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Question: Galaxy API: Re-running job causes error
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gravatar for ivar.grytten
3.4 years ago by
ivar.grytten • 50
Norway
ivar.grytten • 50 wrote:

Hello,

I am using the galaxy API to rerun a tool doing a POST to /api/tools with action set to "rerun", target_dataset_id set to an api_id of a previous job and inputs set to empty (so that previous inputs will be used).

My debugging shows that the galaxy server correctly starts to rerun the tool. However, it fails on line 476 in the tool api (see https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/api/tools.py#L476) with python reporting that tool.trackster_conf is None. If i remove this section in the code of my local instance, the job re-runs correctly.

So my questions are:

Is this an error in the galaxy API, crashing if tool.trackster_conf is None?
What is tool.trackster_conf anyway? It seems from code elsewhere in galaxy that it often is set to None.

Appreciate any help!


 
api galaxy • 861 views
ADD COMMENT • link •
modified 3.4 years ago by Dannon Baker ♦ 3.7k • written 3.4 years ago by ivar.grytten • 50
2
gravatar for Dannon Baker
3.4 years ago by
Dannon Baker ♦ 3.7k
United States
Dannon Baker ♦ 3.7k wrote:

Hi Ivar,

I'm looking into this, but the code is very old and hasn't changed in a long time so I'm a little bit surprised we haven't seen this before.  I *think* this particular method of rerun is only used by trackster and that the other endpoints support what you want to do more correctly.  That said, this functionality should *probably* be unified.  I'll dig at this and post an update here when I know more, but hopefully this gives you some background.

-Dannon

 

Edit:  I can confirm that this functionality wasn't intended to be used outside Trackster and that as the API has grown the intended way to do this would be two requests:   1) get the details (the tool dict with params) for the particular job you want to rerun, 2) send a second request with these parameters (modified to point to a new dataset, slightly different parameters, etc) to execute the job.
ADD COMMENT • link modified 3.4 years ago • written 3.4 years ago by Dannon Baker ♦ 3.7k

I see! Thank you!

ADD REPLY • link written 3.4 years ago by ivar.grytten • 50
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