October 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] 48e2dd: Updated integrated_tool_panel.xml from Main
by GitHub 25 Oct '16

25 Oct '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 48e2ddcc7436782a270393ded55859f00b4bd24f https://github.com/galaxyproject/usegalaxy-playbook/commit/48e2ddcc7436782a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-10-25 (Tue, 25 Oct 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml Log Message: ----------- Updated integrated_tool_panel.xml from Main Commit: c346c541753039291d17459f1b9ab9886bee41b8 https://github.com/galaxyproject/usegalaxy-playbook/commit/c346c54175303929… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-10-25 (Tue, 25 Oct 2016) Changed paths: M production/secret_vars/galaxyservers.yml M stage/secret_vars/galaxyservers.yml Log Message: ----------- Update Test/Main admin users Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/fe578b76e94d...…

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[galaxyproject/galaxy] 575373: Remove run_complete.mako -- unused and cruft from ...
by GitHub 25 Oct '16

25 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 575373c8f304967b224af128774ad646a40cde3b https://github.com/galaxyproject/galaxy/commit/575373c8f304967b224af128774a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-23 (Sun, 23 Oct 2016) Changed paths: R templates/webapps/galaxy/workflow/run_complete.mako Log Message: ----------- Remove run_complete.mako -- unused and cruft from merge chaos in webhooks PR. Commit: d2ff7345a8c0fbdb8c5d88e86e428f79c263d462 https://github.com/galaxyproject/galaxy/commit/d2ff7345a8c0fbdb8c5d88e86e42… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-25 (Tue, 25 Oct 2016) Changed paths: R templates/webapps/galaxy/workflow/index.mako R templates/webapps/galaxy/workflow/missing_tools.mako R templates/webapps/galaxy/workflow/myexp_export_content.mako R templates/webapps/galaxy/workflow/rename.mako Log Message: ----------- Remove 4 additional mako files per nsoranzo Commit: 8da4ad6563f2d37309494aa86e1f8ed2595a6af9 https://github.com/galaxyproject/galaxy/commit/8da4ad6563f2d37309494aa86e1f… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-10-25 (Tue, 25 Oct 2016) Changed paths: R templates/webapps/galaxy/workflow/index.mako R templates/webapps/galaxy/workflow/missing_tools.mako R templates/webapps/galaxy/workflow/myexp_export_content.mako R templates/webapps/galaxy/workflow/rename.mako R templates/webapps/galaxy/workflow/run_complete.mako Log Message: ----------- Merge pull request #3082 from dannon/remove_run_complete Remove run_complete.mako -- unused and cruft from merge chaos in webh… Compare: https://github.com/galaxyproject/galaxy/compare/62c77e2cc457...8da4ad6563f2

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[galaxyproject/galaxy] ae0d0a: Update the schema to be correct and recent
by GitHub 25 Oct '16

25 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ae0d0a23e273d39f64da2550da34adee9a540bb2 https://github.com/galaxyproject/galaxy/commit/ae0d0a23e273d39f64da2550da34… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-25 (Tue, 25 Oct 2016) Changed paths: M doc/source/slideshow/architecture/images/galaxy_schema.png Log Message: ----------- Update the schema to be correct and recent Commit: 62c77e2cc457a5cb2f33b7d75e247ecf13ba57d8 https://github.com/galaxyproject/galaxy/commit/62c77e2cc457a5cb2f33b7d75e24… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-25 (Tue, 25 Oct 2016) Changed paths: M doc/source/slideshow/architecture/images/galaxy_schema.png Log Message: ----------- Merge pull request #3091 from dannon/update_old_schema Update the schema image in architecture slides to be correct and recent (and use git-lfs for doc pngs) Compare: https://github.com/galaxyproject/galaxy/compare/9d402eaf1ab1...62c77e2cc457

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[galaxyproject/galaxy] a431d8: Add tool xml reload to tool run page - for admins ...
by GitHub 25 Oct '16

25 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a431d88293faf8f6286cae416f8842ce186692c4 https://github.com/galaxyproject/galaxy/commit/a431d88293faf8f6286cae416f88… Author: tmcgowan <mcgo0092(a)umn.edu> Date: 2016-10-18 (Tue, 18 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js 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.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Add tool xml reload to tool run page - for admins only Commit: f9357ea07ddf0525b3a82021c9e11f690c700d67 https://github.com/galaxyproject/galaxy/commit/f9357ea07ddf0525b3a82021c9e1… Author: tmcgowan <mcgo0092(a)umn.edu> Date: 2016-10-20 (Thu, 20 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js 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.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Add modal confirmation for tool reload. Commit: 9d402eaf1ab13b03894a27645368f12a9d42289c https://github.com/galaxyproject/galaxy/commit/9d402eaf1ab13b03894a27645368… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-25 (Tue, 25 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js 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.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Merge remote-tracking branch 'tmcgowan/frequest_943' into dev Compare: https://github.com/galaxyproject/galaxy/compare/05be84ba47c0...9d402eaf1ab1

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[galaxyproject/usegalaxy-playbook] fe578b: Add a manual dependency path to Main for SRA Tools...
by GitHub 25 Oct '16

25 Oct '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: fe578b76e94d3078ec07a6d187f88038d0f6730e https://github.com/galaxyproject/usegalaxy-playbook/commit/fe578b76e94d3078… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-10-25 (Tue, 25 Oct 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Add a manual dependency path to Main for SRA Tools to find ascp.

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[galaxyproject/galaxy] 0f0bcb: fix bad merge in #3060
by GitHub 24 Oct '16

24 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0f0bcb6a088f669a5c1272d238bbe79e29002742 https://github.com/galaxyproject/galaxy/commit/0f0bcb6a088f669a5c1272d238bb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-24 (Mon, 24 Oct 2016) Changed paths: M Makefile Log Message: ----------- fix bad merge in #3060 Commit: 00c48e4878a0b22ce7045692d67d72af7d540215 https://github.com/galaxyproject/galaxy/commit/00c48e4878a0b22ce7045692d67d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-24 (Mon, 24 Oct 2016) Changed paths: M Makefile Log Message: ----------- remove the rest of the badle merged target Commit: 05be84ba47c0932a393cb9925ae10db4fae27396 https://github.com/galaxyproject/galaxy/commit/05be84ba47c0932a393cb9925ae1… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-10-24 (Mon, 24 Oct 2016) Changed paths: M Makefile Log Message: ----------- Merge pull request #3087 from martenson/fix-makefile fix bad merge in #3060 Compare: https://github.com/galaxyproject/galaxy/compare/5662a6a5c6fd...05be84ba47c0

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[galaxyproject/galaxy] e4b376: Change remaining __all__ from list to tuple
by GitHub 24 Oct '16

24 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e4b3766c1b8798ab20a00c98d10f7bbf29da16ab https://github.com/galaxyproject/galaxy/commit/e4b3766c1b8798ab20a00c98d10f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-18 (Tue, 18 Oct 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/localdb.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/dataproviders/__init__.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/deferred/data_transfer.py M lib/galaxy/jobs/deferred/manual_data_transfer.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/collectl/subsystems.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/metrics/instrumenters/uname.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/godocker.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/jobs/runners/util/__init__.py M lib/galaxy/jobs/runners/util/drmaa/__init__.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/json.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/properties.py M lib/galaxy/util/topsort.py M lib/galaxy/web/__init__.py M lib/galaxy/web/buildapp.py M lib/galaxy/web/framework/__init__.py M lib/galaxy/web/framework/middleware/error.py M lib/galaxy/web/framework/middleware/static.py M lib/galaxy/webapps/galaxy/api/tours.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/galaxy/webapps/reports/__init__.py M lib/galaxy/webapps/tool_shed/__init__.py M lib/galaxy/webapps/tool_shed/controllers/user.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/workflow_util.py M scripts/db_shell.py M test/api/test_histories.py M test/api/test_libraries.py M test/unit/tools/test_tool_dependency_description.py Log Message: ----------- Change remaining __all__ from list to tuple Also fix import order and Python3 compatibility. Commit: 5662a6a5c6fd7166b9f5092308e3ff2ca2bb3738 https://github.com/galaxyproject/galaxy/commit/5662a6a5c6fd7166b9f5092308e3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-24 (Mon, 24 Oct 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/localdb.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/dataproviders/__init__.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/deferred/data_transfer.py M lib/galaxy/jobs/deferred/manual_data_transfer.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/collectl/subsystems.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/metrics/instrumenters/uname.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/godocker.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/jobs/runners/util/__init__.py M lib/galaxy/jobs/runners/util/drmaa/__init__.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/json.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/properties.py M lib/galaxy/util/topsort.py M lib/galaxy/web/__init__.py M lib/galaxy/web/buildapp.py M lib/galaxy/web/framework/__init__.py M lib/galaxy/web/framework/middleware/error.py M lib/galaxy/web/framework/middleware/static.py M lib/galaxy/webapps/galaxy/api/tours.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/galaxy/webapps/reports/__init__.py M lib/galaxy/webapps/tool_shed/__init__.py M lib/galaxy/webapps/tool_shed/controllers/user.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/workflow_util.py M scripts/db_shell.py M test/api/test_histories.py M test/api/test_libraries.py M test/unit/tools/test_tool_dependency_description.py Log Message: ----------- Merge pull request #3071 from nsoranzo/fix__all__ Change __all__ from list to tuple [2/2] Compare: https://github.com/galaxyproject/galaxy/compare/a6d52cdbdc83...5662a6a5c6fd

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[galaxyproject/galaxy] 096a7b: fix the incorrect handling of root when prefix is ...
by GitHub 23 Oct '16

23 Oct '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 096a7bf94d799f905013f7052c1bdf87062a45a7 https://github.com/galaxyproject/galaxy/commit/096a7bf94d799f905013f7052c1b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-20 (Thu, 20 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js 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-folderrow-view.js.map 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-dataset-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- fix the incorrect handling of root when prefix is in play Commit: 65dc4f22aa7b717109aca6fac7947a84d2bd587a https://github.com/galaxyproject/galaxy/commit/65dc4f22aa7b717109aca6fac794… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-23 (Sun, 23 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js 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-folderrow-view.js.map 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-dataset-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #3074 from martenson/fix-libraries-prefix [16.07] Fix libraries prefix Compare: https://github.com/galaxyproject/galaxy/compare/cf0e4e84ce41...65dc4f22aa7b

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[galaxyproject/galaxy] afe5e0: Merge branch 'release_16.01'
by GitHub 23 Oct '16

