Migrating from older non-docker version to recent docker-compose version #2971

chrisAta · 2022-09-21T09:32:50Z

chrisAta
Sep 21, 2022

Hello!

We've got an old seqr instance that was manually installed back in 2017 that I'm interested in migrating to the newer version using the seqr docker-compose. I've tried a couple of things based off this issue from 2020:

I've created a data dump using the command pg_dump -U postgres seqrdb | gzip -c - > backup.gz
I then started the seqr docker-compose (docker-compose up -d seqr) and entered the postgres container, and ran these commands to drop the database and replace it with my backup:

psql -U postgres postgres -c "drop database seqrdb"
psql -U postgres postgres -c "create database seqrdb"
psql -U postgres seqrdb <  <(gunzip -c backup.gz)

This all seems to run fine.

I then do:
3. python -m manage makemigrations
Which results in 'no changes detected', I assume because the migrations folder of each app (like seqr/migrations) is full of old migrations that were uploaded to the github repo.
4. python -m manage migrate
And at this point it finally errors out:

Operations to perform:
  Apply all migrations: admin, auth, contenttypes, guardian, matchmaker, panelapp, reference_data, seqr, sessions, social_django
Running migrations:
  Applying matchmaker.0001_initial...Traceback (most recent call last):
  File "/usr/local/lib/python3.7/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/usr/local/lib/python3.7/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/seqr/manage.py", line 10, in <module>
    execute_from_command_line(sys.argv)
  File "/opt/venv/lib/python3.7/site-packages/django/core/management/__init__.py", line 419, in execute_from_command_line
    utility.execute()
  File "/opt/venv/lib/python3.7/site-packages/django/core/management/__init__.py", line 413, in execute
    self.fetch_command(subcommand).run_from_argv(self.argv)
  File "/opt/venv/lib/python3.7/site-packages/django/core/management/base.py", line 354, in run_from_argv
    self.execute(*args, **cmd_options)
  File "/opt/venv/lib/python3.7/site-packages/django/core/management/base.py", line 398, in execute
    output = self.handle(*args, **options)
  File "/opt/venv/lib/python3.7/site-packages/django/core/management/base.py", line 89, in wrapped
    res = handle_func(*args, **kwargs)
  File "/opt/venv/lib/python3.7/site-packages/django/core/management/commands/migrate.py", line 246, in handle
    fake_initial=fake_initial,
  File "/opt/venv/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 "/opt/venv/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 "/opt/venv/lib/python3.7/site-packages/django/db/migrations/executor.py", line 227, in apply_migration
    state = migration.apply(state, schema_editor)
  File "/opt/venv/lib/python3.7/site-packages/django/db/migrations/migration.py", line 126, in apply
    operation.database_forwards(self.app_label, schema_editor, old_state, project_state)
  File "/opt/venv/lib/python3.7/site-packages/django/db/migrations/operations/models.py", line 92, in database_forwards
    schema_editor.create_model(model)
  File "/opt/venv/lib/python3.7/site-packages/django/db/backends/base/schema.py", line 343, in create_model
    sql, params = self.table_sql(model)
  File "/opt/venv/lib/python3.7/site-packages/django/db/backends/base/schema.py", line 162, in table_sql
    definition, extra_params = self.column_sql(model, field)
  File "/opt/venv/lib/python3.7/site-packages/django/db/backends/base/schema.py", line 215, in column_sql
    db_params = field.db_parameters(connection=self.connection)
  File "/opt/venv/lib/python3.7/site-packages/django/db/models/fields/related.py", line 1004, in db_parameters
    return {"type": self.db_type(connection), "check": self.db_check(connection)}
  File "/opt/venv/lib/python3.7/site-packages/django/db/models/fields/related.py", line 1001, in db_type
    return self.target_field.rel_db_type(connection=connection)
  File "/opt/venv/lib/python3.7/site-packages/django/db/models/fields/related.py", line 897, in target_field
    return self.foreign_related_fields[0]
  File "/opt/venv/lib/python3.7/site-packages/django/utils/functional.py", line 48, in __get__
    res = instance.__dict__[self.name] = self.func(instance)
  File "/opt/venv/lib/python3.7/site-packages/django/db/models/fields/related.py", line 644, in foreign_related_fields
    return tuple(rhs_field for lhs_field, rhs_field in self.related_fields if rhs_field)
  File "/opt/venv/lib/python3.7/site-packages/django/utils/functional.py", line 48, in __get__
    res = instance.__dict__[self.name] = self.func(instance)
  File "/opt/venv/lib/python3.7/site-packages/django/db/models/fields/related.py", line 632, in related_fields
    return self.resolve_related_fields()
  File "/opt/venv/lib/python3.7/site-packages/django/db/models/fields/related.py", line 936, in resolve_related_fields
    related_fields = super().resolve_related_fields()
  File "/opt/venv/lib/python3.7/site-packages/django/db/models/fields/related.py", line 615, in resolve_related_fields
    raise ValueError('Related model %r cannot be resolved' % self.remote_field.model)
ValueError: Related model 'seqr.individual' cannot be resolved

