John Chilton b92074e6ff Implement profile="XX.XX" on tools, better defaults for newer tools. ...

- set -e in tool command scripts.
 - Disable implicit extra file collection. All dynamic extra file collection requires a <discover_datasets tag.
 - Disable format="input" - require explicit metadata targets (metadata_source, format_source).
 - Disable interpreter= - hacky and doesn't work as expected in too many circumstances. Use $__tool_directory__.
 - Disable $param_file - grepping the command for the string is impercise. If useful we can add flag to match the flag used to produce inputs as a JSON file.
 - Disable default version of 1.0.0, the IUC has made it clear they prefer all tools have an explicit version.

Fixes #1609.

2016-02-22 10:47:11 +00:00

..

dataset_collections

Bugfix: Rework collection matching logic so it properly matches combined collection/subcollection mapping.

2014-05-07 15:39:03 -05:00

datatypes

Testing: move managers, web/base, datatypes/dataproviders, and visualization 'unit'(?) tests to using common mock objects and loading system; cleanup

2015-04-16 10:25:34 -04:00

jobs

Introduce strict shell command option.

2016-02-22 09:58:43 +00:00

managers

(merge conflicts with dev)

2016-02-09 10:27:21 -05:00

tool_shed_unit_tests

Revert "Revert "[WIP] Mega flake8 linting""

2015-07-12 21:25:44 +01:00

tools

Implement profile="XX.XX" on tools, better defaults for newer tools.

2016-02-22 10:47:11 +00:00

unittest_utils

CORS: move check/setter to webapp.GalaxyWebTransaction from base.WebApplication, bail on lack of config key, rework tests, add test files

2016-01-07 12:39:18 -05:00

visualizations

Use os.pardir everywhere instead of '..' .

2015-07-14 16:20:29 +01:00

web

CORS: try fixing tests again, this time by avoiding use of Configuration altogether

2016-01-14 16:45:28 -05:00

workflows

Merge pull request #1308 from jmchilton/multi_collection_types

2016-01-04 14:43:37 -06:00

test_galaxy_mapping.py

Implement nested workflows.

2015-12-16 15:22:18 +00:00

test_galaxy_transactions.py

Fix bunch import; fix unit test imports

2014-09-03 15:18:55 -04:00

test_lazy_process.py

Attempt fix of test/unit/test_lazy_process.py which transiently fails.

2014-11-25 23:02:05 -05:00

test_objectstore.py

More Python 3 fixes.

2015-12-20 13:38:34 +00:00

test_routes.py

API-ify tool dependency resolution.

2015-12-30 20:17:44 +00:00

test_security_helper.py

Rework encode_all_ids in BaseController so it can be used outside of controllers.

2014-05-06 08:54:31 -05:00

test_sockets.py

Revert "Revert "[WIP] Mega flake8 linting""

2015-07-12 21:25:44 +01:00

test_sqlite_utils.py

Better sqlite query whitelisting via the sqlparse library

2014-07-25 11:02:53 +10:00

test_topsort.py

Ensure topological sorting is 'stable' w.r.t to first element of tuple.

2014-08-04 09:33:40 -04:00

tools_support.py

Merge pull request #1556 from jmchilton/datatype_imports

2016-02-09 12:44:59 -05:00