- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 07a92f: Remove tool_model usage from client
by GitHub 21 Feb '17

21 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 07a92fd3ef084a6d7cbe27199d281e534e35cec1 https://github.com/galaxyproject/galaxy/commit/07a92fd3ef084a6d7cbe27199d28… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-09 (Thu, 09 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M lib/galaxy/webapps/galaxy/api/workflows.py M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/tool/tool-form-workflow.js Log Message: ----------- Remove tool_model usage from client Commit: 171655930aa44227d6b88709aac638dea77a6cd0 https://github.com/galaxyproject/galaxy/commit/171655930aa44227d6b88709aac6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-09 (Thu, 09 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Move populate state to parameter handling module Commit: 3e3eb4d1397effc8b46c913bb80f3c02773ac506 https://github.com/galaxyproject/galaxy/commit/3e3eb4d1397effc8b46c913bb80f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-09 (Thu, 09 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/tool/tool-form-workflow.js Log Message: ----------- Unify build_module handler Commit: 62d42f711e26e0ab176041ce9a552d1af1290f1a https://github.com/galaxyproject/galaxy/commit/62d42f711e26e0ab176041ce9a55… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-09 (Thu, 09 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Parse payload directly to from_dict handler, handle tool specific attributes in corresponding module wrapper Commit: d27e0570cb0b372288114498fa1ad26a1f5df188 https://github.com/galaxyproject/galaxy/commit/d27e0570cb0b372288114498fa1a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/workflow/modules.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Remove name handling field from workflow module forms Commit: 1858e43d46355be344c0fab9e61a2e5a57dc8947 https://github.com/galaxyproject/galaxy/commit/1858e43d46355be344c0fab9e61a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Unify handling/parsing of label and fixed module name to build title in workflow run form Commit: d484355832a1c6518d38326ef4fbb526423c0e34 https://github.com/galaxyproject/galaxy/commit/d484355832a1c6518d38326ef4fb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Provide attributes to front-end, build title on client side Commit: b9f1e29eaf32cda146fea2b102157489a639ea51 https://github.com/galaxyproject/galaxy/commit/b9f1e29eaf32cda146fea2b10215… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Remove redundant label handling from subworkflows Commit: 7ac954f757d2485ae7543db15f400dca0b94fdf3 https://github.com/galaxyproject/galaxy/commit/7ac954f757d2485ae7543db15f40… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/util/workflow_util.py Log Message: ----------- Strip name handler Commit: 11f9e1863f9616d58fc00a22526f71b2bca7b880 https://github.com/galaxyproject/galaxy/commit/11f9e1863f9616d58fc00a22526f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix label and annotation handling for subworkflows Commit: c6c210a4fa47d0fc47306d30b9dbf40589f68cd8 https://github.com/galaxyproject/galaxy/commit/c6c210a4fa47d0fc47306d30b9db… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M lib/galaxy/workflow/run_request.py Log Message: ----------- Remove uncommented code block from request builder Commit: eb95131ab3a03a3675c3e6d6db23caca524b3da6 https://github.com/galaxyproject/galaxy/commit/eb95131ab3a03a3675c3e6d6db23… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Export label instead of name for description export Commit: d298c1c0da5871105898166ca72dd224f7897fc6 https://github.com/galaxyproject/galaxy/commit/d298c1c0da5871105898166ca72d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-11 (Sat, 11 Feb 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Fix lint issues Commit: 047c833db79fef8daa25ddf022f85d2ef9386d63 https://github.com/galaxyproject/galaxy/commit/047c833db79fef8daa25ddf022f8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-11 (Sat, 11 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py Log Message: ----------- Align subworkflow handling, fix run request through input name Commit: dfa1ddacb93acf341b71148114450c993379adc1 https://github.com/galaxyproject/galaxy/commit/dfa1ddacb93acf341b7114811445… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Restore legacy name handling for backward compatibility Commit: 93f190dd0518005f195960333895b645556860cd https://github.com/galaxyproject/galaxy/commit/93f190dd0518005f195960333895… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Restore previous export behavior Commit: c4491b2d834cdbb61cf009d57c1d3f1086bcfbdb https://github.com/galaxyproject/galaxy/commit/c4491b2d834cdbb61cf009d57c1d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix quotes Commit: 79c24066b444b7bd7a85f0ec2ccdd4b131c4da9e https://github.com/galaxyproject/galaxy/commit/79c24066b444b7bd7a85f0ec2ccd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/run_tests.sh M .ci/py3_sources.txt M CONTRIBUTING.md M client/galaxy/scripts/mvc/tool/tool-form-base.js M config/datatypes_conf.xml.sample M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml M contrib/nagios/check_galaxy M contrib/nagios/check_galaxy.py M doc/source/slideshow/architecture/galaxy_architecture.md M doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg M doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg M doc/source/slideshow/architecture/images/objectstore.plantuml.svg M doc/source/slideshow/architecture/images/plantuml_options.txt M doc/source/slideshow/architecture/images/server_client.plantuml.svg M doc/source/slideshow/architecture/images/server_client_old.plantuml.svg M doc/source/slideshow/architecture/images/webapp.plantuml.svg M doc/source/slideshow/architecture/style.css M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/workflow/steps.py M scripts/slideshow/slideshow_template.html 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 templates/admin/reload_tool.mako M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/base/populators.py A test/functional/tools/output_format_deprecated_when.xml M test/functional/tools/samples_tool_conf.xml M test/selenium_tests/framework.py M test/selenium_tests/test_stock_tours.py M test/selenium_tests/test_uploads.py Log Message: ----------- Merge branch 'dev' into unify_name_label Commit: 1cb8a5da38006cace8c48966a5326b2d3747c574 https://github.com/galaxyproject/galaxy/commit/1cb8a5da38006cace8c48966a532… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix import order Commit: 6330f6051790b7d86bdd5674697163efc3c2a0f0 https://github.com/galaxyproject/galaxy/commit/6330f6051790b7d86bdd56746971… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/mvc/user/user-quotameter.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js Log Message: ----------- Merge branch 'dev' into unify_name_label Commit: dcda376c9ca68742eb58efe6f3438d4d6c5f834f https://github.com/galaxyproject/galaxy/commit/dcda376c9ca68742eb58efe6f343… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Restore subworkflow behavior, no need for modifications anymore Commit: 5cd05161413b73c5eb6ea7393b78cafd213409b9 https://github.com/galaxyproject/galaxy/commit/5cd05161413b73c5eb6ea7393b78… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/mapping.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge branch 'dev' into unify_name_label Commit: 678a8627984852ea4282f6a25bf8c5176783c7c3 https://github.com/galaxyproject/galaxy/commit/678a8627984852ea4282f6a25bf8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/run_request.py Log Message: ----------- Fix Commit: 7ad46c22694ac7b58acdaefca59ca82cca328f25 https://github.com/galaxyproject/galaxy/commit/7ad46c22694ac7b58acdaefca59c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Fix subworkflow caller Commit: c75671484058bc5c0cec8f07dda081cff7c0eb57 https://github.com/galaxyproject/galaxy/commit/c75671484058bc5c0cec8f07dda0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Properly initialize subworkflow parameter Commit: 841cbfd9c7bf1efe2c10bbbff59da22ce67e800c https://github.com/galaxyproject/galaxy/commit/841cbfd9c7bf1efe2c10bbbff59d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/workflow/modules.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Fix content id parsing, through error if subworkflow could not be found Commit: 4610da47863c9ca9c5eb092bfd031f32c6984b96 https://github.com/galaxyproject/galaxy/commit/4610da47863c9ca9c5eb092bfd03… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix style Commit: f548af88076b11d33e3a24b50102108a076df1b4 https://github.com/galaxyproject/galaxy/commit/f548af88076b11d33e3a24b50102… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Add test case for state populating Commit: 8557c32034c9723dc110719b26082312dde1a998 https://github.com/galaxyproject/galaxy/commit/8557c32034c9723dc110719b2608… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Fix sanitization Commit: cdb15f63925e9879744ae38e5e140e5eb9cc6c19 https://github.com/galaxyproject/galaxy/commit/cdb15f63925e9879744ae38e5e14… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/util/workflow_util.py M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge pull request #3593 from guerler/unify_name_label Introduce label and annotation attributes to subworkflows, fix annotation display, unify module form update handler Compare: https://github.com/galaxyproject/galaxy/compare/430ac221baea...cdb15f63925e

