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

[galaxyproject/galaxy] 585c10: Display an error message when IE loading raises an...
by GitHub 24 Feb '17

24 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 585c1070f29260895497c01bc7723317e3751934 https://github.com/galaxyproject/galaxy/commit/585c1070f29260895497c01bc772… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Display an error message when IE loading raises an exception Commit: a5ea10622bf2616278827221d43a4ab635932edd https://github.com/galaxyproject/galaxy/commit/a5ea10622bf2616278827221d43a… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Merge pull request #3662 from natefoo/ie-error-message Display an error message when IE loading raises an exception Compare: https://github.com/galaxyproject/galaxy/compare/0baae35c56cf...a5ea10622bf2

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[galaxyproject/galaxy] b4ba27: Ignore Node modules installed for the IE proxy whe...
by GitHub 24 Feb '17

24 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b4ba2768a246c3788bc9f4adc5f2741dd7ab4956 https://github.com/galaxyproject/galaxy/commit/b4ba2768a246c3788bc9f4adc5f2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M .ci/flake8_blacklist.txt Log Message: ----------- Ignore Node modules installed for the IE proxy when linting Commit: 0baae35c56cfa26908ebff9a3124640489459c31 https://github.com/galaxyproject/galaxy/commit/0baae35c56cfa26908ebff9a3124… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M .ci/flake8_blacklist.txt Log Message: ----------- Merge pull request #3664 from natefoo/lint-ignore-js-proxy Ignore Node modules installed for the IE proxy when linting Compare: https://github.com/galaxyproject/galaxy/compare/77a47d2f6f94...0baae35c56cf

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[galaxyproject/galaxy] 10d0f6: Bump Jupyter container version to 16.01.1
by GitHub 24 Feb '17

24 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 10d0f627dcdfac2bd24085a599a7087809cec1bf https://github.com/galaxyproject/galaxy/commit/10d0f627dcdfac2bd24085a599a7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample Log Message: ----------- Bump Jupyter container version to 16.01.1 Commit: 77a47d2f6f947a1ec7d24d068538bbabdf5e88dd https://github.com/galaxyproject/galaxy/commit/77a47d2f6f947a1ec7d24d068538… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample Log Message: ----------- Merge pull request #3665 from natefoo/jupyter-16.01.1 Bump Jupyter container version to 16.01.1 Compare: https://github.com/galaxyproject/galaxy/compare/d5e4dc4753b8...77a47d2f6f94

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[galaxyproject/galaxy] 99397f: add the mzData datatype
by GitHub 24 Feb '17

24 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 99397fad74d3e47c27073f44e36300d43f48a181 https://github.com/galaxyproject/galaxy/commit/99397fad74d3e47c27073f44e363… Author: lecorguille <lecorguille(a)users.noreply.github.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/proteomics.py Log Message: ----------- add the mzData datatype Commit: 036df2ac2003ab378f6a0227e4642d980639a5ab https://github.com/galaxyproject/galaxy/commit/036df2ac2003ab378f6a0227e464… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M lib/galaxy/datatypes/proteomics.py Log Message: ----------- Fix linting Commit: d5e4dc4753b8e6ab4a079b5fedb0ad1834bda157 https://github.com/galaxyproject/galaxy/commit/d5e4dc4753b8e6ab4a079b5fedb0… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/proteomics.py Log Message: ----------- Merge pull request #3661 from lecorguille/datatype_mzdata add the mzData datatype Compare: https://github.com/galaxyproject/galaxy/compare/73c444eaf407...d5e4dc4753b8

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[galaxyproject/usegalaxy-playbook] 02dfd5: Wait up to 65 seconds for uWSGI to stop (it brutal...
by GitHub 23 Feb '17

23 Feb '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 02dfd5bb9fecf1a99eb84e94158482afdfbe6d50 https://github.com/galaxyproject/usegalaxy-playbook/commit/02dfd5bb9fecf1a9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M templates/supervisor/galaxy.j2 Log Message: ----------- Wait up to 65 seconds for uWSGI to stop (it brutally kills workers after 60) Commit: 358979ed7b084c9f63b7b7e82d59ae50a67dcd6f https://github.com/galaxyproject/usegalaxy-playbook/commit/358979ed7b084c9f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Mutable configs Commit: b13a169e3f6ac22eb0722423a93374a8dd6a90d1 https://github.com/galaxyproject/usegalaxy-playbook/commit/b13a169e3f6ac22e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M galaxy.yml Log Message: ----------- Fix the no-restart tag so it actually updates Galaxy Commit: e018710445c6c3935df2985d39adf69cc51b2186 https://github.com/galaxyproject/usegalaxy-playbook/commit/e018710445c6c393… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M templates/galaxy/usegalaxy.org/config/uwsgi.ini.j2 Log Message: ----------- Update Main, switch to new zerg mode setup Commit: 3f3d614c52f0fbea7c9de5600799ee33ca724b7d https://github.com/galaxyproject/usegalaxy-playbook/commit/3f3d614c52f0fbea… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M production/galaxy_version.yml M production/group_vars/all.yml M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Update Main, use NVC dynamic rule Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/a83ebd9b4ee4...…

