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[galaxyproject/galaxy] 5def7e: refactor rest of JS templates;
by GitHub 30 Mar '16

30 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5def7ee035645ae155a7c712a068a5a9bc6fdc42 https://github.com/galaxyproject/galaxy/commit/5def7ee035645ae155a7c712a068… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/style/less/library.less M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-model.js.map M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-model.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- refactor rest of JS templates; move all text outside of the fontawesome spans convert console. calls to Galaxy.emit calls Commit: 971b987f0b5d110e51022fcc7d0bfc9fd6c52502 https://github.com/galaxyproject/galaxy/commit/971b987f0b5d110e51022fcc7d0b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js Log Message: ----------- libraries: fetch nondeleted only first to speed up fetch the deleted only when specifically requested Commit: 565f11f142de7cee37faea056f9def237b2d870d https://github.com/galaxyproject/galaxy/commit/565f11f142de7cee37faea056f9d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/style/less/library.less M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Merge branch 'lib-refactor-cleanup' into dev Compare: https://github.com/galaxyproject/galaxy/compare/35767b138012...565f11f142de

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[galaxyproject/galaxy] 516f4f: Fix transiently failing tool shed tests.
by GitHub 30 Mar '16

30 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 516f4f017f1635a961d50ea47c36a15053aa9689 https://github.com/galaxyproject/galaxy/commit/516f4f017f1635a961d50ea47c36… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Fix transiently failing tool shed tests. Comments inline - I don't know why but the retry would fix the transient problems acording to the Jenkins tests with the previous exception added to verify this would fix the problem. Commit: 35767b1380121121dddebc6751f072510be8b5cb https://github.com/galaxyproject/galaxy/commit/35767b1380121121dddebc6751f0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Merge pull request #2030 from jmchilton/capsule_fix Fix transiently failing tool shed tests. Compare: https://github.com/galaxyproject/galaxy/compare/d15b1030c5ba...35767b138012

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[galaxyproject/galaxy] f27ff0: Fix to 9acbfdf: initial fix borked fa-2x, instead ...
by GitHub 29 Mar '16

29 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: f27ff0c7ba829a48f9c0eae443baa36cda92cf98 https://github.com/galaxyproject/galaxy/commit/f27ff0c7ba829a48f9c0eae443ba… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/fontawesome/core.less M static/style/blue/base.css Log Message: ----------- Fix to 9acbfdf: initial fix borked fa-2x, instead remove second woff loaded due to fa-icon font-family rule by aliasing that to fa Commit: 7a9d4943cd0571f5adebf850b4e167065289700b https://github.com/galaxyproject/galaxy/commit/7a9d4943cd0571f5adebf850b4e1… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Fix tool shed tests for e4a1d5727805168a9fd15aca1cdd21630ada2bbc . Commit: 15c08d80e4a2c027a01dd8dabc16b802be4c18a1 https://github.com/galaxyproject/galaxy/commit/15c08d80e4a2c027a01dd8dabc16… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/fontawesome/core.less M static/style/blue/base.css Log Message: ----------- Merge pull request #1791 from carlfeberhard/release_16.01 [16.01] Fix to 9acbfdf: initial fix borked fa-2x, instead remove second woff … Commit: 5546211c0dddb23bbeae34c0cddbd7ad9cebf6b5 https://github.com/galaxyproject/galaxy/commit/5546211c0dddb23bbeae34c0cddb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Merge pull request #1798 from nsoranzo/release_16.01_tool_shed_test_fixes [16.01] Fix tool shed tests for e4a1d5727805168a9fd15aca1cdd21630ada2bbc . Commit: 1aa1d6164a63438b49beb2fd6cc4b80a57bbdb5d https://github.com/galaxyproject/galaxy/commit/1aa1d6164a63438b49beb2fd6cc4… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Fix workflow parameters not rendered when tool parameter wrapped in