Docker-Compose: `name 'basestring' is not defined` #412

JakobMiksch · 2021-12-21T09:33:04Z

Describe the bug

Starting GHC with docker-compose fails with error name 'basestring' is not defined

To Reproduce

Go to ./docker/compose
run docker-compose -f docker-compose.yml up

Expected Behavior
GHC should run without errors.

Screenshots or Logfiles

ghc_web       | ---> pavement.upgrade                                                                                
ghc_web       | Upgrading database...                                                                                
ghc_web       | cd /GeoHealthCheck/GeoHealthCheck                                                                    
ghc_web       | python manage.py db upgrade                                                                          
ghc_web       | 2021-12-21 09:28:22,156 - init - INFO - created GHC App instance #1                                  
ghc_web       | INFO  [alembic.runtime.migration] Context impl SQLiteImpl.                                           
ghc_web       | INFO  [alembic.runtime.migration] Will assume non-transactional DDL.                                 
ghc_web       | cd /GeoHealthCheck                                                                                   
ghc_web       | Running GHC WSGI on 0.0.0.0:80 with 4 workers and SCRIPT_NAME=                                       
ghc_web       | [2021-12-21 09:28:22 +0000] [1] [INFO] Starting gunicorn 20.1.0                                      
ghc_web       | [2021-12-21 09:28:22 +0000] [1] [INFO] Listening at: http://0.0.0.0:80 (1)                           
ghc_web       | [2021-12-21 09:28:22 +0000] [1] [INFO] Using worker: eventlet                                        
ghc_web       | [2021-12-21 09:28:22 +0000] [16] [INFO] Booting worker with pid: 16                                  
ghc_web       | [2021-12-21 09:28:22 +0000] [16] [ERROR] Exception in worker process                                 
ghc_web       | Traceback (most recent call last):                                                                   
ghc_web       |   File "/venv/lib/python3.7/site-packages/gunicorn/arbiter.py", line 589, in spawn_worker            
ghc_web       |     worker.init_process()                                                                            
ghc_web       |   File "/venv/lib/python3.7/site-packages/gunicorn/workers/geventlet.py", line 133, in init_process  
ghc_web       |     self.patch()                                                                                     
ghc_web       |   File "/venv/lib/python3.7/site-packages/gunicorn/workers/geventlet.py", line 124, in patch         
ghc_web       |     eventlet.monkey_patch()                                                                          
ghc_web       |   File "/venv/lib/python3.7/site-packages/eventlet/patcher.py", line 296, in monkey_patch            
ghc_web       |     from eventlet.support import psycopg2_patcher                                                    
ghc_web       |   File "/venv/lib/python3.7/site-packages/eventlet/support/psycopg2_patcher.py", line 27, in <module>
ghc_web       |     import psycopg2                                                                                  
ghc_web       |   File "/venv/lib/python3.7/site-packages/psycopg2/__init__.py", line 68, in <module>                
ghc_web       |     from psycopg2 import extensions as _ext                                                          
ghc_web       |   File "/venv/lib/python3.7/site-packages/psycopg2/extensions.py", line 211, in <module>             
ghc_web       |     from psycopg2. _range import Range                              # noqa                           
ghc_web       |   File "/venv/lib/python3.7/site-packages/psycopg2/_range.py", line 502, in <module>                 
ghc_web       |     oid=3904, subtype_oid=23, array_oid=3905)                                                        
ghc_web       |   File "/venv/lib/python3.7/site-packages/psycopg2/_range.py", line 283, in __init__                 
ghc_web       |     self._create_ranges(pgrange, pyrange)                                                            
ghc_web       |   File "/venv/lib/python3.7/site-packages/psycopg2/_range.py", line 302, in _create_ranges           
ghc_web       |     if isinstance(pgrange, basestring):                                                              
ghc_web       | NameError: name 'basestring' is not defined                                                          
ghc_web       | [2021-12-21 09:28:22 +0000] [16] [INFO] Worker exiting (pid: 16)                                                                                                                                                              
ghc_web       | [2021-12-21 09:28:22 +0000] [17] [INFO] Booting worker with pid: 17                                                                                                                                                           
ghc_web       | [2021-12-21 09:28:22 +0000] [17] [ERROR] Exception in worker process                                                                                                                                                          
ghc_web       | Traceback (most recent call last):                                                                                                                                                                                            
ghc_web       |   File "/venv/lib/python3.7/site-packages/gunicorn/arbiter.py", line 589, in spawn_worker                                                                                                                                     
ghc_web       |     worker.init_process()                                                                                                                                                                                                     
ghc_web       |   File "/venv/lib/python3.7/site-packages/gunicorn/workers/geventlet.py", line 133, in init_process                                                                                                                           
ghc_web       |     self.patch()                                                                                                                                                                                                              
ghc_web       |   File "/venv/lib/python3.7/site-packages/gunicorn/workers/geventlet.py", line 124, in patch                                                                                                                                  
ghc_web       |     eventlet.monkey_patch()                                                                                                                                                                                                   
ghc_web       |   File "/venv/lib/python3.7/site-packages/eventlet/patcher.py", line 296, in monkey_patch                                                                                                                                     
ghc_web       |     from eventlet.support import psycopg2_patcher                                                                                                                                                                             
ghc_web       |   File "/venv/lib/python3.7/site-packages/eventlet/support/psycopg2_patcher.py", line 27, in <module>                                                                                                                         
ghc_web       |     import psycopg2                                                                                                                                                                                                           
ghc_web       |   File "/venv/lib/python3.7/site-packages/psycopg2/__init__.py", line 68, in <module>                                                                                                                                         
ghc_web       |     from psycopg2 import extensions as _ext
ghc_web       |   File "/venv/lib/python3.7/site-packages/psycopg2/extensions.py", line 211, in <module>
ghc_web       |     from psycopg2. _range import Range                              # noqa
ghc_web       |   File "/venv/lib/python3.7/site-packages/psycopg2/_range.py", line 502, in <module>
ghc_web       |     oid=3904, subtype_oid=23, array_oid=3905)
ghc_web       |   File "/venv/lib/python3.7/site-packages/psycopg2/_range.py", line 283, in __init__
ghc_web       |     self._create_ranges(pgrange, pyrange)
ghc_web       |   File "/venv/lib/python3.7/site-packages/psycopg2/_range.py", line 302, in _create_ranges
ghc_web       |     if isinstance(pgrange, basestring):
ghc_web       | NameError: name 'basestring' is not defined
ghc_web       | [2021-12-21 09:28:22 +0000] [17] [INFO] Worker exiting (pid: 17)
ghc_web       | [2021-12-21 09:28:22 +0000] [1] [WARNING] Worker with pid 17 was terminated due to signal 15
ghc_web       | [2021-12-21 09:28:22 +0000] [1] [INFO] Shutting down: Master
ghc_web       | [2021-12-21 09:28:22 +0000] [1] [INFO] Reason: Worker failed to boot.
ghc_web exited with code 3

