- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 12ce4e: Strip legacy request helpers
by GitHub 15 Dec '17

15 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 12ce4e7266b2fb5985e8384eda62ff764930e60e https://github.com/galaxyproject/galaxy/commit/12ce4e7266b2fb5985e8384eda62… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Strip legacy request helpers Commit: 67cf6944894f71a1408e0b596558039d00306f68 https://github.com/galaxyproject/galaxy/commit/67cf6944894f71a1408e0b596558… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Remove field value helper Commit: de5d29a6f2e66bf2792c4cde0a7eb2a56e018234 https://github.com/galaxyproject/galaxy/commit/de5d29a6f2e66bf2792c4cde0a7e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: A lib/galaxy/webapps/reports/framework/grids.py Log Message: ----------- Move grid helper to reports Commit: 7961dcc75ca8f9932b0c1f674347dbaf91190ce6 https://github.com/galaxyproject/galaxy/commit/7961dcc75ca8f9932b0c1f674347… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Strip mako support from galaxy grid helper Commit: f600a1dd99998e9415215a045bafd3a47ffb4975 https://github.com/galaxyproject/galaxy/commit/f600a1dd99998e9415215a045baf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Remove comma from root controller config dict Commit: 24cd0893e5f9ad5aab1befa2aa311ba9b597302a https://github.com/galaxyproject/galaxy/commit/24cd0893e5f9ad5aab1befa2aa31… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py Log Message: ----------- Link jobs mako to legacy reports module Commit: a8f59df445cbe36f9cdc281f2fe5aa91a809be5c https://github.com/galaxyproject/galaxy/commit/a8f59df445cbe36f9cdc281f2fe5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: M lib/galaxy/webapps/reports/controllers/workflows.py Log Message: ----------- Same for worflows grid in reports Commit: 47578b641fadee5b9dd2d0e65fe06da1dfb5ccfd https://github.com/galaxyproject/galaxy/commit/47578b641fadee5b9dd2d0e65fe0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py Log Message: ----------- Redirect for admin toolshed grids Commit: b726cda3a7abbc49a0532b942fcf6923475d51df https://github.com/galaxyproject/galaxy/commit/b726cda3a7abbc49a0532b942fcf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_review_grids.py Log Message: ----------- More redirects for toolshed grids Commit: d4dda34f1214df3389d779e9b835d7557a7499c8 https://github.com/galaxyproject/galaxy/commit/d4dda34f1214df3389d779e9b835… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: R templates/webapps/reports/grid.mako Log Message: ----------- Remove reports default grid mako Commit: d930b114558814945bd0d5f054904318c2f83b35 https://github.com/galaxyproject/galaxy/commit/d930b114558814945bd0d5f05490… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: R templates/grid_base.mako R templates/grid_base_async.mako A templates/webapps/reports/grid_base.mako A templates/webapps/reports/grid_base_asyn.mako Log Message: ----------- Move grid makos from galaxy to reports app Commit: 6c974dd81b0f6fb2dec6c65d1a0c3a98983cda5b https://github.com/galaxyproject/galaxy/commit/6c974dd81b0f6fb2dec6c65d1a0c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: M templates/webapps/reports/grid_base.mako R templates/webapps/reports/grid_base_asyn.mako A templates/webapps/reports/grid_base_async.mako M templates/webapps/tool_shed/category/grid.mako M templates/webapps/tool_shed/category/valid_grid.mako M templates/webapps/tool_shed/common/grid_common.mako M templates/webapps/tool_shed/repository_review/grid.mako Log Message: ----------- Redirect makos to new grid helper location in reports Commit: d2752dc7b7977f6d887fe7b7c88f53141a2b46bf https://github.com/galaxyproject/galaxy/commit/d2752dc7b7977f6d887fe7b7c88f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: A lib/galaxy/webapps/reports/framework/__init__.py Log Message: ----------- Add init file to framework module Commit: 96b9b151aea1236cc754bdabc9c1ebe29f23533c https://github.com/galaxyproject/galaxy/commit/96b9b151aea1236cc754bdabc9c1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/webapps/reports/framework/grids.py M lib/tool_shed/grids/repository_grids.py Log Message: ----------- Remove dict format from legacy grid helper Commit: c9783de884db11c77c05303fbf36591fba84030a https://github.com/galaxyproject/galaxy/commit/c9783de884db11c77c05303fbf36… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/config.py R lib/galaxy/webapps/reports/controllers/sample_tracking.py M templates/webapps/reports/index.mako R templates/webapps/reports/requests_per_month_all.mako R templates/webapps/reports/requests_per_user.mako R templates/webapps/reports/requests_user_per_month.mako Log Message: ----------- Merge branch 'clear_sample_tracking' into remove_gridhelper Commit: 1c8ed722c221de5baaf437085c0b3e84b1ee5689 https://github.com/galaxyproject/galaxy/commit/1c8ed722c221de5baaf437085c0b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: A client/galaxy/scripts/reports/run_stats.js R client/galaxy/scripts/reports_webapp/run_stats.js R static/scripts/reports_webapp/run_stats.js M templates/webapps/reports/grid_base.mako M templates/webapps/reports/run_stats.mako Log Message: ----------- Copy legacy grid code to reports app, redirect imports Commit: f01a597480909c53ca3fadd3a1e01922ccf430b3 https://github.com/galaxyproject/galaxy/commit/f01a597480909c53ca3fadd3a1e0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/webapps/reports/framework/grids.py M templates/webapps/reports/grid_base_async.mako M templates/webapps/tool_shed/repository_review/grid.mako Log Message: ----------- Fix imports to new mako location Commit: cbe7cab090398695431acc3b87b11e2c0e66a36b https://github.com/galaxyproject/galaxy/commit/cbe7cab090398695431acc3b87b1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py Log Message: ----------- Fix grids used within Galaxy's admin interface Commit: f2d12a5d699b30532e5a73ea24a0f599ebe42481 https://github.com/galaxyproject/galaxy/commit/f2d12a5d699b30532e5a73ea24a0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Remove async attribute from grid helper Commit: d12e65652e7eb001b9e274de5ccff2665276ec7c https://github.com/galaxyproject/galaxy/commit/d12e65652e7eb001b9e274de5ccf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.