- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 27e7da: Fix bug: 4247 in search overlay
by GitHub 02 Aug '17

02 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 27e7da9406486fc2a7d40c36332e480d84aab407 https://github.com/galaxyproject/galaxy/commit/27e7da9406486fc2a7d40c36332e… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-27 (Thu, 27 Jul 2017) Changed paths: M config/plugins/webhooks/demo/search/static/script.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Fix bug: 4247 in search overlay Commit: 1e18e6b0795c303172c21c038cd145ef75b51720 https://github.com/galaxyproject/galaxy/commit/1e18e6b0795c303172c21c038cd1… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-27 (Thu, 27 Jul 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/model/mapping.py Log Message: ----------- Merge branch 'dev' of https://github.com/bgruening/galaxy into searchoverlay_bugfix Commit: bcecec0713e6778ab6850320943ad12b5f184f16 https://github.com/galaxyproject/galaxy/commit/bcecec0713e6778ab6850320943a… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/nls/fr/locale.js M config/tool_shed.ini.sample M lib/galaxy/jobs/runners/cli.py M lib/galaxy/model/metadata.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/deps/conda_util.py R lib/galaxy/web/base/controllers/__init__.py R lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/workflow/modules.py A lib/tool_shed/util/admin_util.py A static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/nls/fr/locale.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 A static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/nls/fr/locale.js R templates/webapps/galaxy/dataset/edit_attributes.mako Log Message: ----------- Merge with dev Commit: f41d2ba8ecf6440901fd1106b6bafa6377098ad9 https://github.com/galaxyproject/galaxy/commit/f41d2ba8ecf6440901fd1106b6ba… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M config/plugins/webhooks/demo/search/static/script.js Log Message: ----------- Merge pull request #4348 from bgruening/searchoverlay_bugfix Search Overlay plugin bug fix Compare: https://github.com/galaxyproject/galaxy/compare/98292a0a124a...f41d2ba8ecf6

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[galaxyproject/usegalaxy-playbook] 0a1838: Run unicycler on Bridges
by GitHub 02 Aug '17

02 Aug '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0a1838527f6a1a7cb98f6e13ee12d1317726f813 https://github.com/galaxyproject/usegalaxy-playbook/commit/0a1838527f6a1a7c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Run unicycler on Bridges Commit: aafd5807943b509fb8c32b6c16a199c4d844fba3 https://github.com/galaxyproject/usegalaxy-playbook/commit/aafd5807943b509f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Test mutable configs Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/3ea4cacef518...…

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[galaxyproject/galaxy] 81af55: Delete conda_exec_home instead of env['HOME']
by GitHub 01 Aug '17

01 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 81af55cfea7853b177782c3d6550b0c62b5d7446 https://github.com/galaxyproject/galaxy/commit/81af55cfea7853b177782c3d6550… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-31 (Mon, 31 Jul 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Delete conda_exec_home instead of env['HOME'] This should always be the same in the current code, but this feels a little safer, given that env is mutable. Commit: 98292a0a124a106bde64dd977f0e505e599ff864 https://github.com/galaxyproject/galaxy/commit/98292a0a124a106bde64dd977f0e… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #4360 from mvdbeek/shutil_rmtree_headache Delete conda_exec_home instead of env['HOME'] Compare: https://github.com/galaxyproject/galaxy/compare/bd0f804085bf...98292a0a124a

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[galaxyproject/galaxy] e7f971: Set up scripts for removing edit attributes mako o...
by GitHub 01 Aug '17

