Remove entry from Tool Data Table using via Data Manager

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Remove entry from Tool Data Table using via Data Manager

Dan Fornika
Hello,

I'm working on galaxy integration for an MLST tool called MentaLiST:


I've created data managers that create kmer databases and store their locations in a Tool Data Table. I'd like to allow users to remove entries from the Tool Data Table. Has anyone seen a Data Manager that provides that functionality? Should I create separate data managers for add and remove functionality, or can it be integrated into one?

Thanks,

Dan

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Re: Remove entry from Tool Data Table using via Data Manager

Dan Fornika
Here is the documentation for Data Managers:


I don't see any reference to removing entries from a Tool Data Table. Is there a technical reason why it can't be done?

As I understand it, each Tool Data Table must have one column called 'value' that acts as a unique ID for that row of the table. So the data manager would just need the name of the Tool Data Table and a string to look up in the 'value' table, and it would remove that row if it found a match.

In my case, another column in the Tool Data Table stores the path to a kmer database that should be removed from the disk.

Will this be possible with the currently-available xml & json syntax? Are there any postgresql database entries that should be cleaned up if a Tool Data Table entry is removed? Is there some reason why this is a bad idea or is there another way of accomplishing this (removing Tool Data Table entries) that I've missed?

Thanks

Dan



On Tue, Mar 27, 2018 at 2:09 PM, Dan Fornika <[hidden email]> wrote:
Hello,

I'm working on galaxy integration for an MLST tool called MentaLiST:


I've created data managers that create kmer databases and store their locations in a Tool Data Table. I'd like to allow users to remove entries from the Tool Data Table. Has anyone seen a Data Manager that provides that functionality? Should I create separate data managers for add and remove functionality, or can it be integrated into one?

Thanks,

Dan


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Re: Remove entry from Tool Data Table using via Data Manager

Björn Grüning-3
In reply to this post by Dan Fornika
Hi Dan,

as far as I know data-tables are admin only and users can not interact
with them. You can think about it like a frozen set of reference data,
that should not be touched for reproducibility reasons.

Can I ask for the use-case?

Cheers,
Bjoern

Am 27.03.2018 um 23:09 schrieb Dan Fornika:

> Hello,
>
> I'm working on galaxy integration for an MLST tool called MentaLiST:
>
> https://github.com/WGS-TB/MentaLiST/tree/master/galaxy
>
> I've created data managers that create kmer databases and store their
> locations in a Tool Data Table. I'd like to allow users to remove
> entries from the Tool Data Table. Has anyone seen a Data Manager that
> provides that functionality? Should I create separate data managers for
> add and remove functionality, or can it be integrated into one?
>
> Thanks,
>
> Dan
>
>
> ___________________________________________________________
> 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/
>
> To search Galaxy mailing lists use the unified search at:
>    http://galaxyproject.org/search/
>
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Re: Remove entry from Tool Data Table using via Data Manager

Dan Fornika
Sorry, I should have been more clear. I'd like to create a Data Manager tool that an Admin can use to remove items from a Tool Data Table.

I agree that reproducibility is an important concern and the Admin should keep that in mind when managing the data tables.

In our case, MentaLiST is designed to pull MLST schemes from public data sources (pubmlst.org, cgmlst.orgenterobase.warwick.ac.uk), and build kmer databases. Those public datasets are updated periodically, so an Admin may decide to build new versions of the databases at various timepoints. We do stamp the data table entries with the creation date, so each new database gets a new entry in the tool data table. 

At some point an Admin may want to remove older versions of a database. They might find that there is some sort of error or corruption in one of the existing databases. They might want to free up a bit of storage, or just make the user interface a bit cleaner by removing old entries.

I noticed that the galaxy API provides a method to do this and it's also included in bioblend, so I'm curious to know if there's a way to call that method from a Data Manager tool.


Dan


On Sun, Apr 22, 2018 at 3:16 AM, Björn Grüning <[hidden email]> wrote:
Hi Dan,

as far as I know data-tables are admin only and users can not interact with them. You can think about it like a frozen set of reference data, that should not be touched for reproducibility reasons.

Can I ask for the use-case?

Cheers,
Bjoern


Am 27.03.2018 um 23:09 schrieb Dan Fornika:
Hello,

I'm working on galaxy integration for an MLST tool called MentaLiST:

https://github.com/WGS-TB/MentaLiST/tree/master/galaxy

I've created data managers that create kmer databases and store their locations in a Tool Data Table. I'd like to allow users to remove entries from the Tool Data Table. Has anyone seen a Data Manager that provides that functionality? Should I create separate data managers for add and remove functionality, or can it be integrated into one?

Thanks,

Dan


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