- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 47ed81: Remove unreachable print statement
by John Chilton 26 Feb '19

26 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 47ed81feb95c092587c68deb07e247c3a4d29bff https://github.com/galaxyproject/galaxy/commit/47ed81feb95c092587c68deb07e2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M tools/data_source/upload.py Log Message: ----------- Remove unreachable print statement I don't think an exception could ever occur here. Commit: ed375993ebc43112e03f58779d7c8c104e67956a https://github.com/galaxyproject/galaxy/commit/ed375993ebc43112e03f58779d7c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M lib/galaxy/datatypes/proteomics.py Log Message: ----------- Fix analyze75 hdr file upload when convert newlines is on Commit: bd25ff919c2f94dea446e656a757c61f8237db89 https://github.com/galaxyproject/galaxy/commit/bd25ff919c2f94dea446e656a757… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M lib/galaxy/datatypes/proteomics.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #7414 from mvdbeek/fix_analyze_75 [19.01] Fix analyze 75 datatype upload Commit: 14f3ce3b5092467e3d9dde9bd94fdab5f6b604b2 https://github.com/galaxyproject/galaxy/commit/14f3ce3b5092467e3d9dde9bd94f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Fix workflow interface drop to import Commit: 1583eecfdb338aae17fbb199160f7937e3b0ec01 https://github.com/galaxyproject/galaxy/commit/1583eecfdb338aae17fbb199160f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/components/admin/ErrorStack.vue M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/scss/base.scss Log Message: ----------- Client formatting sync for 19.01 Commit: 7553326ba1af32e50c3695cbb67795fc11f0ecdc https://github.com/galaxyproject/galaxy/commit/7553326ba1af32e50c3695cbb677… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/components/admin/ErrorStack.vue M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/scss/base.scss Log Message: ----------- Merge pull request #7415 from dannon/fix-workflow-drop-hack [19.01] Fix workflow list drop-to-upload Commit: 574cc22a08d6c109abf12bad02cbb6e47c512df6 https://github.com/galaxyproject/galaxy/commit/574cc22a08d6c109abf12bad02cb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/datatypes/proteomics.py M tools/data_source/upload.py Log Message: ----------- Merge branch 'release_19.01' into dev Commit: fdb18045b76220b847163857e6e58acc19cef347 https://github.com/galaxyproject/galaxy/commit/fdb18045b76220b847163857e6e5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 19.01 Commit: 68c835e8ac2c68a3ddc2d02ec7e39e5b78c08485 https://github.com/galaxyproject/galaxy/commit/68c835e8ac2c68a3ddc2d02ec7e3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: Log Message: ----------- Merge branch 'release_19.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/ccdf4fb0b60e...68c835e8ac2c

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[galaxyproject/galaxy] fdb180: Update version to 19.01
by John Chilton 26 Feb '19

26 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: fdb18045b76220b847163857e6e58acc19cef347 https://github.com/galaxyproject/galaxy/commit/fdb18045b76220b847163857e6e5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 19.01

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[galaxyproject/galaxy] 14f3ce: Fix workflow interface drop to import
by John Chilton 26 Feb '19

26 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 14f3ce3b5092467e3d9dde9bd94fdab5f6b604b2 https://github.com/galaxyproject/galaxy/commit/14f3ce3b5092467e3d9dde9bd94f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Fix workflow interface drop to import Commit: 1583eecfdb338aae17fbb199160f7937e3b0ec01 https://github.com/galaxyproject/galaxy/commit/1583eecfdb338aae17fbb199160f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/components/admin/ErrorStack.vue M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/scss/base.scss Log Message: ----------- Client formatting sync for 19.01 Commit: 7553326ba1af32e50c3695cbb67795fc11f0ecdc https://github.com/galaxyproject/galaxy/commit/7553326ba1af32e50c3695cbb677… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/components/admin/ErrorStack.vue M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/scss/base.scss Log Message: ----------- Merge pull request #7415 from dannon/fix-workflow-drop-hack [19.01] Fix workflow list drop-to-upload Compare: https://github.com/galaxyproject/galaxy/compare/bd25ff919c2f...7553326ba1af

