Re: [galaxy-dev] Storing data in the user session

[Steve Cassidy]

Thanks Bjoern, look forward to seeing this, happy to test it when it’s ready.

Steve


—
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy

On 17 Oct. 2016, at 5:41 pm, Björn Grüning 
mailto:bjoern.gruen...@gmail.com>> wrote:

Hi Steve and Katherine,

we are working on this branch and it is working:
https://github.com/bgruening/galaxy/tree/extra_user_preferences

But are a little bit sidetracked by porting the user-preferences from
mako to JS before we can include this into Main Galaxy, but the main
idea should work for tools and all other features we have in mind.

Cheers,
Bjoern

Am 17.10.2016 um 23:31 schrieb Katherine Beaulieu:
Ah I see, we had a similar problem except our service used a password
and username so we ended up implementing a password parameter that
didn't persist in the database.

On Mon, Oct 17, 2016 at 5:29 PM, Steve Cassidy 
mailto:steve.cass...@mq.edu.au>
> wrote:

   Thanks Katherine, in my case I want to store the API key for an
   external service (not Galaxy) and get access to that from a tool so
   that the tool can act on behalf of the user.

   Steve

   —
   Department of Computing, Macquarie University
   http://web.science.mq.edu.au/~cassidy
   

   On 17 Oct. 2016, at 5:26 pm, Katherine Beaulieu
   mailto:katherine.beaulieu...@gmail.com>
   > wrote:

   Hi Steve,
   In terms of accessing the user's api key within a tool definition
   file, have a look at this thread I had started. John had suggested
   something but I haven't gotten it to work but maybe you will have
   more luck than me.
   
http://dev.list.galaxyproject.org/Workflow-ID-Galaxy-Instance-URL-API-Key-in-Galaxy-Tool-Config-td4669906.html#a4670104
   

   Cheers,
   Katherine

   On Mon, Oct 17, 2016 at 5:17 PM, Steve Cassidy
   mailto:steve.cass...@mq.edu.au> 
> wrote:

   Hi Bjoern,
just wanting to revisit this question and perhaps get an
   update on what you were doing for extending the user profile.

   I just noticed in the galaxy sources the option to add ‘forms’
   to be filled out at registration time. The admin interface
   seems to allow me to create  a form but it doesn’t appear when
   I try to register.  The code for this seems to be 2-5 years
   old so perhaps it’s a forgotten corner?

   https://github.com/galaxyproject/galaxy/tree/dev/templates/admin/forms
   

   Anyway, if you have made any progress on this I’d be happy to
   hear about it.  I’d like to be able to store the user’s API
   key in the profile and access it from a tool definition file.

   Cheers,

   Steve
   —
   Department of Computing, Macquarie University
   http://web.science.mq.edu.au/~cassidy
   

   On 28 Jul. 2016, at 2:59 pm, Björn Grüning
   mailto:bjoern.gruen...@gmail.com>
   > wrote:

   Hi Steve & Mohammed,

   I'm working on a user-profile extension to get credentials
   for a user,
   but this will take a few more weeks sorry.

   In the meantime can you look at the following idea:

   my_programm.py --credentials $USER_CREDENTIALS --arguments

   The variable $USER_CREDENTIALS is set during job execution
   with dynamic
   destination mappings
   
https://wiki.galaxyproject.org/Admin/Config/Jobs#Dynamic_Destination_Mapping
   


   What do you think, would this work for you?
   This assumes you as admin can pass along the user credentials
   if you
   know the username.

   If not please get in touch and I will tell you about my plans
   to extend
   the user-preferences maybe you can help me with this to speed
   things up.

   Ciao,
   Bjoern


   Hi Bjorn,
   sure, I don’t want to have the credentials stored in the
   tool but the tool
   needs to act on behalf of the user to retrieve data from the
   repository, so
   it needs access to credentials.  This could for example be a
   token generated
   via an OAuth2 exchange - basically something that is sent
   along with every
   http request to the remote resource to authenticate the user.

   My thought is that this could be stored in the user profile
   if this can be made
   available to the tool in the same way that __user_email__ is
   now.

   When you say ‘on the framework level’ do you mean by Galaxy?

   Steve
   —
   Department of Computing, Macquarie University
   http://web.science.m

Re: [galaxy-dev] Storing data in the user session

[Björn Grüning]

Hi Steve and Katherine,

we are working on this branch and it is working:
https://github.com/bgruening/galaxy/tree/extra_user_preferences

But are a little bit sidetracked by porting the user-preferences from
mako to JS before we can include this into Main Galaxy, but the main
idea should work for tools and all other features we have in mind.

Cheers,
Bjoern

Am 17.10.2016 um 23:31 schrieb Katherine Beaulieu:
> Ah I see, we had a similar problem except our service used a password
> and username so we ended up implementing a password parameter that
> didn't persist in the database.
> 
> On Mon, Oct 17, 2016 at 5:29 PM, Steve Cassidy  > wrote:
> 
> Thanks Katherine, in my case I want to store the API key for an
> external service (not Galaxy) and get access to that from a tool so
> that the tool can act on behalf of the user. 
> 
> Steve
> 
> —
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy
> 
> 
>> On 17 Oct. 2016, at 5:26 pm, Katherine Beaulieu
>> > > wrote:
>>
>> Hi Steve, 
>> In terms of accessing the user's api key within a tool definition
>> file, have a look at this thread I had started. John had suggested
>> something but I haven't gotten it to work but maybe you will have
>> more luck than me.
>> 
>> http://dev.list.galaxyproject.org/Workflow-ID-Galaxy-Instance-URL-API-Key-in-Galaxy-Tool-Config-td4669906.html#a4670104
>> 
>> 
>> Cheers,
>> Katherine
>>
>> On Mon, Oct 17, 2016 at 5:17 PM, Steve Cassidy
>> mailto:steve.cass...@mq.edu.au>> wrote:
>>
>> Hi Bjoern, 
>>  just wanting to revisit this question and perhaps get an
>> update on what you were doing for extending the user profile. 
>>
>> I just noticed in the galaxy sources the option to add ‘forms’
>> to be filled out at registration time. The admin interface
>> seems to allow me to create  a form but it doesn’t appear when
>> I try to register.  The code for this seems to be 2-5 years
>> old so perhaps it’s a forgotten corner? 
>>
>> 
>> https://github.com/galaxyproject/galaxy/tree/dev/templates/admin/forms
>> 
>> 
>>
>> Anyway, if you have made any progress on this I’d be happy to
>> hear about it.  I’d like to be able to store the user’s API
>> key in the profile and access it from a tool definition file. 
>>
>> Cheers,
>>
>> Steve
>> —
>> Department of Computing, Macquarie University
>> http://web.science.mq.edu.au/~cassidy
>> 
>>
>>> On 28 Jul. 2016, at 2:59 pm, Björn Grüning
>>> >> > wrote:
>>>
>>> Hi Steve & Mohammed,
>>>
>>> I'm working on a user-profile extension to get credentials
>>> for a user,
>>> but this will take a few more weeks sorry.
>>>
>>> In the meantime can you look at the following idea:
>>>
>>> my_programm.py --credentials $USER_CREDENTIALS --arguments
>>>
>>> The variable $USER_CREDENTIALS is set during job execution
>>> with dynamic
>>> destination mappings
>>> 
>>> https://wiki.galaxyproject.org/Admin/Config/Jobs#Dynamic_Destination_Mapping
>>> 
>>> 
>>>
>>> What do you think, would this work for you?
>>> This assumes you as admin can pass along the user credentials
>>> if you
>>> know the username.
>>>
>>> If not please get in touch and I will tell you about my plans
>>> to extend
>>> the user-preferences maybe you can help me with this to speed
>>> things up.
>>>
>>> Ciao,
>>> Bjoern
>>>
>>>
 Hi Bjorn,
 sure, I don’t want to have the credentials stored in the
 tool but the tool
 needs to act on behalf of the user to retrieve data from the
 repository, so
 it needs access to credentials.  This could for example be a
 token generated
 via an OAuth2 exchange - basically something that is sent
 along with every
 http request to the remote resource to authenticate the user.  

 My thought is that this could be stored in the user profile
 if this can be made
 available to the tool in the same way that __user_email__ is
 now.

