galaxy-commits March 2016

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[galaxyproject/galaxy] 09a0e9: More job related timing logging.
by GitHub 21 Mar '16

21 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 09a0e9395d159d51c017204eb64d63e207a1eea6 https://github.com/galaxyproject/galaxy/commit/09a0e9395d159d51c017204eb64d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- More job related timing logging. - Log time of big flush statement. - Log time of adding datasets to history. - Log time for setting up job. These log statements would make the output of the following gist (https://gist.github.com/blankenberg/43db2e0f61a566126c45) from #1831 a lot more informative. Commit: 901cab12cb124b39177fa919842de8463533dd8b https://github.com/galaxyproject/galaxy/commit/901cab12cb124b39177fa919842d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #1956 from jmchilton/more_job_logging More job related timing logging. Compare: https://github.com/galaxyproject/galaxy/compare/d0ceb29bd8eb...901cab12cb12

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[galaxyproject/galaxy] 9e9dfd: Fix workflow scheduler log message.
by GitHub 21 Mar '16

21 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 9e9dfdfd55b2b8d2377f8ef4e288a1fa482105b9 https://github.com/galaxyproject/galaxy/commit/9e9dfdfd55b2b8d2377f8ef4e288… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Fix workflow scheduler log message. Commit: 5f5f0af5cd5e21c64810d29202e149915226c34a https://github.com/galaxyproject/galaxy/commit/5f5f0af5cd5e21c64810d29202e1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Merge pull request #1955 from jmchilton/fix_wf_log_message [16.01] Fix workflow scheduler log message. Compare: https://github.com/galaxyproject/galaxy/compare/19bf334c7763...5f5f0af5cd5e

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[galaxyproject/galaxy] 9d362a: log warning if user account is not active
by GitHub 20 Mar '16

20 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9d362a2400bb1d36b1dec8df5316fca75ea05c08 https://github.com/galaxyproject/galaxy/commit/9d362a2400bb1d36b1dec8df5316… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-20 (Sun, 20 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- log warning if user account is not active Commit: 3b71020dfc1ef6ad4b4ccb09de6317dd059cdb1a https://github.com/galaxyproject/galaxy/commit/3b71020dfc1ef6ad4b4ccb09de63… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-20 (Sun, 20 Mar 2016) Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Account for anonymous user. Commit: 34dedb3eb97f914e67563ffe84cb791ca7ceb936 https://github.com/galaxyproject/galaxy/commit/34dedb3eb97f914e67563ffe84cb… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-20 (Sun, 20 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- linting fixes Commit: d0ceb29bd8eb83cfd0ba1dd40ebf03d830c60c3c https://github.com/galaxyproject/galaxy/commit/d0ceb29bd8eb83cfd0ba1dd40ebf… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-20 (Sun, 20 Mar 2016) Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Merge pull request #1953 from mvdbeek/warn_if_user_inactive Warn if tool is executed and user account is inactive Compare: https://github.com/galaxyproject/galaxy/compare/53daf30dd284...d0ceb29bd8eb

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[galaxyproject/usegalaxy-playbook] 3bcb74: add labels to main and move deeptools seciton
by GitHub 20 Mar '16

20 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3bcb74a5d931e65e3987bb16b4497ea3e6db3198 https://github.com/galaxyproject/usegalaxy-playbook/commit/3bcb74a5d931e65e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-19 (Sat, 19 Mar 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml Log Message: ----------- add labels to main and move deeptools seciton

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[galaxyproject/usegalaxy-playbook] cbbbc2: update MTS and TTS
by GitHub 19 Mar '16

19 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: cbbbc2025f418bf83dfc21931faa6958339fda3f https://github.com/galaxyproject/usegalaxy-playbook/commit/cbbbc2025f418bf8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M production/group_vars/toolshedservers.yml M stage/group_vars/toolshedservers.yml Log Message: ----------- update MTS and TTS

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[galaxyproject/usegalaxy-playbook] ec3aba: things that showed up after updating Galaxy's vers...
by GitHub 19 Mar '16

19 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ec3abaa9fee94c4a852f3eb14acea2483b0f03ab https://github.com/galaxyproject/usegalaxy-playbook/commit/ec3abaa9fee94c4a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M production/files/interactive_environments/plugins/.ansible_ie_role_current_version M production/files/interactive_environments/proxy/.ansible_ie_role_current_version Log Message: ----------- things that showed up after updating Galaxy's version

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[galaxyproject/usegalaxy-playbook] c78ef2: install deeptools; update Main to latest 16.01
by GitHub 19 Mar '16

