Re: [galaxy-dev] Galaxy Not Displacing History
Hi Dannon, Clearing the browser cache worked! Thanks so much. Jeremy Liu On Thu, Nov 6, 2014 at 2:04 AM, ofer fridman ofer.frid...@mail.huji.ac.il wrote: I Had the same problem, after moving to stable everything is working. I know it's not a solution but for the meantime this is what I have. Best, Ofer On Wed Nov 05 2014 at 11:04:01 PM Dannon Baker dannon.ba...@gmail.com wrote: This is usually an old cached version of the history panel interfering, or a javascript error that you'd see in the console. Can you clear browser cache, close out all Galaxy windows, and try again? If that still doesn't work, can you look in the javascript console to see if there are any errors? Dropping the database and whatnot definitely shouldn't ever be required. On Wed, Nov 5, 2014 at 3:52 PM, Jeremy Liu jeremy@yale.edu wrote: Hi Galaxy Dev, I just pulled the latest updates for galaxy-dist with hg pull -u and then migrated over the postgres database with: sh manage_db.sh -c ./universe_wsgi.ini upgrade After restarting the server, my Galaxy instance would not show the history of datasets. The history was still there, since I could see it when I clicked Saved Datasets - View - Show Structure and jobs would be executed normally. However the history toolbar was entirely missing. Is there any fix for this other than dropping the database, deleting galaxy and clean install galaxy? (then reinstall the tools that I had downloaded from the toolshed). Note: After running sh run.sh --reload, Galaxy noted that some of the tools were not moved over, so I tried running sh ./scripts/migrate_tools/0012_tools.sh and sh ./scripts/migrate_tools/0012_tools.sh install_dependencies but I was unable to locate the scripts. Thanks, Jeremy Liu ___ 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/ ___ 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/
[galaxy-dev] data_columns
Dear list, I tried to make a tool that takes tsv input and have some data_columns selection parameters in the xml definition. It seems to work, but I get ‘invalid option was selected’ in the browser interface for each of the data_columns. No logging errors or stacktraces. Digging a bit, I found out that the legal_values of the ColumnParameter (in lib/galaxy/tools/parameters/basic.py ) is empty. It is returned empty by get_column_list when this does if not dataset.metadata.columns: on line 1184 of the above mentioned file. Now I’m a bit at a loss, how do I set these columns, or where are those columns set on the metadata? Is it stored, generated from the input file? My files are not official formats, just tsv subclasses. I’m on changeset 14567:007f6a80629a in galaxy-dist. cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden ___ 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/
Re: [galaxy-dev] data_columns
No, I am not subclassing from Tabular. But when I do, it suddenly works. Thanks loads Dan! cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden On 07 Nov 2014, at 19:07, Daniel Blankenberg d...@bx.psu.edu wrote: Hi Jorrit, Are you subclassing your tsv datatypes from tabular? If you can post your tool xml and datatype_conf.xml additions then we should be to provide more assistance. Thanks for using Galaxy, Dan On Nov 7, 2014, at 12:27 PM, Jorrit Boekel jorrit.boe...@scilifelab.se wrote: Dear list, I tried to make a tool that takes tsv input and have some data_columns selection parameters in the xml definition. It seems to work, but I get ‘invalid option was selected’ in the browser interface for each of the data_columns. No logging errors or stacktraces. Digging a bit, I found out that the legal_values of the ColumnParameter (in lib/galaxy/tools/parameters/basic.py ) is empty. It is returned empty by get_column_list when this does if not dataset.metadata.columns: on line 1184 of the above mentioned file. Now I’m a bit at a loss, how do I set these columns, or where are those columns set on the metadata? Is it stored, generated from the input file? My files are not official formats, just tsv subclasses. I’m on changeset 14567:007f6a80629a in galaxy-dist. cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden ___ 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/
[galaxy-dev] Error in creating admin user during tool shed bootstrap
I'm setting up a local development Tool Shed according to Greg Von Kuster's blog post http://gregvonkuster.org/galaxy-tool-shed-june-2-2014-release/. During the bootstrapping process, it seems that the creation of the admin user based on the information in user_info.xml fails because of a SQLAlchemy error (see attached stdout.txt). As a result, I believe the API calls for creating categories and users also fail, because they depend on the existence of admin user. This error seems to be due to a missing repository table in the database. I ran the SQL query against the Tool Shed database within PostgreSQL after the failed bootstrapping command and it returned no error, because the repository table actually exists. So, I don't know whether the SQL query is being run against the wrong database (*e.g.* the Galaxy database) or if the database schema isn't properly set up by the time SQLAlchemy attempts the query. I'm using the latest version of Galaxy (revision 83f821c5ecc1). Best regards, Bruno $ sh ~/galaxy_dist/run_tool_shed.sh -bootstrap_from_tool_shed testtoolshed.g2.bx.psu.edu Bootstrapping from tool shed at testtoolshed.g2.bx.psu.edu. Creating database... done. Creating user 'bgrande' with email address 'bgra...@sfu.ca'...Traceback (most recent call last): File lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py, line 152, in module app = BootstrapApplication( config ) File lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py, line 46, in __init__ create_tables=False ) File /home/galaxy/galaxy_dist/lib/galaxy/webapps/tool_shed/model/mapping.py, line 330, in init result.shed_counter = shed_statistics.ShedCounter( result ) File /home/galaxy/galaxy_dist/lib/galaxy/webapps/tool_shed/util/shed_statistics.py, line 20, in __init__ self.generate_statistics() File /home/galaxy/galaxy_dist/lib/galaxy/webapps/tool_shed/util/shed_statistics.py, line 39, in generate_statistics for repository in self.sa_session.query( self.model.Repository ): File /home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py, line 2227, in __iter__ File /home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py, line 2242, in _execute_and_instances File /home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py, line 1449, in execute File /home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py, line 1584, in _execute_clauseelement File /home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py, line 1698, in _execute_context File /home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py, line 1691, in _execute_context File /home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py, line 331, in do_execute sqlalchemy.exc.OperationalError: (OperationalError) no such table: repository u'SELECT repository.id AS repository_id, repository.create_time AS repository_create_time, repository.update_time AS repository_update_time, repository.name AS repository_name, repository.type AS repository_type, repository.description AS repository_description, repository.long_description AS repository_long_description, repository.user_id AS repository_user_id, repository.private AS repository_private, repository.deleted AS repository_deleted, repository.email_alerts AS repository_email_alerts, repository.times_downloaded AS repository_times_downloaded, repository.deprecated AS repository_deprecated \nFROM repository' () done. Starting tool shed in order to populate users and categories... done. Retrieving admin user's API key from http://127.0.0.1:9009... done. Creating users... done. Creating categories... done. Bootstrap complete, shutting down temporary tool shed process. A log has been saved to tool_shed_bootstrap.log tool_shed_bootstrap.log Description: Binary data ___ 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/
