- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] f1d245: Installed MiModD 0.8.1
by GitHub 15 Nov '17

15 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f1d2455635aec3d88c354061f106adb53081465f https://github.com/galaxyproject/usegalaxy-playbook/commit/f1d2455635aec3d8… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Installed MiModD 0.8.1

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[galaxyproject/usegalaxy-playbook] f01373: Fix BAM metadata issues on Jetstream
by GitHub 15 Nov '17

15 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f01373fe9596a3eafec883d7c3bcc76cab433c91 https://github.com/galaxyproject/usegalaxy-playbook/commit/f01373fe9596a3ea… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M CHANGELOG.md M env/main/templates/galaxy/config/job_conf.xml.j2 M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Fix BAM metadata issues on Jetstream

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[galaxyproject/galaxy] 0a6c29: Add missing ipaddress requirement
by GitHub 15 Nov '17

15 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0a6c2974204b3048456bc7ceba7793ab4774de9f https://github.com/galaxyproject/galaxy/commit/0a6c2974204b3048456bc7ceba77… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Add missing ipaddress requirement Broken in https://github.com/galaxyproject/galaxy/pull/4289 . Fix https://github.com/galaxyproject/galaxy/issues/4999 . Commit: 18467e9b2cecb2102d17fd6734f1fb40c5321623 https://github.com/galaxyproject/galaxy/commit/18467e9b2cecb2102d17fd6734f1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Merge pull request #5000 from nsoranzo/release_17.09_add_ipaddress_requirement [17.09] Add missing ipaddress requirement Commit: 7bede53beff349b393c3c5a293902def1d8bdb76 https://github.com/galaxyproject/galaxy/commit/7bede53beff349b393c3c5a29390… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Merge branch 'release_17.09' into dev Conflicts: lib/galaxy/dependencies/pinned-requirements.txt lib/galaxy/dependencies/requirements.txt Compare: https://github.com/galaxyproject/galaxy/compare/f34e6a1e2e18...7bede53beff3

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[galaxyproject/galaxy] c99400: add askomics interactive environment
by GitHub 15 Nov '17

15 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c994005fcc2b06bacfaf992be9de9002c47b5ab3 https://github.com/galaxyproject/galaxy/commit/c994005fcc2b06bacfaf992be9de… Author: xgaia <xgaia(a)gmx.com> Date: 2017-10-03 (Tue, 03 Oct 2017) Changed paths: A config/plugins/interactive_environments/askomics/LICENSE A config/plugins/interactive_environments/askomics/README.md A config/plugins/interactive_environments/askomics/config/allowed_images.yml A config/plugins/interactive_environments/askomics/config/allowed_images.yml.sample A config/plugins/interactive_environments/askomics/config/askomics.ini.sample A config/plugins/interactive_environments/askomics/config/askomics.xml A config/plugins/interactive_environments/askomics/static/js/askomics.js A config/plugins/interactive_environments/askomics/templates/askomics.mako Log Message: ----------- add askomics interactive environment Commit: 4d5facb9857e2f7b70282e74f40d0b31d1120d41 https://github.com/galaxyproject/galaxy/commit/4d5facb9857e2f7b70282e74f40d… Author: xgaia <xgaia(a)gmx.com> Date: 2017-10-03 (Tue, 03 Oct 2017) Changed paths: R config/plugins/interactive_environments/askomics/README.md R config/plugins/interactive_environments/askomics/config/allowed_images.yml Log Message: ----------- remove files Commit: e55121f655ca105f2d9ac7ea473cca77c6f07b75 https://github.com/galaxyproject/galaxy/commit/e55121f655ca105f2d9ac7ea473c… Author: xgaia <xgaia(a)gmx.com> Date: 2017-10-03 (Tue, 03 Oct 2017) Changed paths: R config/plugins/interactive_environments/askomics/LICENSE Log Message: ----------- remove license file Commit: 04370ebff931ed2f591531f2cf58b8248e71f956 https://github.com/galaxyproject/galaxy/commit/04370ebff931ed2f591531f2cf58… Author: xgaia <xgaia(a)gmx.com> Date: 2017-10-05 (Thu, 05 Oct 2017) Changed paths: M config/plugins/interactive_environments/askomics/templates/askomics.mako Log Message: ----------- use build-in password generator for api key Commit: 1d5f0d2b611c3685cc12b95a0efdb91e3e4d872b https://github.com/galaxyproject/galaxy/commit/1d5f0d2b611c3685cc12b95a0efd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M config/plugins/interactive_environments/askomics/static/js/askomics.js M config/plugins/interactive_environments/askomics/templates/askomics.mako Log Message: ----------- Fixes to askomics javascript Commit: 7d674e1de0d23b48d3f6a8cf0fc4c5a2d883d9e7 https://github.com/galaxyproject/galaxy/commit/7d674e1de0d23b48d3f6a8cf0fc4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M config/plugins/interactive_environments/askomics/static/js/askomics.js Log Message: ----------- Left off semicolon. Commit: 8d3c8c6d40521ec513b936dd4b15693edf0f280b https://github.com/galaxyproject/galaxy/commit/8d3c8c6d40521ec513b936dd4b15… Author: Xavier Garnier <xgaia(a)gmx.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M config/plugins/interactive_environments/askomics/static/js/askomics.js M config/plugins/interactive_environments/askomics/templates/askomics.mako Log Message: ----------- Merge pull request #1 from dannon/askomics-fixes Small javascript fixes for askomics IE integration Commit: f34e6a1e2e182c10a36172d63740559723058086 https://github.com/galaxyproject/galaxy/commit/f34e6a1e2e182c10a36172d63740… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: A config/plugins/interactive_environments/askomics/config/allowed_images.yml.sample A config/plugins/interactive_environments/askomics/config/askomics.ini.sample A config/plugins/interactive_environments/askomics/config/askomics.xml A config/plugins/interactive_environments/askomics/static/js/askomics.js A config/plugins/interactive_environments/askomics/templates/askomics.mako Log Message: ----------- Merge pull request #4737 from xgaia/askomics-ie AskOmics Interactive Environment Compare: https://github.com/galaxyproject/galaxy/compare/e27a16953d5f...f34e6a1e2e18

