- galaxy-commits - lists.galaxyproject.org

[galaxyproject/infrastructure-playbook] 85852a: Break internally queued jobs down by handler
by GitHub 04 Oct '18

04 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 85852a755a27701994399ddf33ac3450d2ec6f2f https://github.com/galaxyproject/infrastructure-playbook/commit/85852a755a2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M roles/stats/templates/galaxy_slurp.py.j2 Log Message: ----------- Break internally queued jobs down by handler **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 546459: Wrap onclick functions with a tooltip de-tipper fo...
by GitHub 04 Oct '18

04 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 546459f3536ca7b1504550794e8d1d77e68985d0 https://github.com/galaxyproject/galaxy/commit/546459f3536ca7b1504550794e8d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M client/galaxy/scripts/ui/fa-icon-button.js Log Message: ----------- Wrap onclick functions with a tooltip de-tipper for faIconButtons. Commit: 35b72ff508a860ed297780345d213c9155f014aa https://github.com/galaxyproject/galaxy/commit/35b72ff508a860ed297780345d21… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Remove now-unnecessary tooltip dispose Commit: 3146c57b310fedc525aa6a5b8ab87d8bacf2784d https://github.com/galaxyproject/galaxy/commit/3146c57b310fedc525aa6a5b8ab8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M client/galaxy/scripts/ui/fa-icon-button.js Log Message: ----------- Blur buttons onclick Commit: 7c290b1743b03c1eb1711df8218f5733a8f791c8 https://github.com/galaxyproject/galaxy/commit/7c290b1743b03c1eb1711df8218f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M client/galaxy/scripts/ui/fa-icon-button.js Log Message: ----------- Set a reasonable nearby focus instead of blur, to prevent tabindex loss. Commit: 34d54558b3dc40d54a507128b8a45b691151f863 https://github.com/galaxyproject/galaxy/commit/34d54558b3dc40d54a507128b8a4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M client/galaxy/scripts/ui/fa-icon-button.js Log Message: ----------- Simplify wrapping logic, fix context. Commit: 7320752138dc186b96f53746b1811dcc2c212dc1 https://github.com/galaxyproject/galaxy/commit/7320752138dc186b96f53746b181… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M client/galaxy/scripts/ui/fa-icon-button.js Log Message: ----------- Client formatting. Commit: fd6af5eb0e0ba79679f8395d9333cf3e7331ba05 https://github.com/galaxyproject/galaxy/commit/fd6af5eb0e0ba79679f8395d9333… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- No memory leaks here Commit: b7187f0e62e172dd7d2db1bbd51f9c3f9a5058c5 https://github.com/galaxyproject/galaxy/commit/b7187f0e62e172dd7d2db1bbd51f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Don't delete referenced Datasets when purging users. Commit: 74d82096d8eef3cbd05b52cf956d0dc654d05533 https://github.com/galaxyproject/galaxy/commit/74d82096d8eef3cbd05b52cf956d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M client/galaxy/scripts/ui/fa-icon-button.js Log Message: ----------- Merge pull request #6745 from dannon/more-generic-tooltip-handling-for-fa-buttons [18.09] Generic tooltip hide for onclick faIconButtons Commit: f6a5cae8e1af10003e3553cb27b2512977bc0c8e https://github.com/galaxyproject/galaxy/commit/f6a5cae8e1af10003e3553cb27b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Merge pull request #6809 from natefoo/purge-user-fix [18.05] Don't delete referenced Datasets when purging users Commit: 266ebdb225a6e3aec28bbd2a4b356c1e83f49429 https://github.com/galaxyproject/galaxy/commit/266ebdb225a6e3aec28bbd2a4b35… Author: Saskia Hiltemann <zazkia(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- cast row count to integer in filter first/last N rows rule Commit: e54dd1d19c0e7e36ec4e8bd9b0d5b21f298b0d17 https://github.com/galaxyproject/galaxy/commit/e54dd1d19c0e7e36ec4e8bd9b0d5… Author: Saskia Hiltemann <zazkia(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/rules/rule-definitions.js Log Message: ----------- build client Commit: 87d2c20dbfc86bf0dd5136e274b6e960d2543a91 https://github.com/galaxyproject/galaxy/commit/87d2c20dbfc86bf0dd5136e274b6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Merge pull request #6814 from shiltemann/rulebuilder-fix [18.05] Fix apply rules bug in filter first/last N rows. Commit: 4a345b99c3cc1ee21b648386dafb4c15edcbb856 https://github.com/galaxyproject/galaxy/commit/4a345b99c3cc1ee21b648386dafb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M lib/galaxy/util/compression_utils.py A test-data/safetar_with_symlink.tar A test-data/testdir.tar A test-data/unsafe.tar A test-data/unsafe.zip A test-data/unsafe_relative_symlink.tar A test/unit/test_compression_util.py Log Message: ----------- Fix security problems when extracting untrusted tar files. Fixes GX-2018-0006. Commit: 1c4a4ed8cb60ab67d8b1cf71f231d4cf4acfb077 https://github.com/galaxyproject/galaxy/commit/1c4a4ed8cb60ab67d8b1cf71f231… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js M lib/galaxy/util/compression_utils.py M lib/galaxy/webapps/galaxy/controllers/admin.py A test-data/safetar_with_symlink.tar A test-data/testdir.tar A test-data/unsafe.tar A test-data/unsafe.zip A test-data/unsafe_relative_symlink.tar A test/unit/test_compression_util.py Log Message: ----------- Merge remote-tracking branch 'galaxyproject/release_18.05' into release_18.09 Commit: 493816e245fdd17cbf9edb9de492228477518a6a https://github.com/galaxyproject/galaxy/commit/493816e245fdd17cbf9edb9de492… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/ui/fa-icon-button.js M lib/galaxy/util/compression_utils.py M lib/galaxy/webapps/galaxy/controllers/admin.py A test-data/safetar_with_symlink.tar A test-data/testdir.tar A test-data/unsafe.tar A test-data/unsafe.zip A test-data/unsafe_relative_symlink.tar A test/unit/test_compression_util.py Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/b7334253a75d...493816e245fd **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] b7187f: Don't delete referenced Datasets when purging user...
by GitHub 04 Oct '18