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[galaxyproject/galaxy] 47ed81: Remove unreachable print statement
by Martin Cech 26 Feb '19

26 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 47ed81feb95c092587c68deb07e247c3a4d29bff https://github.com/galaxyproject/galaxy/commit/47ed81feb95c092587c68deb07e2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M tools/data_source/upload.py Log Message: ----------- Remove unreachable print statement I don't think an exception could ever occur here. Commit: ed375993ebc43112e03f58779d7c8c104e67956a https://github.com/galaxyproject/galaxy/commit/ed375993ebc43112e03f58779d7c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M lib/galaxy/datatypes/proteomics.py Log Message: ----------- Fix analyze75 hdr file upload when convert newlines is on Commit: bd25ff919c2f94dea446e656a757c61f8237db89 https://github.com/galaxyproject/galaxy/commit/bd25ff919c2f94dea446e656a757… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M lib/galaxy/datatypes/proteomics.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #7414 from mvdbeek/fix_analyze_75 [19.01] Fix analyze 75 datatype upload Compare: https://github.com/galaxyproject/galaxy/compare/808aa5bef7fb...bd25ff919c2f

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[galaxyproject/galaxy] f7a3c0: Fix settings of pie charts
by Dannon 26 Feb '19

26 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f7a3c0b6fef1e55b0012b1287931644e5afd6e8e https://github.com/galaxyproject/galaxy/commit/f7a3c0b6fef1e55b0012b1287931… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M config/plugins/visualizations/nvd3/nvd3_bar/package.json M config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.css M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js M config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml Log Message: ----------- Fix settings of pie charts Commit: 402fd2896bf8e9556db5322e13e3485303d166d2 https://github.com/galaxyproject/galaxy/commit/402fd2896bf8e9556db5322e13e3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M client/galaxy/style/scss/ui.scss Log Message: ----------- Set portlet height to auto Commit: 96b4d1efc23c22c2085a7810f1b62d8bdd2c5cc8 https://github.com/galaxyproject/galaxy/commit/96b4d1efc23c22c2085a7810f1b6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml Log Message: ----------- Fix setting remaining setting for label column placement Commit: ccdf4fb0b60eb1af6131ab20ce827d4549a75c97 https://github.com/galaxyproject/galaxy/commit/ccdf4fb0b60eb1af6131ab20ce82… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M client/galaxy/style/scss/ui.scss M config/plugins/visualizations/nvd3/nvd3_bar/package.json M config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.css M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js M config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml Log Message: ----------- Merge pull request #7396 from guerler/fix_pie_chart Fix pie chart and portlet height in flexboxes Compare: https://github.com/galaxyproject/galaxy/compare/9d5e532df2d5...ccdf4fb0b60e

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[galaxyproject/infrastructure-playbook] 82c4d3: Certbot support for the Mailman server
by Nate Coraor 25 Feb '19

25 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 82c4d3bc724b85cfef9aa5b7d682ec4a6bec991b https://github.com/galaxyproject/infrastructure-playbook/commit/82c4d3bc724… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-25 (Mon, 25 Feb 2019) Changed paths: M env/mailman/TODO.txt M env/mailman/group_vars/listservers.yml R env/mailman/templates/nginx/anvil-lists.j2 R env/mailman/templates/nginx/galaxy-lists.j2 M env/mailman/templates/nginx/mailman.j2 A env/mailman/templates/nginx/mailman_ssl.j2 M env/mailman/webservers.yml Log Message: ----------- Certbot support for the Mailman server

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[galaxyproject/usegalaxy-playbook] 55f1d4: Installed column_maker 1.2.0
by Dave B. 25 Feb '19

25 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 55f1d464eb2bdbcce25accc72ddae3e49cfba539 https://github.com/galaxyproject/usegalaxy-playbook/commit/55f1d464eb2bdbcc… Author: Dave B <dave(a)bx.psu.edu> Date: 2019-02-25 (Mon, 25 Feb 2019) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Installed column_maker 1.2.0