conditional. Commit: dad1784a087623c990e0b3f05d1c8026f7bd957c https://github.com/galaxyproject/galaxy/commit/dad1784a087623c990e0b3f05d1c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #1799 from mvdbeek/fix_workflow_parameters_conditional [16.01] Fix workflow parameters not rendered when tool parameter wrapped in conditional. Commit: 56076db848459cb1da39b04dc635538ff013d3a9 https://github.com/galaxyproject/galaxy/commit/56076db848459cb1da39b04dc635… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Disable command isolation for Pulsar... ... it builds its own job script - no need to have Galaxy do this isolation on the Galaxy end. The more Pulsar can handle the better. Commit: cb19630bd4e04b21653a2cb9848e888805dfabcc https://github.com/galaxyproject/galaxy/commit/cb19630bd4e04b21653a2cb9848e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M test/unit/jobs/test_job_wrapper.py M test/unit/tools_support.py Log Message: ----------- Fix unit tests for 56076db848459cb1da39b04dc635538ff013d3a9 Commit: 47c93180708eb138c1fa0393cd18b24d27249359 https://github.com/galaxyproject/galaxy/commit/47c93180708eb138c1fa0393cd18… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-02-28 (Sun, 28 Feb 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py M test/unit/jobs/test_job_wrapper.py M test/unit/tools_support.py Log Message: ----------- Merge pull request #1812 from jmchilton/pulsar_16.01_fixes [16.01] Disable command isolation for Pulsar... Commit: 865f2d49bd04b636552002cd0e4830f2dbad5c75 https://github.com/galaxyproject/galaxy/commit/865f2d49bd04b636552002cd0e48… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M create_db.sh M manage_db.sh Log Message: ----------- Fix create/manage db scripts to respect GALAXY_VIRTUAL_ENV. Commit: 5bc55f9fa2fd6af9142df644bf82e830b56f9ce4 https://github.com/galaxyproject/galaxy/commit/5bc55f9fa2fd6af9142df644bf82… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- Add js for mako based masthead Commit: 281f5b734610963b437b72837e7b71cebbb3c5bd https://github.com/galaxyproject/galaxy/commit/281f5b734610963b437b72837e7b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/ui/popup-menu.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/style/less/base.less M client/galaxy/style/less/fontawesome/core.less M client/galaxy/style/less/ui/icon-btn.less M doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst M lib/galaxy/config.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/version.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/encoding_util.py M lib/tool_shed/util/repository_content_util.py M lib/tool_shed/util/shed_util_common.py M static/maps/mvc/ui/popup-menu.js.map M static/maps/mvc/workflow/workflow-terminals.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/ui/popup-menu.js M static/scripts/mvc/workflow/workflow-terminals.js M static/style/blue/base.css R templates/admin/requests/select_datasets_to_transfer.mako M templates/admin/tool_shed_repository/common.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/tool_shed/repository/common.mako M test/functional/tools/output_format.xml M test/qunit/tests/workflow_editor_tests.js M test/tool_shed/base/twilltestcase.py M test/unit/jobs/test_job_wrapper.py M test/unit/tools_support.py Log Message: ----------- Merge branch 'release_16.01' of https://github.com/galaxyproject/galaxy into release_16.01 Commit: fa8beb225004d27da24065f8f633c7917b5be942 https://github.com/galaxyproject/galaxy/commit/fa8beb225004d27da24065f8f633… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- Merge pull request #1823 from martenson/port-masthead-fix [16.01] Port masthead fix Commit: 50bc127a3b55432884ed6350bee3e0ea67beb95f https://github.com/galaxyproject/galaxy/commit/50bc127a3b55432884ed6350bee3… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M create_db.sh M manage_db.sh Log Message: ----------- Merge pull request #1820 from jmchilton/db_script_fixes [16.01] Fix create/manage db scripts to respect GALAXY_VIRTUAL_ENV. Commit: 93494a833ee390811bdc1d13c1ef54b52ed005f2 https://github.com/galaxyproject/galaxy/commit/93494a833ee390811bdc1d13c1ef… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- This