01 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e7f9714a29893177f479270f7017aec3a976d6df https://github.com/galaxyproject/galaxy/commit/e7f9714a29893177f479270f7017… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-10 (Mon, 10 Jul 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M lib/galaxy/webapps/galaxy/buildapp.py A static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Set up scripts for removing edit attributes mako of Dataset edit action Commit: 6a493ac3001cb0e3345355025ca4a79008ec8d36 https://github.com/galaxyproject/galaxy/commit/6a493ac3001cb0e3345355025ca4… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-10 (Mon, 10 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.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/mvc/dataset/dataset-edit-attributes.js Log Message: ----------- Adding tabs for different sections of edit dataset attributes view Commit: 19ede9b477f8c32d6915152869e73959dc10677c https://github.com/galaxyproject/galaxy/commit/19ede9b477f8c32d6915152869e7… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-11 (Tue, 11 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-edit-attributes.js Log Message: ----------- Updating edit attributes view Commit: 5e59549ddf47d12ed03326a65d5858a9d9ec030c https://github.com/galaxyproject/galaxy/commit/5e59549ddf47d12ed03326a65d58… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-11 (Tue, 11 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-edit-attributes.js Log Message: ----------- Adding messages to the actions Commit: 95032151fa56681148529eba2d27140db80b7c98 https://github.com/galaxyproject/galaxy/commit/95032151fa56681148529eba2d27… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-11 (Tue, 11 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-edit-attributes.js Log Message: ----------- Adding Convert tab to Dataset Edit Attributes page Commit: b3ae53c1e7f8de207aabeb55d96526be07c29752 https://github.com/galaxyproject/galaxy/commit/b3ae53c1e7f8de207aabeb55d965… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-11 (Tue, 11 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-edit-attributes.js Log Message: ----------- Updating logic for extra fields like comments lines Commit: 7ba4f22b61aa248383d99dc2caf1ec747299539a https://github.com/galaxyproject/galaxy/commit/7ba4f22b61aa248383d99dc2caf1… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-16 (Sun, 16 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-edit-attributes.js Log Message: ----------- Adding form builder for edit attributes tabs Commit: 3572bad66fd4b1d3899378d5493975c43751c67b https://github.com/galaxyproject/galaxy/commit/3572bad66fd4b1d3899378d54939… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-17 (Mon, 17 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-edit-attributes.js Log Message: ----------- Adding permissions tab Commit: 69934d9f02787a66082a6841e39406198905c936 https://github.com/galaxyproject/galaxy/commit/69934d9f02787a66082a6841e394… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-17 (Mon, 17 Jul 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js A client/package-lock.json M config/galaxy.ini.sample M config/tool_conf.xml.main M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/tags.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py A lib/galaxy/objectstore/pithos.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M scripts/runtime_stats.py M static/maps/galaxy.pages.js.map M static/maps/layout/menu.js.map M static/maps/layout/scratchbook.js.map M static/maps/mvc/dataset/data.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/grid/grid-model.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/nls/ja/locale.js.map M static/maps/nls/locale.js.map M static/maps/viz/circster.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/visualization.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/galaxy.pages.js M static/scripts/layout/menu.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/grid/grid-view.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js R templates/webapps/galaxy/history/list_published.mako M templates/webapps/galaxy/page/editor.mako R templates/webapps/galaxy/page/select_items_grid.mako R templates/webapps/galaxy/tracks/add_to_viz.mako R templates/webapps/galaxy/tracks/add_tracks.mako R templates/webapps/galaxy/tracks/history_datasets_select_grid.mako R templates/webapps/galaxy/tracks/history_select_grid.mako R templates/webapps/galaxy/tracks/library_datasets_select_grid.mako Log Message: ----------- Merging with dev Commit: 9604fb3844bcf936bd73581d7adefabd7f99f491 https://github.com/galaxyproject/galaxy/commit/9604fb3844bcf936bd73581d7ade… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-17 (Mon, 17 Jul 2017) Changed paths: M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Resolve the save permission issue Commit: 44d24c39f7873ea86d21d56c15565f041fbaab20 https://github.com/galaxyproject/galaxy/commit/44d24c39f7873ea86d21d56c1556… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-17 (Mon, 17 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-edit-attributes.js Log Message: ----------- Add form builder for the attributes tab Commit: 212ffc7476551568136391e9bfd2c34d84269731 https://github.com/galaxyproject/galaxy/commit/212ffc7476551568136391e9bfd2… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/model/metadata.