- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] fe251e: Ensure removal of temporary files.
by GitHub 18 Aug '15

18 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fe251e3c2de4d986b3654130b317fe5fe9b2cffb https://github.com/galaxyproject/galaxy/commit/fe251e3c2de4d986b3654130b317… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Ensure removal of temporary files. Specifically, export_info.xml and manifest.xml were not being deleted after the capsule was created. Commit: ed4bb86c3355cad578354696394dd6364b5a898d https://github.com/galaxyproject/galaxy/commit/ed4bb86c3355cad578354696394d… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Also delete uploaded file data after processing. API uploads, e.g. with planemo, would leave upload_file_data_XXXXXX lying around in the configured temporary directory. Forever. Commit: 9c8edf106bd61851b0668ceb6047104784f2cb1a https://github.com/galaxyproject/galaxy/commit/9c8edf106bd61851b0668ceb6047… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Merge pull request #607 from davebx/ts_tempfiles Ensure removal of temporary files. Compare: https://github.com/galaxyproject/galaxy/compare/634799803ef3...9c8edf106bd6

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[galaxyproject/galaxy] c938e6: Fix output collection terminal base class
by GitHub 17 Aug '15

17 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c938e66e98512d85120c1c06d485a13000ff82c1 https://github.com/galaxyproject/galaxy/commit/c938e66e98512d85120c1c06d485… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Fix output collection terminal base class Commit: 79dbff19674dbe667887b92d070165ade85ae834 https://github.com/galaxyproject/galaxy/commit/79dbff19674dbe667887b92d0701… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Merge pull request #602 from guerler/fix_collections_000 [15.07] Fix output collection terminal base class Commit: 4463676e2cf70989b4a036f155356418ef22b049 https://github.com/galaxyproject/galaxy/commit/4463676e2cf70989b4a036f15535… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-17 (Mon, 17 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Merge branch 'release_15.07' into dev Commit: 634799803ef36b9ea1a615bc980425f224d5d958 https://github.com/galaxyproject/galaxy/commit/634799803ef36b9ea1a615bc9804… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-17 (Mon, 17 Aug 2015) Changed paths: M static/maps/mvc/history/options-menu.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Merge from release and rebuild. Compare: https://github.com/galaxyproject/galaxy/compare/c0119de12eee...634799803ef3

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[galaxyproject/galaxy] 646086: Add a --develop flag to grunt that is compatible w...
by GitHub 17 Aug '15

17 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 64608685393a235bad5c161421861af6c5609048 https://github.com/galaxyproject/galaxy/commit/64608685393a235bad5c16142186… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M client/grunt-tasks/scripts.js Log Message: ----------- Add a --develop flag to grunt that is compatible with both standard build *and* watch to allow for easier debugging instead of requiring the 'decompress' task -- though this still works. This makes it possible to drop in 'debugger' statements, etc., and should help when working on the client. Additionally enable drop_console for the compressor, since it's now much easier to use local development tweaks. Commit: 63d6c37a39a53bae6806e3bb9267a1659313f878 https://github.com/galaxyproject/galaxy/commit/63d6c37a39a53bae6806e3bb9267… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M static/maps/galaxy.interactive_environments.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/toastr.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/data.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/visualization.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/toastr.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/data.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-jobs.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-select.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/utils.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/visualization.js Log Message: ----------- Rebuild client w/ new options. Commit: 2666499da649fdbb3524d11ceab90b9af86205da https://github.com/galaxyproject/galaxy/commit/2666499da649fdbb3524d11ceab9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M client/grunt-tasks/scripts.js Log Message: ----------- One minor styling issue Commit: c0119de12eeeba5308c72b98811a2d140cdccbd4 https://github.com/galaxyproject/galaxy/commit/c0119de12eeeba5308c72b98811a… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-08-17 (Mon, 17 Aug 2015) Changed paths: M client/grunt-tasks/scripts.js M static/maps/galaxy.interactive_environments.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/toastr.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/data.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/visualization.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/toastr.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/data.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-jobs.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-select.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/utils.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/visualization.js Log Message: ----------- Merge pull request #601 from dannon/grunt_develop_mode Grunt develop mode Compare: https://github.com/galaxyproject/galaxy/compare/ed54c343e66d...c0119de12eee

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[galaxyproject/galaxy] 0f2e21: Cleanup of the toolshed's url handling methods.
by GitHub 17 Aug '15

