Nate Coraor
126c02eb71
Experimental/alpha/in-development/incomplete object store plugin for iRODS. This plugin will probably set your iRODS instance on fire: do not use except in development/testing.
2013-08-28 16:20:19 -04:00
Greg Von Kuster
0a704cdb6d
Automatically eliminate tool entries from non-shed-related tool panel configs for tools contained in tool shed repositories that were migrated out of the Galaxy distribution.
2013-08-22 10:12:08 -04:00
Carl Eberhard
89c8698169
Functional tests: fix sqlite db_path var; fix api test for hda update with nonsense key
2013-08-21 10:00:09 -07:00
Dave Bouvier
aa5d0ca8a7
Merge in bugfix from stable.
2013-08-19 13:06:42 -04:00
Dave Bouvier
7adc736e16
Fix for case where running functional tests might overwrite certain files in database/files.
2013-08-19 13:06:17 -04:00
Dannon Baker
67ff535694
Merged in lance_parsons/galaxy-central-pull-requests/cleanup_datasets_unicode_fix (pull request #196 )
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Fix unicode issue when printing history names in cleanup_datasets.py script
2013-08-15 11:18:37 -04:00
Greg Von Kuster
cf96dccddb
Add the ability to export a specified repository revision from the tool shed to a gzip compressed archive saved locally. The ability to import this archive to the same or another tool shed is not yet implemented, but coming soon. All of the repository's repository dependencies can optionally be exported into the same archive. The archive includes a manifest.xml file that contains the order in whcih the repositories in the archive must be imported.
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This feature is now available for any installable revision of a repository using the new "Export this revision" option in the Repository actions menu in the browser. It is also available via the Tool Shed API using a command like the following:
export.py --url http://testtoolshed.g2.bx.psu.edu --name chemicaltoolbox --owner bgruening --revision 4133dbf7ff4d --export_repository_dependencies True --download_dir /tmp
2013-08-02 19:30:03 -04:00
Lance Parsons
91ba836a00
Fix unicode issue when printing history names in cleanup_datasets.py script
2013-07-22 14:24:13 -04:00
Nate Coraor
86f25f3bcf
GCC2013 Advanced Tool and Data Source Configuration workshop: "The test framework uses tool_conf.xml.sample for reasons unknown and lost to time."
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Use tool_conf.xml for running functional tests, rather than tool_conf.xml.sample.
2013-06-30 10:04:58 -04:00
Greg Von Kuster
586c673338
Add support for repairing an installed tool shed repository and all of it's repository dependency hierarchy. Repairing a repository hierarchy will attempt to ensure all repositories in the hierarchy are correctly installed and all tool dependencies of each repository in the hierarchy are correctly installed.
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There is a new Repository Actions pop-up menu item for each repository labeled "Repair repository" that enables this in the browser.
This is also supported in the enhanced Galaxy API using a command like the following from the ~/scripts/api directory:
python ./repair_tool_shed_repository.py --api <Galaxy admin API key> -l http://localhost:8763 --url http://localhost:9009/ -o test -r 1018e3cee313 --name chemicaltoolbox
2013-06-26 21:17:00 -04:00
Dannon Baker
b66c39c951
galaxy.model.orm is a more sensible location than mapping for dialect_to_egg
2013-06-20 10:58:52 -04:00
Dannon Baker
be4bc4694a
Consolidate dialect_to_egg to a single location.
2013-06-20 10:50:31 -04:00
Carl Eberhard
c86637486b
scripts/api: Fixes to upload_to_history.py
2013-06-12 10:35:11 -04:00
Carl Eberhard
4512eeab3f
API: libaray_contents.create: add support for copying an HDA; scripts/api: add copy_hda_to_library_folder.py, rename upload_to_history.py
2013-06-07 16:06:22 -04:00
Dannon Baker
62736bdc84
Merged in lance_parsons/galaxy-central_postgres-user-disk-usage-fix (pull request #97 )
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Fix for Postgres versions < 9
2013-06-06 10:21:57 -04:00
Dannon Baker
111837de21
Require decorator in manage_db.py -- resolves decorator not found for particular deployments
2013-06-05 11:24:55 -04:00
Carl Eberhard
be2bb18e83
Tools API: better error handling in create, encode ids returned; Scripts: add history_upload script to api
2013-05-29 17:28:47 -04:00
Nate Coraor
b9cbf89ce6
merge next-stable.
2013-05-29 16:16:24 -04:00
Nate Coraor
c1fb32d7c6
Update pgcleanup.py for dialect name change.
2013-05-29 16:16:11 -04:00
Greg Von Kuster
a787646f92
Delete the original copy of the install_repository_tools.py Galaxy API script since it has been renamed to install_tool_shed_repositories.py
2013-05-22 14:36:08 -04:00
Dave Bouvier
aa0c5c86eb
Fix for setting metadata externally when running functional tests.
2013-05-08 15:48:16 -04:00
Dannon Baker
ae36520d56
Metadata setting: Always set externally.
2013-05-06 12:50:06 -04:00
Dave Bouvier
9cf536f537
Rename install_repository_tools to install_tool_shed_repositories. Use shed_util_common.url_join to generate the API url.
2013-05-03 15:55:56 -04:00
Dannon Baker
f51719aaa9
Fix install_repository_tools script to appropriately handle a trailing slash in the URL.
