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

[galaxyproject/galaxy] 83628d: Add conditional statsd requirement. Wheel is live...
by GitHub 22 Apr '16

22 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 83628d5ecda9d353594e97e5ee329dd1a80d3e30 https://github.com/galaxyproject/galaxy/commit/83628d5ecda9d353594e97e5ee32… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Add conditional statsd requirement. Wheel is live on wheels.galaxyproject.org. Commit: 581e5ccdcb21f92d108021bf8fbc8e834999a157 https://github.com/galaxyproject/galaxy/commit/581e5ccdcb21f92d108021bf8fbc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-22 (Fri, 22 Apr 2016) Log Message: ----------- Merge pull request #2227 from dannon/stats_req_backport [16.04] Add conditional statsd requirement Compare: https://github.com/galaxyproject/galaxy/compare/f23c3ae662b7...581e5ccdcb21

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[galaxyproject/galaxy] 6460b1: Correctly check set_environment declarations when ...
by GitHub 22 Apr '16

22 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6460b19045a951ac2594ee2d606f923b9fdedc25 https://github.com/galaxyproject/galaxy/commit/6460b19045a951ac2594ee2d606f… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Correctly check set_environment declarations when updating repository. Commit: f23c3ae662b72b56175be5d8daf01dcfec43d814 https://github.com/galaxyproject/galaxy/commit/f23c3ae662b72b56175be5d8daf0… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-22 (Fri, 22 Apr 2016) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #2116 from davebx/update_environment Correctly check set_environment declarations when updating repository. Compare: https://github.com/galaxyproject/galaxy/compare/bbf5722f27ef...f23c3ae662b7

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[galaxyproject/galaxy] e5b3c9: Fix js value validator
by GitHub 22 Apr '16

22 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e5b3c94c5e03a963059a58243858b7244508fb63 https://github.com/galaxyproject/galaxy/commit/e5b3c94c5e03a963059a58243858… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-22 (Fri, 22 Apr 2016) Changed paths: M client/galaxy/scripts/utils/utils.js M static/maps/utils/utils.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/utils.js Log Message: ----------- Fix js value validator Commit: 62bc415ae6ed331d0dacaafb2e62a79055972500 https://github.com/galaxyproject/galaxy/commit/62bc415ae6ed331d0dacaafb2e62… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-22 (Fri, 22 Apr 2016) Changed paths: M client/galaxy/scripts/utils/utils.js M static/maps/utils/utils.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/utils.js Log Message: ----------- Merge pull request #2234 from guerler/fix_validator_000 [16.04] Fix js value validator Commit: bbf5722f27efe4a477ed21e876f14d300f03cff0 https://github.com/galaxyproject/galaxy/commit/bbf5722f27efe4a477ed21e876f1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-22 (Fri, 22 Apr 2016) Changed paths: M client/galaxy/scripts/utils/utils.js M static/maps/utils/utils.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/utils.js Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/1243bd5eb200...bbf5722f27ef

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[galaxyproject/galaxy] e5b3c9: Fix js value validator
by GitHub 22 Apr '16

22 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: e5b3c94c5e03a963059a58243858b7244508fb63 https://github.com/galaxyproject/galaxy/commit/e5b3c94c5e03a963059a58243858… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-22 (Fri, 22 Apr 2016) Changed paths: M client/galaxy/scripts/utils/utils.js M static/maps/utils/utils.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/utils.js Log Message: ----------- Fix js value validator Commit: 62bc415ae6ed331d0dacaafb2e62a79055972500 https://github.com/galaxyproject/galaxy/commit/62bc415ae6ed331d0dacaafb2e62… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-22 (Fri, 22 Apr 2016) Changed paths: M client/galaxy/scripts/utils/utils.js M static/maps/utils/utils.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/utils.js Log Message: ----------- Merge pull request #2234 from guerler/fix_validator_000 [16.04] Fix js value validator Compare: https://github.com/galaxyproject/galaxy/compare/0b9ed993d6eb...62bc415ae6ed

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[galaxyproject/galaxy] 7dcc7a: Fixes #2230
by GitHub 22 Apr '16