23 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: afe5e0446ea3a943eb69616fda84fc9870c3b584 https://github.com/galaxyproject/galaxy/commit/afe5e0446ea3a943eb69616fda84… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py M templates/show_params.mako M templates/webapps/galaxy/data_manager/view_job.mako Log Message: ----------- Merge branch 'release_16.01' Commit: f730f2d1abff763d35fa8514762d55f8a863c791 https://github.com/galaxyproject/galaxy/commit/f730f2d1abff763d35fa8514762d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: A .ci/first_startup.sh M .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh M .ci/py3_sources.txt M .gitignore M .travis.yml M Makefile M README.rst M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.js R client/galaxy/scripts/libs/handlebars.runtime.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-list.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/dataset/states.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js R client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hda-model.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/job-dag.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/library/library-dataset-view.js 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-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-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/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.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/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/onload.js R client/galaxy/scripts/templates/compiled/panel_section.js R client/galaxy/scripts/templates/compiled/tool_form.js R client/galaxy/scripts/templates/compiled/tool_link.js R client/galaxy/scripts/templates/compiled/tool_search.js R client/galaxy/scripts/templates/panel_section.handlebars R client/galaxy/scripts/templates/tool_form.handlebars R client/galaxy/scripts/templates/tool_link.handlebars R client/galaxy/scripts/templates/tool_search.handlebars M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/base.less M client/galaxy/style/less/library.less A client/galaxy/style/less/tour.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M client/grunt-tasks/install-libs.js M client/grunt-tasks/style.js R client/grunt-tasks/templates.js A client/grunt-tasks/webpack.js M client/package.json M client/webpack.config.js M config/datatypes_conf.xml.sample M 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Merge branch 'release_16.04' Commit: a5b836e9eeead2eab752d79b0e15197b82cb0720 https://github.com/galaxyproject/galaxy/commit/a5b836e9eeead2eab752d79b0e15… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/data.js M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/js/lib/proxy.js M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M static/maps/mvc/dataset/data.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/data.js M templates/webapps/galaxy/history/grid.mako A test/unit/datatypes/test_data.py Log Message: ----------- Merge branch 'release_16.04' Commit: 5dfdf90dd09a53e9bc5108f22e439fae961102d5 https://github.com/galaxyproject/galaxy/commit/5dfdf90dd09a53e9bc5108f22e43… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-07-30 (Sat, 30 Jul 2016) Changed paths: M config/galaxy.ini.sample A config/plugins/plugin1.xml A config/plugins/plugin2.xml A config/plugins/webhooks/plugin1/config/plugin1.yaml A config/plugins/webhooks/plugin2/config/plugin2.yml M lib/galaxy/app.py M lib/galaxy/config.py A lib/galaxy/webapps/galaxy/api/webhooks.py A lib/galaxy/webhooks/__init__.py Log Message: ----------- add Webhooks draft Commit: 9551343c605f3f8895f75f7ba0fc295ee678ae1a https://github.com/galaxyproject/galaxy/commit/9551343c605f3f8895f75f7ba0fc… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-07-30 (Sat, 30 Jul 2016) Changed paths: R config/plugins/plugin1.xml R config/plugins/plugin2.xml Log Message: ----------- remove extra files Commit: b00c18c26709483df26a0a2878b059e08d697c22 https://github.com/galaxyproject/galaxy/commit/b00c18c26709483df26a0a2878b0… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-07-30 (Sat, 30 Jul 2016) Changed paths: M config/galaxy.ini.sample A config/plugins/webhooks/plugin1/config/plugin1.yaml A config/plugins/webhooks/plugin2/config/plugin2.yml M lib/galaxy/app.py M lib/galaxy/config.py A lib/galaxy/webapps/galaxy/api/webhooks.py A lib/galaxy/webhooks/__init__.py Log Message: ----------- add Webhooks draft remove extra files Commit: 05823a8d1499f5db150942039b31efce4ec97e6b https://github.com/galaxyproject/galaxy/commit/05823a8d1499f5db150942039b31… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-07-30 (Sat, 30 Jul 2016) Log Message: ----------- Merge branch 'feature/plugin-system' of github.com:bgruening/galaxy into feature/plugin-system Commit: fb76aa0a938a2498d3206e6039bc1d9906e6c2ce https://github.com/galaxyproject/galaxy/commit/fb76aa0a938a2498d3206e6039bc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M .ci/flake8_blacklist.txt M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-contents.js M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/wrappers.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/render.py M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-contents.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/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-contents.js M test/base/driver_util.py M tool-data/shared/ucsc/ucsc_build_sites.txt.sample Log Message: ----------- Merge branch 'release_16.04' Commit: f8cf6f834bd92b82a05250b1c1f0e42957bffb15 https://github.com/galaxyproject/galaxy/commit/f8cf6f834bd92b82a05250b1c1f0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M .ci/flake8_blacklist.txt M lib/galaxy/tools/parameters/basic.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M tox.ini Log Message: ----------- Merge branch 'release_16.04' Commit: bcfcd8184f297abc9f2e90fbf7504be08725600e https://github.com/galaxyproject/galaxy/commit/bcfcd8184f297abc9f2e90fbf750… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge branch 'release_16.04' Commit: 12b020548689b973bc1b99379b35678317b412da https://github.com/galaxyproject/galaxy/commit/12b020548689b973bc1b99379b35… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-08-18 (Thu, 18 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/tool/tool-webhooks.js M config/plugins/webhooks/plugin2/config/plugin2.yml A config/plugins/webhooks/plugin2/static/style.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py M static/maps/mvc/tool/tool-form.js.map A static/maps/mvc/tool/tool-webhooks.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/tool/tool-form.js A static/scripts/mvc/tool/tool-webhooks.js Log Message: ----------- add very basic plugin system (for tools) Commit: d01677618058a9ac7cb3758a4f6f1c3484790012 https://github.com/galaxyproject/galaxy/commit/d01677618058a9ac7cb3758a4f6f… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin2/config/plugin2.yml R config/plugins/webhooks/plugin2/static/style.css A config/plugins/webhooks/xkcd/config/xkcd.yml A config/plugins/webhooks/xkcd/static/script.js A config/plugins/webhooks/xkcd/static/styles.css M lib/galaxy/webhooks/__init__.py M static/maps/mvc/tool/tool-webhooks.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/tool/tool-webhooks.js Log Message: ----------- add first webhook Commit: 08a2d275fa5f8b3713b28be52fcc78eea609a21d https://github.com/galaxyproject/galaxy/commit/08a2d275fa5f8b3713b28be52fcc… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js A config/plugins/webhooks/phdcomics/config/phdcomics.yaml A config/plugins/webhooks/phdcomics/helper/__init__.py A config/plugins/webhooks/phdcomics/static/script.js A config/plugins/webhooks/phdcomics/static/styles.css R config/plugins/webhooks/plugin1/config/plugin1.yaml M config/plugins/webhooks/xkcd/static/script.js M config/plugins/webhooks/xkcd/static/styles.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py M static/maps/mvc/tool/tool-webhooks.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/tool/tool-webhooks.js Log Message: ----------- add one more plugin Commit: 3b9d1c96e0ea48e09c17c48fb9da8d1f65bbc791 https://github.com/galaxyproject/galaxy/commit/3b9d1c96e0ea48e09c17c48fb9da… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js R client/galaxy/scripts/mvc/tool/tool-webhooks.js A client/galaxy/scripts/mvc/webhooks.js A config/plugins/webhooks/topbar_test/config/topbar_test.yml M lib/galaxy/webhooks/__init__.py M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form.js.map A static/maps/mvc/webhooks.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/mvc/tool/tool-form.js A static/scripts/mvc/webhooks.js Log Message: ----------- topbar webhooks testing Commit: a4497004ac47a25d6f9cefbfcb08183c5b6b8564 https://github.com/galaxyproject/galaxy/commit/a4497004ac47a25d6f9cefbfcb08… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: M config/galaxy.ini.sample A config/plugins/plugin1.xml A config/plugins/plugin2.xml A config/plugins/webhooks/plugin1/config/plugin1.yaml A config/plugins/webhooks/plugin2/config/plugin2.yml M lib/galaxy/app.py M lib/galaxy/config.py A lib/galaxy/webapps/galaxy/api/webhooks.py A lib/galaxy/webhooks/__init__.py Log Message: ----------- add Webhooks draft Commit: 356e7ad3982da9916da927c52dad29e86a1e0ceb https://github.com/galaxyproject/galaxy/commit/356e7ad3982da9916da927c52dad… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: R config/plugins/plugin1.xml R config/plugins/plugin2.xml Log Message: ----------- remove extra files Commit: 649bdd2aa947e11ab300152f4d9054be74229020 https://github.com/galaxyproject/galaxy/commit/649bdd2aa947e11ab300152f4d90… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/tool/tool-webhooks.js M config/plugins/webhooks/plugin2/config/plugin2.yml A config/plugins/webhooks/plugin2/static/style.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py M static/maps/mvc/tool/tool-form.js.map A static/maps/mvc/tool/tool-webhooks.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/tool/tool-form.js A static/scripts/mvc/tool/tool-webhooks.js Log Message: ----------- add very basic plugin system (for tools) Commit: 6ea52120840ac0e89aa6b6cfbce414a81a1c42e7 https://github.com/galaxyproject/galaxy/commit/6ea52120840ac0e89aa6b6cfbce4… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin2/config/plugin2.yml R config/plugins/webhooks/plugin2/static/style.css A config/plugins/webhooks/xkcd/config/xkcd.yml A config/plugins/webhooks/xkcd/static/script.js A config/plugins/webhooks/xkcd/static/styles.css M lib/galaxy/webhooks/__init__.py M static/maps/mvc/tool/tool-webhooks.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/tool/tool-webhooks.js Log Message: ----------- add first webhook Commit: 4cbc8a0c0ce1587a52418d91e2918ecdc07cf7ca https://github.com/galaxyproject/galaxy/commit/4cbc8a0c0ce1587a52418d91e291… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js A config/plugins/webhooks/phdcomics/config/phdcomics.yaml A config/plugins/webhooks/phdcomics/helper/__init__.py A config/plugins/webhooks/phdcomics/static/script.js A config/plugins/webhooks/phdcomics/static/styles.css R config/plugins/webhooks/plugin1/config/plugin1.yaml M config/plugins/webhooks/xkcd/static/script.js M config/plugins/webhooks/xkcd/static/styles.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py M static/maps/mvc/tool/tool-webhooks.