cwl-WES

cwl-WES copied to clipboard

Upgrade python image to v3.8 as v3.7 is broken and un supported since…

1

… 5 months ago **IMPORTANT: Please create an issue before filing a pull request! Changes need to be discussed before proceeding. Please read the [contribution guidelines](CONTRIBUTING.md).** **Details** Please provide enough...

lvarin

WIP Upgrade requirements to fix the netloc bug

2

**Details** Closes #246 ```py >>> from six.moves import urllib >>> p=urllib.parse.urlparse('ftp://user:[email protected]/hola') >>> p.username 'user' >>> p.hostname 'server.csc.fi' >>> p.netloc 'user:[email protected]' ``` Upgrading `cwl-tes` and fixing build

lvarin

Remove support for task monitor in cwl-WES

1

Currently, the executed task runs are monitored using the evening send and receive methods provided by Celery. This implementation needs to be changed as it might pose a possible vulnerability...

kushagra189

WIP Instruct Helm to load the configuration from disk

1

Helm will now load the `app-config.yaml` file form disk. This cleans also up the previous method to load the configuration. In order to modify the configuration, one has to edit...

lvarin

**Describe the bug** Funnel (https://ohsu-comp-bio.github.io/funnel/docs/storage/ftp/) requires (for the moment) to add the username and password to any FTP URL sent in a task. If you do so, cwl-WES fails as...

lvarin

**Describe the bug** Unable to launch the latest version from GitHub w/ ImportError: cannot import name 'escape' from 'jinja2' **To Reproduce** Steps to reproduce the behavior: 1. mkdir -p data/cwl_wes/db...

superbsky

build: add securityContext and fix rabbitMQ cookie

2

**Details** For details see issue #232 **Note** PR includes old commits from my repo. However, they are not relevant anymore and I removed the changes as they were not good....

viktoriaas

Issue introduces 2 problems together with a PR solving them. 1. Clusters with security policy enabled often forbid the usage of root. Therefore it is necessary to add optional `securityContext`...

viktoriaas

Environment vairables `WES_CONFIG` and `WES_CONFIG_LOG` are passed through and mounted inside the app and worker containers.

uniqueg

Run the CWL 1.0 and 1.1 conformance tests against a cwl-WES endpoint during CI

1

**Is your feature request related to a problem? Please describe.** Users need to know that they will have no problems running the CWL workflow against a `cwl-WES` endpoint. **Describe the...

mr-c