 When you say ‘on the framework level’ do you mean by Galaxy?

 Steve

Re: [galaxy-dev] Storing data in the user session

[Katherine Beaulieu]

Ah I see, we had a similar problem except our service used a password and
username so we ended up implementing a password parameter that didn't
persist in the database.

On Mon, Oct 17, 2016 at 5:29 PM, Steve Cassidy 
wrote:

> Thanks Katherine, in my case I want to store the API key for an external
> service (not Galaxy) and get access to that from a tool so that the tool
> can act on behalf of the user.
>
> Steve
>
> —
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy
>
> On 17 Oct. 2016, at 5:26 pm, Katherine Beaulieu <
> katherine.beaulieu...@gmail.com> wrote:
>
> Hi Steve,
> In terms of accessing the user's api key within a tool definition file,
> have a look at this thread I had started. John had suggested something but
> I haven't gotten it to work but maybe you will have more luck than me.
> http://dev.list.galaxyproject.org/Workflow-ID-Galaxy-
> Instance-URL-API-Key-in-Galaxy-Tool-Config-td4669906.html#a4670104
> Cheers,
> Katherine
>
> On Mon, Oct 17, 2016 at 5:17 PM, Steve Cassidy 
> wrote:
>
>> Hi Bjoern,
>>  just wanting to revisit this question and perhaps get an update on what
>> you were doing for extending the user profile.
>>
>> I just noticed in the galaxy sources the option to add ‘forms’ to be
>> filled out at registration time. The admin interface seems to allow me to
>> create  a form but it doesn’t appear when I try to register.  The code for
>> this seems to be 2-5 years old so perhaps it’s a forgotten corner?
>>
>> https://github.com/galaxyproject/galaxy/tree/dev/templates/admin/forms
>>
>> Anyway, if you have made any progress on this I’d be happy to hear about
>> it.  I’d like to be able to store the user’s API key in the profile and
>> access it from a tool definition file.
>>
>> Cheers,
>>
>> Steve
>> —
>> Department of Computing, Macquarie University
>> http://web.science.mq.edu.au/~cassidy
>>
>> On 28 Jul. 2016, at 2:59 pm, Björn Grüning 
>> wrote:
>>
>> Hi Steve & Mohammed,
>>
>> I'm working on a user-profile extension to get credentials for a user,
>> but this will take a few more weeks sorry.
>>
>> In the meantime can you look at the following idea:
>>
>> my_programm.py --credentials $USER_CREDENTIALS --arguments
>>
>> The variable $USER_CREDENTIALS is set during job execution with dynamic
>> destination mappings
>> https://wiki.galaxyproject.org/Admin/Config/Jobs#Dynamic_Des
>> tination_Mapping
>>
>> What do you think, would this work for you?
>> This assumes you as admin can pass along the user credentials if you
>> know the username.
>>
>> If not please get in touch and I will tell you about my plans to extend
>> the user-preferences maybe you can help me with this to speed things up.
>>
>> Ciao,
>> Bjoern
>>
>>
>> Hi Bjorn,
>> sure, I don’t want to have the credentials stored in the tool but the
>> tool
>> needs to act on behalf of the user to retrieve data from the repository,
>> so
>> it needs access to credentials.  This could for example be a token
>> generated
>> via an OAuth2 exchange - basically something that is sent along with
>> every
>> http request to the remote resource to authenticate the user.
>>
>> My thought is that this could be stored in the user profile if this can
>> be made
>> available to the tool in the same way that __user_email__ is now.
>>
>> When you say ‘on the framework level’ do you mean by Galaxy?
>>
>> Steve
>> —
>> Department of Computing, Macquarie University
>> http://web.science.mq.edu.au/~cassidy
>>
>> On 28 Jul 2016, at 5:23 PM, Björn Grüning 
>> wrote:
>>
>> Hi Steve,
>>
>> can you explain the larger use-case behind it. Imho you should not
>> populate a tool with credentials, this should be handled on the
>> framework level.
>>
>> Hope you are fine,
>> Bjoern
>>
>> Am 28.07.2016 um 03:15 schrieb Steve Cassidy:
>>
>> Hi again,
>>  I’m looking for the right way to store some user credentials in the
>> galaxy session so that tools can work on behalf of the user with our
>> repository.
>>
>> Currently users have an API key and they need to upload it as a data
>> item to that is then passed to each tool that needs it as input.  This
>> doesn’t seem like the right solution since the API key becomes part of
>> the history and so would be shared if the history were shared.
>>
>> What would be better would be a way of storing the API key in the user
>> session and then being able to pass that into a tool.
>>
>> I note that there are a few user session variables available in the tool
>> xml file: __user__, __user_email__, __user_name__ and __user_id__.
>> There is also a user preferences page where they can fill out a few
>> details.  However, I can’t see a mechanism to extend this in any way and
>> have extra properties in the preferences pane that would then be
>> available to tools via the template file.
>>
>> I can see that the standard practice for the data sources on
>> usegalaxy.org  is to send the user off to a
>> repository website to find data that is then posted back t

Re: [galaxy-dev] Storing data in the user session

[Steve Cassidy]

Thanks Katherine, in my case I want to store the API key for an external 
service (not Galaxy) and get access to that from a tool so that the tool can 
act on behalf of the user.

Steve

—
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy

On 17 Oct. 2016, at 5:26 pm, Katherine Beaulieu 
mailto:katherine.beaulieu...@gmail.com>> wrote:

Hi Steve,
In terms of accessing the user's api key within a tool definition file, have a 
look at this thread I had started. John had suggested something but I haven't 
gotten it to work but maybe you will have more luck than me.
http://dev.list.galaxyproject.org/Workflow-ID-Galaxy-Instance-URL-API-Key-in-Galaxy-Tool-Config-td4669906.html#a4670104
Cheers,
Katherine

On Mon, Oct 17, 2016 at 5:17 PM, Steve Cassidy 
mailto:steve.cass...@mq.edu.au>> wrote:
Hi Bjoern,
 just wanting to revisit this question and perhaps get an update on what you 
were doing for extending the user profile.

I just noticed in the galaxy sources the option to add ‘forms’ to be filled out 
at registration time. The admin interface seems to allow me to create  a form 
but it doesn’t appear when I try to register.  The code for this seems to be 
2-5 years old so perhaps it’s a forgotten corner?

https://github.com/galaxyproject/galaxy/tree/dev/templates/admin/forms

Anyway, if you have made any progress on this I’d be happy to hear about it.  
I’d like to be able to store the user’s API key in the profile and access it 
from a tool definition file.

Cheers,

Steve
—
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy

On 28 Jul. 2016, at 2:59 pm, Björn Grüning 
mailto:bjoern.gruen...@gmail.com>> wrote:

Hi Steve & Mohammed,

I'm working on a user-profile extension to get credentials for a user,
but this will take a few more weeks sorry.

In the meantime can you look at the following idea:

my_programm.py --credentials $USER_CREDENTIALS --arguments

The variable $USER_CREDENTIALS is set during job execution with dynamic
destination mappings
https://wiki.galaxyproject.org/Admin/Config/Jobs#Dynamic_Destination_Mapping

What do you think, would this work for you?
This assumes you as admin can pass along the user credentials if you
know the username.

If not please get in touch and I will tell you about my plans to extend
the user-preferences maybe you can help me with this to speed things up.

Ciao,
Bjoern


Hi Bjorn,
sure, I don’t want to have the credentials stored in the tool but the tool
needs to act on behalf of the user to retrieve data from the repository, so
it needs access to credentials.  This could for example be a token generated
via an OAuth2 exchange - basically something that is sent along with every
http request to the remote resource to authenticate the user.

My thought is that this could be stored in the user profile if this can be made
available to the tool in the same way that __user_email__ is now.

When you say ‘on the framework level’ do you mean by Galaxy?

Steve
—
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy

On 28 Jul 2016, at 5:23 PM, Björn Grüning 
mailto:bjoern.gruen...@gmail.com>> wrote:

Hi Steve,

can you explain the larger use-case behind it. Imho you should not
populate a tool with credentials, this should be handled on the
framework level.