Context (please complete the following information):

OS: RaspberryPi OS
docker: 20.10.12
docker-compose: 1.29.2

The text was updated successfully, but these errors were encountered:

justb4 · 2021-12-21T12:30:05Z

Guess this is with the Docker Image built for ARM? NameError: name 'basestring' is not defined, strange, is referred as error when running Python2 code on Python3 or with certain Python 3 versions. I tried running the same command on an empty Docker system with the standard GHC geopython/geohealthcheck:latest without a problem.

Using Alpine for Python has more issues (one is massive slower builds) at least it is harder to get right. Recent versions of Docker Ubuntu and Debian (-slim) images are small as well. You may want to try.
In time we also want to migrate GHC Docker to Ubuntu or Debian.

JakobMiksch · 2021-12-21T14:30:32Z

I had this error on "normal" architecture on my laptop as well, but I could fix it by cleaning up my local Docker setup and re-downloading the GHC Docker image.

But I also have this problem on RaspberryPi with the base image arm32v7/python:3.7.9-alpine
Things I do not understand:

I am running Python3 in the image. It is strange to me getting an Python 3 error 🤔
The error is apparently connected with psycopg - however, I do use SQLite and not Postgres

JakobMiksch · 2021-12-21T17:59:16Z

I changed the context in the description to Raspberry Pi

justb4 · 2021-12-22T15:24:53Z

Ok, I just found it this problem is not unique to Rpi. The latest GHC Docker Image running demo.geohealthcheck.org was just rebuilt (triggered by doc updates) and is now failing with similar error:

START /run-web.sh
Container timezone set to: Europe/London
START /configure.sh
Using DB_TYPE=postgresql
Check if Postgres is avail/ready...
ghc_demo_postgis:5432 - no response
Exit code=2 - Postgres not ready - sleeping
ghc_demo_postgis:5432 - accepting connections
Postgres is up - check if DB populated
 count 
-------
   102
(1 row)

