Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: d2394aa172e2030c301f7b50863fb3d96664a2db https://github.com/galaxyproject/galaxy/commit/d2394aa172e2030c301f7b50863fb... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-07 (Mon, 07 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/async.py

Log Message: ----------- Merge pull request #4198 from fabio-cumbo/data-source-async

Async update: support to collections

Commit: d698d32ceb043fdb9820b68615748ca13e0825c8 https://github.com/galaxyproject/galaxy/commit/d698d32ceb043fdb9820b68615748... Author: guerler aysam.guerler@gmail.com Date: 2017-08-07 (Mon, 07 Aug 2017)

Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js

Log Message: ----------- Manage users and groups for role

Commit: 9ee062bd4622481165d4cb1e783454a49fcdd704 https://github.com/galaxyproject/galaxy/commit/9ee062bd4622481165d4cb1e78345... Author: guerler aysam.guerler@gmail.com Date: 2017-08-07 (Mon, 07 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Show current name and description when renaming roles

Commit: 183176a05c95e063a710ff469a368c463e18db2f https://github.com/galaxyproject/galaxy/commit/183176a05c95e063a710ff469a368... Author: guerler aysam.guerler@gmail.com Date: 2017-08-07 (Mon, 07 Aug 2017)

Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map

Log Message: ----------- Add create role form

Commit: 663c6c13975b01cf0472a083a68164d9bd010871 https://github.com/galaxyproject/galaxy/commit/663c6c13975b01cf0472a083a6816... Author: guerler aysam.guerler@gmail.com Date: 2017-08-07 (Mon, 07 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py R templates/admin/dataset_security/role/role.mako R templates/admin/dataset_security/role/role_create.mako R templates/admin/dataset_security/role/role_rename.mako A templates/webapps/tool_shed/admin/dataset_security/role/role.mako A templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako A templates/webapps/tool_shed/admin/dataset_security/role/role_rename.mako

Log Message: ----------- Fix boolean title, and move unused role makos to toolshed

Commit: e77fd47b034e6af5b19756bd778f5081332e7c85 https://github.com/galaxyproject/galaxy/commit/e77fd47b034e6af5b19756bd778f5... Author: guerler aysam.guerler@gmail.com Date: 2017-08-07 (Mon, 07 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Fix boolean handling

Commit: 419f3db64fb3614d5a70ed9a9eea8a260b6f5865 https://github.com/galaxyproject/galaxy/commit/419f3db64fb3614d5a70ed9a9eea8... Author: guerler aysam.guerler@gmail.com Date: 2017-08-07 (Mon, 07 Aug 2017)

Changed paths: M lib/tool_shed/util/admin_util.py

Log Message: ----------- Remove unused information feature for toolshed

Commit: 7b423e19c92868a6a3e7abee2a4ad6e92a03aad8 https://github.com/galaxyproject/galaxy/commit/7b423e19c92868a6a3e7abee2a4ad... Author: Brad Langhorst langhorst@neb.com Date: 2017-08-07 (Mon, 07 Aug 2017)

Changed paths: M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py

Log Message: ----------- Merge pull request #1 from dannon/library_tags

Swap two more spots initializing TagManagers to new session

Commit: c49e749534f76c8bb2d0ea8bb629a6ee236ff5cc https://github.com/galaxyproject/galaxy/commit/c49e749534f76c8bb2d0ea8bb629a... Author: guerler aysam.guerler@gmail.com Date: 2017-08-07 (Mon, 07 Aug 2017)

Changed paths: M lib/tool_shed/util/admin_util.py

Log Message: ----------- Fix user info link for toolshed

Commit: 733e225ec96b058dd159dda4e18ba1f7572573fd https://github.com/galaxyproject/galaxy/commit/733e225ec96b058dd159dda4e18ba... Author: guerler aysam.guerler@gmail.com Date: 2017-08-07 (Mon, 07 Aug 2017)

Changed paths: M client/galaxy/scripts/utils/query-string-parsing.js M static/maps/utils/query-string-parsing.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/query-string-parsing.js

Log Message: ----------- Fix message handling in user preference main view

Commit: a5d7c0fa84d8fe24fc94ac814b9f7502283de7c2 https://github.com/galaxyproject/galaxy/commit/a5d7c0fa84d8fe24fc94ac814b9f7... Author: guerler aysam.guerler@gmail.com Date: 2017-08-07 (Mon, 07 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/form/form-wrapper.js M static/maps/mvc/form/form-wrapper.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/form/form-wrapper.js

Log Message: ----------- Scroll to highlight message

Commit: 4b2eca373e936308b0550b9fabfc6494228b837a https://github.com/galaxyproject/galaxy/commit/4b2eca373e936308b0550b9fabfc6... Author: guerler aysam.guerler@gmail.com Date: 2017-08-07 (Mon, 07 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/api/users.py

Log Message: ----------- Remove duplicate roles from selection list

Commit: 5a8adbf8b77dc985353803a724fc4344dcbbdc79 https://github.com/galaxyproject/galaxy/commit/5a8adbf8b77dc985353803a724fc4... Author: guerler aysam.guerler@gmail.com Date: 2017-08-07 (Mon, 07 Aug 2017)

Changed paths: M doc/source/admin/special_topics/grt.rst M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/history.py R scripts/grt.py R scripts/grt.yml.sample A scripts/grt/export.py A scripts/grt/grt.yml.sample A scripts/grt/upload.py M test/api/test_tools.py A test/functional/tools/identifier_source.xml M test/functional/tools/samples_tool_conf.xml A test/unit/test_remote_shell.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py M tox.ini

Log Message: ----------- Merge branch 'remove_duplicates' into admin_grid_roles

Commit: 305f9f94c04579a8414e0034e0ec90311119431b https://github.com/galaxyproject/galaxy/commit/305f9f94c04579a8414e0034e0ec9... Author: Bjoern Gruening bjoern.gruening@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map

Log Message: ----------- revert static files

Commit: a06ec3e58dc1c53a8bcf515f38c89976eae1a074 https://github.com/galaxyproject/galaxy/commit/a06ec3e58dc1c53a8bcf515f38c89... Author: Björn Grüning bjoern@gruenings.eu Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/api/users.py

Log Message: ----------- change xml to yml

Commit: a71f64c8da2427b6f5808b9f4e91612fe82efe10 https://github.com/galaxyproject/galaxy/commit/a71f64c8da2427b6f5808b9f4e916... Author: Björn Grüning bjoern@gruenings.eu Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M config/user_preferences_extra_conf.yml.sample

Log Message: ----------- fix apollo spelling

Commit: 338fffad0bcaea709cc552dcab5310e4b73ea4c7 https://github.com/galaxyproject/galaxy/commit/338fffad0bcaea709cc552dcab531... Author: Björn Grüning bjoern@gruenings.eu Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/config.py

Log Message: ----------- Remove user_preferences_extra_conf.yml sample file from the default list

Commit: eb8f7f0da328b0fd440f67bdf0c6f9c5e366a32d https://github.com/galaxyproject/galaxy/commit/eb8f7f0da328b0fd440f67bdf0c6f... Author: Björn Grüning bjoern@gruenings.eu Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/api/users.py

Log Message: ----------- remove debug statement

Commit: 20f90254bfae5e2e0579a69fa37b0c45e874d9ce https://github.com/galaxyproject/galaxy/commit/20f90254bfae5e2e0579a69fa37b0... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/utility_containers/utility_container_manager.py M templates/webapps/tool_shed/repository/common.mako

Log Message: ----------- Show minimum required galaxy version in tool shed and galaxy installation process

Commit: a77c4587fb9eadfc62da6b8b430154ad18ce1136 https://github.com/galaxyproject/galaxy/commit/a77c4587fb9eadfc62da6b8b43015... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/tool_shed/utility_containers/utility_container_manager.py

Log Message: ----------- Shorten 'Minimum required Galaxy version' to 'Minimum Galaxy Version'

Commit: 210d3e31ab8bd71569ed6399cfc1894223e4ec36 https://github.com/galaxyproject/galaxy/commit/210d3e31ab8bd71569ed6399cfc18... Author: John Chilton jmchilton@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/tools/__init__.py

Log Message: ----------- Refactor to clean up args in one method of galaxy.tools.

Commit: 997e7114be722e56e5633cd10b554d6d1428dfc8 https://github.com/galaxyproject/galaxy/commit/997e7114be722e56e5633cd10b554... Author: John Chilton jmchilton@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/tools/__init__.py M test/unit/tools_support.py

Log Message: ----------- More correct tool creation in tools_support.

Now supports creating tool subclasses based on tool source.

Commit: db91b29df96d354c8972f63513ed755b5dd4418d https://github.com/galaxyproject/galaxy/commit/db91b29df96d354c8972f63513ed7... Author: John Chilton jmchilton@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py

Log Message: ----------- Have more tests use mock_galaxy's MockApp.

Commit: ecad3996f1f4715db5ff326f9f6ae5067cd2e0fc https://github.com/galaxyproject/galaxy/commit/ecad3996f1f4715db5ff326f9f6ae... Author: John Chilton jmchilton@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/tools/parser/output_objects.py

Log Message: ----------- Refactor ToolOutputCollectionStructure to allow it be more easily consumed.

Make complex arguments optional.

Commit: e8112210429d710a9eb9702f541cfaed6e219454 https://github.com/galaxyproject/galaxy/commit/e8112210429d710a9eb9702f541cf... Author: John Chilton jmchilton@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/tools/parser/output_objects.py

Log Message: ----------- Improve cohesion of interaction between ToolOutputCollectionStructure and ToolOutputCollection.

Shield more of ToolOutputCollectionStructure internals from ToolOutputCollection.

Commit: 71db6b461da3d3b2e3c6880c9d2bf90bcd44098e https://github.com/galaxyproject/galaxy/commit/71db6b461da3d3b2e3c6880c9d2bf... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Fix lint

Fix

Commit: bf68966accd18af2da1e4fa518d01119f5a696f2 https://github.com/galaxyproject/galaxy/commit/bf68966accd18af2da1e4fa518d01... Author: John Chilton jmchilton@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/tools/toolbox/base.py

Log Message: ----------- Fix get_tool returning list when it shouldn't.

Commit: c72aca479729ddee6a8bf8e19431b41e98d39d89 https://github.com/galaxyproject/galaxy/commit/c72aca479729ddee6a8bf8e19431b... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map

Log Message: ----------- Revise admin groups endpoint

Commit: a7c6c69cbf6a6eeffdf53815144e623576c47b13 https://github.com/galaxyproject/galaxy/commit/a7c6c69cbf6a6eeffdf53815144e6... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Fix lint

Commit: 097cae67956b972cd609f1155890d122c5bb3742 https://github.com/galaxyproject/galaxy/commit/097cae67956b972cd609f1155890d... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Merge branch 'admin_grid_roles' into admin_grid_groups

Commit: 9822dede69c95796c24e87a1c60cd845788095d1 https://github.com/galaxyproject/galaxy/commit/9822dede69c95796c24e87a1c60cd... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M client/galaxy/scripts/apps/admin.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map

Log Message: ----------- Add client route

Commit: 1bf2d1782fca4c79708261ca98cabe92822e86cb https://github.com/galaxyproject/galaxy/commit/1bf2d1782fca4c79708261ca98cab... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map

Log Message: ----------- Use client side formbuilder for rename group form

Commit: 7a58fd113d32659c9ea6e0c4fdb830d5c1ca7a72 https://github.com/galaxyproject/galaxy/commit/7a58fd113d32659c9ea6e0c4fdb83... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Remove self directed operation

Commit: b2d54b377c6c78f016ccb730178afd3f7a70c0b3 https://github.com/galaxyproject/galaxy/commit/b2d54b377c6c78f016ccb730178af... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Add async support for group deleting

Commit: afdfbf69ff8d1636c661c5758f52c636f9160220 https://github.com/galaxyproject/galaxy/commit/afdfbf69ff8d1636c661c5758f52c... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Add async support for undeleting groups

Commit: 96557cd136730033c3a4b84e506b3cc5831d06af https://github.com/galaxyproject/galaxy/commit/96557cd136730033c3a4b84e506b3... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Add async support for purging groups

Commit: fe2d607675acf5e18994957fb8ff4422079987ea https://github.com/galaxyproject/galaxy/commit/fe2d607675acf5e18994957fb8ff4... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py

Log Message: ----------- Replace list with generator when iterating headers

This should be more memory-friendly. @blankenberg suggested doing this in #4319.

Commit: 037b7fa75754ae90917d0ee25b1565c9ab29cd03 https://github.com/galaxyproject/galaxy/commit/037b7fa75754ae90917d0ee25b156... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Remove exposure of async operation handlers, align naming

Commit: 3840c6d61735fa674239be19a10af04d0d3647f9 https://github.com/galaxyproject/galaxy/commit/3840c6d61735fa674239be19a10af... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Fix purge handler for groups

Commit: 1e83a48c4635ba05576cdb8e42bbdf8f971b825a https://github.com/galaxyproject/galaxy/commit/1e83a48c4635ba05576cdb8e42bbd... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Remove exposure of user related operations

Commit: 1795247bd849e3d7d1c034416d27d5c1672039e8 https://github.com/galaxyproject/galaxy/commit/1795247bd849e3d7d1c034416d27d... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Remove new line

Commit: d53a5424967e46d683f7baafe06cb53703e86adf https://github.com/galaxyproject/galaxy/commit/d53a5424967e46d683f7baafe06cb... Author: Nicola Soranzo nsoranzo@tiscali.it Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/tools/parser/output_objects.py

Log Message: ----------- Merge pull request #4389 from jmchilton/output_collect_refactor

Refactor ToolOutputCollectionStructure...

Commit: e805db6896352042aa5eb8482febbd75af46b008 https://github.com/galaxyproject/galaxy/commit/e805db6896352042aa5eb8482febb... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map

Log Message: ----------- Use client to build create groups form

Commit: a462afa0b7094a5fa439b0aa3b751e26cc18bd98 https://github.com/galaxyproject/galaxy/commit/a462afa0b7094a5fa439b0aa3b751... Author: John Chilton jmchilton@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_execution.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py

Log Message: ----------- Eliminate second unit test variant of MockApp.

As well as my failed experiment in mocking out sqlalchemy - I think the in-memory database is more useful than mocking out sqlalchemy in retrospect.

Commit: 5605f390fe36c8ab562d049b105db7164b8097c1 https://github.com/galaxyproject/galaxy/commit/5605f390fe36c8ab562d049b105db... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map

Log Message: ----------- Build manage users and roles for groups with client form builder

Commit: c827bb0a867e2fcdf89417bb7ea912641e49cf8a https://github.com/galaxyproject/galaxy/commit/c827bb0a867e2fcdf89417bb7ea91... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/tool_shed/util/admin_util.py R templates/admin/dataset_security/group/group.mako R templates/admin/dataset_security/group/group_create.mako R templates/admin/dataset_security/group/group_rename.mako A templates/webapps/tool_shed/admin/dataset_security/group/group.mako A templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako A templates/webapps/tool_shed/admin/dataset_security/group/group_rename.mako

Log Message: ----------- Move unused mako templates to toolshed, adjust paths

Commit: d3b8889c04ef22d740f8b668a8212c728ba5832c https://github.com/galaxyproject/galaxy/commit/d3b8889c04ef22d740f8b668a8212... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 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: ----------- Fix second role link in admin panel

Commit: dbad2556d05dead2ac0991a7897d95f1eda16087 https://github.com/galaxyproject/galaxy/commit/dbad2556d05dead2ac0991a7897d9... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 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: ----------- Merge branch 'admin_grid_roles' into admin_grid_groups

Commit: 4a35bd3532ce3a9e0af84c3a86ee33585e9e0ba3 https://github.com/galaxyproject/galaxy/commit/4a35bd3532ce3a9e0af84c3a86ee3... Author: Nicola Soranzo nsoranzo@tiscali.it Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/tools/toolbox/base.py

Log Message: ----------- Merge pull request #4390 from jmchilton/toollist

Fix get_tool returning list when it shouldn't.

Commit: 613f4fb1ced3c9a7e0d1417b8c9c14b681479bdd https://github.com/galaxyproject/galaxy/commit/613f4fb1ced3c9a7e0d1417b8c9c1... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map

Log Message: ----------- Use dict format for admin tool versions grid

Commit: 381bf173d095ce51ba66d9cf19f5827c75c36dc8 https://github.com/galaxyproject/galaxy/commit/381bf173d095ce51ba66d9cf19f58... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Remove message from tool versions

Commit: cdfaebdaa4722226cf121454aa02b455d324d265 https://github.com/galaxyproject/galaxy/commit/cdfaebdaa4722226cf121454aa02b... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map

Log Message: ----------- Switch quotas grid to dict format

Commit: a060690c3afa8f296404eb52e4986202d1d985ca https://github.com/galaxyproject/galaxy/commit/a060690c3afa8f296404eb52e4986... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/web/base/controller.py M lib/galaxy/workflow/extract.py M lib/tool_shed/util/workflow_util.py

Log Message: ----------- Get tools with tool_version in more places

Commit: e6c238e234ae4d16d1fd1118c1b7e585ba541645 https://github.com/galaxyproject/galaxy/commit/e6c238e234ae4d16d1fd1118c1b7e... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/datatypes/interval.py

Log Message: ----------- Move iter_headers into try clause (thx @nsoranzo)

Commit: 43702ccacdbfe925d921dac413c02bb7f65b9c4f https://github.com/galaxyproject/galaxy/commit/43702ccacdbfe925d921dac413c02... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/datatypes/mothur.py

Log Message: ----------- Process the first line when setting metdata for mother.otu files

Commit: 196a2bbcf50c4f9fa41588d8e087e5b5cee9da65 https://github.com/galaxyproject/galaxy/commit/196a2bbcf50c4f9fa41588d8e087e... Author: Eric Rasche hxr@hx42.org Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: A config/user_preferences_extra_conf.yml.sample M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/api/users.py

Log Message: ----------- Merge pull request #3383 from bgruening/extra_user_preferences

Add extension point for user preferences

Commit: f8648b658629d1313029bb1ad707023c44b626df https://github.com/galaxyproject/galaxy/commit/f8648b658629d1313029bb1ad7070... Author: Björn Grüning bjoern@gruenings.eu Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M config/datatypes_conf.xml.sample

Log Message: ----------- Add deeptools datatypes to Galaxy

Commit: 0e1b80b28f7558104c9a36bd1d224c60d91c2c70 https://github.com/galaxyproject/galaxy/commit/0e1b80b28f7558104c9a36bd1d224... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M lib/galaxy/actions/admin.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map

Log Message: ----------- Add async quota grid operations

Commit: ad60f5a8ea4eaf574b4ffa1e51baa5bbe8282d47 https://github.com/galaxyproject/galaxy/commit/ad60f5a8ea4eaf574b4ffa1e51baa... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/actions/admin.py

Log Message: ----------- Allow empty params

Commit: 83a48f8f336a4c73dd1faabe3c84ce8801fb181d https://github.com/galaxyproject/galaxy/commit/83a48f8f336a4c73dd1faabe3c84c... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/actions/admin.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map

Log Message: ----------- Build quota renaming form in admin panel using client side form builder

Commit: 0da4768c3535d13c0a141cc30f39e8b86b0c98d1 https://github.com/galaxyproject/galaxy/commit/0da4768c3535d13c0a141cc30f39e... Author: John Chilton jmchilton@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py

Log Message: ----------- Merge pull request #4388 from mvdbeek/iter_headers

Replace list with generator when iterating headers

Commit: ff197fe915a67c1ad2ba10ed9a6d433a55b45ee1 https://github.com/galaxyproject/galaxy/commit/ff197fe915a67c1ad2ba10ed9a6d4... Author: John Chilton jmchilton@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/utility_containers/utility_container_manager.py M templates/webapps/tool_shed/repository/common.mako

Log Message: ----------- Merge pull request #4386 from mvdbeek/display_minimum_required_galaxy_version

Show minimum required galaxy version in tool shed and galaxy installation process

Commit: 9dcc181f72d5f31b3d5feb45f673996714aca913 https://github.com/galaxyproject/galaxy/commit/9dcc181f72d5f31b3d5feb45f6739... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Fix error message handling for quota operations, set default value for payloads to none

Commit: 643f262ea913e8cc0f3bb5e39acf2af80194c71f https://github.com/galaxyproject/galaxy/commit/643f262ea913e8cc0f3bb5e39acf2... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/actions/admin.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map

Log Message: ----------- Use client form builder to render edit quota amount form

Commit: ad2dc168307037070205db27d7bdb09fb82d549f https://github.com/galaxyproject/galaxy/commit/ad2dc168307037070205db27d7bdb... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Fix link to edit quota

Commit: ae181d776fb9a565d7b51c18aa8edcae09018bc3 https://github.com/galaxyproject/galaxy/commit/ae181d776fb9a565d7b51c18aa8ed... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Provide async support for unsetting default quotas

Commit: bd542000fa9ec420ba0f2e17d2b8f8047eb72f8c https://github.com/galaxyproject/galaxy/commit/bd542000fa9ec420ba0f2e17d2b8f... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map

Log Message: ----------- Build set default quota forms using client form builder

Commit: 17cd7d16c2db988581e26ad59a88a57302a202c9 https://github.com/galaxyproject/galaxy/commit/17cd7d16c2db988581e26ad59a88a... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/actions/admin.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map

Log Message: ----------- Add manage role support for quotas

Commit: 9f580d0630026157f2727651cce2e8f444f78cdc https://github.com/galaxyproject/galaxy/commit/9f580d0630026157f2727651cce2e... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Use consistent naming for group and role parameters

Commit: e901a0c867cfa9af3420536c4725cbc001621cf8 https://github.com/galaxyproject/galaxy/commit/e901a0c867cfa9af3420536c4725c... Author: John Chilton jmchilton@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/managers/workflows.py

Log Message: ----------- Bugfix for loading subworkflows from workflow descriptions.

