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767 Commits
Author SHA1 Message Date
Nicola Soranzo 408827e251 Merge branch 'release_16.04' into dev 2016-04-12 14:35:37 +01:00
Nicola Soranzo a9d675f5e8 Fix sys.path.insert() after #2093. 2016-04-11 20:27:25 +01:00
Nicola Soranzo 27f418c52d Remove scripts which depend on install_and_test_tool_shed_repositories. 2016-04-11 20:27:25 +01:00
John Chilton bf83b39e0d Merge pull request #2113 from martenson/fix-blocking-issue-check 
fix blocking issue check
 2016-04-08 20:30:55 -04:00
John Chilton af42338ecc Automate and clarify more of the release process. 
upstream is used repeatedly and just assumed to be a remote - this tests for it and adds it if it doesn't exist before using in make commands now. This also automates the previous release to dev merge in the instructions with a new Make command.

Additionally, two PRs need to be created to update versions. This prints a reminder to do this and adds it to the release checklist. Ideally, these PRs could be avoided with a direct push or automatically created with hub (https://github.com/github/hub).
 2016-04-08 14:17:55 -04:00
Martin Cech 2651587e82 fix blocking issue check; 
it would check the issues created by galaxybot before I think
 2016-04-08 13:10:02 -04:00
John Chilton 2744d5541f Merge pull request #2093 from davebx/move_scripts 
Move scripts out of lib/tool_shed.
 2016-04-08 09:54:44 -04:00
Dave Bouvier fbf8cfce2a Remove unused import. 2016-04-05 14:23:56 -04:00
Dave Bouvier 9f1490cc60 Fix sys.path.insert some more. 2016-04-05 13:55:21 -04:00
Dave Bouvier 9bf3976e8a Fix sys.path.insert 2016-04-05 13:50:51 -04:00
Dave Bouvier 77353902ee Move scripts out of lib/tool_shed. 2016-04-05 13:04:44 -04:00
John Chilton 7aa2d6840a Implement IntegrationTestCase and EmbeddedPulsarTestCase. 
IntegrationTestCases differ from functional tests in that they start up a Galaxy instance configured on a per test class basis - so this new class of "integration tests" can test configuration modalities of Galaxy that cannot be tested with traditional Galaxy functional tests.
 2016-04-04 20:08:55 -04:00
John Chilton b3881f86c1 For non-shed tool data - read loc from sample if available. 2016-04-01 17:25:47 -04:00
John Chilton 05a2f44126 Separate different style Galaxy testing behaviors into classes. 2016-03-29 08:04:28 -04:00
John Chilton 6faef4df2e Introduce a TestDriver class to reduce duplication between test drivers. 
Classes allow de-duplicating logic and state organization in a different way than methods. Use a common setup, run, tear down paradigm for these tests.
 2016-03-29 08:04:28 -04:00
John Chilton eac6c10ec9 Allow running Galaxy tests on an existing external instance. 2016-03-29 08:04:27 -04:00
John Chilton 915b7edcb7 Unify and simplify script driver argument processing. 2016-03-29 08:04:27 -04:00
John Chilton fc1861c4d9 Move "with framework test tools" logic out of nose driver and into run_tests. 2016-03-29 08:04:27 -04:00
John Chilton 8fdecbb3bf Another simplifcation to method structure in scripts/functional_tests.py. 2016-03-29 08:04:27 -04:00
John Chilton 93cfdff910 Eliminate last custom config value setup in scripts/functional_tests.py... 
... outside of driver_util. So now we can just use the driver_util config object.
 2016-03-29 08:04:27 -04:00
John Chilton 586fa6801b Move yet more logic into driver_util to reduce driver method for scripts/functional_tests.py. 2016-03-29 08:04:27 -04:00
John Chilton e1aa0b3acc Simplify/unify tool conf handling logic across two driver util... 2016-03-29 08:04:27 -04:00
John Chilton f3c757ff1c Move more galaxy config into driver_util... 
Handle logging and enabling of beta formats consistently across driver scripts.
 2016-03-29 08:04:26 -04:00
John Chilton a8033a543b Move galaxy test data manager setup logic into driver_util. 2016-03-29 08:04:26 -04:00
John Chilton 3546bdf22b Cleanup Galaxy tempdir handling in driver util. 2016-03-29 08:04:26 -04:00
John Chilton 362194b2c0 Cleanup logic for GALAXY_TEST_TMP_DIR add docs. 2016-03-29 08:04:26 -04:00
John Chilton 3c72c2129b Move data_manager_config_file setup into driver_util. 
Seems it doesn't hurt tool shed tests to configure this.