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 lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Remove async attribute from grids Commit: e32d965034f791756b3107cf6f6055ae0784ffab https://github.com/galaxyproject/galaxy/commit/e32d965034f791756b3107cf6f60… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-view.js M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Remove async flag handling from grid client Commit: 134b3cc47fd3f1f94fb896f8c7a4d5843d8f2280 https://github.com/galaxyproject/galaxy/commit/134b3cc47fd3f1f94fb896f8c7a4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/visualization.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/grid/grid-model.js M static/scripts/mvc/grid/grid-view.js Log Message: ----------- Remove dict format flag from grid client Commit: efbd02743ed3be506c608662ae6e649f1695d675 https://github.com/galaxyproject/galaxy/commit/efbd02743ed3be506c608662ae6e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/forms.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 lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Remove dict format from controllers Commit: 7624ce25ed1f224f3df1423fa30f88e02186012c https://github.com/galaxyproject/galaxy/commit/7624ce25ed1f224f3df1423fa30f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/viz/trackster.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/galaxy.pages.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-list.js M static/scripts/viz/trackster.js M static/scripts/viz/visualization.js Log Message: ----------- Repack client Commit: 0f7bc19e30d37acb3a2b7da14972ba6c046d4112 https://github.com/galaxyproject/galaxy/commit/0f7bc19e30d37acb3a2b7da14972… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/galaxy/webapps/reports/framework/grids.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py Log Message: ----------- Remove unused preserve state attribute from grids Commit: 1bb521b8ed693775e7e52322737f58c1867f9552 https://github.com/galaxyproject/galaxy/commit/1bb521b8ed693775e7e52322737f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: A client/galaxy/scripts/reports/grid/grid-model.js A client/galaxy/scripts/reports/grid/grid-template.js A client/galaxy/scripts/reports/grid/grid-view.js A static/scripts/reports/grid/grid-model.js A static/scripts/reports/grid/grid-template.js A static/scripts/reports/grid/grid-view.js Log Message: ----------- Add separated grid client for reports and toolshed Commit: 52ce746b64457d46ea8f6f7c72d90cb9b851243b https://github.com/galaxyproject/galaxy/commit/52ce746b64457d46ea8f6f7c72d9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/reports/framework/grids.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py Log Message: ----------- Remove unused imports, fix import order Commit: 85fef66272014df1ad944117a017368253253b9f https://github.com/galaxyproject/galaxy/commit/85fef66272014df1ad944117a017… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Remove unused expose attribute from grid helper Commit: 73749b748276802c66a112cf181723036fcbef0f https://github.com/galaxyproject/galaxy/commit/73749b748276802c66a112cf1817… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Remove unused pass_through_operations from grid helper Commit: ced73c02e8acdebda9523ef6f3054eeea7845dd0 https://github.com/galaxyproject/galaxy/commit/ced73c02e8acdebda9523ef6f305… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/webapps/reports/framework/grids.py Log Message: ----------- Remove flags from legacy grid helper in reports Commit: b703a4c525911dd9bf98a847b549417a589ad299 https://github.com/galaxyproject/galaxy/commit/b703a4c525911dd9bf98a847b549… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: R templates/panels.mako Log Message: ----------- Remove legacy panels mako for grids Commit: 6586ce2b6dcab1ac866062e0e4c486daf489afc6 https://github.com/galaxyproject/galaxy/commit/6586ce2b6dcab1ac866062e0e4c4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Remove legacy comment Commit: 644977c6a538db4829c33a0cd7d0827138a8f8e6 https://github.com/galaxyproject/galaxy/commit/644977c6a538db4829c33a0cd7d0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/cram_to_bam.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/test/1.bam A lib/galaxy/datatypes/test/1.vcf A lib/galaxy/datatypes/test/1.vcf.gz A lib/galaxy/datatypes/test/2.cram A lib/galaxy/datatypes/test/2.shuffled.bam M lib/galaxy/visualization/data_providers/genome.py M static/scripts/bundled/extended.bundled.