22 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7dcc7a5af007483dc18a139ded42474d1f690d39 https://github.com/galaxyproject/galaxy/commit/7dcc7a5af007483dc18a139ded42… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-04-22 (Fri, 22 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M static/maps/mvc/form/form-input.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/form/form-input.js M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Fixes #2230 This sanitizes some instances where tool parameters were included directly into the DOM. workflow/run.mako displayed the parameter as a value in a hidden input. This was base64 encoded as there was no better solution apparent at the time. I'm not sure where this parameter is POSTed to but we should figure that out and b64decode it, or remove the hidden parameter. client/... added the parameter value into the DOM. This was easily sanitized using a standard method. workflow/display.mako included the parameter value directly into the HTML. This was cgi.esacped Commit: 1243bd5eb20083c9832d0bb6dbe1c5830c480ff7 https://github.com/galaxyproject/galaxy/commit/1243bd5eb20083c9832d0bb6dbe1… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-04-22 (Fri, 22 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M static/maps/mvc/form/form-input.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/form/form-input.js M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #2231 from erasche/fix-2230 Fixes #2230 Compare: https://github.com/galaxyproject/galaxy/compare/46585014c09b...1243bd5eb200

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[galaxyproject/infrastructure-playbook] 42df2d: More IU JS nodes
by GitHub 21 Apr '16

21 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 42df2d8517e76d1525b9ff55573cf92bfc37f12f https://github.com/galaxyproject/infrastructure-playbook/commit/42df2d8517e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M jetstreamiuenv/group_vars/slurmclients.yml M jetstreamiuenv/inventory Log Message: ----------- More IU JS nodes

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[galaxyproject/usegalaxy-playbook] 3eec59: Test and Main updates, Jetstream config changes an...
by GitHub 21 Apr '16

21 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3eec599a7c17e57f3d1d85ce5d740fb98e162af0 https://github.com/galaxyproject/usegalaxy-playbook/commit/3eec599a7c17e57f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: A files/galaxy/common/config/pulsar_jetstream_actions.yml M files/galaxy/common/dynamic_rules/multi_dynamic_walltime.py M files/galaxy/test.galaxyproject.org/config/job_resource_params_conf.xml A files/galaxy/test.galaxyproject.org/config/pulsar_jetstream.yml M files/galaxy/test.galaxyproject.org/config/pulsar_jetstream_actions.yml R files/galaxy/test.galaxyproject.org/config/pulsar_jetstream_iu.yml R files/galaxy/test.galaxyproject.org/config/pulsar_jetstream_tacc.yml M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/config/job_resource_params_conf.xml A files/galaxy/usegalaxy.org/config/pulsar_jetstream.yml A files/galaxy/usegalaxy.org/config/pulsar_jetstream_actions.yml M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M production/group_vars/all.yml M production/group_vars/galaxyservers.yml M stage/group_vars/all.yml M stage/group_vars/galaxyservers.yml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Test and Main updates, Jetstream config changes and fixes for Test, enable Jetstream destinations for Main

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[galaxyproject/galaxy] e65cfe: Add pyparsing dependency of svgwrite. Unpin mercur...
by GitHub 21 Apr '16

21 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e65cfe57487566760de82b2ed1992744d9820f59 https://github.com/galaxyproject/galaxy/commit/e65cfe57487566760de82b2ed199… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Add pyparsing dependency of svgwrite. Unpin mercurial. Also sync missing dependencies of dependencies and move some Galaxy dependencies to the correct section. Commit: 46585014c09baffc42eb9627303eabd880f81247 https://github.com/galaxyproject/galaxy/commit/46585014c09baffc42eb9627303e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Merge pull request #2223 from nsoranzo/fix_requirements Add pyparsing dependency of svgwrite. Unpin mercurial. Compare: https://github.com/galaxyproject/galaxy/compare/5cda797832c8...46585014c09b

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[galaxyproject/galaxy] ebb49d: Make client, somehow this got out of sync.
by GitHub 21 Apr '16

