[galaxy-dev] Error when changing default permissions for new histories
Hello, when I go to the user preferences and try to change the default permissions for new histories, I always get the following error (full message in attachment): Error - type 'exceptions.TypeError': set_default_permissions() takes exactly 3 non-keyword arguments (2 given) URL: http://solweb2.immunbio.mpg.de/user/set_default_permissions File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) TypeError: set_default_permissions() takes exactly 3 non-keyword arguments (2 given) I would greatly appreciate any help to solve this problem. Thanks in advance! Best regards, Sarah 10.1.5.190 - - [08/Jul/2011:09:36:14 +0200] POST /user/set_default_permissions HTTP/1.1 500 - http://solweb2.immunbio.mpg.de/user/set_default_permissions?cntrller=user; Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.17) Gecko/20110428 Fedora/3.6.17-1.fc14 Firefox/3.6.17 Error - type 'exceptions.TypeError': set_default_permissions() takes exactly 3 non-keyword arguments (2 given) URL: http://solweb2.immunbio.mpg.de/user/set_default_permissions File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) TypeError: set_default_permissions() takes exactly 3 non-keyword arguments (2 given) CGI Variables - CONTENT_LENGTH: '-1' CONTENT_TYPE: 'application/x-www-form-urlencoded' HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' HTTP_ACCEPT_CHARSET: 'ISO-8859-1,utf-8;q=0.7,*;q=0.7' HTTP_ACCEPT_ENCODING: 'gzip,deflate' HTTP_ACCEPT_LANGUAGE: 'en-us,en;q=0.5' HTTP_CONNECTION: 'Keep-Alive' HTTP_COOKIE: 'galaxysession=f611411aa8a0c665b61db8293a8ea068714c7d705211c2d710c72adcfca0d053c2f647fee2d5d9cd' HTTP_HOST: 'solweb2.immunbio.mpg.de' HTTP_REFERER: 'http://solweb2.immunbio.mpg.de/user/set_default_permissions?cntrller=user' HTTP_USER_AGENT: 'Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.17) Gecko/20110428 Fedora/3.6.17-1.fc14 Firefox/3.6.17' HTTP_X_FORWARDED_FOR: '10.1.5.190' HTTP_X_FORWARDED_HOST: 'solweb2.immunbio.mpg.de' HTTP_X_FORWARDED_SERVER: 'solweb2' ORGINAL_HTTP_HOST: 'localhost:8081' ORGINAL_REMOTE_ADDR: '127.0.0.1' PATH_INFO: '/user/set_default_permissions' REMOTE_ADDR: '10.1.5.190' REQUEST_METHOD: 'POST' SERVER_NAME: '0.0.0.0' SERVER_PORT: '8081' SERVER_PROTOCOL: 'HTTP/1.1' Configuration - __file__: '/galaxy/galaxy_server/universe_wsgi.webapp.ini' admin_users: 'di...@immunbio.mpg.de' allow_library_path_paste: 'False' allow_user_creation: 'True' allow_user_dataset_purge: 'True' allow_user_deletion: 'True' apache_xsendfile: 'True' bugs_email: 'di...@immunbio.mpg.de' cookie_path: '/' database_connection: 'postgres://user:password@localhost/galaxy' database_engine_option_server_side_cursors: 'True' database_engine_option_strategy: 'threadlocal' datatypes_config_file: 'datatypes_conf.xml' debug: 'False' enable_api: 'True' enable_job_running: 'False' enable_pages: 'True' enable_tracks: 'True' error_email_to: 'di...@immunbio.mpg.de' external_service_type_config_file: 'external_service_types_conf.xml' external_service_type_path: 'external_service_types' file_path: 'database/files' fulltext_max_size: '200' fulltext_noindex_filetypes: 'bam,sam,wig,bigwig,fasta,fastq,fastqsolexa,fastqillumina,fastqsanger' gbrowse_display_sites: 'wormbase,tair,modencode_worm,modencode_fly,local_mouse,local_human,local_fly' genetrack_display_sites: 'main,test' here: '/galaxy/galaxy_server' id_secret: 'MPI-IE' job_working_directory: 'database/job_working_directory' len_file_path: 'tool-data/shared/ucsc/chrom' library_import_dir: '/galaxy/galaxy_server/data' local_job_queue_workers: '15' log_actions: 'True' log_events: 'True' log_level: 'DEBUG' new_file_path: 'database/tmp' new_user_dataset_access_role_default_private: 'False' nglims_config_file: 'tool-data/nglims.yaml' require_login: 'False' set_metadata_externally:
Re: [galaxy-dev] problems with 'Profile Annotations' tool UI
Hi Dan
Thank you very much. The display works nicely, now.
Thanks, Hans
On 07/07/2011 06:14 PM, Daniel Blankenberg wrote:
Hi Hans,
Very sorry for the delay in response. The sample file that was included was
incorrect, but has been updated in changeset 5775:4220f8a5c571 and should now
display an interface.
If you would like to use or run the tool, you may find
$GALAXY_ROOT/scripts/tools/annotation_profiler/README.txt helpful. Please let
us know if you encounter further difficulties.
Thanks for using Galaxy,
Dan
On Jun 8, 2011, at 8:10 AM, Hans-Rudolf Hotz wrote:
Hi
we are looking into different methods to display dynamic contents in the tool
user interface.