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[galaxyproject/galaxy] 140a0a: Add DELETE /api/jobs/<job_id> as a job cancellatio...
by GitHub 15 Nov '17

15 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 140a0a49d3af5f5d6ffaa50cc0cac5b5f4cd1bcc https://github.com/galaxyproject/galaxy/commit/140a0a49d3af5f5d6ffaa50cc0ca… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-08 (Wed, 08 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/base/populators.py A test/functional/tools/cat_data_and_sleep.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigates_galaxy.py A test/integration/test_local_job_cancellation.py Log Message: ----------- Add DELETE /api/jobs/<job_id> as a job cancellation API endpoint. Commit: e27a16953d5faadbfa8d2be1e0a09afe4bd7df87 https://github.com/galaxyproject/galaxy/commit/e27a16953d5faadbfa8d2be1e0a0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/base/populators.py A test/functional/tools/cat_data_and_sleep.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigates_galaxy.py A test/integration/test_local_job_cancellation.py Log Message: ----------- Merge pull request #4961 from jmchilton/job_delete_api Add DELETE /api/jobs/<job_id> as a job cancellation API endpoint. Compare: https://github.com/galaxyproject/galaxy/compare/bbd96c435b86...e27a16953d5f

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[galaxyproject/galaxy] a1e912: If installing dev dependencies, do so along side r...
by GitHub 15 Nov '17

15 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a1e91231aa5dba34c10f039446177d0f55871623 https://github.com/galaxyproject/galaxy/commit/a1e91231aa5dba34c10f03944617… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-02 (Thu, 02 Nov 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M scripts/common_startup.sh Log Message: ----------- If installing dev dependencies, do so along side regular dependencies. Catch conflicts and works faster. Commit: bbd96c435b866a2cab7299fadf0687d7e2c99e3e https://github.com/galaxyproject/galaxy/commit/bbd96c435b866a2cab7299fadf06… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M scripts/common_startup.sh Log Message: ----------- Merge pull request #4903 from jmchilton/dev_at_same_time Install dev and regular dependencies at the same time. Compare: https://github.com/galaxyproject/galaxy/compare/54c6a794e9c6...bbd96c435b86

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[galaxyproject/galaxy] 0a6c29: Add missing ipaddress requirement
by GitHub 15 Nov '17

15 Nov '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 0a6c2974204b3048456bc7ceba7793ab4774de9f https://github.com/galaxyproject/galaxy/commit/0a6c2974204b3048456bc7ceba77… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Add missing ipaddress requirement Broken in https://github.com/galaxyproject/galaxy/pull/4289 . Fix https://github.com/galaxyproject/galaxy/issues/4999 . Commit: 18467e9b2cecb2102d17fd6734f1fb40c5321623 https://github.com/galaxyproject/galaxy/commit/18467e9b2cecb2102d17fd6734f1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Merge pull request #5000 from nsoranzo/release_17.09_add_ipaddress_requirement [17.09] Add missing ipaddress requirement Compare: https://github.com/galaxyproject/galaxy/compare/b25de8b00316...18467e9b2cec

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[galaxyproject/galaxy] 6c32ed: start writing tests for TDT
by GitHub 15 Nov '17