I have tried clearing out the migrations folders (by removing the 00*.py and pycache files and folders) for all the apps (seqr, matchmaker, panelapp, reference_data), and trying the last two commands again:

python -m manage makemigrations
Migrations for 'reference_data':
  reference_data/migrations/0001_initial.py
    - Create model GeneInfo
    - Create model HumanPhenotypeOntology
    - Create model TranscriptInfo
    - Create model PrimateAI
    - Create model GeneCopyNumberSensitivity
    - Create model GeneConstraint
    - Create model GenCC
    - Create model dbNSFPGene
    - Create model ClinGen
    - Create model Omim
    - Create model MGI
Migrations for 'matchmaker':
  matchmaker/migrations/0001_initial.py
    - Create model MatchmakerContactNotes
    - Create model MatchmakerIncomingQuery
    - Create model MatchmakerResult
    - Create model MatchmakerSubmission
  matchmaker/migrations/0002_initial.py
    - Add field individual to matchmakersubmission
    - Add field created_by to matchmakerresult
    - Add field last_modified_by to matchmakerresult
    - Add field originating_query to matchmakerresult
    - Add field originating_submission to matchmakerresult
    - Add field submission to matchmakerresult
    - Add field created_by to matchmakerincomingquery
    - Add field created_by to matchmakercontactnotes
Migrations for 'seqr':
  seqr/migrations/0001_initial.py
    - Create model Family
    - Create model Individual
    - Create model LocusList
    - Create model Project
    - Create model SavedVariant
    - Create model UserPolicy
    - Create model VariantSearch
    - Create model WarningMessage
    - Create model VariantTagType
    - Create model VariantTag
    - Create model VariantSearchResults
    - Create model VariantNote
    - Create model VariantFunctionalData
    - Create model Sample
    - Create model RnaSeqOutlier
    - Create model ProjectCategory
    - Create model LocusListInterval
    - Create model LocusListGene
    - Add field projects to locuslist
    - Create model IgvSample
    - Create model GeneNote
    - Create model FamilyNote
    - Create model FamilyAnalysedBy
    - Add field project to family
    - Create model AnalysisGroup
    - Create model RnaSeqTpm
    - Create index seqr_rnaseq_gene_id_a6ad2f_idx on field(s) gene_id of model rnaseqoutlier
    - Create index seqr_rnaseq_p_adjus_59a417_idx on field(s) p_adjust of model rnaseqoutlier
    - Alter unique_together for rnaseqoutlier (1 constraint(s))
    - Alter unique_together for locuslistinterval (1 constraint(s))
    - Alter unique_together for locuslistgene (1 constraint(s))
    - Alter unique_together for locuslist (1 constraint(s))
    - Alter unique_together for individual (1 constraint(s))
    - Alter unique_together for igvsample (1 constraint(s))
    - Alter unique_together for family (1 constraint(s))
    - Alter unique_together for analysisgroup (1 constraint(s))
Migrations for 'panelapp':
  panelapp/migrations/0001_initial.py
    - Create model PaLocusList
    - Create model PaLocusListGene

Which seems to create new migrations, followed by:

python -m manage migrate
Operations to perform:
  Apply all migrations: admin, auth, contenttypes, guardian, matchmaker, panelapp, reference_data, seqr, sessions, social_django
Running migrations:
  Applying matchmaker.0001_initial... OK
  Applying matchmaker.0002_initial... OK
  Applying panelapp.0001_initial...Traceback (most recent call last):
  File "/opt/venv/lib/python3.7/site-packages/django/db/backends/utils.py", line 84, in _execute
    return self.cursor.execute(sql, params)
psycopg2.errors.UndefinedTable: relation "seqr_locuslistgene" does not exist


