John Chilton a2e3140375 Give tool executions a clean working directory. ...

Rather then massively renaming job_directory and job_working_directory, I introduce the concept of the tool execution working directory (tool_working_directory) that is the job working directory + "/working" and that will not be populated with job files.

Some legacy cruft in there for the upgrade, things like galaxy.json and dynamic outputs may be in the job working directory or the tool execution working directory.

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

Give tool executions a clean working directory.

2016-02-22 10:47:11 +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

Rename config.job_working_directory to config.jobs_directory.

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

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

Rename config.job_working_directory to config.jobs_directory.

2016-02-22 10:47:11 +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