17 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0f2e2152ee17532488a8231cf1220ed9ddddb3aa https://github.com/galaxyproject/galaxy/commit/0f2e2152ee17532488a8231cf122… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Cleanup of the toolshed's url handling methods. Commit: 9f975e85067c1c5f695979f13d26ae4d132cb36f https://github.com/galaxyproject/galaxy/commit/9f975e85067c1c5f695979f13d26… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Make travis happier. Commit: 624cf19ba5bec88dfee58380722720fc47d68eb3 https://github.com/galaxyproject/galaxy/commit/624cf19ba5bec88dfee583807227… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/util/common_util.py Log Message: ----------- More linting. Commit: d7e6d627d0679a5cc95f30e71f5a9d30cc753802 https://github.com/galaxyproject/galaxy/commit/d7e6d627d0679a5cc95f30e71f5a… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Correct errors found by Nicola. Commit: 84329f8f3d7423106f197fb880fc12aee2d2b71d https://github.com/galaxyproject/galaxy/commit/84329f8f3d7423106f197fb880fc… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/tool_shed/util/common_util.py Log Message: ----------- Remove debug output. Commit: 0efc866a07699067beb930dc0275aab7dfb40cd5 https://github.com/galaxyproject/galaxy/commit/0efc866a07699067beb930dc0275… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Correct additional errors discovered by Nicola. Commit: 5ddd2c92a3caeb75bcb379f297f2967af26afc47 https://github.com/galaxyproject/galaxy/commit/5ddd2c92a3caeb75bcb379f297f2… Author: Dave B. <dave(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Fix missing parameter. Commit: ed54c343e66d7dee79dd785da837f2ce55f69138 https://github.com/galaxyproject/galaxy/commit/ed54c343e66d7dee79dd785da837… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-16 (Sun, 16 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #586 from davebx/ts_url_cleanup Cleanup of the toolshed's url handling methods. Compare: https://github.com/galaxyproject/galaxy/compare/2da0083cdfdf...ed54c343e66d

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[galaxyproject/galaxy] d6ef04: Applied paging to all pages
by GitHub 15 Aug '15

15 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d6ef0458309a9cfea12cb33b9d0931fd75eeb04a https://github.com/galaxyproject/galaxy/commit/d6ef0458309a9cfea12cb33b9d09… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py M templates/page_base.mako M templates/spark_base.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_in_error.mako Log Message: ----------- Applied paging to all pages Commit: 21ab4d2dbfa8576f89a13018d962cd8dc3738239 https://github.com/galaxyproject/galaxy/commit/21ab4d2dbfa8576f89a13018d962… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js A client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/style/less/reports.less M config/datatypes_conf.xml.sample M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M lib/galaxy/dataset_collections/builder.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/output.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/history.py A lib/galaxy/webapps/reports/controllers/home.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/basic_util.py R static/help.css R static/help.html R static/help.rst R static/images/SetAttr.png R static/images/SetGenome.png R static/images/brochure.pdf R static/images/galaxy.png R static/images/galaxyLogo_small.png R static/images/lock.jpg R static/images/qk/quickie1_small.png R static/images/qk/quickie2_small.png R static/images/qk/quickie3_small.png R static/images/qk/quickie4_small.png R static/images/qk/quickie5_small.png R static/images/qk/quickie6_small.png R static/images/qk/quickie7_small.png R static/images/screencast.png R static/images/sequencer.png R static/images/tools.gif R static/images/toolsExpandingMenu.gif R static/images/welcomePhoto.jpg M static/maps/mvc/upload/upload-view.js.map A static/maps/reports_webapp/run_stats.js.map M static/scripts/mvc/upload/upload-view.js A static/scripts/reports_webapp/run_stats.js M static/style/blue/base.css M static/style/blue/reports.css R static/welcome.rst M templates/base.mako M templates/webapps/reports/base_panels.mako M templates/webapps/reports/index.mako A templates/webapps/reports/run_stats.mako R templates/webapps/tool_shed/message.mako M templates/webapps/tool_shed/repository/manage_repository.mako M test/functional/test_toolbox.py A test/functional/tools/collection_creates_dynamic_list_of_pairs.xml A test/functional/tools/collection_creates_dynamic_nested.xml A test/functional/tools/collection_creates_list_of_pairs.xml M test/functional/tools/samples_tool_conf.xml M tool-data/all_fasta.loc.sample M tool-data/faseq.loc.sample M tool-data/liftOver.loc.sample M tool-data/mosaik_index.loc.sample M tool-data/ngs_sim_fasta.loc.sample M tool-data/perm_base_index.loc.sample M tool-data/perm_color_index.loc.sample M tool-data/picard_index.loc.sample M tool-data/regions.loc.sample M tool-data/srma_index.loc.sample Log Message: ----------- Merge branch 'dev' of https://github.com/Airistotal/galaxy into Reports_pages Commit: dd51cfe6e0ae23e8faab7b43673f9f3bc6cc6dcf https://github.com/galaxyproject/galaxy/commit/dd51cfe6e0ae23e8faab7b43673f… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/workflows.py M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako Log Message: ----------- Added Paging to Workflows Commit: a27ff9b2922aff5f863cf7d2e84094e236d8c6bb https://github.com/galaxyproject/galaxy/commit/a27ff9b2922aff5f863cf7d2e840… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M lib/galaxy/webapps/reports/controllers/workflows.py M static/style/blue/base.css M static/style/blue/reports.css Log Message: ----------- Added limits to queries (bug fix) Changed homepage button location (small style change) Changes for CI Commit: 1d3e304644f0f5b7b3cb828a9016e2b679791f46 https://github.com/galaxyproject/galaxy/commit/1d3e304644f0f5b7b3cb828a9016… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py M templates/webapps/reports/jobs_per_user.mako Log Message: ----------- Timing of the queries on the jobs per user page. Commit: 266d96bcb0c34365b1f3ea136909abad7180a118 https://github.com/galaxyproject/galaxy/commit/266d96bcb0c34365b1f3ea136909… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-14 (Fri, 14 Aug 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py M templates/webapps/reports/jobs_per_user.mako Log Message: ----------- Changed for CI, added total time for page load Commit: 2da0083cdfdfc268229d730ef2a8f5432da781f1 https://github.com/galaxyproject/galaxy/commit/2da0083cdfdfc268229d730ef2a8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-15 (Sat, 15 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/workflows.py M static/style/blue/base.css M static/style/blue/reports.css M templates/page_base.mako M templates/spark_base.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako Log Message: ----------- Merge pull request #576 from Airistotal/Reports_pages Reports: Applied paging to all pages Compare: https://github.com/galaxyproject/galaxy/compare/5b2e208b775f...2da0083cdfdf

