February 2019 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 4372b4: Simplify tag handling in history export.
by Dannon 25 Feb '19

25 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4372b493aa3781857c30926933e0324ac30f8517 https://github.com/galaxyproject/galaxy/commit/4372b493aa3781857c30926933e0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Simplify tag handling in history export. Not yet used in import so we might as well simplify our lives and synchronize this with API exports before we actually start using them. Commit: 9d5e532df2d5c7ec976a28e4f7591694baaf3077 https://github.com/galaxyproject/galaxy/commit/9d5e532df2d5c7ec976a28e4f759… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-02-25 (Mon, 25 Feb 2019) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Merge pull request #7369 from jmchilton/imp_exp_simple_3 Simplify tag handling in history export. Compare: https://github.com/galaxyproject/galaxy/compare/67bb91348bb2...9d5e532df2d5

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[galaxyproject/galaxy] 73fc69: specify generic exceptions more precisely
by Nicola Soranzo 24 Feb '19

24 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 73fc69d7899984446d52091ea179320dd08da0f2 https://github.com/galaxyproject/galaxy/commit/73fc69d7899984446d52091ea179… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- specify generic exceptions more precisely Commit: 564d0d7f9584f09c2ebf1af1f24c61c4226132c5 https://github.com/galaxyproject/galaxy/commit/564d0d7f9584f09c2ebf1af1f24c… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- choose better exceptions class Co-Authored-By: martenson <marten(a)bx.psu.edu> Commit: c459d9a98ac1101438bc0b3cf747b84958b69e0c https://github.com/galaxyproject/galaxy/commit/c459d9a98ac1101438bc0b3cf747… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- choose better exceptions class Co-Authored-By: martenson <marten(a)bx.psu.edu> Commit: 09a3802602c512ed51e02c243447db0776921f56 https://github.com/galaxyproject/galaxy/commit/09a3802602c512ed51e02c243447… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- choose better exceptions class Co-Authored-By: martenson <marten(a)bx.psu.edu> Commit: b197fedf60b8e82f68bdb61e05d2f6d2bad33a7b https://github.com/galaxyproject/galaxy/commit/b197fedf60b8e82f68bdb61e05d2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M lib/galaxy/exceptions/error_codes.json Log Message: ----------- improve exception message per @nsoranzo Commit: 67bb91348bb26584b83592542424d329714d6b47 https://github.com/galaxyproject/galaxy/commit/67bb91348bb26584b83592542424… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-24 (Sun, 24 Feb 2019) Changed paths: M lib/galaxy/exceptions/error_codes.json M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Merge pull request #7397 from martenson/focus-exceptions specify generic exceptions more precisely Compare: https://github.com/galaxyproject/galaxy/compare/7324db1273da...67bb91348bb2

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[galaxyproject/infrastructure-playbook] d52874: WIP Mailman 3 server
by Nate Coraor 22 Feb '19

22 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: d52874f9e445bf86950e3beb7945f212ead2c9fb https://github.com/galaxyproject/infrastructure-playbook/commit/d52874f9e44… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: A env/mailman/TODO.txt A env/mailman/baseenv.yml A env/mailman/bootstrap.yml A env/mailman/files/ssl A env/mailman/group_vars/all.yml A env/mailman/group_vars/listservers.yml A env/mailman/group_vars/mailservers-mx.yml A env/mailman/group_vars/sslservers A env/mailman/inventory A env/mailman/listservers.yml A env/mailman/mailservers.yml A env/mailman/playbook.yml A env/mailman/templates/nginx/anvil-lists.j2 A env/mailman/templates/nginx/galaxy-lists.j2 A env/mailman/templates/nginx/mailman.j2 A env/mailman/templates/postfix/relay_restrictions.j2 A env/mailman/webservers.yml Log Message: ----------- WIP Mailman 3 server

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[galaxyproject/infrastructure-playbook] 9e3bb0: Proxy training site instead of redirecting
by Nate Coraor 22 Feb '19

22 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 9e3bb0847d99cff0a7a721cc0d9566f12d0deb2c https://github.com/galaxyproject/infrastructure-playbook/commit/9e3bb0847d9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-08 (Fri, 08 Feb 2019) Changed paths: M env/galaxy/templates/nginx/training.j2 Log Message: ----------- Proxy training site instead of redirecting