Hope you are fine,
Bjoern

Am 28.07.2016 um 03:15 schrieb Steve Cassidy:
Hi again,
 I’m looking for the right way to store some user credentials in the
galaxy session so that tools can work on behalf of the user with our
repository.

Currently users have an API key and they need to upload it as a data
item to that is then passed to each tool that needs it as input.  This
doesn’t seem like the right solution since the API key becomes part of
the history and so would be shared if the history were shared.

What would be better would be a way of storing the API key in the user
session and then being able to pass that into a tool.

I note that there are a few user session variables available in the tool
xml file: __user__, __user_email__, __user_name__ and __user_id__.
There is also a user preferences page where they can fill out a few
details.  However, I can’t see a mechanism to extend this in any way and
have extra properties in the preferences pane that would then be
available to tools via the template file.

I can see that the standard practice for the data sources on
usegalaxy.org 
> is to send the user off to a
repository website to find data that is then posted back to the galaxy
server.  This isn’t appropriate for us since the interaction with the
repository is not just for downloading a single dataset - tools will
query the repository, download various kinds of data and possibly upload
new data, so we need to store user credentials in some way.

Is there already a good way to achieve this or is this an enhancement to
Galaxy?

Thanks,

Steve


—
Department of Comp

Re: [galaxy-dev] Storing data in the user session

[Katherine Beaulieu]

Hi Steve,
In terms of accessing the user's api key within a tool definition file,
have a look at this thread I had started. John had suggested something but
I haven't gotten it to work but maybe you will have more luck than me.
http://dev.list.galaxyproject.org/Workflow-ID-Galaxy-Instance-URL-API-Key-in-Galaxy-Tool-Config-td4669906.html#a4670104
Cheers,
Katherine

On Mon, Oct 17, 2016 at 5:17 PM, Steve Cassidy 
wrote:

> Hi Bjoern,
>  just wanting to revisit this question and perhaps get an update on what
> you were doing for extending the user profile.
>
> I just noticed in the galaxy sources the option to add ‘forms’ to be
> filled out at registration time. The admin interface seems to allow me to
> create  a form but it doesn’t appear when I try to register.  The code for
> this seems to be 2-5 years old so perhaps it’s a forgotten corner?
>
> https://github.com/galaxyproject/galaxy/tree/dev/templates/admin/forms
>
> Anyway, if you have made any progress on this I’d be happy to hear about
> it.  I’d like to be able to store the user’s API key in the profile and
> access it from a tool definition file.
>
> Cheers,
>
> Steve
> —
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy
>
> On 28 Jul. 2016, at 2:59 pm, Björn Grüning 
> wrote:
>
> Hi Steve & Mohammed,
>
> I'm working on a user-profile extension to get credentials for a user,
> but this will take a few more weeks sorry.
>
> In the meantime can you look at the following idea:
>
> my_programm.py --credentials $USER_CREDENTIALS --arguments
>
> The variable $USER_CREDENTIALS is set during job execution with dynamic
> destination mappings
> https://wiki.galaxyproject.org/Admin/Config/Jobs#Dynamic_
> Destination_Mapping
>
> What do you think, would this work for you?
> This assumes you as admin can pass along the user credentials if you
> know the username.
>
> If not please get in touch and I will tell you about my plans to extend
> the user-preferences maybe you can help me with this to speed things up.
>
> Ciao,
> Bjoern
>
>
> Hi Bjorn,
> sure, I don’t want to have the credentials stored in the tool but the tool
> needs to act on behalf of the user to retrieve data from the repository, so
> it needs access to credentials.  This could for example be a token
> generated
> via an OAuth2 exchange - basically something that is sent along with every
> http request to the remote resource to authenticate the user.
>
> My thought is that this could be stored in the user profile if this can be
> made
> available to the tool in the same way that __user_email__ is now.
>
> When you say ‘on the framework level’ do you mean by Galaxy?
>
> Steve
> —
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy
>
> On 28 Jul 2016, at 5:23 PM, Björn Grüning 
> wrote:
>
> Hi Steve,
>
> can you explain the larger use-case behind it. Imho you should not
> populate a tool with credentials, this should be handled on the
> framework level.
>
> Hope you are fine,
> Bjoern
>
> Am 28.07.2016 um 03:15 schrieb Steve Cassidy:
>
> Hi again,
>  I’m looking for the right way to store some user credentials in the
> galaxy session so that tools can work on behalf of the user with our
> repository.
>
> Currently users have an API key and they need to upload it as a data
> item to that is then passed to each tool that needs it as input.  This
> doesn’t seem like the right solution since the API key becomes part of
> the history and so would be shared if the history were shared.
>
> What would be better would be a way of storing the API key in the user
> session and then being able to pass that into a tool.
>
> I note that there are a few user session variables available in the tool
> xml file: __user__, __user_email__, __user_name__ and __user_id__.
> There is also a user preferences page where they can fill out a few
> details.  However, I can’t see a mechanism to extend this in any way and
> have extra properties in the preferences pane that would then be
> available to tools via the template file.
>
> I can see that the standard practice for the data sources on
> usegalaxy.org  is to send the user off to a
> repository website to find data that is then posted back to the galaxy
> server.  This isn’t appropriate for us since the interaction with the
> repository is not just for downloading a single dataset - tools will
> query the repository, download various kinds of data and possibly upload
> new data, so we need to store user credentials in some way.
>
> Is there already a good way to achieve this or is this an enhancement to
> Galaxy?
>
> Thanks,
>
> Steve
>
>
> —
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy
> 
>
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy 

Re: [galaxy-dev] Storing data in the user session

[Steve Cassidy]

Hi Bjoern,
 just wanting to revisit this question and perhaps get an update on what you 
were doing for extending the user profile.

I just noticed in the galaxy sources the option to add ‘forms’ to be filled out 
at registration time. The admin interface seems to allow me to create  a form 
but it doesn’t appear when I try to register.  The code for this seems to be 
2-5 years old so perhaps it’s a forgotten corner?

https://github.com/galaxyproject/galaxy/tree/dev/templates/admin/forms

Anyway, if you have made any progress on this I’d be happy to hear about it.  
I’d like to be able to store the user’s API key in the profile and access it 
from a tool definition file.

Cheers,

Steve
—
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy

On 28 Jul. 2016, at 2:59 pm, Björn Grüning 
mailto:bjoern.gruen...@gmail.com>> wrote:

Hi Steve & Mohammed,

I'm working on a user-profile extension to get credentials for a user,
but this will take a few more weeks sorry.

In the meantime can you look at the following idea:

my_programm.py --credentials $USER_CREDENTIALS --arguments

The variable $USER_CREDENTIALS is set during job execution with dynamic
destination mappings
https://wiki.galaxyproject.org/Admin/Config/Jobs#Dynamic_Destination_Mapping

What do you think, would this work for you?
This assumes you as admin can pass along the user credentials if you
know the username.

If not please get in touch and I will tell you about my plans to extend
the user-preferences maybe you can help me with this to speed things up.

Ciao,
Bjoern


Hi Bjorn,
sure, I don’t want to have the credentials stored in the tool but the tool
needs to act on behalf of the user to retrieve data from the repository, so
it needs access to credentials.  This could for example be a token generated
via an OAuth2 exchange - basically something that is sent along with every
http request to the remote resource to authenticate the user.

My thought is that this could be stored in the user profile if this can be made
available to the tool in the same way that __user_email__ is now.

When you say ‘on the framework level’ do you mean by Galaxy?

Steve
—
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy

On 28 Jul 2016, at 5:23 PM, Björn Grüning  wrote:

Hi Steve,

can you explain the larger use-case behind it. Imho you should not
populate a tool with credentials, this should be handled on the
framework level.

Hope you are fine,
Bjoern

Am 28.07.2016 um 03:15 schrieb Steve Cassidy:
Hi again,
 I’m looking for the right way to store some user credentials in the
galaxy session so that tools can work on behalf of the user with our
repository.

Currently users have an API key and they need to upload it as a data
item to that is then passed to each tool that needs it as input.  This
doesn’t seem like the right solution since the API key becomes part of
the history and so would be shared if the history were shared.

What would be better would be a way of storing the API key in the user
session and then being able to pass that into a tool.