Sometimes unrelated workflow steps can be flushed in a half complete state and violate integrity constraints when a subworkflow step causes a flush of during the load of a different step. This fixes that by preloading all subworkflows during workflow import.

This PR doesn't include a test case but one will be included if the CWL branch is merged at a later date (xref https://github.com/common-workflow-language/common-workflow-language/pull/49...).

Commit: cf34d8b75958db007dcaa5368557dda6850d6e95 https://github.com/galaxyproject/galaxy/commit/cf34d8b75958db007dcaa5368557d... Author: John Chilton jmchilton@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M config/datatypes_conf.xml.sample

Log Message: ----------- Merge pull request #4392 from bgruening/deeptools_datatypes

Add deepTools datatypes to Galaxy

Commit: 7de7f3f63a438a9d2b2b452d61e3118a710826c7 https://github.com/galaxyproject/galaxy/commit/7de7f3f63a438a9d2b2b452d61e31... Author: John Chilton jmchilton@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M test/unit/tools_support.py

Log Message: ----------- "Fix" import order of tools_support for Travis.

Commit: bc23c26cf4210b46f4d17369902fdaec48a16e98 https://github.com/galaxyproject/galaxy/commit/bc23c26cf4210b46f4d17369902fd... Author: John Chilton jmchilton@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/web/base/controller.py M lib/galaxy/workflow/extract.py M lib/tool_shed/util/workflow_util.py

Log Message: ----------- Merge pull request #4391 from mvdbeek/more_version_fixes

Get tools with tool_version in more places

Commit: c03b29f4855dcce9677e2fe16779d2eb64b1646d https://github.com/galaxyproject/galaxy/commit/c03b29f4855dcce9677e2fe16779d... Author: John Chilton jmchilton@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/jobs/command_factory.py

Log Message: ----------- Revise comment thanks to note from @mvdbeek.

Commit: 11365e9620a5198ca88a35f5a10902744d94a7a3 https://github.com/galaxyproject/galaxy/commit/11365e9620a5198ca88a35f5a1090... Author: John Chilton jmchilton@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M lib/galaxy/tools/parser/interface.py M test/unit/tools/test_parsing.py

Log Message: ----------- Bugfix: __str__ method on tool parsers would throw an Exception.

Commit: d39483bf0a88aa6c62cb69928abc8195e9082db7 https://github.com/galaxyproject/galaxy/commit/d39483bf0a88aa6c62cb69928abc8... Author: John Chilton jmchilton@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M test/base/interactor.py

Log Message: ----------- Revise summarize history errors to display more data and outline collections.

Commit: 67f9e34f530d1d505e12fcca9fef2648025d877e https://github.com/galaxyproject/galaxy/commit/67f9e34f530d1d505e12fcca9fef2... Author: John Chilton jmchilton@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M test/api/test_tools.py M test/base/populators.py

Log Message: ----------- Implement test lib history context.

Commit: b7fe2fa2ecc44bde964be1c44e73e2ea11586bf5 https://github.com/galaxyproject/galaxy/commit/b7fe2fa2ecc44bde964be1c44e73e... Author: John Chilton jmchilton@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)