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[galaxyproject/galaxy] 3bc903: Add a brief security note for 19.01.
by Martin Cech 22 Feb '19

22 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3bc90381a535aa4ca42c772e1bfca92765230f04 https://github.com/galaxyproject/galaxy/commit/3bc90381a535aa4ca42c772e1bfc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M doc/source/releases/19.01_announce.rst Log Message: ----------- Add a brief security note for 19.01. Commit: 7324db1273da3ff1ea6ab60cfd7da60959d1bb47 https://github.com/galaxyproject/galaxy/commit/7324db1273da3ff1ea6ab60cfd7d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M doc/source/releases/19.01_announce.rst Log Message: ----------- Merge pull request #7405 from jmchilton/release_notes_update Add a brief security note for 19.01. Compare: https://github.com/galaxyproject/galaxy/compare/ef8f20800299...7324db1273da

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[galaxyproject/galaxy] b6d567: Update galaxy.yml.sample for prefix config
by Nate Coraor 22 Feb '19

22 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b6d5675f5da1e91aece2df4af5d037072e897185 https://github.com/galaxyproject/galaxy/commit/b6d5675f5da1e91aece2df4af5d0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Update galaxy.yml.sample for prefix config Commit: ae8bf6f793edda9211b59c68d6c029b9fa74154a https://github.com/galaxyproject/galaxy/commit/ae8bf6f793edda9211b59c68d6c0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: A doc/source/releases/19.01.rst M doc/source/releases/19.01_announce.rst A doc/source/releases/19.05_announce.rst Log Message: ----------- Release notes raw. Commit: b5713ca170cfeb574063a2ec9dca8adbee1f7d74 https://github.com/galaxyproject/galaxy/commit/b5713ca170cfeb574063a2ec9dca… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M doc/source/releases/19.01.rst M doc/source/releases/19.01_announce.rst M doc/source/releases/index.rst Log Message: ----------- Progress on 19.01 release notes... Commit: 16af73423f2c5a1181b016dcc01955c1c2ab037a https://github.com/galaxyproject/galaxy/commit/16af73423f2c5a1181b016dcc019… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M doc/source/releases/19.01.rst Log Message: ----------- Update doc/source/releases/19.01.rst Co-Authored-By: jmchilton <jmchilton(a)gmail.com> Commit: 072b8d73eca68201bcf691c7dc9fa22272433ac3 https://github.com/galaxyproject/galaxy/commit/072b8d73eca68201bcf691c7dc9f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M doc/source/releases/19.01.rst Log Message: ----------- Update doc/source/releases/19.01.rst Co-Authored-By: jmchilton <jmchilton(a)gmail.com> Commit: 2a3555d9d73e4a9f72b003a319698f7e8fb01d3c https://github.com/galaxyproject/galaxy/commit/2a3555d9d73e4a9f72b003a31969… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M doc/source/releases/19.01.rst M doc/source/releases/19.01_announce.rst Log Message: ----------- Better Singularity summary thanks to @mvdbeek. Commit: 94bcb8d00f3fc8817cdca5ef3ab383e705b950d6 https://github.com/galaxyproject/galaxy/commit/94bcb8d00f3fc8817cdca5ef3ab3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M doc/source/releases/19.01.rst Log Message: ----------- More fixes to 19.01 release notes. Commit: ca4acf78df6cfc89f76b0f09143d0301aac234b4 https://github.com/galaxyproject/galaxy/commit/ca4acf78df6cfc89f76b0f09143d… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M doc/source/releases/19.01_announce.rst Log Message: ----------- Sort PR numbers Small fixes. Commit: 37a93972d59459ffd50d340d53c5f278b3e15dae https://github.com/galaxyproject/galaxy/commit/37a93972d59459ffd50d340d53c5… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M doc/source/releases/19.01.rst Log Message: ----------- Fix PR link Commit: d72f82de98f464ace59db312fe9db398793c3494 https://github.com/galaxyproject/galaxy/commit/d72f82de98f464ace59db312fe9d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- remove Paste config option, reword URL prefix Commit: 6d24026ba59fbe3e534067cd8dce76d4e6a2f38f https://github.com/galaxyproject/galaxy/commit/6d24026ba59fbe3e534067cd8dce… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #11 from martenson/fix_galaxy_yml_prefix_comments remove Paste config option, reword URL prefix Commit: b4fc7c19a80c38b595cb08f05fd6765a07f95920 https://github.com/galaxyproject/galaxy/commit/b4fc7c19a80c38b595cb08f05fd6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-20 (Wed, 20 Feb 2019) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Report line number mismatch in sort collection tool Otherwise this would just fail because sorted_elements is undefined. I don't think there can be a HDA without metadata, so I've dropped that check. Commit: 015ce5cedc21c1a318d6455534f52f8acc3d36ca