March 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] e3255f: made collection ops help sections slightly more re...
by GitHub 21 Mar '17

21 Mar '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: e3255fd3cb7c1b0cf9ce9fa82f0a4a9c39719f19 https://github.com/galaxyproject/galaxy/commit/e3255fd3cb7c1b0cf9ce9fa82f0a… Author: nekrut <anton(a)nekrut.org> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/tools/filter_failed_collection.xml M lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/unzip_collection.xml M lib/galaxy/tools/zip_collection.xml Log Message: ----------- made collection ops help sections slightly more readable Commit: d9c3a0bb57e63a1849bb3f55c056ae0384a2279a https://github.com/galaxyproject/galaxy/commit/d9c3a0bb57e63a1849bb3f55c056… Author: Anton Nekrutenko <anekrut(a)gmail.com> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/tools/unzip_collection.xml Log Message: ----------- Update unzip_collection.xml fixed typos identified by @mvdbeek Commit: c84b3ba0b8f9de983d43ea17c165856d23960911 https://github.com/galaxyproject/galaxy/commit/c84b3ba0b8f9de983d43ea17c165… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/tools/filter_failed_collection.xml M lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/unzip_collection.xml M lib/galaxy/tools/zip_collection.xml Log Message: ----------- Merge pull request #3788 from jmchilton/backport_collection_option_help_fixes [17.01] Backport collection operation help fixes Compare: https://github.com/galaxyproject/galaxy/compare/ec88dda1e9c9...c84b3ba0b8f9

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[galaxyproject/galaxy] 12eb38: fix xss thanks to @erasche
by GitHub 21 Mar '17

21 Mar '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 12eb3838496f373e429235cd8e75117baf682005 https://github.com/galaxyproject/galaxy/commit/12eb3838496f373e429235cd8e75… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- fix xss thanks to @erasche Commit: 2528a89bd087786c458c86d6ac78c24e8fb7f51d https://github.com/galaxyproject/galaxy/commit/2528a89bd087786c458c86d6ac78… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #3776 from martenson/xss-fix [16.04] fix xss vuln in grids Commit: 80ecc79a4cb8fa3dbaf9b3348216df6f9387a91c https://github.com/galaxyproject/galaxy/commit/80ecc79a4cb8fa3dbaf9b3348216… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #3789 from galaxyproject/release_16.04 merge 16.04 into 16.07 Commit: 490e565611b5e3a22124d937e22cf0363afb62f6 https://github.com/galaxyproject/galaxy/commit/490e565611b5e3a22124d937e22c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #3790 from galaxyproject/release_16.07 merge 16.07 into 16.10 Commit: ec88dda1e9c926341b87bc7e19b7b5842eb92ddb https://github.com/galaxyproject/galaxy/commit/ec88dda1e9c926341b87bc7e19b7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #3791 from galaxyproject/release_16.10 merge 16.10 into 17.01 Compare: https://github.com/galaxyproject/galaxy/compare/e3e24facc721...ec88dda1e9c9

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[galaxyproject/galaxy] 12eb38: fix xss thanks to @erasche
by GitHub 21 Mar '17

21 Mar '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 12eb3838496f373e429235cd8e75117baf682005 https://github.com/galaxyproject/galaxy/commit/12eb3838496f373e429235cd8e75… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- fix xss thanks to @erasche Commit: 2528a89bd087786c458c86d6ac78c24e8fb7f51d https://github.com/galaxyproject/galaxy/commit/2528a89bd087786c458c86d6ac78… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #3776 from martenson/xss-fix [16.04] fix xss vuln in grids Commit: 80ecc79a4cb8fa3dbaf9b3348216df6f9387a91c https://github.com/galaxyproject/galaxy/commit/80ecc79a4cb8fa3dbaf9b3348216… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #3789 from galaxyproject/release_16.04 merge 16.04 into 16.07 Commit: 490e565611b5e3a22124d937e22cf0363afb62f6 https://github.com/galaxyproject/galaxy/commit/490e565611b5e3a22124d937e22c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #3790 from galaxyproject/release_16.07 merge 16.07 into 16.10 Compare: https://github.com/galaxyproject/galaxy/compare/1b9a2868a178...490e565611b5

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[galaxyproject/galaxy] 12eb38: fix xss thanks to @erasche
by GitHub 21 Mar '17

