Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 75a3aecbbeddf7124ab9e6d7b885bdd28765e0e0 https://github.com/galaxyproject/galaxy/commit/75a3aecbbeddf7124ab9e6d7b885b... Author: John Chilton <jmchilton@gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/utils/utils.js M config/plugins/visualizations/charts/static/app.css M config/plugins/visualizations/charts/static/app.js R config/plugins/visualizations/charts/static/charts/forms/default.js M config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js M config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js M config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js M config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/config.js M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/line/config.js M config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/scatter/config.js M config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/bar/config.js M config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/config.js M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/config.js M 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config/plugins/visualizations/charts/static/charts/others/example/logo.png A config/plugins/visualizations/charts/static/charts/others/example/wrapper.js M config/plugins/visualizations/charts/static/charts/others/heatmap/config.js M config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-parameters.js M config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js M config/plugins/visualizations/charts/static/charts/others/heatmap/wrapper.js M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/config.js M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js A config/plugins/visualizations/charts/static/charts/overview.js R config/plugins/visualizations/charts/static/charts/tools.js M config/plugins/visualizations/charts/static/charts/types.js A config/plugins/visualizations/charts/static/charts/utilities/tabular-datasets.js A 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config/plugins/visualizations/charts/static/views/editor.js M 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 M config/plugins/visualizations/charts/templates/charts.mako M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-color-picker.js.map M static/maps/mvc/ui/ui-tabs.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/ui/ui-tabs.js M static/scripts/utils/utils.js Log Message: ----------- Merge pull request #2820 from guerler/charts_revision Charts revision, part 2 Commit: e8eb48a9c42de08edd6e9a4ea529bcac0d698df9 https://github.com/galaxyproject/galaxy/commit/e8eb48a9c42de08edd6e9a4ea529b... Author: guerler <aysam.guerler@gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Remove unused app variable Commit: f9758f2871e3b21b25d76f7b62bcc2aae99b9249 https://github.com/galaxyproject/galaxy/commit/f9758f2871e3b21b25d76f7b62bcc... Author: John Chilton <jmchilton@gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #2858 from martenson/rn_tweaks alter release notes template Commit: f98ade125f0fbe5d90ca0f005a84f8f7d91fb3d5 https://github.com/galaxyproject/galaxy/commit/f98ade125f0fbe5d90ca0f005a84f... Author: guerler <aysam.guerler@gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/biojs/msa/config.js Log Message: ----------- Add basic description for msa viewer Commit: c4e9ecfe4c9dec4f9c58597fc755a4c4ab944a83 https://github.com/galaxyproject/galaxy/commit/c4e9ecfe4c9dec4f9c58597fc755a... Author: guerler <aysam.guerler@gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/biojs/msa/config.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js M config/plugins/visualizations/charts/static/charts/others/example/config.js M config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js M config/plugins/visualizations/charts/static/views/types.js Log Message: ----------- Allow multiple datatype matching Commit: edfdef2853e2df3f5058d97e1578c4129fb292de https://github.com/galaxyproject/galaxy/commit/edfdef2853e2df3f5058d97e1578c... Author: guerler <aysam.guerler@gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js M static/maps/mvc/ui/ui-buttons.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/ui/ui-buttons.js Log Message: ----------- Enhance ui menu button view Commit: 633f958e1b6f2179264cdad06d9cda8cc13d0e93 https://github.com/galaxyproject/galaxy/commit/633f958e1b6f2179264cdad06d9cd... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Open tool executions in a different tab from admin/tool_lineage, instead of loading galaxy(whole) within the tab Commit: 72f89a4c262de328d398ebbb4c6ccfefc483b75d https://github.com/galaxyproject/galaxy/commit/72f89a4c262de328d398ebbb4c6cc... Author: guerler <aysam.guerler@gmail.com> Date: 2016-08-26 (Fri, 26 Aug 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: ----------- Fix requirements message Commit: ed76484af2ba5d86a9cfee82118f74dde70f21ae https://github.com/galaxyproject/galaxy/commit/ed76484af2ba5d86a9cfee82118f7... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix toolbox's get_tool 'exact' matching. Previously it'd return a tool even when exact was specified, though no exact match was made (so, exact=False behavior, always) Commit: c53585e8b5227e9d9f3536fa1434ae74acc0ef68 https://github.com/galaxyproject/galaxy/commit/c53585e8b5227e9d9f3536fa1434a... Author: zipho <zipho.m@gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M tools/data_source/upload.py Log Message: ----------- added cProfile Commit: d14b43abf2694ce3ef6933a9bede181ff1d7f79d https://github.com/galaxyproject/galaxy/commit/d14b43abf2694ce3ef6933a9bede1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Probably still want to match identical tool guids against multiple sheds? Commit: 66e3f8540f4dff918a90c2d02eca4a3f46f7fbdd https://github.com/galaxyproject/galaxy/commit/66e3f8540f4dff918a90c2d02eca4... Author: zipho <zipho.m@gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M tools/data_source/upload.py Log Message: ----------- removed traces of cProfile and use Commit: d6639bee403a8cc79df647a21b79e905c3b6474d https://github.com/galaxyproject/galaxy/commit/d6639bee403a8cc79df647a21b79e... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- encourage wittiness in release notes Commit: 4ad0bee5523b1a05423eaa21624ebe146412d423 https://github.com/galaxyproject/galaxy/commit/4ad0bee5523b1a05423eaa21624eb... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M doc/source/releases/16.07.rst 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' into dev Commit: c29f481dceeaaa790be1d8fdadfd58f1cb2d68c6 https://github.com/galaxyproject/galaxy/commit/c29f481dceeaaa790be1d8fdadfd5... Author: takadonet <philipmabon@gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/append_collection.xml Log Message: ----------- initial version of append collection tool. Allow's user to add one or more datasets to an existing collection. Provides options when we have name conflicts Commit: b97ddd7ea52da1215c8251029f632cc972c6dba3 https://github.com/galaxyproject/galaxy/commit/b97ddd7ea52da1215c8251029f632... Author: takadonet <philipmabon@gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M .ci/first_startup.sh M .ci/flake8_lint_include_list.txt M Makefile M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/form/form-data.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/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/library.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/plugins/visualizations/charts/static/app.css M config/plugins/visualizations/charts/static/app.js R config/plugins/visualizations/charts/static/charts/forms/default.js M config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js M 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doc/source/admin/communication_server.png A doc/source/admin/communication_server_rooms.png A doc/source/admin/conda_faq.rst M doc/source/admin/index.rst A doc/source/dev/build_a_job_runner.rst A doc/source/releases/16.07.rst M doc/source/releases/16.07_announce.rst A doc/source/releases/16.10_announce.rst M lib/galaxy/app.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/triples.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/managers/datasets.py M lib/galaxy/model/__init__.py M lib/galaxy/model/migrate/check.py M lib/galaxy/queues.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/__init__.py A lib/galaxy/util/postfork.py M lib/galaxy/util/template.py M lib/galaxy/web/framework/base.py A lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/proxy/js/lib/main.js M lib/galaxy/web/proxy/js/lib/proxy.js M lib/galaxy/web/proxy/js/package.json M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/hg.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/workflow/modules.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/galaxy_install/update_repository_manager.py M run.sh M scripts/bootstrap_history.py M scripts/common_startup.sh M static/maps/mvc/dataset/data.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/ui/ui-color-picker.js.map M static/maps/mvc/ui/ui-tabs.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/data.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/ui/ui-tabs.js M static/scripts/utils/utils.js M static/style/blue/base.css M static/style/blue/library.css M templates/webapps/galaxy/workflow/run.mako M templates/webapps/tool_shed/index.mako A test/api/test_api_batch.py M test/base/interactor.py A test/casperjs/api-batch-tests.js A test/functional/tools/dbkey_output_action.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_1.xml A test/functional/tools/tool_provided_metadata_2.xml A test/functional/tools/tool_provided_metadata_3.xml M test/qunit/test-data/fakeserver.js M test/qunit/tests/form_tests.js M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into collection_tools Commit: 5159f878cfbdaa2627be76db1d69741b3579b68f https://github.com/galaxyproject/galaxy/commit/5159f878cfbdaa2627be76db1d697... Author: takadonet <philipmabon@gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M lib/galaxy/tools/append_collection.xml Log Message: ----------- change tool description Commit: b1f4a0f61aeb8ddfec26c4b51bf92bdd50606c91 https://github.com/galaxyproject/galaxy/commit/b1f4a0f61aeb8ddfec26c4b51bf92... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-29 (Mon, 29 Aug 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#L61) and perhaps why that bug made it into the release in the first place). Commit: f6c1aa0770508c552f074771078a4b7cc4cce400 https://github.com/galaxyproject/galaxy/commit/f6c1aa0770508c552f074771078a4... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M templates/webapps/galaxy/workflow/display.mako Log Message: ----------- Create a new trans method for getting the most recently touched history. Swap several uses of get_history (with create=True, only), to use this new functionality where it makes sense. Commit: f88e8a19fa270615bdfe482ca4f2d1175f56d10b https://github.com/galaxyproject/galaxy/commit/f88e8a19fa270615bdfe482ca4f2d... Author: takadonet <philipmabon@gmail.com> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M lib/galaxy/tools/append_collection.xml Log Message: ----------- changed tool name and description Commit: f54bf1bb3b0afc28d948a511001895abcaf8b15f https://github.com/galaxyproject/galaxy/commit/f54bf1bb3b0afc28d948a51100189... Author: takadonet <philipmabon@gmail.com> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/filter_failed_collection.xml Log Message: ----------- Now allow filter_failed_collection to accept and filter out list:paired collection Commit: 97ba98037992a577a9a1a6b844893f63a7339034 https://github.com/galaxyproject/galaxy/commit/97ba98037992a577a9a1a6b844893... Author: takadonet <philipmabon@gmail.com> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- now change to see if the element has dataset_instance before attempting to call it. Commit: 4729565dfdc32482b177e3e2740f8abcbc23ab0f https://github.com/galaxyproject/galaxy/commit/4729565dfdc32482b177e3e2740f8... Author: takadonet <philipmabon@gmail.com> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- added AppendCollectionTool to list of tool_classes Commit: 9ff882944ee1fd78b6244dad5893ac7390eb76fa https://github.com/galaxyproject/galaxy/commit/9ff882944ee1fd78b6244dad5893a... Author: anatskiy <evgeny.anatskiy@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/d2ec87548a22273a2e0d94bbe1b41... Author: anatskiy <evgeny.anatskiy@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: d86ee3706089e59868c16a3352ce61e0257dbb40 https://github.com/galaxyproject/galaxy/commit/d86ee3706089e59868c16a3352ce6... Author: Rémi Marenco <remi.marenco@gmail.com> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Add the <conda_prefix> in 12. and fix typo I am adding the ``<conda_prefix>/envs`` to check for the package to have been properly installed (if people have brought their own Conda). And fixing ``conda_prefix`` to stay consistent in the doc (``<conda_prefix>``). Commit: 040dd33980668ecb74a44dfc9c4e39e1a1339cef https://github.com/galaxyproject/galaxy/commit/040dd33980668ecb74a44dfc9c4e3... Author: Rémi Marenco <remi.marenco@gmail.com> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M doc/source/admin/chat.rst Log Message: ----------- Fix typo Commit: dbde38c951cdbb539def102ca55ddf5a4da3ced2 https://github.com/galaxyproject/galaxy/commit/dbde38c951cdbb539def102ca55dd... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M doc/source/admin/chat.rst Log Message: ----------- Merge pull request #2872 from remimarenco/patch-9 Fix typo Commit: 569ceb4405bef72c420c91c86f4c203f6d7ed29f https://github.com/galaxyproject/galaxy/commit/569ceb4405bef72c420c91c86f4c2... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- Try reloading tool via control_task Commit: 1223c420cb48ef05db61303ef784ff276716cdc3 https://github.com/galaxyproject/galaxy/commit/1223c420cb48ef05db61303ef784f... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Explicitly monitor shed_tool_conf for changes Commit: 1d04755fa39657bb824ca986e41224e77d59d35f https://github.com/galaxyproject/galaxy/commit/1d04755fa39657bb824ca986e4122... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Reference app instead of self when reloading toolbox Commit: 6e4897dee7d66587d75b445f9211b51f07490241 https://github.com/galaxyproject/galaxy/commit/6e4897dee7d66587d75b445f9211b... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py Log Message: ----------- Do not load individual new toolpanel elements (We rely on the tool watcher to reload the toolbox) Commit: f7693802ce0d2e555cb283a09d0a83740e8664e2 https://github.com/galaxyproject/galaxy/commit/f7693802ce0d2e555cb283a09d0a8... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py Log Message: ----------- Remove in-memory removal of tools (rely on toolbox reload) Commit: 7b259fb10a5f1289ba81ec749a1e86ccf3fb7303 https://github.com/galaxyproject/galaxy/commit/7b259fb10a5f1289ba81ec749a1e8... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Remove one more unused panel manipulation function Commit: 128ee9b72a6c7f693a990c65b1c4b34d9be193c5 https://github.com/galaxyproject/galaxy/commit/128ee9b72a6c7f693a990c65b1c4b... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py Log Message: ----------- Remove unused variable Commit: 81bf7b382bc1003c0d1a3b0a019ea7e57d6ecce9 https://github.com/galaxyproject/galaxy/commit/81bf7b382bc1003c0d1a3b0a019ea... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M test/unit/tools/test_watcher.py Log Message: ----------- Start conf_watcher thread in unit tests Commit: e340fd4e06f7b8a2063448bad8e2c594af39cdb9 https://github.com/galaxyproject/galaxy/commit/e340fd4e06f7b8a2063448bad8e2c... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M test/unit/tools/test_watcher.py Log Message: ----------- Wait before triggering a callback in test_watcher.py Commit: 3206421b91a305d1e38672a1bccd52c732705266 https://github.com/galaxyproject/galaxy/commit/3206421b91a305d1e38672a1bccd5... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Remove update_shed_conf test We do not update the toolbox in memory, so this test is obsolete Commit: fe158de11109140b22c408cd6640b547ffd4db30 https://github.com/galaxyproject/galaxy/commit/fe158de11109140b22c408cd6640b... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_toolbox.py Log Message: ----------- Remove panel_manager tests for deactivated tools Deactivate tests that rely on deactivating, but not removing entries from tool_conf. For tests that test changes in tool_panel, load a new toolbox after making the changes. Commit: ad86e2c7840fa9129263fdfb144959c158653874 https://github.com/galaxyproject/galaxy/commit/ad86e2c7840fa9129263fdfb14495... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_1060_install_repository_with_workflow.py Log Message: ----------- Add sleep to allow toolbox to finish loading Commit: ded1db8b3834bf3de6897b2163a9d208828d259d https://github.com/galaxyproject/galaxy/commit/ded1db8b3834bf3de6897b2163a9d... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py M test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py Log Message: ----------- Remove test for deactivated tools and sections These are tests that verify that deactivated tools were present in the correct tool panel section. Commit: 579ea41085501139eebbbeb5b3f72c9c04c03e4c https://github.com/galaxyproject/galaxy/commit/579ea41085501139eebbbeb5b3f72... Author: Rémi Marenco <remi.marenco@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Update Marius advice Commit: e6450369730230bc844db67d3df05f1cffd3cdad https://github.com/galaxyproject/galaxy/commit/e6450369730230bc844db67d3df05... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Merge pull request #2871 from remimarenco/patch-8 Add the <conda_prefix> in 12. and fix typo Commit: 0bd1ea108e7f6000759583afd3e6d2d7daa3e7be https://github.com/galaxyproject/galaxy/commit/0bd1ea108e7f6000759583afd3e6d... Author: John Chilton <jmchilton@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M templates/webapps/galaxy/workflow/display.mako Log Message: ----------- Merge pull request #2870 from dannon/histories.most_recent_v_default Create a new trans method for getting the most recently touched history. Commit: ba6a0a36476cd5db46777e99b84b6440ec6073b0 https://github.com/galaxyproject/galaxy/commit/ba6a0a36476cd5db46777e99b84b6... Author: John Chilton <jmchilton@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #2869 from mvdbeek/upgrade_conda_instead_of_downgrading Fix initial conda version at 4.0.5 Commit: 19a09e18a84a860d60e66517b3b68b58628843c7 https://github.com/galaxyproject/galaxy/commit/19a09e18a84a860d60e66517b3b68... Author: takadonet <philipmabon@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py R lib/galaxy/tools/append_collection.xml Log Message: ----------- removed append_collection tool due to John request. MergeCollection should cover all cases that append would have anyway. Commit: 59852d0e0f4897b09a964091d5792458de48deb0 https://github.com/galaxyproject/galaxy/commit/59852d0e0f4897b09a964091d5792... 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config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.cursor.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.enhancedLegendRenderer.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.highlighter.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.ohlcRenderer.min.js R config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.css R config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.js M config/plugins/visualizations/charts/static/views/description.js M config/plugins/visualizations/charts/static/views/types.js M config/plugins/visualizations/charts/static/views/viewport.js M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Use remote repo for chart plugins Commit: 54e589ebad000535c384850df7abe6c195fbe5f5 https://github.com/galaxyproject/galaxy/commit/54e589ebad000535c384850df7abe... Author: John Chilton <jmchilton@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py R templates/admin/tool_shed_repository/browse_categories.mako A templates/admin/tool_shed_repository/browse_toolsheds.mako R templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Merge pull request #2769 from davebx/api_install_performance Cleanup of and performance enhancements to the API installation of repositories. Commit: af45adb7e6e57d4180b49581c5f48274df54117f https://github.com/galaxyproject/galaxy/commit/af45adb7e6e57d4180b49581c5f48... Author: guerler <aysam.guerler@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/views/types.js M config/plugins/visualizations/charts/static/views/viewport.js M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Add error message if charts fails to retrieve plugin resources from its repository Commit: 3e7302fc3c6d8f0713d8698f6536662fc46f42b0 https://github.com/galaxyproject/galaxy/commit/3e7302fc3c6d8f0713d8698f65366... Author: guerler <aysam.guerler@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/viewport.js Log Message: ----------- Fix remote url Commit: 5ebdefe40f1d816339c21f553cbe67365a9d7285 https://github.com/galaxyproject/galaxy/commit/5ebdefe40f1d816339c21f553cbe6... Author: John Chilton <jmchilton@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Merge pull request #2862 from dannon/fix_lineage_onclick Open tool executions in a different tab from admin/tool_lineage, inst… Commit: ecc415369ff50dce02f5db73bdaf6fe8e60b6020 https://github.com/galaxyproject/galaxy/commit/ecc415369ff50dce02f5db73bdaf6... Author: takadonet <philipmabon@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/merge_collection.xml Log Message: ----------- added support to merge two list:paired collection together. Added single test to reflect new changes. Commit: 693eb5d0c91061fdbe052b41be1e78f4c58f57cb https://github.com/galaxyproject/galaxy/commit/693eb5d0c91061fdbe052b41be1e7... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_1060_install_repository_with_workflow.py Log Message: ----------- Wait 2 seconds after touch shed_tool_conf.xml The file watcher monitors for changes every second, so 2 seconds should be enough to let tests that check the tool panel after installing new tools pass. Commit: 2fb4045abd61b9ccb1afb4e5e422ad6e73167db8 https://github.com/galaxyproject/galaxy/commit/2fb4045abd61b9ccb1afb4e5e422a... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Also reload data managers upon touching data_manager.conf Commit: f6fc5ed44299f2d1a9ac1c966d43281fd9515bf0 https://github.com/galaxyproject/galaxy/commit/f6fc5ed44299f2d1a9ac1c966d432... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Shut down old data manager watchers Commit: abd4fa611a3f1d4d089a03aef48ecb43383bb101 https://github.com/galaxyproject/galaxy/commit/abd4fa611a3f1d4d089a03aef48ec... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/hash_util.py Log Message: ----------- Implement hashing for tool conf watcher If modification time of watched files changes, only trigger event if hashes differ as well Commit: 49ab74827cd0905cd0fa62eee7a5643b43ad41d9 https://github.com/galaxyproject/galaxy/commit/49ab74827cd0905cd0fa62eee7a56... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Log who's triggering a reload Commit: a2669c565ae7c25bcd20c9831a470bbc0731597c https://github.com/galaxyproject/galaxy/commit/a2669c565ae7c25bcd20c9831a470... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py Log Message: ----------- Add back integrated_tool_panel saving Commit: 6fc46a8c46549bc43fca00cfbd2e32b07db158d5 https://github.com/galaxyproject/galaxy/commit/6fc46a8c46549bc43fca00cfbd2e3... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Directly reload toolbox or data manager when watcher triggers reload Commit: 054fbd05cb2ca3918f0dd2819cc71e5485ef4580 https://github.com/galaxyproject/galaxy/commit/054fbd05cb2ca3918f0dd2819cc71... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Use the tool_data_tables.tool_data_path, to avoid persisting the temporary in-memory path to the data table Commit: 612eea85e6e2322d277f4210005d2efbddaae3e1 https://github.com/galaxyproject/galaxy/commit/612eea85e6e2322d277f4210005d2... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Fix reload thread for uwsgi workers. and fix typos Commit: 1bc84e0b4f5a77d018126656fc2808ed66c4712e https://github.com/galaxyproject/galaxy/commit/1bc84e0b4f5a77d018126656fc280... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Do not call start() method of watchter as this happens when it starts watching a file. Commit: b8695b36280f195242215c56cffad9aff5a7fad4 https://github.com/galaxyproject/galaxy/commit/b8695b36280f195242215c56cffad... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- One last attempt to revive launched thread Commit: 9e36a15e22f92fd3913a1dbed0700bcae91b61e7 https://github.com/galaxyproject/galaxy/commit/9e36a15e22f92fd3913a1dbed0700... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Transplant tool conf watcher thread Commit: 95c0e3cbf78e45f7786cab918835004dc67c156d https://github.com/galaxyproject/galaxy/commit/95c0e3cbf78e45f7786cab9188350... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Also reload conf_watchers for data managers Commit: c0cef19eb7a68e61ac30d9eb55b6bef14705648d https://github.com/galaxyproject/galaxy/commit/c0cef19eb7a68e61ac30d9eb55b6b... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Reload data managers after reloading the toolbox Commit: 3d42be5f234d837ff5fa3792c53d138d3e28fcac https://github.com/galaxyproject/galaxy/commit/3d42be5f234d837ff5fa3792c53d1... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Trigger event with lock Commit: 42854e31ea50eae1e26ce2112696cd86ccb247be https://github.com/galaxyproject/galaxy/commit/42854e31ea50eae1e26ce2112696c... Author: guerler <aysam.guerler@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/types.js Log Message: ----------- Bundle thumbnail view Commit: d4d403d678a9c6d5a5dbf1df5c23b8425f1a1311 https://github.com/galaxyproject/galaxy/commit/d4d403d678a9c6d5a5dbf1df5c23b... Author: guerler <aysam.guerler@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/app.css M config/plugins/visualizations/charts/static/views/types.js Log Message: ----------- Show list instead Commit: 6f444e5cdbc69ba0fdca4a04c1dce7d7493420be https://github.com/galaxyproject/galaxy/commit/6f444e5cdbc69ba0fdca4a04c1dce... Author: guerler <aysam.guerler@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/app.css M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/views/types.js Log Message: ----------- Restore regular selection view Commit: ccd265ed0705d3166f792d7d1473f229c8b5accb https://github.com/galaxyproject/galaxy/commit/ccd265ed0705d3166f792d7d1473f... Author: guerler <aysam.guerler@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/types.js Log Message: ----------- Fix tab creation behavior Commit: d65bf1e4f773c6c6d27b83e7a850b51bfd3d3faa https://github.com/galaxyproject/galaxy/commit/d65bf1e4f773c6c6d27b83e7a850b... Author: guerler <aysam.guerler@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/types.js Log Message: ----------- Fix sorting Commit: bee75fb77909ddc938290c134eb689a7f5729254 https://github.com/galaxyproject/galaxy/commit/bee75fb77909ddc938290c134eb68... Author: guerler <aysam.guerler@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/types.js Log Message: ----------- Fix order Commit: 9601a0f607b71e8725dafff90288ee8486dbfcf1 https://github.com/galaxyproject/galaxy/commit/9601a0f607b71e8725dafff90288e... Author: guerler <aysam.guerler@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/app.css M config/plugins/visualizations/charts/static/views/types.js Log Message: ----------- Revise thumbnail view Commit: ec038cb0904b24c6df8cb5f7b16e671997004aa7 https://github.com/galaxyproject/galaxy/commit/ec038cb0904b24c6df8cb5f7b16e6... Author: guerler <aysam.guerler@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/types.js Log Message: ----------- Use original order Commit: 5cae6f7735436800c586065be690a43c1a1683e5 https://github.com/galaxyproject/galaxy/commit/5cae6f7735436800c586065be690a... Author: guerler <aysam.guerler@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/types.js Log Message: ----------- Fix spacing Commit: 71fe20ab040df9393c8ac0c083a31006a65ab848 https://github.com/galaxyproject/galaxy/commit/71fe20ab040df9393c8ac0c083a31... Author: guerler <aysam.guerler@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M client/galaxy/scripts/utils/utils.js M config/plugins/visualizations/charts/static/views/description.js M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/utils.js Log Message: ----------- Identify links in visualizations plugins descriptions Commit: e0617bb29b280f5f7f756ccbfdd6678ed3e185ef https://github.com/galaxyproject/galaxy/commit/e0617bb29b280f5f7f756ccbfdd66... Author: guerler <aysam.guerler@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/types.js Log Message: ----------- Add tooltip to thumbnail view? Commit: f03a06488feb0e1c471c92d11cff14c6bf5c0cf1 https://github.com/galaxyproject/galaxy/commit/f03a06488feb0e1c471c92d11cff1... Author: guerler <aysam.guerler@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/types.js Log Message: ----------- Limit title length for thumbnails Commit: f2b26a61cb14ff468ecc2971d6394e6cea64f889 https://github.com/galaxyproject/galaxy/commit/f2b26a61cb14ff468ecc2971d6394... Author: guerler <aysam.guerler@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/views/types.js M config/plugins/visualizations/charts/static/views/viewport.js Log Message: ----------- Filter suitable visualization types on initialization Commit: 84942582b57499a753cf9e8039486c3bc9efa4f3 https://github.com/galaxyproject/galaxy/commit/84942582b57499a753cf9e8039486... Author: guerler <aysam.guerler@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/app.js Log Message: ----------- Modify error message Commit: 3e79da902163b131aff677a7b1bad9fa87e61d89 https://github.com/galaxyproject/galaxy/commit/3e79da902163b131aff677a7b1bad... Author: guerler <aysam.guerler@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/components/screenshot.js M config/plugins/visualizations/charts/static/views/description.js M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Fix error messages Commit: bc1be68bb6f0eef840465dd2b578136d0094ae20 https://github.com/galaxyproject/galaxy/commit/bc1be68bb6f0eef840465dd2b5781... Author: zipho <zipho.m@gmail.com> Date: 2016-08-31 (Wed, 31 Aug 2016) Changed paths: M tools/data_source/upload.py Log Message: ----------- added the extra blank line Commit: e85cd284d099af16329d6592b46dc3d6ce37dba4 https://github.com/galaxyproject/galaxy/commit/e85cd284d099af16329d6592b46dc... Author: zipho <zipho.m@gmail.com> Date: 2016-08-31 (Wed, 31 Aug 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- fixed the line tabs Commit: 271959d1345077baa064c60fe79ff00a6ed0b021 https://github.com/galaxyproject/galaxy/commit/271959d1345077baa064c60fe79ff... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-31 (Wed, 31 Aug 2016) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/toolbox/watcher.py M lib/tool_shed/metadata/metadata_generator.py M test/unit/tools/test_watcher.py Log Message: ----------- Reload data table managers and data tables ... before reloading data managers. Data managers need to have access to the data tables, so that they can process the results. Do not explicitly start watcher thread for shed_data_manager_conf changes. Commit: f92d496bd9ae42387e5017e2ef84a032de6e49ea https://github.com/galaxyproject/galaxy/commit/f92d496bd9ae42387e5017e2ef84a... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-31 (Wed, 31 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Remove debugging statements and mention uwsgi/threads in line Commit: 7afb25d5fbf8bcb37d4c9fc7e25b20b8d8373011 https://github.com/galaxyproject/galaxy/commit/7afb25d5fbf8bcb37d4c9fc7e25b2... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-08-31 (Wed, 31 Aug 2016) Changed paths: M lib/tool_shed/galaxy_install/tools/data_manager.py Log Message: ----------- Wait for shed_data_manager_conf watcher to pick up changes Commit: 1a2e34561aa634de4ff1a4d793e32de1d1ff316e https://github.com/galaxyproject/galaxy/commit/1a2e34561aa634de4ff1a4d793e32... Author: John Chilton <jmchilton@gmail.com> Date: 2016-08-31 (Wed, 31 Aug 2016) Changed paths: R lib/galaxy/tools/toolbox/requirements.py Log Message: ----------- Remove empty file in toolbox module. Assuming it was accidentally added by @mvdbeek in 753587931ed3a460e57334de398d5048bc35f6b9. Commit: 75d2c0eac7a320a06ac1173045606fbd4bfbff72 https://github.com/galaxyproject/galaxy/commit/75d2c0eac7a320a06ac1173045606... Author: John Chilton <jmchilton@gmail.com> Date: 2016-08-31 (Wed, 31 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py A lib/galaxy/util/filelock.py M lib/galaxy/web/proxy/__init__.py R lib/galaxy/web/proxy/filelock.py Log Message: ----------- Refactor - move filelock.py to galaxy.util. galaxy.tools.deps.resolvers.conda should not depend on galaxy.web.proxy - this is a smell that indicates filelock belongs in galaxy.util IMO. Commit: 7b44cc5470728b59a2b47c64aedd27774706dd8b https://github.com/galaxyproject/galaxy/commit/7b44cc5470728b59a2b47c64aedd2... Author: jgoecks <jgoecks@gwu.edu> Date: 2016-08-31 (Wed, 31 Aug 2016) Changed paths: M .ci/flake8_lint_include_list.txt M Makefile M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/utils/utils.js M config/galaxy.ini.sample M config/plugins/visualizations/charts/static/app.css M config/plugins/visualizations/charts/static/app.js R config/plugins/visualizations/charts/static/charts/forms/default.js M config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js M config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js M 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lib/galaxy/jobs/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/web/framework/base.py A lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M scripts/bootstrap_history.py M static/maps/mvc/dataset/data.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-color-picker.js.map M static/maps/mvc/ui/ui-tabs.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M 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Author: Scott Szakonyi <sszakony@nd.edu> Date: 2016-08-31 (Wed, 31 Aug 2016) Changed paths: M .ci/flake8_lint_include_list.txt M Makefile M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/utils/utils.js M config/galaxy.ini.sample M config/plugins/visualizations/charts/static/app.css M config/plugins/visualizations/charts/static/app.js R config/plugins/visualizations/charts/static/charts/forms/default.js M config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js M config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js M 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doc/source/releases/16.10_announce.rst M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/postfork.py M lib/galaxy/web/framework/base.py A lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/tool_shed/config.py M scripts/bootstrap_history.py M static/maps/mvc/dataset/data.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-color-picker.js.map M static/maps/mvc/ui/ui-tabs.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/data.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/ui/ui-tabs.js M static/scripts/utils/utils.js R templates/admin/tool_shed_repository/browse_categories.mako A templates/admin/tool_shed_repository/browse_toolsheds.mako R templates/admin/tool_shed_repository/preview_repository.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/tool_shed/index.mako A test/api/test_api_batch.py A test/casperjs/api-batch-tests.js Log Message: ----------- Merge remote branch 'upstream/dev' into dev Commit: 5d780d68d1a2ec5d1928a0156637a1d522f5b743 https://github.com/galaxyproject/galaxy/commit/5d780d68d1a2ec5d1928a0156637a... Author: guerler <aysam.guerler@gmail.com> Date: 2016-08-31 (Wed, 31 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/components/screenshot.js Log Message: ----------- Revise exporting functions, increase png quality, remove unused libraries Commit: 0d160900ace430f370330a3343e3c3ed79c78450 https://github.com/galaxyproject/galaxy/commit/0d160900ace430f370330a3343e3c... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2016-08-31 (Wed, 31 Aug 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js R database/info.txt M static/maps/layout/menu.js.map M static/maps/layout/scratchbook.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/layout/scratchbook.js Log Message: ----------- Merge pull request #2808 from sszakony/dev Addressing issue 2747, login appearing in scratchbook window Commit: 78bd9e8f867eb5747218644e2a5a1f5417079b73 https://github.com/galaxyproject/galaxy/commit/78bd9e8f867eb5747218644e2a5a1... Author: guerler <aysam.guerler@gmail.com> Date: 2016-08-31 (Wed, 31 Aug 2016) Changed paths: M Makefile M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js R database/info.txt A doc/source/admin/chat-0.png A doc/source/admin/chat-1.png A doc/source/admin/chat-2.png A doc/source/admin/chat-3.png A doc/source/admin/chat-4.png A doc/source/admin/chat.rst A doc/source/admin/communication_server.png A doc/source/admin/communication_server_rooms.png A doc/source/admin/conda_faq.rst M doc/source/admin/index.rst A doc/source/releases/16.07.rst M doc/source/releases/16.07_announce.rst A doc/source/releases/16.10_announce.rst M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M scripts/bootstrap_history.py M static/maps/layout/menu.js.map M static/maps/layout/scratchbook.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/layout/scratchbook.js R templates/admin/tool_shed_repository/browse_categories.mako A templates/admin/tool_shed_repository/browse_toolsheds.mako R templates/admin/tool_shed_repository/preview_repository.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/tool_shed/index.mako Log Message: ----------- Merge branch 'dev' into remote_chart_plugins Commit: 3908a9a8361da77427392b7d90a1ace780839cc2 https://github.com/galaxyproject/galaxy/commit/3908a9a8361da77427392b7d90a1a... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2016-08-31 (Wed, 31 Aug 2016) Changed paths: R lib/galaxy/tools/toolbox/requirements.py Log Message: ----------- Merge pull request #2877 from jmchilton/remove_empty_file Remove empty file in toolbox module. Commit: 5518c20a20e6fc38ac1edfbbdaa2a8a4f1737c95 https://github.com/galaxyproject/galaxy/commit/5518c20a20e6fc38ac1edfbbdaa2a... Author: jgoecks <jgoecks@gwu.edu> Date: 2016-08-31 (Wed, 31 Aug 2016) Changed paths: M client/galaxy/scripts/viz/bbi-data-manager.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M static/maps/viz/bbi-data-manager.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/tracks.js.map M static/scripts/viz/bbi-data-manager.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/tracks.js Log Message: ----------- Cleanup: (a) remove debugging statements; (b) use Galaxy app; and (c) fix offset issue for LinePainter using floor instead of ceil. Commit: a97b4bae546a5621dc37b6beaaba747d51c8ed9e https://github.com/galaxyproject/galaxy/commit/a97b4bae546a5621dc37b6beaaba7... Author: guerler <aysam.guerler@gmail.com> Date: 2016-08-31 (Wed, 31 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/app.js Log Message: ----------- Rename types to registry to avoid confusion Commit: 494141c260514071c5187a83a8dd1700643b5423 https://github.com/galaxyproject/galaxy/commit/494141c260514071c5187a83a8dd1... Author: guerler <aysam.guerler@gmail.com> Date: 2016-08-31 (Wed, 31 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/settings.js M config/plugins/visualizations/charts/static/views/viewport.js Log Message: ----------- Use underscores for internal parameters to avoid conflicts Commit: 61839637f098130ccd54bfe408ff9955dbffc883 https://github.com/galaxyproject/galaxy/commit/61839637f098130ccd54bfe408ff9... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/components/model.js R config/plugins/visualizations/charts/static/components/storage.js M config/plugins/visualizations/charts/static/views/editor.js Log Message: ----------- Simplify storage handling Commit: 7d20e9055e1be434c7914fc540ceb64a8e4d1051 https://github.com/galaxyproject/galaxy/commit/7d20e9055e1be434c7914fc540ceb... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M config/plugins/visualizations/charts/static/components/model.js Log Message: ----------- Remove unused options variable Commit: a19f67f8be85c4d5b459082ea9343cbda0a298b3 https://github.com/galaxyproject/galaxy/commit/a19f67f8be85c4d5b459082ea9343... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Try locking load_item Commit: 426ea3b726a085f1a89033ed875584468db7b321 https://github.com/galaxyproject/galaxy/commit/426ea3b726a085f1a89033ed87558... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/toolbox/base.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py Log Message: ----------- Keep a count of reloads Commit: c4aa171ae4bc16667b082122ef14dfc0f08891c8 https://github.com/galaxyproject/galaxy/commit/c4aa171ae4bc16667b082122ef14d... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/data_manager/manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py Log Message: ----------- Always wait for reload action to be finished Commit: 55cd6d86333b63747c257911a16a68a42bb34828 https://github.com/galaxyproject/galaxy/commit/55cd6d86333b63747c257911a16a6... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py A lib/galaxy/util/filelock.py M lib/galaxy/web/proxy/__init__.py R lib/galaxy/web/proxy/filelock.py Log Message: ----------- Merge pull request #2879 from jmchilton/refactor_filelock Refactor - move filelock.py to galaxy.util. Commit: 7f893f39f6d1087afe50af9d9a61da77fcbe14db https://github.com/galaxyproject/galaxy/commit/7f893f39f6d1087afe50af9d9a61d... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M lib/galaxy/queue_worker.py M test/unit/tools_support.py Log Message: ----------- Mock the Lock; fix linting problems Commit: c1d66d1fbc7281cb2cd5b050e8516818093d3e6a https://github.com/galaxyproject/galaxy/commit/c1d66d1fbc7281cb2cd5b050e8516... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M test/unit/tools_support.py Log Message: ----------- One more linting fix Commit: 4adc872e5864d9a8262948a56a4552fbafe68390 https://github.com/galaxyproject/galaxy/commit/4adc872e5864d9a8262948a56a455... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M test/unit/tools_support.py Log Message: ----------- Fix indentation Commit: 30d4e338b473797816e8b8a5da93dcd5420e24fc https://github.com/galaxyproject/galaxy/commit/30d4e338b473797816e8b8a5da93d... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/components/model.js M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Revise visualization config handling Commit: 57b41b201964b57daf9a95c06120cbe1bba14e1b https://github.com/galaxyproject/galaxy/commit/57b41b201964b57daf9a95c06120c... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M config/plugins/visualizations/charts/static/components/model.js Log Message: ----------- Fix chart saving Commit: 22e79f7aa943edb9ca6a80d1b035931ab8c9232f https://github.com/galaxyproject/galaxy/commit/22e79f7aa943edb9ca6a80d1b0359... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M config/plugins/visualizations/charts/static/components/model.js M config/plugins/visualizations/charts/static/components/screenshot.js M config/plugins/visualizations/charts/static/views/editor.js M config/plugins/visualizations/charts/static/views/types.js Log Message: ----------- Improve handling for cases with missing plugins Commit: 21ccf76b1009301365171d7a33afb380b40dd3a3 https://github.com/galaxyproject/galaxy/commit/21ccf76b1009301365171d7a33afb... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/history_contents.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- API, history contents: contents download endpoint - Adds an api endpoint at 'histories/{id}/contents/archive' for creating an archive from all history contents or a filtered subset of contents - Contents are returned in 'tgz' format currently - Datasets are located in the archive in paths roughly matching the nesting relationships of their parent collections - Filters can be applied using the same syntax as index - Adding 'dry_run=True' will return a JSON list of archive paths and dataset file paths for debugging - Adds map_datasets method for walking the datasets of histories and HDCAs Commit: 76c9948742d659b2dd73452cc2d3c49f44f00cd7 https://github.com/galaxyproject/galaxy/commit/76c9948742d659b2dd73452cc2d3c... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/components/model.js M config/plugins/visualizations/charts/static/views/editor.js Log Message: ----------- Enhance notification and handling when chart type is unavailable Commit: 81dffca58cab841dfcf0fda42b42d5c97f54f245 https://github.com/galaxyproject/galaxy/commit/81dffca58cab841dfcf0fda42b42d... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M config/plugins/visualizations/charts/static/components/model.js M config/plugins/visualizations/charts/static/views/editor.js Log Message: ----------- Remove test case, replace change listeners Commit: fa7930d20e10309aee666f280963b759571e3884 https://github.com/galaxyproject/galaxy/commit/fa7930d20e10309aee666f280963b... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M config/plugins/visualizations/charts/static/views/editor.js Log Message: ----------- Fix message persistence for missing column notification Commit: b3451ed03d5104442b4935905e330b006e492204 https://github.com/galaxyproject/galaxy/commit/b3451ed03d5104442b4935905e330... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M config/plugins/visualizations/charts/static/views/editor.js Log Message: ----------- Fix message persistence for missing data groups Commit: 4669d5ee26410faec0c6e49aed512352631066e3 https://github.com/galaxyproject/galaxy/commit/4669d5ee26410faec0c6e49aed512... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Remove warning notification when leaving charts, data is saved upon drawing Commit: 00053b6d30b21ce2eed5419a3537caa0b8cd7797 https://github.com/galaxyproject/galaxy/commit/00053b6d30b21ce2eed5419a3537c... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M config/plugins/visualizations/charts/static/components/model.js Log Message: ----------- Fix spacing Commit: ffba835195737c4705e5b2717c384be05edeae91 https://github.com/galaxyproject/galaxy/commit/ffba835195737c4705e5b2717c384... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M config/plugins/visualizations/charts/static/components/screenshot.js M config/plugins/visualizations/charts/static/views/types.js M config/plugins/visualizations/charts/static/views/viewport.js Log Message: ----------- Remove spacing Commit: 99acb36da32ec2d2d4d7d1ce7cdc4da426e51645 https://github.com/galaxyproject/galaxy/commit/99acb36da32ec2d2d4d7d1ce7cdc4... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M test/unit/tools_support.py Log Message: ----------- Add server_name to unit test app's config. Required for messaging stuff. Commit: 7351d67967a0750a5e351660b457d92dcb01b516 https://github.com/galaxyproject/galaxy/commit/7351d67967a0750a5e351660b457d... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M config/plugins/visualizations/charts/static/views/types.js Log Message: ----------- Remove unused listener Commit: 9f7c749638340fb63ac00a417a9e328875296885 https://github.com/galaxyproject/galaxy/commit/9f7c749638340fb63ac00a417a9e3... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/tools/toolbox/base.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M test/unit/tools_support.py Log Message: ----------- Fix test case for tool manager. Commit: 05fa9b9f5adcd96456348754225c72554d4e12af https://github.com/galaxyproject/galaxy/commit/05fa9b9f5adcd96456348754225c7... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/views/description.js M config/plugins/visualizations/charts/static/views/types.js M config/plugins/visualizations/charts/static/views/viewport.js M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Rename remote to repository to avoid confusion Commit: 3d9df6437073484d243d64fc9606dc137dc6bfb7 https://github.com/galaxyproject/galaxy/commit/3d9df6437073484d243d64fc9606d... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Rename optional config attributes name accordingly Commit: efac63f7cd5a46a26eb9f27a78510f06e072b6b9 https://github.com/galaxyproject/galaxy/commit/efac63f7cd5a46a26eb9f27a78510... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: A database/info.txt Log Message: ----------- Restore database/info.txt. It was problematically removed with a recent PR and is causing Travis breakages - Galaxy assumes this directory exists. Commit: 50c8302b1525ebc2168bb0a9ab4439105d9317e7 https://github.com/galaxyproject/galaxy/commit/50c8302b1525ebc2168bb0a9ab443... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M lib/galaxy/tools/cwl/parser.py Log Message: ----------- Small cwl fixes to sync with galaxy-lib. description became doc in draft 1.0. Commit: 0d35f9435ad6d9cd1636d7626dae97ad8d08027d https://github.com/galaxyproject/galaxy/commit/0d35f9435ad6d9cd1636d7626dae9... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: A database/info.txt Log Message: ----------- Merge pull request #2887 from jmchilton/database_info_restore Restore database/info.txt. Commit: 07cf96c26053d8a0d0fe1a6365f6bf4272a3593d https://github.com/galaxyproject/galaxy/commit/07cf96c26053d8a0d0fe1a6365f6b... Author: Enis Afgan <afgane@gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Update Conda FAQ Commit: 9a9a1f9becf185db5a778f1436913bc6942b2ac3 https://github.com/galaxyproject/galaxy/commit/9a9a1f9becf185db5a778f1436913... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py Log Message: ----------- Lint for last commit. Commit: 4479bcebbe6984c06d0b5b9411d6d9e8bc2f22ca https://github.com/galaxyproject/galaxy/commit/4479bcebbe6984c06d0b5b9411d6d... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js M doc/source/admin/conda_faq.rst M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/toolbox/base.py R lib/galaxy/tools/toolbox/requirements.py A lib/galaxy/util/filelock.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/__init__.py R lib/galaxy/web/proxy/filelock.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M static/maps/layout/menu.js.map M static/maps/layout/scratchbook.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/layout/scratchbook.js R templates/admin/tool_shed_repository/browse_categories.mako A templates/admin/tool_shed_repository/browse_toolsheds.mako R templates/admin/tool_shed_repository/preview_repository.mako M templates/webapps/galaxy/workflow/display.mako Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into reload_toolbox_across_handlers Commit: b1940945607448f3795f98f6ffd8c8dd37c7b3d5 https://github.com/galaxyproject/galaxy/commit/b1940945607448f3795f98f6ffd8c... Author: nturaga <nitesh.turaga@gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M templates/admin/tool_shed_repository/common.mako Log Message: ----------- Changed wording on common.mako when selecting how to install tool and handle dependencies Commit: a199590efa2378e2f1f865b8da68cc4fe12a33c1 https://github.com/galaxyproject/galaxy/commit/a199590efa2378e2f1f865b8da68c... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M lib/galaxy/tools/cwl/parser.py Log Message: ----------- Merge pull request #2888 from jmchilton/cwl_fixes_from_lib Small cwl fixes to sync with galaxy-lib. Commit: ecdbf4d0b579f4dbae79a56aea1398224d9f2c93 https://github.com/galaxyproject/galaxy/commit/ecdbf4d0b579f4dbae79a56aea139... Author: Enis Afgan <afgane@gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Address PR #2891 comments Commit: 53d387d771b3bb95cd17cf0c74ec90099122f376 https://github.com/galaxyproject/galaxy/commit/53d387d771b3bb95cd17cf0c74ec9... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Another linting fix. Commit: ff301c562b87a1843d18819eb79dd580d207e9c8 https://github.com/galaxyproject/galaxy/commit/ff301c562b87a1843d18819eb79dd... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-02 (Fri, 02 Sep 2016) Changed paths: M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Add debug log, fix config name, add comment for local repository Commit: 36c1384d020bcb2d3a89da83861cccfae23e8916 https://github.com/galaxyproject/galaxy/commit/36c1384d020bcb2d3a89da83861cc... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-02 (Fri, 02 Sep 2016) Changed paths: M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Use rawgit for proper MIME type handling Commit: 819cb65d2e1ecc905b22e97b9972fa8901ac09c1 https://github.com/galaxyproject/galaxy/commit/819cb65d2e1ecc905b22e97b9972f... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-02 (Fri, 02 Sep 2016) Changed paths: M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Add repository revision to url Commit: 3cee333011bff6aed673429f361659132804f33c https://github.com/galaxyproject/galaxy/commit/3cee333011bff6aed673429f36165... Author: Enis Afgan <afgane@gmail.com> Date: 2016-09-02 (Fri, 02 Sep 2016) Changed paths: M lib/galaxy/tools/cwl/parser.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into dev Commit: 97b748c73a4eb169c5e1c6894ea2b30dbcc0343a https://github.com/galaxyproject/galaxy/commit/97b748c73a4eb169c5e1c6894ea2b... Author: Enis Afgan <afgane@gmail.com> Date: 2016-09-02 (Fri, 02 Sep 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Shorten Conda environment naming as per https://github.com/galaxyproject/galaxy/commit/e9d81500caa3526200b204270aca1... Thanks @lparsons. Commit: d5440f7ac4170adf27f757fdfbc888a67e20cf27 https://github.com/galaxyproject/galaxy/commit/d5440f7ac4170adf27f757fdfbc88... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-02 (Fri, 02 Sep 2016) Changed paths: M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Upgrade repository version, allow pdb rendering type selection Commit: 14ef3e3d448dc4190707312443b6f60e187ee962 https://github.com/galaxyproject/galaxy/commit/14ef3e3d448dc4190707312443b6f... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-02 (Fri, 02 Sep 2016) Changed paths: M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Upgrade repository version Commit: 2b6b5c82754a3ca9722e55d9828042e70d95d028 https://github.com/galaxyproject/galaxy/commit/2b6b5c82754a3ca9722e55d982804... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-02 (Fri, 02 Sep 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Merge pull request #2891 from afgane/dev Update Conda FAQ Commit: cd8daaab1f30fd0a45dd4903d0d3de2c9ed5633b https://github.com/galaxyproject/galaxy/commit/cd8daaab1f30fd0a45dd4903d0d3d... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2016-09-02 (Fri, 02 Sep 2016) Changed paths: M templates/admin/tool_shed_repository/common.mako Log Message: ----------- Merge pull request #2893 from nturaga/change_dependency_wording Changed wording on common.mako when selecting how to install tool and… Commit: 5483e9f5bf4d725e3bb2a746db1d9c1a911a5291 https://github.com/galaxyproject/galaxy/commit/5483e9f5bf4d725e3bb2a746db1d9... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-02 (Fri, 02 Sep 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js M static/maps/layout/menu.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 Log Message: ----------- Fix indention for noscratchbook flag Commit: fed59596a37176b388d74346cd7fce6bba224c8e https://github.com/galaxyproject/galaxy/commit/fed59596a37176b388d74346cd7fc... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-02 (Fri, 02 Sep 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Fix the infinite loop. Thanks @mvdbeek! Commit: afefb9dd831ff5aed21c74cc159dc6d62eebe64a https://github.com/galaxyproject/galaxy/commit/afefb9dd831ff5aed21c74cc159dc... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-02 (Fri, 02 Sep 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js M static/maps/layout/menu.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 Log Message: ----------- Merge pull request #2894 from guerler/revise_noscratchbook_flag Fix indention for noscratchbook flag Commit: d98a72d58e1cf462eb89f4a9cd3e04a5c6fea9fb https://github.com/galaxyproject/galaxy/commit/d98a72d58e1cf462eb89f4a9cd3e0... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-02 (Fri, 02 Sep 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js A database/info.txt M doc/source/admin/conda_faq.rst M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/deps/resolvers/conda.py R lib/galaxy/tools/toolbox/requirements.py A lib/galaxy/util/filelock.py M lib/galaxy/web/proxy/__init__.py R lib/galaxy/web/proxy/filelock.py M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js.map M templates/admin/tool_shed_repository/common.mako Log Message: ----------- Merge branch 'dev' into remote_chart_plugins Commit: 61fb26181c7dfaefa821f616171a281928153b70 https://github.com/galaxyproject/galaxy/commit/61fb26181c7dfaefa821f616171a2... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-02 (Fri, 02 Sep 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/hash_util.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py M test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/tools_support.py Log Message: ----------- Merge pull request #2840 from mvdbeek/reload_toolbox_across_handlers Allow reloading tools without restarting galaxy, simplify tool panel handling for tool shed installed tools Commit: d092bd8ec2d29bd05a701c0edae1c915e392d257 https://github.com/galaxyproject/galaxy/commit/d092bd8ec2d29bd05a701c0edae1c... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-02 (Fri, 02 Sep 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Enable new run workflow form by default Commit: e510f86a05b2a8ad368e0b99f521bfcce207cfc1 https://github.com/galaxyproject/galaxy/commit/e510f86a05b2a8ad368e0b99f521b... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-02 (Fri, 02 Sep 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Update default value in sample config file Commit: 0c8dadcede0609ed1a8aed997c57adceaf8dce83 https://github.com/galaxyproject/galaxy/commit/0c8dadcede0609ed1a8aed997c57a... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-06 (Tue, 06 Sep 2016) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Seemingly fix #2806. I guess this would make sense if somehow the step of this workflow has its tool parameters double wrapped. Commit: cbd55b20d373538d2b8019344dd08a0fd190752c https://github.com/galaxyproject/galaxy/commit/cbd55b20d373538d2b8019344dd08... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-09-06 (Tue, 06 Sep 2016) Changed paths: M config/galaxy.ini.sample M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #2895 from guerler/activate_new_run_form Enable new run workflow form Commit: b710ed1e8519fc6ed85f1d9cef4b63e679294a93 https://github.com/galaxyproject/galaxy/commit/b710ed1e8519fc6ed85f1d9cef4b6... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-06 (Tue, 06 Sep 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix over encoding of dataset ids Commit: 94338632e005da8a9e90eabdbf915b9102b9308e https://github.com/galaxyproject/galaxy/commit/94338632e005da8a9e90eabdbf915... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-07 (Wed, 07 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Rename lda id parameter Commit: d6b9348f377d48f85286fdf57b826ec99e29a856 https://github.com/galaxyproject/galaxy/commit/d6b9348f377d48f85286fdf57b826... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-07 (Wed, 07 Sep 2016) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/instrumenters/__init__.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/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/brew_exts.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/dockerfiles.py M lib/galaxy/tools/deps/resolvers/__init__.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/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.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/loader.py M lib/galaxy/tools/parser/__init__.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/toolbox/tags.py M lib/galaxy/tools/verify/asserts/xml.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/util/__init__.py M lib/galaxy/util/biostar.py M lib/galaxy/util/checkers.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/json.py M lib/galaxy/util/lazy_process.py M lib/galaxy/util/none_like.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/util/permutations.py M lib/galaxy/util/properties.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/sockets.py M lib/galaxy/util/sqlite.py M lib/galaxy/util/streamball.py M lib/galaxy/util/submodules.py M lib/galaxy/util/topsort.py M lib/galaxy/util/validation.py M lib/galaxy/util/xml_macros.py M setup.cfg M test/unit/test_objectstore.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/tools/test_watcher.py M test/unit/tools/test_wrappers.py Log Message: ----------- Extend import order linting to all of galaxy-lib w/fixes. Includes a bit linting of order for galaxy.util. Commit: 825c7287a57dabe465f86bb5b66730aba080d000 https://github.com/galaxyproject/galaxy/commit/825c7287a57dabe465f86bb5b6673... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-07 (Wed, 07 Sep 2016) Changed paths: M lib/galaxy/tools/parser/yaml.py M lib/galaxy/util/topsort.py Log Message: ----------- Lint fixes thanks to @nsoranzo's eagle eyes. Commit: 259e6730c21dae72c6bd60ba38b52f6954b9ca83 https://github.com/galaxyproject/galaxy/commit/259e6730c21dae72c6bd60ba38b52... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-07 (Wed, 07 Sep 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Rename to use_security Commit: 69ee5afaeca5dce6acb814cf292a009e9fd2f0c5 https://github.com/galaxyproject/galaxy/commit/69ee5afaeca5dce6acb814cf292a0... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-07 (Wed, 07 Sep 2016) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/instrumenters/__init__.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/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/brew_exts.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/dockerfiles.py M lib/galaxy/tools/deps/resolvers/__init__.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/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.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/loader.py M lib/galaxy/tools/parser/__init__.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/toolbox/tags.py M lib/galaxy/tools/verify/asserts/xml.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/util/__init__.py M lib/galaxy/util/biostar.py M lib/galaxy/util/checkers.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/json.py M lib/galaxy/util/lazy_process.py M lib/galaxy/util/none_like.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/util/permutations.py M lib/galaxy/util/properties.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/sockets.py M lib/galaxy/util/sqlite.py M lib/galaxy/util/streamball.py M lib/galaxy/util/submodules.py M lib/galaxy/util/topsort.py M lib/galaxy/util/validation.py M lib/galaxy/util/xml_macros.py M setup.cfg M test/unit/test_objectstore.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/tools/test_watcher.py M test/unit/tools/test_wrappers.py Log Message: ----------- Merge pull request #2889 from jmchilton/import-order-linting Extend import order linting to all of galaxy-lib w/fixes. Commit: 2d36ab52dee7085628f30ecd58c7c920158804d8 https://github.com/galaxyproject/galaxy/commit/2d36ab52dee7085628f30ecd58c7c... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-07 (Wed, 07 Sep 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #2902 from guerler/fix_id_storage Fix over encoding of dataset ids Commit: d5ba73b0c84f6bfa297d4b75296e5614d25a07cf https://github.com/galaxyproject/galaxy/commit/d5ba73b0c84f6bfa297d4b75296e5... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py Log Message: ----------- Fix hang when installing data managers Commit: 82c1da4709a5ae5b52ee60b2b197f91d64c5d5d3 https://github.com/galaxyproject/galaxy/commit/82c1da4709a5ae5b52ee60b2b197f... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Add data managers to new toolbox before replacing the old toolbox, to avoid 'Tool not found or not accessible.' while installing new tools Commit: a8f794290dc1e529dd9564a95a55f4b808b2e6d9 https://github.com/galaxyproject/galaxy/commit/a8f794290dc1e529dd9564a95a55f... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Handle xml ParseError Occasionally the following Traceback can be seen in the log files: ``` Traceback (most recent call last): File "lib/galaxy/tools/toolbox/base.py", line 112, in _init_tools_from_configs self._init_tools_from_config( config_filename ) File "lib/galaxy/tools/toolbox/base.py", line 136, in _init_tools_from_config tool_conf_source = get_toolbox_parser(config_filename) File "lib/galaxy/tools/toolbox/parser.py", line 152, in get_toolbox_parser return XmlToolConfSource(config_filename) File "lib/galaxy/tools/toolbox/parser.py", line 40, in __init__ tree = parse_xml(config_filename) File "lib/galaxy/util/__init__.py", line 210, in parse_xml root = tree.parse( fname, parser=ElementTree.XMLParser( target=DoctypeSafeCallbackTarget() ) ) File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 657, in parse self._root = parser.close() File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1654, in close self._raiseerror(v) File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1506, in _raiseerror raise err ParseError: unclosed token: line 2636, column 0 ``` We just try parsing again, which seems to solve the issue. This may be a problem with concurrently reading/writing to the file. Commit: 89bafff06170c02e5089800a5062e3de0421ad23 https://github.com/galaxyproject/galaxy/commit/89bafff06170c02e5089800a5062e... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/tool_shed/galaxy_install/tools/data_manager.py Log Message: ----------- Whitespace fix Commit: c3886b373e8954c1f7bb193cf28357aebd8cd459 https://github.com/galaxyproject/galaxy/commit/c3886b373e8954c1f7bb193cf2835... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/queue_worker.py Log Message: ----------- Specifically index new toolbox Commit: 6fd4c5a5be75a39e941ab4b4b4df95c9456ca1e9 https://github.com/galaxyproject/galaxy/commit/6fd4c5a5be75a39e941ab4b4b4df9... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Keep track of toolbox reload time Commit: 230e7df4ae293e46e4f15bf2cf811f788a9f811d https://github.com/galaxyproject/galaxy/commit/230e7df4ae293e46e4f15bf2cf811... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/cache.py Log Message: ----------- Use cache to get the repository containing a tool when reloading toolbox. This should prevent lots of (slow) database requests when reloading the toolbox. Commit: c5406eb192a0e2355602e5e5d7eb1e218a632d07 https://github.com/galaxyproject/galaxy/commit/c5406eb192a0e2355602e5e5d7eb1... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Improve logic handling of loading tools Commit: ab9be8c311a7943d778842522a706451e9996943 https://github.com/galaxyproject/galaxy/commit/ab9be8c311a7943d778842522a706... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fetch cached tools repository Commit: 894b77ba23fa66a8852b554aacf18cc123f5d7cd https://github.com/galaxyproject/galaxy/commit/894b77ba23fa66a8852b554aacf18... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/tools/toolbox/lineages/factory.py Log Message: ----------- Simplify lineage registration Commit: acc5b4ceb6525a9cf53bf39c3d6c00abf9069990 https://github.com/galaxyproject/galaxy/commit/acc5b4ceb6525a9cf53bf39c3d6c0... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/tools/toolbox/base.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 Log Message: ----------- Load all versions in a single request Commit: 971227c59dd1d32b537c04c59a16e7572aa7acbd https://github.com/galaxyproject/galaxy/commit/971227c59dd1d32b537c04c59a16e... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/panel.py A lib/galaxy/util/profiling.py Log Message: ----------- Use tool version cache to boost tool panel loading Commit: 833af5e8c2121947e16bdfb99b2794b7a130d045 https://github.com/galaxyproject/galaxy/commit/833af5e8c2121947e16bdfb99b279... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/toolbox/base.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/util/profiling.py Log Message: ----------- Restore peacemeal tool registration Commit: 8bed867fcfcf249838b6b24a1b5985af401b9b5a https://github.com/galaxyproject/galaxy/commit/8bed867fcfcf249838b6b24a1b598... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py Log Message: ----------- Reload tool_version_cache after new installs in the unit-testing code. Commit: 894ac295207430d5ec1b02a0be7ee76ce4dc2cc0 https://github.com/galaxyproject/galaxy/commit/894ac295207430d5ec1b02a0be7ee... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Reload tool_version_cache when adding new tool version relationships to the database. Commit: 09173cc6070bc914759f15854367d62ca6323c79 https://github.com/galaxyproject/galaxy/commit/09173cc6070bc914759f15854367d... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/util/profiling.py M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Rebase and linting fixes Commit: d06e2a672b0c81e5391e077288bf36001f72dbb5 https://github.com/galaxyproject/galaxy/commit/d06e2a672b0c81e5391e077288bf3... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M test/functional/tools/column_multi_param.xml M test/functional/tools/column_param.xml M test/functional/tools/identifier_collection.xml M test/functional/tools/identifier_multiple.xml M test/functional/tools/identifier_single.xml M test/functional/tools/inputs_as_json.xml M test/functional/tools/multi_output.xml M test/functional/tools/multi_output_assign_primary.xml M test/functional/tools/multi_output_configured.xml M test/functional/tools/tool_directory.xml M test/functional/tools/validation_repeat.xml M tools/data_source/upload.xml Log Message: ----------- XSD discovered tool problems. Commit: d98dcd75db307de955391c46e4121a0cd3036f3e https://github.com/galaxyproject/galaxy/commit/d98dcd75db307de955391c46e4121... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Merge pull request #2898 from jmchilton/fix_2806 Seemingly fix #2806. Commit: c08db31ab22aefa23a0e6472c4f115cff537668f https://github.com/galaxyproject/galaxy/commit/c08db31ab22aefa23a0e6472c4f11... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/tools/toolbox/lineages/tool_shed.py R lib/galaxy/util/profiling.py Log Message: ----------- Document ToolVersionCache class Commit: 92d028cbae55d120326cfac61f2fd4fb5d425b35 https://github.com/galaxyproject/galaxy/commit/92d028cbae55d120326cfac61f2fd... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M test/unit/tools_support.py Log Message: ----------- Remove unnecessary self.install_model from unittest app Commit: 0c3b5272eb53256b892a313aa6fcc4d5d5b5daa0 https://github.com/galaxyproject/galaxy/commit/0c3b5272eb53256b892a313aa6fcc... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M test/functional/tools/column_multi_param.xml M test/functional/tools/column_param.xml M test/functional/tools/identifier_collection.xml M test/functional/tools/identifier_multiple.xml M test/functional/tools/identifier_single.xml M test/functional/tools/inputs_as_json.xml M test/functional/tools/multi_output.xml M test/functional/tools/multi_output_assign_primary.xml M test/functional/tools/multi_output_configured.xml M test/functional/tools/tool_directory.xml M test/functional/tools/validation_repeat.xml M tools/data_source/upload.xml Log Message: ----------- Merge pull request #2903 from jmchilton/format_fixes XSD discovered tool problems. Commit: 5c45da362ad27c788fe5f7e62fd5c779b7fa24bf https://github.com/galaxyproject/galaxy/commit/5c45da362ad27c788fe5f7e62fd5c... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/cache.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/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/tools/tool_version_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py Log Message: ----------- Merge pull request #2901 from mvdbeek/fix_data_manager_hangs All-around improvements to toolbox loading/reloading Commit: 4df654d7da363afad10c7dc78a35a3f6c3a3d1bf https://github.com/galaxyproject/galaxy/commit/4df654d7da363afad10c7dc78a35a... Author: nturaga <nitesh.turaga@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M .gitignore Log Message: ----------- Add `database/dependencies` gitignore Since the galaxy.ini.sample file is shipped with `#tool_dependency_dir = database/dependencies` as default, and we don't want anyone commiting dependencies. Commit: 14c0365b22d238e8c48b20dc64654cc412386059 https://github.com/galaxyproject/galaxy/commit/14c0365b22d238e8c48b20dc64654... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M config/plugins/visualizations/charts/static/views/groups.js M config/plugins/visualizations/charts/static/views/types.js M config/plugins/visualizations/charts/static/views/viewport.js M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Upgrade repository revision Commit: 9b414cd1fa2eb87187daff9677d5b0d552355009 https://github.com/galaxyproject/galaxy/commit/9b414cd1fa2eb87187daff9677d5b... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-09 (Fri, 09 Sep 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M test/unit/tools_support.py Log Message: ----------- Minor fixes to shed tool lineage get_installed_tool_version needs to look up the tool_version object using the tool_id, not the tool_version id. Make sure toolshed tools in cache have toolshed attribute. Commit: 5e8a2ced3a819a238227bbde0627d90cfd3cf728 https://github.com/galaxyproject/galaxy/commit/5e8a2ced3a819a238227bbde0627d... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-09 (Fri, 09 Sep 2016) Changed paths: M config/plugins/visualizations/charts/static/components/model.js M config/plugins/visualizations/charts/static/views/editor.js M config/plugins/visualizations/charts/static/views/viewer.js Log Message: ----------- Distinguish draw and save to avoid accumulation of saved visualizations Commit: cf9db96a1d7076474873c5b1f6e7ed2e32a3d79e https://github.com/galaxyproject/galaxy/commit/cf9db96a1d7076474873c5b1f6e7e... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-09 (Fri, 09 Sep 2016) Changed paths: M config/plugins/visualizations/charts/static/views/editor.js Log Message: ----------- Change label from draw to visualize Commit: a88942b0875f659e799d65bd00cea1d771c82570 https://github.com/galaxyproject/galaxy/commit/a88942b0875f659e799d65bd00cea... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-09 (Fri, 09 Sep 2016) Changed paths: M config/plugins/visualizations/charts/static/components/model.js M config/plugins/visualizations/charts/static/components/screenshot.js M config/plugins/visualizations/charts/static/views/editor.js M config/plugins/visualizations/charts/static/views/groups.js M config/plugins/visualizations/charts/static/views/settings.js M config/plugins/visualizations/charts/static/views/viewer.js Log Message: ----------- Unify labels and tooltips Commit: 052b6e367bdeeffa5811853612a3bb1759c27039 https://github.com/galaxyproject/galaxy/commit/052b6e367bdeeffa5811853612a3b... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-09 (Fri, 09 Sep 2016) Changed paths: M config/plugins/visualizations/charts/static/views/editor.js Log Message: ----------- Fix tooltip Commit: 48a841c0d9c80f03512314d31ac9f63358a186dc https://github.com/galaxyproject/galaxy/commit/48a841c0d9c80f03512314d31ac9f... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-09 (Fri, 09 Sep 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M test/unit/tools_support.py Log Message: ----------- Merge pull request #2905 from mvdbeek/minor_lineage_bug Minor fixes to shed tool lineage Commit: c158d0b0611ed233b4b3d39fd23822e38d69d4db https://github.com/galaxyproject/galaxy/commit/c158d0b0611ed233b4b3d39fd2382... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-09 (Fri, 09 Sep 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py Log Message: ----------- Refactor shed tool lineage registration to avoid using tool.tool_shed_repository if possible, since this is a property of the tool instance, which results in a database query. These sequential queries slow down reloading a large number of tools. Commit: 7cc1579c5908186d02aa04f9e72495530d63fe75 https://github.com/galaxyproject/galaxy/commit/7cc1579c5908186d02aa04f9e7249... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-12 (Mon, 12 Sep 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py Log Message: ----------- Merge pull request #2909 from mvdbeek/last_speed_fix Refactor shed tool lineage registration Commit: b102e2012342078a3b8bcab8348b2aaa485aa2a6 https://github.com/galaxyproject/galaxy/commit/b102e2012342078a3b8bcab8348b2... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-12 (Mon, 12 Sep 2016) Changed paths: M .gitignore Log Message: ----------- Merge pull request #2904 from nturaga/update_gitignore Add `database/dependencies` gitignore Commit: 85c1a8f2e2c7e4a93a9df7c8c2a0b8aff952774d https://github.com/galaxyproject/galaxy/commit/85c1a8f2e2c7e4a93a9df7c8c2a0b... Author: Marius van den Beek <m.vandenbeek@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: 167286ad93bea7853eb6d95b6112bd04ff4fa20c https://github.com/galaxyproject/galaxy/commit/167286ad93bea7853eb6d95b6112b... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M templates/show_params.mako M test/unit/jobs/test_job_wrapper.py Log Message: ----------- Track used dependencies in job metadata and expose with job info. Commit: 04db0a2348e671ff0b80612d001bd62f69c2e32b https://github.com/galaxyproject/galaxy/commit/04db0a2348e671ff0b80612d001bd... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py Log Message: ----------- Correct comment (thanks @martenson) Commit: 63f758f9976b5e5810cae8648fa926d2d4855e5e https://github.com/galaxyproject/galaxy/commit/63f758f9976b5e5810cae8648fa92... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py M templates/show_params.mako M test/unit/jobs/test_job_wrapper.py Log Message: ----------- Merge pull request #2917 from mvdbeek/log_dependency_type Log the resolved dependency type Commit: 8b13f63f423800bf17e51a99231fa35099b58519 https://github.com/galaxyproject/galaxy/commit/8b13f63f423800bf17e51a99231fa... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .gitignore M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/instrumenters/__init__.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/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/brew_exts.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/dockerfiles.py M lib/galaxy/tools/deps/resolvers/__init__.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/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.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/loader.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parser/__init__.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/filters/__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/panel.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/toolbox/tags.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/verify/asserts/xml.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/__init__.py M lib/galaxy/util/biostar.py M lib/galaxy/util/checkers.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/json.py M lib/galaxy/util/lazy_process.py M lib/galaxy/util/none_like.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/util/permutations.py M lib/galaxy/util/properties.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/sockets.py M lib/galaxy/util/sqlite.py M lib/galaxy/util/streamball.py M lib/galaxy/util/submodules.py M lib/galaxy/util/topsort.py M lib/galaxy/util/validation.py M lib/galaxy/util/xml_macros.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/tools/tool_version_manager.py M setup.cfg M templates/show_params.mako M templates/webapps/galaxy/workflow/run.mako M test/functional/tools/column_multi_param.xml M test/functional/tools/column_param.xml M test/functional/tools/identifier_collection.xml M test/functional/tools/identifier_multiple.xml M test/functional/tools/identifier_single.xml M test/functional/tools/inputs_as_json.xml M test/functional/tools/multi_output.xml M test/functional/tools/multi_output_assign_primary.xml M test/functional/tools/multi_output_configured.xml M test/functional/tools/tool_directory.xml M test/functional/tools/validation_repeat.xml M test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py M test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py M test/unit/jobs/test_job_wrapper.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_objectstore.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/tools/test_watcher.py M test/unit/tools/test_wrappers.py M test/unit/tools_support.py M tools/data_source/upload.xml Log Message: ----------- Merge branch 'dev' into remote_chart_plugins Commit: 921933ea9cb108a45f804f36adc0dc76d447ed11 https://github.com/galaxyproject/galaxy/commit/921933ea9cb108a45f804f36adc0d... Author: carlfeberhard <carlfeberhard@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_16.07' into dev Commit: 694fac5f567491471dadd11bb934dbec5746cafd https://github.com/galaxyproject/galaxy/commit/694fac5f567491471dadd11bb934d... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Implement on random validator ``split``. Commit: 7e8bee8830d5d82e222b350d4bc240d1206e5af3 https://github.com/galaxyproject/galaxy/commit/7e8bee8830d5d82e222b350d4bc24... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: A galaxy.xsd Log Message: ----------- Deleting directories from SVN that should have been ignored. git-svn-id: https://svn.msi.umn.edu/tint/trunk@427 29e1c259-b37a-0410-ae23-5fb2df606144 Commit: 39fb238e666bb404b140b9ec37f1caeeb8a2637f https://github.com/galaxyproject/galaxy/commit/39fb238e666bb404b140b9ec37f1c... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Work on galaxy support, implemented repeat blocks in the UI. Commit: a718608e838f796bddb159b4e303194db52b3085 https://github.com/galaxyproject/galaxy/commit/a718608e838f796bddb159b4e3031... Author: Jean-Frédéric <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: A README.md Log Message: ----------- Add basic ReadMe Commit: 6e689fa77eef72020f62e00149bddfae825e299f https://github.com/galaxyproject/galaxy/commit/6e689fa77eef72020f62e00149bdd... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Remove custom namespaces Commit: e1fc626fc1d6f2e49519784bea217ea3022d4073 https://github.com/galaxyproject/galaxy/commit/e1fc626fc1d6f2e49519784bea217... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Change tool element to <xs:all> Element order is not enforced by Galaxy. Commit: 025a22b0e7bbb8f9fc89dac33c8e18fdfc49b36f https://github.com/galaxyproject/galaxy/commit/025a22b0e7bbb8f9fc89dac33c8e1... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add <requirements> tag set This includes: -<requirements> -<requirement> -Enumeration RequirementType Commit: 08f1faad44fde20cf0748d7c12785300d67942ec https://github.com/galaxyproject/galaxy/commit/08f1faad44fde20cf0748d7c12785... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Complete <repeat> tag set Add attributes min and max to Repeat element Commit: 9a9ba49caab8c63cff05153948160acccd80f912 https://github.com/galaxyproject/galaxy/commit/9a9ba49caab8c63cff05153948160... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add <options> tag to <param> The <param> tag can contain <options> to dynamically create a list of options. Commit: 6b828d2b29b1612c82bcd7348625318628712aaf https://github.com/galaxyproject/galaxy/commit/6b828d2b29b1612c82bcd73486253... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add <label> tag to <param> Commit: 150939e16a242a992d69bb771a6bf87f1936be40 https://github.com/galaxyproject/galaxy/commit/150939e16a242a992d69bb771a6bf... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add missing attributes to <param> tag Add seven missing attributes to <param> tag Add the necessary datatypes for display, hierarchy and checked. Commit: 62c32df6f1d7de93f04cd3a9b5fd7572f91f4363 https://github.com/galaxyproject/galaxy/commit/62c32df6f1d7de93f04cd3a9b5fd7... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add missing attributes and element to <data> tag Add three missing attributes to <data> tag Add <filter> element to sequence Commit: 73edfd6cf03c4366d4fd1036aa6fe3760958cd2a https://github.com/galaxyproject/galaxy/commit/73edfd6cf03c4366d4fd1036aa6fe... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Fix indentation Commit: 91a166b7f5f42ee60495da20443b73d4bda1a502 https://github.com/galaxyproject/galaxy/commit/91a166b7f5f42ee60495da20443b7... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add <parallelism> tag Add the <parallelism> tag (which serves for splitting job) and the datatype for the 'method' attribute. Commit: f9c5cf28ef2f60867a81dd8b6da3454e46d2936a https://github.com/galaxyproject/galaxy/commit/f9c5cf28ef2f60867a81dd8b6da34... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add <stdio> tag set to <tool> Add <stdio> tag set, to handle tool messages on standard output and standard error. - Add <stdio> tag - Add <regex> and <exit_code> sub elements - Add datatypes for 'range', 'level' and 'source' attributes Commit: 6e1d7e40a333d717a7c877c18eb94048dd99a7f0 https://github.com/galaxyproject/galaxy/commit/6e1d7e40a333d717a7c877c18eb94... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Change type for requirement version Version information can be too complex for xs:decimal (eg "0.12.7"). Change for xs:string. Commit: 642e88857caa09d968f4e5c740dc44475a64e288 https://github.com/galaxyproject/galaxy/commit/642e88857caa09d968f4e5c740dc4... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add column, filter and validator tags Commit: 1787f1e89b4a311d9bae2c60effc851347da50e2 https://github.com/galaxyproject/galaxy/commit/1787f1e89b4a311d9bae2c60effc8... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add ftype attribute to param tag in tests Commit: 6181d24704fd23b3370a961ba3fb573d0100f099 https://github.com/galaxyproject/galaxy/commit/6181d24704fd23b3370a961ba3fb5... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add <code> tag set Commit: 0da4d3c85361954a82fb8a0aa4c0f6bd742b9033 https://github.com/galaxyproject/galaxy/commit/0da4d3c85361954a82fb8a0aa4c0f... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Remove required use from <requirement> version Commit: 8164cfd3ba691dbb11fc5f623610b726ad5f2b85 https://github.com/galaxyproject/galaxy/commit/8164cfd3ba691dbb11fc5f623610b... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Edit <options> tag set Commit: bb285e4caee908cf4be30f0bf19ae21ffba20ebe https://github.com/galaxyproject/galaxy/commit/bb285e4caee908cf4be30f0bf19ae... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add <validator> to <param> Commit: 02aa90c4a477bb595540914df08ef9402275d84d https://github.com/galaxyproject/galaxy/commit/02aa90c4a477bb595540914df08ef... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add 'split' attribute to <validator> Commit: e200148feef9ff553820272d7893b387e6e4723d https://github.com/galaxyproject/galaxy/commit/e200148feef9ff553820272d7893b... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add <actions> tag set Commit: 1c9513d6cb64315e742eab7befec7536dee766c8 https://github.com/galaxyproject/galaxy/commit/1c9513d6cb64315e742eab7befec7... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Extend CheckedType to accept unspecified values According to the documentation, CheckedType can either be 'yes', 'true' or 'on' ; but many tools use '[Ff]alse' which seems to be accepted/ignored by Galaxy. Commit: b35b9fd52c78a891555660d7512e617b03d36cc0 https://github.com/galaxyproject/galaxy/commit/b35b9fd52c78a891555660d7512e6... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add PermissiveBoolean datatype <xs:boolean> can either be 'true', 'false', '1' or 'O' ; but many Galaxy tools use 'True' and 'False' (capitalized), which appears to be ignored/accepted by Galaxy. This PermissiveBoolean type is meant to be used in place of xs:boolean when needed. Commit: dd0ba4293dc03db422a7b33e974c3b7554c287e9 https://github.com/galaxyproject/galaxy/commit/dd0ba4293dc03db422a7b33e974c3... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add attributes 'ftype' and 'sort' to test <output> These are undocumented attributes. Commit: 4578e0a0f957ef7f851257b7bb605764712c5a44 https://github.com/galaxyproject/galaxy/commit/4578e0a0f957ef7f851257b7bb605... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add (undocumented) attributes to <filter> Add attributes 'compare', 'keep' and 'value' to <filter> tag (though these attributes are not documented). Add CompareType for possible 'compare' values. Commit: 4bdfd455c58d00c5a28fdf1e6fc80d70648cb57a https://github.com/galaxyproject/galaxy/commit/4bdfd455c58d00c5a28fdf1e6fc80... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Edit filter tag for output tag Commit: 566e279172c98e417c7fca9cf04bda2e3abd2da5 https://github.com/galaxyproject/galaxy/commit/566e279172c98e417c7fca9cf04bd... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Rewrite <actions> handling Commit: 1cda2e4439f28229d000f30120ecf69709606b6f https://github.com/galaxyproject/galaxy/commit/1cda2e4439f28229d000f30120ecf... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add (undocumented) 'dbkey' attribute to TestParam Commit: 081c39e55161e1d1babebed1d159f2415a8e0adb https://github.com/galaxyproject/galaxy/commit/081c39e55161e1d1babebed1d159f... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add 'from_file' value to ActionsOptionType Commit: b466de7e0a5e019d1a4264f2982f8c2012715241 https://github.com/galaxyproject/galaxy/commit/b466de7e0a5e019d1a4264f2982f8... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Use PermissiveBoolean for ParamOption 'selected' Commit: 92b1076261ee0403ff8fb6f8e2601ba5149e9807 https://github.com/galaxyproject/galaxy/commit/92b1076261ee0403ff8fb6f8e2601... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add attributes tool_type and URL_method to <tool> And corresponding enumeration Datatypes. Commit: e8f236a52e5c4081ef9a228e15ffefb50185db7f https://github.com/galaxyproject/galaxy/commit/e8f236a52e5c4081ef9a228e15ffe... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- use PermissiveBoolean on two attributes of <param> Commit: 7d7b5a8d3dfc604335626f0abf806377dc2b630c https://github.com/galaxyproject/galaxy/commit/7d7b5a8d3dfc604335626f0abf806... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add (undocumented) value 'no' to CheckedType Commit: e19f1fb99a982cedebc74a3b42f0c376e19d46bc https://github.com/galaxyproject/galaxy/commit/e19f1fb99a982cedebc74a3b42f0c... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add (undocumented) <uihints> to <tool> See /lib/galaxy/tools/__init__.py:1069 for usage Commit: 836aff4b3f70d6073bbd5f4d78d4b6688aed7baa https://github.com/galaxyproject/galaxy/commit/836aff4b3f70d6073bbd5f4d78d4b... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add (undocumented) attributes to <inputs> Add attributes 'action', 'check_values', 'method' and 'target' to <inputs>. Add relevant Target datatype. Commit: c4769e701302625031db4a7730e572b32c019ead https://github.com/galaxyproject/galaxy/commit/c4769e701302625031db4a7730e57... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add <sanitizer> tag Commit: 5419b1a4bce60a4459b59711acbf9c2652d5722d https://github.com/galaxyproject/galaxy/commit/5419b1a4bce60a4459b59711acbf9... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add (undocumented) attribute metadata_name to <param> Commit: 79cf1c57d8b6a1add066bf61ec18936bf1a8f6ee https://github.com/galaxyproject/galaxy/commit/79cf1c57d8b6a1add066bf61ec189... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add (undocumented) attributes to <options> Add 'options_filter_attribute' attribute (see lib/galaxy/tools/parameters/basic.py) Add 'transform_lines' attribute (see lib/galaxy/tools/parameters/dynamic_options.py) transform_lines and Commit: 11b013f402b90c742789df87b6810e156a173171 https://github.com/galaxyproject/galaxy/commit/11b013f402b90c742789df87b6810... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add (undocumented) 'ref_attribute' to <filter> Add attribute 'ref_attribute' to <filter> (see lib/galaxy/tools/parameters/dynamic_options.py:153) Commit: 65903327fa21536d44822ef94a9e75b2d29cf11d https://github.com/galaxyproject/galaxy/commit/65903327fa21536d44822ef94a9e7... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add (undocumented) 'startswith' to <options> Add attribute 'startswith' to <options> tag (see lib/galaxy/tools/parameters/dynamic_options.py:416) Commit: d12766e260ea8d1e6ebe61806cb7e2b3eb55b886 https://github.com/galaxyproject/galaxy/commit/d12766e260ea8d1e6ebe61806cb7e... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add (undocumented) attribute 'display' to <inputs> See lib/galaxy/tools/__init__.py:1531 Commit: 091b3b85687eeb8ef5becdf30ff81211b12f6f45 https://github.com/galaxyproject/galaxy/commit/091b3b85687eeb8ef5becdf30ff81... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Fix value baseurl in <param> 'type' attribute Commit: 395780d3d143982204c1f9ccf188df1deff51d55 https://github.com/galaxyproject/galaxy/commit/395780d3d143982204c1f9ccf188d... Author: JeanFred <jean-frederic.berthelot@lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Fix type of min and max in <validator> Commit: 2fdf2267b841d2701db424f9d2f458d8fbc2309b https://github.com/galaxyproject/galaxy/commit/2fdf2267b841d2701db424f9d2f45... Author: Pierre Lindenbaum <plindenbaum@yahoo.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: A .gitignore A Makefile M README.md A citation.xsd A citations.xsd A galaxy.jxb M galaxy.xsd A test.urls Log Message: ----------- added doc and JXB bindings Commit: 2cecbe1922a9b5d75f34d42bedcd025a83fbae09 https://github.com/galaxyproject/galaxy/commit/2cecbe1922a9b5d75f34d42bedcd0... Author: Pierre Lindenbaum <plindenbaum@yahoo.