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

[galaxyproject/infrastructure-playbook] d79b82: Swap from testing to stable channel for Grafana (t...
by GitHub 11 May '16

11 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: d79b820cac421179516fb5b452d214990fea592a https://github.com/galaxyproject/infrastructure-playbook/commit/d79b820cac4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M roles/stats/tasks/main.yml Log Message: ----------- Swap from testing to stable channel for Grafana (though this commit also disables use of that channel, in lieu of the remote .rpm until the channel is updated) Commit: 6c8914ec1a0300e8338c3ed9342a2a707ad73054 https://github.com/galaxyproject/infrastructure-playbook/commit/6c8914ec1a0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M roles/stats/tasks/main.yml Log Message: ----------- Direct rpm grafana installation Commit: e4a6f1c85cfeee1e49c07d2f31fa6a4d76f2eae0 https://github.com/galaxyproject/infrastructure-playbook/commit/e4a6f1c85cf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M roles/stats/tasks/main.yml Log Message: ----------- Merge branch 'stats_role' Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/38b3aaf764…

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[galaxyproject/infrastructure-playbook] 6c8914: Direct rpm grafana installation
by GitHub 11 May '16

11 May '16

Branch: refs/heads/stats_role Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 6c8914ec1a0300e8338c3ed9342a2a707ad73054 https://github.com/galaxyproject/infrastructure-playbook/commit/6c8914ec1a0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M roles/stats/tasks/main.yml Log Message: ----------- Direct rpm grafana installation

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[galaxyproject/usegalaxy-playbook] b14d78: Disable TACC Jetstream until Ceph @ TACC stabilize...
by GitHub 11 May '16

11 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b14d7836394d5515cefd39d88d099c030986ddf6 https://github.com/galaxyproject/usegalaxy-playbook/commit/b14d7836394d5515… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M files/galaxy/test.galaxyproject.org/config/pulsar_jetstream.yml M files/galaxy/usegalaxy.org/config/pulsar_jetstream.yml Log Message: ----------- Disable TACC Jetstream until Ceph @ TACC stabilizes Commit: 21dda40651195a3d7c4d273f0831592e37cf378b https://github.com/galaxyproject/usegalaxy-playbook/commit/21dda40651195a3d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update Test Commit: 89ad6d275775a850cf50d43d089c82f30ef303fd https://github.com/galaxyproject/usegalaxy-playbook/commit/89ad6d275775a850… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Multiple multi handlers for Test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/f41f0d01033b...…

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[galaxyproject/infrastructure-playbook] d79b82: Swap from testing to stable channel for Grafana (t...
by GitHub 11 May '16

11 May '16

Branch: refs/heads/stats_role Home: https://github.com/galaxyproject/infrastructure-playbook Commit: d79b820cac421179516fb5b452d214990fea592a https://github.com/galaxyproject/infrastructure-playbook/commit/d79b820cac4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M roles/stats/tasks/main.yml Log Message: ----------- Swap from testing to stable channel for Grafana (though this commit also disables use of that channel, in lieu of the remote .rpm until the channel is updated)

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[galaxyproject/infrastructure-playbook] a98bdd: Influx stack packages.
by GitHub 11 May '16

