Displaying tool select list according to user

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Displaying tool select list according to user

Laure QUINTRIC
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

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


___________________________________________________________
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: Displaying tool select list according to user

Laure QUINTRIC
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

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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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

SAPET, Frederic
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:
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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/

 



___________________________________________________________
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:
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Re: Displaying tool select list according to user

Laure QUINTRIC
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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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

SAPET, Frederic

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:
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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
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Re: Displaying tool select list according to user

SAPET, Frederic
Hi Peter,

Good idea, I will keep that in mind for other needs.
I'm not sure that it will be suitable for what I want to do. Users will have to first import database to their history (yet another step as they ask me for less, even the upload process is sometimes one step they would like to avoid !)

But it could be a way of achieving what I want, if Galaxy could get files (or .loc files) from a data library, within the tool form itself !

Maybe I will create an issue on the Galaxy git in order to discuss about that. I will be glad to help if something can be done.

Maybe some explanations about the fact that my users ask me for "less steps".
I really want Galaxy to be the main tool of our analysis platform.
Right now I still maintain a plain old perl/php/CGI web interface. With a blast tool (among a lot of others tools). This proprietary Blast interface is really like you will find on NCBI or EBI sites. And you can quickly paste your sequences, pick up a database, a Blast algorythm and then launch. Few seconds later I have a 'htmlized' Blast report, with a nice picture.
This use case (is this sequence a part of this database ?) is still faster on this plain old interface. And I afraid that I will have to keep it until they found Galaxy better than it...

Maybe it could be another (or two) idea(s)  : the user can drag and drop his file within the tool form, Galaxy will handle the creation of this file within the history and then launch the tool. Or user can copy/paste a sequence within a text-area, and Galaxy will handle the creation of a file from these data within the history and then launch the tool.
This skips upload process.

thank you again for sharing your ideas, it helps!

Fred

-----Message d'origine-----
De : Peter Cock [mailto:[hidden email]]
Envoyé : mercredi 20 septembre 2017 12:37
À : SAPET, Frederic <[hidden email]>
Cc : Laure QUINTRIC <[hidden email]>; Galaxy-dev <[hidden email]>
Objet : Re: [galaxy-dev] Displaying tool select list according to user

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/

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Re: Displaying tool select list according to user

Gildas Le Corguillé
As it was already mention, about the filtering we presented at Baltimore this project : https://github.com/abims-sbr/galaxy-blastprivate

And about the report, we also have something about that :https://github.com/abims-sbr/galaxy-blastvisu

But shame on us, there is a lot of dust on them.
Although, if we can build a little group around this project, we are stil interesting in. Our goal was also to drop out our W3Blast server. 

Gildas

-----------------------------------------------------------------
Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
http://abims.sb-roscoff.fr

Member of the Workflow4Metabolomics project
http://workflow4metabolomics.org

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
------------------------------------------------------------------



Le 21 sept. 2017 à 13:50, SAPET, Frederic <[hidden email]> a écrit :

Hi Peter,

Good idea, I will keep that in mind for other needs.
I'm not sure that it will be suitable for what I want to do. Users will have to first import database to their history (yet another step as they ask me for less, even the upload process is sometimes one step they would like to avoid !)

But it could be a way of achieving what I want, if Galaxy could get files (or .loc files) from a data library, within the tool form itself !

Maybe I will create an issue on the Galaxy git in order to discuss about that. I will be glad to help if something can be done.

Maybe some explanations about the fact that my users ask me for "less steps".
I really want Galaxy to be the main tool of our analysis platform.
Right now I still maintain a plain old perl/php/CGI web interface. With a blast tool (among a lot of others tools). This proprietary Blast interface is really like you will find on NCBI or EBI sites. And you can quickly paste your sequences, pick up a database, a Blast algorythm and then launch. Few seconds later I have a 'htmlized' Blast report, with a nice picture.
This use case (is this sequence a part of this database ?) is still faster on this plain old interface. And I afraid that I will have to keep it until they found Galaxy better than it...

Maybe it could be another (or two) idea(s)  : the user can drag and drop his file within the tool form, Galaxy will handle the creation of this file within the history and then launch the tool. Or user can copy/paste a sequence within a text-area, and Galaxy will handle the creation of a file from these data within the history and then launch the tool.
This skips upload process.

thank you again for sharing your ideas, it helps!

Fred

-----Message d'origine-----
De : Peter Cock [[hidden email]]
Envoyé : mercredi 20 septembre 2017 12:37
À : SAPET, Frederic <[hidden email]>
Cc : Laure QUINTRIC <[hidden email]>; Galaxy-dev <[hidden email]>
Objet : Re: [galaxy-dev] Displaying tool select list according to user

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 [[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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and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/


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Re: Displaying tool select list according to user

Peter Cock
In reply to this post by SAPET, Frederic


On Thu, Sep 21, 2017 at 12:50 PM, SAPET, Frederic <[hidden email]> wrote:
Hi Peter,

Good idea, I will keep that in mind for other needs.
I'm not sure that it will be suitable for what I want to do. Users will have to first import database to their history (yet another step as they ask me for less, even the upload process is sometimes one step they would like to avoid !) 
 
