"Edit attributes" for interval dataset not consistent with documentation

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"Edit attributes" for interval dataset not consistent with documentation

Peter Briggs
Dear Devs

One of my local users has noticed that the "edit attributes" function for "interval"-type datasets is not consistent with the documentation at:

https://galaxyproject.org/learn/datatypes/#interval

This states that only CHROM, START, and END are required, with the implication that other fields are optional.

However when editing the attributes for a dataset, if either of "Strand" or "Name" are not set to an explicit column number then "Save attributes" fails with the message: "Error occurred while saving. Please fill all the required fields and try again."

This is true on both our local Galaxy running release_17.09 and also on Galaxy main.

Is this a bug in the documentation, or the implementation?

Thanks,

Peter

--
Peter Briggs [hidden email]
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482

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Re: "Edit attributes" for interval dataset not consistent with documentation

Nicola Soranzo-2
Dear Peter,
this bug has been recently reported in https://github.com/galaxyproject/galaxy/issues/4966 and fixed in https://github.com/galaxyproject/galaxy/pull/5027 for the upcoming 18.01 Galaxy release.
Not sure if this is worth a backport, but if you need it for 17.09 and want to try, it should be feasible.

Cheers,
Nicola

------ Messaggio originale------
Da: Peter Briggs
Data: gio 18 gen 2018 12:11
CC:
Oggetto:[galaxy-dev] "Edit attributes" for interval dataset not consistent with documentation

Dear Devs

One of my local users has noticed that the "edit attributes" function for "interval"-type datasets is not consistent with the documentation at:

https://galaxyproject.org/learn/datatypes/#interval

This states that only CHROM, START, and END are required, with the implication that other fields are optional.

However when editing the attributes for a dataset, if either of "Strand" or "Name" are not set to an explicit column number then "Save attributes" fails with the message: "Error occurred while saving. Please fill all the required fields and try again."

This is true on both our local Galaxy running release_17.09 and also on Galaxy main.

Is this a bug in the documentation, or the implementation?

Thanks,

Peter

--
Peter Briggs[hidden email]
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: <a href="tel:(0161) 2751482">(0161) 2751482

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

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  http://galaxyproject.org/search/

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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: "Edit attributes" for interval dataset not consistent with documentation

Peter Briggs
Hello Nicola

Thanks for pointing this out, much appreciated.

I've tried a naive patch of our 17.09 release (i.e. just putting the edits from the PR into the code base) but it didn't seem to make any difference for the specific case of the 'interval' file. I don't know if some other change is required from elsewhere or if I messed up somehow.

Anyway: I think we'll wait for 18.01 to fix it. In the meantime thanks again for your help!

Best wishes

Peter

-- 
Peter Briggs [hidden email]
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482


From: Nicola Soranzo [[hidden email]] on behalf of [hidden email] [[hidden email]]
Sent: Thursday, January 18, 2018 9:58 PM
To: Peter Briggs; [hidden email]
Subject: Re: [galaxy-dev] "Edit attributes" for interval dataset not consistent with documentation

Dear Peter,
this bug has been recently reported in https://github.com/galaxyproject/galaxy/issues/4966 and fixed in https://github.com/galaxyproject/galaxy/pull/5027 for the upcoming 18.01 Galaxy release.
Not sure if this is worth a backport, but if you need it for 17.09 and want to try, it should be feasible.

Cheers,
Nicola

------ Messaggio originale------
Da: Peter Briggs
Data: gio 18 gen 2018 12:11
CC:
Oggetto:[galaxy-dev] "Edit attributes" for interval dataset not consistent with documentation

Dear Devs

One of my local users has noticed that the "edit attributes" function for "interval"-type datasets is not consistent with the documentation at:

https://galaxyproject.org/learn/datatypes/#interval

This states that only CHROM, START, and END are required, with the implication that other fields are optional.

However when editing the attributes for a dataset, if either of "Strand" or "Name" are not set to an explicit column number then "Save attributes" fails with the message: "Error occurred while saving. Please fill all the required fields and try again."

This is true on both our local Galaxy running release_17.09 and also on Galaxy main.

Is this a bug in the documentation, or the implementation?

Thanks,

Peter

--
Peter Briggs[hidden email]
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: <a href="tel:(0161) 2751482" target="_blank">(0161) 2751482

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

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  http://galaxyproject.org/search/

___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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  http://galaxyproject.org/search/