- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 3cb2bb: Start work on synchronizing functional test driver...
by GitHub 29 Mar '16

29 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3cb2bb1c359a7dd9f66e07e04490262b753e83e6 https://github.com/galaxyproject/galaxy/commit/3cb2bb1c359a7dd9f66e07e04490… Author: John Chilton <jmchilton(a)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/9d1a54e88c9ce55e9473cfd823c2… Author: John Chilton <jmchilton(a)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/3369dfafa0ed12886d1adea7ea21… Author: John Chilton <jmchilton(a)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/55297b75e10a49ffe081087e5a7d… Author: John Chilton <jmchilton(a)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/173d98484bc50cec7f755d85c46a… Author: John Chilton <jmchilton(a)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/d60fe9f5aa3bb264d2a1873aaa38… Author: John Chilton <jmchilton(a)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/b7c75f20a5bfb625d01c85d1821d… Author: John Chilton <jmchilton(a)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/103098c7e421043b79b3629c8c6f… Author: John Chilton <jmchilton(a)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/d0ee53f8017ef4fde97efb05ee82… Author: John Chilton <jmchilton(a)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/34f154d92e162bcb56e4ffa9524b… Author: John Chilton <jmchilton(a)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/8c857694f3792520950cbdf6a2dc… Author: John Chilton <jmchilton(a)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/e0a9d6b67fd9a7063b292a7f2ede… Author: John Chilton <jmchilton(a)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/887edb647b5175c9e24a3e432a0e… Author: John Chilton <jmchilton(a)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/fe39f5bf553dd3b2a41b5bfaf960… Author: John Chilton <jmchilton(a)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/db37011d700d3ba174033dc68808… Author: John Chilton <jmchilton(a)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/91a71068979ca19763ca18cde73d… Author: John Chilton <jmchilton(a)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/ce9a55207fe5f467a71e03fb3f36… Author: John Chilton <jmchilton(a)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/97070b4b532b2fd8f11276d8056d… Author: John Chilton <jmchilton(a)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/fd46a1f987fe6c9fa95b62e9b21b… Author: John Chilton <jmchilton(a)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/9804eb56bf6d4ba4df0ec7875013… Author: John Chilton <jmchilton(a)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/72716750d1f6ba1b91781144d12c… Author: John Chilton <jmchilton(a)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/75f0cb470c69d05ad69ff4e4d96d… Author: John Chilton <jmchilton(a)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/16c0ae216aa5414b4a9d19c53b47… Author: John Chilton <jmchilton(a)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/c2b260539b58291c6a207f1d779a… Author: John Chilton <jmchilton(a)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/e86fa83e863b7da20ba1cc1b2ce9… Author: John Chilton <jmchilton(a)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/a18cbd5930cc21a3997cdc0d69fc… Author: John Chilton <jmchilton(a)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/ec3f0506c9ee791b8c2e3ba22eb1… Author: John Chilton <jmchilton(a)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/e309c7f6ebaf7b29a00902af9fb7… Author: John Chilton <jmchilton(a)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/7eab64eed0e06872d3eb209f68f1… Author: John Chilton <jmchilton(a)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/dcbdcbe081bdeebdc8e2539007d2… Author: John Chilton <jmchilton(a)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/5af770972d47fcabf7d2c062fa9b… Author: John Chilton <jmchilton(a)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/6b278478d30f03298ac9cc8a5ebe… Author: John Chilton <jmchilton(a)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/18c366c6d064147a118ab8397a1c… Author: John Chilton <jmchilton(a)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/88ce7a2fa4ac7a5c44e08ca4dcea… Author: John Chilton <jmchilton(a)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/d03651f4ef7c5e5540d3a23c84b3… Author: John