04 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: b7187f0e62e172dd7d2db1bbd51f9c3f9a5058c5 https://github.com/galaxyproject/galaxy/commit/b7187f0e62e172dd7d2db1bbd51f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Don't delete referenced Datasets when purging users. Commit: f6a5cae8e1af10003e3553cb27b2512977bc0c8e https://github.com/galaxyproject/galaxy/commit/f6a5cae8e1af10003e3553cb27b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Merge pull request #6809 from natefoo/purge-user-fix [18.05] Don't delete referenced Datasets when purging users Commit: 266ebdb225a6e3aec28bbd2a4b356c1e83f49429 https://github.com/galaxyproject/galaxy/commit/266ebdb225a6e3aec28bbd2a4b35… Author: Saskia Hiltemann <zazkia(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- cast row count to integer in filter first/last N rows rule Commit: e54dd1d19c0e7e36ec4e8bd9b0d5b21f298b0d17 https://github.com/galaxyproject/galaxy/commit/e54dd1d19c0e7e36ec4e8bd9b0d5… Author: Saskia Hiltemann <zazkia(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/rules/rule-definitions.js Log Message: ----------- build client Commit: 87d2c20dbfc86bf0dd5136e274b6e960d2543a91 https://github.com/galaxyproject/galaxy/commit/87d2c20dbfc86bf0dd5136e274b6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Merge pull request #6814 from shiltemann/rulebuilder-fix [18.05] Fix apply rules bug in filter first/last N rows. Commit: 4a345b99c3cc1ee21b648386dafb4c15edcbb856 https://github.com/galaxyproject/galaxy/commit/4a345b99c3cc1ee21b648386dafb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M lib/galaxy/util/compression_utils.py A test-data/safetar_with_symlink.tar A test-data/testdir.tar A test-data/unsafe.tar A test-data/unsafe.zip A test-data/unsafe_relative_symlink.tar A test/unit/test_compression_util.py Log Message: ----------- Fix security problems when extracting untrusted tar files. Fixes GX-2018-0006. Commit: 1c4a4ed8cb60ab67d8b1cf71f231d4cf4acfb077 https://github.com/galaxyproject/galaxy/commit/1c4a4ed8cb60ab67d8b1cf71f231… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js M lib/galaxy/util/compression_utils.py M lib/galaxy/webapps/galaxy/controllers/admin.py A test-data/safetar_with_symlink.tar A test-data/testdir.tar A test-data/unsafe.tar A test-data/unsafe.zip A test-data/unsafe_relative_symlink.tar A test/unit/test_compression_util.py Log Message: ----------- Merge remote-tracking branch 'galaxyproject/release_18.05' into release_18.09 Compare: https://github.com/galaxyproject/galaxy/compare/74d82096d8ee...1c4a4ed8cb60 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 4a345b: Fix security problems when extracting untrusted ta...
by GitHub 04 Oct '18

