Error after stopping/starting docker containers

[bnouyou]

Hello again,

I have stop and start my docker containers. And now I have this error message in the browser:

These are the logs:

seqr_1             | {"timestamp": "2021-10-22 08:48:20,845", "severity": "ERROR", "httpRequest": {"requestMethod": "GET", "requestUrl": "http://lx165/", "status": 500, "responseSize": 137414, "userAgent": "Mozilla/5.0 (Windows NT 10.0; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/75.0.3770.100 Safari/537.36", "remoteIp": "172.18.8.26", "referer": null, "protocol": "HTTP/1.1"}, "message": "relation \"seqr_warningmessage\" does not exist\nLINE 1: ...e\".\"message\", \"seqr_warningmessage\".\"header\" FROM \"seqr_warn...\n                                                             ^\n", "user": "benedicte.nouyou@chu-rennes.fr", "traceback": "Traceback (most recent call last):\n  File \"/usr/local/lib/python3.7/site-packages/django/db/backends/utils.py\", line 84, in _execute\n    return self.cursor.execute(sql, params)\npsycopg2.errors.UndefinedTable: relation \"seqr_warningmessage\" does not exist\nLINE 1: ...e\".\"message\", \"seqr_warningmessage\".\"header\" FROM \"seqr_warn...\n                                                             ^\n\n\nThe above exception was the direct cause of the following exception:\n\nTraceback (most recent call last):\n  File \"/usr/local/lib/python3.7/site-packages/django/core/handlers/base.py\", line 181, in _get_response\n    response = wrapped_callback(request, *callback_args, **callback_kwargs)\n  File \"/seqr/seqr/views/react_app.py\", line 31, in no_login_main_app\n    return render_app_html(request, **render_kwargs)\n  File \"/seqr/seqr/views/react_app.py\", line 41, in render_app_html\n    'warningMessages': [message.json() for message in WarningMessage.objects.all()],\n  File \"/usr/local/lib/python3.7/site-packages/django/db/models/query.py\", line 287, in __iter__\n    self._fetch_all()\n  File \"/usr/local/lib/python3.7/site-packages/django/db/models/query.py\", line 1308, in _fetch_all\n    self._result_cache = list(self._iterable_class(self))\n  File \"/usr/local/lib/python3.7/site-packages/django/db/models/query.py\", line 53, in __iter__\n    results = compiler.execute_sql(chunked_fetch=self.chunked_fetch, chunk_size=self.chunk_size)\n  File \"/usr/local/lib/python3.7/site-packages/django/db/models/sql/compiler.py\", line 1156, in execute_sql\n    cursor.execute(sql, params)\n  File \"/usr/local/lib/python3.7/site-packages/django/db/backends/utils.py\", line 98, in execute\n    return super().execute(sql, params)\n  File \"/usr/local/lib/python3.7/site-packages/django/db/backends/utils.py\", line 66, in execute\n    return self._execute_with_wrappers(sql, params, many=False, executor=self._execute)\n  File \"/usr/local/lib/python3.7/site-packages/django/db/backends/utils.py\", line 75, in _execute_with_wrappers\n    return executor(sql, params, many, context)\n  File \"/usr/local/lib/python3.7/site-packages/django/db/backends/utils.py\", line 84, in _execute\n    return self.cursor.execute(sql, params)\n  File \"/usr/local/lib/python3.7/site-packages/django/db/utils.py\", line 90, in __exit__\n    raise dj_exc_value.with_traceback(traceback) from exc_value\n  File \"/usr/local/lib/python3.7/site-packages/django/db/backends/utils.py\", line 84, in _execute\n    return self.cursor.execute(sql, params)\ndjango.db.utils.ProgrammingError: relation \"seqr_warningmessage\" does not exist\nLINE 1: ...e\".\"message\", \"seqr_warningmessage\".\"header\" FROM \"seqr_warn...\n                                                             ^\n\n", "@type": "type.googleapis.com/google.devtools.clouderrorreporting.v1beta1.ReportedErrorEvent"}