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/tool/tool-webhooks.js Log Message: ----------- add one more plugin Commit: d2b58c80993c42b3add50a0266d4b8f9ca269a6d https://github.com/galaxyproject/galaxy/commit/d2b58c80993c42b3add50a0266d4… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js R client/galaxy/scripts/mvc/tool/tool-webhooks.js A client/galaxy/scripts/mvc/webhooks.js A config/plugins/webhooks/topbar_test/config/topbar_test.yml M lib/galaxy/webhooks/__init__.py M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form.js.map A static/maps/mvc/webhooks.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/mvc/tool/tool-form.js A static/scripts/mvc/webhooks.js Log Message: ----------- topbar webhooks testing Commit: 763aa1026dc6071cab0687859d5d764ac9f438ed https://github.com/galaxyproject/galaxy/commit/763aa1026dc6071cab0687859d5d… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Log Message: ----------- Merge branch 'feature/plugin-system' of github.com:bgruening/galaxy into feature/plugin-system Commit: bec41c889def0b012ec809d5e3e97fe2bc006492 https://github.com/galaxyproject/galaxy/commit/bec41c889def0b012ec809d5e3e9… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js A config/plugins/webhooks/masthead_test/config/masthead_test.yml M config/plugins/webhooks/phdcomics/config/phdcomics.yaml R config/plugins/webhooks/topbar_test/config/topbar_test.yml M config/plugins/webhooks/xkcd/config/xkcd.yml M lib/galaxy/webhooks/__init__.py M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/webhooks.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/mvc/tool/tool-form.js M static/scripts/mvc/webhooks.js Log Message: ----------- renamings and fixes 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client/galaxy/scripts/libs/underscore.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js R client/galaxy/scripts/mvc/tool/tool-template.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/popup-menu.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/ui/hoverhighlight.js M client/galaxy/scripts/ui/loading-indicator.js M client/galaxy/scripts/ui/mode-button.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/galaxy/scripts/utils/localization.js M client/galaxy/scripts/utils/metrics-logger.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/base.less M client/galaxy/style/less/frame.less M client/galaxy/style/less/library.less M client/galaxy/style/less/ui.less M client/grunt-tasks/install-libs.js M client/grunt-tasks/scripts.js M client/grunt-tasks/style.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/object_store_conf.xml.sample M config/plugins/interactive_environments/jupyter/config/jupyter.xml A config/plugins/interactive_environments/neo/config/allowed_images.yml.sample A config/plugins/interactive_environments/neo/config/neo.ini.sample A config/plugins/interactive_environments/neo/config/neo.xml A config/plugins/interactive_environments/neo/static/js/neo.js A config/plugins/interactive_environments/neo/templates/neo.mako M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.scratchbook.yaml M config/plugins/visualizations/charts/static/app.css M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/charts/forms/default.js M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js M config/plugins/visualizations/charts/static/library/datasets.js M config/plugins/visualizations/charts/static/library/jobs.js M config/plugins/visualizations/charts/static/library/storage.js R config/plugins/visualizations/charts/static/library/ui-table-form.js M config/plugins/visualizations/charts/static/models/chart.js M config/plugins/visualizations/charts/static/models/config.js R config/plugins/visualizations/charts/static/models/group.js R config/plugins/visualizations/charts/static/models/groups.js M config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.css M config/plugins/visualizations/charts/static/views/editor.js R config/plugins/visualizations/charts/static/views/group.js A config/plugins/visualizations/charts/static/views/groups.js M config/plugins/visualizations/charts/static/views/settings.js M config/plugins/visualizations/charts/static/views/types.js M config/plugins/visualizations/charts/static/views/viewer.js M config/plugins/visualizations/charts/static/views/viewport.js R config/plugins/visualizations/graphview/config/graphview.xml R config/plugins/visualizations/graphview/static/graphview.css R 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test/unit/test_galaxy_mapping.py M test/unit/test_objectstore.py M test/unit/tools/test_actions.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_execution.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_toolbox.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_run_parameters.py M tool_list.py M tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/hbvar_filter.py M tools/data_source/import.py M 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tools/genomespace/genomespace_file_browser.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_split_by_species.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/filtering.xml M tools/stats/grouping.py M tools/stats/gsummary.py M tools/stats/gsummary.xml M tox.ini Log Message: ----------- Merge branch 'release_16.07' Commit: 9ff882944ee1fd78b6244dad5893ac7390eb76fa https://github.com/galaxyproject/galaxy/commit/9ff882944ee1fd78b6244dad5893… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M config/plugins/webhooks/masthead_test/config/masthead_test.yml A config/plugins/webhooks/masthead_test/static/script.js M config/plugins/webhooks/phdcomics/helper/__init__.py M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webhooks/__init__.py M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/webhooks.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/mvc/tool/tool-form.js M static/scripts/mvc/webhooks.js Log Message: ----------- - unify webhooks entry point - simlify webhooks code (on load) - improve code readability - clean up Commit: d2ec87548a22273a2e0d94bbe1b415fbf6352b36 https://github.com/galaxyproject/galaxy/commit/d2ec87548a22273a2e0d94bbe1b4… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M config/plugins/webhooks/masthead_test/config/masthead_test.yml M config/plugins/webhooks/phdcomics/config/phdcomics.yaml M config/plugins/webhooks/xkcd/config/xkcd.yml M lib/galaxy/webapps/galaxy/api/webhooks.py M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/webhooks.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.js M static/scripts/mvc/webhooks.js M templates/webapps/galaxy/workflow/run_complete.mako Log Message: ----------- - add new entry point (Workflow) - temporarily hide masthead webhook (due to instability) Commit: e320b1aaa70aea38b7108ca6ae372b1d06fd30bc https://github.com/galaxyproject/galaxy/commit/e320b1aaa70aea38b7108ca6ae37… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-09-07 (Wed, 07 Sep 2016) Changed paths: M config/galaxy.ini.sample M doc/source/releases/16.07.rst M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Merge branch 'release_16.07' Commit: b46d55e30fd3f8a2832130dd3f917082f442836f https://github.com/galaxyproject/galaxy/commit/b46d55e30fd3f8a2832130dd3f91… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-04 (Tue, 04 Oct 2016) Changed paths: M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/webhooks.js A config/plugins/webhooks/history_test1/config/history_test1.yml A config/plugins/webhooks/history_test2/config/history_test2.yml M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/webhooks.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/history/options-menu.js M static/scripts/mvc/webhooks.js Log Message: ----------- add new entry point for History Panel menu Commit: b98e49f2bc88e62b4835aa8d23f8d3386f81f66a https://github.com/galaxyproject/galaxy/commit/b98e49f2bc88e62b4835aa8d23f8… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M config/plugins/webhooks/history_test1/config/history_test1.yml M config/plugins/webhooks/history_test2/config/history_test2.yml M config/plugins/webhooks/masthead_test/config/masthead_test.yml M config/plugins/webhooks/phdcomics/config/phdcomics.yaml M config/plugins/webhooks/xkcd/config/xkcd.yml M lib/galaxy/webhooks/__init__.py M static/maps/layout/menu.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/webhooks.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/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/webhooks.js Log Message: ----------- bug fixes and improvements Commit: 58e0d6e1a61b06c444b2086d7725e1100d49441a https://github.com/galaxyproject/galaxy/commit/58e0d6e1a61b06c444b2086d7725… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M config/galaxy.ini.sample A config/plugins/plugin1.xml A config/plugins/plugin2.xml A config/plugins/webhooks/plugin1/config/plugin1.yaml A config/plugins/webhooks/plugin2/config/plugin2.yml M lib/galaxy/app.py M lib/galaxy/config.py A lib/galaxy/webapps/galaxy/api/webhooks.py A lib/galaxy/webhooks/__init__.py Log Message: ----------- add Webhooks draft Commit: cbbcf3d625a1625e89bbe7c59997d3658d23ea55 https://github.com/galaxyproject/galaxy/commit/cbbcf3d625a1625e89bbe7c59997… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: R config/plugins/plugin1.xml R config/plugins/plugin2.xml Log Message: ----------- remove extra files Commit: cf1fde577e9b918bacfe2d78d9f2b632a81ee20b https://github.com/galaxyproject/galaxy/commit/cf1fde577e9b918bacfe2d78d9f2… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: A client/galaxy/scripts/mvc/tool/tool-webhooks.js A client/galaxy/scripts/mvc/webhooks.js M config/plugins/webhooks/plugin2/config/plugin2.yml A config/plugins/webhooks/plugin2/static/style.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py A static/maps/mvc/tool/tool-webhooks.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map A static/scripts/mvc/tool/tool-webhooks.js Log Message: ----------- add very basic plugin system (for tools) Commit: ac5a0f5a6adea3493549d69627d1d2223b97c09e https://github.com/galaxyproject/galaxy/commit/ac5a0f5a6adea3493549d69627d1… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin2/config/plugin2.yml R config/plugins/webhooks/plugin2/static/style.css A config/plugins/webhooks/xkcd/config/xkcd.yml A config/plugins/webhooks/xkcd/static/script.js A config/plugins/webhooks/xkcd/static/styles.css M lib/galaxy/webhooks/__init__.py M static/maps/mvc/tool/tool-webhooks.js.map M static/scripts/mvc/tool/tool-webhooks.js Log Message: ----------- add first webhook Commit: fecf493ecde3590e9da4629a063d5885dde99502 https://github.com/galaxyproject/galaxy/commit/fecf493ecde3590e9da4629a063d… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js A config/plugins/webhooks/phdcomics/config/phdcomics.yaml A config/plugins/webhooks/phdcomics/helper/__init__.py A config/plugins/webhooks/phdcomics/static/script.js A config/plugins/webhooks/phdcomics/static/styles.css R config/plugins/webhooks/plugin1/config/plugin1.yaml M config/plugins/webhooks/xkcd/static/script.js M config/plugins/webhooks/xkcd/static/styles.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py M static/maps/mvc/tool/tool-webhooks.