42 sqlalchemy.exc.ProgrammingError: (psycopg2.errors.UndefinedTable) relation "galaxy_user" does not exist 2025-02-25 16:32:42 LINE 3: FROM galaxy_user 2025-02-25 16:32:42 ^ 2025-02-25 16:32:42 2025-02-25 16:32:42 [SQL: SELECT count(*) AS count_1 2025-02-25 16:32:42 FROM (SELECT galaxy_user.id AS galaxy_user_id, galaxy_user.create_time AS galaxy_user_create_time, galaxy_user.update_time AS galaxy_user_update_time, galaxy_user.email AS galaxy_user_email, galaxy_user.username AS galaxy_user_username, galaxy_user.password AS galaxy_user_password, galaxy_user.last_password_change AS galaxy_user_last_password_change, galaxy_user.external AS galaxy_user_external, galaxy_user.form_values_id AS galaxy_user_form_values_id, galaxy_user.preferred_object_store_id AS galaxy_user_preferred_object_store_id, galaxy_user.deleted AS galaxy_user_deleted, galaxy_user.purged AS galaxy_user_purged, galaxy_user.disk_usage AS galaxy_user_disk_usage, galaxy_user.active AS galaxy_user_active, galaxy_user.activation_token AS galaxy_user_activation_token 2025-02-25 16:32:42 FROM galaxy_user 2025-02-25 16:32:42 WHERE galaxy_user.email = %(email_1)s) AS anon_1] 2025-02-25 16:32:42 [parameters: {'email_1': ***@***.***'}] 2025-02-25 16:32:42 (Background on this error at: https://sqlalche.me/e/20/f405)

…

On Tue, Feb 25, 2025 at 2:46 PM Björn Grüning ***@***.***> wrote: Can you please test the new 24.2 image and let me know if you still have problems? — Reply to this email directly, view it on GitHub <#619 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AINESA7GYDDN2JUNNGGJ4DD2RTXC7AVCNFSM6AAAAABWBPAFQWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMOBTGQ3DENRXGA> . You are receiving this because you authored the thread.Message ID: ***@***.***> [image: bgruening]*bgruening* left a comment (bgruening/docker-galaxy#619) <#619 (comment)> Can you please test the new 24.2 image and let me know if you still have problems? — Reply to this email directly, view it on GitHub <#619 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AINESA7GYDDN2JUNNGGJ4DD2RTXC7AVCNFSM6AAAAABWBPAFQWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMOBTGQ3DENRXGA> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[jtdbod]

When I start the container in interactive mode, install psycopg2-binary in the virtual environment, and then run the startup script, everything works fine.

[jtdbod]

I found a workaround. I build with a Dockerfile that copies and runs an alternative startup script via CMD in the container. The startup script is below:

#!/bin/bash

. /galaxy_venv/bin/activate
/galaxy_venv/bin/pip install psycopg2-binary
/usr/bin/startup