Re: Displaying tool select list according to user

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Re: Displaying tool select list according to user

Peter Cock
Hi Laure,

I don't think there is any easy to use mechanism for this in Galaxy.
Unfortunately Galaxy loads all the *.loc files at startup and treats
them as global values available to all users equally.

I can't find the email thread, but I recall someone previously trying
to do something with a single large example.loc file for all users
but with an extra column for filtering by account name. I forget if
they got these changes to work or not.

Assuming you only have a few separate versions of the example.loc
file, you could create copies of the BLAST wrapper XML file which
use the specific *.loc file - and then restrict the tool by user?

In either case at a minimum you would have to maintain local
changes to the BLAST wrappers (and potentially changes to
Galaxy itself), which is not a good situation.

Peter

On Tue, Sep 12, 2017 at 1:41 PM, Laure QUINTRIC <[hidden email]> wrote:
Hello Galaxy users,

I try to figure out how I can display a select list into a galaxy tool according to the connected user.

I have several .loc files containing the paths for custom blast databases I have created for several users (user1.loc, user2.loc, and so on). I would like the blast tool to display the specific databases for the connected user (user1 or user2).

Any idea on how to proceed ?
Regards,
Laure


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Re: Displaying tool select list according to user

Yvan Le Bras-2
Hi Laure,

Maybe you can use the toolbox filtering https://galaxyproject.org/user-defined-toolbox-filters/ option to do that ? For example defining group of users and filtering toolbox regarding the user group...


Cheers,

Yvan

De: "Laure Quintric" <[hidden email]>
À: "Peter Cock" <[hidden email]>
Cc: "Galaxy-dev" <[hidden email]>
Envoyé: Mardi 12 Septembre 2017 15:16:56
Objet: Re: [galaxy-dev] Displaying tool select list according to user

Hi Peter,

Thank you for your answer. Maybe I should try your option below :

Le 12/09/2017 à 14:56, Peter Cock a écrit :

 I can't find the email thread, but I recall someone previously trying
 to do something with a single large example.loc file for all users
 but with an extra column for filtering by account name. I forget if
 they got these changes to work or not.

But in this case, did you remember how to write the filter to match the
extra column with the username to the connected account name ? as he
$__user_id__ variable could not be user between <filter> tags ?

Laure

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Re: Displaying tool select list according to user

FredBGA
In reply to this post by Peter Cock

Hi Laure,

 

There are others users (including me! ) that need this kind of function :

http://dev.list.galaxyproject.org/Blast-db-permission-td4670440.html

 

@Galaxy team:

Do we need to add an issue in GitHub ?

Do you think that it could be enabled one day ?

 

I think this something that could be nice to develop !

I would be glad to help.

 

Thank a lot

 

Fred

 

De : galaxy-dev [mailto:[hidden email]] De la part de Peter Cock
Envoyé : mardi 12 septembre 2017 14:56
À : Laure QUINTRIC <[hidden email]>
Cc : Galaxy-dev <[hidden email]>
Objet : Re: [galaxy-dev] Displaying tool select list according to user

 

Hi Laure,

 

I don't think there is any easy to use mechanism for this in Galaxy.

Unfortunately Galaxy loads all the *.loc files at startup and treats

them as global values available to all users equally.

 

I can't find the email thread, but I recall someone previously trying

to do something with a single large example.loc file for all users

but with an extra column for filtering by account name. I forget if

they got these changes to work or not.

 

Assuming you only have a few separate versions of the example.loc

file, you could create copies of the BLAST wrapper XML file which

use the specific *.loc file - and then restrict the tool by user?

 

In either case at a minimum you would have to maintain local

changes to the BLAST wrappers (and potentially changes to

Galaxy itself), which is not a good situation.

 

Peter

 

On Tue, Sep 12, 2017 at 1:41 PM, Laure QUINTRIC <[hidden email]> wrote:

Hello Galaxy users,

I try to figure out how I can display a select list into a galaxy tool according to the connected user.