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/tool/tool-webhooks.js Log Message: ----------- add one more plugin Commit: 239731d45aa5019eecc4d65a771102bb38a79851 https://github.com/galaxyproject/galaxy/commit/239731d45aa5019eecc4d65a7711… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js R client/galaxy/scripts/mvc/tool/tool-webhooks.js A config/plugins/webhooks/topbar_test/config/topbar_test.yml M lib/galaxy/webhooks/__init__.py A static/maps/mvc/webhooks.js.map A static/scripts/mvc/webhooks.js Log Message: ----------- topbar webhooks testing Commit: d35d99727b76ab71173ad7cccca1a4d66aa9ce70 https://github.com/galaxyproject/galaxy/commit/d35d99727b76ab71173ad7cccca1… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: A config/plugins/plugin1.xml A config/plugins/plugin2.xml A config/plugins/webhooks/plugin1/config/plugin1.yaml A config/plugins/webhooks/plugin2/config/plugin2.yml Log Message: ----------- add Webhooks draft Commit: 1f7a4135318f0d6940e2a65a2b9f7ab29cdb0a41 https://github.com/galaxyproject/galaxy/commit/1f7a4135318f0d6940e2a65a2b9f… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: R config/plugins/plugin1.xml R config/plugins/plugin2.xml Log Message: ----------- remove extra files Commit: adc92fd31740ebe4fe66bfec32fe14ef5b736c72 https://github.com/galaxyproject/galaxy/commit/adc92fd31740ebe4fe66bfec32fe… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: A client/galaxy/scripts/mvc/tool/tool-webhooks.js M config/plugins/webhooks/plugin2/config/plugin2.yml A config/plugins/webhooks/plugin2/static/style.css Log Message: ----------- add very basic plugin system (for tools) Commit: d490415b0500dcbadca9a1f959cf0b996abe326e https://github.com/galaxyproject/galaxy/commit/d490415b0500dcbadca9a1f959cf… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin2/config/plugin2.yml R config/plugins/webhooks/plugin2/static/style.css Log Message: ----------- add first webhook Commit: 86af65a7d6889086e1f16ef3ef4fcfa77ba3c88e https://github.com/galaxyproject/galaxy/commit/86af65a7d6889086e1f16ef3ef4f… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin1/config/plugin1.yaml Log Message: ----------- add one more plugin Commit: 4635ff4575ea1a47fac8da2bbb50092cc3352c3f https://github.com/galaxyproject/galaxy/commit/4635ff4575ea1a47fac8da2bbb50… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: R client/galaxy/scripts/mvc/tool/tool-webhooks.js Log Message: ----------- topbar webhooks testing Commit: 482e0b2bffe992c329f22e4f9b50a34cfd835518 https://github.com/galaxyproject/galaxy/commit/482e0b2bffe992c329f22e4f9b50… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: A config/plugins/webhooks/masthead_test/config/masthead_test.yml M config/plugins/webhooks/phdcomics/config/phdcomics.yaml R config/plugins/webhooks/topbar_test/config/topbar_test.yml M config/plugins/webhooks/xkcd/config/xkcd.yml M lib/galaxy/webhooks/__init__.py M static/maps/mvc/webhooks.js.map M static/scripts/mvc/webhooks.js Log Message: ----------- renamings and fixes Commit: 6e534213e12820f69bb849b74aa8924787d9023e https://github.com/galaxyproject/galaxy/commit/6e534213e12820f69bb849b74aa8… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M config/plugins/webhooks/masthead_test/config/masthead_test.yml A config/plugins/webhooks/masthead_test/static/script.js M config/plugins/webhooks/phdcomics/helper/__init__.py M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webhooks/__init__.py M static/maps/mvc/webhooks.js.map M static/scripts/mvc/webhooks.js Log Message: ----------- - unify webhooks entry point - simlify webhooks code (on load) - improve code readability - clean up Commit: fce44d257b9d05e68ca4323036e7e509d329e789 https://github.com/galaxyproject/galaxy/commit/fce44d257b9d05e68ca4323036e7… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M config/plugins/webhooks/masthead_test/config/masthead_test.yml M config/plugins/webhooks/phdcomics/config/phdcomics.yaml M config/plugins/webhooks/xkcd/config/xkcd.yml M lib/galaxy/webapps/galaxy/api/webhooks.py M static/maps/mvc/webhooks.js.map M static/scripts/mvc/webhooks.js M templates/webapps/galaxy/workflow/run_complete.mako Log Message: ----------- - add new entry point (Workflow) - temporarily hide masthead webhook (due to instability) Commit: 3c3819900fd293de1532a4c0a15685927a8fd2dd https://github.com/galaxyproject/galaxy/commit/3c3819900fd293de1532a4c0a156… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/mvc/history/options-menu.js A config/plugins/webhooks/history_test1/config/history_test1.yml A config/plugins/webhooks/history_test2/config/history_test2.yml M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/webhooks.js.map M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/webhooks.js Log Message: ----------- add new entry point for History Panel menu Commit: 6f109176d16a162b9f5a132927eef13e096bdce4 https://github.com/galaxyproject/galaxy/commit/6f109176d16a162b9f5a132927ee… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M config/plugins/webhooks/history_test1/config/history_test1.yml M config/plugins/webhooks/history_test2/config/history_test2.yml M config/plugins/webhooks/masthead_test/config/masthead_test.yml M config/plugins/webhooks/phdcomics/config/phdcomics.yaml M config/plugins/webhooks/xkcd/config/xkcd.yml M lib/galaxy/webhooks/__init__.py M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/webhooks.js.map M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/webhooks.js Log Message: ----------- bug fixes and improvements Commit: 31674ef5b789b9c9557bb78efaa5d13961744c1d https://github.com/galaxyproject/galaxy/commit/31674ef5b789b9c9557bb78efaa5… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M static/maps/layout/menu.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/mvc/tool/tool-form.js Log Message: ----------- Merge branch 'feature/plugin-system' of github.com:bgruening/galaxy into feature/plugin-system # Conflicts: # client/galaxy/scripts/layout/menu.js # client/galaxy/scripts/mvc/tool/tool-form.js # static/maps/layout/menu.js.map # static/maps/mvc/tool/tool-form.js.map # static/scripts/bundled/analysis.bundled.js # static/scripts/bundled/analysis.bundled.js.map # static/scripts/bundled/libs.bundled.js # static/scripts/bundled/libs.bundled.js.map # static/scripts/layout/menu.js # static/scripts/mvc/tool/tool-form.js Commit: 2bf0549a371a1a3f683d375233b9b3f5b1e37944 https://github.com/galaxyproject/galaxy/commit/2bf0549a371a1a3f683d375233b9… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M config/plugins/webhooks/xkcd/config/xkcd.yml M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/webhooks.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/mvc/tool/tool-form.js Log Message: ----------- fix bugs after previous commit Commit: d821c2745c014bc0e2e2cc31eac8d70bb576ea7e https://github.com/galaxyproject/galaxy/commit/d821c2745c014bc0e2e2cc31eac8… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/webhooks.js M config/plugins/webhooks/masthead_test/config/masthead_test.yml R config/plugins/webhooks/masthead_test/static/script.js M config/plugins/webhooks/phdcomics/helper/__init__.py M lib/galaxy/webapps/galaxy/api/webhooks.py M static/maps/mvc/webhooks.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/webhooks.js Log Message: ----------- pass trans object into the helper function Commit: 1a80a0df7f371347976f0b9fb3ff1cb651d4170b https://github.com/galaxyproject/galaxy/commit/1a80a0df7f371347976f0b9fb3ff… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: A doc/source/admin/webhooks.rst Log Message: ----------- Add initial docs Commit: 5361d7c03d23ed4fe4701b2e126f56114673cf7f https://github.com/galaxyproject/galaxy/commit/5361d7c03d23ed4fe4701b2e126f… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M config/galaxy.ini.sample A config/plugins/plugin1.xml A config/plugins/plugin2.xml A config/plugins/webhooks/plugin1/config/plugin1.yaml A config/plugins/webhooks/plugin2/config/plugin2.yml M lib/galaxy/app.py M lib/galaxy/config.py A lib/galaxy/webapps/galaxy/api/webhooks.py A lib/galaxy/webhooks/__init__.py Log Message: ----------- add Webhooks draft Commit: a34a1201fc72abff092ccb8c0366b07dfde31987 https://github.com/galaxyproject/galaxy/commit/a34a1201fc72abff092ccb8c0366… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: R config/plugins/plugin1.xml R config/plugins/plugin2.xml Log Message: ----------- remove extra files Commit: 6e66fbeca8741748aa823e34432bd62527096491 https://github.com/galaxyproject/galaxy/commit/6e66fbeca8741748aa823e34432b… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/tool/tool-webhooks.js M config/plugins/webhooks/plugin2/config/plugin2.yml A config/plugins/webhooks/plugin2/static/style.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py A static/maps/mvc/tool/tool-webhooks.js.map A static/scripts/mvc/tool/tool-webhooks.js Log Message: ----------- add very basic plugin system (for tools) Commit: eb46e70206ba43a5e191153df74aa47dc441ed19 https://github.com/galaxyproject/galaxy/commit/eb46e70206ba43a5e191153df74a… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin2/config/plugin2.yml R config/plugins/webhooks/plugin2/static/style.css A config/plugins/webhooks/xkcd/config/xkcd.yml A config/plugins/webhooks/xkcd/static/script.js A config/plugins/webhooks/xkcd/static/styles.css M lib/galaxy/webhooks/__init__.py M static/maps/mvc/tool/tool-webhooks.js.map M static/scripts/mvc/tool/tool-webhooks.js Log Message: ----------- add first webhook Commit: 40bcaaecf531920275d8f9f82d5e57bac60c43ae https://github.com/galaxyproject/galaxy/commit/40bcaaecf531920275d8f9f82d5e… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js A config/plugins/webhooks/phdcomics/config/phdcomics.yaml A config/plugins/webhooks/phdcomics/helper/__init__.py A config/plugins/webhooks/phdcomics/static/script.js A config/plugins/webhooks/phdcomics/static/styles.css R config/plugins/webhooks/plugin1/config/plugin1.yaml M config/plugins/webhooks/xkcd/static/script.js M config/plugins/webhooks/xkcd/static/styles.