21 Mar '17

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 12eb3838496f373e429235cd8e75117baf682005 https://github.com/galaxyproject/galaxy/commit/12eb3838496f373e429235cd8e75… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- fix xss thanks to @erasche Commit: 2528a89bd087786c458c86d6ac78c24e8fb7f51d https://github.com/galaxyproject/galaxy/commit/2528a89bd087786c458c86d6ac78… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #3776 from martenson/xss-fix [16.04] fix xss vuln in grids Commit: 80ecc79a4cb8fa3dbaf9b3348216df6f9387a91c https://github.com/galaxyproject/galaxy/commit/80ecc79a4cb8fa3dbaf9b3348216… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #3789 from galaxyproject/release_16.04 merge 16.04 into 16.07 Compare: https://github.com/galaxyproject/galaxy/compare/915b653b91af...80ecc79a4cb8

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[galaxyproject/galaxy] 61677d: made collection ops help sections slightly more re...
by GitHub 21 Mar '17

21 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 61677d2026f155868ad57a1289609c1aad1044e6 https://github.com/galaxyproject/galaxy/commit/61677d2026f155868ad57a128960… Author: nekrut <anton(a)nekrut.org> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M lib/galaxy/tools/filter_failed_collection.xml M lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/unzip_collection.xml M lib/galaxy/tools/zip_collection.xml Log Message: ----------- made collection ops help sections slightly more readable Commit: a8d0c46ee97b37df20ac2022af4309890ca0c6e0 https://github.com/galaxyproject/galaxy/commit/a8d0c46ee97b37df20ac2022af43… Author: Anton Nekrutenko <anekrut(a)gmail.com> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/tools/unzip_collection.xml Log Message: ----------- Update unzip_collection.xml fixed typos identified by @mvdbeek Commit: eadbb16462f2bd6f6f8f8cf71d992f0c5389c80f https://github.com/galaxyproject/galaxy/commit/eadbb16462f2bd6f6f8f8cf71d99… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/tools/filter_failed_collection.xml M lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/unzip_collection.xml M lib/galaxy/tools/zip_collection.xml Log Message: ----------- Merge pull request #3784 from nekrut/collection_ops_help_fixes made collection ops help sections slightly more readable Compare: https://github.com/galaxyproject/galaxy/compare/a5b0e760503d...eadbb16462f2

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[galaxyproject/infrastructure-playbook] 92e004: Decrease squid memory usage on stratum 1s
by GitHub 21 Mar '17

21 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 92e004b615d7297191f06b5a3c729d8ec6533207 https://github.com/galaxyproject/infrastructure-playbook/commit/92e004b615d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M galaxyenv/group_vars/cvmfsstratum1servers.yml Log Message: ----------- Decrease squid memory usage on stratum 1s Commit: 9ad75c96e7be125768960f0bdd62fb30f569512f https://github.com/galaxyproject/infrastructure-playbook/commit/9ad75c96e7b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M galaxyenv/host_vars/cvmfs0-psu0.galaxyproject.org.yml M galaxyenv/host_vars/cvmfs0-tacc0.galaxyproject.org.yml M galaxyenv/host_vars/cvmfs1-psu0.galaxyproject.org.yml A galaxyenv/host_vars/jetstream-iu0.galaxyproject.org.yml A galaxyenv/host_vars/jetstream-tacc0.galaxyproject.org.yml M galaxyenv/inventory M galaxyenv/playbook.yml A galaxyenv/secret_group_vars/dockersslservers.yml A jetstream_common/files/etc/dhclient.conf A jetstream_common/files/etc/ifcfg-eth1 M jetstreamiuenv/group_vars/controllers.yml A jetstreamtaccenv/files M jetstreamtaccenv/group_vars/controllers.yml A roles/cvmfs/meta/main.yml A roles/docker/README.md A roles/docker/defaults/main.yml A roles/docker/handlers/main.yml A roles/docker/tasks/install_debian.yml A roles/docker/tasks/install_redhat.yml A roles/docker/tasks/main.yml A roles/docker/tasks/ssl-ca-passphrase.yml A roles/docker/tasks/ssl-gen-ca.yml A roles/docker/tasks/ssl-gen-client-cert.yml A roles/docker/tasks/ssl-gen-server-cert.yml A roles/docker/tasks/ssl-server.yml A roles/docker_swarm/meta/main.yml A roles/docker_swarm/tasks/main.yml A roles/docker_swarm/tasks/swarm-init.yml Log Message: ----------- Add roles for docker and docker swarm, create a swarm on Jetstream and PSU Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/c1e9057120…

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[galaxyproject/galaxy] 18cb50: Abstraction for re-use between collection creators...
by GitHub 21 Mar '17

