October 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] b5a2fa: do not rule out numbers that are accessed with shi...
by GitHub 04 Oct '18

04 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b5a2fafa07fcf1580989d51dd64f335387a568b8 https://github.com/galaxyproject/galaxy/commit/b5a2fafa07fcf1580989d51dd64f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js Log Message: ----------- do not rule out numbers that are accessed with shift modifier closes #5370 I think there are more problems with this code: - it assumes too much about the keyboard used and puts unnecessary restrictions on the user - the implementation should be refactored to use KeyboardEvent.key instead of the deprecated charCode Commit: 8ea455303ab76cf94e5c7acdf22d14d75260b188 https://github.com/galaxyproject/galaxy/commit/8ea455303ab76cf94e5c7acdf22d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js Log Message: ----------- Merge pull request #6810 from martenson/fix-nonUS-keyboards [18.09] do not rule out numbers that are accessed with shift modifier Commit: 18f351ae31ae767db01888bf3c2304325c4f6e22 https://github.com/galaxyproject/galaxy/commit/18f351ae31ae767db01888bf3c23… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/493816e245fd...18f351ae31ae **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] afffd9: Add final PR.
by GitHub 04 Oct '18

04 Oct '18

Branch: refs/heads/18.09_release_notes Home: https://github.com/galaxyproject/galaxy Commit: afffd9bdaa66b4fcadbd790a25387654c23e4aa6 https://github.com/galaxyproject/galaxy/commit/afffd9bdaa66b4fcadbd790a2538… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add final PR. **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] b5a2fa: do not rule out numbers that are accessed with shi...
by GitHub 04 Oct '18

04 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: b5a2fafa07fcf1580989d51dd64f335387a568b8 https://github.com/galaxyproject/galaxy/commit/b5a2fafa07fcf1580989d51dd64f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js Log Message: ----------- do not rule out numbers that are accessed with shift modifier closes #5370 I think there are more problems with this code: - it assumes too much about the keyboard used and puts unnecessary restrictions on the user - the implementation should be refactored to use KeyboardEvent.key instead of the deprecated charCode Commit: 8ea455303ab76cf94e5c7acdf22d14d75260b188 https://github.com/galaxyproject/galaxy/commit/8ea455303ab76cf94e5c7acdf22d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js Log Message: ----------- Merge pull request #6810 from martenson/fix-nonUS-keyboards [18.09] do not rule out numbers that are accessed with shift modifier Compare: https://github.com/galaxyproject/galaxy/compare/1c4a4ed8cb60...8ea455303ab7 **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] 758dd7: Update Test/Main
by GitHub 04 Oct '18

04 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 758dd7e496cdcccd52a226e5f9a95bb81c30adcc https://github.com/galaxyproject/usegalaxy-playbook/commit/758dd7e496cdcccd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test/Main **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] 907188: Add deprecation notice for username being null
by GitHub 04 Oct '18

04 Oct '18

Branch: refs/heads/18.09_release_notes Home: https://github.com/galaxyproject/galaxy Commit: 90718843096f115324be8a086d7a6089e0086703 https://github.com/galaxyproject/galaxy/commit/90718843096f115324be8a086d7a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Add deprecation notice for username being null **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] 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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