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py M static/maps/mvc/tool/tool-webhooks.js.map M static/scripts/mvc/tool/tool-webhooks.js Log Message: ----------- add one more plugin Commit: bf4a1aa1a87050e030ead0e5ff8922bcb7338d98 https://github.com/galaxyproject/galaxy/commit/bf4a1aa1a87050e030ead0e5ff89… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js R client/galaxy/scripts/mvc/tool/tool-webhooks.js A client/galaxy/scripts/mvc/webhooks.js A config/plugins/webhooks/topbar_test/config/topbar_test.yml M lib/galaxy/webhooks/__init__.py A static/maps/mvc/webhooks.js.map A static/scripts/mvc/webhooks.js Log Message: ----------- topbar webhooks testing Commit: 17440d7b11b5013e52033efe4668115a466115b0 https://github.com/galaxyproject/galaxy/commit/17440d7b11b5013e52033efe4668… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: A config/plugins/plugin1.xml A config/plugins/plugin2.xml A config/plugins/webhooks/plugin1/config/plugin1.yaml A config/plugins/webhooks/plugin2/config/plugin2.yml M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webhooks/__init__.py Log Message: ----------- add Webhooks draft Commit: 143a740dc38fec9f92211d26364cb0b40235a24e https://github.com/galaxyproject/galaxy/commit/143a740dc38fec9f92211d26364c… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: R config/plugins/plugin1.xml R config/plugins/plugin2.xml Log Message: ----------- remove extra files Commit: 117c5263acdfb8853cc6771810ef87c755b006ce https://github.com/galaxyproject/galaxy/commit/117c5263acdfb8853cc6771810ef… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: A client/galaxy/scripts/mvc/tool/tool-webhooks.js M config/plugins/webhooks/plugin2/config/plugin2.yml A config/plugins/webhooks/plugin2/static/style.css M lib/galaxy/webhooks/__init__.py Log Message: ----------- add very basic plugin system (for tools) Commit: ed2282d60b3f41c653e61be13d24ace6e83215ca https://github.com/galaxyproject/galaxy/commit/ed2282d60b3f41c653e61be13d24… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin2/config/plugin2.yml R config/plugins/webhooks/plugin2/static/style.css M lib/galaxy/webhooks/__init__.py Log Message: ----------- add first webhook Commit: 29129463a0be1778c69fce6e783dd75da05d53c0 https://github.com/galaxyproject/galaxy/commit/29129463a0be1778c69fce6e783d… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin1/config/plugin1.yaml Log Message: ----------- add one more plugin Commit: 411674521cf1d9d3c5479ae334fbead783d737fe https://github.com/galaxyproject/galaxy/commit/411674521cf1d9d3c5479ae334fb… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: R client/galaxy/scripts/mvc/tool/tool-webhooks.js Log Message: ----------- topbar webhooks testing Commit: b215de947c007dfc84ae4325d1a6b0be846986b5 https://github.com/galaxyproject/galaxy/commit/b215de947c007dfc84ae4325d1a6… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js A config/plugins/webhooks/masthead_test/config/masthead_test.yml M config/plugins/webhooks/phdcomics/config/phdcomics.yaml R config/plugins/webhooks/topbar_test/config/topbar_test.yml M config/plugins/webhooks/xkcd/config/xkcd.yml M lib/galaxy/webhooks/__init__.py M static/maps/mvc/webhooks.js.map M static/scripts/mvc/webhooks.js Log Message: ----------- renamings and fixes Commit: bb9dc0560ade3f44037a4d03a24651b91af36dbd https://github.com/galaxyproject/galaxy/commit/bb9dc0560ade3f44037a4d03a246… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M config/plugins/webhooks/masthead_test/config/masthead_test.yml A config/plugins/webhooks/masthead_test/static/script.js M config/plugins/webhooks/phdcomics/helper/__init__.py M lib/galaxy/webapps/galaxy/api/webhooks.py M static/maps/mvc/webhooks.js.map M static/scripts/mvc/webhooks.js Log Message: ----------- - unify webhooks entry point - simlify webhooks code (on load) - improve code readability - clean up Commit: e95392b4b62b5ff803390287d0eac4f385504ef1 https://github.com/galaxyproject/galaxy/commit/e95392b4b62b5ff803390287d0ea… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M config/plugins/webhooks/masthead_test/config/masthead_test.yml M config/plugins/webhooks/phdcomics/config/phdcomics.yaml M config/plugins/webhooks/xkcd/config/xkcd.yml M lib/galaxy/webapps/galaxy/api/webhooks.py M static/maps/mvc/webhooks.js.map M static/scripts/mvc/webhooks.js Log Message: ----------- - add new entry point (Workflow) - temporarily hide masthead webhook (due to instability) Commit: f3b1232bdb46e9ccb4f27b3a1fc668d987d650cc https://github.com/galaxyproject/galaxy/commit/f3b1232bdb46e9ccb4f27b3a1fc6… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/webhooks.js A config/plugins/webhooks/history_test1/config/history_test1.yml A config/plugins/webhooks/history_test2/config/history_test2.yml M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/webhooks.js.map M static/scripts/mvc/webhooks.js Log Message: ----------- add new entry point for History Panel menu Commit: 578bdf679f0575e98922ddea004248de9b8b965c https://github.com/galaxyproject/galaxy/commit/578bdf679f0575e98922ddea0042… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M config/plugins/webhooks/history_test1/config/history_test1.yml M config/plugins/webhooks/history_test2/config/history_test2.yml M config/plugins/webhooks/masthead_test/config/masthead_test.yml M config/plugins/webhooks/phdcomics/config/phdcomics.yaml M config/plugins/webhooks/xkcd/config/xkcd.yml M lib/galaxy/webhooks/__init__.py M static/maps/mvc/webhooks.js.map M static/scripts/mvc/webhooks.js Log Message: ----------- bug fixes and improvements Commit: 42adc9c7dfa1485162b78742f5ac3a7e8935902f https://github.com/galaxyproject/galaxy/commit/42adc9c7dfa1485162b78742f5ac… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: A config/plugins/plugin1.xml A config/plugins/plugin2.xml A config/plugins/webhooks/plugin1/config/plugin1.yaml A config/plugins/webhooks/plugin2/config/plugin2.yml Log Message: ----------- add Webhooks draft Commit: 6bc57ec0209f22970c4303870ba48cfea528e0ff https://github.com/galaxyproject/galaxy/commit/6bc57ec0209f22970c4303870ba4… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: R config/plugins/plugin1.xml R config/plugins/plugin2.xml Log Message: ----------- remove extra files Commit: ca769ab848209be8e4e48a6b28c13ecf52744e0f https://github.com/galaxyproject/galaxy/commit/ca769ab848209be8e4e48a6b28c1… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: A client/galaxy/scripts/mvc/tool/tool-webhooks.js M config/plugins/webhooks/plugin2/config/plugin2.yml A config/plugins/webhooks/plugin2/static/style.css Log Message: ----------- add very basic plugin system (for tools) Commit: 1a8a82370bcfd157f1d82ee6f6634bfcbcfb62af https://github.com/galaxyproject/galaxy/commit/1a8a82370bcfd157f1d82ee6f663… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin2/config/plugin2.yml R config/plugins/webhooks/plugin2/static/style.css M config/plugins/webhooks/xkcd/config/xkcd.yml Log Message: ----------- add first webhook Commit: 454a88b45174cfddae5ad79c31d92edffb07cabe https://github.com/galaxyproject/galaxy/commit/454a88b45174cfddae5ad79c31d9… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin1/config/plugin1.yaml Log Message: ----------- add one more plugin Commit: 53f56c3426714b3531dd1c49ecca431f73b77de9 https://github.com/galaxyproject/galaxy/commit/53f56c3426714b3531dd1c49ecca… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: R client/galaxy/scripts/mvc/tool/tool-webhooks.js A config/plugins/webhooks/topbar_test/config/topbar_test.yml M lib/galaxy/webhooks/__init__.py Log Message: ----------- topbar webhooks testing Commit: c7f35c41d72a6131bfd0a4a7b3525518ed29d78a https://github.com/galaxyproject/galaxy/commit/c7f35c41d72a6131bfd0a4a7b352… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: A config/plugins/plugin1.xml A config/plugins/plugin2.xml A config/plugins/webhooks/plugin1/config/plugin1.yaml A config/plugins/webhooks/plugin2/config/plugin2.yml Log Message: ----------- add Webhooks draft Commit: a73d00fc04695b1f27a3cdf6091d352ee61f8f45 https://github.com/galaxyproject/galaxy/commit/a73d00fc04695b1f27a3cdf6091d… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: R config/plugins/plugin1.xml R config/plugins/plugin2.xml Log Message: ----------- remove extra files Commit: 2b2be226ee9425742e0a629459e126b0c90e5e86 https://github.com/galaxyproject/galaxy/commit/2b2be226ee9425742e0a629459e1… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: A client/galaxy/scripts/mvc/tool/tool-webhooks.js M config/plugins/webhooks/plugin2/config/plugin2.yml A config/plugins/webhooks/plugin2/static/style.css Log Message: ----------- add very basic plugin system (for tools) Commit: 211491fdf31a814590250edd4447916a5213120b https://github.com/galaxyproject/galaxy/commit/211491fdf31a814590250edd4447… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin2/config/plugin2.yml R config/plugins/webhooks/plugin2/static/style.css Log Message: ----------- add first webhook Commit: 060df24ff5b329c37103f9c90caf65c4889c964d https://github.com/galaxyproject/galaxy/commit/060df24ff5b329c37103f9c90caf… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin1/config/plugin1.yaml Log Message: ----------- add one more plugin Commit: 00cf0cb85ec2cca9091de22fcaa6579d611530f1 https://github.com/galaxyproject/galaxy/commit/00cf0cb85ec2cca9091de22fcaa6… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: R client/galaxy/scripts/mvc/tool/tool-webhooks.js Log Message: ----------- topbar webhooks testing Commit: 27e0302ea3926e0a3ce6955317f6d1f38bc6f8b4 https://github.com/galaxyproject/galaxy/commit/27e0302ea3926e0a3ce6955317f6… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: R config/plugins/webhooks/topbar_test/config/topbar_test.yml M config/plugins/webhooks/xkcd/config/xkcd.yml M lib/galaxy/webhooks/__init__.py Log Message: ----------- renamings and fixes Commit: 29a57ba0fdd9ab066e19110715bbb091014e3f7a https://github.com/galaxyproject/galaxy/commit/29a57ba0fdd9ab066e19110715bb… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M config/plugins/webhooks/xkcd/config/xkcd.yml Log Message: ----------- - add new entry point (Workflow) - temporarily hide masthead webhook (due to instability) Commit: e58fe7ca49f7b01244d1e6f4bfc92586459c799d https://github.com/galaxyproject/galaxy/commit/e58fe7ca49f7b01244d1e6f4bfc9… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M config/plugins/webhooks/xkcd/config/xkcd.yml Log Message: ----------- bug fixes and improvements Commit: 8b5716ddfda7d8d4bc604cf6d396d59fa45498c7 https://github.com/galaxyproject/galaxy/commit/8b5716ddfda7d8d4bc604cf6d396… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M config/plugins/webhooks/xkcd/config/xkcd.yml M static/maps/mvc/webhooks.js.map Log Message: ----------- fix bugs after previous commit Commit: ce346b6ad4482a1e6a0e8e9f92e79ea1d90a33b4 https://github.com/galaxyproject/galaxy/commit/ce346b6ad4482a1e6a0e8e9f92e7… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/webhooks.js M config/plugins/webhooks/masthead_test/config/masthead_test.yml R config/plugins/webhooks/masthead_test/static/script.js M config/plugins/webhooks/phdcomics/helper/__init__.py M static/maps/mvc/webhooks.js.map M static/scripts/mvc/webhooks.js Log Message: ----------- pass trans object into the helper function Commit: 2cc133f32507cd2aec8784e247106cef540a1c17 https://github.com/galaxyproject/galaxy/commit/2cc133f32507cd2aec8784e24710… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: A doc/source/admin/webhooks.rst Log Message: ----------- Add initial docs Commit: 69a9344c529e34cdb70fdd71634ba2944bf0a7e8 https://github.com/galaxyproject/galaxy/commit/69a9344c529e34cdb70fdd71634b… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js A config/plugins/webhooks/trans_object/config/trans_object.yaml A config/plugins/webhooks/trans_object/helper/__init__.py M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webhooks/__init__.py M static/maps/layout/menu.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/webhooks.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/layout/menu.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js Log Message: ----------- - show Webhook on a workflow page - fix merge errors Commit: ef304a2223ca080c9181fad4117919c71d539211 https://github.com/galaxyproject/galaxy/commit/ef304a2223ca080c9181fad41179… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M lib/galaxy/webapps/galaxy/api/webhooks.py M static/maps/layout/menu.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/webhooks.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/layout/menu.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form.js A templates/webapps/galaxy/workflow/run_complete.mako Log Message: ----------- - merge Commit: a3627b98ab8f5940af529e1387c8da8a4595a9e0 https://github.com/galaxyproject/galaxy/commit/a3627b98ab8f5940af529e1387c8… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M static/maps/mvc/webhooks.