November 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] a9dab6: Preserve custom event handler for form inputs
by GitHub 22 Nov '16

22 Nov '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: a9dab631fb00252ac122ea297262e89f63887019 https://github.com/galaxyproject/galaxy/commit/a9dab631fb00252ac122ea297262… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M static/maps/mvc/form/form-section.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/mvc/form/form-section.js Log Message: ----------- Preserve custom event handler for form inputs Commit: 0b2d0c1746c9b7d7cc5781fedc5c6a02af3bdfdb https://github.com/galaxyproject/galaxy/commit/0b2d0c1746c9b7d7cc5781fedc5c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M static/maps/mvc/form/form-section.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/mvc/form/form-section.js Log Message: ----------- Merge pull request #3210 from guerler/fix_output_label_handler [16.10] Preserve custom event handler for form inputs Compare: https://github.com/galaxyproject/galaxy/compare/ec08ec60bb4d...0b2d0c1746c9

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[galaxyproject/infrastructure-playbook] 33ddca: Move new.galaxyproject.org ownership to gxsite and...
by GitHub 22 Nov '16

22 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 33ddca9740b4b37bf66efaf0554fc25b3d13f234 https://github.com/galaxyproject/infrastructure-playbook/commit/33ddca9740b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M galaxyenv/host_vars/chouffe.galaxyproject.org.yml M galaxyenv/secret_group_vars/all.yml M galaxyenv/secret_host_vars/chouffe.galaxyproject.org.yml M galaxyenv/secret_host_vars/leeroy.galaxyproject.org.yml Log Message: ----------- Move new.galaxyproject.org ownership to gxsite and allow Jenkins access.

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[galaxyproject/infrastructure-playbook] 50f4d0: Migrate more web stuff from the private playbook, ...
by GitHub 22 Nov '16

22 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 50f4d01ef91a41ff21f2c181cdc2aa707d60982a https://github.com/galaxyproject/infrastructure-playbook/commit/50f4d01ef91… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M common_env/secret_group_vars/sslwebservers.yml M galaxyenv/files/ssl/wildcard_cert.pem M galaxyenv/host_vars/chouffe.galaxyproject.org.yml M galaxyenv/inventory A galaxyenv/secret_host_vars/chouffe.galaxyproject.org.yml M galaxyenv/secret_host_vars/delirium.galaxyproject.org.yml A galaxyenv/templates/nginx/intron.j2 A galaxyenv/templates/nginx/new.j2 A galaxyenv/templates/nginx/wiki.j2 Log Message: ----------- Migrate more web stuff from the private playbook, add new.galaxyproject.org

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[galaxyproject/usegalaxy-playbook] 56bf24: Fix IEs
by GitHub 22 Nov '16

22 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 56bf24a6db259bb80f0fddfea082175185be70cc https://github.com/galaxyproject/usegalaxy-playbook/commit/56bf24a6db259bb8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M galaxy.yml M production/secret_vars/galaxyservers.yml M roles/galaxyprojectdotorg.interactive_environments/defaults/main.yml M roles/galaxyprojectdotorg.interactive_environments/meta/.galaxy_install_info R roles/galaxyprojectdotorg.interactive_environments/templates/ipython_apache.conf.j2 R roles/galaxyprojectdotorg.interactive_environments/templates/ipython_nginx.conf.j2 A roles/galaxyprojectdotorg.interactive_environments/templates/jupyter_apache.conf.j2 A roles/galaxyprojectdotorg.interactive_environments/templates/jupyter_nginx.conf.j2 M stage/secret_vars/galaxyservers.yml Log Message: ----------- Fix IEs

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[galaxyproject/usegalaxy-playbook] 7bd0ad: Disable sentry logging on Main so logs are readabl...
by GitHub 22 Nov '16

22 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7bd0ad190d148494f9430b23b1f9ab68e9936524 https://github.com/galaxyproject/usegalaxy-playbook/commit/7bd0ad190d148494… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M production/group_vars/galaxyservers.yml Log Message: ----------- Disable sentry logging on Main so logs are readable