[hanars]

It looks like your version of the seqr codebase is out of sync with you database. Run

docker-compose exec seqr python -u manage.py makemigrations
docker-compose exec seqr python -u manage.py migrate

[hanars]

Okay, I pushed up another fix to the branch which will hopefully get you all the way to the end this time. Again, you should run

docker-compose exec seqr git checkout partial-migration-fix
docker-compose exec seqr git pull
docker-compose exec seqr python -u manage.py migrate
docker-compose exec seqr git checkout master

[bnouyou]

I did this, it failed on step 0031.
The I did the migrate on branch master, step 0031 passed.
And now it failed at 0032:

[cytogen@LX165 SEQR]$ docker-compose exec seqr python -u manage.py migrate
/usr/local/lib/python3.7/site-packages/requests/__init__.py:91: RequestsDependencyWarning: urllib3 (1.26.5) or chardet (3.0.4) doesn't match a supported version!
  RequestsDependencyWarning)
/usr/local/lib/python3.7/site-packages/pandas/compat/__init__.py:120: UserWarning: Could not import the lzma module. Your installed Python is incomplete. Attempting to use lzma compression will result in a RuntimeError.
  warnings.warn(msg)
System check identified some issues:

WARNINGS:
social_django.Partial.data: (fields.W904) django.contrib.postgres.fields.JSONField is deprecated. Support for it (except in historical migrations) will be removed in Django 4.0.
        HINT: Use django.db.models.JSONField instead.
social_django.UserSocialAuth.extra_data: (fields.W904) django.contrib.postgres.fields.JSONField is deprecated. Support for it (except in historical migrations) will be removed in Django 4.0.
        HINT: Use django.db.models.JSONField instead.
Operations to perform:
  Apply all migrations: admin, auth, contenttypes, guardian, matchmaker, panelapp, reference_data, seqr, sessions, social_django
Running migrations:
  Applying seqr.0032_warningmessage...Traceback (most recent call last):
  File "/usr/local/lib/python3.7/site-packages/django/db/backends/utils.py", line 82, in _execute
    return self.cursor.execute(sql)
psycopg2.errors.DuplicateTable: relation "seqr_warningmessage" already exists


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

Traceback (most recent call last):
  File "manage.py", line 10, in <module>
    execute_from_command_line(sys.argv)
  File "/usr/local/lib/python3.7/site-packages/django/core/management/__init__.py", line 401, in execute_from_command_line
    utility.execute()
  File "/usr/local/lib/python3.7/site-packages/django/core/management/__init__.py", line 395, in execute
    self.fetch_command(subcommand).run_from_argv(self.argv)
  File "/usr/local/lib/python3.7/site-packages/django/core/management/base.py", line 330, in run_from_argv
    self.execute(*args, **cmd_options)
  File "/usr/local/lib/python3.7/site-packages/django/core/management/base.py", line 371, in execute
    output = self.handle(*args, **options)
  File "/usr/local/lib/python3.7/site-packages/django/core/management/base.py", line 85, in wrapped
    res = handle_func(*args, **kwargs)
  File "/usr/local/lib/python3.7/site-packages/django/core/management/commands/migrate.py", line 245, in handle
    fake_initial=fake_initial,
  File "/usr/local/lib/python3.7/site-packages/django/db/migrations/executor.py", line 117, in migrate
    state = self._migrate_all_forwards(state, plan, full_plan, fake=fake, fake_initial=fake_initial)
  File "/usr/local/lib/python3.7/site-packages/django/db/migrations/executor.py", line 147, in _migrate_all_forwards
    state = self.apply_migration(state, migration, fake=fake, fake_initial=fake_initial)
  File "/usr/local/lib/python3.7/site-packages/django/db/migrations/executor.py", line 227, in apply_migration
    state = migration.apply(state, schema_editor)
  File "/usr/local/lib/python3.7/site-packages/django/db/migrations/migration.py", line 124, in apply
    operation.database_forwards(self.app_label, schema_editor, old_state, project_state)
  File "/usr/local/lib/python3.7/site-packages/django/db/migrations/operations/models.py", line 92, in database_forwards
    schema_editor.create_model(model)
  File "/usr/local/lib/python3.7/site-packages/django/db/backends/base/schema.py", line 324, in create_model
    self.execute(sql, params or None)
  File "/usr/local/lib/python3.7/site-packages/django/db/backends/base/schema.py", line 142, in execute
    cursor.execute(sql, params)
  File "/usr/local/lib/python3.7/site-packages/django/db/backends/utils.py", line 98, in execute
    return super().execute(sql, params)
  File "/usr/local/lib/python3.7/site-packages/django/db/backends/utils.py", line 66, in execute
    return self._execute_with_wrappers(sql, params, many=False, executor=self._execute)
  File "/usr/local/lib/python3.7/site-packages/django/db/backends/utils.py", line 75, in _execute_with_wrappers
    return executor(sql, params, many, context)
  File "/usr/local/lib/python3.7/site-packages/django/db/backends/utils.py", line 84, in _execute
    return self.cursor.execute(sql, params)
  File "/usr/local/lib/python3.7/site-packages/django/db/utils.py", line 90, in __exit__
    raise dj_exc_value.with_traceback(traceback) from exc_value
  File "/usr/local/lib/python3.7/site-packages/django/db/backends/utils.py", line 82, in _execute
    return self.cursor.execute(sql)
django.db.utils.ProgrammingError: relation "seqr_warningmessage" already exists