silences logging when display whitelist isn't explicitly defined and the default file doesn't exist. Explicit usage still logs a failure. Commit: 16280c63236621082ce4c3b3d93eb679294cd515 https://github.com/galaxyproject/galaxy/commit/16280c63236621082ce4c3b3d93e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py Log Message: ----------- Only attempt to read/load sanitize_whitelist_file when starting an actual galaxy application. Commit: 7534182d7afd8c997df7d919d0633345ee5c4dfa https://github.com/galaxyproject/galaxy/commit/7534182d7afd8c997df7d919d063… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M lib/galaxy/app.py Log Message: ----------- Add a default logger prior to full logging configuration. We currently attempt to log at various places in config parsing/etc that fail with 'No handlers could be found for logger ...', and this resolves that. Commit: cf91ab4511897ef5ac4beb8d56219119073073c4 https://github.com/galaxyproject/galaxy/commit/cf91ab4511897ef5ac4beb8d5621… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py Log Message: ----------- Merge pull request #1828 from dannon/cherrypick_logging [16.01] Fix startup logging Commit: f67cbe72d571f87a87e868161650e5965e681881 https://github.com/galaxyproject/galaxy/commit/f67cbe72d571f87a87e868161650… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M templates/webapps/tool_shed/repository/view_repository.mako Log Message: ----------- revert escaping added in a24e206ff7762d5b86d3dc7240190f043dc532b5 that prevented line endings and spaces to be rendered properly Commit: 0051cab4f35240ff8b85f010b1ae0d66de7273c0 https://github.com/galaxyproject/galaxy/commit/0051cab4f35240ff8b85f010b1ae… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M templates/webapps/tool_shed/repository/view_repository.mako Log Message: ----------- Merge pull request #1830 from martenson/revert-ts-repo-rendering [16.01] revert ts repo long desc escaping Commit: a49401189735daa55e44dec7af6b84a646e8bbc9 https://github.com/galaxyproject/galaxy/commit/a49401189735daa55e44dec7af6b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Improve dataset error log message Commit: 4992684d1fc58d4774e5d6a6c1df9c193218c460 https://github.com/galaxyproject/galaxy/commit/4992684d1fc58d4774e5d6a6c1df… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M config/tool_conf.xml.main Log Message: ----------- Hide tools that have been replaced. Commit: dfef64db75c43cd4001a67cf48143e28df3efe60 https://github.com/galaxyproject/galaxy/commit/dfef64db75c43cd4001a67cf4814… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #1836 from natefoo/dataset-error-log [16.01] Improve dataset error log message Commit: de70306407c0682834814c479c91f8b8adc615ce https://github.com/galaxyproject/galaxy/commit/de70306407c0682834814c479c91… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M config/tool_conf.xml.main Log Message: ----------- Merge pull request #1837 from davebx/release_16.01 [16.01] Hide tools that have been replaced. Commit: 26d5561b4ff48eb770970bee5f2ba49d425e9902 https://github.com/galaxyproject/galaxy/commit/26d5561b4ff48eb770970bee5f2b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M manage_tools.sh M run_reports.sh M run_tool_shed.sh Log Message: ----------- Update more scripts to respect GALAXY_VIRTUAL_ENV. Drop explicit sourcing in run_reports and run_tool_shed since they source common_startup. Commit: e0ce68cc58a6d6eeb306f5c0445563e71bcc1d12 https://github.com/galaxyproject/galaxy/commit/e0ce68cc58a6d6eeb306f5c04455… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Fix lack of output when discovering large collections... Example log statement collected for each dataset: ``` galaxy.tools.parameters.output_collect DEBUG 2016-03-03 11:47:31,302 (8) Created dynamic collection dataset for path [/home/john/workspace/galaxy/database/job_working_directory/000/8/oe2_ie2.fq] with element identifier [oe2:ie2] for output [list_output]. ``` Commit: 0fbd22c9a30686afe62de1e1f23ff309dd6374a8 https://github.com/galaxyproject/galaxy/commit/0fbd22c9a30686afe62de1e1f23f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Merge pull request #1852 from