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[galaxyproject/usegalaxy-playbook] 9f32b1: Update Main shed_tool_conf
by Martin Cech 25 Feb '19

25 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9f32b1951135d95f8bf25cd6487a0b5f4b4d2ee9 https://github.com/galaxyproject/usegalaxy-playbook/commit/9f32b1951135d95f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-25 (Mon, 25 Feb 2019) Changed paths: M env/main/files/galaxy/galaxy_version.yml M env/main/files/galaxy/var/migrated_tools_conf.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Main shed_tool_conf

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

22 Feb '19

Branch: refs/heads/release_18.05 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 Compare: https://github.com/galaxyproject/galaxy/compare/c17c20b8cf7c...1529758ecb78

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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_18.01 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.

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[galaxyproject/ansible-galaxy] e4fbb8: Replace: pip_virtualenv_command > galaxy_virtualen...
by Enis Afgan 22 Feb '19

22 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: e4fbb80576d44b22c69eda13b8d3909e9c7b1fbb https://github.com/galaxyproject/ansible-galaxy/commit/e4fbb80576d44b22c69e… Author: Sergey Golitsynskiy <sgolitsynskiy(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M README.md M tasks/dependencies.yml M tasks/virtualenv.yml Log Message: ----------- Replace: pip_virtualenv_command > galaxy_virtualenv_command Keep backword compatible. Commit: badffb979b9ab537b7ce542cb3d5d8219606ae39 https://github.com/galaxyproject/ansible-galaxy/commit/badffb979b9ab537b7ce… Author: Enis Afgan <afgane(a)gmail.com> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M README.md M tasks/dependencies.yml M tasks/virtualenv.yml Log Message: ----------- Merge pull request #62 from ic4f/master Replace: pip_virtualenv_command > galaxy_virtualenv_command Compare: https://github.com/galaxyproject/ansible-galaxy/compare/3e9ff5520254...badf…

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[galaxyproject/galaxy] f00fb3: Place oidc login button under regular login form
by Dannon 22 Feb '19

22 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f00fb3e4add155268aaf7e17228699734b0bfeab https://github.com/galaxyproject/galaxy/commit/f00fb3e4add155268aaf7e172286… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M client/galaxy/scripts/components/login/Login.vue Log Message: ----------- Place oidc login button under regular login form Commit: 87261f625368f55b2d7ba7aa1711fd462e2afcb6 https://github.com/galaxyproject/galaxy/commit/87261f625368f55b2d7ba7aa1711… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M client/galaxy/scripts/components/login/Login.vue Log Message: ----------- Hide oidc options based on config setting Commit: 61a5c3b14f7e606b7d0513b2ae1cec3acf6b75b0 https://github.com/galaxyproject/galaxy/commit/61a5c3b14f7e606b7d0513b2ae1c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M client/galaxy/scripts/components/login/Login.vue Log Message: ----------- Use lower-case galaxy local variable name Commit: 66b01d2b32181b6ae526f90e0c4cbde85f19c4c3 https://github.com/galaxyproject/galaxy/commit/66b01d2b32181b6ae526f90e0c4c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M client/galaxy/scripts/components/login/Login.vue Log Message: ----------- Avoid computing oidc setting Commit: 2a05323daa84db46479f5ee9ca756dba51da45e7 https://github.com/galaxyproject/galaxy/commit/2a05323daa84db46479f5ee9ca75… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M client/galaxy/scripts/components/login/Login.vue M client/galaxy/scripts/entry/panels/tool-panel.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/user/user-model.js Log Message: ----------- Client formatting. Commit: 830c21d6f5ef34e4ddce498b2c02c9c4ae7ff027 https://github.com/galaxyproject/galaxy/commit/830c21d6f5ef34e4ddce498b2c02… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M client/galaxy/scripts/components/login/Login.vue M client/galaxy/scripts/entry/panels/tool-panel.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/user/user-model.js Log Message: ----------- Merge branch 'move_google_login_button' into dev Compare: https://github.com/galaxyproject/galaxy/compare/c53fb623d8cf...830c21d6f5ef

