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common-workflow-language / workflow-service

Implementation of the GA4GH Workflow Execution Service, a REST service for running workflows
Apache License 2.0
36 stars 21 forks source link

ModuleNotFoundError: No module named 'jsonschema.compat' #119

Open golharam opened 3 years ago

golharam commented 3 years ago

Folllowing the install instructions in README.md, I get this error.

python3 -m venv ga4gh-python-env
source ga4gh-python-env/bin/activate
pip install wes-service
wes-client --info
Traceback (most recent call last):
  File "/Users/golharr/workspace/ga4gh/ga4gh-python-env/bin/wes-client", line 7, in <module>
    from wes_client.wes_client_main import main
  File "/Users/golharr/workspace/ga4gh/ga4gh-python-env/lib/python3.6/site-packages/wes_client/wes_client_main.py", line 11, in <module>
    from wes_client.util import modify_jsonyaml_paths, WESClient
  File "/Users/golharr/workspace/ga4gh/ga4gh-python-env/lib/python3.6/site-packages/wes_client/util.py", line 10, in <module>
    from wes_service.util import visit
  File "/Users/golharr/workspace/ga4gh/ga4gh-python-env/lib/python3.6/site-packages/wes_service/util.py", line 7, in <module>
    import connexion
  File "/Users/golharr/workspace/ga4gh/ga4gh-python-env/lib/python3.6/site-packages/connexion/__init__.py", line 3, in <module>
    from .apis import AbstractAPI  # NOQA
  File "/Users/golharr/workspace/ga4gh/ga4gh-python-env/lib/python3.6/site-packages/connexion/apis/__init__.py", line 1, in <module>
    from .abstract import AbstractAPI  # NOQA
  File "/Users/golharr/workspace/ga4gh/ga4gh-python-env/lib/python3.6/site-packages/connexion/apis/abstract.py", line 11, in <module>
    from swagger_spec_validator.validator20 import validate_spec
  File "/Users/golharr/workspace/ga4gh/ga4gh-python-env/lib/python3.6/site-packages/swagger_spec_validator/__init__.py", line 8, in <module>
    from swagger_spec_validator.util import validate_spec_url
  File "/Users/golharr/workspace/ga4gh/ga4gh-python-env/lib/python3.6/site-packages/swagger_spec_validator/util.py", line 9, in <module>
    from swagger_spec_validator import validator12
  File "/Users/golharr/workspace/ga4gh/ga4gh-python-env/lib/python3.6/site-packages/swagger_spec_validator/validator12.py", line 29, in <module>
    from swagger_spec_validator.ref_validators import default_handlers
  File "/Users/golharr/workspace/ga4gh/ga4gh-python-env/lib/python3.6/site-packages/swagger_spec_validator/ref_validators.py", line 14, in <module>
    from jsonschema.compat import iteritems
ModuleNotFoundError: No module named 'jsonschema.compat'
golharam commented 3 years ago

Per https://stackoverflow.com/questions/69426664/modulenotfounderror-no-module-named-jsonschema-compat, looks like downgrading jsonschema is the solution.

pip install -U 'jsonschema<4.0'

which then leads to another error

ImportError: cannot import name 'FileStorage'
golharam commented 3 years ago

Referencing #85