galaxy-commits July 2017

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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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[galaxyproject/galaxy] 12f0ac: Revert "Revert "[release_17.05] Patch bug preventi...
by GitHub 28 Jul '17

28 Jul '17

Branch: refs/heads/revert-4356-revert-4355-patch-wrong-folder-id 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""

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[galaxyproject/galaxy]
by GitHub 28 Jul '17

28 Jul '17

Branch: refs/heads/revert-4355-patch-wrong-folder-id Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] ecfb90: Revert "[release_17.05] Patch bug preventing creat...
by GitHub 28 Jul '17

28 Jul '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: ecfb90ef9f8037575db2e62ae49d8bbb7e4e427b https://github.com/galaxyproject/galaxy/commit/ecfb90ef9f8037575db2e62ae49d… 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 R 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 R static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Revert "[release_17.05] Patch bug preventing creation of dataset library folders" Commit: 163e4ebbe1fbfc5f1f97b5aabc804621fdd426c9 https://github.com/galaxyproject/galaxy/commit/163e4ebbe1fbfc5f1f97b5aabc80… 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 R 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 R static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #4356 from galaxyproject/revert-4355-patch-wrong-folder-id Revert "[release_17.05] Patch bug preventing creation of dataset library folders" Compare: https://github.com/galaxyproject/galaxy/compare/a2229783177b...163e4ebbe1fb

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[galaxyproject/galaxy] ecfb90: Revert "[release_17.05] Patch bug preventing creat...
by GitHub 28 Jul '17

28 Jul '17

Branch: refs/heads/revert-4355-patch-wrong-folder-id Home: https://github.com/galaxyproject/galaxy Commit: ecfb90ef9f8037575db2e62ae49d8bbb7e4e427b https://github.com/galaxyproject/galaxy/commit/ecfb90ef9f8037575db2e62ae49d… 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 R 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 R static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Revert "[release_17.05] Patch bug preventing creation of dataset library folders"

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galaxy-commits July 2017