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[galaxyproject/galaxy] eca238: Make pykube a conditional requirement
by John Chilton 22 Feb '19

22 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: eca238d7837928c7ee962f10435fd667d61ccc4c https://github.com/galaxyproject/galaxy/commit/eca238d7837928c7ee962f10435f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Make pykube a conditional requirement Commit: c82cd04ca820d65c9279872c029d712358e4c65f https://github.com/galaxyproject/galaxy/commit/c82cd04ca820d65c9279872c029d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Use standard os.environ Commit: 879d7c22b63733dfd5f9e1c6cbe368c97e06495d https://github.com/galaxyproject/galaxy/commit/879d7c22b63733dfd5f9e1c6cbe3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M test/base/integration_util.py A test/integration/test_kubernetes_runner.py Log Message: ----------- Add basic kubernetes integration test Currently times out becasue jobs aren't monitored succesfully. Commit: 4eed32dc4c86da17a525419ba985d4d06d7a768b https://github.com/galaxyproject/galaxy/commit/4eed32dc4c86da17a525419ba985… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pbs.py Log Message: ----------- Propagate selected shell to job_script Commit: 912fc61592a92fbed329501b38b35a591e556b2d https://github.com/galaxyproject/galaxy/commit/912fc61592a92fbed329501b38b3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Allow skipping pod_retrial Commit: e7b89122489083f80b0c183ff0a958a58d823118 https://github.com/galaxyproject/galaxy/commit/e7b89122489083f80b0c183ff0a9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Use galaxy's exisiting job_file abstraction This allows setting environment variables, job instrumentation, exit code checking and so on. Commit: 3498f87d8734ce5bc3341e546842dabe29b93d40 https://github.com/galaxyproject/galaxy/commit/3498f87d8734ce5bc3341e546842… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M test/integration/test_kubernetes_runner.py Log Message: ----------- Use sh as job shell for kubernetes test, bash is not available in default container Commit: 5dd10c4f86b07d9483b76c59511148bdce8949d3 https://github.com/galaxyproject/galaxy/commit/5dd10c4f86b07d9483b76c595111… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/tools/deps/dependencies.py Log Message: ----------- Drop mutable defaults Commit: 1a007682737af1b466a6a8545922e17c7f42fb19 https://github.com/galaxyproject/galaxy/commit/1a007682737af1b466a6a8545922… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Skip broken string encoding logic Commit: d2ed543ecd39fee1876fcbad063c1aa4c4c3ce33 https://github.com/galaxyproject/galaxy/commit/d2ed543ecd39fee1876fcbad063c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/godocker.py M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Remove return statements from queue_job, this is never consumed anywhere Commit: 1103ce1dccd0ac3dda0dca715da4cb0feafde4ee https://github.com/galaxyproject/galaxy/commit/1103ce1dccd0ac3dda0dca715da4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Remove commented out non-functional code in kubernetes runner. Commit: a23063b2dc3fdf82c645383fd36c3b6439b68f52 https://github.com/galaxyproject/galaxy/commit/a23063b2dc3fdf82c645383fd36c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Cleanup of kubernetes exception logging Commit: 4e39c0fc8488a4794870752f8895f61dc8d704cf https://github.com/galaxyproject/galaxy/commit/4e39c0fc8488a4794870752f8895… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py M test/integration/test_containerized_jobs.py M test/integration/test_job_recovery.py M test/integration/test_kubernetes_runner.py Log Message: ----------- Test cancelling jobs, running mulled containers on kubernetes Commit: 9019916ae2180afe6f35b6ead45f1ae294c2bfe9 https://github.com/galaxyproject/galaxy/commit/9019916ae2180afe6f35b6ead45f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M test/integration/test_kubernetes_runner.py Log Message: ----------- Fix test skipping Commit: 34c0a2940b69c59b20bbdd8df0944332cb59e64c https://github.com/galaxyproject/galaxy/commit/34c0a2940b69c59b20bbdd8df094… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Don't write fake stderr file Commit: 5c5f199f812ff68e7d061c047956aeaa3627632f https://github.com/galaxyproject/galaxy/commit/5c5f199f812ff68e7d061c047956… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M test/integration/test_kubernetes_runner.py Log Message: ----------- Add job properties test Commit: b43f1985d71fadf3f907feeab2b529408dc05588 https://github.com/galaxyproject/galaxy/commit/b43f1985d71fadf3f907feeab2b5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Capture stdout and stderr for kubernetes runner There is currently no way to discriminate stdout and stderr from kubernetes logs (https://github.com/kubernetes/kubernetes/issues/28167) but Galaxy really needs to know about the stderr. To work around this we capture the stdout and stderr into files using the approach outined in https://stackoverflow.com/a/692407. Commit: d0e749375a2e703f9f59e8794825867760ee7b44 https://github.com/galaxyproject/galaxy/commit/d0e749375a2e703f9f59e8794825… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Drop custom fail_job and stderr logging methods We now log stdout and stderr to files, so this isn't needed. Commit: 98b571e19aec1b182dbb636d23ab8a3ff290f30d https://github.com/galaxyproject/galaxy/commit/98b571e19aec1b182dbb636d23ab… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Remove user-cancelled jobs from monitor queue Commit: dc184567376ec25eba3d317c9a70d2a27d4aefed https://github.com/galaxyproject/galaxy/commit/dc184567376ec25eba3d317c9a70… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: A lib/galaxy/util/bytesize.py Log Message: ----------- Add utility class for manipulating byte sizes Commit: c61c790fccc84f06991d48dcbea70ef8181fe452 https://github.com/galaxyproject/galaxy/commit/c61c790fccc84f06991d48dcbea7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh M test/functional/tools/samples_tool_conf.xml M test/integration/test_kubernetes_runner.py Log Message: ----------- Make kubernetes pass GALAXY_SLOTS and GALAXY_MEMORY_MB Also drops __transform_cpu_value, incoming values are always strings, so this wasn't functional in any case. Commit: fe02dbbf8107b8ded12cb9c76fd1686515a47dd4 https://github.com/galaxyproject/galaxy/commit/fe02dbbf8107b8ded12cb9c76fd1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M config/job_conf.xml.sample_advanced Log Message: ----------- Fix typo in config/job_conf.xml.sample_advanced Commit: 54c964011a29eca1c72360f17f5114022ad626bf https://github.com/galaxyproject/galaxy/commit/54c964011a29eca1c72360f17f51… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py M test/integration/test_kubernetes_runner.py Log Message: ----------- Take ceiling of kubernetes cpu value Commit: 936679ea817151438ff76d2e14ac2557c4caa3a0 https://github.com/galaxyproject/galaxy/commit/936679ea817151438ff76d2e14ac… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Inject env vars for k8s job to avoid changing tool environment inside container. Commit: e52bb5daa78eb040304919299dc624491573c53f https://github.com/galaxyproject/galaxy/commit/e52bb5daa78eb040304919299dc6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M test/integration/test_kubernetes_runner.py Log Message: ----------- Import from correct module Commit: 626657e3c2b8dc3325a4c2dee35777ac45ac8f0c https://github.com/galaxyproject/galaxy/commit/626657e3c2b8dc3325a4c2dee357… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Revert "job script returns tool exit code in any case" This breaks exit code reporting and leads to pod re-scheduling. This reverts commit 6beeec836f6c6ab479700e6a1e1accbe5069dacf. Commit: 7cf161ba0155abf02582cbbf4636d1ca8681efbe https://github.com/galaxyproject/galaxy/commit/7cf161ba0155abf02582cbbf4636… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/kubernetes.py M test/integration/test_kubernetes_runner.py Log Message: ----------- Allow adding multiple volume claims Commit: e293a74e66002a28adc1045fda0e3415c6f2e08b https://github.com/galaxyproject/galaxy/commit/e293a74e66002a28adc1045fda0e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M test/integration/test_kubernetes_runner.py Log Message: ----------- Add test for tool using python dependencies Commit: 32cad5977b102c33088111abe80887ab1a567a19 https://github.com/galaxyproject/galaxy/commit/32cad5977b102c33088111abe808… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Set galaxy_virtual_env to None for kubernetes runner This prevents attempts of activating Galaxy's virtualenv inside the container. Commit: b931576ed1ebcdfc0f9e0d5cbab74d199e8bbb2a https://github.com/galaxyproject/galaxy/commit/b931576ed1ebcdfc0f9e0d5cbab7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Drop GALAXY_VIRTUAL_ENV env hack GALAXY_VIRTUAL_ENV is injected through job_wrapper.galaxy_virtual_env, which does `os.environ.get(VIRTUAL_ENV, None)`, so this didn't work. The previous commit addresses that. Commit: db387ab898cf47076279ac9d97407ba0fdc45e49 https://github.com/galaxyproject/galaxy/commit/db387ab898cf47076279ac9d9740… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M test/unit/jobs/test_command_factory.py Log Message: ----------- Fix typo fixed by reverted commit 6beeec8 Commit: c53fb623d8cf3af99732a3fe9d1f513f9b538c2b https://github.com/galaxyproject/galaxy/commit/c53fb623d8cf3af99732a3fe9d1f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/godocker.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/deps/dependencies.py A lib/galaxy/util/bytesize.py M test/base/integration_util.py M test/functional/tools/samples_tool_conf.xml M test/integration/test_containerized_jobs.py M test/integration/test_job_recovery.py A test/integration/test_kubernetes_runner.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Merge pull request #6958 from mvdbeek/kubernetes_integration_test Kubernetes job runner integration test and enhancements Compare: https://github.com/galaxyproject/galaxy/compare/65f0c2ac8da8...c53fb623d8cf

