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

[galaxyproject/galaxy] 70a64b: Refactor bug reporting into plugins
by GitHub 10 Aug '17

10 Aug '17

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

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[galaxyproject/galaxy] 3164fc: Allow app specific client side routing
by GitHub 10 Aug '17

10 Aug '17

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 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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 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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 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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 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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 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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

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[galaxyproject/galaxy] 64a1e5: Adds tags to library dataset items, and allows use...
by GitHub 09 Aug '17

09 Aug '17

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

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[galaxyproject/galaxy] 7ca5cd: Fix import order and Python3 compatibility for lib...
by GitHub 09 Aug '17

09 Aug '17

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

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[galaxyproject/galaxy] 11365e: Bugfix: __str__ method on tool parsers would throw...
by GitHub 09 Aug '17

09 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 11365e9620a5198ca88a35f5a10902744d94a7a3 https://github.com/galaxyproject/galaxy/commit/11365e9620a5198ca88a35f5a109… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/tools/parser/interface.py M test/unit/tools/test_parsing.py Log Message: ----------- Bugfix: __str__ method on tool parsers would throw an Exception. Commit: c7d7b6c4695b300739b572b9a94e0de312a0f6ef https://github.com/galaxyproject/galaxy/commit/c7d7b6c4695b300739b572b9a94e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-08-09 (Wed, 09 Aug 2017) Changed paths: M lib/galaxy/tools/parser/interface.py M test/unit/tools/test_parsing.py Log Message: ----------- Merge pull request #4395 from jmchilton/parser_to_str_fix Bugfix: __str__ method on tool parsers would throw an Exception. Compare: https://github.com/galaxyproject/galaxy/compare/a001145278fb...c7d7b6c4695b

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[galaxyproject/galaxy] aa29b3: Fix job splitting so it happens before dependency ...
by GitHub 09 Aug '17

09 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aa29b3a1a18d9ee528bd33e58eb2cd8ff180f544 https://github.com/galaxyproject/galaxy/commit/aa29b3a1a18d9ee528bd33e58eb2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/jobs/command_factory.py Log Message: ----------- Fix job splitting so it happens before dependency resolution? Commit: 061eb256409938179d29163ffb522abdc8d9796e https://github.com/galaxyproject/galaxy/commit/061eb256409938179d29163ffb52… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/jobs/command_factory.py Log Message: ----------- Add comment about fix for #4381. Commit: c03b29f4855dcce9677e2fe16779d2eb64b1646d https://github.com/galaxyproject/galaxy/commit/c03b29f4855dcce9677e2fe16779… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/jobs/command_factory.py Log Message: ----------- Revise comment thanks to note from @mvdbeek. Commit: a001145278fb0642325214123da0c5cec6fc6704 https://github.com/galaxyproject/galaxy/commit/a001145278fb0642325214123da0… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-08-09 (Wed, 09 Aug 2017) Changed paths: M lib/galaxy/jobs/command_factory.py Log Message: ----------- Merge pull request #4383 from jmchilton/split_conda Bugfix: Ensure task splitting handles before job resolution. Compare: https://github.com/galaxyproject/galaxy/compare/bc23c26cf421...a001145278fb

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[galaxyproject/galaxy] a06069: Get tools with tool_version in more places
by GitHub 09 Aug '17

09 Aug '17

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

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[galaxyproject/galaxy] f8648b: Add deeptools datatypes to Galaxy
by GitHub 09 Aug '17

09 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f8648b658629d1313029bb1ad707023c44b626df https://github.com/galaxyproject/galaxy/commit/f8648b658629d1313029bb1ad707… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Add deeptools datatypes to Galaxy Commit: cf34d8b75958db007dcaa5368557dda6850d6e95 https://github.com/galaxyproject/galaxy/commit/cf34d8b75958db007dcaa5368557… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #4392 from bgruening/deeptools_datatypes Add deepTools datatypes to Galaxy Compare: https://github.com/galaxyproject/galaxy/compare/ff197fe915a6...cf34d8b75958

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[galaxyproject/galaxy] 20f902: Show minimum required galaxy version in tool shed ...
by GitHub 08 Aug '17

08 Aug '17

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

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[galaxyproject/galaxy] fe2d60: Replace list with generator when iterating headers
by GitHub 08 Aug '17

08 Aug '17

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

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