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 )
...
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...
...
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
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
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
Dave Bouvier