John Chilton 79c8f59341 Models: Introduce real class for app.model (ModelMapping). ...

Shared across Tool Shed and Galaxy to reduce code duplication. Previously this was just a bunch, making it a real class allows placing some shared logic in there.

This refactoring also eliminates some global variables galaxy.model.mapping.Session, galaxy.model.mapping.context, and same for tool shed. This may break things, but these are things that should probably be fixed anyway.

In particular small changes to db_shell.py and a unit test that depended on these global variables have been updated. The functional test frameworks likewise needed to be updated to not depend on these - these changes were more substantial.

To fix these functional tests, I essentially replace old references to global variables in Galaxy with references to global variables just defined in the test framework in test/functional/database_contexts.py (a slight improvement).

2013-12-05 00:20:54 -06:00

..

api

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

cleanup_datasets

Merged in lance_parsons/galaxy-central-pull-requests/dataset-cleanup (pull request #158)

2013-09-10 13:14:10 -04:00

data_libraries

Brad Chapman's patch for fixing an issue where the current user roles were not passed to a template.

2011-02-01 13:11:24 -05:00

galaxy_messaging

Fix the data transfer script to work with new API library content ids.

2012-03-30 09:51:04 -04:00

loc_files

Fix create_all_fasta_loc to work when inspect_dir is not set.

2012-09-18 20:49:29 -04:00

metagenomics

Sync hashbangs

2010-04-01 20:36:31 -04:00

microbes

Eliminated all Python2.4 references, added necessary assert statements to ensure minimum version of Python 2.4.

2008-03-28 15:24:50 +00:00

migrate_tools

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

others

Script to enumerate GOPS JOIN jobs that could have returned an incorrect result before the issue with minimum overlap was fixed last week.

2008-12-22 13:35:01 -05:00

scramble

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

taxonomy

Tweaks to taxonomy tools

2010-11-15 15:04:59 -05:00

tool_shed

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

tools

Fix minor typo in 5233:b5f4df8c3956

2011-03-18 13:40:58 -04:00

__init__.py

Adding db_shell.py that can be used to simplify writing command line

2012-03-05 12:11:53 -06:00

build_toolbox.py

* Remove Todo's that have been done

2011-04-14 14:07:36 +02:00

build_universe_config.py

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.

2012-09-21 22:04:15 -05:00

check_eggs.py

minor docstring adds in /scripts

2012-08-03 13:31:48 -04:00

check_galaxy.py

Fix job manager/handler shutdown, functional tests due to referer -> redirect rename, and check_galaxy script for dataset display -> html table change.

2012-04-16 14:56:24 -04:00

check_python.py

Require Python 2.6+ and remove various compatibility patches for 2.4 and 2.5

2013-04-09 11:57:38 -04:00

create_db.py

Modles: Clean up stand-alone database scripts.

2013-12-05 00:20:54 -06:00

db_shell.py

Models: Introduce real class for app.model (ModelMapping).

2013-12-05 00:20:54 -06:00

dist-scramble.py

minor docstring adds in /scripts

2012-08-03 13:31:48 -04:00

drmaa_external_killer.py

minor docstring adds in /scripts

2012-08-03 13:31:48 -04:00

drmaa_external_runner.py

Fix passing of job name when running jobs as a system user.

2012-10-03 11:51:07 -04:00

egg_packager_template.py

Fix the platform argument to fetch_eggs.py and create an egg packager for easing the installation/updating of Galaxy on systems without a direct connection to the internet.

2010-08-30 11:31:58 -04:00

external_chown_script.py

Some fixes to actual user code to negate the need for world-writable directories and write external metadata and job stdout/stderr to the job working directory.

2011-10-31 16:15:00 -04:00

extract_dataset_part.py

Metadata setting: Always set externally.

2013-05-06 12:50:06 -04:00

extract_toolbox_sections.py

introduction of toolboxposition elements

2011-04-14 15:09:00 +02:00

fetch_eggs.py

minor docstring adds in /scripts

2012-08-03 13:31:48 -04:00

functional_tests.py

Models: Introduce real class for app.model (ModelMapping).

2013-12-05 00:20:54 -06:00

get_platforms.py

Egg support overhaul, introduces a number of fixes to the ABI recognition, better build scripts, a rewrite of the eggs library and eliminition of the need for python -ES

2010-03-01 15:41:30 -05:00

helper.py

Merge

2011-10-07 13:25:19 -07:00

make_egg_packager.py

Bugfix for the offline egg packaging script.

2011-08-03 10:13:01 -04:00

manage_db.py

Modles: Clean up stand-alone database scripts.

2013-12-05 00:20:54 -06:00

manage_tools.py

galaxy.model.orm is a more sensible location than mapping for dialect_to_egg

2013-06-20 10:58:52 -04:00

nosetests.py

Separate framework and tool environments.

2008-04-11 20:11:21 +00:00

paster.py

core: add PasteDeploy dependency back, used inside Paste#httpserver

2013-02-01 17:30:58 -05:00

rst2html.py

Cleaning up modules. Still a few stragglers that can't be easily eggified.

2006-11-15 18:27:21 +00:00

run_selenium_tests.sh

Adding workflow tests using Selenium. These actually drive the web browser to test the Javascript UI effectively. Currently can't run under buildbot.

2009-03-27 18:55:00 -04:00

scramble.py

Typo in scramble.py.

2011-09-02 14:37:09 -04:00

set_dataset_sizes.py

Merge

2011-10-07 13:25:19 -07:00

set_metadata.py

Metadata setting: Always set externally.

2013-05-06 12:50:06 -04:00

set_user_disk_usage.py

Fix a few postgres dialect renaming misses.

2013-09-26 09:34:27 -04:00

sync_reports_config.py

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.

2012-09-21 22:04:15 -05:00

test_dist_egg.py

Add numpy egg, update bx_python egg (now with 100% more numpy) and include code that allows scrambling to depend on other eggs existing and being importable.

2010-03-15 14:35:35 -04:00

transfer.py

1. Add support for manual file transfer from external services to a Galaxy data library using scp. This is currently enabled via the enable_beta_job_managers flag. This should not currently be used because it hits the db significantly to determine if dererred jobs are queued for running. The plan is to use messaging for this, but that approach is not yet implemented. Rabbit mq is still being used to enable manual file transfer to Galaxy data libraries when the enable_beta_job_managers flag is not set.

2011-04-13 13:52:05 -04:00

yuicompressor.jar

Updating the packed versions of all javascripts.

2009-02-25 14:24:46 -05:00