Chilton <jmchilton(a)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/e7b5293534d6cf9a704b9d295271… Author: John Chilton <jmchilton(a)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/651b91248b350de951c95e5c2bd8… Author: John Chilton <jmchilton(a)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/be0107b6204b5b47b9c6e8ea3196… Author: John Chilton <jmchilton(a)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/246ea04cc7ee1d0d470a514302bf…. Commit: 528b74ca1e470499d53719ccbeb8acd78002ee33 https://github.com/galaxyproject/galaxy/commit/528b74ca1e470499d53719ccbeb8… Author: John Chilton <jmchilton(a)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/fe460008faf33a673185672ee2f3… Author: John Chilton <jmchilton(a)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/2729699bf69c7b4ca6750fbc628f… Author: John Chilton <jmchilton(a)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/ec0a123849947745223801653029… Author: John Chilton <jmchilton(a)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/ecbb7326658ee4f400be865cfc7d… Author: John Chilton <jmchilton(a)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/ee537a119b381b78ce1d58769970… Author: John Chilton <jmchilton(a)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/0f362294000b005073c8167ac553… Author: John Chilton <jmchilton(a)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/671b6933dd602e47ba8d99ba8e39… Author: John Chilton <jmchilton(a)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/33d312b906ac4c50554fb1bff1e0… Author: John Chilton <jmchilton(a)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/3c47105732febe5ca69a6ba20df8… Author: John Chilton <jmchilton(a)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/d657855b7f075bbcc1b2c7aa7f2e… Author: John Chilton <jmchilton(a)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/65806641c1aa0260923f0733bff7… Author: John Chilton <jmchilton(a)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/5b826a0839f6545ee94b3c3cd3ff… Author: John Chilton <jmchilton(a)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/e356c80c02e23ff42d0c3ba0b945… Author: John Chilton <jmchilton(a)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/1b80e6e8d1e4e2ecddaac4b37337… Author: John Chilton <jmchilton(a)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/3c72c2129bd5a92e4fe0722e50e5… Author: John Chilton <jmchilton(a)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/362194b2c023dc54cd220038a529… Author: John Chilton <jmchilton(a)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/3546bdf22b0defd8236e184331a0… Author: John Chilton <jmchilton(a)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/a8033a543baa7f919e0d7c061baa… Author: John Chilton <jmchilton(a)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/f3c757ff1c5349ef683a092cc8b7… Author: John Chilton <jmchilton(a)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/e1aa0b3acc83ef219752cad75b26… Author: John Chilton <jmchilton(a)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/586fa6801b9d7cec1db1ceaf5488… Author: John Chilton <jmchilton(a)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/93cfdff9103dc4216893ed494e22… Author: John Chilton <jmchilton(a)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/8fdecbb3bf5c6ba02393531117c3… Author: John Chilton <jmchilton(a)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/fc1861c4d9ab8b7ecae5b959c3e5… Author: John Chilton <jmchilton(a)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/915b7edcb7b0120d4690c3fa59b9… Author: John Chilton <jmchilton(a)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/eac6c10ec93a6f5a610a9d07d1e7… Author: John Chilton <jmchilton(a)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/8538c0ed774c89416c80e8688723… Author: John Chilton <jmchilton(a)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/6faef4df2ec5a1b189594bf528de… Author: John Chilton <jmchilton(a)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/05a2f441261c176dfe2cc802d474… Author: John Chilton <jmchilton(a)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/b8ecf36f2ae52af1cda3eac64f53… Author: John Chilton <jmchilton(a)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/d693aaf624ce1ca1f501e3ed98fe… Author: Aysam Guerler <aysam.guerler(a)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

