- galaxy-commits - lists.galaxyproject.org

[galaxyproject/infrastructure-playbook] dede28: Use supervisor instead of systemd
by GitHub 18 Mar '16

18 Mar '16

Branch: refs/heads/memcached_tweak Home: https://github.com/galaxyproject/infrastructure-playbook Commit: dede2824ad219409ab4210d6ab32390754549171 https://github.com/galaxyproject/infrastructure-playbook/commit/dede2824ad2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M roles/sentry/tasks/main.yml M taccenv/templates/supervisor/sentry.j2 Log Message: ----------- Use supervisor instead of systemd

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[galaxyproject/infrastructure-playbook] 0f91b8: Enable and start memcached on statsservers
by GitHub 18 Mar '16

18 Mar '16

Branch: refs/heads/memcached_tweak Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 0f91b8b9e33a229423252d6aed2ea6cd692afc85 https://github.com/galaxyproject/infrastructure-playbook/commit/0f91b8b9e33… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M roles/sentry/tasks/main.yml Log Message: ----------- Enable and start memcached on statsservers

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[galaxyproject/galaxy] f277f9: Fix handling of time in fluent logger.
by GitHub 18 Mar '16

18 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy 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 Compare: https://github.com/galaxyproject/galaxy/compare/00a7c3af057c...19bf334c7763

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[galaxyproject/infrastructure-playbook] 51f6f6: Install memcached for sentry
by GitHub 18 Mar '16

18 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 51f6f60c38b89591912b731b0b28f18290ab54ed https://github.com/galaxyproject/infrastructure-playbook/commit/51f6f60c38b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M taccenv/group_vars/statsservers.yml Log Message: ----------- Install memcached for sentry

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[galaxyproject/galaxy] 87bb98: Add "new" state to list of dataset states in saved...
by GitHub 18 Mar '16

18 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 87bb98eed23634c2684e6b246051e871068aca0c https://github.com/galaxyproject/galaxy/commit/87bb98eed23634c2684e6b246051… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Add "new" state to list of dataset states in saved history list. Commit: 6fff01c01c59a1ebe9a4906c47e1f550d2019f6f https://github.com/galaxyproject/galaxy/commit/6fff01c01c59a1ebe9a4906c47e1… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #1949 from blankenberg/history-list-new-hda Add "new" state to list of dataset states in saved history list. Compare: https://github.com/galaxyproject/galaxy/compare/2bc3da6b4988...6fff01c01c59

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[galaxyproject/galaxy] 6a123b: Use database query rather than dataset iteration t...
by GitHub 17 Mar '16

17 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6a123b12e9a6fd2c8ace506d6a6318504aa6fa81 https://github.com/galaxyproject/galaxy/commit/6a123b12e9a6fd2c8ace506d6a63… Author: jgoecks <jgoecks(a)gwu.edu> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Use database query rather than dataset iteration to compute dataset counts in saved histories grid. Commit: 4520a619abd638d49d07c8deac1a120f6181fad0 https://github.com/galaxyproject/galaxy/commit/4520a619abd638d49d07c8deac1a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Minor style tweaks to pass flake8 Commit: 8c1defe60e6b1195eb2a2fbaba167fec11ed5bce https://github.com/galaxyproject/galaxy/commit/8c1defe60e6b1195eb2a2fbaba16… Author: Jeremy Goecks <jgoecks(a)users.noreply.github.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #2 from dannon/history-grid-state-optimization Minor style tweaks to pass flake8 Commit: 78da8df812393778841e97465993e3ce7199f45f https://github.com/galaxyproject/galaxy/commit/78da8df812393778841e97465993… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Oops. Commit: 38d7bbb712cd2523e3c9ba31df5f49c2b9f2ce83 https://github.com/galaxyproject/galaxy/commit/38d7bbb712cd2523e3c9ba31df5f… Author: Jeremy Goecks <jgoecks(a)users.noreply.github.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #3 from dannon/history-grid-state-optimization It's a function, not a true-y value :/ Commit: 2bc3da6b4988d5fbb5c3aa1e2562452a654f7c6a https://github.com/galaxyproject/galaxy/commit/2bc3da6b4988d5fbb5c3aa1e2562… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #1948 from jgoecks/history-grid-state-optimization Use database query rather than dataset iteration to compute dataset c… Compare: https://github.com/galaxyproject/galaxy/compare/c7d1f009a163...2bc3da6b4988

