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

[galaxyproject/galaxy] 6fd17e: Add a gulp plumber.
by GitHub 25 Oct '17

25 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6fd17e36696d02835af943d55cb721f0d109d5cd https://github.com/galaxyproject/galaxy/commit/6fd17e36696d02835af943d55cb7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M client/gulpfile.js M client/package.json M client/yarn.lock Log Message: ----------- Add a gulp plumber. Commit: 561ccfe815e025c44ecc6fbb825ab5a2a23324c2 https://github.com/galaxyproject/galaxy/commit/561ccfe815e025c44ecc6fbb825a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M client/gulpfile.js M client/package.json M client/yarn.lock Log Message: ----------- Merge pull request #4867 from dannon/plumber Add a gulp plumber. Compare: https://github.com/galaxyproject/galaxy/compare/9b3d217a2e5d...561ccfe815e0

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[galaxyproject/galaxy] 4dcba2: initial release notes for 17.09
by GitHub 25 Oct '17

25 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4dcba21d838bd2bad806687d7c212d7da0b8e85e https://github.com/galaxyproject/galaxy/commit/4dcba21d838bd2bad806687d7c21… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: A doc/source/releases/17.09.rst M doc/source/releases/17.09_announce.rst A doc/source/releases/18.01_announce.rst Log Message: ----------- initial release notes for 17.09 Commit: 272ed6217d4662f7bdc6b385206a7f301295a033 https://github.com/galaxyproject/galaxy/commit/272ed6217d4662f7bdc6b385206a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- add deprecations Commit: 06d3f4051543e7c319e775884ea3aab8abef9a2c https://github.com/galaxyproject/galaxy/commit/06d3f4051543e7c319e775884ea3… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- amend add missing line Commit: eab76b9ae014c4fa2dd3a1ba09199f3351536924 https://github.com/galaxyproject/galaxy/commit/eab76b9ae014c4fa2dd3a1ba0919… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M doc/source/releases/index.rst Log Message: ----------- add listing of 17.09 release to index Commit: 812b04d14eb1c3d3ec016efb6aa8f1024811c560 https://github.com/galaxyproject/galaxy/commit/812b04d14eb1c3d3ec016efb6aa8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M doc/source/releases/17.09.rst M doc/source/releases/17.09_announce.rst Log Message: ----------- more work on RN Commit: 5bde1d1c3a0239ef37369f59e90ceca863d6821f https://github.com/galaxyproject/galaxy/commit/5bde1d1c3a0239ef37369f59e90c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M doc/source/releases/17.09.rst M doc/source/releases/17.09_announce.rst Log Message: ----------- Small progress on 17.09 release notes. Commit: ee27188b59d174f4db16d2ce4b7cd2181ea93517 https://github.com/galaxyproject/galaxy/commit/ee27188b59d174f4db16d2ce4b7c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: A client/galaxy/scripts/libs/jquery/jquery.complexify.js A doc/source/api/api.rst A doc/source/api/ts_api.rst M doc/source/releases/17.09_announce.rst Log Message: ----------- add security release notes Commit: 180472a3d8ceb40f6d015c0bfe5ef1dd08da5513 https://github.com/galaxyproject/galaxy/commit/180472a3d8ceb40f6d015c0bfe5e… Author: Dave Clements <clements(a)galaxyproject.org> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- Small edits to 17.09 release notes. Commit: c8efbb3327cb4e2805c0099975c5a2be70b95a21 https://github.com/galaxyproject/galaxy/commit/c8efbb3327cb4e2805c0099975c5… Author: Dave Clements <clements(a)galaxyproject.org> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- Fixed indenting in release notes. Commit: 4252f4f813c3d5a390ead3d86c4eec78273163cb https://github.com/galaxyproject/galaxy/commit/4252f4f813c3d5a390ead3d86c4e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M doc/source/releases/17.09.rst Log Message: ----------- Small 17.09 release note improvements. Commit: 199ec6dd4c70c733edd200e61d6470dedcf0da85 https://github.com/galaxyproject/galaxy/commit/199ec6dd4c70c733edd200e61d64… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M doc/source/releases/17.09.rst Log Message: ----------- Condense several 17.09 release notes items. Commit: 3e8bf27fca44f5b70ac9e7e1f66acbdb11c98162 https://github.com/galaxyproject/galaxy/commit/3e8bf27fca44f5b70ac9e7e1f66a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M doc/source/releases/17.09.rst Log Message: ----------- More release notes improvements. Move a couple things higher, merge a couple more things, improved language (toward sentences). Commit: 1b5421c1df5392ce83a66de22dceb6ef404134bf https://github.com/galaxyproject/galaxy/commit/1b5421c1df5392ce83a66de22dce… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- Merge pull request #24 from tnabtaf/17.09_release_notes 17.09 release notes edits Commit: 00bc7a51f9c780e15041b465e0245848f7b26244 https://github.com/galaxyproject/galaxy/commit/00bc7a51f9c780e15041b465e024… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M doc/source/releases/17.09.rst Log Message: ----------- More 17.09 release note fixes. Merge more items, fix more sentences, etc... Commit: d1190bb067146d76bc16ec403562d4ba2d905710 https://github.com/galaxyproject/galaxy/commit/d1190bb067146d76bc16ec403562… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- deprecate undocumented refresh_on_change functionality Commit: fe440d27367ef00b663057bf8ebe30b7b9ab0344 https://github.com/galaxyproject/galaxy/commit/fe440d27367ef00b663057bf8ebe… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M doc/source/releases/17.09.rst Log Message: ----------- Merge branch '17.09_release_notes' of github.com:martenson/galaxy into 17.09_release_notes Commit: 6bbf345c282782efac6a026d36f60296571deabe https://github.com/galaxyproject/galaxy/commit/6bbf345c282782efac6a026d36f6… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: R client/galaxy/scripts/libs/jquery/jquery.complexify.js R doc/source/api/api.rst R doc/source/api/ts_api.rst Log Message: ----------- remove wrongly added files Commit: 73b31ce3199ac73a0208dd784420800064278454 https://github.com/galaxyproject/galaxy/commit/73b31ce3199ac73a0208dd784420… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: A doc/source/releases/17.09.rst M doc/source/releases/17.09_announce.rst A doc/source/releases/18.01_announce.rst M doc/source/releases/index.rst Log Message: ----------- Merge pull request #4772 from martenson/17.09_release_notes [17.09] release notes Commit: f5981e6ef381d5c4be33e0725cdb697a5515ca7b https://github.com/galaxyproject/galaxy/commit/f5981e6ef381d5c4be33e0725cdb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- add tldr for security Commit: add3a97bb014392d773c7a5bb8243f7341c1219c https://github.com/galaxyproject/galaxy/commit/add3a97bb014392d773c7a5bb824… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- this is not markdown Commit: cfb61e069659fa43b4ad290b4cc4a93ebd71e3e0 https://github.com/galaxyproject/galaxy/commit/cfb61e069659fa43b4ad290b4cc4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- Rework security wording a bit. I waffle on adding security notes for the 17.09-only issues... Commit: 01b244a810434a1184d3e72ff9476af2a1243dcc https://github.com/galaxyproject/galaxy/commit/01b244a810434a1184d3e72ff947… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- Merge pull request #4853 from martenson/improve-RN [17.09] release notes - add tldr for security Commit: 9791dd22d4d9084989cafa3498ae313dd4cd13f0 https://github.com/galaxyproject/galaxy/commit/9791dd22d4d9084989cafa3498ae… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M lib/galaxy/util/path/ntpath.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Fix regressions in library API Introduced in commit 93a8bfc7cb5e9c3395c5057910ec39d68ad787b4 Commit: a4a8f155376119277df2cfebd13376e919873c4f https://github.com/galaxyproject/galaxy/commit/a4a8f155376119277df2cfebd133… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M lib/galaxy/util/path/ntpath.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Merge pull request #4854 from nsoranzo/release_16.07_fix_test_regressions [16.07] Fix regressions in library API Commit: 899b0d806808d29291bf132a8c9e45df31fc28e1 https://github.com/galaxyproject/galaxy/commit/899b0d806808d29291bf132a8c9e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M lib/galaxy/util/path/__init__.py Log Message: ----------- Fix galaxy.util.in_directory() - broken because it takes realpath of just one argument. Easy to see on Mac OS X since /tmp isn't really /tmp for instance: ``` % touch /tmp/moo % python >>> import galaxy.util >>> galaxy.util.in_directory("/tmp/moo", "/tmp/moo") False ``` ... and this is why the Travis tests are failing under Mac OS X. Broken with 93a8bfc7cb5e9c3395c5057910ec39d68ad787b4. Commit: 4b5dc399b934542092bfe66c3c4e03acc3980d49 https://github.com/galaxyproject/galaxy/commit/4b5dc399b934542092bfe66c3c4e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add basic test for in_directory. Commit: fcb23eb8f878700bfd77384ef679a569c59f7a62 https://github.com/galaxyproject/galaxy/commit/fcb23eb8f878700bfd77384ef679… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Some documentation to clarify discussion on #4856. Commit: 95f8f48416c5a4d2590120e965cf9714c752ed61 https://github.com/galaxyproject/galaxy/commit/95f8f48416c5a4d2590120e965cf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/path/__init__.py Log Message: ----------- Doc fix thanks to @nsoranzo. Commit: 7e08ba6f19346668350d358ee4eb01ef722e74e7 https://github.com/galaxyproject/galaxy/commit/7e08ba6f19346668350d358ee4eb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/path/__init__.py Log Message: ----------- Rework in_directory fix to move realpath expansion into galaxy.util. Commit: e3e28ddc2dac1c4faaa45a9764abc7970129beb3 https://github.com/galaxyproject/galaxy/commit/e3e28ddc2dac1c4faaa45a9764ab… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/path/__init__.py Log Message: ----------- Merge pull request #4856 from jmchilton/release_16.07_fix_in_directory [16.07] Fix galaxy.util.in_directory()... Commit: 90289b6116c6a6ba1f6f0b4cbdee059003f916a3 https://github.com/galaxyproject/galaxy/commit/90289b6116c6a6ba1f6f0b4cbdee… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/path/ntpath.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: a7bf1601a1ad34e5896978e1bce9c8081aafbb05 https://github.com/galaxyproject/galaxy/commit/a7bf1601a1ad34e5896978e1bce9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/path/ntpath.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Commit: 20621b7d09443fc80c8326d91bdd204decb80b81 https://github.com/galaxyproject/galaxy/commit/20621b7d09443fc80c8326d91bdd… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/path/ntpath.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Commit: 986031bf190b82317cf687ed7e82ebd6b2646957 https://github.com/galaxyproject/galaxy/commit/986031bf190b82317cf687ed7e82… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/path/ntpath.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Conflicts: lib/galaxy/webapps/galaxy/controllers/library_common.py Commit: 1baed58e1e7c813e6a87b5a83883c5940a78035d https://github.com/galaxyproject/galaxy/commit/1baed58e1e7c813e6a87b5a83883… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- Backport fix for E201 and E202 errors >From commit 9b4de72ca68afc2353beff333775422039baae25 Commit: 9b3d217a2e5d9ccaa37b345cdd9487599fc5b699 https://github.com/galaxyproject/galaxy/commit/9b3d217a2e5d9ccaa37b345cdd94… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: A doc/source/releases/17.09.rst M doc/source/releases/17.09_announce.rst A doc/source/releases/18.01_announce.rst M doc/source/releases/index.rst M lib/galaxy/util/__init__.py M lib/galaxy/util/path/__init__.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Merge branch 'release_17.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/0f5927b628ea...9b3d217a2e5d

