Pull last docker image : how can I get my data back ?

[bnouyou]

Discussed in #1987

^{Originally posted by bnouyou July 23, 2021}
Hello,

I am not very familiar with docker, so my issue is maybe very easy to solve.
I used seqr installed as local instance on my server since few months and it worked well.
I just pulled the last docker image, and now when I start seqr container with docker-compose up -d seqr (still with the "old" docker-compose.yml, maybe that's the problem ?), here I have nothing in the interface (I mean I haven't my projects anymore here).
How can I put them back ?

Thank you in advance for your hep.

[bnouyou]

Hello,
I just tried with new docker-compose, and it seems that postgres is not working, the container isn't running. And this is what I have in logs:

Attaching to seqr_postgres_1
postgres_1         | The files belonging to this database system will be owned by user "postgres".
postgres_1         | This user must also own the server process.
postgres_1         |
postgres_1         | The database cluster will be initialized with locale "en_US.utf8".
postgres_1         | The default database encoding has accordingly been set to "UTF8".
postgres_1         | The default text search configuration will be set to "english".
postgres_1         |
postgres_1         | Data page checksums are disabled.
postgres_1         |
postgres_1         | initdb: error: directory "/var/lib/postgresql/data" exists but is not empty
postgres_1         | If you want to create a new database system, either remove or empty
postgres_1         | the directory "/var/lib/postgresql/data" or run initdb
postgres_1         | with an argument other than "/var/lib/postgresql/data".
postgres_1         | The files belonging to this database system will be owned by user "postgres".
postgres_1         | This user must also own the server process.

[bnouyou]

I have put the "old" postgres in the docker-compose, which is:

postgres:
    image: gcr.io/seqr-project/postgres:gcloud-prod
    environment:
      - PGPORT=5433
      - POSTGRES_PASSWORD=docker-compose-postgres-password
    volumes:
      - ./data/postgres:/var/lib/postgresql/data
    healthcheck:
      test: pg_isready -h postgres -U postgres
      interval: 5s
      timeout: 10s
      retries: 100

This time, the postgres container starts.
I can access to the interface but project list is still empty.
In the logs of postgres container I have that:

Attaching to seqr_postgres_1
postgres_1         | LOG:  database system was shut down at 2021-07-23 11:51:16 UTC
postgres_1         | LOG:  MultiXact member wraparound protections are now enabled
postgres_1         | LOG:  database system is ready to accept connections
postgres_1         | LOG:  autovacuum launcher started
postgres_1         | ERROR:  column seqr_family.case_review_notes does not exist at character 629
postgres_1         | STATEMENT:  SELECT "seqr_family"."id", "seqr_family"."guid", "seqr_family"."created_date", "seqr_family"."created_by_id", "seqr_family"."last_modified_date", "seqr_family"."project_id", "seqr_family"."family_id", "seqr_family"."display_name", "seqr_family"."description", "seqr_family"."pedigree_image", "seqr_family"."assigned_analyst_id", "seqr_family"."success_story_types", "seqr_family"."success_story", "seqr_family"."mme_notes", "seqr_family"."analysis_notes", "seqr_family"."analysis_summary", "seqr_family"."coded_phenotype", "seqr_family"."post_discovery_omim_number", "seqr_family"."pubmed_ids", "seqr_family"."analysis_status", "seqr_family"."case_review_notes", "seqr_family"."case_review_summary", "seqr_project"."id", "seqr_project"."guid", "seqr_project"."created_date", "seqr_project"."created_by_id", "seqr_project"."last_modified_date", "seqr_project"."name", "seqr_project"."description", "seqr_project"."can_edit_group_id", "seqr_project"."can_view_group_id", "seqr_project"."genome_version", "seqr_project"."is_mme_enabled", "seqr_project"."mme_primary_data_owner", "seqr_project"."mme_contact_url", "seqr_project"."mme_contact_institution", "seqr_project"."has_case_review", "seqr_project"."last_accessed_date", "seqr_project"."workspace_namespace", "seqr_project"."workspace_name", "auth_group"."id", "auth_group"."name", T4."id", T4."name" FROM "seqr_family" INNER JOIN "seqr_project" ON ("seqr_family"."project_id" = "seqr_project"."id") INNER JOIN "auth_group" ON ("seqr_project"."can_edit_group_id" = "auth_group"."id") INNER JOIN "auth_group" T4 ON ("seqr_project"."can_view_group_id" = T4."id") ORDER BY "seqr_family"."id" DESC

How can I do to solve this problem ?