https://github.com/galaxyproject/galaxy/commit/015ce5cedc21c1a318d6455534f5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-20 (Wed, 20 Feb 2019) Changed paths: A doc/source/releases/19.01.rst M doc/source/releases/19.01_announce.rst A doc/source/releases/19.05_announce.rst M doc/source/releases/index.rst Log Message: ----------- Merge pull request #7308 from jmchilton/19.01_release_notes [19.01] Release notes for 19.01. Commit: 648d01685bf26c9dcb5231cc61755d95a4696928 https://github.com/galaxyproject/galaxy/commit/648d01685bf26c9dcb5231cc6175… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-20 (Wed, 20 Feb 2019) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #7390 from mvdbeek/more_useful_error_message [19.01] Report line number mismatch in sort collection tool Commit: 8c9c27b7f6bd14581af870b0d38339d90501e464 https://github.com/galaxyproject/galaxy/commit/8c9c27b7f6bd14581af870b0d383… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst Log Message: ----------- Drop filter-with from docs / .sample Commit: 726ad9a0f68d134d7bc2ffa37ad3f369787d19da https://github.com/galaxyproject/galaxy/commit/726ad9a0f68d134d7bc2ffa37ad3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M Makefile M scripts/common_startup.sh Log Message: ----------- Bump yarn's network timeout from 2 minutes to 5 minutes. Commit: 4ad4fe59be7bbcc1917d3a1e039fa3f3a8367709 https://github.com/galaxyproject/galaxy/commit/4ad4fe59be7bbcc1917d3a1e039f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M Makefile M scripts/common_startup.sh Log Message: ----------- Merge pull request #7399 from dannon/bump_yarn_network_tolerance [19.01] Bump yarn network tolerance Commit: 1a0f067590d8dcd88857e38d58f62b95a467c641 https://github.com/galaxyproject/galaxy/commit/1a0f067590d8dcd88857e38d58f6… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- change config schema to reflect removing paste options Commit: 351c188830793946ce6fa71dfaab95fe3af7cf7a https://github.com/galaxyproject/galaxy/commit/351c188830793946ce6fa71dfaab… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml Log Message: ----------- Remove ``filter-with`` and update ``cookie_path`` options also for Tool Shed and Reports Commit: a83eb67775442f37b22ff20203b88a234ab11bec https://github.com/galaxyproject/galaxy/commit/a83eb67775442f37b22ff20203b8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml Log Message: ----------- Slight rewording of the cookie_path option description, and corrections to file_path and new_file_path descriptions. Commit: 5fc5b4aaab373d344f6d286e9dab4b2ce78f98eb https://github.com/galaxyproject/galaxy/commit/5fc5b4aaab373d344f6d286e9dab… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml Log Message: ----------- Merge pull request #12 from natefoo/mvdbeek-fix_galaxy_yml_prefix_comments Slight rewording of the cookie_path option description, and corrections to file_path and new_file_path descriptions Commit: 656b3c2f87a0dfd49284e113d7df6f2b88b43464 https://github.com/galaxyproject/galaxy/commit/656b3c2f87a0dfd49284e113d7df… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Refactor dataset fetching in get/set dataset method in web controller. Commit: 1529758ecb781a8bcbfe727acad9e7f2209c824b https://github.com/galaxyproject/galaxy/commit/1529758ecb781a8bcbfe727acad9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: 2f973ac7fa7726ff309a8a8893962fbcd58ffded https://github.com/galaxyproject/galaxy/commit/2f973ac7fa7726ff309a8a889396… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Commit: 8651e1eea3779233c1dff3c28ae7b4a0c3fb9735 https://github.com/galaxyproject/galaxy/commit/8651e1eea3779233c1dff3c28ae7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Merge branch 'release_18.09' into release_19.01 Commit: 9b72f5a880e39d1a3fd99d8aa6b1509f4e8d6ad1 https://github.com/galaxyproject/galaxy/commit/9b72f5a880e39d1a3fd99d8aa6b1… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml Log Message: ----------- Merge pull request #7216 from mvdbeek/fix_galaxy_yml_prefix_comments [18.09] Update configuration samples Commit: 808aa5bef7fb5e0aa24818cc4bd9da647ccd3f01 https://github.com/galaxyproject/galaxy/commit/808aa5bef7fb5e0aa24818cc4bd9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.09' into release_19.01 Commit: ef8f208002993b4e2051a8851e0bdcad804ee339 https://github.com/galaxyproject/galaxy/commit/ef8f208002993b4e2051a8851e0b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M Makefile M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst A doc/source/releases/19.01.rst M doc/source/releases/19.01_announce.rst A doc/source/releases/19.05_announce.rst M doc/source/releases/index.rst M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml M scripts/common_startup.sh Log Message: ----------- Merge remote-tracking branch 'upstream/release_19.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/830c21d6f5ef...ef8f20800299