This is the state of showmigration:

/usr/local/lib/python3.7/site-packages/requests/__init__.py:91: RequestsDependencyWarning: urllib3 (1.26.5) or chardet (3.0.4) doesn't match a supported version!
  RequestsDependencyWarning)
/usr/local/lib/python3.7/site-packages/pandas/compat/__init__.py:120: UserWarning: Could not import the lzma module. Your installed Python is incomplete. Attempting to use lzma compression will result in a RuntimeError.
  warnings.warn(msg)
System check identified some issues:

WARNINGS:
social_django.Partial.data: (fields.W904) django.contrib.postgres.fields.JSONField is deprecated. Support for it (except in historical migrations) will be removed in Django 4.0.
        HINT: Use django.db.models.JSONField instead.
social_django.UserSocialAuth.extra_data: (fields.W904) django.contrib.postgres.fields.JSONField is deprecated. Support for it (except in historical migrations) will be removed in Django 4.0.
        HINT: Use django.db.models.JSONField instead.
admin
 [X] 0001_initial
 [X] 0002_logentry_remove_auto_add
 [X] 0003_logentry_add_action_flag_choices
auth
 [X] 0001_initial
 [X] 0002_alter_permission_name_max_length
 [X] 0003_alter_user_email_max_length
 [X] 0004_alter_user_username_opts
 [X] 0005_alter_user_last_login_null
 [X] 0006_require_contenttypes_0002
 [X] 0007_alter_validators_add_error_messages
 [X] 0008_alter_user_username_max_length
 [X] 0009_alter_user_last_name_max_length
 [X] 0010_alter_group_name_max_length
 [X] 0011_update_proxy_permissions
 [X] 0012_alter_user_first_name_max_length
contenttypes
 [X] 0001_initial
 [X] 0002_remove_content_type_name
guardian
 [X] 0001_initial
 [X] 0002_generic_permissions_index
matchmaker
 [X] 0001_initial
 [X] 0002_matchmakerresult_originating_submission
 [X] 0003_auto_20201123_2111
panelapp
 [X] 0001_initial
 [X] 0002_auto_20210915_1049
reference_data
 [X] 0001_initial
 [X] 0002_auto_20170319_0332
 [X] 0003_clinvar
 [X] 0004_auto_20170626_1401
 [X] 0005_auto_20170627_0318
 [X] 0006_auto_20170630_1754
 [X] 0007_auto_20180809_2053
 [X] 0008_geneexpression
 [X] 0009_auto_20180917_2015
 [X] 0010_auto_20190319_1518
 [X] 0011_primateai
 [X] 0012_auto_20190321_1656
 [X] 0013_auto_20190404_1953
 [X] 0014_auto_20190510_2150
 [X] 0015_auto_20190625_1813
 [X] 0016_dbnsfpgene_gene_names
 [X] 0017_auto_20190909_2102
 [X] 0018_genecopynumbersensitivity
seqr
 [X] 0001_squashed_0067_remove_project_custom_reference_populations (78 squashed migrations)
 [X] 0002_auto_20191203_1913
 [X] 0003_auto_20191203_1130
 [X] 0004_auto_20200124_1912
 [X] 0005_locuslist_projects
 [X] 0006_family_mme_notes
 [X] 0007_auto_20200303_1842
 [X] 0008_auto_20200317_1716
 [X] 0009_auto_20200402_2219
 [X] 0010_auto_20200413_2159