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[galaxyproject/galaxy] f1f6bf: Fix annotation display for data inputs
by GitHub 21 Feb '17

21 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: f1f6bf6c3a765e05f8a2dc2b127ee480a485b42e https://github.com/galaxyproject/galaxy/commit/f1f6bf6c3a765e05f8a2dc2b127e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Fix annotation display for data inputs Commit: 09c08d1f61f93ec7973cab1d2cd24532d20e3bb7 https://github.com/galaxyproject/galaxy/commit/09c08d1f61f93ec7973cab1d2cd2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge pull request #3636 from guerler/fix_annotation [17.01] Fix annotation display for data inputs Compare: https://github.com/galaxyproject/galaxy/compare/493cf2816134...09c08d1f61f9

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[galaxyproject/galaxy] ab6ae4: Cancel existing delayed updates when changing page...
by GitHub 21 Feb '17

21 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: ab6ae42c7a7d76b3fbf024edbbdec407b7b1f490 https://github.com/galaxyproject/galaxy/commit/ab6ae42c7a7d76b3fbf024edbbde… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view.js Log Message: ----------- Cancel existing delayed updates when changing pages in the history. Commit: f155a9420a23241c6dc7e404ce487c803a911726 https://github.com/galaxyproject/galaxy/commit/f155a9420a23241c6dc7e404ce48… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M tools/filters/random_lines_two_pass.py Log Message: ----------- temp Commit: ce264f9542df6d4ba779309fb8e7822c6f351f2e https://github.com/galaxyproject/galaxy/commit/ce264f9542df6d4ba779309fb8e7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: 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 static/maps/mvc/history/options-menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Reimplement *old* method for unhide/delete-all-hidden using a temporary web controller endpoint. Commit: a3a7e1001cc0ffa985fd7e987c7190f2d74492ff https://github.com/galaxyproject/galaxy/commit/a3a7e1001cc0ffa985fd7e987c71… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M tools/filters/random_lines_two_pass.py Log Message: ----------- Strip stashed-yet-merged debug detritus from history UI fixes. Commit: bf602a8add58289900fa64cc5c1163c0721f1d10 https://github.com/galaxyproject/galaxy/commit/bf602a8add58289900fa64cc5c11… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Yet more debugging cruft. This is why we have reviews. Commit: 493cf2816134562188ba009e8bf04ffbcc18a2ac https://github.com/galaxyproject/galaxy/commit/493cf2816134562188ba009e8bf0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.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 static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/options-menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/options-menu.js Log Message: ----------- Merge pull request #3621 from dannon/fix-paginated-history-updates [17.01] History Fixes Compare: https://github.com/galaxyproject/galaxy/compare/f6cc1dcf077f...493cf2816134