To start, we looked at the 'Operate on Genomic Intervals:Profile Annotations' tool. We
turned it on in a local installation (May 20, 8c11dd28a3cf release), but we
struggled to get the interface to work.
On 'http://main.g2.bx.psu.edu/', the tables to choose from are only displayed if there is
a history item with: format: bed, database: hg18.
But in our local test installation, we don't get the list of tables, no matter whether we have a
('hg18') bed file in our history or not. It looks like as if the
'from_file=annotation_profiler_options.xml' statement in the
annotation_profiler.xml is ignored.
I know, the file 'annotation_profiler_options.xml' is read, since I get an
error during restart, if I provide invalid xml.
Is there anything else, I have to enable, in order to get this interface to
work? Currently, I don't care about the tools functionality, I just want the
(cool) interface to work.
Thank you very much for your help.
Regards, Hans
PS: this question is connected to Tim's question yesterday - I just
should have sent mine first - sorry.
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[galaxy-dev] Galaxy - UCSC Authentication issues
Dear list, I have recently finished to set local installations of both Galaxy and UCSC servers. Because of the required set-up, access to these is password protected. Galaxy uses the Apache authentication system (as by instructions in galaxy pages) and the username:password combos are the same used by our local UCSC server. Now, whenever I try to export tables to Galaxy from the UCSC hgTables tool, I get the following error on Galaxy: Dataset generation errors Dataset 33: UCSC Main on Mouse: Rbbp5_Ang2011 (genome) Tool execution generated the following error message: The remote data source application may be off line, please try again later. Error: EOF when reading a line The tool produced the following additional output: Enter username for UCSC-Galaxy at ucsc.cbs.dtu.dk Similarly, if I try to use UCSC to visualise a track I just created on Galaxy, no track will appear on UCSC I will get this error Expected 200 http://galaxy.cbs.dtu.dk/display_application/48916fac0de9a85d/ucsc_bigwig/main/b9ba5eb40e0fec32/param/track: 401 Authorization Required Did anyone have this issue? How can I solve this? Thanks a lot, Fred -- Federico De Masi, PhD, Assistant Professor The Technical University of Denmark - DTU Center for Biological Sequence Analysis - CBS Kemitorvet 208/002 DK-2800 KGS. LYNGBY, DENMARK Telephone: (+45) 45 25 24 21 Fax: (+45) 45 93 15 85 http://rg.cbs.dtu.dk ___ 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/
Re: [galaxy-dev] Error when changing default permissions for new histories
Hello Sarah, This is a bug which I've fixed in change set 5776:a787213d08e1, which is currently available from our development repository and should be available in the distribution within the next few weeks. Thanks for finding this. Greg Von Kuster On Jul 8, 2011, at 3:53 AM, Sarah Diehl wrote: Hello, when I go to the user preferences and try to change the default permissions for new histories, I always get the following error (full message in attachment): Error - type 'exceptions.TypeError': set_default_permissions() takes exactly 3 non-keyword arguments (2 given) URL: http://solweb2.immunbio.mpg.de/user/set_default_permissions File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) TypeError: set_default_permissions() takes exactly 3 non-keyword arguments (2 given) I would greatly appreciate any help to solve this problem. Thanks in advance! Best regards, Sarah galaxy_error.txt___ 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/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ 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/
Re: [galaxy-dev] Saved Histories - default view on deleted histories (bug)
Hi Michal, Can you elaborate on set on deleted items by default? It is always active by default for me. Thanks, K On Wed, Jul 6, 2011 at 3:23 AM, Michal Stuglik michal.stug...@gmail.com wrote: hi all, in galaxy-central: 1. default view in Saved Histories section is set on deleted items ( Jeremy, I did double check this morning on fresh instance :)) 2. in advanced search option: one of the filter switch is deleted and does the same job as active switch 3. Sugestion: Saved Histories-Advanced Search sharing: private | shared | accessible | published | all deleted: active | deleted | all maybe it is better to change it to: sharing: private | shared | accessible | published | all status: active | deleted | all I think deleted is not clear.. all the best, michal ___ 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/ ___ 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/
[galaxy-dev] admin users
Dear All, I have a local galaxy instance and I have problems with admin users. I have a comma separated list of valid galaxy users in the universe_wsgi.ini file but only the first one has access to the admin tab, it doesn't appear for the other ones. Am I missing something? Thanks in advance, Yann ___ 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/
Re: [galaxy-dev] admin users
Hi Ross, thanks that was the problem, it works fine with no space. I'll raise a ticket about it. yann On 07/08/2011 04:29 PM, Ross wrote: I seem to remember being bitten by this once years ago when I had spaces between the comma and the next email address - but I never fixed it - someone else may have. If that turns out to be your problem please raise a ticket since it means the parsing is wrong - spaces should be ignored around the comma delims. On Sat, Jul 9, 2011 at 2:50 AM, Yann Surget-Grobaysurg...@ucsc.edu wrote: Dear All, I have a local galaxy instance and I have problems with admin users. I have a comma separated list of valid galaxy users in the universe_wsgi.ini file but only the first one has access to the admin tab, it doesn't appear for the other ones. Am I missing something? Thanks in advance, Yann ___ 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/ ___ 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/
