Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 70a64b304eb2b5c9642581061f345e669251eac6
https://github.com/galaxyproject/galaxy/commit/70a64b304eb2b5c9642581061f34…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
A config/error_report.xml.sample
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/jobs/__init__.py
A lib/galaxy/tools/error_reports/__init__.py
A lib/galaxy/tools/error_reports/sinks/__init__.py
A lib/galaxy/tools/error_reports/sinks/email.py
A lib/galaxy/tools/error_reports/sinks/json.py
A lib/galaxy/tools/error_reports/sinks/sentry.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
A templates/messages.mako
Log Message:
-----------
Refactor bug reporting into plugins
Commit: 9dd27dcc3de5eff03c4a37c34fc810d3f295c85c
https://github.com/galaxyproject/galaxy/commit/9dd27dcc3de5eff03c4a37c34fc8…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/tools/error_reports/__init__.py
M lib/galaxy/tools/error_reports/sinks/__init__.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
Log Message:
-----------
flake8
Commit: 181a72a6f383aa54c4a053cedba05e345eda2584
https://github.com/galaxyproject/galaxy/commit/181a72a6f383aa54c4a053cedba0…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/tools/error_reports/sinks/email.py
M lib/galaxy/tools/error_reports/sinks/json.py
M lib/galaxy/tools/error_reports/sinks/sentry.py
Log Message:
-----------
flake8 import
Commit: 437ab325da8b49b9f0e9b796f8515899aa10d035
https://github.com/galaxyproject/galaxy/commit/437ab325da8b49b9f0e9b796f851…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
A doc/source/admin/special_topics/bug_reports.rst
M doc/source/admin/special_topics/index.rst
Log Message:
-----------
document
Commit: 46b621708aa4b9973c3e6bf6b02417dc3931523c
https://github.com/galaxyproject/galaxy/commit/46b621708aa4b9973c3e6bf6b024…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M doc/source/admin/special_topics/bug_reports.rst
M lib/galaxy/tools/error_reports/sinks/sentry.py
Log Message:
-----------
Allow sentry to be verbose
Commit: d7e400c96ddf51caca3df26e8dc8a75089be2b06
https://github.com/galaxyproject/galaxy/commit/d7e400c96ddf51caca3df26e8dc8…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
R config/error_report.xml.sample
A config/error_report.yml.sample
M lib/galaxy/config.py
Log Message:
-----------
Per @jmchilton comment, rewrite as yml
Commit: f4a823c27a9b533994c593670cf5a13740e5bf7a
https://github.com/galaxyproject/galaxy/commit/f4a823c27a9b533994c593670cf5…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
Log Message:
-----------
add bug reporter
Commit: ed7551e09679b940bd084fd5e5ce5fcf97320ffa
https://github.com/galaxyproject/galaxy/commit/ed7551e09679b940bd084fd5e5ce…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
A client/galaxy/scripts/mvc/dataset/dataset-error.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
A client/galaxy/scripts/mvc/job/job-params.js
Log Message:
-----------
redirect to new url
Commit: 2f8347d5bc4bdf52a7d2b10d3e69b55290d104ca
https://github.com/galaxyproject/galaxy/commit/2f8347d5bc4bdf52a7d2b10d3e69…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
add clientside route
Commit: ef6b8cbeea5a0578683df8f013a0739a1e022fe0
https://github.com/galaxyproject/galaxy/commit/ef6b8cbeea5a0578683df8f013a0…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M client/galaxy/style/less/galaxy_bootstrap/overrides.less
M templates/show_params.mako
Log Message:
-----------
move css rule to a more generic location
Commit: 98ac18661865e958249f9a21bc847ba558b00893
https://github.com/galaxyproject/galaxy/commit/98ac18661865e958249f9a21bc84…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/tools/error_reports/sinks/email.py
M lib/galaxy/tools/error_reports/sinks/json.py
M lib/galaxy/tools/error_reports/sinks/sentry.py
Log Message:
-----------
change report code
Commit: 6f8f38170c976b2152ef2e21fc46a47922da4b56
https://github.com/galaxyproject/galaxy/commit/6f8f38170c976b2152ef2e21fc46…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
Log Message:
-----------
refactor into an API
Commit: 838b23358e6d00ce2d65f6a5fde6a413505eaf10
https://github.com/galaxyproject/galaxy/commit/838b23358e6d00ce2d65f6a5fde6…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-error.js
Log Message:
-----------
Handle error report submission
Commit: 64174113bfd8e18b2e87581137a134f8f4520bd7
https://github.com/galaxyproject/galaxy/commit/64174113bfd8e18b2e87581137a1…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-error.js
Log Message:
-----------
refactor a bit
Commit: 73369a2e8dd098d59083c61f67ec140a7c3cd102
https://github.com/galaxyproject/galaxy/commit/73369a2e8dd098d59083c61f67ec…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-error.js
Log Message:
-----------
Add extra parameter to allow multiple messages
Commit: cdb82dd8e64b83e14244b3b46163be1715afcfe2
https://github.com/galaxyproject/galaxy/commit/cdb82dd8e64b83e14244b3b46163…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/tools/error_reports/__init__.py
M lib/galaxy/webapps/galaxy/api/jobs.py
Log Message:
-----------
Change invocation to pass user information
Commit: 5980bd91bb0f916b576b27386d2b052609610d57
https://github.com/galaxyproject/galaxy/commit/5980bd91bb0f916b576b27386d2b…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/tools/errors.py
Log Message:
-----------
Link in expected places
Commit: fd6c247398133d6f8df26b447328ec64801fcd11
https://github.com/galaxyproject/galaxy/commit/fd6c247398133d6f8df26b447328…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
A lib/galaxy/tools/error_reports/sinks/biostars.py
M lib/galaxy/util/biostar.py
Log Message:
-----------
Switch biostars to using HTML submission
Commit: fb78a2118d0e45a11378bbc5e0daf0e351c8b763
https://github.com/galaxyproject/galaxy/commit/fb78a2118d0e45a11378bbc5e0da…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/style/blue/base.css
Log Message:
-----------
merge
Commit: e8a5b48da9ce98c72ac92171be56435ca2b9565f
https://github.com/galaxyproject/galaxy/commit/e8a5b48da9ce98c72ac92171be56…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
R templates/webapps/galaxy/dataset/errors.mako
Log Message:
-----------
Now unused
Commit: 550cb7dfae8706e06a2b7638b078c9b9b134281d
https://github.com/galaxyproject/galaxy/commit/550cb7dfae8706e06a2b7638b078…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/tools/error_reports/__init__.py
A lib/galaxy/tools/error_reports/plugins/__init__.py
A lib/galaxy/tools/error_reports/plugins/biostars.py
A lib/galaxy/tools/error_reports/plugins/email.py