Postgres DB already populated
END /configure.sh
---> pavement.upgrade
Upgrading database...
cd /GeoHealthCheck/GeoHealthCheck
python manage.py db upgrade
2021-12-22 15:27:46,607 - init - INFO - created GHC App instance #1
Traceback (most recent call last):
  File "manage.py", line 53, in <module>
    manager.run()
  File "/venv/lib/python3.7/site-packages/flask_script/__init__.py", line 417, in run
    result = self.handle(argv[0], argv[1:])
  File "/venv/lib/python3.7/site-packages/flask_script/__init__.py", line 386, in handle
    res = handle(*args, **config)
  File "/venv/lib/python3.7/site-packages/flask_script/commands.py", line 216, in __call__
    return self.run(*args, **kwargs)
  File "/venv/lib/python3.7/site-packages/flask_migrate/__init__.py", line 95, in wrapped
    f(*args, **kwargs)
  File "/venv/lib/python3.7/site-packages/flask_migrate/__init__.py", line 280, in upgrade
    command.upgrade(config, revision, sql=sql, tag=tag)
  File "/venv/lib/python3.7/site-packages/alembic/command.py", line 320, in upgrade
    script.run_env()
  File "/venv/lib/python3.7/site-packages/alembic/script/base.py", line 563, in run_env
    util.load_python_file(self.dir, "env.py")
  File "/venv/lib/python3.7/site-packages/alembic/util/pyfiles.py", line 92, in load_python_file
    module = load_module_py(module_id, path)
  File "/venv/lib/python3.7/site-packages/alembic/util/pyfiles.py", line 108, in load_module_py
    spec.loader.exec_module(module)  # type: ignore
  File "<frozen importlib._bootstrap_external>", line 728, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "migrations/env.py", line 87, in <module>
    run_migrations_online()
  File "migrations/env.py", line 70, in run_migrations_online
    poolclass=pool.NullPool)
  File "/venv/lib/python3.7/site-packages/sqlalchemy/engine/__init__.py", line 499, in engine_from_config
    return create_engine(url, **options)
  File "/venv/lib/python3.7/site-packages/sqlalchemy/engine/__init__.py", line 456, in create_engine
    return strategy.create(*args, **kwargs)
  File "/venv/lib/python3.7/site-packages/sqlalchemy/engine/strategies.py", line 87, in create
    dbapi = dialect_cls.dbapi(**dbapi_args)
  File "/venv/lib/python3.7/site-packages/sqlalchemy/dialects/postgresql/psycopg2.py", line 737, in dbapi
    import psycopg2
  File "/venv/lib/python3.7/site-packages/psycopg2/__init__.py", line 68, in <module>
    from psycopg2 import extensions as _ext
  File "/venv/lib/python3.7/site-packages/psycopg2/extensions.py", line 211, in <module>
    from psycopg2. _range import Range                              # noqa
  File "/venv/lib/python3.7/site-packages/psycopg2/_range.py", line 502, in <module>
    oid=3904, subtype_oid=23, array_oid=3905)
  File "/venv/lib/python3.7/site-packages/psycopg2/_range.py", line 283, in __init__
    self._create_ranges(pgrange, pyrange)
  File "/venv/lib/python3.7/site-packages/psycopg2/_range.py", line 302, in _create_ranges
    if isinstance(pgrange, basestring):
NameError: name 'basestring' is not defined

justb4 · 2021-12-22T15:26:02Z

The failing build is not due to the changes, there is a problem in a unit test involving ArcGIS server...

justb4 · 2021-12-22T15:27:11Z

So the fix, upgrading to psycopg2 2.9.2 works! @JakobMiksch : this may also now work for Docker on Raspberry Pi.

JakobMiksch added the bug label Dec 21, 2021

justb4 self-assigned this Dec 22, 2021

justb4 added this to the Version 0.9.0 milestone Dec 22, 2021

justb4 added a commit that referenced this issue Dec 22, 2021

#412 upgrade psycopg2 to 2.9.2 to fix basestring not defined error

378a692

justb4 closed this as completed Dec 22, 2021

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Docker-Compose: `name 'basestring' is not defined` #412

Docker-Compose: `name 'basestring' is not defined` #412

JakobMiksch commented Dec 21, 2021 •

edited

justb4 commented Dec 21, 2021

JakobMiksch commented Dec 21, 2021

JakobMiksch commented Dec 21, 2021

justb4 commented Dec 22, 2021

justb4 commented Dec 22, 2021

justb4 commented Dec 22, 2021

Docker-Compose: name 'basestring' is not defined #412

Docker-Compose: name 'basestring' is not defined #412

Comments

JakobMiksch commented Dec 21, 2021 • edited

justb4 commented Dec 21, 2021

JakobMiksch commented Dec 21, 2021

JakobMiksch commented Dec 21, 2021

justb4 commented Dec 22, 2021

justb4 commented Dec 22, 2021

justb4 commented Dec 22, 2021

Docker-Compose: `name 'basestring' is not defined` #412

Docker-Compose: `name 'basestring' is not defined` #412

JakobMiksch commented Dec 21, 2021 •

edited