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-view.js A test/unit/datatypes/converters/__init__.py A test/unit/datatypes/converters/test_interval_to_tabix.py A test/unit/datatypes/test_bam.py A test/unit/datatypes/test_bcf.py A test/unit/datatypes/test_cram.py A test/unit/datatypes/test_vcf.py A test/unit/datatypes/util.py M tools/data_source/upload.xml Log Message: ----------- Merge branch 'dev' into remove_gridhelper Commit: 5c12a9a9bdbf6da453edf0259dcd1eb3400cbaed https://github.com/galaxyproject/galaxy/commit/5c12a9a9bdbf6da453edf0259dcd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Log Message: ----------- Merge branch 'dev' into remove_gridhelper Commit: 4411189f2589ca366098f93dfc48942b0d2cb7a9 https://github.com/galaxyproject/galaxy/commit/4411189f2589ca366098f93dfc48… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Log Message: ----------- Merge branch 'dev' into remove_gridhelper Commit: 364804f40a176ab5bf2350c85a62bcb72a3cdddc https://github.com/galaxyproject/galaxy/commit/364804f40a176ab5bf2350c85a62… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/user.py M static/scripts/bundled/analysis.bundled.js M static/scripts/mvc/user/user-preferences.js M templates/user/openid_manage.mako Log Message: ----------- Use client side grid builder for openids table Commit: 200d8a229a7f51cb7a1a3fbade94fca0412d492e https://github.com/galaxyproject/galaxy/commit/200d8a229a7f51cb7a1a3fbade94… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Add error message if openids are disabled Commit: 241de16c327c6e92d8127382770b8e1d9bdaf715 https://github.com/galaxyproject/galaxy/commit/241de16c327c6e92d8127382770b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Add delete operation to new openid controller Commit: f2fd3b1626ee86d228102d9a5368f67b94ae6bbd https://github.com/galaxyproject/galaxy/commit/f2fd3b1626ee86d228102d9a5368… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Remove previous delete operation caller Commit: 7fd3bfb36566ad5d18814c081b136e0e13d688f9 https://github.com/galaxyproject/galaxy/commit/7fd3bfb36566ad5d18814c081b13… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/user.py M static/scripts/bundled/analysis.bundled.js Log Message: ----------- Prepare openid creation form Commit: 8e4ab4012620fc4a28d6baa0eb2ca2bb186ba01b https://github.com/galaxyproject/galaxy/commit/8e4ab4012620fc4a28d6baa0eb2c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py M templates/user/openid_manage.mako Log Message: ----------- Remove table view from manage mako Commit: cf7cc197e7fd16bf6fb0619d08b449ca3f051d4c https://github.com/galaxyproject/galaxy/commit/cf7cc197e7fd16bf6fb0619d08b4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/user.py M templates/user/openid_manage.mako Log Message: ----------- Use mako to display add account form Commit: e942e4b3e2ccea0505dcfaef6d8a11444238485a https://github.com/galaxyproject/galaxy/commit/e942e4b3e2ccea0505dcfaef6d8a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Show openid form in center panel Commit: 87777cf52db6b811a99691a7bd2104decd7eecb5 https://github.com/galaxyproject/galaxy/commit/87777cf52db6b811a99691a7bd21… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py M templates/user/index.mako Log Message: ----------- Fix redirects to new client side route Commit: 7bc92610a25db4d1480130a3022905eea8f27234 https://github.com/galaxyproject/galaxy/commit/7bc92610a25db4d1480130a30229… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M lib/galaxy/webapps/galaxy/controllers/user.py M static/scripts/bundled/analysis.bundled.js Log Message: ----------- Fix delete operation, remove unused route to client form Commit: 74d4ea8eef26cb83ede4a3f53be617cc9872b6e1 https://github.com/galaxyproject/galaxy/commit/74d4ea8eef26cb83ede4a3f53be6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M templates/user/openid_manage.mako Log Message: ----------- Remove unused mako properties Commit: 1952e738a703afab2db0cffe615498536f74bb31 https://github.com/galaxyproject/galaxy/commit/1952e738a703afab2db0cffe6154… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/user.py M static/scripts/bundled/analysis.bundled.js M static/scripts/mvc/user/user-preferences.js M templates/user/index.mako M templates/user/openid_manage.mako Log Message: ----------- Merge branch 'replace_openid_table' into remove_gridhelper Commit: d0a5a35dfd567ea8ce13fec38d1761fd44cd0ff2 https://github.com/galaxyproject/galaxy/commit/d0a5a35dfd567ea8ce13fec38d17… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Require only regular login to create openids Commit: f239ef45465149964b30438b717cc30e7b2716ca https://github.com/galaxyproject/galaxy/commit/f239ef45465149964b30438b717c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: A client/galaxy/scripts/reports/run_stats.js R client/galaxy/scripts/reports_webapp/run_stats.js Log Message: ----------- Move reports app to reports Commit: 52cee726621e0281fde10c9ebb2820e8cc94a083 https://github.com/galaxyproject/galaxy/commit/52cee726621e0281fde10c9ebb28… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: R client/galaxy/scripts/mvc/grid/grid-model.js R client/galaxy/scripts/mvc/grid/grid-shared.js R client/galaxy/scripts/mvc/grid/grid-template.js R client/galaxy/scripts/mvc/grid/grid-view.js A client/galaxy/scripts/reports/grid/grid-model.js A client/galaxy/scripts/reports/grid/grid-shared.js A client/galaxy/scripts/reports/grid/grid-template.js A client/galaxy/scripts/reports/grid/grid-view.js Log Message: ----------- Move legacy grid client to reports Commit: 5ed7b143eb457695bf230c5912e48dfabbfa7fb0 https://github.com/galaxyproject/galaxy/commit/5ed7b143eb457695bf230c5912e4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/reports/grid/grid-shared.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/visualization.js M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/workflows.py A lib/galaxy/webapps/reports/framework/__init__.py A lib/galaxy/webapps/reports/framework/grids.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/galaxy.pages.js M static/scripts/mvc/grid/grid-model.