I note that there are a few user session variables available in the tool
xml file: __user__, __user_email__, __user_name__ and __user_id__.
There is also a user preferences page where they can fill out a few
details.  However, I can’t see a mechanism to extend this in any way and
have extra properties in the preferences pane that would then be
available to tools via the template file.

I can see that the standard practice for the data sources on
usegalaxy.org  is to send the user off to a
repository website to find data that is then posted back to the galaxy
server.  This isn’t appropriate for us since the interaction with the
repository is not just for downloading a single dataset - tools will
query the repository, download various kinds of data and possibly upload
new data, so we need to store user credentials in some way.

Is there already a good way to achieve this or is this an enhancement to
Galaxy?

Thanks,

Steve


—
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy




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Re: [galaxy-dev] Storing data in the user session

[Mohamed Kassam]

Dear Bjoern,
I think it should work for me.

I will contatct you to see how it can work for my purpose.

Thank you in advance,

Mohamed

2016-07-28 20:59 GMT+02:00 Björn Grüning :

> Hi Steve & Mohammed,
>
> I'm working on a user-profile extension to get credentials for a user,
> but this will take a few more weeks sorry.
>
> In the meantime can you look at the following idea:
>
> my_programm.py --credentials $USER_CREDENTIALS --arguments
>
> The variable $USER_CREDENTIALS is set during job execution with dynamic
> destination mappings
>
> https://wiki.galaxyproject.org/Admin/Config/Jobs#Dynamic_Destination_Mapping
>
> What do you think, would this work for you?
> This assumes you as admin can pass along the user credentials if you
> know the username.
>
> If not please get in touch and I will tell you about my plans to extend
> the user-preferences maybe you can help me with this to speed things up.
>
> Ciao,
> Bjoern
>
>
> > Hi Bjorn,
> >  sure, I don’t want to have the credentials stored in the tool but the
> tool
> > needs to act on behalf of the user to retrieve data from the repository,
> so
> > it needs access to credentials.  This could for example be a token
> generated
> > via an OAuth2 exchange - basically something that is sent along with
> every
> > http request to the remote resource to authenticate the user.
> >
> > My thought is that this could be stored in the user profile if this can
> be made
> > available to the tool in the same way that __user_email__ is now.
> >
> > When you say ‘on the framework level’ do you mean by Galaxy?
> >
> > Steve
> > —
> > Department of Computing, Macquarie University
> > http://web.science.mq.edu.au/~cassidy
> >
> >> On 28 Jul 2016, at 5:23 PM, Björn Grüning 
> wrote:
> >>
> >> Hi Steve,
> >>
> >> can you explain the larger use-case behind it. Imho you should not
> >> populate a tool with credentials, this should be handled on the
> >> framework level.
> >>
> >> Hope you are fine,
> >> Bjoern
> >>
> >> Am 28.07.2016 um 03:15 schrieb Steve Cassidy:
> >>> Hi again,
> >>>   I’m looking for the right way to store some user credentials in the
> >>> galaxy session so that tools can work on behalf of the user with our
> >>> repository.
> >>>
> >>> Currently users have an API key and they need to upload it as a data
> >>> item to that is then passed to each tool that needs it as input.  This
> >>> doesn’t seem like the right solution since the API key becomes part of
> >>> the history and so would be shared if the history were shared.
> >>>
> >>> What would be better would be a way of storing the API key in the user
> >>> session and then being able to pass that into a tool.
> >>>
> >>> I note that there are a few user session variables available in the
> tool
> >>> xml file: __user__, __user_email__, __user_name__ and __user_id__.
> >>> There is also a user preferences page where they can fill out a few
> >>> details.  However, I can’t see a mechanism to extend this in any way
> and
> >>> have extra properties in the preferences pane that would then be
> >>> available to tools via the template file.
> >>>
> >>> I can see that the standard practice for the data sources on
> >>> usegalaxy.org  is to send the user off to a
> >>> repository website to find data that is then posted back to the galaxy
> >>> server.  This isn’t appropriate for us since the interaction with the
> >>> repository is not just for downloading a single dataset - tools will
> >>> query the repository, download various kinds of data and possibly
> upload
> >>> new data, so we need to store user credentials in some way.
> >>>
> >>> Is there already a good way to achieve this or is this an enhancement
> to
> >>> Galaxy?
> >>>
> >>> Thanks,
> >>>
> >>> Steve
> >>>
> >>>
> >>> —
> >>> Department of Computing, Macquarie University
> >>> http://web.science.mq.edu.au/~cassidy
> >>> 
> >>>
> >>>
> >>>
> >>> ___
> >>> 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/mailinglists/
> >
>
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Re: [galaxy-dev] Storing data in the user session

[Björn Grüning]

Hi Eric,

I think they are. What you described is more the user-facing part.
My current proof-of-concept does not have a tool-user-interface, it just
stores the credentials in the framework and makes it accessible through
the user-object. Which should be enough for dynamic job destinations.
A dedicated user-interface for tools is a nice idea and we can put this
ontop I think very easily!

Thanks for sharing!
Bjoern

Am 28.07.2016 um 21:09 schrieb Eric Rasche:
> Hey Björn,
> 
> I talked a bit about this with Katherine today, her group is quite
> interested in working on this as well.
> 
> I know we had discussed this a bit at GCC, and I posted a message today,
> outlining my plans which were formulated when I was at PSU the other
> month. Were those suggestions compatible with the existing work you'd
> done on generic KV store stuff?
> 
> Cheers,
> Eric
> 
> On 28. juli 2016 18:59, Björn Grüning wrote:
>> Hi Steve & Mohammed,
>>
>> I'm working on a user-profile extension to get credentials for a user,
>> but this will take a few more weeks sorry.
>>
>> In the meantime can you look at the following idea:
>>
>> my_programm.py --credentials $USER_CREDENTIALS --arguments
>>
>> The variable $USER_CREDENTIALS is set during job execution with dynamic
>> destination mappings
>> https://wiki.galaxyproject.org/Admin/Config/Jobs#Dynamic_Destination_Mapping
>>
>> What do you think, would this work for you?
>> This assumes you as admin can pass along the user credentials if you
>> know the username.
>>
>> If not please get in touch and I will tell you about my plans to extend
>> the user-preferences maybe you can help me with this to speed things up.
>>
>> Ciao,
>> Bjoern
>>
>>
>>> Hi Bjorn,
>>>  sure, I don’t want to have the credentials stored in the tool but the tool 
>>> needs to act on behalf of the user to retrieve data from the repository, so
>>> it needs access to credentials.  This could for example be a token generated
>>> via an OAuth2 exchange - basically something that is sent along with every 
>>> http request to the remote resource to authenticate the user.  
>>>
>>> My thought is that this could be stored in the user profile if this can be 
>>> made
>>> available to the tool in the same way that __user_email__ is now. 
>>>
>>> When you say ‘on the framework level’ do you mean by Galaxy? 
>>>
>>> Steve
>>> —
>>> Department of Computing, Macquarie University
>>> http://web.science.mq.edu.au/~cassidy
>>>
 On 28 Jul 2016, at 5:23 PM, Björn Grüning  
 wrote:

 Hi Steve,

 can you explain the larger use-case behind it. Imho you should not
 populate a tool with credentials, this should be handled on the
 framework level.

 Hope you are fine,
 Bjoern

 Am 28.07.2016 um 03:15 schrieb Steve Cassidy:
> Hi again,
>   I’m looking for the right way to store some user credentials in the
> galaxy session so that tools can work on behalf of the user with our
> repository. 
>
> Currently users have an API key and they need to upload it as a data
> item to that is then passed to each tool that needs it as input.  This
> doesn’t seem like the right solution since the API key becomes part of
> the history and so would be shared if the history were shared.  
>
> What would be better would be a way of storing the API key in the user
> session and then being able to pass that into a tool.
>
> I note that there are a few user session variables available in the tool
> xml file: __user__, __user_email__, __user_name__ and __user_id__.
> There is also a user preferences page where they can fill out a few
> details.  However, I can’t see a mechanism to extend this in any way and
> have extra properties in the preferences pane that would then be
> available to tools via the template file.  
>
> I can see that the standard practice for the data sources on
> usegalaxy.org  is to send the user off to a
> repository website to find data that is then posted back to the galaxy
> server.  This isn’t appropriate for us since the interaction with the
> repository is not just for downloading a single dataset - tools will
> query the repository, download various kinds of data and possibly upload
> new data, so we need to store user credentials in some way. 
>
> Is there already a good way to achieve this or is this an enhancement to
> Galaxy? 
>
> Thanks,
>
> Steve
>
>
> —
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy
> 
>
>
>
> ___
> 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/
>
>

Re: [galaxy-dev] Storing data in the user session

[Eric Rasche]

Hey Björn,

I talked a bit about this with Katherine today, her group is quite
interested in working on this as well.