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[galaxyproject/galaxy] 9f0ddf: Revise input wrapper, add test cases
by GitHub 29 Mar '16

29 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9f0ddf57bb0b82b0225b2975982ef0579957a03f https://github.com/galaxyproject/galaxy/commit/9f0ddf57bb0b82b0225b2975982e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/style/less/ui.less M static/maps/mvc/form/form-input.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-input.js M static/style/blue/base.css A test/qunit/tests/form_tests.html A test/qunit/tests/form_tests.js Log Message: ----------- Revise input wrapper, add test cases Commit: 2687002a27adf43ec526077cbd8bdaca214dc83b https://github.com/galaxyproject/galaxy/commit/2687002a27adf43ec526077cbd8b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/style/less/ui.less M static/maps/mvc/form/form-input.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-input.js M static/style/blue/base.css A test/qunit/tests/form_tests.html A test/qunit/tests/form_tests.js Log Message: ----------- Merge pull request #2027 from guerler/revise_input_000 Revise input wrapper, add test cases Compare: https://github.com/galaxyproject/galaxy/compare/aee2ed98a01e...2687002a27ad

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[galaxyproject/galaxy] 991e06: enable obfs datatype during upload
by GitHub 29 Mar '16

29 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 991e069ef284e7669e5dece818aef510189b2d15 https://github.com/galaxyproject/galaxy/commit/991e069ef284e7669e5dece818ae… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- enable obfs datatype during upload Commit: aee2ed98a01ef9f93623dc33b0b5730c3fbfc30b https://github.com/galaxyproject/galaxy/commit/aee2ed98a01ef9f93623dc33b0b5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #2028 from bgruening/obfs_in_upload enable obfs datatype during upload Compare: https://github.com/galaxyproject/galaxy/compare/ad12042f5f17...aee2ed98a01e

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[galaxyproject/galaxy] e6d352: [16.01] Fix for running jobs when metadata tool is...
by GitHub 29 Mar '16

29 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: e6d3529b4c85708bb0b1fbea32e8ce36921e60e1 https://github.com/galaxyproject/galaxy/commit/e6d3529b4c85708bb0b1fbea32e8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-28 (Mon, 28 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: 68ca4b9237a5c44a88377c32cecc9014013c32cc https://github.com/galaxyproject/galaxy/commit/68ca4b9237a5c44a88377c32cecc… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #2024 from jmchilton/metadata_tool_fix [16.01] Fix for running jobs when metadata tool is not in toolbox. Compare: https://github.com/galaxyproject/galaxy/compare/948a4aa55bf9...68ca4b9237a5

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[galaxyproject/galaxy] a9d51f: Don't setup a default tool_data_table_config_path ...
by GitHub 29 Mar '16

29 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a9d51f6dfe3748f7db5bfd1d128f03a8b6558656 https://github.com/galaxyproject/galaxy/commit/a9d51f6dfe3748f7db5bfd1d128f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-28 (Mon, 28 Mar 2016) Changed paths: M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Don't setup a default tool_data_table_config_path in the TS. Commit: ad12042f5f17fc2b7facc08dc5628bdafc94eca3 https://github.com/galaxyproject/galaxy/commit/ad12042f5f17fc2b7facc08dc562… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Merge pull request #2025 from jmchilton/ts_tool_data_table_config Don't setup a default tool_data_table_config_path in the shed. Compare: https://github.com/galaxyproject/galaxy/compare/71d8b4a6c123...ad12042f5f17

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[galaxyproject/galaxy] 1be896: data_column to json config file
by GitHub 28 Mar '16

28 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1be896fd157dffcd5c2f9b20dd0a5fc866faadbe https://github.com/galaxyproject/galaxy/commit/1be896fd157dffcd5c2f9b20dd0a… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/wrapped_json.py Log Message: ----------- data_column to json config file Commit: 71d8b4a6c123f05aaedffd0e38db0d921b7a0410 https://github.com/galaxyproject/galaxy/commit/71d8b4a6c123f05aaedffd0e38db… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-28 (Mon, 28 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/wrapped_json.py Log Message: ----------- Merge pull request #2026 from bgruening/param_configfile_data_column data_column to json config file Compare: https://github.com/galaxyproject/galaxy/compare/5a7ba04cd9f8...71d8b4a6c123

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[galaxyproject/galaxy] 962866: Remove install and test framework.
by GitHub 28 Mar '16

28 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 962866478a020b3fc794f76f89696ada60881d17 https://github.com/galaxyproject/galaxy/commit/962866478a020b3fc794f76f8969… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: R test/install_and_test_tool_shed_repositories/__init__.py R test/install_and_test_tool_shed_repositories/base/__init__.py R test/install_and_test_tool_shed_repositories/base/test_db_util.py R test/install_and_test_tool_shed_repositories/base/twilltestcase.py R test/install_and_test_tool_shed_repositories/base/util.py R test/install_and_test_tool_shed_repositories/functional/__init__.py R test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py R test/install_and_test_tool_shed_repositories/repositories_with_tools/__init__.py R test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py R test/install_and_test_tool_shed_repositories/tool_dependency_definitions/__init__.py R test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py Log Message: ----------- Remove install and test framework. Commit: 5a7ba04cd9f85661a4681b00427b3c1aa815d988 https://github.com/galaxyproject/galaxy/commit/5a7ba04cd9f85661a4681b00427b… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-03-28 (Mon, 28 Mar 2016) Changed paths: R test/install_and_test_tool_shed_repositories/__init__.py R test/install_and_test_tool_shed_repositories/base/__init__.py R test/install_and_test_tool_shed_repositories/base/test_db_util.py R test/install_and_test_tool_shed_repositories/base/twilltestcase.py R test/install_and_test_tool_shed_repositories/base/util.py R test/install_and_test_tool_shed_repositories/functional/__init__.py R test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py R test/install_and_test_tool_shed_repositories/repositories_with_tools/__init__.py R test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py R test/install_and_test_tool_shed_repositories/tool_dependency_definitions/__init__.py R test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py Log Message: ----------- Merge pull request #2018 from jmchilton/remove_iat Remove install and test code. Compare: https://github.com/galaxyproject/galaxy/compare/62fae769345e...5a7ba04cd9f8

