workflow-service

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Bumps [toil[cwl]](https://github.com/DataBiosphere/toil) from 5.6.0 to 5.9.2. Release notes Sourced from toil[cwl]'s releases. 5.9.2 Changelog Bug Fixes Change build tag import (#4329) Thank you to our contributors: @​adamnovak , @​Hexotical !...

dependabot[bot]

Keeping your Docker base image up-to-date means you’ll benefit from security fixes in the latest version of your chosen image. #### Changes included in this PR - Dockerfile We recommend...

snyk-bot

jyotsnapagid

``` $ ./wes-docker.sh + python setup.py sdist running sdist running egg_info creating wes_service.egg-info writing wes_service.egg-info/PKG-INFO writing dependency_links to wes_service.egg-info/dependency_links.txt writing entry points to wes_service.egg-info/entry_points.txt writing requirements to wes_service.egg-info/requires.txt writing top-level...

golharam

ModuleNotFoundError: No module named 'jsonschema.compat'

2

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...

golharam

ImportError: cannot import name 'FileStorage'

7

Following the docs shown on https://pypi.org/project/wes-service/, I just installed via 'pip install wes-service' into a python 3.6 virtual env. When I run 'wes-server' I get the error: ``` $ wes-server...

golharam

WESClient.cancel doesn't seem to do much

1

When I call `WESClient.cancel` on the client I see a `DELETE` call in the server logs but the workflow remains untouched.

gijzelaerr

Incorrect exit code / status for CWL run with Toil backend

1

When running the `md5sum.cwl` workflow using Toil, the job seems to hang indefinitely in "RUNNING" state. Looking at the run log, the workflow appears to have completed successfully, but the...

jaeddy

So that a username/password combination can be provided by environment variables to the service. All endpoints (except service info?) should be under auth. Close with tests that demonstrate the server...

david4096

## Update virtualenv set up and requirements process. `virtualenv venv && source venv/bin/activate && pip install toil==3.16.0 && pip install . --process-dependency-links && pip install -r dev-requirements.txt`

achave11-ucsc