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[galaxyproject/galaxy] f53b64: WIP: Fix for conda=4.3
by GitHub 20 Feb '17

20 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: f53b6474828d1f8ab1170630ce5851bb913ebec7 https://github.com/galaxyproject/galaxy/commit/f53b6474828d1f8ab1170630ce58… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- WIP: Fix for conda=4.3 Commit: d37ed7e7dadcf568b22836f477ce5afd2a377af7 https://github.com/galaxyproject/galaxy/commit/d37ed7e7dadcf568b22836f477ce… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Adjust offline fix to work for a broader range of potential target Condas. This logic could in theory be backported all the way to 16.01 I suppose now. Commit: 1e3c9ab945c4616510b5b4ff2726aab89585bef4 https://github.com/galaxyproject/galaxy/commit/1e3c9ab945c4616510b5b4ff2726… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py A test/functional/tools/mulled_example_multi_incomplete.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- More revisions to fixing --offline mode to Conda. Incorporate package extraction fixes thanks to @nsoranzo, the fix for version 4.1 and 4.0 thanks to @mvdbeek, a comment for @bgruening and a new test tool that makes it a bit easier to test this. Commit: 0024aa458216589589d35b9366c6347c0c280860 https://github.com/galaxyproject/galaxy/commit/0024aa458216589589d35b9366c6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M test/functional/tools/mulled_example_multi_incomplete.xml Log Message: ----------- Add a clarification to new test tool. Commit: f6cc1dcf077f9d98c38afdd93d47e60c42ac06e5 https://github.com/galaxyproject/galaxy/commit/f6cc1dcf077f9d98c38afdd93d47… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py A test/functional/tools/mulled_example_multi_incomplete.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3632 from jmchilton/conda_43_fix [17.01] Fix Conda --offline logic for bug in 4.0,4.1,4.3. Compare: https://github.com/galaxyproject/galaxy/compare/851f08cb00ea...f6cc1dcf077f

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[galaxyproject/galaxy] 409f50: Add default docker_connect_port to interactive env...
by GitHub 17 Feb '17

17 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 409f50e282885a686b2cdbe75bfe5a5f0e8dde38 https://github.com/galaxyproject/galaxy/commit/409f50e282885a686b2cdbe75bfe… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Add default docker_connect_port to interactive environments config dictionary. Commit: 851f08cb00eac7582a90bafe660b561ebea4c50b https://github.com/galaxyproject/galaxy/commit/851f08cb00eac7582a90bafe660b… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #3631 from blankenberg/gie-jupyter-fix-17.01 [17.01] Add default docker_connect_port to interactive environments config dictionary. Commit: 430ac221baea4c18af247eee8e9106869a570390 https://github.com/galaxyproject/galaxy/commit/430ac221baea4c18af247eee8e91… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge branch 'release_17.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/28089a3ae1ea...430ac221baea

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[galaxyproject/galaxy] 409f50: Add default docker_connect_port to interactive env...
by GitHub 17 Feb '17

17 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 409f50e282885a686b2cdbe75bfe5a5f0e8dde38 https://github.com/galaxyproject/galaxy/commit/409f50e282885a686b2cdbe75bfe… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Add default docker_connect_port to interactive environments config dictionary. Commit: 851f08cb00eac7582a90bafe660b561ebea4c50b https://github.com/galaxyproject/galaxy/commit/851f08cb00eac7582a90bafe660b… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #3631 from blankenberg/gie-jupyter-fix-17.01 [17.01] Add default docker_connect_port to interactive environments config dictionary. Compare: https://github.com/galaxyproject/galaxy/compare/56f7af455c56...851f08cb00ea

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[galaxyproject/usegalaxy-playbook] 1fb776: more 16gb tools
by GitHub 17 Feb '17

17 Feb '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1fb7764538cc15c7ddc6b474753c333b447295ab https://github.com/galaxyproject/usegalaxy-playbook/commit/1fb7764538cc15c7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- more 16gb tools add sailfish, weightedaverage and cummerbund Commit: 2e3403866b618fa15a9cc34b8c6e1bb8d30c6113 https://github.com/galaxyproject/usegalaxy-playbook/commit/2e3403866b618fa1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Merge pull request #22 from galaxyproject/add-16gb-tools allocate more 16gb tools Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/2e21c55a4645...…

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[galaxyproject/galaxy] e5da52: Fix kombu documentation link, add a tiny bit more ...
by GitHub 17 Feb '17

