October 2015 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] b6f378: remove test_map_over_two_collections_legacy as it ...
by GitHub 15 Oct '15

15 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b6f3783acd03b4979448ba51395af8e1fc605d27 https://github.com/galaxyproject/galaxy/commit/b6f3783acd03b4979448ba51395a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M test/api/test_tools.py Log Message: ----------- remove test_map_over_two_collections_legacy as it is obsolete Commit: e540c2cc7781c82d842103de1db9b1c38e7888a5 https://github.com/galaxyproject/galaxy/commit/e540c2cc7781c82d842103de1db9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M test/api/test_tools.py Log Message: ----------- Merge pull request #924 from martenson/remove-legacy-test remove test_map_over_two_collections_legacy as it is obsolete Compare: https://github.com/galaxyproject/galaxy/compare/6c7ebdbbcb6b...e540c2cc7781

1 0

[galaxyproject/usegalaxy-playbook] fa5668: Update Test and admin_users
by GitHub 15 Oct '15

15 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: fa5668b25e5ced931dea1062c1cf7b0689083244 https://github.com/galaxyproject/usegalaxy-playbook/commit/fa5668b25e5ced93… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M stage/group_vars/all.yml M stage/secret_vars/galaxyservers.yml Log Message: ----------- Update Test and admin_users

1 0

[galaxyproject/galaxy] 8cb894: Fix data library test case
by GitHub 15 Oct '15

15 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8cb894b34a162b4082a49b3c41df8e96dfedd04b https://github.com/galaxyproject/galaxy/commit/8cb894b34a162b4082a49b3c41df… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-12 (Mon, 12 Oct 2015) Changed paths: M test/api/test_tools.py Log Message: ----------- Fix data library test case Fix library data test case Commit: 6c7ebdbbcb6b9c93229d7586ddff133a03776271 https://github.com/galaxyproject/galaxy/commit/6c7ebdbbcb6b9c93229d7586ddff… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M test/api/test_tools.py Log Message: ----------- Merge pull request #898 from guerler/fix_library_test_000 Fix data library test case Compare: https://github.com/galaxyproject/galaxy/compare/296dab0588ba...6c7ebdbbcb6b

1 0

[galaxyproject/galaxy] a9c91d: reorder workflow inputs to top
by GitHub 15 Oct '15

15 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a9c91d3a5606dbcdc42d2181b3085d6b41d50a31 https://github.com/galaxyproject/galaxy/commit/a9c91d3a5606dbcdc42d2181b308… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M lib/galaxy/workflow/modules.py M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- reorder workflow inputs to top Commit: 296dab0588badfe7b9aba436988daf5e0872f384 https://github.com/galaxyproject/galaxy/commit/296dab0588badfe7b9aba436988d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M lib/galaxy/workflow/modules.py M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #912 from scholtalbers/reorder-workflow-controls Reorder workflow inputs to top Compare: https://github.com/galaxyproject/galaxy/compare/2d01cae6b200...296dab0588ba

1 0

[galaxyproject/galaxy] a74219: Fixes for switching history (standard as well as m...
by GitHub 14 Oct '15

14 Oct '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: a742198a36d700f299019ef8929a9dc55d58c17a https://github.com/galaxyproject/galaxy/commit/a742198a36d700f299019ef8929a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Fixes for switching history (standard as well as multiview) when using IE11. Intentionally minimal fix for 15.10, more comprehensive refactoring+solution forthcoming for dev. Commit: 11d17b3e7b305a28aaa0fb8392424dbb650e70d6 https://github.com/galaxyproject/galaxy/commit/11d17b3e7b305a28aaa0fb839242… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #920 from dannon/release_15.10 [15.10] IE11 history-stuck fix Compare: https://github.com/galaxyproject/galaxy/compare/cf59e8bd3c52...11d17b3e7b30

1 0

[galaxyproject/galaxy] 7a5e8f: Add check for HTTP_GX_SECRET
by GitHub 14 Oct '15

14 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7a5e8f7749db9ac1822a00d2e77b23279b72f719 https://github.com/galaxyproject/galaxy/commit/7a5e8f7749db9ac1822a00d2e77b… Author: Ryan <ngsbioinformatics(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Add check for HTTP_GX_SECRET If not provided, safe_str_cmp crashes and present debug trace log to user. Commit: 63e30dac5d4a6b4be5176464e6f744fbb51c900f https://github.com/galaxyproject/galaxy/commit/63e30dac5d4a6b4be5176464e6f7… Author: Ryan <ngsbioinformatics(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Removed trailing white space Commit: 100ed418e8f2361b5c83ab3dee9b318bec222a2d https://github.com/galaxyproject/galaxy/commit/100ed418e8f2361b5c83ab3dee9b… Author: Ryan <ngsbioinformatics(a)gmail.com> Date: 2015-10-03 (Sat, 03 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Update remoteuser.py removed empty lines Commit: 973e70103373d49e5100fb3262aae8df4fc5bc5e https://github.com/galaxyproject/galaxy/commit/973e70103373d49e5100fb3262aa… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Remove trailing whitespace Commit: e54df2e6ac4337265e9aba95c6e62d8e49eb5f48 https://github.com/galaxyproject/galaxy/commit/e54df2e6ac4337265e9aba95c6e6… Author: Ryan <ngsbioinformatics(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #2 from erasche/whitespace-fix-827 Remove trailing whitespace Commit: 2d01cae6b2002d966ede39bd435c35da4f3d9764 https://github.com/galaxyproject/galaxy/commit/2d01cae6b2002d966ede39bd435c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #827 from golharam/patch-2 Add check for HTTP_GX_SECRET Compare: https://github.com/galaxyproject/galaxy/compare/005561c22a40...2d01cae6b200

