- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 6a25d9: fix _query method to return a query instead of a l...
by GitHub 12 Aug '15

12 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6a25d979e1329aec4366bf6943aa65d9b41ec18f https://github.com/galaxyproject/galaxy/commit/6a25d979e1329aec4366bf6943aa… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/managers/sharable.py Log Message: ----------- fix _query method to return a query instead of a list Commit: 40f61610f1133e142de32389aad1a04294cb3164 https://github.com/galaxyproject/galaxy/commit/40f61610f1133e142de32389aad1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- introduce new API endpoint&method for published histories Commit: a4274913e195d0c1d6f558f5f877346a18c1e310 https://github.com/galaxyproject/galaxy/commit/a4274913e195d0c1d6f558f5f877… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/managers/sharable.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #594 from martenson/expose-api-pub-hist new API for published histories Compare: https://github.com/galaxyproject/galaxy/compare/01b69e327b52...a4274913e195

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[galaxyproject/usegalaxy-playbook] f891ab: Fix path to zfs for postgres backups from radegast
by GitHub 12 Aug '15

12 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f891abde3e3da083bbc9edd8af4bfb7b87daf806 https://github.com/galaxyproject/usegalaxy-playbook/commit/f891abde3e3da083… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M common/host_vars/radegast.galaxyproject.org.yml Log Message: ----------- Fix path to zfs for postgres backups from radegast

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[galaxyproject/galaxy] bb6a78: Include valid_tools as part of metadata returned w...
by GitHub 12 Aug '15

12 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bb6a784f13ff3f91762244d4488437ffef9e5acf https://github.com/galaxyproject/galaxy/commit/bb6a784f13ff3f91762244d44884… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Include valid_tools as part of metadata returned with the repository install info. Otherwise, no linkage exists bwtween tool version and a revision that can be used via the API. Commit: 01b69e327b524be014f86b9e98375f3e5d660141 https://github.com/galaxyproject/galaxy/commit/01b69e327b524be014f86b9e9837… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Merge pull request #592 from afgane/dev Include valid_tools as part of metadata returned with the repository … Compare: https://github.com/galaxyproject/galaxy/compare/1d325e217e03...01b69e327b52

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[galaxyproject/galaxy] 790713: Code style cleanup.
by GitHub 11 Aug '15

11 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7907136ffd4e3ee293ec96d39bf48357cf433539 https://github.com/galaxyproject/galaxy/commit/7907136ffd4e3ee293ec96d39bf4… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/utility_containers/__init__.py M lib/tool_shed/utility_containers/utility_container_manager.py Log Message: ----------- Code style cleanup. Commit: f1fc95e3655950a9f2064c5bc1506fecc936e4d4 https://github.com/galaxyproject/galaxy/commit/f1fc95e3655950a9f2064c5bc150… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/tool_shed/utility_containers/utility_container_manager.py Log Message: ----------- Use correct formatting for multi-line if. Commit: 1d325e217e03e13fbfcfc8c4ed46a00277382ed9 https://github.com/galaxyproject/galaxy/commit/1d325e217e03e13fbfcfc8c4ed46… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/utility_containers/__init__.py M lib/tool_shed/utility_containers/utility_container_manager.py Log Message: ----------- Merge pull request #591 from davebx/ts_lint Code style cleanup. Compare: https://github.com/galaxyproject/galaxy/compare/db4461177162...1d325e217e03

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[galaxyproject/galaxy] d9d365: Fix wrong call to LDAPObject.result() by using sea...
by GitHub 11 Aug '15

11 Aug '15

Branch: refs/heads/release_15.05 Home: https://github.com/galaxyproject/galaxy Commit: d9d365b36e827adf859759fd41113a74204ce376 https://github.com/galaxyproject/galaxy/commit/d9d365b36e827adf859759fd4111… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- Fix wrong call to LDAPObject.result() by using search_ext_s(). result() second parameter is 'all', which should be 0 or 1. result() call was passing 60 as second parameter, which was probably intended to be a timeout (third parameter). By using search_ext_s(), the search() and result() calls are combined in one and the number of search results retrieved is limited to 1. Also, if the search return no results, this is now logged separately at warning level. Commit: 15b5a336c4c09524bacdc445ad47ce8a0be60168 https://github.com/galaxyproject/galaxy/commit/15b5a336c4c09524bacdc445ad47… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- Merge pull request #590 from nsoranzo/release_15.05 [15.05] Fix wrong call to LDAPObject.result() by using search_ext_s(). Compare: https://github.com/galaxyproject/galaxy/compare/395e103ee5ff...15b5a336c4c0

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[galaxyproject/usegalaxy-playbook] f59034: Mutable configs from Test
by GitHub 11 Aug '15