17 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e5da52e388af093e432efeae9f395a7f92ce97da https://github.com/galaxyproject/galaxy/commit/e5da52e388af093e432efeae9f39… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Fix kombu documentation link, add a tiny bit more description to handle the old TODO. Commit: 28089a3ae1ea4eb8be62364aaaef65ae019dc127 https://github.com/galaxyproject/galaxy/commit/28089a3ae1ea4eb8be62364aaaef… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Merge pull request #3629 from dannon/kombu_url_fix Fix kombu documentation link in galaxy.ini.sample Compare: https://github.com/galaxyproject/galaxy/compare/2ff6f910373a...28089a3ae1ea

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[galaxyproject/galaxy] 792bd4: Implementation of slow query logging. Disabled by...
by GitHub 17 Feb '17

17 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 792bd4f8835e9aef355a904b773f208a022e5e95 https://github.com/galaxyproject/galaxy/commit/792bd4f8835e9aef355a904b773f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/mapping.py M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Implementation of slow query logging. Disabled by default. Commit: 9135226ae40dd2222172fd6883511f682c72f7a4 https://github.com/galaxyproject/galaxy/commit/9135226ae40dd2222172fd688351… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Aarrghs spacing. Commit: 42d2a1a4e33b28c98faef4f003edebb600710562 https://github.com/galaxyproject/galaxy/commit/42d2a1a4e33b28c98faef4f003ed… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Add forgotten sample change. Commit: 28fe37c977b18d83d91e7a1d604112f62857073f https://github.com/galaxyproject/galaxy/commit/28fe37c977b18d83d91e7a1d6041… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Style tweaks. My flake8-in-editor had silently died and was not warning me anymore, super. Commit: b14dccab631b2a68ca0131ceca27426668d9b2e2 https://github.com/galaxyproject/galaxy/commit/b14dccab631b2a68ca0131ceca27… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Import formatting... Commit: 56f7af455c5638aef16d2fd7ac07cd0644f7009a https://github.com/galaxyproject/galaxy/commit/56f7af455c5638aef16d2fd7ac07… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/mapping.py M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Merge pull request #3625 from dannon/backport_query_logging [17.01] Usable slow query logging Commit: 2ff6f910373a2eaf547472f8b4be7f92cda495bb https://github.com/galaxyproject/galaxy/commit/2ff6f910373a2eaf547472f8b4be… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Log Message: ----------- Merge branch 'release_17.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/f6649f890499...2ff6f910373a

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[galaxyproject/galaxy] 792bd4: Implementation of slow query logging. Disabled by...
by GitHub 17 Feb '17

17 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 792bd4f8835e9aef355a904b773f208a022e5e95 https://github.com/galaxyproject/galaxy/commit/792bd4f8835e9aef355a904b773f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/mapping.py M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Implementation of slow query logging. Disabled by default. Commit: 9135226ae40dd2222172fd6883511f682c72f7a4 https://github.com/galaxyproject/galaxy/commit/9135226ae40dd2222172fd688351… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Aarrghs spacing. Commit: 42d2a1a4e33b28c98faef4f003edebb600710562 https://github.com/galaxyproject/galaxy/commit/42d2a1a4e33b28c98faef4f003ed… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Add forgotten sample change. Commit: 28fe37c977b18d83d91e7a1d604112f62857073f https://github.com/galaxyproject/galaxy/commit/28fe37c977b18d83d91e7a1d6041… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Style tweaks. My flake8-in-editor had silently died and was not warning me anymore, super. Commit: b14dccab631b2a68ca0131ceca27426668d9b2e2 https://github.com/galaxyproject/galaxy/commit/b14dccab631b2a68ca0131ceca27… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Import formatting... Commit: 56f7af455c5638aef16d2fd7ac07cd0644f7009a https://github.com/galaxyproject/galaxy/commit/56f7af455c5638aef16d2fd7ac07… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/mapping.py M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Merge pull request #3625 from dannon/backport_query_logging [17.01] Usable slow query logging Compare: https://github.com/galaxyproject/galaxy/compare/d2ec75084b2e...56f7af455c56

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[galaxyproject/galaxy] 0e9eb7: deprecate repair repository feature
by GitHub 16 Feb '17

16 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0e9eb78636da19c68ff3c981ff8090b63a7d11ae https://github.com/galaxyproject/galaxy/commit/0e9eb78636da19c68ff3c981ff80… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- deprecate repair repository feature Commit: 29d229cedd697ff79595b223d651dd0d97ded457 https://github.com/galaxyproject/galaxy/commit/29d229cedd697ff79595b223d651… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- Merge pull request #3615 from martenson/release_17.01 [17.01] deprecate repair repository feature Commit: ac191f5f2a10c003788a291501331b68fb521bc7 https://github.com/galaxyproject/galaxy/commit/ac191f5f2a10c003788a29150133… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- [17.01] Make active_datasets_children_and_roles just active_datasets_and_roles. I guess somewhere in the tool building process we eliminated children from appearing the form. Remove unused code that used the children selector in the tool form. Commit: eb42d130d34c9393f3386ba115de6fe561e9ef18 https://github.com/galaxyproject/galaxy/commit/eb42d130d34c9393f3386ba115de… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py Log Message: ----------- Fix unit tests for that last commit. Commit: d2ec75084b2eeae30ce61168462fec03f1211b6e https://github.com/galaxyproject/galaxy/commit/d2ec75084b2eeae30ce61168462f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py Log Message: ----------- Merge pull request #3624 from jmchilton/active_children_drop [17.01] Drop children from query that prefetches data for dataset matching. Commit: f6649f890499a2e4569057e4b1921f0c95426e11 https://github.com/galaxyproject/galaxy/commit/f6649f890499a2e4569057e4b192… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py Log Message: ----------- Merge branch 'release_17.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/89e32ee526e7...f6649f890499