11 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: a98bdd24183c8185424265cfa4358dc39880bfd1 https://github.com/galaxyproject/infrastructure-playbook/commit/a98bdd24183… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: A roles/stats/defaults/main.yml A roles/stats/tasks/main.yml M taccenv/host_vars/galaxy06.tacc.utexas.edu.yml M taccenv/playbook.yml Log Message: ----------- Influx stack packages. Commit: 4cb6510b3e5278c55278e72f770e0a95256f9c7e https://github.com/galaxyproject/infrastructure-playbook/commit/4cb6510b3e5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M roles/stats/tasks/main.yml A roles/stats/templates/influxdb.conf.j2 A roles/stats/templates/telegraf.conf.j2 Log Message: ----------- Add stats configs, defaults for now. Commit: 52c4b7f3ac2a14367e6e21bfe4a925651ceb3202 https://github.com/galaxyproject/infrastructure-playbook/commit/52c4b7f3ac2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M roles/stats/tasks/main.yml A roles/stats/templates/grafana.conf.j2 M taccenv/group_vars/statsservers.yml A taccenv/templates/supervisor/stats.j2 Log Message: ----------- Supervisor configs and more for stats role. Commit: 4bc99b4dfb69263e7895729dbaa3c0a69b46e2c4 https://github.com/galaxyproject/infrastructure-playbook/commit/4bc99b4dfb6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M roles/stats/tasks/main.yml M roles/stats/templates/grafana.conf.j2 M roles/stats/templates/influxdb.conf.j2 M taccenv/templates/supervisor/stats.j2 Log Message: ----------- Stats startup fixes. Commit: d8006eecfab6822ea881bcd5d2d20018e7593992 https://github.com/galaxyproject/infrastructure-playbook/commit/d8006eecfab… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M taccenv/host_vars/galaxy06.tacc.utexas.edu.yml A taccenv/templates/nginx/stats.j2 Log Message: ----------- Basic nginx config for stats.galaxyproject.org Commit: d0bf01aa82c6eedbaadd94720a2ac78ab766cd7d https://github.com/galaxyproject/infrastructure-playbook/commit/d0bf01aa82c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M roles/stats/templates/grafana.conf.j2 M taccenv/playbook.yml A taccenv/secret_group_vars/stats.yml Log Message: ----------- Configure default user, add vault. Commit: c978f4625c72f5b95b898d84d6bf76a71b86a12e https://github.com/galaxyproject/infrastructure-playbook/commit/c978f4625c7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: R taccenv/templates/nginx/graphite.j2 M taccenv/templates/nginx/sentry.j2 M taccenv/templates/nginx/stats.j2 Log Message: ----------- Update nginx confs, remove graphite subdomain. is interesting in nginx, it always returns the first server (which was sentry), and http://stats.galaxyproject.org was redirecting to https://sentry.* before this change. Commit: 6094b47bdc5785c8be93c7af38f36741f3d65314 https://github.com/galaxyproject/infrastructure-playbook/commit/6094b47bdc5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M roles/stats/templates/grafana.conf.j2 M roles/stats/templates/telegraf.conf.j2 Log Message: ----------- Connecting all the things. Commit: 38b3aaf764521c812da0f04c58f508c6c86f6a4c https://github.com/galaxyproject/infrastructure-playbook/commit/38b3aaf7645… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: A roles/stats/defaults/main.yml A roles/stats/tasks/main.yml A roles/stats/templates/grafana.conf.j2 A roles/stats/templates/influxdb.conf.j2 A roles/stats/templates/telegraf.conf.j2 M taccenv/group_vars/statsservers.yml M taccenv/host_vars/galaxy06.tacc.utexas.edu.yml M taccenv/playbook.yml A taccenv/secret_group_vars/stats.yml R taccenv/templates/nginx/graphite.j2 M taccenv/templates/nginx/sentry.j2 A taccenv/templates/nginx/stats.j2 A taccenv/templates/supervisor/stats.j2 Log Message: ----------- Merge pull request #8 from galaxyproject/stats_role Stats role Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/2f0cbfceda…

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[galaxyproject/galaxy] fac2ef: Wrap statsd timing middleware more closely around ...
by GitHub 11 May '16

11 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fac2efc4bd6b2214fa6d17e27b43d26fe4de7d37 https://github.com/galaxyproject/galaxy/commit/fac2efc4bd6b2214fa6d17e27b43… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Wrap statsd timing middleware more closely around the core application in an attempt to prevent manipulation of keys it uses in environ Commit: fcc0d123ea4ea04c77dea5d71b3ff3e1fd984cd1 https://github.com/galaxyproject/galaxy/commit/fcc0d123ea4ea04c77dea5d71b3f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #2342 from dannon/stats_layering_fix Wrap statsd timing middleware more closely around the core applicatio… Compare: https://github.com/galaxyproject/galaxy/compare/f3e4cd4ddafc...fcc0d123ea4e

