Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3cb2bb1c359a7dd9f66e07e04490262b753e83e6 https://github.com/galaxyproject/galaxy/commit/3cb2bb1c359a7dd9f66e07e044902... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py A test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Start work on synchronizing functional test drivers. - Tweak paths in same way. - Don't write tool shed temp files to GALAXY_ROOT - respect /tmp. - Build identical loggers. Commit: 9d1a54e88c9ce55e9473cfd823c2d1ebe5cd7b8e https://github.com/galaxyproject/galaxy/commit/9d1a54e88c9ce55e9473cfd823c2d... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M test/tool_shed/functional_tests.py Log Message: ----------- Synchronize main() handling between functional test driver scripts. Commit: 3369dfafa0ed12886d1adea7ea2155fc3ebe31aa https://github.com/galaxyproject/galaxy/commit/3369dfafa0ed12886d1adea7ea215... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Synchronize a bunch of test launch and nose configure stuff. Commit: 55297b75e10a49ffe081087e5a7d5a1140af38ff https://github.com/galaxyproject/galaxy/commit/55297b75e10a49ffe081087e5a7d5... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Sync code for retrieving prepopulated databases. Commit: 173d98484bc50cec7f755d85c46ae941b1e5bc50 https://github.com/galaxyproject/galaxy/commit/173d98484bc50cec7f755d85c46ae... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/tool_shed/functional_tests.py Log Message: ----------- Eliminate always True variable to simplify test driver logic. For now, always serve static content with these tests. Commit: d60fe9f5aa3bb264d2a1873aaa383ee9657487ad https://github.com/galaxyproject/galaxy/commit/d60fe9f5aa3bb264d2a1873aaa383... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Synchronize static configuration stuff. Commit: b7c75f20a5bfb625d01c85d1821d11ff50fb5949 https://github.com/galaxyproject/galaxy/commit/b7c75f20a5bfb625d01c85d1821d1... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Eliminate duplication in waiting for HTTP servers in test drivers. Commit: 103098c7e421043b79b3629c8c6f61b1ee792fb1 https://github.com/galaxyproject/galaxy/commit/103098c7e421043b79b3629c8c6f6... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- De-duplicate and simplify launching a webapp for functional tests. Commit: d0ee53f8017ef4fde97efb05ee82b4f95d037b62 https://github.com/galaxyproject/galaxy/commit/d0ee53f8017ef4fde97efb05ee82b... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py Log Message: ----------- Simplify ignore_files logic in scripts/functional_tests.py. These details are taken care of by run_tests.sh. Commit: 34f154d92e162bcb56e4ffa9524bdaae4cb4f140 https://github.com/galaxyproject/galaxy/commit/34f154d92e162bcb56e4ffa9524bd... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py A test/functional/tools/upload_tool_conf.xml Log Message: ----------- Rework upload tool. Commit: 8c857694f3792520950cbdf6a2dcd5df4e7f332c https://github.com/galaxyproject/galaxy/commit/8c857694f3792520950cbdf6a2dcd... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Synchronize locale handling for test drivers. Commit: e0a9d6b67fd9a7063b292a7f2ede04ae70c470fc https://github.com/galaxyproject/galaxy/commit/e0a9d6b67fd9a7063b292a7f2ede0... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- De-duplicate code for setting up Galaxy database. Commit: 887edb647b5175c9e24a3e432a0ef38fe84ed02c https://github.com/galaxyproject/galaxy/commit/887edb647b5175c9e24a3e432a0ef... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/tool_shed/functional_tests.py Log Message: ----------- Remove no longer valid sample references in scripts/functional_tests.py. Commit: fe39f5bf553dd3b2a41b5bfaf960b9a175e8d904 https://github.com/galaxyproject/galaxy/commit/fe39f5bf553dd3b2a41b5bfaf960b... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M test/base/driver_util.py Log Message: ----------- Revise test driver logging so log is available in driver_util. Commit: db37011d700d3ba174033dc68808a9882525268d https://github.com/galaxyproject/galaxy/commit/db37011d700d3ba174033dc68808a... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- De-duplicate code for cleaning up test directories. Commit: 91a71068979ca19763ca18cde73d350a37546ec4 https://github.com/galaxyproject/galaxy/commit/91a71068979ca19763ca18cde73d3... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/tool_shed/functional_tests.py Log Message: ----------- Remove unused proxy port stuff in test drivers. Commit: ce9a55207fe5f467a71e03fb3f364fc08ed4f943 https://github.com/galaxyproject/galaxy/commit/ce9a55207fe5f467a71e03fb3f364... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M test/tool_shed/functional_tests.py Log Message: ----------- Remove unused or un-useful code from tool shed test driver. Commit: 97070b4b532b2fd8f11276d8056dc036a4155d50 https://github.com/galaxyproject/galaxy/commit/97070b4b532b2fd8f11276d8056dc... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Move tool shed test data handling into driver_util. Commit: fd46a1f987fe6c9fa95b62e9b21bc00273c36fe9 https://github.com/galaxyproject/galaxy/commit/fd46a1f987fe6c9fa95b62e9b21bc... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Move tool_conf logic for drivers into driver_util. - Don't generate a tool_conf for upload in tool shed tests - just use the fixed one setup for framework tools. - Move every mention of that directory and files into constants in driver_util. Commit: 9804eb56bf6d4ba4df0ec787501366d1dab8102e https://github.com/galaxyproject/galaxy/commit/9804eb56bf6d4ba4df0ec78750136... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- De-duplicate test driver logic for install database connection. Commit: 72716750d1f6ba1b91781144d12c6fd90ce51bca https://github.com/galaxyproject/galaxy/commit/72716750d1f6ba1b91781144d12c6... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py Log Message: ----------- Simplify GALAXY_TEST_SAVE logic... ... script/functional_tests.py was just pulling it out of the environ and sticking it back in - made no sense. Commit: 75f0cb470c69d05ad69ff4e4d96d83ff036940cd https://github.com/galaxyproject/galaxy/commit/75f0cb470c69d05ad69ff4e4d96d8... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M test/tool_shed/functional_tests.py Log Message: ----------- Eliminate ability to set Galaxy tool path for tool shed tests... Makes sense in Galaxy tests but not for tool shed tests, I see no reason for this extension point. If it is needed GALAXY_CONFIG_TOOL_PATH will work instead of TOOL_SHED_TEST_TOOL_PATH. Commit: 16c0ae216aa5414b4a9d19c53b47a9d94fc6e3af https://github.com/galaxyproject/galaxy/commit/16c0ae216aa5414b4a9d19c53b47a... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- De-duplicate XXX_TEST_DBPATH logic. Commit: c2b260539b58291c6a207f1d779ac8465302c831 https://github.com/galaxyproject/galaxy/commit/c2b260539b58291c6a207f1d779ac... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M run_tests.sh Log Message: ----------- Start list of environment variables used for testing. Commit: e86fa83e863b7da20ba1cc1b2ce96bec6dd76896 https://github.com/galaxyproject/galaxy/commit/e86fa83e863b7da20ba1cc1b2ce96... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Begin work on test driver function for setting up Galaxy config. Commit: a18cbd5930cc21a3997cdc0d69fcf4f0ba53ea55 https://github.com/galaxyproject/galaxy/commit/a18cbd5930cc21a3997cdc0d69fcf... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- De-duplicate test driver - move more Galaxy config into common method. Commit: ec3f0506c9ee791b8c2e3ba22eb158e14375a267 https://github.com/galaxyproject/galaxy/commit/ec3f0506c9ee791b8c2e3ba22eb15... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/tool_shed/functional_tests.py Log Message: ----------- Remove unused config variable from test drivers. Commit: e309c7f6ebaf7b29a00902af9fb71fd69fac4070 https://github.com/galaxyproject/galaxy/commit/e309c7f6ebaf7b29a00902af9fb71... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- 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. Commit: 7eab64eed0e06872d3eb209f68f1f32667dda65e https://github.com/galaxyproject/galaxy/commit/7eab64eed0e06872d3eb209f68f1f... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M test/tool_shed/functional_tests.py Log Message: ----------- Remove unused shed tool dependency logic in tool shed tests. Commit: dcbdcbe081bdeebdc8e2539007d210db267dcb37 https://github.com/galaxyproject/galaxy/commit/dcbdcbe081bdeebdc8e2539007d21... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Unify tool dependency dir handling between test driver scripts. Commit: 5af770972d47fcabf7d2c062fa9b4f1739ec146a https://github.com/galaxyproject/galaxy/commit/5af770972d47fcabf7d2c062fa9b4... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/tool_shed/functional_tests.py Log Message: ----------- Fix naming and comment best practices for test driver scripts. Commit: 6b278478d30f03298ac9cc8a5ebeaf6c2f1bd04f https://github.com/galaxyproject/galaxy/commit/6b278478d30f03298ac9cc8a5ebea... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py Log Message: ----------- Move tool_path logic into setup_galaxy_config. Commit: 18c366c6d064147a118ab8397a1c2cbc3b0ec4d0 https://github.com/galaxyproject/galaxy/commit/18c366c6d064147a118ab8397a1c2... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M test/tool_shed/functional_tests.py Log Message: ----------- Remove now unused variable and documentation. Commit: 88ce7a2fa4ac7a5c44e08ca4dcea9fcfe257f406 https://github.com/galaxyproject/galaxy/commit/88ce7a2fa4ac7a5c44e08ca4dcea9... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M test/tool_shed/functional_tests.py Log Message: ----------- Remove unused branch for tool shed test driver code. Commit: d03651f4ef7c5e5540d3a23c84b38e840900b500 https://github.com/galaxyproject/galaxy/commit/d03651f4ef7c5e5540d3a23c84b38... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Move more shared galaxy configuration into driver_util. Commit: e7b5293534d6cf9a704b9d295271abffda0f3c5d https://github.com/galaxyproject/galaxy/commit/e7b5293534d6cf9a704b9d295271a... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M run_tests.sh M scripts/functional_tests.py M test/base/driver_util.py Log Message: ----------- 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. Commit: 651b91248b350de951c95e5c2bd8edd6e517b9d2 https://github.com/galaxyproject/galaxy/commit/651b91248b350de951c95e5c2bd8e... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py Log Message: ----------- Restructure scripts/functional_test.py's main() to reflect recent simplifications. Commit: be0107b6204b5b47b9c6e8ea3196a893d4409c05 https://github.com/galaxyproject/galaxy/commit/be0107b6204b5b47b9c6e8ea3196a... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py Log Message: ----------- Simplify test tool_data_table_config logic. Added with https://github.com/galaxyproject/galaxy/commit/246ea04cc7ee1d0d470a514302bf2.... Commit: 528b74ca1e470499d53719ccbeb8acd78002ee33 https://github.com/galaxyproject/galaxy/commit/528b74ca1e470499d53719ccbeb8a... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py Log Message: ----------- 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. Commit: fe460008faf33a673185672ee2f34b26b8878ea5 https://github.com/galaxyproject/galaxy/commit/fe460008faf33a673185672ee2f34... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- More work on syncrhonized test database configuration... for test drivers. Commit: 2729699bf69c7b4ca6750fbc628f4eb147c12717 https://github.com/galaxyproject/galaxy/commit/2729699bf69c7b4ca6750fbc628f4... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Further unification of how to setup Galaxy databases for testing. Reuse setup_galaxy_config for this task. Commit: ec0a12384994774522380165302934531ca12901 https://github.com/galaxyproject/galaxy/commit/ec0a1238499477452238016530293... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/tool_shed/functional_tests.py Log Message: ----------- Unify and simplify how Galaxy is launched across test drivers. Commit: ecbb7326658ee4f400be865cfc7d3a4baf199b39 https://github.com/galaxyproject/galaxy/commit/ecbb7326658ee4f400be865cfc7d3... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- 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. Commit: ee537a119b381b78ce1d58769970c0302fe5b684 https://github.com/galaxyproject/galaxy/commit/ee537a119b381b78ce1d58769970c... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py Log Message: ----------- 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. Commit: 0f362294000b005073c8167ac553c88403316951 https://github.com/galaxyproject/galaxy/commit/0f362294000b005073c8167ac553c... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- 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. Commit: 671b6933dd602e47ba8d99ba8e39e0419dde51f3 https://github.com/galaxyproject/galaxy/commit/671b6933dd602e47ba8d99ba8e39e... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- De-duplicate test driver logic for closing apps and stopping severs... Commit: 33d312b906ac4c50554fb1bff1e0dc39bdaea077 https://github.com/galaxyproject/galaxy/commit/33d312b906ac4c50554fb1bff1e0d... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- [16.01] Fix for running jobs when metadata tool is not in toolbox. Happens when -installed or -migrated are passed into run_tests.sh because of the way the tool shed hacks up Galaxy's tool config. Commit: 3c47105732febe5ca69a6ba20df875177fb7a31a https://github.com/galaxyproject/galaxy/commit/3c47105732febe5ca69a6ba20df87... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py Log Message: ----------- 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. Commit: d657855b7f075bbcc1b2c7aa7f2e7b679ff1a6dd https://github.com/galaxyproject/galaxy/commit/d657855b7f075bbcc1b2c7aa7f2e7... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/tool_shed/config.py M scripts/functional_tests.py Log Message: ----------- Remove unused test_conf variable. Commit: 65806641c1aa0260923f0733bff7b1f81304d3a3 https://github.com/galaxyproject/galaxy/commit/65806641c1aa0260923f0733bff7b... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Simplify(?) tool data table config logic at lest in scripts/functional_tests.py. Commit: 5b826a0839f6545ee94b3c3cd3ff710e5b8747f3 https://github.com/galaxyproject/galaxy/commit/5b826a0839f6545ee94b3c3cd3ff7... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py Log Message: ----------- Move more galaxy config logic into driver_util. This time for galaxy master API key. Commit: e356c80c02e23ff42d0c3ba0b94575865793168c https://github.com/galaxyproject/galaxy/commit/e356c80c02e23ff42d0c3ba0b9457... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Move enable_tool_shed_check test driver logic into driver_util. Commit: 1b80e6e8d1e4e2ecddaac4b37337e7cfd7016d57 https://github.com/galaxyproject/galaxy/commit/1b80e6e8d1e4e2ecddaac4b37337e... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py Log Message: ----------- Move another galaxy config (clean up job) into driver_util. Commit: 3c72c2129bd5a92e4fe0722e50e5f6d31c5d3737 https://github.com/galaxyproject/galaxy/commit/3c72c2129bd5a92e4fe0722e50e5f... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py Log Message: ----------- Move data_manager_config_file setup into driver_util. Seems it doesn't hurt tool shed tests to configure this. Commit: 362194b2c023dc54cd220038a529ae411e6a2ea3 https://github.com/galaxyproject/galaxy/commit/362194b2c023dc54cd220038a529a... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M run_tests.sh M scripts/functional_tests.py M test/base/driver_util.py Log Message: ----------- Cleanup logic for GALAXY_TEST_TMP_DIR add docs. Commit: 3546bdf22b0defd8236e184331a041bb3f4f8840 https://github.com/galaxyproject/galaxy/commit/3546bdf22b0defd8236e184331a04... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py Log Message: ----------- Cleanup Galaxy tempdir handling in driver util. Commit: a8033a543baa7f919e0d7c061baa62263c7f633e https://github.com/galaxyproject/galaxy/commit/a8033a543baa7f919e0d7c061baa6... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py Log Message: ----------- Move galaxy test data manager setup logic into driver_util. Commit: f3c757ff1c5349ef683a092cc8b758b93cf84614 https://github.com/galaxyproject/galaxy/commit/f3c757ff1c5349ef683a092cc8b75... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py Log Message: ----------- Move more galaxy config into driver_util... Handle logging and enabling of beta formats consistently across driver scripts. Commit: e1aa0b3acc83ef219752cad75b262b71cd232199 https://github.com/galaxyproject/galaxy/commit/e1aa0b3acc83ef219752cad75b262... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Simplify/unify tool conf handling logic across two driver util... Commit: 586fa6801b9d7cec1db1ceaf5488f66dadfbc183 https://github.com/galaxyproject/galaxy/commit/586fa6801b9d7cec1db1ceaf5488f... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- Move yet more logic into driver_util to reduce driver method for scripts/functional_tests.py. Commit: 93cfdff9103dc4216893ed494e22bdc2d870ff22 https://github.com/galaxyproject/galaxy/commit/93cfdff9103dc4216893ed494e22b... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- 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. Commit: 8fdecbb3bf5c6ba02393531117c3e2160e5ea22b https://github.com/galaxyproject/galaxy/commit/8fdecbb3bf5c6ba02393531117c3e... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py Log Message: ----------- Another simplifcation to method structure in scripts/functional_tests.py. Commit: fc1861c4d9ab8b7ecae5b959c3e59f33146e6802 https://github.com/galaxyproject/galaxy/commit/fc1861c4d9ab8b7ecae5b959c3e59... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M run_tests.sh M scripts/functional_tests.py Log Message: ----------- Move "with framework test tools" logic out of nose driver and into run_tests. Commit: 915b7edcb7b0120d4690c3fa59b97e7dbdcb4a2a https://github.com/galaxyproject/galaxy/commit/915b7edcb7b0120d4690c3fa59b97... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M run_tests.sh M scripts/functional_tests.py M test/functional/workflow.py Log Message: ----------- Unify and simplify script driver argument processing. Commit: eac6c10ec93a6f5a610a9d07d1e7601049f4f7cf https://github.com/galaxyproject/galaxy/commit/eac6c10ec93a6f5a610a9d07d1e76... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M run_tests.sh M scripts/functional_tests.py M test/base/twilltestcase.py Log Message: ----------- Allow running Galaxy tests on an existing external instance. Commit: 8538c0ed774c89416c80e8688723238386a90736 https://github.com/galaxyproject/galaxy/commit/8538c0ed774c89416c80e86887232... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Add comment describing metadata_tool hack. Commit: 6faef4df2ec5a1b189594bf528debd521e869d96 https://github.com/galaxyproject/galaxy/commit/6faef4df2ec5a1b189594bf528deb... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py M test/tool_shed/functional_tests.py Log Message: ----------- 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. Commit: 05a2f441261c176dfe2cc802d4743aad6652a9ea https://github.com/galaxyproject/galaxy/commit/05a2f441261c176dfe2cc802d4743... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py Log Message: ----------- Separate different style Galaxy testing behaviors into classes. Commit: b8ecf36f2ae52af1cda3eac64f53400e56e895db https://github.com/galaxyproject/galaxy/commit/b8ecf36f2ae52af1cda3eac64f534... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M run_tests.sh Log Message: ----------- Improve testing environment variable and CLI documentation. Document many more variables and improve documentation of what is there. Include fixes recommended by @nsoranzo. Commit: d693aaf624ce1ca1f501e3ed98fe2ad74ca0836d https://github.com/galaxyproject/galaxy/commit/d693aaf624ce1ca1f501e3ed98fe2... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/webapps/tool_shed/config.py M run_tests.sh M scripts/functional_tests.py A test/base/driver_util.py M test/base/twilltestcase.py A test/functional/tools/upload_tool_conf.xml M test/functional/workflow.py M test/tool_shed/functional_tests.py Log Message: ----------- Merge pull request #2016 from jmchilton/test_driver_cleanup Functional Test Drivers Overhaul Compare: https://github.com/galaxyproject/galaxy/compare/2687002a27ad...d693aaf624ce