John Chilton 3ac17e09f1 Rework test framework testing and tools. ...

-framework will still cause just a small set of non-default, non-user facing tools to be tested and exerise various aspects of the tool and test frameworks, but now an argument can be passed in -with_framework_test_tools to allow these tools to be used as part of the normal test framework (i.e. when not using -framework). This serves two purposes - to ensure the feature coverage of existing tests remains high as the tests are migrated out of the distribution and to allow a set of tests to be available for functional (e.g. API tests) that users don't need to see.

2014-04-28 11:48:51 -05:00

..

api

Add a very simple example script that uses API to run data managers.

2014-02-10 11:59:58 -05:00

cleanup_datasets

Correct usage of "it's" versus "its".

2014-04-17 15:49:32 -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

Swap amqplib for amqp. This was mostly a drop-in replacement, since it's a currently-maintained fork of amqplib, with slight updates to work with amqp 0-9-1.

2014-02-19 14:27:10 -05:00

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

Fixed tool help image for gops complement.

2014-04-14 13:17:12 -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

Correct usage of "it's" versus "its".

2014-04-17 15:49:32 -04:00

taxonomy

Tweaks to taxonomy tools

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

tool_shed

Add a script to check toolshed dependency files for broken/invalid download URLs.

2014-02-17 12:51:34 -05:00

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

Models: Database migrations for stand-alone tool_shed_install models.

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

Fix old wiki links.

2014-04-10 20:00:45 +02:00

drmaa_external_killer.py

Remove dependency on simplejson; convert everything over to using the json module in the python standard library.

2014-01-10 07:29:05 -05:00

drmaa_external_runner.py

Remove dependency on simplejson; convert everything over to using the json module in the python standard library.

2014-01-10 07:29:05 -05:00

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

Remove dependency on simplejson; convert everything over to using the json module in the python standard library.

2014-01-10 07:29:05 -05:00

extract_dataset_part.py

Remove dependency on simplejson; convert everything over to using the json module in the python standard library.

2014-01-10 07:29:05 -05:00

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

Rework test framework testing and tools.

2014-04-28 11:48:51 -05:00

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

Tools now properly migrated into install_database_connection database...

2013-12-17 11:19:41 -06:00

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

Remove dependency on simplejson; convert everything over to using the json module in the python standard library.

2014-01-10 07:29:05 -05:00

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