15 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6c32edebc1b36136759a055fe3032d51a24f1f68 https://github.com/galaxyproject/galaxy/commit/6c32edebc1b36136759a055fe303… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) 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 A test/selenium_tests/test_tool_describing_tours.py Log Message: ----------- start writing tests for TDT Commit: 7431cb13123f091fc13d5cb2b2756a4bd0726d1f https://github.com/galaxyproject/galaxy/commit/7431cb13123f091fc13d5cb2b275… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- fix TDT's dependency Commit: b0973391640248f29765bacdc0ff0faf68db5f52 https://github.com/galaxyproject/galaxy/commit/b0973391640248f29765bacdc0ff… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M test/selenium_tests/test_tool_describing_tours.py Log Message: ----------- test successful tour generation Commit: 9d646c605cbab0c59e34379818e2e63f7269e5b6 https://github.com/galaxyproject/galaxy/commit/9d646c605cbab0c59e34379818e2… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M test/selenium_tests/test_tool_describing_tours.py Log Message: ----------- improve the test Commit: 323e1ad64e9f3fa75c32a283b82694474d49ceb0 https://github.com/galaxyproject/galaxy/commit/323e1ad64e9f3fa75c32a283b826… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M .ci/flake8_lint_include_list.txt R .ci/flake8_py3_wrapper.sh M .ci/jenkins/selenium/Dockerfile M .ci/jenkins/selenium/docker-compose.yml M .ci/jenkins/selenium/galaxy.ini M .ci/jenkins/selenium/run_galaxy.bash M .ci/jenkins/selenium/run_tests.sh M .ci/py3_sources.txt A .ci/tox_envs/flake8/Pipfile A .ci/tox_envs/flake8/requirements.txt A .ci/tox_envs/flake8_imports/Pipfile A .ci/tox_envs/flake8_imports/requirements.txt A .ci/tox_envs/update.sh M .gitignore M .travis.yml M CITATION M Makefile A client/.babelrc M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/login.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/i18n.js M client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.js R client/galaxy/scripts/libs/backbone.js R client/galaxy/scripts/libs/bibtex.js R client/galaxy/scripts/libs/d3.js R client/galaxy/scripts/libs/jquery.complexify.js R client/galaxy/scripts/libs/jquery/jquery.cookie.js R client/galaxy/scripts/libs/jquery/jquery.js R client/galaxy/scripts/libs/jquery/jquery.migrate.js R client/galaxy/scripts/libs/jquery/jquery.mousewheel.js R client/galaxy/scripts/libs/raven.js R client/galaxy/scripts/libs/require.js R client/galaxy/scripts/libs/underscore.js M client/galaxy/scripts/mvc/annotation.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-list.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/dataset/states.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hda-model.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-preferences.js M client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/job-dag.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/job/job-li.js M client/galaxy/scripts/mvc/job/job-model.js M client/galaxy/scripts/mvc/job/job-params.js A client/galaxy/scripts/mvc/lazy/lazy-limited.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js A client/galaxy/scripts/mvc/library/library-util.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repo-queue-view.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/toolshed-model.js M client/galaxy/scripts/mvc/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/error-modal.js M client/galaxy/scripts/mvc/ui/icon-button.js M client/galaxy/scripts/mvc/ui/popup-menu.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M 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test/qunit/tests/upload_dialog_tests.js M test/qunit/tests/utils_test.js M test/qunit/tests/workflow_editor_tests.js M test/selenium_tests/framework.py M test/selenium_tests/test_anon_history.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_custom_builds.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_options.py M test/selenium_tests/test_history_panel.py M test/selenium_tests/test_history_sharing.py A test/selenium_tests/test_jupyter.py A test/selenium_tests/test_library_contents.py A test/selenium_tests/test_library_landing.py M test/selenium_tests/test_login.py A test/selenium_tests/test_navigates_galaxy.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_registration.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_sizzle_loading.py M test/selenium_tests/test_stock_tours.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py 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tools/data_source/import.py M tools/data_source/microbial_import.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/evolution/codingSnps_filter.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/extract/liftOver_wrapper.xml M tools/filters/axt_to_lav.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_to_bed_converter.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/sff_extract.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_exon_bed.xml M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/genomespace/genomespace_importer.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_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/vcf_to_maf_customtrack.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/solid2fastq.py M tools/plotting/bar_chart.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/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tox.ini Log Message: ----------- Merge branch 'dev' into tdt_tests # Conflicts: # client/galaxy/scripts/mvc/tool/tool-form-base.js # static/maps/mvc/tool/tool-form-base.js.map # static/scripts/bundled/analysis.bundled.js # static/scripts/bundled/analysis.bundled.js.map # static/scripts/bundled/libs.bundled.js.map # static/scripts/mvc/tool/tool-form-base.js Commit: f419c85955dc9885ef09f77db7e10e5145ef99fd https://github.com/galaxyproject/galaxy/commit/f419c85955dc9885ef09f77db7e1… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-11-01 (Wed, 01 Nov 2017) 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 M test/selenium_tests/test_tool_describing_tours.py Log Message: ----------- add test for TDT Commit: c52ebfca26710b8c9883bbfdba04187d53295427 https://github.com/galaxyproject/galaxy/commit/c52ebfca26710b8c9883bbfdba04… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: A test/functional/webhooks/tour_generator M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_tool_describing_tours.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Improvements for tour generator Selenium tests. - Replace test using Cut1 with two tests each using framework test tools loaded with Selenium tests by default. - Create a symbolic link so that tour generator is configured with default test webhooks. - Establish and use components and navigates_galaxy.py abstractions for tour generation and navigation. - In one of the tool tests actually walk the tour (previously we only verified the initial tour popover). Commit: cecef90915abf0383aed8b56deb4ec237ca9a712 https://github.com/galaxyproject/galaxy/commit/cecef90915abf0383aed8b56deb4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: R .ci/flake8_lint_include_list.txt R .ci/flake8_wrapper_imports.sh A .ci/jenkins/selenium-compose/Dockerfile A .ci/jenkins/selenium-compose/docker-compose.yml A .ci/jenkins/selenium-compose/galaxy.ini A .ci/jenkins/selenium-compose/run_galaxy.bash A .ci/jenkins/selenium-compose/run_tests.sh R .ci/jenkins/selenium/Dockerfile R .ci/jenkins/selenium/docker-compose.yml R .ci/jenkins/selenium/galaxy.ini R .ci/jenkins/selenium/run_galaxy.bash M .ci/jenkins/selenium/run_tests.sh R .ci/tox_envs/flake8/Pipfile R .ci/tox_envs/flake8/requirements.txt R .ci/tox_envs/flake8_imports/Pipfile R .ci/tox_envs/flake8_imports/requirements.txt R .ci/tox_envs/update.sh M .travis.yml M Makefile M README.rst M client/.babelrc M client/galaxy/scripts/admin.toolshed.js M 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client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M 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templates/webapps/galaxy/library/common/library_item_info.mako R templates/webapps/galaxy/library/common/library_permissions.mako R templates/webapps/galaxy/library/common/move_library_item.mako R templates/webapps/galaxy/library/common/new_folder.mako R templates/webapps/galaxy/library/common/upload.mako R templates/webapps/galaxy/library/grid.mako R templates/webapps/galaxy/library/index.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/phyloviz.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/group/index.mako M test/api/test_dataset_collections.py M test/api/test_history_contents.py M test/api/test_jobs.py M test/api/test_page_revisions.py M test/api/test_tools_upload.py M test/base/driver_util.py M test/base/integration_util.py M test/base/populators.py M test/base/testcase.py M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh A test/docker/base/selenium/LICENSE A test/docker/base/selenium/README A test/docker/base/selenium/entry_point.sh A test/docker/base/selenium/functions.sh A test/docker/base/selenium/generate_config A test/docker/base/selenium/wrap_chrome_binary M test/functional/test_toolbox.py M test/galaxy_selenium/components.py M test/galaxy_selenium/data.py M test/galaxy_selenium/driver_factory.py M test/galaxy_selenium/navigates_galaxy.py M test/manual/workflows_scaling.py M test/qunit/test-app.js M test/qunit/tests/form_tests.js M test/qunit/tests/galaxy-app-base.js M test/qunit/tests/graph.js M test/qunit/tests/hda-base.js M test/qunit/tests/history_contents_model_tests.js M test/qunit/tests/job-dag.js M test/qunit/tests/list-of-pairs-collection-creator.js M test/qunit/tests/masthead_tests.js M test/qunit/tests/metrics-logger.js M test/qunit/tests/modal_tests.js M test/qunit/tests/page_tests.js M test/qunit/tests/popover_tests.js M test/qunit/tests/ui_tests.js M test/qunit/tests/upload_dialog_tests.js M test/qunit/tests/utils_test.js M test/qunit/tests/workflow_editor_tests.js M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_library_contents.py M test/selenium_tests/test_library_landing.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_stock_tours.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py M test/shed_functional/base/twilltestcase.py M test/unit/config/1607_root_filters/config/galaxy.ini M test/unit/config/1607_root_samples/config/galaxy.ini 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_job_wrapper.py M test/unit/jobs/test_mapper.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_installed_repository_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_objectstore.py M test/unit/tools/test_actions.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_parsing.py M test/unit/tools/test_select_parameters.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_watcher.py M test/unit/tools_support.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.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 tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/phenotype_association/senatag.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into tdt_tests Commit: 9273d7a1c73df1aeb2271dcad6495d1b6fd4f036 https://github.com/galaxyproject/galaxy/commit/9273d7a1c73df1aeb2271dcad649… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M test/selenium_tests/test_tool_describing_tours.py Log Message: ----------- Add screenshots for TDT Selenium tests. Commit: fb91302458f1ab8c1d8dbd59ef0d7ebf29932536 https://github.com/galaxyproject/galaxy/commit/fb91302458f1ab8c1d8dbd59ef0d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- Fix TDT fors ES6 module switchover. Commit: 54c6a794e9c6c3b5e51990875516e026cbac94c0 https://github.com/galaxyproject/galaxy/commit/54c6a794e9c6c3b5e51990875516… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M config/plugins/webhooks/demo/tour_generator/static/script.js M static/maps/mvc/tool/tool-form-base.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 A test/functional/webhooks/tour_generator M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml A test/selenium_tests/test_tool_describing_tours.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Merge pull request #4909 from anatskiy/tdt_tests Selenium test for Tool-Describing-Tours Compare: https://github.com/galaxyproject/galaxy/compare/a12b50c08ecf...54c6a794e9c6