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/user/user-preferences.js A static/scripts/reports/grid/grid-model.js A static/scripts/reports/grid/grid-template.js A static/scripts/reports/grid/grid-view.js R static/scripts/reports_webapp/run_stats.js M static/scripts/viz/trackster.js M static/scripts/viz/visualization.js R templates/grid_base.mako R templates/grid_base_async.mako R templates/panels.mako M templates/user/index.mako M templates/user/openid_manage.mako R templates/webapps/reports/grid.mako A templates/webapps/reports/grid_base.mako A templates/webapps/reports/grid_base_async.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/category/grid.mako M templates/webapps/tool_shed/category/valid_grid.mako M templates/webapps/tool_shed/common/grid_common.mako M templates/webapps/tool_shed/repository_review/grid.mako Log Message: ----------- Merge branch 'remove_gridhelper' into remove_gridhelper_001 Commit: 170b2431c9f61ea320a19ed04834e2f836f1c740 https://github.com/galaxyproject/galaxy/commit/170b2431c9f61ea320a19ed04834… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: A client/galaxy/scripts/mvc/grid/grid-model.js A client/galaxy/scripts/mvc/grid/grid-shared.js A client/galaxy/scripts/mvc/grid/grid-template.js A client/galaxy/scripts/mvc/grid/grid-view.js Log Message: ----------- Add grid modules Commit: 6e8100f274648cb57fe5f2cda34dd22806b540ac https://github.com/galaxyproject/galaxy/commit/6e8100f274648cb57fe5f2cda34d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: A static/scripts/reports/grid/grid-shared.js Log Message: ----------- Pack client Commit: c19ef1aacea869b33651fa3352970531150b0e07 https://github.com/galaxyproject/galaxy/commit/c19ef1aacea869b33651fa335297… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: R client/galaxy/scripts/reports/grid/grid-shared.js R static/scripts/reports/grid/grid-shared.js Log Message: ----------- Remove shared grid view Commit: cbc4e55fda91dde884c9be474d7a95c62ccd98c7 https://github.com/galaxyproject/galaxy/commit/cbc4e55fda91dde884c9be474d7a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js Log Message: ----------- Client format. Commit: 85ba7c56e8ff0f2f6797a0e2b25f577ff7ee0071 https://github.com/galaxyproject/galaxy/commit/85ba7c56e8ff0f2f6797a0e2b25f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: A client/galaxy/scripts/legacy/grid/grid-model.js A client/galaxy/scripts/legacy/grid/grid-template.js A client/galaxy/scripts/legacy/grid/grid-view.js R client/galaxy/scripts/reports/grid/grid-model.js R client/galaxy/scripts/reports/grid/grid-template.js R client/galaxy/scripts/reports/grid/grid-view.js Log Message: ----------- Relocate to legacy* templates to be very clear on the status of this code. Commit: 8ecb6ecdfb6c7943b627bc63299d606fefe21c49 https://github.com/galaxyproject/galaxy/commit/8ecb6ecdfb6c7943b627bc63299d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M client/galaxy/scripts/legacy/grid/grid-view.js Log Message: ----------- Correct legacy grid* to point to the correct copied code (this was broken before the shift to legacy -- instead pointing back to the mvc version instead of the reports version Commit: 8db84bea66615687d1ffba2f6b0af1fd770883b5 https://github.com/galaxyproject/galaxy/commit/8db84bea66615687d1ffba2f6b0a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M lib/galaxy/webapps/reports/framework/grids.py A templates/legacy/grid_base.mako A templates/legacy/grid_base_async.mako R templates/webapps/reports/grid_base.mako R templates/webapps/reports/grid_base_async.mako M templates/webapps/tool_shed/category/grid.mako M templates/webapps/tool_shed/category/valid_grid.mako M templates/webapps/tool_shed/repository_review/grid.mako Log Message: ----------- Move templates (commonly used legacy grid code) from reports to legacy Commit: 28653132bec89eab6bd3cdebebb334bd3fcb1345 https://github.com/galaxyproject/galaxy/commit/28653132bec89eab6bd3cdebebb3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: R .ci/py3_sources.txt M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/gulpfile.js M client/package.json M client/webpack.config.js M client/yarn.lock M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/workflows.py M lib/galaxy/openid/providers.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/util/permutations.py M lib/galaxy/util/script.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/authenticate.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/webapps/tool_shed/util/hgweb_config.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M scripts/build_universe_config.py M scripts/data_libraries/build_lucene_index.py M scripts/galaxy-main M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/microbes/util.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/sync_reports_config.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/transfer.py M scripts/update_shed_config_path.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/libs.bundled.js R static/scripts/libs/vue.js M static/scripts/mvc/tool/tool-form-base.js M test/selenium_tests/test_tool_form.py M tools/data_source/upload.py M tools/genomespace/genomespace_importer.