Changed paths: M test/base/interactor.py M test/base/populators.py

Log Message: ----------- Rework summarizing histories on errors to include all datasets.

``` -------------------- >> begin captured stdout << --------------------- Problem in history with id adb5f5c93f827949 - summary of datasets below. -------------------------------------- | 1 - Test Dataset (HID - NAME) | Dataset State: | ok | Dataset Blurb: | 1 line | Dataset Info: | uploaded txt file | Peek: | <table cellspacing="0" cellpadding="3"><tr><td>1 2 3</td></tr></table> | Dataset Job Standard Output: | *Standard output was empty.* | Dataset Job Standard Error: | *Standard error was empty.* | -------------------------------------- | 2 - Test Dataset (HID - NAME) | Dataset State: | ok | Dataset Blurb: | 1 line | Dataset Info: | uploaded txt file | Peek: | <table cellspacing="0" cellpadding="3"><tr><td>4 5 6</td></tr></table> | Dataset Job Standard Output: | *Standard output was empty.* | Dataset Job Standard Error: | *Standard error was empty.* | -------------------------------------- | 3 - multi_data_param on data 1 and data 2 (HID - NAME) | Dataset State: | ok | Dataset Blurb: | 2 lines | Dataset Info: | *Dataset info is empty.* | Peek: | <table cellspacing="0" cellpadding="3"><tr><td>1 2 3</td></tr><tr><td>4 5 6</td></tr></table> | Dataset Job Standard Output: | *Standard output was empty.* | Dataset Job Standard Error: | *Standard error was empty.* | -------------------------------------- | 4 - multi_data_param on data 1 and data 2 (HID - NAME) | Dataset State: | ok | Dataset Blurb: | 2 lines | Dataset Info: | *Dataset info is empty.* | Peek: | <table cellspacing="0" cellpadding="3"><tr><td>4 5 6</td></tr><tr><td>1 2 3</td></tr></table> | Dataset Job Standard Output: | *Standard output was empty.* | Dataset Job Standard Error: | *Standard error was empty.* | -------------------------------------- ```

Commit: a001145278fb0642325214123da0c5cec6fc6704 https://github.com/galaxyproject/galaxy/commit/a001145278fb0642325214123da0c... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2017-08-09 (Wed, 09 Aug 2017)

Changed paths: M lib/galaxy/jobs/command_factory.py

Log Message: ----------- Merge pull request #4383 from jmchilton/split_conda

Bugfix: Ensure task splitting handles before job resolution.

Commit: c7d7b6c4695b300739b572b9a94e0de312a0f6ef https://github.com/galaxyproject/galaxy/commit/c7d7b6c4695b300739b572b9a94e0... Author: Nicola Soranzo nsoranzo@tiscali.it Date: 2017-08-09 (Wed, 09 Aug 2017)

Changed paths: M lib/galaxy/tools/parser/interface.py M test/unit/tools/test_parsing.py

Log Message: ----------- Merge pull request #4395 from jmchilton/parser_to_str_fix

Bugfix: __str__ method on tool parsers would throw an Exception.

Commit: 7ca5cd6585ef8a69f07cfa8362287a800b48281a https://github.com/galaxyproject/galaxy/commit/7ca5cd6585ef8a69f07cfa8362287... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-08-09 (Wed, 09 Aug 2017)

Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py

Log Message: ----------- Fix import order and Python3 compatibility for lib/galaxy/web/base/

Commit: 0f84d8bd91722c4bd36d5a736d6ca02a57460cfc https://github.com/galaxyproject/galaxy/commit/0f84d8bd91722c4bd36d5a736d6ca... Author: guerler aysam.guerler@gmail.com Date: 2017-08-09 (Wed, 09 Aug 2017)

Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map

Log Message: ----------- Add client side form to create new quota

Commit: 5647dfe5dbb22b7d09b1b760e41a2e0cd96cd8c8 https://github.com/galaxyproject/galaxy/commit/5647dfe5dbb22b7d09b1b760e41a2... Author: guerler aysam.guerler@gmail.com Date: 2017-08-09 (Wed, 09 Aug 2017)

Changed paths: R templates/admin/quota/quota.mako R templates/admin/quota/quota_create.mako R templates/admin/quota/quota_edit.mako R templates/admin/quota/quota_rename.mako R templates/admin/quota/quota_set_default.mako

Log Message: ----------- Remove unused quota makos

Commit: c57c36b51465b1bfaefcf486b9814c32f7f92840 https://github.com/galaxyproject/galaxy/commit/c57c36b51465b1bfaefcf486b9814... Author: guerler aysam.guerler@gmail.com Date: 2017-08-09 (Wed, 09 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Remove over indent

Commit: 4a77956dc8756300825c3744ccfa3a4646be5775 https://github.com/galaxyproject/galaxy/commit/4a77956dc8756300825c3744ccfa3... Author: guerler aysam.guerler@gmail.com Date: 2017-08-09 (Wed, 09 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Merge branch 'admin_grid_roles' into admin_grid_groups

Commit: 2e53858a2973aa6d4f95c3e8401d9709809d1da3 https://github.com/galaxyproject/galaxy/commit/2e53858a2973aa6d4f95c3e8401d9... Author: John Chilton jmchilton@gmail.com Date: 2017-08-09 (Wed, 09 Aug 2017)

Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py

Log Message: ----------- Merge pull request #4403 from nsoranzo/flake8-import-order

Fix import order and Python3 compatibility for lib/galaxy/web/base/

Commit: 8f056c2bbc78040c790255c874b6c321c4ba5b97 https://github.com/galaxyproject/galaxy/commit/8f056c2bbc78040c790255c874b6c... Author: guerler aysam.guerler@gmail.com Date: 2017-08-09 (Wed, 09 Aug 2017)

Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/user/user-preferences.js M config/datatypes_conf.xml.sample A config/user_preferences_extra_conf.yml.sample M doc/source/admin/special_topics/grt.rst M lib/galaxy/config.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/workflow/extract.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/utility_container_manager.py R scripts/grt.py R scripts/grt.yml.sample A scripts/grt/export.py A scripts/grt/grt.yml.sample A scripts/grt/upload.py M static/maps/galaxy.js.map M static/maps/layout/menu.js.map M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/galaxy.js M static/scripts/layout/menu.js M static/scripts/mvc/user/user-preferences.js M templates/galaxy_client_app.mako M templates/user/login.mako M templates/user/register.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako M templates/webapps/tool_shed/repository/common.mako M test/api/test_tools.py A test/functional/tools/identifier_source.xml M test/functional/tools/samples_tool_conf.xml M test/shed_functional/base/twilltestcase.py A test/unit/test_remote_shell.py M test/unit/tools/test_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py M tox.ini

Log Message: ----------- Merge branch 'dev' into revise_page

Commit: c01023b5adc402a6a8662e9f319afcd9e4f5fc6e https://github.com/galaxyproject/galaxy/commit/c01023b5adc402a6a8662e9f319af... Author: guerler aysam.guerler@gmail.com Date: 2017-08-09 (Wed, 09 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Fix indention

Commit: d32a3a58a50bdbdbe6144a265ef3424a2f011ae2 https://github.com/galaxyproject/galaxy/commit/d32a3a58a50bdbdbe6144a265ef34... Author: guerler aysam.guerler@gmail.com Date: 2017-08-09 (Wed, 09 Aug 2017)

Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M config/datatypes_conf.xml.sample A config/user_preferences_extra_conf.yml.sample M lib/galaxy/config.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/managers/workflows.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/workflow/extract.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/utility_container_manager.py M templates/webapps/tool_shed/repository/common.mako M test/unit/tools/test_parsing.py

Log Message: ----------- Merge branch 'revise_page' into admin_grid_roles

Commit: 06c70d34e2c218b826d813d3dd4e52d077ab94d4 https://github.com/galaxyproject/galaxy/commit/06c70d34e2c218b826d813d3dd4e5... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-09 (Wed, 09 Aug 2017)

Changed paths: M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js

Log Message: ----------- make client

Commit: cff21d350dc71b1e7b088985eeeb3f27b0fec1d0 https://github.com/galaxyproject/galaxy/commit/cff21d350dc71b1e7b088985eeeb3... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-09 (Wed, 09 Aug 2017)

Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/data.js A client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/grid/grid-model.js A client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-view.js R client/galaxy/scripts/mvc/page/page-list.js M client/galaxy/scripts/mvc/user/user-preferences.js R client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M client/galaxy/style/less/base.less M client/galaxy/style/less/galaxy_bootstrap/overrides.less A client/package-lock.json M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js A config/plugins/visualizations/unipept/README.md A config/plugins/visualizations/unipept/config/unipept.xml A config/plugins/visualizations/unipept/static/style.css A config/plugins/visualizations/unipept/static/tooltip.css A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js.map A config/plugins/visualizations/unipept/static/unipept_viz.js A config/plugins/visualizations/unipept/templates/glyphicons-86-repeat.png A config/plugins/visualizations/unipept/templates/unipept.mako M config/plugins/webhooks/demo/search/static/script.js M config/tool_conf.xml.main M config/tool_shed.ini.sample A config/user_preferences_extra_conf.yml.sample M doc/source/admin/special_topics/grt.rst M lib/galaxy/config.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/objectstore/__init__.py A lib/galaxy/objectstore/pithos.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/web/base/controller.py R lib/galaxy/web/base/controllers/__init__.py R lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/tool_shed/metadata/metadata_generator.py A lib/tool_shed/util/admin_util.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/utility_container_manager.py R scripts/grt.py R scripts/grt.yml.sample A scripts/grt/export.py A scripts/grt/grt.yml.sample A scripts/grt/upload.py M scripts/runtime_stats.py M static/maps/galaxy.js.map M static/maps/galaxy.pages.js.map M static/maps/layout/menu.js.map M static/maps/layout/scratchbook.js.map M static/maps/mvc/dataset/data.js.map A static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/grid/grid-model.js.map A static/maps/mvc/grid/grid-shared.js.map M static/maps/mvc/grid/grid-view.js.map R static/maps/mvc/page/page-list.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/nls/fr/locale.js.map M static/maps/nls/ja/locale.js.map M static/maps/nls/locale.js.map M static/maps/viz/circster.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/visualization.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/galaxy.js M static/scripts/galaxy.pages.js M static/scripts/layout/menu.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/dataset/data.js A static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-li-edit.js A static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-view.js R static/scripts/mvc/page/page-list.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js M static/style/blue/base.css M templates/galaxy_client_app.mako M templates/user/login.mako M templates/user/register.mako R templates/webapps/galaxy/dataset/edit_attributes.mako M templates/webapps/galaxy/history/display_structured.mako R templates/webapps/galaxy/history/list_published.mako M templates/webapps/galaxy/page/editor.mako R templates/webapps/galaxy/page/select_items_grid.mako M templates/webapps/galaxy/requests/common/common.mako R templates/webapps/galaxy/tracks/add_to_viz.mako R templates/webapps/galaxy/tracks/add_tracks.mako R templates/webapps/galaxy/tracks/history_datasets_select_grid.mako R templates/webapps/galaxy/tracks/history_select_grid.mako R templates/webapps/galaxy/tracks/library_datasets_select_grid.mako R templates/webapps/galaxy/visualization/list.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako M templates/webapps/tool_shed/repository/common.mako M test/api/test_tools.py A test/functional/tools/identifier_source.xml M test/functional/tools/samples_tool_conf.xml M test/shed_functional/base/twilltestcase.py A test/unit/test_remote_shell.py M test/unit/tools/test_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py M tox.ini

Log Message: ----------- Merge branch 'dev' into library_tags

Commit: fd0ce1284a9663fab95558fd38ad9477c98d8311 https://github.com/galaxyproject/galaxy/commit/fd0ce1284a9663fab95558fd38ad9... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-09 (Wed, 09 Aug 2017)

Changed paths: M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map

Log Message: ----------- make client again...

Commit: d52ac533daa8bcfef209f66f8c4e3020d93c09df https://github.com/galaxyproject/galaxy/commit/d52ac533daa8bcfef209f66f8c4e3... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-09 (Wed, 09 Aug 2017)

Changed paths: M lib/galaxy/model/migrate/versions/0135_add_library_tags.py

Log Message: ----------- fix indentation

Commit: 429771820200acd1a0d0b12c85a39ab7fe530195 https://github.com/galaxyproject/galaxy/commit/429771820200acd1a0d0b12c85a39... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-09 (Wed, 09 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/managers/tags.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0135_add_library_tags.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js

Log Message: ----------- Merge pull request #4262 from bwlang/library_tags

Library tags

Commit: cfa3220d9f2d257b94795b6f63592459d3011f30 https://github.com/galaxyproject/galaxy/commit/cfa3220d9f2d257b94795b6f63592... Author: guerler aysam.guerler@gmail.com Date: 2017-08-09 (Wed, 09 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/managers/tags.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0135_add_library_tags.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js

Log Message: ----------- Merge branch 'dev' into revise_page

Commit: bdbe3603059b84bb2a91646ebcad003477bb9590 https://github.com/galaxyproject/galaxy/commit/bdbe3603059b84bb2a91646ebcad0... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M scripts/grt/export.py

Log Message: ----------- fix pardir

Commit: f4383bd983ee14d4e85ef610dba4b11266b196ed https://github.com/galaxyproject/galaxy/commit/f4383bd983ee14d4e85ef610dba4b... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M scripts/grt/export.py

Log Message: ----------- Fun things you find in production

Commit: c5b36128644310e1ac52647df53f226c1457aaeb https://github.com/galaxyproject/galaxy/commit/c5b36128644310e1ac52647df53f2... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M scripts/grt/upload.py

Log Message: ----------- cleanup url in case

Commit: 847df13fc0ea349ab2103099b696715a6d66b38f https://github.com/galaxyproject/galaxy/commit/847df13fc0ea349ab2103099b6967... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M scripts/grt/upload.py

Log Message: ----------- this should not have been missed

Commit: 496169719465e18c899b991152a9e327d83e2446 https://github.com/galaxyproject/galaxy/commit/496169719465e18c899b991152a9e... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M scripts/grt/upload.py

Log Message: ----------- fix extension

Commit: a177ccd0268805e0079f39d5d141ae4da39c0a00 https://github.com/galaxyproject/galaxy/commit/a177ccd0268805e0079f39d5d141a... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M scripts/grt/upload.py

Log Message: ----------- not needed

Commit: 5e43fcef3c94e9b3f6d700fc5258067d0547e30d https://github.com/galaxyproject/galaxy/commit/5e43fcef3c94e9b3f6d700fc52580... Author: John Chilton jmchilton@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js A client/galaxy/scripts/layout/router.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/root.py M static/maps/galaxy.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.js.map A static/maps/layout/router.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/galaxy.js M static/scripts/layout/menu.js M static/scripts/layout/page.js A static/scripts/layout/router.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M templates/admin/user/reset_password.mako M templates/admin/user/user.mako

Log Message: ----------- Merge pull request #4341 from guerler/revise_page

Admin user grid conversion

Commit: e477cce9b68d90a313d1534c3ad156f9eb8cc6ec https://github.com/galaxyproject/galaxy/commit/e477cce9b68d90a313d1534c3ad15... Author: guerler aysam.guerler@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M config/datatypes_conf.xml.sample A config/user_preferences_extra_conf.yml.sample M doc/source/admin/special_topics/grt.rst M lib/galaxy/config.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0135_add_library_tags.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/workflow/extract.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/utility_container_manager.py R scripts/grt.py R scripts/grt.yml.sample A scripts/grt/export.py A scripts/grt/grt.yml.sample A scripts/grt/upload.py M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M templates/webapps/tool_shed/repository/common.mako M test/api/test_tools.py A test/functional/tools/identifier_source.xml M test/functional/tools/samples_tool_conf.xml A test/unit/test_remote_shell.py M test/unit/tools/test_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py M tox.ini

Log Message: ----------- Merge branch 'revise_page' into revise_grid_forms

Commit: 938bf525f46c8d3c7568d9b2a97edfa958ba900f https://github.com/galaxyproject/galaxy/commit/938bf525f46c8d3c7568d9b2a97ed... Author: guerler aysam.guerler@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/managers/tags.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0135_add_library_tags.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/user/user-preferences.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/user/user-preferences.js

Log Message: ----------- Merge branch 'revise_grid_forms' into admin_grid_roles

Commit: b8c05ede4dd188dce24c914912f8fa35963d9562 https://github.com/galaxyproject/galaxy/commit/b8c05ede4dd188dce24c914912f8f... Author: guerler aysam.guerler@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Log Message: ----------- Merge branch 'dev' into revise_grid_forms

Commit: 70a64b304eb2b5c9642581061f345e669251eac6 https://github.com/galaxyproject/galaxy/commit/70a64b304eb2b5c9642581061f345... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: A config/error_report.xml.sample M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py A lib/galaxy/tools/error_reports/__init__.py A lib/galaxy/tools/error_reports/sinks/__init__.py A lib/galaxy/tools/error_reports/sinks/email.py A lib/galaxy/tools/error_reports/sinks/json.py A lib/galaxy/tools/error_reports/sinks/sentry.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py A templates/messages.mako

Log Message: ----------- Refactor bug reporting into plugins

Commit: 9dd27dcc3de5eff03c4a37c34fc810d3f295c85c https://github.com/galaxyproject/galaxy/commit/9dd27dcc3de5eff03c4a37c34fc81... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M lib/galaxy/tools/error_reports/__init__.py M lib/galaxy/tools/error_reports/sinks/__init__.py M lib/galaxy/webapps/galaxy/controllers/dataset.py

Log Message: ----------- flake8

Commit: 181a72a6f383aa54c4a053cedba05e345eda2584 https://github.com/galaxyproject/galaxy/commit/181a72a6f383aa54c4a053cedba05... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M lib/galaxy/tools/error_reports/sinks/email.py M lib/galaxy/tools/error_reports/sinks/json.py M lib/galaxy/tools/error_reports/sinks/sentry.py

Log Message: ----------- flake8 import

Commit: 437ab325da8b49b9f0e9b796f8515899aa10d035 https://github.com/galaxyproject/galaxy/commit/437ab325da8b49b9f0e9b796f8515... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: A doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/index.rst

Log Message: ----------- document

Commit: 46b621708aa4b9973c3e6bf6b02417dc3931523c https://github.com/galaxyproject/galaxy/commit/46b621708aa4b9973c3e6bf6b0241... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M doc/source/admin/special_topics/bug_reports.rst M lib/galaxy/tools/error_reports/sinks/sentry.py

Log Message: ----------- Allow sentry to be verbose

Commit: d7e400c96ddf51caca3df26e8dc8a75089be2b06 https://github.com/galaxyproject/galaxy/commit/d7e400c96ddf51caca3df26e8dc8a... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: R config/error_report.xml.sample A config/error_report.yml.sample M lib/galaxy/config.py

Log Message: ----------- Per @jmchilton comment, rewrite as yml

Commit: f4a823c27a9b533994c593670cf5a13740e5bf7a https://github.com/galaxyproject/galaxy/commit/f4a823c27a9b533994c593670cf5a... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M client/galaxy/scripts/apps/analysis.js

Log Message: ----------- add bug reporter

Commit: ed7551e09679b940bd084fd5e5ce5fcf97320ffa https://github.com/galaxyproject/galaxy/commit/ed7551e09679b940bd084fd5e5ce5... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: A client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js A client/galaxy/scripts/mvc/job/job-params.js

Log Message: ----------- redirect to new url

Commit: 2f8347d5bc4bdf52a7d2b10d3e69b55290d104ca https://github.com/galaxyproject/galaxy/commit/2f8347d5bc4bdf52a7d2b10d3e69b... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py

Log Message: ----------- add clientside route

Commit: ef6b8cbeea5a0578683df8f013a0739a1e022fe0 https://github.com/galaxyproject/galaxy/commit/ef6b8cbeea5a0578683df8f013a07... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M client/galaxy/style/less/galaxy_bootstrap/overrides.less M templates/show_params.mako

Log Message: ----------- move css rule to a more generic location

Commit: 98ac18661865e958249f9a21bc847ba558b00893 https://github.com/galaxyproject/galaxy/commit/98ac18661865e958249f9a21bc847... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M lib/galaxy/tools/error_reports/sinks/email.py M lib/galaxy/tools/error_reports/sinks/json.py M lib/galaxy/tools/error_reports/sinks/sentry.py

Log Message: ----------- change report code

Commit: 6f8f38170c976b2152ef2e21fc46a47922da4b56 https://github.com/galaxyproject/galaxy/commit/6f8f38170c976b2152ef2e21fc46a... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py

Log Message: ----------- refactor into an API

Commit: 838b23358e6d00ce2d65f6a5fde6a413505eaf10 https://github.com/galaxyproject/galaxy/commit/838b23358e6d00ce2d65f6a5fde6a... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js

Log Message: ----------- Handle error report submission

Commit: 64174113bfd8e18b2e87581137a134f8f4520bd7 https://github.com/galaxyproject/galaxy/commit/64174113bfd8e18b2e87581137a13... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js

Log Message: ----------- refactor a bit

Commit: 73369a2e8dd098d59083c61f67ec140a7c3cd102 https://github.com/galaxyproject/galaxy/commit/73369a2e8dd098d59083c61f67ec1... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js

Log Message: ----------- Add extra parameter to allow multiple messages

Commit: cdb82dd8e64b83e14244b3b46163be1715afcfe2 https://github.com/galaxyproject/galaxy/commit/cdb82dd8e64b83e14244b3b46163b... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M lib/galaxy/tools/error_reports/__init__.py M lib/galaxy/webapps/galaxy/api/jobs.py

Log Message: ----------- Change invocation to pass user information

Commit: 5980bd91bb0f916b576b27386d2b052609610d57 https://github.com/galaxyproject/galaxy/commit/5980bd91bb0f916b576b27386d2b0... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M lib/galaxy/tools/errors.py

Log Message: ----------- Link in expected places

Commit: fd6c247398133d6f8df26b447328ec64801fcd11 https://github.com/galaxyproject/galaxy/commit/fd6c247398133d6f8df26b447328e... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: A lib/galaxy/tools/error_reports/sinks/biostars.py M lib/galaxy/util/biostar.py

Log Message: ----------- Switch biostars to using HTML submission

Commit: fb78a2118d0e45a11378bbc5e0daf0e351c8b763 https://github.com/galaxyproject/galaxy/commit/fb78a2118d0e45a11378bbc5e0daf... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M static/maps/mvc/dataset/dataset-li-edit.js.map M static/scripts/mvc/dataset/dataset-li-edit.js M static/style/blue/base.css

Log Message: ----------- merge

Commit: e8a5b48da9ce98c72ac92171be56435ca2b9565f https://github.com/galaxyproject/galaxy/commit/e8a5b48da9ce98c72ac92171be564... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: R templates/webapps/galaxy/dataset/errors.mako

Log Message: ----------- Now unused

