Hi all,
I am trying to build a REST API around an existing command line tool I had which is connected to a postgres db using rdkit cartridge. I am trying to use django for building the server around the app and using the existing DB.
After setting up the project, the app etc. and configuring settings.py to use the existing db, I run an inspectdb with good results. I copied the output to models.py file with the suggested models. I replaced the generic types suggested by django by the models provided in django-rdkit (I have some Mol and BFP columns). When I finally call the manage.py migrate
, I get the following error:
what am I doing wrong?? I'd really appreaciate your help!
`Running migrations:
Applying chemspace_server.0001_initial... OK
Applying django_rdkit.0001_setup...Traceback (most recent call last):
File "/home/dalvarez/miniconda3/envs/chemspace/lib/python3.7/site-packages/django/db/backends/utils.py", line 82, in _execute
return self.cursor.execute(sql)
psycopg2.errors.UndefinedObject: type "mol" does not exist
LINE 1: SELECT mol_to_smiles('C'::mol)
^
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "manage.py", line 22, in
main()
File "manage.py", line 18, in main
execute_from_command_line(sys.argv)
File "/home/dalvarez/miniconda3/envs/chemspace/lib/python3.7/site-packages/django/core/management/init.py", line 401, in execute_from_command_line
utility.execute()
File "/home/dalvarez/miniconda3/envs/chemspace/lib/python3.7/site-packages/django/core/management/init.py", line 395, in execute
self.fetch_command(subcommand).run_from_argv(self.argv)
File "/home/dalvarez/miniconda3/envs/chemspace/lib/python3.7/site-packages/django/core/management/base.py", line 330, in run_from_argv
self.execute(*args, **cmd_options)
File "/home/dalvarez/miniconda3/envs/chemspace/lib/python3.7/site-packages/django/core/management/base.py", line 371, in execute
output = self.handle(*args, **options)
File "/home/dalvarez/miniconda3/envs/chemspace/lib/python3.7/site-packages/django/core/management/base.py", line 85, in wrapped
res = handle_func(*args, **kwargs)
File "/home/dalvarez/miniconda3/envs/chemspace/lib/python3.7/site-packages/django/core/management/commands/migrate.py", line 245, in handle
fake_initial=fake_initial,
File "/home/dalvarez/miniconda3/envs/chemspace/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 "/home/dalvarez/miniconda3/envs/chemspace/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 "/home/dalvarez/miniconda3/envs/chemspace/lib/python3.7/site-packages/django/db/migrations/executor.py", line 227, in apply_migration
state = migration.apply(state, schema_editor)
File "/home/dalvarez/miniconda3/envs/chemspace/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 "/home/dalvarez/miniconda3/envs/chemspace/lib/python3.7/site-packages/django_rdkit/operations.py", line 16, in database_forwards
c.execute("SELECT mol_to_smiles('C'::mol)")
File "/home/dalvarez/miniconda3/envs/chemspace/lib/python3.7/site-packages/django/db/backends/utils.py", line 98, in execute
return super().execute(sql, params)
File "/home/dalvarez/miniconda3/envs/chemspace/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 "/home/dalvarez/miniconda3/envs/chemspace/lib/python3.7/site-packages/django/db/backends/utils.py", line 75, in _execute_with_wrappers
return executor(sql, params, many, context)
File "/home/dalvarez/miniconda3/envs/chemspace/lib/python3.7/site-packages/django/db/backends/utils.py", line 84, in _execute
return self.cursor.execute(sql, params)
File "/home/dalvarez/miniconda3/envs/chemspace/lib/python3.7/site-packages/django/db/utils.py", line 90, in exit
raise dj_exc_value.with_traceback(traceback) from exc_value
File "/home/dalvarez/miniconda3/envs/chemspace/lib/python3.7/site-packages/django/db/backends/utils.py", line 82, in _execute
return self.cursor.execute(sql)
django.db.utils.ProgrammingError: type "mol" does not exist
LINE 1: SELECT mol_to_smiles('C'::mol)`