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M README.md Log Message: ----------- updated README Commit: f692d3a5ae244ce638be596723f369dade3ed501 https://github.com/galaxyproject/galaxy/commit/f692d3a5ae244ce638be596723f36... Author: Jean-Fred <JeanFred@github> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: A .travis.yml Log Message: ----------- Add Continuous integration with Travis for XSD linting At the very least these XSD files should be XML valid. Commit: cdbe79b4b657609724081c991466b0be13460d36 https://github.com/galaxyproject/galaxy/commit/cdbe79b4b657609724081c991466b... Author: Jean-Fred <JeanFred@github> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M .travis.yml Log Message: ----------- Fix dependency installation for Travis Build was failing with $ apt-get install libxml2-utils E: Could not open lock file /var/lib/dpkg/lock - open (13: Permission denied) E: Unable to lock the administration directory (/var/lib/dpkg/), are you root? APT dependencies must be installed as sudoer. Commit: 00a560ce1dbb093989b36f628abf08bf5ad3ee91 https://github.com/galaxyproject/galaxy/commit/00a560ce1dbb093989b36f628abf0... Author: Jean-Fred <JeanFred@github> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M README.md Log Message: ----------- Add Travis badge to ReadMe Commit: 3315e9a8c424281df01e7521a9c9715447356059 https://github.com/galaxyproject/galaxy/commit/3315e9a8c424281df01e7521a9c97... Author: Jean-Fred <JeanFred@github> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: A test.sh Log Message: ----------- Add Shell test script Following the idea of @lindenb in the Makefile. This tests all the given URLs in test.urls and outputs a compliant TAP. Commit: bcc20e289fc9c4df1615530b264a6cada2e39974 https://github.com/galaxyproject/galaxy/commit/bcc20e289fc9c4df1615530b264a6... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M README.md Log Message: ----------- Add me (@jmchilton) to authors list. My name is on the earliest commits (thanks for preserving that). Commit: 1b7f2a54f6c2b12d9340fe4c8c3e8de0f0f68afb https://github.com/galaxyproject/galaxy/commit/1b7f2a54f6c2b12d9340fe4c8c3e8... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M citation.xsd M test.urls Log Message: ----------- Fix CitationType attribute. Add Galaxy's test tool for citations to test.urls. Commit: 057c36997bd5c4c75a85acd5a9346f8c28eee015 https://github.com/galaxyproject/galaxy/commit/057c36997bd5c4c75a85acd5a9346... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd M test.urls Log Message: ----------- Update XSD for container tags. Add Galaxy test tool for Docker container tags to test.urls. Commit: bdf36556fbf4c4db4c343e51d6d78c1ac2030464 https://github.com/galaxyproject/galaxy/commit/bdf36556fbf4c4db4c343e51d6d78... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Drop embeddedValue for test stuff. These were an extension to the Galaxy XML syntax for TINT - which is no longer actively maintained. Commit: f0799b5fbb9dfe54241b702c450f258c946bf326 https://github.com/galaxyproject/galaxy/commit/f0799b5fbb9dfe54241b702c450f2... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd M test.urls Log Message: ----------- Start work on implementing assert_contents tag in tests. Just enough to get Galaxy's simple_contructrs.xml to validate - add this to test.urls. More work should be done on these - but it should be automated derived from Galaxy somehow. Commit: b479b7334fc6649606c5144da7c9225c82857e6b https://github.com/galaxyproject/galaxy/commit/b479b7334fc6649606c5144da7c92... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd M test.urls Log Message: ----------- Update XSD for very basic data collection usage. - Allow 'data_collection' parameters and allow them to specify a 'collection_type'. - Allow test parameters to be flat collections. - Add test/functional/tools/collection_paired_test.xml to test.urls to check all of this. Lots more TODO for recent tool collection support - output collections definitions, output collection tests, dynamic discovery tags, specifying nested collections for test inputs. Commit: 49f7d51f57eb2f72e01e37fdaf6c44ffe11898de https://github.com/galaxyproject/galaxy/commit/49f7d51f57eb2f72e01e37fdaf6c4... Author: Jean-Fred <JeanFred@github> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: A LICENSE M README.md Log Message: ----------- Add MIT license Per agreement of all authors. Closes #2. Commit: 8947f29ef2596e750d2783206df547efc7ef40fd https://github.com/galaxyproject/galaxy/commit/8947f29ef2596e750d2783206df54... Author: Jean-Fred <JeanFred@github> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M README.md Log Message: ----------- Expand history in ReadMe Commit: 5d40c7b3e2b66d91a52ae12cf48cda30d245d180 https://github.com/galaxyproject/galaxy/commit/5d40c7b3e2b66d91a52ae12cf48cd... Author: Jean-Fred <JeanFred@github> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M LICENSE Log Message: ----------- Fix authors in License file Follow up on #2. Commit: a4e5568af7f206c61ebf7afd9165bd1e34181d0b https://github.com/galaxyproject/galaxy/commit/a4e5568af7f206c61ebf7afd9165b... Author: Michael R. Crusoe <crusoe@ucdavis.edu> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- first try Commit: 8f8cc890bcfaceaf4870daa2d4e22e10018119c2 https://github.com/galaxyproject/galaxy/commit/8f8cc890bcfaceaf4870daa2d4e22... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Improvements to XSD: - Implement section. - Implement and document request_parameter_translation, request_parameter and its children (value_translation and append_param). - Implement detect_errors on the command block and document defaults. Commit: 63c019b13b44fedc9159909eb7995294d3653244 https://github.com/galaxyproject/galaxy/commit/63c019b13b44fedc9159909eb7995... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- More progress... - Fix to previous commit. - Remove downstream config file type that was abandoned work and not in galaxy-core. - More documentation for configfile stuff. - Improvements to representation for output and santizer. Commit: 1125f1b8ea8b993ac5493f663b76c4ba54350ee4 https://github.com/galaxyproject/galaxy/commit/1125f1b8ea8b993ac5493f663b76c... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Simplify schema and improve docs related to sanitization. Commit: 21cd752e252d17fdba2401cbe78bc3ef62ffd327 https://github.com/galaxyproject/galaxy/commit/21cd752e252d17fdba2401cbe78bc... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Improve docs on filter and change_format of outputs. Commit: 804c072d5af2e5704d57a503a84ad6733f03c1c0 https://github.com/galaxyproject/galaxy/commit/804c072d5af2e5704d57a503a84ad... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- And more progress... - Docs for help. - Docs for tests. - Docs for code files. - Implementing more of the assert_xxx test flags. - Improved coverage of test assertion element descriptions. Commit: 23449750d46e4df208fc46d1c2a4d3840cd080f4 https://github.com/galaxyproject/galaxy/commit/23449750d46e4df208fc46d1c2a4d... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- More progress... - Refine test outputs and include syntax for testing extra files and md5sums. Commit: 3d3c3fee4f576408c223c723b57b003ae6ccf4c1 https://github.com/galaxyproject/galaxy/commit/3d3c3fee4f576408c223c723b57b0... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- More progress. - Add strict to command. - Add conditional and repeat to test params. - Add count to output collections. - Implement more collection output attributes (type_source, etc...). - Reduce need for type on collection defs (since type_source can be defined). Commit: 80d086b861f1401568b967d96e2e37461ca677a2 https://github.com/galaxyproject/galaxy/commit/80d086b861f1401568b967d96e2e3... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- More progress... - Allow section in test parameters. - Implement basic metadata testing. Commit: 19b273cdf55df6b2593715d7daaf4690d8d6935b https://github.com/galaxyproject/galaxy/commit/19b273cdf55df6b2593715d7daaf4... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- More progress... - Allow nested elements in test output collections (hackily) - Implement ``compare`` and ``delta`` for test output comparison. - Implement the new ``checksum`` output test. Commit: 7f5cc04c114bd5e696e7e54697e5a7bf58277fa7 https://github.com/galaxyproject/galaxy/commit/7f5cc04c114bd5e696e7e54697e5a... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- More progress... - Add tool action. - Stub workflow_compatible and profile_version attributes on tool. - Add many more attributes to parallelism tag. - Add maxseconds and expect_num_outputs to tool test tag. - Small fix to <repeat> block in test cases. - Implement assigning metadata in test params. - Allow more versitle ordering of test blocks (too permissive now). - Implement testing of output metadata and discovered datasets. - Add nginx_upload attribute used by upload.xml and various conditional attributes for pulling in values from Galaxy internals. - Implement the stub of a ``upload_dataset`` param and say not to use it. - Add color and library data parameter types. - More attributes to filters and validators. - Implement auto_format on outputs. - Implement filters and explicit data outputs on output collections. - Implement inputs as json element. - Add empty dataset validator. Commit: 49ff357854ff1a8dab9d792c0d97881f33c5a603 https://github.com/galaxyproject/galaxy/commit/49ff357854ff1a8dab9d792c0d978... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Stub out environment variables and add a new tool type. Commit: c6ae6ee8cb3c240923e4738f0e8f0a4a1134cbd5 https://github.com/galaxyproject/galaxy/commit/c6ae6ee8cb3c240923e4738f0e8f0... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: R citation.xsd R citations.xsd M galaxy.xsd Log Message: ----------- Embed citations right in galaxy.xsd. Not that I mind splitting it up - but it will make a couple things easier downstream and those few tags weren't enough to warrent breaking things up like that. Commit: dcfdd3ceaa62ccee0a8d22c6d299eab2742df47f https://github.com/galaxyproject/galaxy/commit/dcfdd3ceaa62ccee0a8d22c6d299e... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Many more fixes derived from testing tools-iuc. Commit: 8c2a4e12758827b0855181de962ef0f0a61515a7 https://github.com/galaxyproject/galaxy/commit/8c2a4e12758827b0855181de962ef... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- And more progress - now covers all Galaxy test tools and all IUC. - Add <options> block. - Add <trackster_conf> block. - Add a newerish validator and allow filter/validator columns to be column names. - More permissives boolean values to match Galaxy in various places. - Other mostly obsecure features. Commit: ff6cca8635e6ce1c906dd316dcc0d6ab0bed7fb3 https://github.com/galaxyproject/galaxy/commit/ff6cca8635e6ce1c906dd316dcc0d... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Doc updates Commit: 491efe8c4951eedecc1635dbc972fb49ec883230 https://github.com/galaxyproject/galaxy/commit/491efe8c4951eedecc1635dbc972f... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Doc improvements. Commit: 94ad78da97b98eee05a5ff0f890eec0e518845b7 https://github.com/galaxyproject/galaxy/commit/94ad78da97b98eee05a5ff0f890ee... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Much richer documentation for a few tags including ``command``. Commit: e9f08b411a0bf4ef8620bc66fb7c10d61112fb49 https://github.com/galaxyproject/galaxy/commit/e9f08b411a0bf4ef8620bc66fb7c1... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- More work on documentation - revise last commit and add repeats and sections. Commit: 2e31bc932dd9bd96d403cd8e6ef20715785c3eef https://github.com/galaxyproject/galaxy/commit/2e31bc932dd9bd96d403cd8e6ef20... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Work on docs. Commit: 8f2f62a75a7aa256904821888c09682ebde99c83 https://github.com/galaxyproject/galaxy/commit/8f2f62a75a7aa256904821888c096... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- More docs... - Added docs for param's option. - Started work on validators and options, but are WIP though. Commit: 4bcfe568b713e9369d0d1e5090e140d7ebfee17c https://github.com/galaxyproject/galaxy/commit/4bcfe568b713e9369d0d1e5090e14... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- More docs for validators. Commit: 2980835dc7ec8b2ba2e1cde39142e0697c4fc9f8 https://github.com/galaxyproject/galaxy/commit/2980835dc7ec8b2ba2e1cde39142e... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- A lot more documentation around parameter options. Also fixed a bit of a problem - turns out <filter> in action conditionals is very different than filter in options so I've split these types out. Commit: cd5328dce2aff381df95fa7b523dc40bc525f704 https://github.com/galaxyproject/galaxy/commit/cd5328dce2aff381df95fa7b523dc... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- More documentation... Cleaned up the stdio tags and help section, flushed out citations and parameter options. Small touchups other places also. Commit: 24f46245e09ef044cca6804c48c994e49b70b69a https://github.com/galaxyproject/galaxy/commit/24f46245e09ef044cca6804c48c99... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Mention code files as a way to generate dynamic options. Transplant example from Galaxy wiki of doing this. Commit: 6481a00f88bff4bb7a7adbf2aaaee639e4649147 https://github.com/galaxyproject/galaxy/commit/6481a00f88bff4bb7a7adbf2aaaee... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Flush out docs for requirements and child tags. Commit: 3af76de52ff56fca6b65d993ce91fb39c30af2d2 https://github.com/galaxyproject/galaxy/commit/3af76de52ff56fca6b65d993ce91f... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Flush out docs for sanitizers, configfiles, etc... Commit: b059c8b592b0f45dd669f8e9cbca714ed292ccac https://github.com/galaxyproject/galaxy/commit/b059c8b592b0f45dd669f8e9cbca7... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Working my way through basic parameter documentation. Commit: 366def7026a68e2bde75a140e3e4f1496966b1f2 https://github.com/galaxyproject/galaxy/commit/366def7026a68e2bde75a140e3e4f... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- More work on parameters and environment variables. Commit: 4ba421e2f67de03dfa51ad8493f9a27beb159f27 https://github.com/galaxyproject/galaxy/commit/4ba421e2f67de03dfa51ad8493f9a... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Finishing first pass at filling out wiki docs for ``param``. And other small fixes. Commit: 5ad6e790e2f1a752beb748581469aa2e9f73477f https://github.com/galaxyproject/galaxy/commit/5ad6e790e2f1a752beb748581469a... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Starting to polish and flush out data outputs documentation. Commit: e2d55ccf1685ec767d2c09715b189c7a1ff411cb https://github.com/galaxyproject/galaxy/commit/e2d55ccf1685ec767d2c09715b189... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- More docs - conditional output actions and some more on discover datasets. Commit: 89c8934727c7a8b8cc4ca7db10e7882d22542a87 https://github.com/galaxyproject/galaxy/commit/89c8934727c7a8b8cc4ca7db10e78... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- A bunch of work on cleaning up and flushing out documentation for test tags. Commit: c607727d83c079a2859ed9026d26edbb52f4bcf9 https://github.com/galaxyproject/galaxy/commit/c607727d83c079a2859ed9026d26e... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Document the test ``output_collection`` tag. Commit: fc440a87c4883a9244d5e45783e2f27b639319cb https://github.com/galaxyproject/galaxy/commit/fc440a87c4883a9244d5e45783e2f... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Fix missing annotation. Commit: 60def6204d1ba2299442a76856f19ab53ffe1e92 https://github.com/galaxyproject/galaxy/commit/60def6204d1ba2299442a76856f19... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Fixes of structure broken with docs. Commit: b74c1a5b0baa6da94ca45f11a1e8e2057fcf2790 https://github.com/galaxyproject/galaxy/commit/b74c1a5b0baa6da94ca45f11a1e8e... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Use the new action conditional filter. Commit: 195fd46604a64ad8928ead83d6cd6f7f51a2639c https://github.com/galaxyproject/galaxy/commit/195fd46604a64ad8928ead83d6cd6... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add a fictious XML schema with Galaxy stuff. New attributes: - deprecated - best_practices (provides links of the form http://planemo.readthedocs.io/en/latest/standards/docs/best_practices/tool_x...) Commit: 4dd8da09b8bd1917094622039adfe01cffa2fd40 https://github.com/galaxyproject/galaxy/commit/4dd8da09b8bd1917094622039adfe... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Remove embedded best practice stuff - the help will have links now. Commit: c4f03079d7fefb2e37790b4d07fe7d0a67990d8d https://github.com/galaxyproject/galaxy/commit/c4f03079d7fefb2e37790b4d07fe7... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Fill out some docs for test sections... Commit: 0c6be2095710fbb79bd9b9fdd231e960bb9f2ce8 https://github.com/galaxyproject/galaxy/commit/0c6be2095710fbb79bd9b9fdd231e... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M test.sh Log Message: ----------- Revise automated testing, check against test tools and IUC tools. Commit: b9d25b848c333226e503d4f301187a43dbebc584 https://github.com/galaxyproject/galaxy/commit/b9d25b848c333226e503d4f301187... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Document testing discovered datasets and metadata. Commit: 8b7ae4bc7b446b0b00758f6cf0c98e7eaece96ce https://github.com/galaxyproject/galaxy/commit/8b7ae4bc7b446b0b00758f6cf0c98... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Fix a syntax error. Commit: 236bdf5a40d0d720a72b7c71b03e2cb79fc576d4 https://github.com/galaxyproject/galaxy/commit/236bdf5a40d0d720a72b7c71b03e2... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Update the link for multiple outputs. Commit: 3d7ae4e38fea3d7f84368ccb57f107f0c13f9749 https://github.com/galaxyproject/galaxy/commit/3d7ae4e38fea3d7f84368ccb57f10... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: R .gitignore R .travis.yml R LICENSE R Makefile R README.md R galaxy.jxb R galaxy.xsd A lib/galaxy/tools/xsd/LICENSE A lib/galaxy/tools/xsd/Makefile A lib/galaxy/tools/xsd/README.md A lib/galaxy/tools/xsd/galaxy.jxb A lib/galaxy/tools/xsd/galaxy.xsd A lib/galaxy/tools/xsd/test.sh A lib/galaxy/tools/xsd/test.urls R test.sh R test.urls Log Message: ----------- Relocate Galaxy XSD files into Galaxy directory structure. Commit: 491c9fd519be37b6c6f57cd4082d981c9f411ba5 https://github.com/galaxyproject/galaxy/commit/491c9fd519be37b6c6f57cd4082d9... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: R lib/galaxy/tools/xsd/Makefile R lib/galaxy/tools/xsd/test.urls Log Message: ----------- Cleanup XSD for move to Galaxy core. Commit: c4d8dddc5cbfe416e5931e409db9e63804688f1e https://github.com/galaxyproject/galaxy/commit/c4d8dddc5cbfe416e5931e409db9e... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: A lib/galaxy/tools/xsd/LICENSE A lib/galaxy/tools/xsd/README.md A lib/galaxy/tools/xsd/galaxy.jxb A lib/galaxy/tools/xsd/galaxy.xsd A lib/galaxy/tools/xsd/test.sh Log Message: ----------- Merge branch 'master' of Galaxy-XSD into 'dev' Commit: babaf7a2c675648e2851f81d985a72321b4eeb44 https://github.com/galaxyproject/galaxy/commit/babaf7a2c675648e2851f81d985a7... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd R lib/galaxy/tools/xsd/test.sh Log Message: ----------- Address reviewer comments on XSD. - Merge in @bgruening's numerous awesome fixes. - Remove test script with issues that make if not a fit for this repo in that form (noted by @nsoranzo). - Incorporate other changes to the XSD suggested by @nsoranzo. Commit: f553d387a47d0ef1a58a1522c0f437e3b1783a59 https://github.com/galaxyproject/galaxy/commit/f553d387a47d0ef1a58a1522c0f43... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: A client/galaxy/scripts/libs/bbi/bigwig.js A client/galaxy/scripts/libs/bbi/jquery-ajax-native.js A client/galaxy/scripts/libs/bbi/jszlib.js A client/galaxy/scripts/libs/bbi/spans.js A client/galaxy/scripts/viz/bbi-data-manager.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js A static/maps/libs/bbi/bigwig.js.map A static/maps/libs/bbi/jquery-ajax-native.js.map A static/maps/libs/bbi/jszlib.js.map A static/maps/libs/bbi/spans.js.map A static/maps/viz/bbi-data-manager.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/tracks.js.map A static/scripts/libs/bbi/bigwig.js A static/scripts/libs/bbi/jquery-ajax-native.js A static/scripts/libs/bbi/jszlib.js A static/scripts/libs/bbi/spans.js A static/scripts/viz/bbi-data-manager.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/tracks.js Log Message: ----------- Merge pull request #2880 from jgoecks/bbi-js3 Trackster: Read numerical data directly from bigwig files Commit: e76bbf53b62f29f2d05459ecea13fd8e98449aa4 https://github.com/galaxyproject/galaxy/commit/e76bbf53b62f29f2d05459ecea13f... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/history_contents.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #2885 from carlfeberhard/file-walker API, history contents: contents download endpoint Commit: 70251b5b6a8363a627fccf90f642c3a02cc57cd5 https://github.com/galaxyproject/galaxy/commit/70251b5b6a8363a627fccf90f642c... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M lib/galaxy/tools/xsd/LICENSE Log Message: ----------- Update the LICENSE for the XSD file. Commit: a698fa52b3aef236cbf6bad729e286552b84114c https://github.com/galaxyproject/galaxy/commit/a698fa52b3aef236cbf6bad729e28... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M LICENSE.txt Log Message: ----------- Update the Copyright year in the LICENSE.txt. Commit: 9d24d55cb5e515b8e8f9654e070ae17aae864367 https://github.com/galaxyproject/galaxy/commit/9d24d55cb5e515b8e8f9654e070ae... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M CONTRIBUTORS.md Log Message: ----------- Add XSD contributors to CONTRIBUTORS.md. Commit: c576f27d4fba92c1066964fc1b32d24921a65771 https://github.com/galaxyproject/galaxy/commit/c576f27d4fba92c1066964fc1b32d... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M LICENSE.txt Log Message: ----------- Merge pull request #2926 from jmchilton/copyright Update the Copyright year in the LICENSE.txt. Commit: f34ab79d22b261e6606ae994f7c2b8bb14273ca2 https://github.com/galaxyproject/galaxy/commit/f34ab79d22b261e6606ae994f7c2b... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Merge pull request #2921 from jmchilton/implement_split Implement ``split`` on a validator. Commit: 4c60b812030423f7e4c755f7cbc57c83083ea834 https://github.com/galaxyproject/galaxy/commit/4c60b812030423f7e4c755f7cbc57... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-09-16 (Fri, 16 Sep 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge branch 'release_16.07' into dev Conflicts: lib/galaxy/tools/deps/__init__.py Commit: 7a8d9af16b97677656234c68d88c760495b4d322 https://github.com/galaxyproject/galaxy/commit/7a8d9af16b97677656234c68d88c7... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-09-16 (Fri, 16 Sep 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Catch failure to import grp in util (for Pulsar on Windows) Commit: 31b4eb155fa8f9f9d13d17ed60592f9cd99f23db https://github.com/galaxyproject/galaxy/commit/31b4eb155fa8f9f9d13d17ed60592... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-16 (Fri, 16 Sep 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #2928 from natefoo/windows-util-fix Catch failure to import grp in util (for Pulsar on Windows) Commit: f12723dc8311b35c9cf7271dc3bc46f640bde00b https://github.com/galaxyproject/galaxy/commit/f12723dc8311b35c9cf7271dc3bc4... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-16 (Fri, 16 Sep 2016) Changed paths: M CONTRIBUTORS.md A lib/galaxy/tools/xsd/LICENSE A lib/galaxy/tools/xsd/README.md A lib/galaxy/tools/xsd/galaxy.jxb A lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #2923 from jmchilton/merge_xsd_into_core Merge Galaxy-XSD into project Commit: bbf72ef932f7e7ef314b905e17b4958180f4eb11 https://github.com/galaxyproject/galaxy/commit/bbf72ef932f7e7ef314b905e17b49... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-16 (Fri, 16 Sep 2016) Changed paths: A .ci/validate_test_tools.sh M .travis.yml R test/functional/tools/multi_page.xml M test/functional/tools/samples_tool_conf.xml M tox.ini Log Message: ----------- CI testing of newly integrated tool schema (XSD). - Add CI script that lints the XSD definition and then validates all test tools against it. - Add tox environment to run the aforementioned script. - Add Travis check through tox to run the script. - Drop the multi_page.xml test tool - pages have been removed from the framework and are not part of the schema (xref https://github.com/galaxyproject/galaxy/issues/1776). This will hopefully ensure that all new tool features get added to the schema (as long as there is a test tool for the feature). xref https://github.com/galaxyproject/galaxy/pull/2923 https://github.com/galaxyproject/galaxy/pull/2903 Largely based on work done in Galaxy-XSD by JeanFred (e.g. https://github.com/galaxyproject/Galaxy-XSD/commit/386ba087881877093d4be1f6d...) Commit: 05ae9959078a94da25a16ed8ef13f2a2d6aceb45 https://github.com/galaxyproject/galaxy/commit/05ae9959078a94da25a16ed8ef13f... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-16 (Fri, 16 Sep 2016) Changed paths: M .ci/validate_test_tools.sh A scripts/validate_tools.sh Log Message: ----------- Refactor most of tool validation for CI into a standalone script. Commit: 8ca517dc8b937e5f435e2a5046e3ecc32c27d504 https://github.com/galaxyproject/galaxy/commit/8ca517dc8b937e5f435e2a5046e3e... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-16 (Fri, 16 Sep 2016) Changed paths: M .travis.yml M tox.ini Log Message: ----------- More fixes pointed out by @nsoranzo for validation CI. Commit: a58d50e14f31c0639069959ef4d68b75ef331580 https://github.com/galaxyproject/galaxy/commit/a58d50e14f31c0639069959ef4d68... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-16 (Fri, 16 Sep 2016) Changed paths: M .travis.yml Log Message: ----------- Another fix thanks to @nsoranzo. Commit: 71cea6604d43c5fe6215f5656462ba6c1af69bb6 https://github.com/galaxyproject/galaxy/commit/71cea6604d43c5fe6215f5656462b... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2016-09-16 (Fri, 16 Sep 2016) Changed paths: A .ci/validate_test_tools.sh M .travis.yml A scripts/validate_tools.sh R test/functional/tools/multi_page.xml M test/functional/tools/samples_tool_conf.xml M tox.ini Log Message: ----------- Merge pull request #2932 from jmchilton/validate_test_tools CI testing of newly integrated tool schema (XSD). Commit: b58b83e56e458efd749fb9966cfe087cfbf41c3d https://github.com/galaxyproject/galaxy/commit/b58b83e56e458efd749fb9966cfe0... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-09-19 (Mon, 19 Sep 2016) Changed paths: M lib/galaxy/web/framework/decorators.py Log Message: ----------- Allow JSONP in api calls Commit: ffd0ac78cd3920768ed84f6ab780c13d69532a45 https://github.com/galaxyproject/galaxy/commit/ffd0ac78cd3920768ed84f6ab780c... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-09-19 (Mon, 19 Sep 2016) Changed paths: M lib/galaxy/web/framework/decorators.py Log Message: ----------- Extend JSONP to older decorators Commit: c69a20f76109754c846ac2d42e22ce87cdc96bca https://github.com/galaxyproject/galaxy/commit/c69a20f76109754c846ac2d42e22c... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: M lib/galaxy/web/framework/decorators.py Log Message: ----------- API, jsonp: better var name Commit: a312ef29e113f510d7fffa0343824b4491206c0a https://github.com/galaxyproject/galaxy/commit/a312ef29e113f510d7fffa0343824... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: M lib/galaxy/web/framework/decorators.py Log Message: ----------- API, jsonp: switch off for certain decorators Commit: 35d0fed80145c7d07c0512ebcb9b4a23c4293072 https://github.com/galaxyproject/galaxy/commit/35d0fed80145c7d07c0512ebcb9b4... Author: Nicola Soranzo <nicola.soranzo@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_16.07' into dev Commit: 97532515ea24325ba26877696991b24401733ee6 https://github.com/galaxyproject/galaxy/commit/97532515ea24325ba26877696991b... Author: Jim Johnson <jj@umn.edu> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/genomes.py Log Message: ----------- API access to genome fasta index and sequence Allows visualization components, e.g. IGV.js, to incrementally retrieve sequence as needed. Commit: 9ae56b782a241c373d3ef4496d9110763b31c951 https://github.com/galaxyproject/galaxy/commit/9ae56b782a241c373d3ef4496d911... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: M lib/galaxy/web/framework/decorators.py Log Message: ----------- Merge pull request #2937 from carlfeberhard/jsonp Allow JSONP to be returned from API endpoints Commit: 10b310b87142a9f34a1ce5340575d6c351a2279b https://github.com/galaxyproject/galaxy/commit/10b310b87142a9f34a1ce5340575d... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/extract.py M templates/webapps/galaxy/workflow/build_from_current_history.mako Log Message: ----------- Allow naming Dataset/collection inputs during workflow extraction. Default name is now the original input dataset name. Commit: 9890cb63f12d2d2e5eccd40e931c5563732efd44 https://github.com/galaxyproject/galaxy/commit/9890cb63f12d2d2e5eccd40e931c5... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: M templates/webapps/galaxy/workflow/build_from_current_history.mako Log Message: ----------- Text inputs can't be checked. Commit: 36b514c6e963b44b27003e7f64f0a9fe019f305e https://github.com/galaxyproject/galaxy/commit/36b514c6e963b44b27003e7f64f0a... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/util/checkers.py Log Message: ----------- Remove unnecessary use of binascii Also explicitly specify binary mode for file opening and header strings. Fix import order. Commit: a8bc9d5d16244badb023a9c5097efd826b26db56 https://github.com/galaxyproject/galaxy/commit/a8bc9d5d16244badb023a9c5097ef... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M .gitignore M Makefile A doc/parse_gx_xsd.py A doc/schema_template.md Log Message: ----------- XSD Generated Tool Documentation. - Add script to generate Markdown documentation from the XSD. - Add Makefile target to build these docs, convert to HTML, and open respectively. Commit: 0e0b773edc85c3e36ae25f38ee929e8a95cc520b https://github.com/galaxyproject/galaxy/commit/0e0b773edc85c3e36ae25f38ee929... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/security/validate_user_input.py M templates/user/info.mako M templates/user/register.mako M test/unit/managers/test_UserManager.py Log Message: ----------- Allow '.' and '_' for public names Fix #2593. Also standardise error messages. Commit: 70db2b7c4ad253b3ce0443d66df3832e4fc2a189 https://github.com/galaxyproject/galaxy/commit/70db2b7c4ad253b3ce0443d66df38... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/mobile.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Validate public name when auto-registering a user Commit: 8fb3cd9c5bc52495e6055c0a2a5bb4339e31612b https://github.com/galaxyproject/galaxy/commit/8fb3cd9c5bc52495e6055c0a2a5bb... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M templates/user/info.mako M templates/user/register.mako M templates/user/username.mako Log Message: ----------- propagate allowed changes to hints Commit: 736df5a0717089f815e0ba02ef7e9502fef36814 https://github.com/galaxyproject/galaxy/commit/736df5a0717089f815e0ba02ef7e9... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M templates/user/info.mako M templates/user/register.mako M templates/user/username.mako Log Message: ----------- Merge pull request #4 from martenson/nsoranzo-publicnames propagate allowed username changes to form hints Commit: f799656b1117d74afac0cd0c4ad1ca19625ca625 https://github.com/galaxyproject/galaxy/commit/f799656b1117d74afac0cd0c4ad1c... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/security/validate_user_input.py M lib/galaxy/webapps/galaxy/controllers/mobile.py M lib/galaxy/webapps/galaxy/controllers/user.py M templates/user/info.mako M templates/user/register.mako M templates/user/username.mako M test/unit/managers/test_UserManager.py Log Message: ----------- Merge pull request #2947 from nsoranzo/publicnames Allow '.' and '_' for public names Commit: 7d76bfe046fef24e25d4d04ef68b8228971aa79c https://github.com/galaxyproject/galaxy/commit/7d76bfe046fef24e25d4d04ef68b8... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/extract.py M templates/webapps/galaxy/workflow/build_from_current_history.mako Log Message: ----------- Merge pull request #2943 from blankenberg/wf_input_name Allow naming Dataset/collection inputs during workflow extraction. Commit: b30d331a811f2c5621ba81ff5bd54dc4ee93d755 https://github.com/galaxyproject/galaxy/commit/b30d331a811f2c5621ba81ff5bd54... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge branch 'release_16.07' into dev Commit: c81ec07c6d39f7dbb080f0db3680d6a29747608a https://github.com/galaxyproject/galaxy/commit/c81ec07c6d39f7dbb080f0db3680d... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/util/checkers.py Log Message: ----------- Merge pull request #2946 from nsoranzo/binascii_reduction Remove unnecessary use of binascii Commit: 9c43103630eb8bceb10021b282b8296218c04729 https://github.com/galaxyproject/galaxy/commit/9c43103630eb8bceb10021b282b82... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Remove html builders for tool parameters, strip run workflow mako Commit: cd93da35c11f9374c5ffd03a44cbf33876dffb29 https://github.com/galaxyproject/galaxy/commit/cd93da35c11f9374c5ffd03a44cbf... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py R templates/webapps/galaxy/workflow/run_complete.mako Log Message: ----------- Remove old run controller Commit: 289ac4845ad79cc7ee2079784d31182d3df23027 https://github.com/galaxyproject/galaxy/commit/289ac4845ad79cc7ee2079784d311... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove unused checked list state for booleans Commit: 9f6a88a28f968a03301e8a516f10a5322bc77f4e https://github.com/galaxyproject/galaxy/commit/9f6a88a28f968a03301e8a516f10a... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove unused to_dict parameters Commit: cd91e3141c7d031b092091ce22345d87b8aa76d2 https://github.com/galaxyproject/galaxy/commit/cd91e3141c7d031b092091ce22345... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Rename regex parameter, fix spacing Commit: b38b9fe2e1663d724651a0c6e1aa78e87acaa43d https://github.com/galaxyproject/galaxy/commit/b38b9fe2e1663d724651a0c6e1aa7... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove comment Commit: 13f498568c505b24f1b9753aaf158be324542219 https://github.com/galaxyproject/galaxy/commit/13f498568c505b24f1b9753aaf158... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove unused repeat handling Commit: d5ca00d6892874dc7da54be0a45da3cea4acb878 https://github.com/galaxyproject/galaxy/commit/d5ca00d6892874dc7da54be0a45da... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Adjust first half of test cases in basic paramter handling Commit: 143a3ecffcc8da4469245b40336901f944b531e0 https://github.com/galaxyproject/galaxy/commit/143a3ecffcc8da4469245b4033690... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix test cases Commit: adfaa948e9f65c07bf8cf8a67791bb3dd0e30bc6 https://github.com/galaxyproject/galaxy/commit/adfaa948e9f65c07bf8cf8a67791b... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Remove unused imports Commit: c61933d1b1c0289735945bf97bf8b1f4bf5e5fc8 https://github.com/galaxyproject/galaxy/commit/c61933d1b1c0289735945bf97bf8b... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M test/unit/tools/test_data_parameters.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Fix dataset parameter tests Commit: 979bdd44c60d5aab27e472b19afa8dd704ee195a https://github.com/galaxyproject/galaxy/commit/979bdd44c60d5aab27e472b19afa8... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix drilldown tests Commit: 05923e210c41e0f3a6d14a3bd914356c042f4670 https://github.com/galaxyproject/galaxy/commit/05923e210c41e0f3a6d14a3bd9143... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Undo name change for workflow regex Commit: 9863e35368066975fe049adee716c5cabad4c60f https://github.com/galaxyproject/galaxy/commit/9863e35368066975fe049adee716c... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M test/unit/tools/test_data_parameters.py Log Message: ----------- Attempt to remove value_mapper parsing Commit: 29cfd1635879987de9d1efc49d704894454a3ddf https://github.com/galaxyproject/galaxy/commit/29cfd1635879987de9d1efc49d704... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M test/unit/tools/test_parameter_parsing.py Log Message: ----------- Fix test_parameter_parsing Commit: 474c9a26c495ddddeb6ba7c1966de6ae32cedea7 https://github.com/galaxyproject/galaxy/commit/474c9a26c495ddddeb6ba7c1966de... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M templates/webapps/tool_shed/repository/tool_form.mako M test/unit/tools/test_data_parameters.py Log Message: ----------- Fix toolshed tool form preview, import order Commit: 6b40607e7917b98c481c4e47ac31d31698ce2660 https://github.com/galaxyproject/galaxy/commit/6b40607e7917b98c481c4e47ac31d... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove debug output Commit: 0ef6f7826c621235beef70e8e4c3352d2ab2e2b6 https://github.com/galaxyproject/galaxy/commit/0ef6f7826c621235beef70e8e4c33... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Move controller build endpoint to api Commit: 057485b6f6a8c545478907d01bd6ceadfea0d1f6 https://github.com/galaxyproject/galaxy/commit/057485b6f6a8c545478907d01bd6c... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Import exception, fix parameter names Commit: a537daa9ed24fe4a4fd7c9e7c54ba30f6de6e156 https://github.com/galaxyproject/galaxy/commit/a537daa9ed24fe4a4fd7c9e7c54ba... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/tool/tool-form-composite.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-composite.js M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Move run form model builder to workflow data manager Commit: b2014fe44ce7b5af42956cf74cd6e75c51a8df0f https://github.com/galaxyproject/galaxy/commit/b2014fe44ce7b5af42956cf74cd6e... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Disable target history specification for run workflow form Commit: 2c79755ba2fb752418d7405efdfdcd46bf14d8a4 https://github.com/galaxyproject/galaxy/commit/2c79755ba2fb752418d7405efdfdc... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix stored/workflow handling Commit: 667d5e83cb6ccb7b46084b73101cb85cc81dd9fa https://github.com/galaxyproject/galaxy/commit/667d5e83cb6ccb7b46084b73101cb... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M templates/webapps/tool_shed/repository/tool_form.mako Log Message: ----------- Fix value parsing Commit: 21b5246c913fbf5ae8361f359e17252718f1f87d https://github.com/galaxyproject/galaxy/commit/21b5246c913fbf5ae8361f359e172... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Remove unused data manager Commit: c5d00518fe409d4876c18ceaeeef2ad5b6829385 https://github.com/galaxyproject/galaxy/commit/c5d00518fe409d4876c18ceaeeef2... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix error messages Commit: 86719ce90e2cb8ee8439b2f4e8a947cc239e1957 https://github.com/galaxyproject/galaxy/commit/86719ce90e2cb8ee8439b2f4e8a94... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Remove redundant imports Commit: 675398c91263eaed37007b76e4856a6d81f888a3 https://github.com/galaxyproject/galaxy/commit/675398c91263eaed37007b76e4856... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Use message exception to parse errors Commit: a0da06d842a6488ee355c0cf37c06f7ffb8ee837 https://github.com/galaxyproject/galaxy/commit/a0da06d842a6488ee355c0cf37c06... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Revise comment Commit: 05b1c988961e9e002e10d4e4cc21f49ff4ab958a https://github.com/galaxyproject/galaxy/commit/05b1c988961e9e002e10d4e4cc21f... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Add basic step version changes notification Commit: 680e34c1adf87e3f6181bc2d6508f3f5ab84c903 https://github.com/galaxyproject/galaxy/commit/680e34c1adf87e3f6181bc2d6508f... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Fix form preview height style Commit: 80b5e5da91cdf65b8f06e75a9a6b2c202b94d409 https://github.com/galaxyproject/galaxy/commit/80b5e5da91cdf65b8f06e75a9a6b2... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/style/less/ui.less M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/ui/ui-portlet.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-composite.js M static/scripts/mvc/ui/ui-portlet.js M static/style/blue/base.css Log Message: ----------- Remove unused portlet footer Commit: 1ab673a4ed5de36db49e24edae821d226040d183 https://github.com/galaxyproject/galaxy/commit/1ab673a4ed5de36db49e24edae821... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js 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/ui/ui-select-content.js Log Message: ----------- Fix padding distance Commit: 9dc412921e5b5446aa4493aca8c7c0105f7d0725 https://github.com/galaxyproject/galaxy/commit/9dc412921e5b5446aa4493aca8c7c... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Fix bottom margin Commit: bb91a10a4cc17f73a051ffec41b796290505b35d https://github.com/galaxyproject/galaxy/commit/bb91a10a4cc17f73a051ffec41b79... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M Makefile Log Message: ----------- modify target for tool schema html builder to use pandoc this is @jmchilton committing as @martenson...pssst Commit: 7a736818a6c32615c396a2a18d9ebd884ddccebb https://github.com/galaxyproject/galaxy/commit/7a736818a6c32615c396a2a18d9eb... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M static/maps/mvc/tool/tool-form-workflow.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.map M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js M test/qunit/tests/form_tests.js Log Message: ----------- Avoid inheritance in tool-form view Avoid inheritance for workflow editor form Fix test cases Commit: f3c79e6aa97d8d8bf319c4e9105f0b68f09fda54 https://github.com/galaxyproject/galaxy/commit/f3c79e6aa97d8d8bf319c4e9105f0... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M templates/webapps/galaxy/dataset/copy_view.mako Log Message: ----------- Fix for displaying empty history message in copy datasets. Likely cause is change from a list to a generator at some point. Commit: 55582a790312a70324fd0dbbb1f6ea00cd992b9c https://github.com/galaxyproject/galaxy/commit/55582a790312a70324fd0dbbb1f6e... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- add TS deployments to freeze/release procedures Commit: 0e324460165900cfba231bc729006f80f46b95e2 https://github.com/galaxyproject/galaxy/commit/0e324460165900cfba231bc729006... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Bump pysam, remove 'already_compressed' usage due to new wheel with autodetect Commit: 356367fc73185de2bf0dd932ea19d3a4eb4be2c3 https://github.com/galaxyproject/galaxy/commit/356367fc73185de2bf0dd932ea19d... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Fix for copy datasets to respect the '-OR-' and only copy to a new history when name is provided. Commit: c595ace8da858f9cc7718060cbd29515578932e5 https://github.com/galaxyproject/galaxy/commit/c595ace8da858f9cc7718060cbd29... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M templates/webapps/galaxy/dataset/copy_view.mako Log Message: ----------- Add "All" and "None" buttons to copy dataset view. Commit: fb56a799fd0a0823df82c9946fea70df7764a18d https://github.com/galaxyproject/galaxy/commit/fb56a799fd0a0823df82c9946fea7... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M .gitignore M Makefile A doc/parse_gx_xsd.py A doc/schema_template.md Log Message: ----------- Merge pull request #2936 from jmchilton/xsd_docs XSD Generated Tool Documentation. Commit: 623110d85fb3d4b8d742fed315c28fb35d3a9595 https://github.com/galaxyproject/galaxy/commit/623110d85fb3d4b8d742fed315c28... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M templates/webapps/galaxy/dataset/copy_view.mako Log Message: ----------- Style tweak. Commit: 51a6d849342f57d426a762ef6fe51e049466e265 https://github.com/galaxyproject/galaxy/commit/51a6d849342f57d426a762ef6fe51... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #2952 from martenson/adjust-release-check add TS deployments to freeze/release procedures checklist Commit: 42ebe00c060d6fcbc69fd16973995c33aba48207 https://github.com/galaxyproject/galaxy/commit/42ebe00c060d6fcbc69fd16973995... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form.js Log Message: ----------- Add listener to properly clean up deferred form building processes Commit: 2cf7b8ee15856626bff5dfad735023a43ace978b https://github.com/galaxyproject/galaxy/commit/2cf7b8ee15856626bff5dfad73502... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/utils/utils.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/utils/utils.js Log Message: ----------- Fix status handling for ajax requests Commit: c5a51967173b7e5b0ecf6bbb1340db9ff54a3aed https://github.com/galaxyproject/galaxy/commit/c5a51967173b7e5b0ecf6bbb1340d... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/style/less/base.less M static/maps/mvc/tool/tool-form-workflow.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-workflow.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Change wording to be more clear about how workflow output cleanup works. Also adjust styling so that the rows in the workflow editor box are less smashed together. Commit: 317fb472c96296c6de4d094b7236b9c3f25610da https://github.com/galaxyproject/galaxy/commit/317fb472c96296c6de4d094b7236b... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> 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 branch 'release_16.07' into dev Commit: 7a604c67d95f51f0afdaa980d01ab4061b4631f0 https://github.com/galaxyproject/galaxy/commit/7a604c67d95f51f0afdaa980d01ab... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- Merge branch 'release_16.07' into dev Commit: 4de55ae51a64c34ab3636e58ea35f43904969d18 https://github.com/galaxyproject/galaxy/commit/4de55ae51a64c34ab3636e58ea35f... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Document setting column names in tool XSD. This is a transplant of a @yhoogstrate wiki update to the XSD docs. Commit: 277d3c3e58d28904752674c9210f02b88e481eb7 https://github.com/galaxyproject/galaxy/commit/277d3c3e58d28904752674c9210f0... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/tool/tool-form-workflow.js Log Message: ----------- Slight wording tweak. Commit: 5549a9ee2bd01940254c49e58ab143d4aa95049a https://github.com/galaxyproject/galaxy/commit/5549a9ee2bd01940254c49e58ab14... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Fix link in galaxy.xsd. Commit: e8f35310ba581e8f88d719053979c4c3603c930a https://github.com/galaxyproject/galaxy/commit/e8f35310ba581e8f88d719053979c... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M doc/schema_template.md M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/samples_tool_conf.xml A test/functional/tools/version_command.py A test/functional/tools/version_command_interpreter.xml A test/functional/tools/version_command_plain.xml A test/functional/tools/version_command_tool_dir.xml M test/unit/jobs/test_job_wrapper.py Log Message: ----------- Revise and improve ``version_command`` tag. - Include deprecated ``interpreter`` tag in XSD. (Closes galaxyproject/planemo#574) - Allow the use of ``$__tool_directory__`` in interpreter command (so we can actually call ``interpreter`` deprecated). - Include sample tools of both of these styles. - General improvements to the version command documentation. Commit: 4df2530847ffee6d280f841c39beabaf7163d5f0 https://github.com/galaxyproject/galaxy/commit/4df2530847ffee6d280f841c39bea... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py M templates/webapps/galaxy/dataset/copy_view.mako Log Message: ----------- Merge pull request #2957 from blankenberg/copy_datasets Add "All" and "None" buttons to copy dataset view. And fix 2 minor bugs Commit: e3346e1d273b277445844e38e9e8d29873b4d619 https://github.com/galaxyproject/galaxy/commit/e3346e1d273b277445844e38e9e8d... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M .gitignore M Makefile A doc/parse_gx_xsd.py A doc/schema_template.md M lib/galaxy/webapps/galaxy/controllers/dataset.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/bootstrap_history.py M scripts/tool_shed/build_ts_whoosh_index.py M templates/webapps/galaxy/dataset/copy_view.mako M test/shed_functional/functional/test_1400_review_migration_stages.py Log Message: ----------- Merge branch 'dev' into strip_run_form_mako Commit: cbb957028f0c8b740e7b00d1315262dbe55a6b82 https://github.com/galaxyproject/galaxy/commit/cbb957028f0c8b740e7b00d131526... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #2965 from jmchilton/more_action_docs Document setting column names in tool XSD. Commit: 5095fc02c4cfb830748179c29ea9e1b1aaf0b455 https://github.com/galaxyproject/galaxy/commit/5095fc02c4cfb830748179c29ea9e... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-25 (Sun, 25 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js M test/unit/workflows/test_run_parameters.py Log Message: ----------- Remove internal api endpoint, merge into invocations endpoint Commit: 7f19ba817c4d8e7d82380bd6fe8d03a7247488f3 https://github.com/galaxyproject/galaxy/commit/7f19ba817c4d8e7d82380bd6fe8d0... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-25 (Sun, 25 Sep 2016) Changed paths: 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-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/ui.less M lib/galaxy/managers/workflows.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/run.mako R templates/webapps/galaxy/workflow/run_complete.mako M templates/webapps/tool_shed/repository/tool_form.mako M test/qunit/tests/form_tests.js M test/unit/tools/test_data_parameters.py M test/unit/tools/test_parameter_parsing.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge pull request #2935 from guerler/strip_run_form_mako Strip workflow run mako Commit: 9d9e5f026dff5523e7e6aef1a9442c872f5fb77c https://github.com/galaxyproject/galaxy/commit/9d9e5f026dff5523e7e6aef1a9442... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M .gitignore M Makefile A doc/parse_gx_xsd.py A doc/schema_template.md M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/galaxy/controllers/dataset.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/bootstrap_history.py M scripts/tool_shed/build_ts_whoosh_index.py M templates/webapps/galaxy/dataset/copy_view.mako M test/shed_functional/functional/test_1400_review_migration_stages.py Log Message: ----------- Merge branch 'dev' into unite_api Commit: c840730101823107396104dcc7364534577a2dd4 https://github.com/galaxyproject/galaxy/commit/c840730101823107396104dcc7364... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py Log Message: ----------- Convert dict keys to integers Commit: 9a9726e9a174a230b3a71bdb40bceb9e5b0d28c7 https://github.com/galaxyproject/galaxy/commit/9a9726e9a174a230b3a71bdb40bce... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M lib/galaxy/workflow/run_request.py Log Message: ----------- Fix name generation Commit: 25ca456697f30671290859fbbcc14b126f2bbd51 https://github.com/galaxyproject/galaxy/commit/25ca456697f30671290859fbbcc14... Author: yhoogstrate <y.hoogstrate@gmail.com> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: A test/functional/tools/metadata_column_names.xml Log Message: ----------- Fuctional test case for testing column names as meta-data Commit: 838fad39a14674986680edfccfbd24232308c07d https://github.com/galaxyproject/galaxy/commit/838fad39a14674986680edfccfbd2... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js 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.map M static/scripts/mvc/tool/tool-form.js Log Message: ----------- Add details to error modal Commit: 1d16200759895b6ede6c38655d085fa7bb0a1e17 https://github.com/galaxyproject/galaxy/commit/1d16200759895b6ede6c38655d085... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Refactor recent toolbox changes for galaxy-lib. The abstracttoolbox class is supposed to shield Galaxy from the internals of the toolbox organization and vice versa, so having a reload method that uses Galaxy-specific queueing stuff is less than ideal. The concrete toolbox class is where I have been putting such functionality. In addition to this being the abstract design I prefer, it is definitely needed for galaxy-lib which contains the abstracttoolbox but not the concrete toolbox or the queue worker functionality. xref #2840 Commit: 780473a751ae52868e29b4e34ba2b0894598dc7b https://github.com/galaxyproject/galaxy/commit/780473a751ae52868e29b4e34ba2b... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #2971 from jmchilton/galaxy-lib-import-fix Refactor recent toolbox changes for galaxy-lib. Commit: 8414e909a664855a82eda19b9a9fa26cf9178c3f https://github.com/galaxyproject/galaxy/commit/8414e909a664855a82eda19b9a9fa... Author: yhoogstrate <y.hoogstrate@gmail.com> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Registration of metadata column name test into appropriate XML file - thanks to @nsoranzo Commit: 750cb7c5843fee4c82f7b028fa59d718a0629927 https://github.com/galaxyproject/galaxy/commit/750cb7c5843fee4c82f7b028fa59d... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M doc/schema_template.md Log Message: ----------- encourage bug reporting in tool schema Commit: 051d2b285487fb99a065448b20f69f0d82d3a100 https://github.com/galaxyproject/galaxy/commit/051d2b285487fb99a065448b20f69... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M doc/schema_template.md Log Message: ----------- Merge pull request #2972 from martenson/tool-schema-report encourage bug reporting in tool schema document Commit: 8b452c9dc3dca9c4ba8804e0a3e6edd8d06946c0 https://github.com/galaxyproject/galaxy/commit/8b452c9dc3dca9c4ba8804e0a3e6e... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Remove invalid attribute metadata_name from param examples in XSD docs. Pointed out by @peterjc in https://github.com/galaxyproject/tools-iuc/pull/964#issuecomment-249632638. Commit: 0a767d4d5343d7eaf3697373922d056251c5b802 https://github.com/galaxyproject/galaxy/commit/0a767d4d5343d7eaf3697373922d0... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix error handling Commit: 0df6ff9f2d7d841b322ee690a84ec8baa822b336 https://github.com/galaxyproject/galaxy/commit/0df6ff9f2d7d841b322ee690a84ec... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #2974 from jmchilton/schema_fix_0 Remove invalid attribute metadata_name from param examples in XSD docs. Commit: 9eba273202873abab5b9f302a9c2ae1cf21c7431 https://github.com/galaxyproject/galaxy/commit/9eba273202873abab5b9f302a9c2a... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M lib/galaxy/model/mapping.py M test/unit/test_galaxy_mapping.py Log Message: ----------- Optimized workflow invocation step update. Commit: 002d974f8adae4cfc52c434c46c4966ac90918bd https://github.com/galaxyproject/galaxy/commit/002d974f8adae4cfc52c434c46c49... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/requirements.py Log Message: ----------- Merge pull request #2790 from jmchilton/docker_container_xml More configurability for containerized jobs Commit: 7ecf9377bf3780faa2bb93594cf41435a15ff40a https://github.com/galaxyproject/galaxy/commit/7ecf9377bf3780faa2bb93594cf41... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M lib/galaxy/tools/deps/containers.py Log Message: ----------- Fix import order in containers.py (broken in cad4002efed5547ccc1f89a3a45d2d4b9b12f76d). Commit: 8ff8af7b248b79436113e03d3c01e2cc4cd2a88c https://github.com/galaxyproject/galaxy/commit/8ff8af7b248b79436113e03d3c01e... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M lib/galaxy/tools/deps/containers.py Log Message: ----------- Merge pull request #2975 from jmchilton/fix_import_order Fix import order in containers.py Commit: 8966b741317431275100c24ab3cc69a221de646c https://github.com/galaxyproject/galaxy/commit/8966b741317431275100c24ab3cc6... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M client/galaxy/style/less/ui.less M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css Log Message: ----------- Swap to section row selector Commit: 32064b338d619031112298dc489338cdbc67ec5b https://github.com/galaxyproject/galaxy/commit/32064b338d619031112298dc48933... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Lazy load workflow invocation steps Fix job handler going OOM when executing Job.set_final_state() for a step processing a 30K elements collection in parallel. Commit: 8054da9fb4d858b7ff9dd461f8baa923fea99425 https://github.com/galaxyproject/galaxy/commit/8054da9fb4d858b7ff9dd461f8baa... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M doc/source/project/issues.rst Log Message: ----------- Update issues.rst Commit: 23fc1e5d577291a86ba9eed1e027ba7516bbfb9d https://github.com/galaxyproject/galaxy/commit/23fc1e5d577291a86ba9eed1e027b... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/model/mapping.py Log Message: ----------- Fix import order and Python3 compatibility for lib/galaxy/model/mapping.py Commit: aa70a97e1e570507121320d9f2370265fd25fca8 https://github.com/galaxyproject/galaxy/commit/aa70a97e1e570507121320d9f2370... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/library_common.py M templates/webapps/galaxy/library/common/common.mako Log Message: ----------- Merge pull request #2819 from SANBI-SA/upload_admin_line_endings Functionality to allow admins to switch on/off the line endings conversion on import Commit: 477d3f9ae94acf2b9c57eba641c2dcdd66d5af27 https://github.com/galaxyproject/galaxy/commit/477d3f9ae94acf2b9c57eba641c2d... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M lib/galaxy/workflow/run_request.py A test/api/test_workflow_input_params.ga M test/api/test_workflows.py Log Message: ----------- Add batch mode test case for invocations api Commit: 10703fac3a00a854bb3d4d548ab1dd22485199c5 https://github.com/galaxyproject/galaxy/commit/10703fac3a00a854bb3d4d548ab1d... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M doc/source/project/issues.rst Log Message: ----------- Merge pull request #2976 from martenson/issues-on-par-with-reality bring issues.rst on par with reality Commit: 695a759c9d8301ef447cd30a2c2efd4ef958e79e https://github.com/galaxyproject/galaxy/commit/695a759c9d8301ef447cd30a2c2ef... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2016-09-28 (Wed, 28 Sep 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/model/mapping.py Log Message: ----------- Merge pull request #2978 from nsoranzo/lazy_workflow_invocation Lazy load workflow invocation steps Commit: ab68b951da7a766f06cc5fbbfaea34a2ea1b5dac https://github.com/galaxyproject/galaxy/commit/ab68b951da7a766f06cc5fbbfaea3... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-28 (Wed, 28 Sep 2016) Changed paths: M test/base/interactor.py M test/functional/tools/metadata_column_names.xml Log Message: ----------- Implement metadata testing for list metadata. Commit: efbc06eb0178f495d1581aec7a8c1467af93f2d7 https://github.com/galaxyproject/galaxy/commit/efbc06eb0178f495d1581aec7a8c1... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-28 (Wed, 28 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/genomes.py Log Message: ----------- Cleanup 97532515ea24325ba26877696991b24401733ee6. Commit: 860c2854b78ac4c6aff2c8524a42225476f8b513 https://github.com/galaxyproject/galaxy/commit/860c2854b78ac4c6aff2c8524a422... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2016-09-28 (Wed, 28 Sep 2016) Changed paths: M test/base/interactor.py A test/functional/tools/metadata_column_names.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #2970 from yhoogstrate/functional_test_metadata_columns Fuctional test case for testing column names as meta-data Commit: 98ea43700dd635b6b0c7d6a274d5f3a22ba7829b https://github.com/galaxyproject/galaxy/commit/98ea43700dd635b6b0c7d6a274d5f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-09-28 (Wed, 28 Sep 2016) Changed paths: M lib/galaxy/dependencies/pinned-hashed-requirements.txt Log Message: ----------- Update hashes for new pysam wheel. Commit: fcd86c5e586256438aa8b53035ecf2e1f1e98429 https://github.com/galaxyproject/galaxy/commit/fcd86c5e586256438aa8b53035ecf... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-28 (Wed, 28 Sep 2016) Changed paths: M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Merge pull request #2953 from dannon/pysam_update_gx5 Bump pysam, remove 'already_compressed' usage due to new wheel with a… Commit: 7d2e3be0b0e989a0ffe72bd8e974998a30353357 https://github.com/galaxyproject/galaxy/commit/7d2e3be0b0e989a0ffe72bd8e9749... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-09-28 (Wed, 28 Sep 2016) Changed paths: M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Update sqlalchemy to 1.0.15 (from 1.0.8). This is likely the last 1.0 series release before we'll be able to upgrade to a live 1.1. Commit: 1fee06e4e360f442e2e621e084ca3b313b07138a https://github.com/galaxyproject/galaxy/commit/1fee06e4e360f442e2e621e084ca3... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-28 (Wed, 28 Sep 2016) Changed paths: M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #2979 from dannon/sqlalchemy_1.0.15 Update sqlalchemy to 1.0.15 (from 1.0.8). This is likely the last 1.… Commit: 991d81cdbeeca43891b2ed5464c73052fbe20ef3 https://github.com/galaxyproject/galaxy/commit/991d81cdbeeca43891b2ed5464c73... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-29 (Thu, 29 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix phrasing of error message Commit: 3d7bfeb6dd08b0241d8fa75f37c5010762146eeb https://github.com/galaxyproject/galaxy/commit/3d7bfeb6dd08b0241d8fa75f37c50... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-29 (Thu, 29 Sep 2016) Changed paths: M test/api/test_workflows.py Log Message: ----------- Revise target url Commit: 1cb67308771edf40716ef5f30f4321051debc4bb https://github.com/galaxyproject/galaxy/commit/1cb67308771edf40716ef5f30f432... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-29 (Thu, 29 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Always return a list for formats with batch mode option Commit: e34019e52806fde224781cfe3bc408b633f86179 https://github.com/galaxyproject/galaxy/commit/e34019e52806fde224781cfe3bc40... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-29 (Thu, 29 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Improve invocations success message Commit: 3545a0ef1f8a2fbde86558fcaf5da43e9563710b https://github.com/galaxyproject/galaxy/commit/3545a0ef1f8a2fbde86558fcaf5da... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-29 (Thu, 29 Sep 2016) Changed paths: M test/api/test_workflows.py Log Message: ----------- Remove unused history wait Commit: 6f7e9cd5df6eb444974e3d45f1df11f1e3f77281 https://github.com/galaxyproject/galaxy/commit/6f7e9cd5df6eb444974e3d45f1df1... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-29 (Thu, 29 Sep 2016) Changed paths: M test/api/test_workflows.py Log Message: ----------- Use hid from hda Commit: b1eaf85480fbfef5166925294257e2b2cc954b4d https://github.com/galaxyproject/galaxy/commit/b1eaf85480fbfef5166925294257e... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-29 (Thu, 29 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/meta.py Log Message: ----------- Fix indent Commit: 1cc8e04c819487c898c09471132b385642dd7b8e https://github.com/galaxyproject/galaxy/commit/1cc8e04c819487c898c09471132b3... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-29 (Thu, 29 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M lib/galaxy/tools/__init__.py M static/maps/mvc/tool/tool-form.js.map Log Message: ----------- Merge all errors from batch mode run for regular tool executions Commit: 11b4f3a60c3f24ddbfdf1421391c9b443060a3cf https://github.com/galaxyproject/galaxy/commit/11b4f3a60c3f24ddbfdf1421391c9... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-09-29 (Thu, 29 Sep 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M tools/data_source/data_source.py M tools/data_source/hbvar_filter.py M tools/data_source/microbial_import_code.py M tools/evolution/add_scores.py M tools/evolution/codingSnps_filter.py M tools/extract/extract_genomic_dna.py M tools/filters/axt_to_concat_fasta.py M tools/filters/axt_to_fasta.py M tools/filters/axt_to_lav.py M tools/filters/axt_to_lav_code.py M tools/filters/bed_to_gff_converter.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/secure_hash_message_digest.py M tools/filters/sff_extract.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/vcf_to_maf_customtrack.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/solid2fastq.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/velvetg_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ_code.py Log Message: ----------- Fix import order and Python3 compatibility for tools/ xref #1715 Commit: 7dadb932d827ee168acefacbf041dad671d36c7f https://github.com/galaxyproject/galaxy/commit/7dadb932d827ee168acefacbf041d... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-29 (Thu, 29 Sep 2016) Changed paths: M lib/galaxy/model/mapping.py M test/unit/test_galaxy_mapping.py Log Message: ----------- Merge pull request #2973 from jmchilton/optimize_invocation_update Optimized workflow invocation step update. Commit: 46d05ba08017cf10467eb0334272e48733c9f684 https://github.com/galaxyproject/galaxy/commit/46d05ba08017cf10467eb0334272e... 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doc/schema_template.md M doc/source/project/issues.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/history_contents.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/mapping.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/toolbox/base.py A lib/galaxy/tools/xsd/LICENSE A lib/galaxy/tools/xsd/README.md A lib/galaxy/tools/xsd/galaxy.jxb A lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/mobile.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/workflow.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/galaxy/workflow/extract.py M lib/tool_shed/util/metadata_util.py M scripts/bootstrap_history.py M scripts/tool_shed/build_ts_whoosh_index.py A scripts/validate_tools.sh A static/maps/libs/bbi/bigwig.js.map A static/maps/libs/bbi/jquery-ajax-native.js.map A static/maps/libs/bbi/jszlib.js.map A static/maps/libs/bbi/spans.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/utils/utils.js.map A static/maps/viz/bbi-data-manager.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/tracks.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 A static/scripts/libs/bbi/bigwig.js A static/scripts/libs/bbi/jquery-ajax-native.js A static/scripts/libs/bbi/jszlib.js A static/scripts/libs/bbi/spans.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/utils/utils.js A static/scripts/viz/bbi-data-manager.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/tracks.js M static/style/blue/base.css M templates/user/info.mako M templates/user/register.mako M templates/user/username.mako M templates/webapps/galaxy/dataset/copy_view.mako M templates/webapps/galaxy/library/common/common.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako M templates/webapps/galaxy/workflow/run.mako R templates/webapps/galaxy/workflow/run_complete.mako M templates/webapps/tool_shed/repository/tool_form.mako M test/base/interactor.py A test/functional/tools/metadata_column_names.xml R test/functional/tools/multi_page.xml M test/functional/tools/samples_tool_conf.xml M test/qunit/tests/form_tests.js M test/shed_functional/functional/test_1400_review_migration_stages.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_UserManager.py M test/unit/test_galaxy_mapping.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_parameter_parsing.py M test/unit/unittest_utils/galaxy_mock.py M tox.ini Log Message: ----------- Merge branch 'dev' into remote_chart_plugins Commit: 494d50f52c33a7465e0d466a3e43fba9fd5a1dbd https://github.com/galaxyproject/galaxy/commit/494d50f52c33a7465e0d466a3e43f... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-29 (Thu, 29 Sep 2016) Changed paths: M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Repack client Commit: e14fe506434e55d999995b3da115c7a36f7376be https://github.com/galaxyproject/galaxy/commit/e14fe506434e55d999995b3da115c... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/workflow/run_request.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js M test/api/test_workflows.py Log Message: ----------- Use order_index instead of step_id Commit: a1158a79059a47cd928eee2acdbb81df9fbdabcb https://github.com/galaxyproject/galaxy/commit/a1158a79059a47cd928eee2acdbb8... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M tools/data_source/data_source.py M tools/data_source/hbvar_filter.py M tools/data_source/microbial_import_code.py M tools/evolution/add_scores.py M tools/evolution/codingSnps_filter.py M tools/extract/extract_genomic_dna.py M tools/filters/axt_to_concat_fasta.py M tools/filters/axt_to_fasta.py M tools/filters/axt_to_lav.py M tools/filters/axt_to_lav_code.py M tools/filters/bed_to_gff_converter.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/secure_hash_message_digest.py M tools/filters/sff_extract.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/vcf_to_maf_customtrack.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/solid2fastq.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/velvetg_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ_code.py Log Message: ----------- Merge pull request #2983 from nsoranzo/python3 Fix import order and Python3 compatibility for tools/ Commit: 67eb2c6530bd62f4b6542937f38f373e6022c000 https://github.com/galaxyproject/galaxy/commit/67eb2c6530bd62f4b6542937f38f3... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/run_request.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js M test/api/test_workflows.py Log Message: ----------- Use parameters/batch instead of input_params Commit: 70df25e74b306337e18ce0c2d8291a998da23024 https://github.com/galaxyproject/galaxy/commit/70df25e74b306337e18ce0c2d8291... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: A test/api/test_workflow_batch.ga R test/api/test_workflow_input_params.ga M test/api/test_workflows.py Log Message: ----------- Rename test associated workflow export Commit: 1a91c603892f7ea574197de67f738df6b7008dd8 https://github.com/galaxyproject/galaxy/commit/1a91c603892f7ea574197de67f738... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Fix startswith method spelling Introduced in commit 4b2e0c84e19001c8071b374a8e7daf609bb3aa88 Commit: ed7bba5e2027bf239bf86359b68a360149c027dd https://github.com/galaxyproject/galaxy/commit/ed7bba5e2027bf239bf86359b68a3... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/run_request.py Log Message: ----------- Increased consistency in backend workflow run code. Rename build_workflow_run_config to build_workflow_run_configs since it sometimes returned a list, make it always return a list, one path out of run_request.py:build_workflow_run_configs, ensure batch parameter is respected and throw an exception if it is not and build_workflow_run_configs returns multiple invocations. Commit: c71c1300a2f2797a1009c1c86c9c9449b42e05d5 https://github.com/galaxyproject/galaxy/commit/c71c1300a2f2797a1009c1c86c9c9... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Merge pull request #2990 from nsoranzo/fix_for_2761 Fix startswith method spelling Commit: 8166276679cb1d1bf90d9cf473102b3e2eda3b99 https://github.com/galaxyproject/galaxy/commit/8166276679cb1d1bf90d9cf473102... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/workflow/run_request.py Log Message: ----------- Do not copy tags from source history Commit: 8fab4f141b93e298487e1a5ed58fda24289be7ef https://github.com/galaxyproject/galaxy/commit/8fab4f141b93e298487e1a5ed58fd... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/workflow/run_request.py Log Message: ----------- Unify workflow API history options across approaches. The old variant of specifying a history attribute should work with new batch parameter mode and the new variant of specifing new_history_name or history_id should work with the existing invocation API stuff. Commit: f4ca27d50dbac3d89ad758262633777545ee32f4 https://github.com/galaxyproject/galaxy/commit/f4ca27d50dbac3d89ad7582626337... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/workflow/run_request.py Log Message: ----------- Add error response to validate expansion result Commit: 5b70453e5ea2d98052635c509ee5502574144c06 https://github.com/galaxyproject/galaxy/commit/5b70453e5ea2d98052635c509ee55... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Log Message: ----------- Merge remote-tracking branch 'guerler/unite_api' into unite_api_history Conflicts: lib/galaxy/workflow/run_request.py Commit: 2eadece71e8ff8cff76ed58d56cb5eba7ac99c87 https://github.com/galaxyproject/galaxy/commit/2eadece71e8ff8cff76ed58d56cb5... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Add flake8 pinning to Branch procedures Commit: ab2a5198afeb0b651643b84c0dd3eb6a0e611bb6 https://github.com/galaxyproject/galaxy/commit/ab2a5198afeb0b651643b84c0dd3e... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/workflow/run_request.py Log Message: ----------- Resolve this comment/discussion (https://github.com/galaxyproject/galaxy/pull/2969#issuecomment-250830186). Commit: 92034e67766c0e608b8cec6c63e29e3405e80333 https://github.com/galaxyproject/galaxy/commit/92034e67766c0e608b8cec6c63e29... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/workflow/run_request.py Log Message: ----------- Revert to an exception instead of an assertion. I'm close to winning @guerler over - but not quite there yet. Commit: 72980bc967a8fb7b988b4c33a79af9c3af94bcc2 https://github.com/galaxyproject/galaxy/commit/72980bc967a8fb7b988b4c33a79af... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Log Message: ----------- Merge remote-tracking branch 'guerler/unite_api' into unite_api_history Conflicts: lib/galaxy/workflow/run_request.py Commit: 3d4e02f1314cdeeae6fc6285e7b0c35fb2b6f136 https://github.com/galaxyproject/galaxy/commit/3d4e02f1314cdeeae6fc6285e7b0c... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/run_request.py Log Message: ----------- Fixup previous commits bugs. Commit: 4fea03acc917089498cb2a897e931a5d1cec8a7b https://github.com/galaxyproject/galaxy/commit/4fea03acc917089498cb2a897e931... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Use explicit order_index when assigning workflow steps Commit: 55cce84189510e14b55a042168e5f63c71be7fe3 https://github.com/galaxyproject/galaxy/commit/55cce84189510e14b55a042168e5f... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Reload metadata and lib tools on toolbox reload Should close #2988. Commit: c67e4ac1a391348fdac942ebe2918cb7e0e08235 https://github.com/galaxyproject/galaxy/commit/c67e4ac1a391348fdac942ebe2918... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test case Commit: 66a5bd45bd3c72e497b2098337de652b2c5d5f51 https://github.com/galaxyproject/galaxy/commit/66a5bd45bd3c72e497b2098337de6... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #2991 from nsoranzo/fix_for_2665 Add flake8 pinning to Branch procedures Commit: 9df99d2bb0f5c34c66f1d0730c012b5cd268899b https://github.com/galaxyproject/galaxy/commit/9df99d2bb0f5c34c66f1d0730c012... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js M test/api/test_workflows.py Log Message: ----------- Merge remote-tracking branch 'guerler/unite_api' into unite_api_history Commit: 0263c3259ebcf7d604bfc9da8ba1bb69800a27aa https://github.com/galaxyproject/galaxy/commit/0263c3259ebcf7d604bfc9da8ba1b... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/workflow/run_request.py Log Message: ----------- Refactor run_request to reuse step parameter normalization. Lessens the difference between GUI and API approaches. Commit: eb288cd4e122b0c5ff11a75fbac34374b080bc3a https://github.com/galaxyproject/galaxy/commit/eb288cd4e122b0c5ff11a75fbac34... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/workflow/run_request.py Log Message: ----------- Refactor build_workflow_run_configs toward unification of API and UI approaches. Commit: a2e265e8b148da7e4a6ba50eb9b64cdaf6765a93 https://github.com/galaxyproject/galaxy/commit/a2e265e8b148da7e4a6ba50eb9b64... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/workflow/run_request.py Log Message: ----------- Refactor build_workflow_run_configs toward unification of API and UI approaches. Swap expansion of raw parameters and normalization of parmeters so that we can move the loop outside of the conditional ... and thus elimiante the conditional that distinguishes between API and UI approaches. Commit: e60fd0490526e76f58210151d9ea6090d9277317 https://github.com/galaxyproject/galaxy/commit/e60fd0490526e76f58210151d9ea6... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/workflow/run_request.py Log Message: ----------- Refine workflow target history handling with bug fix and improved error message. Commit: b106c48b68f87b2c9008e6f03b5cdb51b951051a https://github.com/galaxyproject/galaxy/commit/b106c48b68f87b2c9008e6f03b5cd... Author: John Chilton <jmchilton@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/workflow/run_request.py M static/maps/mvc/tool/tool-form-composite.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-composite.js M test/api/test_workflows.py Log Message: ----------- Unify build_workflow_run_configs for API and UI approaches to running workflows. No more branches - the method runs top to bottom for each approach. One loop for batching regardless and completely available to all API options. Only call WorkflowRunConfig in one place. Remove duplicate fetching of replacement_params. One call to _normalize_step_parameters. Commit: aaf5cc4075fcf3951850b979b4b4eec288fd5393 https://github.com/galaxyproject/galaxy/commit/aaf5cc4075fcf3951850b979b4b4e... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/run_request.py M static/maps/mvc/tool/tool-form-composite.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-composite.js M test/api/test_workflows.py Log Message: ----------- Merge pull request #13 from jmchilton/unite_api_history Unify workflow API history options across approaches. Commit: dc209c7a003bbc63d590cbbc45fbdf48340bbe8c https://github.com/galaxyproject/galaxy/commit/dc209c7a003bbc63d590cbbc45fbd... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Encode unencoded step id when exposing workflow dictionary for execution Commit: 76201eba45c39e9b5b62be865bc56331bb775d57 https://github.com/galaxyproject/galaxy/commit/76201eba45c39e9b5b62be865bc56... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/workflow/run_request.py Log Message: ----------- Move get target history out of build_workflow_run_configs Commit: 5e6af483d799137c2a956d98aad79ee30f636101 https://github.com/galaxyproject/galaxy/commit/5e6af483d799137c2a956d98aad79... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-01 (Sat, 01 Oct 2016) Changed paths: M lib/galaxy/workflow/run_request.py Log Message: ----------- Refactor target history mode validation, remove spaces Commit: 824f556ea7d04b5141307ede3258850fcc17ed77 https://github.com/galaxyproject/galaxy/commit/824f556ea7d04b5141307ede32588... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Merge pull request #2992 from mvdbeek/reload_special_tools Reload metadata and lib tools on toolbox reload Commit: 0f6ad3f41469816cbb31b6c5a2a663cf30f0ecf1 https://github.com/galaxyproject/galaxy/commit/0f6ad3f41469816cbb31b6c5a2a66... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Use order index to link connected datasets Commit: ce7cf6cc230827c1ad485579a7efd4a2fa807381 https://github.com/galaxyproject/galaxy/commit/ce7cf6cc230827c1ad485579a7efd... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Rename step_id to step_index to avoid confusion Commit: d5c54907dad35d5ba8578f4d563c36c8b06fa43d https://github.com/galaxyproject/galaxy/commit/d5c54907dad35d5ba8578f4d563c3... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Rename step_id to step_index to avoid confusion, fix error message response handling Commit: 0b03a800abdab4540152adea44ed820cbc2782e0 https://github.com/galaxyproject/galaxy/commit/0b03a800abdab4540152adea44ed8... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Improve error display robustness for run workflow form Commit: f3ce9a927caf193ee7f681553c6209dfa3fd05ff https://github.com/galaxyproject/galaxy/commit/f3ce9a927caf193ee7f681553c620... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/meta.py Log Message: ----------- Remove sorting from workflow expansion test cases Commit: b865952bab1a659e70e65aaf63740d776fbb3249 https://github.com/galaxyproject/galaxy/commit/b865952bab1a659e70e65aaf63740... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M config/job_conf.xml.sample_advanced Log Message: ----------- Add reference to Go-Docker repository and a little blurb. Commit: 4664a64c15d9989a5fd0589e0551d7a681db8f9e https://github.com/galaxyproject/galaxy/commit/4664a64c15d9989a5fd0589e0551d... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M lib/galaxy/jobs/runners/godocker.py Log Message: ----------- Remove ssl warning disable -- these are good to have/see when using unverified SSL connections. Commit: ea1879d4410eda95506e9645adada1bc8a2247dc https://github.com/galaxyproject/galaxy/commit/ea1879d4410eda95506e9645adada... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/meta.py Log Message: ----------- Remove sorting from last expansion test case Commit: 00f471156574cb1a5bba3cf62ee26c8dc4a6e41e https://github.com/galaxyproject/galaxy/commit/00f471156574cb1a5bba3cf62ee26... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/meta.py Log Message: ----------- Fix order in workflow expansion Commit: c2f1b635cc65aafd32309b788d809c5d6cf53615 https://github.com/galaxyproject/galaxy/commit/c2f1b635cc65aafd32309b788d809... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/meta.py M test/api/test_workflows.py Log Message: ----------- Rely on deterministic invocations order in batch mode test case Commit: 4d871fa734e0982e685fb1bf356f4147ff1ae143 https://github.com/galaxyproject/galaxy/commit/4d871fa734e0982e685fb1bf356f4... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-04 (Tue, 04 Oct 2016) Changed paths: M test/api/test_workflows.py Log Message: ----------- Check both invocation orders when using the new batch mode feature Commit: b46d55e30fd3f8a2832130dd3f917082f442836f https://github.com/galaxyproject/galaxy/commit/b46d55e30fd3f8a2832130dd3f917... Author: Evgeny Anatskiy <evgeny.anatskiy@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: 17c4af285d75e4a271880b37f4727df59987655a https://github.com/galaxyproject/galaxy/commit/17c4af285d75e4a271880b37f4727... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-04 (Tue, 04 Oct 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/__init__.py M lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/subsystems.py M lib/galaxy/jobs/metrics/formatting.py M lib/galaxy/jobs/metrics/instrumenters/__init__.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 Log Message: ----------- Docstring fixes for galaxy.exceptions and galaxy.jobs.metrics. xref https://github.com/galaxyproject/galaxy-lib/pull/21. Rebase with spelling fixes thanks to @nsoranzo. Commit: d9af95b401ebec1db5cd6653f5ebbb9a7fd5c3f5 https://github.com/galaxyproject/galaxy/commit/d9af95b401ebec1db5cd6653f5ebb... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2016-10-04 (Tue, 04 Oct 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/__init__.py M lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/subsystems.py M lib/galaxy/jobs/metrics/formatting.py M lib/galaxy/jobs/metrics/instrumenters/__init__.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 Log Message: ----------- Merge pull request #3003 from jmchilton/docstrings1 Docstring fixes for galaxy.exceptions and galaxy.jobs.metrics. Commit: 329ee052510c0c720ae5d44bac23becf639f6506 https://github.com/galaxyproject/galaxy/commit/329ee052510c0c720ae5d44bac23b... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-04 (Tue, 04 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Hide children elements instead of destroying them upon successful workflow submission Commit: 56721e7a0fe67e9aba55d4b52d97601b75b2beb9 https://github.com/galaxyproject/galaxy/commit/56721e7a0fe67e9aba55d4b52d976... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-04 (Tue, 04 Oct 2016) Changed paths: A .ci/flake8_docstrings_include_list.txt M .ci/flake8_wrapper.sh A .ci/flake8_wrapper_docstrings.sh M .travis.yml M lib/galaxy/util/__init__.py M setup.cfg M tox.ini Log Message: ----------- Initial docstring linting. - Apply one docstring lint to the global lint list (D302 - unicode docstrings should start with u"""). - Create an inclusion list with many more docstring checks (public modules need a docstring, white space and quoting issue, check imperative mood and capitializaton). Add a couple modules to this inclusion list. - Add tox and Travis targets for this linting. This gives a person who wants to work on improving Galaxy's in-code docstring documentation three ways to "raise the bar" for the project. One could: - Add more modules to the inclusion list (.ci/flake8_docstrings_include_list.txt). Many more modules should contain docstrings - especially things in galaxy-lib and web controllers. - Add more checks to the existing inclusion list checks - I'd say D101 and/or D103 first or any of the missing D2XX or D4XX options. D102 seems a bit too ambitious and I worry it'd be too much of a burden. - Pick some DXXX check that is ignored globally and fix it for the whole project and then remove it from the exclude list in setup.cfg. Commit: 922d9ee53a9d9400cda622c12d6f79fc190673f6 https://github.com/galaxyproject/galaxy/commit/922d9ee53a9d9400cda622c12d6f7... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-04 (Tue, 04 Oct 2016) Changed paths: M lib/galaxy/workflow/run_request.py Log Message: ----------- Fix for unite_api branch for API key specification without explicit history target. It is good to not depend on trans.history being set I think and this is required to fix bioblend tests. Commit: 5a5d770455f5a41f0630cf6b7fad40a2e0e939e0 https://github.com/galaxyproject/galaxy/commit/5a5d770455f5a41f0630cf6b7fad4... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2016-10-04 (Tue, 04 Oct 2016) Changed paths: M lib/galaxy/workflow/run_request.py Log Message: ----------- Merge pull request #14 from jmchilton/unite_api_apikey_fix Fix for unite_api branch for API key specification without explicit history target. Commit: b595cd3f4775c1435a28ee80159fe16a2b4581b6 https://github.com/galaxyproject/galaxy/commit/b595cd3f4775c1435a28ee80159fe... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-04 (Tue, 04 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Always submit either history_id or new history name through run form Commit: 2ca1af225f8fe1715ef058fd0f516a48d32fa325 https://github.com/galaxyproject/galaxy/commit/2ca1af225f8fe1715ef058fd0f516... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-04 (Tue, 04 Oct 2016) Changed paths: M lib/galaxy/workflow/run_request.py Log Message: ----------- Remove trans.history from target history identification Commit: 240781811e3f6f6b05dc53bee69850745f71d5c2 https://github.com/galaxyproject/galaxy/commit/240781811e3f6f6b05dc53bee6985... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-04 (Tue, 04 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove unnecessary line from test cases Commit: 5595bf2e40687f6e67e34748867f57eedbd7ceab https://github.com/galaxyproject/galaxy/commit/5595bf2e40687f6e67e34748867f5... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #3005 from guerler/simplify_basic_py Remove unnecessary line from parameter unit test cases Commit: f0f26e0654b2f9f3bdd3a159ea2800745980abd2 https://github.com/galaxyproject/galaxy/commit/f0f26e0654b2f9f3bdd3a159ea280... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M static/maps/mvc/tool/tool-form-composite.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/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js A test/api/test_workflow_batch.ga M test/api/test_workflows.py M test/unit/workflows/test_run_parameters.py Log Message: ----------- Merge pull request #2969 from guerler/unite_api Unite workflow execution api endpoints Commit: 16c2227b93151c31caefa369e17e36cdfb75e381 https://github.com/galaxyproject/galaxy/commit/16c2227b93151c31caefa369e17e3... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/genomes.py Log Message: ----------- Merge pull request #2939 from jj-umn/patch-4 API access to genome fasta index and sequence Commit: 9ae35cb64a57a67976459de1a9c589f3b70ab3f1 https://github.com/galaxyproject/galaxy/commit/9ae35cb64a57a67976459de1a9c58... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M tox.ini Log Message: ----------- Fix typo spotted by @nsoranzo. Commit: b98e49f2bc88e62b4835aa8d23f8d3386f81f66a https://github.com/galaxyproject/galaxy/commit/b98e49f2bc88e62b4835aa8d23f8d... Author: Evgeny Anatskiy <evgeny.anatskiy@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/58e0d6e1a61b06c444b2086d7725e... Author: anatskiy <evgeny.anatskiy@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/cbbcf3d625a1625e89bbe7c59997d... Author: anatskiy <evgeny.anatskiy@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/cf1fde577e9b918bacfe2d78d9f2b... Author: anatskiy <evgeny.anatskiy@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/ac5a0f5a6adea3493549d69627d1d... Author: anatskiy <evgeny.anatskiy@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/fecf493ecde3590e9da4629a063d5... Author: anatskiy <evgeny.anatskiy@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/239731d45aa5019eecc4d65a77110... Author: anatskiy <evgeny.anatskiy@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/d35d99727b76ab71173ad7cccca1a... Author: anatskiy <evgeny.anatskiy@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/1f7a4135318f0d6940e2a65a2b9f7... Author: anatskiy <evgeny.anatskiy@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/adc92fd31740ebe4fe66bfec32fe1... Author: anatskiy <evgeny.anatskiy@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/d490415b0500dcbadca9a1f959cf0... Author: anatskiy <evgeny.anatskiy@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/86af65a7d6889086e1f16ef3ef4fc... Author: anatskiy <evgeny.anatskiy@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/4635ff4575ea1a47fac8da2bbb500... Author: anatskiy <evgeny.anatskiy@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/482e0b2bffe992c329f22e4f9b50a... Author: anatskiy <evgeny.anatskiy@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/6e534213e12820f69bb849b74aa89... Author: anatskiy <evgeny.anatskiy@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/fce44d257b9d05e68ca4323036e7e... Author: anatskiy <evgeny.anatskiy@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/3c3819900fd293de1532a4c0a1568... Author: Evgeny Anatskiy <evgeny.anatskiy@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/6f109176d16a162b9f5a132927eef... Author: Evgeny Anatskiy <evgeny.anatskiy@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/31674ef5b789b9c9557bb78efaa5d... Author: Evgeny Anatskiy <evgeny.anatskiy@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: be3c347a37fd0a84ff08fbac00af7816158db634 https://github.com/galaxyproject/galaxy/commit/be3c347a37fd0a84ff08fbac00af7... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add rgb option for color picker Commit: c6fca34428bdf62d74ff476f5a1bd4b2b9f97790 https://github.com/galaxyproject/galaxy/commit/c6fca34428bdf62d74ff476f5a1bd... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove unused value map argument from basic parameter handling Commit: 2bf0549a371a1a3f683d375233b9b3f5b1e37944 https://github.com/galaxyproject/galaxy/commit/2bf0549a371a1a3f683d375233b9b... Author: Evgeny Anatskiy <evgeny.anatskiy@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: a2ee8d10af84332bf1afa1e32f0acf9cdb754f0a https://github.com/galaxyproject/galaxy/commit/a2ee8d10af84332bf1afa1e32f0ac... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-modal.js M doc/source/admin/conda_faq.rst M lib/galaxy/tools/deps/__init__.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.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 Log Message: ----------- Merge branch 'release_16.07' into dev Conflicts: doc/source/admin/conda_faq.rst static/maps/mvc/ui/ui-modal.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map static/scripts/mvc/ui/ui-modal.js Commit: f283a6248cc6638c58074286f7dfa3e34a2e1a00 https://github.com/galaxyproject/galaxy/commit/f283a6248cc6638c58074286f7dfa... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add space Commit: f6d395c7cb9c217a2c653781a5702a1ae8449342 https://github.com/galaxyproject/galaxy/commit/f6d395c7cb9c217a2c653781a5702... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix whitespace after comma Commit: e93c9b42d648537fed89569373d83f20ebeaf3c7 https://github.com/galaxyproject/galaxy/commit/e93c9b42d648537fed89569373d83... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove two unused private functions for data tool parameters Commit: 5f9bfd5fc078043bce9fa10c0063a1989887aae2 https://github.com/galaxyproject/galaxy/commit/5f9bfd5fc078043bce9fa10c0063a... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Add an XSD entry for this new feature. Commit: a6da9ab00006fc21ebbf511f1210a9685ce9ddfa https://github.com/galaxyproject/galaxy/commit/a6da9ab00006fc21ebbf511f1210a... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py Log Message: ----------- Rename private function to indicate public use Commit: 2b9034d597941ad055975fb776506b8de2382c67 https://github.com/galaxyproject/galaxy/commit/2b9034d597941ad055975fb776506... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M doc/source/api/guidelines.rst Log Message: ----------- Update some old information in API guideline docs. Commit: c03748dd49c060a68d07bce56eae33e0ba154414 https://github.com/galaxyproject/galaxy/commit/c03748dd49c060a68d07bce56eae3... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M doc/source/api/guidelines.rst Log Message: ----------- Merge pull request #3011 from jmchilton/api_docs Update some old information in API guideline docs. Commit: f599a7b8c025a60781216450f00a81c5a497bfd7 https://github.com/galaxyproject/galaxy/commit/f599a7b8c025a60781216450f00a8... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2016-10-06 (Thu, 06 Oct 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #15 from guerler/XSD_addition Add an XSD entry for this new feature. Commit: 59a6d07b7b02f2b23719acdc83122eae89e49b78 https://github.com/galaxyproject/galaxy/commit/59a6d07b7b02f2b23719acdc83122... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-10-06 (Thu, 06 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-modal.js M doc/source/admin/conda_faq.rst M lib/galaxy/tools/deps/__init__.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.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 Log Message: ----------- Merge pull request #3010 from nsoranzo/merge_release_16.07 Merge release_16.07 into dev Commit: 51aa341fe5ac7859233081af3ce5fab934349b1c https://github.com/galaxyproject/galaxy/commit/51aa341fe5ac7859233081af3ce5f... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-10-06 (Thu, 06 Oct 2016) Changed paths: A .ci/flake8_docstrings_include_list.txt M .ci/flake8_wrapper.sh A .ci/flake8_wrapper_docstrings.sh M .travis.yml M lib/galaxy/util/__init__.py M setup.cfg M tox.ini Log Message: ----------- Merge pull request #3004 from jmchilton/docstring_lint Initial docstring linting. Commit: 5e15d3b79d0fee4f469e2e3a1b0e2acdddeda15c https://github.com/galaxyproject/galaxy/commit/5e15d3b79d0fee4f469e2e3a1b0e2... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M test/base/driver_util.py Log Message: ----------- Use requests in driver_util for better proxy handling Commit: d0b9e2ca9f19453a74a478426c3e2d2236bf8788 https://github.com/galaxyproject/galaxy/commit/d0b9e2ca9f19453a74a478426c3e2... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py Log Message: ----------- Merge pull request #3007 from guerler/remove_unused_value_map Remove unused value map argument from basic parameter handling Commit: 2b10e2047293ee95ea8084657c55a5e354ce3b23 https://github.com/galaxyproject/galaxy/commit/2b10e2047293ee95ea8084657c55a... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #3006 from guerler/add_rgb_option Add rgb option for color picker Commit: 5e8da4ec82848407a4f1127da57eed5006b6ea39 https://github.com/galaxyproject/galaxy/commit/5e8da4ec82848407a4f1127da57ee... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix bare exception. https://docs.python.org/2/howto/doanddont.html#except Commit: 9e299e93468041e984518d0992ad4b2041b681f6 https://github.com/galaxyproject/galaxy/commit/9e299e93468041e984518d0992ad4... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M test/base/driver_util.py Log Message: ----------- Merge pull request #3013 from mvdbeek/proxy_planemo Use requests in driver_util for better proxy handling Commit: e310453fd0bde9c0c565c6f68b2fcd09942ac49a https://github.com/galaxyproject/galaxy/commit/e310453fd0bde9c0c565c6f68b2fc... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/color_param.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Improved docs and testing for color params. Commit: f72b46198ef7f03533b7d400195828d0976027c4 https://github.com/galaxyproject/galaxy/commit/f72b46198ef7f03533b7d40019582... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M config/job_conf.xml.sample_advanced A lib/galaxy/jobs/runners/godocker.py Log Message: ----------- Merge pull request #2791 from dannon/godocker Godocker job runner Commit: 3345dd4a92b9224a6a4e864326b60c8e92f29ad0 https://github.com/galaxyproject/galaxy/commit/3345dd4a92b9224a6a4e864326b60... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #2865 from martenson/forced-wittiness encourage wittiness in release notes Commit: a08b849f6db5041dc56173051bc45aaa8c469ae4 https://github.com/galaxyproject/galaxy/commit/a08b849f6db5041dc56173051bc45... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/color_param.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3016 from jmchilton/color_followup Improved docs and testing for color params. Commit: 604dfb27ce0acba176c059f08642aae7a390ddf0 https://github.com/galaxyproject/galaxy/commit/604dfb27ce0acba176c059f08642a... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Fix for reruning tool with workflow resume that is part of a collection. The special casing of "__identifier__" that occurs here and elsewhere in the code is less than ideal. Commit: c39f8c92ea47c73e2cef8295e4816f06a6e72f44 https://github.com/galaxyproject/galaxy/commit/c39f8c92ea47c73e2cef8295e4816... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Fix for XSD Commit: 056a7e0d1e7a6e3bb78f22903df6b941b44fad69 https://github.com/galaxyproject/galaxy/commit/056a7e0d1e7a6e3bb78f22903df6b... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #3020 from bgruening/xsd_fix Fix for XSD Commit: 415c7fa67be28885fa92246fb63efdf5bfd777bf https://github.com/galaxyproject/galaxy/commit/415c7fa67be28885fa92246fb63ef... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Verify tools coming from cache have correct id. Commit: 56dfaf003f3239d2475715b478e319ff359e08d4 https://github.com/galaxyproject/galaxy/commit/56dfaf003f3239d2475715b478e31... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-10-08 (Sat, 08 Oct 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix tool reload in 415c7fa67be28885fa92246fb63efdf5bfd777bf Previous commit changed the if/elif/else logic. The else was now applying also to cached tools, which it should not. Instead, explicitly check that we still don't have a tool object. Commit: 5a72449246be6f0f2fe3955bebf6f42ae89966bc https://github.com/galaxyproject/galaxy/commit/5a72449246be6f0f2fe3955bebf6f... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-08 (Sat, 08 Oct 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.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 A test/functional/tools/mulled_example_multi_1.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Implement beta support for dynamically discovering mulled containers for dependencies. Contains all mulled fixes and enhancements through 16.10.7 including several bug fixes from @bgruening. Commit: e389e1939160dfef7c364785a17869f5de30198b https://github.com/galaxyproject/galaxy/commit/e389e1939160dfef7c364785a1786... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-08 (Sat, 08 Oct 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M test/unit/jobs/test_runner_local.py Log Message: ----------- Implement option to require containerization of jobs. This is great for security in production. For my own greedy concerns, I'm adding it for development however. I don't want someone to be testing mulled containers and accidently run the job locally. Commit: fdc81bd84a76082249474782367b7b7a59706af3 https://github.com/galaxyproject/galaxy/commit/fdc81bd84a76082249474782367b7... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-08 (Sat, 08 Oct 2016) Changed paths: M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Upgrade repository revision Commit: 2316075f0caf7771bafabbfa00bfe2c5ecdfacec https://github.com/galaxyproject/galaxy/commit/2316075f0caf7771bafabbfa00bfe... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-08 (Sat, 08 Oct 2016) Changed paths: A .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/flake8_wrapper.sh A .ci/flake8_wrapper_docstrings.sh M .ci/py3_sources.txt M .travis.yml M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-modal.js M config/job_conf.xml.sample_advanced M doc/source/admin/conda_faq.rst M doc/source/api/guidelines.rst M lib/galaxy/datatypes/data.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/__init__.py M lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/subsystems.py M lib/galaxy/jobs/metrics/formatting.py M lib/galaxy/jobs/metrics/instrumenters/__init__.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 A lib/galaxy/jobs/runners/godocker.py M lib/galaxy/managers/workflows.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/genomes.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M scripts/bootstrap_history.py M setup.cfg M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/ui-modal.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-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/ui-modal.js A test/api/test_workflow_batch.ga M test/api/test_workflows.py M test/base/driver_util.py A test/functional/tools/color_param.xml M test/functional/tools/samples_tool_conf.xml M test/unit/workflows/test_run_parameters.py M tools/data_source/data_source.py M tools/data_source/hbvar_filter.py M tools/data_source/microbial_import_code.py M tools/evolution/add_scores.py M tools/evolution/codingSnps_filter.py M tools/extract/extract_genomic_dna.py M tools/filters/axt_to_concat_fasta.py M tools/filters/axt_to_fasta.py M tools/filters/axt_to_lav.py M tools/filters/axt_to_lav_code.py M tools/filters/bed_to_gff_converter.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/secure_hash_message_digest.py M tools/filters/sff_extract.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/vcf_to_maf_customtrack.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/solid2fastq.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/velvetg_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Merge branch 'dev' into remote_chart_plugins Commit: b7a25fc653fa30a78d97b2aa23e9a5ad43814694 https://github.com/galaxyproject/galaxy/commit/b7a25fc653fa30a78d97b2aa23e9a... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-08 (Sat, 08 Oct 2016) Changed paths: M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Update repository revision to new drawrnajs logo Commit: 654b5e9322f5c54332c8d8861bc8ed34c6e71a8e https://github.com/galaxyproject/galaxy/commit/654b5e9322f5c54332c8d8861bc8e... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: A doc/source/admin/mulled_containers.rst Log Message: ----------- Add initial documentation about the new mulled features. Commit: d821c2745c014bc0e2e2cc31eac8d70bb576ea7e https://github.com/galaxyproject/galaxy/commit/d821c2745c014bc0e2e2cc31eac8d... Author: Evgeny Anatskiy <evgeny.anatskiy@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/1a80a0df7f371347976f0b9fb3ff1... Author: Björn Grüning <bjoern@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/5361d7c03d23ed4fe4701b2e126f5... Author: anatskiy <evgeny.anatskiy@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/a34a1201fc72abff092ccb8c0366b... Author: anatskiy <evgeny.anatskiy@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/6e66fbeca8741748aa823e34432bd... Author: anatskiy <evgeny.anatskiy@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/eb46e70206ba43a5e191153df74aa... Author: anatskiy <evgeny.anatskiy@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/40bcaaecf531920275d8f9f82d5e5... Author: anatskiy <evgeny.anatskiy@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/bf4a1aa1a87050e030ead0e5ff892... Author: anatskiy <evgeny.anatskiy@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/17440d7b11b5013e52033efe46681... Author: anatskiy <evgeny.anatskiy@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/143a740dc38fec9f92211d26364cb... Author: anatskiy <evgeny.anatskiy@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/117c5263acdfb8853cc6771810ef8... Author: anatskiy <evgeny.anatskiy@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/ed2282d60b3f41c653e61be13d24a... Author: anatskiy <evgeny.anatskiy@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/29129463a0be1778c69fce6e783dd... Author: anatskiy <evgeny.anatskiy@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/411674521cf1d9d3c5479ae334fbe... Author: anatskiy <evgeny.anatskiy@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/b215de947c007dfc84ae4325d1a6b... Author: anatskiy <evgeny.anatskiy@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/bb9dc0560ade3f44037a4d03a2465... Author: anatskiy <evgeny.anatskiy@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/e95392b4b62b5ff803390287d0eac... Author: anatskiy <evgeny.anatskiy@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/f3b1232bdb46e9ccb4f27b3a1fc66... Author: Evgeny Anatskiy <evgeny.anatskiy@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/578bdf679f0575e98922ddea00424... Author: Evgeny Anatskiy <evgeny.anatskiy@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/42adc9c7dfa1485162b78742f5ac3... Author: anatskiy <evgeny.anatskiy@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/6bc57ec0209f22970c4303870ba48... Author: anatskiy <evgeny.anatskiy@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/ca769ab848209be8e4e48a6b28c13... Author: anatskiy <evgeny.anatskiy@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/1a8a82370bcfd157f1d82ee6f6634... Author: anatskiy <evgeny.anatskiy@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/454a88b45174cfddae5ad79c31d92... Author: anatskiy <evgeny.anatskiy@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/53f56c3426714b3531dd1c49ecca4... Author: anatskiy <evgeny.anatskiy@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/c7f35c41d72a6131bfd0a4a7b3525... Author: anatskiy <evgeny.anatskiy@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/a73d00fc04695b1f27a3cdf6091d3... Author: anatskiy <evgeny.anatskiy@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/2b2be226ee9425742e0a629459e12... Author: anatskiy <evgeny.anatskiy@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/211491fdf31a814590250edd44479... Author: anatskiy <evgeny.anatskiy@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/060df24ff5b329c37103f9c90caf6... Author: anatskiy <evgeny.anatskiy@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/00cf0cb85ec2cca9091de22fcaa65... Author: anatskiy <evgeny.anatskiy@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/27e0302ea3926e0a3ce6955317f6d... Author: anatskiy <evgeny.anatskiy@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/29a57ba0fdd9ab066e19110715bbb... Author: anatskiy <evgeny.anatskiy@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/e58fe7ca49f7b01244d1e6f4bfc92... Author: Evgeny Anatskiy <evgeny.anatskiy@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/8b5716ddfda7d8d4bc604cf6d396d... Author: Evgeny Anatskiy <evgeny.anatskiy@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/ce346b6ad4482a1e6a0e8e9f92e79... Author: Evgeny Anatskiy <evgeny.anatskiy@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/2cc133f32507cd2aec8784e247106... Author: Björn Grüning <bjoern@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/69a9344c529e34cdb70fdd71634ba... Author: Evgeny Anatskiy <evgeny.anatskiy@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/ef304a2223ca080c9181fad411791... Author: Evgeny Anatskiy <evgeny.anatskiy@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/a3627b98ab8f5940af529e1387c8d... Author: Evgeny Anatskiy <evgeny.anatskiy@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: ad0d0bc7cec7c281052610b9453db42cfce8dcea https://github.com/galaxyproject/galaxy/commit/ad0d0bc7cec7c281052610b9453db... Author: ramezrawas <ramezrawas@gmail.com> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Missing double quotation line 3664: name="output_vcf> Commit: 217854827ac7dfc88c5388cd2ecb24fffd86c060 https://github.com/galaxyproject/galaxy/commit/217854827ac7dfc88c5388cd2ecb2... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #3027 from ramezrawas/patch-1 Missing double quotation Commit: 4b5114bed1c09c655654972b084274e74310ebe8 https://github.com/galaxyproject/galaxy/commit/4b5114bed1c09c655654972b08427... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: A doc/source/admin/mulled_containers.rst Log Message: ----------- Merge pull request #50 from jmchilton/mulled_docs Add initial documentation about the new mulled features. Commit: fad562876f886e3384fec1a9782685251d12e2c1 https://github.com/galaxyproject/galaxy/commit/fad562876f886e3384fec1a978268... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Datatypes: include base classes in search by name Fixes #2982 Adds the base class 'images.Image' to the list of classes returnable by 'datatypes_registry.get_datatype_class_by_name'. Normally that method searches the registry's list of datatypes and those are instantiable classes only. The images.Image can be considered an abstract base class and you'd never create a dataset of that datatype. The method is used for getting classes for 'isinstance' tests, however, so including base classes like 'images.Image' allow testing for all its image subclasses. This change makes that possible and allows the method (and its consumers) to behave in a much more predictable and useful manner. Commit: 91bfecea67b78f7e459a250a7844c6344154367f https://github.com/galaxyproject/galaxy/commit/91bfecea67b78f7e459a250a7844c... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/multi_data_optional.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add documentation on optional ``multiple="true"`` data parameters. Thanks to detailed biostar question from @lindenb (sorry these parameters are so counter-intuitive - I don't have an excuse other than a need to preserve backward compatibility). Rebased with indention requested by @nsoranzo and fixes for the test case tool. Commit: f0b988da78f081bf6845ce2d280d153e221f3633 https://github.com/galaxyproject/galaxy/commit/f0b988da78f081bf6845ce2d280d1... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/util.py Log Message: ----------- Bring in latest galaxy-lib fixes. Commit: 1e32c0926ca3fcee79f355577c5525c4bf73c8e4 https://github.com/galaxyproject/galaxy/commit/1e32c0926ca3fcee79f355577c552... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/style/source_material/circle.py M doc/parse_gx_xsd.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 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 Log Message: ----------- Fix import order and Python3 compatibility for most of test/ Commit: 20dcc4d693ae8fa7e846eb32e65292c3c4a38863 https://github.com/galaxyproject/galaxy/commit/20dcc4d693ae8fa7e846eb32e6529... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- remove duplicated option from config sample Commit: bcabbd8707e0064e041e730e5abd1d8dfc0a692c https://github.com/galaxyproject/galaxy/commit/bcabbd8707e0064e041e730e5abd1... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M doc/source/admin/mulled_containers.rst Log Message: ----------- minor changes to mulled admin docs Commit: 7db241faa6d505427108c5ddeae8dbc77c384613 https://github.com/galaxyproject/galaxy/commit/7db241faa6d505427108c5ddeae8d... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced A doc/source/admin/mulled_containers.rst M lib/galaxy/config.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 A test/functional/tools/mulled_example_multi_1.xml M test/functional/tools/samples_tool_conf.xml M test/unit/jobs/test_runner_local.py Log Message: ----------- Merge pull request #2986 from jmchilton/mulled Implement beta support for discovering mulled containers for dependencies. Commit: 1a2d75fade1077359b2a9b1072feab793022b7f4 https://github.com/galaxyproject/galaxy/commit/1a2d75fade1077359b2a9b1072fea... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M doc/source/admin/index.rst Log Message: ----------- add muled docs to admin index Commit: 7d642c063f18b18b438a4840705f09652f3b586d https://github.com/galaxyproject/galaxy/commit/7d642c063f18b18b438a4840705f0... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M doc/source/admin/index.rst Log Message: ----------- Merge pull request #3032 from martenson/link-mulled-docs add muled docs to admin index Commit: 75d1f8496acc060e8bd91cdaffd082fc9685ef1f https://github.com/galaxyproject/galaxy/commit/75d1f8496acc060e8bd91cdaffd08... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/style/source_material/circle.py M doc/parse_gx_xsd.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 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 Log Message: ----------- Merge pull request #3031 from nsoranzo/flake8-import-order Fix import order and Python3 compatibility for most of test/ Commit: 191bae9a2b9d06bb7d461633b0a43ce320a042c4 https://github.com/galaxyproject/galaxy/commit/191bae9a2b9d06bb7d461633b0a43... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Merge pull request #3028 from carlfeberhard/fix.tiff Datatypes: include base classes in search by name Commit: bf5cc30b843838f30a4b40faa9834cbc28a01991 https://github.com/galaxyproject/galaxy/commit/bf5cc30b843838f30a4b40faa9834... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: R config/plugins/visualizations/charts/sample.txt M config/plugins/visualizations/charts/static/views/groups.js M config/plugins/visualizations/charts/static/views/viewport.js Log Message: ----------- Remove tabular file from repo, fix comments Commit: 6639a181df3ba8f2a26e6a9bde27e53866cf110a https://github.com/galaxyproject/galaxy/commit/6639a181df3ba8f2a26e6a9bde27e... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #3025 from mvdbeek/cache_fix Cache fix Commit: 1156006733001fb06520a70f54a9227f5b4c7061 https://github.com/galaxyproject/galaxy/commit/1156006733001fb06520a70f54a92... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M .travis.yml M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst Log Message: ----------- Merge branch 'release_16.07' into dev Conflicts: lib/galaxy/tools/deps/__init__.py Commit: d93cedef8a3e727bc0a089ad6eda4c5734cd55c7 https://github.com/galaxyproject/galaxy/commit/d93cedef8a3e727bc0a089ad6eda4... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Increase min number of columns for pileup sniffing to 5 Fix #3001. Commit: 3be66005dc4cbd2a7d45e2a482f297dcaf493c02 https://github.com/galaxyproject/galaxy/commit/3be66005dc4cbd2a7d45e2a482f29... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Check that chromosome number is >=0 Commit: 1288cf0505eea6139bf9f34d60e6b255268d717d https://github.com/galaxyproject/galaxy/commit/1288cf0505eea6139bf9f34d60e6b... Author: tmcgowan <mcgo0092@umn.edu> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/workflow/workflow-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/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Add workflow save-as functionality. Issue 3000 Commit: 2ab0b18706dc54cde3507e194a935f513c68119c https://github.com/galaxyproject/galaxy/commit/2ab0b18706dc54cde3507e194a935... Author: tmcgowan <mcgo0092@umn.edu> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Allow names with spaces Commit: 2b9281a37832346b0a3e5aed1b13ee84270ffe44 https://github.com/galaxyproject/galaxy/commit/2b9281a37832346b0a3e5aed1b13e... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Fix dependency ordering broken in #2917. We will store dependencies in an OrderedDict, matching the order of `<requirements>`. Fixes an issue where an R library was being sourced before R itself during shell command generation, the sourcing of R afterwards overwrote the `R_LIBS` env setting. Commit: 58d608b9060d7608c33d711183790e3b19c313cc https://github.com/galaxyproject/galaxy/commit/58d608b9060d7608c33d711183790... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge pull request #3036 from blankenberg/fix-dep-shell-order Fix dependency ordering broken in #2917. Commit: 1805ac8b5948ded11e154c887a2da99481ac70c6 https://github.com/galaxyproject/galaxy/commit/1805ac8b5948ded11e154c887a2da... 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config/plugins/visualizations/charts/static/views/editor.js R config/plugins/visualizations/charts/static/views/groups.js R config/plugins/visualizations/charts/static/views/settings.js R config/plugins/visualizations/charts/static/views/types.js R config/plugins/visualizations/charts/static/views/viewer.js R config/plugins/visualizations/charts/static/views/viewport.js M config/plugins/visualizations/charts/templates/charts.mako A config/plugins/visualizations/charts/webpack.config.js Log Message: ----------- Add chart plugins back to plugins directory of visualization framework Commit: f467384fdd97dba43ee0f9b7c3592498de738ee8 https://github.com/galaxyproject/galaxy/commit/f467384fdd97dba43ee0f9b7c3592... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Use fixed repository path Commit: fe73009db5248a04844db86584064b48a86f2cb2 https://github.com/galaxyproject/galaxy/commit/fe73009db5248a04844db86584064... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M config/plugins/visualizations/charts/static/client/components/model.js Log Message: ----------- Fix default options for storing request Commit: cc36793cd0d249fd2794c5de54af6ff10695b88e https://github.com/galaxyproject/galaxy/commit/cc36793cd0d249fd2794c5de54af6... Author: Evgeny Anatskiy <evgeny.anatskiy@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/812aca5b34df584a09d3f82f9d938... Author: Evgeny Anatskiy <evgeny.anatskiy@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/5f9154a6179f194a8186d0f91a375... Author: Evgeny Anatskiy <evgeny.anatskiy@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/cd92be8802e520a2f53eceb385f01... Author: Björn Grüning <bjoern@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/0ad7c99ea20ba49725fffe5a356ab... Author: Joachim Wolff <wolffj@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/f29b003a8cd6a277ee67cb5536530... Author: Joachim Wolff <wolffj@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/95c1f186935a77ee71de59a3a616d... Author: Joachim Wolff <wolffj@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/eb32ad229f5f22c8b2cb497344fd5... Author: Joachim Wolff <wolffj@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/d1737110bf2d870346df43d5969b3... Author: Joachim Wolff <wolffj@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/76b9e004d204b6569ef6d19b6e808... Author: Joachim Wolff <wolffj@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 https://github.com/galaxyproject/galaxy/commit/8030d2025ddaa0ca5f5d58f12a24f... Author: Joachim Wolff <wolffj@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: acd99f76fc967445cc9b8cd1317793a6074997b7 https://github.com/galaxyproject/galaxy/commit/acd99f76fc967445cc9b8cd131779... Author: Joachim Wolff <wolffj@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: 6684fd4e262f97c313d907bf44409d94172338c8 https://github.com/galaxyproject/galaxy/commit/6684fd4e262f97c313d907bf44409... Author: Joachim Wolff <wolffj@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: fafeedc286035d78d1033220717b346e4c0d3c99 https://github.com/galaxyproject/galaxy/commit/fafeedc286035d78d1033220717b3... Author: Joachim Wolff <wolffj@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/af8a3f11048c86f91f17044344211... Author: Joachim Wolff <wolffj@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: dcde64ce407b332072525c66885adf03a26eeb5e https://github.com/galaxyproject/galaxy/commit/dcde64ce407b332072525c66885ad... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/workflow/extract.py M test/api/test_workflow_extraction.py Log Message: ----------- Fix import order. Fix typos and improve readability Commit: 04bf2153b8f61c60288cb180d448e7c20352f6e7 https://github.com/galaxyproject/galaxy/commit/04bf2153b8f61c60288cb180d448e... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M lib/galaxy/workflow/extract.py Log Message: ----------- WorkflowSummary: add dict to map a job id to its representative job Fix #2742 introduced in commit 9ede8e556be1f6038361b579c1457068e50e951a . The representative job is the first in the returned query, so substantially random and not necessarily the one with the lowest job id. Mapping a job id to its representative job in extract_steps() makes it robust also against API requests with manually chosen collection job ids. Commit: d5dc39ab0f034d79252a9fb0875824cbf8b02e04 https://github.com/galaxyproject/galaxy/commit/d5dc39ab0f034d79252a9fb087582... Author: Björn Grüning <bjoern@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/0a15289d31a189df71490bba53927... Author: Evgeny Anatskiy <evgeny.anatskiy@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/bc51dc3ec72dc7a5bbcc42bcd4f1c... Author: Evgeny Anatskiy <evgeny.anatskiy@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/95d6990cf3f6f1e4ade87b6ba6557... Author: Evgeny Anatskiy <evgeny.anatskiy@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/4f89528c94d33f1e3eca8df9dd34c... Author: Björn Grüning <bjoern@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: 1e2688f1578552ea03e7a601d927c4475b96fdd2 https://github.com/galaxyproject/galaxy/commit/1e2688f1578552ea03e7a601d927c... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/multi_data_optional.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3024 from jmchilton/multi_optional_param Add documentation on optional ``multiple="true"`` data parameters. Commit: c6713e7c31d5ffe576af5af7de56d3536d196786 https://github.com/galaxyproject/galaxy/commit/c6713e7c31d5ffe576af5af7de56d... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/workflow/extract.py M test/api/test_workflow_extraction.py Log Message: ----------- Merge pull request #3039 from nsoranzo/fix_for_2742 Fix workflow extraction API tests on PostgreSQL Commit: 2d915a42f6329bd31dfdc76b5bfa56376a57c841 https://github.com/galaxyproject/galaxy/commit/2d915a42f6329bd31dfdc76b5bfa5... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- tense changes Commit: 77f78cfbc79ddc345bc22277afc335f11e189491 https://github.com/galaxyproject/galaxy/commit/77f78cfbc79ddc345bc22277afc33... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt 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/workflow/extract.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/schedulers/core.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 M test/unit/tools_support.py M test/unit/unittest_utils/utility.py Log Message: ----------- Change __all__ from list to tuple Also fix import order and Python3 compatibility. Commit: bb4428896839898fb5d0c9b88ae18fc9b705a27b https://github.com/galaxyproject/galaxy/commit/bb4428896839898fb5d0c9b88ae18... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/util/image_util.py M lib/galaxy/util/checkers.py M tools/data_source/upload.py Log Message: ----------- Failthrough to using imghdr when PIL does not detect an image correctly. Some misc cleanup, avoiding use of system functions as variable names, etc. Commit: cb6e25278c4a59d4ea2edd9ce5e9c757b1ebf7f8 https://github.com/galaxyproject/galaxy/commit/cb6e25278c4a59d4ea2edd9ce5e9c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/sequence.py R lib/galaxy/datatypes/util/image_util.py M lib/galaxy/util/checkers.py A lib/galaxy/util/image_util.py M tools/data_source/upload.py Log Message: ----------- Refactoring, because it was bugging me. Commit: ba07956117e5e4527fa5d2837da2c267f6ab981d https://github.com/galaxyproject/galaxy/commit/ba07956117e5e4527fa5d2837da2c... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M tools/stats/filtering.py Log Message: ----------- Fix tabular filtering tool broken in #2983 Commit: 5d294ea7d3a14561a15c30f3527dfcd21d517369 https://github.com/galaxyproject/galaxy/commit/5d294ea7d3a14561a15c30f3527df... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py Log Message: ----------- Fix GFF attribute filtering tool broken in #2983 Commit: 32bc17cdaa636ba0ba2a97a372b37d518cdd6390 https://github.com/galaxyproject/galaxy/commit/32bc17cdaa636ba0ba2a97a372b37... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py Log Message: ----------- Whitespace fix Commit: b6d4473aa0975f88b2d2cf8aa1372aecfc92919b https://github.com/galaxyproject/galaxy/commit/b6d4473aa0975f88b2d2cf8aa1372... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix for displaying parameters to the user, that have a False value. Previously, e.g. an integer with a value of 0 would display "Not available.". Commit: ed263bf8a52b37199cc7822126598a75a9984335 https://github.com/galaxyproject/galaxy/commit/ed263bf8a52b37199cc7822126598... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/util/image_util.py Log Message: ----------- import order. Commit: 4bc429776853239961c45c9656c69b3be0ae01bc https://github.com/galaxyproject/galaxy/commit/4bc429776853239961c45c9656c69... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/util/image_util.py Log Message: ----------- Simplify, strip out passing of image. Commit: 6c17d1a823b4367b93fff61d7f2fbed23dc5de3b https://github.com/galaxyproject/galaxy/commit/6c17d1a823b4367b93fff61d7f2fb... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Remove outdated warning After digging through the code I am not finding evidence that this was ever possible to do, at least not since sometime pre-2010. Commit: a22a4d0bd5a2376c130ad84e4bc0313b9f252e45 https://github.com/galaxyproject/galaxy/commit/a22a4d0bd5a2376c130ad84e4bc03... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Merge pull request #3046 from erasche/remove_warning Remove outdated warning on ID_SECRET Commit: 36ae57c6e028fc814af1cd4740e9222dfcb56021 https://github.com/galaxyproject/galaxy/commit/36ae57c6e028fc814af1cd4740e92... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M tools/stats/filtering.py Log Message: ----------- Merge pull request #3043 from blankenberg/fix-filter-tool Fix tabular filtering tool broken in #2983 Commit: f6d5f3c4a2e51bd6b75a99dc015360e4ca9a6461 https://github.com/galaxyproject/galaxy/commit/f6d5f3c4a2e51bd6b75a99dc01536... Author: Dave B <dave@bx.psu.edu> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix downloading tool tarball with boolean test input values. Commit: b52d5be75b3f2bf9cae86d4a278689cb614095be https://github.com/galaxyproject/galaxy/commit/b52d5be75b3f2bf9cae86d4a27868... Author: Björn Grüning <bjoern@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/290c48b16c54fab54ec35601e04d6... Author: Björn Grüning <bjoern@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/a231e240ed1a8002318678dde5979... Author: Björn Grüning <bjoern@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/6a62dbc91a0f2ed282c2cc1e3c422... Author: Bjoern Gruening <bjoern.gruening@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/8f5b54141dd2b46d3b532915b082c... Author: Björn Grüning <bjoern@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/773d85453f965712cdd8bcc209b9a... Author: Bjoern Gruening <bjoern.gruening@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: 277727ada67d32404dc953d393716af8aa2aabdc https://github.com/galaxyproject/galaxy/commit/277727ada67d32404dc953d393716... Author: Dannon Baker <dannon.baker@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 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/workflow/extract.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/schedulers/core.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 M test/unit/tools_support.py M test/unit/unittest_utils/utility.py Log Message: ----------- Merge pull request #3041 from nsoranzo/flake8-import-order Change __all__ from list to tuple [1/2] Commit: a676d6e8234dd9db59376df7f54633a78e503f86 https://github.com/galaxyproject/galaxy/commit/a676d6e8234dd9db59376df7f5463... Author: Bjoern Gruening <bjoern.gruening@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: 0062eacfdf86fbfe8fda3de88b2b5b122cdc567e https://github.com/galaxyproject/galaxy/commit/0062eacfdf86fbfe8fda3de88b2b5... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py Log Message: ----------- Merge pull request #3044 from blankenberg/gff-filter-tool-fix Fix GFF attribute filtering tool broken in #2983 Commit: 6894df3dcb0f308724331bceceff46dba23156a1 https://github.com/galaxyproject/galaxy/commit/6894df3dcb0f308724331bceceff4... Author: Evgeny Anatskiy <evgeny.anatskiy@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/3f8d45b388e5788b23c39c2b544e4... Author: Evgeny Anatskiy <evgeny.anatskiy@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/fb516d9387a2df9a1ccdd2c7a1a1c... Author: Evgeny Anatskiy <evgeny.anatskiy@gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/webhooks/__init__.py Log Message: ----------- remove blank line Commit: b9e4bf58c5b656089ac8402632677503e6a86c65 https://github.com/galaxyproject/galaxy/commit/b9e4bf58c5b656089ac8402632677... Author: Lance Parsons <lparsons@princeton.edu> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml Log Message: ----------- Sort bedtools output in bam_to_bigwig conversion Bedtools genomecov seems to output bedgraph files with chromosomes sorted in the order given in the chromInfo file. This can cause issues with bedGraphToBigWig which requires them sorted in a specific way. Fixes #2582. Commit: e220ed097067124f5ab616d0ece35d0af4cb2539 https://github.com/galaxyproject/galaxy/commit/e220ed097067124f5ab616d0ece35... Author: Bjoern Gruening <bjoern.gruening@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/b0b5157f36ec26090c9c11c0a1335... Author: Bjoern Gruening <bjoern.gruening@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/f4dc38a54da3539f4d63f7e33708b... Author: Bjoern Gruening <bjoern.gruening@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/2703ba1a0cc3a28314018299b8f1a... Author: Evgeny Anatskiy <evgeny.anatskiy@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: afbea0dbfda0ad231a101aa0d7c25ee3822d9f7e https://github.com/galaxyproject/galaxy/commit/afbea0dbfda0ad231a101aa0d7c25... Author: tmcgowan <mcgo0092@umn.edu> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M static/maps/mvc/dataset/dataset-li.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/dataset/dataset-li.js Log Message: ----------- Present tool help from history entry. Issue 2100 Commit: 8694356ab7057c47164a92f8d4e47a800fca2f4d https://github.com/galaxyproject/galaxy/commit/8694356ab7057c47164a92f8d4e47... Author: Björn Grüning <bjoern@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/3aadd84b80bca7fc588ffccaa27f0... Author: Bjoern Gruening <bjoern.gruening@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/0dc2c95bd07e2a53dec27c8d0d4fc... Author: Bjoern Gruening <bjoern.gruening@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/3cb8189e1fa48c58afaf609691a08... Author: Bjoern Gruening <bjoern.gruening@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: 4446ccc98c970f5077080f563585c90b1f84dc3a https://github.com/galaxyproject/galaxy/commit/4446ccc98c970f5077080f563585c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #3045 from blankenberg/value_to_display_text-fix Fix for displaying parameters to the user, that have a False value. Commit: 37702392817107dfd12cbb54f0af1dcb18bd848e https://github.com/galaxyproject/galaxy/commit/37702392817107dfd12cbb54f0af1... Author: Evgeny Anatskiy <evgeny.anatskiy@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/bd20ab1aa57381b36e16dc08c20b6... Author: Evgeny Anatskiy <evgeny.anatskiy@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/3d4f302c4734e9afc7e065645c915... Author: Bjoern Gruening <bjoern.gruening@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: d26f46423e5d79dd8d0519d90350389838fece3c https://github.com/galaxyproject/galaxy/commit/d26f46423e5d79dd8d0519d903503... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/sequence.py R lib/galaxy/datatypes/util/image_util.py M lib/galaxy/util/checkers.py A lib/galaxy/util/image_util.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #3042 from dannon/image_detection_fixes Image detection fixes Commit: 4bbab51c0500922c9a191d022de295daa48f0dd5 https://github.com/galaxyproject/galaxy/commit/4bbab51c0500922c9a191d022de29... Author: Björn Grüning <bjoern@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: e5913a49e260be47ff4f32ae21780264731d98d5 https://github.com/galaxyproject/galaxy/commit/e5913a49e260be47ff4f32ae21780... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3047 from galaxyproject/tool_tarball_fix Fix downloading tool tarball with boolean test input values. Commit: 36134bca694c9dc6b2584fb661dfbce4ddb793e6 https://github.com/galaxyproject/galaxy/commit/36134bca694c9dc6b2584fb661dfb... Author: Scott Szakonyi <sszakony@nd.edu> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js Log Message: ----------- Added code to adjust top setting of tool search if messagebox is visible, issue 2907 Commit: 6312d8052b9668a03b3bb25ea02b9d42ac32de6d https://github.com/galaxyproject/galaxy/commit/6312d8052b9668a03b3bb25ea02b9... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js M static/maps/mvc/tool/tools.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/tools.js Log Message: ----------- Rebuild cilent. Commit: 28bb83f0ab5e93b5f961f12dac555bf96a9073ea https://github.com/galaxyproject/galaxy/commit/28bb83f0ab5e93b5f961f12dac555... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js M static/maps/mvc/tool/tools.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/tools.js Log Message: ----------- Merge pull request #3055 from dannon/cherrypick_masthead_fix Cherrypick masthead fix Commit: a895c823daaf01c2b1b883dc256452411de9a728 https://github.com/galaxyproject/galaxy/commit/a895c823daaf01c2b1b883dc25645... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Merge pull request #3019 from blankenberg/collection-wf-resume-error Fix for rerunning tool with workflow resume that is part of a collection. Commit: 868658c7e72e3d0f37e36c51316a72a56a270376 https://github.com/galaxyproject/galaxy/commit/868658c7e72e3d0f37e36c51316a7... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Always display text, with test cases Commit: f053f9bb3d2820c09aab1a0bc3b29e27eed56d09 https://github.com/galaxyproject/galaxy/commit/f053f9bb3d2820c09aab1a0bc3b29... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-14 (Fri, 14 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/mvc/tool/tools.js 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/images.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py R lib/galaxy/datatypes/util/image_util.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py 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/__init__.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/__init__.py M lib/galaxy/tools/deps/commands.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 M lib/galaxy/tools/deps/docker_util.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/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/basic.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/base.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/util/checkers.py A lib/galaxy/util/image_util.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/schedulers/core.py M static/maps/mvc/tool/tools.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/tools.js 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/api/workflows_format_2/main.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 A test/functional/tools/multi_data_optional.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 M test/unit/tools_support.py M test/unit/unittest_utils/utility.py M tools/data_source/upload.py M tools/filters/gff/gff_filter_by_attribute.py M tools/stats/filtering.py Log Message: ----------- Merge branch 'dev' into remote_chart_plugins Commit: ebaffa2e0d6a030dfc3c78a3b9515093b14f7103 https://github.com/galaxyproject/galaxy/commit/ebaffa2e0d6a030dfc3c78a3b9515... Author: Evgeny Anatskiy <evgeny.anatskiy@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: 15ad14e6620706d6dbb39176783e274e01eebb3b https://github.com/galaxyproject/galaxy/commit/15ad14e6620706d6dbb39176783e2... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-16 (Sun, 16 Oct 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/merge_collection.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Enhance merge collection work from @Takadonet with more merge conflict actions. And allow it to work over any number of input collections. Commit: 448a27a4a1ebe2b25b40eca11b7aa319f7345c61 https://github.com/galaxyproject/galaxy/commit/448a27a4a1ebe2b25b40eca11b7aa... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-16 (Sun, 16 Oct 2016) Changed paths: M .ci/flake8_blacklist.txt A .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/flake8_wrapper.sh A .ci/flake8_wrapper_docstrings.sh M .ci/py3_sources.txt A .ci/validate_test_tools.sh M .gitignore M .travis.yml M CONTRIBUTORS.md M LICENSE.txt M Makefile M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js A client/galaxy/scripts/libs/bbi/bigwig.js A client/galaxy/scripts/libs/bbi/jquery-ajax-native.js A client/galaxy/scripts/libs/bbi/jszlib.js A client/galaxy/scripts/libs/bbi/spans.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-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/utils/utils.js A client/galaxy/scripts/viz/bbi-data-manager.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/ui.less M client/galaxy/style/source_material/circle.py M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced A doc/parse_gx_xsd.py A doc/schema_template.md M doc/source/admin/chat.rst M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst M doc/source/admin/index.rst A doc/source/admin/mulled_containers.rst M doc/source/api/guidelines.rst M doc/source/project/issues.rst M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M 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tools/next_gen_conversion/solid2fastq.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/velvetg_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into collection_tools Commit: 49eac93882226e6f29624c676d593ae78719d7e5 https://github.com/galaxyproject/galaxy/commit/49eac93882226e6f29624c676d593... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-16 (Sun, 16 Oct 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/merge_collection.xml Log Message: ----------- Cleanup merge collection and get test cases working again. Commit: 7d938e2a23ca3ce8e3fac430bce494ce8f5238c3 https://github.com/galaxyproject/galaxy/commit/7d938e2a23ca3ce8e3fac430bce49... Author: Philip Mabon <philipmabon@gmail.com> Date: 2016-10-17 (Mon, 17 Oct 2016) Changed paths: M .ci/flake8_blacklist.txt A .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/flake8_wrapper.sh A .ci/flake8_wrapper_docstrings.sh M .ci/py3_sources.txt A .ci/validate_test_tools.sh M .gitignore M .travis.yml M CONTRIBUTORS.md M LICENSE.txt M Makefile M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js A client/galaxy/scripts/libs/bbi/bigwig.js A client/galaxy/scripts/libs/bbi/jquery-ajax-native.js A client/galaxy/scripts/libs/bbi/jszlib.js A client/galaxy/scripts/libs/bbi/spans.