 [X] 0011_individual_proband_relationship
 [X] 0012_auto_20200603_1924
 [X] 0013_individual_sv_flags
 [X] 0014_userpolicy
 [X] 0015_auto_20201112_1617
 [X] 0016_auto_20201120_1636
 [X] 0017_auto_20201124_1446
 [X] 0018_auto_20201202_1553
 [X] 0019_auto_20201221_1718
 [X] 0020_remove_project_disable_staff_access
 [X] 0021_auto_20210125_2221
 [X] 0022_auto_20210201_2151
 [X] 0023_auto_20210304_2315
 [X] 0024_varianttag_metadata
 [X] 0025_auto_20210428_1619
 [X] 0026_auto_20210521_1836
 [X] 0027_family_pedigree_dataset
 [X] 0028_auto_20210826_1528
 [X] 0029_auto_20210826_1748
 [X] 0030_project_enable_hgmd
 [X] 0031_project_all_user_demo
 [ ] 0032_warningmessage
sessions
 [X] 0001_initial
social_django
 [ ] 0001_initial (2 squashed migrations)
 [ ] 0002_add_related_name (2 squashed migrations)
 [ ] 0003_alter_email_max_length (2 squashed migrations)
 [ ] 0004_auto_20160423_0400 (2 squashed migrations)
 [ ] 0005_auto_20160727_2333 (1 squashed migrations)
 [ ] 0006_partial
 [ ] 0007_code_timestamp
 [ ] 0008_partial_timestamp
 [ ] 0009_auto_20191118_0520
 [ ] 0010_uid_db_index

[hanars]

okay I updated the branch so hopefully this should be the last fix you need:

docker-compose exec seqr git checkout partial-migration-fix
docker-compose exec seqr git pull
docker-compose exec seqr python -u manage.py migrate
docker-compose exec seqr git checkout master

[bnouyou]

Thank you so much for your help. It finally works!
The migration is now "OK" for all steps:

Operations to perform:
  Apply all migrations: admin, auth, contenttypes, guardian, matchmaker, panelapp, reference_data, seqr, sessions, social_django
Running migrations:
  Applying seqr.0032_warningmessage... OK
  Applying social_django.0001_initial... OK
  Applying social_django.0002_add_related_name... OK
  Applying social_django.0003_alter_email_max_length... OK
  Applying social_django.0004_auto_20160423_0400... OK
  Applying social_django.0005_auto_20160727_2333... OK
  Applying social_django.0006_partial... OK
  Applying social_django.0007_code_timestamp... OK
  Applying social_django.0008_partial_timestamp... OK
  Applying social_django.0009_auto_20191118_0520... OK
  Applying social_django.0010_uid_db_index... OK

And in the showmigration, everything is checked.

Now I will pay very attention when I need to restart containers, because it pull the last version of the code, and I need to use the migration script then.

[hanars]

Great, I'm glad you are all set! We are planning work for next year that will hopefully make the docker image more stable, so it doesn't pull the latest code automatically when you restart the container and only does it if you actually want to update. But yes, in the meantime that sounds good