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[galaxyproject/galaxy] 62ee8e: Fix Python environment hack to allow "fixing" tool...
by GitHub 23 Feb '17

23 Feb '17

Branch: refs/heads/usegalaxy Home: https://github.com/galaxyproject/galaxy Commit: 62ee8e8404fb86155d9893a8eeab1cf58473d795 https://github.com/galaxyproject/galaxy/commit/62ee8e8404fb86155d9893a8eeab… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix Python environment hack to allow "fixing" tool ids at some version. This is a less broken alternative to #3620 and something I intended to ultimately do anyway. sam-to-bam used to be broken but now it isn't, we need to express that. Ideally we would move most of the things from the unversioned list to the versioned list as they are fixed. xref https://github.com/galaxyproject/galaxy/pull/3620#issuecomment-280674067 xref https://github.com/galaxyproject/galaxy/commit/fe2a1d8ade4fbda158ae035c7813… xref #3351 xref galaxyproject/tools-iuc#1148 Commit: eb6c0e410e600171fa3ce4fffb78bc205aad5292 https://github.com/galaxyproject/galaxy/commit/eb6c0e410e600171fa3ce4fffb78… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Rework preserve python environment expression according to :eagle::eyes: suggestion. https://github.com/galaxyproject/galaxy/pull/3630#discussion_r101798306 Commit: 6733c36318bacce0bbf33a8d266f6a08de3ba019 https://github.com/galaxyproject/galaxy/commit/6733c36318bacce0bbf33a8d266f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- [17.01] Restore logging statement missing when resolve_all is used. Broken in #3391. Commit: 49ef352235f7c998e79ca5423fab9725ea28d8be https://github.com/galaxyproject/galaxy/commit/49ef352235f7c998e79ca5423fab… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge pull request #3646 from jmchilton/resolve_all_logging [17.01] Restore logging statement missing when resolve_all is used. Commit: 9ebe2d2dd6efde7a66c52681aa57c52342ad992d https://github.com/galaxyproject/galaxy/commit/9ebe2d2dd6efde7a66c52681aa57… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3630 from jmchilton/python_hack_scalpel [17.01] Fix Python environment hack to allow "fixing" tool ids at some version. Commit: 90de3f2588a61382e70b6209ea39293c6a3987f1 https://github.com/galaxyproject/galaxy/commit/90de3f2588a61382e70b6209ea39… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 17.01 Commit: d10f740cff8e3520383c004a16830700b2789c9f https://github.com/galaxyproject/galaxy/commit/d10f740cff8e3520383c004a1683… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py A templates/webapps/galaxy/user/manage_info.mako Log Message: ----------- The user controller functions for changing information were ripped out before providing a way for admin functionality to use the new javascript stuff. Seems nontrivial, so this puts the endpoint back temporarily until the adminjs rewrite which can include the new functionality. Commit: 6f3c8c7447e9a71c580ef9307395cd5dcd314915 https://github.com/galaxyproject/galaxy/commit/6f3c8c7447e9a71c580ef9307395… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- This template inherited field never worked apparently, but nobody noticed. This correctly sets the is_admin flag here. Commit: 4be00d3058396ed30da4f6f0958ad6fa989249cb https://github.com/galaxyproject/galaxy/commit/4be00d3058396ed30da4f6f0958a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M templates/webapps/galaxy/user/manage_info.mako Log Message: ----------- Strip out unnecessary user address editing. Commit: 456acf0b84004c85c94d3129f0a89af9be2d5452 https://github.com/galaxyproject/galaxy/commit/456acf0b84004c85c94d3129f0a8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Update docstring to explicitly mention this as a temporary endpoint. Commit: b46ac475a93fbf0da71272861677a00a3877b91b https://github.com/galaxyproject/galaxy/commit/b46ac475a93fbf0da71272861677… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Fix verbiage in temporary method. Commit: 64036a441284151e1b1a3e9305537d526005ff3a https://github.com/galaxyproject/galaxy/commit/64036a441284151e1b1a3e930553… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py A templates/webapps/galaxy/user/manage_info.mako Log Message: ----------- Merge pull request #3656 from dannon/admin-userinfo-edit-fix [17.01] Admin user information editing Commit: a352b3c490c7f5d7fbcf4e28a129bc8a537d3b53 https://github.com/galaxyproject/galaxy/commit/a352b3c490c7f5d7fbcf4e28a129… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/version.py M lib/galaxy/webapps/galaxy/controllers/user.py A templates/webapps/galaxy/user/manage_info.mako Log Message: ----------- Merge branch 'release_17.01' into usegalaxy Compare: https://github.com/galaxyproject/galaxy/compare/277c4ed20bdf...a352b3c490c7