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

Traceback (most recent call last):
  File "/usr/local/lib/python3.7/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/usr/local/lib/python3.7/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/seqr/manage.py", line 10, in <module>
    execute_from_command_line(sys.argv)
  File "/opt/venv/lib/python3.7/site-packages/django/core/management/__init__.py", line 419, in execute_from_command_line
    utility.execute()
  File "/opt/venv/lib/python3.7/site-packages/django/core/management/__init__.py", line 413, in execute
    self.fetch_command(subcommand).run_from_argv(self.argv)
  File "/opt/venv/lib/python3.7/site-packages/django/core/management/base.py", line 354, in run_from_argv
    self.execute(*args, **cmd_options)
  File "/opt/venv/lib/python3.7/site-packages/django/core/management/base.py", line 398, in execute
    output = self.handle(*args, **options)
  File "/opt/venv/lib/python3.7/site-packages/django/core/management/base.py", line 89, in wrapped
    res = handle_func(*args, **kwargs)
  File "/opt/venv/lib/python3.7/site-packages/django/core/management/commands/migrate.py", line 246, in handle
    fake_initial=fake_initial,
  File "/opt/venv/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 "/opt/venv/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 "/opt/venv/lib/python3.7/site-packages/django/db/migrations/executor.py", line 230, in apply_migration
    migration_recorded = True
  File "/opt/venv/lib/python3.7/site-packages/django/db/backends/base/schema.py", line 118, in __exit__
    self.execute(sql)
  File "/opt/venv/lib/python3.7/site-packages/django/db/backends/base/schema.py", line 145, in execute
    cursor.execute(sql, params)
  File "/opt/venv/lib/python3.7/site-packages/django/db/backends/utils.py", line 98, in execute
    return super().execute(sql, params)
  File "/opt/venv/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 "/opt/venv/lib/python3.7/site-packages/django/db/backends/utils.py", line 75, in _execute_with_wrappers
    return executor(sql, params, many, context)
  File "/opt/venv/lib/python3.7/site-packages/django/db/backends/utils.py", line 84, in _execute
    return self.cursor.execute(sql, params)
  File "/opt/venv/lib/python3.7/site-packages/django/db/utils.py", line 90, in __exit__
    raise dj_exc_value.with_traceback(traceback) from exc_value
  File "/opt/venv/lib/python3.7/site-packages/django/db/backends/utils.py", line 84, in _execute
    return self.cursor.execute(sql, params)
django.db.utils.ProgrammingError: relation "seqr_locuslistgene" does not exist

Which errors out again. At this point I'm a little out of my depth, so I was wondering whether you'd have any help or other instructions for porting an old non-docker instance of seqr to a newer docker instance of it.

Thanks in advance!

Chris

hanars · 2022-09-21T15:42:18Z

hanars
Sep 21, 2022
Maintainer

I am a little confused about where exactly you are running your commands, you mention in step 2 that you "entered the postgres container" but I'm not 100% sure what that means. You then mention manage commands you are running in steps 3 and 4 but are not entirely clear on where they are being run. In general, when using docker you want to run commands as docker-composes exec <postgres/seqr/etc...> <command>

It seems like the state of your database right now is pretty broken, so I would recommend you delete all the docker postgres databases by clearing out any data in the mounted volume for that pod and start again cleanly. Then I would recommend you make sure you have a working empty seqr instance. Run docker-compose up -d seqr and make sure you have a running seqr instance with no data in it. Once you confirm that seqr is working as expected without all the old database data, then work on restoring it as follows:

docker-compose exec seqr psql --host postgres -U postgres -c 'DROP DATABASE seqrdb';
docker-compose exec seqr psql --host postgres -U postgres -c 'CREATE DATABASE seqrdb';
docker-compose exec seqr psql --host postgres -U postgres seqrdb < <(gunzip -c backup.gz)
docker-compose exec seqr python -u manage.py makemigrations
docker-compose exec seqr python -u manage.py migrate seqr
docker-compose exec seqr python -u manage.py migrate matchmaker

Keep the output from each step and let me know if any of them fail

Also, how old exactly is the version of the manual instance you are running? If it is pre 2019 and has all the old xbrowse models you will need to locally transfer to the updated schema before you can switch to docker compose

1 reply

chrisAta Oct 4, 2022
Author

Hi hanars!