A lib/galaxy/tools/error_reports/plugins/json.py
A lib/galaxy/tools/error_reports/plugins/sentry.py
R lib/galaxy/tools/error_reports/sinks/__init__.py
R lib/galaxy/tools/error_reports/sinks/biostars.py
R lib/galaxy/tools/error_reports/sinks/email.py
R lib/galaxy/tools/error_reports/sinks/json.py
R lib/galaxy/tools/error_reports/sinks/sentry.py
Log Message:
-----------
Requested renames, sink + yml
Commit: fcd94f0483c119a4db0e84e469af3aade0f2847c
https://github.com/galaxyproject/galaxy/commit/fcd94f0483c119a4db0e84e469af…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M config/error_report.yml.sample
M lib/galaxy/app.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/tools/error_reports/__init__.py
M lib/galaxy/webapps/galaxy/api/jobs.py
Log Message:
-----------
more renames
Commit: 7c1c60d82643b100a55edefb6f88d13671defafa
https://github.com/galaxyproject/galaxy/commit/7c1c60d82643b100a55edefb6f88…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
A static/maps/mvc/dataset/dataset-error.js.map
A static/maps/mvc/job/job-params.js.map
A static/scripts/mvc/dataset/dataset-error.js
A static/scripts/mvc/job/job-params.js
Log Message:
-----------
forgot static files
Commit: 61a5b7c9e139cfa73fefa048f6ec34a7511b741c
https://github.com/galaxyproject/galaxy/commit/61a5b7c9e139cfa73fefa048f6ec…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
Log Message:
-----------
another merge
Commit: a6aedc695336b122c5e552ced771a97b5f62ee52
https://github.com/galaxyproject/galaxy/commit/a6aedc695336b122c5e552ced771…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/tools/error_reports/plugins/biostars.py
Log Message:
-----------
address flaking
Commit: 1e9c31241c419cb53306232856ed7c368d8c6e92
https://github.com/galaxyproject/galaxy/commit/1e9c31241c419cb53306232856ed…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/jobs.py
Log Message:
-----------
remove comment
Commit: 538ef006f36b3e525bb87d18944d596afb5f1639
https://github.com/galaxyproject/galaxy/commit/538ef006f36b3e525bb87d18944d…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/util/plugin_config.py
Log Message:
-----------
Also load yaml sample files. cc @jmchilton, is this ok?
Commit: 3e8919c41643352feb6df50d04a71f2291024ef7
https://github.com/galaxyproject/galaxy/commit/3e8919c41643352feb6df50d04a7…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M config/error_report.yml.sample
Log Message:
-----------
correct name to type
Commit: 5563ecc3ffa7d0565be42eea99276d64ec5232dd
https://github.com/galaxyproject/galaxy/commit/5563ecc3ffa7d0565be42eea9927…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/tools/error_reports/plugins/biostars.py
Log Message:
-----------
fix import order
Commit: 00ee109ed4538b6a032489a07807deb7e13c9882
https://github.com/galaxyproject/galaxy/commit/00ee109ed4538b6a032489a07807…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/tools/error_reports/plugins/email.py
Log Message:
-----------
fix css class
Commit: 4c36b5a7a189f9586c061460bfdec7a84b6774c4
https://github.com/galaxyproject/galaxy/commit/4c36b5a7a189f9586c061460bfde…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/tools/error_reports/plugins/sentry.py
Log Message:
-----------
not a useful test in this location
Commit: a2b02065ebbfa9759aad5e56db0c251f7ad514bc
https://github.com/galaxyproject/galaxy/commit/a2b02065ebbfa9759aad5e56db0c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M lib/galaxy/web/framework/webapp.py
R templates/messages.mako
Log Message:
-----------
Remove unneeded messages.mako.
Commit: 41461235b2429ef84c50336021d9921ca6ef8a4a
https://github.com/galaxyproject/galaxy/commit/41461235b2429ef84c50336021d9…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js.map
Log Message:
-----------
rebuild client
Commit: 6d7d4e9e8e55cfcaa504f43e6288c1d39c0ed932
https://github.com/galaxyproject/galaxy/commit/6d7d4e9e8e55cfcaa504f43e6288…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
A client/galaxy/scripts/mvc/dataset/dataset-error.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
A client/galaxy/scripts/mvc/job/job-params.js
M client/galaxy/style/less/galaxy_bootstrap/overrides.less
A config/error_report.yml.sample
A doc/source/admin/special_topics/bug_reports.rst
M doc/source/admin/special_topics/index.rst
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/jobs/__init__.py
A lib/galaxy/tools/error_reports/__init__.py
A lib/galaxy/tools/error_reports/plugins/__init__.py
A lib/galaxy/tools/error_reports/plugins/biostars.py
A lib/galaxy/tools/error_reports/plugins/email.py
A lib/galaxy/tools/error_reports/plugins/json.py
A lib/galaxy/tools/error_reports/plugins/sentry.py
M lib/galaxy/tools/errors.py
M lib/galaxy/util/biostar.py
M lib/galaxy/util/plugin_config.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
A static/maps/mvc/dataset/dataset-error.js.map
M static/maps/mvc/dataset/dataset-li-edit.js.map
A static/maps/mvc/job/job-params.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js.map
A static/scripts/mvc/dataset/dataset-error.js
M static/scripts/mvc/dataset/dataset-li-edit.js
A static/scripts/mvc/job/job-params.js
M static/style/blue/base.css
M templates/show_params.mako
R templates/webapps/galaxy/dataset/errors.mako
Log Message:
-----------
Merge pull request #4305 from erasche/bug-report-actions
Refactor bug reporting into plugins / Remove bug report mako
Compare: https://github.com/galaxyproject/galaxy/compare/5e43fcef3c94...6d7d4e9e8e55
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 3164fc88d0861f5ea1853803741cdc008e4f9459
https://github.com/galaxyproject/galaxy/commit/3164fc88d0861f5ea1853803741c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-19 (Wed, 19 Jul 2017)
Changed paths:
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/root.py
Log Message:
-----------
Allow app specific client side routing
Commit: e5e390d829e373301ab169a4ecb1a01c4fb6548d
https://github.com/galaxyproject/galaxy/commit/e5e390d829e373301ab169a4ecb1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-19 (Wed, 19 Jul 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M lib/galaxy/webapps/galaxy/buildapp.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
Log Message:
-----------
Create admin specific client router
Commit: 0679534a1ff6ade2e3c9341f5a6e95fb59509248
https://github.com/galaxyproject/galaxy/commit/0679534a1ff6ade2e3c9341f5a6e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-19 (Wed, 19 Jul 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
Log Message:
-----------
Load grid client
