Re: [galaxy-dev] how to create users through Galaxy API?

2016-09-02 Thread Björn Grüning 
Hi,

and here a script used by the Galaxy Docker project:

https://github.com/bgruening/docker-galaxy-stable/blob/master/galaxy/setup_postgresql.py

Cheers,
Bjoern

Am 30.08.2016 um 11:56 schrieb Peter Cock:
> Thanks Nicola & Peter B.,
> 
> I was hoping we could script new-user creation like this, and
> that someone else had already done this with the Galaxy API
> (and Bioblend). This looks great!
> 
> Thank you both,
> 
> Peter C.
> 
> On Tue, Aug 30, 2016 at 10:43 AM, Peter Briggs
>  wrote:
>> Hello Peter
>>
>> Following on from Nicola's suggestion: a while ago I had a go at writing
>> some command line tools using Bioblend to try and do some of my Galaxy admin
>> tasks via the API, including creating new user accounts so I'd also
>> recommend this route as much much easier than attempting to interact with
>> the API directly.
>>
>> The tools I wrote are here if you'd like to look at some an example of using
>> Bioblend for this, to get you started:
>>
>> https://github.com/pjbriggs/nebulizer/blob/master/nebulizer/users.py
>>
>> As long as the user that the API key belongs to is an admin user (or if
>> you're using a master API key) this works fine.
>>
>> HTH
>>
>> Best wishes
>>
>> Peter
>>
>>
>> On 29/08/16 17:37, Nicola Soranzo wrote:
>>>
>>> Hi Peter,
>>> why not use BioBlend?
>>>
>>>
>>> https://bioblend.readthedocs.io/en/latest/api_docs/galaxy/all.html#module-bioblend.galaxy.users
>>>
>>> Cheers,
>>> Nicola
>>>
>>>  Peter Cock ha scritto 
>>>
 Thanks Hans-Rudolf,

 Yes - you are right. The wiki does link there but it wasn't obvious to
 me.
 Reading the UserAPIController link source code suggests as long as
 I am authenticated as a Galaxy Admin, I could use this to create new
 user accounts:


 https://docs.galaxyproject.org/en/master/_modules/galaxy/webapps/galaxy/api/users.html#UserAPIController.create

 Thank looks very promising...

 Peter

 On Mon, Aug 29, 2016 at 4:36 PM, Hans-Rudolf Hotz  wrote:
>
> Hi Peter
>
> I guess it is here:
>
> https://docs.galaxyproject.org/en/master/api_doc.html
>
>
> Regards,  Hans-Rudolf
>
> On 08/29/2016 05:27 PM, Peter Cock wrote:
>>
>>
>> Hi Martin,
>>
>> I'd like to look into creating new users via the API (where we can
>> control the email address and username format for integration with our
>> cluster), and have the web-interface forbid users from
>> self-registration.
>>
>> The read-the-docs site you mentioned in this old email (below) doesn't
>> exist anymore, and the API wiki page doesn't seem to link to something
>> similar:
>>
>> https://wiki.galaxyproject.org/Admin/API
>>
>> Where is the official API documentation now?
>>
>> Thanks,
>>
>> Peter
>>
>> On Mon, Dec 30, 2013 at 4:34 AM, Martin Čech > > wrote:
>>
>> Hi,
>>
>> you specify username, password and email in the body (payload) of
>> the POST as Key:Value pairs.
>>
>> Code from the API method: (
>>
>>
>> https://galaxy-central.readthedocs.org/en/latest/_modules/galaxy/webapps/galaxy/api/users.html#UserAPIController.create
>>
>>
>> 
>> )
>>
>>
>>
>> username=payload['username']email=payload['email']password=payload['password']
>>
>> There are also other conditions that need to be fulfilled (e.g.
>> user
>> creation has to be turned on in the configuration) - you will find
>> these when you look at the source code of the method (because the
>> documentation is not perfect yet, sorry).
>>
>> M.
>>
>>
>>
>>
>> ___
>> 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:
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 To search Galaxy mailing lists use the unified search at:
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>>>
>>> ___
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>>> in your mail client.  To manage your subscriptions to this
>>>

Re: [galaxy-dev] how to create users through Galaxy API?

2016-08-30 Thread Peter Cock 
Thanks Nicola & Peter B.,

I was hoping we could script new-user creation like this, and
that someone else had already done this with the Galaxy API
(and Bioblend). This looks great!

Thank you both,

Peter C.