I know we had discussed this a bit at GCC, and I posted a message today,
outlining my plans which were formulated when I was at PSU the other
month. Were those suggestions compatible with the existing work you'd
done on generic KV store stuff?

Cheers,
Eric

On 28. juli 2016 18:59, Björn Grüning wrote:
> Hi Steve & Mohammed,
>
> I'm working on a user-profile extension to get credentials for a user,
> but this will take a few more weeks sorry.
>
> In the meantime can you look at the following idea:
>
> my_programm.py --credentials $USER_CREDENTIALS --arguments
>
> The variable $USER_CREDENTIALS is set during job execution with dynamic
> destination mappings
> https://wiki.galaxyproject.org/Admin/Config/Jobs#Dynamic_Destination_Mapping
>
> What do you think, would this work for you?
> This assumes you as admin can pass along the user credentials if you
> know the username.
>
> If not please get in touch and I will tell you about my plans to extend
> the user-preferences maybe you can help me with this to speed things up.
>
> Ciao,
> Bjoern
>
>
>> Hi Bjorn,
>>  sure, I don’t want to have the credentials stored in the tool but the tool 
>> needs to act on behalf of the user to retrieve data from the repository, so
>> it needs access to credentials.  This could for example be a token generated
>> via an OAuth2 exchange - basically something that is sent along with every 
>> http request to the remote resource to authenticate the user.  
>>
>> My thought is that this could be stored in the user profile if this can be 
>> made
>> available to the tool in the same way that __user_email__ is now. 
>>
>> When you say ‘on the framework level’ do you mean by Galaxy? 
>>
>> Steve
>> —
>> Department of Computing, Macquarie University
>> http://web.science.mq.edu.au/~cassidy
>>
>>> On 28 Jul 2016, at 5:23 PM, Björn Grüning  wrote:
>>>
>>> Hi Steve,
>>>
>>> can you explain the larger use-case behind it. Imho you should not
>>> populate a tool with credentials, this should be handled on the
>>> framework level.
>>>
>>> Hope you are fine,
>>> Bjoern
>>>
>>> Am 28.07.2016 um 03:15 schrieb Steve Cassidy:
 Hi again,
   I’m looking for the right way to store some user credentials in the
 galaxy session so that tools can work on behalf of the user with our
 repository. 

 Currently users have an API key and they need to upload it as a data
 item to that is then passed to each tool that needs it as input.  This
 doesn’t seem like the right solution since the API key becomes part of
 the history and so would be shared if the history were shared.  

 What would be better would be a way of storing the API key in the user
 session and then being able to pass that into a tool.

 I note that there are a few user session variables available in the tool
 xml file: __user__, __user_email__, __user_name__ and __user_id__.
 There is also a user preferences page where they can fill out a few
 details.  However, I can’t see a mechanism to extend this in any way and
 have extra properties in the preferences pane that would then be
 available to tools via the template file.  

 I can see that the standard practice for the data sources on
 usegalaxy.org  is to send the user off to a
 repository website to find data that is then posted back to the galaxy
 server.  This isn’t appropriate for us since the interaction with the
 repository is not just for downloading a single dataset - tools will
 query the repository, download various kinds of data and possibly upload
 new data, so we need to store user credentials in some way. 

 Is there already a good way to achieve this or is this an enhancement to
 Galaxy? 

 Thanks,

 Steve


 —
 Department of Computing, Macquarie University
 http://web.science.mq.edu.au/~cassidy
 



 ___
 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/mailinglists/
> ___
> 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/mailinglists/

-- 

Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
Col

Re: [galaxy-dev] Storing data in the user session

[Björn Grüning]

Hi Steve & Mohammed,

I'm working on a user-profile extension to get credentials for a user,
but this will take a few more weeks sorry.

In the meantime can you look at the following idea:

my_programm.py --credentials $USER_CREDENTIALS --arguments

The variable $USER_CREDENTIALS is set during job execution with dynamic
destination mappings
https://wiki.galaxyproject.org/Admin/Config/Jobs#Dynamic_Destination_Mapping

What do you think, would this work for you?
This assumes you as admin can pass along the user credentials if you
know the username.

If not please get in touch and I will tell you about my plans to extend
the user-preferences maybe you can help me with this to speed things up.

Ciao,
Bjoern


> Hi Bjorn,
>  sure, I don’t want to have the credentials stored in the tool but the tool 
> needs to act on behalf of the user to retrieve data from the repository, so
> it needs access to credentials.  This could for example be a token generated
> via an OAuth2 exchange - basically something that is sent along with every 
> http request to the remote resource to authenticate the user.  
> 
> My thought is that this could be stored in the user profile if this can be 
> made
> available to the tool in the same way that __user_email__ is now. 
> 
> When you say ‘on the framework level’ do you mean by Galaxy? 
> 
> Steve
> —
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy
> 
>> On 28 Jul 2016, at 5:23 PM, Björn Grüning  wrote:
>>
>> Hi Steve,
>>
>> can you explain the larger use-case behind it. Imho you should not
>> populate a tool with credentials, this should be handled on the
>> framework level.
>>
>> Hope you are fine,
>> Bjoern
>>
>> Am 28.07.2016 um 03:15 schrieb Steve Cassidy:
>>> Hi again,
>>>   I’m looking for the right way to store some user credentials in the
>>> galaxy session so that tools can work on behalf of the user with our
>>> repository. 
>>>
>>> Currently users have an API key and they need to upload it as a data
>>> item to that is then passed to each tool that needs it as input.  This
>>> doesn’t seem like the right solution since the API key becomes part of
>>> the history and so would be shared if the history were shared.  
>>>
>>> What would be better would be a way of storing the API key in the user
>>> session and then being able to pass that into a tool.
>>>
>>> I note that there are a few user session variables available in the tool
>>> xml file: __user__, __user_email__, __user_name__ and __user_id__.
>>> There is also a user preferences page where they can fill out a few
>>> details.  However, I can’t see a mechanism to extend this in any way and
>>> have extra properties in the preferences pane that would then be
>>> available to tools via the template file.  
>>>
>>> I can see that the standard practice for the data sources on
>>> usegalaxy.org  is to send the user off to a
>>> repository website to find data that is then posted back to the galaxy
>>> server.  This isn’t appropriate for us since the interaction with the
>>> repository is not just for downloading a single dataset - tools will
>>> query the repository, download various kinds of data and possibly upload
>>> new data, so we need to store user credentials in some way. 
>>>
>>> Is there already a good way to achieve this or is this an enhancement to
>>> Galaxy? 
>>>
>>> Thanks,
>>>
>>> Steve
>>>
>>>
>>> —
>>> Department of Computing, Macquarie University
>>> http://web.science.mq.edu.au/~cassidy
>>> 
>>>
>>>
>>>
>>> ___
>>> 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/mailinglists/
> 
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and other Galaxy lists, please use the interface at:
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Re: [galaxy-dev] Storing data in the user session

[Mohamed Kassam]

Hi Steve
so what you can do create a web authentification tool with Galaxy and bring
back the information as it is done with the ucsc genopme browser.
Maybe it should work, then you don't need to show the password in the
history .