1 0

[galaxyproject/galaxy] 4cebca: Redo total disk calculation adjustments to be less...
by GitHub 14 Oct '15

14 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4cebca81c677a6692e22006468310d0e21195251 https://github.com/galaxyproject/galaxy/commit/4cebca81c677a6692e2200646831… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-12 (Mon, 12 Oct 2015) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M test/unit/test_galaxy_mapping.py Log Message: ----------- Redo total disk calculation adjustments to be less race condition-y. ... at least when finishing the job. Method should probably be used other places as well. Commit: b77496ec638e5e15f6cb8b1e83077fdf266634d2 https://github.com/galaxyproject/galaxy/commit/b77496ec638e5e15f6cb8b1e8307… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M lib/galaxy/managers/hdas.py M lib/galaxy/model/__init__.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M scripts/cleanup_datasets/cleanup_datasets.py Log Message: ----------- Update other quota manipulations to use the new user.adjust_quota_usage function. Commit: 3e5b91ceca04bc2ce040617a0ba17ab73d274469 https://github.com/galaxyproject/galaxy/commit/3e5b91ceca04bc2ce040617a0ba1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Remove duplicate func import Commit: c05315c7d38790b5de75f386fab06db0f241212d https://github.com/galaxyproject/galaxy/commit/c05315c7d38790b5de75f386fab0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/web/framework/webapp.py Log Message: ----------- Avoid overriding 'bytes' type with the local variable. Commit: 005561c22a40d74693318ccfd0c94e41bbd309e0 https://github.com/galaxyproject/galaxy/commit/005561c22a40d74693318ccfd0c9… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/hdas.py M lib/galaxy/model/__init__.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M scripts/cleanup_datasets/cleanup_datasets.py M test/unit/test_galaxy_mapping.py Log Message: ----------- Merge pull request #907 from dannon/quota_bugfix Quota bugfixes Compare: https://github.com/galaxyproject/galaxy/compare/977ef6b7c7c0...005561c22a40

1 0

[galaxyproject/galaxy] 4657ce: Add support for constructive solid geometry dataty...
by GitHub 14 Oct '15

14 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4657ce6f34ab16d1b4ab472cf3b7faf39086e572 https://github.com/galaxyproject/galaxy/commit/4657ce6f34ab16d1b4ab472cf3b7… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/constructive_solid_geometry.py Log Message: ----------- Add support for constructive solid geometry datatypes ply and vtk. Commit: 977ef6b7c7c0e8dc627333dca093dce0762b2888 https://github.com/galaxyproject/galaxy/commit/977ef6b7c7c0e8dc627333dca093… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/constructive_solid_geometry.py Log Message: ----------- Merge pull request #905 from gregvonkuster/dev Add support for constructive solid geometry datatypes ply and vtk. Compare: https://github.com/galaxyproject/galaxy/compare/744ed8cd4c80...977ef6b7c7c0

1 0

[galaxyproject/galaxy] 120ec6: Fix command quoting and remove size from text inpu...
by GitHub 14 Oct '15

14 Oct '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 120ec61264dadb90b0386e46bd4c33a2f6481c52 https://github.com/galaxyproject/galaxy/commit/120ec61264dadb90b0386e46bd4c… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M tools/filters/cutWrapper.xml Log Message: ----------- Fix command quoting and remove size from text input for Cut tool. Commit: cf59e8bd3c52f52ae717ca9755e6b10f48382b07 https://github.com/galaxyproject/galaxy/commit/cf59e8bd3c52f52ae717ca9755e6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M tools/filters/cutWrapper.xml Log Message: ----------- Merge pull request #913 from blankenberg/cut_15.10 [15.10] Fix command quoting and remove size from text input for Cut tool. Compare: https://github.com/galaxyproject/galaxy/compare/ee42fd053191...cf59e8bd3c52

1 0

[galaxyproject/galaxy] c64f27: Only return repository if it is not None ( This ha...
by GitHub 14 Oct '15

14 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c64f27e014ea4f79b45c2a7172ccee10edf11ec7 https://github.com/galaxyproject/galaxy/commit/c64f27e014ea4f79b45c2a7172cc… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-10-10 (Sat, 10 Oct 2015) Changed paths: M lib/tool_shed/galaxy_install/repair_repository_manager.py Log Message: ----------- Only return repository if it is not None ( This happends for the repository that we try to repair). Add the repository to be repaired to installed_repository list. Commit: 744ed8cd4c80c742d12762202f52795b56f0fcf0 https://github.com/galaxyproject/galaxy/commit/744ed8cd4c80c742d12762202f52… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M lib/tool_shed/galaxy_install/repair_repository_manager.py Log Message: ----------- Merge pull request #891 from mvdbeek/repair_repository_id_fix Only return repository if it is not None ( This happens for the repo… Compare: https://github.com/galaxyproject/galaxy/compare/6c95ef9d969a...744ed8cd4c80

1 0