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qiita-spots / qiita

Qiita - A multi-omics databasing effort
http://qiita.microbio.me
BSD 3-Clause "New" or "Revised" License
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Allow admins to define a workflow via an existing processing. #3369

Open sjanssen2 opened 5 months ago

sjanssen2 commented 5 months ago

Is there a mechanism to insert the latest default workflows into a fresh new qiita DB? Do you provide these information as some file or do they just live in qiita.ucsd.edu database?

https://github.com/qiita-spots/qiita/blob/57d1b146729223da9daa286a1cc75db6f2923746/qiita_db/support_files/patches/81.sql#L30-L32

antgonza commented 5 months ago

Yes, information in the dev help: https://qiita.ucsd.edu/static/doc/html/dev/workflows.html

Note that currently they are added by hand - really carefully - as there is no GUI or easy way to do it - in case you have any ideas on how to make it user friendly and/or are interested in implementing something easier.

sjanssen2 commented 5 months ago

I found the stup about which DB tables to extend in the documentation. My goal was to insert the same values for default workflows as in qiita.ucsd.edu i.e. carry over your expert knowledge on best practice processing. What I am saying is: where do I get the information from, not how do I technically insert it.

Regarding a "user interface", one could adopt the Galaxy way of upgrading/generalizing an individual processing into a workflow by providing an according button to a privileged user like: image We might want to double check before adding that no non-deprecated default-workflow already exists for this kind of input.

To do so, we could provide a deprecation action for privileged users to the workflow overview: image

Thus, the privileged user does not have to manually insert values into the database. However, my use case (inject pre-defined workflows into a fresh new productive database) would not be covered by this approach as one first needs to create studies / processing pipelines to generalized those.

antgonza commented 5 months ago

I see, the issue with "copying" a given workflow between systems is that the database identifiers will not match; for example, command X in system A can have the id of n, while that same command in system B can have m.

Anyway, I really like these ideas of the add/deprecate button for admins. FWIW we haven't spent a lot of time making the admin easier as the impact is only for admins (vs. all users) but will love to have them available.

antgonza commented 2 months ago

Renaming issue based on discussion.