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into remove_gridhelper_001 Commit: bb6e58b40dbc64b77dcf31291c28d1af7138e42a https://github.com/galaxyproject/galaxy/commit/bb6e58b40dbc64b77dcf31291c28… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M client/galaxy/scripts/legacy/grid/grid-template.js Log Message: ----------- Formatting in grid-template Commit: 985c65e677eb1dee5190685e85a429c8d1eab842 https://github.com/galaxyproject/galaxy/commit/985c65e677eb1dee5190685e85a4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M client/galaxy/scripts/legacy/grid/grid-model.js M client/galaxy/scripts/legacy/grid/grid-template.js Log Message: ----------- Remove a little cruft in now-legacy grids. Commit: e08a2839867b5214e830fe6a3df84dddca66521f https://github.com/galaxyproject/galaxy/commit/e08a2839867b5214e830fe6a3df8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js Log Message: ----------- Remove the same cruft from the mvc/grid/grid-template. Commit: b832fec9e71694caf233627dd09c2f8921841534 https://github.com/galaxyproject/galaxy/commit/b832fec9e71694caf233627dd09c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M static/scripts/bundled/libs.bundled.js A static/scripts/legacy/grid/grid-model.js A static/scripts/legacy/grid/grid-template.js A static/scripts/legacy/grid/grid-view.js M static/scripts/mvc/grid/grid-template.js R static/scripts/reports/grid/grid-model.js R static/scripts/reports/grid/grid-template.js R static/scripts/reports/grid/grid-view.js A static/scripts/reports/run_stats.js Log Message: ----------- Build client Commit: 609020da0fa8b2d3171e157bf609b30dd4b54067 https://github.com/galaxyproject/galaxy/commit/609020da0fa8b2d3171e157bf609… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: R .ci/py3_sources.txt M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/modal.js A client/galaxy/scripts/legacy/grid/grid-model.js A client/galaxy/scripts/legacy/grid/grid-template.js A client/galaxy/scripts/legacy/grid/grid-view.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js R client/galaxy/scripts/reports/grid/grid-model.js R client/galaxy/scripts/reports/grid/grid-template.js R client/galaxy/scripts/reports/grid/grid-view.js M client/gulpfile.js M client/package.json M client/webpack.config.js M client/yarn.lock M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/workflows.py M lib/galaxy/openid/providers.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/util/permutations.py M lib/galaxy/util/script.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/authenticate.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/framework/grids.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/webapps/tool_shed/util/hgweb_config.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M scripts/build_universe_config.py M scripts/data_libraries/build_lucene_index.py M scripts/galaxy-main M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/microbes/util.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/sync_reports_config.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/transfer.py M scripts/update_shed_config_path.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/libs.bundled.js A static/scripts/legacy/grid/grid-model.js A static/scripts/legacy/grid/grid-template.js A static/scripts/legacy/grid/grid-view.js R static/scripts/libs/vue.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/tool/tool-form-base.js R static/scripts/reports/grid/grid-model.js R static/scripts/reports/grid/grid-template.js R static/scripts/reports/grid/grid-view.js A static/scripts/reports/run_stats.js A templates/legacy/grid_base.mako A templates/legacy/grid_base_async.mako R templates/webapps/reports/grid_base.mako R templates/webapps/reports/grid_base_async.mako M templates/webapps/tool_shed/category/grid.mako M templates/webapps/tool_shed/category/valid_grid.mako M templates/webapps/tool_shed/repository_review/grid.mako M test/selenium_tests/test_tool_form.py M tools/data_source/upload.py M tools/genomespace/genomespace_importer.py Log Message: ----------- Merge pull request #23 from dannon/remove_gridhelper_001 Some fixes and cleanup, makes the merge clean. Commit: 9aa596df8b6853bcf63635fdbd38790f634a0888 https://github.com/galaxyproject/galaxy/commit/9aa596df8b6853bcf63635fdbd38… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.pages.js A client/galaxy/scripts/legacy/grid/grid-model.js A client/galaxy/scripts/legacy/grid/grid-template.js A client/galaxy/scripts/legacy/grid/grid-view.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/user/user-preferences.js A client/galaxy/scripts/reports/run_stats.js R client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/visualization.js M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/workflows.py A lib/galaxy/webapps/reports/framework/__init__.py A lib/galaxy/webapps/reports/framework/grids.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/galaxy.pages.js A static/scripts/legacy/grid/grid-model.js A static/scripts/legacy/grid/grid-template.js A static/scripts/legacy/grid/grid-view.js M static/scripts/mvc/grid/grid-model.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/user/user-preferences.js A static/scripts/reports/run_stats.js R static/scripts/reports_webapp/run_stats.js M static/scripts/viz/trackster.js M static/scripts/viz/visualization.js R templates/grid_base.mako R templates/grid_base_async.mako A templates/legacy/grid_base.mako A templates/legacy/grid_base_async.mako R templates/panels.mako M templates/user/index.mako M templates/user/openid_manage.mako R templates/webapps/reports/grid.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/category/grid.mako M templates/webapps/tool_shed/category/valid_grid.mako M templates/webapps/tool_shed/common/grid_common.mako M templates/webapps/tool_shed/repository_review/grid.mako Log Message: ----------- Merge pull request #5212 from guerler/remove_gridhelper_001 Remove html producing grid helpers Compare: https://github.com/galaxyproject/galaxy/compare/b96c428cde5e...9aa596df8b68