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[galaxyproject/galaxy] 9791dd: Fix regressions in library API
by GitHub 25 Oct '17

25 Oct '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 9791dd22d4d9084989cafa3498ae313dd4cd13f0 https://github.com/galaxyproject/galaxy/commit/9791dd22d4d9084989cafa3498ae… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M lib/galaxy/util/path/ntpath.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Fix regressions in library API Introduced in commit 93a8bfc7cb5e9c3395c5057910ec39d68ad787b4 Commit: a4a8f155376119277df2cfebd13376e919873c4f https://github.com/galaxyproject/galaxy/commit/a4a8f155376119277df2cfebd133… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M lib/galaxy/util/path/ntpath.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Merge pull request #4854 from nsoranzo/release_16.07_fix_test_regressions [16.07] Fix regressions in library API Commit: 899b0d806808d29291bf132a8c9e45df31fc28e1 https://github.com/galaxyproject/galaxy/commit/899b0d806808d29291bf132a8c9e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M lib/galaxy/util/path/__init__.py Log Message: ----------- Fix galaxy.util.in_directory() - broken because it takes realpath of just one argument. Easy to see on Mac OS X since /tmp isn't really /tmp for instance: ``` % touch /tmp/moo % python >>> import galaxy.util >>> galaxy.util.in_directory("/tmp/moo", "/tmp/moo") False ``` ... and this is why the Travis tests are failing under Mac OS X. Broken with 93a8bfc7cb5e9c3395c5057910ec39d68ad787b4. Commit: 4b5dc399b934542092bfe66c3c4e03acc3980d49 https://github.com/galaxyproject/galaxy/commit/4b5dc399b934542092bfe66c3c4e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add basic test for in_directory. Commit: fcb23eb8f878700bfd77384ef679a569c59f7a62 https://github.com/galaxyproject/galaxy/commit/fcb23eb8f878700bfd77384ef679… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Some documentation to clarify discussion on #4856. Commit: 95f8f48416c5a4d2590120e965cf9714c752ed61 https://github.com/galaxyproject/galaxy/commit/95f8f48416c5a4d2590120e965cf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/path/__init__.py Log Message: ----------- Doc fix thanks to @nsoranzo. Commit: 7e08ba6f19346668350d358ee4eb01ef722e74e7 https://github.com/galaxyproject/galaxy/commit/7e08ba6f19346668350d358ee4eb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/path/__init__.py Log Message: ----------- Rework in_directory fix to move realpath expansion into galaxy.util. Commit: e3e28ddc2dac1c4faaa45a9764abc7970129beb3 https://github.com/galaxyproject/galaxy/commit/e3e28ddc2dac1c4faaa45a9764ab… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/path/__init__.py Log Message: ----------- Merge pull request #4856 from jmchilton/release_16.07_fix_in_directory [16.07] Fix galaxy.util.in_directory()... Commit: 90289b6116c6a6ba1f6f0b4cbdee059003f916a3 https://github.com/galaxyproject/galaxy/commit/90289b6116c6a6ba1f6f0b4cbdee… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/path/ntpath.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: a7bf1601a1ad34e5896978e1bce9c8081aafbb05 https://github.com/galaxyproject/galaxy/commit/a7bf1601a1ad34e5896978e1bce9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/path/ntpath.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Commit: 20621b7d09443fc80c8326d91bdd204decb80b81 https://github.com/galaxyproject/galaxy/commit/20621b7d09443fc80c8326d91bdd… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/path/ntpath.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Commit: 986031bf190b82317cf687ed7e82ebd6b2646957 https://github.com/galaxyproject/galaxy/commit/986031bf190b82317cf687ed7e82… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/path/ntpath.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Conflicts: lib/galaxy/webapps/galaxy/controllers/library_common.py Commit: 1baed58e1e7c813e6a87b5a83883c5940a78035d https://github.com/galaxyproject/galaxy/commit/1baed58e1e7c813e6a87b5a83883… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- Backport fix for E201 and E202 errors >From commit 9b4de72ca68afc2353beff333775422039baae25 Compare: https://github.com/galaxyproject/galaxy/compare/01b244a81043...1baed58e1e7c