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[galaxyproject/galaxy] b4e041: Removed unneeded skip_install tags in tox.ini.
by GitHub 15 Nov '17

15 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b4e041d14d4b036c0c6fac3565e92f265d62f079 https://github.com/galaxyproject/galaxy/commit/b4e041d14d4b036c0c6fac3565e9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M tox.ini Log Message: ----------- Removed unneeded skip_install tags in tox.ini. Alternative to #4995 thanks to @nsoranzo's detective work. Commit: a12b50c08ecffa383f97342ae53f874be20aff56 https://github.com/galaxyproject/galaxy/commit/a12b50c08ecffa383f97342ae53f… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M tox.ini Log Message: ----------- Merge pull request #5011 from jmchilton/remove_skip_install_tox Removed unneeded skip_install tags in tox.ini. Compare: https://github.com/galaxyproject/galaxy/compare/482ff776e596...a12b50c08ecf

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[galaxyproject/galaxy] 68a83c: dataset info: present decoded IDs for admins and a...
by GitHub 14 Nov '17

14 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 68a83ce08395fabf9c388fd0d8fa84cd4ba85e85 https://github.com/galaxyproject/galaxy/commit/68a83ce08395fabf9c388fd0d8fa… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M templates/show_params.mako Log Message: ----------- dataset info: present decoded IDs for admins and add peek Commit: 482ff776e59612a5130e8af45661e514764bb0b5 https://github.com/galaxyproject/galaxy/commit/482ff776e59612a5130e8af45661… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M templates/show_params.mako Log Message: ----------- Merge pull request #5006 from martenson/decode_for_admins dataset info: present decoded IDs for admins and add peek Compare: https://github.com/galaxyproject/galaxy/compare/39bd5c6a194a...482ff776e596

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[galaxyproject/galaxy] 63f039: remove the default override
by GitHub 14 Nov '17