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[galaxyproject/galaxy] b6d567: Update galaxy.yml.sample for prefix config
by Nate Coraor 22 Feb '19

22 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: b6d5675f5da1e91aece2df4af5d037072e897185 https://github.com/galaxyproject/galaxy/commit/b6d5675f5da1e91aece2df4af5d0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Update galaxy.yml.sample for prefix config Commit: d72f82de98f464ace59db312fe9db398793c3494 https://github.com/galaxyproject/galaxy/commit/d72f82de98f464ace59db312fe9d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- remove Paste config option, reword URL prefix Commit: 6d24026ba59fbe3e534067cd8dce76d4e6a2f38f https://github.com/galaxyproject/galaxy/commit/6d24026ba59fbe3e534067cd8dce… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #11 from martenson/fix_galaxy_yml_prefix_comments remove Paste config option, reword URL prefix Commit: 8c9c27b7f6bd14581af870b0d38339d90501e464 https://github.com/galaxyproject/galaxy/commit/8c9c27b7f6bd14581af870b0d383… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst Log Message: ----------- Drop filter-with from docs / .sample Commit: 1a0f067590d8dcd88857e38d58f62b95a467c641 https://github.com/galaxyproject/galaxy/commit/1a0f067590d8dcd88857e38d58f6… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- change config schema to reflect removing paste options Commit: 351c188830793946ce6fa71dfaab95fe3af7cf7a https://github.com/galaxyproject/galaxy/commit/351c188830793946ce6fa71dfaab… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml Log Message: ----------- Remove ``filter-with`` and update ``cookie_path`` options also for Tool Shed and Reports Commit: a83eb67775442f37b22ff20203b88a234ab11bec https://github.com/galaxyproject/galaxy/commit/a83eb67775442f37b22ff20203b8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml Log Message: ----------- Slight rewording of the cookie_path option description, and corrections to file_path and new_file_path descriptions. Commit: 5fc5b4aaab373d344f6d286e9dab4b2ce78f98eb https://github.com/galaxyproject/galaxy/commit/5fc5b4aaab373d344f6d286e9dab… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml Log Message: ----------- Merge pull request #12 from natefoo/mvdbeek-fix_galaxy_yml_prefix_comments Slight rewording of the cookie_path option description, and corrections to file_path and new_file_path descriptions Commit: 9b72f5a880e39d1a3fd99d8aa6b1509f4e8d6ad1 https://github.com/galaxyproject/galaxy/commit/9b72f5a880e39d1a3fd99d8aa6b1… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml Log Message: ----------- Merge pull request #7216 from mvdbeek/fix_galaxy_yml_prefix_comments [18.09] Update configuration samples Commit: 808aa5bef7fb5e0aa24818cc4bd9da647ccd3f01 https://github.com/galaxyproject/galaxy/commit/808aa5bef7fb5e0aa24818cc4bd9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.09' into release_19.01 Compare: https://github.com/galaxyproject/galaxy/compare/8651e1eea377...808aa5bef7fb

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[galaxyproject/galaxy] b6d567: Update galaxy.yml.sample for prefix config
by Nicola Soranzo 22 Feb '19