Mohamed

2016-07-28 10:17 GMT+02:00 Steve Cassidy :

> Hi Mohamed,
>
> The problem with this solution is that the password again becomes part of
> the history since it is one of the inputs to the tool.  If I want to
> publish this workflow then the password can’t be visible.  For this reason
> password storage needs to be outside of workflows and handled somewhere
> else in Galaxy.
>
> Steve
>
>
>
> —
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy
>
> On 28 Jul 2016, at 6:04 PM, Mohamed Kassam  wrote:
>
> Hi Steve,
> there is another solution is that the user is giving his credential via
> the tool. The only thing is missing the tag password on the xml then you
> can encrypt the password.
> I tried to add the new paramter on the build.py but I have some errors,
> don't know if someone arrived to fixed it.
>
> Mohamed
>
> 2016-07-28 10:00 GMT+02:00 Steve Cassidy :
>
>> Hi Mohamed,
>>In my case, the credentials on Galaxy are not generally the same as on
>> the remote system so we need some way to store a second set of credentials
>> in the galaxy session.
>>
>> So, for example, user Fred has an account on Galaxy (f...@here.com) and
>> wants to get data from Alveo as input to a workflow. For the Alveo tools to
>> get data, they need Fred’s access token from Alveo which Fred can retrieve
>> by logging in to the Alveo website.  Fred enters the access key into his
>> preferences in Galaxy.  This key is then passed to one or more tools that
>> access Alveo on his behalf:
>>
>>  - the query tool finds words matching a given pattern from a spoken
>> corpus (needs the token)
>>  - the get-data tool retrieves the audio files for each word (needs the
>> token)
>>  - the automatic alignment tool finds the locations of the vowel sounds
>> in each word
>>  - the annotation storer tool sends these locations back to Alveo as a
>> new annotation set (needs the token)
>>
>> and so on, at various times in the workflow, the tools need to talk to
>> the repository to query, get data or add new data.
>>
>> At the moment, I need the token to be a data item in the history, but it
>> would be better if it were part of the user session in Galaxy.
>>
>> Steve
>>
>>
>> —
>> Department of Computing, Macquarie University
>> http://web.science.mq.edu.au/~cassidy
>>
>> On 28 Jul 2016, at 5:46 PM, Mohamed Kassam  wrote:
>>
>> Hello Cassidy,
>> I have the same problem like you because I need the user credential to
>> access to an external tools.
>> I tried the user session variables available in the tool
>>  xml file: __user__, __user_email__, __user_name__ and __user_id__. I t
>> works perfectly I don't know if you need the password, because this is the
>> only information is missing.
>>
>> Mohamed
>>
>> 2016-07-28 9:42 GMT+02:00 Steve Cassidy :
>>
>>> Hi Bjorn,
>>>  sure, I don’t want to have the credentials stored in the tool but the
>>> tool
>>> needs to act on behalf of the user to retrieve data from the repository,
>>> so
>>> it needs access to credentials.  This could for example be a token
>>> generated
>>> via an OAuth2 exchange - basically something that is sent along with
>>> every
>>> http request to the remote resource to authenticate the user.
>>>
>>> My thought is that this could be stored in the user profile if this can
>>> be made
>>> available to the tool in the same way that __user_email__ is now.
>>>
>>> When you say ‘on the framework level’ do you mean by Galaxy?
>>>
>>> Steve
>>> —
>>> Department of Computing, Macquarie University
>>> http://web.science.mq.edu.au/~cassidy
>>>
>>> > On 28 Jul 2016, at 5:23 PM, Björn Grüning 
>>> wrote:
>>> >
>>> > Hi Steve,
>>> >
>>> > can you explain the larger use-case behind it. Imho you should not
>>> > populate a tool with credentials, this should be handled on the
>>> > framework level.
>>> >
>>> > Hope you are fine,
>>> > Bjoern
>>> >
>>> > Am 28.07.2016 um 03:15 schrieb Steve Cassidy:
>>> >> Hi again,
>>> >>   I’m looking for the right way to store some user credentials in the
>>> >> galaxy session so that tools can work on behalf of the user with our
>>> >> repository.
>>> >>
>>> >> Currently users have an API key and they need to upload it as a data
>>> >> item to that is then passed to each tool that needs it as input.  This
>>> >> doesn’t seem like the right solution since the API key becomes part of
>>> >> the history and so would be shared if the history were shared.
>>> >>
>>> >> What would be better would be a way of storing the API key in the user
>>> >> session and then being able to pass that into a tool.
>>> >>
>>> >> I note that there are a few user session variables available in the
>>> tool
>>> >> xml file: __user__, __user_email__, __user_name__ and __user_id__.
>>> >> There is also a user p

Re: [galaxy-dev] Storing data in the user session

[Steve Cassidy]

Hi Mohamed,

The problem with this solution is that the password again becomes part of the 
history since it is one of the inputs to the tool.  If I want to publish this 
workflow then the password can’t be visible.  For this reason password storage 
needs to be outside of workflows and handled somewhere else in Galaxy.

Steve



—
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy

On 28 Jul 2016, at 6:04 PM, Mohamed Kassam 
mailto:k.mam...@gmail.com>> wrote:

Hi Steve,
there is another solution is that the user is giving his credential via the 
tool. The only thing is missing the tag password on the xml then you can 
encrypt the password.
I tried to add the new paramter on the build.py but I have some errors, don't 
know if someone arrived to fixed it.

Mohamed

2016-07-28 10:00 GMT+02:00 Steve Cassidy 
mailto:steve.cass...@mq.edu.au>>:
Hi Mohamed,
   In my case, the credentials on Galaxy are not generally the same as on the 
remote system so we need some way to store a second set of credentials in the 
galaxy session.

So, for example, user Fred has an account on Galaxy 
(f...@here.com) and wants to get data from Alveo as input 
to a workflow. For the Alveo tools to get data, they need Fred’s access token 
from Alveo which Fred can retrieve by logging in to the Alveo website.  Fred 
enters the access key into his preferences in Galaxy.  This key is then passed 
to one or more tools that access Alveo on his behalf:

 - the query tool finds words matching a given pattern from a spoken corpus 
(needs the token)
 - the get-data tool retrieves the audio files for each word (needs the token)
 - the automatic alignment tool finds the locations of the vowel sounds in each 
word
 - the annotation storer tool sends these locations back to Alveo as a new 
annotation set (needs the token)

and so on, at various times in the workflow, the tools need to talk to the 
repository to query, get data or add new data.

At the moment, I need the token to be a data item in the history, but it would 
be better if it were part of the user session in Galaxy.

Steve


—
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy

On 28 Jul 2016, at 5:46 PM, Mohamed Kassam 
mailto:k.mam...@gmail.com>> wrote:

Hello Cassidy,
I have the same problem like you because I need the user credential to access 
to an external tools.
I tried the user session variables available in the tool
 xml file: __user__, __user_email__, __user_name__ and __user_id__. I t works 
perfectly I don't know if you need the password, because this is the only 
information is missing.

Mohamed

2016-07-28 9:42 GMT+02:00 Steve Cassidy 
mailto:steve.cass...@mq.edu.au>>:
Hi Bjorn,
 sure, I don’t want to have the credentials stored in the tool but the tool
needs to act on behalf of the user to retrieve data from the repository, so
it needs access to credentials.  This could for example be a token generated
via an OAuth2 exchange - basically something that is sent along with every
http request to the remote resource to authenticate the user.

My thought is that this could be stored in the user profile if this can be made
available to the tool in the same way that __user_email__ is now.

When you say ‘on the framework level’ do you mean by Galaxy?

Steve
—
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy

> On 28 Jul 2016, at 5:23 PM, Björn Grüning 
> mailto:bjoern.gruen...@gmail.com>> wrote:
>
> Hi Steve,
>
> can you explain the larger use-case behind it. Imho you should not
> populate a tool with credentials, this should be handled on the
> framework level.
>
> Hope you are fine,
> Bjoern
>
> Am 28.07.2016 um 03:15 schrieb Steve Cassidy:
>> Hi again,
>>   I’m looking for the right way to store some user credentials in the
>> galaxy session so that tools can work on behalf of the user with our
>> repository.
>>
>> Currently users have an API key and they need to upload it as a data
>> item to that is then passed to each tool that needs it as input.  This
>> doesn’t seem like the right solution since the API key becomes part of
>> the history and so would be shared if the history were shared.
>>
>> What would be better would be a way of storing the API key in the user
>> session and then being able to pass that into a tool.
>>
>> I note that there are a few user session variables available in the tool
>> xml file: __user__, __user_email__, __user_name__ and __user_id__.
>> There is also a user preferences page where they can fill out a few
>> details.  However, I can’t see a mechanism to extend this in any way and
>> have extra properties in the preferences pane that would then be
>> available to tools via the template file.
>>
>> I can see that the standard practice for the data sources on
>> usegalaxy.org 
>> > is to send the user off to a
>> repository website to find data that is then 

Re: [galaxy-dev] Storing data in the user session

[Mohamed Kassam]

Hi Steve,
there is another solution is that the user is giving his credential via the
tool. The only thing is missing the tag password on the xml then you can
encrypt the password.
I tried to add the new paramter on the build.py but I have some errors,
don't know if someone arrived to fixed it.