[bnouyou]

Hello,

I did these commands and this is what I have after "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, reference_data, seqr, sessions, social_django
Running migrations:
  Applying admin.0003_logentry_add_action_flag_choices... OK
  Applying auth.0009_alter_user_last_name_max_length... OK
  Applying auth.0010_alter_group_name_max_length... OK
  Applying auth.0011_update_proxy_permissions... OK
  Applying auth.0012_alter_user_first_name_max_length... OK
  Applying guardian.0002_generic_permissions_index... OK
  Applying matchmaker.0003_auto_20201123_2111... OK
  Applying reference_data.0018_genecopynumbersensitivity... OK
  Applying seqr.0014_userpolicy... OK
  Applying seqr.0015_auto_20201112_1617... OK
  Applying seqr.0016_auto_20201120_1636... OK
  Applying seqr.0017_auto_20201124_1446... OK
  Applying seqr.0018_auto_20201202_1553... OK
  Applying seqr.0019_auto_20201221_1718... OK
  Applying seqr.0020_remove_project_disable_staff_access...Creating analyst project group with 3 projects
Creating user groups
Adding 2 analysts
Updating 2 staff users
 OK
  Applying seqr.0021_auto_20210125_2221... OK
  Applying seqr.0022_auto_20210201_2151... OK
  Applying seqr.0023_auto_20210304_2315... OK
  Applying seqr.0024_varianttag_metadata...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/special.py", line 190, in database_forwards
    self.code(from_state.apps, schema_editor)
  File "/seqr/seqr/migrations/0024_varianttag_metadata.py", line 74, in update_validation_tag_types
    _update_tag_type(tag_type, {'name': new_name, 'description': None, 'metadata_title': 'Test Type(s)'})
  File "/seqr/seqr/migrations/0024_varianttag_metadata.py", line 17, in _update_tag_type
    log_model_update(logger, tag_type, user=None, update_type='update', update_fields=list(json.keys()) + ['last_modified_date'])
  File "/seqr/seqr/utils/logging_utils.py", line 72, in log_model_update
    logger.info('{} {} {}'.format(update_type, db_entity, entity_id), user, db_update=db_update)
  File "/usr/local/lib/python3.7/logging/__init__.py", line 1378, in info
    self._log(INFO, msg, args, **kwargs)
TypeError: _log() got an unexpected keyword argument 'db_update'

In the interface I see that only one project has been imported (I had 3), and the variant information are not available (error message about database).
Do you know how I can do ?

Thank you.

[hanars]

I think this is actually a permission error, rather than a data missing error. Are you logging in as a superuser?

[bnouyou]

No I am not loggued as root. Should I need to be root to lauch these commands ?

[hanars]

So when you are logged in to seqr and are saying "In the interface I see that only one project has been imported" are you logged in as a superuser? Are you sure the user you logged in as still has permission to view all the projects? The fact that the application is loading and any of the data is there means your database has been restored, so I think what has happened is since seqr was last updated the way permissions work have been changed. You should make sure the user you are logging in as has a "superuser" permission if you want to be able to see every project in seqr

[bnouyou]

Ok I see what you mean. I just checked and my user is "superuser" in seqr interface. I see it's not "staff user". In the Django Admin interface I have seen that groups and user permissions are not good for my user, so I put back the good groups just now. But I still don't see the other projects after refreshing the interface.

The migrate script has still an error at test 0024 :

Running migrations:
  Applying seqr.0024_varianttag_metadata...Traceback (most recent call last):
  File "/usr/local/lib/python3.7/site-packages/django/db/backends/utils.py", line 84, in _execute
    return self.cursor.execute(sql, params)
psycopg2.errors.DuplicateColumn: column "metadata" of relation "seqr_varianttag" already exists

I see it concerns the "variant tag". Could it be problematic because I had created some custom tags before ?

[bnouyou]

I have refreshed the cache and now I see all projects ! That's a good thing.

But I still have some issues:

• for the variant search, I have this error message after clicking on search:
  

• And in the selected variants (the ones I have taggued before), I see there is no gene names:
  

Is it because the migrate.py script has not work correctly ?

[hanars]

try docker-compose exec seqr python -u manage.py migrate reference_data

[bnouyou]

I did that and it's saying "no migration to apply":

/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: reference_data
Running migrations:
  No migrations to apply.

[bnouyou]

Hello,
What could be the next step ? I still don't have the gene names (only the ENSG ids for all genes).
In the Django Admin interface I see that the "Reference Data" part is empty. Should I do other migration steps ?
In the Migration documentation, I see the steps "Update gene-level reference datasets", should I do that ?

Edit:
I think I know the problem, I see that the database "reference_data_db" has empty tables. So I suppose I need to do the steps described in the Migration documentation about reference_data_db. Am I right ?
Should I do this:

psql -U postgres postgres -c "drop database reference_data_db"
psql -U postgres postgres -c "create database reference_data_db"
REFERENCE_DATA_BACKUP_FILE=gene_reference_data_backup.gz
wget -N https://storage.googleapis.com/seqr-reference-data/gene_reference_data_backup.gz -O ${REFERENCE_DATA_BACKUP_FILE}
psql -U postgres reference_data_db <  <(gunzip -c ${REFERENCE_DATA_BACKUP_FILE})
rm ${REFERENCE_DATA_BACKUP_FILE}

Edit 2:
I have done the commands for importing the "gene_reference_data" and it works.

My problem is solved.
Thank you for your help. Have a nice day.

[hanars]

I'm glad you figured this out and I'm glad it worked!