From kmuret@sb-roscoff.fr Tue Apr 15 03:17:52 2014 From: Kevin Muret To: galaxy-dev@lists.galaxyproject.org Subject: [galaxy-dev] Problem with the "set_library_permissions" function on bioblend Date: Tue, 15 Apr 2014 09:17:34 +0200 Message-ID: <534CDD0E.7030302@sb-roscoff.fr> In-Reply-To: <5754ab7e223f1f2ebbbd42b03ce792d2.squirrel@application.sb-roscoff.fr> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============6052147176930542059==" --===============6052147176930542059== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Hello to all, In recent days, I try to do the "set_library_permissions ()" bioblend's f= unction working. =20 I tried the following syntaxes, and it was unsuccessful. Anybody know ho= w to use it? Or otherwise,how would it be possible to modify user access= to libraries (or contents)? ---------------------------------------------- Bonjour =C3=A0 tous, Depuis quelques jours, je tente de faire fonctionner la fonction "set_library= _permissions()". J'ai tent=C3=A9 les syntaxes suivantes, et ce f=C3=BBt sans succ=C3=A8s. Quel= qu'un saurait-il comment l'utiliser ? Ou comment serait-il possible de modifi= er les acc=C3=A8s utilisateurs d'une autre mani=C3=A8re ? ---------------------------------------------- "instance" is opened with an admin API key. 1 --> print instance.libraries.set_library_permissions(library_id=3D"417e331= 44b294c21", access_in=3DNone, modify_in=3DNone, add_in=3DNone, manage_in=3DNo= ne) Traceback (most recent call last): File "Workflow_Lib/work_test.py", line 76, in main() File "Workflow_Lib/work_test.py", line 39, in main print instance.libraries.set_library_permissions(library_id=3D"417e33144= b294c21", access_in=3DNone, modify_in=3DNone, add_in=3DNone, manage_in=3DNone) File "/home/gcc2013/lib/bioblend/lib/python2.7/site-packages/bioblend-0.4.= 3_dev-py2.7.egg/bioblend/galaxy/libraries/__init__.py", line 308, in set_libr= ary_permissions return Client._post(self, payload, url=3Durl) File "/home/gcc2013/lib/bioblend/lib/python2.7/site-packages/bioblend-0.4.= 3_dev-py2.7.egg/bioblend/galaxy/client.py", line 181, in _post r =3D self.gi.make_post_request(url, payload=3Dpayload, files_attached= =3Dfiles_attached) File "/home/gcc2013/lib/bioblend/lib/python2.7/site-packages/bioblend-0.4.= 3_dev-py2.7.egg/bioblend/galaxyclient.py", line 99, in make_post_request r.status_code, body=3Dr.text) # @see self.body for HTTP response body bioblend.galaxy.client.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

2 --> print instance.libraries.set_library_permissions(library_id=3D"417e3314= 4b294c21", access_in=3D[admin_id], modify_in=3D[admin_id], add_in=3D[admin_id= ], manage_in=3D[admin_id]) 3 --> Moreover,are we supposed to view the content of this page?http://lo= calhost:8080/api/libraries/417e33144b294c21/permissions =20 ---------------------------------------------- Thank you in advance to the community for your help, Kevin MURET Intern at Station Biologique de Roscoff ABiMS platform --===============6052147176930542059== Content-Type: text/html Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="attachment.htm" MIME-Version: 1.0 PGh0bWw+CiAgPGhlYWQ+CiAgICA8bWV0YSBjb250ZW50PSJ0ZXh0L2h0bWw7IGNoYXJzZXQ9SVNP LTg4NTktMSIKICAgICAgaHR0cC1lcXVpdj0iQ29udGVudC1UeXBlIj4KICA8L2hlYWQ+CiAgPGJv ZHkgYmdjb2xvcj0iI0ZGRkZGRiIgdGV4dD0iIzAwMDAwMCI+CiAgICA8cHJlIHdyYXA9IiI+SGVs bG8gdG8gYWxsLAoKPHNwYW4gaWQ9InJlc3VsdF9ib3giIGNsYXNzPSIiIGxhbmc9ImVuIj48c3Bh 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b2dpcXVlIGRlIFJvc2NvZmYKQUJpTVMgcGxhdGZvcm0KPC9wcmU+CiAgPC9ib2R5Pgo8L2h0bWw+ Cg== --===============6052147176930542059==-- From jmchilton@gmail.com Thu Apr 17 15:32:11 2014 From: John Chilton To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Problem