On Tue, Aug 30, 2016 at 10:43 AM, Peter Briggs
 wrote:
> Hello Peter
>
> Following on from Nicola's suggestion: a while ago I had a go at writing
> some command line tools using Bioblend to try and do some of my Galaxy admin
> tasks via the API, including creating new user accounts so I'd also
> recommend this route as much much easier than attempting to interact with
> the API directly.
>
> The tools I wrote are here if you'd like to look at some an example of using
> Bioblend for this, to get you started:
>
> https://github.com/pjbriggs/nebulizer/blob/master/nebulizer/users.py
>
> As long as the user that the API key belongs to is an admin user (or if
> you're using a master API key) this works fine.
>
> HTH
>
> Best wishes
>
> Peter
>
>
> On 29/08/16 17:37, Nicola Soranzo wrote:
>>
>> Hi Peter,
>> why not use BioBlend?
>>
>>
>> https://bioblend.readthedocs.io/en/latest/api_docs/galaxy/all.html#module-bioblend.galaxy.users
>>
>> Cheers,
>> Nicola
>>
>>  Peter Cock ha scritto 
>>
>>> Thanks Hans-Rudolf,
>>>
>>> Yes - you are right. The wiki does link there but it wasn't obvious to
>>> me.
>>> Reading the UserAPIController link source code suggests as long as
>>> I am authenticated as a Galaxy Admin, I could use this to create new
>>> user accounts:
>>>
>>>
>>> https://docs.galaxyproject.org/en/master/_modules/galaxy/webapps/galaxy/api/users.html#UserAPIController.create
>>>
>>> Thank looks very promising...
>>>
>>> Peter
>>>
>>> On Mon, Aug 29, 2016 at 4:36 PM, Hans-Rudolf Hotz  wrote:

 Hi Peter

 I guess it is here:

 https://docs.galaxyproject.org/en/master/api_doc.html


 Regards,  Hans-Rudolf

 On 08/29/2016 05:27 PM, Peter Cock wrote:
>
>
> Hi Martin,
>
> I'd like to look into creating new users via the API (where we can
> control the email address and username format for integration with our
> cluster), and have the web-interface forbid users from
> self-registration.
>
> The read-the-docs site you mentioned in this old email (below) doesn't
> exist anymore, and the API wiki page doesn't seem to link to something
> similar:
>
> https://wiki.galaxyproject.org/Admin/API
>
> Where is the official API documentation now?
>
> Thanks,
>
> Peter
>
> On Mon, Dec 30, 2013 at 4:34 AM, Martin Čech  > wrote:
>
> Hi,
>
> you specify username, password and email in the body (payload) of
> the POST as Key:Value pairs.
>
> Code from the API method: (
>
>
> https://galaxy-central.readthedocs.org/en/latest/_modules/galaxy/webapps/galaxy/api/users.html#UserAPIController.create
>
>
> 
> )
>
>
>
> username=payload['username']email=payload['email']password=payload['password']
>
> There are also other conditions that need to be fulfilled (e.g.
> user
> creation has to be turned on in the configuration) - you will find
> these when you look at the source code of the method (because the
> documentation is not perfect yet, sorry).
>
> M.
>
>
>
>
> ___
> 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/
>>
>
> --
> Peter Briggs peter.bri...@manchester.ac.uk
> Bioinformatics Core Facility University of Manchester
> B.1083 Michael Smith Bldg Tel: (0161) 2751482
>
>

Re: [galaxy-dev] how to create users through Galaxy API?

2016-08-30 Thread Peter Briggs 

Hello Peter

Following on from Nicola's suggestion: a while ago I had a go at writing 
some command line tools using Bioblend to try and do some of my Galaxy 
admin tasks via the API, including creating new user accounts so I'd 
also recommend this route as much much easier than attempting to 
interact with the API directly.


The tools I wrote are here if you'd like to look at some an example of 
using Bioblend for this, to get you started:


https://github.com/pjbriggs/nebulizer/blob/master/nebulizer/users.py

As long as the user that the API key belongs to is an admin user (or if 
you're using a master API key) this works fine.


HTH

Best wishes

Peter

On 29/08/16 17:37, Nicola Soranzo wrote:

Hi Peter,
why not use BioBlend?

https://bioblend.readthedocs.io/en/latest/api_docs/galaxy/all.html#module-bioblend.galaxy.users

Cheers,
Nicola

 Peter Cock ha scritto 


Thanks Hans-Rudolf,

Yes - you are right. The wiki does link there but it wasn't obvious to me.
Reading the UserAPIController link source code suggests as long as
I am authenticated as a Galaxy Admin, I could use this to create new
user accounts:

https://docs.galaxyproject.org/en/master/_modules/galaxy/webapps/galaxy/api/users.html#UserAPIController.create

Thank looks very promising...

Peter

On Mon, Aug 29, 2016 at 4:36 PM, Hans-Rudolf Hotz  wrote:

Hi Peter

I guess it is here:

https://docs.galaxyproject.org/en/master/api_doc.html


Regards,  Hans-Rudolf

On 08/29/2016 05:27 PM, Peter Cock wrote:


Hi Martin,

I'd like to look into creating new users via the API (where we can
control the email address and username format for integration with our
cluster), and have the web-interface forbid users from self-registration.