Mohamed

2016-07-28 10:00 GMT+02:00 Steve Cassidy :

> Hi Mohamed,
>In my case, the credentials on Galaxy are not generally the same as on
> the remote system so we need some way to store a second set of credentials
> in the galaxy session.
>
> So, for example, user Fred has an account on Galaxy (f...@here.com) and
> wants to get data from Alveo as input to a workflow. For the Alveo tools to
> get data, they need Fred’s access token from Alveo which Fred can retrieve
> by logging in to the Alveo website.  Fred enters the access key into his
> preferences in Galaxy.  This key is then passed to one or more tools that
> access Alveo on his behalf:
>
>  - the query tool finds words matching a given pattern from a spoken
> corpus (needs the token)
>  - the get-data tool retrieves the audio files for each word (needs the
> token)
>  - the automatic alignment tool finds the locations of the vowel sounds in
> each word
>  - the annotation storer tool sends these locations back to Alveo as a new
> annotation set (needs the token)
>
> and so on, at various times in the workflow, the tools need to talk to the
> repository to query, get data or add new data.
>
> At the moment, I need the token to be a data item in the history, but it
> would be better if it were part of the user session in Galaxy.
>
> Steve
>
>
> —
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy
>
> On 28 Jul 2016, at 5:46 PM, Mohamed Kassam  wrote:
>
> Hello Cassidy,
> I have the same problem like you because I need the user credential to
> access to an external tools.
> I tried the user session variables available in the tool
>  xml file: __user__, __user_email__, __user_name__ and __user_id__. I t
> works perfectly I don't know if you need the password, because this is the
> only information is missing.
>
> Mohamed
>
> 2016-07-28 9:42 GMT+02:00 Steve Cassidy :
>
>> Hi Bjorn,
>>  sure, I don’t want to have the credentials stored in the tool but the
>> tool
>> needs to act on behalf of the user to retrieve data from the repository,
>> so
>> it needs access to credentials.  This could for example be a token
>> generated
>> via an OAuth2 exchange - basically something that is sent along with every
>> http request to the remote resource to authenticate the user.
>>
>> My thought is that this could be stored in the user profile if this can
>> be made
>> available to the tool in the same way that __user_email__ is now.
>>
>> When you say ‘on the framework level’ do you mean by Galaxy?
>>
>> Steve
>> —
>> Department of Computing, Macquarie University
>> http://web.science.mq.edu.au/~cassidy
>>
>> > On 28 Jul 2016, at 5:23 PM, Björn Grüning 
>> wrote:
>> >
>> > Hi Steve,
>> >
>> > can you explain the larger use-case behind it. Imho you should not
>> > populate a tool with credentials, this should be handled on the
>> > framework level.
>> >
>> > Hope you are fine,
>> > Bjoern
>> >
>> > Am 28.07.2016 um 03:15 schrieb Steve Cassidy:
>> >> Hi again,
>> >>   I’m looking for the right way to store some user credentials in the
>> >> galaxy session so that tools can work on behalf of the user with our
>> >> repository.
>> >>
>> >> Currently users have an API key and they need to upload it as a data
>> >> item to that is then passed to each tool that needs it as input.  This
>> >> doesn’t seem like the right solution since the API key becomes part of
>> >> the history and so would be shared if the history were shared.
>> >>
>> >> What would be better would be a way of storing the API key in the user
>> >> session and then being able to pass that into a tool.
>> >>
>> >> I note that there are a few user session variables available in the
>> tool
>> >> xml file: __user__, __user_email__, __user_name__ and __user_id__.
>> >> There is also a user preferences page where they can fill out a few
>> >> details.  However, I can’t see a mechanism to extend this in any way
>> and
>> >> have extra properties in the preferences pane that would then be
>> >> available to tools via the template file.
>> >>
>> >> I can see that the standard practice for the data sources on
>> >> usegalaxy.org  is to send the user off to a
>> >> repository website to find data that is then posted back to the galaxy
>> >> server.  This isn’t appropriate for us since the interaction with the
>> >> repository is not just for downloading a single dataset - tools will
>> >> query the repository, download various kinds of data and possibly
>> upload
>> >> new data, so we need to store user credentials in some way.
>> >>
>> >> Is there already a good way to achieve this or is this an enhancement
>> to
>> >> Galaxy?
>> >>
>> >> Thanks,
>> >>
>> >> St

Re: [galaxy-dev] Storing data in the user session

[Steve Cassidy]

Hi Mohamed,
   In my case, the credentials on Galaxy are not generally the same as on the 
remote system so we need some way to store a second set of credentials in the 
galaxy session.

So, for example, user Fred has an account on Galaxy 
(f...@here.com) and wants to get data from Alveo as input 
to a workflow. For the Alveo tools to get data, they need Fred’s access token 
from Alveo which Fred can retrieve by logging in to the Alveo website.  Fred 
enters the access key into his preferences in Galaxy.  This key is then passed 
to one or more tools that access Alveo on his behalf:

 - the query tool finds words matching a given pattern from a spoken corpus 
(needs the token)
 - the get-data tool retrieves the audio files for each word (needs the token)
 - the automatic alignment tool finds the locations of the vowel sounds in each 
word
 - the annotation storer tool sends these locations back to Alveo as a new 
annotation set (needs the token)

and so on, at various times in the workflow, the tools need to talk to the 
repository to query, get data or add new data.

At the moment, I need the token to be a data item in the history, but it would 
be better if it were part of the user session in Galaxy.

Steve


—
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy

On 28 Jul 2016, at 5:46 PM, Mohamed Kassam 
mailto:k.mam...@gmail.com>> wrote:

Hello Cassidy,
I have the same problem like you because I need the user credential to access 
to an external tools.
I tried the user session variables available in the tool
 xml file: __user__, __user_email__, __user_name__ and __user_id__. I t works 
perfectly I don't know if you need the password, because this is the only 
information is missing.

Mohamed

2016-07-28 9:42 GMT+02:00 Steve Cassidy 
mailto:steve.cass...@mq.edu.au>>:
Hi Bjorn,
 sure, I don’t want to have the credentials stored in the tool but the tool
needs to act on behalf of the user to retrieve data from the repository, so
it needs access to credentials.  This could for example be a token generated
via an OAuth2 exchange - basically something that is sent along with every
http request to the remote resource to authenticate the user.

My thought is that this could be stored in the user profile if this can be made
available to the tool in the same way that __user_email__ is now.

When you say ‘on the framework level’ do you mean by Galaxy?