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[galaxyproject/usegalaxy-playbook] a4218f: Replaced GCC2016 abstracts due slide: March 25 is ...
by GitHub 28 Mar '16

28 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a4218f633e911fc458dcdf30516b2820b4fbdd38 https://github.com/galaxyproject/usegalaxy-playbook/commit/a4218f633e911fc4… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2016-03-28 (Mon, 28 Mar 2016) Changed paths: A files/galaxy/common/static/welcome_img/GCC2016OralAbstractsDueApril8.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Replaced GCC2016 abstracts due slide: March 25 is now April 8

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[galaxyproject/galaxy] 207af3: Fix multiple flag for workflow dataset inputs
by GitHub 28 Mar '16

28 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 207af3d97565885491096488621c0f7bd664b8e4 https://github.com/galaxyproject/galaxy/commit/207af3d97565885491096488621c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-27 (Sun, 27 Mar 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix multiple flag for workflow dataset inputs Commit: 62fae769345e75c3852fc89f867bbc36cdb3423e https://github.com/galaxyproject/galaxy/commit/62fae769345e75c3852fc89f867b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-28 (Mon, 28 Mar 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #2021 from guerler/fix_collection_002 Fix multiple flag for workflow dataset inputs Compare: https://github.com/galaxyproject/galaxy/compare/18300c9dc66a...62fae769345e

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[galaxyproject/galaxy] ee0a65: fix duplication of select2 entries
by GitHub 28 Mar '16

28 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ee0a65bf13a1fff8084aa19fdfd4831b66dd096d https://github.com/galaxyproject/galaxy/commit/ee0a65bf13a1fff8084aa19fdfd4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-28 (Mon, 28 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- fix duplication of select2 entries leverage caching Commit: 2c76ba7502c9fa99d2b02f44d79009b119a243f8 https://github.com/galaxyproject/galaxy/commit/2c76ba7502c9fa99d2b02f44d790… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-28 (Mon, 28 Mar 2016) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- repack client Commit: 18300c9dc66af06fb24601a5f907be8e5ff18dcb https://github.com/galaxyproject/galaxy/commit/18300c9dc66af06fb24601a5f907… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-28 (Mon, 28 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #2022 from martenson/fix-select-dup fix duplication of select2 entries Compare: https://github.com/galaxyproject/galaxy/compare/625d9e53c3c9...18300c9dc66a

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[galaxyproject/galaxy] f70df2: Upgrade content selector, add test cases
by GitHub 28 Mar '16

28 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f70df2206097ec99683e0433c597ad2b2ac2decf https://github.com/galaxyproject/galaxy/commit/f70df2206097ec99683e0433c597… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-27 (Sun, 27 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js R client/galaxy/scripts/mvc/form/form-select-content.js A client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/ui.less M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/utils/utils.js M static/style/blue/base.css M test/qunit/test-app.js M test/qunit/tests/ui_tests.js Log Message: ----------- Upgrade content selector, add test cases Commit: d0f7ce260d42daf21a26a30dd0d5ae1d4cf01ebb https://github.com/galaxyproject/galaxy/commit/d0f7ce260d42daf21a26a30dd0d5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-27 (Sun, 27 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/utils/utils.js R static/maps/mvc/form/form-select-content.js.map A static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map R static/scripts/mvc/form/form-select-content.js A static/scripts/mvc/ui/ui-select-content.js M static/scripts/utils/utils.js M test/qunit/tests/ui_tests.js Log Message: ----------- Add workflow content selectors and test cases Commit: 625d9e53c3c91ddde6c59b6a02e5163acbc5add3 https://github.com/galaxyproject/galaxy/commit/625d9e53c3c91ddde6c59b6a02e5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-28 (Mon, 28 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js R client/galaxy/scripts/mvc/form/form-select-content.js A client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/ui.less M static/maps/mvc/form/form-parameters.js.map R static/maps/mvc/form/form-select-content.js.map A static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-parameters.js R static/scripts/mvc/form/form-select-content.js A static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/utils/utils.js M static/style/blue/base.css M test/qunit/test-app.js M test/qunit/tests/ui_tests.js Log Message: ----------- Merge pull request #2011 from guerler/revise_content_select_000 Revise content selection, add test cases Compare: https://github.com/galaxyproject/galaxy/compare/5b16589f2901...625d9e53c3c9