19 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c78ef2fec723ea8784b5c2ea9a63c714a1167e63 https://github.com/galaxyproject/usegalaxy-playbook/commit/c78ef2fec723ea87… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_data_manager_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml M production/group_vars/all.yml Log Message: ----------- install deeptools; update Main to latest 16.01 Please enter the commit message for your changes. Lines starting

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[galaxyproject/galaxy] 29c78e: Fix virtualenv broken with #1847.
by GitHub 19 Mar '16

19 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 29c78e984e52ac08b1b36a03e39b65c6edbe6200 https://github.com/galaxyproject/galaxy/commit/29c78e984e52ac08b1b36a03e39b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M run_reports.sh M run_tool_shed.sh Log Message: ----------- Fix virtualenv broken with #1847. Commit: 5824bc04af9270afbebcb2c8f9b6b3bea371b788 https://github.com/galaxyproject/galaxy/commit/5824bc04af9270afbebcb2c8f9b6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M run_reports.sh M run_tool_shed.sh Log Message: ----------- Fix duplicate print statement reported by @dannon... https://github.com/galaxyproject/galaxy/pull/1890#issuecomment-193873380 Commit: 438661e8945c1bb317f75dabe3db429ea779255d https://github.com/galaxyproject/galaxy/commit/438661e8945c1bb317f75dabe3db… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M run_reports.sh M run_tool_shed.sh Log Message: ----------- Another fix for virtualenv fixes. Commit: 00a7c3af057c0689a53748802740bc2002df375c https://github.com/galaxyproject/galaxy/commit/00a7c3af057c0689a53748802740… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: M run_reports.sh M run_tool_shed.sh Log Message: ----------- Merge pull request #1890 from jmchilton/fix_virtualenvs [16.01] Fix virtual env handling broken with #1847. Commit: f277f99aed411fede7d1cb91d3177469922a58ae https://github.com/galaxyproject/galaxy/commit/f277f99aed411fede7d1cb91d317… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/util/log/fluent_log.py Log Message: ----------- Fix handling of time in fluent logger. Commit: 87bcb5f5a1b6801e948b2cc0f5dc676c7faca682 https://github.com/galaxyproject/galaxy/commit/87bcb5f5a1b6801e948b2cc0f5dc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/util/log/fluent_log.py Log Message: ----------- Fix in a different way not requiring signature change; still not thrilled about overlapping kwarg names w/ stdlib module names. Commit: c8e48bfaccb5d10552df4200e616a9eee49206b0 https://github.com/galaxyproject/galaxy/commit/c8e48bfaccb5d10552df4200e616… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Add fluentd configuration to galaxy.ini.sample Commit: 98c65dcee08338ea80a7e34251f8fa4ed6bd8dd5 https://github.com/galaxyproject/galaxy/commit/98c65dcee08338ea80a7e34251f8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/util/log/fluent_log.py M lib/galaxy/webapps/galaxy/api/metrics.py Log Message: ----------- Swap back to the first fix, update metrics api to use new signature. Commit: 19bf334c7763c2418408083b9a7369386e50ad66 https://github.com/galaxyproject/galaxy/commit/19bf334c7763c2418408083b9a73… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/util/log/fluent_log.py M lib/galaxy/webapps/galaxy/api/metrics.py Log Message: ----------- Merge pull request #1945 from dannon/fluent_logging_fix [16.01] Fix handling of time in fluent logger Commit: 53daf30dd284004c7e0b85ce8dbe6daf94622ef1 https://github.com/galaxyproject/galaxy/commit/53daf30dd284004c7e0b85ce8dbe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/util/log/fluent_log.py M lib/galaxy/webapps/galaxy/api/metrics.py M run_reports.sh M run_tool_shed.sh Log Message: ----------- Merge branch 'release_16.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/6fff01c01c59...53daf30dd284

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[galaxyproject/infrastructure-playbook] b55fdb: Add celery beat for sentry, should be the last pie...
by GitHub 18 Mar '16

18 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: b55fdbafe09e758a51466cf633f016ebab820039 https://github.com/galaxyproject/infrastructure-playbook/commit/b55fdbafe09… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M taccenv/templates/supervisor/sentry.j2 Log Message: ----------- Add celery beat for sentry, should be the last piece of the puzzle.

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[galaxyproject/usegalaxy-playbook] b3de5c: update Test mutable configs and common_roles subre...
by GitHub 18 Mar '16

18 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b3de5c2b03848640a2cbf3210faf165be774a720 https://github.com/galaxyproject/usegalaxy-playbook/commit/b3de5c2b03848640… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M common_roles M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml Log Message: ----------- update Test mutable configs and common_roles subrepo that has not been committed

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galaxy-commits March 2016