Hello Olivia,

Great, thanks for the clarification! It took me a little bit, but I
have caught up. First - you don't need to justify using bioblend over
the provided scripts in galaxy distribution. Anything non-trivial
should be using bioblend (if it weren't going to make me very
unpopular I would just delete scripts/api out of Galaxy).

There are a couple problems here - but the main one is simply that the
roles param is taking in something odd as an argument - namely the
unencoded integer id of the role as a string - it probably makes
perfect sense for the UI to deal with things this way but it doesn't
fit well with the API. Here
(https://github.com/jmchilton/galaxy-central/commit/11377929a679fb3391481e35227bcccd7e96a497.patch)
is a patch you can apply to Galaxy to make it work the way you are
trying to get it to work (allowing roles to take in a single role
name). Just apply that to Galaxy and I imagine your example will work
as is.

However, this is not "the right" way for it to work however so I am
not going to apply it Galaxy directly but it is a very isolated change
you can apply to your Galaxy instance if your comfortable with that.
In an ideal implementation - there are many different permission types
that should be exposed and the API should be consuming encoded role
ids (as obtained from /api/roles) - but the backend isn't implemented
for this first part and bioblend doesn't have a roles client for the
second.

I have created a Trello card for this feature: https://trello.com/c/qsQHnFlG.

Let me know if you have any additional questions or if this is unclear
in any way.

-John

On Sun, Jan 5, 2014 at 3:35 AM, Olivia Doppelt
<olivia.dopp...@pasteur.fr> wrote:
> Hello again,
> I just reminded a capital thing concerning the api script
> library_upload_from_import_dir.py. Actually it only works for admin users.
> simple users don't have the authorization to upload anything in their galaxy
> library using this script. It is the main reason why we choose to user
> bioblend.
> --
> Olivia
>
>
> Le 04/01/14 22:10, Olivia Doppelt a écrit :
>
>
> Le 03/01/14 15:44, John Chilton a écrit :
>
> I am not sure I understand the problem. Can you clarify a few points:
>
> Is bioblend letting users associate roles with data libraries that
> they shouldn't be able to and the operation is succeeding -or- are you
> trying to add roles and the operation is failing?
>
> Dear John,
>
> In our Galaxy instance, each user connecting to Galaxy has a library
> associated to its user role which is created automatically as well as two
> directories; one in the links directory corresponding to our
> "user_library_import_dir" and one in an "output" directory to enable the
> users to export their results from the instance.
>
> The user directories are readable by Galaxy and by themselves (unix rights
> are set using a root cron script)
>
> For a project, we need to do basic galaxy stuff using either the API scripts
> or bioblend api. We have tried both and bioblend is a little simpler to use.
>
> Using the api script library_upload_from_import_dir.py, using a user api
> key, only files from the user directory are "uploadable".
>
> However, using bioblend function from libraries class
> "upload_file_from_server", a user with its key can upload within its galaxy
> library, the data of anyone.
>
> #giOlivia.libraries.upload_file_from_server("OLIVIA_API_key","/xxxxxxx/links/otheru...@pasteur.fr/","F0045a9ffd77d1226")
>
>
> To disable this, i'm trying to add an associate role when I launch the
> upload_file_from_server command but I get an error.
>
> giOlivia.libraries.upload_file_from_server("OLIVIA_API_key","/xxxxxxxx/links/oli...@pasteur.fr/",
> "F0045a9ffd77d1226", roles='oli...@pasteur.fr')
>
> and I get the following error:
>
> Traceback (most recent call last):   File "<input>", line 1, in <module>
> File
> "/usr/local/lib/python2.7/dist-packages/bioblend-0.4.2_dev-py2.7.egg/bioblend/galaxy/libraries/__init__.py",
> line 242, in upload_file_from_server     return self._do_upload(**vars)
> File
> "/usr/local/lib/python2.7/dist-packages/bioblend-0.4.2_dev-py2.7.egg/bioblend/galaxy/libraries/__init__.py",
> line 190, in _do_upload     files_attached=files_attached)   File
> "/usr/local/lib/python2.7/dist-packages/bioblend-0.4.2_dev-py2.7.egg/bioblend/galaxy/client.py",
> line 71, in _post     r = self.gi.make_post_request(url, payload=payload,
> files_attached=files_attached)   File
> "/usr/local/lib/python2.7/dist-packages/bioblend-0.4.2_dev-py2.7.egg/bioblend/galaxyclient.py",
> line 94, in make_post_request     r.status_code, body=r.text)     # @see
> self.body for HTTP response body ConnectionError: Unexpected response from
> galaxy: 500: <html>   <head><title>Internal Server Error</title></head>
> <body>     <h1>Internal Server Error</h1>     <p>The server has either erred
> or is incapable of performing the requested operation.
> <br/> <!--  --></p>     <hr noshade>     <div align="right">WSGI
> Server</div>   </body> </html>
>
>
> If the API is producing an error message can you share that: in
> particular this code is probably resulting in an error or some kind?
>
>             elif roles:
>                 # Check to see if the user selected roles to associate
> with the DATASET_ACCESS permission
>                 # on the dataset that would cause accessibility issues.
>                 vars = dict( DATASET_ACCESS_in=roles )
>                 permissions, in_roles, error, message = \
>                     trans.app.security_agent.derive_roles_from_access(
> trans, library.id, cntrller, library=True, **vars )
>             if error:
>                 if cntrller == 'api':
>                     return 400, message
>
>
> the api does not produce any error when the api key corresponds to the user
> which tries to import its own data.
>
>
> Has your institute made modifications Galaxy to enforce this
> constraint - ("it can't be possible that any user may upload any other
> user's data in their Galaxy Data library")? Also is the thing you are
> trying to do something that is working through the web ui but not
> through the API, or have you only tried through the API?
>
>
> I did a few tests yesterday, and to resume, it works as it should using the
> api script but there is a problem using bioblend.
> I'm not sure that roles are really needed here, i only thought that it could
> guide galaxy (and bioblend) to not upload data that does not belong to user
> (corresponding to the API key)
>
> I looked at the sources, and my major doubt was that bioblend didn't pass
> all the arguments but it does, everything is transmitted to galaxy do it
> should work.
>
> Tell me if you need more information. I'll look further on monday but i'm
> kind of stuck.
>
> Thank you for your help,
>
> Cheers,
>
> --
> Olivia Doppelt-Azeroual, PhD
> CIB - Institut Pasteur
>
>
>
> On Fri, Jan 3, 2014 at 5:36 AM, Olivia Doppelt
> <olivia.dopp...@pasteur.fr> wrote:
>
> Hello to all,
>
> I'm trying to use the function  "upload_file_from_server" from the galaxy
> libraries api of Bioblend.
>
> It's working correctly when i don't associate any role to the arguments.
> However, in our architecture (Institut Pasteur, Paris) it can't be possible
> that any user may upload any other user's data in their Galaxy Data library.
>
> Thus, it is how ""upload_file_from_server" is working at the moment.
>
> As I understand the problem, it doesn't come from Bioblend itself, as all
> arguments (as well as roles) are well transmitted on the server side.
>
> could somebody help me with that ?
>
> Happy new Year !!! and Have a nice day,
>
> --
> Olivia Doppelt-Azeroual, PhD
> Tel: 92 15
> CIB - Institut Pasteur
>
>
> ___________________________________________________________
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>
>
>
> ___________________________________________________________
> 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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>
>
>
> --
> Olivia Doppelt-Azeroual, PhD
> Tel: 92 15
> CIB - Institut Pasteur

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