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[galaxyproject/usegalaxy-playbook] a83ebd: Don't leave unused zerglings around tying up memor...
by GitHub 23 Feb '17

23 Feb '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a83ebd9b4ee4f020e87ebd4178b39fc21c8f7c20 https://github.com/galaxyproject/usegalaxy-playbook/commit/a83ebd9b4ee4f020… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M templates/galaxy/test.galaxyproject.org/config/uwsgi.ini.j2 M templates/supervisor/galaxy.j2 Log Message: ----------- Don't leave unused zerglings around tying up memory/swap, fix the zergling startup race condition.

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[galaxyproject/galaxy] d10f74: The user controller functions for changing informa...
by GitHub 23 Feb '17

23 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: d10f740cff8e3520383c004a16830700b2789c9f https://github.com/galaxyproject/galaxy/commit/d10f740cff8e3520383c004a1683… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py A templates/webapps/galaxy/user/manage_info.mako Log Message: ----------- The user controller functions for changing information were ripped out before providing a way for admin functionality to use the new javascript stuff. Seems nontrivial, so this puts the endpoint back temporarily until the adminjs rewrite which can include the new functionality. Commit: 6f3c8c7447e9a71c580ef9307395cd5dcd314915 https://github.com/galaxyproject/galaxy/commit/6f3c8c7447e9a71c580ef9307395… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- This template inherited field never worked apparently, but nobody noticed. This correctly sets the is_admin flag here. Commit: 4be00d3058396ed30da4f6f0958ad6fa989249cb https://github.com/galaxyproject/galaxy/commit/4be00d3058396ed30da4f6f0958a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M templates/webapps/galaxy/user/manage_info.mako Log Message: ----------- Strip out unnecessary user address editing. Commit: 456acf0b84004c85c94d3129f0a89af9be2d5452 https://github.com/galaxyproject/galaxy/commit/456acf0b84004c85c94d3129f0a8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Update docstring to explicitly mention this as a temporary endpoint. Commit: b46ac475a93fbf0da71272861677a00a3877b91b https://github.com/galaxyproject/galaxy/commit/b46ac475a93fbf0da71272861677… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Fix verbiage in temporary method. Commit: 64036a441284151e1b1a3e9305537d526005ff3a https://github.com/galaxyproject/galaxy/commit/64036a441284151e1b1a3e930553… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py A templates/webapps/galaxy/user/manage_info.mako Log Message: ----------- Merge pull request #3656 from dannon/admin-userinfo-edit-fix [17.01] Admin user information editing Compare: https://github.com/galaxyproject/galaxy/compare/90de3f2588a6...64036a441284

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[galaxyproject/galaxy] d9d3b2: Update dynamic_tool_destination.py
by GitHub 23 Feb '17

23 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d9d3b22efdf5d7e0f4c9b371b0ea74a64ab53f46 https://github.com/galaxyproject/galaxy/commit/d9d3b22efdf5d7e0f4c9b371b0ea… Author: Gildas Le Corguillé <lecorguille(a)users.noreply.github.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Update dynamic_tool_destination.py Commit: 73c444eaf4074c98262b9de0011e686170b1b125 https://github.com/galaxyproject/galaxy/commit/73c444eaf4074c98262b9de0011e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Merge pull request #3655 from lecorguille/patch-3 Update dynamic_tool_destination.py Compare: https://github.com/galaxyproject/galaxy/compare/99fdc37b815a...73c444eaf407

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[galaxyproject/galaxy] 8130d8: Update against the latest changes in galaxy-dev.
by GitHub 23 Feb '17

23 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8130d8b4c88343cdd44243fe700eae3fb863cc1a https://github.com/galaxyproject/galaxy/commit/8130d8b4c88343cdd44243fe700e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/exceptions/error_codes.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/linters/general.py M lib/galaxy/tools/linters/outputs.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Update against the latest changes in galaxy-dev. Commit: 99fdc37b815ab9c26f15250d722f2d30ab9691b2 https://github.com/galaxyproject/galaxy/commit/99fdc37b815ab9c26f15250d722f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/exceptions/error_codes.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/linters/general.py M lib/galaxy/tools/linters/outputs.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #3654 from jmchilton/galaxy-lib-update Update against the latest changes in galaxy-lib Compare: https://github.com/galaxyproject/galaxy/compare/647fcad924a9...99fdc37b815a

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