1 0

[galaxyproject/galaxy] 9791dd: Fix regressions in library API
by GitHub 25 Oct '17

25 Oct '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 9791dd22d4d9084989cafa3498ae313dd4cd13f0 https://github.com/galaxyproject/galaxy/commit/9791dd22d4d9084989cafa3498ae… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M lib/galaxy/util/path/ntpath.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Fix regressions in library API Introduced in commit 93a8bfc7cb5e9c3395c5057910ec39d68ad787b4 Commit: a4a8f155376119277df2cfebd13376e919873c4f https://github.com/galaxyproject/galaxy/commit/a4a8f155376119277df2cfebd133… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M lib/galaxy/util/path/ntpath.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Merge pull request #4854 from nsoranzo/release_16.07_fix_test_regressions [16.07] Fix regressions in library API Commit: 899b0d806808d29291bf132a8c9e45df31fc28e1 https://github.com/galaxyproject/galaxy/commit/899b0d806808d29291bf132a8c9e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M lib/galaxy/util/path/__init__.py Log Message: ----------- Fix galaxy.util.in_directory() - broken because it takes realpath of just one argument. Easy to see on Mac OS X since /tmp isn't really /tmp for instance: ``` % touch /tmp/moo % python >>> import galaxy.util >>> galaxy.util.in_directory("/tmp/moo", "/tmp/moo") False ``` ... and this is why the Travis tests are failing under Mac OS X. Broken with 93a8bfc7cb5e9c3395c5057910ec39d68ad787b4. Commit: 4b5dc399b934542092bfe66c3c4e03acc3980d49 https://github.com/galaxyproject/galaxy/commit/4b5dc399b934542092bfe66c3c4e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add basic test for in_directory. Commit: fcb23eb8f878700bfd77384ef679a569c59f7a62 https://github.com/galaxyproject/galaxy/commit/fcb23eb8f878700bfd77384ef679… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Some documentation to clarify discussion on #4856. Commit: 95f8f48416c5a4d2590120e965cf9714c752ed61 https://github.com/galaxyproject/galaxy/commit/95f8f48416c5a4d2590120e965cf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/path/__init__.py Log Message: ----------- Doc fix thanks to @nsoranzo. Commit: 7e08ba6f19346668350d358ee4eb01ef722e74e7 https://github.com/galaxyproject/galaxy/commit/7e08ba6f19346668350d358ee4eb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/path/__init__.py Log Message: ----------- Rework in_directory fix to move realpath expansion into galaxy.util. Commit: e3e28ddc2dac1c4faaa45a9764abc7970129beb3 https://github.com/galaxyproject/galaxy/commit/e3e28ddc2dac1c4faaa45a9764ab… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/path/__init__.py Log Message: ----------- Merge pull request #4856 from jmchilton/release_16.07_fix_in_directory [16.07] Fix galaxy.util.in_directory()... Commit: 90289b6116c6a6ba1f6f0b4cbdee059003f916a3 https://github.com/galaxyproject/galaxy/commit/90289b6116c6a6ba1f6f0b4cbdee… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/path/ntpath.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: a7bf1601a1ad34e5896978e1bce9c8081aafbb05 https://github.com/galaxyproject/galaxy/commit/a7bf1601a1ad34e5896978e1bce9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/path/ntpath.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Commit: 20621b7d09443fc80c8326d91bdd204decb80b81 https://github.com/galaxyproject/galaxy/commit/20621b7d09443fc80c8326d91bdd… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/path/ntpath.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Compare: https://github.com/galaxyproject/galaxy/compare/b35fe934d424...20621b7d0944

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[galaxyproject/galaxy] 9791dd: Fix regressions in library API
by GitHub 25 Oct '17

25 Oct '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 9791dd22d4d9084989cafa3498ae313dd4cd13f0 https://github.com/galaxyproject/galaxy/commit/9791dd22d4d9084989cafa3498ae… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M lib/galaxy/util/path/ntpath.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Fix regressions in library API Introduced in commit 93a8bfc7cb5e9c3395c5057910ec39d68ad787b4 Commit: a4a8f155376119277df2cfebd13376e919873c4f https://github.com/galaxyproject/galaxy/commit/a4a8f155376119277df2cfebd133… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M lib/galaxy/util/path/ntpath.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Merge pull request #4854 from nsoranzo/release_16.07_fix_test_regressions [16.07] Fix regressions in library API Commit: 899b0d806808d29291bf132a8c9e45df31fc28e1 https://github.com/galaxyproject/galaxy/commit/899b0d806808d29291bf132a8c9e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M lib/galaxy/util/path/__init__.py Log Message: ----------- Fix galaxy.util.in_directory() - broken because it takes realpath of just one argument. Easy to see on Mac OS X since /tmp isn't really /tmp for instance: ``` % touch /tmp/moo % python >>> import galaxy.util >>> galaxy.util.in_directory("/tmp/moo", "/tmp/moo") False ``` ... and this is why the Travis tests are failing under Mac OS X. Broken with 93a8bfc7cb5e9c3395c5057910ec39d68ad787b4. Commit: 4b5dc399b934542092bfe66c3c4e03acc3980d49 https://github.com/galaxyproject/galaxy/commit/4b5dc399b934542092bfe66c3c4e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add basic test for in_directory. Commit: fcb23eb8f878700bfd77384ef679a569c59f7a62 https://github.com/galaxyproject/galaxy/commit/fcb23eb8f878700bfd77384ef679… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Some documentation to clarify discussion on #4856. Commit: 95f8f48416c5a4d2590120e965cf9714c752ed61 https://github.com/galaxyproject/galaxy/commit/95f8f48416c5a4d2590120e965cf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/path/__init__.py Log Message: ----------- Doc fix thanks to @nsoranzo. Commit: 7e08ba6f19346668350d358ee4eb01ef722e74e7 https://github.com/galaxyproject/galaxy/commit/7e08ba6f19346668350d358ee4eb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/path/__init__.py Log Message: ----------- Rework in_directory fix to move realpath expansion into galaxy.util. Commit: e3e28ddc2dac1c4faaa45a9764abc7970129beb3 https://github.com/galaxyproject/galaxy/commit/e3e28ddc2dac1c4faaa45a9764ab… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/path/__init__.py Log Message: ----------- Merge pull request #4856 from jmchilton/release_16.07_fix_in_directory [16.07] Fix galaxy.util.in_directory()... Commit: 90289b6116c6a6ba1f6f0b4cbdee059003f916a3 https://github.com/galaxyproject/galaxy/commit/90289b6116c6a6ba1f6f0b4cbdee… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/path/ntpath.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: a7bf1601a1ad34e5896978e1bce9c8081aafbb05 https://github.com/galaxyproject/galaxy/commit/a7bf1601a1ad34e5896978e1bce9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/path/ntpath.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Compare: https://github.com/galaxyproject/galaxy/compare/c4855af7d516...a7bf1601a1ad