jmchilton/dataset_collection_log [16.01] Fix lack of log output when discovering large collections... Commit: 97793ab81ab5601466fa89bba7b3250118e95de4 https://github.com/galaxyproject/galaxy/commit/97793ab81ab5601466fa89bba7b3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M manage_tools.sh M run_reports.sh M run_tool_shed.sh Log Message: ----------- Merge pull request #1847 from jmchilton/more_virtualenv_fixes [16.01] Update more scripts to respect GALAXY_VIRTUAL_ENV. Commit: e14e8a074c1344ab62dae2254f1e4a250e963b22 https://github.com/galaxyproject/galaxy/commit/e14e8a074c1344ab62dae2254f1e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-04 (Fri, 04 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Allow rerun of datasets new yet queued by job manager. Commit: 0445fcda51cad08a0b2969140b48948a9e7d759b https://github.com/galaxyproject/galaxy/commit/0445fcda51cad08a0b2969140b48… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-04 (Fri, 04 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add workflow building mode check to collection parameter handling Commit: 8905bafe10845545bedbd1c6b9e758e1b9523b4d https://github.com/galaxyproject/galaxy/commit/8905bafe10845545bedbd1c6b9e7… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-03-06 (Sun, 06 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #1859 from guerler/fix_collection_000 [16.01] Add workflow building mode check to collection parameter handling Commit: 0e0c1caec4f14e0a5240763e697bd5d3613db719 https://github.com/galaxyproject/galaxy/commit/0e0c1caec4f14e0a5240763e697b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: 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 Log Message: ----------- Fixing subworkflow migration (0131) to work with mysql Commit: 6442cbc3d4340ea3d03dad01c3ebf2dce05ed6e1 https://github.com/galaxyproject/galaxy/commit/6442cbc3d4340ea3d03dad01c3eb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py Log Message: ----------- Fix downgrade attempting to drop parent_workflow_id off the wrong table. Commit: b23c354f91f9d1a572f488a4d49f25b8681e58ba https://github.com/galaxyproject/galaxy/commit/b23c354f91f9d1a572f488a4d49f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py Log Message: ----------- Replace testing keynames with real ones. Commit: ad6273307da4b971ea4354d9ad33cb08ca912577 https://github.com/galaxyproject/galaxy/commit/ad6273307da4b971ea4354d9ad33… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py Log Message: ----------- We can't flip storedworkflow back to non-nullable in a downgrade step here, so don't try. Just leave it alone. Commit: 0c34d5bd3ff414d6beb669e106306066f663d75f https://github.com/galaxyproject/galaxy/commit/0c34d5bd3ff414d6beb669e10630… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Merge pull request #1858 from jmchilton/rerun_new_datasets [16.01] Allow rerun of datasets new yet queued by job manager. Commit: 0f97b50e9ca8ca8b54e8d30769cd3fe46204f27c https://github.com/galaxyproject/galaxy/commit/0f97b50e9ca8ca8b54e8d30769cd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py Log Message: ----------- Different logic for mysql (just don't worry about keys, due to the agony -- access to the database is entirely procedural and due to this we'd likely see any issues breaking these fk constraints in postgres before mysql (if ever) anyway. Commit: 29c78e984e52ac08b1b36a03e39b65c6edbe6200 https://github.com/galaxyproject/galaxy/commit/29c78e984e52ac08b1b36a03e39b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M run_reports.sh M run_tool_shed.sh Log Message: ----------- Fix virtualenv broken with #1847. Commit: 5824bc04af9270afbebcb2c8f9b6b3bea371b788 https://github.com/galaxyproject/galaxy/commit/5824bc04af9270afbebcb2c8f9b6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M run_reports.sh M run_tool_shed.sh Log Message: ----------- Fix duplicate print statement reported by @dannon... https://github.com/galaxyproject/galaxy/pull/1890#issuecomment-193873380 Commit: 50f1089c72ff46397e525d4aa99dc80569081509 https://github.com/galaxyproject/galaxy/commit/50f1089c72ff46397e525d4aa99d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Slight