Commit: 550cb7dfae8706e06a2b7638b078c9b9b134281d https://github.com/galaxyproject/galaxy/commit/550cb7dfae8706e06a2b7638b078c... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M lib/galaxy/config.py M lib/galaxy/tools/error_reports/__init__.py A lib/galaxy/tools/error_reports/plugins/__init__.py A lib/galaxy/tools/error_reports/plugins/biostars.py A lib/galaxy/tools/error_reports/plugins/email.py A lib/galaxy/tools/error_reports/plugins/json.py A lib/galaxy/tools/error_reports/plugins/sentry.py R lib/galaxy/tools/error_reports/sinks/__init__.py R lib/galaxy/tools/error_reports/sinks/biostars.py R lib/galaxy/tools/error_reports/sinks/email.py R lib/galaxy/tools/error_reports/sinks/json.py R lib/galaxy/tools/error_reports/sinks/sentry.py

Log Message: ----------- Requested renames, sink + yml

Commit: fcd94f0483c119a4db0e84e469af3aade0f2847c https://github.com/galaxyproject/galaxy/commit/fcd94f0483c119a4db0e84e469af3... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M config/error_report.yml.sample M lib/galaxy/app.py M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/error_reports/__init__.py M lib/galaxy/webapps/galaxy/api/jobs.py

Log Message: ----------- more renames

Commit: 7c1c60d82643b100a55edefb6f88d13671defafa https://github.com/galaxyproject/galaxy/commit/7c1c60d82643b100a55edefb6f88d... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: A static/maps/mvc/dataset/dataset-error.js.map A static/maps/mvc/job/job-params.js.map A static/scripts/mvc/dataset/dataset-error.js A static/scripts/mvc/job/job-params.js

Log Message: ----------- forgot static files

Commit: 61a5b7c9e139cfa73fefa048f6ec34a7511b741c https://github.com/galaxyproject/galaxy/commit/61a5b7c9e139cfa73fefa048f6ec3... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.js.map M static/scripts/mvc/dataset/dataset-li-edit.js

Log Message: ----------- another merge

Commit: a6aedc695336b122c5e552ced771a97b5f62ee52 https://github.com/galaxyproject/galaxy/commit/a6aedc695336b122c5e552ced771a... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M lib/galaxy/tools/error_reports/plugins/biostars.py

Log Message: ----------- address flaking

Commit: 1e9c31241c419cb53306232856ed7c368d8c6e92 https://github.com/galaxyproject/galaxy/commit/1e9c31241c419cb53306232856ed7... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py

Log Message: ----------- remove comment

Commit: 538ef006f36b3e525bb87d18944d596afb5f1639 https://github.com/galaxyproject/galaxy/commit/538ef006f36b3e525bb87d18944d5... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M lib/galaxy/util/plugin_config.py

Log Message: ----------- Also load yaml sample files. cc @jmchilton, is this ok?

Commit: 3e8919c41643352feb6df50d04a71f2291024ef7 https://github.com/galaxyproject/galaxy/commit/3e8919c41643352feb6df50d04a71... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M config/error_report.yml.sample

Log Message: ----------- correct name to type

Commit: 5563ecc3ffa7d0565be42eea99276d64ec5232dd https://github.com/galaxyproject/galaxy/commit/5563ecc3ffa7d0565be42eea99276... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M lib/galaxy/tools/error_reports/plugins/biostars.py

Log Message: ----------- fix import order

Commit: 00ee109ed4538b6a032489a07807deb7e13c9882 https://github.com/galaxyproject/galaxy/commit/00ee109ed4538b6a032489a07807d... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M lib/galaxy/tools/error_reports/plugins/email.py

Log Message: ----------- fix css class

Commit: 4c36b5a7a189f9586c061460bfdec7a84b6774c4 https://github.com/galaxyproject/galaxy/commit/4c36b5a7a189f9586c061460bfdec... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py

Log Message: ----------- not a useful test in this location

Commit: a2b02065ebbfa9759aad5e56db0c251f7ad514bc https://github.com/galaxyproject/galaxy/commit/a2b02065ebbfa9759aad5e56db0c2... Author: John Chilton jmchilton@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M lib/galaxy/web/framework/webapp.py R templates/messages.mako

Log Message: ----------- Remove unneeded messages.mako.

Commit: 41461235b2429ef84c50336021d9921ca6ef8a4a https://github.com/galaxyproject/galaxy/commit/41461235b2429ef84c50336021d99... Author: E Rasche hxr@hx42.org Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map

Log Message: ----------- rebuild client

Commit: 6d7d4e9e8e55cfcaa504f43e6288c1d39c0ed932 https://github.com/galaxyproject/galaxy/commit/6d7d4e9e8e55cfcaa504f43e6288c... Author: John Chilton jmchilton@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js A client/galaxy/scripts/mvc/job/job-params.js M client/galaxy/style/less/galaxy_bootstrap/overrides.less A config/error_report.yml.sample A doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/index.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py A lib/galaxy/tools/error_reports/__init__.py A lib/galaxy/tools/error_reports/plugins/__init__.py A lib/galaxy/tools/error_reports/plugins/biostars.py A lib/galaxy/tools/error_reports/plugins/email.py A lib/galaxy/tools/error_reports/plugins/json.py A lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/errors.py M lib/galaxy/util/biostar.py M lib/galaxy/util/plugin_config.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py A static/maps/mvc/dataset/dataset-error.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map A static/maps/mvc/job/job-params.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map A static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js A static/scripts/mvc/job/job-params.js M static/style/blue/base.css M templates/show_params.mako R templates/webapps/galaxy/dataset/errors.mako

Log Message: ----------- Merge pull request #4305 from erasche/bug-report-actions

Refactor bug reporting into plugins / Remove bug report mako

Commit: fcd06a96d61342564febfaf652198bd009c9c76f https://github.com/galaxyproject/galaxy/commit/fcd06a96d61342564febfaf652198... Author: John Chilton jmchilton@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M scripts/grt/export.py M scripts/grt/upload.py

Log Message: ----------- Merge pull request #4408 from erasche/grt-pardir

Small GRT bugfixes

Commit: e3de5e250d02d105aff4265a0caf13553e3c3ade https://github.com/galaxyproject/galaxy/commit/e3de5e250d02d105aff4265a0caf1... Author: John Chilton jmchilton@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/sort_collection_list.xml M test/functional/tools/samples_tool_conf.xml

Log Message: ----------- Merge pull request #4329 from glormph/collection_list_sort

Created alphabetic and numerical sort tool for collection operations

Commit: bcdf2c84f6df020e81c8868b10bcf337e2d72630 https://github.com/galaxyproject/galaxy/commit/bcdf2c84f6df020e81c8868b10bcf... Author: John Chilton jmchilton@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/tabular.py A test-data/test.vcf.gz M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/vcf_bgzip.xml

Log Message: ----------- Merge pull request #4254 from ffinfo/vcf_gz_datatype

Vcf gz datatype

Commit: 583765c7c087c77c6d1f2756e4233ce97a71240f https://github.com/galaxyproject/galaxy/commit/583765c7c087c77c6d1f2756e4233... Author: guerler aysam.guerler@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js A client/galaxy/scripts/mvc/job/job-params.js M client/galaxy/style/less/galaxy_bootstrap/overrides.less M config/datatypes_conf.xml.sample A config/error_report.yml.sample M config/tool_conf.xml.sample A doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/index.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py A lib/galaxy/tools/error_reports/__init__.py A lib/galaxy/tools/error_reports/plugins/__init__.py A lib/galaxy/tools/error_reports/plugins/biostars.py A lib/galaxy/tools/error_reports/plugins/email.py A lib/galaxy/tools/error_reports/plugins/json.py A lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/errors.py A lib/galaxy/tools/sort_collection_list.xml M lib/galaxy/util/biostar.py M lib/galaxy/util/plugin_config.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M scripts/grt/export.py M scripts/grt/upload.py A static/maps/mvc/dataset/dataset-error.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map A static/maps/mvc/job/job-params.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js A static/scripts/mvc/job/job-params.js M static/style/blue/base.css M templates/show_params.mako R templates/webapps/galaxy/dataset/errors.mako A test-data/test.vcf.gz M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/vcf_bgzip.xml

Log Message: ----------- Merge branch 'dev' into revise_grid_forms

Commit: be19b36ecaab43dd9cbf2fd5f80995e7ac9ff507 https://github.com/galaxyproject/galaxy/commit/be19b36ecaab43dd9cbf2fd5f8099... Author: guerler aysam.guerler@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js A client/galaxy/scripts/mvc/job/job-params.js M client/galaxy/style/less/galaxy_bootstrap/overrides.less M config/datatypes_conf.xml.sample A config/error_report.yml.sample M config/tool_conf.xml.sample A doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/index.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py A lib/galaxy/tools/error_reports/__init__.py A lib/galaxy/tools/error_reports/plugins/__init__.py A lib/galaxy/tools/error_reports/plugins/biostars.py A lib/galaxy/tools/error_reports/plugins/email.py A lib/galaxy/tools/error_reports/plugins/json.py A lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/errors.py A lib/galaxy/tools/sort_collection_list.xml M lib/galaxy/util/biostar.py M lib/galaxy/util/plugin_config.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M scripts/grt/export.py M scripts/grt/upload.py A static/maps/mvc/dataset/dataset-error.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map A static/maps/mvc/job/job-params.js.map M static/maps/mvc/user/user-preferences.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 A static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js A static/scripts/mvc/job/job-params.js M static/scripts/mvc/user/user-preferences.js M static/style/blue/base.css M templates/show_params.mako R templates/webapps/galaxy/dataset/errors.mako A test-data/test.vcf.gz M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/vcf_bgzip.xml

Log Message: ----------- Merge branch 'revise_grid_forms' into admin_grid_roles

Commit: b38ccbc10547ded7e3afec262a5819bd3d44613f https://github.com/galaxyproject/galaxy/commit/b38ccbc10547ded7e3afec262a581... Author: guerler aysam.guerler@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js A client/galaxy/scripts/mvc/job/job-params.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/style/less/galaxy_bootstrap/overrides.less M config/datatypes_conf.xml.sample A config/error_report.yml.sample M config/tool_conf.xml.sample A config/user_preferences_extra_conf.yml.sample A doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/index.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0135_add_library_tags.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload_common.py A lib/galaxy/tools/error_reports/__init__.py A lib/galaxy/tools/error_reports/plugins/__init__.py A lib/galaxy/tools/error_reports/plugins/biostars.py A lib/galaxy/tools/error_reports/plugins/email.py A lib/galaxy/tools/error_reports/plugins/json.py A lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_objects.py A lib/galaxy/tools/sort_collection_list.xml M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/biostar.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/workflow/extract.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/utility_container_manager.py M scripts/grt/export.py M scripts/grt/upload.py A static/maps/mvc/dataset/dataset-error.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/admin.bundled.js 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 A static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/style/blue/base.css M templates/show_params.mako R templates/webapps/galaxy/dataset/errors.mako M templates/webapps/tool_shed/repository/common.mako A test-data/test.vcf.gz M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/vcf_bgzip.xml M test/unit/tools/test_parsing.py

Log Message: ----------- Merge branch 'admin_grid_roles' into admin_grid_groups

Commit: ad2f39c1e6475c65fcb1e300201c035701640f10 https://github.com/galaxyproject/galaxy/commit/ad2f39c1e6475c65fcb1e300201c0... Author: guerler aysam.guerler@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Fix lint

Commit: 6a7cc34e1b1ade9580e464570fc6b83a488e941f https://github.com/galaxyproject/galaxy/commit/6a7cc34e1b1ade9580e464570fc6b... Author: John Chilton jmchilton@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M run.sh M run_reports.sh M run_tool_shed.sh A scripts/common_startup_functions.sh

Log Message: ----------- Bring Galaxy, reports, and shed run scripts in sync.

- They now uniformly handle server option processing. - Reports and Tool Shed now respect many new and important options such as --skip_venv. - Reports and Tool Shed now do extra checking around Python version that Galaxy does.

In addition to improving the reports and tool shed startup scripts and reducing cognative load with respect to option handling, this is an important pre-condition to us being able us to switch on uwsgi by default for all three services simultaneously without a bunch of copy and pasting.

Commit: 72e5a00ba0ad9c1a8e56ad9544bec23c843d900d https://github.com/galaxyproject/galaxy/commit/72e5a00ba0ad9c1a8e56ad9544bec... Author: John Chilton jmchilton@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M run_reports.sh M run_tool_shed.sh M scripts/common_startup_functions.sh

Log Message: ----------- Centralize launching server for reports and tool shed.

Initial outline of allowing launch via uwsgi.

Commit: 1bdb99bbd76d0827cd3a7e617d288564584863ea https://github.com/galaxyproject/galaxy/commit/1bdb99bbd76d0827cd3a7e617d288... Author: John Chilton jmchilton@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/util/properties.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/tool_shed/buildapp.py M scripts/manage_tools.py

Log Message: ----------- Update galaxy.util.properties to allow YAML.

Commit: 8189a1f1e289e14d362fcb8871b9339c3355e8b2 https://github.com/galaxyproject/galaxy/commit/8189a1f1e289e14d362fcb8871b93... Author: John Chilton jmchilton@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: A lib/galaxy/webapps/config_manage.py A scripts/config_sample_to_kwalify.py A test/unit/config/1607_root_filters/config/galaxy.ini A test/unit/config/1607_root_filters/config/tool_shed.ini A test/unit/config/1607_root_samples/config/galaxy.ini A test/unit/config/1607_root_samples/config/reports.ini A test/unit/config/1607_root_samples/config/tool_shed.ini A test/unit/config/test_config_manage.py

Log Message: ----------- Scripts to manage configuration infrastructure.

This has been rebased several times and includes a variety of fixes (some thanks to martenson).

Commit: 7973a914e0beef9680475d54947bd953c0b062cd https://github.com/galaxyproject/galaxy/commit/7973a914e0beef9680475d54947bd... Author: John Chilton jmchilton@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: A lib/galaxy/webapps/uwsgi_schema.yml

Log Message: ----------- Add uwsgi_schema.yml.

Commit: 90e899d68fbf21effad1cf309efbd786c54be556 https://github.com/galaxyproject/galaxy/commit/90e899d68fbf21effad1cf309efbd... Author: John Chilton jmchilton@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: R config/tool_shed.ini.sample A config/tool_shed.yml.sample M lib/galaxy/webapps/tool_shed/buildapp.py A lib/galaxy/webapps/tool_shed/config_schema.yml A lib/galaxy/webapps/tool_shed/uwsgi_schema.yml M run_tool_shed.sh

Log Message: ----------- Update tool shed to use newer configuration schema.

- Implement kwalify schema to validate/define the schema. - Replace ini configuration with YAML (completely backward compatible). - Rebuild a sample configuration from the schema (config/tool_shed.yml.sample).

Commit: 102566dd5e1c5903726057f1077a1d7fc614b815 https://github.com/galaxyproject/galaxy/commit/102566dd5e1c5903726057f1077a1... Author: John Chilton jmchilton@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: R config/reports.ini.sample A config/reports.yml.sample M lib/galaxy/webapps/reports/buildapp.py A lib/galaxy/webapps/reports/config_schema.yml A lib/galaxy/webapps/reports/uwsgi_schema.yml M run_reports.sh

Log Message: ----------- Update Galaxy Reports to use newer configuration schema.

- Implement kwalify schema to validate/define the schema. - Replace ini configuration with YAML (completely backward compatible). - Rebuild a sample configuration from the schema (config/reports.yml.sample).

Commit: 50d426ed2b9ae2aff8b243143478ce84c7731816 https://github.com/galaxyproject/galaxy/commit/50d426ed2b9ae2aff8b243143478c... Author: John Chilton jmchilton@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: A doc/source/admin/reports.rst A doc/source/admin/reports_options.rst

Log Message: ----------- Add reports documentation to ``doc/``.

- Automatically generate RST docs from config schema. - Describe older functionality as well as new YAML-based configuration. - Replace https://wiki.galaxyproject.org/Admin/UsageReports.

Commit: 4945f55e4fe28842b58c025b37c4d6c96a07028f https://github.com/galaxyproject/galaxy/commit/4945f55e4fe28842b58c025b37c4d... Author: John Chilton jmchilton@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M Makefile

Log Message: ----------- Makefile shortcuts for configuration script.

Commit: ef46a60a829e3dae44d935f6f886feef39b873e3 https://github.com/galaxyproject/galaxy/commit/ef46a60a829e3dae44d935f6f886f... Author: John Chilton jmchilton@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt

Log Message: ----------- Add required dependency on uwsgi.

Required for the new out-of-the-box configuration of tool shed and reports.

Commit: 8191fd492819214b12c0aa28b35e5b6c4ea7bfa1 https://github.com/galaxyproject/galaxy/commit/8191fd492819214b12c0aa28b35e5... Author: John Chilton jmchilton@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt

Log Message: ----------- Add pykwalify as dependency for the new config validation stuff.

xref https://github.com/galaxyproject/starforge/pull/110

Commit: ffe295e96dbd82615c987a2b9ba9bd15ea253826 https://github.com/galaxyproject/galaxy/commit/ffe295e96dbd82615c987a2b9ba9b... Author: John Chilton jmchilton@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M test/unit/config/test_config_manage.py

Log Message: ----------- Fix Python 3 linting problem with test_config_manage.py.

Commit: 1ce93ccfdf7b54ec1efcf08b04c9f28b67ab0615 https://github.com/galaxyproject/galaxy/commit/1ce93ccfdf7b54ec1efcf08b04c9f... Author: John Chilton jmchilton@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt

Log Message: ----------- Pin version of uWSGI to freshly released 2.0.15 available on wheels.galaxyproject.org.

Commit: 539a62f642ada1f2d832f1f88ab339cafe672c1f https://github.com/galaxyproject/galaxy/commit/539a62f642ada1f2d832f1f88ab33... Author: John Chilton jmchilton@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M lib/galaxy/model/orm/scripts.py M lib/galaxy/util/properties.py

Log Message: ----------- Fix ORM scripts for #3179.

Commit: 98ca8ce7a68d18533f3bf85097490c5b66e9f876 https://github.com/galaxyproject/galaxy/commit/98ca8ce7a68d18533f3bf85097490... Author: John Chilton jmchilton@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/buildapp.py

Log Message: ----------- Update config overhaul branch for introduction of galaxy.web.stack package.

Commit: 23db89ba3ddf54420b40e881bd92edbfeff869c6 https://github.com/galaxyproject/galaxy/commit/23db89ba3ddf54420b40e881bd92e... Author: John Chilton jmchilton@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/flake8_wrapper_docstrings.sh A .ci/jenkins/api/run_tests.sh A .ci/jenkins/framework/run_tests.sh A .ci/jenkins/integration/run_tests.sh A .ci/jenkins/selenium/Dockerfile A .ci/jenkins/selenium/docker-compose.yml A .ci/jenkins/selenium/galaxy.ini A .ci/jenkins/selenium/run_galaxy.bash A .ci/jenkins/selenium/run_tests.sh A .ci/jenkins/toolshed/run_tests.sh M .ci/py3_sources.txt M .gitignore M .travis.yml M CITATION M CONTRIBUTING.md M CONTRIBUTORS.md M Makefile M README.rst A SECURITY_POLICY.md A client/galaxy/scripts/admin.toolshed.js A client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js R client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/apps/login.js A client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/apps/panels/history-panel.js A client/galaxy/scripts/apps/panels/tool-panel.js R client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js A client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/libs/jquery/jquery.autocomplete.js M client/galaxy/scripts/mvc/citation/citation-view.js A client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js A client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js A client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/grid/grid-model.js A client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/history-contents.js A client/galaxy/scripts/mvc/history/history-list.js M 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client/galaxy/style/less/ui.less M client/galaxy/style/less/ui/paired-collection-creator.less M client/galaxy/style/less/upload.less M client/galaxy/style/source_material/circle.py A client/package-lock.json M client/package.json M client/webpack.config.js A config/build_sites.yml.sample A config/containers_conf.yml.sample M config/datatypes_conf.xml.sample M config/dependency_resolvers_conf.xml.sample A config/error_report.yml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced A config/local_conda_mapping.yml.sample M config/openid_conf.xml.sample M config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample M config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/common/templates/ie.mako A config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample A 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test/selenium_tests/test_history_panel.py A test/selenium_tests/test_history_sharing.py A test/selenium_tests/test_login.py A test/selenium_tests/test_registration.py A test/selenium_tests/test_stock_tours.py A test/selenium_tests/test_tool_form.py A test/selenium_tests/test_uploads.py A test/selenium_tests/test_workflow_editor.py A test/selenium_tests/test_workflow_management.py A test/selenium_tests/test_workflow_run.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1090_repository_dependency_handling.py M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py M test/shed_functional/functional/test_1150_datatype_converters.py M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py M test/unit/dataset_collections/test_matching.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py A test/unit/jobs/conditional_runners_job_conf.xml M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_rule_helper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_fabric_util.py A test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_td_common_util.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_galaxy_transactions.py A test/unit/test_remote_shell.py M test/unit/test_routes.py M test/unit/test_sockets.py M test/unit/tools/test_actions.py M test/unit/tools/test_citations.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_dependency_description.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_external_files.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/tools/test_wrappers.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/unittest_utils/utility.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py A tool-data/blastdb.loc.sample A tool-data/blastdb_d.loc.sample A tool-data/blastdb_p.loc.sample M tool-data/shared/ucsc/builds.txt.sample M tool-data/shared/ucsc/ucsc_build_sites.txt.sample M tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/upload.py M tools/evolution/add_scores.py M tools/evolution/add_scores.xml M tools/extract/extract_genomic_dna.py M tools/extract/extract_genomic_dna.xml M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_fasta.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_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml M tools/filters/gff/gtf_filter_by_attribute_values_list.py R tools/filters/gff/sort_gtf.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed.py M tools/filters/mergeCols.py M tools/filters/pasteWrapper.xml M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/secure_hash_message_digest.py M tools/filters/sorter.py M tools/filters/trimmer.py M tools/filters/trimmer.xml 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/filters/uniq.py M tools/filters/wc_gnu.xml M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.py M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/macros.xml M tools/maf/maf_by_block_number.py M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.py M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.py M tools/maf/maf_limit_size.xml M tools/maf/maf_limit_to_species.py M tools/maf/maf_limit_to_species.xml M tools/maf/maf_reverse_complement.py M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.py M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.py M tools/maf/maf_stats.xml M tools/maf/maf_thread_for_species.py M tools/maf/maf_thread_for_species.xml M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta.xml M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/maf_to_interval.xml M tools/maf/vcf_to_maf_customtrack.py M tools/maf/vcf_to_maf_customtrack.xml M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/fastq_gen_conv.xml M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/plotting/bar_chart.xml M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/stats/aggregate_binned_scores_in_intervals.xml M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tox.ini

Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into install_workflow_and_tools

Conflicts: lib/galaxy/webapps/galaxy/api/workflows.py

Commit: 7dd3ddccafee8f5cc185f1b0dd711056576a92ce https://github.com/galaxyproject/galaxy/commit/7dd3ddccafee8f5cc185f1b0dd711... Author: John Chilton jmchilton@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py

Log Message: ----------- Require admin for new import_tools function in workflows API.

Includes test case.

Commit: 6353704e4b44e9eded6571b467f52a6dd288387d https://github.com/galaxyproject/galaxy/commit/6353704e4b44e9eded6571b467f52... Author: John Chilton jmchilton@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py M openid/yahoo.xml

Log Message: ----------- Merge pull request #4039 from VJalili/patch-11

Updated parameters check for OpenID

Commit: e49ba40d771dae0d7056ed089c99f3d53a81b933 https://github.com/galaxyproject/galaxy/commit/e49ba40d771dae0d7056ed089c99f... Author: John Chilton jmchilton@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/parameters/grouping.py

Log Message: ----------- Generalize allow_library_path_paste to allow_path_paste.

Enable pasting paths in the history upload GUI & general purpose tools API for admin users if enabled.

Commit: f97efa6f90f80ced8bd0c794841e450813238710 https://github.com/galaxyproject/galaxy/commit/f97efa6f90f80ced8bd0c794841e4... Author: John Chilton jmchilton@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M lib/galaxy/tools/parameters/grouping.py

Log Message: ----------- Remove unused dataset_info in parameters.grouping.

Commit: 33acc1f8a337977eb85e9ba570f3404476411edc https://github.com/galaxyproject/galaxy/commit/33acc1f8a337977eb85e9ba570f34... Author: guerler aysam.guerler@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)

Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js A client/galaxy/scripts/mvc/job/job-params.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/style/less/galaxy_bootstrap/overrides.less M config/datatypes_conf.xml.sample A config/error_report.yml.sample M config/tool_conf.xml.sample A config/user_preferences_extra_conf.yml.sample A doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/index.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0135_add_library_tags.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload_common.py A lib/galaxy/tools/error_reports/__init__.py A lib/galaxy/tools/error_reports/plugins/__init__.py A lib/galaxy/tools/error_reports/plugins/biostars.py A lib/galaxy/tools/error_reports/plugins/email.py A lib/galaxy/tools/error_reports/plugins/json.py A lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_objects.py A lib/galaxy/tools/sort_collection_list.xml M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/biostar.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/workflow/extract.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/utility_container_manager.py M scripts/grt/export.py M scripts/grt/upload.py A static/maps/mvc/dataset/dataset-error.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/admin.bundled.js 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 A static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/style/blue/base.css M templates/show_params.mako R templates/webapps/galaxy/dataset/errors.mako M templates/webapps/tool_shed/repository/common.mako A test-data/test.vcf.gz M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/vcf_bgzip.xml M test/unit/tools/test_parsing.py

Log Message: ----------- Merge branch 'admin_grid_groups' into admin_grid_toolversion

Commit: ef2c32ae84706897e70fa41808f46d95f1132ec9 https://github.com/galaxyproject/galaxy/commit/ef2c32ae84706897e70fa41808f46... Author: guerler aysam.guerler@gmail.com Date: 2017-08-11 (Fri, 11 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Fix lint

Commit: 600b0aad7ce10c1e427513684c4cd7423f5b52aa https://github.com/galaxyproject/galaxy/commit/600b0aad7ce10c1e427513684c4cd... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-11 (Fri, 11 Aug 2017)

Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/form/form-view.js A client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/utils/query-string-parsing.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/util/admin_util.py M static/maps/mvc/form/form-view.js.map A static/maps/mvc/form/form-wrapper.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/utils/query-string-parsing.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-view.js A static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/user/user-preferences.js M static/scripts/utils/query-string-parsing.js R templates/admin/dataset_security/group/grid.mako R templates/admin/dataset_security/role/grid.mako R templates/admin/quota/grid.mako R templates/admin/tool_shed_repository/grid.mako R templates/admin/tool_version/grid.mako R templates/admin/user/grid.mako R templates/admin/user/reset_password.mako R templates/admin/user/user.mako A templates/webapps/tool_shed/admin/user/reset_password.mako A templates/webapps/tool_shed/admin/user/user.mako R templates/webapps/tool_shed/repository/grid.mako

Log Message: ----------- Merge pull request #4377 from guerler/revise_grid_forms

Remove makos of admin user grid forms

Commit: 33c794d273271b14732fb8037c2ea8105a3c688e https://github.com/galaxyproject/galaxy/commit/33c794d273271b14732fb8037c2ea... Author: John Chilton jmchilton@gmail.com Date: 2017-08-11 (Fri, 11 Aug 2017)

Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/utils/query-string-parsing.js M client/galaxy/style/less/ui.less M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/tool_shed/util/admin_util.py M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-wrapper.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/ui-buttons.js.map M static/maps/mvc/ui/ui-list.js.map M static/maps/mvc/user/user-custom-builds.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/utils/query-string-parsing.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/mvc/form/form-repeat.js M static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/ui-buttons.js M static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-preferences.js M static/scripts/utils/query-string-parsing.js M static/style/blue/base.css R templates/admin/dataset_security/role/role.mako R templates/admin/dataset_security/role/role_create.mako R templates/admin/dataset_security/role/role_rename.mako A templates/webapps/tool_shed/admin/dataset_security/role/role.mako A templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako A templates/webapps/tool_shed/admin/dataset_security/role/role_rename.mako

Log Message: ----------- Merge pull request #4385 from guerler/admin_grid_roles

Admin grid roles revision

Commit: 10285b8ecbbc6891a4954b5067198df2839a2957 https://github.com/galaxyproject/galaxy/commit/10285b8ecbbc6891a4954b5067198... Author: John Chilton jmchilton@gmail.com Date: 2017-08-11 (Fri, 11 Aug 2017)

Changed paths: M lib/galaxy/datatypes/binary.py

Log Message: ----------- Tweak Excel format phrasing based on review from @nsoranzo.

Commit: fbde34f8c8e823badd0f565bce4922512448b532 https://github.com/galaxyproject/galaxy/commit/fbde34f8c8e823badd0f565bce492... Author: John Chilton jmchilton@gmail.com Date: 2017-08-11 (Fri, 11 Aug 2017)

Changed paths: M lib/galaxy/datatypes/binary.py

Log Message: ----------- Add EDAM format for excel.xls datatype.

Commit: cca00ea5d87fb0baba3ceca715038158cf2ceba0 https://github.com/galaxyproject/galaxy/commit/cca00ea5d87fb0baba3ceca715038... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-11 (Fri, 11 Aug 2017)

Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/parameters/grouping.py

Log Message: ----------- Merge pull request #4404 from jmchilton/allow_path_paste

Generalize allow_library_path_paste to allow_path_paste.

Commit: c6e45e7b0720376886626393ae355e3398561035 https://github.com/galaxyproject/galaxy/commit/c6e45e7b0720376886626393ae355... Author: Björn Grüning bjoern@gruenings.eu Date: 2017-08-11 (Fri, 11 Aug 2017)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/1.xls

Log Message: ----------- Merge pull request #4410 from jmchilton/excel97

Add Excel97 Datatype

Commit: 331851b0495d429220450ceb3a540fbba900143a https://github.com/galaxyproject/galaxy/commit/331851b0495d429220450ceb3a540... Author: Björn Grüning bjoern@gruenings.eu Date: 2017-08-12 (Sat, 12 Aug 2017)

Changed paths: M Makefile R config/reports.ini.sample A config/reports.yml.sample R config/tool_shed.ini.sample A config/tool_shed.yml.sample A doc/source/admin/reports.rst A doc/source/admin/reports_options.rst M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/model/orm/scripts.py M lib/galaxy/util/properties.py M lib/galaxy/web/framework/webapp.py A lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py A lib/galaxy/webapps/reports/config_schema.yml A lib/galaxy/webapps/reports/uwsgi_schema.yml M lib/galaxy/webapps/tool_shed/buildapp.py A lib/galaxy/webapps/tool_shed/config_schema.yml A lib/galaxy/webapps/tool_shed/uwsgi_schema.yml A lib/galaxy/webapps/uwsgi_schema.yml M run.sh M run_reports.sh M run_tool_shed.sh A scripts/common_startup_functions.sh A scripts/config_sample_to_kwalify.py M scripts/manage_tools.py A test/unit/config/1607_root_filters/config/galaxy.ini A test/unit/config/1607_root_filters/config/tool_shed.ini A test/unit/config/1607_root_samples/config/galaxy.ini A test/unit/config/1607_root_samples/config/reports.ini A test/unit/config/1607_root_samples/config/tool_shed.ini A test/unit/config/test_config_manage.py

Log Message: ----------- Merge pull request #3179 from jmchilton/web_config_overhaul_0

Configuration & Server Overhaul - Tool Shed and Reports

Commit: 7a1fbd37e9fb262432daed6eefc4e9c54ceff406 https://github.com/galaxyproject/galaxy/commit/7a1fbd37e9fb262432daed6eefc4e... Author: John Chilton jmchilton@gmail.com Date: 2017-08-12 (Sat, 12 Aug 2017)

Changed paths: M lib/galaxy/util/checkers.py

Log Message: ----------- Fix bug in upload HTML checker.

If a chunk was passed into the check_html function - e.g. it was read from a compressed file - it would search through each character in the string for certain HTML content instead of each line in the string.

Commit: 59aa11864a795861484133dfc85212bf9150cf4a https://github.com/galaxyproject/galaxy/commit/59aa11864a795861484133dfc8521... Author: John Chilton jmchilton@gmail.com Date: 2017-08-12 (Sat, 12 Aug 2017)

Changed paths: M lib/galaxy/config.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/util/checkers.py M tools/data_source/upload.py

Log Message: ----------- Add configuration option to disable upload content checking.

Commit: 53b0b25456c170990ad3345021aab16f68e6e185 https://github.com/galaxyproject/galaxy/commit/53b0b25456c170990ad3345021aab... Author: John Chilton jmchilton@gmail.com Date: 2017-08-12 (Sat, 12 Aug 2017)

Changed paths: M test/base/populators.py

Log Message: ----------- Better error reporting in test/base/populators.py.

Commit: bee6af1e4117e7ff6f7caac0d9c84253ec1c4882 https://github.com/galaxyproject/galaxy/commit/bee6af1e4117e7ff6f7caac0d9c84... Author: John Chilton jmchilton@gmail.com Date: 2017-08-12 (Sat, 12 Aug 2017)

Changed paths: M test/base/api.py

Log Message: ----------- Allow API tests to work with admin users (not just admin keys).

Commit: fec1eab82dc6dea2d03711127ed08b3038ad5bf1 https://github.com/galaxyproject/galaxy/commit/fec1eab82dc6dea2d03711127ed08... Author: John Chilton jmchilton@gmail.com Date: 2017-08-12 (Sat, 12 Aug 2017)

Changed paths: M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M test/base/populators.py M tools/data_source/upload.py M tools/data_source/upload.xml

Log Message: ----------- Add ability to arbitrarily not decompress files on upload via API.

Commit: fc861cdf38d1d20fd611e8bcb042328eb905b3c4 https://github.com/galaxyproject/galaxy/commit/fc861cdf38d1d20fd611e8bcb0423... Author: John Chilton jmchilton@gmail.com Date: 2017-08-12 (Sat, 12 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py

Log Message: ----------- Merge pull request #3064 from manabuishii/install_workflow_and_tools

Install tools and workflow

Commit: 06ca789f92ad2f4dfaffc36d3fa0bafb3c74920d https://github.com/galaxyproject/galaxy/commit/06ca789f92ad2f4dfaffc36d3fa0b... Author: John Chilton jmchilton@gmail.com Date: 2017-08-12 (Sat, 12 Aug 2017)

Changed paths: A test-data/1.sam.gz A test-data/bad.html.gz A test-data/random-file M test/functional/tools/sample_datatypes_conf.xml A test/integration/test_upload_configuration_options.py

Log Message: ----------- Configuration tests for the last few upload enhancements.

Commit: 5f1b7d5a5060c3c45601b499a953113e0b1b3125 https://github.com/galaxyproject/galaxy/commit/5f1b7d5a5060c3c45601b499a9531... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-13 (Sun, 13 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js

Log Message: ----------- Show verison button in workflow editor and trigger on_change

Commit: 25e05b62c7b529b0379e3ff50fc75ccb5b8c28b6 https://github.com/galaxyproject/galaxy/commit/25e05b62c7b529b0379e3ff50fc75... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-13 (Sun, 13 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js

Log Message: ----------- Do postchange action only when modifiying tool versions in the workflow editor

Commit: 5afe490822325d4aa6c9be726183175743dc88f6 https://github.com/galaxyproject/galaxy/commit/5afe490822325d4aa6c9be7261831... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-13 (Sun, 13 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js

Log Message: ----------- Fix qunit test

Commit: 36ce9113f7ccb6372bc2d1f8e92e95a8aafdd066 https://github.com/galaxyproject/galaxy/commit/36ce9113f7ccb6372bc2d1f8e92e9... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-13 (Sun, 13 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js

Log Message: ----------- Keep spacing consistent (thx @nsoranzo)

Commit: 526e98e372e61747b1e3cd4b86a04603ca08959b https://github.com/galaxyproject/galaxy/commit/526e98e372e61747b1e3cd4b86a04... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-13 (Sun, 13 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-node.js

Log Message: ----------- Reset outputs when changing tool versions in wf-editor

Commit: db2ea853f699bf6b55b67cf7199ab355196910bc https://github.com/galaxyproject/galaxy/commit/db2ea853f699bf6b55b67cf7199ab... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-13 (Sun, 13 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js

Log Message: ----------- Now thing are mostly working -- input and output connections are correctly altered ... but saving the workflow and reloading occasionally loads the wrong workflow

Commit: ea1f4f866658e77465d1272b4d7f37bb85ee488b https://github.com/galaxyproject/galaxy/commit/ea1f4f866658e77465d1272b4d7f3... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-13 (Sun, 13 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js

Log Message: ----------- Fix the occasional loading of the wrong workflow. Turns out that sometimes the tool_version is undefined (i.e) if the exact node had not been manipulated, but config_form.version is always up to date

Commit: bc95f5e81b46a0bee54f6ffdd5c3a6615258af20 https://github.com/galaxyproject/galaxy/commit/bc95f5e81b46a0bee54f6ffdd5c3a... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-13 (Sun, 13 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js

Log Message: ----------- Now adding/removing datasets and multiple version switches work fine, but PJA parameters are still problematic

Commit: 92fedc0ae86127d670f3ff8e829d07ee657f30d7 https://github.com/galaxyproject/galaxy/commit/92fedc0ae86127d670f3ff8e829d0... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-13 (Sun, 13 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js

Log Message: ----------- Fix logic for adding and removing outputs

Commit: 1c286b158a8304380f499709b2f14c958b6fe203 https://github.com/galaxyproject/galaxy/commit/1c286b158a8304380f499709b2f14... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-13 (Sun, 13 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-node.js

Log Message: ----------- Remove extra newlines

Commit: 2e95026317e2e781163cf8bd4449bfd5ddfb894f https://github.com/galaxyproject/galaxy/commit/2e95026317e2e781163cf8bd4449b... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-13 (Sun, 13 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js

Log Message: ----------- Remove unused old_version variable

Commit: 31c423a45a4186c41981f71d41a590177bad033d https://github.com/galaxyproject/galaxy/commit/31c423a45a4186c41981f71d41a59... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-13 (Sun, 13 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js

Log Message: ----------- Fix typo and remove leftover comment (thanks @nsoranzo)

Commit: df91881c1f4dba06a9fb6a1720db68d059664041 https://github.com/galaxyproject/galaxy/commit/df91881c1f4dba06a9fb6a1720db6... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-13 (Sun, 13 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js

Log Message: ----------- Remove unused workflow outputs

Commit: 73f4141d96ad54c25fdf7a3ffb458f2b1933e14e https://github.com/galaxyproject/galaxy/commit/73f4141d96ad54c25fdf7a3ffb458... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-14 (Mon, 14 Aug 2017)

Changed paths: M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view.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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js

Log Message: ----------- Add static JS

Commit: f849c7e6feafabf905653bd008fde23dc1413a85 https://github.com/galaxyproject/galaxy/commit/f849c7e6feafabf905653bd008fde... Author: Björn Grüning bjoern@gruenings.eu Date: 2017-08-14 (Mon, 14 Aug 2017)

Changed paths: M lib/galaxy/config.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/checkers.py A test-data/1.sam.gz A test-data/bad.html.gz A test-data/random-file M test/base/api.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml A test/integration/test_upload_configuration_options.py M tools/data_source/upload.py M tools/data_source/upload.xml

Log Message: ----------- Merge pull request #4417 from jmchilton/upload_enhance

Fixes and enhancements for the upload API

Commit: 8e192dbf4ca2f7c6c0860430a4d8085de7732ab1 https://github.com/galaxyproject/galaxy/commit/8e192dbf4ca2f7c6c0860430a4d80... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2017-08-14 (Mon, 14 Aug 2017)

Changed paths: M test/api/test_tools.py M test/base/interactor.py M test/base/populators.py

Log Message: ----------- Merge pull request #4397 from jmchilton/api_test_enhancement

Better Error Summaries for API Tests

Commit: e594152de2dd33dbdff2feb8e05f05ad5810ab27 https://github.com/galaxyproject/galaxy/commit/e594152de2dd33dbdff2feb8e05f0... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2017-08-14 (Mon, 14 Aug 2017)

Changed paths: M lib/galaxy/managers/workflows.py

Log Message: ----------- Merge pull request #4394 from jmchilton/subworkflow_loading_fix

Bugfix for loading subworkflows from workflow descriptions.

Commit: 9cbabef17e9afb4953324516d0883976edd51e87 https://github.com/galaxyproject/galaxy/commit/9cbabef17e9afb4953324516d0883... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-08-14 (Mon, 14 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/molecules.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js

Log Message: ----------- Merge branch 'release_17.05' into dev

Conflicts: static/maps/mvc/library/library-foldertoolbar-view.js.map static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map static/scripts/mvc/library/library-foldertoolbar-view.js

Commit: 4dd503046f59b13e925a76f88862882747dc6ad7 https://github.com/galaxyproject/galaxy/commit/4dd503046f59b13e925a76f888628... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-08-14 (Mon, 14 Aug 2017)

Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/resolvers/conda.py

Log Message: ----------- Update conda channel order to sync with Bioconda

Commit: 420e7a4f3408ec064403a4283ba22a134b65ece5 https://github.com/galaxyproject/galaxy/commit/420e7a4f3408ec064403a4283ba22... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-08-14 (Mon, 14 Aug 2017)

Changed paths: M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py

Log Message: ----------- Remove _ensure_conda_context() function

and make conda_context argument mandatory in functions/methods. This should help making sure the correct context (e.g. channels) is used for all Conda operations.

Also remove unused is_target_available() function.

Commit: cdbac056cb664e4c51f84c41c2519993d0412d74 https://github.com/galaxyproject/galaxy/commit/cdbac056cb664e4c51f84c41c2519... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-08-14 (Mon, 14 Aug 2017)

Changed paths: M lib/galaxy/tools/deps/conda_util.py

Log Message: ----------- Override channel list on the command line instead of modifying condarc

The way we were modifying condarc in the ensure_channels_configured() method was broken because we were appending the missing channels at the end, so the final order may not be the one specified in conda_ensure_channels .

Also: - not modifying the user condarc is a much better approach - overriding the channel list on the command line will make debugging easier

Commit: eccdc8c248fabef6bc5a988cdb1889c1aa32ca7a https://github.com/galaxyproject/galaxy/commit/eccdc8c248fabef6bc5a988cdb188... Author: guerler aysam.guerler@gmail.com Date: 2017-08-14 (Mon, 14 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Removed unreached message line

Commit: fd5f42dc17009cfdfbfc08583549ba608efb166a https://github.com/galaxyproject/galaxy/commit/fd5f42dc17009cfdfbfc08583549b... Author: guerler aysam.guerler@gmail.com Date: 2017-08-14 (Mon, 14 Aug 2017)

Changed paths: M Makefile M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample R config/reports.ini.sample A config/reports.yml.sample R config/tool_shed.ini.sample A config/tool_shed.yml.sample A doc/source/admin/reports.rst A doc/source/admin/reports_options.rst M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/1.xls M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/managers/workflows.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/checkers.py M lib/galaxy/util/properties.py M lib/galaxy/web/framework/webapp.py A lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/reports/buildapp.py A lib/galaxy/webapps/reports/config_schema.yml A lib/galaxy/webapps/reports/uwsgi_schema.yml M lib/galaxy/webapps/tool_shed/buildapp.py A lib/galaxy/webapps/tool_shed/config_schema.yml A lib/galaxy/webapps/tool_shed/uwsgi_schema.yml A lib/galaxy/webapps/uwsgi_schema.yml M openid/yahoo.xml M run.sh M run_reports.sh M run_tool_shed.sh A scripts/common_startup_functions.sh A scripts/config_sample_to_kwalify.py M scripts/manage_tools.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js A test-data/1.sam.gz A test-data/bad.html.gz A test-data/random-file M test/api/test_tools.py M test/api/test_workflows.py M test/base/api.py M test/base/interactor.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml A test/integration/test_upload_configuration_options.py A test/unit/config/1607_root_filters/config/galaxy.ini A test/unit/config/1607_root_filters/config/tool_shed.ini A test/unit/config/1607_root_samples/config/galaxy.ini A test/unit/config/1607_root_samples/config/reports.ini A test/unit/config/1607_root_samples/config/tool_shed.ini A test/unit/config/test_config_manage.py M tools/data_source/upload.py M tools/data_source/upload.xml

