workflow-service
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ModuleNotFoundError: No module named 'jsonschema.compat'
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'
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'
Referencing #85