broadinstitute/widdler

A command-line tool for executing, managing, and querying WDL workflows on Cromwell servers.

widdler's Issues

Package up widdler so it can be imported.

This will likely require some refactoring some code since widdler wasn't originally written with packaging in mind.

Widdler Monitor Polling Mode

This functionality exists in Widdler, but is not functioning properly, so it needs to be fixed.

To address the requirement:

-Has function to poll workflow status in a loop until it's terminal

Widdler CaaS Support

To address requirement: works with both standalone Cromwell and CaaS.

Widdler currently doesn't support Cromwell-as-a-Service. As such this will need to be implemented and should also address the requirement:
-Supports submitting workflows, including options file, dependencies zip, labels, CaaS collection name

Widdler Query Review/Update

To address the requirement:
-Supports metadata and status endpoints, supports query endpoint including ability to filter by status

This functionality exists, but we need to make sure it supports the expectations of Mint team.

No log file error

hello,

I have run this wdl successfully with the cromwell run mode.
But I run widdler with some errors:

python2 widdler-1.4.5a/widdler.py run pipeline_udocker.wdl inputs.json -S localhost

Traceback (most recent call last):
File "widdler-1.4.5a/widdler.py", line 35, in
fh = logging.FileHandler(os.path.join(c.log_dir, '{}.widdler.log'.format(str(time.strftime("%m.%d.%Y")))))
File "/path/lib/python2.7/logging/init.py", line 913, in init
StreamHandler.init(self, self._open())
File "/path/lib/python2.7/logging/init.py", line 943, in _open
stream = open(self.baseFilename, self.mode)
IOError: [Errno 2] No such file or directory: '/cil/shed/resources/widdler/logs/07.04.2019.widdler.log'

Best

Widdler Authentication Support

To address the requirement:
-Supports OAuth2 and Basic Auth