14 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 63f039b66fef6448f10ea639f2be5fb376cca05e https://github.com/galaxyproject/galaxy/commit/63f039b66fef6448f10ea639f2be… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- remove the default override since it is wrong and ignores the access permissions Commit: 9a13a4af7fe44f6482b075bba6cf3fc500226956 https://github.com/galaxyproject/galaxy/commit/9a13a4af7fe44f6482b075bba6cf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Merge pull request #5008 from martenson/fix-ldda-access-check [16.07] history contents api - remove the default flag override Commit: 4a2814227cd7509ee62a8f5a64190934b4169ae9 https://github.com/galaxyproject/galaxy/commit/4a2814227cd7509ee62a8f5a6419… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.07' into HEAD Commit: 54b9b09fb2d232b53fa9430606040060d6b21a4e https://github.com/galaxyproject/galaxy/commit/54b9b09fb2d232b53fa943060604… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.10' into HEAD Commit: eab30c96522a5a558de4232320c87c1ef102d2d2 https://github.com/galaxyproject/galaxy/commit/eab30c96522a5a558de4232320c8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.01' into release_17.05 Commit: b25de8b003168ebced8fbc3bfce5274d32cc1ab7 https://github.com/galaxyproject/galaxy/commit/b25de8b003168ebced8fbc3bfce5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.05' into HEAD Commit: 39bd5c6a194ac15b155514ea3ea0f06073dd9d5a https://github.com/galaxyproject/galaxy/commit/39bd5c6a194ac15b155514ea3ea0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Merge branch 'release_17.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/7c1afa8f16b6...39bd5c6a194a

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[galaxyproject/galaxy] 63f039: remove the default override
by GitHub 14 Nov '17

14 Nov '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 63f039b66fef6448f10ea639f2be5fb376cca05e https://github.com/galaxyproject/galaxy/commit/63f039b66fef6448f10ea639f2be… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- remove the default override since it is wrong and ignores the access permissions Commit: 9a13a4af7fe44f6482b075bba6cf3fc500226956 https://github.com/galaxyproject/galaxy/commit/9a13a4af7fe44f6482b075bba6cf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Merge pull request #5008 from martenson/fix-ldda-access-check [16.07] history contents api - remove the default flag override Commit: 4a2814227cd7509ee62a8f5a64190934b4169ae9 https://github.com/galaxyproject/galaxy/commit/4a2814227cd7509ee62a8f5a6419… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.07' into HEAD Commit: 54b9b09fb2d232b53fa9430606040060d6b21a4e https://github.com/galaxyproject/galaxy/commit/54b9b09fb2d232b53fa943060604… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.10' into HEAD Commit: eab30c96522a5a558de4232320c87c1ef102d2d2 https://github.com/galaxyproject/galaxy/commit/eab30c96522a5a558de4232320c8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.01' into release_17.05 Commit: b25de8b003168ebced8fbc3bfce5274d32cc1ab7 https://github.com/galaxyproject/galaxy/commit/b25de8b003168ebced8fbc3bfce5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.05' into HEAD Compare: https://github.com/galaxyproject/galaxy/compare/1a412bfb1b04...b25de8b00316

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[galaxyproject/galaxy] 63f039: remove the default override
by GitHub 14 Nov '17

14 Nov '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 63f039b66fef6448f10ea639f2be5fb376cca05e https://github.com/galaxyproject/galaxy/commit/63f039b66fef6448f10ea639f2be… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- remove the default override since it is wrong and ignores the access permissions Commit: 9a13a4af7fe44f6482b075bba6cf3fc500226956 https://github.com/galaxyproject/galaxy/commit/9a13a4af7fe44f6482b075bba6cf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Merge pull request #5008 from martenson/fix-ldda-access-check [16.07] history contents api - remove the default flag override Commit: 4a2814227cd7509ee62a8f5a64190934b4169ae9 https://github.com/galaxyproject/galaxy/commit/4a2814227cd7509ee62a8f5a6419… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.07' into HEAD Commit: 54b9b09fb2d232b53fa9430606040060d6b21a4e https://github.com/galaxyproject/galaxy/commit/54b9b09fb2d232b53fa943060604… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.10' into HEAD Commit: eab30c96522a5a558de4232320c87c1ef102d2d2 https://github.com/galaxyproject/galaxy/commit/eab30c96522a5a558de4232320c8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.01' into release_17.05 Compare: https://github.com/galaxyproject/galaxy/compare/e5587dcb6489...eab30c96522a

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[galaxyproject/galaxy] 63f039: remove the default override
by GitHub 14 Nov '17

14 Nov '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 63f039b66fef6448f10ea639f2be5fb376cca05e https://github.com/galaxyproject/galaxy/commit/63f039b66fef6448f10ea639f2be… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- remove the default override since it is wrong and ignores the access permissions Commit: 9a13a4af7fe44f6482b075bba6cf3fc500226956 https://github.com/galaxyproject/galaxy/commit/9a13a4af7fe44f6482b075bba6cf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Merge pull request #5008 from martenson/fix-ldda-access-check [16.07] history contents api - remove the default flag override Commit: 4a2814227cd7509ee62a8f5a64190934b4169ae9 https://github.com/galaxyproject/galaxy/commit/4a2814227cd7509ee62a8f5a6419… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.07' into HEAD Commit: 54b9b09fb2d232b53fa9430606040060d6b21a4e https://github.com/galaxyproject/galaxy/commit/54b9b09fb2d232b53fa943060604… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.10' into HEAD Compare: https://github.com/galaxyproject/galaxy/compare/c7b09f870d31...54b9b09fb2d2

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[galaxyproject/galaxy] 63f039: remove the default override
by GitHub 14 Nov '17

14 Nov '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 63f039b66fef6448f10ea639f2be5fb376cca05e https://github.com/galaxyproject/galaxy/commit/63f039b66fef6448f10ea639f2be… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- remove the default override since it is wrong and ignores the access permissions Commit: 9a13a4af7fe44f6482b075bba6cf3fc500226956 https://github.com/galaxyproject/galaxy/commit/9a13a4af7fe44f6482b075bba6cf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Merge pull request #5008 from martenson/fix-ldda-access-check [16.07] history contents api - remove the default flag override Commit: 4a2814227cd7509ee62a8f5a64190934b4169ae9 https://github.com/galaxyproject/galaxy/commit/4a2814227cd7509ee62a8f5a6419… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.07' into HEAD Compare: https://github.com/galaxyproject/galaxy/compare/7bf2bbfa4050...4a2814227cd7