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[galaxyproject/galaxy] 504343: Selenium - little pause to let extension form in u...
by GitHub 14 Dec '17

14 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5043439df2ca694254623887d351905be1d9b698 https://github.com/galaxyproject/galaxy/commit/5043439df2ca694254623887d351… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Selenium - little pause to let extension form in upload dialog render. xref https://github.com/galaxyproject/galaxy/issues/5169 Commit: 6fd6595238b5189e89f54ad01079b4d34fbcfea7 https://github.com/galaxyproject/galaxy/commit/6fd6595238b5189e89f54ad01079… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Another try to fix flakey tool form Selenium test. Commit: b96c428cde5e9786376d0ecd5eba5f5233b6fec2 https://github.com/galaxyproject/galaxy/commit/b96c428cde5e9786376d0ecd5eba… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M test/selenium_tests/test_tool_form.py Log Message: ----------- Merge pull request #5211 from jmchilton/selenium_test_fixes Mark transiently failing test_run_data as flakey. Compare: https://github.com/galaxyproject/galaxy/compare/3b7f40198e96...b96c428cde5e

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[galaxyproject/galaxy] 14259b: Python3: finish first pass on whole codebase
by GitHub 14 Dec '17

14 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 14259b11d9a5f6238153556ed5a28bf89468e2b4 https://github.com/galaxyproject/galaxy/commit/14259b11d9a5f6238153556ed5a2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: R .ci/py3_sources.txt M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/workflows.py M lib/galaxy/openid/providers.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/util/permutations.py M lib/galaxy/util/script.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/authenticate.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/webapps/tool_shed/util/hgweb_config.py M scripts/build_universe_config.py M scripts/data_libraries/build_lucene_index.py M scripts/galaxy-main M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/microbes/util.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/sync_reports_config.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/transfer.py M scripts/update_shed_config_path.py M tools/genomespace/genomespace_importer.py Log Message: ----------- Python3: finish first pass on whole codebase Commit: 820d1e259c625f2472f79ee46654bbf91b19dea4 https://github.com/galaxyproject/galaxy/commit/820d1e259c625f2472f79ee46654… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Mercurial does not support Python3 yet Commit: 3b7f40198e968d7c2bbda533551686688cfd8f48 https://github.com/galaxyproject/galaxy/commit/3b7f40198e968d7c2bbda5335516… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: R .ci/py3_sources.txt M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/workflows.py M lib/galaxy/openid/providers.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/util/permutations.py M lib/galaxy/util/script.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/authenticate.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/webapps/tool_shed/util/hgweb_config.py M scripts/build_universe_config.py M scripts/data_libraries/build_lucene_index.py M scripts/galaxy-main M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/microbes/util.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/sync_reports_config.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/transfer.py M scripts/update_shed_config_path.py M tools/genomespace/genomespace_importer.py Log Message: ----------- Merge pull request #5215 from nsoranzo/python3 Python3: finish first pass on whole codebase Compare: https://github.com/galaxyproject/galaxy/compare/fd4f0e6aa6f7...3b7f40198e96