tweaks to our tabix usage. This fixes trackster without more divergence in our version of pysam. Commit: c6f3e9b5b28268cba1ef8d7be5f1bed90b6ecc00 https://github.com/galaxyproject/galaxy/commit/c6f3e9b5b28268cba1ef8d7be5f1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Slight cleanup, remove outdated comment regarding tabixfile.close() Commit: f0b7a34dd3ea5b3b10494c7e186fb10fda30441f https://github.com/galaxyproject/galaxy/commit/f0b7a34dd3ea5b3b10494c7e186f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/quotas.py Log Message: ----------- Apply patch from Fabien Mareuil to resolve json serialization of Decimal error; for more see http://dev.list.galaxyproject.org/quota-api-error-td4669081.html Commit: a351c75687921bb8d2487577c5c4c0a64bee5e5f https://github.com/galaxyproject/galaxy/commit/a351c75687921bb8d2487577c5c4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Extra documentation for @mvdbeek Commit: 438661e8945c1bb317f75dabe3db429ea779255d https://github.com/galaxyproject/galaxy/commit/438661e8945c1bb317f75dabe3db… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M run_reports.sh M run_tool_shed.sh Log Message: ----------- Another fix for virtualenv fixes. Commit: 62b5f207566eb9666df58f1ab107d3e7b1f0c736 https://github.com/galaxyproject/galaxy/commit/62b5f207566eb9666df58f1ab107… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Remove unnecessary encoding in remote_files. This allows paths and filenames like Ăfile.txt Commit: 0c225bec2e9af0c941ccc943d9ad010f2893a6e0 https://github.com/galaxyproject/galaxy/commit/0c225bec2e9af0c941ccc943d9ad… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M templates/webapps/galaxy/library/common/library_info.mako Log Message: ----------- Update library_info.mako escaping. This allows use of non-ascii characters like 'This is Ă data library' Commit: afb4e9c8f40da5331412c2a8f83ece814fb54b05 https://github.com/galaxyproject/galaxy/commit/afb4e9c8f40da5331412c2a8f83e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Merge pull request #1897 from dannon/pysam_compat [16.01] Slight tweaks to our tabix usage. Commit: 3abd2c213ae508bd3547d08729c96bbff4a5b740 https://github.com/galaxyproject/galaxy/commit/3abd2c213ae508bd3547d08729c9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/quotas.py Log Message: ----------- Merge pull request #1898 from dannon/quota_api_fix_fabien [16.01] Quota API issue with serialization to JSON of Decimal Commit: b3e9398c3affa964fdc8cf090eb5c149f7a6bf47 https://github.com/galaxyproject/galaxy/commit/b3e9398c3affa964fdc8cf090eb5… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-11 (Fri, 11 Mar 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py Log Message: ----------- Replace get_tool_shed_repository_by_tool_shed_name_owner_changeset_revision with get_repository_for_dependency_relationship Commit: d6e38c7d482eae65fc135cd65a13b7f215220cd5 https://github.com/galaxyproject/galaxy/commit/d6e38c7d482eae65fc135cd65a13… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-11 (Fri, 11 Mar 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py Log Message: ----------- remove unused import Commit: 5a50a4691c11edb9366f2e0d3eeb68aaaabb9c80 https://github.com/galaxyproject/galaxy/commit/5a50a4691c11edb9366f2e0d3eeb… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-03-11 (Fri, 11 Mar 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py Log Message: ----------- Merge pull request #1909 from mvdbeek/backport_repository_for_dependency_relationship [16.01] Backport PR #1868 Commit: 90fcd8c668865ce109b3fbc011319a9794e9e47f https://github.com/galaxyproject/galaxy/commit/90fcd8c668865ce109b3fbc01131… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-03-14 (Mon, 14 Mar 2016) Changed paths: M templates/webapps/galaxy/workflow/display.mako Log Message: ----------- Handle sections in view workflow Fixes 1723 Commit: 65a5b08c7129462a310fc741fb64e7f883bd8b0f https://github.com/galaxyproject/galaxy/commit/65a5b08c7129462a310fc741fb64… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: M templates/webapps/galaxy/workflow/display.mako Log Message: ----------- Merge pull request #1916 from erasche/fix-1723-back [16.01] Handle sections in view workflow Commit: 18473a187e019421933746abb31f8b226e828b80 https://github.com/galaxyproject/galaxy/commit/18473a187e019421933746abb31f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Ensure chrom, start, end as bytestring in BamDataProvider Commit: 9a343efe8b7dd393842e0f971e59d575f2286de2 https://github.com/galaxyproject/galaxy/commit/9a343efe8b7dd393842e0f971e59… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Merge pull request #1930 from mvdbeek/more_bytestring_for_pysam [16.01] Ensure chrom, start, end as bytestring in BamDataProvider Commit: 00a7c3af057c0689a53748802740bc2002df375c https://github.com/galaxyproject/galaxy/commit/00a7c3af057c0689a53748802740… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: M run_reports.sh M run_tool_shed.sh Log Message: ----------- Merge pull request #1890 from jmchilton/fix_virtualenvs [16.01] Fix virtual env handling broken with #1847. Commit: f277f99aed411fede7d1cb91d3177469922a58ae https://github.com/galaxyproject/galaxy/commit/f277f99aed411fede7d1cb91d317… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/util/log/fluent_log.py Log Message: ----------- Fix handling of time in fluent logger. Commit: 87bcb5f5a1b6801e948b2cc0f5dc676c7faca682 https://github.com/galaxyproject/galaxy/commit/87bcb5f5a1b6801e948b2cc0f5dc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/util/log/fluent_log.py Log Message: ----------- Fix in a different way not requiring signature change; still not thrilled about overlapping kwarg names w/ stdlib module names. Commit: c8e48bfaccb5d10552df4200e616a9eee49206b0 https://github.com/galaxyproject/galaxy/commit/c8e48bfaccb5d10552df4200e616… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Add fluentd configuration to galaxy.ini.sample Commit: 98c65dcee08338ea80a7e34251f8fa4ed6bd8dd5 https://github.com/galaxyproject/galaxy/commit/98c65dcee08338ea80a7e34251f8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/util/log/fluent_log.py M lib/galaxy/webapps/galaxy/api/metrics.py Log Message: ----------- Swap back to the first fix, update metrics api to use new signature. Commit: 4ef186812f1d3f16b36080654ee043065237d0c5 https://github.com/galaxyproject/galaxy/commit/4ef186812f1d3f16b36080654ee0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Encode user_login as utf8 prior to directory manipulation. Commit: e3e49a477d96ec5fc4623646e7ea240090f80ae2 https://github.com/galaxyproject/galaxy/commit/e3e49a477d96ec5fc4623646e7ea… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- extreme casting to 1) make this code actually work with python 2, and 3) work should the web framework ever be functional in python3 Commit: 19bf334c7763c2418408083b9a7369386e50ad66 https://github.com/galaxyproject/galaxy/commit/19bf334c7763c2418408083b9a73… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/util/log/fluent_log.py M lib/galaxy/webapps/galaxy/api/metrics.py Log Message: ----------- Merge pull request #1945 from dannon/fluent_logging_fix [16.01] Fix handling of time in fluent logger Commit: bd0439d9b724bb72c1fab4c27a4c72814abef0b9 https://github.com/galaxyproject/galaxy/commit/bd0439d9b724bb72c1fab4c27a4c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py M static/maps/mvc/tool/tool-form-base.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/tool/tool-form-base.js Log Message: ----------- Fix tool access rights and forwarding Commit: 054fdf76f09faf35662adf0f4a8a6f6428abab4f https://github.com/galaxyproject/galaxy/commit/054fdf76f09faf35662adf0f4a8a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Parse user when filtering tools Commit: 9e9dfdfd55b2b8d2377f8ef4e288a1fa482105b9 https://github.com/galaxyproject/galaxy/commit/9e9dfdfd55b2b8d2377f8ef4e288… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Fix workflow scheduler log message. Commit: 5f5f0af5cd5e21c64810d29202e149915226c34a https://github.com/galaxyproject/galaxy/commit/5f5f0af5cd5e21c64810d29202e1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Merge pull request #1955 from jmchilton/fix_wf_log_message [16.01] Fix workflow scheduler log message. Commit: 2efd9c2687d2ca818520249cdb3484e781659069 https://github.com/galaxyproject/galaxy/commit/2efd9c2687d2ca818520249cdb34… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix #1721. TODO: write test... Commit: 377ccbe23b717f9c8cb0d571de9f0d6da08a1ee8 https://github.com/galaxyproject/galaxy/commit/377ccbe23b717f9c8cb0d571de9f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #1967 from jmchilton/fix_optional_numeric_params [16.01] Fix #1721. Commit: 566f556b076db164ce73750f33c9824fe0285530 https://github.com/galaxyproject/galaxy/commit/566f556b076db164ce73750f33c9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py M static/maps/mvc/tool/tool-form-base.