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-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M 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tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/solid2fastq.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/velvetg_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Merge pull request #1 from jmchilton/collection_tools Enhance the Merge Collections Tool Commit: 31cb477e1a538c74360f039dda23907d0856adb6 https://github.com/galaxyproject/galaxy/commit/31cb477e1a538c74360f039dda239... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-17 (Mon, 17 Oct 2016) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py M lib/galaxy/tools/filter_failed_collection.xml A lib/galaxy/tools/merge_collection.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #2771 from Takadonet/dev Collection Operator tools Commit: 762337e110d7a8d4058d7fcc7fd41147b0d89020 https://github.com/galaxyproject/galaxy/commit/762337e110d7a8d4058d7fcc7fd41... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-17 (Mon, 17 Oct 2016) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/object_wrapper.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/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/workflow_util.py M test/api/test_histories.py M test/api/test_libraries.py M test/unit/tools/test_tool_dependency_description.py Log Message: ----------- Fix import orders for updates to flake8_import_order. Commit: 4bf1994fc3fd09b874c9ea29a8871269d44ad193 https://github.com/galaxyproject/galaxy/commit/4bf1994fc3fd09b874c9ea29a8871... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-10-17 (Mon, 17 Oct 2016) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/object_wrapper.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/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/workflow_util.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 #3059 from jmchilton/import_update Fix import orders for updates to flake8_import_order. Commit: 7207c15090385a397493da0503b06dbea1004d68 https://github.com/galaxyproject/galaxy/commit/7207c15090385a397493da0503b06... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-17 (Mon, 17 Oct 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #3033 from nsoranzo/fix_for_3001 Increase min number of columns for pileup sniffing to 5 Commit: 22839eeee0b0909bc2726e60ffb26a213ddfc553 https://github.com/galaxyproject/galaxy/commit/22839eeee0b0909bc2726e60ffb26... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-17 (Mon, 17 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #3052 from guerler/always_display_text Always display text Commit: 7eb413f4e8ee97d68a6fa466d9c5189b324dde52 https://github.com/galaxyproject/galaxy/commit/7eb413f4e8ee97d68a6fa466d9c51... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-10-17 (Mon, 17 Oct 2016) Changed paths: M doc/schema_template.md M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/samples_tool_conf.xml A test/functional/tools/version_command.py A test/functional/tools/version_command_interpreter.xml A test/functional/tools/version_command_plain.xml A test/functional/tools/version_command_tool_dir.xml M test/unit/jobs/test_job_wrapper.py Log Message: ----------- Merge pull request #2961 from jmchilton/xsd_fixes_1 Improve ``version_command`` tag. Commit: 1dc2d6a4ead34b9d8bdaecf85f146ca17b5e803c https://github.com/galaxyproject/galaxy/commit/1dc2d6a4ead34b9d8bdaecf85f146... 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config/plugins/visualizations/charts/static/repository/visualizations/others/example/config.js A config/plugins/visualizations/charts/static/repository/visualizations/others/example/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/others/example/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/config.js A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-parameters.js A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-plugin.js A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/config.js A 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config/plugins/visualizations/charts/static/views/settings.js R config/plugins/visualizations/charts/static/views/types.js R config/plugins/visualizations/charts/static/views/viewer.js R config/plugins/visualizations/charts/static/views/viewport.js M config/plugins/visualizations/charts/templates/charts.mako A config/plugins/visualizations/charts/webpack.config.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/ui/ui-buttons.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/ui/ui-buttons.js M static/scripts/utils/utils.js Log Message: ----------- Merge pull request #2875 from guerler/remote_chart_plugins Link charts to external repo, adjust interface Commit: 3e737c99ea21dcb7ea3a326d36aee9c715c8d70b https://github.com/galaxyproject/galaxy/commit/3e737c99ea21dcb7ea3a326d36aee... Author: Remi Marenco <remi.marenco@gmail.com> Date: 2016-10-17 (Mon, 17 Oct 2016) Changed paths: M .gitignore M Makefile M doc/source/conf.py A doc/source/slideshow/architecture/galaxy_architecture.md A doc/source/slideshow/architecture/images/backbone-model-view.svg A doc/source/slideshow/architecture/images/cluster_support.svg A doc/source/slideshow/architecture/images/data_managers.svg A doc/source/slideshow/architecture/images/docker-chart.png A doc/source/slideshow/architecture/images/family/team.png A doc/source/slideshow/architecture/images/galaxy_schema.png A doc/source/slideshow/architecture/images/hda.svg A doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg A doc/source/slideshow/architecture/images/hda_dataset.plantuml.txt A doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg A doc/source/slideshow/architecture/images/hda_hdca.plantuml.txt A doc/source/slideshow/architecture/images/jsload.png A doc/source/slideshow/architecture/images/libraries.svg A doc/source/slideshow/architecture/images/library_permissions.svg A doc/source/slideshow/architecture/images/objectstore.plantuml.svg A doc/source/slideshow/architecture/images/objectstore.plantuml.txt A doc/source/slideshow/architecture/images/objectstore_diagram.svg A doc/source/slideshow/architecture/images/plantuml_options.txt A doc/source/slideshow/architecture/images/sequence.json A doc/source/slideshow/architecture/images/server_client.plantuml.svg A doc/source/slideshow/architecture/images/server_client.plantuml.txt A doc/source/slideshow/architecture/images/server_client_old.plantuml.svg A doc/source/slideshow/architecture/images/server_client_old.plantuml.txt A doc/source/slideshow/architecture/images/sqla_arch_small.png A doc/source/slideshow/architecture/images/usegalaxy_webservers.svg A doc/source/slideshow/architecture/images/usegalaxyorg.svg A doc/source/slideshow/architecture/images/webapp.plantuml.svg A doc/source/slideshow/architecture/images/webapp.plantuml.txt A doc/source/slideshow/architecture/images/what-is-webpack.svg A doc/source/slideshow/architecture/images/workflow_definition.svg A doc/source/slideshow/architecture/images/workflow_run.svg A doc/source/slideshow/architecture/images/wsgi_app.svg A doc/source/slideshow/architecture/images/wsgi_request.svg A doc/source/slideshow/architecture/remark-latest.min.js A doc/source/slideshow/architecture/style.css M lib/galaxy/model/migrate/check.py A scripts/slideshow/__init__.py A scripts/slideshow/build_slideshow.py A scripts/slideshow/example.md A scripts/slideshow/slideshow_template.html A scripts/slideshow/style.sample.css Log Message: ----------- Add Galaxy Architecture slides in .md + the plumbing for slides creation Init of #2244, second part: Python converter md to html + wip on GCC 2015 talk conversion Add the 2. Galaxy app architecture. Need images Add the 3. Galaxy components and object model Add more content in md Fix linting error by adding newline at the end of build_slideshow.py Moved the galaxyArchitecture.md into a folder dedicated to it Add 7th and 17th image + add style.css to have a better management of layout + added first slide as the first in GCC2015 slide Set properly the CSS used in the whole presentation + add special to p and first slide Add special orange for regular text and green emphasis (emphasis_2_galaxy) Changed the font to PT Sans Add 3. with images + few modifications Removed the images integrated using background-image by now Markdown imaging (still need work, image's size seems not good by default Add Makefile target to build architecture slides... 2016 Updates to 2015 architecture talk. More intro slides for Galaxy architecture. Update author line. Progress on architecture slides... - Improved styling (use Oxygen - closer to Galaxy font) - Add ability to generate SVG diagrams to slide infrastructure - Add newer client-server sequence diagram based on that. Improved logging when there are problems with SQL migrations. More misc work on architecture talk. More images, slides, slide formatting, and initial work on an IPython notebook. Improved styling for architecture slides... Updates to architecture talk... - Infrastructure for building class diagrams with plantuml - Bring in move SVGs from last year's google docs. - Fill out section on client architecture. More work on slides for architecture talk. Add startup_output. Replace mermaid diagrams with plantuml diagrams. Fill out these diagrams more and style them for a black background in Galaxy oranges. Commit: 564aeeccd7379a5717de2180f5eb3208e479ea98 https://github.com/galaxyproject/galaxy/commit/564aeeccd7379a5717de2180f5eb3... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-10-17 (Mon, 17 Oct 2016) Changed paths: M Makefile Log Message: ----------- remove the duplicated variable Commit: 32d0db8bb3b3b64a96beb1f09908cb1e3c1e3c28 https://github.com/galaxyproject/galaxy/commit/32d0db8bb3b3b64a96beb1f09908c... Author: tmcgowan <mcgo0092@umn.edu> Date: 2016-10-17 (Mon, 17 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M static/maps/mvc/dataset/dataset-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li.js Log Message: ----------- Job ID comes from creating_job value in dataset metadata. Commit: bdc8829dd2363c759b362a275757448173afcd22 https://github.com/galaxyproject/galaxy/commit/bdc8829dd2363c759b362a2757574... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-17 (Mon, 17 Oct 2016) Changed paths: M config/plugins/visualizations/charts/static/client/app.js Log Message: ----------- Dataset metadata should not be cached when building chart visualizations Commit: 5a2d01b267398bb01620faeec0d665291ac953ad https://github.com/galaxyproject/galaxy/commit/5a2d01b267398bb01620faeec0d66... Author: tmcgowan <mcgo0092@umn.edu> Date: 2016-10-18 (Tue, 18 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js Log Message: ----------- Move help button to last position of left group, add 5px padding to help text. Commit: 569723a4e5487c4eab25dfe619cda5b044b6115b https://github.com/galaxyproject/galaxy/commit/569723a4e5487c4eab25dfe619cda... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-18 (Tue, 18 Oct 2016) Changed paths: M .gitignore M Makefile M doc/source/conf.py A doc/source/slideshow/architecture/galaxy_architecture.md A doc/source/slideshow/architecture/images/backbone-model-view.svg A doc/source/slideshow/architecture/images/cluster_support.svg A doc/source/slideshow/architecture/images/data_managers.svg A doc/source/slideshow/architecture/images/docker-chart.png A doc/source/slideshow/architecture/images/family/team.png A doc/source/slideshow/architecture/images/galaxy_schema.png A doc/source/slideshow/architecture/images/hda.svg A doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg A doc/source/slideshow/architecture/images/hda_dataset.plantuml.txt A doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg A doc/source/slideshow/architecture/images/hda_hdca.plantuml.txt A doc/source/slideshow/architecture/images/jsload.png A doc/source/slideshow/architecture/images/libraries.svg A doc/source/slideshow/architecture/images/library_permissions.svg A doc/source/slideshow/architecture/images/objectstore.plantuml.svg A doc/source/slideshow/architecture/images/objectstore.plantuml.txt A doc/source/slideshow/architecture/images/objectstore_diagram.svg A doc/source/slideshow/architecture/images/plantuml_options.txt A doc/source/slideshow/architecture/images/sequence.json A doc/source/slideshow/architecture/images/server_client.plantuml.svg A doc/source/slideshow/architecture/images/server_client.plantuml.txt A doc/source/slideshow/architecture/images/server_client_old.plantuml.svg A doc/source/slideshow/architecture/images/server_client_old.plantuml.txt A doc/source/slideshow/architecture/images/sqla_arch_small.png A doc/source/slideshow/architecture/images/usegalaxy_webservers.svg A doc/source/slideshow/architecture/images/usegalaxyorg.svg A doc/source/slideshow/architecture/images/webapp.plantuml.svg A doc/source/slideshow/architecture/images/webapp.plantuml.txt A doc/source/slideshow/architecture/images/what-is-webpack.svg A doc/source/slideshow/architecture/images/workflow_definition.svg A doc/source/slideshow/architecture/images/workflow_run.svg A doc/source/slideshow/architecture/images/wsgi_app.svg A doc/source/slideshow/architecture/images/wsgi_request.svg A doc/source/slideshow/architecture/remark-latest.min.js A doc/source/slideshow/architecture/style.css M lib/galaxy/model/migrate/check.py A scripts/slideshow/__init__.py A scripts/slideshow/build_slideshow.py A scripts/slideshow/example.md A scripts/slideshow/slideshow_template.html A scripts/slideshow/style.sample.css Log Message: ----------- Merge pull request #3060 from martenson/remimarenco-gcc2015_talk Add Galaxy Architecture slides in .md Commit: a431d88293faf8f6286cae416f8842ce186692c4 https://github.com/galaxyproject/galaxy/commit/a431d88293faf8f6286cae416f884... Author: tmcgowan <mcgo0092@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: 2a7e4f79c0c04158fe37dbd6c1b95cc251537173 https://github.com/galaxyproject/galaxy/commit/2a7e4f79c0c04158fe37dbd6c1b95... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2016-10-18 (Tue, 18 Oct 2016) Changed paths: M config/plugins/visualizations/charts/static/client/app.js Log Message: ----------- Merge pull request #3062 from guerler/fix_dataset_caching Dataset metadata should not be cached when building chart visualizations Commit: e4b3766c1b8798ab20a00c98d10f7bbf29da16ab https://github.com/galaxyproject/galaxy/commit/e4b3766c1b8798ab20a00c98d10f7... Author: Nicola Soranzo <nicola.soranzo@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: 38464b5b284289c66263adc19afa0a6be2e24389 https://github.com/galaxyproject/galaxy/commit/38464b5b284289c66263adc19afa0... Author: tmcgowan <mcgo0092@umn.edu> Date: 2016-10-18 (Tue, 18 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Originating workflow must be unchanged, load save as workflow to editor on save. Commit: 3a99bbae0716c98aa8e8d290a666909ac88c0817 https://github.com/galaxyproject/galaxy/commit/3a99bbae0716c98aa8e8d290a6669... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-19 (Wed, 19 Oct 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Add deprecated, legacy attribute default_value to XSD. Cleanup use of ``gxdocs:deprecated``. Commit: 69636f5e65e6b3ad2c8d7e3c300cd81418bb6206 https://github.com/galaxyproject/galaxy/commit/69636f5e65e6b3ad2c8d7e3c300cd... Author: nturaga <nitesh.turaga@gmail.com> Date: 2016-10-19 (Wed, 19 Oct 2016) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Add CEL file as a datatype Commit: 7e2725d1250fef33d1d03cc4e15b29de6f1a540f https://github.com/galaxyproject/galaxy/commit/7e2725d1250fef33d1d03cc4e15b2... Author: nturaga <nitesh.turaga@gmail.com> Date: 2016-10-19 (Wed, 19 Oct 2016) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- add CEL datatypes to datatypes conf sample Commit: 05f792edcd4bf779d0e9c91f5f4c92396979f17b https://github.com/galaxyproject/galaxy/commit/05f792edcd4bf779d0e9c91f5f4c9... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-19 (Wed, 19 Oct 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Specify actual parameter to use in lieu of default_value in XSD. As suggested by @nsoranzo. Commit: cfeb0135ac5fc3334d5a3afcfdfd1e586ce5d32f https://github.com/galaxyproject/galaxy/commit/cfeb0135ac5fc3334d5a3afcfdfd1... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-10-19 (Wed, 19 Oct 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #3072 from jmchilton/default_value_legacy_xsd Add deprecated, legacy attribute default_value to XSD. Commit: f9357ea07ddf0525b3a82021c9e11f690c700d67 https://github.com/galaxyproject/galaxy/commit/f9357ea07ddf0525b3a82021c9e11... Author: tmcgowan <mcgo0092@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: 096a7bf94d799f905013f7052c1bdf87062a45a7 https://github.com/galaxyproject/galaxy/commit/096a7bf94d799f905013f7052c1bd... Author: Martin Cech <cech.marten@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: b31bd5be35b207ce3be3c287c5fa7831a40986d7 https://github.com/galaxyproject/galaxy/commit/b31bd5be35b207ce3be3c287c5fa7... Author: tmcgowan <mcgo0092@umn.edu> Date: 2016-10-21 (Fri, 21 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Extend PUT /api/workflows/{id} with additional workflow properties Commit: a6d52cdbdc837c427c0971c6586eb5169a786752 https://github.com/galaxyproject/galaxy/commit/a6d52cdbdc837c427c0971c6586eb... Author: Dannon Baker <dannon.baker@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 Commit: 575373c8f304967b224af128774ad646a40cde3b https://github.com/galaxyproject/galaxy/commit/575373c8f304967b224af128774ad... Author: Dannon Baker <dannon.baker@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: 65dc4f22aa7b717109aca6fac7947a84d2bd587a https://github.com/galaxyproject/galaxy/commit/65dc4f22aa7b717109aca6fac7947... Author: Dannon Baker <dannon.baker@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 Commit: 20f98df554f502bddff1f22879bf867f97ab7288 https://github.com/galaxyproject/galaxy/commit/20f98df554f502bddff1f22879bf8... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-10-24 (Mon, 24 Oct 2016) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- Finish job for Torque SSH runner Commit: 5662a6a5c6fd7166b9f5092308e3ff2ca2bb3738 https://github.com/galaxyproject/galaxy/commit/5662a6a5c6fd7166b9f5092308e3f... Author: John Chilton <jmchilton@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] Commit: 0f0bcb6a088f669a5c1272d238bbe79e29002742 https://github.com/galaxyproject/galaxy/commit/0f0bcb6a088f669a5c1272d238bbe... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-10-24 (Mon, 24 Oct 2016) Changed paths: M Makefile Log Message: ----------- fix bad merge in #3060 Commit: 61d25720661cb120afc7b44c57f41a1b245e21e4 https://github.com/galaxyproject/galaxy/commit/61d25720661cb120afc7b44c57f41... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-10-24 (Mon, 24 Oct 2016) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- More explcit logging of CLI runner state change (thx @nsoranzo) Commit: 00c48e4878a0b22ce7045692d67d72af7d540215 https://github.com/galaxyproject/galaxy/commit/00c48e4878a0b22ce7045692d67d7... Author: Martin Cech <cech.marten@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/05be84ba47c0932a393cb9925ae10... Author: Nicola Soranzo <nsoranzo@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 Commit: 4bfac4536971c54a704c76de083de0600332442c https://github.com/galaxyproject/galaxy/commit/4bfac4536971c54a704c76de083de... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-10-24 (Mon, 24 Oct 2016) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M doc/patch.py Log Message: ----------- Fix flake8 errors and Python3 compatibility for doc/patch.py Commit: a21ed34efb695fb71f1c7616dc1655de8b54be41 https://github.com/galaxyproject/galaxy/commit/a21ed34efb695fb71f1c7616dc165... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-10-24 (Mon, 24 Oct 2016) Changed paths: R doc/source/admin/interactive_environments_success.png A doc/source/dev/interactive_environments_success.png Log Message: ----------- Move png in the right directory Broken in #2543. Commit: 8a17143bc77ce370974e35f51d699f8029edd647 https://github.com/galaxyproject/galaxy/commit/8a17143bc77ce370974e35f51d699... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-10-24 (Mon, 24 Oct 2016) Changed paths: R doc/source/lib/galaxy.util.backports.importlib.rst R scripts/bootstrap_history_announce_template.rst Log Message: ----------- Remove unused files Commit: e6d0b69ec89786f56fa71d2e893b2361bbe55d0e https://github.com/galaxyproject/galaxy/commit/e6d0b69ec89786f56fa71d2e893b2... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-10-24 (Mon, 24 Oct 2016) Changed paths: M doc/source/dev/build_a_job_runner.rst A doc/source/dev/inherit.png A doc/source/dev/queue.png A doc/source/dev/queue_b.png A doc/source/dev/runner_diag.png Log Message: ----------- Add and use local images for build runner doc Commit: 3180b631662ced589fe9db42d27caa58638b5f8d https://github.com/galaxyproject/galaxy/commit/3180b631662ced589fe9db42d27ca... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-10-24 (Mon, 24 Oct 2016) Changed paths: M .gitignore M Makefile M doc/Makefile M doc/parse_gx_xsd.py M doc/schema_template.md M doc/source/dev/index.rst M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Properly integrate tool XML schema with docs Generate intermediate rst file instead of html Move generation to doc/Makefile Use pandoc to generate table of contents and fragment ids. Remove nested inline markup (not supported by reStructuredText) Fix https and other links. Commit: 527e332aa39e82224965e6aaef94ffaa1cf956bf https://github.com/galaxyproject/galaxy/commit/527e332aa39e82224965e6aaef94f... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-10-24 (Mon, 24 Oct 2016) Changed paths: M doc/source/admin/conda_faq.rst M doc/source/admin/interactive_environments.rst M doc/source/admin/mulled_containers.rst M doc/source/conf.py M doc/source/index.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.jobs.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.tools.linters.rst M doc/source/lib/galaxy.tools.parameters.rst M doc/source/lib/galaxy.util.backports.rst M doc/source/lib/galaxy.util.rst M doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst M doc/source/releases/16.07.rst M doc/source/releases/index.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/__init__.py M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/decorators.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/metrics/instrumenters/__init__.py M lib/galaxy/managers/__init__.py M lib/galaxy/managers/base.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/roles.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/util/simplegraph.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M scripts/bootstrap_history.py M scripts/galaxy-main Log Message: ----------- Fix a bunch of errors reported by Sphinx Commit: 10ce532c15a5ab7373f40a1452f3e1ed236d3ec7 https://github.com/galaxyproject/galaxy/commit/10ce532c15a5ab7373f40a1452f3e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-10-25 (Tue, 25 Oct 2016) Changed paths: M test/qunit/package.json Log Message: ----------- Fix qunit local testing install -- now runs on modern node (v6.9.1) with no system packages, just 'npm install', 'grunt'. Commit: ae0d0a23e273d39f64da2550da34adee9a540bb2 https://github.com/galaxyproject/galaxy/commit/ae0d0a23e273d39f64da2550da34a... Author: Dannon Baker <dannon.baker@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: d2ff7345a8c0fbdb8c5d88e86e428f79c263d462 https://github.com/galaxyproject/galaxy/commit/d2ff7345a8c0fbdb8c5d88e86e428... Author: Dannon Baker <dannon.baker@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: 9d402eaf1ab13b03894a27645368f12a9d42289c https://github.com/galaxyproject/galaxy/commit/9d402eaf1ab13b03894a27645368f... Author: Dannon Baker <dannon.baker@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 Commit: 62c77e2cc457a5cb2f33b7d75e247ecf13ba57d8 https://github.com/galaxyproject/galaxy/commit/62c77e2cc457a5cb2f33b7d75e247... Author: Martin Cech <cech.marten@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) Commit: 8da4ad6563f2d37309494aa86e1f8ed2595a6af9 https://github.com/galaxyproject/galaxy/commit/8da4ad6563f2d37309494aa86e1f8... Author: Nicola Soranzo <nsoranzo@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… Commit: 17da51abdc61e9fb1e3f76b36316c9dbf3c836e6 https://github.com/galaxyproject/galaxy/commit/17da51abdc61e9fb1e3f76b36316c... Author: Peter Cock <p.j.a.cock@googlemail.com> Date: 2016-10-25 (Tue, 25 Oct 2016) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Include filenames in loc file DEBUG lines This will help debugging where multiple (possibly conflicting) ``*.loc`` files come from, e.g. ``` galaxy.tools.data DEBUG 2016-10-25 18:34:50,841 Loaded tool data table 'blastdb_p' galaxy.tools.data DEBUG 2016-10-25 18:34:51,356 Loaded tool data table 'blastdb' galaxy.tools.data DEBUG 2016-10-25 18:34:51,359 Loading another instance of data table 'blastdb_p', attempting to merge content. galaxy.tools.data DEBUG 2016-10-25 18:34:51,375 Loaded tool data table 'blastdb_d' ``` Evidently I may have at least two copies of ``blastdb_p.loc``, but where are they? Commit: f891034390908bd6a374bf140a57ac76afefefd9 https://github.com/galaxyproject/galaxy/commit/f891034390908bd6a374bf140a57a... Author: nturaga <nitesh.turaga@gmail.com> Date: 2016-10-25 (Tue, 25 Oct 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Lowercase the datatypes, add edam_data, thanks @nsoranzo Commit: 35346fdb3e6764b14ae3359fb9ea31c03d932ea0 https://github.com/galaxyproject/galaxy/commit/35346fdb3e6764b14ae3359fb9ea3... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge pull request #3095 from peterjc/patch-4 Include filenames in loc file DEBUG lines Commit: ca8cd524a1f882b7de2aaf5f56d8b2878c07739a https://github.com/galaxyproject/galaxy/commit/ca8cd524a1f882b7de2aaf5f56d8b... Author: Peter Cock <p.j.a.cock@googlemail.com> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Avoid pointless lambda function The lambda function used a ternary if/else anyway, just do this directly - its shorter and clearer. Commit: fc027124e73ee391e4b4045b2abc68fd942f910c https://github.com/galaxyproject/galaxy/commit/fc027124e73ee391e4b4045b2abc6... Author: Peter Cock <p.j.a.cock@googlemail.com> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M config/tool_data_table_conf.xml.sample Log Message: ----------- Fix BLAST database *.loc files inconsistency We should have all of the ``blast*.loc`` files in the sample configuration, or none of them. Historically Galaxy included only the nucleotide BLAST database ``blastdb.loc`` file for use with mega-blast, with ``blastdb_p.loc`` later for protein databases added as part of the BLAST+ suite (which initially was in the main Galaxy repository). In a3018feb028658fc3a7071803b7b49cb575e7358 the mega-blast tool was moved to the Tool Shed, and the ``blastdb.loc`` entry removed. Likewise the BLAST+ tools were moved to the Tool Shed, but the ``blastdb_p.loc`` entry remains. Later (on the Tool Shed only?) ``blastdb_d.loc``was added for protein domain databases. Commit: ab42b7b15c50c7ae4a4a582ebc1df2780e1538de https://github.com/galaxyproject/galaxy/commit/ab42b7b15c50c7ae4a4a582ebc1df... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge pull request #3097 from peterjc/patch-4 Avoid pointless lambda function Commit: 90d143cda16d7c7a0938e255c08bf9db7fea727c https://github.com/galaxyproject/galaxy/commit/90d143cda16d7c7a0938e255c08bf... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M config/tool_data_table_conf.xml.sample Log Message: ----------- Merge pull request #3098 from peterjc/patch-6 Fix BLAST database *.loc files inconsistency Commit: 2ec9c05380356ba543b29bae44cc3bdd947196a2 https://github.com/galaxyproject/galaxy/commit/2ec9c05380356ba543b29bae44cc3... Author: Peter Cock <p.j.a.cock@googlemail.com> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Log loading of resources from *.loc files Example output: ``` $ grep "lines from" paster.log galaxy.tools.data DEBUG 2016-10-26 10:24:22,742 Loaded 0 lines from 'tool-data/all_fasta.loc' for 'all_fasta' galaxy.tools.data DEBUG 2016-10-26 10:24:22,753 Loaded 0 lines from 'tool-data/bfast_indexes.loc' for 'bfast_indexes' galaxy.tools.data DEBUG 2016-10-26 10:24:22,848 Loaded 24 lines from 'tool-data/blastdb_p.loc' for 'blastdb_p' galaxy.tools.data DEBUG 2016-10-26 10:24:22,859 Loaded 0 lines from 'tool-data/maf_index.loc' for 'indexed_maf_files' galaxy.tools.data DEBUG 2016-10-26 10:24:22,865 Loaded 0 lines from 'tool-data/ngs_sim_fasta.loc' for 'ngs_sim_fasta' galaxy.tools.data DEBUG 2016-10-26 10:24:22,878 Loaded 0 lines from 'tool-data/perm_base_index.loc' for 'perm_base_indexes' galaxy.tools.data DEBUG 2016-10-26 10:24:22,890 Loaded 0 lines from 'tool-data/perm_color_index.loc' for 'perm_color_indexes' galaxy.tools.data DEBUG 2016-10-26 10:24:22,895 Loaded 0 lines from 'tool-data/picard_index.loc' for 'picard_indexes' galaxy.tools.data DEBUG 2016-10-26 10:24:22,899 Loaded 0 lines from 'tool-data/picard_index.loc' for 'srma_indexes' galaxy.tools.data DEBUG 2016-10-26 10:24:22,937 Loaded 0 lines from 'tool-data/mosaik_index.loc' for 'mosaik_indexes' galaxy.tools.data DEBUG 2016-10-26 10:24:22,943 Loaded 0 lines from 'tool-data/twobit.loc' for 'twobit' ... galaxy.tools.data DEBUG 2016-10-26 10:24:24,036 Loaded 0 lines from '/mnt/shared/galaxy/galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/7f3c448e119b/blastdb.loc' for 'blastdb' galaxy.tools.data DEBUG 2016-10-26 10:24:24,106 Loaded 0 lines from '/mnt/shared/galaxy/galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/7f3c448e119b/blastdb_p.loc' for 'blastdb_p' galaxy.tools.data DEBUG 2016-10-26 10:24:24,112 Loaded 0 lines from '/mnt/shared/galaxy/galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/7f3c448e119b/blastdb_d.loc' for 'blastdb_d' ``` Commit: f21279d473fa8f19d3881af35d3066e79d757304 https://github.com/galaxyproject/galaxy/commit/f21279d473fa8f19d3881af35d306... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge pull request #3099 from peterjc/patch-5 Log loading of resources from *.loc files Commit: a6f1783b366293a0d87ee941882e449f092cce95 https://github.com/galaxyproject/galaxy/commit/a6f1783b366293a0d87ee941882e4... Author: nturaga <nitesh.turaga@gmail.com> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: A lib/galaxy/datatypes/test/test.CEL Log Message: ----------- Small test case CEL datatype, v4 Commit: 827e61a98cdfb3074d49df25b3ac0b30ce32d0bc https://github.com/galaxyproject/galaxy/commit/827e61a98cdfb3074d49df25b3ac0... Author: nturaga <nitesh.turaga@gmail.com> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Add doctests Commit: 5c1d0982e33e3c5464bb6374d33ed9a7bb76a648 https://github.com/galaxyproject/galaxy/commit/5c1d0982e33e3c5464bb6374d33ed... Author: nturaga <nitesh.turaga@gmail.com> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- lint issues Commit: 541643d7fe28abeac4a69147aa3ae30f84d438ae https://github.com/galaxyproject/galaxy/commit/541643d7fe28abeac4a69147aa3ae... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/test.CEL Log Message: ----------- Merge pull request #3073 from nturaga/add_cel_datatype Add CEL datatype Commit: 66dec1d580b426ad955db03608ec7da7eb5c5018 https://github.com/galaxyproject/galaxy/commit/66dec1d580b426ad955db03608ec7... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M test/base/driver_util.py Log Message: ----------- Add download_to_file function to galaxy.util Use it in 2 places: - test/base/driver_util.py (thus adding timeout and chunking) - lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py where the total download timeout is substituted with the usual urllib timeout Commit: 0eff2ec6479b321d9fc653aa9eaf79559fc50e56 https://github.com/galaxyproject/galaxy/commit/0eff2ec6479b321d9fc653aa9eaf7... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-10-27 (Thu, 27 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge remote-tracking branch 'tmcgowan/issue_3000' into dev Commit: 6e4f3d9d2d1a01b539d412aad5bb8fbe0ba95a17 https://github.com/galaxyproject/galaxy/commit/6e4f3d9d2d1a01b539d412aad5bb8... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-10-27 (Thu, 27 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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/tool/tool-form.js Log Message: ----------- Revert menu.js, tool-form.js to pre-webhooks-PR Commit: 83a29454caea72915386c58a7188e08cd4597d35 https://github.com/galaxyproject/galaxy/commit/83a29454caea72915386c58a7188e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-10-27 (Thu, 27 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Lint fixes to workflow controller Commit: 660d70f8b4da32f5ebd5981ad9eb27e87a79da73 https://github.com/galaxyproject/galaxy/commit/660d70f8b4da32f5ebd5981ad9eb2... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2016-10-27 (Thu, 27 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #3103 from dannon/minor_style_fixes Lint fixes to workflow controller Commit: 62773a72c728b8bab46804d2128e46f62d45cd1d https://github.com/galaxyproject/galaxy/commit/62773a72c728b8bab46804d2128e4... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-10-27 (Thu, 27 Oct 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.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 Log Message: ----------- Reapply isolated menu.js webhook changes Commit: 67b1d45e3657af077005ed7b0b1469a7fd3f42d0 https://github.com/galaxyproject/galaxy/commit/67b1d45e3657af077005ed7b0b146... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-10-27 (Thu, 27 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js 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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form.js Log Message: ----------- Reapply isolated tool-form.js webhook changes Commit: 2458c5455fe07c7832cb30fd5bdedc9770db6f42 https://github.com/galaxyproject/galaxy/commit/2458c5455fe07c7832cb30fd5bded... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2016-10-27 (Thu, 27 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 pull request #3102 from dannon/fix_webhook_js_merge Fixes for remaining webhooks PR issues. Commit: d9dfc2cc78339f9b2158a07fff3df0a24d081865 https://github.com/galaxyproject/galaxy/commit/d9dfc2cc78339f9b2158a07fff3df... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-27 (Thu, 27 Oct 2016) Changed paths: A client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/galaxy/style/less/ui.less M config/plugins/visualizations/charts/static/client/app.css M config/plugins/visualizations/charts/static/client/views/editor.js R config/plugins/visualizations/charts/static/client/views/types.js A static/maps/mvc/ui/ui-thumbnails.js.map A static/scripts/mvc/ui/ui-thumbnails.js M static/style/blue/base.css Log Message: ----------- Move thumbnail list view to shared ui elements Commit: 296ef7e232468a2311ba18763752d97e10c63a2d https://github.com/galaxyproject/galaxy/commit/296ef7e232468a2311ba18763752d... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-27 (Thu, 27 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.js M static/maps/mvc/ui/ui-tabs.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/ui/ui-tabs.js Log Message: ----------- Hide tabs navigation if there is only one tab Commit: aab59be19160a97f41c60b7dab741825c90be934 https://github.com/galaxyproject/galaxy/commit/aab59be19160a97f41c60b7dab741... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-27 (Thu, 27 Oct 2016) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Fix margin Commit: ec9ca3ffd1bcb2a6e70a5a1f2c8e0183e80ddc1a https://github.com/galaxyproject/galaxy/commit/ec9ca3ffd1bcb2a6e70a5a1f2c8e0... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-27 (Thu, 27 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-thumbnails.js M config/plugins/visualizations/charts/static/client/views/editor.js M static/maps/mvc/ui/ui-thumbnails.js.map M static/scripts/mvc/ui/ui-thumbnails.js Log Message: ----------- Fix list view title Commit: 0b1c171ebc2b9b0605a6ef1e8e5b68e20d579c74 https://github.com/galaxyproject/galaxy/commit/0b1c171ebc2b9b0605a6ef1e8e5b6... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-27 (Thu, 27 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.js M config/plugins/visualizations/charts/static/client/views/editor.js M static/maps/mvc/ui/ui-tabs.js.map M static/maps/mvc/ui/ui-thumbnails.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/ui/ui-tabs.js M static/scripts/mvc/ui/ui-thumbnails.js M test/qunit/tests/ui_tests.js Log Message: ----------- Revise tab viewer, add test cases Commit: c4526bdaba29ccc9b045dea429dbc0c3fa0e5b15 https://github.com/galaxyproject/galaxy/commit/c4526bdaba29ccc9b045dea429dbc... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-27 (Thu, 27 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-tabs.js M static/maps/mvc/ui/ui-tabs.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/ui/ui-tabs.js Log Message: ----------- Hide tab navbar if there is only one tab available Commit: 05fbef510c7497911a2abea83c5bdc26bf338460 https://github.com/galaxyproject/galaxy/commit/05fbef510c7497911a2abea83c5bd... Author: Anthony Bretaudeau <abretaud@irisa.fr> Date: 2016-10-28 (Fri, 28 Oct 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Add doc for conda_copy_dependencies option Discussed on IUC gitter, related to https://github.com/galaxyproject/galaxy/issues/3008 Commit: 16866b5e8075d648bd17ac3786f76356e23c43a2 https://github.com/galaxyproject/galaxy/commit/16866b5e8075d648bd17ac3786f76... Author: Anthony Bretaudeau <anthony.bretaudeau@inria.fr> Date: 2016-10-28 (Fri, 28 Oct 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- add extra time problem Commit: 69cda7ee10d78a61830f90f957500ba41821640b https://github.com/galaxyproject/galaxy/commit/69cda7ee10d78a61830f90f957500... Author: Anthony Bretaudeau <anthony.bretaudeau@inria.fr> Date: 2016-10-28 (Fri, 28 Oct 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- clarify links Commit: 19b568cb9310b03b0cc74d3e6a7745b83074a0b8 https://github.com/galaxyproject/galaxy/commit/19b568cb9310b03b0cc74d3e6a774... Author: Greg Von Kuster <ghv2@psu.edu> Date: 2016-10-28 (Fri, 28 Oct 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Fix XSD for exclude_min and exclude_max attributes of tool param validator Commit: 838e2cbb66f2d7138eed51e434e623f057625042 https://github.com/galaxyproject/galaxy/commit/838e2cbb66f2d7138eed51e434e62... Author: Jim Johnson <jj@umn.edu> Date: 2016-10-28 (Fri, 28 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add routes to get genomes indexes and sequences So igv.js can retrieve genome data Commit: ac9d21d510320de98d7db87fd97e1246d468728a https://github.com/galaxyproject/galaxy/commit/ac9d21d510320de98d7db87fd97e1... Author: James Taylor <james@jamestaylor.org> Date: 2016-10-28 (Fri, 28 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Eagerload tags and annotations in history display Commit: c626ff8b2effa390de4816eafe507ea5b1fd1d6b https://github.com/galaxyproject/galaxy/commit/c626ff8b2effa390de4816eafe507... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-10-28 (Fri, 28 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #3110 from jxtx/dev Eagerload tags and annotations in history display Commit: a1e5118050ee5cf827396e2b2b38f147c51ed772 https://github.com/galaxyproject/galaxy/commit/a1e5118050ee5cf827396e2b2b38f... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-31 (Mon, 31 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #3109 from jj-umn/patch-5 Add routes to get genomes indexes and sequences Commit: 29b07cbb2a5aa05eb3636dcd9c3f0e15c42d21a1 https://github.com/galaxyproject/galaxy/commit/29b07cbb2a5aa05eb3636dcd9c3f0... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-31 (Mon, 31 Oct 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #3108 from gregvonkuster/xsd Fix XSD for exclude_min and exclude_max Commit: f0c5d5ca39d1e7456aea0d81fdcba345ce28a868 https://github.com/galaxyproject/galaxy/commit/f0c5d5ca39d1e7456aea0d81fdcba... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-31 (Mon, 31 Oct 2016) Changed paths: M test/qunit/package.json Log Message: ----------- Merge pull request #3089 from dannon/fix_local_qunit Fix qunit local testing install -- now runs on modern node (v6.9.1) w… Commit: f9ee0f86376f90ede636e4874cca120d30e7cd8c https://github.com/galaxyproject/galaxy/commit/f9ee0f86376f90ede636e4874cca1... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-31 (Mon, 31 Oct 2016) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M .gitignore M Makefile M doc/Makefile M doc/parse_gx_xsd.py M doc/patch.py M doc/schema_template.md M doc/source/admin/conda_faq.rst M doc/source/admin/interactive_environments.rst R doc/source/admin/interactive_environments_success.png M doc/source/admin/mulled_containers.rst M doc/source/conf.py M doc/source/dev/build_a_job_runner.rst M doc/source/dev/index.rst A doc/source/dev/inherit.png A doc/source/dev/interactive_environments_success.png A doc/source/dev/queue.png A doc/source/dev/queue_b.png A doc/source/dev/runner_diag.png M doc/source/index.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.jobs.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.tools.linters.rst M doc/source/lib/galaxy.tools.parameters.rst R doc/source/lib/galaxy.util.backports.importlib.rst M doc/source/lib/galaxy.util.backports.rst M doc/source/lib/galaxy.util.rst M doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst M doc/source/releases/16.07.rst M doc/source/releases/index.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/__init__.py M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/decorators.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/metrics/instrumenters/__init__.py M lib/galaxy/managers/__init__.py M lib/galaxy/managers/base.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/roles.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/simplegraph.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M scripts/bootstrap_history.py R scripts/bootstrap_history_announce_template.rst M scripts/galaxy-main Log Message: ----------- Merge pull request #3086 from nsoranzo/fix_doc Properly integrate tool XML schema with docs Commit: 25527bec32b2431f1a8769ef79f34ad9af38c0db https://github.com/galaxyproject/galaxy/commit/25527bec32b2431f1a8769ef79f34... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-31 (Mon, 31 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-tabs.js A client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/galaxy/style/less/ui.less M config/plugins/visualizations/charts/static/client/app.css M config/plugins/visualizations/charts/static/client/views/editor.js R config/plugins/visualizations/charts/static/client/views/types.js M static/maps/mvc/ui/ui-tabs.js.map A static/maps/mvc/ui/ui-thumbnails.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/ui/ui-tabs.js A static/scripts/mvc/ui/ui-thumbnails.js M static/style/blue/base.css M test/qunit/tests/ui_tests.js Log Message: ----------- Merge pull request #3079 from guerler/reusable_grid_view Move thumbnail list view to shared ui elements, revise tabs, add test cases Commit: 9e1331f1b37a40d8894fc724bb745589bc5e213b https://github.com/galaxyproject/galaxy/commit/9e1331f1b37a40d8894fc724bb745... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-31 (Mon, 31 Oct 2016) Changed paths: M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml Log Message: ----------- Merge pull request #3049 from lparsons/bam_to_bigwig Sort bedtools output in bam_to_bigwig conversion Commit: aaf5b4d0f8a823d9b3d659b55f25ce207c47e25e https://github.com/galaxyproject/galaxy/commit/aaf5b4d0f8a823d9b3d659b55f25c... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-31 (Mon, 31 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #3080 from tmcgowan/frequest_1842 Extend PUT /api/workflows/{id} with additional workflow properties Commit: 6082f790438d6fc04f313c2eef273bfa43ff0715 https://github.com/galaxyproject/galaxy/commit/6082f790438d6fc04f313c2eef273... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-11-01 (Tue, 01 Nov 2016) Changed paths: M run_tool_shed.sh Log Message: ----------- Fix path Broken in #2131. Reported by @dnbenso at https://github.com/galaxyproject/galaxy/commit/f2bd242a2c28954215fb84d289d19... Commit: ce1c7e41c6d90e1ca7d00c68afbd4fca8f55115e https://github.com/galaxyproject/galaxy/commit/ce1c7e41c6d90e1ca7d00c68afbd4... Author: John Chilton <jmchilton@gmail.com> Date: 2016-11-01 (Tue, 01 Nov 2016) Changed paths: M doc/Makefile Log Message: ----------- Restore XML formatting for schema document. Commit: 38dd9ca509ed50b3cf48689522ee884226cc1219 https://github.com/galaxyproject/galaxy/commit/38dd9ca509ed50b3cf48689522ee8... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2016-11-01 (Tue, 01 Nov 2016) Changed paths: M doc/Makefile Log Message: ----------- Merge pull request #3113 from jmchilton/schema_build Restore XML formatting for tool schema document. Commit: 9abe863f26ba742c9f362b3a8177af5c8efa5741 https://github.com/galaxyproject/galaxy/commit/9abe863f26ba742c9f362b3a8177a... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-11-01 (Tue, 01 Nov 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix loading of collection operations If MODEL_TOOLS_PATH is not absolute, it will be joined with tool_path (i.e. './tools' ) inside _load_tool_tag_set(), so Galaxy will try to load e.g. './tools/lib/galaxy/tools/unzip_collection.xml' Commit: 5963a2fa22e64b5494a1aa00931808a11d792cbd https://github.com/galaxyproject/galaxy/commit/5963a2fa22e64b5494a1aa0093180... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #3115 from nsoranzo/release_16.07_fix_collection_ops_loading [16.07] Fix loading of collection operations Commit: ef3e63e6d7327719a4581bb939dff8fd1ac1fcd9 https://github.com/galaxyproject/galaxy/commit/ef3e63e6d7327719a4581bb939dff... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-11-02 (Wed, 02 Nov 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 lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py 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/bundled/login.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 M templates/user/index.mako Log Message: ----------- Merge branch 'release_16.07' into dev Conflicts: 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 Commit: 892237bf0042e458db7c7220eb4faf022b5a7650 https://github.com/galaxyproject/galaxy/commit/892237bf0042e458db7c7220eb4fa... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix linting broken in #3080 Also fix import order and Python3 compatibility. Commit: aa72f4a0b62a7795bc726dd75bdb7635d29afef5 https://github.com/galaxyproject/galaxy/commit/aa72f4a0b62a7795bc726dd75bdb7... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #3116 from nsoranzo/fix_for_3080 Fix linting broken in #3080 Commit: e06581c587cdfe24822fba2f79ddaf60619858d2 https://github.com/galaxyproject/galaxy/commit/e06581c587cdfe24822fba2f79dda... Author: Joachim Wolff <wolffj@informatik.uni-freiburg.de> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Extended the linter rules to accept a help attribute for sections Commit: 8f89a04eae27e615434e268f93d492b6c0cd54be https://github.com/galaxyproject/galaxy/commit/8f89a04eae27e615434e268f93d49... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Fix job_working_directory commented default Follow-up to commit 0eab8346b3dd3ee7788c9cdda0f10f8aea4b2726. Commit: 83760e6a01cd3fa16a17158bb1182ffebb00c5d7 https://github.com/galaxyproject/galaxy/commit/83760e6a01cd3fa16a17158bb1182... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M doc/source/conf.py Log Message: ----------- Don't skip __init__() methods when generating docs Commit: 402f2815c23d695f0673d0af9acb9cf0e3527afa https://github.com/galaxyproject/galaxy/commit/402f2815c23d695f0673d0af9acb9... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Drop code which is never executed After commit 59583f26ea11b44cb17f260230be820b304cd918, self.object_store_config_file is always set. Commit: ad515397388056b8587c80350b755444602a49d0 https://github.com/galaxyproject/galaxy/commit/ad515397388056b8587c80350b755... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M lib/galaxy/jobs/command_factory.py Log Message: ----------- Fix typo Commit: 0c28a64269048ea21701e6c5b358d783bdde8eed https://github.com/galaxyproject/galaxy/commit/0c28a64269048ea21701e6c5b358d... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M lib/galaxy/objectstore/rods.py Log Message: ----------- Remove redundant ObjectStore superclass Commit: 1c68e0af3e9a02250d0d12c2149dcdbb1caf2da2 https://github.com/galaxyproject/galaxy/commit/1c68e0af3e9a02250d0d12c2149dc... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M lib/galaxy/objectstore/__init__.py Log Message: ----------- Fix object stores' __init__() methods doc Also: - remove unused parameters when calling the parent constructors - Python3 compatibility Commit: 94fd3a51a2a3a46aa4a834ed6d7d0bb50e6154a5 https://github.com/galaxyproject/galaxy/commit/94fd3a51a2a3a46aa4a834ed6d7d0... Author: John Chilton <jmchilton@gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M config/galaxy.ini.sample M doc/source/conf.py M lib/galaxy/config.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py Log Message: ----------- Merge pull request #3119 from nsoranzo/misc_fixes Object store and other misc fixes Commit: 65338b3adb925f27142c6fdf45af7f8d01e57f9d https://github.com/galaxyproject/galaxy/commit/65338b3adb925f27142c6fdf45af7... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M run_tool_shed.sh Log Message: ----------- Merge pull request #3112 from nsoranzo/release_16.04_fix_for_2131 [16.04] Fix path in run_tool_shed.sh Commit: d72cc77bebd46b0e60d09e19cee2496777503f11 https://github.com/galaxyproject/galaxy/commit/d72cc77bebd46b0e60d09e19cee24... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M run_tool_shed.sh Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Commit: 1d8f31c4f488dc380ffe657e5fa4a9d9cdd697ae https://github.com/galaxyproject/galaxy/commit/1d8f31c4f488dc380ffe657e5fa4a... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M run_tool_shed.sh Log Message: ----------- Merge branch 'release_16.07' into dev Commit: d3a5c4c7205b269830547fcb647528e3e2a9663f https://github.com/galaxyproject/galaxy/commit/d3a5c4c7205b269830547fcb64752... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Catch and display exceptions triggered by tool filter functions Commit: 300c9616306f69579b1d492aa78a17985e21f738 https://github.com/galaxyproject/galaxy/commit/300c9616306f69579b1d492aa78a1... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Use as instead of comma Commit: 5e19d6c57465ce79d4ee96e3206542ac655d137d https://github.com/galaxyproject/galaxy/commit/5e19d6c57465ce79d4ee96e320654... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py Log Message: ----------- Escape section id and name when writing integrated_tool_panel.xml This should fix #3084. Commit: 4866e72ad22b1772f93c8973e51f32086896277f https://github.com/galaxyproject/galaxy/commit/4866e72ad22b1772f93c8973e51f3... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py Log Message: ----------- Merge pull request #3122 from mvdbeek/escape_sections Escape section name when writing to xml, Commit: d5132a374c25d17e63a19379bcec1d42b99f8547 https://github.com/galaxyproject/galaxy/commit/d5132a374c25d17e63a19379bcec1... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Log invalid xml filename Commit: 51c586c264f2acd912060297804d61c2539f2483 https://github.com/galaxyproject/galaxy/commit/51c586c264f2acd912060297804d6... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix tools placed outside of panel section Occasionally tools were being installed outside of the selected too panel section. In the log one would find contradicting messages such as ``` tool_shed.util.repository_util DEBUG 2016-11-04 11:06:17,854 Adding new row for repository 'sra_tools' in the tool_shed_repository table, status set to 'New'. galaxy.tools.toolbox.base DEBUG 2016-11-04 11:06:17,886 Appending to tool panel section: NCBI SRA Tools 172.17.0.1 - - [04/Nov/2016:11:06:15 +0000] "POST /admin_toolshed/prepare_for_install HTTP/1.1" 200 - "http://localhost/admin_toolshed/prepare_for_install?changeset_revisions=62e4d56ebb6f&repository_ids=cb2d31dfab58ee88&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F" " Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/54.0.2840.71 Safari/537.36 nvalid tool_panel_section_key "ncbi_sra_tools" specified. Tools will be loaded outside of sections in the tool panel. ``` The intermittent POST is picked up by a different thread, that didn't have its toolbox updated with the new section. To circumvent this, we send the `create_panel_section` task to all threads. Commit: 4365b907293e366d4ad48396bb5c9dc00f134611 https://github.com/galaxyproject/galaxy/commit/4365b907293e366d4ad48396bb5c9... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Fix toolbox unittests Commit: a3ac57dbc532320c98e0b4a72772663293ab3b06 https://github.com/galaxyproject/galaxy/commit/a3ac57dbc532320c98e0b4a727726... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Remove verbose_install_check option This option was introduced with #2554 and #2538, in reponse to a false positive conda install. This would have been caught by simply checking the exit code, which we are doing by default now. The additional verification is too strigent and not in line with the conda resolver. Activating this option will report perfectly well installed conda environments as having failed and will cause them to be uninstalled. Commit: 37399049552dd1f2f4492e4eb9f168ac8a9abd5f https://github.com/galaxyproject/galaxy/commit/37399049552dd1f2f4492e4eb9f16... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #3124 from mvdbeek/escape_sections Log invalid xml filename Commit: c94b2205b27d1d527f159bcf13ba62ce937457f6 https://github.com/galaxyproject/galaxy/commit/c94b2205b27d1d527f159bcf13ba6... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py Log Message: ----------- Escape section id and name when writing integrated_tool_panel.xml This should fix #3084. Commit: f6ca913809330922a3bc96bcf0f77d3f60e9bbe9 https://github.com/galaxyproject/galaxy/commit/f6ca913809330922a3bc96bcf0f77... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Log invalid xml filename Commit: 2956f94aa06f62fc0adde93d5aacc69e693a62d8 https://github.com/galaxyproject/galaxy/commit/2956f94aa06f62fc0adde93d5aacc... Author: peterjc <p.j.a.cock@googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: A tool-data/blastdb.loc.sample A tool-data/blastdb_d.loc.sample A tool-data/blastdb_p.loc.sample Log Message: ----------- BLAST database *.loc.sample files Commit: 2e36fdb0bd0fff246eeff6322542c31150804eb2 https://github.com/galaxyproject/galaxy/commit/2e36fdb0bd0fff246eeff6322542c... Author: peterjc <p.j.a.cock@googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M config/tool_data_table_conf.xml.sample Log Message: ----------- Include all three BLAST .loc files in data table conf Commit: f060795335e564f79ed3f28b5390db4ac8e7d735 https://github.com/galaxyproject/galaxy/commit/f060795335e564f79ed3f28b5390d... Author: peterjc <p.j.a.cock@googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: A lib/galaxy/datatypes/blast.py Log Message: ----------- BLAST datatypes as of standalone blast_datatypes v0.0.21 Copied from separate BLAST+ Galaxy repository, https://github.com/peterjc/galaxy_blast/blob/master/datatypes/blast_datatype... Currently available from the Galaxy Tool Shed, http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes Primary contributors to the BLAST datatypes for Galaxy: * Peter Cock (The James Hutton Institute, UK) * Edward Kirton * Nicola Soranzo * Bjoern Gruening This work and the associated BLAST+ wrappers can be cited as: NCBI BLAST+ integrated into Galaxy. P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo *GigaScience* 2015, 4:39 DOI: http://dx.doi.org/10.1186/s13742-015-0080-7 Commit: a53e9fa9dbd635ee6359fb6b68371a3d0e5159c6 https://github.com/galaxyproject/galaxy/commit/a53e9fa9dbd635ee6359fb6b68371... Author: peterjc <p.j.a.cock@googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/datatypes/blast.py Log Message: ----------- Remove unused imports Commit: bdd046a2e86c935e1c932421a25e7ed480aacdf8 https://github.com/galaxyproject/galaxy/commit/bdd046a2e86c935e1c932421a25e7... Author: peterjc <p.j.a.cock@googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/datatypes/blast.py Log Message: ----------- Missing import required for use as doctest Commit: 193651c88d325a5c1710def37386524e956ac147 https://github.com/galaxyproject/galaxy/commit/193651c88d325a5c1710def373865... Author: peterjc <p.j.a.cock@googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: A lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml Log Message: ----------- Sample blastxml file for sniff doctest Commit: ea717dd0013c9ef69d5ea0cd8edb72f44546e5d8 https://github.com/galaxyproject/galaxy/commit/ea717dd0013c9ef69d5ea0cd8edb7... Author: peterjc <p.j.a.cock@googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Add BLAST datatypes to datatypes_conf.xml.sample Commit: 8b73de6f50572ea2fb815fa75460f5850b877f12 https://github.com/galaxyproject/galaxy/commit/8b73de6f50572ea2fb815fa75460f... Author: peterjc <p.j.a.cock@googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/datatypes/blast.py Log Message: ----------- Adjust import order as per Galaxy tox flake8 checks Commit: f9eff95613cdf27f5300ea393418f017da8e8012 https://github.com/galaxyproject/galaxy/commit/f9eff95613cdf27f5300ea393418f... Author: peterjc <p.j.a.cock@googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/datatypes/blast.py Log Message: ----------- More accurate module docstring Commit: 0152254a6f455bae538c96f3ce85baee1ae1c9f8 https://github.com/galaxyproject/galaxy/commit/0152254a6f455bae538c96f3ce85b... Author: peterjc <p.j.a.cock@googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- megablast_xml_parser_test1.blastxml should now sniff as blastxml Commit: 48664fa2fe7f43ee667e9fa4ece51852632570e7 https://github.com/galaxyproject/galaxy/commit/48664fa2fe7f43ee667e9fa4ece51... Author: peterjc <p.j.a.cock@googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M CONTRIBUTORS.md Log Message: ----------- Ensure all BLAST datatype contributors in CONTRIBUTORS.md Commit: ce5ceeb29b134a84cf577f0bf2244011ac0cdfe4 https://github.com/galaxyproject/galaxy/commit/ce5ceeb29b134a84cf577f0bf2244... Author: peterjc <p.j.a.cock@googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M CONTRIBUTORS.md Log Message: ----------- Give my work email address as well. My Galaxy work to date has been while employed at The James Hutton Institute (UK). Commit: 17783cec36f4bf0d3b79137842dad52a64f80da2 https://github.com/galaxyproject/galaxy/commit/17783cec36f4bf0d3b79137842dad... Author: peterjc <p.j.a.cock@googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py Log Message: ----------- Tweak testing installing BLAST datatypes from Tool Shed This is a short term pragmatic solution for the planned return of the BLAST datatypes to the main Galaxy distribution. Long term an additional test using an alternative Tool Shed defined datatype may be needed. Commit: 7fe47735209e43501e6116453a2fd961e5934429 https://github.com/galaxyproject/galaxy/commit/7fe47735209e43501e6116453a2fd... Author: peterjc <p.j.a.cock@googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/datatypes/blast.py Log Message: ----------- Clearer error message if BLAST XML header too long Commit: 4159770ed9d173a2a3b45f7615aa764be9e99188 https://github.com/galaxyproject/galaxy/commit/4159770ed9d173a2a3b45f7615aa7... Author: peterjc <p.j.a.cock@googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/datatypes/blast.py Log Message: ----------- Explicitly label blast.py as MIT licensed. Edward Kirton's contributions were made under the MIT license while this code was developed outside of the main Galaxy Project and distributed via the Galaxy Tool Shed). We have not been able to contact him to authorise re-licensing under the main Galaxy Project's license instead. Commit: b5ba9605e56b8a8c8a827c6bd83208314ab8ccf0 https://github.com/galaxyproject/galaxy/commit/b5ba9605e56b8a8c8a827c6bd8320... Author: peterjc <p.j.a.cock@googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/datatypes/blast.py Log Message: ----------- Mark BLAST XML with EDAM ontology terms. As per Herve Menager, EDAM format should be 3331 and data 0857 (sequence search results). Commit: b1892b7e30f9e2a9be94bd8ee064c0f548525bfe https://github.com/galaxyproject/galaxy/commit/b1892b7e30f9e2a9be94bd8ee064c... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M test/base/driver_util.py Log Message: ----------- Merge pull request #3100 from nsoranzo/followup_on_3013 Add download_to_file function to galaxy.util Commit: 1c740833e0c1884d43a42dc4417eb3f02adfafab https://github.com/galaxyproject/galaxy/commit/1c740833e0c1884d43a42dc4417eb... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix import order Commit: c5245219567562f67556548cbc0b8a9624ea0308 https://github.com/galaxyproject/galaxy/commit/c5245219567562f67556548cbc0b8... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Make catching XML parsing errors python2.6 compatible Commit: 7456b1f9218dabd6eab0d2fa6c3acc285c6c20c3 https://github.com/galaxyproject/galaxy/commit/7456b1f9218dabd6eab0d2fa6c3ac... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Remove unnecessary slashes Commit: 4d623a4d5a391a6aed2faf4b45f03c87b8f11a90 https://github.com/galaxyproject/galaxy/commit/4d623a4d5a391a6aed2faf4b45f03... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Ensure that label key exists before attempting removal Commit: 58b7b6cf15c57a9a42340baeb2131e42cc76d02d https://github.com/galaxyproject/galaxy/commit/58b7b6cf15c57a9a42340baeb2131... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2016-11-05 (Sat, 05 Nov 2016) Changed paths: M CONTRIBUTORS.md M config/datatypes_conf.xml.sample M config/tool_data_table_conf.xml.sample A lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py A tool-data/blastdb.loc.sample A tool-data/blastdb_d.loc.sample A tool-data/blastdb_p.loc.sample Log Message: ----------- Merge pull request #2696 from peterjc/blast_datatypes Returning Blast datatypes to Galaxy core (work-in-progress) Commit: a274e635a6f7f2b169506ebf4a5a2363578bbfb1 https://github.com/galaxyproject/galaxy/commit/a274e635a6f7f2b169506ebf4a5a2... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2016-11-05 (Sat, 05 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #3128 from mvdbeek/backport_3122_3124 [16.01] Backport #3122 #3124 - fix unescaped & in integrated_tool_panel.xml Commit: 202f96c73114fe9f05ed295505243ba17716b0e2 https://github.com/galaxyproject/galaxy/commit/202f96c73114fe9f05ed295505243... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2016-11-06 (Sun, 06 Nov 2016) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge pull request #3125 from mvdbeek/fix_invalid_section_key Fix tools placed outside of panel section Commit: 51050653b44c24328d9225b69d9b1b6971b0354c https://github.com/galaxyproject/galaxy/commit/51050653b44c24328d9225b69d9b1... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-06 (Sun, 06 Nov 2016) Changed paths: M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Rework dependency shell command handling The approach is to always log a warning with stdout and stderr when the exit code is not 0. With this change, one can expect logs like the follwing: ``` galaxy.tools.deps.conda_util DEBUG 2016-11-05 15:14:17,373 Executing command: /home/mvandenb/miniconda3/bin/conda create -y --name __bowtie@0.12.7 bowtie=0.12.7 127.0.0.1 - - [05/nov./2016:15:14:19 +0200] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://127.0.0.1:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/54.0.2840.90 Safari/537.36" 127.0.0.1 - - [05/nov./2016:15:14:22 +0200] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://127.0.0.1:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/54.0.2840.90 Safari/537.36" galaxy.tools.deps.conda_util WARNING 2016-11-05 15:14:24,029 Failed to execute command-line /home/mvandenb/miniconda3/bin/conda create -y --name __bowtie@0.12.7 bowtie=0.12.7, stderr was: -------->>begin stderr<<-------- PackageNotFoundError: Package not found: '' Package missing in current linux-64 channels: - bowtie 0.12.7* You can search for packages on anaconda.org with anaconda search -t conda bowtie You may need to install the anaconda-client command line client with conda install anaconda-client -------->>end stderr<<-------- -------->>begin stdout<<-------- Fetching package metadata ............... Solving package specifications: . -------->>end stdout<<-------- galaxy.tools.deps.resolvers.conda DEBUG 2016-11-05 15:14:24,030 Removing failed conda install of bowtie, version '0.12.7' ``` This should be helpful for the more obscure errors that can occur with conda. Commit: 8a972cc325fd39b71d89f28d9eec62630d9859ac https://github.com/galaxyproject/galaxy/commit/8a972cc325fd39b71d89f28d9eec6... Author: Anthony Bretaudeau <anthony.bretaudeau@inria.fr> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- be stronger Commit: 788dc1ebef5110fded19d23e4a2c48e06e3c5e63 https://github.com/galaxyproject/galaxy/commit/788dc1ebef5110fded19d23e4a2c4... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Conflicts: lib/galaxy/util/__init__.py Commit: 53a66c9d46780a4910a8a03de565eb3fb53f5bdc https://github.com/galaxyproject/galaxy/commit/53a66c9d46780a4910a8a03de565e... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Commit: 3200fa343b12b2c40ad6b3e29b77c6628d66b7a0 https://github.com/galaxyproject/galaxy/commit/3200fa343b12b2c40ad6b3e29b77c... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-11-07 (Mon, 07 Nov 2016) Log Message: ----------- Merge branch 'release_16.07' into dev Conflicts: lib/galaxy/util/__init__.py Commit: fb69afae28c434f35860ccaa4591e95fe3acfe91 https://github.com/galaxyproject/galaxy/commit/fb69afae28c434f35860ccaa4591e... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Update ToolPanelElements instance locally in addition to Galaxy's IPC call via send_control_task. Commit: b169299b5efbd144d5ab43f28e079a3fa5cf45a8 https://github.com/galaxyproject/galaxy/commit/b169299b5efbd144d5ab43f28e079... Author: Joachim Wolff <wolffj@informatik.uni-freiburg.de> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Extended linter rule for help attribute in section Commit: 192f66a714f3c7dd320550def43d7cd283dfa6af https://github.com/galaxyproject/galaxy/commit/192f66a714f3c7dd320550def43d7... Author: Gildas Le Corguillé <lecorguille@users.noreply.github.com> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Update galaxy.xsd Add `hidden_data` in `ParamType` The context [cufflinks](https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/...) `planemo lint .` ``` Applying linter tool_xsd... FAIL .. ERROR: Invalid tmpw5U2MV found. Errors [/tmp/tmpw5U2MV:144:0:ERROR:SCHEMASV:SCHEMAV_CVC_ENUMERATION_VALID: Element 'param', attribute 'type': [facet 'enumeration'] The value 'hidden_data' is not an element of the set {'text', 'integer', 'float', 'color', 'boolean', 'genomebuild', 'library_data', 'select', 'data_column', 'hidden', 'baseurl', 'file', 'data', 'drill_down', 'data_collection'}. /tmp/tmpw5U2MV:144:0:ERROR:SCHEMASV:SCHEMAV_CVC_DATATYPE_VALID_1_2_1: Element 'param', attribute 'type': 'hidden_data' is not a valid value of the atomic type 'ParamType'. ``` I don’t know so much this tag `hidden_data`, but it seems that it’s still in the [Galaxy doc](https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-inputs-param) Commit: 04935ce94b864a7898dc62895a11023dec805580 https://github.com/galaxyproject/galaxy/commit/04935ce94b864a7898dc62895a110... Author: John Chilton <jmchilton@gmail.com> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Merge pull request #3105 from abretaud/patch-2 Add doc for conda_copy_dependencies option Commit: 78dfb95f0264e349ee03b5c1a7c1cde9c6e38ba4 https://github.com/galaxyproject/galaxy/commit/78dfb95f0264e349ee03b5c1a7c1c... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #3131 from joachimwolff/dev Extended the linter rules to accept a help attribute for sections Commit: 7c030ebf2f51c6800966a2fc2d1b0048f0930f1d https://github.com/galaxyproject/galaxy/commit/7c030ebf2f51c6800966a2fc2d1b0... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M doc/Makefile Log Message: ----------- Use sed instead of pandoc to insert TOC in schema doc pandoc < 1.14 adds the TOC depth as a float, which is not recognised by Sphinx. Also, move the TOC after the introduction, which looks nicer. Commit: 3b8f543ebdd1307c91c3ae719bbb7072476d7b9a https://github.com/galaxyproject/galaxy/commit/3b8f543ebdd1307c91c3ae719bbb7... Author: John Chilton <jmchilton@gmail.com> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #3132 from lecorguille/patch-2 Update galaxy.xsd Commit: 6a8ca92dd70bc88bee962cd079460118f998c351 https://github.com/galaxyproject/galaxy/commit/6a8ca92dd70bc88bee962cd079460... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M doc/Makefile Log Message: ----------- Merge pull request #3135 from nsoranzo/followup_on_3086 Use sed instead of pandoc to insert TOC in schema doc Commit: 0ba54e922046733e582b7c5b4066525edc3957aa https://github.com/galaxyproject/galaxy/commit/0ba54e922046733e582b7c5b40665... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-11-08 (Tue, 08 Nov 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Treat the value of `message_box_visible` in galaxy.ini as a boolean Commit: 7bee2651aa8f08ea0495d167e33d317a22ae3ef9 https://github.com/galaxyproject/galaxy/commit/7bee2651aa8f08ea0495d167e33d3... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-11-08 (Tue, 08 Nov 2016) Changed paths: M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- string_as_bool for message_box_visible on webapps Commit: 1e142dd33d505436e081306bc08f044bb7b5886a https://github.com/galaxyproject/galaxy/commit/1e142dd33d505436e081306bc08f0... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-11-08 (Tue, 08 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- User activation emails are sent without a From: address if email_from is unset. Fix this by using `galaxy-no-reply@host` as with other emails we send. Commit: 3d69a2d1a5f7ee5606834c45e34e341fa4822721 https://github.com/galaxyproject/galaxy/commit/3d69a2d1a5f7ee5606834c45e34e3... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-11-08 (Tue, 08 Nov 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Merge pull request #3139 from natefoo/message-box-bool Treat the value of `message_box_visible` in galaxy.ini as a boolean Commit: 00edc474274a671c1ba4d7e2a64335e0abb614c5 https://github.com/galaxyproject/galaxy/commit/00edc474274a671c1ba4d7e2a6433... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2016-11-08 (Tue, 08 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Merge pull request #3140 from natefoo/activation-from Ensure a From: address is set for user activation emails Commit: 7f630ea2ddb279ce963070d87573bac4c66d5027 https://github.com/galaxyproject/galaxy/commit/7f630ea2ddb279ce963070d87573b... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-11-09 (Wed, 09 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/webapps/reports/config.py Log Message: ----------- Fix flake8 linting broken in 7bee2651aa8f08ea0495d167e33d317a22ae3ef9 Also fix import order and Python3 compatibility. Commit: 93a09d2eb033d8bc8b98a7ca94e80bbb1a80fe60 https://github.com/galaxyproject/galaxy/commit/93a09d2eb033d8bc8b98a7ca94e80... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-11-09 (Wed, 09 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/webapps/reports/config.py Log Message: ----------- Merge pull request #3141 from nsoranzo/followup_on_3139 Fix flake8 linting broken in 7bee2651aa8f08ea0495d167e33d317a22ae3ef9 Commit: 4b2e875802dcdc0015fb1c05d669e31eb60f01ab https://github.com/galaxyproject/galaxy/commit/4b2e875802dcdc0015fb1c05d669e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-11-09 (Wed, 09 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #3123 from guerler/fix_tool_filters Display an error message when toolbox filters fails Commit: 019f554e4e8425635c4ba36d7d2500d3a3a7502c https://github.com/galaxyproject/galaxy/commit/019f554e4e8425635c4ba36d7d250... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Copy hid attribute to converted datasets for hdas only Commit: 9c37c6df896312de5d07f93d2c6e1bdcaeff3e53 https://github.com/galaxyproject/galaxy/commit/9c37c6df896312de5d07f93d2c6e1... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/tool_shed/tools/tool_validator.py M scripts/api/filter_failed_datasets_from_collection.py Log Message: ----------- Fixes for flake8-import-order 0.11 Also fix Python3 compatibility. Commit: 2d8cf6b3376b41a6dd9a9ff3f4a82aaae1baa209 https://github.com/galaxyproject/galaxy/commit/2d8cf6b3376b41a6dd9a9ff3f4a82... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/tool_shed/tools/tool_validator.py M scripts/api/filter_failed_datasets_from_collection.py Log Message: ----------- Merge pull request #3154 from nsoranzo/fixes_for_new_flake8_import_order Fixes for flake8-import-order 0.11 Commit: d144f18e7a6eaa5276b2d63f51457eda1befd679 https://github.com/galaxyproject/galaxy/commit/d144f18e7a6eaa5276b2d63f51457... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Fix typo in GIE nginx proxy docs Commit: b748ad1565a1e5064f6e08640c19b09a41b4b2bc https://github.com/galaxyproject/galaxy/commit/b748ad1565a1e5064f6e08640c19b... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Merge pull request #3157 from galaxyproject/gie-doc-fix [16.07] Fix typo in GIE nginx proxy docs Commit: 3ec7be27952b57cf7e0ad87fdf067cacc5e66856 https://github.com/galaxyproject/galaxy/commit/3ec7be27952b57cf7e0ad87fdf067... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #3149 from guerler/fix_hid Explicitly specify attributes which should be copied to converted datasets Commit: d3f7510b2db932228c76402062bad9095549f5f0 https://github.com/galaxyproject/galaxy/commit/d3f7510b2db932228c76402062bad... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/datatypes/data.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Remove unnecessary set_output_history parameter Also fix import order and Python3 compatibility. Commit: 133fd3adfc76216d8808ed7200e7278bdaf87488 https://github.com/galaxyproject/galaxy/commit/133fd3adfc76216d8808ed7200e72... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-12 (Sat, 12 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/bed_to_fli_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.xml M lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml M lib/galaxy/datatypes/converters/fasta_to_2bit.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_len.xml M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml M lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml M lib/galaxy/datatypes/converters/gff_to_bed_converter.xml M lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/gff_to_fli_converter.xml M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed_converter.xml M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml M lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/interval_to_coverage.xml M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml M lib/galaxy/datatypes/converters/len_to_linecount.xml M lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml M lib/galaxy/datatypes/converters/maf_to_interval_converter.xml M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml M lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml M lib/galaxy/tools/imp_exp/exp_history_to_archive.xml Log Message: ----------- Quote all paths in converter tools Commit: 89e6f77feb4404ecb9e0ba025b5d2168e627ed71 https://github.com/galaxyproject/galaxy/commit/89e6f77feb4404ecb9e0ba025b5d2... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-12 (Sat, 12 Nov 2016) Changed paths: M lib/galaxy/tools/imp_exp/exp_history_to_archive.xml Log Message: ----------- Don't quote Commit: 46bd40bdc4c0dbad20084937e1e3ac606def9a3a https://github.com/galaxyproject/galaxy/commit/46bd40bdc4c0dbad20084937e1e3a... Author: John Chilton <jmchilton@gmail.com> Date: 2016-11-13 (Sun, 13 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/bed_to_fli_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.xml M lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml M lib/galaxy/datatypes/converters/fasta_to_2bit.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_len.xml M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml M lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml M lib/galaxy/datatypes/converters/gff_to_bed_converter.xml M lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/gff_to_fli_converter.xml M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed_converter.xml M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml M lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/interval_to_coverage.xml M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml M lib/galaxy/datatypes/converters/len_to_linecount.xml M lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml M lib/galaxy/datatypes/converters/maf_to_interval_converter.xml M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml M lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml M lib/galaxy/tools/imp_exp/exp_history_to_archive.xml Log Message: ----------- Merge pull request #3165 from mvdbeek/quote_data_converters Quote all paths in converter tool xml Commit: 7955077e635f09b4a0c3fda621406686affe0c0f https://github.com/galaxyproject/galaxy/commit/7955077e635f09b4a0c3fda621406... Author: John Chilton <jmchilton@gmail.com> Date: 2016-11-13 (Sun, 13 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/datatypes/data.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #3155 from nsoranzo/remove_set_output_history Remove unnecessary set_output_history parameter Commit: bfabe00ea8f07782f0af307b124da8090f2906f2 https://github.com/galaxyproject/galaxy/commit/bfabe00ea8f07782f0af307b124da... Author: John Chilton <jmchilton@gmail.com> Date: 2016-11-13 (Sun, 13 Nov 2016) Changed paths: M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3129 from mvdbeek/conda_error_reporting Pass dependency shell command errors to log Commit: ae3bdf31dc815dfce305316fe67776bc6802ec1a https://github.com/galaxyproject/galaxy/commit/ae3bdf31dc815dfce305316fe6777... Author: John Chilton <jmchilton@gmail.com> Date: 2016-11-13 (Sun, 13 Nov 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3127 from mvdbeek/remove_verbose_install_check_16.07 [16.07] Remove verbose_install_check option Commit: 6c4d430d75781dac112f0c7b56fe61208d081f1c https://github.com/galaxyproject/galaxy/commit/6c4d430d75781dac112f0c7b56fe6... Author: John Chilton <jmchilton@gmail.com> Date: 2016-11-14 (Mon, 14 Nov 2016) Changed paths: M Makefile Log Message: ----------- Add note about building docs to Makefile. Commit: 727270261750fc71979e7ba9fec96b10091ff104 https://github.com/galaxyproject/galaxy/commit/727270261750fc71979e7ba9fec96... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2016-11-14 (Mon, 14 Nov 2016) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- Merge pull request #3085 from mvdbeek/fix_torque_ssh [16.07] Finish job for Torque SSH/CLI runner Commit: ca4e8914ecddbba007c1f65ff17f51e719c0c149 https://github.com/galaxyproject/galaxy/commit/ca4e8914ecddbba007c1f65ff17f5... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-11-14 (Mon, 14 Nov 2016) Changed paths: M config/galaxy.ini.sample M doc/source/admin/interactive_environments.rst M lib/galaxy/jobs/runners/cli.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge branch 'release_16.07' into dev Conflicts: lib/galaxy/tools/deps/conda_util.py Commit: 66cc4c3bbe4a90cd68d935574691c31b8053804e https://github.com/galaxyproject/galaxy/commit/66cc4c3bbe4a90cd68d935574691c... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-11-14 (Mon, 14 Nov 2016) Changed paths: M Makefile Log Message: ----------- Merge pull request #3167 from jmchilton/doc_note Add note about building docs to Makefile. Commit: 00b147a6649b8fd1112fa76c573fa78db8e58621 https://github.com/galaxyproject/galaxy/commit/00b147a6649b8fd1112fa76c573fa... Author: John Chilton <jmchilton@gmail.com> Date: 2016-11-14 (Mon, 14 Nov 2016) Changed paths: M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/subsystems.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/objectstore/rods.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.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/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/util/__init__.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/object_wrapper.py Log Message: ----------- Bring in updates from galaxy-lib. Commit: 7e988bbe097f4f4e3d1f7c5dc3d149ee0c201bd8 https://github.com/galaxyproject/galaxy/commit/7e988bbe097f4f4e3d1f7c5dc3d14... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2016-11-14 (Mon, 14 Nov 2016) Changed paths: M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/subsystems.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/objectstore/rods.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.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/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/util/__init__.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/object_wrapper.py Log Message: ----------- Merge pull request #3169 from jmchilton/galaxy-lib-update-3 Bring in updates from galaxy-lib. Commit: 3f4033c05d1f2f1437d42da21e5d26e8e3b46ced https://github.com/galaxyproject/galaxy/commit/3f4033c05d1f2f1437d42da21e5d2... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-11-15 (Tue, 15 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.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/dataset/dataset-li-edit.js Log Message: ----------- Merge remote-tracking branch 'tmcgowan/issue_2100' into dev Commit: 1d17a29c7947993ae7cca998eff25c1ff998ebdb https://github.com/galaxyproject/galaxy/commit/1d17a29c7947993ae7cca998eff25... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-11-15 (Tue, 15 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M client/galaxy/style/source_material/circle.py M contrib/galaxy_config_merger.py M contrib/nagios/check_galaxy.py M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M doc/parse_gx_xsd.py M doc/patch.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/fasta_to_len.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/display_applications/parameters.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/triples.py M lib/galaxy/external_services/actions.py M lib/galaxy/external_services/parameters.py M lib/galaxy/external_services/result_handlers/basic.py M lib/galaxy/external_services/service.py M lib/galaxy/forms/forms.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/managers/collections_util.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/versions/0007_sharing_histories.py M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0012_user_address.py M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0020_library_upload_job.py M lib/galaxy/model/migrate/versions/0026_cloud_tables.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py M lib/galaxy/queue_worker.py M lib/galaxy/sample_tracking/data_transfer.py M lib/galaxy/sample_tracking/request_types.py M lib/galaxy/sample_tracking/sample.py M lib/galaxy/security/passwords.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/util/galaxyops/__init__.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/middleware/error.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/schedulers/core.py M lib/galaxy_utils/sequence/fastq.py M lib/galaxy_utils/sequence/vcf.py M lib/mimeparse.py M lib/tool_shed/util/workflow_util.py M scripts/api/data_manager_example_execute.py M scripts/api/example_watch_folder.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/install_tool_shed_repositories.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/reset_metadata_on_installed_repositories.py M scripts/api/search.py M scripts/api/sequencer_configuration_create.py M scripts/api/workflow_execute.py M scripts/api/workflow_execute_parameters.py M scripts/api/workflow_import.py M scripts/auth/pam_auth_helper.py M scripts/build_toolbox.py M scripts/build_universe_config.py M scripts/check_galaxy.py M scripts/check_python.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/communication/communication_server.py M scripts/create_db.py M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/drmaa_external_killer.py M scripts/drmaa_external_runner.py M scripts/external_chown_script.py M scripts/extract_dataset_part.py M scripts/extract_toolbox_sections.py M scripts/functional_tests.py M scripts/grt.py M scripts/loc_files/create_all_fasta_loc.py M scripts/manage_db.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/slideshow/build_slideshow.py M scripts/summarize_timings.py M scripts/sync_reports_config.py M scripts/tool_shed/api/add_repository_registry_entry.py M scripts/tool_shed/api/create_categories.py M scripts/tool_shed/api/create_users.py M scripts/tool_shed/api/export.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/api/import_capsule.py M scripts/tool_shed/api/remove_repository_registry_entry.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/clean_up_tool_dependency_directory.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py M scripts/tools/maf/check_loc_file.py M scripts/tools/re_escape_output.py M scripts/transfer.py M scripts/update_shed_config_path.py M test/api/test_workflows.py M test/api/workflows_format_2/main.py M test/base/api_asserts.py M test/base/driver_util.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/workflows/test_modules.py M tools/data_source/data_source.py M tools/data_source/genbank.py M tools/data_source/upload.py M tools/evolution/add_scores.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_fasta.py M tools/filters/bed_to_gff_converter.py M tools/filters/catWrapper.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/secure_hash_message_digest.py M tools/filters/sorter.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.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/sr_mapping/srma_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py Log Message: ----------- Fixes for pycodestyle 2.2.0 Commit: 594e44b4fbca2a1d128f81c8a10d5a4e0c334b01 https://github.com/galaxyproject/galaxy/commit/594e44b4fbca2a1d128f81c8a10d5... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-11-15 (Tue, 15 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M client/galaxy/style/source_material/circle.py M contrib/galaxy_config_merger.py M contrib/nagios/check_galaxy.py M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M doc/parse_gx_xsd.py M doc/patch.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/fasta_to_len.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/display_applications/parameters.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/triples.py M lib/galaxy/external_services/actions.py M lib/galaxy/external_services/parameters.py M lib/galaxy/external_services/result_handlers/basic.py M lib/galaxy/external_services/service.py M lib/galaxy/forms/forms.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/managers/collections_util.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/versions/0007_sharing_histories.py M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0012_user_address.py M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0020_library_upload_job.py M lib/galaxy/model/migrate/versions/0026_cloud_tables.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py M lib/galaxy/queue_worker.py M lib/galaxy/sample_tracking/data_transfer.py M lib/galaxy/sample_tracking/request_types.py M lib/galaxy/sample_tracking/sample.py M lib/galaxy/security/passwords.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/util/galaxyops/__init__.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/middleware/error.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/schedulers/core.py M lib/galaxy_utils/sequence/fastq.py M lib/galaxy_utils/sequence/vcf.py M lib/mimeparse.py M lib/tool_shed/util/workflow_util.py M scripts/api/data_manager_example_execute.py M scripts/api/example_watch_folder.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/install_tool_shed_repositories.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/reset_metadata_on_installed_repositories.py M scripts/api/search.py M scripts/api/sequencer_configuration_create.py M scripts/api/workflow_execute.py M scripts/api/workflow_execute_parameters.py M scripts/api/workflow_import.py M scripts/auth/pam_auth_helper.py M scripts/build_toolbox.py M scripts/build_universe_config.py M scripts/check_galaxy.py M scripts/check_python.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/communication/communication_server.py M scripts/create_db.py M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/drmaa_external_killer.py M scripts/drmaa_external_runner.py M scripts/external_chown_script.py M scripts/extract_dataset_part.py M scripts/extract_toolbox_sections.py M scripts/functional_tests.py M scripts/grt.py M scripts/loc_files/create_all_fasta_loc.py M scripts/manage_db.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/slideshow/build_slideshow.py M scripts/summarize_timings.py M scripts/sync_reports_config.py M scripts/tool_shed/api/add_repository_registry_entry.py M scripts/tool_shed/api/create_categories.py M scripts/tool_shed/api/create_users.py M scripts/tool_shed/api/export.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/api/import_capsule.py M scripts/tool_shed/api/remove_repository_registry_entry.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/clean_up_tool_dependency_directory.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py M scripts/tools/maf/check_loc_file.py M scripts/tools/re_escape_output.py M scripts/transfer.py M scripts/update_shed_config_path.py M test/api/test_workflows.py M test/api/workflows_format_2/main.py M test/base/api_asserts.py M test/base/driver_util.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/workflows/test_modules.py M tools/data_source/data_source.py M tools/data_source/genbank.py M tools/data_source/upload.py M tools/evolution/add_scores.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_fasta.py M tools/filters/bed_to_gff_converter.py M tools/filters/catWrapper.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/secure_hash_message_digest.py M tools/filters/sorter.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.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/sr_mapping/srma_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py Log Message: ----------- Merge pull request #3170 from nsoranzo/dev Fixes for pycodestyle 2.2.0 Commit: db63b131c1728493a87901764c102dbc47f74f3f https://github.com/galaxyproject/galaxy/commit/db63b131c1728493a87901764c102... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-11-15 (Tue, 15 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Fix styling, we don't need to force rounded edges here. Commit: ca24098883fda1c35241d4c380f8b0765de7bb95 https://github.com/galaxyproject/galaxy/commit/ca24098883fda1c35241d4c380f8b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-11-15 (Tue, 15 Nov 2016) Changed paths: M client/galaxy/style/less/dataset.less M static/style/blue/base.css Log Message: ----------- Remove unused style, we can rely on the :last pseudoclasses for this. Commit: f8974acba2884dc2fc1728aaa81021708ad05493 https://github.com/galaxyproject/galaxy/commit/f8974acba2884dc2fc1728aaa8102... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-11-15 (Tue, 15 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Fix styling when only one visualization type exists Commit: 063bb61d07177f2736805521a888003d705e516e https://github.com/galaxyproject/galaxy/commit/063bb61d07177f2736805521a8880... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-11-15 (Tue, 15 Nov 2016) Changed paths: M static/welcome.html.sample Log Message: ----------- add links to local tours to sample welcome Commit: 2c756ff170da94b88829866f43082861a625b9fb https://github.com/galaxyproject/galaxy/commit/2c756ff170da94b88829866f43082... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-11-15 (Tue, 15 Nov 2016) Changed paths: M static/welcome.html.sample Log Message: ----------- drop leading slash to work with proxy prefix, thanks @dannon Commit: a86a457230e87ab02de29bba13686ad0c1243a63 https://github.com/galaxyproject/galaxy/commit/a86a457230e87ab02de29bba13686... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-11-15 (Tue, 15 Nov 2016) Changed paths: M static/welcome.html.sample Log Message: ----------- Merge pull request #3176 from martenson/add-tours-to-welcome add links to local tours to sample welcome Commit: dd556090c158b5062f0b7f6e0775281fcaabcb7e https://github.com/galaxyproject/galaxy/commit/dd556090c158b5062f0b7f6e07752... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M test/manual/workflows_scaling.py Log Message: ----------- Fix import broken in b4c77b761799b3a8752a6fec500717b1a6f3818b Commit: a8746c4f52295e5133950c0bffc3a9f07a2818ec https://github.com/galaxyproject/galaxy/commit/a8746c4f52295e5133950c0bffc3a... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M test/unit/dataset_collections/test_matching.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_rule_helper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_fabric_util.py M test/unit/shed_unit/test_td_common_util.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_galaxy_transactions.py M test/unit/test_routes.py M test/unit/tools/test_actions.py M test/unit/tools/test_citations.