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[galaxyproject/galaxy] a8c22e: Remove twill functional tests we don't actively ru...
by GitHub 26 Mar '16

26 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a8c22ee9dbc8eb0f59ea55748db7a9c5cae50bc0 https://github.com/galaxyproject/galaxy/commit/a8c22ee9dbc8eb0f59ea55748db7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: R test/functional/test_admin_features.py R test/functional/test_data_security.py R test/functional/test_dataset_features.py R test/functional/test_get_data.py R test/functional/test_library_features.py R test/functional/test_library_security.py R test/functional/test_metadata_editing.py R test/functional/test_sample_tracking.py R test/functional/test_tags.py R test/functional/test_ucsc_table_browser.py R test/functional/test_user_info.py Log Message: ----------- Remove twill functional tests we don't actively run. Commit: 5b16589f290139cba11b693452bae5570a60e47d https://github.com/galaxyproject/galaxy/commit/5b16589f290139cba11b693452ba… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-26 (Sat, 26 Mar 2016) Changed paths: R test/functional/test_admin_features.py R test/functional/test_data_security.py R test/functional/test_dataset_features.py R test/functional/test_get_data.py R test/functional/test_library_features.py R test/functional/test_library_security.py R test/functional/test_metadata_editing.py R test/functional/test_sample_tracking.py R test/functional/test_tags.py R test/functional/test_ucsc_table_browser.py R test/functional/test_user_info.py Log Message: ----------- Merge pull request #2019 from jmchilton/remove_twill_tests Remove twill functional tests we don't actively run. Compare: https://github.com/galaxyproject/galaxy/compare/c093c793b7ba...5b16589f2901

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[galaxyproject/galaxy] 85ef86: Improvements to workflow scaling performance testi...
by GitHub 26 Mar '16

26 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 85ef86ab2ee904c62d00f84e7220c661bd31e58c https://github.com/galaxyproject/galaxy/commit/85ef86ab2ee904c62d00f84e7220… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/workflow/scheduling_manager.py M scripts/summarize_timings.py A test/functional/tools/for_workflows/create_input_collection.xml A test/functional/tools/for_workflows/split.xml M test/functional/tools/samples_tool_conf.xml A test/manual/launch_and_run.sh A test/manual/workflow_job_conf.xml M test/manual/workflows_scaling.py Log Message: ----------- Improvements to workflow scaling performance testing scripts. - Implement a wrapper script for launching a docker-galaxy-stable setup a many ways for this task including: - Configure container's Galaxy with outer Galaxy's lib and test directory. - Collect log files. - Log a statement for interacting with the container easily while the test is running. - Disable unneeded services. - Implement a fan-in-fan-out style workflow for performance testing. - Add an option to test performance of scheduling workflows without actually running jobs. - Sample tool for creating large collections easily at beginning of tests (much faster than uploads). - Sample tool for splitting a file into a collection for fan in and out workflow test. - Assume Python 2.7 in scripts to simplify things. - Add documentation. Commit: da1f1bd8b2ae1ce7910b14c3dab0791dc0a67050 https://github.com/galaxyproject/galaxy/commit/da1f1bd8b2ae1ce7910b14c3dab0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M test/functional/tools/for_workflows/create_input_collection.xml Log Message: ----------- Fixes to create_input_collection.xml based on comments from @nsoranzo. Commit: c093c793b7ba589c41e7df3041585922ddc840d8 https://github.com/galaxyproject/galaxy/commit/c093c793b7ba589c41e7df304158… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M lib/galaxy/workflow/scheduling_manager.py M scripts/summarize_timings.py A test/functional/tools/for_workflows/create_input_collection.xml A test/functional/tools/for_workflows/split.xml M test/functional/tools/samples_tool_conf.xml A test/manual/launch_and_run.sh A test/manual/workflow_job_conf.xml M test/manual/workflows_scaling.py Log Message: ----------- Merge pull request #1958 from jmchilton/workflow_scheduling_testing Improvements to workflow scaling performance testing scripts. Compare: https://github.com/galaxyproject/galaxy/compare/d9177a81e548...c093c793b7ba

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[galaxyproject/galaxy] 142383: Fix collection handling
by GitHub 25 Mar '16