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[galaxyproject/galaxy] ac191f: [17.01] Make active_datasets_children_and_roles ju...
by GitHub 16 Feb '17

16 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: ac191f5f2a10c003788a291501331b68fb521bc7 https://github.com/galaxyproject/galaxy/commit/ac191f5f2a10c003788a29150133… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- [17.01] Make active_datasets_children_and_roles just active_datasets_and_roles. I guess somewhere in the tool building process we eliminated children from appearing the form. Remove unused code that used the children selector in the tool form. Commit: eb42d130d34c9393f3386ba115de6fe561e9ef18 https://github.com/galaxyproject/galaxy/commit/eb42d130d34c9393f3386ba115de… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py Log Message: ----------- Fix unit tests for that last commit. Commit: d2ec75084b2eeae30ce61168462fec03f1211b6e https://github.com/galaxyproject/galaxy/commit/d2ec75084b2eeae30ce61168462f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py Log Message: ----------- Merge pull request #3624 from jmchilton/active_children_drop [17.01] Drop children from query that prefetches data for dataset matching. Compare: https://github.com/galaxyproject/galaxy/compare/29d229cedd69...d2ec75084b2e

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[galaxyproject/galaxy] be5eaf: Util to encode or decode values
by GitHub 15 Feb '17

15 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: be5eaf4881b9624c67a7e3125dbb080032502477 https://github.com/galaxyproject/galaxy/commit/be5eaf4881b9624c67a7e3125dbb… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: A scripts/cookie.py Log Message: ----------- Util to encode or decode values Commit: 6849752fb68b018aaf30f61d9d3c564894ed9e2b https://github.com/galaxyproject/galaxy/commit/6849752fb68b018aaf30f61d9d3c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: R scripts/cookie.py A scripts/secret_decoder_ring.py Log Message: ----------- Rename, Strip F for Folder Commit: fb2450ff33ebdbdeb3f1205bdc58c38519921e7a https://github.com/galaxyproject/galaxy/commit/fb2450ff33ebdbdeb3f1205bdc58… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M scripts/secret_decoder_ring.py Log Message: ----------- document scriptg Commit: 89e32ee526e7f2ebc64be8bd46337a6edef78cab https://github.com/galaxyproject/galaxy/commit/89e32ee526e7f2ebc64be8bd4633… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: A scripts/secret_decoder_ring.py Log Message: ----------- Merge pull request #3622 from erasche/encode-decode-util Util to encode or decode values Compare: https://github.com/galaxyproject/galaxy/compare/43f2a648230b...89e32ee526e7

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[galaxyproject/galaxy] 412d8e: Adding NGL viewer for molecule representation
by GitHub 15 Feb '17

15 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 412d8e1bb6c82a9aa8a86971e64e4242a5341419 https://github.com/galaxyproject/galaxy/commit/412d8e1bb6c82a9aa8a86971e64e… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-02-12 (Sun, 12 Feb 2017) Changed paths: A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js A config/plugins/visualizations/charts/static/repository/plugins/ngl/viewer.js M config/plugins/visualizations/charts/static/repository/registry.json A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/config.js A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js Log Message: ----------- Adding NGL viewer for molecule representation Commit: 6864bc30b4a02495220d1552026c0cacb5d41af7 https://github.com/galaxyproject/galaxy/commit/6864bc30b4a02495220d1552026c… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js M config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js Log Message: ----------- Replacing url by download_url to fetch files Commit: 48639028df5b59e7547a2e716b9c7e34e9743a41 https://github.com/galaxyproject/galaxy/commit/48639028df5b59e7547a2e716b9c… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js M config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js Log Message: ----------- Removing utils.get to fetch pdb files Commit: c390da3cbd933c27ad0c731bc3b557ad916a72cd https://github.com/galaxyproject/galaxy/commit/c390da3cbd933c27ad0c731bc3b5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js M config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js Log Message: ----------- Change default settings, avoid flickering on startup Commit: 7472568fe5102a77ff69c47db0f19d7fd0a8487a https://github.com/galaxyproject/galaxy/commit/7472568fe5102a77ff69c47db0f1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js M config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js Log Message: ----------- Remove unused name from stage parameter Commit: 43f2a648230b5b0ee46c124cc3df95b758e50fb2 https://github.com/galaxyproject/galaxy/commit/43f2a648230b5b0ee46c124cc3df… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js A config/plugins/visualizations/charts/static/repository/plugins/ngl/viewer.js M config/plugins/visualizations/charts/static/repository/registry.json A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/config.js A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js Log Message: ----------- Merge pull request #3601 from bgruening/ngl_viewer NGL Viewer for molecule representation Compare: https://github.com/galaxyproject/galaxy/compare/a7572145e9c0...43f2a648230b

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[galaxyproject/galaxy] 0e9eb7: deprecate repair repository feature
by GitHub 15 Feb '17