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 Log Message: ----------- make client Commit: cc36793cd0d249fd2794c5de54af6ff10695b88e https://github.com/galaxyproject/galaxy/commit/cc36793cd0d249fd2794c5de54af… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/webhooks.js M lib/galaxy/webapps/galaxy/api/webhooks.py M static/maps/layout/menu.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/webhooks.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/mvc/history/options-menu.js M static/scripts/mvc/webhooks.js Log Message: ----------- - remove separate functions for adding masthead/history-menu plugins - choose a random tool/workflow plugin only among active ones Commit: 812aca5b34df584a09d3f82f9d938e89d396b2bd https://github.com/galaxyproject/galaxy/commit/812aca5b34df584a09d3f82f9d93… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/webhooks.py Log Message: ----------- bug fix Commit: 5f9154a6179f194a8186d0f91a375d449cb26ea2 https://github.com/galaxyproject/galaxy/commit/5f9154a6179f194a8186d0f91a37… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- tiny fixes Commit: cd92be8802e520a2f53eceb385f018ded4aea218 https://github.com/galaxyproject/galaxy/commit/cd92be8802e520a2f53eceb385f0… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- Include a section about plugin dependencies. Commit: 0ad7c99ea20ba49725fffe5a356ab39bf601111d https://github.com/galaxyproject/galaxy/commit/0ad7c99ea20ba49725fffe5a356a… Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- Extended the documentation of webhooks and added an images directory. Commit: f29b003a8cd6a277ee67cb553653063fbc53dbfe https://github.com/galaxyproject/galaxy/commit/f29b003a8cd6a277ee67cb553653… Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: A doc/source/admin/images_webhooks/history-menu.png A doc/source/admin/images_webhooks/masthead.png A doc/source/admin/images_webhooks/masthead_trans_object.png A doc/source/admin/images_webhooks/tool.png A doc/source/admin/images_webhooks/workflow.png Log Message: ----------- Added images directory for webhooks documentation Commit: 95c1f186935a77ee71de59a3a616dc5d7f11c8c2 https://github.com/galaxyproject/galaxy/commit/95c1f186935a77ee71de59a3a616… Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- Fixed formatting errors Commit: eb32ad229f5f22c8b2cb497344fd545f14f6eae3 https://github.com/galaxyproject/galaxy/commit/eb32ad229f5f22c8b2cb497344fd… Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- Fixed formatting errors Commit: d1737110bf2d870346df43d5969b329cea1b16d8 https://github.com/galaxyproject/galaxy/commit/d1737110bf2d870346df43d5969b… Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- Fixing errors Commit: 76b9e004d204b6569ef6d19b6e808b77db9984f2 https://github.com/galaxyproject/galaxy/commit/76b9e004d204b6569ef6d19b6e80… Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- Fixing errors Commit: 8030d2025ddaa0ca5f5d58f12a24f85e860f9339 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Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- Fixing errors Commit: af8a3f11048c86f91f17044344211a5cdba98b13 https://github.com/galaxyproject/galaxy/commit/af8a3f11048c86f91f1704434421… Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- Fixing errors Commit: d5dc39ab0f034d79252a9fb0875824cbf8b02e04 https://github.com/galaxyproject/galaxy/commit/d5dc39ab0f034d79252a9fb08758… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: A doc/source/admin/images_webhooks/history-menu.png A doc/source/admin/images_webhooks/masthead.png A doc/source/admin/images_webhooks/masthead_trans_object.png A doc/source/admin/images_webhooks/tool.png A doc/source/admin/images_webhooks/workflow.png M doc/source/admin/webhooks.rst Log Message: ----------- Merge pull request #21 from joachimwolff/feature/plugin-system Feature/plugin system Commit: 0a15289d31a189df71490bba5392726ac0f6db47 https://github.com/galaxyproject/galaxy/commit/0a15289d31a189df71490bba5392… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M config/plugins/webhooks/phdcomics/helper/__init__.py Log Message: ----------- added missing dependencies check Commit: bc51dc3ec72dc7a5bbcc42bcd4f1cc834c1a69b6 https://github.com/galaxyproject/galaxy/commit/bc51dc3ec72dc7a5bbcc42bcd4f1… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- Update webhooks.rst escape missing dependencies Commit: 95d6990cf3f6f1e4ade87b6ba6557c99471ff924 https://github.com/galaxyproject/galaxy/commit/95d6990cf3f6f1e4ade87b6ba655… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- Update webhooks.rst Commit: 4f89528c94d33f1e3eca8df9dd34c06965e7beec https://github.com/galaxyproject/galaxy/commit/4f89528c94d33f1e3eca8df9dd34… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- make activation procedure more clear Commit: 2d915a42f6329bd31dfdc76b5bfa56376a57c841 https://github.com/galaxyproject/galaxy/commit/2d915a42f6329bd31dfdc76b5bfa… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- tense changes Commit: b52d5be75b3f2bf9cae86d4a278689cb614095be https://github.com/galaxyproject/galaxy/commit/b52d5be75b3f2bf9cae86d4a2786… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- Change according to Aysam's review Commit: 290c48b16c54fab54ec35601e04d6877071a78db https://github.com/galaxyproject/galaxy/commit/290c48b16c54fab54ec35601e04d… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- Change according to Aysam's review Commit: a231e240ed1a8002318678dde5979c3febb11770 https://github.com/galaxyproject/galaxy/commit/a231e240ed1a8002318678dde597… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- remove obsolete code Commit: 6a62dbc91a0f2ed282c2cc1e3c4227faed870ace https://github.com/galaxyproject/galaxy/commit/6a62dbc91a0f2ed282c2cc1e3c42… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M .travis.yml M client/galaxy/style/source_material/circle.py M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M doc/parse_gx_xsd.py M doc/source/admin/dependency_resolvers.rst M doc/source/admin/index.rst A doc/source/admin/mulled_containers.rst M lib/galaxy/config.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/__init__.py A lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/conda_util.py A lib/galaxy/tools/deps/container_resolvers/__init__.py A lib/galaxy/tools/deps/container_resolvers/explicit.py A lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py A lib/galaxy/tools/deps/installable.py A lib/galaxy/tools/deps/mulled/__init__.py A lib/galaxy/tools/deps/mulled/_cli.py A lib/galaxy/tools/deps/mulled/invfile.lua A lib/galaxy/tools/deps/mulled/mulled_build.py A lib/galaxy/tools/deps/mulled/mulled_build_channel.py A lib/galaxy/tools/deps/mulled/mulled_build_files.py A lib/galaxy/tools/deps/mulled/mulled_build_tool.py A lib/galaxy/tools/deps/mulled/mulled_search.py A lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/xsd/galaxy.xsd M test/api/helpers.py M test/api/test_api_batch.py M test/api/test_authenticate.py M test/api/test_dataset_collections.py M test/api/test_history_contents.py M test/api/test_page_revisions.py M test/api/test_pages.py M test/api/test_tool_data.py M test/api/test_tools.py M test/api/test_users.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/workflows_format_2/__init__.py M test/api/workflows_format_2/converter.py M test/base/api.py M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/base/test_logging.py M test/base/twilltestcase.py M test/functional/test_data_managers.py M test/functional/test_library_templates.py M test/functional/test_toolbox.py A test/functional/tools/mulled_example_multi_1.xml M test/functional/tools/samples_tool_conf.xml M test/functional/workflow.py M test/integration/test_resolvers.py M test/manual/workflows_scaling.py M test/shed_functional/base/test_db_util.py M test/shed_functional/functional/test_0300_reset_all_metadata.py M test/shed_functional/functional/test_1300_reset_all_metadata.py M test/shed_functional/functional_tests.py M test/unit/jobs/test_runner_local.py Log Message: ----------- Merge branch 'dev' into feature/plugin-system Commit: 8f5b54141dd2b46d3b532915b082c4bd5eeff44c https://github.com/galaxyproject/galaxy/commit/8f5b54141dd2b46d3b532915b082… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- code optimization, thanks Sam Commit: 773d85453f965712cdd8bcc209b9a05897959994 https://github.com/galaxyproject/galaxy/commit/773d85453f965712cdd8bcc209b9… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: A config/plugins/webhooks/demo/history_test1/config/history_test1.yml A config/plugins/webhooks/demo/history_test2/config/history_test2.yml A config/plugins/webhooks/demo/masthead_test/config/masthead_test.yml A config/plugins/webhooks/demo/phdcomics/config/phdcomics.yaml A config/plugins/webhooks/demo/phdcomics/helper/__init__.py A config/plugins/webhooks/demo/phdcomics/static/script.js A config/plugins/webhooks/demo/phdcomics/static/styles.css A config/plugins/webhooks/demo/trans_object/config/trans_object.yaml A config/plugins/webhooks/demo/trans_object/helper/__init__.py A config/plugins/webhooks/demo/xkcd/config/xkcd.yml A config/plugins/webhooks/demo/xkcd/static/script.js A config/plugins/webhooks/demo/xkcd/static/styles.css R config/plugins/webhooks/history_test1/config/history_test1.yml R config/plugins/webhooks/history_test2/config/history_test2.yml R config/plugins/webhooks/masthead_test/config/masthead_test.yml R config/plugins/webhooks/phdcomics/config/phdcomics.yaml R config/plugins/webhooks/phdcomics/helper/__init__.py R config/plugins/webhooks/phdcomics/static/script.js R config/plugins/webhooks/phdcomics/static/styles.css R config/plugins/webhooks/trans_object/config/trans_object.yaml R config/plugins/webhooks/trans_object/helper/__init__.py R config/plugins/webhooks/xkcd/config/xkcd.yml R config/plugins/webhooks/xkcd/static/script.js R config/plugins/webhooks/xkcd/static/styles.css Log Message: ----------- move all plugins into a demo folder Commit: a676d6e8234dd9db59376df7f54633a78e503f86 https://github.com/galaxyproject/galaxy/commit/a676d6e8234dd9db59376df7f546… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/webhooks/__init__.py Log Message: ----------- allow multiple webhook dirs Commit: 6894df3dcb0f308724331bceceff46dba23156a1 https://github.com/galaxyproject/galaxy/commit/6894df3dcb0f308724331bceceff… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M .travis.yml M client/galaxy/scripts/layout/menu.js M client/galaxy/style/source_material/circle.py M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced A config/plugins/webhooks/demo/history_test1/config/history_test1.yml A config/plugins/webhooks/demo/history_test2/config/history_test2.yml A config/plugins/webhooks/demo/masthead_test/config/masthead_test.yml A config/plugins/webhooks/demo/phdcomics/config/phdcomics.yaml A config/plugins/webhooks/demo/phdcomics/helper/__init__.py A config/plugins/webhooks/demo/phdcomics/static/script.js A config/plugins/webhooks/demo/phdcomics/static/styles.css A config/plugins/webhooks/demo/trans_object/config/trans_object.yaml A config/plugins/webhooks/demo/trans_object/helper/__init__.py A config/plugins/webhooks/demo/xkcd/config/xkcd.yml A config/plugins/webhooks/demo/xkcd/static/script.js A config/plugins/webhooks/demo/xkcd/static/styles.css R config/plugins/webhooks/history_test1/config/history_test1.yml R config/plugins/webhooks/history_test2/config/history_test2.yml R config/plugins/webhooks/masthead_test/config/masthead_test.yml R config/plugins/webhooks/phdcomics/config/phdcomics.yaml R config/plugins/webhooks/phdcomics/helper/__init__.py R config/plugins/webhooks/phdcomics/static/script.js R config/plugins/webhooks/phdcomics/static/styles.css R config/plugins/webhooks/trans_object/config/trans_object.yaml R config/plugins/webhooks/trans_object/helper/__init__.py R config/plugins/webhooks/xkcd/config/xkcd.yml R config/plugins/webhooks/xkcd/static/script.js R config/plugins/webhooks/xkcd/static/styles.css M doc/parse_gx_xsd.py M doc/source/admin/dependency_resolvers.rst A doc/source/admin/images_webhooks/history-menu.png A doc/source/admin/images_webhooks/masthead.png A doc/source/admin/images_webhooks/masthead_trans_object.png A doc/source/admin/images_webhooks/tool.png A doc/source/admin/images_webhooks/workflow.png M doc/source/admin/index.rst A doc/source/admin/mulled_containers.rst M doc/source/admin/webhooks.