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[galaxyproject/galaxy] 63f039: remove the default override
by GitHub 14 Nov '17

14 Nov '17

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 63f039b66fef6448f10ea639f2be5fb376cca05e https://github.com/galaxyproject/galaxy/commit/63f039b66fef6448f10ea639f2be… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- remove the default override since it is wrong and ignores the access permissions Commit: 9a13a4af7fe44f6482b075bba6cf3fc500226956 https://github.com/galaxyproject/galaxy/commit/9a13a4af7fe44f6482b075bba6cf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Merge pull request #5008 from martenson/fix-ldda-access-check [16.07] history contents api - remove the default flag override Compare: https://github.com/galaxyproject/galaxy/compare/e3e28ddc2dac...9a13a4af7fe4

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[galaxyproject/galaxy] 2cd95c: Fix import order everywhere
by GitHub 14 Nov '17

14 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2cd95c48f6dabfe79ec9a5c440bff8cfc29c68df https://github.com/galaxyproject/galaxy/commit/2cd95c48f6dabfe79ec9a5c440bf… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: R .ci/flake8_lint_include_list.txt R .ci/flake8_wrapper_imports.sh M .travis.yml M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/registry.py M lib/galaxy/dataset_collections/types/list.py M lib/galaxy/dataset_collections/types/paired.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/dependencies/pipfiles/flake8/Pipfile M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock M lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt R lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile R lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile.lock R lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-hashed-requirements.txt R lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh M lib/galaxy/external_services/actions.py M lib/galaxy/external_services/service.py M lib/galaxy/forms/forms.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/jobs/runners/util/__init__.py M lib/galaxy/jobs/splitters/multi.py M lib/galaxy/managers/citations.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/managers/library_datasets.py M lib/galaxy/managers/pages.py M lib/galaxy/managers/ratable.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/roles.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/users.py M lib/galaxy/managers/visualizations.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/migrate/check.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/pithos.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/openid/providers.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py M lib/galaxy/sample_tracking/request_types.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/mulled/mulled_build.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/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/error_reports/plugins/biostars.py M lib/galaxy/tools/error_reports/plugins/email.py M lib/galaxy/tools/error_reports/plugins/github.py M lib/galaxy/tools/error_reports/plugins/influxdb.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/locations/__init__.py M lib/galaxy/tools/locations/dockstore.py M lib/galaxy/tools/locations/http.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.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/lineages/interface.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/util/biostar.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/submodules.py M lib/galaxy/util/xml_macros.py M lib/galaxy/visualization/data_providers/phyloviz/__init__.py M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py M lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py M lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py M lib/galaxy/visualization/data_providers/registry.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/formbuilder.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/annotations.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/dataset_collections.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/extended_metadata.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/forms.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/item_tags.py M lib/galaxy/webapps/galaxy/api/job_files.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/metrics.py M lib/galaxy/webapps/galaxy/api/page_revisions.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/api/provenance.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/search.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/biostar.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/reports/controllers/history.py M lib/galaxy/webapps/reports/controllers/home.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/root.py M lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/galaxy/webapps/tool_shed/api/authenticate.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/configuration.py M lib/galaxy/webapps/tool_shed/api/groups.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/api/users.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/controllers/user.py M lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/galaxy/webapps/tool_shed/util/hgweb_config.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/schedulers/core.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/repository_types/registry.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/utility_containers/__init__.py M scripts/functional_tests.py M test/api/test_jobs.py M test/api/test_page_revisions.py M test/base/driver_util.py M test/base/testcase.py M test/functional/test_toolbox.py M test/galaxy_selenium/components.py M test/galaxy_selenium/data.py M test/galaxy_selenium/navigates_galaxy.py M test/manual/workflows_scaling.py M test/selenium_tests/test_stock_tours.py M test/shed_functional/base/twilltestcase.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_job_wrapper.py M test/unit/jobs/test_mapper.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_installed_repository_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_objectstore.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.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_parsing.py M test/unit/tools/test_select_parameters.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_watcher.py M test/unit/tools_support.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.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 tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/phenotype_association/senatag.py M tox.ini Log Message: ----------- Fix import order everywhere - Add flake8-import-order to flake8 Pipfile and remove py27-lint-imports and py27-lint-imports-include-list tox envs - Fix most E201 and E202 errors reported by flake8-import-order v0.15, but pin flake8-import-order to v0.14.3 until https://github.com/PyCQA/flake8-import-order/issues/123 is fixed This let us drop 2 jobs on Travis per each job. Commit: 7c1afa8f16b68fcb8948c760862d4beb68187118 https://github.com/galaxyproject/galaxy/commit/7c1afa8f16b68fcb8948c760862d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: R .ci/flake8_lint_include_list.txt R .ci/flake8_wrapper_imports.sh M .travis.yml M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/registry.py M lib/galaxy/dataset_collections/types/list.py M lib/galaxy/dataset_collections/types/paired.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/dependencies/pipfiles/flake8/Pipfile M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock M lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt R lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile R lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile.lock R lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-hashed-requirements.txt R lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh M lib/galaxy/external_services/actions.py M lib/galaxy/external_services/service.py M lib/galaxy/forms/forms.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/jobs/runners/util/__init__.py M lib/galaxy/jobs/splitters/multi.py M lib/galaxy/managers/citations.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/managers/library_datasets.py M lib/galaxy/managers/pages.py M lib/galaxy/managers/ratable.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/roles.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/users.py M lib/galaxy/managers/visualizations.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/migrate/check.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/pithos.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/openid/providers.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py M lib/galaxy/sample_tracking/request_types.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/mulled/mulled_build.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/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/error_reports/plugins/biostars.py M lib/galaxy/tools/error_reports/plugins/email.py M lib/galaxy/tools/error_reports/plugins/github.py M lib/galaxy/tools/error_reports/plugins/influxdb.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/locations/__init__.py M lib/galaxy/tools/locations/dockstore.py M lib/galaxy/tools/locations/http.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.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/lineages/interface.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/util/biostar.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/submodules.py M lib/galaxy/util/xml_macros.py M lib/galaxy/visualization/data_providers/phyloviz/__init__.py M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py M lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py M lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py M lib/galaxy/visualization/data_providers/registry.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/formbuilder.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/annotations.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/dataset_collections.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/extended_metadata.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/forms.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/item_tags.py M lib/galaxy/webapps/galaxy/api/job_files.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/metrics.py M lib/galaxy/webapps/galaxy/api/page_revisions.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/api/provenance.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/search.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/biostar.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/reports/controllers/history.py M lib/galaxy/webapps/reports/controllers/home.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/root.py M lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/galaxy/webapps/tool_shed/api/authenticate.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/configuration.py M lib/galaxy/webapps/tool_shed/api/groups.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/api/users.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/controllers/user.py M lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/galaxy/webapps/tool_shed/util/hgweb_config.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/schedulers/core.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/repository_types/registry.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/utility_containers/__init__.py M scripts/functional_tests.py M test/api/test_jobs.py M test/api/test_page_revisions.py M test/base/driver_util.py M test/base/testcase.py M test/functional/test_toolbox.py M test/galaxy_selenium/components.py M test/galaxy_selenium/data.py M test/galaxy_selenium/navigates_galaxy.py M test/manual/workflows_scaling.py M test/selenium_tests/test_stock_tours.py M test/shed_functional/base/twilltestcase.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_job_wrapper.py M test/unit/jobs/test_mapper.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_installed_repository_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_objectstore.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.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_parsing.py M test/unit/tools/test_select_parameters.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_watcher.py M test/unit/tools_support.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.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 tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/phenotype_association/senatag.py M tox.ini Log Message: ----------- Merge pull request #5005 from nsoranzo/flake8-import-order Fix import order everywhere Compare: https://github.com/galaxyproject/galaxy/compare/f86dd647da54...7c1afa8f16b6