Steve
—
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy

> On 28 Jul 2016, at 5:23 PM, Björn Grüning 
> mailto:bjoern.gruen...@gmail.com>> wrote:
>
> Hi Steve,
>
> can you explain the larger use-case behind it. Imho you should not
> populate a tool with credentials, this should be handled on the
> framework level.
>
> Hope you are fine,
> Bjoern
>
> Am 28.07.2016 um 03:15 schrieb Steve Cassidy:
>> Hi again,
>>   I’m looking for the right way to store some user credentials in the
>> galaxy session so that tools can work on behalf of the user with our
>> repository.
>>
>> Currently users have an API key and they need to upload it as a data
>> item to that is then passed to each tool that needs it as input.  This
>> doesn’t seem like the right solution since the API key becomes part of
>> the history and so would be shared if the history were shared.
>>
>> What would be better would be a way of storing the API key in the user
>> session and then being able to pass that into a tool.
>>
>> I note that there are a few user session variables available in the tool
>> xml file: __user__, __user_email__, __user_name__ and __user_id__.
>> There is also a user preferences page where they can fill out a few
>> details.  However, I can’t see a mechanism to extend this in any way and
>> have extra properties in the preferences pane that would then be
>> available to tools via the template file.
>>
>> I can see that the standard practice for the data sources on
>> usegalaxy.org 
>> > is to send the user off to a
>> repository website to find data that is then posted back to the galaxy
>> server.  This isn’t appropriate for us since the interaction with the
>> repository is not just for downloading a single dataset - tools will
>> query the repository, download various kinds of data and possibly upload
>> new data, so we need to store user credentials in some way.
>>
>> Is there already a good way to achieve this or is this an enhancement to
>> Galaxy?
>>
>> Thanks,
>>
>> Steve
>>
>>
>> —
>> Department of Computing, Macquarie University
>> http://web.science.mq.edu.au/~cassidy
>> 
>>
>>
>>
>> ___
>> 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 ma

Re: [galaxy-dev] Storing data in the user session

[Mohamed Kassam]

Hello Cassidy,
I have the same problem like you because I need the user credential to
access to an external tools.
I tried the user session variables available in the tool
 xml file: __user__, __user_email__, __user_name__ and __user_id__. I t
works perfectly I don't know if you need the password, because this is the
only information is missing.

Mohamed

2016-07-28 9:42 GMT+02:00 Steve Cassidy :

> Hi Bjorn,
>  sure, I don’t want to have the credentials stored in the tool but the tool
> needs to act on behalf of the user to retrieve data from the repository, so
> it needs access to credentials.  This could for example be a token
> generated
> via an OAuth2 exchange - basically something that is sent along with every
> http request to the remote resource to authenticate the user.
>
> My thought is that this could be stored in the user profile if this can be
> made
> available to the tool in the same way that __user_email__ is now.
>
> When you say ‘on the framework level’ do you mean by Galaxy?
>
> Steve
> —
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy
>
> > On 28 Jul 2016, at 5:23 PM, Björn Grüning 
> wrote:
> >
> > Hi Steve,
> >
> > can you explain the larger use-case behind it. Imho you should not
> > populate a tool with credentials, this should be handled on the
> > framework level.
> >
> > Hope you are fine,
> > Bjoern
> >
> > Am 28.07.2016 um 03:15 schrieb Steve Cassidy:
> >> Hi again,
> >>   I’m looking for the right way to store some user credentials in the
> >> galaxy session so that tools can work on behalf of the user with our
> >> repository.
> >>
> >> Currently users have an API key and they need to upload it as a data
> >> item to that is then passed to each tool that needs it as input.  This
> >> doesn’t seem like the right solution since the API key becomes part of
> >> the history and so would be shared if the history were shared.
> >>
> >> What would be better would be a way of storing the API key in the user
> >> session and then being able to pass that into a tool.
> >>
> >> I note that there are a few user session variables available in the tool
> >> xml file: __user__, __user_email__, __user_name__ and __user_id__.
> >> There is also a user preferences page where they can fill out a few
> >> details.  However, I can’t see a mechanism to extend this in any way and
> >> have extra properties in the preferences pane that would then be
> >> available to tools via the template file.
> >>
> >> I can see that the standard practice for the data sources on
> >> usegalaxy.org  is to send the user off to a
> >> repository website to find data that is then posted back to the galaxy
> >> server.  This isn’t appropriate for us since the interaction with the
> >> repository is not just for downloading a single dataset - tools will
> >> query the repository, download various kinds of data and possibly upload
> >> new data, so we need to store user credentials in some way.
> >>
> >> Is there already a good way to achieve this or is this an enhancement to
> >> Galaxy?
> >>
> >> Thanks,
> >>
> >> Steve
> >>
> >>
> >> —
> >> Department of Computing, Macquarie University
> >> http://web.science.mq.edu.au/~cassidy
> >> 
> >>
> >>
> >>
> >> ___
> >> 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/mailinglists/
>
> ___
> 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/mailinglists/
___
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/mailinglists/

Re: [galaxy-dev] Storing data in the user session

[Steve Cassidy]

Hi Bjorn,
 sure, I don’t want to have the credentials stored in the tool but the tool 
needs to act on behalf of the user to retrieve data from the repository, so
it needs access to credentials.  This could for example be a token generated
via an OAuth2 exchange - basically something that is sent along with every 
http request to the remote resource to authenticate the user.  

My thought is that this could be stored in the user profile if this can be made
available to the tool in the same way that __user_email__ is now. 

When you say ‘on the framework level’ do you mean by Galaxy? 

Steve
—
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy

> On 28 Jul 2016, at 5:23 PM, Björn Grüning  wrote:
> 
> Hi Steve,
> 
> can you explain the larger use-case behind it. Imho you should not
> populate a tool with credentials, this should be handled on the
> framework level.
> 
> Hope you are fine,
> Bjoern
> 
> Am 28.07.2016 um 03:15 schrieb Steve Cassidy:
>> Hi again,
>>   I’m looking for the right way to store some user credentials in the
>> galaxy session so that tools can work on behalf of the user with our
>> repository. 
>> 
>> Currently users have an API key and they need to upload it as a data
>> item to that is then passed to each tool that needs it as input.  This
>> doesn’t seem like the right solution since the API key becomes part of
>> the history and so would be shared if the history were shared.  
>> 
>> What would be better would be a way of storing the API key in the user
>> session and then being able to pass that into a tool.
>> 
>> I note that there are a few user session variables available in the tool
>> xml file: __user__, __user_email__, __user_name__ and __user_id__.
>> There is also a user preferences page where they can fill out a few
>> details.  However, I can’t see a mechanism to extend this in any way and
>> have extra properties in the preferences pane that would then be
>> available to tools via the template file.  
>> 
>> I can see that the standard practice for the data sources on
>> usegalaxy.org  is to send the user off to a
>> repository website to find data that is then posted back to the galaxy
>> server.  This isn’t appropriate for us since the interaction with the
>> repository is not just for downloading a single dataset - tools will
>> query the repository, download various kinds of data and possibly upload
>> new data, so we need to store user credentials in some way. 
>> 
>> Is there already a good way to achieve this or is this an enhancement to
>> Galaxy? 
>> 
>> Thanks,
>> 
>> Steve
>> 
>> 
>> —
>> Department of Computing, Macquarie University
>> http://web.science.mq.edu.au/~cassidy
>> 
>> 
>> 
>> 
>> ___
>> 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/mailinglists/

___
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/mailinglists/

Re: [galaxy-dev] Storing data in the user session

[Björn Grüning]

Hi Steve,

can you explain the larger use-case behind it. Imho you should not
populate a tool with credentials, this should be handled on the
framework level.

Hope you are fine,
Bjoern

Am 28.07.2016 um 03:15 schrieb Steve Cassidy:
> Hi again,
>I’m looking for the right way to store some user credentials in the
> galaxy session so that tools can work on behalf of the user with our
> repository. 
> 
> Currently users have an API key and they need to upload it as a data
> item to that is then passed to each tool that needs it as input.  This
> doesn’t seem like the right solution since the API key becomes part of
> the history and so would be shared if the history were shared.  
> 
> What would be better would be a way of storing the API key in the user
> session and then being able to pass that into a tool.
> 
> I note that there are a few user session variables available in the tool
> xml file: __user__, __user_email__, __user_name__ and __user_id__.
>  There is also a user preferences page where they can fill out a few
> details.  However, I can’t see a mechanism to extend this in any way and
> have extra properties in the preferences pane that would then be
> available to tools via the template file.  
> 
> I can see that the standard practice for the data sources on
> usegalaxy.org  is to send the user off to a
> repository website to find data that is then posted back to the galaxy
> server.  This isn’t appropriate for us since the interaction with the
> repository is not just for downloading a single dataset - tools will
> query the repository, download various kinds of data and possibly upload
> new data, so we need to store user credentials in some way. 
> 
> Is there already a good way to achieve this or is this an enhancement to
> Galaxy? 
> 
> Thanks,
> 
> Steve
> 
> 
> —
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy
> 
> 
> 
> 
> ___
> 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/mailinglists/
> 
___
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/mailinglists/