Log Message: ----------- Merge branch 'dev' into admin_grid_groups

Commit: 68555f5571b5b872a39a34f8fa6035bfad67ea43 https://github.com/galaxyproject/galaxy/commit/68555f5571b5b872a39a34f8fa603... Author: E Rasche hxr@hx42.org Date: 2017-08-15 (Tue, 15 Aug 2017)

Changed paths: M lib/galaxy/jobs/__init__.py

Log Message: ----------- some unicoding

Commit: 8721da8ca2e1f78a018baf4c43d8229327eb477f https://github.com/galaxyproject/galaxy/commit/8721da8ca2e1f78a018baf4c43d82... Author: John Chilton jmchilton@gmail.com Date: 2017-08-15 (Tue, 15 Aug 2017)

Changed paths: M lib/galaxy/jobs/__init__.py

Log Message: ----------- Merge pull request #4426 from erasche/local-runner-unicode

some unicoding for local runner

Commit: 44548f8f2fe258051ad2df45b153642586b85e00 https://github.com/galaxyproject/galaxy/commit/44548f8f2fe258051ad2df45b1536... Author: John Chilton jmchilton@gmail.com Date: 2017-08-15 (Tue, 15 Aug 2017)

Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py

Log Message: ----------- Merge pull request #4409 from nsoranzo/fix_conda_channel_order

Update conda channel order to sync with Bioconda

Commit: 07a30499994b33e27c0b1765df9f32c9bfcea0b2 https://github.com/galaxyproject/galaxy/commit/07a30499994b33e27c0b1765df9f3... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-08-15 (Tue, 15 Aug 2017)

Changed paths: M lib/galaxy/workflow/modules.py

Log Message: ----------- Merge branch 'release_17.05' into dev

Conflicts: lib/galaxy/model/tool_shed_install/__init__.py

Commit: aa7be28960a43802bd476be1d7d996c85134c055 https://github.com/galaxyproject/galaxy/commit/aa7be28960a43802bd476be1d7d99... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-15 (Tue, 15 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/config.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/checkers.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js A test-data/1.sam.gz A test-data/bad.html.gz A test-data/random-file M test/api/test_tools.py M test/base/api.py M test/base/interactor.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml A test/integration/test_upload_configuration_options.py M tools/data_source/upload.py M tools/data_source/upload.xml

Log Message: ----------- Merge branch 'dev' into switch_versions_in_workflows

Commit: 27be24963837354af6cac1f429c1bc06e95626e1 https://github.com/galaxyproject/galaxy/commit/27be24963837354af6cac1f429c1b... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-15 (Tue, 15 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view.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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js

Log Message: ----------- Merge pull request #4373 from mvdbeek/switch_versions_in_workflows

Allow switching tool versions in workflow editor

Commit: 462b7def5d9b9298d50cea2e62cfbf89bd463d25 https://github.com/galaxyproject/galaxy/commit/462b7def5d9b9298d50cea2e62cfb... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-08-15 (Tue, 15 Aug 2017)

Changed paths: M lib/galaxy/workflow/modules.py

Log Message: ----------- Merge pull request #4427 from nsoranzo/merge_release_17.05

Merge release_17.05 into dev

Commit: e72948cb743e50b50a21bf7f778792ba36ec38bd https://github.com/galaxyproject/galaxy/commit/e72948cb743e50b50a21bf7f77879... Author: guerler aysam.guerler@gmail.com Date: 2017-08-15 (Tue, 15 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view.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/tool-form-base.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js

Log Message: ----------- Merge branch 'dev' into admin_grid_groups

Commit: b726c33c80b33ece878343b6208e65f3d983008f https://github.com/galaxyproject/galaxy/commit/b726c33c80b33ece878343b6208e6... Author: guerler aysam.guerler@gmail.com Date: 2017-08-15 (Tue, 15 Aug 2017)

Changed paths: M Makefile M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample R config/reports.ini.sample A config/reports.yml.sample R config/tool_shed.ini.sample A config/tool_shed.yml.sample M doc/source/admin/dependency_resolvers.rst A doc/source/admin/reports.rst A doc/source/admin/reports_options.rst M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/1.xls M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/checkers.py M lib/galaxy/util/properties.py M lib/galaxy/web/framework/webapp.py A lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/reports/buildapp.py A lib/galaxy/webapps/reports/config_schema.yml A lib/galaxy/webapps/reports/uwsgi_schema.yml M lib/galaxy/webapps/tool_shed/buildapp.py A lib/galaxy/webapps/tool_shed/config_schema.yml A lib/galaxy/webapps/tool_shed/uwsgi_schema.yml A lib/galaxy/webapps/uwsgi_schema.yml M lib/galaxy/workflow/modules.py M openid/yahoo.xml M run.sh M run_reports.sh M run_tool_shed.sh A scripts/common_startup_functions.sh A scripts/config_sample_to_kwalify.py M scripts/manage_tools.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view.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/library/library-foldertoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js A test-data/1.sam.gz A test-data/bad.html.gz A test-data/random-file M test/api/test_tools.py M test/api/test_workflows.py M test/base/api.py M test/base/interactor.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml A test/integration/test_upload_configuration_options.py A test/unit/config/1607_root_filters/config/galaxy.ini A test/unit/config/1607_root_filters/config/tool_shed.ini A test/unit/config/1607_root_samples/config/galaxy.ini A test/unit/config/1607_root_samples/config/reports.ini A test/unit/config/1607_root_samples/config/tool_shed.ini A test/unit/config/test_config_manage.py M tools/data_source/upload.py M tools/data_source/upload.xml

Log Message: ----------- Merge branch 'admin_grid_groups' into admin_grid_toolversion

Commit: a078ee025f02732e108cf2d790e18cc826829ac5 https://github.com/galaxyproject/galaxy/commit/a078ee025f02732e108cf2d790e18... Author: guerler aysam.guerler@gmail.com Date: 2017-08-15 (Tue, 15 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-view.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/tool-form-base.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-view.js

Log Message: ----------- Move form augmentation to form handler

Commit: 5cebb086b2849f92ac8da10d7e776e4334c28ff5 https://github.com/galaxyproject/galaxy/commit/5cebb086b2849f92ac8da10d7e776... Author: Greg Von Kuster ghv2@psu.edu Date: 2017-08-15 (Tue, 15 Aug 2017)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py A lib/galaxy/datatypes/test/1.psp

Log Message: ----------- Add support for the MEME psp format

Commit: 4bddd617fe5df41efcebacdda7a6bb1d280ac2ce https://github.com/galaxyproject/galaxy/commit/4bddd617fe5df41efcebacdda7a6b... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-15 (Tue, 15 Aug 2017)

Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/tool_shed/util/admin_util.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map R templates/admin/dataset_security/group/group.mako R templates/admin/dataset_security/group/group_create.mako R templates/admin/dataset_security/group/group_rename.mako A templates/webapps/tool_shed/admin/dataset_security/group/group.mako A templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako A templates/webapps/tool_shed/admin/dataset_security/group/group_rename.mako

Log Message: ----------- Merge pull request #4405 from guerler/admin_grid_groups

Admin grid groups revision

Commit: 9dfee375e9782f421832ecc44981a2cbdfc4f183 https://github.com/galaxyproject/galaxy/commit/9dfee375e9782f421832ecc44981a... Author: guerler aysam.guerler@gmail.com Date: 2017-08-15 (Tue, 15 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.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/form/form-parameters.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js

Log Message: ----------- Optionally allow to show or hide select all

Commit: a1897bd32a112e68ce09b71fd6ad98e6b97f267b https://github.com/galaxyproject/galaxy/commit/a1897bd32a112e68ce09b71fd6ad9... Author: guerler aysam.guerler@gmail.com Date: 2017-08-15 (Tue, 15 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Hide select all for role and group selectors

Commit: d6f6a78ab8464bf1a10cbca74632873993744933 https://github.com/galaxyproject/galaxy/commit/d6f6a78ab8464bf1a10cbca746328... Author: guerler aysam.guerler@gmail.com Date: 2017-08-15 (Tue, 15 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/form/form-wrapper.js M static/maps/mvc/form/form-wrapper.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/form/form-wrapper.js

Log Message: ----------- Use 'Save' as default title for configuration forms

Commit: 4688eef2a41e79b44e8cb19ad87d5f2fc9a3aaf1 https://github.com/galaxyproject/galaxy/commit/4688eef2a41e79b44e8cb19ad87d5... Author: guerler aysam.guerler@gmail.com Date: 2017-08-15 (Tue, 15 Aug 2017)

Changed paths: M lib/galaxy/actions/admin.py M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Fix user id decoding, fix optional array handling

Commit: 96cad03980b314a7a89a01a5e1d442b2855a22e8 https://github.com/galaxyproject/galaxy/commit/96cad03980b314a7a89a01a5e1d44... Author: guerler aysam.guerler@gmail.com Date: 2017-08-15 (Tue, 15 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Fix label for default quotas

Commit: 09c4b1037b0034093488ed679628b9f614849a5e https://github.com/galaxyproject/galaxy/commit/09c4b1037b0034093488ed679628b... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-15 (Tue, 15 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js

Log Message: ----------- Break connection in workflow editor if necessary

When switching tool versions in the workflow editor connections are maintained by default. If a tool changes the datatype one may end up with a connection between incompatible input/outputs. Therefore we update the datatypes and explicitly destroy invalid connections.

Commit: 246489a7aa2b950d7a12bf2610faaaed26d90a55 https://github.com/galaxyproject/galaxy/commit/246489a7aa2b950d7a12bf2610faa... Author: guerler aysam.guerler@gmail.com Date: 2017-08-15 (Tue, 15 Aug 2017)

Changed paths: M lib/galaxy/actions/admin.py

Log Message: ----------- Fix messages

Commit: f9e889215021f7a99a4ccfe4612431caa963f63c https://github.com/galaxyproject/galaxy/commit/f9e889215021f7a99a4ccfe461243... Author: guerler aysam.guerler@gmail.com Date: 2017-08-15 (Tue, 15 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Catch user input error for auto created roles and groups

Commit: bebc5ff56ae41a2660f884a2b04604b2a473dd11 https://github.com/galaxyproject/galaxy/commit/bebc5ff56ae41a2660f884a2b0460... Author: guerler aysam.guerler@gmail.com Date: 2017-08-15 (Tue, 15 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Move decode id to correct location

Commit: f1e13cef05759bc7782248c08d595043d03161fe https://github.com/galaxyproject/galaxy/commit/f1e13cef05759bc7782248c08d595... Author: guerler aysam.guerler@gmail.com Date: 2017-08-15 (Tue, 15 Aug 2017)

Changed paths: M lib/galaxy/actions/admin.py

Log Message: ----------- More messages to validate inputs

Commit: 86cdaaf610011b2b0c43f1bd93d36d87907b30e7 https://github.com/galaxyproject/galaxy/commit/86cdaaf610011b2b0c43f1bd93d36... Author: guerler aysam.guerler@gmail.com Date: 2017-08-15 (Tue, 15 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Add validation messages if resource ids are not correct

Commit: 522ca9e5c2ebbf274af26b466c1bab5fb5bc5625 https://github.com/galaxyproject/galaxy/commit/522ca9e5c2ebbf274af26b466c1ba... Author: guerler aysam.guerler@gmail.com Date: 2017-08-15 (Tue, 15 Aug 2017)

Changed paths: M lib/galaxy/security/__init__.py

Log Message: ----------- Fix private role validation

Commit: 2073151bf2f6b2c2427c10934b1feea967d010ff https://github.com/galaxyproject/galaxy/commit/2073151bf2f6b2c2427c10934b1fe... Author: guerler aysam.guerler@gmail.com Date: 2017-08-15 (Tue, 15 Aug 2017)

Log Message: ----------- Merge branch 'dev' into admin_grid_toolversion

Commit: abe8117b650bb9ab6575294d2892d33daeb32e4b https://github.com/galaxyproject/galaxy/commit/abe8117b650bb9ab6575294d2892d... Author: guerler aysam.guerler@gmail.com Date: 2017-08-15 (Tue, 15 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M static/maps/mvc/workflow/workflow-forms.js.map M static/scripts/mvc/workflow/workflow-forms.js

Log Message: ----------- Fix

Fix

Commit: 8eb487e7c1383cedd971de8128bb9ba143abaa41 https://github.com/galaxyproject/galaxy/commit/8eb487e7c1383cedd971de8128bb9... Author: John Chilton jmchilton@gmail.com Date: 2017-08-15 (Tue, 15 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js

Log Message: ----------- Merge pull request #4431 from mvdbeek/break_connections

Break connection in workflow editor if necessary

Commit: 806370123b028eb0728e05fff2f9f9853c5cd6c5 https://github.com/galaxyproject/galaxy/commit/806370123b028eb0728e05fff2f9f... Author: Björn Grüning bjoern@gruenings.eu Date: 2017-08-16 (Wed, 16 Aug 2017)

Changed paths: M config/datatypes_conf.xml.sample

Log Message: ----------- fix XML error

Commit: 338abee984c6915a3f32f60ff1c448245c030376 https://github.com/galaxyproject/galaxy/commit/338abee984c6915a3f32f60ff1c44... Author: guerler aysam.guerler@gmail.com Date: 2017-08-16 (Wed, 16 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-view.js

Log Message: ----------- Separate input augmentation helpers from form views, augment inputs for regular form

Commit: b6f0600e98b74a301c2eb787263cd89e5ca487ca https://github.com/galaxyproject/galaxy/commit/b6f0600e98b74a301c2eb787263cd... Author: Björn Grüning bjoern@gruenings.eu Date: 2017-08-16 (Wed, 16 Aug 2017)

Changed paths: M lib/galaxy/tools/__init__.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_execution.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py

Log Message: ----------- Merge pull request #4387 from jmchilton/tool_unit_test_cleanup

Cleanup of Unit Test Code for Loading Tools

Commit: 7af41d472f360c02d41e9113307385141e85ade6 https://github.com/galaxyproject/galaxy/commit/7af41d472f360c02d41e911330738... Author: guerler aysam.guerler@gmail.com Date: 2017-08-16 (Wed, 16 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js

Log Message: ----------- Simplify form wrapper calling

Commit: c5a91491c64610ede9421af8b89ddf8389238be3 https://github.com/galaxyproject/galaxy/commit/c5a91491c64610ede9421af8b89dd... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-08-16 (Wed, 16 Aug 2017)

Changed paths: M lib/galaxy/security/__init__.py

Log Message: ----------- Merge pull request #4432 from guerler/fix_role_association_check

Fix private role validation

Commit: 7dae650fdbde77336250341832c928f604b41bab https://github.com/galaxyproject/galaxy/commit/7dae650fdbde77336250341832c92... Author: Greg Von Kuster ghv2@psu.edu Date: 2017-08-16 (Wed, 16 Aug 2017)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py A lib/galaxy/datatypes/test/1.memepsp R lib/galaxy/datatypes/test/1.psp

Log Message: ----------- Change Psp to MemePsp and misc fixes per initial review

Commit: 7ef9b4cdafd0e2c6e68cba3729d9bd99645ef15f https://github.com/galaxyproject/galaxy/commit/7ef9b4cdafd0e2c6e68cba3729d9b... Author: Max Schaefer max@semmle.com Date: 2017-08-16 (Wed, 16 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/job/job-params.js

Log Message: ----------- Remove spurious null check.

Commit: 43ddd4732034ca2ee658ccd4ab0ae17d4a1bbe40 https://github.com/galaxyproject/galaxy/commit/43ddd4732034ca2ee658ccd4ab0ae... Author: Max Schaefer max@semmle.com Date: 2017-08-16 (Wed, 16 Aug 2017)

Changed paths: M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.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-folderrow-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-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/scripts/ui/scroll-panel.js M client/galaxy/scripts/utils/graph.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/toolshed/scripts/mvc/groups/group-list-view.js M config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.big.js M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/base64.js M config/plugins/interactive_environments/rstudio/static/js/crypto/wu/base64.js M config/plugins/visualizations/charts/static/client/components/screenshot.js M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js M config/plugins/webhooks/demo/search/static/script.js M lib/galaxy/web/proxy/js/lib/proxy.js M scripts/communication/template/communication.js

Log Message: ----------- Add missing `var` declarations.

In all these cases, a variable was not declared to be a local using `var` (and hence was implicitly interpreted as a global variable), but all uses of that variable were preceded by a definition within the same function, suggesting that the variable was, in fact, meant to be local, not global.

Commit: 48b835c35cd746c23c185ae69577ab6ae9fc4ee8 https://github.com/galaxyproject/galaxy/commit/48b835c35cd746c23c185ae69577a... Author: Max Schaefer max@semmle.com Date: 2017-08-16 (Wed, 16 Aug 2017)

Changed paths: M client/galaxy/scripts/viz/circster.js

Log Message: ----------- Remove an unused variable.

The result of the `_.map` call was never used, so I replaced it with `_.each`.

Commit: 8950d4423ff7d02bcf95b417676b2ef1c311333a https://github.com/galaxyproject/galaxy/commit/8950d4423ff7d02bcf95b417676b2... Author: Max Schaefer max@semmle.com Date: 2017-08-16 (Wed, 16 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js

Log Message: ----------- Move two variable definitions to combine them with their declarations.

Commit: 57c6284269c3256529f9c55953279eccb07dfabf https://github.com/galaxyproject/galaxy/commit/57c6284269c3256529f9c55953279... Author: Max Schaefer max@semmle.com Date: 2017-08-16 (Wed, 16 Aug 2017)

Changed paths: M static/maps/galaxy.pages.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/dataset/data.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.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-folderrow-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-libraryrow-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/toolshed/categories-view.js.map M static/maps/mvc/toolshed/repo-status-view.js.map M static/maps/mvc/toolshed/repositories-view.js.map M static/maps/mvc/toolshed/repository-queue-view.js.map M static/maps/mvc/toolshed/repository-view.js.map M static/maps/mvc/toolshed/util.js.map M static/maps/mvc/toolshed/workflows-view.js.map M static/maps/mvc/ui/ui-drilldown.js.map M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/reports_webapp/run_stats.js.map M static/maps/ui/scroll-panel.js.map M static/maps/utils/graph.js.map M static/maps/utils/uploadbox.js.map M static/maps/viz/circster.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/tracks.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/galaxy.pages.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.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-folderrow-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-libraryrow-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/util.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/reports_webapp/run_stats.js M static/scripts/ui/scroll-panel.js M static/scripts/utils/graph.js M static/scripts/utils/uploadbox.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/tracks.js

Log Message: ----------- Run `make client`.

Commit: 3026bf56c9662f47062fbd37904803156a4fe0db https://github.com/galaxyproject/galaxy/commit/3026bf56c9662f47062fbd3790480... Author: Greg Von Kuster ghv2@psu.edu Date: 2017-08-16 (Wed, 16 Aug 2017)

Changed paths: M lib/galaxy/datatypes/sequence.py

Log Message: ----------- Remove strange import - no idea from where it originated

Commit: 1b7f25eeaec96ae8b6a5336090dca675076b07bd https://github.com/galaxyproject/galaxy/commit/1b7f25eeaec96ae8b6a5336090dca... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-08-16 (Wed, 16 Aug 2017)

Changed paths: M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/job/job-params.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-folderrow-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-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/scripts/ui/scroll-panel.js M client/galaxy/scripts/utils/graph.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/toolshed/scripts/mvc/groups/group-list-view.js M config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.big.js M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/base64.js M config/plugins/interactive_environments/rstudio/static/js/crypto/wu/base64.js M config/plugins/visualizations/charts/static/client/components/screenshot.js M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js M config/plugins/webhooks/demo/search/static/script.js M lib/galaxy/web/proxy/js/lib/proxy.js M scripts/communication/template/communication.js M static/maps/galaxy.pages.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/dataset/data.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.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-folderrow-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-libraryrow-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/toolshed/categories-view.js.map M static/maps/mvc/toolshed/repo-status-view.js.map M static/maps/mvc/toolshed/repositories-view.js.map M static/maps/mvc/toolshed/repository-queue-view.js.map M static/maps/mvc/toolshed/repository-view.js.map M static/maps/mvc/toolshed/util.js.map M static/maps/mvc/toolshed/workflows-view.js.map M static/maps/mvc/ui/ui-drilldown.js.map M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/reports_webapp/run_stats.js.map M static/maps/ui/scroll-panel.js.map M static/maps/utils/graph.js.map M static/maps/utils/uploadbox.js.map M static/maps/viz/circster.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/tracks.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/galaxy.pages.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.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-folderrow-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-libraryrow-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/util.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/reports_webapp/run_stats.js M static/scripts/ui/scroll-panel.js M static/scripts/utils/graph.js M static/scripts/utils/uploadbox.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/tracks.js

Log Message: ----------- Merge pull request #4421 from xiemaisi/fix-lgtm-alerts

Fix lgtm alerts

Commit: c72f43dc5fb48e358d65caf6c59876ba0f15324e https://github.com/galaxyproject/galaxy/commit/c72f43dc5fb48e358d65caf6c5987... Author: Matt Chambers matt.chambers42@gmail.com Date: 2017-08-16 (Wed, 16 Aug 2017)

Changed paths: M lib/galaxy/managers/workflows.py

Log Message: ----------- Avoid adding `(imported from API)` to workflows

This should fail a few tests which I will fix with additional commits. Doing this from GitHub...

Commit: 9ef13a1c724a2bb326bba3556019448ef69ae8fd https://github.com/galaxyproject/galaxy/commit/9ef13a1c724a2bb326bba35560194... Author: Matt Chambers matt.chambers42@gmail.com Date: 2017-08-16 (Wed, 16 Aug 2017)

Changed paths: M test/api/test_search.py

Log Message: ----------- Remove `(imported from API)` suffix from test

Commit: 03a3d34f1e2326c99798299d53fc6b7026aadb09 https://github.com/galaxyproject/galaxy/commit/03a3d34f1e2326c99798299d53fc6... Author: Matt Chambers matt.chambers42@gmail.com Date: 2017-08-16 (Wed, 16 Aug 2017)

Changed paths: M test/api/test_workflows.py

Log Message: ----------- Remove `(imported from API)` suffix from test

Commit: 73d6bd09d30859ca3dfd14debc8f20ed750598a9 https://github.com/galaxyproject/galaxy/commit/73d6bd09d30859ca3dfd14debc8f2... Author: guerler aysam.guerler@gmail.com Date: 2017-08-16 (Wed, 16 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-view.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/tool-form-base.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-view.js

Log Message: ----------- Restore build model bypass

Pack

Commit: 1fc4bb1a62d493412f9b28a30c806d10c56474cf https://github.com/galaxyproject/galaxy/commit/1fc4bb1a62d493412f9b28a30c806... Author: guerler aysam.guerler@gmail.com Date: 2017-08-16 (Wed, 16 Aug 2017)

Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/job/job-params.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-folderrow-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-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/scripts/ui/scroll-panel.js M client/galaxy/scripts/utils/graph.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/toolshed/scripts/mvc/groups/group-list-view.js M config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.big.js M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/base64.js M config/plugins/interactive_environments/rstudio/static/js/crypto/wu/base64.js M config/plugins/visualizations/charts/static/client/components/screenshot.js M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js M config/plugins/webhooks/demo/search/static/script.js M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/web/proxy/js/lib/proxy.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/tool_shed/util/admin_util.py M scripts/communication/template/communication.js M static/maps/galaxy.pages.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/dataset/data.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.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-folderrow-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-libraryrow-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/toolshed/categories-view.js.map M static/maps/mvc/toolshed/repo-status-view.js.map M static/maps/mvc/toolshed/repositories-view.js.map M static/maps/mvc/toolshed/repository-queue-view.js.map M static/maps/mvc/toolshed/repository-view.js.map M static/maps/mvc/toolshed/util.js.map M static/maps/mvc/toolshed/workflows-view.js.map M static/maps/mvc/ui/ui-drilldown.js.map M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/reports_webapp/run_stats.js.map M static/maps/ui/scroll-panel.js.map M static/maps/utils/graph.js.map M static/maps/utils/uploadbox.js.map M static/maps/viz/circster.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/tracks.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/galaxy.pages.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.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-folderrow-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-libraryrow-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/util.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/reports_webapp/run_stats.js M static/scripts/ui/scroll-panel.js M static/scripts/utils/graph.js M static/scripts/utils/uploadbox.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/tracks.js R templates/admin/dataset_security/group/group.mako R templates/admin/dataset_security/group/group_create.mako R templates/admin/dataset_security/group/group_rename.mako A templates/webapps/tool_shed/admin/dataset_security/group/group.mako A templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako A templates/webapps/tool_shed/admin/dataset_security/group/group_rename.mako M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_execution.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py

Log Message: ----------- Merge branch 'dev' into improve_form_modules

Commit: a0217cb2372bfd83bee833299b3ea956a4d9b5b1 https://github.com/galaxyproject/galaxy/commit/a0217cb2372bfd83bee833299b3ea... Author: guerler aysam.guerler@gmail.com Date: 2017-08-16 (Wed, 16 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-view.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/tool-form-base.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-view.js

Log Message: ----------- Attempt to customize build model

Commit: fdcd46918d52c4ee8ab7c2c421fd3e559c9a1fdc https://github.com/galaxyproject/galaxy/commit/fdcd46918d52c4ee8ab7c2c421fd3... Author: guerler aysam.guerler@gmail.com Date: 2017-08-16 (Wed, 16 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Remove unfilterable columns from group and quota search grids

Commit: 2c4cf686f8fffd17bb7a248571fa7d502f52a046 https://github.com/galaxyproject/galaxy/commit/2c4cf686f8fffd17bb7a248571fa7... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-16 (Wed, 16 Aug 2017)

Changed paths: M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/job/job-params.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-folderrow-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-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/scripts/ui/scroll-panel.js M client/galaxy/scripts/utils/graph.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/toolshed/scripts/mvc/groups/group-list-view.js M config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.big.js M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/base64.js M config/plugins/interactive_environments/rstudio/static/js/crypto/wu/base64.js M config/plugins/visualizations/charts/static/client/components/screenshot.js M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js M config/plugins/webhooks/demo/search/static/script.js M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/web/proxy/js/lib/proxy.js M scripts/communication/template/communication.js M static/maps/galaxy.pages.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/dataset/data.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.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-folderrow-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-libraryrow-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/toolshed/categories-view.js.map M static/maps/mvc/toolshed/repo-status-view.js.map M static/maps/mvc/toolshed/repositories-view.js.map M static/maps/mvc/toolshed/repository-queue-view.js.map M static/maps/mvc/toolshed/repository-view.js.map M static/maps/mvc/toolshed/util.js.map M static/maps/mvc/toolshed/workflows-view.js.map M static/maps/mvc/ui/ui-drilldown.js.map M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/reports_webapp/run_stats.js.map M static/maps/ui/scroll-panel.js.map M static/maps/utils/graph.js.map M static/maps/utils/uploadbox.js.map M static/maps/viz/circster.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/tracks.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/galaxy.pages.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.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-folderrow-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-libraryrow-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/util.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/reports_webapp/run_stats.js M static/scripts/ui/scroll-panel.js M static/scripts/utils/graph.js M static/scripts/utils/uploadbox.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/tracks.js M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_execution.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py

Log Message: ----------- Merge branch 'dev' into admin_grid_toolversion and repack

Commit: 04583346a1970f9bab4f0cd3b9e8693de4fedbf9 https://github.com/galaxyproject/galaxy/commit/04583346a1970f9bab4f0cd3b9e86... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-16 (Wed, 16 Aug 2017)

Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M lib/galaxy/actions/admin.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-wrapper.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js R templates/admin/quota/quota.mako R templates/admin/quota/quota_create.mako R templates/admin/quota/quota_edit.mako R templates/admin/quota/quota_rename.mako R templates/admin/quota/quota_set_default.mako

Log Message: ----------- Merge pull request #4411 from guerler/admin_grid_toolversion

replace mako templates for tool lineage and quotas grids

Commit: 25bd7178c157f24523333caaf7f5a0a54f264abe https://github.com/galaxyproject/galaxy/commit/25bd7178c157f24523333caaf7f5a... Author: Matt Chambers matt.chambers42@gmail.com Date: 2017-08-16 (Wed, 16 Aug 2017)

Changed paths: M scripts/api/upload_to_history.py

Log Message: ----------- Remove print of non-existent attribute 'content'

Commit: 5b64e6d0032f515093a2e2d589839da451081546 https://github.com/galaxyproject/galaxy/commit/5b64e6d0032f515093a2e2d589839... Author: guerler aysam.guerler@gmail.com Date: 2017-08-16 (Wed, 16 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form.js M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form.js

Log Message: ----------- Decouple model building

Commit: 2b94fa3b890a00bbe170ac1bec68d29e8d19c75a https://github.com/galaxyproject/galaxy/commit/2b94fa3b890a00bbe170ac1bec68d... Author: Greg Von Kuster ghv2@psu.edu Date: 2017-08-16 (Wed, 16 Aug 2017)

Changed paths: M config/datatypes_conf.xml.sample

Log Message: ----------- Fix MemePsp sniff entry

Commit: 3c4e8927e398e8468b232c2d6a5e49b3206c19b9 https://github.com/galaxyproject/galaxy/commit/3c4e8927e398e8468b232c2d6a5e4... Author: guerler aysam.guerler@gmail.com Date: 2017-08-16 (Wed, 16 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.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/tool-form-base.js

Log Message: ----------- Hide initial tool version message

Commit: 8b43348b676161d7d1aa799dd6988040767c7f6f https://github.com/galaxyproject/galaxy/commit/8b43348b676161d7d1aa799dd6988... Author: guerler aysam.guerler@gmail.com Date: 2017-08-16 (Wed, 16 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/workflow/workflow-forms.js

Log Message: ----------- Move workflow tool form model rebuilding to workflow forms

Commit: 192c4b1141a5a58b45d42afad93f1565579b31e0 https://github.com/galaxyproject/galaxy/commit/192c4b1141a5a58b45d42afad93f1... Author: guerler aysam.guerler@gmail.com Date: 2017-08-16 (Wed, 16 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M static/maps/mvc/workflow/workflow-forms.js.map M static/scripts/mvc/workflow/workflow-forms.js

Log Message: ----------- Properly update workflow tool module

Commit: 6d87448b45074b52298c71dfbca562d8c1950343 https://github.com/galaxyproject/galaxy/commit/6d87448b45074b52298c71dfbca56... Author: guerler aysam.guerler@gmail.com Date: 2017-08-16 (Wed, 16 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/workflow/workflow-forms.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/tool-form-base.js M static/scripts/mvc/workflow/workflow-forms.js

Log Message: ----------- Add optional initial model caller

Pack

Commit: 409867230cac37572779199d5210210a37663145 https://github.com/galaxyproject/galaxy/commit/409867230cac37572779199d52102... Author: guerler aysam.guerler@gmail.com Date: 2017-08-16 (Wed, 16 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js

Log Message: ----------- Remove form dom removal through workflow manager

Commit: 0092600cf384df8888fcb982aadfe1964b4d7a37 https://github.com/galaxyproject/galaxy/commit/0092600cf384df8888fcb982aadfe... Author: guerler aysam.guerler@gmail.com Date: 2017-08-16 (Wed, 16 Aug 2017)

Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M lib/galaxy/actions/admin.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-wrapper.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.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/form/form-parameters.js M static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js R templates/admin/quota/quota.mako R templates/admin/quota/quota_create.mako R templates/admin/quota/quota_edit.mako R templates/admin/quota/quota_rename.mako R templates/admin/quota/quota_set_default.mako

Log Message: ----------- Merge branch 'dev' into improve_form_modules

Commit: d8925d73c5ba7b4e0bcbb36c98d45e45bb3b9e78 https://github.com/galaxyproject/galaxy/commit/d8925d73c5ba7b4e0bcbb36c98d45... Author: guerler aysam.guerler@gmail.com Date: 2017-08-16 (Wed, 16 Aug 2017)

Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css

Log Message: ----------- Fix message style

Commit: 1b69b9a5fedbd232e76ef684734170e7b06fe3e9 https://github.com/galaxyproject/galaxy/commit/1b69b9a5fedbd232e76ef68473417... Author: Björn Grüning bjoern@gruenings.eu Date: 2017-08-17 (Thu, 17 Aug 2017)

Changed paths: M scripts/api/upload_to_history.py

Log Message: ----------- Merge pull request #4439 from chambm/patch-2

Remove print of non-existent attribute 'content'

Commit: 008a1d849c4eb86ab52fd032ae611e4844c3cf09 https://github.com/galaxyproject/galaxy/commit/008a1d849c4eb86ab52fd032ae611... Author: Björn Grüning bjoern@gruenings.eu Date: 2017-08-17 (Thu, 17 Aug 2017)

Changed paths: M lib/galaxy/managers/workflows.py M test/api/test_search.py M test/api/test_workflows.py

Log Message: ----------- Merge pull request #4434 from chambm/patch-1

Avoid adding `(imported from API)` to workflows

Commit: 5799fbc3d13ae6ec41ef5a17e55faf6f58059ae3 https://github.com/galaxyproject/galaxy/commit/5799fbc3d13ae6ec41ef5a17e55fa... Author: Björn Grüning bjoern@gruenings.eu Date: 2017-08-17 (Thu, 17 Aug 2017)

Changed paths: M lib/galaxy/datatypes/sequence.py

Log Message: ----------- change file_ext to be inline with memexml and co

Commit: 21b44bf348ae10d170ab96a3b6f30bf9dbbd5a4a https://github.com/galaxyproject/galaxy/commit/21b44bf348ae10d170ab96a3b6f30... Author: Nicola Soranzo nicola.soranzo@tgac.ac.uk Date: 2017-08-17 (Thu, 17 Aug 2017)

Changed paths: M client/galaxy/style/source_material/circle.py M contrib/nagios/check_galaxy.py M cron/build_chrom_db.py M lib/galaxy/__init__.py M lib/galaxy/actions/admin.py M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/config.py M lib/galaxy/dataset_collections/builder.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/registry.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/dataset_collections/types/__init__.py M lib/galaxy/dataset_collections/types/list.py M lib/galaxy/dataset_collections/types/paired.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/chrominfo.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/fasta_to_len.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_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/gff_to_interval_index_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/interval_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.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/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_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/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/coverage.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/dataproviders/chunk.py M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/decorators.py M lib/galaxy/datatypes/dataproviders/exceptions.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/datatypes/dataproviders/hierarchy.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/display_applications/parameters.py M lib/galaxy/datatypes/display_applications/util.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/registry.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/triples.py M lib/galaxy/datatypes/util/generic_util.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/datatypes/xml.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/external_services/actions.py M 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Log Message: ----------- Fix all E201 and E202 style errors

using the following command: ``` autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E201,E202 . ```

Commit: a353b2e88fc0693c8b9a60017cbc012448c4f4e0 https://github.com/galaxyproject/galaxy/commit/a353b2e88fc0693c8b9a60017cbc0... Author: Nicola Soranzo nicola.soranzo@tgac.ac.uk Date: 2017-08-17 (Thu, 17 Aug 2017)

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tools/data_source/upload.py M tools/filters/axt_to_lav.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_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py

Log Message: ----------- Fix E127 errors introduced by previous commit

using: ``` autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E127 . ```

Commit: a8d7b2df8bb0ccf49b2ca7247f2451b6123a5fd8 https://github.com/galaxyproject/galaxy/commit/a8d7b2df8bb0ccf49b2ca7247f245... Author: Nicola Soranzo nicola.soranzo@tgac.ac.uk Date: 2017-08-17 (Thu, 17 Aug 2017)

Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/error_level.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/model/__init__.py M lib/galaxy/model/tool_shed_install/mapping.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/groups.py M lib/galaxy/webapps/tool_shed/controllers/user.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/util/admin_util.py M lib/tool_shed/utility_containers/__init__.py M lib/tool_shed/utility_containers/utility_container_manager.py M scripts/microbes/BeautifulSoup.py M scripts/tool_shed/deprecate_repositories_without_metadata.py

Log Message: ----------- Fix more indentation errors

Commit: a85ee599ffc66ce3a5954ad819c864064bff838a https://github.com/galaxyproject/galaxy/commit/a85ee599ffc66ce3a5954ad819c86... Author: John Chilton jmchilton@gmail.com Date: 2017-08-17 (Thu, 17 Aug 2017)

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lib/galaxy/model/migrate/versions/0014_pages.py M lib/galaxy/model/migrate/versions/0015_tagging.py M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0019_request_library_folder.py M lib/galaxy/model/migrate/versions/0020_library_upload_job.py M lib/galaxy/model/migrate/versions/0021_user_prefs.py M lib/galaxy/model/migrate/versions/0022_visualization_tables.py M lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py M lib/galaxy/model/migrate/versions/0025_user_info.py M lib/galaxy/model/migrate/versions/0026_cloud_tables.py M lib/galaxy/model/migrate/versions/0027_request_events.py M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py M 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test/shed_functional/functional/test_0400_repository_component_reviews.py M test/shed_functional/functional/test_0410_repository_component_review_access_control.py M test/shed_functional/functional/test_0420_citable_urls_for_repositories.py M test/shed_functional/functional/test_0430_browse_utilities.py M test/shed_functional/functional/test_0440_deleting_dependency_definitions.py M test/shed_functional/functional/test_0460_upload_to_repository.py M test/shed_functional/functional/test_0470_tool_dependency_repository_type.py M test/shed_functional/functional/test_0480_tool_dependency_xml_verification.py M test/shed_functional/functional/test_0490_export_import_repositories.py M test/shed_functional/functional/test_0500_export_repository_simple_dependency.py M test/shed_functional/functional/test_0510_export_import_repository_complex_dependencies.py M test/shed_functional/functional/test_0520_import_export_circular_dependencies.py M test/shed_functional/functional/test_0530_repository_admin_feature.py M test/shed_functional/functional/test_0540_get_all_metadata_from_api.py M test/shed_functional/functional/test_0550_metadata_updated_dependencies.py M test/shed_functional/functional/test_1000_install_basic_repository.py M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1020_install_repository_with_repository_dependencies.py M test/shed_functional/functional/test_1030_install_repository_with_dependency_revisions.py M test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py M test/shed_functional/functional/test_1050_circular_dependencies_4_levels.py M test/shed_functional/functional/test_1060_install_repository_with_workflow.py M test/shed_functional/functional/test_1070_invalid_tool.py M test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py M test/shed_functional/functional/test_1090_repository_dependency_handling.py M test/shed_functional/functional/test_1100_install_updated_repository_dependencies.py M test/shed_functional/functional/test_1110_install_tool_from_tool_search.py M test/shed_functional/functional/test_1120_install_repository_with_complex_dependencies.py M test/shed_functional/functional/test_1130_install_repository_with_invalid_repository_dependency.py M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py M test/shed_functional/functional/test_1150_datatype_converters.py M test/shed_functional/functional/test_1160_tool_help_images.py M test/shed_functional/functional/test_1170_prior_installation_required.py M test/shed_functional/functional/test_1180_circular_prior_installation_required.py M test/shed_functional/functional/test_1190_complex_prior_installation_required.py M test/shed_functional/functional/test_1200_uninstall_and_reinstall_basic_repository.py M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py M test/shed_functional/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py M test/shed_functional/functional/test_1300_reset_all_metadata.py M test/shed_functional/functional/test_1400_review_migration_stages.py M test/shed_functional/functional/test_1410_update_manager.py M test/shed_functional/functional/test_1420_tool_dependency_environment_inheritance.py M test/shed_functional/functional/test_1430_repair_installed_repository.py M test/shed_functional/functional/test_1440_missing_env_sh_files.py M test/shed_functional/functional/test_1450_installing_datatypes_sniffers.py M test/shed_functional/functional/test_1460_data_managers.py M test/shed_functional/functional/test_1470_updating_installed_repositories.py M test/shed_functional/functional_tests.py M test/unit/dataset_collections/test_matching.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/datatypes/test_data.py M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_datasets.py M test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_rule_helper.py M test/unit/jobs/test_rules/10_site.py M test/unit/jobs/test_runner_local.py M test/unit/jobs/test_runner_params.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_fabric_util.py M test/unit/shed_unit/test_td_common_util.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_galaxy_mapping.py M test/unit/test_galaxy_transactions.py M test/unit/test_routes.py M test/unit/test_security_helper.py M test/unit/test_sqlite_utils.py M test/unit/test_topsort.py M test/unit/tools/filter_modules/filtermod.py M test/unit/tools/test_actions.py M test/unit/tools/test_citations.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_panel.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/tools/test_watcher.py M test/unit/tools/test_wrappers.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/unittest_utils/utility.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_extract_summary.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py M tool_list.py M tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/hbvar_filter.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/add_scores.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/axt_to_lav_code.py M tools/filters/bed_to_gff_converter.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/gtf_filter_by_attribute_values_list.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/secure_hash_message_digest.py M tools/filters/sorter.py M tools/filters/trimmer.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/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.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_split_by_species.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/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/meme/fimo_wrapper.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/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.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_assembly/velvetg_wrapper.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_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 M tools/visualization/LAJ.py M tools/visualization/LAJ_code.py

Log Message: ----------- Merge pull request #4440 from nsoranzo/fix_E201_E202

Fix E201 and E202 style errors

Commit: 03df496540a6e2099aa4012fb2d46ec44be9bdbf https://github.com/galaxyproject/galaxy/commit/03df496540a6e2099aa4012fb2d46... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-08-17 (Thu, 17 Aug 2017)

Changed paths: M test/api/test_workflows.py

Log Message: ----------- Fix API tests broken in #4434

Commit: 56c1f25bf385fa3610e447ddc6fad0f063cc2de1 https://github.com/galaxyproject/galaxy/commit/56c1f25bf385fa3610e447ddc6fad... Author: guerler aysam.guerler@gmail.com Date: 2017-08-17 (Thu, 17 Aug 2017)

Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css

Log Message: ----------- Fix help text style

Commit: b8f11dfee4efa1d4df47ae3d753af3e9b5c69b82 https://github.com/galaxyproject/galaxy/commit/b8f11dfee4efa1d4df47ae3d753af... Author: John Chilton jmchilton@gmail.com Date: 2017-08-17 (Thu, 17 Aug 2017)

Changed paths: M lib/galaxy/workflow/modules.py

Log Message: ----------- Improve error message for unknown module types when encountered.

Commit: 213137028182942b372f2483e3b0bb1e20c79518 https://github.com/galaxyproject/galaxy/commit/213137028182942b372f2483e3b0b... Author: John Chilton jmchilton@gmail.com Date: 2017-08-17 (Thu, 17 Aug 2017)