15 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 0e9eb78636da19c68ff3c981ff8090b63a7d11ae https://github.com/galaxyproject/galaxy/commit/0e9eb78636da19c68ff3c981ff80… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- deprecate repair repository feature Commit: 29d229cedd697ff79595b223d651dd0d97ded457 https://github.com/galaxyproject/galaxy/commit/29d229cedd697ff79595b223d651… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- Merge pull request #3615 from martenson/release_17.01 [17.01] deprecate repair repository feature Compare: https://github.com/galaxyproject/galaxy/compare/c82530fd2384...29d229cedd69

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[galaxyproject/galaxy] eb5ded: Remove likely un-needed check.
by GitHub 15 Feb '17

15 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: eb5ded2a439d1c9491700650842f9ece04cfad33 https://github.com/galaxyproject/galaxy/commit/eb5ded2a439d1c9491700650842f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Remove likely un-needed check. Commit: a7572145e9c0d4872cde027d547ef4c31c87af10 https://github.com/galaxyproject/galaxy/commit/a7572145e9c0d4872cde027d547e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Merge pull request #3618 from jmchilton/remove_unneeded_15 Remove un-needed check in histories manager code Compare: https://github.com/galaxyproject/galaxy/compare/149dfa007f70...a7572145e9c0

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[galaxyproject/galaxy] 452ab0: Implementation of slow query logging. Disabled by...
by GitHub 15 Feb '17

15 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 452ab0d509171033e901bf65cf2556ef411e5161 https://github.com/galaxyproject/galaxy/commit/452ab0d509171033e901bf65cf25… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/mapping.py M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Implementation of slow query logging. Disabled by default. Commit: 78282a288bd1528dfd5222f47baaaeaaf1480f17 https://github.com/galaxyproject/galaxy/commit/78282a288bd1528dfd5222f47baa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Aarrghs spacing. Commit: 19e18dd5719abe08e361bf4b50a7bf4bbbd554e1 https://github.com/galaxyproject/galaxy/commit/19e18dd5719abe08e361bf4b50a7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Add forgotten sample change. Commit: 7810f5a8648c913045ae042a7c991642dbc045c8 https://github.com/galaxyproject/galaxy/commit/7810f5a8648c913045ae042a7c99… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Style tweaks. My flake8-in-editor had silently died and was not warning me anymore, super. Commit: da24f4c8ad03a34da9323041e634d4bbe55617b4 https://github.com/galaxyproject/galaxy/commit/da24f4c8ad03a34da9323041e634… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Import formatting... Commit: 149dfa007f70fe6794b8c1f37708ac8fbb7cccef https://github.com/galaxyproject/galaxy/commit/149dfa007f70fe6794b8c1f37708… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/mapping.py M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Merge pull request #3616 from dannon/slow_query_logging Slow query logging Compare: https://github.com/galaxyproject/galaxy/compare/8ce1291359c8...149dfa007f70

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[galaxyproject/galaxy] 255aa0: Fix workflow save-as url not using galaxy's prefix...
by GitHub 14 Feb '17

14 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 255aa0470f44ea90d2b4d738e07b8f6d08874c3b https://github.com/galaxyproject/galaxy/commit/255aa0470f44ea90d2b4d738e07b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Fix workflow save-as url not using galaxy's prefix. Commit: c86d2ee8bcbdde82ac5e6f450241ef7fed076665 https://github.com/galaxyproject/galaxy/commit/c86d2ee8bcbdde82ac5e6f450241… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #3610 from dannon/fix-editor-save-as-url [17.01] Fix workflow save-as url not using galaxy's prefix. Commit: 4689cf16bf77b0e7b0d22d193b695d7d5df24d6c https://github.com/galaxyproject/galaxy/commit/4689cf16bf77b0e7b0d22d193b69… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Recalculate user disk usage on logout. Not as ideal as just having it be accurate all the time, but it 1) avoids adding yet another control people need to dig for when they need to recalculate, and 2) makes things right when following 'turn it off and on again' Commit: 43d80a0b6052b59f8be768ad810fee952a436ce3 https://github.com/galaxyproject/galaxy/commit/43d80a0b6052b59f8be768ad810f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M static/maps/mvc/user/user-quotameter.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js Log Message: ----------- Tooltips to suggest relog for quota correction. Commit: 966d578b47f4999ba0f8db874bf927e5f4246d7f https://github.com/galaxyproject/galaxy/commit/966d578b47f4999ba0f8db874bf9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Slightly more defensive programming -- we don't expose this in the UI unless there *is* a trans.user, but we might as well be careful here. Commit: 944feb2411d1381b1743f3365b6380e883c9cccb https://github.com/galaxyproject/galaxy/commit/944feb2411d1381b1743f3365b63… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M static/maps/mvc/user/user-quotameter.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js Log Message: ----------- Minor tooltip tweaks. Commit: c82530fd2384f5df2457e8f5dd33368cc13abc48 https://github.com/galaxyproject/galaxy/commit/c82530fd2384f5df2457e8f5dd33… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/mvc/user/user-quotameter.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js Log Message: ----------- Merge pull request #3614 from dannon/logout-recalc-backport [17.01] Logout recalc backport and additional logic Commit: 8ce1291359c88148023e5bb3f44a9eb38c78a864 https://github.com/galaxyproject/galaxy/commit/8ce1291359c88148023e5bb3f44a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge branch 'release_17.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/df22e40522d7...8ce1291359c8