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[galaxyproject/galaxy] d9d86e: Update contact email address for security issues.
by GitHub 15 Aug '15

15 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d9d86ee8a749550d052ef4f7dc3ff4be51e00734 https://github.com/galaxyproject/galaxy/commit/d9d86ee8a749550d052ef4f7dc3f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M CONTRIBUTING.md Log Message: ----------- Update contact email address for security issues. Commit: 55e0f109fcebbee3da19e0d5a568ff5b4cedcddb https://github.com/galaxyproject/galaxy/commit/55e0f109fcebbee3da19e0d5a568… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M CONTRIBUTING.md Log Message: ----------- Mention GitHub issues. Commit: 86aa07d87e61a980b98cf6fa6e6360e7d649f5e5 https://github.com/galaxyproject/galaxy/commit/86aa07d87e61a980b98cf6fa6e63… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M CONTRIBUTING.md Log Message: ----------- Require PRs to pass the CI tests. Commit: 3df58181cdf13f6a8e7e41fb813c49de4c5a6dd6 https://github.com/galaxyproject/galaxy/commit/3df58181cdf13f6a8e7e41fb813c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M CONTRIBUTING.md Log Message: ----------- Small fixes for CONTRIBUTING.md . Commit: 5b2e208b775f8284c651f67dad86fd55929456ac https://github.com/galaxyproject/galaxy/commit/5b2e208b775f8284c651f67dad86… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-15 (Sat, 15 Aug 2015) Changed paths: M CONTRIBUTING.md Log Message: ----------- Merge pull request #574 from nsoranzo/dev [PROCEDURES] GitHub issues, security email contact and CI testing Compare: https://github.com/galaxyproject/galaxy/compare/cb1538588d8a...5b2e208b775f

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[galaxyproject/usegalaxy-playbook] e989ab: update MTS
by GitHub 14 Aug '15

14 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e989abf5130cfc80c69b50260ce2d5a3b5f276f1 https://github.com/galaxyproject/usegalaxy-playbook/commit/e989abf5130cfc80… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-14 (Fri, 14 Aug 2015) Changed paths: M production/group_vars/toolshedservers.yml Log Message: ----------- update MTS