04 Oct '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 4a345b99c3cc1ee21b648386dafb4c15edcbb856 https://github.com/galaxyproject/galaxy/commit/4a345b99c3cc1ee21b648386dafb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M lib/galaxy/util/compression_utils.py A test-data/safetar_with_symlink.tar A test-data/testdir.tar A test-data/unsafe.tar A test-data/unsafe.zip A test-data/unsafe_relative_symlink.tar A test/unit/test_compression_util.py Log Message: ----------- Fix security problems when extracting untrusted tar files. Fixes GX-2018-0006. **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/infrastructure-playbook] c6d551: Slurp queued jobs
by GitHub 04 Oct '18

04 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c6d5516b037c17dfbeaafaff50bfc598c2c7882b https://github.com/galaxyproject/infrastructure-playbook/commit/c6d5516b037… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M roles/stats/templates/galaxy_slurp.py.j2 Log Message: ----------- Slurp queued jobs **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] b5f795: Announce Python 3 Beta Support
by GitHub 04 Oct '18

04 Oct '18

Branch: refs/heads/18.09_release_notes Home: https://github.com/galaxyproject/galaxy Commit: b5f7955c5addba2664b6375aa87c9873b2949fad https://github.com/galaxyproject/galaxy/commit/b5f7955c5addba2664b6375aa87c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Announce Python 3 Beta Support **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] a1f1d9: adding itp and mdp datatypes (for gromacs)
by GitHub 04 Oct '18

04 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a1f1d9ef7ea6f7c46b8517ba5bdee3cdaa0fb451 https://github.com/galaxyproject/galaxy/commit/a1f1d9ef7ea6f7c46b8517ba5bde… Author: Simon Bray <32272674+simonbray(a)users.noreply.github.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- adding itp and mdp datatypes (for gromacs) Commit: b7334253a75d82b9a4d1cf30974f644f375cb05c https://github.com/galaxyproject/galaxy/commit/b7334253a75d82b9a4d1cf30974f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #6812 from simonbray/dev adding itp and mdp datatypes (for gromacs) Compare: https://github.com/galaxyproject/galaxy/compare/260e37f2bc31...b7334253a75d **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 266ebd: cast row count to integer in filter first/last N r...
by GitHub 04 Oct '18

04 Oct '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 266ebdb225a6e3aec28bbd2a4b356c1e83f49429 https://github.com/galaxyproject/galaxy/commit/266ebdb225a6e3aec28bbd2a4b35… Author: Saskia Hiltemann <zazkia(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- cast row count to integer in filter first/last N rows rule Commit: e54dd1d19c0e7e36ec4e8bd9b0d5b21f298b0d17 https://github.com/galaxyproject/galaxy/commit/e54dd1d19c0e7e36ec4e8bd9b0d5… Author: Saskia Hiltemann <zazkia(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/rules/rule-definitions.js Log Message: ----------- build client Commit: 87d2c20dbfc86bf0dd5136e274b6e960d2543a91 https://github.com/galaxyproject/galaxy/commit/87d2c20dbfc86bf0dd5136e274b6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Merge pull request #6814 from shiltemann/rulebuilder-fix [18.05] Fix apply rules bug in filter first/last N rows. Compare: https://github.com/galaxyproject/galaxy/compare/f6a5cae8e1af...87d2c20dbfc8 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 441f4c: Increase shared_buffers on galaxy-db-02
by GitHub 03 Oct '18

03 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 441f4cfe584ddbe46d8a04bde620f1b903bdc40d https://github.com/galaxyproject/usegalaxy-playbook/commit/441f4cfe584ddbe4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-03 (Wed, 03 Oct 2018) Changed paths: M env/main/group_vars/dbservers/vars.yml Log Message: ----------- Increase shared_buffers on galaxy-db-02 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/infrastructure-playbook] 2fb5a4: Upgrade Grafana/InfluxDB and enable Github auth in...
by GitHub 03 Oct '18

03 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 2fb5a46911118c7f505cdf2c63604725b3de33b2 https://github.com/galaxyproject/infrastructure-playbook/commit/2fb5a469111… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-03 (Wed, 03 Oct 2018) Changed paths: M env/tacc/group_vars/statsservers/vars.yml M env/tacc/group_vars/statsservers/vault.yml M roles/stats/tasks/redhat.yml M roles/stats/templates/grafana.ini.j2 Log Message: ----------- Upgrade Grafana/InfluxDB and enable Github auth in Grafana **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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