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[galaxyproject/galaxy] 4689cf: Recalculate user disk usage on logout. Not as ide...
by GitHub 14 Feb '17

14 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 4689cf16bf77b0e7b0d22d193b695d7d5df24d6c https://github.com/galaxyproject/galaxy/commit/4689cf16bf77b0e7b0d22d193b69… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Recalculate user disk usage on logout. Not as ideal as just having it be accurate all the time, but it 1) avoids adding yet another control people need to dig for when they need to recalculate, and 2) makes things right when following 'turn it off and on again' Commit: 43d80a0b6052b59f8be768ad810fee952a436ce3 https://github.com/galaxyproject/galaxy/commit/43d80a0b6052b59f8be768ad810f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M static/maps/mvc/user/user-quotameter.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js Log Message: ----------- Tooltips to suggest relog for quota correction. Commit: 966d578b47f4999ba0f8db874bf927e5f4246d7f https://github.com/galaxyproject/galaxy/commit/966d578b47f4999ba0f8db874bf9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Slightly more defensive programming -- we don't expose this in the UI unless there *is* a trans.user, but we might as well be careful here. Commit: 944feb2411d1381b1743f3365b6380e883c9cccb https://github.com/galaxyproject/galaxy/commit/944feb2411d1381b1743f3365b63… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M static/maps/mvc/user/user-quotameter.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js Log Message: ----------- Minor tooltip tweaks. Commit: c82530fd2384f5df2457e8f5dd33368cc13abc48 https://github.com/galaxyproject/galaxy/commit/c82530fd2384f5df2457e8f5dd33… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/mvc/user/user-quotameter.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js Log Message: ----------- Merge pull request #3614 from dannon/logout-recalc-backport [17.01] Logout recalc backport and additional logic Compare: https://github.com/galaxyproject/galaxy/compare/c86d2ee8bcbd...c82530fd2384

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[galaxyproject/galaxy] 9bb9fe: Recalculate user disk usage on logout. Not as ide...
by GitHub 14 Feb '17

14 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9bb9feb0a8aeec36ded548aa8d28927e2b26d678 https://github.com/galaxyproject/galaxy/commit/9bb9feb0a8aeec36ded548aa8d28… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-12 (Sun, 12 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Recalculate user disk usage on logout. Not as ideal as just having it be accurate all the time, but it 1) avoids adding yet another control people need to dig for when they need to recalculate, and 2) makes things right when following 'turn it off and on again' Commit: fcbb7c3de17841027da5c2ec16cf11f78e709872 https://github.com/galaxyproject/galaxy/commit/fcbb7c3de17841027da5c2ec16cf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-12 (Sun, 12 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M static/maps/mvc/user/user-quotameter.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js Log Message: ----------- Tooltips to suggest relog for quota correction. Commit: 3f07555173f89f39b4823767daaa25bd92ec7d68 https://github.com/galaxyproject/galaxy/commit/3f07555173f89f39b4823767daaa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M CONTRIBUTING.md M client/galaxy/scripts/mvc/tool/tool-form-base.js M config/plugins/tours/core.galaxy_ui.yaml M doc/source/slideshow/architecture/galaxy_architecture.md M doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg M doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg M doc/source/slideshow/architecture/images/objectstore.plantuml.svg M doc/source/slideshow/architecture/images/plantuml_options.txt M doc/source/slideshow/architecture/images/server_client.plantuml.svg M doc/source/slideshow/architecture/images/server_client_old.plantuml.svg M doc/source/slideshow/architecture/images/webapp.plantuml.svg M doc/source/slideshow/architecture/style.css M lib/galaxy/datatypes/interval.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/workflow/steps.py M scripts/slideshow/slideshow_template.html 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 templates/admin/reload_tool.mako A test/functional/tools/output_format_deprecated_when.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'dev' into recalc-on-logout Commit: df22e40522d7777cc3c82a4e32b64fe2d95d9273 https://github.com/galaxyproject/galaxy/commit/df22e40522d7777cc3c82a4e32b6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/mvc/user/user-quotameter.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js Log Message: ----------- Merge pull request #3600 from dannon/recalc-on-logout Recalculate user disk usage on logout. Compare: https://github.com/galaxyproject/galaxy/compare/9597b9b62b66...df22e40522d7

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[galaxyproject/galaxy] 4f80b1: Revert "Set 'deleted' to True when purging a histo...
by GitHub 14 Feb '17

14 Feb '17

Branch: refs/heads/revert-3572-fix_3548 Home: https://github.com/galaxyproject/galaxy Commit: 4f80b11e9c513b4ca1a9442fbf955a3116c07436 https://github.com/galaxyproject/galaxy/commit/4f80b11e9c513b4ca1a9442fbf95… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/managers/deletable.py R lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py M lib/galaxy/webapps/galaxy/api/histories.py M test/api/test_histories.py M test/api/test_history_contents.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Revert "Set 'deleted' to True when purging a history dataset association"

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[galaxyproject/galaxy] 255aa0: Fix workflow save-as url not using galaxy's prefix...
by GitHub 14 Feb '17

