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bird-house / flyingpigeon

WPS processes for climate model data, indices and extreme events
http://flyingpigeon.readthedocs.io/en/latest/
Apache License 2.0
19 stars 15 forks source link

conda env: add psycopg2 and remove birdhouse channel #297

Closed tlvu closed 4 years ago

tlvu commented 4 years ago

"psycopg2" is to fix the following error:

2019-10-24 19:10:04,943] [ERROR] line=45 module=exceptions Exception: code: 500, description: No applicable error code, please check error log., locator:
Traceback (most recent call last):
  File "/opt/conda/envs/wps/lib/python3.7/site-packages/pywps/app/Service.py", line 314, in call
    log_request(request_uuid, wps_request)
  File "/opt/conda/envs/wps/lib/python3.7/site-packages/pywps/dblog.py", line 71, in log_request
    session = get_session()
  File "/opt/conda/envs/wps/lib/python3.7/site-packages/pywps/dblog.py", line 175, in get_session
    engine = sqlalchemy.create_engine(database, echo=echo, poolclass=NullPool)
  File "/opt/conda/envs/wps/lib/python3.7/site-packages/sqlalchemy/engine/__init__.py", line 479, in create_engine
    return strategy.create(*args, **kwargs)
  File "/opt/conda/envs/wps/lib/python3.7/site-packages/sqlalchemy/engine/strategies.py", line 87, in create
    dbapi = dialect_cls.dbapi(**dbapi_args)
  File "/opt/conda/envs/wps/lib/python3.7/site-packages/sqlalchemy/dialects/postgresql/psycopg2.py", line 737, in dbapi
    import psycopg2
ModuleNotFoundError: No module named 'psycopg2'

When the following config is used when running the docker image:

[logging]
level = INFO
database=postgresql://user:pass@postgres/flyingpigeon

"psycopg2" technically is only needed for production deployment so potentially be added via individual conda install inside Dockerfile instead. I choose to add it to environment.yml so that during dev/testing, we can also replicate "production environment".

It's always a best practice that dev/test environment mirror as much as possible the production environment to smoke out all the relevant bugs.

"birdhouse" channel is removed because supposedly none of the packages need to come from birdhouse anymore.

Leaving birdhouse channel in place might inadvertently use older releases from birdhouse and overshadow the good one.

Additional Information

No more ModuleNotFoundError error in logs but unable to use existing notebook to test since FP is also affected by this bug: https://github.com/geopython/pywps/pull/499

tlvu commented 4 years ago

Don't think the Travis-CI error has to do with my changes. It could not install conda !

$ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh

$ bash miniconda.sh -b -p $HOME/miniconda

PREFIX=/home/travis/miniconda

Unpacking payload ...

  0%|                                                    | 0/35 [00:00<?, ?it/s]

No output has been received in the last 10m0s, this potentially indicates a stalled build or something wrong with the build itself.

Check the details on how to adjust your build configuration on: https://docs.travis-ci.com/user/common-build-problems/#build-times-out-because-no-output-was-received

The build has been terminated
cehbrecht commented 4 years ago

@tlvu merged. Thanks.