Commit: 2671f2ae01a53d67c9f38f0cc77c12926b78055b
https://github.com/galaxyproject/galaxy/commit/2671f2ae01a53d67c9f38f0cc77c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-19 (Wed, 19 Jul 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
A client/galaxy/scripts/layout/router.js
A static/maps/layout/router.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
A static/scripts/layout/router.js
Log Message:
-----------
Add shared base router
Commit: f74947b816843da19a80060e78996c1e53a9de83
https://github.com/galaxyproject/galaxy/commit/f74947b816843da19a80060e7899…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-19 (Wed, 19 Jul 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/layout/page.js
M static/maps/layout/page.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/layout/page.js
Log Message:
-----------
Used shared base router for admin and analysis app
Repack scripts
Commit: 770deb58f08bfe2c5c7e885bffe5dd73da12fa8c
https://github.com/galaxyproject/galaxy/commit/770deb58f08bfe2c5c7e885bffe5…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-19 (Wed, 19 Jul 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Use transformed user grid list endpoint
Commit: c95ea0956f632d3c874b5c5035ec12fa66c89af0
https://github.com/galaxyproject/galaxy/commit/c95ea0956f632d3c874b5c5035ec…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-19 (Wed, 19 Jul 2017)
Changed paths:
M client/galaxy/scripts/apps/panels/admin-panel.js
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Move user list endpoint to admin controller
Commit: dba9c5cbf3aeacd65f41e2e7a6e5be55f9787379
https://github.com/galaxyproject/galaxy/commit/dba9c5cbf3aeacd65f41e2e7a6e5…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-19 (Wed, 19 Jul 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Fix base operations
Commit: 8dd816d6db39bb6da9b7f82339df001af6610ef3
https://github.com/galaxyproject/galaxy/commit/8dd816d6db39bb6da9b7f82339df…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-19 (Wed, 19 Jul 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/history.py
Log Message:
-----------
Remove out commented legacy operation
Commit: 95cf5f7e07c1af2cdb3d08a99af22261291807e8
https://github.com/galaxyproject/galaxy/commit/95cf5f7e07c1af2cdb3d08a99af2…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-19 (Wed, 19 Jul 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Reset passwords individually
Commit: 9b7a7a2398b185217cc06b526083c7512019074d
https://github.com/galaxyproject/galaxy/commit/9b7a7a2398b185217cc06b526083…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-19 (Wed, 19 Jul 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Remove unused roles operation
Commit: 7f4d199256628fa6f8c4b24c051670d819781206
https://github.com/galaxyproject/galaxy/commit/7f4d199256628fa6f8c4b24c0516…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-20 (Thu, 20 Jul 2017)
Changed paths:
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/tool_shed/controllers/admin.py
Log Message:
-----------
Separate toolshed and galaxy, index and center endpoints
Commit: 0a7202d68014ceadb408e47b455dfe7e6a348f86
https://github.com/galaxyproject/galaxy/commit/0a7202d68014ceadb408e47b455d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-20 (Thu, 20 Jul 2017)
Changed paths:
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/webapps/tool_shed/controllers/admin.py
Log Message:
-----------
Restore mako based users endpoint for toolshed
Commit: c075eae1d5b8425d62c3a4ea47a52c0f44ef4d6a
https://github.com/galaxyproject/galaxy/commit/c075eae1d5b8425d62c3a4ea47a5…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-20 (Thu, 20 Jul 2017)
Changed paths:
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/tool_shed/controllers/admin.py
Log Message:
-----------
Move tool version and role grid
Commit: dca5e70c02cbbc3e443fab13586ced4296baea3c
https://github.com/galaxyproject/galaxy/commit/dca5e70c02cbbc3e443fab13586c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-20 (Thu, 20 Jul 2017)
Changed paths:
M lib/galaxy/webapps/tool_shed/controllers/admin.py
Log Message:
-----------
Replicate legacy admin handler in toolshed before modification
Commit: ce2938b6204685862c26fd8a3bc61cb6c4664d37
https://github.com/galaxyproject/galaxy/commit/ce2938b6204685862c26fd8a3bc6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-20 (Thu, 20 Jul 2017)
Changed paths:
M lib/galaxy/webapps/tool_shed/controllers/admin.py
Log Message:
-----------
Remove functions not used in toolshed admin, package and reload tools
Commit: b504095183be4d3b0b3abea792fc45d12c79de46
https://github.com/galaxyproject/galaxy/commit/b504095183be4d3b0b3abea792fc…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-20 (Thu, 20 Jul 2017)
Changed paths:
M lib/galaxy/webapps/tool_shed/controllers/admin.py
Log Message:
-----------
Combine both toolshed controllers into one
Commit: e967a3321b7209cd10c0079e109bd4c7ed2508a4
https://github.com/galaxyproject/galaxy/commit/e967a3321b7209cd10c0079e109b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-24 (Mon, 24 Jul 2017)
Changed paths:
R lib/galaxy/web/base/controllers/__init__.py
R lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/webapps/galaxy/api/quotas.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/tool_shed/controllers/admin.py
A lib/tool_shed/util/admin_util.py
Log Message:
-----------
Merge branch 'separate_admin_controllers' into revise_page
Commit: b6379a9ede442c0e76d50bcea51c91cc8ec22b53
https://github.com/galaxyproject/galaxy/commit/b6379a9ede442c0e76d50bcea51c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-24 (Mon, 24 Jul 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Remove legacy user controller endpoint
Commit: 3decf1bed960e9daee09adffa993ab4fb46f6d09
https://github.com/galaxyproject/galaxy/commit/3decf1bed960e9daee09adffa993…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-24 (Mon, 24 Jul 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Restore multiple password option
Commit: b9beb4723b16e270b16597e89039a3880041dc38
https://github.com/galaxyproject/galaxy/commit/b9beb4723b16e270b16597e89039…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-24 (Mon, 24 Jul 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Move user identification to shared method
Commit: 50948f23695fd1cc9e95c2f95296103212ff3ae1
https://github.com/galaxyproject/galaxy/commit/50948f23695fd1cc9e95c2f95296…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-25 (Tue, 25 Jul 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Align admin user grid operations and messages