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[galaxyproject/galaxy] 1383ce: flake8 lib/galaxy_utils/
by GitHub 14 Aug '15

14 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1383ced0bdf55d3355a2927db42b584d3b00b15f https://github.com/galaxyproject/galaxy/commit/1383ced0bdf55d3355a2927db42b… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-14 (Fri, 14 Aug 2015) Changed paths: M .ci/flake8_blacklist.txt M lib/galaxy_utils/sequence/fasta.py M lib/galaxy_utils/sequence/fastq.py M lib/galaxy_utils/sequence/sequence.py M lib/galaxy_utils/sequence/transform.py M lib/galaxy_utils/sequence/vcf.py Log Message: ----------- flake8 lib/galaxy_utils/ Commit: cb1538588d8a7632dcb29232bbad1b299173a84c https://github.com/galaxyproject/galaxy/commit/cb1538588d8a7632dcb29232bbad… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-14 (Fri, 14 Aug 2015) Changed paths: M .ci/flake8_blacklist.txt M lib/galaxy_utils/sequence/fasta.py M lib/galaxy_utils/sequence/fastq.py M lib/galaxy_utils/sequence/sequence.py M lib/galaxy_utils/sequence/transform.py M lib/galaxy_utils/sequence/vcf.py Log Message: ----------- Merge pull request #604 from nsoranzo/flake8_fixes flake8 lib/galaxy_utils/ Compare: https://github.com/galaxyproject/galaxy/compare/4459e9411b61...cb1538588d8a

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[galaxyproject/galaxy] bf8d74: UI, Histories: move unhide_datasets and delete_hid...
by GitHub 14 Aug '15