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[galaxyproject/galaxy] dda410: #3002 update to newer version of virtualenv.
by GitHub 14 Dec '17

14 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dda410da63ef26c7d86a40bd764adadb19cbbcd5 https://github.com/galaxyproject/galaxy/commit/dda410da63ef26c7d86a40bd764a… Author: Peter Selten <peter.selten98(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- #3002 update to newer version of virtualenv. Commit: fd4f0e6aa6f7178639c3af556da86a0805460808 https://github.com/galaxyproject/galaxy/commit/fd4f0e6aa6f7178639c3af556da8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #5202 from selten/dev #3002 update to newer version of virtualenv. Compare: https://github.com/galaxyproject/galaxy/compare/7b04c834e0ff...fd4f0e6aa6f7

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[galaxyproject/galaxy] 6eaa73: Swap to vue via node_module; no staging.
by GitHub 14 Dec '17

14 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6eaa73e37ee5f795d8b96c9abe274403dfa62753 https://github.com/galaxyproject/galaxy/commit/6eaa73e37ee5f795d8b96c9abe27… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/gulpfile.js M client/webpack.config.js R static/scripts/libs/vue.js Log Message: ----------- Swap to vue via node_module; no staging. Commit: 1a6065b0c3ee7178acbf96028672a33ee32bb195 https://github.com/galaxyproject/galaxy/commit/1a6065b0c3ee7178acbf96028672… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: R static/scripts/libs/bibtex.js Log Message: ----------- Remove old bibtex.js cruft. Commit: 662f35df490c66c2d9443f9815820c2041ee7fdd https://github.com/galaxyproject/galaxy/commit/662f35df490c66c2d9443f981582… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Upgrade vue. Commit: 2ca7b90262a6ef5e833df0c65da4c3a5a45a6d9b https://github.com/galaxyproject/galaxy/commit/2ca7b90262a6ef5e833df0c65da4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Upgrade webpack to 3.10 Commit: 0a92f5b80bea2b593a9d37ab9d606e5ac97c2e71 https://github.com/galaxyproject/galaxy/commit/0a92f5b80bea2b593a9d37ab9d60… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Update vue-template-compiler Commit: 8cd62168d8eda3e5480ffcfb25e87c62b44163c6 https://github.com/galaxyproject/galaxy/commit/8cd62168d8eda3e5480ffcfb25e8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Upgrade minor devDependencies. Commit: 4dbe7c420e6f6c1515183bf44838a4f2ed3fa453 https://github.com/galaxyproject/galaxy/commit/4dbe7c420e6f6c1515183bf44838… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Upgrade prettier 1.7->1.9 Commit: a363d81b7314bd41fba5ea15b2ff432a9bc83dad https://github.com/galaxyproject/galaxy/commit/a363d81b7314bd41fba5ea15b2ff… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Rerun new version of prettier. Commit: c09643d57bac206bc101434f4623c0d63d75ca16 https://github.com/galaxyproject/galaxy/commit/c09643d57bac206bc101434f4623… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Build client. Commit: 7b04c834e0ff03eddedd81303ea0242d0e44fbc6 https://github.com/galaxyproject/galaxy/commit/7b04c834e0ff03eddedd81303ea0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/gulpfile.js M client/package.json M client/webpack.config.js M client/yarn.lock M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/libs.bundled.js R static/scripts/libs/vue.js M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Merge pull request #5190 from dannon/vue_dep_tweaks Client dependency upgrades, changes. Compare: https://github.com/galaxyproject/galaxy/compare/fce9f13eba7f...7b04c834e0ff

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[galaxyproject/galaxy] 099c15: Re-organize edge case upload options for my own cl...
by GitHub 14 Dec '17