Commit: f33c06dd8d8328dd1abdf846d9ba11037c1fb8ec
https://github.com/galaxyproject/galaxy/commit/f33c06dd8d8328dd1abdf846d9ba…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-25 (Tue, 25 Jul 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Fix message and user information link
Commit: 3829d3dea5b9128b5f7b4e1b5b4d4c6cff10f40a
https://github.com/galaxyproject/galaxy/commit/3829d3dea5b9128b5f7b4e1b5b4d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-25 (Tue, 25 Jul 2017)
Changed paths:
M client/galaxy/scripts/mvc/grid/grid-view.js
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M static/maps/mvc/grid/grid-view.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/grid/grid-view.js
Log Message:
-----------
Add support for redirecting multiple select operations to the client instead of redirecting through controller
Commit: 415939709448ffe9fdec44e749f022eaea9ddcec
https://github.com/galaxyproject/galaxy/commit/415939709448ffe9fdec44e749f0…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-26 (Wed, 26 Jul 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Keep error messages on form page, remove duplicate center function
Commit: 17eff91b2335428d8a5a4b2c86545acae2a96498
https://github.com/galaxyproject/galaxy/commit/17eff91b2335428d8a5a4b2c8654…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-26 (Wed, 26 Jul 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/tool_shed/util/admin_util.py
Log Message:
-----------
Fix toolshed center endpoint
Commit: 149de8b44f621aac8274770f813e2b471e025ed5
https://github.com/galaxyproject/galaxy/commit/149de8b44f621aac8274770f813e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-26 (Wed, 26 Jul 2017)
Changed paths:
M client/galaxy/scripts/mvc/grid/grid-view.js
M static/maps/mvc/grid/grid-view.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/grid/grid-view.js
Log Message:
-----------
Fix request submission
Commit: a8720aaf8cecb3182c676a74ef16107e8ecbd047
https://github.com/galaxyproject/galaxy/commit/a8720aaf8cecb3182c676a74ef16…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-26 (Wed, 26 Jul 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Make disk size calculation operation async
Commit: f449f7e4b7309b7b230187fcf0fdd374c76cb72c
https://github.com/galaxyproject/galaxy/commit/f449f7e4b7309b7b230187fcf0fd…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-26 (Wed, 26 Jul 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Remove unused dependency
Commit: fa9ac881e0b600b73912bf29eac06e3a3dabb609
https://github.com/galaxyproject/galaxy/commit/fa9ac881e0b600b73912bf29eac0…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-28 (Fri, 28 Jul 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Remove duplicate callers
Commit: d46adeff19d9b36326f70ed15a647676d7d812fe
https://github.com/galaxyproject/galaxy/commit/d46adeff19d9b36326f70ed15a64…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-28 (Fri, 28 Jul 2017)
Changed paths:
M lib/galaxy/web/framework/helpers/grids.py
Log Message:
-----------
Fix href parsing for multiselect operation with redirect
Commit: ba0cb1d6058acc4347f751979c950795cb4e1c3b
https://github.com/galaxyproject/galaxy/commit/ba0cb1d6058acc4347f751979c95…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-28 (Fri, 28 Jul 2017)
Changed paths:
M client/galaxy/scripts/layout/page.js
M static/maps/layout/page.js.map
M static/scripts/bundled/admin.bundled.js.map
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/layout/page.js
Log Message:
-----------
Only initialize router if passed
Commit: 876b1ca9040b0d1fa586654d5443331f45e3d845
https://github.com/galaxyproject/galaxy/commit/876b1ca9040b0d1fa586654d5443…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-31 (Mon, 31 Jul 2017)
Changed paths:
M templates/admin/user/user.mako
Log Message:
-----------
Add masthead header to manage user page
Commit: 38125518aff32b6589ea52396f9340ab5db94c32
https://github.com/galaxyproject/galaxy/commit/38125518aff32b6589ea52396f93…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-31 (Mon, 31 Jul 2017)
Changed paths:
M lib/tool_shed/util/admin_util.py
Log Message:
-----------
Fix user grid controller for toolshed
Commit: 308a4adaf5f4034943a7cf4cb2f245f5763b7c0b
https://github.com/galaxyproject/galaxy/commit/308a4adaf5f4034943a7cf4cb2f2…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-31 (Mon, 31 Jul 2017)
Changed paths:
M templates/admin/user/user.mako
Log Message:
-----------
Fix js insertion in user roles mako
Commit: 9fdfb41852db80eaaafde4e69e0f3d25b6bb1fbd
https://github.com/galaxyproject/galaxy/commit/9fdfb41852db80eaaafde4e69e0f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-31 (Mon, 31 Jul 2017)
Changed paths:
M templates/admin/user/reset_password.mako
Log Message:
-----------
Add panels to reset_password mako
Commit: 13e09b58550b7e805240e618f98991bb3bebe053
https://github.com/galaxyproject/galaxy/commit/13e09b58550b7e805240e618f989…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-31 (Mon, 31 Jul 2017)
Changed paths:
M templates/admin/user/reset_password.mako
M templates/admin/user/user.mako
Log Message:
-----------
Add messages to form makos
Commit: b44e780867999464a1c1cb6675bb622c50848347
https://github.com/galaxyproject/galaxy/commit/b44e780867999464a1c1cb6675bb…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-07-31 (Mon, 31 Jul 2017)
Changed paths:
M templates/admin/user/reset_password.mako
M templates/admin/user/user.mako
Log Message:
-----------
Enable overflow for form makos
Commit: 41a2904128db4f642834754931305791a38db0c3
https://github.com/galaxyproject/galaxy/commit/41a2904128db4f64283475493130…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-01 (Tue, 01 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
A client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/nls/fr/locale.js
M config/tool_shed.ini.sample
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/jobs/runners/cli.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/metadata.py
M lib/galaxy/security/__init__.py
M lib/galaxy/webapps/galaxy/api/quotas.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/workflow/modules.py
A static/maps/mvc/dataset/dataset-edit-attributes.js.map
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/maps/nls/fr/locale.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
A static/scripts/mvc/dataset/dataset-edit-attributes.js
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/nls/fr/locale.js
R templates/webapps/galaxy/dataset/edit_attributes.mako
Log Message:
-----------
