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

[galaxyproject/infrastructure-playbook] d45011: Configure telegraf on Galaxy servers to log nginx.
by GitHub 07 Sep '18

07 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: d45011459599ad8d6985b8d891113ae6463f73a7 https://github.com/galaxyproject/infrastructure-playbook/commit/d4501145959… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M env/tacc/group_vars/galaxyservers.yml Log Message: ----------- Configure telegraf on Galaxy servers to log nginx. **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] 384a16: Allow schema to validate
by GitHub 07 Sep '18

07 Sep '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 384a165aab2d579ee4c2dceba61f21c42c8c2dc4 https://github.com/galaxyproject/galaxy/commit/384a165aab2d579ee4c2dceba61f… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Allow schema to validate Commit: 0b95898ccf68b8497dff9f322b44abc5668dfce6 https://github.com/galaxyproject/galaxy/commit/0b95898ccf68b8497dff9f322b44… Author: E Rasche <hxr(a)hx42.org> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Document pbkdf2 Commit: 3efda23b4fe84f1a61d83aba07186e46c81990ce https://github.com/galaxyproject/galaxy/commit/3efda23b4fe84f1a61d83aba0718… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Restore logging block in galaxy config schema. Commit: 7d7a875af398c440040e78dcc2516aae1c6eb041 https://github.com/galaxyproject/galaxy/commit/7d7a875af398c440040e78dcc251… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #5919 from erasche/fix-config-validate [18.01] Allow schema to validate Compare: https://github.com/galaxyproject/galaxy/compare/6d9df51f36e2...7d7a875af398 **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] 828cac: Set data type for logflux
by GitHub 07 Sep '18

07 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 828cac65b3e7d6ec6960cc2c649e940da4841383 https://github.com/galaxyproject/usegalaxy-playbook/commit/828cac65b3e7d6ec… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M env/test/group_vars/logfluxservers.yml Log Message: ----------- Set data type for logflux **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] ee0c83: Serialize select field options
by GitHub 07 Sep '18

07 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ee0c8327e4b2f848c9f9d3c0003cc49781c149f4 https://github.com/galaxyproject/galaxy/commit/ee0c8327e4b2f848c9f9d3c0003c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Serialize select field options This fixes the empty select list in the beta install interface. Commit: 95462754c09facf8ae767b88767003b2d00c1da1 https://github.com/galaxyproject/galaxy/commit/95462754c09facf8ae767b887670… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Merge pull request #6677 from mvdbeek/fix_shed_tool_conf_selection Serialize select field options, fixes beta install Compare: https://github.com/galaxyproject/galaxy/compare/ba22818ff45e...95462754c09f **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] 933fc3: Try using slurmd -b to prevent permanent node fail...
by GitHub 07 Sep '18

07 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 933fc3603339cf58082a3094dbf94780649938e0 https://github.com/galaxyproject/infrastructure-playbook/commit/933fc360333… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M roles/slurmscale/files/resume.yml Log Message: ----------- Try using slurmd -b to prevent permanent node failure **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] cef8f1: Install logflux for nginx rate limit logs
by GitHub 07 Sep '18

07 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: cef8f1beb4139a2939f9e92c1462315a73a0f870 https://github.com/galaxyproject/usegalaxy-playbook/commit/cef8f1beb4139a29… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M env/common/stack.yml A env/test/group_vars/logfluxservers.yml M env/test/inventory A roles/logflux/defaults/main.yml A roles/logflux/handlers/main.yml A roles/logflux/tasks/main.yml A roles/logflux/templates/logflux.service.j2 A roles/logflux/templates/rsyslog.conf.j2 Log Message: ----------- Install logflux for nginx rate limit logs Commit: 2c8b698a762a0dba51321f2d0b6dad97f78fd7a5 https://github.com/galaxyproject/usegalaxy-playbook/commit/2c8b698a762a0dba… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Fix Main version number (it was updated to this version on 2018-07-18, not sure why it wasn't committed) Commit: b278079d0e2cdb3e3a94e741ee8d622e648818d5 https://github.com/galaxyproject/usegalaxy-playbook/commit/b278079d0e2cdb3e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M env/main/group_vars/cvmfsstratum0servers.yml Log Message: ----------- Build client on Main Commit: c05443511ed2ec153a4930130e789096c9a71d75 https://github.com/galaxyproject/usegalaxy-playbook/commit/c05443511ed2ec15… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M env/test/group_vars/logfluxservers.yml M env/test/templates/nginx/galaxy_test.j2 M roles/logflux/defaults/main.yml M roles/logflux/tasks/main.yml M roles/logflux/templates/rsyslog.conf.j2 Log Message: ----------- Fixes for logflux Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/3ebe796f2020...… **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] c867c6: Upgraded genomespaceclient to newer version
by GitHub 07 Sep '18