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[galaxyproject/galaxy] df117b: Add warning for sort-of-defunct workflow options.
by GitHub 14 Nov '17

14 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: df117b86f2edd9dcc1f6c09c9c6cfa1a5ff48c9e https://github.com/galaxyproject/galaxy/commit/df117b86f2edd9dcc1f6c09c9c6c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Add warning for sort-of-defunct workflow options. Commit: f86dd647da54d524f5a9a840de7b66c355954078 https://github.com/galaxyproject/galaxy/commit/f86dd647da54d524f5a9a840de7b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Merge pull request #5002 from jmchilton/beta_workflow_options Add warning for sort-of-defunct workflow options in galaxy.ini. Compare: https://github.com/galaxyproject/galaxy/compare/61fda75d1f22...f86dd647da54

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[galaxyproject/galaxy] 241a22: Random ES6-ing of files working on in collection_s...
by GitHub 14 Nov '17

14 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 241a2229f42fb6f64b50a1dd5238f79ec3aa40fa https://github.com/galaxyproject/galaxy/commit/241a2229f42fb6f64b50a1dd5238… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js A client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js Log Message: ----------- Random ES6-ing of files working on in collection_state branch downstream. A few of these actually bump into things I'm touching, a few of these are just me exploring ES6 and cleaning up the code a bit. Commit: 53cbbeefca74f64699cad2cc935a5c8a319dfc45 https://github.com/galaxyproject/galaxy/commit/53cbbeefca74f64699cad2cc935a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map A static/maps/mvc/history/history-item-li.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/collection/collection-model.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js A static/scripts/mvc/history/history-item-li.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js Log Message: ----------- Rebuild client. Commit: 61fda75d1f22654417ab66a7896da834d607c28c https://github.com/galaxyproject/galaxy/commit/61fda75d1f22654417ab66a7896d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js A client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map A static/maps/mvc/history/history-item-li.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/collection/collection-model.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js A static/scripts/mvc/history/history-item-li.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js Log Message: ----------- Merge pull request #5001 from jmchilton/es6_collections_2 ES6 refactoring of files touched in collection_state branch. Compare: https://github.com/galaxyproject/galaxy/compare/049b3550f773...61fda75d1f22

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[galaxyproject/galaxy] 062ab4: Remove extraneous subclass for DMND datatype
by GitHub 14 Nov '17

14 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 062ab412b20b245f80a17b673aa0451e08b8ca56 https://github.com/galaxyproject/galaxy/commit/062ab412b20b245f80a17b673aa0… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Remove extraneous subclass for DMND datatype Commit: 049b3550f773b403847d0cbdeef347cbc231e0a8 https://github.com/galaxyproject/galaxy/commit/049b3550f773b403847d0cbdeef3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #4990 from nsoranzo/fix_dmnd_datatype Remove extraneous subclass for DMND datatype Compare: https://github.com/galaxyproject/galaxy/compare/fb78cb6be3fa...049b3550f773

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[galaxyproject/galaxy] c0a3e6: Update imports for galaxy.util.path moves
by GitHub 14 Nov '17