with the "set_library_permissions" function on bioblend Date: Thu, 17 Apr 2014 14:32:00 -0500 Message-ID: In-Reply-To: <534CDD0E.7030302@sb-roscoff.fr> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============7429089423217456389==" --===============7429089423217456389== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable This API controller broke with the latest release from earlier this week - I have since fixed this in galaxy-central and opened a pull request to have it fixed in the stable branch. Otherwise I think it was worked for quite some time. The bioblend commands should be something like this... >>> gi =3D galaxy.GalaxyInstance(url=3D"", key=3D"") >>> l =3D gi.libraries.create_library("testlib") >>> gi.libraries.set_library_permissions( l['id'], access_in=3D[''] = ) # Require a role id to access get from /api/roles >>> gi.libraries.set_library_permissions( l['id'], access_in=3D[], modify_in= =3D[], add_in=3D[], manage_in=3D[] ) # reset all permissions If you have a very new Galaxy, please apply this patch - https://bitbucket.org/galaxy/galaxy-central/commits/c4291f95313abcb1ad91ffe4f= aaa2c30b05149dc. Otherwise can you try using the commands as shown above - lists of role ids. If that doesn't work there should be some stack traces in the galaxy log to help diagnose the problem. Please feel free to follow up with these. Hope this helps - let me know if there are still problems. -John On Tue, Apr 15, 2014 at 2:17 AM, Kevin Muret wrote: > Hello to all, > > In recent days, I try to do the "set_library_permissions ()" bioblend's > function working. > > I tried the following syntaxes, and it was unsuccessful. Anybody know how to > use it? Or otherwise, how would it be possible to modify user access to > libraries (or contents)? > > ---------------------------------------------- > > Bonjour =C3=A0 tous, > > Depuis quelques jours, je tente de faire fonctionner la fonction > "set_library_permissions()". > > J'ai tent=C3=A9 les syntaxes suivantes, et ce f=C3=BBt sans succ=C3=A8s. Qu= elqu'un > saurait-il comment l'utiliser ? Ou comment serait-il possible de modifier > les acc=C3=A8s utilisateurs d'une autre mani=C3=A8re ? > > ---------------------------------------------- > > "instance" is opened with an admin API key. > > 1 --> print > instance.libraries.set_library_permissions(library_id=3D"417e33144b294c21", > access_in=3DNone, modify_in=3DNone, add_in=3DNone, manage_in=3DNone) > > Traceback (most recent call last): > File "Workflow_Lib/work_test.py", line 76, in > main() > File "Workflow_Lib/work_test.py", line 39, in main > print > instance.libraries.set_library_permissions(library_id=3D"417e33144b294c21", > access_in=3DNone, modify_in=3DNone, add_in=3DNone, manage_in=3DNone) > File > "/home/gcc2013/lib/bioblend/lib/python2.7/site-packages/bioblend-0.4.3_dev-= py2.7.egg/bioblend/galaxy/libraries/__init__.py", > line 308, in set_library_permissions > return Client._post(self, payload, url=3Durl) > File > "/home/gcc2013/lib/bioblend/lib/python2.7/site-packages/bioblend-0.4.3_dev-= py2.7.egg/bioblend/galaxy/client.py", > line 181, in _post > r =3D self.gi.make_post_request(url, payload=3Dpayload, > files_attached=3Dfiles_attached) > File > "/home/gcc2013/lib/bioblend/lib/python2.7/site-packages/bioblend-0.4.3_dev-= py2.7.egg/bioblend/galaxyclient.py", > line 99, in make_post_request > r.status_code, body=3Dr.text) # @see self.body for HTTP response bo= dy > bioblend.galaxy.client.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