But it could be a way of achieving what I want, if Galaxy could get files (or .loc files) from a data library, within the tool form itself ! 
 
Maybe I will create an issue on the Galaxy git in order to discuss about that. I will be glad to help if something can be done.

Good idea! I wonder if the Galaxy UI team can think of a good way to integrate this, which would make Shared Data library files available to any tool without the import to current history step? Can you reply with a link to the new GitHub issue for this?
 
Maybe some explanations about the fact that my users ask me for "less steps".
I really want Galaxy to be the main tool of our analysis platform.
Right now I still maintain a plain old perl/php/CGI web interface. With a blast tool (among a lot of others tools). This proprietary Blast interface is really like you will find on NCBI or EBI sites. And you can quickly paste your sequences, pick up a database, a Blast algorythm and then launch. Few seconds later I have a 'htmlized' Blast report, with a nice picture.
This use case (is this sequence a part of this database ?) is still faster on this plain old interface. And I afraid that I will have to keep it until they found Galaxy better than it...

We used to run wwwBLAST locally for similar reasons. If I was trying to setup up something similar now, I'd look at http://www.sequenceserver.com/ for this - but making the Galaxy alternative easier to use would be neater.
 
Maybe it could be another (or two) idea(s)  : the user can drag and drop his file within the tool form, Galaxy will handle the creation of this file within the history and then launch the tool. Or user can copy/paste a sequence within a text-area, and Galaxy will handle the creation of a file from these data within the history and then launch the tool.
This skips upload process.

The Galaxy upload does now support drag and drop, so again in principle the Galaxy team might be able to extend the tool interface as well. The tool input's expected file formats could be used to guide the data-type sniffer and/or short list the choices shown to the use.

As well or instead, I could imagine having an upload icon associated with each tool input (again, creating a history item and selecting it for you)? This could take advantage of the fact that each tool's input parameter specifies the expected input file formats, so that might be mapped to known file extensions for a file picker?
 

thank you again for sharing your ideas, it helps!

Fred

These are great usability ideas you are putting forward here - as a Galaxy Tool Author they sound positive, but I cannot comment on how complicated it would be for the Galaxy UI team. Or indeed if the UI would actually be practical - or just overly complicate things which is always a risk.

Peter


___________________________________________________________
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

SAPET, Frederic

Hi,

 

I have created 3 issues!

 

Use different .loc files depending on user's parameters

https://github.com/galaxyproject/galaxy/issues/4666

 

Access DataLibrary files from tool form

https://github.com/galaxyproject/galaxy/issues/4667

 

File upload enhancement

https://github.com/galaxyproject/galaxy/issues/4668

 

thank you Peter for pointing me out http://www.sequenceserver.com/

 

and of course as I also develop and maintain tools, I understand that all ‘craziest’ ideas cannot become a reality.

 

Fred

 

 

De : Peter Cock [mailto:[hidden email]]
Envoyé : jeudi 21 septembre 2017 14:46
À : SAPET, Frederic <[hidden email]>
Cc : Laure QUINTRIC <[hidden email]>; Galaxy-dev <[hidden email]>
Objet : Re: [galaxy-dev] Displaying tool select list according to user

 

 

 

On Thu, Sep 21, 2017 at 12:50 PM, SAPET, Frederic <[hidden email]> wrote:

Hi Peter,

Good idea, I will keep that in mind for other needs.
I'm not sure that it will be suitable for what I want to do. Users will have to first import database to their history (yet another step as they ask me for less, even the upload process is sometimes one step they would like to avoid !) 

 

But it could be a way of achieving what I want, if Galaxy could get files (or .loc files) from a data library, within the tool form itself ! 

 

Maybe I will create an issue on the Galaxy git in order to discuss about that. I will be glad to help if something can be done.

 

Good idea! I wonder if the Galaxy UI team can think of a good way to integrate this, which would make Shared Data library files available to any tool without the import to current history step? Can you reply with a link to the new GitHub issue for this?

 

Maybe some explanations about the fact that my users ask me for "less steps".
I really want Galaxy to be the main tool of our analysis platform.
Right now I still maintain a plain old perl/php/CGI web interface. With a blast tool (among a lot of others tools). This proprietary Blast interface is really like you will find on NCBI or EBI sites. And you can quickly paste your sequences, pick up a database, a Blast algorythm and then launch. Few seconds later I have a 'htmlized' Blast report, with a nice picture.
This use case (is this sequence a part of this database ?) is still faster on this plain old interface. And I afraid that I will have to keep it until they found Galaxy better than it...

 

We used to run wwwBLAST locally for similar reasons. If I was trying to setup up something similar now, I'd look at http://www.sequenceserver.com/ for this - but making the Galaxy alternative easier to use would be neater.