Merge branch 'dev' into revise_page
Commit: b3e095d66c499a31f3b0a9b0e25690e70f653bec
https://github.com/galaxyproject/galaxy/commit/b3e095d66c499a31f3b0a9b0e256…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-01 (Tue, 01 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/galaxy.js
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M static/maps/galaxy.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/galaxy.js
Log Message:
-----------
Parse url parameters for all client apps
Commit: 1f27ad541d7d3dd542152d70ca2d0e207904286b
https://github.com/galaxyproject/galaxy/commit/1f27ad541d7d3dd542152d70ca2d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-01 (Tue, 01 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M lib/galaxy/webapps/galaxy/controllers/admin.py
M static/maps/mvc/grid/grid-view.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/grid/grid-view.js
Log Message:
-----------
Fix url parameter forwarding to grid view
Commit: 068ff8c55d1b7b0c8c22fe2beebd583fa52c4634
https://github.com/galaxyproject/galaxy/commit/068ff8c55d1b7b0c8c22fe2beebd…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-01 (Tue, 01 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/panels/admin-panel.js
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Use router to load grid, avoids page refresh
Commit: e952a45af9271ce72f676a9df2f799fd5d910031
https://github.com/galaxyproject/galaxy/commit/e952a45af9271ce72f676a9df2f7…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-01 (Tue, 01 Aug 2017)
Changed paths:
M client/galaxy/scripts/layout/router.js
M static/maps/layout/router.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/layout/router.js
Log Message:
-----------
Reset url parameters when pushing new states
Commit: f800b38dbd6957b4b2d21342c5a53aaef72fa23b
https://github.com/galaxyproject/galaxy/commit/f800b38dbd6957b4b2d21342c5a5…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-02 (Wed, 02 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/mvc/user/user-preferences.js
R client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js
M client/galaxy/scripts/mvc/workflow/workflow.js
M client/galaxy/style/less/base.less
M config/plugins/webhooks/demo/search/static/script.js
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/maps/mvc/user/user-preferences.js.map
M static/maps/mvc/workflow/workflow.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/user/user-preferences.js
M static/scripts/mvc/workflow/workflow.js
M static/style/blue/base.css
Log Message:
-----------
Merge branch 'dev' into revise_page
Commit: 11244ac2ee3d6c3acae5c44ac1e74d3f61da2767
https://github.com/galaxyproject/galaxy/commit/11244ac2ee3d6c3acae5c44ac1e7…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-02 (Wed, 02 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/grid/grid-template.js
M static/maps/mvc/grid/grid-template.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/grid/grid-template.js
Log Message:
-----------
Escape grid messages
Commit: 2626eec1ab893371ea9e2d9ea723bbd1edf9c86a
https://github.com/galaxyproject/galaxy/commit/2626eec1ab893371ea9e2d9ea723…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-03 (Thu, 03 Aug 2017)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
Use regular anchors for masthead routes
Commit: 88b8016b4638e1da23826b9241df1da617ea6245
https://github.com/galaxyproject/galaxy/commit/88b8016b4638e1da23826b9241df…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-03 (Thu, 03 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/managers/tags.py
M static/maps/mvc/workflow/workflow-forms.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Merge branch 'dev' into revise_page
Commit: 8f056c2bbc78040c790255c874b6c321c4ba5b97
https://github.com/galaxyproject/galaxy/commit/8f056c2bbc78040c790255c874b6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-09 (Wed, 09 Aug 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M client/galaxy/scripts/galaxy.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M config/datatypes_conf.xml.sample
A config/user_preferences_extra_conf.yml.sample
M doc/source/admin/special_topics/grt.rst
M lib/galaxy/config.py
M lib/galaxy/dataset_collections/matching.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/rule_helper.py
M lib/galaxy/jobs/runners/util/cli/__init__.py
M lib/galaxy/jobs/runners/util/cli/shell/local.py
M lib/galaxy/jobs/runners/util/cli/shell/rsh.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/objectstore/s3_multipart_upload.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/base/pluginframework.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/controllers/async.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/workflow/extract.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/util/workflow_util.py
M lib/tool_shed/utility_containers/utility_container_manager.py
R scripts/grt.py
R scripts/grt.yml.sample
A scripts/grt/export.py
A scripts/grt/grt.yml.sample
A scripts/grt/upload.py
M static/maps/galaxy.js.map
M static/maps/layout/menu.js.map
M static/maps/mvc/user/user-preferences.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/galaxy.js
M static/scripts/layout/menu.js
M static/scripts/mvc/user/user-preferences.js
M templates/galaxy_client_app.mako
M templates/user/login.mako
M templates/user/register.mako
M templates/webapps/galaxy/history/display_structured.mako
M templates/webapps/galaxy/workflow/build_from_current_history.mako
M templates/webapps/tool_shed/repository/common.mako
M test/api/test_tools.py
A test/functional/tools/identifier_source.xml
M test/functional/tools/samples_tool_conf.xml
M test/shed_functional/base/twilltestcase.py
A test/unit/test_remote_shell.py
M test/unit/tools/test_parsing.py
M test/unit/tools/test_toolbox.py
M test/unit/tools_support.py
M tox.ini
Log Message:
-----------
Merge branch 'dev' into revise_page
Commit: cfa3220d9f2d257b94795b6f63592459d3011f30
https://github.com/galaxyproject/galaxy/commit/cfa3220d9f2d257b94795b6f6359…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-09 (Wed, 09 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M lib/galaxy/managers/tags.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
A lib/galaxy/model/migrate/versions/0135_add_library_tags.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M static/maps/mvc/library/library-dataset-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
Merge branch 'dev' into revise_page
Commit: 5e43fcef3c94e9b3f6d700fc5258067d0547e30d
https://github.com/galaxyproject/galaxy/commit/5e43fcef3c94e9b3f6d700fc5258…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/panels/admin-panel.js
