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
James Taylor
15ec130bfb
core: add PasteDeploy dependency back, used inside Paste#httpserver
2013-02-01 17:30:58 -05:00
James Taylor
f6629fd8c4
changeset: 8701:c3ac9849dd1b
...
branch: unstable
tag: tip
user: James Taylor <james@jamestaylor.org >
summary: core: pull the pieces of PasteScript we use into galaxy.util.pastescript. Remove all dependencies on PasteScript and PasteDeploy. Begin stripping down the serve command so we can start to enhance it for our needs.
2013-01-30 15:26:00 -05:00
Lance Parsons
f98cf656a2
Fix for Postgres versions < 9 (see https://trello.com/c/Z0EynAV2 )
2012-12-10 16:23:11 -05:00
Carl Eberhard
fdbf75864f
Enable serving static files when running functional tests
2013-01-17 14:58:43 -05:00
Greg Von Kuster
1c7ef874b5
Utility code cleanup and import tweaking.
2012-12-13 11:41:31 -05:00
Carl Eberhard
b6d4e00bc2
Fixes to history functional tests; Twilltestcase: added function to parse and check json, exact string matcher
2012-12-10 17:44:11 -05:00
Greg Von Kuster
c48f54ee3c
Merged in lance_parsons/galaxy-central_installed-tools-functional-tests-fix (pull request #95 )
2012-12-07 19:09:00 -05:00
Lance Parsons
0e7a2b7324
Fix for finding test-data for installed tools
...
See bug: https://trello.com/c/Z0vhJEq6
2012-12-07 17:22:48 -05:00
Dave Bouvier
de7cb21382
Migrate tools to tool shed: addValue, ChangeCase, Condense characters1, Convert characters1, Cut1, mergeCols1, Remove beginning1, Show beginning1, Show tail1, trimmer
2012-12-07 16:08:40 -05:00
Kyle Ellrott
53e4dc4f6b
Patch to make extended_metadata loader work better, and fixing library loader to catch non-ascii errors
2012-11-30 10:58:39 -08:00
Dave Bouvier
917d5a72e8
Migrated lastz and bowtie tools to the tool shed. Added a target_file feature to the tool dependency installation process.
2012-11-26 10:18:47 -05:00
Dannon Baker
e660fb2591
Merged in jmchilton/galaxy-central-reports-config-enhancements (pull request #71 )
2012-11-12 12:00:18 -05:00
Dannon Baker
e4b98ca9b5
Merged in kellrott/galaxy-central (pull request #81 )
2012-11-12 11:54:45 -05:00
Dave Bouvier
576ceb7829
Revert tool migration.
2012-12-07 16:38:26 -05:00
Greg Von Kuster
ed060ddcbe
Add the shed_tool_data_table_config to the functional test's app.
2012-11-08 11:41:21 -05:00
Greg Von Kuster
d0438ecb2f
Since tool migration scripts can be executed any number of times, make sure that no repositories are installed if not tools associated with the migration are defined in the tool_conf.xml file (or equivalent). This fix is associated only with the recently introduced Galaxy admin UI feature displaying the list of migration stages currently available. This is the way the migration process at server startup has always worked so no changes are needed in that scenario.
2012-11-07 10:51:35 -05:00
Daniel Blankenberg
e316254e28
Change indent from 3 spaces to 4 for 8171:4b62ed46e5b6.
2012-11-07 10:45:10 -05:00
Daniel Blankenberg
bbeed4dc0b
Use check_python() to verify python version in set_metadata.py instead of hardcoded minimum version check.
2012-11-07 10:35:56 -05:00
Kyle Ellrott
4e8d938ff7
Adding the initial componenents of an extended metadata system for datasets.
...
The idea behind an 'extended metadata' for datasets is to provide a mechanism to encode
and index user generated metadata and keep it attached to files. Users can provide a
JSON style data structure which will then be indexed and stored. Later this index can
be used to search and discover datasets via a pseudo-formal schema.
This patch introduces the tables, and makes it possible to inject user metadata into a file
load using the 'extended_metadata' field in the query.
2012-10-28 00:28:42 -07:00
Dave Bouvier
cc608c31b2
Updated migration script to reference repository with correct use of tool dependency tag sets.
2012-10-25 13:25:39 -04:00
Dave Bouvier
c968460662
Migrate Picard tools to the tool shed.
2012-10-24 11:09:20 -04:00
Scott McManus
a0afee842e
Re-commit new /api/folders section
2012-10-15 18:09:25 -04:00
Scott McManus
0148eabc72
Backout
2012-10-15 17:53:37 -04:00
Scott McManus
954e96fc34
Added /api/folders. The api_folders configuration variable controls access to it (and is False by default).
2012-10-15 17:29:29 -04:00
Daniel Blankenberg
94a2f94529
Fix minor typos in db_shell.py
2012-10-11 16:43:37 -04:00
Nate Coraor
9213c344db
Fix reporting in the set_user_disk_usage.py script.
2012-10-03 13:40:54 -04:00
Nate Coraor
9ab95a9fa9
Fix passing of job name when running jobs as a system user.
2012-10-03 11:51:07 -04:00
Nate Coraor
1e2256fe0e
pgcleanup: Print a useful message if no options are given.
2012-10-01 13:45:37 -04:00
Nate Coraor
8193489dda
pgcleanup/set_user_disk_usage: set usage to 0, not null, when the user has no active data.
2012-09-28 16:11:38 -04:00
Dave Bouvier
c2eeee7b9f
Migrate BWA to the tool shed.
2012-09-28 15:35:44 -04:00
Nate Coraor
caa06bbc20
Allow Postgres users to update user disk usage with a fast wCTE rather than a slower computation in Python.
2012-09-28 14:30:10 -04:00
John Chilton
c3e99bc384
Improvements to reports management script (run_reports.sh) to enable managing the reports app from CloudMan. These enhancements are all "optional", the default behavior of run_reports.sh is unchanged.
...
Added flag (--sync-config) to run_reports.sh script that will cause it to synchronize the database connection and file path properties in reports_wsgi.ini with those in universe_wsgi.ini prior to starting paster app.
Allow specification of reports configuration directory mirroring similar extensions previously accepted for universe config and run.sh
Added usage documentation to run_reports.sh.
Added extension points to tweak pid and log location for reports application via environment variables.
2012-09-21 22:04:15 -05:00
Dannon Baker
ba6114ca3e
Fix create_all_fasta_loc to work when inspect_dir is not set.
2012-09-18 20:49:29 -04:00
Nate Coraor
459d3a2c1d
More pgcleanup.py fixes and addition of cleanup event tables for library items.
2012-09-17 12:51:17 -04:00
Nate Coraor
71d7f7c132
Distributed object store fixes for pgcleanup.py.
2012-09-11 12:22:03 -04:00
Nate Coraor
0e1b041cde
Bug fixes for pgcleanup.py
2012-09-10 16:59:33 -04:00
Nate Coraor
c8e49cdd6d
Bugfix for pgcleanup.py
2012-09-10 14:07:05 -04:00
Greg Von Kuster