22 Feb '19

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: b6d5675f5da1e91aece2df4af5d037072e897185 https://github.com/galaxyproject/galaxy/commit/b6d5675f5da1e91aece2df4af5d0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Update galaxy.yml.sample for prefix config Commit: d72f82de98f464ace59db312fe9db398793c3494 https://github.com/galaxyproject/galaxy/commit/d72f82de98f464ace59db312fe9d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- remove Paste config option, reword URL prefix Commit: 6d24026ba59fbe3e534067cd8dce76d4e6a2f38f https://github.com/galaxyproject/galaxy/commit/6d24026ba59fbe3e534067cd8dce… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #11 from martenson/fix_galaxy_yml_prefix_comments remove Paste config option, reword URL prefix Commit: 8c9c27b7f6bd14581af870b0d38339d90501e464 https://github.com/galaxyproject/galaxy/commit/8c9c27b7f6bd14581af870b0d383… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst Log Message: ----------- Drop filter-with from docs / .sample Commit: 1a0f067590d8dcd88857e38d58f62b95a467c641 https://github.com/galaxyproject/galaxy/commit/1a0f067590d8dcd88857e38d58f6… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- change config schema to reflect removing paste options Commit: 351c188830793946ce6fa71dfaab95fe3af7cf7a https://github.com/galaxyproject/galaxy/commit/351c188830793946ce6fa71dfaab… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml Log Message: ----------- Remove ``filter-with`` and update ``cookie_path`` options also for Tool Shed and Reports Commit: a83eb67775442f37b22ff20203b88a234ab11bec https://github.com/galaxyproject/galaxy/commit/a83eb67775442f37b22ff20203b8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml Log Message: ----------- Slight rewording of the cookie_path option description, and corrections to file_path and new_file_path descriptions. Commit: 5fc5b4aaab373d344f6d286e9dab4b2ce78f98eb https://github.com/galaxyproject/galaxy/commit/5fc5b4aaab373d344f6d286e9dab… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml Log Message: ----------- Merge pull request #12 from natefoo/mvdbeek-fix_galaxy_yml_prefix_comments Slight rewording of the cookie_path option description, and corrections to file_path and new_file_path descriptions Commit: 9b72f5a880e39d1a3fd99d8aa6b1509f4e8d6ad1 https://github.com/galaxyproject/galaxy/commit/9b72f5a880e39d1a3fd99d8aa6b1… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml Log Message: ----------- Merge pull request #7216 from mvdbeek/fix_galaxy_yml_prefix_comments [18.09] Update configuration samples Compare: https://github.com/galaxyproject/galaxy/compare/2f973ac7fa77...9b72f5a880e3

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[galaxyproject/galaxy] 656b3c: Refactor dataset fetching in get/set dataset metho...
by John Chilton 22 Feb '19

22 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 656b3c2f87a0dfd49284e113d7df6f2b88b43464 https://github.com/galaxyproject/galaxy/commit/656b3c2f87a0dfd49284e113d7df… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Refactor dataset fetching in get/set dataset method in web controller. Commit: 1529758ecb781a8bcbfe727acad9e7f2209c824b https://github.com/galaxyproject/galaxy/commit/1529758ecb781a8bcbfe727acad9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: 2f973ac7fa7726ff309a8a8893962fbcd58ffded https://github.com/galaxyproject/galaxy/commit/2f973ac7fa7726ff309a8a889396… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Commit: 8651e1eea3779233c1dff3c28ae7b4a0c3fb9735 https://github.com/galaxyproject/galaxy/commit/8651e1eea3779233c1dff3c28ae7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Merge branch 'release_18.09' into release_19.01 Compare: https://github.com/galaxyproject/galaxy/compare/4ad4fe59be7b...8651e1eea377

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[galaxyproject/galaxy] 656b3c: Refactor dataset fetching in get/set dataset metho...
by John Chilton 22 Feb '19

22 Feb '19

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 656b3c2f87a0dfd49284e113d7df6f2b88b43464 https://github.com/galaxyproject/galaxy/commit/656b3c2f87a0dfd49284e113d7df… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Refactor dataset fetching in get/set dataset method in web controller. Commit: 1529758ecb781a8bcbfe727acad9e7f2209c824b https://github.com/galaxyproject/galaxy/commit/1529758ecb781a8bcbfe727acad9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: 2f973ac7fa7726ff309a8a8893962fbcd58ffded https://github.com/galaxyproject/galaxy/commit/2f973ac7fa7726ff309a8a889396… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Compare: https://github.com/galaxyproject/galaxy/compare/9c9c8a5d50d7...2f973ac7fa77

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