11 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f59034d1e3dccdfeb7a41a5166de7ba0f8302d31 https://github.com/galaxyproject/usegalaxy-playbook/commit/f59034d1e3dccdfe… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: 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: ----------- Mutable configs from Test Commit: 4c97ad68efeb863c6ac2a4c98933b6d5038bf668 https://github.com/galaxyproject/usegalaxy-playbook/commit/4c97ad68efeb863c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M production/group_vars/galaxyservers.yml Log Message: ----------- Corral is back up Commit: bd7bc13a6a102a798f9b7128f3d381f10a80b045 https://github.com/galaxyproject/usegalaxy-playbook/commit/bd7bc13a6a102a79… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update Test Commit: 0531e6047534313b1a33b0466b708c7d7edf3272 https://github.com/galaxyproject/usegalaxy-playbook/commit/0531e6047534313b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M production/group_vars/all.yml Log Message: ----------- Update Main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/e22a25d404ed...…

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[galaxyproject/galaxy] 249d18: Minor cleanup of some iterators.
by GitHub 11 Aug '15

11 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 249d185d88bfdca668ca08775ef8c93bef34557c https://github.com/galaxyproject/galaxy/commit/249d185d88bfdca668ca08775ef8… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/grids/repository_grids.py Log Message: ----------- Minor cleanup of some iterators. Commit: 5885ce870e4b42b94be9115180880b7e2a1c96db https://github.com/galaxyproject/galaxy/commit/5885ce870e4b42b94be911518088… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/tool_shed/grids/repository_grids.py Log Message: ----------- Address Nicola's concerns. Commit: db4461177162fae94b2100363d3e617c213d09df https://github.com/galaxyproject/galaxy/commit/db4461177162fae94b2100363d3e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/grids/repository_grids.py Log Message: ----------- Merge pull request #589 from davebx/cleanup_ts Minor cleanup of some iterators. Compare: https://github.com/galaxyproject/galaxy/compare/a04147dc56cc...db4461177162

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[galaxyproject/infrastructure-playbook] 7b6c08: Removed invalid flags from ssh keys.
by GitHub 11 Aug '15

11 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 7b6c0858acd570c47ebdf3f16a09db0710ad3cbe https://github.com/galaxyproject/infrastructure-playbook/commit/7b6c0858acd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M galaxyenv/secret_group_vars/all.yml Log Message: ----------- Removed invalid flags from ssh keys.

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[galaxyproject/infrastructure-playbook] ca2d50: Ensure debconf utils are installed for Mailman
by GitHub 11 Aug '15

11 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: ca2d50b595141bce623e55ac9fbea9f94f84fa64 https://github.com/galaxyproject/infrastructure-playbook/commit/ca2d50b5951… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M roles/mailman/tasks/main.yml Log Message: ----------- Ensure debconf utils are installed for Mailman

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[galaxyproject/infrastructure-playbook] 229fea: Fix mail on SmartOS (non-GZ, anyway). As a result, ...
by GitHub 11 Aug '15

11 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 229feae52598cc3a09fbe9ac6830c05063823b6e https://github.com/galaxyproject/infrastructure-playbook/commit/229feae5259… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: A roles/mailman/files/default-spamassassin A roles/mailman/files/mm_discard_report.py A roles/mailman/handlers/main.yml A roles/mailman/meta/main.yml A roles/mailman/tasks/main.yml A roles/mailman/templates/mailman.ini.j2 A roles/mailman/templates/mm_cfg.py.j2 A roles/mailman/templates/mm_genaliases_ldap.j2 A roles/postfix/defaults/main.yml A roles/postfix/handlers/main.yml A roles/postfix/tasks/main.yml A roles/postfix/tasks/mx.yml A roles/postfix/tasks/relay.yml A roles/postfix/templates/15-content_filter_mode.j2 A roles/postfix/templates/50-user.j2 A roles/postfix/templates/ldap-aliases.cf.j2 A roles/postfix/templates/ldap-lists.cf.j2 A roles/postfix/templates/ldap-local.cf.j2 A roles/postfix/templates/local.cf.j2 A roles/postfix/templates/mailer.conf.j2 A roles/postfix/templates/main.cf.j2 A roles/postfix/templates/master.cf.j2 A roles/postfix/vars/default.yml A roles/postfix/vars/smartos.yml Log Message: ----------- Fix mail on SmartOS (non-GZ, anyway). As a result, bring the postfix and mailman roles over from the private playbook. So far, putting almost everything in a single play seems to be working out well. The only downside here is that as more stuff is added, there will be a *lot* of skipped tasks. Commit: 5f2cd8c675fa3659788f83dcd8d20689b1806b9a https://github.com/galaxyproject/infrastructure-playbook/commit/5f2cd8c675f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M galaxyenv/group_vars/all.yml A galaxyenv/group_vars/listservers.yml A galaxyenv/group_vars/mailservers.yml A galaxyenv/host_vars/chouffe.galaxyproject.org.yml A galaxyenv/host_vars/delirium.galaxyproject.org.yml M galaxyenv/inventory M playbook.yml Log Message: ----------- Data for the previously added postfix and mailman roles. Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/b04320d9c6…

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