14 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bf8d74da29ba02c08cc1debed38dbf63a13dd686 https://github.com/galaxyproject/galaxy/commit/bf8d74da29ba02c08cc1debed38d… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/options-menu.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/options-menu.js Log Message: ----------- UI, Histories: move unhide_datasets and delete_hidden_datasets to the client, remove them from the web controller Commit: d20add4ff8abe54cbc15704edc0222935631c767 https://github.com/galaxyproject/galaxy/commit/d20add4ff8abe54cbc15704edc02… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/root.py A templates/webapps/galaxy/history/as_xml.mako M templates/webapps/galaxy/history/view.mako R templates/webapps/galaxy/root/history.mako R templates/webapps/galaxy/root/history_as_xml.mako Log Message: ----------- UI, Histories: use /history/view with current to replace /history, move history_as_xml to /history/as_xml Commit: ff13fb85cc46cdf8399e3477ba8808dfc6078ed5 https://github.com/galaxyproject/galaxy/commit/ff13fb85cc46cdf8399e3477ba88… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M client/bower.json M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/farbtastic.js A client/galaxy/scripts/libs/jquery.sparklines.js M client/galaxy/scripts/libs/jquery/jqtouch.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/libs/tracekit.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-panel-edit.js M client/galaxy/scripts/mvc/ui/ui-select-library.js A client/galaxy/scripts/utils/query-string-parsing.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/style/less/base.less M client/galaxy/style/less/history.less A client/galaxy/style/less/reports.less M client/grunt-tasks/install-libs.js M client/grunt-tasks/style.js M config/galaxy.ini.sample M config/plugins/visualizations/trackster/config/trackster.xml A doc/source/api/guidelines.rst M doc/source/api_doc.rst M doc/source/index.rst M doc/source/releases/_header.rst A doc/source/ts_api_doc.rst M lib/galaxy/config.py M lib/galaxy/dataset_collections/builder.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/histories.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/output.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/util/basic_util.py M scripts/tool_shed/build_ts_whoosh_index.py M static/maps/libs/d3.js.map M static/maps/libs/farbtastic.js.map A static/maps/libs/jquery.sparklines.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/require.js.map M static/maps/libs/tracekit.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-panel-edit.js.map M static/maps/mvc/ui/ui-select-library.js.map A static/maps/utils/query-string-parsing.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster.js.map M static/scripts/libs/d3.js M static/scripts/libs/farbtastic.js A static/scripts/libs/jquery.sparklines.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/require.js M static/scripts/libs/tracekit.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-panel-edit.js M static/scripts/mvc/ui/ui-select-library.js A static/scripts/utils/query-string-parsing.js M static/scripts/utils/utils.js M static/scripts/viz/trackster.js M static/style/blue/base.css A static/style/blue/reports.css M templates/base.mako M templates/display_base.mako M templates/page_base.mako M templates/search/index.mako M templates/sorting_base.mako A templates/spark_base.mako M templates/webapps/galaxy/cloud/index.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/library/common/ldda_info.mako M templates/webapps/galaxy/library/common/ldda_permissions.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako M templates/webapps/reports/base_panels.mako M templates/webapps/reports/index.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/registered_users_specified_month.mako M templates/webapps/reports/requests_per_month_all.mako M templates/webapps/reports/requests_per_user.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako A templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako R templates/webapps/tool_shed/message.mako M test/functional/test_toolbox.py A test/functional/tool-data/fasta_indexes.loc M test/functional/tool-data/sample_tool_data_tables.xml A test/functional/tools/collection_creates_dynamic_list_of_pairs.xml A test/functional/tools/collection_creates_dynamic_nested.xml A test/functional/tools/collection_creates_list_of_pairs.xml A test/functional/tools/dbkey_filter_input.xml A test/functional/tools/dbkey_filter_multi_input.xml M test/functional/tools/samples_tool_conf.xml M tools/extract/extract_genomic_dna.py M tools/extract/extract_genomic_dna.xml Log Message: ----------- Merge conflicts Commit: 971b96ddd6855e0e2fd61b89499a15d9e6fb3b93 https://github.com/galaxyproject/galaxy/commit/971b96ddd6855e0e2fd61b89499a… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/options-menu.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- UI, Histories: when calling 'Delete hidden', both delete *and* unhide the datasets (preventing them from being both deleted and hidden) Commit: 3e212507defb88e91799883754d4a1d1ae8c0876 https://github.com/galaxyproject/galaxy/commit/3e212507defb88e91799883754d4… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py M templates/webapps/galaxy/history/view.mako Log Message: ----------- UI, Histories: fix view.mako json ref, remove unused import in root Commit: b0a8c6f52bfda10244e12b08ff3143c1f4ef0d45 https://github.com/galaxyproject/galaxy/commit/b0a8c6f52bfda10244e12b08ff31… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/options-menu.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- UI, Histories: use renderItems for batched changes in options menu Commit: 4459e9411b610ea106fe2db74d20dfd27363aa23 https://github.com/galaxyproject/galaxy/commit/4459e9411b610ea106fe2db74d20… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-14 (Fri, 14 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/root.py M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/options-menu.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/options-menu.js A templates/webapps/galaxy/history/as_xml.mako M templates/webapps/galaxy/history/view.mako R templates/webapps/galaxy/root/history.mako R templates/webapps/galaxy/root/history_as_xml.mako Log Message: ----------- Merge pull request #578 from carlfeberhard/history.s-n-d Remove more history UIController methods. Compare: https://github.com/galaxyproject/galaxy/compare/d0a053608582...4459e9411b61

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[galaxyproject/galaxy] c00196: Fix StockLineage.get_versions() when reverse=True ...
by GitHub 14 Aug '15

14 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c00196fd2cb4eb7f999bd2176c570b0834c81c2d https://github.com/galaxyproject/galaxy/commit/c00196fd2cb4eb7f999bd2176c57… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/tools/toolbox/lineages/stock.py Log Message: ----------- Fix StockLineage.get_versions() when reverse=True . Commit: 4b3a34f1d25cd00c12a5ee3815f609f238f83aa5 https://github.com/galaxyproject/galaxy/commit/4b3a34f1d25cd00c12a5ee3815f6… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Simplify ToolVersion.get_version_ids() . Commit: 9c318ac1f7dac48e25e8b1c315c372e36dc0323e https://github.com/galaxyproject/galaxy/commit/9c318ac1f7dac48e25e8b1c315c3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Remove existing wrong tool version associations in ToolVersionManager.handle_tool_versions() . Fix #552. To fix a tool with a wrong lineage, click on "Set tool versions" on the "Repository Actions" menu. Commit: d0a0536085821e667d39cc30423d7bdcbc8e5115 https://github.com/galaxyproject/galaxy/commit/d0a0536085821e667d39cc30423d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-14 (Fri, 14 Aug 2015) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/toolbox/lineages/stock.py M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge pull request #596 from nsoranzo/lineage_fixes Tool lineage fixes. Compare: https://github.com/galaxyproject/galaxy/compare/cafe872bfb20...d0a053608582

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