07 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c867c6863fbbb75f473f209fea7a805e2da63a47 https://github.com/galaxyproject/galaxy/commit/c867c6863fbbb75f473f209fea7a… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M tools/genomespace/genomespace_importer.py Log Message: ----------- Upgraded genomespaceclient to newer version This fixes issue reported in: https://github.com/galaxyproject/usegalaxy-playbook/issues/100 Also related to PR: https://github.com/galaxyproject/galaxy/pull/6660 Commit: ba22818ff45ee639fb1a199a6dff5085a28f8365 https://github.com/galaxyproject/galaxy/commit/ba22818ff45ee639fb1a199a6dff… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M tools/genomespace/genomespace_importer.py Log Message: ----------- Merge pull request #6668 from gvlproject/genomespaceclient_upgrade Upgraded genomespaceclient to newer version Compare: https://github.com/galaxyproject/galaxy/compare/1ba4b47d7335...ba22818ff45e **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] 3ebe79: Install multigps 0.74 wrapper by Greg.
by GitHub 07 Sep '18

07 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3ebe796f2020f47eedd043519c51789ae003c9f5 https://github.com/galaxyproject/usegalaxy-playbook/commit/3ebe796f2020f47e… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Install multigps 0.74 wrapper by Greg. **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] 69252d: Tell pytest not to execute Python code in node_mod...
by GitHub 07 Sep '18

07 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 69252d711a1d7112e3340a25d5b3b821cb027e39 https://github.com/galaxyproject/galaxy/commit/69252d711a1d7112e3340a25d5b3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M run_tests.sh Log Message: ----------- Tell pytest not to execute Python code in node_modules for web proxy. Causes test execution to fail for me. Commit: 1ba4b47d7335c097a189a15859c58ddac1e2dadd https://github.com/galaxyproject/galaxy/commit/1ba4b47d7335c097a189a15859c5… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #6676 from jmchilton/pytest_fix Tell pytest not to execute Python code in node_modules for web proxy. Compare: https://github.com/galaxyproject/galaxy/compare/3824a8948a43...1ba4b47d7335 **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] 5e7415: Optimize initial validation of collection input pa...
by GitHub 07 Sep '18

07 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5e74154c930326f4c7a69f7dbd33ea88189fb257 https://github.com/galaxyproject/galaxy/commit/5e74154c930326f4c7a69f7dbd33… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Optimize initial validation of collection input parameters. Commit: ca26c3d5aff4d92192bfef744348c94b6e41ea7e https://github.com/galaxyproject/galaxy/commit/ca26c3d5aff4d92192bfef744348… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M lib/galaxy/dataset_collections/matching.py M lib/galaxy/model/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/execute.py Log Message: ----------- Optimize permission loading and checking collection parameters. We were checking permissions twice it seems like to me, only do it once. Avoid loading dataset permissions for each individual dataset in a collection - work with summary sets of role ids. Commit: 3824a8948a43a8a0def879df73087ce190182b3f https://github.com/galaxyproject/galaxy/commit/3824a8948a43a8a0def879df7308… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/dataset_collections/matching.py M lib/galaxy/model/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/execute.py Log Message: ----------- Merge pull request #6635 from jmchilton/permission_opts Optimize tool execution permission checking Compare: https://github.com/galaxyproject/galaxy/compare/da18624067c8...3824a8948a43 **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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