14 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c0a3e6c12a32f0e2fc1c657493a9a2ad3e515b03 https://github.com/galaxyproject/galaxy/commit/c0a3e6c12a32f0e2fc1c657493a9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/pithos.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Update imports for galaxy.util.path moves Commit: ae720d6f4cea03268e8303454088c89c4849cf41 https://github.com/galaxyproject/galaxy/commit/ae720d6f4cea03268e8303454088… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Log a more useful error message when tool loading fails due to IOError/OSError or a nonexistent tool config. Commit: f8e59b922a8bad9f1ca0b6b62eae6707144e4456 https://github.com/galaxyproject/galaxy/commit/f8e59b922a8bad9f1ca0b6b62eae… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Improve util.listify documentation and allow it to accept tuples Commit: f5ee540df102526219f8347bbcb7217fbb704b11 https://github.com/galaxyproject/galaxy/commit/f5ee540df102526219f8347bbcb7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: A lib/galaxy/util/script.py M scripts/manage_tool_dependencies.py Log Message: ----------- To avoid duplication, move common utilities used by external scripts to galaxy.util.script. Update one such script to use the new module. Commit: eed12ad15c9bd3f5ba9122826e5f6be0e8a4e615 https://github.com/galaxyproject/galaxy/commit/eed12ad15c9bd3f5ba9122826e5f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Docstring fixes Commit: fb78cb6be3fa6e7debb6ac4e5e528322571afd03 https://github.com/galaxyproject/galaxy/commit/fb78cb6be3fa6e7debb6ac4e5e52… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/pithos.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py A lib/galaxy/util/script.py M lib/tool_shed/capsule/capsule_manager.py M scripts/manage_tool_dependencies.py Log Message: ----------- Merge pull request #4994 from natefoo/non-mule-changes Changes made while working on uWSGI mules that don't belong in the mules PR Compare: https://github.com/galaxyproject/galaxy/compare/95c297c5560c...fb78cb6be3fa

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[galaxyproject/infrastructure-playbook] f54bfe: Redirect training.galaxyproject.org ->
by GitHub 14 Nov '17

14 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: f54bfe05fd383af1439e84f31c4afcc27752b231 https://github.com/galaxyproject/infrastructure-playbook/commit/f54bfe05fd3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M galaxyenv/templates/nginx/training.j2 Log Message: ----------- Redirect training.galaxyproject.org -> galaxyproject.github.io/training-material with the $request_uri appended (previously all pages redirected to the training root).

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[galaxyproject/galaxy] 538d63: Remove unused galaxy-side set_tool_version code
by GitHub 13 Nov '17

13 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 538d63a8c6b9d5ad138ba377808c8f32e4fae5c9 https://github.com/galaxyproject/galaxy/commit/538d63a8c6b9d5ad138ba377808c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-12 (Sun, 12 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/tools/tool_version_manager.py M templates/admin/tool_shed_repository/repository_actions_menu.mako M templates/admin/tool_shed_repository/view_tool_metadata.mako M test/unit/shed_unit/test_tool_panel_manager.py Log Message: ----------- Remove unused galaxy-side set_tool_version code This is all unnecessary or handled by the tool lineage. Commit: 95c297c5560c50f1cb9992c630193c3d06392ba9 https://github.com/galaxyproject/galaxy/commit/95c297c5560c50f1cb9992c63019… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/tools/tool_version_manager.py M templates/admin/tool_shed_repository/repository_actions_menu.mako M templates/admin/tool_shed_repository/view_tool_metadata.mako M test/unit/shed_unit/test_tool_panel_manager.py Log Message: ----------- Merge pull request #4986 from mvdbeek/remove_galaxy_set_tool_versions Remove unused galaxy-side set_tool_version code Compare: https://github.com/galaxyproject/galaxy/compare/9d9c323f735f...95c297c5560c

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[galaxyproject/galaxy] 80ba1c: Fix allow-register option in auth module
by GitHub 13 Nov '17

13 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 80ba1c07bf614f8d116249ed904f61cd43bbaa35 https://github.com/galaxyproject/galaxy/commit/80ba1c07bf614f8d116249ed904f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/pam_auth.py Log Message: ----------- Fix allow-register option in auth module config/auth_conf.xml.sample specifies that the possible values are True, False and Challenge. Broken in commit b3174efa8e2996dc8e05e85d563e546cc66e2848 . Also remove _get_bool(d, k, o) function in favour of the more explicit `string_as_bool(d.get(k, o))` . Commit: 9d9c323f735faca44d70eee817f87f17146b9ec6 https://github.com/galaxyproject/galaxy/commit/9d9c323f735faca44d70eee817f8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/pam_auth.py Log Message: ----------- Merge pull request #4989 from nsoranzo/fix_allow-register Fix allow-register option in auth module Compare: https://github.com/galaxyproject/galaxy/compare/148e91f5b711...9d9c323f735f

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[galaxyproject/galaxy] aa640f: Fix tox envlist to contain all envs that should pa...
by GitHub 13 Nov '17

13 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aa640f493d3fc7f709607c7c4777f9957b2f6ff9 https://github.com/galaxyproject/galaxy/commit/aa640f493d3fc7f709607c7c4777… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M tox.ini Log Message: ----------- Fix tox envlist to contain all envs that should pass Now simply running: ``` $ tox ``` is the equivalent of running all the Travis jobs that are not in the `allow_failures` list. Also: - remove py33-lint env - sort envs alphabetically Commit: 148e91f5b71121a203a82c33bf20a34102ec4277 https://github.com/galaxyproject/galaxy/commit/148e91f5b71121a203a82c33bf20… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M tox.ini Log Message: ----------- Merge pull request #4992 from nsoranzo/fix_tox_envlist Fix tox envlist to contain all envs that should pass Compare: https://github.com/galaxyproject/galaxy/compare/c83a8260fd62...148e91f5b711

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