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[galaxyproject/usegalaxy-playbook] f41f0d: nginx config fixes for Jupyter changes
by GitHub 11 May '16

11 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f41f0d01033b5b9626190b76b32f83d6b23a102e https://github.com/galaxyproject/usegalaxy-playbook/commit/f41f0d01033b5b96… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M templates/nginx/usegalaxy.j2 Log Message: ----------- nginx config fixes for Jupyter changes

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[galaxyproject/galaxy] bd25ae: Re-fix the bug with multiple preceding '/' charact...
by GitHub 11 May '16

11 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bd25ae95f900cef379214caa43c5b0bfc7705baf https://github.com/galaxyproject/galaxy/commit/bd25ae95f900cef379214caa43c5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Re-fix the bug with multiple preceding '/' characters in the GIE proxy prefix Commit: 013813691ac1d67a432a267c0c596a8efde611fb https://github.com/galaxyproject/galaxy/commit/013813691ac1d67a432a267c0c59… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #2339 from natefoo/gie-proxy-path [16.04] Re-fix the bug with multiple preceding '/' characters in the GIE proxy prefix Commit: 073f37a81bfd805b4ccf174d40133da7fe78c9a8 https://github.com/galaxyproject/galaxy/commit/073f37a81bfd805b4ccf174d4013… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge branch 'release_16.04' into dev Commit: f3e4cd4ddafc8691e7a84d17feba259ad21a6f3d https://github.com/galaxyproject/galaxy/commit/f3e4cd4ddafc8691e7a84d17feba… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Make client. Compare: https://github.com/galaxyproject/galaxy/compare/6ca6ba198de0...f3e4cd4ddafc

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[galaxyproject/galaxy] bd25ae: Re-fix the bug with multiple preceding '/' charact...
by GitHub 11 May '16

11 May '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: bd25ae95f900cef379214caa43c5b0bfc7705baf https://github.com/galaxyproject/galaxy/commit/bd25ae95f900cef379214caa43c5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Re-fix the bug with multiple preceding '/' characters in the GIE proxy prefix Commit: 013813691ac1d67a432a267c0c596a8efde611fb https://github.com/galaxyproject/galaxy/commit/013813691ac1d67a432a267c0c59… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #2339 from natefoo/gie-proxy-path [16.04] Re-fix the bug with multiple preceding '/' characters in the GIE proxy prefix Compare: https://github.com/galaxyproject/galaxy/compare/d0830e0c226b...013813691ac1

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[galaxyproject/galaxy] 3672ed: UI, history: update using xhr date header
by GitHub 10 May '16

10 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3672eda0ea82ece74dae918503518e0d19c5dee6 https://github.com/galaxyproject/galaxy/commit/3672eda0ea82ece74dae91850351… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M static/maps/mvc/history/history-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-model.js Log Message: ----------- UI, history: update using xhr date header Makes the 'updated since' contents query based on any previous update's ajax Date response header instead of the client time. This may offer more protection against incorrect client time. This works (and may work better than the previous method) because the Date header is floored and not rounded and seems to mark a time before the contents query is made. Resolves #2242 (hopefully) Commit: 5437c9a7d9131fa4748ee7d338d7a01ba5618fec https://github.com/galaxyproject/galaxy/commit/5437c9a7d9131fa4748ee7d338d7… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M Makefile Log Message: ----------- (merge conflicts) Commit: 6ca6ba198de0d71652c18ee8007103fdb3fad3d9 https://github.com/galaxyproject/galaxy/commit/6ca6ba198de0d71652c18ee80071… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M static/maps/mvc/history/history-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-model.js Log Message: ----------- Merge pull request #2335 from carlfeberhard/history.updating-sync UI, history: update using xhr date header Compare: https://github.com/galaxyproject/galaxy/compare/75a99eb11235...6ca6ba198de0

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