> > > > 2 --> print > instance.libraries.set_library_permissions(library_id=3D"417e33144b294c21", > access_in=3D[admin_id], modify_in=3D[admin_id], add_in=3D[admin_id], > manage_in=3D[admin_id]) > > 3 --> Moreover, are we supposed to view the content of this page? > http://localhost:8080/api/libraries/417e33144b294c21/permissions > > ---------------------------------------------- > > Thank you in advance to the community for your help, > > Kevin MURET > Intern at Station Biologique de Roscoff > ABiMS platform > > > ___________________________________________________________ > 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/ --===============7429089423217456389==-- From kmuret@sb-roscoff.fr Wed Apr 30 05:59:11 2014 From: Kevin Muret To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Problem with the "set_library_permissions" function on bioblend Date: Wed, 30 Apr 2014 11:58:55 +0200 Message-ID: <5360C95F.8090707@sb-roscoff.fr> In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============7229970240948369978==" --===============7229970240948369978== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Hi John, I tried what you suggested: #!/usr/bin/env python import os, sys from bioblend.galaxy import GalaxyInstance url=3D"http://#####" key=3D"#######" def main(): gi =3D GalaxyInstance(url=3Durl, key=3Dkey) l =3D gi.libraries.create_library("testlib") print l['id'] # ok gi.libraries.set_library_permissions( l['id'], access_in=3D[],=20 modify_in=3D[], add_in=3D[], manage_in=3D[]) if __name__ =3D=3D '__main__': main() I have the same error message : Traceback (most recent call last): File "./test.py", line 17, in main() File "./test.py", line 14, in main gi.libraries.set_library_permissions( l['id'], access_in=3D[],=20 modify_in=3D[], add_in=3D[], manage_in=3D[]) File=20 "build/bdist.linux-x86_64/egg/bioblend/galaxy/libraries/__init__.py",=20 line 307, in set_library_permissions File "build/bdist.linux-x86_64/egg/bioblend/galaxy/client.py", line=20 71, in _post File "build/bdist.linux-x86_64/egg/bioblend/galaxyclient.py", line=20 94, in make_post_request bioblend.galaxy.client.ConnectionError: Unexpected response from galaxy:=20 500: Internal Server Error

Internal Server Error

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

WSGI Server

I never success running the allocation of permissions. Thank you for your help, Kevin MURET Intern at Station Biologique de Roscoff ABiMS platform Le 17/04/2014 21:32, John Chilton a =C3=A9crit : > This API controller broke with the latest release from earlier this > week - I have since fixed this in galaxy-central and opened a pull > request to have it fixed in the stable branch. Otherwise I think it > was worked for quite some time. The bioblend commands should be > something like this... > >>>> gi =3D galaxy.GalaxyInstance(url=3D"", key=3D"") >>>> l =3D gi.libraries.create_library("testlib") >>>> gi.libraries.set_library_permissions( l['id'], access_in=3D['']= ) # Require a role id to access get from /api/roles >>>> gi.libraries.set_library_permissions( l['id'], access_in=3D[], modify_in= =3D[], add_in=3D[], manage_in=3D[] ) # reset all permissions > If you have a very new Galaxy, please apply this patch - > https://bitbucket.org/galaxy/galaxy-central/commits/c4291f95313abcb1ad91ffe= 4faaa2c30b05149dc. > Otherwise can you try using the commands as shown above - lists of > role ids. If that doesn't work there should be some stack traces in > the galaxy log to help diagnose the problem. Please feel free to > follow up with these. > > Hope this helps - let me know if there are still problems. > > -John > > On Tue, Apr 15, 2014 at 2:17 AM, Kevin Muret wrote: >> Hello to all, >> >> In recent days, I try to do the "set_library_permissions ()" bioblend's >> function working. >> >> I tried the following syntaxes, and it was unsuccessful. Anybody know how = to >> use it? Or otherwise, how would it be possible to modify user access to >> libraries (or