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-edit-attributes.js Log Message: ----------- Add metadata fields Commit: 90247d7432ac7942797a574c3e241316d18f5bcf https://github.com/galaxyproject/galaxy/commit/90247d7432ac7942797a574c3e24… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M lib/galaxy/model/metadata.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Build inputs in controller Commit: 9853625e905c14fd9b9fd706a0c7a174da9135e0 https://github.com/galaxyproject/galaxy/commit/9853625e905c14fd9b9fd706a0c7… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js A client/galaxy/scripts/mvc/grid/grid-shared.js R client/galaxy/scripts/mvc/page/page-list.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/trackster.js M client/package-lock.json A config/plugins/visualizations/unipept/README.md A config/plugins/visualizations/unipept/config/unipept.xml A config/plugins/visualizations/unipept/static/style.css A config/plugins/visualizations/unipept/static/tooltip.css A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js.map A config/plugins/visualizations/unipept/static/unipept_viz.js A config/plugins/visualizations/unipept/templates/glyphicons-86-repeat.png A config/plugins/visualizations/unipept/templates/unipept.mako M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M static/maps/layout/menu.js.map A static/maps/mvc/grid/grid-shared.js.map R static/maps/mvc/page/page-list.js.map M static/maps/viz/circster.js.map M static/maps/viz/trackster.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js A static/scripts/mvc/grid/grid-shared.js R static/scripts/mvc/page/page-list.js M static/scripts/viz/circster.js M static/scripts/viz/trackster.js M templates/webapps/galaxy/requests/common/common.mako R templates/webapps/galaxy/visualization/list.mako Log Message: ----------- Merge with def Commit: 9c83253c41645ec253e8320604c9b9ae5254412c https://github.com/galaxyproject/galaxy/commit/9c83253c41645ec253e8320604c9… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-23 (Sun, 23 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-edit-attributes.js Log Message: ----------- Changes for setting values of select box in metadata Commit: ac6ad5aabac9ca34baf8d0ebede25073e2fa7bae https://github.com/galaxyproject/galaxy/commit/ac6ad5aabac9ca34baf8d0ebede2… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-23 (Sun, 23 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-edit-attributes.js Log Message: ----------- Update the help text Commit: a302dee11e4f66244992655c51dbf8affa1a88e8 https://github.com/galaxyproject/galaxy/commit/a302dee11e4f66244992655c51db… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-23 (Sun, 23 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Correct the indentations and spacings Commit: f4ffef05ce501f8f40efb4461c678d7a3b1ca01d https://github.com/galaxyproject/galaxy/commit/f4ffef05ce501f8f40efb4461c67… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-23 (Sun, 23 Jul 2017) Changed paths: R templates/webapps/galaxy/dataset/edit_attributes.mako Log Message: ----------- Removing the edit attributes mako file Commit: 315fd58fcac02097efc42dac7e2db68fa6bd6db3 https://github.com/galaxyproject/galaxy/commit/315fd58fcac02097efc42dac7e2d… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-23 (Sun, 23 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Fixing build fail comments Commit: 8fa3b2b97a07c2b9a6c015aec56445c2d049bfd0 https://github.com/galaxyproject/galaxy/commit/8fa3b2b97a07c2b9a6c015aec564… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-25 (Tue, 25 Jul 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-edit-attributes.js Log Message: ----------- Fixing PR review comments Commit: f8e6fcaebc8b7968daba841fd172636bf37e3858 https://github.com/galaxyproject/galaxy/commit/f8e6fcaebc8b7968daba841fd172… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-30 (Sun, 30 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-edit-attributes.js Log Message: ----------- Removing unsued self vars and using just Backbone.Model Commit: 2f5b26e8b6dcb47b5ca69466b6510fa58bea1f7c https://github.com/galaxyproject/galaxy/commit/2f5b26e8b6dcb47b5ca69466b651… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-30 (Sun, 30 Jul 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js M config/tool_shed.ini.sample M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/runners/cli.py M lib/galaxy/model/mapping.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge branch 'dev' of https://github.com/bgruening/galaxy into edit_attributes_mako Commit: 8502a6854a363eca1f8180e25f11f322d4a094f4 https://github.com/galaxyproject/galaxy/commit/8502a6854a363eca1f8180e25f11… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-31 (Mon, 31 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/nls/fr/locale.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/nls/fr/locale.js Log Message: ----------- Updating the dataset id Commit: bd0f804085bf1fa467001554dd8e51ad999aa261 https://github.com/galaxyproject/galaxy/commit/bd0f804085bf1fa467001554dd8e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M lib/galaxy/model/metadata.py M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py A static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/nls/fr/locale.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 A static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/nls/fr/locale.js R templates/webapps/galaxy/dataset/edit_attributes.mako Log Message: ----------- Merge pull request #4334 from bgruening/edit_attributes_mako Replacing Edit Attributes Mako by JavaScript Compare: https://github.com/galaxyproject/galaxy/compare/2659718a6d71...bd0f804085bf