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[galaxyproject/usegalaxy-playbook] 34b210: Update Main
by GitHub 21 Nov '16

21 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 34b210bb6ad8ed489b3466cc041f32518c203fe8 https://github.com/galaxyproject/usegalaxy-playbook/commit/34b210bb6ad8ed48… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M production/galaxy_version.yml Log Message: ----------- Update Main

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[galaxyproject/galaxy] c122e7: Fixes for core.galaxy_ui.yaml.
by GitHub 21 Nov '16

21 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c122e74240fb35222d5d2d0f0b08e783dc0d561a https://github.com/galaxyproject/galaxy/commit/c122e74240fb35222d5d2d0f0b08… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml Log Message: ----------- Fixes for core.galaxy_ui.yaml. Neither of these prevent the tour from working but I think they are bugs. The extra click isn't an elemment that is clickable at that point in the tour and the referenced id isn't available so nothing in particular is tagged in the UI at that point. Commit: 097300ea6219e14b66b23a0e05f2808b16f10015 https://github.com/galaxyproject/galaxy/commit/097300ea6219e14b66b23a0e05f2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml Log Message: ----------- Merge pull request #3206 from jmchilton/tour_fixes Fixes for core.galaxy_ui.yaml. Compare: https://github.com/galaxyproject/galaxy/compare/d2c95b43fa33...097300ea6219

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[galaxyproject/galaxy] 74d8fa: Change 'History Actions' to 'Current History' in h...
by GitHub 21 Nov '16

21 Nov '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 74d8faac9f07407ac9df344a78c9ecb06c178f93 https://github.com/galaxyproject/galaxy/commit/74d8faac9f07407ac9df344a78c9… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js 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.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Change 'History Actions' to 'Current History' in history options menu. as it was before 1cc57b1eb2c295dbd68837c864740b6ff079b83d. Commit: ec08ec60bb4dadaf6f8759f9dce79f764f26c909 https://github.com/galaxyproject/galaxy/commit/ec08ec60bb4dadaf6f8759f9dce7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js 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.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Merge pull request #3205 from blankenberg/history-current-options-name_16.10 [16.10] Change 'History Actions' to 'Current History' in history options menu. Compare: https://github.com/galaxyproject/galaxy/compare/aadc14d967c3...ec08ec60bb4d

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[galaxyproject/usegalaxy-playbook] 74f97c: First pass at a uWSGI zerg mode setup. Requires th...
by GitHub 21 Nov '16

21 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 74f97c6ac5b03d254759e2f5582d28348ad7f9e4 https://github.com/galaxyproject/usegalaxy-playbook/commit/74f97c6ac5b03d25… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M templates/galaxy/test.galaxyproject.org/config/uwsgi.ini.j2 M templates/galaxy/usegalaxy.org/config/uwsgi.ini.j2 M templates/supervisor/galaxy.j2 Log Message: ----------- First pass at a uWSGI zerg mode setup. Requires the uWSGI author's one-off spinningfifo plugin from an email and has a bad race condition encountered when starting zerglings simultaneously: Both will attempt to write `2p` to the running fifo at the same time and both will attempt to grab the `new` fifo at the same time, and one or both will end up in the running state, unpaused. Staggering starting/restarting can be used to solve this but hopefully I can come up with a better solution. uWSGI/server full restarts will need to be hand-held for now. But `galaxy graceful` and the new `galaxy gracefuluwsgi` work very nice.

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[galaxyproject/usegalaxy-playbook] 70201c: Take down downtime message
by GitHub 21 Nov '16

21 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 70201ca9de45477f2a7c082fce3d4799580c0ff0 https://github.com/galaxyproject/usegalaxy-playbook/commit/70201ca9de45477f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M production/group_vars/galaxyservers.yml M stage/group_vars/galaxyservers.yml Log Message: ----------- Take down downtime message

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