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/tool/tool-form-base.js Log Message: ----------- Merge pull request #1952 from guerler/fix_tool_access_000 [16.01] Fix tool access rights and forwarding Commit: 30750c32e4817de18aecba8bc4f523f4369e7292 https://github.com/galaxyproject/galaxy/commit/30750c32e4817de18aecba8bc4f5… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: 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 Log Message: ----------- Merge pull request #1880 from dannon/fix_migration_0131_mysql [16.01] Fixes to subworkflow migration 0131 Commit: 58346169dfbe89f845a3f2317bde514c3e65f79f https://github.com/galaxyproject/galaxy/commit/58346169dfbe89f845a3f2317bde… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Fix dom duplication Commit: fa1414759e604073bc45fe3f2b15dc9f21c72c4c https://github.com/galaxyproject/galaxy/commit/fa1414759e604073bc45fe3f2b15… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Merge pull request #1976 from guerler/fix_ui_000 [16.01] Fix dom duplication Commit: 133f77413e9fb933ec1964d279408c1fb8846db4 https://github.com/galaxyproject/galaxy/commit/133f77413e9fb933ec1964d27940… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map 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/page.js Log Message: ----------- Fix 'Resend verification' link in inactive user message box which would display as [Object object] Commit: fef166545c36df5c7ba73924c7b0ea4e1d44ec82 https://github.com/galaxyproject/galaxy/commit/fef166545c36df5c7ba73924c7b0… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/page.js 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 static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Layout: Fix optional panel rendering and associated inline css Commit: dd476fc42c57b5e17d8e1e342d7a597b986b6b3e https://github.com/galaxyproject/galaxy/commit/dd476fc42c57b5e17d8e1e342d7a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map 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/page.js Log Message: ----------- Merge pull request #1978 from carlfeberhard/release_16.01 [16.01] Fixes to page.js Commit: 79d16f71f9064c1f35a0bf4c7de1191872398428 https://github.com/galaxyproject/galaxy/commit/79d16f71f9064c1f35a0bf4c7de1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/page.js M static/maps/layout/masthead.js.map M static/maps/layout/page.js.map 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/masthead.js M static/scripts/layout/page.js Log Message: ----------- Fix scratchbook Commit: 9eb1db82ca4bbae598d0070de8da78172ca90fa9 https://github.com/galaxyproject/galaxy/commit/9eb1db82ca4bbae598d0070de8da… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Do not convert spaces to tabs when importing datasets into a library. Reported (with fix provided) by Fabien Mareuil in http://dev.list.galaxyproject.org/automatic-adding-of-a-tab-in-a-fastq-head… Commit: cf16b1d692d0e96f3d0aa4d2cf0f9f52c8dd7bb3 https://github.com/galaxyproject/galaxy/commit/cf16b1d692d0e96f3d0aa4d2cf0f… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Merge pull request #1985 from nsoranzo/release_16.01_lda_fixes [16.01] Do not convert spaces to tabs when importing datasets into a library. Commit: 8e41fda58a6b8def4f261121269c321e5dd8ff34 https://github.com/galaxyproject/galaxy/commit/8e41fda58a6b8def4f261121269c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/page.js M static/maps/layout/masthead.js.map M static/maps/layout/page.js.map 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/masthead.js M static/scripts/layout/page.js