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Submitting genotyping analysis to Galaxy fails

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Submitting genotyping analysis to Galaxy fails eva pujadas  2015-03-24 08:25
Status: Closed
 
We are running LabKey 14.2 and wanted to test the LabKey-Galaxy integration.

After setting up the Genotyping Dashboard and loading the sample data as documented in:
https://www.labkey.org/wiki/home/Documentation/page.view?name=genotypingSetup
we tried to submit a workflow to Galaxy in the way described in your documentation:
https://www.labkey.org/wiki/home/Documentation/page.view?name=genotut

That produced the following error:

24 Mar 2015 16:08:38,961 ERROR: Submitting genotyping analysis failed
org.json.JSONException: A JSONArray text must start with '[' at character 1 of {
    "id": "ebfb8f50c6abde6d",
    "name": "genotypingSampleData_6",
    "url": "/galaxy/api/libraries/ebfb8f50c6abde6d"
}

Any ideas why that could happen?

Thanks for your help,
Eva Pujadas
 
 
jeckels responded:  2015-03-24 10:26
Hi Eva,

What version of Galaxy are you running? It's possible that they've changed their API responses.

Thanks,
Josh
 
eva pujadas responded:  2015-03-26 04:34
Hi Josh,

Thank you very much for your answer.

In order to avoid that the Galaxy instance version is too old, I tried to submit the analysis to the public Galaxy instance https://usegalaxy.org/ which is in version 15.03.1, currently the last release.

The error message is very similar:

26 Mar 2015 12:21:06,800 ERROR: Submitting genotyping analysis failed
org.json.JSONException: A JSONArray text must start with '[' at character 1 of {"can_user_add": false, "description": "MHC analysis 1 for run 1", "deleted": false, "can_user_manage": false, "can_user_modify": false, "public": true, "synopsis": "An MHC genotyping analysis", "root_folder_id": "Fd3823c748ae2205d", "model_class": "Library", "id": "5d49318e008bb870", "name": "genotypingSampleData_1"}

Do you think that the cause has to do with Galaxy API having changed their response definitions?

All the best,
Eva
 
Jon (LabKey DevOps) responded:  2015-03-30 14:49
Hi Eva,

This may be the case. I have setup a developer ticket in the meantime. Are you exclusively using the 14.2 version of LabKey? We just recently released 15.1 a few weeks ago. If we manage to get a fix put in place for the problem, this will appear in our 15.2 release at the earliest.

Regards,

Jon
 
Jon (LabKey DevOps) responded:  2015-03-30 14:52
Developer ticket created: https://www.labkey.org/issues/home/Developer/issues/details.view?issueId=22975
 
eva pujadas responded:  2015-04-07 07:00
Hi Jon,

Thanks for your support.
We'll wait with updating of our LabKey instance until release 15.2 is out.

Best,
Eva
 
Jon (LabKey DevOps) responded:  2022-10-31 14:01
Update: https://www.labkey.org/home/Developer/issues/issues-details.view?issueId=22975 has been closed due to no longer supporting Galaxy Integration.