25 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1423836f1e3ef1032ce38128a5fd1191fb7d217a https://github.com/galaxyproject/galaxy/commit/1423836f1e3ef1032ce38128a5fd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix collection handling Commit: d9177a81e5488f0248fba7a6e22e55885779f4a5 https://github.com/galaxyproject/galaxy/commit/d9177a81e5488f0248fba7a6e22e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #2015 from guerler/fix_collection_001 Fix collection handling Compare: https://github.com/galaxyproject/galaxy/compare/494b2f3e2726...d9177a81e548

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[galaxyproject/galaxy] 3240c2: Swap analyse to analyze to be consistent.
by GitHub 25 Mar '16

25 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3240c20a4b5cd29a1f2e3764a8aa6cf84ca1e48d https://github.com/galaxyproject/galaxy/commit/3240c20a4b5cd29a1f2e3764a8aa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Swap analyse to analyze to be consistent. Commit: 494b2f3e272662d2f497ab9dd1a870f3f661554c https://github.com/galaxyproject/galaxy/commit/494b2f3e272662d2f497ab9dd1a8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #2020 from dannon/analyse Swap analyse to analyze to be consistent across the app. Compare: https://github.com/galaxyproject/galaxy/compare/b9ccf17376f6...494b2f3e2726

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[galaxyproject/galaxy] 87ea37: add 'create history &import to it' feature
by GitHub 25 Mar '16

25 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 87ea37ca28f791624eeabdbaa26d5fd01d7a9297 https://github.com/galaxyproject/galaxy/commit/87ea37ca28f791624eeabdbaa26d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/style/less/library.less M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- add 'create history &import to it' feature various refactorings and fixes to UX glitches Commit: ce1b9aeb38d68893004c0d9de6d0637983145de7 https://github.com/galaxyproject/galaxy/commit/ce1b9aeb38d68893004c0d9de6d0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- minor adjustments to markup; improve logging; repack Commit: b9ccf17376f631cf1d004ee3af0571d2925cd7aa https://github.com/galaxyproject/galaxy/commit/b9ccf17376f631cf1d004ee3af05… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/style/less/library.less M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Merge pull request #2017 from martenson/import-to-new-history libraries: add 'create history &import to it' feature Compare: https://github.com/galaxyproject/galaxy/compare/0d5001eea78e...b9ccf17376f6

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[galaxyproject/galaxy] 4f2661: Fix PJA creation in tool bursting threads.
by GitHub 25 Mar '16

25 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 4f2661a1e9b3179b8df7ff773b71d15aa756dd8d https://github.com/galaxyproject/galaxy/commit/4f2661a1e9b3179b8df7ff773b71… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Fix PJA creation in tool bursting threads. Potentially fixes #1657. Commit: 948a4aa55bf9409a69b7af75b9987d60f09890f3 https://github.com/galaxyproject/galaxy/commit/948a4aa55bf9409a69b7af75b998… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #2013 from jmchilton/fix_1657_stable [16.01] Fix PJA creation in tool bursting threads. Compare: https://github.com/galaxyproject/galaxy/compare/425f0daa2d90...948a4aa55bf9

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[galaxyproject/galaxy] 7d1b52: The response from dataproviders here can return da...
by GitHub 25 Mar '16

25 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 7d1b525682c9dd0786b7ccca23c3b0695b3c0751 https://github.com/galaxyproject/galaxy/commit/7d1b525682c9dd0786b7ccca23c3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js M lib/galaxy/webapps/galaxy/api/datasets.py M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/viz/trackster/tracks.js Log Message: ----------- The response from dataproviders here can return data===null in addition to being simply undefined. This corrects the logic shortcutting and prevents errors like 'Cannot read property 'min' of null' Commit: 425f0daa2d9030a36c2af5b144a4d563542153a2 https://github.com/galaxyproject/galaxy/commit/425f0daa2d9030a36c2af5b144a4… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js M lib/galaxy/webapps/galaxy/api/datasets.py M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/viz/trackster/tracks.js Log Message: ----------- Merge pull request #2014 from dannon/trackster_dataprovider_fix [16.01] Fix trackster erroring when fetching data from regions or datasets with no content. Compare: https://github.com/galaxyproject/galaxy/compare/8accc56132ff...425f0daa2d90

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[galaxyproject/galaxy] dc49a9: Fix unbound error that is possible if using tool b...
by GitHub 25 Mar '16