14 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 255aa0470f44ea90d2b4d738e07b8f6d08874c3b https://github.com/galaxyproject/galaxy/commit/255aa0470f44ea90d2b4d738e07b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Fix workflow save-as url not using galaxy's prefix. Commit: c86d2ee8bcbdde82ac5e6f450241ef7fed076665 https://github.com/galaxyproject/galaxy/commit/c86d2ee8bcbdde82ac5e6f450241… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #3610 from dannon/fix-editor-save-as-url [17.01] Fix workflow save-as url not using galaxy's prefix. Compare: https://github.com/galaxyproject/galaxy/compare/5db0b7681bb6...c86d2ee8bcbd

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[galaxyproject/galaxy] ac4630: Minor fix of core.galaxy-ui tour in more robustly ...
by GitHub 14 Feb '17

14 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ac46305686c81a94b60a76dd6904a772a784ff24 https://github.com/galaxyproject/galaxy/commit/ac46305686c81a94b60a76dd6904… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml Log Message: ----------- Minor fix of core.galaxy-ui tour in more robustly selecting first reload icon in the active history. Commit: 9597b9b62b66d933ae5d891ff45550d23a86b6f2 https://github.com/galaxyproject/galaxy/commit/9597b9b62b66d933ae5d891ff455… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml Log Message: ----------- Merge pull request #3608 from dannon/minor-tour-fix Minor fix of core.galaxy-ui tour in more robustly selecting first rel… Compare: https://github.com/galaxyproject/galaxy/compare/4fc0b84910ad...9597b9b62b66

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[galaxyproject/galaxy] 93453e: Avoid html response when reloading tool through th...
by GitHub 13 Feb '17

13 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 93453e490f2490899d818473d79eeddf9f6d0808 https://github.com/galaxyproject/galaxy/commit/93453e490f2490899d818473d79e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/tools.py M templates/admin/reload_tool.mako Log Message: ----------- Avoid html response when reloading tool through the api Commit: b466ff6cd8dc86c03f0d6322e26b94605087bb39 https://github.com/galaxyproject/galaxy/commit/b466ff6cd8dc86c03f0d6322e26b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 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 Log Message: ----------- Fix root location for tool reloader Commit: 1aa459f19d45221957ff0be6a5f708bf6bd41a41 https://github.com/galaxyproject/galaxy/commit/1aa459f19d45221957ff0be6a5f7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 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/mvc/tool/tool-form-base.js Log Message: ----------- Use shared modal viewer Commit: cd52f20961fcdee3453b5c5ce28b84f25b50f3f3 https://github.com/galaxyproject/galaxy/commit/cd52f20961fcdee3453b5c5ce28b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 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 Log Message: ----------- Align code style to existing code in tool form base Commit: 727bfbd258c548917d2025708368f73b57199648 https://github.com/galaxyproject/galaxy/commit/727bfbd258c548917d2025708368… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/tools.py M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Fix error message style, raise message exception if tool has not been found Commit: 8e59ec1e2be863dc00cb86d1689e7169cd43b6e5 https://github.com/galaxyproject/galaxy/commit/8e59ec1e2be863dc00cb86d1689e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/tools.py M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Remove unused tooltips for submenu options, fix response Commit: 10943712b829ac48760fc5ecd25405d768cc9dd4 https://github.com/galaxyproject/galaxy/commit/10943712b829ac48760fc5ecd254… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 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 Log Message: ----------- Revise dropdown item label Commit: 9590d4551439c7b9ae13f704508bfef376ff1fc4 https://github.com/galaxyproject/galaxy/commit/9590d4551439c7b9ae13f704508b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Improve success message upon tool xml reloading Commit: 73b8fc45aa088b17970c5309108442d968c70a7b https://github.com/galaxyproject/galaxy/commit/73b8fc45aa088b17970c53091084… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 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 Log Message: ----------- Check once for admin operations when building dropdown list in tool form Commit: 4fc0b84910adef446daa20a68cd69b0721a4d362 https://github.com/galaxyproject/galaxy/commit/4fc0b84910adef446daa20a68cd6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/toolbox/base.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/tools.py M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M templates/admin/reload_tool.mako Log Message: ----------- Merge remote-tracking branch 'guerler/fix_tool_reload_003' into dev Compare: https://github.com/galaxyproject/galaxy/compare/9f9d0cb4082b...4fc0b84910ad

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[galaxyproject/galaxy] 4483f0: Fix ScIdx datatype sniffer
by GitHub 13 Feb '17

13 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4483f014107d92340573c7113745821e4863c148 https://github.com/galaxyproject/galaxy/commit/4483f014107d92340573c7113745… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Fix ScIdx datatype sniffer Check for EOF before line stripping, otherwise empty or whitespace lines will be considered EOF. Found when uploading a GFF file which was erroneously sniffed as scidx. Commit: 5db0b7681bb60e0671c0d80d06e3d980ef3aab6e https://github.com/galaxyproject/galaxy/commit/5db0b7681bb60e0671c0d80d06e3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Merge pull request #3602 from nsoranzo/release_17.01_fix_scidx_sniffer Fix ScIdx datatype sniffer Commit: 9f9d0cb4082b66e385bd43e31995cbaa5a2a0e09 https://github.com/galaxyproject/galaxy/commit/9f9d0cb4082b66e385bd43e31995… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Merge branch 'release_17.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/b4b75b276c9d...9f9d0cb4082b

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