September 2015 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] 659dbc: Update Test
by GitHub 16 Sep '15

16 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 659dbced678c878d79b396982d9b046fb03dc4f5 https://github.com/galaxyproject/usegalaxy-playbook/commit/659dbced678c878d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-16 (Wed, 16 Sep 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update Test

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[galaxyproject/galaxy] d41c13: Fix for logging in using OpenID when the OpenID is...
by GitHub 16 Sep '15

16 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d41c137e2d6b4d9871bb25c5162745dda36e2f31 https://github.com/galaxyproject/galaxy/commit/d41c137e2d6b4d9871bb25c51627… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M templates/user/login.mako Log Message: ----------- Fix for logging in using OpenID when the OpenID isn't associated with a user yet. (cherry picked from commit 451196e4d39800995d7b1ea1f69b177294c3c632) Commit: 358dc4071462347dacecd1f6ec125d650b261db0 https://github.com/galaxyproject/galaxy/commit/358dc4071462347dacecd1f6ec12… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M templates/user/login.mako Log Message: ----------- Merge pull request #718 from blankenberg/openid_15.07 [15.07] Fix for logging in using OpenID when the OpenID isn't associated with a user yet. Commit: 88abd3451d1b8cb7161fde7559684d5378dc76fc https://github.com/galaxyproject/galaxy/commit/88abd3451d1b8cb7161fde755968… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M lib/pulsar/client/amqp_exchange.py Log Message: ----------- Merge pull request #719 from natefoo/amqp_ack [15.07] Pulsar client: Fix deepcopy() error with copying the errback method from PulsarExchange. Commit: d3bd0fa57765bd2d03f255099c2b4f0501ac6466 https://github.com/galaxyproject/galaxy/commit/d3bd0fa57765bd2d03f255099c2b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-16 (Wed, 16 Sep 2015) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py Log Message: ----------- Do not change the state of jobs if a state update is received after they are set to a terminal state. Commit: 85552f73f712a9491af8d141a27369b21b615075 https://github.com/galaxyproject/galaxy/commit/85552f73f712a9491af8d141a273… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-16 (Wed, 16 Sep 2015) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #737 from natefoo/job-terminal-update [15.07] Don't update the state of terminal jobs Commit: 43c13ee1626779a4127f67b564ee88bb6b9af3ca https://github.com/galaxyproject/galaxy/commit/43c13ee1626779a4127f67b564ee… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-16 (Wed, 16 Sep 2015) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge branch 'release_15.07' into dev Conflicts: lib/galaxy/model/__init__.py Compare: https://github.com/galaxyproject/galaxy/compare/1e2adc6b5703...43c13ee16267

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[galaxyproject/galaxy] d3bd0f: Do not change the state of jobs if a state update ...
by GitHub 16 Sep '15

16 Sep '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: d3bd0fa57765bd2d03f255099c2b4f0501ac6466 https://github.com/galaxyproject/galaxy/commit/d3bd0fa57765bd2d03f255099c2b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-16 (Wed, 16 Sep 2015) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py Log Message: ----------- Do not change the state of jobs if a state update is received after they are set to a terminal state. Commit: 85552f73f712a9491af8d141a27369b21b615075 https://github.com/galaxyproject/galaxy/commit/85552f73f712a9491af8d141a273… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-16 (Wed, 16 Sep 2015) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #737 from natefoo/job-terminal-update [15.07] Don't update the state of terminal jobs Compare: https://github.com/galaxyproject/galaxy/compare/88abd3451d1b...85552f73f712

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[galaxyproject/infrastructure-playbook] dc91d3: add jenkins to the docker group
by GitHub 16 Sep '15

16 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: dc91d3c8e8dc57e05bd9efa0022c0d237edfbcd9 https://github.com/galaxyproject/infrastructure-playbook/commit/dc91d3c8e8d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-16 (Wed, 16 Sep 2015) Changed paths: M galaxyenv/host_vars/n2.galaxyproject.org.yml Log Message: ----------- add jenkins to the docker group jenkins user was created by apt