Log Message: ----------- Merge pull request #1984 from guerler/fix_scratchbook_000 [16.01] Fix scratchbook Commit: 21e71a9b46b9f4cd90b8fe5023981460775e4b59 https://github.com/galaxyproject/galaxy/commit/21e71a9b46b9f4cd90b8fe502398… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py M templates/webapps/galaxy/library/common/library_info.mako Log Message: ----------- Merge pull request #1905 from dannon/library_errors [16.01] Encoding in libraries 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: 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: 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. 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. 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. Commit: 7b2a2b1ef1154699d064482ffc41b4d3b6efdabb https://github.com/galaxyproject/galaxy/commit/7b2a2b1ef1154699d064482ffc41… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M test/unit/test_lazy_process.py Log Message: ----------- [16.01] More robust test_lazy_process. Hopefully this will fix a transiently failing test (I've only seen in fail on OS X). Commit: 7c94ac8d93b8c7fd2dd2f18d3939fa23a1589ad9 https://github.com/galaxyproject/galaxy/commit/7c94ac8d93b8c7fd2dd2f18d3939… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M test/unit/test_lazy_process.py Log Message: ----------- Merge pull request #2032 from jmchilton/lazy_process_test_fix [16.01] More robust test_lazy_process. Compare: https://github.com/galaxyproject/galaxy/compare/5677c2ee4fce...7c94ac8d93b8

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[galaxyproject/galaxy] 7d1b52: The response from dataproviders here can return da...
by GitHub 29 Mar '16

29 Mar '16

Branch: refs/heads/dev 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. 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. 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. Commit: 7b2a2b1ef1154699d064482ffc41b4d3b6efdabb https://github.com/galaxyproject/galaxy/commit/7b2a2b1ef1154699d064482ffc41… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M test/unit/test_lazy_process.py Log Message: ----------- [16.01] More robust test_lazy_process. Hopefully this will fix a transiently failing test (I've only seen in fail on OS X). Commit: 7c94ac8d93b8c7fd2dd2f18d3939fa23a1589ad9 https://github.com/galaxyproject/galaxy/commit/7c94ac8d93b8c7fd2dd2f18d3939… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M test/unit/test_lazy_process.py Log Message: ----------- Merge pull request #2032 from jmchilton/lazy_process_test_fix [16.01] More robust test_lazy_process. Commit: d15b1030c5bad75f41e46bdc38d860ebb35bd4fe https://github.com/galaxyproject/galaxy/commit/d15b1030c5bad75f41e46bdc38d8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/workflow/modules.py M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/viz/trackster/tracks.js M test/unit/test_lazy_process.py Log Message: ----------- Merge, rebuild. Compare: https://github.com/galaxyproject/galaxy/compare/d693aaf624ce...d15b1030c5ba

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[galaxyproject/galaxy] 7b2a2b: [16.01] More robust test_lazy_process.
by GitHub 29 Mar '16

29 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 7b2a2b1ef1154699d064482ffc41b4d3b6efdabb https://github.com/galaxyproject/galaxy/commit/7b2a2b1ef1154699d064482ffc41… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M test/unit/test_lazy_process.py Log Message: ----------- [16.01] More robust test_lazy_process. Hopefully this will fix a transiently failing test (I've only seen in fail on OS X). Commit: 7c94ac8d93b8c7fd2dd2f18d3939fa23a1589ad9 https://github.com/galaxyproject/galaxy/commit/7c94ac8d93b8c7fd2dd2f18d3939… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M test/unit/test_lazy_process.py Log Message: ----------- Merge pull request #2032 from jmchilton/lazy_process_test_fix [16.01] More robust test_lazy_process. Compare: https://github.com/galaxyproject/galaxy/compare/68ca4b9237a5...7c94ac8d93b8

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[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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