Database migrations fail to apply automatically

[hackdna]

• Specific code commit: 775728
• Version of the web browser and OS: N/A
• Environment where the error occurred: any

Steps to reproduce

(refinery-platform)vagrant@refinery:/vagrant/refinery$ ./manage.py migrate --noinput

Observed behavior

Operations to perform:
  Synchronize unmigrated apps: djangular, visualization_manager, chunked_upload, rest_framework_swagger, flatblocks, django_markwhat, registration, django_extensions, workflow_manager, rest_framework, haystack
  Apply all migrations: core, annotation_server, sessions, admin, data_set_manager, djcelery, sites, auth, tastypie, galaxy_connector, contenttypes, file_server, tool_manager, file_store, guardian, httpproxy, analysis_manager
Synchronizing apps without migrations:
  Creating tables...
  Installing custom SQL...
  Installing indexes...
Running migrations:
  No migrations to apply.
  Your models have changes that are not yet reflected in a migration, and so won't be applied.
  Run 'manage.py makemigrations' to make new migrations, and then re-run 'manage.py migrate' to apply them.

Expected behavior

Migrations should apply automatically.

Notes

Additional information displayed when running the migrate command without the --noinput:

The following content types are stale and need to be deleted:

    core | workflowfilesdl

Any objects related to these content types by a foreign key will also
be deleted. Are you sure you want to delete these content types?
If you're unsure, answer 'no'.

    Type 'yes' to continue, or 'no' to cancel:

[scottx611x]

@hackdna I'm fairly sure the migration applies. You can check with /manage.py migrate --list | grep 0013_auto_20171117_1058

We'll always have stale content types if we're suppressing user input. I'm not sure if newer Django versions have taken care of this.

As for:

Your models have changes that are not yet reflected in a migration, and so won't be applied.
  Run 'manage.py makemigrations' to make new migrations, and then re-run 'manage.py migrate' to apply them.

That seems unrelated to this with the migrations created all being related to UUIDFields

(refinery-platform)vagrant@refinery:/vagrant/refinery$ ./manage.py makemigrations
Migrations for 'core':
  0014_auto_20171208_1634.py:
    - Alter field analysis_uuid on analysisresult
    - Alter field file_store_uuid on analysisresult
    - Alter field data_uuid on workflowdatainputmap
Migrations for 'analysis_manager':
  0004_auto_20171208_1634.py:
    - Alter field galaxy_export_task_group_id on analysisstatus
    - Alter field galaxy_import_task_group_id on analysisstatus
    - Alter field galaxy_workflow_task_group_id on analysisstatus
    - Alter field refinery_import_task_group_id on analysisstatus
Migrations for 'file_store':
  0006_auto_20171208_1634.py:
    - Alter field import_task_id on filestoreitem
Migrations for 'data_set_manager':
  0004_auto_20171208_1634.py:
    - Alter field node_analysis_uuid on annotatednode
    - Alter field isarchive_file on investigation
    - Alter field pre_isarchive_file on investigation
    - Alter field analysis_uuid on node
    - Alter field file_uuid on node

Probably related to 811e1d7

[hackdna]

It looks like it is possible to remove stale content types in a migration using update_contenttypes management command. So, it should be added to core/migrations/0013_auto_20171117_1058.py.

[scottx611x]

@hackdna To me it looks like we couldn't utilize that code without manual intervention.

ok_to_delete can't be == 'yes' here without a users input.

[hackdna]

OK, in that case, a note about running migrations interactively should be added to the release changelog.
Here is the result of running migrations on a test instance running 21682e2 with the latest data snapshots:

(refinery-platform)ubuntu@ip-172-31-49-47:/srv/refinery-platform/refinery$ ./manage.py migrate
Operations to perform:
  Synchronize unmigrated apps: djangular, visualization_manager, chunked_upload, rest_framework_swagger, flatblocks, django_markwhat, registration, workflow_manager, rest_framework, haystack
  Apply all migrations: core, annotation_server, sessions, admin, data_set_manager, djcelery, sites, auth, tastypie, galaxy_connector, contenttypes, file_server, tool_manager, file_store, guardian, httpproxy, analysis_manager
Synchronizing apps without migrations:
  Creating tables...
  Installing custom SQL...
  Installing indexes...
Running migrations:
  No migrations to apply.
The following content types are stale and need to be deleted:

    core | workflowfilesdl
    core | nodeset
    core | nodegroup
    core | noderelationship
    core | nodepair

Any objects related to these content types by a foreign key will also
be deleted. Are you sure you want to delete these content types?
If you're unsure, answer 'no'.

    Type 'yes' to continue, or 'no' to cancel: yes
The following content types are stale and need to be deleted:

    tool_manager | outputfile

Any objects related to these content types by a foreign key will also
be deleted. Are you sure you want to delete these content types?
If you're unsure, answer 'no'.

    Type 'yes' to continue, or 'no' to cancel: yes

So, this note should have been added to several previous releases where models where deleted.

[scottx611x]

@hackdna Okay I can go ahead and add notes to past releases that have included the deletion of these models, and close this after I'm done.

[scottx611x]

I've update Releases v1.6.1 & v1.5.7 accordingly