Hi all,
I noticed something strange in my (latest) galaxy-dist. I have around 10-20 workflows, which are in certain cases very similar for e.g. slightly different experimental setups with the same output. I then usually copy the first wf and adapt a few steps to fit the second one. Anyway, they are on a testserver and I export them to import in my production instance. There I noticed that sometimes in (always the same 3) workflows, the export to json changes the ‘name’ attribute of the workflow. So when importing them in production, the wf has a different name.
I haven’t been able to pinpoint where the problem lies, but the new name is very similar to the old one. I therefore believe that it may be that I have copied the workflow and the name of the source-wf is hanging around in some db table somewhere. Unlikely as it sounds. To be more specific it doesn’t show up when I do bioblend: workflows.show_workflow(id=x), but only when export_workflow_json(). It only happens in 3 of my workflows and I have surely copied more of them.
Easy enough to workaround though, and kind of hoping this is a glitch in my setup only but wanted to let you know.
cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden
Hi Jorrit,
Would you like to share the workflow names? Maybe before and after for the three? I could test in a default local to see if reproducible.
Your question was from a few weeks ago and I am not sure if you are using the master branch of 15_10 or something earlier or the dev branch, so sharing a bit about your setup would probably help (including if this is even still a problem).
Thanks!
Jen
-- Jennifer Hillman-Jackson Galaxy Application Support http://usegalaxy.org http://galaxyproject.org http://biostar.usegalaxy.org
On Sun, Nov 22, 2015 at 12:48 PM, Jorrit Boekel <jorrit.boekel@scilifelab.se
wrote:
Hi all,
I noticed something strange in my (latest) galaxy-dist. I have around 10-20 workflows, which are in certain cases very similar for e.g. slightly different experimental setups with the same output. I then usually copy the first wf and adapt a few steps to fit the second one. Anyway, they are on a testserver and I export them to import in my production instance. There I noticed that sometimes in (always the same 3) workflows, the export to json changes the ‘name’ attribute of the workflow. So when importing them in production, the wf has a different name.
I haven’t been able to pinpoint where the problem lies, but the new name is very similar to the old one. I therefore believe that it may be that I have copied the workflow and the name of the source-wf is hanging around in some db table somewhere. Unlikely as it sounds. To be more specific it doesn’t show up when I do bioblend: workflows.show_workflow(id=x), but only when export_workflow_json(). It only happens in 3 of my workflows and I have surely copied more of them.
Easy enough to workaround though, and kind of hoping this is a glitch in my setup only but wanted to let you know.
cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden
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Jorrit Boekel