Greg Von Kuster
a610d0d458
Enhance the Tool Shed and Galaxy APIs to support resetting metadata on repositories in the Tool Shed or installed into Galaxy respectively. When resetting repository metadata in the Tool Shed, if the API key is associated with an admin user, then setting the my_writable param value to True will restrict resetting metadata to only repositories that are writable by the user in addition to those repositories of type tool_dependency_definition. This param is ignored if the current user is not an admin user, in which case this same restriction is automatic. Also, when resetting metadata in the Tool Shed, repositories of type tool_dependency_definition are reset before repositories of type unrestricted. When setting metadata for installed repositories in Galaxy, neither repository types nor order are considered since these concepts are irrelevant in that environment.
2013-10-16 14:19:26 -04:00
John Chilton
0f63caaff0
Bug fix in scripts/functional_tests.py.
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A tempdir is referenced before it is created in certain cases.
2013-10-14 21:50:12 -05:00
Ross Lazarus
8c4f96ed81
backout -r 10808
2013-10-08 10:55:24 +11:00
Ross Lazarus
87b1203b4a
branch merge
2013-10-05 09:56:05 +10:00
Ross Lazarus
7938d1fc81
local changes
2013-10-05 09:51:18 +10:00
Dave Bouvier
962be8d8ec
Remove sam_fa_indices.loc.sample from tool-data. Update migration xml to the correct revisions of cufflinks repositories.
2013-10-01 15:49:08 -04:00
Dave Bouvier
695aa8f44d
Migrate cuffcompare, cuffdiff, cufflinks, and cuffmerge from the distribution to the tool shed. Update the 'Review migration stages' layout.
2013-10-01 13:54:57 -04:00
Dave Bouvier
b0efe4ddea
Migrate tools from the distribution to the tool shed, including but not limited to samtools and fastx_toolkit tools.
2013-09-26 10:05:00 -04:00
Nate Coraor
ed9fc69f33
Fix a few postgres dialect renaming misses.
2013-09-26 09:34:27 -04:00
Greg Von Kuster
b5ecae6f3b
Enhance the Galaxy API to display the list of exported workflows contained in an installed tool shed repository and to import one or more of those exported workflows into Galaxy. This change set is loosely based on John Chilton's pull request # 223 titled "Implement API methods for interfacing with an installed tool shed repository's workflows", but the implementation has been re-worked. All of John's contributed features should be available in this change set.
2013-09-24 12:05:17 -04:00
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
Dannon Baker
eed1f76001
Merged in lance_parsons/galaxy-central-pull-requests/dataset-cleanup (pull request #158 )
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Basic administrative dataset cleanup script
2013-09-10 13:14:10 -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
Lance Parsons
d37fabc834
Fix admin_cleanup_datasets.py for copied datasets
2013-04-18 15:43:00 -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
Lance Parsons
bd8cd477bc
Basic administrative dataset cleanup script
2013-04-18 11:24:09 -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