From olivia.doppelt@pasteur.fr Sun Jan 5 04:35:12 2014 From: Olivia Doppelt To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] BioBlend AND Galaxy: Problem using upload_file_from_server function with an associated role Date: Sun, 05 Jan 2014 10:35:03 +0100 Message-ID: <52C92747.6010903@pasteur.fr> In-Reply-To: <52C878DE.8020501@pasteur.fr> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============6857669158848256682==" --===============6857669158848256682== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Hello again, I just reminded a capital thing concerning the api script=20 library_upload_from_import_dir.py. Actually it only works for admin=20 users. simple users don't have the authorization to upload anything in=20 their galaxy library using this script. It is the main reason why we=20 choose to user bioblend. -- Olivia Le 04/01/14 22:10, Olivia Doppelt a =C3=A9crit : > > Le 03/01/14 15:44, John Chilton a =C3=A9crit : >> 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=20 > associated to its user role which is created automatically as well as=20 > two directories; one in the links directory corresponding to our=20 > "user_library_import_dir" and one in an "output" directory to enable=20 > the users to export their results from the instance. > > The user directories are readable by Galaxy and by themselves (unix=20 > rights are set using a root cron script) > > For a project, we need to do basic galaxy stuff using either the API=20 > scripts or bioblend api. We have tried both and bioblend is a little=20 > simpler to use. > > Using the api script library_upload_from_import_dir.py, using a user=20 > api key, only files from the user directory are "uploadable". > > However, using bioblend function from libraries class=20 > "upload_file_from_server", a user with its key can upload within its=20 > galaxy library, the data of anyone. > > #giOlivia.libraries.upload_file_from_server("OLIVIA_API_key","/xxxxxxx/link= s/otherUser(a)pasteur.fr/","F0045a9ffd77d1226") > > > To disable this, i'm trying to add an associate role when I launch the=20 > upload_file_from_server command but I get an error. > > giOlivia.libraries.upload_file_from_server("OLIVIA_API_key","/xxxxxxxx/link= s/olivia(a)pasteur.fr/",=20 > "F0045a9ffd77d1226", roles=3D'olivia(a)pasteur.fr') > > and I get the following error: >> Traceback (most recent call last): >> >> File "", line 1, in >> >> File=20 >> "/usr/local/lib/python2.7/dist-packages/bioblend-0.4.2_dev-py2.7.egg/biobl= end/galaxy/libraries/__init__.py",=20 >> line 242, in upload_file_from_server >> >> return self._do_upload(**vars) >> >> File=20 >> "/usr/local/lib/python2.7/dist-packages/bioblend-0.4.2_dev-py2.7.egg/biobl= end/galaxy/libraries/__init__.py",=20 >> line 190, in _do_upload >> >> files_attached=3Dfiles_attached) >> >> File=20 >> "/usr/local/lib/python2.7/dist-packages/bioblend-0.4.2_dev-py2.7.egg/biobl= end/galaxy/client.py",=20 >> line 71, in _post >> >> r =3D self.gi.make_post_request(url, payload=3Dpayload,=20 >> files_attached=3Dfiles_attached) >> >> File=20 >> "/usr/local/lib/python2.7/dist-packages/bioblend-0.4.2_dev-py2.7.egg/biobl= end/galaxyclient.py",=20 >> line 94, in make_post_request >> >> r.status_code, body=3Dr.text) # @see self.body for HTTP=20 >> response body >> >> ConnectionError: Unexpected response from galaxy: 500: >> >> Internal Server Error >> >> >> >>

Internal Server Error

>> >>

The server has either erred or is incapable of performing >> >> the requested operation. >> >> >>
>> >>

>> >>

WSGI Server

>> >> >> >> >> > >> 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 =3D dict( DATASET_ACCESS_in=3Droles ) >> permissions, in_roles, error, message =3D \ >> trans.app.security_agent.derive_roles_from_access( >> trans, library.id, cntrller, library=3DTrue, **vars ) >> if error: >> if cntrller =3D=3D 'api': >> return 400, message > > the api does not produce any error when the api key corresponds to the=20 > 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=20 > 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=20 > could guide galaxy (and bioblend) to not upload data that does not=20 > belong to user (corresponding to the API key) > > I looked at the sources, and my major doubt was that bioblend didn't=20 > pass all the arguments but it does, everything is transmitted to=20 > galaxy do it should work. > > Tell me if you need more information. I'll look further on monday but=20 > i'm kind of stuck. > > Thank you for your help, > > Cheers, > > --=20 > Olivia Doppelt-Azeroual, PhD > CIB - Institut Pasteur > > >> On Fri, Jan 3, 2014 at 5:36 AM, Olivia Doppelt >> 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 possib= le >>> that any user may upload any other user's data in their Galaxy Data libra= ry. >>> >>> 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 >>> >>> >>> ___________________________________________________________ >>> 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: >>> http://lists.bx.psu.edu/ >>> >>> 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: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ --=20 Olivia Doppelt-Azeroual, PhD Tel: 92 15 CIB - Institut Pasteur --===============6857669158848256682== Content-Type: text/html Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="attachment.htm" MIME-Version: 1.0 PGh0bWw+CiAgPGhlYWQ+CiAgICA8bWV0YSBjb250ZW50PSJ0ZXh0L2h0bWw7IGNoYXJzZXQ9SVNP LTg4NTktMSIKICAgICAgaHR0cC1lcXVpdj0iQ29udGVudC1UeXBlIj4KICA8L2hlYWQ+CiAgPGJv ZHkgYmdjb2xvcj0iI0ZGRkZGRiIgdGV4dD0iIzAwMDAwMCI+CiAgICA8ZGl2IGNsYXNzPSJtb3ot Y2l0ZS1wcmVmaXgiPkhlbGxvIGFnYWluLCA8YnI+CiAgICAgIEkganVzdCByZW1pbmRlZCBhIGNh cGl0YWwgdGhpbmcgY29uY2VybmluZyB0aGUgYXBpIHNjcmlwdAogICAgICBsaWJyYXJ5X3VwbG9h ZF9mcm9tX2ltcG9ydF9kaXIucHkuIEFjdHVhbGx5IGl0IG9ubHkgd29ya3MgZm9yCiAgICAgIGFk 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