Thanks for your reply - I finally was able to have a look into these instructions, and I'm afraid I'm still stuck. I did what you suggested and completely wiped the database, and got an empty seqr instance working.

However, once I attempted step 3, I get this error:

docker-compose exec -T seqr psql --host postgres -U postgres seqrdb < <(gunzip -c ./backup_2020_03_03.gz)
SET
SET
SET
SET
SET
SET
CREATE EXTENSION
COMMENT
SET
SET
SET
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
CREATE TABLE
ERROR:  role "seqr" does not exist
CREATE SEQUENCE
ERROR:  role "seqr" does not exist
ALTER SEQUENCE
ALTER TABLE
ALTER TABLE
ALTER TABLE
ALTER TABLE
ALTER TABLE
ALTER TABLE
ALTER TABLE
ALTER TABLE
ALTER TABLE
ALTER TABLE
ALTER TABLE
ALTER TABLE
ALTER TABLE
ALTER TABLE
ALTER TABLE
ALTER TABLE
ALTER TABLE
ALTER TABLE
ALTER TABLE
ALTER TABLE
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ALTER TABLE
ALTER TABLE
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COPY 0
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    171
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--------
     43
(1 row)

COPY 404
 setval 
--------
   1042
(1 row)

COPY 7
COPY 17
 setval 
--------
     17
(1 row)

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--------
      7
(1 row)

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      1
(1 row)

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      1
(1 row)

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 setval 
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   2079
(1 row)

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   2168
(1 row)

COPY 0
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      1
(1 row)

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 setval 
--------
     30
(1 row)

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      1
(1 row)

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     41
(1 row)

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     11
(1 row)

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      1
(1 row)

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    456
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      2
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     29
(1 row)

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    202
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    255
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(1 row)

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     68
(1 row)

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 setval 
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     12
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 setval 
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   5985
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      1
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      1
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 196520
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      1
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 setval 
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  14705
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COPY 0
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      1
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      1
(1 row)

COPY 0
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      1
(1 row)

COPY 0
 setval 
--------
      1
(1 row)

COPY 0
 setval 
--------
      1
(1 row)

COPY 0
COPY 0
 setval 
--------
      1
(1 row)

 setval 
--------
      1
(1 row)

COPY 0
 setval 
--------
      1
(1 row)

COPY 0
 setval 
--------
      1
(1 row)

COPY 0
 setval 
--------
      1
(1 row)

COPY 0
 setval 
--------
      1
(1 row)

COPY 0
 setval 
--------
      1
(1 row)

COPY 0
 setval 
--------
      1
(1 row)

COPY 0
 setval 
--------
      1
(1 row)

COPY 0
 setval 
--------
      1
(1 row)

COPY 0
 setval 
--------
      1
(1 row)

COPY 0
 setval 
--------
      1
(1 row)

ALTER TABLE
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CREATE INDEX
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REVOKE
ERROR:  role "seqr" does not exist
ERROR:  role "seqr" does not exist
GRANT

Attempting to continue from this and performing steps 4 and 5 leads to No changes detected for step 4, followed by this error trace for step 5:

docker-compose exec seqr python -u manage.py migrate seqr
Operations to perform:
  Apply all migrations: seqr
Running migrations:
  Applying matchmaker.0001_initial...Traceback (most recent call last):
  File "manage.py", line 10, in <module>
    execute_from_command_line(sys.argv)
  File "/opt/venv/lib/python3.7/site-packages/django/core/management/__init__.py", line 419, in execute_from_command_line
    utility.execute()
  File "/opt/venv/lib/python3.7/site-packages/django/core/management/__init__.py", line 413, in execute
    self.fetch_command(subcommand).run_from_argv(self.argv)
  File "/opt/venv/lib/python3.7/site-packages/django/core/management/base.py", line 354, in run_from_argv
    self.execute(*args, **cmd_options)
  File "/opt/venv/lib/python3.7/site-packages/django/core/management/base.py", line 398, in execute
    output = self.handle(*args, **options)
  File "/opt/venv/lib/python3.7/site-packages/django/core/management/base.py", line 89, in wrapped
    res = handle_func(*args, **kwargs)
  File "/opt/venv/lib/python3.7/site-packages/django/core/management/commands/migrate.py", line 246, in handle
    fake_initial=fake_initial,
  File "/opt/venv/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 "/opt/venv/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 "/opt/venv/lib/python3.7/site-packages/django/db/migrations/executor.py", line 227, in apply_migration
    state = migration.apply(state, schema_editor)
  File "/opt/venv/lib/python3.7/site-packages/django/db/migrations/migration.py", line 126, in apply
    operation.database_forwards(self.app_label, schema_editor, old_state, project_state)
  File "/opt/venv/lib/python3.7/site-packages/django/db/migrations/operations/models.py", line 92, in database_forwards
    schema_editor.create_model(model)
  File "/opt/venv/lib/python3.7/site-packages/django/db/backends/base/schema.py", line 343, in create_model
    sql, params = self.table_sql(model)
  File "/opt/venv/lib/python3.7/site-packages/django/db/backends/base/schema.py", line 162, in table_sql
    definition, extra_params = self.column_sql(model, field)
  File "/opt/venv/lib/python3.7/site-packages/django/db/backends/base/schema.py", line 215, in column_sql
    db_params = field.db_parameters(connection=self.connection)
  File "/opt/venv/lib/python3.7/site-packages/django/db/models/fields/related.py", line 1004, in db_parameters
    return {"type": self.db_type(connection), "check": self.db_check(connection)}
  File "/opt/venv/lib/python3.7/site-packages/django/db/models/fields/related.py", line 1001, in db_type
    return self.target_field.rel_db_type(connection=connection)
  File "/opt/venv/lib/python3.7/site-packages/django/db/models/fields/related.py", line 897, in target_field
    return self.foreign_related_fields[0]
  File "/opt/venv/lib/python3.7/site-packages/django/utils/functional.py", line 48, in __get__
    res = instance.__dict__[self.name] = self.func(instance)
  File "/opt/venv/lib/python3.7/site-packages/django/db/models/fields/related.py", line 644, in foreign_related_fields
    return tuple(rhs_field for lhs_field, rhs_field in self.related_fields if rhs_field)
  File "/opt/venv/lib/python3.7/site-packages/django/utils/functional.py", line 48, in __get__
    res = instance.__dict__[self.name] = self.func(instance)
  File "/opt/venv/lib/python3.7/site-packages/django/db/models/fields/related.py", line 632, in related_fields
    return self.resolve_related_fields()
  File "/opt/venv/lib/python3.7/site-packages/django/db/models/fields/related.py", line 936, in resolve_related_fields
    related_fields = super().resolve_related_fields()
  File "/opt/venv/lib/python3.7/site-packages/django/db/models/fields/related.py", line 615, in resolve_related_fields
    raise ValueError('Related model %r cannot be resolved' % self.remote_field.model)
ValueError: Related model 'seqr.individual' cannot be resolved

Do you have any further advice?

Thanks in advance!

Chris

hanars · 2022-10-06T15:18:25Z

hanars
Oct 6, 2022
Maintainer

Per my previous comment:

Also, how old exactly is the version of the manual instance you are running? If it is pre 2019 and has all the old xbrowse models you will need to locally transfer to the updated schema before you can switch to docker compose

If this is the case you need to migrate your current, non-docker seqr to use the new schema first, and then dump that migrated db and prceed with the steps to transfer to the docker compose seqr. Instructions can be found here, and you will need to check out the secific commit that they are found at (3f85f1f) : https://github.com/broadinstitute/seqr/blob/3f85f1f226e374c4dff50f3f642991ef7aaa6065/deploy/MIGRATE.md

0 replies

AunErki · 2024-03-08T09:33:15Z

AunErki
Mar 8, 2024

Hi,
I got "the input device is not a TTY" while running step 3.
However i ran "docker compose" not "docker-compose".
Do you know what causes it and how to fix this @hanars

Regards,
Erki

2 replies

hanars Mar 11, 2024
Maintainer

Hi Erki, this appears to be a totally unrelated issue to this original discussion. Please submit a new discussion post containing all the relevant information - when you originally set up seqr and how, what changes you are trying to make, what steps you were following to make those changes, etc. Also please include all relevant log files. Also, this should go without saying but all commands need to be run exactly as they are provided, so if you are running into errors when modifying commands the first thing you should try is running the commands as provided without modification

AunErki Mar 13, 2024

Hi Hana. This is still related to executing the suggested steps for migrating the seqr data, specifically the step 3. The original python project "docker-compose" is deprecated and new plug-in for docker is "docker compose". The "docker compose exec" just needed -T/--no-TTY flag in addition to run step 3 which has the file input and then it ran as good as it should :)

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