 

Maybe it could be another (or two) idea(s)  : the user can drag and drop his file within the tool form, Galaxy will handle the creation of this file within the history and then launch the tool. Or user can copy/paste a sequence within a text-area, and Galaxy will handle the creation of a file from these data within the history and then launch the tool.
This skips upload process.

 

The Galaxy upload does now support drag and drop, so again in principle the Galaxy team might be able to extend the tool interface as well. The tool input's expected file formats could be used to guide the data-type sniffer and/or short list the choices shown to the use.

 

As well or instead, I could imagine having an upload icon associated with each tool input (again, creating a history item and selecting it for you)? This could take advantage of the fact that each tool's input parameter specifies the expected input file formats, so that might be mapped to known file extensions for a file picker?

 


thank you again for sharing your ideas, it helps!

Fred

 

These are great usability ideas you are putting forward here - as a Galaxy Tool Author they sound positive, but I cannot comment on how complicated it would be for the Galaxy UI team. Or indeed if the UI would actually be practical - or just overly complicate things which is always a risk.

 

Peter

 


___________________________________________________________
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

Mohamed Kassam
Hi Fred,

Thanks a lot,, we are also intereted on that solution for our private database.

Hope that we have any good news soon.

Best regards,

Mohamed 

2017-09-21 16:01 GMT+02:00 SAPET, Frederic <[hidden email]>:

Hi,

 

I have created 3 issues!

 

Use different .loc files depending on user's parameters

https://github.com/galaxyproject/galaxy/issues/4666

 

Access DataLibrary files from tool form

https://github.com/galaxyproject/galaxy/issues/4667

 

File upload enhancement

https://github.com/galaxyproject/galaxy/issues/4668

 

thank you Peter for pointing me out http://www.sequenceserver.com/

 

and of course as I also develop and maintain tools, I understand that all ‘craziest’ ideas cannot become a reality.

 

Fred

 

 

De : Peter Cock [mailto:[hidden email]]
Envoyé : jeudi 21 septembre 2017 14:46
À : SAPET, Frederic <[hidden email]>
Cc : Laure QUINTRIC <[hidden email]>; Galaxy-dev <[hidden email]>
Objet : Re: [galaxy-dev] Displaying tool select list according to user

 

 

 

On Thu, Sep 21, 2017 at 12:50 PM, SAPET, Frederic <[hidden email]> wrote:

Hi Peter,

Good idea, I will keep that in mind for other needs.
I'm not sure that it will be suitable for what I want to do. Users will have to first import database to their history (yet another step as they ask me for less, even the upload process is sometimes one step they would like to avoid !) 

 

But it could be a way of achieving what I want, if Galaxy could get files (or .loc files) from a data library, within the tool form itself ! 

 

Maybe I will create an issue on the Galaxy git in order to discuss about that. I will be glad to help if something can be done.

 

Good idea! I wonder if the Galaxy UI team can think of a good way to integrate this, which would make Shared Data library files available to any tool without the import to current history step? Can you reply with a link to the new GitHub issue for this?

 

Maybe some explanations about the fact that my users ask me for "less steps".
I really want Galaxy to be the main tool of our analysis platform.
Right now I still maintain a plain old perl/php/CGI web interface. With a blast tool (among a lot of others tools). This proprietary Blast interface is really like you will find on NCBI or EBI sites. And you can quickly paste your sequences, pick up a database, a Blast algorythm and then launch. Few seconds later I have a 'htmlized' Blast report, with a nice picture.
This use case (is this sequence a part of this database ?) is still faster on this plain old interface. And I afraid that I will have to keep it until they found Galaxy better than it...

 

We used to run wwwBLAST locally for similar reasons. If I was trying to setup up something similar now, I'd look at http://www.sequenceserver.com/ for this - but making the Galaxy alternative easier to use would be neater.

 

Maybe it could be another (or two) idea(s)  : the user can drag and drop his file within the tool form, Galaxy will handle the creation of this file within the history and then launch the tool. Or user can copy/paste a sequence within a text-area, and Galaxy will handle the creation of a file from these data within the history and then launch the tool.
This skips upload process.

 

The Galaxy upload does now support drag and drop, so again in principle the Galaxy team might be able to extend the tool interface as well. The tool input's expected file formats could be used to guide the data-type sniffer and/or short list the choices shown to the use.

 

As well or instead, I could imagine having an upload icon associated with each tool input (again, creating a history item and selecting it for you)? This could take advantage of the fact that each tool's input parameter specifies the expected input file formats, so that might be mapped to known file extensions for a file picker?

 


thank you again for sharing your ideas, it helps!

Fred

 

These are great usability ideas you are putting forward here - as a Galaxy Tool Author they sound positive, but I cannot comment on how complicated it would be for the Galaxy UI team. Or indeed if the UI would actually be practical - or just overly complicate things which is always a risk.

 

Peter

 


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