14 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 099c1562febbcedee63a431b4314654df5e23301 https://github.com/galaxyproject/galaxy/commit/099c1562febbcedee63a431b4314… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M lib/galaxy/tools/actions/upload_common.py M tools/data_source/upload.py Log Message: ----------- Re-organize edge case upload options for my own clarity. I think setting each of these variables once and simplifing the context they are used in (in the case of purge_upload) makes it more clear what each variable is and how it is set. I also think one, more detailed comment for each variable helps. Note: This will break run-as-user uploads started prior to the upgrade to 18.XX and executed after the upgrade. It is a small switch to restore the old behavior but I'm not sure it is worth the complexity it adds to the file. ``` run_as_real_user = dataset.get('run_as_real_user', False) or dataset_get.('in_place', True) ``` Commit: fce9f13eba7f882025885f10c5f613772a93652e https://github.com/galaxyproject/galaxy/commit/fce9f13eba7f882025885f10c5f6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M lib/galaxy/tools/actions/upload_common.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #5206 from jmchilton/upload_option_clarify Re-organize edge case upload options for my own understanding. Compare: https://github.com/galaxyproject/galaxy/compare/9adfa316913d...fce9f13eba7f

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[galaxyproject/galaxy] e5be2c: Fix Python3 compatibility for lib/galaxy/web/
by GitHub 13 Dec '17

13 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e5be2c363a0df6d847026d584a9e79e935cb268b https://github.com/galaxyproject/galaxy/commit/e5be2c363a0df6d847026d584a9e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M .ci/py3_sources.txt M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/security/__init__.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py Log Message: ----------- Fix Python3 compatibility for lib/galaxy/web/ Commit: 9adfa316913d348e922deb5c96e33046229034d6 https://github.com/galaxyproject/galaxy/commit/9adfa316913d348e922deb5c96e3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M .ci/py3_sources.txt M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/security/__init__.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py Log Message: ----------- Merge pull request #5200 from nsoranzo/python3 Fix Python3 compatibility for lib/galaxy/web/ Compare: https://github.com/galaxyproject/galaxy/compare/c4680394b8ac...9adfa316913d

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[galaxyproject/galaxy] 972b1c: Remove the deprecated OpenID backend of yahoo
by GitHub 13 Dec '17

13 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 972b1cbe236ce3a02d11d7864c59801bd9271ba7 https://github.com/galaxyproject/galaxy/commit/972b1cbe236ce3a02d11d7864c59… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M config/openid_conf.xml.sample Log Message: ----------- Remove the deprecated OpenID backend of yahoo Commit: 5d09c5e85fb3da7ca383144bf21625d51fd0cc20 https://github.com/galaxyproject/galaxy/commit/5d09c5e85fb3da7ca383144bf216… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: R openid/yahoo.xml Log Message: ----------- Deleted Yahoo openid endpoint url. Commit: c4680394b8acd71a012443f041ace33ab52723c0 https://github.com/galaxyproject/galaxy/commit/c4680394b8acd71a012443f041ac… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M config/openid_conf.xml.sample R openid/yahoo.xml Log Message: ----------- Merge pull request #5208 from VJalili/patch-5 Removed Yahoo OpenID support Compare: https://github.com/galaxyproject/galaxy/compare/84c069e65902...c4680394b8ac

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[galaxyproject/galaxy] 41dbb8: Remove SampleDataset and RequestType references fr...
by GitHub 13 Dec '17

13 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 41dbb88e2b1d85d9001d9ded279e1849db8328c5 https://github.com/galaxyproject/galaxy/commit/41dbb88e2b1d85d9001d9ded279e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M templates/display_common.mako Log Message: ----------- Remove SampleDataset and RequestType references from display_common; this prevents any use of this mako currently. Commit: 29c61624d67886d7d252532a24a6ddc8073f7e9f https://github.com/galaxyproject/galaxy/commit/29c61624d67886d7d252532a24a6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- More request type cruft; seems to be unused and it'd blow up if tried to use Commit: 84c069e65902dbe32e53c490a0879988029a981b https://github.com/galaxyproject/galaxy/commit/84c069e65902dbe32e53c490a087… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M lib/galaxy/security/__init__.py M templates/display_common.mako Log Message: ----------- Merge pull request #5204 from dannon/sampletracking-removal-followup Sample tracking removal cleanup Compare: https://github.com/galaxyproject/galaxy/compare/82f9f8eb9896...84c069e65902

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[galaxyproject/galaxy] b3dc79: Python3: use collections.Mapping instead of remove...
by GitHub 12 Dec '17

12 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b3dc7923dbe1b04060d9c173287d3626ce231802 https://github.com/galaxyproject/galaxy/commit/b3dc7923dbe1b04060d9c173287d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M tools/stats/aggregate_scores_in_intervals.py Log Message: ----------- Python3: use collections.Mapping instead of removed DictMixin Commit: 82f9f8eb9896982f2f14e176a44ae6135116df30 https://github.com/galaxyproject/galaxy/commit/82f9f8eb9896982f2f14e176a44a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M tools/stats/aggregate_scores_in_intervals.py Log Message: ----------- Merge pull request #5199 from nsoranzo/python3 Python3: use collections.Mapping instead of removed DictMixin Compare: https://github.com/galaxyproject/galaxy/compare/d84fd9514a54...82f9f8eb9896

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