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[galaxyproject/galaxy] 9791dd: Fix regressions in library API
by GitHub 25 Oct '17

25 Oct '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 9791dd22d4d9084989cafa3498ae313dd4cd13f0 https://github.com/galaxyproject/galaxy/commit/9791dd22d4d9084989cafa3498ae… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M lib/galaxy/util/path/ntpath.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Fix regressions in library API Introduced in commit 93a8bfc7cb5e9c3395c5057910ec39d68ad787b4 Commit: a4a8f155376119277df2cfebd13376e919873c4f https://github.com/galaxyproject/galaxy/commit/a4a8f155376119277df2cfebd133… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M lib/galaxy/util/path/ntpath.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Merge pull request #4854 from nsoranzo/release_16.07_fix_test_regressions [16.07] Fix regressions in library API Commit: 899b0d806808d29291bf132a8c9e45df31fc28e1 https://github.com/galaxyproject/galaxy/commit/899b0d806808d29291bf132a8c9e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M lib/galaxy/util/path/__init__.py Log Message: ----------- Fix galaxy.util.in_directory() - broken because it takes realpath of just one argument. Easy to see on Mac OS X since /tmp isn't really /tmp for instance: ``` % touch /tmp/moo % python >>> import galaxy.util >>> galaxy.util.in_directory("/tmp/moo", "/tmp/moo") False ``` ... and this is why the Travis tests are failing under Mac OS X. Broken with 93a8bfc7cb5e9c3395c5057910ec39d68ad787b4. Commit: 4b5dc399b934542092bfe66c3c4e03acc3980d49 https://github.com/galaxyproject/galaxy/commit/4b5dc399b934542092bfe66c3c4e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add basic test for in_directory. Commit: fcb23eb8f878700bfd77384ef679a569c59f7a62 https://github.com/galaxyproject/galaxy/commit/fcb23eb8f878700bfd77384ef679… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Some documentation to clarify discussion on #4856. Commit: 95f8f48416c5a4d2590120e965cf9714c752ed61 https://github.com/galaxyproject/galaxy/commit/95f8f48416c5a4d2590120e965cf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/path/__init__.py Log Message: ----------- Doc fix thanks to @nsoranzo. Commit: 7e08ba6f19346668350d358ee4eb01ef722e74e7 https://github.com/galaxyproject/galaxy/commit/7e08ba6f19346668350d358ee4eb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/path/__init__.py Log Message: ----------- Rework in_directory fix to move realpath expansion into galaxy.util. Commit: e3e28ddc2dac1c4faaa45a9764abc7970129beb3 https://github.com/galaxyproject/galaxy/commit/e3e28ddc2dac1c4faaa45a9764ab… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/path/__init__.py Log Message: ----------- Merge pull request #4856 from jmchilton/release_16.07_fix_in_directory [16.07] Fix galaxy.util.in_directory()... Commit: 90289b6116c6a6ba1f6f0b4cbdee059003f916a3 https://github.com/galaxyproject/galaxy/commit/90289b6116c6a6ba1f6f0b4cbdee… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/path/ntpath.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Compare: https://github.com/galaxyproject/galaxy/compare/dda175dbf088...90289b6116c6

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[galaxyproject/galaxy] 899b0d: Fix galaxy.util.in_directory() - broken because it...
by GitHub 25 Oct '17

25 Oct '17

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 899b0d806808d29291bf132a8c9e45df31fc28e1 https://github.com/galaxyproject/galaxy/commit/899b0d806808d29291bf132a8c9e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M lib/galaxy/util/path/__init__.py Log Message: ----------- Fix galaxy.util.in_directory() - broken because it takes realpath of just one argument. Easy to see on Mac OS X since /tmp isn't really /tmp for instance: ``` % touch /tmp/moo % python >>> import galaxy.util >>> galaxy.util.in_directory("/tmp/moo", "/tmp/moo") False ``` ... and this is why the Travis tests are failing under Mac OS X. Broken with 93a8bfc7cb5e9c3395c5057910ec39d68ad787b4. Commit: 4b5dc399b934542092bfe66c3c4e03acc3980d49 https://github.com/galaxyproject/galaxy/commit/4b5dc399b934542092bfe66c3c4e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add basic test for in_directory. Commit: fcb23eb8f878700bfd77384ef679a569c59f7a62 https://github.com/galaxyproject/galaxy/commit/fcb23eb8f878700bfd77384ef679… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Some documentation to clarify discussion on #4856. Commit: 95f8f48416c5a4d2590120e965cf9714c752ed61 https://github.com/galaxyproject/galaxy/commit/95f8f48416c5a4d2590120e965cf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/path/__init__.py Log Message: ----------- Doc fix thanks to @nsoranzo. Commit: 7e08ba6f19346668350d358ee4eb01ef722e74e7 https://github.com/galaxyproject/galaxy/commit/7e08ba6f19346668350d358ee4eb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/path/__init__.py Log Message: ----------- Rework in_directory fix to move realpath expansion into galaxy.util. Commit: e3e28ddc2dac1c4faaa45a9764abc7970129beb3 https://github.com/galaxyproject/galaxy/commit/e3e28ddc2dac1c4faaa45a9764ab… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/path/__init__.py Log Message: ----------- Merge pull request #4856 from jmchilton/release_16.07_fix_in_directory [16.07] Fix galaxy.util.in_directory()... Compare: https://github.com/galaxyproject/galaxy/compare/a4a8f1553761...e3e28ddc2dac

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[galaxyproject/galaxy] f67376: expose state, stdout, stderr, uuid in the API
by GitHub 25 Oct '17

25 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f6737618e319b78f874e938c5e68ad70cd7ba746 https://github.com/galaxyproject/galaxy/commit/f6737618e319b78f874e938c5e68… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-20 (Fri, 20 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/style/less/library.less M lib/galaxy/managers/library_datasets.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-libraryrow-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- expose state, stdout, stderr, uuid in the API fix few bugs and UI/UX glitches Commit: 7e667170cd575db5d518efb1335c87eaa697591e https://github.com/galaxyproject/galaxy/commit/7e667170cd575db5d518efb1335c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M lib/galaxy/managers/library_datasets.py Log Message: ----------- optimize the admin query Commit: 0f5927b628eabd8ed82496a65d7eaac46cd3ef1e https://github.com/galaxyproject/galaxy/commit/0f5927b628eabd8ed82496a65d7e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/style/less/library.less M lib/galaxy/managers/library_datasets.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-libraryrow-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Merge pull request #4839 from martenson/library-expose-state expose state, stdout, stderr, uuid in the library API Compare: https://github.com/galaxyproject/galaxy/compare/a1f0895c927e...0f5927b628ea