contents)? >> >> ---------------------------------------------- >> >> Bonjour =C3=A0 tous, >> >> Depuis quelques jours, je tente de faire fonctionner la fonction >> "set_library_permissions()". >> >> J'ai tent=C3=A9 les syntaxes suivantes, et ce f=C3=BBt sans succ=C3=A8s. Q= uelqu'un >> saurait-il comment l'utiliser ? Ou comment serait-il possible de modifier >> les acc=C3=A8s utilisateurs d'une autre mani=C3=A8re ? >> >> ---------------------------------------------- >> >> "instance" is opened with an admin API key. >> >> 1 --> print >> instance.libraries.set_library_permissions(library_id=3D"417e33144b294c21", >> access_in=3DNone, modify_in=3DNone, add_in=3DNone, manage_in=3DNone) >> >> Traceback (most recent call last): >> File "Workflow_Lib/work_test.py", line 76, in >> main() >> File "Workflow_Lib/work_test.py", line 39, in main >> print >> instance.libraries.set_library_permissions(library_id=3D"417e33144b294c21", >> access_in=3DNone, modify_in=3DNone, add_in=3DNone, manage_in=3DNone) >> File >> "/home/gcc2013/lib/bioblend/lib/python2.7/site-packages/bioblend-0.4.3_dev= -py2.7.egg/bioblend/galaxy/libraries/__init__.py", >> line 308, in set_library_permissions >> return Client._post(self, payload, url=3Durl) >> File >> "/home/gcc2013/lib/bioblend/lib/python2.7/site-packages/bioblend-0.4.3_dev= -py2.7.egg/bioblend/galaxy/client.py", >> line 181, in _post >> r =3D self.gi.make_post_request(url, payload=3Dpayload, >> files_attached=3Dfiles_attached) >> File >> "/home/gcc2013/lib/bioblend/lib/python2.7/site-packages/bioblend-0.4.3_dev= -py2.7.egg/bioblend/galaxyclient.py", >> line 99, in make_post_request >> r.status_code, body=3Dr.text) # @see self.body for HTTP response = body >> bioblend.galaxy.client.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

>> >> >> >> 2 --> print >> instance.libraries.set_library_permissions(library_id=3D"417e33144b294c21", >> access_in=3D[admin_id], modify_in=3D[admin_id], add_in=3D[admin_id], >> manage_in=3D[admin_id]) >> >> 3 --> Moreover, are we supposed to view the content of this page? >> http://localhost:8080/api/libraries/417e33144b294c21/permissions >> >> ---------------------------------------------- >> >> Thank you in advance to the community for your help, >> >> Kevin MURET >> Intern at Station Biologique de Roscoff >> ABiMS platform >> >> >> ___________________________________________________________ >> 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/ --===============7229970240948369978== Content-Type: text/html Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="attachment.htm" MIME-Version: 1.0 PGh0bWw+CiAgPGhlYWQ+CiAgICA8bWV0YSBjb250ZW50PSJ0ZXh0L2h0bWw7IGNoYXJzZXQ9VVRG LTgiIGh0dHAtZXF1aXY9IkNvbnRlbnQtVHlwZSI+CiAgPC9oZWFkPgogIDxib2R5IGJnY29sb3I9 IiNGRkZGRkYiIHRleHQ9IiMwMDAwMDAiPgogICAgSGkgSm9obiw8YnI+CiAgICA8YnI+CiAgICA8 ZGl2IGlkPSJndC1zcmMtdG9vbHMiPgogICAgICA8ZGl2IGlkPSJndC1zcmMtdG9vbHMtbCI+CiAg ICAgICAgPGRpdiBzdHlsZT0iZGlzcGxheTogaW5saW5lLWJsb2NrOyIgaWQ9Imd0LWlucHV0LXRv b2wiPgogICAgICAgICAgPGRpdiBpZD0iaXRhbWVudSI+PHNwYW4gY2xhc3M9Iml0YS1rZC1pbnB1 dHRvb2xzLWRpdiI+PC9zcGFuPjwvZGl2PgogICAgICAgIDwvZGl2PgogICAgICA8L2Rpdj4KICAg 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Content-Transfer-Encoding: quoted-printable In addition, the content of "parser.log" file with and without the=20 modification _With modification_ : galaxy.web.framework ERROR 2014-04-30 14:11:52,222 Uncaught exception in=20 exposed API method: Traceback (most recent call last): File=20 "/w/galaxy/galaxy4kevin/galaxy-dist/lib/galaxy/web/framework/__init__.py",=20 line 199, in decorator rval =3D func( self, trans, *args, **kwargs) File=20 "/w/galaxy/galaxy4kevin/galaxy-dist/lib/galaxy/webapps/galaxy/api/permissions= .py",=20 line 50, in create *item =3D