I have several .loc files containing the paths for custom blast databases I have created for several users (user1.loc, user2.loc, and so on). I would like the blast tool to display the specific databases for the connected user (user1 or user2).

Any idea on how to proceed ?
Regards,
Laure


___________________________________________________________
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/

 


___________________________________________________________
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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Re: Displaying tool select list according to user

Peter Cock
Thanks Fred,

That's the previous discussion I was trying to find -
sadly no clear solution but some ideas to explore.

It does seem filtering example.loc by user or role
is not a niche request. I wonder if this could be
linked to the Galaxy data library permissions
structure as a way to manage the access rights?

Peter

On Tue, Sep 12, 2017 at 4:20 PM, SAPET, Frederic <[hidden email]> wrote:

Hi Laure,

 

There are others users (including me! ) that need this kind of function :

http://dev.list.galaxyproject.org/Blast-db-permission-td4670440.html

 

@Galaxy team:

Do we need to add an issue in GitHub ?

Do you think that it could be enabled one day ?

 

I think this something that could be nice to develop !

I would be glad to help.

 

Thank a lot

 

Fred

 

De : galaxy-dev [mailto:[hidden email]] De la part de Peter Cock
Envoyé : mardi 12 septembre 2017 14:56
À : Laure QUINTRIC <[hidden email]>
Cc : Galaxy-dev <[hidden email]>
Objet : Re: [galaxy-dev] Displaying tool select list according to user

 

Hi Laure,

 

I don't think there is any easy to use mechanism for this in Galaxy.

Unfortunately Galaxy loads all the *.loc files at startup and treats

them as global values available to all users equally.

 

I can't find the email thread, but I recall someone previously trying

to do something with a single large example.loc file for all users

but with an extra column for filtering by account name. I forget if

they got these changes to work or not.

 

Assuming you only have a few separate versions of the example.loc

file, you could create copies of the BLAST wrapper XML file which

use the specific *.loc file - and then restrict the tool by user?

 

In either case at a minimum you would have to maintain local

changes to the BLAST wrappers (and potentially changes to

Galaxy itself), which is not a good situation.

 

Peter

 

On Tue, Sep 12, 2017 at 1:41 PM, Laure QUINTRIC <[hidden email]> wrote:

Hello Galaxy users,

I try to figure out how I can display a select list into a galaxy tool according to the connected user.

I have several .loc files containing the paths for custom blast databases I have created for several users (user1.loc, user2.loc, and so on). I would like the blast tool to display the specific databases for the connected user (user1 or user2).

Any idea on how to proceed ?
Regards,
Laure


___________________________________________________________
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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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: Displaying tool select list according to user

FredBGA

Hello Laure

 

this idea cannot be applied in my use case.

indeed I don’t want that users can choose which data to display. I want to hide some data based on their name/group/address (anything that can be useful to clasify my users).

 

Thank you for sharing your ideas :)

 

Fred

De : Laure QUINTRIC [mailto:[hidden email]]
Envoyé : mercredi 13 septembre 2017 13:54
À : Peter Cock <[hidden email]>; SAPET, Frederic <[hidden email]>
Cc : Galaxy-dev <[hidden email]>
Objet : Re: [galaxy-dev] Displaying tool select list according to user

 

A workaround would be to do this :

- first, create a tool which will output a tabular loc file with all the custom banks for the connected user.
- then add in the ncbi_blast wrapper a select list with the attribute from_dataset to load the loc file generated by the previous tool  : see the example here : https://docs.galaxyproject.org/en/latest/dev/schema.html#from-dataset

I have something like this in the ncbi_blast tool:
        <param name="userdb_loc_file" type="data" format="tabular" label="My custom dbs"/>
        <param name="custom_db" type="select" size="120" optional="true" multiple="true" display="checkboxes" label="Select our custom db">
            <options from_dataset="userdb_loc_file">
                <column name="value" index="0"/>
                <column name="name" index="1"/>
                <column name="path" index="2"/>
            </options>

and I set in param userdb_loc_file the loc file which is in my history and looks like this :
NCBI_nt<tab>NCBI_nt 2017-05-19<tab>/path/to/biobanks/n/NCBI_nt/current/NCBI_nt/NCBI_nt

Laure

Le 12/09/2017 à 17:25, Peter Cock a écrit :

Thanks Fred,

 

That's the previous discussion I was trying to find -

sadly no clear solution but some ideas to explore.