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[galaxyproject/galaxy] f8bbc4: Remove sample request links from admin panel
by GitHub 25 Oct '17

25 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f8bbc42167d249e2dcb3130e795dd5e0b384df61 https://github.com/galaxyproject/galaxy/commit/f8bbc42167d249e2dcb3130e795d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-30 (Wed, 30 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: ----------- Remove sample request links from admin panel Commit: a5fab9f67de730bae6ff85e3a579bbbc1b22edcb https://github.com/galaxyproject/galaxy/commit/a5fab9f67de730bae6ff85e3a579… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- Do not serialize if a user has requests Commit: f9e8b4f2ad4cf3d1cb95fce327fda79a2a13e41e https://github.com/galaxyproject/galaxy/commit/f9e8b4f2ad4cf3d1cb95fce327fd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: R lib/galaxy/webapps/galaxy/controllers/external_service.py R lib/galaxy/webapps/galaxy/controllers/external_services.py R lib/galaxy/webapps/galaxy/controllers/request_type.py R lib/galaxy/webapps/galaxy/controllers/requests.py R lib/galaxy/webapps/galaxy/controllers/requests_admin.py R lib/galaxy/webapps/galaxy/controllers/requests_common.py Log Message: ----------- Remove controller endpoints for requests and external services Commit: 413a07878e751497ef39340736f2fa8a3a40c803 https://github.com/galaxyproject/galaxy/commit/413a07878e751497ef39340736f2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: R templates/admin/external_service/common.mako R templates/admin/external_service/create_external_service.mako R templates/admin/external_service/edit_external_service.mako R templates/admin/external_service/grid.mako R templates/admin/external_service/reload_external_service_types.mako R templates/admin/external_service/view_external_service.mako R templates/admin/request_type/common.mako R templates/admin/request_type/create_request_type.mako R templates/admin/request_type/edit_request_type.mako R templates/admin/request_type/grid.mako R templates/admin/request_type/request_type_permissions.mako R templates/admin/request_type/view_request_type.mako R templates/admin/requests/grid.mako R templates/admin/requests/reject.mako R templates/admin/requests/rename_datasets.mako R templates/admin/requests/sample_datasets_grid.mako R templates/admin/requests/view_sample_dataset.mako Log Message: ----------- Remove admin makos for requests and external services Commit: 3b4c124cccf1e343cc075741e93acad30577d934 https://github.com/galaxyproject/galaxy/commit/3b4c124cccf1e343cc075741e93a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: R templates/webapps/galaxy/external_services/generic_jquery_grid.mako R templates/webapps/galaxy/external_services/generic_json.mako R templates/webapps/galaxy/external_services/json_common.mako R templates/webapps/galaxy/requests/common/add_samples.mako R templates/webapps/galaxy/requests/common/common.mako R templates/webapps/galaxy/requests/common/create_request.mako R templates/webapps/galaxy/requests/common/edit_basic_request_info.mako R templates/webapps/galaxy/requests/common/edit_samples.mako R templates/webapps/galaxy/requests/common/find_samples.mako R templates/webapps/galaxy/requests/common/index.mako R templates/webapps/galaxy/requests/common/sample_dataset_transfer_status.mako R templates/webapps/galaxy/requests/common/sample_datasets.mako R templates/webapps/galaxy/requests/common/sample_state.mako R templates/webapps/galaxy/requests/common/view_request.mako R templates/webapps/galaxy/requests/common/view_request_history.mako R templates/webapps/galaxy/requests/common/view_sample.mako R templates/webapps/galaxy/requests/common/view_sample_datasets.mako R templates/webapps/galaxy/requests/common/view_sample_history.mako R templates/webapps/galaxy/requests/find_samples_index.mako R templates/webapps/galaxy/requests/grid.mako R templates/webapps/galaxy/requests/index.mako Log Message: ----------- Remove user makos for requests and external services Commit: 82f5a4cff7da178af841aa9bcd69ec03e90f2c1a https://github.com/galaxyproject/galaxy/commit/82f5a4cff7da178af841aa9bcd69… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: A templates/webapps/galaxy/external_services/generic_jquery_grid.mako A templates/webapps/galaxy/external_services/generic_json.mako A templates/webapps/galaxy/external_services/json_common.mako Log Message: ----------- Leave makos used by external service result handlers in for now Commit: 6237eba32ffaef96e273186d13dbc7de32c2bb95 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lib/galaxy/datatypes/converters/bcf_to_bcf_uncompressed_converter.xml A lib/galaxy/datatypes/converters/bcf_uncompressed_to_bcf_converter.xml M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/1.bcf A lib/galaxy/datatypes/test/1.bcf_uncompressed M lib/galaxy/web/framework/base.py R lib/galaxy/webapps/galaxy/controllers/mobile.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/workflow/modules.py R static/jqtouch/img/backButton.png R static/jqtouch/img/back_button.png R static/jqtouch/img/back_button_clicked.png R static/jqtouch/img/bg_row.gif R static/jqtouch/img/bg_row_select.gif R static/jqtouch/img/blueButton.png R static/jqtouch/img/button.png R static/jqtouch/img/button_clicked.png R static/jqtouch/img/cancel.png R static/jqtouch/img/chevron.png R static/jqtouch/img/chevron_select.png R static/jqtouch/img/grayButton.png R static/jqtouch/img/header.gif R static/jqtouch/img/listGroup.png R static/jqtouch/img/loading.gif R static/jqtouch/img/pinstripes.png R static/jqtouch/img/selection.png R static/jqtouch/img/thumb.png R static/jqtouch/img/toggle.png R static/jqtouch/img/toggleOn.png R static/jqtouch/img/toolButton.png R static/jqtouch/img/toolbar.gif R static/jqtouch/img/toolbar.png R static/jqtouch/img/whiteButton.png R static/jqtouch/jqtouch.css M static/maps/mvc/tool/tools.js.map M static/maps/mvc/ui/ui-select-content.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/tool/tools.js M static/scripts/mvc/ui/ui-select-content.js M static/style/blue/base.css R static/style/blue/iphone.css M templates/webapps/galaxy/dataset/copy_view.mako R templates/webapps/galaxy/mobile/dataset/detail.mako R templates/webapps/galaxy/mobile/dataset/peek.mako R templates/webapps/galaxy/mobile/form.mako R templates/webapps/galaxy/mobile/history/detail.mako R templates/webapps/galaxy/mobile/history/list.mako R templates/webapps/galaxy/mobile/index.mako R templates/webapps/galaxy/mobile/manage_library.mako R templates/webapps/galaxy/mobile/settings.mako M test/api/test_jobs.py M test/functional/tools/sample_datatypes_conf.xml A test/selenium_tests/test_published_histories_grid.py Log Message: ----------- Merge branch 'dev' into remove_samples_000 Commit: ecf5031eef6b591f81a5d799955347f194b0df47 https://github.com/galaxyproject/galaxy/commit/ecf5031eef6b591f81a5d7999553… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/forms.py Log Message: ----------- Remove unused library Commit: c6c7cb855ae579bb1d8a338f526d2231a8ca9c6a https://github.com/galaxyproject/galaxy/commit/c6c7cb855ae579bb1d8a338f526d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M test/unit/managers/test_UserManager.py Log Message: ----------- Fix failing test Commit: ce3e2ebf7db681b8611b47c0c29c121c511ebe02 https://github.com/galaxyproject/galaxy/commit/ce3e2ebf7db681b8611b47c0c29c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-13 (Wed, 13 Sep 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/docker-compose.yml M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/user/user-preferences.js A client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/base.less M client/galaxy/style/less/library.less M config/datatypes_conf.xml.sample M config/dependency_resolvers_conf.xml.sample M config/error_report.yml.sample M config/galaxy.ini.sample A config/lmod_modules_mapping.yml.sample A 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lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/xml_util.py M scripts/tool_shed/build_ts_whoosh_index.py M static/maps/layout/page.js.map M static/maps/mvc/grid/grid-shared.