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.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_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_external_files.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_wrappers.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/unittest_utils/utility.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_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py Log Message: ----------- Fix import order and Python3 compatibility for test/unit/ Commit: d48817adb17b914975c26b90a2dd17887b24744b https://github.com/galaxyproject/galaxy/commit/d48817adb17b914975c26b90a2dd1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M run.sh Log Message: ----------- Remove redundant .venv activation -- this is handled in common_startup Commit: 72d360e942da2a614b7d74d3238d2ee0791a8141 https://github.com/galaxyproject/galaxy/commit/72d360e942da2a614b7d74d3238d2... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Change startup logic for .venv sourcing. If a .venv exists, use it. If not, if conda is there, use it. If no conda, create a .venv. Commit: 7f5d9d2fbd745f2099be15de706112717f9e01f6 https://github.com/galaxyproject/galaxy/commit/7f5d9d2fbd745f2099be15de70611... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- More startup logic tweaks, .venv > conda > new_venv Commit: 2f2d21aea25f45508bccf046f179041f3599c3b0 https://github.com/galaxyproject/galaxy/commit/2f2d21aea25f45508bccf046f1790... Author: John Chilton <jmchilton@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M test/manual/workflows_scaling.py M test/unit/dataset_collections/test_matching.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_rule_helper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_fabric_util.py M test/unit/shed_unit/test_td_common_util.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_galaxy_transactions.py M test/unit/test_routes.py M test/unit/tools/test_actions.py M test/unit/tools/test_citations.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.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_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_external_files.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_wrappers.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/unittest_utils/utility.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_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge pull request #3177 from nsoranzo/flake8-import-order Fix import order and Python3 compatibility for test/unit/ Commit: 985bd0dffd779b55813f6dc1c6bae663e959bd9c https://github.com/galaxyproject/galaxy/commit/985bd0dffd779b55813f6dc1c6bae... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M run.sh Log Message: ----------- Because common_startup is executed and not sourced, this block needs to remain in run.sh Commit: 4e6e7d36f87249b93f4a49249e227409e629305e https://github.com/galaxyproject/galaxy/commit/4e6e7d36f87249b93f4a49249e227... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Validate cycles and step size before building model for workflow execution Commit: 45259b7f168f6c1eb17f4f6aec738ad9f9231518 https://github.com/galaxyproject/galaxy/commit/45259b7f168f6c1eb17f4f6aec738... Author: Enis Afgan <afgane@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml Log Message: ----------- Fix typo Commit: 2f08dd72c3e028855b37dc1d113636dda2db9eab https://github.com/galaxyproject/galaxy/commit/2f08dd72c3e028855b37dc1d11363... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml Log Message: ----------- Merge pull request #3184 from afgane/dev Fix a typo in the intro tour Commit: ac5b7efc5f88da9b337a8d98f36dbdbfe29bb3f6 https://github.com/galaxyproject/galaxy/commit/ac5b7efc5f88da9b337a8d98f36db... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3130 from mvdbeek/fix_invalid_section_key Update ToolPanelElements instance locally Commit: 5028e2a25107e8f4cd2f136ab275853b5e31bb7f https://github.com/galaxyproject/galaxy/commit/5028e2a25107e8f4cd2f136ab2758... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M .ci/flake8_blacklist.txt A .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/flake8_wrapper.sh A .ci/flake8_wrapper_docstrings.sh M .ci/py3_sources.txt M .gitignore M .travis.yml M CONTRIBUTORS.md M Makefile 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/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.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-folderrow-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-workflow.js M 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static/scripts/utils/utils.js M static/style/blue/base.css M static/welcome.html.sample M templates/user/index.mako M templates/webapps/galaxy/dataset/copy_view.mako M templates/webapps/galaxy/library/common/common.mako M templates/webapps/galaxy/workflow/editor.mako 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 M templates/webapps/galaxy/workflow/run.mako R templates/webapps/galaxy/workflow/run_complete.mako M templates/webapps/tool_shed/repository/tool_form.mako 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_histories.py M test/api/test_history_contents.py M test/api/test_libraries.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 A 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tools/stats/gsummary.py M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into workflow_intermediates_ux Commit: 953ee3259999f774887e97d5e72bccb1102540f5 https://github.com/galaxyproject/galaxy/commit/953ee3259999f774887e97d5e72bc... Author: Ignacio <ignacio.eguinoa@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py Log Message: ----------- change parameters to samtools sort command (new samtools vers) Commit: 5bb86a3b687732913dee746732060f973b622cff https://github.com/galaxyproject/galaxy/commit/5bb86a3b687732913dee746732060... Author: Ignacio <ignacio.eguinoa@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py Log Message: ----------- correct indentation Commit: e5b69a711d14fa8e8876041f92160db19da3e9bf https://github.com/galaxyproject/galaxy/commit/e5b69a711d14fa8e8876041f92160... Author: John Chilton <jmchilton@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/tool/tool-form-workflow.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #2966 from dannon/workflow_intermediates_ux Change wording to be more clear about how workflow output cleanup wor… Commit: efde00d80a916afc20869608a7a1922249581a62 https://github.com/galaxyproject/galaxy/commit/efde00d80a916afc20869608a7a19... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py Log Message: ----------- Handle samtools 0.x Commit: 0b8fc7c8cca4b7374f12932b26ef3d854e2d8491 https://github.com/galaxyproject/galaxy/commit/0b8fc7c8cca4b7374f12932b26ef3... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge remote-tracking branch 'guerler/validate_workflow' into dev Commit: 31b73fd5869f1c3ae968fb29773cf1631a3f5843 https://github.com/galaxyproject/galaxy/commit/31b73fd5869f1c3ae968fb29773cf... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #3180 from dannon/venv_over_conda Prefer existing .venv over conda, when both are available. Commit: 92105d99fae6ec892f2eb6eb60c31d68196b061a https://github.com/galaxyproject/galaxy/commit/92105d99fae6ec892f2eb6eb60c31... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako Log Message: ----------- Merge pull request #2818 from erasche/rstudio-1610 Return of RStudio Commit: 592f15c7b5da3f962dda9f98cb978e5c5c6b4a1d https://github.com/galaxyproject/galaxy/commit/592f15c7b5da3f962dda9f98cb978... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: A test-data/bam_from_sam.bam A test-data/sam_with_header.sam A test/functional/tools/sam_to_bam.xml Log Message: ----------- Add sam-to-bam conversion test tool Commit: 0b395a7fb3aaebf5fa3a0448338df73c8774e388 https://github.com/galaxyproject/galaxy/commit/0b395a7fb3aaebf5fa3a0448338df... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Slight clarification of run.sh messaging when using conda. Commit: 164a0ad20cbbd55b40583c633c1c52dde9ecb7ba https://github.com/galaxyproject/galaxy/commit/164a0ad20cbbd55b40583c633c1c5... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #3188 from dannon/startup_output_tweaks Slight clarification of run.sh messaging when using conda. Commit: 8ace021c0af79e5d325d6a590f525bce881715f8 https://github.com/galaxyproject/galaxy/commit/8ace021c0af79e5d325d6a590f525... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py Log Message: ----------- Single quote variables in sam-to-bam conversion Commit: d8c75e2dffbfa754eda4fae4c6d3365d42278a4c https://github.com/galaxyproject/galaxy/commit/d8c75e2dffbfa754eda4fae4c6d33... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py A test-data/bam_from_sam.bam A test-data/sam_with_header.sam A test/functional/tools/sam_to_bam.xml Log Message: ----------- Merge pull request #3187 from mvdbeek/samtools_1_3_fix Make sam to bam converter tool compatible with samtools >= 1.3 Commit: 9d45f1e48a4321d5df0543bcfcf2994affa35612 https://github.com/galaxyproject/galaxy/commit/9d45f1e48a4321d5df0543bcfcf29... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 16.10.rc1 Commit: 6fd58afa6daf708f373513782ac907c154c266da https://github.com/galaxyproject/galaxy/commit/6fd58afa6daf708f373513782ac90... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #3191 from dannon/version-16.10 Update version to 16.10.rc1 Commit: 5c4ac18b44263df72b25826c03d8c2509ca68a1a https://github.com/galaxyproject/galaxy/commit/5c4ac18b44263df72b25826c03d8c... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-11-18 (Fri, 18 Nov 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/mvc/tool/tools.js M lib/galaxy/webapps/galaxy/controllers/root.py M static/maps/mvc/tool/tools.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/tools.js Log Message: ----------- remove unused override this caused Help/Search to point at /root/tool_search Commit: 3f27777e76086ac94c95003882bb82003c277b4e https://github.com/galaxyproject/galaxy/commit/3f27777e76086ac94c95003882bb8... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-11-18 (Fri, 18 Nov 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/mvc/tool/tools.js M lib/galaxy/webapps/galaxy/controllers/root.py M static/maps/mvc/tool/tools.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/tools.js Log Message: ----------- Merge pull request #3198 from martenson/fix-search-config [16.10] remove unused (and unintended) config override Commit: 548d3e6f05b722301deefada71d5dafda81a1881 https://github.com/galaxyproject/galaxy/commit/548d3e6f05b722301deefada71d5d... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js Log Message: ----------- Fixes for deleting histories broken in 1cc57b1eb2c295dbd68837c864740b6ff079b83d Commit: 5ba820116365ad42dd24e099b747b40d399e6dee https://github.com/galaxyproject/galaxy/commit/5ba820116365ad42dd24e099b747b... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M static/maps/mvc/history/options-menu.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.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Pack scripts Commit: aadc14d967c30683a10e68df61b82bb4f805de98 https://github.com/galaxyproject/galaxy/commit/aadc14d967c30683a10e68df61b82... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/options-menu.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.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Merge pull request #3203 from blankenberg/fix_history_delete_16.10 [16.10] Fixes for deleting histories Commit: 74d8faac9f07407ac9df344a78c9ecb06c178f93 https://github.com/galaxyproject/galaxy/commit/74d8faac9f07407ac9df344a78c9e... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Change 'History Actions' to 'Current History' in history options menu. as it was before 1cc57b1eb2c295dbd68837c864740b6ff079b83d. Commit: ec08ec60bb4dadaf6f8759f9dce79f764f26c909 https://github.com/galaxyproject/galaxy/commit/ec08ec60bb4dadaf6f8759f9dce79... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Merge pull request #3205 from blankenberg/history-current-options-name_16.10 [16.10] Change 'History Actions' to 'Current History' in history options menu. Commit: a9dab631fb00252ac122ea297262e89f63887019 https://github.com/galaxyproject/galaxy/commit/a9dab631fb00252ac122ea297262e... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M static/maps/mvc/form/form-section.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-section.js Log Message: ----------- Preserve custom event handler for form inputs Commit: 0b2d0c1746c9b7d7cc5781fedc5c6a02af3bdfdb https://github.com/galaxyproject/galaxy/commit/0b2d0c1746c9b7d7cc5781fedc5c6... Author: John Chilton <jmchilton@gmail.com> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M static/maps/mvc/form/form-section.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-section.js Log Message: ----------- Merge pull request #3210 from guerler/fix_output_label_handler [16.10] Preserve custom event handler for form inputs Commit: ce320b66ea1de3c15f4f080f19a729b1ff2087cb https://github.com/galaxyproject/galaxy/commit/ce320b66ea1de3c15f4f080f19a72... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- A bit of refactoring, handling of unavailable tools or tools with no help. Slight style changes. Commit: 9a2bae7381b1ee8e2411681a76d75767b05ceffe https://github.com/galaxyproject/galaxy/commit/9a2bae7381b1ee8e2411681a76d75... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M templates/admin/tool_shed_repository/common.mako Log Message: ----------- simplify the UI of deps installation by hiding the details under toggle button Commit: 068ee6bd0ceb942ec67e634a7e6e434314cbe7fe https://github.com/galaxyproject/galaxy/commit/068ee6bd0ceb942ec67e634a7e6e4... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py Log Message: ----------- fix install repo test Commit: 29cf7187233bbd031f07df4584f1bef55de612e4 https://github.com/galaxyproject/galaxy/commit/29cf7187233bbd031f07df4584f1b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Minor styling tweaks -- todo: swap from inline to class-based. Commit: 706bc3fbb118087cc057e6559e0262a6aca31127 https://github.com/galaxyproject/galaxy/commit/706bc3fbb118087cc057e6559e026... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M templates/admin/tool_shed_repository/select_tool_panel_section.mako M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py Log Message: ----------- fix test and hide shed_conf select udner details Commit: 73d010efa4236ed8ef0e46bb10d5e39233ae2d6b https://github.com/galaxyproject/galaxy/commit/73d010efa4236ed8ef0e46bb10d5e... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py Log Message: ----------- fix another test Commit: 4b794729b0cfd347d189a9a1e62273ab1788bc3e https://github.com/galaxyproject/galaxy/commit/4b794729b0cfd347d189a9a1e6227... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- fix a bug that renders conda dependency selection everytime Commit: 83e1392cf8d875109d121eb9cf13c274659c02b7 https://github.com/galaxyproject/galaxy/commit/83e1392cf8d875109d121eb9cf13c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/style/less/dataset.less M static/maps/mvc/dataset/dataset-li-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li-edit.js M static/style/blue/base.css Log Message: ----------- Standard styles inclusion in .less, more styling to match rounded edges and spacing. Commit: 94edc94b73e047612ae51ca2e075f17ac8e238bb https://github.com/galaxyproject/galaxy/commit/94edc94b73e047612ae51ca2e075f... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Add cached dependency manager Similar to https://github.com/galaxyproject/galaxy/pull/2986, implement a mechanism that allows tool dependencies to be cached. If the `use_cached_dependency_manager` option is set to True in galaxy.ini, we build a hash of the combination of a tools' requirements, and store the resulting environment in a directory specified by the `tool_dependency_cache_dir` option in galaxy.ini. Commit: 0a9b6d8755dee530232ab893a3bad199407aa0bc https://github.com/galaxyproject/galaxy/commit/0a9b6d8755dee530232ab893a3bad... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Better phrasing of cache options in galaxy.ini.sample (Thanks @nsoranzo) Commit: 2b1765751b29008aecbd782f28269ac4e63db239 https://github.com/galaxyproject/galaxy/commit/2b1765751b29008aecbd782f28269... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M config/galaxy.ini.sample 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 Log Message: ----------- Rework cached dependencies to be more robust to updates or changes in depedencies, folder structure and resolver configuration. Instead of hashing name, type and version of a dependency, hash the json representation of the dependencies returned by the dependency resolver, which include the path to the environment and the depedency type. This is only applied to resolvers whose cacheable attribute is set to True (conda-only, currently). Commit: f919a98601252ab8f87bffff6e449105e770aadf https://github.com/galaxyproject/galaxy/commit/f919a98601252ab8f87bffff6e449... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Build dependency cache at install time and only activate cached environments if they exist. Commit: 82f30e7645156b5f35c2b4cd77314e6275663979 https://github.com/galaxyproject/galaxy/commit/82f30e7645156b5f35c2b4cd77314... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M lib/galaxy/tools/deps/requirements.py M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Only attempt to build cache once per install and override __eq__ for ToolRequirement, to simplify checking if ToolRequirements are already installed/cached. Commit: 64bc9241ed785d4d552c5fac21cd412558c54567 https://github.com/galaxyproject/galaxy/commit/64bc9241ed785d4d552c5fac21cd4... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix NameError Commit: cf769dd09deb73624b22628208fa103cc4f27150 https://github.com/galaxyproject/galaxy/commit/cf769dd09deb73624b22628208fa1... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/fasta_to_2bit.xml M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add API to install resolver tool dependencies and to build a tool dependency cache (if activated in galaxy.ini). An example to install dependencies for the twobit converter: ``` import bioblend.galaxy url = 'http://localhost:8080/' api_key = 'admin_api_key' tool_id = 'CONVERTER_fasta_to_2bit' endpoint = "api/tools/%s/install_dependencies" % tool_id gi = bioblend.galaxy.GalaxyInstance(url, api_key) gi.make_post_request("/".join((url, endpoint)), payload={'id': tool_id}) ``` If `use_cached_dependency_manager` is activated in the galaxy.ini, a cached environment can be built like this: ``` endpoint = "api/tools/%s/build_dependency_cache" % tool_id gi.make_post_request("/".join((url, endpoint)), payload={'id': tool_id}) ``` Commit: cc7cd47ef54a09efbf8272d1e024f6f2ac92594b https://github.com/galaxyproject/galaxy/commit/cc7cd47ef54a09efbf8272d1e024f... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M test/integration/test_resolvers.py Log Message: ----------- Add integration test-case for install tool dependency API endpoint Commit: f10fd793a68ed9413bec708daa48cef65769d09f https://github.com/galaxyproject/galaxy/commit/f10fd793a68ed9413bec708daa48c... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/fasta_to_2bit.xml Log Message: ----------- Install the correct converter dependency Commit: 045a2f0d471f7b4186aff625f3cea9abfa549fa2 https://github.com/galaxyproject/galaxy/commit/045a2f0d471f7b4186aff625f3cea... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Add `force_rebuild` param to build_dependency_cache This will remove a pre-existing cached dependency directory. Commit: 16b49d9140edbf116f83b51b957cd61c4f2d91df https://github.com/galaxyproject/galaxy/commit/16b49d9140edbf116f83b51b957cd... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/buildapp.py M test/integration/test_resolvers.py Log Message: ----------- Add dependency_resolvers/clean endpoint Commit: 1efd4d4b3b99ec40071aa4d6fb7cf4030c51e2e0 https://github.com/galaxyproject/galaxy/commit/1efd4d4b3b99ec40071aa4d6fb7cf... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- add a conda clean function to remove downloaded tarballs after installation Commit: 2a4ccac4039342c98d71bc72177aa951db6c4ba1 https://github.com/galaxyproject/galaxy/commit/2a4ccac4039342c98d71bc72177aa... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/buildapp.py M test/integration/test_resolvers.py Log Message: ----------- Connect `clean` endpoint properly and add `-y` to exec_clean Commit: e3f8b724648cee51636502959096adba88045e14 https://github.com/galaxyproject/galaxy/commit/e3f8b724648cee51636502959096a... Author: John Chilton <jmchilton@gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py Log Message: ----------- Merge pull request #3226 from martenson/16-10-install-ux [16.10] admin installation ux Commit: d6f0e6b37c318a0202e0e266828e6325100cab19 https://github.com/galaxyproject/galaxy/commit/d6f0e6b37c318a0202e0e266828e6... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/datatypes/converters/fasta_to_2bit.xml M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/tool_shed/galaxy_install/install_manager.py M test/integration/test_resolvers.py Log Message: ----------- Merge pull request #3227 from mvdbeek/cached_deps_16.10 [16.10] Backport #3106 and #3222: Cached conda environments and API to manage them Commit: be6a2f8132f3002e0570488a4ad5f80e07b6c2a8 https://github.com/galaxyproject/galaxy/commit/be6a2f8132f3002e0570488a4ad5f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M client/galaxy/style/source_material/circle.py M config/galaxy.ini.sample M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/tours/core.galaxy_ui.yaml M contrib/galaxy_config_merger.py M contrib/nagios/check_galaxy.py M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M doc/parse_gx_xsd.py M doc/patch.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/config.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/fasta_to_2bit.xml M lib/galaxy/datatypes/converters/fasta_to_len.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/display_applications/parameters.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/triples.py M lib/galaxy/external_services/actions.py M lib/galaxy/external_services/parameters.py M lib/galaxy/external_services/result_handlers/basic.py M lib/galaxy/external_services/service.py M lib/galaxy/forms/forms.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/versions/0007_sharing_histories.py M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0012_user_address.py M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0020_library_upload_job.py M lib/galaxy/model/migrate/versions/0026_cloud_tables.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py M lib/galaxy/queue_worker.py M lib/galaxy/sample_tracking/data_transfer.py M lib/galaxy/sample_tracking/request_types.py M lib/galaxy/sample_tracking/sample.py M lib/galaxy/security/passwords.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/util/galaxyops/__init__.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/version.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/middleware/error.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/schedulers/core.py M lib/galaxy_utils/sequence/fastq.py M lib/galaxy_utils/sequence/vcf.py M lib/mimeparse.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/util/workflow_util.py M scripts/api/data_manager_example_execute.py M scripts/api/example_watch_folder.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/install_tool_shed_repositories.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/reset_metadata_on_installed_repositories.py M scripts/api/search.py M scripts/api/sequencer_configuration_create.py M scripts/api/workflow_execute.py M scripts/api/workflow_execute_parameters.py M scripts/api/workflow_import.py M scripts/auth/pam_auth_helper.py M scripts/build_toolbox.py M scripts/build_universe_config.py M scripts/check_galaxy.py M scripts/check_python.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/common_startup.sh M scripts/communication/communication_server.py M scripts/create_db.py M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/drmaa_external_killer.py M scripts/drmaa_external_runner.py M scripts/external_chown_script.py M scripts/extract_dataset_part.py M scripts/extract_toolbox_sections.py M scripts/functional_tests.py M scripts/grt.py M scripts/loc_files/create_all_fasta_loc.py M scripts/manage_db.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/slideshow/build_slideshow.py M scripts/summarize_timings.py M scripts/sync_reports_config.py M scripts/tool_shed/api/add_repository_registry_entry.py M scripts/tool_shed/api/create_categories.py M scripts/tool_shed/api/create_users.py M scripts/tool_shed/api/export.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/api/import_capsule.py M scripts/tool_shed/api/remove_repository_registry_entry.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/clean_up_tool_dependency_directory.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py M scripts/tools/maf/check_loc_file.py M scripts/tools/re_escape_output.py M scripts/transfer.py M scripts/update_shed_config_path.py M static/maps/mvc/form/form-section.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tools.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/form/form-section.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tools.js M static/style/blue/base.css M static/welcome.html.sample M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/webapps/galaxy/workflow/editor.mako A test-data/bam_from_sam.bam A test-data/sam_with_header.sam M test/api/test_workflows.py M test/api/workflows_format_2/main.py M test/base/api_asserts.py M test/base/driver_util.py A test/functional/tools/sam_to_bam.xml M test/integration/test_resolvers.py M test/manual/workflows_scaling.py M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py M test/unit/dataset_collections/test_matching.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_rule_helper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_fabric_util.py M test/unit/shed_unit/test_td_common_util.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_galaxy_transactions.py M test/unit/test_routes.py M test/unit/tools/test_actions.py M test/unit/tools/test_citations.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.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_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_external_files.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_wrappers.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/unittest_utils/utility.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_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py M tools/data_source/data_source.py M tools/data_source/genbank.py M tools/data_source/upload.py M tools/evolution/add_scores.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_fasta.py M tools/filters/bed_to_gff_converter.py M tools/filters/catWrapper.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/secure_hash_message_digest.py M tools/filters/sorter.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.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/sr_mapping/srma_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.10' into fix_help_history Commit: a26568bdfaefc5748ff3b2385fa9424ece6c652c https://github.com/galaxyproject/galaxy/commit/a26568bdfaefc5748ff3b2385fa94... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2016-11-30 (Wed, 30 Nov 2016) Changed paths: M tox.ini Log Message: ----------- Pin flake8 and flake8-import-order Do not pin when forward-merging to dev branch! Commit: 888a8f91537e22dcbdea174a65eaecbced9ea8a8 https://github.com/galaxyproject/galaxy/commit/888a8f91537e22dcbdea174a65eae... Author: John Chilton <jmchilton@gmail.com> Date: 2016-11-30 (Wed, 30 Nov 2016) Changed paths: M tox.ini Log Message: ----------- Merge pull request #3232 from nsoranzo/release_16.10_pin_flake8 [16.10] Pin flake8 and flake8-import-order Commit: bab709c755ef2ba83849c9457f9558d79a11eaf3 https://github.com/galaxyproject/galaxy/commit/bab709c755ef2ba83849c9457f955... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-12-03 (Sat, 03 Dec 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Request information about tool dependencies from toolshed and make available in prepare_for_install Commit: 72f417ef977030ce092219b7565f2cb6650e5a2c https://github.com/galaxyproject/galaxy/commit/72f417ef977030ce092219b7565f2... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-12-03 (Sat, 03 Dec 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Display requirement status on TS install This commit displays tool requirements as defined in the tool xml during the install confirmation dialog. If a tool dependency is defined in the tool XML, but not in a tool_dependencies.xml, a warning is shown if conda is not activated. This should close #3257. Commit: f20c478bd963c9eb907b711af659f17ef47c171f https://github.com/galaxyproject/galaxy/commit/f20c478bd963c9eb907b711af659f... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-12-03 (Sat, 03 Dec 2016) Changed paths: M templates/admin/tool_shed_repository/select_tool_panel_section.mako Log Message: ----------- Use Tool Shed instead of toolshed Commit: 622f2997376bceb30b822f6c5f1b3a0096e5e2f9 https://github.com/galaxyproject/galaxy/commit/622f2997376bceb30b822f6c5f1b3... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-12-05 (Mon, 05 Dec 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Merge pull request #3262 from mvdbeek/conda_only_improvements [16.10] Display tool requirements for conda-only tools Commit: a84601ba80cb8620a396e740e9a69f3d6f1dfd37 https://github.com/galaxyproject/galaxy/commit/a84601ba80cb8620a396e740e9a69... Author: John Chilton <jmchilton@gmail.com> Date: 2016-12-05 (Mon, 05 Dec 2016) Changed paths: A doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst A doc/source/releases/17.01_announce.rst M scripts/bootstrap_history.py Log Message: ----------- Add 16.10 release notes. Commit: 7fa10aa907ad6527f9e71a4d661281d21ac9150c https://github.com/galaxyproject/galaxy/commit/7fa10aa907ad6527f9e71a4d66128... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-12-06 (Tue, 06 Dec 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Simplify dependency list for cached environemnts (many thanks @nsoranzo) Commit: d0ad2ae1ce296e41e88264b0a770bf9c176db814 https://github.com/galaxyproject/galaxy/commit/d0ad2ae1ce296e41e88264b0a770b... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2016-12-06 (Tue, 06 Dec 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge pull request #3272 from mvdbeek/fix_superfluous_brackets [16.10] Simplify dependency list for cached environemnts (many thanks @nsoranzo) Commit: a1e3965eaf7e850486d289d1a2026877177b3c27 https://github.com/galaxyproject/galaxy/commit/a1e3965eaf7e850486d289d1a2026... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-12-06 (Tue, 06 Dec 2016) Changed paths: M static/welcome.html.sample Log Message: ----------- Fix tour URLs in welcome Commit: 8a5ff5df21efc6db7d2df47171f7cbad5cb1f608 https://github.com/galaxyproject/galaxy/commit/8a5ff5df21efc6db7d2df47171f7c... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-12-06 (Tue, 06 Dec 2016) Changed paths: M static/welcome.html.sample Log Message: ----------- Merge pull request #3277 from dannon/fix_tour_welcome_1610 [16.10] port Fix tour URLs in welcome Commit: 8766e125091d0a5a83a0fd4daf274fe93551a443 https://github.com/galaxyproject/galaxy/commit/8766e125091d0a5a83a0fd4daf274... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.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/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js Log Message: ----------- Escape filename in upload dialog, default and composite. Pointed out by David Wyde. Commit: 13ab07030c8ffa5012a123671c2ab450bf14c40b https://github.com/galaxyproject/galaxy/commit/13ab07030c8ffa5012a123671c2ab... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js M static/maps/mvc/upload/default/default-row.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Use consistent spacing. Commit: 75d327f165c730f95e181a2feff1db64074ab3e6 https://github.com/galaxyproject/galaxy/commit/75d327f165c730f95e181a2feff1d... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.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/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js Log Message: ----------- Merge pull request #3278 from dannon/upload_escape_filename [16.10] Escape filename in upload dialog, default and composite. Commit: f6b94dc465a41e0ce25cd0d38b8cfa81ab4c5254 https://github.com/galaxyproject/galaxy/commit/f6b94dc465a41e0ce25cd0d38b8cf... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M lib/tool_shed/util/tool_util.py Log Message: ----------- Fix for ToolShed install when copied sample data target exists, but is broken symlink. Commit: 70fc43b24090e537479a74b34a7ff9bc4e43de84 https://github.com/galaxyproject/galaxy/commit/70fc43b24090e537479a74b34a7ff... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M lib/tool_shed/util/tool_util.py Log Message: ----------- Merge pull request #3279 from blankenberg/16.10_ts_install_broken_symlink [16.10] Fix for ToolShed install when copied sample data target exists, but is broken symlink. Commit: 128a3174ebc425dfe750767eef40374d0b282448 https://github.com/galaxyproject/galaxy/commit/128a3174ebc425dfe750767eef403... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M doc/Makefile Log Message: ----------- Use OSX-compatible sed syntax Commit: d0f39ceff51843a95048dfdaf49035d07ce75c1d https://github.com/galaxyproject/galaxy/commit/d0f39ceff51843a95048dfdaf4903... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: A doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst A doc/source/releases/17.01_announce.rst M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #3270 from jmchilton/16.10_release_notes_0 [16.10] Add 16.10 release notes. Commit: 3e0e96657d765f4023bb6801ace2e96a1ffc4505 https://github.com/galaxyproject/galaxy/commit/3e0e96657d765f4023bb6801ace2e... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M doc/source/admin/index.rst M doc/source/admin/webhooks.rst M doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst Log Message: ----------- add work on release notes 16.10, improve docs for webhooks Conflicts: doc/source/releases/16.10.rst doc/source/releases/16.10_announce.rst Commit: 739fb59cba5b7747a32e685a3632f96effad4c11 https://github.com/galaxyproject/galaxy/commit/739fb59cba5b7747a32e685a3632f... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- fix the fix Commit: 5784a838a554f8dcf9e132e26be01240a37a3e65 https://github.com/galaxyproject/galaxy/commit/5784a838a554f8dcf9e132e26be01... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M doc/source/releases/16.10.rst Log Message: ----------- fix bad merge Commit: 83de83e7edc230d7f9841a6d9770d87d0c89d06f https://github.com/galaxyproject/galaxy/commit/83de83e7edc230d7f9841a6d9770d... Author: John Chilton <jmchilton@gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M doc/source/admin/index.rst M doc/source/admin/webhooks.rst M doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst Log Message: ----------- Merge pull request #3282 from martenson/release_16.10 [16.10] work on release notes 16.10 Commit: 9c435685cded86c36b605bf81eb9bec7f112cce3 https://github.com/galaxyproject/galaxy/commit/9c435685cded86c36b605bf81eb9b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Don't rely on complex, absolute selector, use local element.find() Commit: e3fbbc52b999f9e25e7b02c4edf44ddd43a63622 https://github.com/galaxyproject/galaxy/commit/e3fbbc52b999f9e25e7b02c4edf44... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M doc/source/releases/16.10_announce.rst Log Message: ----------- add small touches to release notes Commit: c01e25ddf8854e20a96040b3c8616136ec517574 https://github.com/galaxyproject/galaxy/commit/c01e25ddf8854e20a96040b3c8616... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M doc/source/releases/16.10_announce.rst Log Message: ----------- missing articles Commit: 2cbf9a9138b6fb89d06f41398539908a5df4585e https://github.com/galaxyproject/galaxy/commit/2cbf9a9138b6fb89d06f413985399... Author: John Chilton <jmchilton@gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M doc/source/releases/16.10_announce.rst Log Message: ----------- Merge pull request #3284 from martenson/notes-tinies [16.10] add small touches to release notes Commit: 4431d735c8908b19bbcd1ca594ec1a194cf4d299 https://github.com/galaxyproject/galaxy/commit/4431d735c8908b19bbcd1ca594ec1... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js Log Message: ----------- Extend list of tabular datatypes for bar diagrams Commit: c315f1d74bc8b4c4c2e5d6f0d4acd02d64b89e43 https://github.com/galaxyproject/galaxy/commit/c315f1d74bc8b4c4c2e5d6f0d4acd... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.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.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js Log Message: ----------- Upload file escaping backport. Commit: 13ae374f84926e71b3dde7080d8d74ad443916e3 https://github.com/galaxyproject/galaxy/commit/13ae374f84926e71b3dde7080d8d7... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M doc/Makefile A doc/fix_schema_rst.sh Log Message: ----------- Move sed commands to a script to resolve interferences with Make which happen only under OSX Commit: ca99753590abf62df2c34e80a87b1ae2ec3424e2 https://github.com/galaxyproject/galaxy/commit/ca99753590abf62df2c34e80a87b1... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M doc/Makefile A doc/fix_schema_rst.sh Log Message: ----------- Merge pull request #3281 from nsoranzo/release_16.10_fix_doc_Makefile [16.10] Use OSX-compatible sed syntax Commit: 22687410c4829dd9a0e44f55ee93b1020c8eab20 https://github.com/galaxyproject/galaxy/commit/22687410c4829dd9a0e44f55ee93b... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2016-12-09 (Fri, 09 Dec 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Ensure Conda prefix and cached environment are absolute paths Otherwise when Conda commands are executed from the job working directory, they will break. Commit: 879e3d69606e1a4b98bd34f75bf905b9da6edcfa https://github.com/galaxyproject/galaxy/commit/879e3d69606e1a4b98bd34f75bf90... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2016-12-09 (Fri, 09 Dec 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Skip building cache if force_rebuild is False Also: - re-raise exception if rmtree() fails - change hash(ed)_requirements to hash(ed)_dependencies Commit: 7c9d9d2231ecc113f7d69737a4aa4ec140b7e48c https://github.com/galaxyproject/galaxy/commit/7c9d9d2231ecc113f7d69737a4aa4... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-12-09 (Fri, 09 Dec 2016) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Apply a fix similar to 36134bca694c9dc6b2584fb661dfbce4ddb793e6 for the workflow editor. Not ideal, but this is old code we're replacing as the editor is overhauled. Commit: 602f2f2f1d431306c9aa64a6818c8feddaabb261 https://github.com/galaxyproject/galaxy/commit/602f2f2f1d431306c9aa64a6818c8... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-12-09 (Fri, 09 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.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.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js Log Message: ----------- Merge pull request #3292 from dannon/backport_upload_fn_escape [16.07] Upload file escaping backport. Commit: d6d2a12ec071e6cfa297944917ed201895f56332 https://github.com/galaxyproject/galaxy/commit/d6d2a12ec071e6cfa297944917ed2... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2016-12-09 (Fri, 09 Dec 2016) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Conflicts: client/galaxy/scripts/mvc/upload/composite/composite-row.js client/galaxy/scripts/mvc/upload/default/default-row.js static/maps/mvc/upload/composite/composite-row.js.map static/maps/mvc/upload/default/default-row.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/bundled/login.bundled.js.map static/scripts/mvc/upload/composite/composite-row.js static/scripts/mvc/upload/default/default-row.js Commit: 5a7f9e876e28ea773b79af9bbb887de7cff4aaa7 https://github.com/galaxyproject/galaxy/commit/5a7f9e876e28ea773b79af9bbb887... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2016-12-11 (Sun, 11 Dec 2016) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Correctly update TS repo status Execute build_dependency_cache() only if using a cached dependency manager. Set tool versions only if the TS repo contains tools. Raise exception if fetch_tool_versions() fails, previously the error message never reached the UI. Commit: 9dda310cd35e18c3ef86c5b09a021fc359fe5011 https://github.com/galaxyproject/galaxy/commit/9dda310cd35e18c3ef86c5b09a021... Author: John Chilton <jmchilton@gmail.com> Date: 2016-12-11 (Sun, 11 Dec 2016) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #3296 from dannon/workflow_editor_toolsearch_messagebox_fix [16.10] Workflow editor 'messagebox' fix. Commit: 22c7fcf3fff19ed9f271ada3cd8c007a96444768 https://github.com/galaxyproject/galaxy/commit/22c7fcf3fff19ed9f271ada3cd8c0... Author: John Chilton <jmchilton@gmail.com> Date: 2016-12-11 (Sun, 11 Dec 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Merge pull request #3295 from nsoranzo/release_16.10_tool_install_fixes [16.10] Tool install fixes Commit: 2c833499b130aca72ab78d112692f2a9f0d4d9e6 https://github.com/galaxyproject/galaxy/commit/2c833499b130aca72ab78d112692f... Author: John Chilton <jmchilton@gmail.com> Date: 2016-12-11 (Sun, 11 Dec 2016) Changed paths: M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js Log Message: ----------- Merge pull request #3287 from guerler/fix_chart_datatypes [16.10] Rely on tabular subclass matching through vizframework layer Commit: bb8a5a2215c2fce0e1c5fb69f4665358d72905f6 https://github.com/galaxyproject/galaxy/commit/bb8a5a2215c2fce0e1c5fb69f4665... Author: John Chilton <jmchilton@gmail.com> Date: 2016-12-13 (Tue, 13 Dec 2016) Changed paths: M lib/galaxy/tools/deps/commands.py Log Message: ----------- [16.10] Revert commands.shell changes from galaxyproject/galaxy#3129. It seems like people prefer to see the interactive shell https://github.com/galaxyproject/galaxy/issues/3259. See follow up here https://github.com/galaxyproject/galaxy/issues/3309. This also fixes an issue caused by the change of the constructor interface for CommandLineException in galaxyproject/galaxy#3129. Commit: 329108f81021e779db43a6a5c3b2808fd6c14b42 https://github.com/galaxyproject/galaxy/commit/329108f81021e779db43a6a5c3b28... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/tools/deps/commands.py Log Message: ----------- Merge pull request #3310 from jmchilton/shell_fix [16.10] Revert commands.shell changes from galaxyproject/galaxy#3129. Commit: 3ab4e1d742fe08701c1b997bf87f8406d1ccdecb https://github.com/galaxyproject/galaxy/commit/3ab4e1d742fe08701c1b997bf87f8... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- The jobs API, which this functionality is based on, requires a logged in user, so prevent anonymous access here. Also shifts to using Galaxy.root correctly, instead of assuming / Commit: d2ab7e701c87f4292b655893103c7842900a47b5 https://github.com/galaxyproject/galaxy/commit/d2ab7e701c87f4292b655893103c7... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/style/less/dataset.less M static/maps/mvc/dataset/dataset-li-edit.js.map A static/maps/mvc/user/change-password.js.map A static/maps/mvc/user/extra-information.js.map A static/maps/mvc/user/manage-user-information.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.map M static/scripts/mvc/dataset/dataset-li-edit.js A static/scripts/mvc/user/change-password.js A static/scripts/mvc/user/extra-information.js A static/scripts/mvc/user/manage-user-information.js M static/style/blue/base.css Log Message: ----------- build the client Commit: c1e3087ca35dbca1b0328954fe4769d666d3f934 https://github.com/galaxyproject/galaxy/commit/c1e3087ca35dbca1b0328954fe476... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Fix an ACE vulnerability with gff filter tools. Thanks to David Wyde for the disclosure. Commit: 9ee3d01c301ca067f7b94ee3c75bd784fafc4572 https://github.com/galaxyproject/galaxy/commit/9ee3d01c301ca067f7b94ee3c75bd... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Merge branch 'release_14.10' into release_15.01 Commit: da7afb4e22f352c40a53da8b3e18319ed7aeb844 https://github.com/galaxyproject/galaxy/commit/da7afb4e22f352c40a53da8b3e183... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Commit: 7c443eda567ece12fb90330e131e7f97c7b63ba2 https://github.com/galaxyproject/galaxy/commit/7c443eda567ece12fb90330e131e7... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Merge branch 'release_15.03' into release_15.05 Commit: 790e60af60093dcb8e26f093c3a87903605da206 https://github.com/galaxyproject/galaxy/commit/790e60af60093dcb8e26f093c3a87... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Commit: 95daf69b372fa829325be561dc0a9907da0bea81 https://github.com/galaxyproject/galaxy/commit/95daf69b372fa829325be561dc0a9... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Merge branch 'release_15.07' into release_15.10 Commit: 4c07734f57453581666fd3994c44d583f3e319b9 https://github.com/galaxyproject/galaxy/commit/4c07734f57453581666fd3994c44d... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Merge branch 'release_15.10' into release_16.01 Commit: 4cf70aea79772780b49dcdff08d63f40ca75ac6d https://github.com/galaxyproject/galaxy/commit/4cf70aea79772780b49dcdff08d63... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Commit: 22fda449f9d4ff2ed21fe4e39080456120aaf95e https://github.com/galaxyproject/galaxy/commit/22fda449f9d4ff2ed21fe4e390804... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Commit: 42cda969281c2d3e2918eb0d376415154e22d1db https://github.com/galaxyproject/galaxy/commit/42cda969281c2d3e2918eb0d37641... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: 5c01c01791ad79bef23388b6892de974ad7b6323 https://github.com/galaxyproject/galaxy/commit/5c01c01791ad79bef23388b6892de... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst Log Message: ----------- Add security disclosure to release notes Commit: c1397908cd1fc81b294849008b1e5ec1b1381660 https://github.com/galaxyproject/galaxy/commit/c1397908cd1fc81b294849008b1e5... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 16.10 Commit: 378ed53a33eee02c3620310c7245e7a85d279427 https://github.com/galaxyproject/galaxy/commit/378ed53a33eee02c3620310c7245e... 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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/velvetg_wrapper.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Merge branch 'release_16.10' Compare: https://github.com/galaxyproject/galaxy/compare/d10758a4f22d...378ed53a33ee