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/__init__.py A lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/conda_util.py A lib/galaxy/tools/deps/container_resolvers/__init__.py A lib/galaxy/tools/deps/container_resolvers/explicit.py A lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py A lib/galaxy/tools/deps/installable.py A lib/galaxy/tools/deps/mulled/__init__.py A lib/galaxy/tools/deps/mulled/_cli.py A lib/galaxy/tools/deps/mulled/invfile.lua A lib/galaxy/tools/deps/mulled/mulled_build.py A lib/galaxy/tools/deps/mulled/mulled_build_channel.py A lib/galaxy/tools/deps/mulled/mulled_build_files.py A lib/galaxy/tools/deps/mulled/mulled_build_tool.py A lib/galaxy/tools/deps/mulled/mulled_search.py A lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webhooks/__init__.py M test/api/helpers.py M test/api/test_api_batch.py M test/api/test_authenticate.py M test/api/test_dataset_collections.py M test/api/test_history_contents.py M test/api/test_page_revisions.py M test/api/test_pages.py M test/api/test_tool_data.py M test/api/test_tools.py M test/api/test_users.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/workflows_format_2/__init__.py M test/api/workflows_format_2/converter.py M test/base/api.py M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/base/test_logging.py M test/base/twilltestcase.py M test/functional/test_data_managers.py M test/functional/test_library_templates.py M test/functional/test_toolbox.py A test/functional/tools/mulled_example_multi_1.xml M test/functional/tools/samples_tool_conf.xml M test/functional/workflow.py M test/integration/test_resolvers.py M test/manual/workflows_scaling.py M test/shed_functional/base/test_db_util.py M test/shed_functional/functional/test_0300_reset_all_metadata.py M test/shed_functional/functional/test_1300_reset_all_metadata.py M test/shed_functional/functional_tests.py M test/unit/jobs/test_runner_local.py Log Message: ----------- Merge branch 'feature/plugin-system' of github.com:bgruening/galaxy into feature/plugin-system Commit: 3f8d45b388e5788b23c39c2b544e4c98eae8018f https://github.com/galaxyproject/galaxy/commit/3f8d45b388e5788b23c39c2b544e… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/webhooks/__init__.py Log Message: ----------- PEP8 Commit: fb516d9387a2df9a1ccdd2c7a1a1ce162f7e52fc https://github.com/galaxyproject/galaxy/commit/fb516d9387a2df9a1ccdd2c7a1a1… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/webhooks/__init__.py Log Message: ----------- remove blank line Commit: e220ed097067124f5ab616d0ece35d0af4cb2539 https://github.com/galaxyproject/galaxy/commit/e220ed097067124f5ab616d0ece3… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/webhooks/__init__.py Log Message: ----------- use config_directories_from_setting Commit: b0b5157f36ec26090c9c11c0a133513083015735 https://github.com/galaxyproject/galaxy/commit/b0b5157f36ec26090c9c11c0a133… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M config/plugins/webhooks/demo/phdcomics/helper/__init__.py Log Message: ----------- merge Commit: f4dc38a54da3539f4d63f7e33708bcc2e33012fb https://github.com/galaxyproject/galaxy/commit/f4dc38a54da3539f4d63f7e33708… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M config/plugins/webhooks/demo/history_test1/config/history_test1.yml M config/plugins/webhooks/demo/history_test2/config/history_test2.yml M config/plugins/webhooks/demo/masthead_test/config/masthead_test.yml M config/plugins/webhooks/demo/phdcomics/config/phdcomics.yaml M config/plugins/webhooks/demo/trans_object/config/trans_object.yaml M config/plugins/webhooks/demo/xkcd/config/xkcd.yml Log Message: ----------- activate all plugins in the demo folder Commit: 2703ba1a0cc3a28314018299b8f1a686dfb6e995 https://github.com/galaxyproject/galaxy/commit/2703ba1a0cc3a28314018299b8f1… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- activate all demo plugins in testing purposes Commit: 8694356ab7057c47164a92f8d4e47a800fca2f4d https://github.com/galaxyproject/galaxy/commit/8694356ab7057c47164a92f8d4e4… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- Adopt help to the latest changes Commit: 3aadd84b80bca7fc588ffccaa27f01c1d599b9d8 https://github.com/galaxyproject/galaxy/commit/3aadd84b80bca7fc588ffccaa27f… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M config/plugins/webhooks/demo/trans_object/helper/__init__.py Log Message: ----------- add case where no user is logged in Commit: 0dc2c95bd07e2a53dec27c8d0d4fc86747aa8878 https://github.com/galaxyproject/galaxy/commit/0dc2c95bd07e2a53dec27c8d0d4f… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- Merge branch 'feature/plugin-system' of https://github.com/bgruening/galaxy into feature/plugin-system Commit: 3cb8189e1fa48c58afaf609691a0801e784484b7 https://github.com/galaxyproject/galaxy/commit/3cb8189e1fa48c58afaf609691a0… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M config/galaxy.ini.sample M lib/galaxy/managers/collections_util.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/metadata.py M lib/galaxy/model/orm/now.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/mulled/_cli.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/mulled_build_tool.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/exception_handling.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/loader.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/parser/__init__.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/schedulers/core.py M test/api/test_workflow_extraction.py M test/api/workflows_format_2/__init__.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/base/driver_util.py A test/functional/tools/multi_data_optional.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools_support.py M test/unit/unittest_utils/utility.py M tools/filters/gff/gff_filter_by_attribute.py M tools/stats/filtering.py Log Message: ----------- Merge branch 'dev' into feature/plugin-system Commit: 37702392817107dfd12cbb54f0af1dcb18bd848e https://github.com/galaxyproject/galaxy/commit/37702392817107dfd12cbb54f0af… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M config/galaxy.ini.sample M config/plugins/webhooks/demo/trans_object/helper/__init__.py M doc/source/admin/webhooks.rst M lib/galaxy/managers/collections_util.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/metadata.py M lib/galaxy/model/orm/now.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/mulled/_cli.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/mulled_build_tool.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/exception_handling.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/loader.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/parser/__init__.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/schedulers/core.py M test/api/test_workflow_extraction.py M test/api/workflows_format_2/__init__.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/base/driver_util.py A test/functional/tools/multi_data_optional.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools_support.py M test/unit/unittest_utils/utility.py M tools/filters/gff/gff_filter_by_attribute.py M tools/stats/filtering.py Log Message: ----------- Merge branch 'feature/plugin-system' of github.com:bgruening/galaxy into feature/plugin-system Commit: bd20ab1aa57381b36e16dc08c20b6b176a7ed724 https://github.com/galaxyproject/galaxy/commit/bd20ab1aa57381b36e16dc08c20b… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M lib/galaxy/webhooks/__init__.py Log Message: ----------- pep8 Commit: 3d4f302c4734e9afc7e065645c915dfd8f37566e https://github.com/galaxyproject/galaxy/commit/3d4f302c4734e9afc7e065645c91… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- change default settings in galaxy.ini.sample Commit: 4bbab51c0500922c9a191d022de295daa48f0dd5 https://github.com/galaxyproject/galaxy/commit/4bbab51c0500922c9a191d022de2… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- Add note about interface stability. Commit: ebaffa2e0d6a030dfc3c78a3b9515093b14f7103 https://github.com/galaxyproject/galaxy/commit/ebaffa2e0d6a030dfc3c78a3b951… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M lib/galaxy/webapps/galaxy/api/webhooks.py Log Message: ----------- fix failing Travis tests #2 (TOX_ENV=py27-lint) and #6 (TOX_ENV=py27-lint-imports) Commit: a6d52cdbdc837c427c0971c6586eb5169a786752 https://github.com/galaxyproject/galaxy/commit/a6d52cdbdc837c427c0971c6586e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-23 (Sun, 23 Oct 2016) Changed paths: M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/webhooks.js M config/galaxy.ini.sample A config/plugins/webhooks/demo/history_test1/config/history_test1.yml A config/plugins/webhooks/demo/history_test2/config/history_test2.yml A config/plugins/webhooks/demo/masthead_test/config/masthead_test.yml A config/plugins/webhooks/demo/phdcomics/config/phdcomics.yaml A config/plugins/webhooks/demo/phdcomics/helper/__init__.py A config/plugins/webhooks/demo/phdcomics/static/script.js A config/plugins/webhooks/demo/phdcomics/static/styles.css A config/plugins/webhooks/demo/trans_object/config/trans_object.yaml A config/plugins/webhooks/demo/trans_object/helper/__init__.py A config/plugins/webhooks/demo/xkcd/config/xkcd.yml A config/plugins/webhooks/demo/xkcd/static/script.js A config/plugins/webhooks/demo/xkcd/static/styles.css A doc/source/admin/images_webhooks/history-menu.png A doc/source/admin/images_webhooks/masthead.png A doc/source/admin/images_webhooks/masthead_trans_object.png A doc/source/admin/images_webhooks/tool.png A doc/source/admin/images_webhooks/workflow.png A doc/source/admin/webhooks.rst M lib/galaxy/app.py M lib/galaxy/config.py A lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py A lib/galaxy/webhooks/__init__.py M static/maps/layout/menu.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form.js.map A static/maps/mvc/tool/tool-webhooks.js.map A static/maps/mvc/webhooks.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/layout/menu.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js A static/scripts/mvc/tool/tool-webhooks.js A static/scripts/mvc/webhooks.js A templates/webapps/galaxy/workflow/run_complete.mako Log Message: ----------- Merge remote-tracking branch 'bgruening/feature/plugin-system' into dev Compare: https://github.com/galaxyproject/galaxy/compare/cfeb0135ac5f...a6d52cdbdc83