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[galaxyproject/galaxy] 268186: Replicate admin controller for toolshed
by GitHub 31 Jul '17

31 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 268186a0d98927d090796c8e5ce21646083d1787 https://github.com/galaxyproject/galaxy/commit/268186a0d98927d090796c8e5ce2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: A lib/tool_shed/util/admin_util.py Log Message: ----------- Replicate admin controller for toolshed Commit: 3cc654836946f0061af4b69130b2b89c79f361b7 https://github.com/galaxyproject/galaxy/commit/3cc654836946f0061af4b69130b2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M lib/tool_shed/util/admin_util.py Log Message: ----------- Remove repository_util dependency Commit: b4506e2a347cb4fbf4becffff2870bfd7277a2c6 https://github.com/galaxyproject/galaxy/commit/b4506e2a347cb4fbf4becffff287… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/admin.py Log Message: ----------- Link to toolshed specific controller Commit: 94391305d8c55fbcb43ab517dad5e2681e08259c https://github.com/galaxyproject/galaxy/commit/94391305d8c55fbcb43ab517dad5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Insert admin base controller endpoints into galaxy admin controller Commit: 6a8841189d51b89da2c9be098440bd0002a6ecb7 https://github.com/galaxyproject/galaxy/commit/6a8841189d51b89da2c9be098440… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: R lib/galaxy/web/base/controllers/__init__.py R lib/galaxy/web/base/controllers/admin.py Log Message: ----------- Remove base admin controller Commit: 2f79e00649aa1863d53d3149c6b1a2e5981a5cc5 https://github.com/galaxyproject/galaxy/commit/2f79e00649aa1863d53d3149c6b1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Transfer non-overlapping dependencies Commit: 616c0326fcd60120e4d4f6d0171fededf48f4c72 https://github.com/galaxyproject/galaxy/commit/616c0326fcd60120e4d4f6d0171f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove redundant dependency Commit: 39cce1abb20ace8f4e988fbb3426476e33cc883b https://github.com/galaxyproject/galaxy/commit/39cce1abb20ace8f4e988fbb3426… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M lib/tool_shed/util/admin_util.py Log Message: ----------- Add new line Commit: 97a4cb9686c260d233e01e08861f0481b63ac670 https://github.com/galaxyproject/galaxy/commit/97a4cb9686c260d233e01e08861f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/quotas.py Log Message: ----------- Avoid inheriting the admin controller for quota api Commit: 917d2d98b42da1561bef1773f1f94ac8f3df8496 https://github.com/galaxyproject/galaxy/commit/917d2d98b42da1561bef1773f1f9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M lib/tool_shed/util/admin_util.py Log Message: ----------- Remove endpoints not needed in toolshed Commit: 7a0c041bc251ea9b122db2adf887db25633e964a https://github.com/galaxyproject/galaxy/commit/7a0c041bc251ea9b122db2adf887… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/tool_shed/util/admin_util.py Log Message: ----------- Remove unused utility functions of controller Commit: e85b3f9951738ed3229ff00a5ed718a916b5c598 https://github.com/galaxyproject/galaxy/commit/e85b3f9951738ed3229ff00a5ed7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M lib/tool_shed/util/admin_util.py Log Message: ----------- Remove unused dependencies Commit: 36cd79b535b98520116a6531dedaf05b15c11c93 https://github.com/galaxyproject/galaxy/commit/36cd79b535b98520116a6531deda… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/quotas.py Log Message: ----------- Remove unused method Commit: 2659718a6d71d89a07a8440a000e2e7b86cf64e6 https://github.com/galaxyproject/galaxy/commit/2659718a6d71d89a07a8440a000e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-07-31 (Mon, 31 Jul 2017) Changed paths: R lib/galaxy/web/base/controllers/__init__.py R lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/admin.py A lib/tool_shed/util/admin_util.py Log Message: ----------- Merge pull request #4327 from guerler/separate_admin_controllers Separate admin controllers Compare: https://github.com/galaxyproject/galaxy/compare/79b1ad601118...2659718a6d71