21 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 18cb50ecea80b3feeac02a2ef07c4cbd816c39d4 https://github.com/galaxyproject/galaxy/commit/18cb50ecea80b3feeac02a2ef07c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: A client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js A static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map A static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- Abstraction for re-use between collection creators. The new mixin reduces the duplication between the list and list of paired collection creators. I'd like to add functionality related to hiding the original datasets (especially useful for direct upload of collections but previously requested also) but I'd like to reduce the duplication related to doing that first. This is a start in that direction. Commit: a5b0e760503dc09ac99d47bbcde1524c7f3e37a4 https://github.com/galaxyproject/galaxy/commit/a5b0e760503dc09ac99d47bbcde1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: A client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js A static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map A static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- Merge pull request #3781 from jmchilton/collection-builders Abstraction for re-use between collection creators. Compare: https://github.com/galaxyproject/galaxy/compare/5428d39adb6b...a5b0e760503d

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[galaxyproject/galaxy] 1578ff: Add tool_list webhook plugin to create the tool li...
by GitHub 20 Mar '17

20 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1578ffe1ca5bf28a34f91a892eed286ab69a14ba https://github.com/galaxyproject/galaxy/commit/1578ffe1ca5bf28a34f91a892eed… Author: Clemens BlanK <blankclemens(a)gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: A config/plugins/webhooks/demo/tool_list/config/tool_list.yml A config/plugins/webhooks/demo/tool_list/helper/__init__.py Log Message: ----------- Add tool_list webhook plugin to create the tool list yaml file for this instance. Commit: 90ae42c3f1d0efc4f8b461e43a158eb5b7b95d4f https://github.com/galaxyproject/galaxy/commit/90ae42c3f1d0efc4f8b461e43a15… Author: Clemens BlanK <blankclemens(a)gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M config/plugins/webhooks/demo/tool_list/helper/__init__.py Log Message: ----------- Reduced API calls to speed it up. Commit: 6ece9acfde69fadd4e8b105c9c14ce572ddbfbcd https://github.com/galaxyproject/galaxy/commit/6ece9acfde69fadd4e8b105c9c14… Author: Clemens BlanK <blankclemens(a)gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M config/plugins/webhooks/demo/tool_list/helper/__init__.py Log Message: ----------- Fix linting. Commit: d7cf8a4b33991c3117f725a1d418706b758703b5 https://github.com/galaxyproject/galaxy/commit/d7cf8a4b33991c3117f725a1d418… Author: Clemens BlanK <blankclemens(a)gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M config/plugins/webhooks/demo/tool_list/helper/__init__.py Log Message: ----------- Fix Python 2.7 linting. Commit: bc203d022f92fd596514d935c0e569163e2cf4d1 https://github.com/galaxyproject/galaxy/commit/bc203d022f92fd596514d935c0e5… Author: Clemens BlanK <blankclemens(a)gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M config/plugins/webhooks/demo/tool_list/config/tool_list.yml M config/plugins/webhooks/demo/tool_list/helper/__init__.py Log Message: ----------- Speed up list creation. Commit: 5428d39adb6bf37c61b8c17efb1b3157e0b242d2 https://github.com/galaxyproject/galaxy/commit/5428d39adb6bf37c61b8c17efb1b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: A config/plugins/webhooks/demo/tool_list/config/tool_list.yml A config/plugins/webhooks/demo/tool_list/helper/__init__.py Log Message: ----------- Merge pull request #3753 from blankclemens/webhook_tool_list Webhook plugin: tool_list Compare: https://github.com/galaxyproject/galaxy/compare/3921aa573c0f...5428d39adb6b

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[galaxyproject/galaxy] 060271: deduplicate obsolete API readme
by GitHub 20 Mar '17

20 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0602712a35015bba52f3bc756b0ce0fa1c20728e https://github.com/galaxyproject/galaxy/commit/0602712a35015bba52f3bc756b0c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M scripts/api/README Log Message: ----------- deduplicate obsolete API readme Commit: 3921aa573c0fa7b900316cdad4d06e23c02b19b2 https://github.com/galaxyproject/galaxy/commit/3921aa573c0fa7b900316cdad4d0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M scripts/api/README Log Message: ----------- Merge pull request #3777 from martenson/dedup-readme deduplicate obsolete API readme Compare: https://github.com/galaxyproject/galaxy/compare/5440889bf6a7...3921aa573c0f

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[galaxyproject/usegalaxy-playbook] 4324d0: update Main
by GitHub 20 Mar '17

20 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4324d0b90e7772248afb9204807c3d9f81d6dfe4 https://github.com/galaxyproject/usegalaxy-playbook/commit/4324d0b90e777224… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M production/galaxy_version.yml Log Message: ----------- update Main

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