1 0

[galaxyproject/galaxy] 91a190: Datasets: allow admin to serialize permissions
by GitHub 21 Oct '16

21 Oct '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 91a190c6eb2f37e041575548bfae85d61b64ce7e https://github.com/galaxyproject/galaxy/commit/91a190c6eb2f37e041575548bfae… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-12 (Mon, 12 Sep 2016) Changed paths: M lib/galaxy/managers/datasets.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Datasets: allow admin to serialize permissions And updates tests. Commit: b88035955d7a81ff43858f092924b60bef1bca9c https://github.com/galaxyproject/galaxy/commit/b88035955d7a81ff43858f092924… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-12 (Mon, 12 Sep 2016) Changed paths: M test/unit/managers/test_DatasetManager.py Log Message: ----------- Datasets: confirm admin ability to set permissions The power was inside you all along. Commit: 8616c0e87c055ed8e41563625498818a76769b2f https://github.com/galaxyproject/galaxy/commit/8616c0e87c055ed8e41563625498… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py Log Message: ----------- Log the resolved dependency type Commit: fc3dcf3b875cbadf75a1eb34ce1395e29dbe0baf https://github.com/galaxyproject/galaxy/commit/fc3dcf3b875cbadf75a1eb34ce13… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M lib/galaxy/managers/datasets.py M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Permissions, datasets: allow admin in RBAC - Admin are considered permitted when calling ** dataset_manager.permssions.access and ** dataset_manager.permissions.manage - Update bad test - Add admin test to other permission checks Commit: 9636ea1b6cb1283ef9e5d8cb210a962eff45bbef https://github.com/galaxyproject/galaxy/commit/9636ea1b6cb1283ef9e5d8cb210a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M test/unit/managers/test_DatasetManager.py Log Message: ----------- Datasets: test for anon access/manage Commit: e7cb0ac2a19f0141336285fdd8fcf9aeb32221f2 https://github.com/galaxyproject/galaxy/commit/e7cb0ac2a19f0141336285fdd8fc… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M test/unit/managers/test_DatasetManager.py Log Message: ----------- Datasets: test for anon deserialization Commit: b301fd42021245f5c3c7291207510659aa66b5ac https://github.com/galaxyproject/galaxy/commit/b301fd42021245f5c3c729120751… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M lib/galaxy/managers/rbac_secured.py Log Message: ----------- Dataset perms: correct comment Commit: 8bf7256ca8ec61a167bca1dcaafa0b83cf12fa5a https://github.com/galaxyproject/galaxy/commit/8bf7256ca8ec61a167bca1dcaafa… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge pull request #2912 from carlfeberhard/dataset.admin-permissions [16.01] Allow admin to serialize/deserialize dataset permissions Commit: b50d07d5bf128ee280eb823f9b2b5677e549b5e5 https://github.com/galaxyproject/galaxy/commit/b50d07d5bf128ee280eb823f9b2b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.01' into release_16.04 Commit: e5f4f2fab6ce44b4e98f1dc54bea138d1185aa85 https://github.com/galaxyproject/galaxy/commit/e5f4f2fab6ce44b4e98f1dc54bea… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.04' into release_16.07 Commit: 646428d73f9cbcd312ed3ff5eff8e36ee12f213e https://github.com/galaxyproject/galaxy/commit/646428d73f9cbcd312ed3ff5eff8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Remove change handler for data and collection multiinput selectors in old run workflow form Commit: b399c086254f35d8536c1afa9fd7a2e50ec339a9 https://github.com/galaxyproject/galaxy/commit/b399c086254f35d8536c1afa9fd7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py Log Message: ----------- Merge pull request #2918 from martenson/pick-dep-log [16.07] cherry pick logging the resolved dependency type Commit: 67a3cf34ca0e639791ac88e849d120dce355d3ef https://github.com/galaxyproject/galaxy/commit/67a3cf34ca0e639791ac88e849d1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #2920 from guerler/fix_collection_refresh [16.07] Prevent refresh for collection selector in old run workflow form Commit: dc5aff7e44e2b0f767b7578935d46db7d7707066 https://github.com/galaxyproject/galaxy/commit/dc5aff7e44e2b0f767b7578935d4… Author: Anthony Bretaudeau <abretaud(a)irisa.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Update python-ldap module Updating to the same version as galaxyproject/starforge#97 Commit: c497ea534897b4c1875186961e96da52129c4a3a https://github.com/galaxyproject/galaxy/commit/c497ea534897b4c1875186961e96… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-09-16 (Fri, 16 Sep 2016) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Merge pull request #2924 from nsoranzo/release_16.07_backport_2738 [16.07] Update python-ldap module Commit: 1f53c32ad68235537d8f6c843d1cd81eda5c11c3 https://github.com/galaxyproject/galaxy/commit/1f53c32ad68235537d8f6c843d1c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-09-19 (Mon, 19 Sep 2016) Changed paths: A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py Log Message: ----------- Add missing tabular_to_dbnsfp.py for dbnsfp.tabular to snpsiftdbnsfp conversion This should have been added in https://bitbucket.org/galaxy/galaxy-central/pull-requests/640/ Actual source code comes from https://github.com/galaxyproject/tools-iuc/blob/master/datatypes/snpsift_db… Commit: b748250193a26ddce4010759b9a22d012d281b81 https://github.com/galaxyproject/galaxy/commit/b748250193a26ddce4010759b9a2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py Log Message: ----------- Merge pull request #2938 from nsoranzo/release_16.04_tabular_to_dbnsfp [16.04] Add missing tabular_to_dbnsfp.py for dbnsfp.tabular to snpsiftdbnsfp conversion Commit: 7627abb3856a4e757b5ed5c55ec05a4f97bd4cac https://github.com/galaxyproject/galaxy/commit/7627abb3856a4e757b5ed5c55ec0… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Commit: 8b3356b869beba70820235c2d0894cee9e590ffe https://github.com/galaxyproject/galaxy/commit/8b3356b869beba70820235c2d089… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Strip stderr message from sacct Commit: 34d60e2b27ab08a3ebc5201d1c3282d346d40af0 https://github.com/galaxyproject/galaxy/commit/34d60e2b27ab08a3ebc5201d1c32… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2945 from nsoranzo/release_16.07_strip_stderr [16.07] Strip stderr message from sacct Commit: b83f0a10247119ef18bf72688d4e0bb8cfee8e36 https://github.com/galaxyproject/galaxy/commit/b83f0a10247119ef18bf72688d4e… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- Fix whoosh indexing. Commit: d7ab1c5cfbfcdff3ce3e201f6fb0684fdb914096 https://github.com/galaxyproject/galaxy/commit/d7ab1c5cfbfcdff3ce3e201f6fb0… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-modal.js M static/maps/mvc/ui/ui-modal.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-modal.js Log Message: ----------- UI, Modal: re-build dom on render Moves templating to render (and updates dom node attributes after) to reset modal and prevent inline styling and other modifications to the singleton from persisting between calls to show. Commit: c0e8a7608351679b8ebdb71207339384161d6616 https://github.com/galaxyproject/galaxy/commit/c0e8a7608351679b8ebdb7120733… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/metadata_util.py Log Message: ----------- [16.07] Fix tool dependencies handling in Tool Shed model (#2950) * Fix the cause of toolshed test 1400 failing. * Fix handling of repositories without tool dependencies. * Fix tool dependency retrieval. In some cases, a process might attempt to fetch tool dependencies for revision 1:7334f6d0ac17, but the repository has been updated, and tool dependency metadata has been reassigned to e.g. 7:ce22ceec214a. This commit resolves that issue. * Correct the logic that returns an empty string for an empty dict. * Fix getting latest revision with tool dependencies. * Use self.app instead of trans.app Commit: 9b3c061addb4f3e61d72465cf492396b9e07464e https://github.com/galaxyproject/galaxy/commit/9b3c061addb4f3e61d72465cf492… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/metadata_util.py Log Message: ----------- [16.07] Fix tool dependencies handling in Tool Shed model (#2950) * Fix the cause of toolshed test 1400 failing. * Fix handling of repositories without tool dependencies. * Fix tool dependency retrieval. In some cases, a process might attempt to fetch tool dependencies for revision 1:7334f6d0ac17, but the repository has been updated, and tool dependency metadata has been reassigned to e.g. 7:ce22ceec214a. This commit resolves that issue. * Correct the logic that returns an empty string for an empty dict. * Fix getting latest revision with tool dependencies. * Use self.app instead of trans.app Conflicts: lib/galaxy/webapps/tool_shed/controllers/repository.py Commit: a78b8bcd2aa02abf787f0974fe567ab4f70f41a1 https://github.com/galaxyproject/galaxy/commit/a78b8bcd2aa02abf787f0974fe56… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge branch 'release_16.04' of https://github.com/galaxyproject/galaxy into release_16.04 Commit: e18d4ed33b8b453229f969f2d05c997b2fa7fe96 https://github.com/galaxyproject/galaxy/commit/e18d4ed33b8b453229f969f2d05c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- UI, datasets: fix optional column form values Updates metadata column checkbox flag from 'true' to '__NOTHING__' to reflect newer form_builder values. Fixes #2175 Commit: aa2e7834f697f02ebf11545b53882baee8b87f4e https://github.com/galaxyproject/galaxy/commit/aa2e7834f697f02ebf11545b5388… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Fix optional flag for library datasets in legacy library ui Commit: c06f8c29968971c6c1e0dfc6847b3baf755f3a96 https://github.com/galaxyproject/galaxy/commit/c06f8c29968971c6c1e0dfc6847b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M lib/galaxy/webapps/tool_shed/model/__init__.py Log Message: ----------- correct the method call Commit: 5e7ee28e0d6937fa53f39b350e04357b554ce9ae https://github.com/galaxyproject/galaxy/commit/5e7ee28e0d6937fa53f39b350e04… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M test/shed_functional/functional/test_1400_review_migration_stages.py Log Message: ----------- bump freebayes in test (since it was updated) Commit: 45e6949eeae88c0d3c4c3f6341ddc5695d329bb2 https://github.com/galaxyproject/galaxy/commit/45e6949eeae88c0d3c4c3f6341dd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/metadata_util.py M test/shed_functional/functional/test_1400_review_migration_stages.py Log Message: ----------- Merge pull request #2959 from martenson/release_16.04 [16.04] backport of model tool dependencies fix Commit: 2c8a5d9d58c49c662aed4193f71caaf3fafe5651 https://github.com/galaxyproject/galaxy/commit/2c8a5d9d58c49c662aed4193f71c… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- Correct import order. Commit: 3b3e2e3358aa73a5374345686581310d37349ff9 https://github.com/galaxyproject/galaxy/commit/3b3e2e3358aa73a5374345686581… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M test/shed_functional/functional/test_1400_review_migration_stages.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Conflicts: lib/galaxy/webapps/tool_shed/controllers/repository.py lib/galaxy/webapps/tool_shed/model/__init__.py Commit: 092a7307c21afa8d66129dca23567b49a540d66a https://github.com/galaxyproject/galaxy/commit/092a7307c21afa8d66129dca2356… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- Merge pull request #2949 from davebx/backport_whoosh [16.07] Fix missing import in whoosh indexing script Commit: 26d381c9a5d77ecfa6bf3e96b2cb77df3d3f846d https://github.com/galaxyproject/galaxy/commit/26d381c9a5d77ecfa6bf3e96b2cb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-24 (Sat, 24 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Merge pull request #2962 from guerler/fix_library_optional_flag [16.07] Fix optional flag for library datasets in legacy library ui Commit: e667f9f360388839d723421b884836acb6974e6c https://github.com/galaxyproject/galaxy/commit/e667f9f360388839d723421b8848… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-25 (Sun, 25 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Merge pull request #2960 from carlfeberhard/fix.bed-columns [16.07] UI, datasets: fix optional column form values Commit: 04d62e242412d0eb6e739f3577256d99b1aaa5bf https://github.com/galaxyproject/galaxy/commit/04d62e242412d0eb6e739f357725… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-modal.js M static/maps/mvc/ui/ui-modal.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-modal.js Log Message: ----------- Merge pull request #2955 from carlfeberhard/fix.modal-resetting [16.07] UI, Modal: re-build dom on render Commit: 375ed8cc81590a18a52b61e32307562488fd551e https://github.com/galaxyproject/galaxy/commit/375ed8cc81590a18a52b61e32307… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- polish resolvers section in conda faq docs Commit: ba274e37f2f0e8c9973b19c46fe99c5565c5118c https://github.com/galaxyproject/galaxy/commit/ba274e37f2f0e8c9973b19c46fe9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- describe the conda installation behavior a bit better Commit: 2899372791fdbba4f8db7c414a5447cf049987f3 https://github.com/galaxyproject/galaxy/commit/2899372791fdbba4f8db7c414a54… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Update conda_faq.rst Commit: fdfe9d8c20a63e6e6e6951d5fe5cbd7d74446d0a https://github.com/galaxyproject/galaxy/commit/fdfe9d8c20a63e6e6e6951d5fe5c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Merge pull request #19 from martenson/nsoranzo-patch-1-1 Small fixes to conda_faq.rst changes Commit: d9fab3345856770a16a98f18cf9e6185a4eae91a https://github.com/galaxyproject/galaxy/commit/d9fab3345856770a16a98f18cf9e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Merge pull request #2998 from martenson/conda-faq-polish [16.07] Conda FAQ polish Commit: 1e8337df5a4acf9e899adc07883f967973cbcac7 https://github.com/galaxyproject/galaxy/commit/1e8337df5a4acf9e899adc07883f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Fix setting conda_copy_dependencies in galaxy.ini. (cherry picked from commit 9246b8629c3831ab623983c9003c4e92cbde97d5) Commit: 6d27a3c4b6184b393e535afd32f87e55e7a07b70 https://github.com/galaxyproject/galaxy/commit/6d27a3c4b6184b393e535afd32f8… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Fix initial conda version at 4.0.5 This should prevent missing `activate` in <conda_prefix>/bin when downgrading to 3.19.3. This is what the conda people use in their CI environment ( [see](https://github.com/conda/conda/blob/master/utils/travis-run-install.sh… and perhaps why that bug made it into the release in the first place). Commit: f7c3e25e5db1a1d99c81380f552719bee07c1790 https://github.com/galaxyproject/galaxy/commit/f7c3e25e5db1a1d99c81380f5527… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #3009 from mvdbeek/conda_downgrade [16.01] Backport #2869 Fix initial conda version at 4.0.5 Commit: 224c2126c73617ec906abc1e08d5f5a7548633b1 https://github.com/galaxyproject/galaxy/commit/224c2126c73617ec906abc1e08d5… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Commit: d6845c249466d013b58ab021540fc5176096aaa0 https://github.com/galaxyproject/galaxy/commit/d6845c249466d013b58ab021540f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Commit: f32b6446a7a4fd5a0bca2fa8e93d4407e0ce3938 https://github.com/galaxyproject/galaxy/commit/f32b6446a7a4fd5a0bca2fa8e93d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge pull request #3008 from natefoo/conda-copy-dependencies [16.07] Fix setting conda_copy_dependencies in galaxy.ini. Commit: 89278b0ec70b7a8f1cf42bda87335cf4f98f175b https://github.com/galaxyproject/galaxy/commit/89278b0ec70b7a8f1cf42bda8733… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix for bioconda recipes depending on conda-forge. Some bioconda recipes now depend on conda forge, this fix is needed for them to work properly. Commit: ddacf38a11a9f752b3cfe13a8b63182ff1d02d06 https://github.com/galaxyproject/galaxy/commit/ddacf38a11a9f752b3cfe13a8b63… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3023 from jmchilton/fix_abyss [16.07] Fix for bioconda recipes depending on conda-forge. Commit: 39fb030f13c45991d4a2ca811b66e7872fb0a4e7 https://github.com/galaxyproject/galaxy/commit/39fb030f13c45991d4a2ca811b66… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M .travis.yml Log Message: ----------- Remove travis-ci python installation, since python2.7 is preinstalled on OSX images now Commit: 2adb98e58cc0f1d0d25aecc260d7108902d4b02c https://github.com/galaxyproject/galaxy/commit/2adb98e58cc0f1d0d25aecc260d7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M .travis.yml Log Message: ----------- Merge pull request #3034 from mvdbeek/skip_python_install_travis [16.04] Remove travis-ci python installation, since python2.7 is preinstalled… Commit: 3300a73c9db6b99cbec6ae952e3e59f8a72e651b https://github.com/galaxyproject/galaxy/commit/3300a73c9db6b99cbec6ae952e3e… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Commit: 600112256970c1024b3ba4e6fa57cd61f9fe199d https://github.com/galaxyproject/galaxy/commit/600112256970c1024b3ba4e6fa57… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M templates/user/index.mako Log Message: ----------- remove the communication server check from non-galaxy calls Commit: cf0e4e84ce4137334ee6e8c20e56a52070179c4d https://github.com/galaxyproject/galaxy/commit/cf0e4e84ce4137334ee6e8c20e56… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M templates/user/index.mako Log Message: ----------- Merge pull request #3053 from martenson/fix-userindex-for-ts [16.07] remove the communication server check Commit: d10758a4f22daa24bdf55863f360493a4a3902f7 https://github.com/galaxyproject/galaxy/commit/d10758a4f22daa24bdf55863f360… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-21 (Fri, 21 Oct 2016) Changed paths: M .travis.yml M client/galaxy/scripts/mvc/ui/ui-modal.js M config/galaxy.ini.sample M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/metadata_util.py M scripts/tool_shed/build_ts_whoosh_index.py M static/maps/mvc/ui/ui-modal.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-modal.js M templates/user/index.mako M templates/webapps/galaxy/workflow/run.mako M test/shed_functional/functional/test_1400_review_migration_stages.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge pull request #3077 from galaxyproject/release_16.07 [master] bring master on par with release_16.07 Compare: https://github.com/galaxyproject/galaxy/compare/e320b1aaa70a...d10758a4f22d

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