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/history-list.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/tag.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/user/user-preferences.js.map A static/maps/mvc/workflow/workflow-model.js.map M 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static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tag.js M static/scripts/mvc/tours.js M static/scripts/mvc/user/user-preferences.js A static/scripts/mvc/workflow/workflow-model.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-terminals.js M static/scripts/mvc/workflow/workflow.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/style/blue/base.css M static/style/blue/library.css M templates/webapps/galaxy/workflow/editor.mako A test-data/joiner_header_in1.tab A test-data/joiner_header_in2.tab A test-data/joiner_out1.bed A test-data/joiner_out2.bed A test-data/joiner_out3.bed A test-data/joiner_out4.bed A test-data/joiner_out5.tab A test-data/joiner_out6.tab A test-data/joiner_out7.tab M test/api/test_histories.py M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/api.py M test/base/driver_util.py M test/base/interactor.py M test/base/populators.py R test/base/test_db_util.py A test/base/testcase.py M test/base/tool_shed_util.py R test/base/twilltestcase.py R test/functional/database_contexts.py R test/functional/test_library_templates.py M test/functional/test_toolbox.py M test/functional/tools/composite.xml M test/functional/tools/composite_output.xml M test/functional/tools/composite_output_tests.xml M test/functional/tools/metadata.xml A test/functional/twilltestcase.py M test/galaxy_selenium/driver_factory.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/sizzle.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/framework.py M test/selenium_tests/test_history_panel.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_login.py M test/selenium_tests/test_published_histories_grid.py A test/selenium_tests/test_saved_histories.py A test/selenium_tests/test_sizzle_loading.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py M test/shed_functional/base/test_db_util.py M test/shed_functional/base/twilltestcase.py M test/unit/tools/test_tool_deps.py M tools/data_source/upload.py M tools/filters/join.py M tools/filters/joiner.xml M tools/sr_assembly/velvetg.xml Log Message: ----------- Merge branch 'dev' into remove_samples_000 Commit: 9045e3fb4eb3023285fe16a55e06e3610babf89f https://github.com/galaxyproject/galaxy/commit/9045e3fb4eb3023285fe16a55e06… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/toolshed/scripts/mvc/groups/group-list-view.js M lib/galaxy/app.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/evaluation.py M lib/galaxy_ext/metadata/set_metadata.py M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js Log Message: ----------- Merge branch 'dev' into remove_samples_000 Commit: 7ea5f3a3a27f4fbfbd90606405eec0d60db5b106 https://github.com/galaxyproject/galaxy/commit/7ea5f3a3a27f4fbfbd90606405ee… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-18 (Mon, 18 Sep 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/layout/menu.js Log Message: ----------- Remove lab tab from masthead Commit: ebbe5a103920c5581bc2b1332a5552002867abce https://github.com/galaxyproject/galaxy/commit/ebbe5a103920c5581bc2b1332a55… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-18 (Mon, 18 Sep 2017) Changed paths: M .travis.yml M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-list-view.js M create_db.sh M extract_dataset_parts.sh M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webhooks/__init__.py M manage_db.sh M manage_tools.sh M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/user/user-custom-builds.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/base/controlled-fetch-collection.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/user/user-custom-builds.js M static/toolshed/scripts/mvc/groups/group-detail-view.js M static/toolshed/scripts/mvc/groups/group-list-view.js M templates/webapps/galaxy/admin/sanitize_whitelist.mako Log Message: ----------- Merge branch 'dev' into remove_samples_000 Commit: 1494207a0decfdd18c0f951a8480372e06bc53f1 https://github.com/galaxyproject/galaxy/commit/1494207a0decfdd18c0f951a8480… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M client/galaxy/style/less/upload.less M lib/galaxy/config.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/managers/libraries.py M lib/galaxy/model/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cache.py M lib/galaxy/tools/loader.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parser/factory.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/util/xml_macros.py M lib/galaxy/version.py A lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py R lib/galaxy/web/base/interactive_environments.py R lib/galaxy/web/base/pluginframework.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_watchers.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/tools/tool_validator.py M static/style/blue/base.css R templates/admin/tool_shed_repository/browse_category.mako R templates/export_base.mako R templates/rss.mako R templates/webapps/galaxy/admin/toolsheds.mako M test/api/test_dataset_collections.py M test/base/driver_util.py M test/base/populators.py A test/integration/test_data_manager_table_reload.py M test/integration/test_resolvers.py A test/integration/tool_sheds_conf.xml M test/selenium_tests/framework.py A test/selenium_tests/test_custom_builds.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py R test/unit/web/base/__init__.py R test/unit/web/base/test_HookPluginManager.py R test/unit/web/base/test_PageServingPluginManager.py R test/unit/web/base/test_PluginManager.py M tools/extract/liftOver_wrapper.xml Log Message: ----------- Merge branch 'dev' into remove_samples_000 Commit: 81f111c720954fd54d54b7604e7be6fd3e4aeeb9 https://github.com/galaxyproject/galaxy/commit/81f111c720954fd54d54b7604e7b… Author: guerler <aysam.guerler(a)gmail.com> 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templates/admin/external_service/edit_external_service.mako R templates/admin/external_service/grid.mako R templates/admin/external_service/reload_external_service_types.mako R templates/admin/external_service/view_external_service.mako R templates/admin/request_type/common.mako R templates/admin/request_type/create_request_type.mako R templates/admin/request_type/edit_request_type.mako R templates/admin/request_type/grid.mako R templates/admin/request_type/request_type_permissions.mako R templates/admin/request_type/view_request_type.mako R templates/admin/requests/grid.mako R templates/admin/requests/reject.mako R templates/admin/requests/rename_datasets.mako R templates/admin/requests/sample_datasets_grid.mako R templates/admin/requests/view_sample_dataset.mako R templates/webapps/galaxy/requests/common/add_samples.mako R templates/webapps/galaxy/requests/common/common.mako R templates/webapps/galaxy/requests/common/create_request.mako R templates/webapps/galaxy/requests/common/edit_basic_request_info.mako R templates/webapps/galaxy/requests/common/edit_samples.mako R templates/webapps/galaxy/requests/common/find_samples.mako R templates/webapps/galaxy/requests/common/index.mako R templates/webapps/galaxy/requests/common/sample_dataset_transfer_status.mako R templates/webapps/galaxy/requests/common/sample_datasets.mako R templates/webapps/galaxy/requests/common/sample_state.mako R templates/webapps/galaxy/requests/common/view_request.mako R templates/webapps/galaxy/requests/common/view_request_history.mako R templates/webapps/galaxy/requests/common/view_sample.mako R templates/webapps/galaxy/requests/common/view_sample_datasets.mako R templates/webapps/galaxy/requests/common/view_sample_history.mako R templates/webapps/galaxy/requests/find_samples_index.mako R templates/webapps/galaxy/requests/grid.mako R templates/webapps/galaxy/requests/index.mako M test/unit/managers/test_UserManager.py Log Message: ----------- 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test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_custom_builds.py M test/selenium_tests/test_history_options.py M test/selenium_tests/test_history_panel.py A test/selenium_tests/test_jupyter.py A test/selenium_tests/test_library_contents.py A test/selenium_tests/test_library_landing.py A test/selenium_tests/test_navigates_galaxy.