2013-05-03 15:46:53 -04:00
Dannon Baker
cd23ac7014
Make sure dependent eggs are loaded for sqlalchemy-migrate, regardless of entry point. This is a hack, and dependency management should/will eventually handle it.
2013-05-03 12:55:55 -04:00
Dannon Baker
e436468f28
Require decorator egg wherever we have sqlalchemy-migrate. Should be able to resolve dependencies and do this automatically
2013-05-03 12:31:20 -04:00
Dannon Baker
57c89d742e
Functional test setup fix for sqlite -- pool_size is an invalid option in sqlalchemy7+.
2013-04-30 23:24:55 -04:00
Dannon Baker
44e7a67ce9
Merge with central
2013-04-18 15:35:22 -04:00
Dannon Baker
c2e71bc003
Postgres migrations successful, model updated
2013-04-18 15:35:00 -04:00
Greg Von Kuster
c1f207b648
White space changes.
2013-04-16 10:38:58 -04:00
Greg Von Kuster
61f5eda689
Merged in BjoernGruening/galaxy-central-bgruening/tool-shed-api (pull request #153 )
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merge install_repository_tool* scripts into one with a commandline interface
2013-04-16 10:19:17 -04:00
Dannon Baker
78a4042517
Fixes for Search API.
2013-04-10 13:59:33 -04:00
James Taylor
d02155ad7b
Require Python 2.6+ and remove various compatibility patches for 2.4 and 2.5
2013-04-09 11:57:38 -04:00
Bjoern Gruening
045f94b651
merge install_repository_tool* scripts into one with a commandline interface
2013-04-06 20:54:40 +02:00
Greg Von Kuster
5d502906e5
Enhance and correct documentation in the new tool_shed_repositories Galaxy API controller as well as the documentation in the example API install scripts. Fix discovery of the tool_path setting in the selected shed-related tool panel config file in the tool_shed_repositories controller's install_repository_revision method.
2013-03-26 09:29:02 -04:00
Greg Von Kuster
ed7248a819
Fix a few typos in my last commit.
2013-03-25 17:18:17 -04:00
Greg Von Kuster
b9c6df9d91
Add baseline cupport for installing tool shed repositories from a specified tool shed into Galaxy via a combination of the tool shed API and the now enhanced Galaxy API. There are 3 new example scripts in ~/scripts/api that demonstrate how this works. The are named like: install_repository...
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In this implementation, all tools contained in repositories will be loaded into the Galaxy tool panel.
The user can specify the following when sending a POST to the new Galaxy API URL:
/api/tool_shed_repositories/new/install_repository_revision
1) an existing tool panel section id for loading tools or a new tool panel section label in which case a new ToolPanelSection will be created for containing the tools.
2) if they want tool dependencies installed along with the repository.
3) if they want repository dependencies installed along with the repository
4) which defined shed-related tool panel config file to use for installed tools
2013-03-25 17:05:14 -04:00
Greg Von Kuster
9dee845318
Eliminate unnecessary resource mappers and api classes in the tool shed api, clean up the remaining tool shed api classes, and enhance the tool shed api by adding the ability to retrieve information about a specified repository and repository revision.
2013-03-22 10:43:58 -04:00
Greg Von Kuster
ae39ab8f2b
Rename community_wsgi.ini.sample to be tool_shed_wsgi.ini.sample, run_community.sh to run_tool_shed.sh, and fix references to these files in the code.
2013-03-18 10:24:03 -04:00
Kyle Ellrott
4aad0ad15e
Enabling dataset UUID setting through library upload, upload1 tool, and galaxy.json file
2013-01-29 15:58:58 -08:00
Dave Bouvier
8d2655503b
Improved documentation for automated repository installation and testing. Handle cases where a repository is missing test data. Limit the list of repositories to test to those that have tools. Update the parse_tool_panel_config method to return a flag specifying whether test data was found for the specified tool panel entry.
2013-03-01 15:13:20 -05:00
Carl Eberhard
2337695990
fix server_env saved output dir name; clean up prev. debugging statements
2013-03-01 12:49:08 -05:00
Greg Von Kuster
f539d3071b
Change the name and path of the community webapp to be tool_shed.
2013-02-27 16:23:19 -05:00
Dave Bouvier
9b30f6c839
Attempt to resolve issue with tool shed registry when running buildbot functional tests.
2013-02-27 14:12:07 -05:00
Greg Von Kuster
280125ee99
Move ~/lib/galaxy/tool_shed to ~/lib/tool_shed, and move the ~/lib/galaxy/util/shed_util componets to ~/lib/tool_shed/util.
2013-02-26 15:52:51 -05:00
Greg Von Kuster
4e91bb120e
Enhancements to the tool shed api to enable the curretnly most important updates for repository_metadata records.
2013-02-22 14:35:34 -05:00
Dave Bouvier
36ea9db697
Extension of framework to automate the installation of a list of tool shed repositories to also run any functional tests in the tools contained within each repository.
2013-02-20 14:27:36 -05:00
Carl Eberhard
c2898ec7f9
More reporting for buildbot corrections
2013-02-19 20:00:27 -05:00
Carl Eberhard
9ef47fd2b6
functional_tests: fix import
2013-02-19 16:21:16 -05:00
Carl Eberhard
ea6393a1a0
functional_tests.py: add debugging statement for app config
2013-02-19 14:31:56 -05:00
Nate Coraor