The read-the-docs site you mentioned in this old email (below) doesn't
exist anymore, and the API wiki page doesn't seem to link to something
similar:

https://wiki.galaxyproject.org/Admin/API

Where is the official API documentation now?

Thanks,

Peter

On Mon, Dec 30, 2013 at 4:34 AM, Martin Čech > wrote:

Hi,

you specify username, password and email in the body (payload) of
the POST as Key:Value pairs.

Code from the API method: (

https://galaxy-central.readthedocs.org/en/latest/_modules/galaxy/webapps/galaxy/api/users.html#UserAPIController.create


)


username=payload['username']email=payload['email']password=payload['password']

There are also other conditions that need to be fulfilled (e.g. user
creation has to be turned on in the configuration) - you will find
these when you look at the source code of the method (because the
documentation is not perfect yet, sorry).

M.




___
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___
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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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--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] how to create users through Galaxy API?

2016-08-29 Thread Nicola Soranzo 
Hi Peter,
why not use BioBlend?

https://bioblend.readthedocs.io/en/latest/api_docs/galaxy/all.html#module-bioblend.galaxy.users

Cheers,
Nicola

 Peter Cock ha scritto 

>Thanks Hans-Rudolf,
>
>Yes - you are right. The wiki does link there but it wasn't obvious to me.
>Reading the UserAPIController link source code suggests as long as
>I am authenticated as a Galaxy Admin, I could use this to create new
>user accounts:
>
>https://docs.galaxyproject.org/en/master/_modules/galaxy/webapps/galaxy/api/users.html#UserAPIController.create
>
>Thank looks very promising...
>
>Peter
>
>On Mon, Aug 29, 2016 at 4:36 PM, Hans-Rudolf Hotz  wrote:
>> Hi Peter
>>
>> I guess it is here:
>>
>> https://docs.galaxyproject.org/en/master/api_doc.html
>>
>>
>> Regards,  Hans-Rudolf
>>
>> On 08/29/2016 05:27 PM, Peter Cock wrote:
>>>
>>> Hi Martin,
>>>
>>> I'd like to look into creating new users via the API (where we can
>>> control the email address and username format for integration with our
>>> cluster), and have the web-interface forbid users from self-registration.
>>>
>>> The read-the-docs site you mentioned in this old email (below) doesn't
>>> exist anymore, and the API wiki page doesn't seem to link to something
>>> similar:
>>>
>>> https://wiki.galaxyproject.org/Admin/API
>>>
>>> Where is the official API documentation now?
>>>
>>> Thanks,
>>>
>>> Peter
>>>
>>> On Mon, Dec 30, 2013 at 4:34 AM, Martin Čech >> > wrote:
>>>
>>> Hi,
>>>
>>> you specify username, password and email in the body (payload) of
>>> the POST as Key:Value pairs.
>>>
>>> Code from the API method: (
>>>
>>> https://galaxy-central.readthedocs.org/en/latest/_modules/galaxy/webapps/galaxy/api/users.html#UserAPIController.create
>>>
>>> 
>>> )
>>>
>>>
>>> username=payload['username']email=payload['email']password=payload['password']
>>>
>>> There are also other conditions that need to be fulfilled (e.g. user
>>> creation has to be turned on in the configuration) - you will find
>>> these when you look at the source code of the method (because the
>>> documentation is not perfect yet, sorry).
>>>
>>> M.
>>>
>>>
>>>
>>>
>>> ___
>>> 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:
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Re: [galaxy-dev] how to create users through Galaxy API?

2016-08-29 Thread Hans-Rudolf Hotz 

Hi Peter

I guess it is here:

https://docs.galaxyproject.org/en/master/api_doc.html


Regards,  Hans-Rudolf

On 08/29/2016 05:27 PM, Peter Cock wrote:

Hi Martin,

I'd like to look into creating new users via the API (where we can
control the email address and username format for integration with our
cluster), and have the web-interface forbid users from self-registration.

The read-the-docs site you mentioned in this old email (below) doesn't
exist anymore, and the API wiki page doesn't seem to link to something
similar:

https://wiki.galaxyproject.org/Admin/API

Where is the official API documentation now?

Thanks,

Peter

On Mon, Dec 30, 2013 at 4:34 AM, Martin Čech > wrote:

Hi,

you specify username, password and email in the body (payload) of
the POST as Key:Value pairs.

Code from the API method: (

https://galaxy-central.readthedocs.org/en/latest/_modules/galaxy/webapps/galaxy/api/users.html#UserAPIController.create


)


username=payload['username']email=payload['email']password=payload['password']

There are also other conditions that need to be fulfilled (e.g. user
creation has to be turned on in the configuration) - you will find
these when you look at the source code of the method (because the
documentation is not perfect yet, sorry).

M.




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

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   http://galaxyproject.org/search/mailinglists/


___
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