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[galaxyproject/infrastructure-playbook]
by GitHub 31 Jul '17

31 Jul '17

Branch: refs/heads/https-include Home: https://github.com/galaxyproject/infrastructure-playbook

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[galaxyproject/infrastructure-playbook] d83c1a: include https in training redirect
by GitHub 31 Jul '17

31 Jul '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: d83c1a7eefa7ea16fbe3b1960efdcd2257271f8c https://github.com/galaxyproject/infrastructure-playbook/commit/d83c1a7eefa… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-07-31 (Mon, 31 Jul 2017) Changed paths: M galaxyenv/templates/nginx/training.j2 Log Message: ----------- include https in training redirect Commit: 7d295c71010067a4e9e9e3831e2cfafaa2b2b228 https://github.com/galaxyproject/infrastructure-playbook/commit/7d295c71010… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-31 (Mon, 31 Jul 2017) Changed paths: M galaxyenv/templates/nginx/training.j2 Log Message: ----------- Merge pull request #18 from galaxyproject/https-include include https in training redirect Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/91921fe770…

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[galaxyproject/infrastructure-playbook] d83c1a: include https in training redirect
by GitHub 31 Jul '17

31 Jul '17

Branch: refs/heads/https-include Home: https://github.com/galaxyproject/infrastructure-playbook Commit: d83c1a7eefa7ea16fbe3b1960efdcd2257271f8c https://github.com/galaxyproject/infrastructure-playbook/commit/d83c1a7eefa… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-07-31 (Mon, 31 Jul 2017) Changed paths: M galaxyenv/templates/nginx/training.j2 Log Message: ----------- include https in training redirect

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[galaxyproject/galaxy] 12f0ac: Revert "Revert "[release_17.05] Patch bug preventi...
by GitHub 31 Jul '17

31 Jul '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 12f0acba1dc1b81bb621ea130a75ec7dfac0fdaa https://github.com/galaxyproject/galaxy/commit/12f0acba1dc1b81bb621ea130a75… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Revert "Revert "[release_17.05] Patch bug preventing creation of dataset library folders"" Commit: 10efd7fac6e38c5ca07d94c351d10473811c7d6c https://github.com/galaxyproject/galaxy/commit/10efd7fac6e38c5ca07d94c351d1… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-07-31 (Mon, 31 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #4357 from galaxyproject/revert-4356-revert-4355-patch-wrong-folder-id [release_17.05] Patch bug preventing creation of dataset library folders Compare: https://github.com/galaxyproject/galaxy/compare/163e4ebbe1fb...10efd7fac6e3

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[galaxyproject/galaxy] 092626: Remove print debug option from toolshed.
by GitHub 28 Jul '17

28 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0926266cbea49a0f30ebeb22cb0a0a95843d7187 https://github.com/galaxyproject/galaxy/commit/0926266cbea49a0f30ebeb22cb0a… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2017-07-21 (Fri, 21 Jul 2017) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Remove print debug option from toolshed. After investigating, I've determined that it's not worth the effort to fix the print debug middleware, so this will remove the option from buildapp.py and tool_shed.ini.sample Commit: 8923912c89c7ada8a9ad7d1a2533eb44d17a9e36 https://github.com/galaxyproject/galaxy/commit/8923912c89c7ada8a9ad7d1a2533… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-07-27 (Thu, 27 Jul 2017) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Fix logic. Commit: 79b1ad6011182075f4a7648f72f3fa7bb5d8fd6f https://github.com/galaxyproject/galaxy/commit/79b1ad6011182075f4a7648f72f3… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Merge pull request #4332 from davebx/remove_printdebug Remove print debug option from toolshed. Compare: https://github.com/galaxyproject/galaxy/compare/e1c54f37d904...79b1ad601118

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