M client/galaxy/scripts/galaxy.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
A client/galaxy/scripts/layout/router.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M static/maps/galaxy.js.map
M static/maps/layout/menu.js.map
M static/maps/layout/page.js.map
A static/maps/layout/router.js.map
M static/maps/mvc/grid/grid-template.js.map
M static/maps/mvc/grid/grid-view.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/galaxy.js
M static/scripts/layout/menu.js
M static/scripts/layout/page.js
A static/scripts/layout/router.js
M static/scripts/mvc/grid/grid-template.js
M static/scripts/mvc/grid/grid-view.js
M templates/admin/user/reset_password.mako
M templates/admin/user/user.mako
Log Message:
-----------
Merge pull request #4341 from guerler/revise_page
Admin user grid conversion
Compare: https://github.com/galaxyproject/galaxy/compare/429771820200...5e43fcef3c94
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 64a1e514587ea4d2d9fa870ebb9230212dbec244
https://github.com/galaxyproject/galaxy/commit/64a1e514587ea4d2d9fa870ebb92…
Author: Brad Langhorst <langhorst(a)neb.com>
Date: 2017-07-05 (Wed, 05 Jul 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M lib/galaxy/managers/tags.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
A lib/galaxy/model/migrate/versions/0135_add_library_tags.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
Adds tags to library dataset items, and allows users to specify that tags should be generated from filenames
Commit: dcdbfd64d1e94c200c023e1d3b51a8a96c60ca1a
https://github.com/galaxyproject/galaxy/commit/dcdbfd64d1e94c200c023e1d3b51…
Author: Brad Langhorst <langhorst(a)neb.com>
Date: 2017-07-05 (Wed, 05 Jul 2017)
Changed paths:
M lib/galaxy/web/base/controller.py
Log Message:
-----------
According to John, this is not actually deprecated
Commit: ce7e10cf07ca0061a168bd637cd8ca5a0b88bec5
https://github.com/galaxyproject/galaxy/commit/ce7e10cf07ca0061a168bd637cd8…
Author: Brad Langhorst <langhorst(a)neb.com>
Date: 2017-07-05 (Wed, 05 Jul 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
Log Message:
-----------
shows tags in library views
Commit: 14a0de0c21e40a88ab9b917db28c5a6365ebc7c9
https://github.com/galaxyproject/galaxy/commit/14a0de0c21e40a88ab9b917db28c…
Author: Brad Langhorst <langhorst(a)neb.com>
Date: 2017-07-05 (Wed, 05 Jul 2017)
Changed paths:
M lib/galaxy/model/__init__.py
Log Message:
-----------
copies tags on library items to history
(and to copies of library items, though I don’t
think anything called this)
Commit: 72e9e69467125afd9cff9e086c3b153c1f20a289
https://github.com/galaxyproject/galaxy/commit/72e9e69467125afd9cff9e086c3b…
Author: Brad Langhorst <langhorst(a)neb.com>
Date: 2017-07-05 (Wed, 05 Jul 2017)
Changed paths:
M lib/galaxy/model/migrate/versions/0135_add_library_tags.py
Log Message:
-----------
Removes unused import
Commit: 3b0c25f73b542022c706787b4cb910a6365c1c75
https://github.com/galaxyproject/galaxy/commit/3b0c25f73b542022c706787b4cb9…
Author: Brad Langhorst <langhorst(a)neb.com>
Date: 2017-07-05 (Wed, 05 Jul 2017)
Changed paths:
M lib/galaxy/model/__init__.py
Log Message:
-----------
Fixes style violation # comment not #comment
Commit: efd6d053bcae0c9eeede93dc17e0069302646967
https://github.com/galaxyproject/galaxy/commit/efd6d053bcae0c9eeede93dc17e0…
Author: Brad Langhorst <langhorst(a)neb.com>
Date: 2017-07-05 (Wed, 05 Jul 2017)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
Log Message:
-----------
fixes import order to comply with flake8
Commit: 5add359cde29a9e6ccc7b94b6b9420522e6d5fea
https://github.com/galaxyproject/galaxy/commit/5add359cde29a9e6ccc7b94b6b94…
Author: Brad Langhorst <langhorst(a)neb.com>
Date: 2017-07-05 (Wed, 05 Jul 2017)
Changed paths:
M lib/galaxy/tools/parameters/grouping.py
Log Message:
-----------
need to construct this field to avoid a conditional
check failure
Commit: 33900e5bc913b494611373a9bd926643e760be95
https://github.com/galaxyproject/galaxy/commit/33900e5bc913b494611373a9bd92…
Author: Brad Langhorst <langhorst(a)neb.com>
Date: 2017-07-05 (Wed, 05 Jul 2017)
Changed paths:
M lib/galaxy/tools/actions/upload_common.py
Log Message:
-----------
Rather than trying to find every path into this
Function, assume no tagging if dataset does not
Have a tag_using_filenames property
Commit: dd2224e92ddab51deaf646b04a23ec3112815733
https://github.com/galaxyproject/galaxy/commit/dd2224e92ddab51deaf646b04a23…
Author: Brad Langhorst <langhorst(a)neb.com>
Date: 2017-07-05 (Wed, 05 Jul 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/library_contents.py
Log Message:
-----------
updates doc to include tag_using_filenames
Commit: 73012c942e77d5fe7993ddbd67559c51c2832813
https://github.com/galaxyproject/galaxy/commit/73012c942e77d5fe7993ddbd6755…
Author: Brad Langhorst <langhorst(a)neb.com>
Date: 2017-07-05 (Wed, 05 Jul 2017)
Changed paths:
M lib/galaxy/tools/parameters/grouping.py
Log Message:
-----------
Allow passing in tag_using_filenames via grouping
Commit: cb7b34f320a82cb8e4efe96e72f4165f72e1930c
https://github.com/galaxyproject/galaxy/commit/cb7b34f320a82cb8e4efe96e72f4…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-07-06 (Thu, 06 Jul 2017)
Changed paths:
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
Log Message:
-----------
Swap two more spots initializing TagManagers to new session instead of app
Commit: 7b423e19c92868a6a3e7abee2a4ad6e92a03aad8
https://github.com/galaxyproject/galaxy/commit/7b423e19c92868a6a3e7abee2a4a…
Author: Brad Langhorst <langhorst(a)neb.com>
Date: 2017-08-07 (Mon, 07 Aug 2017)
Changed paths:
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
Log Message:
-----------
Merge pull request #1 from dannon/library_tags
Swap two more spots initializing TagManagers to new session
Commit: 06c70d34e2c218b826d813d3dd4e52d077ab94d4
https://github.com/galaxyproject/galaxy/commit/06c70d34e2c218b826d813d3dd4e…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-09 (Wed, 09 Aug 2017)
Changed paths:
M static/maps/mvc/library/library-dataset-view.js.map
M static/scripts/bundled/admin.bundled.js.map
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/library/library-dataset-view.js
Log Message:
-----------
make client
Commit: cff21d350dc71b1e7b088985eeeb3f27b0fec1d0
https://github.com/galaxyproject/galaxy/commit/cff21d350dc71b1e7b088985eeeb…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-09 (Wed, 09 Aug 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/galaxy.js