21 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ebb49d460b7cb5573a34cc386502a66594f8e3ad https://github.com/galaxyproject/galaxy/commit/ebb49d460b7cb5573a34cc386502… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Make client, somehow this got out of sync. Commit: 5aefe1b193d866185958645b832f2d731f933c01 https://github.com/galaxyproject/galaxy/commit/5aefe1b193d866185958645b832f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge pull request #2207 from dannon/release_16.01 [16.01] Rebuild client, maps were out of sync. Commit: ef12ae303577b2cc1967a08b341962f0ef1ffc5a https://github.com/galaxyproject/galaxy/commit/ef12ae303577b2cc1967a08b3419… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M templates/webapps/galaxy/library/common/browse_library.mako Log Message: ----------- Test fix for christ-h's french language date abbreviations breaking the old library display Commit: 7e93d462392952d27d414ba87d2dd406c9a60be1 https://github.com/galaxyproject/galaxy/commit/7e93d462392952d27d414ba87d2d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M templates/webapps/galaxy/library/common/ldda_info.mako Log Message: ----------- Another location where the non-ascii month was breaking display. Commit: 3907d83abe98a77dc6ecfb4abe818ea1bf31e9eb https://github.com/galaxyproject/galaxy/commit/3907d83abe98a77dc6ecfb4abe81… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M templates/webapps/galaxy/library/common/browse_library.mako M templates/webapps/galaxy/library/common/ldda_info.mako Log Message: ----------- Merge pull request #2214 from dannon/old_library_fixes [16.01] Browse library date handling for non-ascii month abbreviations Commit: 912e6ea30ffc8c67033c7815d7adee0cc9db5f90 https://github.com/galaxyproject/galaxy/commit/912e6ea30ffc8c67033c7815d7ad… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- port TS test fix so we can rely on jenkins Commit: 9e980862c8b763cf3dd0209be49f0d2d75a90614 https://github.com/galaxyproject/galaxy/commit/9e980862c8b763cf3dd0209be49f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Merge pull request #2220 from martenson/port-tstestfix [16.01] port TS test fix so we can rely on jenkins Commit: 0b9ed993d6eb054dc6c68fcd20d0873fd837b32f https://github.com/galaxyproject/galaxy/commit/0b9ed993d6eb054dc6c68fcd20d0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M templates/webapps/galaxy/library/common/browse_library.mako M templates/webapps/galaxy/library/common/ldda_info.mako Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.01' into release_16.04 Commit: 5cda797832c8823695eca6b82ad25a195e3f194c https://github.com/galaxyproject/galaxy/commit/5cda797832c8823695eca6b82ad2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M templates/webapps/galaxy/library/common/browse_library.mako M templates/webapps/galaxy/library/common/ldda_info.mako Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/d0028bde0fee...5cda797832c8

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[galaxyproject/galaxy] ebb49d: Make client, somehow this got out of sync.
by GitHub 21 Apr '16

21 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: ebb49d460b7cb5573a34cc386502a66594f8e3ad https://github.com/galaxyproject/galaxy/commit/ebb49d460b7cb5573a34cc386502… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Make client, somehow this got out of sync. Commit: 5aefe1b193d866185958645b832f2d731f933c01 https://github.com/galaxyproject/galaxy/commit/5aefe1b193d866185958645b832f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge pull request #2207 from dannon/release_16.01 [16.01] Rebuild client, maps were out of sync. Commit: ef12ae303577b2cc1967a08b341962f0ef1ffc5a https://github.com/galaxyproject/galaxy/commit/ef12ae303577b2cc1967a08b3419… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M templates/webapps/galaxy/library/common/browse_library.mako Log Message: ----------- Test fix for christ-h's french language date abbreviations breaking the old library display Commit: 7e93d462392952d27d414ba87d2dd406c9a60be1 https://github.com/galaxyproject/galaxy/commit/7e93d462392952d27d414ba87d2d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M templates/webapps/galaxy/library/common/ldda_info.mako Log Message: ----------- Another location where the non-ascii month was breaking display. Commit: 3907d83abe98a77dc6ecfb4abe818ea1bf31e9eb https://github.com/galaxyproject/galaxy/commit/3907d83abe98a77dc6ecfb4abe81… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M templates/webapps/galaxy/library/common/browse_library.mako M templates/webapps/galaxy/library/common/ldda_info.mako Log Message: ----------- Merge pull request #2214 from dannon/old_library_fixes [16.01] Browse library date handling for non-ascii month abbreviations Commit: 912e6ea30ffc8c67033c7815d7adee0cc9db5f90 https://github.com/galaxyproject/galaxy/commit/912e6ea30ffc8c67033c7815d7ad… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- port TS test fix so we can rely on jenkins Commit: 9e980862c8b763cf3dd0209be49f0d2d75a90614 https://github.com/galaxyproject/galaxy/commit/9e980862c8b763cf3dd0209be49f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Merge pull request #2220 from martenson/port-tstestfix [16.01] port TS test fix so we can rely on jenkins Commit: 0b9ed993d6eb054dc6c68fcd20d0873fd837b32f https://github.com/galaxyproject/galaxy/commit/0b9ed993d6eb054dc6c68fcd20d0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M templates/webapps/galaxy/library/common/browse_library.mako M templates/webapps/galaxy/library/common/ldda_info.mako Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.01' into release_16.04 Compare: https://github.com/galaxyproject/galaxy/compare/2734c2c4835a...0b9ed993d6eb

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