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[galaxyproject/infrastructure-playbook] 6a54a5: Install packages before managing local users
by GitHub 16 Sep '15

16 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 6a54a5f3801a01a016124167b9dae56a9e227fdd https://github.com/galaxyproject/infrastructure-playbook/commit/6a54a5f3801… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-16 (Wed, 16 Sep 2015) Changed paths: M playbook.yml Log Message: ----------- Install packages before managing local users Allows managing properties of apt managed users.

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[galaxyproject/infrastructure-playbook] c90d0f: add more packages to n2; add backports
by GitHub 16 Sep '15

16 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c90d0f928a4c618ad756eea52b4added68cb5830 https://github.com/galaxyproject/infrastructure-playbook/commit/c90d0f928a4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-16 (Wed, 16 Sep 2015) Changed paths: M galaxyenv/host_vars/n2.galaxyproject.org.yml Log Message: ----------- add more packages to n2; add backports

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[galaxyproject/infrastructure-playbook] 5a2674: fix packages to host_packages so it actually gets ...
by GitHub 16 Sep '15

16 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 5a2674a9c9a06ad8345077298486d19fc4df86e7 https://github.com/galaxyproject/infrastructure-playbook/commit/5a2674a9c9a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-16 (Wed, 16 Sep 2015) Changed paths: M galaxyenv/host_vars/n2.galaxyproject.org.yml Log Message: ----------- fix packages to host_packages so it actually gets recognized

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[galaxyproject/infrastructure-playbook] 49e5db: add TS dependencies in order to get func tests wor...
by GitHub 16 Sep '15

16 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 49e5dba92773f83924e4c145fac09670726fa31b https://github.com/galaxyproject/infrastructure-playbook/commit/49e5dba9277… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-16 (Wed, 16 Sep 2015) Changed paths: M galaxyenv/host_vars/n2.galaxyproject.org.yml Log Message: ----------- add TS dependencies in order to get func tests working

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[galaxyproject/galaxy] 89cc67: Trigger iframe event for history
by GitHub 15 Sep '15

15 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 89cc67baf67e295b3eaa2449e6fd6727317df942 https://github.com/galaxyproject/galaxy/commit/89cc67baf67e295b3eaa2449e6fd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Trigger iframe event for history Commit: 1e2adc6b57034fb27b3a12f0a13d6f0ace1b096a https://github.com/galaxyproject/galaxy/commit/1e2adc6b57034fb27b3a12f0a13d… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Merge pull request #732 from guerler/fix_history_001 Trigger iframe event for history Compare: https://github.com/galaxyproject/galaxy/compare/71a1def3219d...1e2adc6b5703

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[galaxyproject/galaxy] 555b6d: Fix for 13ea86753ad778aaaf6e6470a9370190fc2e91a0.
by GitHub 15 Sep '15

15 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 555b6d745d245d5fa6d6868e92cc3797d6855343 https://github.com/galaxyproject/galaxy/commit/555b6d745d245d5fa6d6868e92cc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Fix for 13ea86753ad778aaaf6e6470a9370190fc2e91a0. Fixes tests and functionality broken with 13ea86753ad778aaaf6e6470a9370190fc2e91a0 as spotted by eagle eye @nsoranzo here https://github.com/galaxyproject/galaxy/commit/13ea86753ad778aaaf6e6470a937…. Commit: 71a1def3219db8763e76b87a4bb1aefdfdc082d3 https://github.com/galaxyproject/galaxy/commit/71a1def3219db8763e76b87a4bb1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Merge pull request #735 from jmchilton/collection_fix Fix for 13ea86753ad778aaaf6e6470a9370190fc2e91a0. Compare: https://github.com/galaxyproject/galaxy/compare/89b42bf06034...71a1def3219d

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