M client/galaxy/scripts/galaxy.pages.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/mvc/dataset/data.js
A client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/grid/grid-model.js
A client/galaxy/scripts/mvc/grid/grid-shared.js
M client/galaxy/scripts/mvc/grid/grid-view.js
R client/galaxy/scripts/mvc/page/page-list.js
M client/galaxy/scripts/mvc/user/user-preferences.js
R client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/mvc/workflow/workflow.js
M client/galaxy/scripts/nls/fr/locale.js
M client/galaxy/scripts/nls/ja/locale.js
M client/galaxy/scripts/nls/locale.js
M client/galaxy/scripts/viz/circster.js
M client/galaxy/scripts/viz/phyloviz.js
M client/galaxy/scripts/viz/trackster.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/scripts/viz/visualization.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/galaxy_bootstrap/overrides.less
A client/package-lock.json
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js
M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js
M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js
A config/plugins/visualizations/unipept/README.md
A config/plugins/visualizations/unipept/config/unipept.xml
A config/plugins/visualizations/unipept/static/style.css
A config/plugins/visualizations/unipept/static/tooltip.css
A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js
A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js.map
A config/plugins/visualizations/unipept/static/unipept_viz.js
A config/plugins/visualizations/unipept/templates/glyphicons-86-repeat.png
A config/plugins/visualizations/unipept/templates/unipept.mako
M config/plugins/webhooks/demo/search/static/script.js
M config/tool_conf.xml.main
M config/tool_shed.ini.sample
A config/user_preferences_extra_conf.yml.sample
M doc/source/admin/special_topics/grt.rst
M lib/galaxy/config.py
M lib/galaxy/dataset_collections/matching.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/rule_helper.py
M lib/galaxy/jobs/runners/cli.py
M lib/galaxy/jobs/runners/util/cli/__init__.py
M lib/galaxy/jobs/runners/util/cli/shell/local.py
M lib/galaxy/jobs/runners/util/cli/shell/rsh.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/tags.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/metadata.py
M lib/galaxy/objectstore/__init__.py
A lib/galaxy/objectstore/pithos.py
M lib/galaxy/objectstore/s3_multipart_upload.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/web/base/controller.py
R lib/galaxy/web/base/controllers/__init__.py
R lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/base/pluginframework.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/api/quotas.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/async.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/controllers/admin.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/modules.py
M lib/tool_shed/metadata/metadata_generator.py
A lib/tool_shed/util/admin_util.py
M lib/tool_shed/util/workflow_util.py
M lib/tool_shed/utility_containers/utility_container_manager.py
R scripts/grt.py
R scripts/grt.yml.sample
A scripts/grt/export.py
A scripts/grt/grt.yml.sample
A scripts/grt/upload.py
M scripts/runtime_stats.py
M static/maps/galaxy.js.map
M static/maps/galaxy.pages.js.map
M static/maps/layout/menu.js.map
M static/maps/layout/scratchbook.js.map
M static/maps/mvc/dataset/data.js.map
A static/maps/mvc/dataset/dataset-edit-attributes.js.map
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/maps/mvc/grid/grid-model.js.map
A static/maps/mvc/grid/grid-shared.js.map
M static/maps/mvc/grid/grid-view.js.map
R static/maps/mvc/page/page-list.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/maps/mvc/workflow/workflow-forms.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/maps/mvc/workflow/workflow.js.map
M static/maps/nls/fr/locale.js.map
M static/maps/nls/ja/locale.js.map
M static/maps/nls/locale.js.map
M static/maps/viz/circster.js.map
M static/maps/viz/phyloviz.js.map
M static/maps/viz/trackster.js.map
M static/maps/viz/trackster/tracks.js.map
M static/maps/viz/visualization.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/galaxy.js
M static/scripts/galaxy.pages.js
M static/scripts/layout/menu.js
M static/scripts/layout/scratchbook.js
M static/scripts/mvc/dataset/data.js
A static/scripts/mvc/dataset/dataset-edit-attributes.js
M static/scripts/mvc/dataset/dataset-li-edit.js
A static/scripts/mvc/grid/grid-shared.js
M static/scripts/mvc/grid/grid-view.js
R static/scripts/mvc/page/page-list.js
M static/scripts/mvc/user/user-preferences.js
M static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/mvc/workflow/workflow-view.js
M static/scripts/mvc/workflow/workflow.js
M static/scripts/nls/fr/locale.js
M static/scripts/nls/ja/locale.js
M static/scripts/nls/locale.js
M static/scripts/viz/circster.js
M static/scripts/viz/phyloviz.js
M static/scripts/viz/trackster.js
M static/scripts/viz/trackster/tracks.js
M static/scripts/viz/visualization.js
M static/style/blue/base.css
M templates/galaxy_client_app.mako
M templates/user/login.mako
M templates/user/register.mako
R templates/webapps/galaxy/dataset/edit_attributes.mako
M templates/webapps/galaxy/history/display_structured.mako
R templates/webapps/galaxy/history/list_published.mako
M templates/webapps/galaxy/page/editor.mako
R templates/webapps/galaxy/page/select_items_grid.mako
M templates/webapps/galaxy/requests/common/common.mako
R templates/webapps/galaxy/tracks/add_to_viz.mako
R templates/webapps/galaxy/tracks/add_tracks.mako
R templates/webapps/galaxy/tracks/history_datasets_select_grid.mako
R templates/webapps/galaxy/tracks/history_select_grid.mako
R templates/webapps/galaxy/tracks/library_datasets_select_grid.mako
R templates/webapps/galaxy/visualization/list.mako
M templates/webapps/galaxy/workflow/build_from_current_history.mako
M templates/webapps/tool_shed/repository/common.mako
M test/api/test_tools.py
A test/functional/tools/identifier_source.xml
M test/functional/tools/samples_tool_conf.xml
M test/shed_functional/base/twilltestcase.py
A test/unit/test_remote_shell.py
M test/unit/tools/test_parsing.py
M test/unit/tools/test_toolbox.py
M test/unit/tools_support.py
M tox.ini
Log Message:
-----------
Merge branch 'dev' into library_tags
Commit: fd0ce1284a9663fab95558fd38ad9477c98d8311
https://github.com/galaxyproject/galaxy/commit/fd0ce1284a9663fab95558fd38ad…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-09 (Wed, 09 Aug 2017)
Changed paths:
M static/scripts/bundled/admin.bundled.js.map
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
Log Message:
-----------
make client again...