library.to_dict( view=3D'element', value_mapper=3D{ 'id' :=20 trans.security.encode_id , 'root_folder_id' : trans.security.encode_id } )* File=20 "/w/galaxy/galaxy4kevin/galaxy-dist/lib/galaxy/model/__init__.py", line=20 1960, in to_dict rval[ 'root_folder_id' ] =3D 'F' + rval[ 'root_folder_id' ] TypeError: cannot concatenate 'str' and 'int' objects _Without modification_ : galaxy.web.framework ERROR 2014-04-30 14:16:56,853 Uncaught exception in=20 exposed API method: Traceback (most recent call last): File=20 "/w/galaxy/galaxy4kevin/galaxy-dist/lib/galaxy/web/framework/__init__.py",=20 line 199, in decorator rval =3D func( self, trans, *args, **kwargs) File=20 "/w/galaxy/galaxy4kevin/galaxy-dist/lib/galaxy/webapps/galaxy/api/permissions= .py",=20 line 50, in create *item =3D library.to_dict( view=3D'element' )** * File=20 "/w/galaxy/galaxy4kevin/galaxy-dist/lib/galaxy/model/__init__.py", line=20 1960, in to_dict rval[ 'root_folder_id' ] =3D 'F' + rval[ 'root_folder_id' ] TypeError: cannot concatenate 'str' and 'int' objects Kevin MURET Intern at Station Biologique de Roscoff ABiMS platform --===============8916518242266184043== Content-Type: text/html Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="attachment.htm" MIME-Version: 1.0 PGh0bWw+CiAgPGhlYWQ+CiAgICA8bWV0YSBjb250ZW50PSJ0ZXh0L2h0bWw7IGNoYXJzZXQ9VVRG LTgiIGh0dHAtZXF1aXY9IkNvbnRlbnQtVHlwZSI+CiAgPC9oZWFkPgogIDxib2R5IGJnY29sb3I9 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Can someone else verify? So my best guess is you guys have modified something in the library code - or you applied that patch but to an older version of galaxy? >>> l =3D gi.libraries.create_library("testlib") >>> gi.libraries.set_library_permissions( l['id'], access_in=3D[], modify_in= =3D[], add_in=3D[], manage_in=3D[] ) {u'description': u'', u'deleted': False, u'synopsis': u'', u'root_folder_id': u'Ff2db41e1fa331b3e', u'model_class': u'Library', u'id': u'f2db41e1fa331b3e', u'name': u'testlib'} Sorry I cannot be of more help. -John On Wed, Apr 30, 2014 at 7:26 AM, Kevin Muret wrote: > In addition, the content of "parser.log" file with and without the > modification > > With modification : > galaxy.web.framework ERROR 2014-04-30 14:11:52,222 Uncaught exception in > exposed API method: > > Traceback (most recent call last): > File > "/w/galaxy/galaxy4kevin/galaxy-dist/lib/galaxy/web/framework/__init__.py", > line 199, in decorator > rval =3D func( self, trans, *args, **kwargs) > File > "/w/galaxy/galaxy4kevin/galaxy-dist/lib/galaxy/webapps/galaxy/api/permissio= ns.py", > line 50, in create > item =3D library.to_dict( view=3D'element', value_mapper=3D{ 'id' : > trans.security.encode_id , 'root_folder_id' : trans.security.encode_id } ) > File "/w/galaxy/galaxy4kevin/galaxy-dist/lib/galaxy/model/__init__.py", > line 1960, in to_dict > rval[ 'root_folder_id' ] =3D 'F' + rval[ 'root_folder_id' ] > TypeError: cannot concatenate 'str' and 'int' objects > > Without modification : > galaxy.web.framework ERROR 2014-04-30 14:16:56,853 Uncaught exception in > exposed API method: > > Traceback (most recent call last): > File > "/w/galaxy/galaxy4kevin/galaxy-dist/lib/galaxy/web/framework/__init__.py", > line 199, in decorator > rval =3D func( self, trans, *args, **kwargs) > File > "/w/galaxy/galaxy4kevin/galaxy-dist/lib/galaxy/webapps/galaxy/api/permissio= ns.py", > line 50, in create > item =3D library.to_dict( view=3D'element' ) > File "/w/galaxy/galaxy4kevin/galaxy-dist/lib/galaxy/model/__init__.py", > line 1960, in to_dict > rval[ 'root_folder_id' ] =3D 'F' + rval[ 'root_folder_id' ] > TypeError: cannot concatenate 'str' and 'int' objects > > > Kevin MURET > Intern at Station Biologique de Roscoff > ABiMS platform --===============2327204409779648975==--