 2016-03-29 08:04:26 -04:00
John Chilton 1b80e6e8d1 Move another galaxy config (clean up job) into driver_util. 2016-03-29 08:04:26 -04:00
John Chilton 5b826a0839 Move more galaxy config logic into driver_util. 
This time for galaxy master API key.
 2016-03-29 08:04:26 -04:00
John Chilton 65806641c1 Simplify(?) tool data table config logic at lest in scripts/functional_tests.py. 2016-03-29 08:04:25 -04:00
John Chilton d657855b7f Remove unused test_conf variable. 2016-03-29 08:04:25 -04:00
John Chilton 3c47105732 Fix shed tool test file shed_tools_dict handling. 
Instead of writing it below GALAXY_ROOT (which it shouldn't do at all) - add to the temp directory managed for the test so that special clean up logic isn't required for it. The global switch GALAXY_TEST_NO_CLEANUP can be used to recover the state of this file if needed now also.
 2016-03-29 08:04:25 -04:00
John Chilton 671b6933dd De-duplicate test driver logic for closing apps and stopping severs... 2016-03-29 08:04:25 -04:00
John Chilton 0f36229400 Unify and simplify configuration and launch of test web servers. 
- Sync up the logic for reading and setting GALAXY_TEST_HOST, GALAXY_TEST_PORT, TOOL_SHED_TEST_HOST, and TOOL_SHED_TEST_PORT.
 - Setup one high level method for taking a Galaxy-style "app" and creating a webapp from a factory method and then launching a paste server for that entity respecting the above variables.
 2016-03-29 08:04:25 -04:00
John Chilton ee537a119b Restructure to simplify the main() in scripts/functional_tests.py. 
Previously this was entering a conditional on the same condition twice. This simplifies this to just do that once and makes the galaxy and tool shed driver code look more similar with respect to launching a Galaxy webapp.
 2016-03-29 08:04:25 -04:00
John Chilton ecbb732665 Move construction of test driver app objects into driver_util. 
This de-duplicates some of the Galaxy stuff and makes the tool shed stuff look very uniform.
 2016-03-29 08:04:25 -04:00
John Chilton ec0a123849 Unify and simplify how Galaxy is launched across test drivers. 2016-03-29 08:04:24 -04:00
John Chilton 2729699bf6 Further unification of how to setup Galaxy databases for testing. 
Reuse setup_galaxy_config for this task.
 2016-03-29 08:04:24 -04:00
John Chilton fe460008fa More work on syncrhonized test database configuration... 
for test drivers.
 2016-03-29 08:04:24 -04:00
John Chilton 528b74ca1e Remove unused test job conf stuff. 
Not that this wouldn't be useful - it would be but it wasn't wired up to do anything currently.
 2016-03-29 08:04:24 -04:00
John Chilton be0107b620 Simplify test tool_data_table_config logic. 
Added with https://github.com/galaxyproject/galaxy/commit/246ea04cc7ee1d0d470a514302bf2623f845ed8f.
 2016-03-29 08:04:24 -04:00
John Chilton 651b91248b Restructure scripts/functional_test.py's main() to reflect recent simplifications. 2016-03-29 08:04:24 -04:00
John Chilton e7b5293534 Refactor toolbox hacks used by installed and migration tool tests out... 
into driver_util. This greatly simplifies the code structure of scripts/functional_tests.py's main method.

Add description of GALAXY_TEST_SHED_TOOL_CONF and some documentation to all of this.
 2016-03-29 08:04:24 -04:00
John Chilton d03651f4ef Move more shared galaxy configuration into driver_util. 2016-03-29 08:04:24 -04:00
John Chilton 6b278478d3 Move tool_path logic into setup_galaxy_config. 2016-03-29 08:04:23 -04:00
John Chilton 5af770972d Fix naming and comment best practices for test driver scripts. 2016-03-29 08:04:23 -04:00
John Chilton dcbdcbe081 Unify tool dependency dir handling between test driver scripts. 2016-03-29 08:04:23 -04:00
John Chilton e309c7f6eb Make XXX_TEST_DBPATH and XXX_TEST_DB_TEMPLATE generic and shared with shed. 
Now the variable TOOL_SHED_TEST_DB_TEMPLATE works as one might expect like GALAXY_TEST_DB_TEMPLATE.
 2016-03-29 08:04:23 -04:00
John Chilton ec3f0506c9 Remove unused config variable from test drivers. 2016-03-29 08:04:23 -04:00
John Chilton a18cbd5930 De-duplicate test driver - move more Galaxy config into common method. 2016-03-29 08:04:22 -04:00