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[galaxyproject/galaxy] 4484eb: Use bootstrapped controller helper for admin app
by Dannon 21 Feb '19

21 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4484eb4b205e865a8bec1874d64e945a562ec30d https://github.com/galaxyproject/galaxy/commit/4484eb4b205e865a8bec1874d64e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-20 (Wed, 20 Feb 2019) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Use bootstrapped controller helper for admin app Commit: ca44e2413a47a843d9b42e266b462d3c5712ec57 https://github.com/galaxyproject/galaxy/commit/ca44e2413a47a843d9b42e266b46… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix the server-side route resolution for admin app, ship same bootstrapped client with additional config. Commit: 420e92917ee33672cf65f7406c285bb48968d255 https://github.com/galaxyproject/galaxy/commit/420e92917ee33672cf65f7406c28… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Filter kwds for admin client bootstrapping. Commit: 65f0c2ac8da8693a6b111b9fbff544aa98cc8b3a https://github.com/galaxyproject/galaxy/commit/65f0c2ac8da8693a6b111b9fbff5… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Merge pull request #7394 from guerler/fix_admin_router Restore admin client router handling Compare: https://github.com/galaxyproject/galaxy/compare/75ac7d8d82ac...65f0c2ac8da8

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[galaxyproject/galaxy] bfcee3: Refactor dataset fetching in get/set dataset metho...
by Nate Coraor 21 Feb '19

21 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bfcee382c7cdabdaeee8acc5c6b066bb10ec3d34 https://github.com/galaxyproject/galaxy/commit/bfcee382c7cdabdaeee8acc5c6b0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-14 (Thu, 14 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: 844dbf39b6a99858c96b5bf6e9794a037248c1aa https://github.com/galaxyproject/galaxy/commit/844dbf39b6a99858c96b5bf6e979… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-14 (Thu, 14 Feb 2019) Changed paths: M test/api/test_history_contents.py M test/api/test_jobs.py Log Message: ----------- testing edit controller. Commit: 75ac7d8d82ac0bb9be0c7c09cf649523770e77f6 https://github.com/galaxyproject/galaxy/commit/75ac7d8d82ac0bb9be0c7c09cf64… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py M test/api/test_history_contents.py M test/api/test_jobs.py Log Message: ----------- Merge pull request #7322 from jmchilton/edit_dataset_refactor Refactor dataset controller to reuse input validation checks between get/set Compare: https://github.com/galaxyproject/galaxy/compare/4bb57e5ffcdf...75ac7d8d82ac

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