Commit: d52ac533daa8bcfef209f66f8c4e3020d93c09df
https://github.com/galaxyproject/galaxy/commit/d52ac533daa8bcfef209f66f8c4e…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-09 (Wed, 09 Aug 2017)
Changed paths:
M lib/galaxy/model/migrate/versions/0135_add_library_tags.py
Log Message:
-----------
fix indentation
Commit: 429771820200acd1a0d0b12c85a39ab7fe530195
https://github.com/galaxyproject/galaxy/commit/429771820200acd1a0d0b12c85a3…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-09 (Wed, 09 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M lib/galaxy/managers/tags.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
A lib/galaxy/model/migrate/versions/0135_add_library_tags.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M static/maps/mvc/library/library-dataset-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/bundled/admin.bundled.js.map
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/library/library-dataset-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
Merge pull request #4262 from bwlang/library_tags
Library tags
Compare: https://github.com/galaxyproject/galaxy/compare/2e53858a2973...429771820200
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 7ca5cd6585ef8a69f07cfa8362287a800b48281a
https://github.com/galaxyproject/galaxy/commit/7ca5cd6585ef8a69f07cfa836228…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-08-09 (Wed, 09 Aug 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/base/pluginframework.py
Log Message:
-----------
Fix import order and Python3 compatibility for lib/galaxy/web/base/
Commit: 2e53858a2973aa6d4f95c3e8401d9709809d1da3
https://github.com/galaxyproject/galaxy/commit/2e53858a2973aa6d4f95c3e8401d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-09 (Wed, 09 Aug 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/base/pluginframework.py
Log Message:
-----------
Merge pull request #4403 from nsoranzo/flake8-import-order
Fix import order and Python3 compatibility for lib/galaxy/web/base/
Compare: https://github.com/galaxyproject/galaxy/compare/c7d7b6c4695b...2e53858a2973
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: a060690c3afa8f296404eb52e4986202d1d985ca
https://github.com/galaxyproject/galaxy/commit/a060690c3afa8f296404eb52e498…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/workflow/extract.py
M lib/tool_shed/util/workflow_util.py
Log Message:
-----------
Get tools with tool_version in more places
Commit: bc23c26cf4210b46f4d17369902fdaec48a16e98
https://github.com/galaxyproject/galaxy/commit/bc23c26cf4210b46f4d17369902f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/workflow/extract.py
M lib/tool_shed/util/workflow_util.py
Log Message:
-----------
Merge pull request #4391 from mvdbeek/more_version_fixes
Get tools with tool_version in more places
Compare: https://github.com/galaxyproject/galaxy/compare/cf34d8b75958...bc23c26cf421
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 20f90254bfae5e2e0579a69fa37b0c45e874d9ce
https://github.com/galaxyproject/galaxy/commit/20f90254bfae5e2e0579a69fa37b…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/utility_containers/utility_container_manager.py
M templates/webapps/tool_shed/repository/common.mako
Log Message:
-----------
Show minimum required galaxy version in tool shed and galaxy installation process
Commit: a77c4587fb9eadfc62da6b8b430154ad18ce1136
https://github.com/galaxyproject/galaxy/commit/a77c4587fb9eadfc62da6b8b4301…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/tool_shed/utility_containers/utility_container_manager.py
Log Message:
-----------
Shorten 'Minimum required Galaxy version' to 'Minimum Galaxy Version'
Commit: ff197fe915a67c1ad2ba10ed9a6d433a55b45ee1
https://github.com/galaxyproject/galaxy/commit/ff197fe915a67c1ad2ba10ed9a6d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/utility_containers/utility_container_manager.py
M templates/webapps/tool_shed/repository/common.mako
Log Message:
-----------
Merge pull request #4386 from mvdbeek/display_minimum_required_galaxy_version
Show minimum required galaxy version in tool shed and galaxy installation process
Compare: https://github.com/galaxyproject/galaxy/compare/0da4768c3535...ff197fe915a6
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: fe2d607675acf5e18994957fb8ff4422079987ea
https://github.com/galaxyproject/galaxy/commit/fe2d607675acf5e18994957fb8ff…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
Log Message:
-----------
Replace list with generator when iterating headers
This should be more memory-friendly. @blankenberg suggested doing this
in #4319.
Commit: e6c238e234ae4d16d1fd1118c1b7e585ba541645
https://github.com/galaxyproject/galaxy/commit/e6c238e234ae4d16d1fd1118c1b7…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/interval.py
Log Message:
-----------
Move iter_headers into try clause (thx @nsoranzo)
Commit: 43702ccacdbfe925d921dac413c02bb7f65b9c4f
https://github.com/galaxyproject/galaxy/commit/43702ccacdbfe925d921dac413c0…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/mothur.py
Log Message:
-----------
Process the first line when setting metdata for mother.otu files
Commit: 0da4768c3535d13c0a141cc30f39e8b86b0c98d1
https://github.com/galaxyproject/galaxy/commit/0da4768c3535d13c0a141cc30f39…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
Log Message:
-----------
Merge pull request #4388 from mvdbeek/iter_headers
Replace list with generator when iterating headers
Compare: https://github.com/galaxyproject/galaxy/compare/196a2bbcf50c...0da4768c3535