25 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dc49a9cbc1b24fb4abd1c5b98eba433218a3042d https://github.com/galaxyproject/galaxy/commit/dc49a9cbc1b24fb4abd1c5b98eba… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-24 (Thu, 24 Mar 2016) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- Fix unbound error that is possible if using tool bursting. Commit: 8accc56132ff5863ff4d0e3127d9aa5c8fc419d4 https://github.com/galaxyproject/galaxy/commit/8accc56132ff5863ff4d0e3127d9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- Merge pull request #2009 from jmchilton/execute_params_fix [16.01] Fix unbound error that is possible if using tool bursting. Commit: 0d5001eea78e21f126299a1f8295e01f84c2d8ee https://github.com/galaxyproject/galaxy/commit/0d5001eea78e21f126299a1f8295… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- Merge branch 'release_16.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/ec3fe67ddd2a...0d5001eea78e

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[galaxyproject/galaxy] edb51d: Rename tool_shed_get to url_get.
by GitHub 25 Mar '16

25 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: edb51d876b763d0fd321c85d429575d465b754d1 https://github.com/galaxyproject/galaxy/commit/edb51d876b763d0fd321c85d4295… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Rename tool_shed_get to url_get. Commit: 9e8890b25bb126a401b17eee616609ce7963f928 https://github.com/galaxyproject/galaxy/commit/9e8890b25bb126a401b17eee6166… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M Makefile M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/style/less/base.less M client/galaxy/style/less/library.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/tool_data_table_conf.xml.sample M contrib/galaxy.fedora-init A contrib/galaxy_reports.fedora-init A display_applications/iobio/bam.xml A display_applications/iobio/vcf.xml M doc/source/releases/index.rst A lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml A lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml A lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml A lib/galaxy/datatypes/converters/cml_to_smi_converter.xml A lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml A lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml A lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml A lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml A lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml A lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml A lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml A lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml A lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml A lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml A lib/galaxy/datatypes/converters/mol_to_cml_converter.xml A lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml A lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml A lib/galaxy/datatypes/converters/mol_to_smi_converter.xml A lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml A lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml A lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml A lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml A lib/galaxy/datatypes/converters/smi_to_cml_converter.xml A lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml A lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml A lib/galaxy/datatypes/converters/smi_to_mol_converter.xml A lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml A lib/galaxy/datatypes/converters/smi_to_smi_converter.xml M lib/galaxy/datatypes/display_applications/application.py A lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/5e5z.pdb A lib/galaxy/datatypes/test/drugbank_drugs.cml A lib/galaxy/datatypes/test/drugbank_drugs.inchi A lib/galaxy/datatypes/test/drugbank_drugs.mol2 A lib/galaxy/datatypes/test/drugbank_drugs.sdf A lib/galaxy/datatypes/test/drugbank_drugs.smi A lib/galaxy/datatypes/test/q.fps M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py R lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/util/log/fluent_log.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/metrics.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/run.py M lib/tool_shed/tool_shed_registry.py M run.sh M run_reports.sh M run_tool_shed.sh M scripts/bootstrap_history.py M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js M static/style/blue/base.css M static/style/blue/library.css M templates/webapps/galaxy/workflow/display.mako M test/base/twilltestcase.py M test/functional/test_toolbox.py M test/functional/tools/collection_creates_list.xml M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0490_export_import_repositories.py M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py M test/unit/jobs/test_runner_local.py A tool-data/bam_iobio.loc.sample A tool-data/vcf_iobio.loc.sample Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into move_tsg Commit: 06b9737e0934823c807b02cbeaf590735437653d https://github.com/galaxyproject/galaxy/commit/06b9737e0934823c807b02cbeaf5… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Cleanup and fix tests. Commit: 7e14f5db6236a5ab1b9df988fe88cd34eaf8ba78 https://github.com/galaxyproject/galaxy/commit/7e14f5db6236a5ab1b9df988fe88… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/util/common_util.py Log Message: ----------- Address travis' complaints. Commit: ec3fe67ddd2a5fc2017b3d402bb2869c70bac368 https://github.com/galaxyproject/galaxy/commit/ec3fe67ddd2a5fc2017b3d402bb2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #1918 from davebx/move_tsg Rename tool_shed_get to url_get. Compare: https://github.com/galaxyproject/galaxy/compare/6e34858e0da7...ec3fe67ddd2a