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_registration.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py M test/unit/test_security_helper.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/filters/joiner.xml Log Message: ----------- Merge branch 'dev' into remove_samples_000 Commit: 0d5d2aea830a44a7c6d805d5f9fee0eebe69f0ae https://github.com/galaxyproject/galaxy/commit/0d5d2aea830a44a7c6d805d5f9fe… 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lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/workflow/modules.py M lib/galaxy_ext/metadata/set_metadata.py M run.sh M run_tests.sh M setup.cfg M static/maps/layout/router.js.map M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-view.js.map A static/maps/mvc/lazy/lazy-limited.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/upload/collection/collection-view.js.map M static/maps/mvc/upload/composite/composite-view.js.map M 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test/selenium_tests/test_history_options.py M test/selenium_tests/test_history_panel.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_library_contents.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_registration.py M test/selenium_tests/test_saved_histories.py M tox.ini Log Message: ----------- Merge branch 'dev' into remove_samples_000 Commit: 3a06f76254497674c627931a560c7f3d3241d547 https://github.com/galaxyproject/galaxy/commit/3a06f76254497674c627931a560c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M .ci/flake8_lint_include_list.txt R .ci/flake8_py3_wrapper.sh M .ci/py3_sources.txt M .gitignore M Makefile A client/.babelrc M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/login.js M 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static/maps/ui/filter-control.js.map M static/maps/ui/hoverhighlight.js.map M static/maps/ui/loading-indicator.js.map M static/maps/ui/mode-button.js.map M static/maps/ui/pagination.js.map M static/maps/ui/peek-column-selector.js.map M static/maps/ui/popupmenu.js.map M static/maps/ui/scroll-panel.js.map M static/maps/ui/search-input.js.map M static/maps/utils/add-logging.js.map M static/maps/utils/ajax-queue.js.map M static/maps/utils/async-save-text.js.map M static/maps/utils/config.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/levenshtein.js.map M static/maps/utils/localization.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/natural-sort.js.map M static/maps/utils/query-string-parsing.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/maps/viz/bbi-data-manager.js.map M static/maps/viz/circster.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/sweepster.js.map M 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test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/filters/bed_to_gff_converter.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_exon_bed.xml M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/metag_tools/shrimp_wrapper.py M tools/sr_assembly/velvetg_wrapper.py M tox.ini Log Message: ----------- Merge branch 'dev' into remove_samples_000 Commit: 454e00d9bf4b3ec97f005373a801765ac8ed7483 https://github.com/galaxyproject/galaxy/commit/454e00d9bf4b3ec97f005373a801… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M static/scripts/libs/d3.js M static/scripts/libs/jquery/jquery.complexify.js M static/scripts/libs/jquery/jquery.cookie.js M static/scripts/libs/jquery/jquery.js M static/scripts/libs/jquery/jquery.migrate.js M static/scripts/libs/jquery/jquery.mousewheel.js M static/scripts/libs/raven.js M static/scripts/libs/require.js M static/scripts/libs/underscore.js Log Message: ----------- Repack scripts Commit: a123bee6cf58f1cd9880cccb575b1dcfbccfec9d https://github.com/galaxyproject/galaxy/commit/a123bee6cf58f1cd9880cccb575b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-18 (Wed, 18 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-parameters.js M config/datatypes_conf.xml.sample M config/plugins/webhooks/demo/tour_generator/static/script.js M doc/source/slideshow/architecture/galaxy_architecture.md A lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/jobs/handler.py M lib/galaxy_ext/metadata/set_metadata.py M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/form/form-parameters.js.map 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/libs/backbone.js M static/scripts/libs/bibtex.js M static/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Merge branch 'dev' into remove_samples_000 Commit: 7c3fdbe1a5a1c8b59c80ce19434fa0f22ec46f00 https://github.com/galaxyproject/galaxy/commit/7c3fdbe1a5a1c8b59c80ce19434f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M config/galaxy.ini.sample M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M lib/galaxy/config.py M lib/galaxy/containers/docker_model.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/__init__.py A lib/galaxy/util/path/__init__.py A lib/galaxy/util/path/ntpath.py A lib/galaxy/util/path/posixpath.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/managers/groups.py M scripts/cleanup_datasets/pgcleanup.py M static/maps/galaxy.interactive_environments.js.map A static/maps/libs/jquery/jquery.complexify.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/galaxy.interactive_environments.js M tools/data_source/data_source.py Log Message: ----------- Merge branch 'dev' into remove_samples_000 Commit: 08913b6f74d19b33ff6ea68b34664652b780c864 https://github.com/galaxyproject/galaxy/commit/08913b6f74d19b33ff6ea68b3466… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- repack Commit: df658082ff36c8ea920b8cb952117ecccffbaeae https://github.com/galaxyproject/galaxy/commit/df658082ff36c8ea920b8cb95211… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M templates/webapps/galaxy/admin/center.mako Log Message: ----------- remove the mentionof sample tracking from admin page Commit: d11ed538c679b2aec889ed8e64153f7c2c1d4176 https://github.com/galaxyproject/galaxy/commit/d11ed538c679b2aec889ed8e6415… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/api/requests.py M lib/galaxy/webapps/galaxy/api/samples.py Log Message: ----------- tie sample tracking api controllers functionality to config introduce enable_legacy_sample_tracking_api config option that controls that disable by default Commit: 8f6e5eb6f578dd9141b511f1d64aa350ee8f9663 https://github.com/galaxyproject/galaxy/commit/8f6e5eb6f578dd9141b511f1d64a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M .ci/flake8_lint_include_list.txt M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/utils/utils.js M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/qualityscore.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/datatypes/tracks.py M lib/galaxy/datatypes/util/generic_util.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/godocker.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/jobs/runners/state_handler_factory.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/jobs/runners/util/cli/job/slurm.py M lib/galaxy/jobs/runners/util/cli/job/torque.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/context.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/check.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py M lib/galaxy/model/migrate/versions/0061_tasks.py M lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py M lib/galaxy/model/tool_shed_install/migrate/check.py M lib/galaxy/sample_tracking/external_service_types.py M lib/galaxy/sample_tracking/request_types.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/dictifiable.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/image_util.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/path/ntpath.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/error.