galaxy-commits March 2018

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[galaxyproject/galaxy] 3da196: [18.01] Fix copying tags for collections when copy...
by GitHub 23 Mar '18

23 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 3da1960c52b2cf893662ec1f865d67050c5500da https://github.com/galaxyproject/galaxy/commit/3da1960c52b2cf893662ec1f865d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- [18.01] Fix copying tags for collections when copying histories. Fixes #5757. Commit: 7dbde33b22ab6c334eec11f88a1596d1cfdcd64d https://github.com/galaxyproject/galaxy/commit/7dbde33b22ab6c334eec11f88a15… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #5766 from jmchilton/copy_tag_fix [18.01] Fix copying tags for collections when copying histories. Compare: https://github.com/galaxyproject/galaxy/compare/c6257f77f100...7dbde33b22ab

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[galaxyproject/usegalaxy-playbook] 4895cd: Remove banner
by GitHub 23 Mar '18

23 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4895cd662d3765ac8553cc6b2a9603d049f26740 https://github.com/galaxyproject/usegalaxy-playbook/commit/4895cd662d3765ac… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Remove banner

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[galaxyproject/galaxy]
by GitHub 23 Mar '18

23 Mar '18

Branch: refs/heads/uwsgi-log-start Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] 5a578b: uWSGI: Log listening URLs at startup.
by GitHub 23 Mar '18

23 Mar '18

Branch: refs/heads/uwsgi-log-start Home: https://github.com/galaxyproject/galaxy Commit: 5a578bfd325777e7e50479b34d1a308940138f82 https://github.com/galaxyproject/galaxy/commit/5a578bfd325777e7e50479b34d1a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- uWSGI: Log listening URLs at startup.

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[galaxyproject/galaxy] d547bc: Downgrade the warning to an info
by GitHub 23 Mar '18

23 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d547bcf11c523a0400ad73328925e9a93934f30a https://github.com/galaxyproject/galaxy/commit/d547bcf11c523a0400ad73328925… Author: E Rasche <hxr(a)hx42.org> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M lib/galaxy/objectstore/__init__.py Log Message: ----------- Downgrade the warning to an info Since this is driving me insane in sentry. We changed to a distributed object store and see this for most dataset accesses. Commit: 8d26be739576924dfa82bfe42a33abb59f9d5acd https://github.com/galaxyproject/galaxy/commit/8d26be739576924dfa82bfe42a33… Author: E Rasche <hxr(a)hx42.org> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M lib/galaxy/objectstore/__init__.py Log Message: ----------- flake8 Commit: 75465deb02c8b5f9614b0fc9446919ff6882a213 https://github.com/galaxyproject/galaxy/commit/75465deb02c8b5f9614b0fc94469… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M lib/galaxy/objectstore/__init__.py Log Message: ----------- Redo logging to be more precise in warnings Commit: 45a541f5c76c4d328c756b27ff58c9d17c072eeb https://github.com/galaxyproject/galaxy/commit/45a541f5c76c4d328c756b27ff58… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/objectstore/__init__.py Log Message: ----------- Merge pull request #5715 from erasche/object-store-annoyance Downgrade the warning to an info Compare: https://github.com/galaxyproject/galaxy/compare/79f027743c23...45a541f5c76c

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[galaxyproject/usegalaxy-playbook] 8c5343: Update Test
by GitHub 23 Mar '18

23 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8c53438cfabb3b53915739f7ffd02fbd61f9a17b https://github.com/galaxyproject/usegalaxy-playbook/commit/8c53438cfabb3b53… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test

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[galaxyproject/galaxy] 4a4909: More backend speed ups for user's workflow index q...
by GitHub 23 Mar '18

23 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4a490970d923043007d8ddd8905dd9d87d9bafb6 https://github.com/galaxyproject/galaxy/commit/4a490970d923043007d8ddd8905d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- More backend speed ups for user's workflow index query. Commit: 79f027743c234035a164522806c4a03b9876f0d9 https://github.com/galaxyproject/galaxy/commit/79f027743c234035a164522806c4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #5755 from jmchilton/workflow_speed_up More backend speed ups for user's workflow index query. Compare: https://github.com/galaxyproject/galaxy/compare/0b580ad13042...79f027743c23

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[galaxyproject/galaxy] 31c1c6: Makes k8s namespace configurable, from the runner'...
by GitHub 23 Mar '18

23 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 31c1c6e5285ad5ce54271ceff1861b87996591b5 https://github.com/galaxyproject/galaxy/commit/31c1c6e5285ad5ce54271ceff186… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Makes k8s namespace configurable, from the runner's perspective. Commit: 0b580ad13042b58c50c3291441f5e5a80d7579ba https://github.com/galaxyproject/galaxy/commit/0b580ad13042b58c50c3291441f5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Merge pull request #5760 from phnmnl/galaxy-prs/k8s-namespace Makes Kubernetes namespace configurable, from the runner's perspective. Compare: https://github.com/galaxyproject/galaxy/compare/c8fc45a44967...0b580ad13042

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[galaxyproject/galaxy] 659721: Add additional validation to numeric input element
by GitHub 22 Mar '18

22 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 659721ac94e909ab31481059ffe1ea092a70047e https://github.com/galaxyproject/galaxy/commit/659721ac94e909ab31481059ffe1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js Log Message: ----------- Add additional validation to numeric input element Commit: c8fc45a44967d700f5b9c9589cf9549b6d800720 https://github.com/galaxyproject/galaxy/commit/c8fc45a44967d700f5b9c9589cf9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js Log Message: ----------- Merge pull request #5750 from guerler/fix_columnassigner Add additional validation to numeric input element Compare: https://github.com/galaxyproject/galaxy/compare/55c052d4da53...c8fc45a44967

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[galaxyproject/galaxy] 6e36af: Fix linking option for library dataset uploads
by GitHub 22 Mar '18

22 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6e36af5c0ec47a3ae14edd99f1044c8fb8b26d9a https://github.com/galaxyproject/galaxy/commit/6e36af5c0ec47a3ae14edd99f104… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Fix linking option for library dataset uploads Broken in commit a45cbfeb8d7d7cc3df5e2561b422023986e805d0 . Found by BioBlend tests: https://travis-ci.org/galaxyproject/bioblend/jobs/356761960 Commit: 55c052d4da53c80611d02e8a815de18b0d8c339d https://github.com/galaxyproject/galaxy/commit/55c052d4da53c80611d02e8a815d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Merge pull request #5758 from nsoranzo/link_to_files Fix linking option for library dataset uploads Compare: https://github.com/galaxyproject/galaxy/compare/d7d888eaed14...55c052d4da53

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galaxy-commits March 2018