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[galaxyproject/galaxy] 72b1ba: Fix parameter expansion for empty collections
by GitHub 25 Mar '16

25 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 72b1ba3714d223f14836a74a841fa811809d488b https://github.com/galaxyproject/galaxy/commit/72b1ba3714d223f14836a74a841f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-24 (Thu, 24 Mar 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix parameter expansion for empty collections Commit: 6e34858e0da7b08075bff946ae5cd2d9d09e6234 https://github.com/galaxyproject/galaxy/commit/6e34858e0da7b08075bff946ae5c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #2010 from guerler/fix_collection_select Fix parameter expansion for empty collections Compare: https://github.com/galaxyproject/galaxy/compare/84044f9a5f3c...6e34858e0da7

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[galaxyproject/galaxy] 975c6f: Much more friendly route mapping.
by GitHub 25 Mar '16

25 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 975c6f5eae19a7f37a828c1d0648f00b2366449a https://github.com/galaxyproject/galaxy/commit/975c6f5eae19a7f37a828c1d0648… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/middleware/statsd.py Log Message: ----------- Much more friendly route mapping. Commit: 84044f9a5f3c5db74ff65eae2544bd61f047f108 https://github.com/galaxyproject/galaxy/commit/84044f9a5f3c5db74ff65eae2544… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/middleware/statsd.py Log Message: ----------- Merge pull request #2002 from dannon/statswork Much more friendly route mapping. Compare: https://github.com/galaxyproject/galaxy/compare/6aaec509edf2...84044f9a5f3c

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[galaxyproject/galaxy] e1fcbc: change default size of fa in iconspans
by GitHub 25 Mar '16

25 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e1fcbc7a208464f9b2a3e6d5eac05bfacd414d38 https://github.com/galaxyproject/galaxy/commit/e1fcbc7a208464f9b2a3e6d5eac0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M client/galaxy/style/less/library.less M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- change default size of fa in iconspans leave as is for the globe icon Commit: 6aaec509edf261ddbe866df0030762c4f0d9943e https://github.com/galaxyproject/galaxy/commit/6aaec509edf261ddbe866df00307… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M client/galaxy/style/less/library.less M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Merge pull request #2000 from martenson/fix-lib-icons libraries: change default size of fa in iconspans Compare: https://github.com/galaxyproject/galaxy/compare/0f099b75b608...6aaec509edf2

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[galaxyproject/galaxy] dc49a9: Fix unbound error that is possible if using tool b...
by GitHub 25 Mar '16

25 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: dc49a9cbc1b24fb4abd1c5b98eba433218a3042d https://github.com/galaxyproject/galaxy/commit/dc49a9cbc1b24fb4abd1c5b98eba… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-24 (Thu, 24 Mar 2016) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- Fix unbound error that is possible if using tool bursting. Commit: 8accc56132ff5863ff4d0e3127d9aa5c8fc419d4 https://github.com/galaxyproject/galaxy/commit/8accc56132ff5863ff4d0e3127d9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- Merge pull request #2009 from jmchilton/execute_params_fix [16.01] Fix unbound error that is possible if using tool bursting. Compare: https://github.com/galaxyproject/galaxy/compare/dede9459b019...8accc56132ff

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[galaxyproject/galaxy] b51bdd: Basepanels don't have Galaxy object, causing failu...
by GitHub 24 Mar '16

24 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b51bdd06b189baccab235def65d15a69c761ac28 https://github.com/galaxyproject/galaxy/commit/b51bdd06b189baccab235def65d1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M templates/base/base_panels.mako Log Message: ----------- Basepanels don't have Galaxy object, causing failures in views like published tracks, etc., when resource urls are generated incorrectly Commit: dede9459b019ceb1212f4f152b4108632f892384 https://github.com/galaxyproject/galaxy/commit/dede9459b019ceb1212f4f152b41… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M templates/base/base_panels.mako Log Message: ----------- Merge pull request #2003 from dannon/trackster_debugging [16.01] Fix shared viz (and other base_panels.mako displays) early URL generation. Commit: 0f099b75b608264bf67d7d88c858cfbd96f3225c https://github.com/galaxyproject/galaxy/commit/0f099b75b608264bf67d7d88c858… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-24 (Thu, 24 Mar 2016) Changed paths: M templates/base/base_panels.mako Log Message: ----------- Merge branch 'release_16.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/86d2b29026fc...0f099b75b608

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