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/galaxy/api/authenticate.py M lib/galaxy/webapps/galaxy/api/forms.py M lib/galaxy/webapps/galaxy/api/group_roles.py M lib/galaxy/webapps/galaxy/api/group_users.py M lib/galaxy/webapps/galaxy/api/groups.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/request_types.py M lib/galaxy/webapps/galaxy/api/requests.py M lib/galaxy/webapps/galaxy/api/roles.py M lib/galaxy/webapps/galaxy/api/samples.py M lib/galaxy/webapps/galaxy/api/tool_data.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_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/migrate/check.py M lib/galaxy_ext/metadata/set_metadata.py M lib/psyco_full.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/grids/util.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/admin_util.py M lib/tool_shed/util/basic_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/workflow_util.py M scripts/bootstrap_history.py M scripts/build_toolbox.py M scripts/check_galaxy.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/drmaa_external_runner.py M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/microbes/util.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py M scripts/rst2html.py M scripts/runtime_stats.py M scripts/tool_shed/migrate_tools_to_repositories.py M setup.cfg M static/maps/layout/page.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/utils/utils.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/layout/page.js M static/scripts/mvc/grid/grid-view.js M static/scripts/utils/utils.js R templates/admin/tool_shed_repository/repair_repository.mako M templates/admin/tool_shed_repository/repository_actions_menu.mako M test/base/testcase.py M test/functional/twilltestcase.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_1100_install_updated_repository_dependencies.py M test/shed_functional/functional/test_1430_repair_installed_repository.py M test/unit/tools/test_tool_deps.py M tools/data_source/data_source.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/evolution/codingSnps_filter.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_lav.py M tools/filters/bed_to_gff_converter.py M tools/filters/catWrapper.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff_to_bed_converter.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/sff_extract.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/genomespace/genomespace_importer.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/vcf_to_maf_customtrack.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/solid2fastq.py M tools/plotting/bar_chart.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py Log Message: ----------- Merge branch 'dev' into remove_samples_000 Commit: 52a566eb056f442e12fcdb79e655e183f1727dd8 https://github.com/galaxyproject/galaxy/commit/52a566eb056f442e12fcdb79e655… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/requests.py Log Message: ----------- Remove api dependency on web controller Commit: 8e9a7e86250ab015309e4fe43171918f33374403 https://github.com/galaxyproject/galaxy/commit/8e9a7e86250ab015309e4fe43171… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/requests.py Log Message: ----------- Remove unused import Commit: d3a6af5f71141eb01392788e87f993f21fe2d758 https://github.com/galaxyproject/galaxy/commit/d3a6af5f71141eb01392788e87f9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 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: ----------- Add legacy data libraries link Commit: 1e23a6397b2383c7b985a765f65b559b5bb6aa2b https://github.com/galaxyproject/galaxy/commit/1e23a6397b2383c7b985a765f65b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 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 M templates/webapps/galaxy/admin/center.mako Log Message: ----------- Fix order in center panel information view Commit: 3dd45099ba5a3a3f4f206553c122994d7746112e https://github.com/galaxyproject/galaxy/commit/3dd45099ba5a3a3f4f206553c122… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 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: ----------- Remove "Lab" from masthead Commit: a1f0895c927e759e30a59dcc1b40a4507eb1e82e https://github.com/galaxyproject/galaxy/commit/a1f0895c927e759e30a59dcc1b40… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/layout/menu.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/managers/users.py M lib/galaxy/webapps/galaxy/api/requests.py M lib/galaxy/webapps/galaxy/api/samples.py R lib/galaxy/webapps/galaxy/controllers/external_service.py R lib/galaxy/webapps/galaxy/controllers/external_services.py R lib/galaxy/webapps/galaxy/controllers/request_type.py R lib/galaxy/webapps/galaxy/controllers/requests.py R lib/galaxy/webapps/galaxy/controllers/requests_admin.py R lib/galaxy/webapps/galaxy/controllers/requests_common.py M static/maps/layout/menu.js.map M static/maps/libs/backbone.js.map M static/maps/libs/bibtex.js.map M static/maps/libs/d3.js.map M static/maps/libs/jquery/jquery.cookie.js.map M static/maps/libs/jquery/jquery.js.map M static/maps/libs/jquery/jquery.migrate.js.map M static/maps/libs/jquery/jquery.mousewheel.js.map M static/maps/libs/raven.js.map M static/maps/libs/require.js.map M static/maps/libs/underscore.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js R templates/admin/external_service/common.mako R templates/admin/external_service/create_external_service.mako R templates/admin/external_service/edit_external_service.mako R templates/admin/external_service/grid.mako R templates/admin/external_service/reload_external_service_types.mako R templates/admin/external_service/view_external_service.mako R templates/admin/request_type/common.mako R templates/admin/request_type/create_request_type.mako R templates/admin/request_type/edit_request_type.mako R templates/admin/request_type/grid.mako R templates/admin/request_type/request_type_permissions.mako R templates/admin/request_type/view_request_type.mako R templates/admin/requests/grid.mako R templates/admin/requests/reject.mako R templates/admin/requests/rename_datasets.mako R templates/admin/requests/sample_datasets_grid.mako R templates/admin/requests/view_sample_dataset.mako M templates/webapps/galaxy/admin/center.mako R templates/webapps/galaxy/requests/common/add_samples.mako R templates/webapps/galaxy/requests/common/common.mako R templates/webapps/galaxy/requests/common/create_request.mako R templates/webapps/galaxy/requests/common/edit_basic_request_info.mako R templates/webapps/galaxy/requests/common/edit_samples.mako R templates/webapps/galaxy/requests/common/find_samples.mako R templates/webapps/galaxy/requests/common/index.mako R templates/webapps/galaxy/requests/common/sample_dataset_transfer_status.mako R templates/webapps/galaxy/requests/common/sample_datasets.mako R templates/webapps/galaxy/requests/common/sample_state.mako R templates/webapps/galaxy/requests/common/view_request.mako R templates/webapps/galaxy/requests/common/view_request_history.mako R templates/webapps/galaxy/requests/common/view_sample.mako R templates/webapps/galaxy/requests/common/view_sample_datasets.mako R templates/webapps/galaxy/requests/common/view_sample_history.mako R templates/webapps/galaxy/requests/find_samples_index.mako R templates/webapps/galaxy/requests/grid.mako R templates/webapps/galaxy/requests/index.mako M test/unit/managers/test_UserManager.py Log Message: ----------- Merge pull request #4526 from guerler/remove_samples_000 Removes Sample request and External services makos/controllers Compare: https://github.com/galaxyproject/galaxy/compare/52b16ecd329d...a1f0895c927e

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[galaxyproject/usegalaxy-playbook] 6e63ec: Run dataset cleanup on Main
by GitHub 25 Oct '17

25 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6e63eccbc5fa5226e3a81173a257a0b5b20a09cf https://github.com/galaxyproject/usegalaxy-playbook/commit/6e63eccbc5fa5226… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M env/main/host_vars/galaxy-web-05.tacc.utexas.edu.yml Log Message: ----------- Run dataset cleanup on Main

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