 

It does seem filtering example.loc by user or role

is not a niche request. I wonder if this could be

linked to the Galaxy data library permissions

structure as a way to manage the access rights?

 

Peter

 

On Tue, Sep 12, 2017 at 4:20 PM, SAPET, Frederic <[hidden email]> wrote:

Hi Laure,

 

There are others users (including me! ) that need this kind of function :

http://dev.list.galaxyproject.org/Blast-db-permission-td4670440.html

 

@Galaxy team:

Do we need to add an issue in GitHub ?

Do you think that it could be enabled one day ?

 

I think this something that could be nice to develop !

I would be glad to help.

 

Thank a lot

 

Fred

 

De : galaxy-dev [mailto:[hidden email]] De la part de Peter Cock
Envoyé : mardi 12 septembre 2017 14:56
À : Laure QUINTRIC <[hidden email]>
Cc : Galaxy-dev <[hidden email]>
Objet : Re: [galaxy-dev] Displaying tool select list according to user

 

Hi Laure,

 

I don't think there is any easy to use mechanism for this in Galaxy.

Unfortunately Galaxy loads all the *.loc files at startup and treats

them as global values available to all users equally.

 

I can't find the email thread, but I recall someone previously trying

to do something with a single large example.loc file for all users

but with an extra column for filtering by account name. I forget if

they got these changes to work or not.

 

Assuming you only have a few separate versions of the example.loc

file, you could create copies of the BLAST wrapper XML file which

use the specific *.loc file - and then restrict the tool by user?

 

In either case at a minimum you would have to maintain local

changes to the BLAST wrappers (and potentially changes to

Galaxy itself), which is not a good situation.

 

Peter

 

On Tue, Sep 12, 2017 at 1:41 PM, Laure QUINTRIC <[hidden email]> wrote:

Hello Galaxy users,

I try to figure out how I can display a select list into a galaxy tool according to the connected user.

I have several .loc files containing the paths for custom blast databases I have created for several users (user1.loc, user2.loc, and so on). I would like the blast tool to display the specific databases for the connected user (user1 or user2).

Any idea on how to proceed ?
Regards,
Laure


___________________________________________________________
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/

 

 



-- 
Laure QUINTRIC
IDM-RIC - Cellule Bio-informatique
02 98 22 49 11

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Re: Displaying tool select list according to user

Peter Cock
Have you tried creating the BLAST databases as files in your history
(by running makeblastdb within Galaxy), and then importing them into
a shared data library (which can then be configured with role based
permissions)?

Peter


On Wed, Sep 20, 2017 at 9:39 AM, SAPET, Frederic
<[hidden email]> wrote:

> Hello Laure
>
>
>
> this idea cannot be applied in my use case.
>
> indeed I don’t want that users can choose which data to display. I want to
> hide some data based on their name/group/address (anything that can be
> useful to clasify my users).
>
>
>
> Thank you for sharing your ideas :)
>
>
>
> Fred
>
> De : Laure QUINTRIC [mailto:[hidden email]]
> Envoyé : mercredi 13 septembre 2017 13:54
> À : Peter Cock <[hidden email]>; SAPET, Frederic
> <[hidden email]>
>
>
> Cc : Galaxy-dev <[hidden email]>
> Objet : Re: [galaxy-dev] Displaying tool select list according to user
>
>
>
> A workaround would be to do this :
>
> - first, create a tool which will output a tabular loc file with all the
> custom banks for the connected user.
> - then add in the ncbi_blast wrapper a select list with the attribute
> from_dataset to load the loc file generated by the previous tool  : see the
> example here :
> https://docs.galaxyproject.org/en/latest/dev/schema.html#from-dataset
>
> I have something like this in the ncbi_blast tool:
>         <param name="userdb_loc_file" type="data" format="tabular" label="My
> custom dbs"/>
>         <param name="custom_db" type="select" size="120" optional="true"
> multiple="true" display="checkboxes" label="Select our custom db">
>             <options from_dataset="userdb_loc_file">
>                 <column name="value" index="0"/>
>                 <column name="name" index="1"/>
>                 <column name="path" index="2"/>
>             </options>
>
> and I set in param userdb_loc_file the loc file which is in my history and
> looks like this :
> NCBI_nt<tab>NCBI_nt
> 2017-05-19<tab>/path/to/biobanks/n/NCBI_nt/current/NCBI_nt/NCBI_nt
>
> Laure
>
> Le 12/09/2017 à 17:25, Peter Cock a écrit :
>
> Thanks Fred,
>
>
>
> That's the previous discussion I was trying to find -
>
> sadly no clear solution but some ideas to explore.
>
>
>
> It does seem filtering example.loc by user or role
>
> is not a niche request. I wonder if this could be
>
> linked to the Galaxy data library permissions
>
> structure as a way to manage the access rights?
>
>
>
> Peter
>
>
>
> On Tue, Sep 12, 2017 at 4:20 PM, SAPET, Frederic
> <[hidden email]> wrote:
>
> Hi Laure,
>
>
>
> There are others users (including me! ) that need this kind of function :
>
> http://dev.list.galaxyproject.org/Blast-db-permission-td4670440.html
>
>
>
> @Galaxy team:
>
> Do we need to add an issue in GitHub ?
>
> Do you think that it could be enabled one day ?
>
>
>
> I think this something that could be nice to develop !
>
> I would be glad to help.
>
>
>
> Thank a lot
>
>
>
> Fred
>
>
>
> De : galaxy-dev [mailto:[hidden email]] De la
> part de Peter Cock
> Envoyé : mardi 12 septembre 2017 14:56
> À : Laure QUINTRIC <[hidden email]>
> Cc : Galaxy-dev <[hidden email]>
> Objet : Re: [galaxy-dev] Displaying tool select list according to user
>
>
>
> Hi Laure,
>
>
>
> I don't think there is any easy to use mechanism for this in Galaxy.
>
> Unfortunately Galaxy loads all the *.loc files at startup and treats
>
> them as global values available to all users equally.
>
>
>
> I can't find the email thread, but I recall someone previously trying
>
> to do something with a single large example.loc file for all users
>
> but with an extra column for filtering by account name. I forget if
>
> they got these changes to work or not.
>
>
>
> Assuming you only have a few separate versions of the example.loc
>
> file, you could create copies of the BLAST wrapper XML file which
>
> use the specific *.loc file - and then restrict the tool by user?
>
>
>
> In either case at a minimum you would have to maintain local
>
> changes to the BLAST wrappers (and potentially changes to
>
> Galaxy itself), which is not a good situation.
>
>
>
> Peter
>
>
>
> On Tue, Sep 12, 2017 at 1:41 PM, Laure QUINTRIC <[hidden email]>
> wrote:
>
> Hello Galaxy users,
>
> I try to figure out how I can display a select list into a galaxy tool
> according to the connected user.
>
> I have several .loc files containing the paths for custom blast databases I
> have created for several users (user1.loc, user2.loc, and so on). I would
> like the blast tool to display the specific databases for the connected user
> (user1 or user2).
>
> Any idea on how to proceed ?
> Regards,
> Laure
>
>
> ___________________________________________________________
> 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/
>
>
>
>
>
>
>
> --
>
> Laure QUINTRIC
>
> IDM-RIC - Cellule Bio-informatique
>
> 02 98 22 49 11
___________________________________________________________
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/