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[galaxyproject/galaxy] b7b04e: Fix tool downloads
by GitHub 17 Mar '16

17 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b7b04ee92033ca9a2e961e296f74378753ab0563 https://github.com/galaxyproject/galaxy/commit/b7b04ee92033ca9a2e961e296f74… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix tool downloads Commit: c7d1f009a163f8e74905c5c4ee5cc2e2288051c9 https://github.com/galaxyproject/galaxy/commit/c7d1f009a163f8e74905c5c4ee5c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1935 from guerler/fix_downloads_000 Fix tool downloads in tool form Compare: https://github.com/galaxyproject/galaxy/compare/cef58abb55e2...c7d1f009a163

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[galaxyproject/galaxy] 80562a: Fix API method broken in 6e13c3999.
by GitHub 17 Mar '16

17 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 80562acfe8979433620da5ad416705c7c845aad5 https://github.com/galaxyproject/galaxy/commit/80562acfe8979433620da5ad4167… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/model/__init__.py Log Message: ----------- Fix API method broken in 6e13c3999. Commit: 381afd7576309409d788a6cf7cfe97f4f1421b04 https://github.com/galaxyproject/galaxy/commit/381afd7576309409d788a6cf7cfe… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Prevent server error if name or owner are missing. Commit: ad6edac562bd2fcfb0c49dc88bde692ced67ae02 https://github.com/galaxyproject/galaxy/commit/ad6edac562bd2fcfb0c49dc88bde… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Also prevent server error when repository is not found. Commit: cef58abb55e261c05de97b9d99906cc60b6416ba https://github.com/galaxyproject/galaxy/commit/cef58abb55e261c05de97b9d9990… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/model/__init__.py Log Message: ----------- Merge pull request #1943 from davebx/ts_api_bug Fix API method broken in 6e13c3999. Compare: https://github.com/galaxyproject/galaxy/compare/89b25edc313d...cef58abb55e2

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[galaxyproject/galaxy] 13f05d: Allow testing element counts in tool output collec...
by GitHub 17 Mar '16

17 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 13f05d2d79a01e0fdde34eb8f7a2a02917a7c607 https://github.com/galaxyproject/galaxy/commit/13f05d2d79a01e0fdde34eb8f7a2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/tools/parser/interface.py M test/functional/test_toolbox.py M test/functional/tools/collection_creates_list.xml Log Message: ----------- Allow testing element counts in tool output collections. Commit: 89b25edc313d4dd411af4f94d8dc830f2b37b945 https://github.com/galaxyproject/galaxy/commit/89b25edc313d4dd411af4f94d8dc… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/tools/parser/interface.py M test/functional/test_toolbox.py M test/functional/tools/collection_creates_list.xml Log Message: ----------- Merge pull request #1942 from jmchilton/element_count_test Allow testing element counts in tool output collections. Compare: https://github.com/galaxyproject/galaxy/compare/7fad23614b2a...89b25edc313d

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[galaxyproject/galaxy] 3e5aa6: More debugging for transiently failing tool test.
by GitHub 17 Mar '16

17 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3e5aa68ccfd1dcb117cc4131134cbe0c410a21cb https://github.com/galaxyproject/galaxy/commit/3e5aa68ccfd1dcb117cc4131134c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M test/base/twilltestcase.py M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0490_export_import_repositories.py M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py Log Message: ----------- More debugging for transiently failing tool test. Commit: 7fad23614b2aaf4de1de4dc07829394ecf1d00c3 https://github.com/galaxyproject/galaxy/commit/7fad23614b2aaf4de1de4dc07829… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M test/base/twilltestcase.py M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0490_export_import_repositories.py M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py Log Message: ----------- Merge pull request #1939 from jmchilton/transient_ts_test More debugging for transiently failing tool shed test. Compare: https://github.com/galaxyproject/galaxy/compare/29b6d545cf22...7fad23614b2a

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