Changed paths: M lib/galaxy/workflow/modules.py

Log Message: ----------- Print warning if any input connections are unused during workflow execution.

Commit: 7bf7f3996373f2528ad7ac88037de3a31f227c23 https://github.com/galaxyproject/galaxy/commit/7bf7f3996373f2528ad7ac88037de... Author: John Chilton jmchilton@gmail.com Date: 2017-08-17 (Thu, 17 Aug 2017)

Changed paths: M lib/galaxy/workflow/modules.py

Log Message: ----------- Cleanup a couple things in #4396 caught by @nsoranzo.

Commit: 35ab7457b9039e9ac6e076ea16bf86dd828faaed https://github.com/galaxyproject/galaxy/commit/35ab7457b9039e9ac6e076ea16bf8... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-08-17 (Thu, 17 Aug 2017)

Changed paths: M test/api/test_workflows.py

Log Message: ----------- Merge pull request #4445 from nsoranzo/followup_on_4434

Fix API tests broken in #4434

Commit: cca1f9e9bcf455b4b655fe9c54707bc34d3c6c32 https://github.com/galaxyproject/galaxy/commit/cca1f9e9bcf455b4b655fe9c54707... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-08-17 (Thu, 17 Aug 2017)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py A lib/galaxy/datatypes/test/1.memepsp

Log Message: ----------- Merge pull request #4430 from gregvonkuster/psp_format

Add support for the MEME psp format

Commit: df442ea51a05541e83e304432ce4aac678a5b7a9 https://github.com/galaxyproject/galaxy/commit/df442ea51a05541e83e304432ce4a... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-08-17 (Thu, 17 Aug 2017)

Changed paths: M lib/galaxy/datatypes/sequence.py

Log Message: ----------- Fix E201 errors (spaces in parens) in new memepsp datatype

Commit: 7ef099f6a6c97f0d9ac202860d6873c9a7aed66c https://github.com/galaxyproject/galaxy/commit/7ef099f6a6c97f0d9ac202860d687... Author: Nicola Soranzo nsoranzo@tiscali.it Date: 2017-08-17 (Thu, 17 Aug 2017)

Changed paths: M lib/galaxy/datatypes/sequence.py

Log Message: ----------- Merge pull request #4446 from dannon/memepsp_formatting

Fix E201 errors (spaces in parens) in new memepsp datatype

Commit: 5a913700221c3734364d70546abfa1b9342d8c1b https://github.com/galaxyproject/galaxy/commit/5a913700221c3734364d70546abfa... Author: guerler aysam.guerler@gmail.com Date: 2017-08-17 (Thu, 17 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.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/tool-form-composite.js

Log Message: ----------- Fix title

Commit: 7bab16ef71c850b3cefab3686beeaee3708e1480 https://github.com/galaxyproject/galaxy/commit/7bab16ef71c850b3cefab3686beea... Author: guerler aysam.guerler@gmail.com Date: 2017-08-17 (Thu, 17 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/mvc/grid/grid-view.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/grid/grid-view.js

Log Message: ----------- Preserve advanced search visibility

Commit: ee4c8e2afac1d16b386c4dc9afa9b0817a0c9325 https://github.com/galaxyproject/galaxy/commit/ee4c8e2afac1d16b386c4dc9afa9b... Author: guerler aysam.guerler@gmail.com Date: 2017-08-17 (Thu, 17 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/mvc/grid/grid-view.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/grid/grid-view.js

Log Message: ----------- Fix filters

Commit: 114997dca6af7483d3ed3f34fafd0f66e3583afc https://github.com/galaxyproject/galaxy/commit/114997dca6af7483d3ed3f34fafd0... Author: guerler aysam.guerler@gmail.com Date: 2017-08-17 (Thu, 17 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/mvc/grid/grid-model.js.map M static/maps/mvc/grid/grid-view.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/grid/grid-model.js M static/scripts/mvc/grid/grid-view.js

Log Message: ----------- Prevent search tag duplication

Commit: 0fa287f76a675c49c2702681ac4404f050b77130 https://github.com/galaxyproject/galaxy/commit/0fa287f76a675c49c2702681ac440... Author: John Chilton jmchilton@gmail.com Date: 2017-08-17 (Thu, 17 Aug 2017)

Changed paths: A .ci/autopep8.sh M lib/galaxy/actions/admin.py M lib/galaxy/app.py M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/dataproviders/chunk.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/exceptions.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/datatypes/dataproviders/hierarchy.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/manager.py M lib/galaxy/jobs/runners/godocker.py M lib/galaxy/jobs/runners/util/drmaa/__init__.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/deletable.py M lib/galaxy/model/__init__.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/metadata.py M lib/galaxy/model/orm/logging_connection_proxy.py M lib/galaxy/model/search.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/pithos.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/queue_worker.py M lib/galaxy/quota/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/brew_exts.py M lib/galaxy/tools/deps/mulled/mulled_search.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/__init__.py M lib/galaxy/util/bunch.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/odict.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/simplegraph.py M lib/galaxy/util/sleeper.py M lib/galaxy/util/ucsc.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/data_providers/phyloviz/baseparser.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/utils.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/formbuilder.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/request_id.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/middleware/xforwardedhost.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/provenance.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/tool_shed/util/ratings_util.py M lib/galaxy/workflow/extract.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M test/casperjs/casperjs_runner.py M test/galaxy_selenium/driver_factory.py M test/shed_functional/functional/test_0060_workflows.py M test/shed_functional/functional/test_0400_repository_component_reviews.py M test/shed_functional/functional/test_0410_repository_component_review_access_control.py M test/shed_functional/functional/test_0420_citable_urls_for_repositories.py M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1060_install_repository_with_workflow.py M test/shed_functional/functional/test_1070_invalid_tool.py M tools/data_source/upload.py

Log Message: ----------- Add autopep8 script to help rebasing branches after #4440.

Fixes a few more PEP8 issues as part of the autopep8'ing as well.

Commit: 8c225ecf3d928b93aceb318dada1e942a510b8ca https://github.com/galaxyproject/galaxy/commit/8c225ecf3d928b93aceb318dada1e... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-08-17 (Thu, 17 Aug 2017)

Log Message: ----------- Merge branch 'release_17.05' into dev

Commit: 68e8abc89aba1263f82c643d1bde89da53d70bc9 https://github.com/galaxyproject/galaxy/commit/68e8abc89aba1263f82c643d1bde8... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-08-17 (Thu, 17 Aug 2017)

Changed paths: A .ci/autopep8.sh M lib/galaxy/actions/admin.py M lib/galaxy/app.py M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/dataproviders/chunk.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/exceptions.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/datatypes/dataproviders/hierarchy.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/manager.py M lib/galaxy/jobs/runners/godocker.py M lib/galaxy/jobs/runners/util/drmaa/__init__.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/deletable.py M lib/galaxy/model/__init__.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/metadata.py M lib/galaxy/model/orm/logging_connection_proxy.py M lib/galaxy/model/search.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/pithos.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/queue_worker.py M lib/galaxy/quota/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/brew_exts.py M lib/galaxy/tools/deps/mulled/mulled_search.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/__init__.py M lib/galaxy/util/bunch.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/odict.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/simplegraph.py M lib/galaxy/util/sleeper.py M lib/galaxy/util/ucsc.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/data_providers/phyloviz/baseparser.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/utils.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/formbuilder.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/request_id.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/middleware/xforwardedhost.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/provenance.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/tool_shed/util/ratings_util.py M lib/galaxy/workflow/extract.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M test/casperjs/casperjs_runner.py M test/galaxy_selenium/driver_factory.py M test/shed_functional/functional/test_0060_workflows.py M test/shed_functional/functional/test_0400_repository_component_reviews.py M test/shed_functional/functional/test_0410_repository_component_review_access_control.py M test/shed_functional/functional/test_0420_citable_urls_for_repositories.py M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1060_install_repository_with_workflow.py M test/shed_functional/functional/test_1070_invalid_tool.py M tools/data_source/upload.py

Log Message: ----------- Merge pull request #4447 from jmchilton/autopep8

Add autopep8 script to help rebasing branches after #4440.

Commit: 706741f30b2ee0a1733e49cafa8c0d0e6b78385a https://github.com/galaxyproject/galaxy/commit/706741f30b2ee0a1733e49cafa8c0... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-17 (Thu, 17 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/mvc/grid/grid-model.js.map M static/maps/mvc/grid/grid-view.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/grid/grid-model.js M static/scripts/mvc/grid/grid-view.js

Log Message: ----------- Merge pull request #4449 from guerler/fix_grid_search

Fixes for advanced grid search

Commit: 042386ff8733874fe7004c900fabb16b7798d031 https://github.com/galaxyproject/galaxy/commit/042386ff8733874fe7004c900fabb... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-17 (Thu, 17 Aug 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-librarytoolbar-view.js M lib/galaxy/webapps/galaxy/api/lda_datasets.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-librarytoolbar-view.js.map M static/scripts/bundled/libs.bundled.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-librarytoolbar-view.js

Log Message: ----------- wip on improving libraries

Commit: 61eb0114034703d5ec225c42e3b781b96b02b7f6 https://github.com/galaxyproject/galaxy/commit/61eb0114034703d5ec225c42e3b78... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-17 (Thu, 17 Aug 2017)

Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py

Log Message: ----------- refactor decode_id method to use base manager

Commit: dc834a52c1dfa2bcca61e3cdb74ed9606c752340 https://github.com/galaxyproject/galaxy/commit/dc834a52c1dfa2bcca61e3cdb74ed... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-17 (Thu, 17 Aug 2017)

Changed paths: M lib/galaxy/managers/libraries.py

Log Message: ----------- fix copypasta error

Commit: e17ab411e338043dce2391672322ebc3468d049e https://github.com/galaxyproject/galaxy/commit/e17ab411e338043dce2391672322e... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-17 (Thu, 17 Aug 2017)

Changed paths: A lib/galaxy/managers/library_datasets.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py

Log Message: ----------- refactor show method to use new manager

Commit: cd09d1327a075f83e0c83323da26377ec0336d03 https://github.com/galaxyproject/galaxy/commit/cd09d1327a075f83e0c83323da263... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-17 (Thu, 17 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py

Log Message: ----------- refactor the rest of the module to use new manager

Commit: 25960121310455e2d5b84933fb76cda8daacc1f7 https://github.com/galaxyproject/galaxy/commit/25960121310455e2d5b84933fb76c... Author: guerler aysam.guerler@gmail.com Date: 2017-08-17 (Thu, 17 Aug 2017)

Changed paths: A .ci/autopep8.sh M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/style/source_material/circle.py M config/datatypes_conf.xml.sample M contrib/nagios/check_galaxy.py M cron/build_chrom_db.py M lib/galaxy/__init__.py M lib/galaxy/actions/admin.py M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/config.py M lib/galaxy/dataset_collections/builder.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/registry.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/dataset_collections/types/__init__.py M lib/galaxy/dataset_collections/types/list.py M lib/galaxy/dataset_collections/types/paired.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/chrominfo.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/fasta_to_len.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_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/gff_to_interval_index_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/interval_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.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/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_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/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/coverage.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/dataproviders/chunk.py M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/decorators.py M lib/galaxy/datatypes/dataproviders/exceptions.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/datatypes/dataproviders/hierarchy.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/display_applications/parameters.py M lib/galaxy/datatypes/display_applications/util.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/1.memepsp M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/triples.py M lib/galaxy/datatypes/util/generic_util.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/datatypes/xml.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/external_services/actions.py M lib/galaxy/external_services/parameters.py M lib/galaxy/external_services/result_handlers/basic.py M lib/galaxy/external_services/service.py M lib/galaxy/forms/forms.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/datasets.py M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/deferred/data_transfer.py M lib/galaxy/jobs/deferred/manual_data_transfer.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/error_level.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/manager.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/collectl/stats.py M lib/galaxy/jobs/metrics/collectl/subsystems.py M lib/galaxy/jobs/metrics/instrumenters/__init__.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/metrics/instrumenters/uname.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/rule_helper.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/local.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/jobs/runners/state_handlers/_safe_eval.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/jobs/runners/util/drmaa/__init__.py M lib/galaxy/jobs/splitters/basic.py M lib/galaxy/jobs/splitters/multi.py M lib/galaxy/jobs/stock_rules.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/annotatable.py M lib/galaxy/managers/api_keys.py M lib/galaxy/managers/base.py M lib/galaxy/managers/citations.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/context.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/deletable.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/managers/lddas.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/pages.py M lib/galaxy/managers/ratable.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/roles.py M lib/galaxy/managers/secured.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/taggable.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/users.py M lib/galaxy/managers/visualizations.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/base.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/item_attrs.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/0001_initial_tables.py M lib/galaxy/model/migrate/versions/0002_metadata_file_table.py M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py M lib/galaxy/model/migrate/versions/0007_sharing_histories.py M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py M lib/galaxy/model/migrate/versions/0009_request_table.py M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0012_user_address.py M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py M lib/galaxy/model/migrate/versions/0014_pages.py M lib/galaxy/model/migrate/versions/0015_tagging.py M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0019_request_library_folder.py M lib/galaxy/model/migrate/versions/0020_library_upload_job.py M lib/galaxy/model/migrate/versions/0021_user_prefs.py M lib/galaxy/model/migrate/versions/0022_visualization_tables.py M lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py M lib/galaxy/model/migrate/versions/0025_user_info.py M lib/galaxy/model/migrate/versions/0026_cloud_tables.py M lib/galaxy/model/migrate/versions/0027_request_events.py M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py M lib/galaxy/model/migrate/versions/0029_user_actions.py M lib/galaxy/model/migrate/versions/0030_history_slug_column.py M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.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/0034_page_user_share_association.py M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0037_samples_library.py M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py M lib/galaxy/model/migrate/versions/0040_page_annotations.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/0043_visualization_sharing_tagging_annotating.py M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py M lib/galaxy/model/migrate/versions/0046_post_job_actions.py M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py M lib/galaxy/model/migrate/versions/0049_api_keys_table.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M 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lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py M lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py M 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Log Message: ----------- Merge branch 'dev' into improve_form_modules

Commit: 50ebc19afd6788125285cbf051f85aec6ac34d00 https://github.com/galaxyproject/galaxy/commit/50ebc19afd6788125285cbf051f85... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-17 (Thu, 17 Aug 2017)

Changed paths: M .ci/flake8_lint_include_list.txt R lib/galaxy/webapps/galaxy/api/lda_datasets.py A lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js

Log Message: ----------- rename lda_datasets to library_datasets

Commit: 517f248ac49caca3f0933c4b1f48cd4d74cf89fe https://github.com/galaxyproject/galaxy/commit/517f248ac49caca3f0933c4b1f48c... Author: John Chilton jmchilton@gmail.com Date: 2017-08-17 (Thu, 17 Aug 2017)

Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/output_collect.py M test/functional/tools/samples_tool_conf.xml M test/functional/tools/tool_provided_metadata_1.xml M test/functional/tools/tool_provided_metadata_2.xml M test/functional/tools/tool_provided_metadata_3.xml A test/functional/tools/tool_provided_metadata_4.xml A test/functional/tools/tool_provided_metadata_5.xml A test/functional/tools/tool_provided_metadata_6.xml M test/unit/tools/test_collect_primary_datasets.py

Log Message: ----------- Overhaul of tool provided job metadata.

- Add another test to demonstrate referencing entries in galaxy.json for datasets by dataset path basename instead of ID. - Add a bit more documentation to test tools. - Redo the structure of galaxy.json for profile >= 17.09 tools with two new test tools to demonstrate the new structure - for both output dataset metadata and discovered dataset metadata. - Improved abstractions for interaction between tools and jobs to enable different tool provided metadata collection depending on tool profile version.

Commit: 72e361bcf14191dae58af8e3963b89a4e8acd38a https://github.com/galaxyproject/galaxy/commit/72e361bcf14191dae58af8e3963b8... Author: John Chilton jmchilton@gmail.com Date: 2017-08-17 (Thu, 17 Aug 2017)

Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/collection_creates_dynamic_nested_from_json.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_7.xml

Log Message: ----------- Allow discovering datasets directly from galaxy.json...

without needing to specify a discovered dataset pattern. If the ``discovered_datasets`` tag includes ``from_tool_provided_metadata="true"`` the datsets listed in galaxy.json will just be used directly without needing to be "discovered" using a dataset pattern. Metadata and such can continue to be specified either in that file or on the discovered_dataset element except things like pattern (which is not used) and sort_by (since the json should describe the order I suppose).

Commit: 6563e387a5d001bb6078469b7ad6a13f9bbed8aa https://github.com/galaxyproject/galaxy/commit/6563e387a5d001bb6078469b7ad6a... Author: John Chilton jmchilton@gmail.com Date: 2017-08-17 (Thu, 17 Aug 2017)

Changed paths: M lib/galaxy/tools/parameters/output_collect.py A test/functional/tools/collection_creates_dynamic_nested_from_json_elements.xml M test/functional/tools/samples_tool_conf.xml

Log Message: ----------- Allow discovering dataset collections in galaxy.json in a nested fashion.

Fixes #2658.

Commit: 39d4411f8c21b307a86340fc5438ed2193abd766 https://github.com/galaxyproject/galaxy/commit/39d4411f8c21b307a86340fc5438e... Author: John Chilton jmchilton@gmail.com Date: 2017-08-17 (Thu, 17 Aug 2017)

Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_8.xml

Log Message: ----------- Move determining tool provided metadata style to tool parser.

Allow override by specifying "provided_metadata_style=" attribute on outputs in tool XML - this should allow newer profile tools to use the older style JSON providing a clear path for upgrades.

Commit: a8bec7a275b5bd387daddf6555b6ff382851e8e8 https://github.com/galaxyproject/galaxy/commit/a8bec7a275b5bd387daddf6555b6f... Author: John Chilton jmchilton@gmail.com Date: 2017-08-17 (Thu, 17 Aug 2017)

Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_9.xml

Log Message: ----------- Allow override of provided metadata location.

Eliminates that terrible circular dependency between tools and jobs.

Commit: 1e1df6786aeb6d02fba1ad84cceb204aa745ea62 https://github.com/galaxyproject/galaxy/commit/1e1df6786aeb6d02fba1ad84cceb2... Author: John Chilton jmchilton@gmail.com Date: 2017-08-17 (Thu, 17 Aug 2017)

Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/xsd/galaxy.xsd

Log Message: ----------- Variety of fixes for #4437.

Commit: 2489499fb656acc61dc9275931dafcdad381d25c https://github.com/galaxyproject/galaxy/commit/2489499fb656acc61dc9275931daf... Author: xgaia xgaia@gmx.com Date: 2017-08-18 (Fri, 18 Aug 2017)

Changed paths: M lib/galaxy/web/base/interactive_environments.py

Log Message: ----------- possibility to don't uppercase env variables

Commit: cff9292f07d1318ce789bcfdab7dbf3e67c8d162 https://github.com/galaxyproject/galaxy/commit/cff9292f07d1318ce789bcfdab7db... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-08-18 (Fri, 18 Aug 2017)

Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/pastescript/serve.py

Log Message: ----------- Uniform indentation of multiline if conditionals

Use 8-spaces indentation for the conditional continuation lines of an `if`-statement where the conditional part spans multiple lines.

According to PEP-8, using 4-spaces "can produce a visual conflict with the indented suite of code nested inside the `if`-statement", but the PEP "takes no explicit position".

There were only 2 places in the whole codebase where 8 spaces were not used, this will make it uniform.

Commit: d2d1f857bbc2b7528e2e17cc8fcfdaad7d79fa75 https://github.com/galaxyproject/galaxy/commit/d2d1f857bbc2b7528e2e17cc8fcfd... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-08-18 (Fri, 18 Aug 2017)

Changed paths: M lib/galaxy/util/pastescript/serve.py

Log Message: ----------- Fix import order and Python3 compatibility for lib/galaxy/util/pastescript/serve.py

Commit: 784e6f5fd360f8374045b256171303f5f795264e https://github.com/galaxyproject/galaxy/commit/784e6f5fd360f8374045b25617130... Author: Nicola Soranzo nsoranzo@tiscali.it Date: 2017-08-18 (Fri, 18 Aug 2017)

Changed paths: M lib/galaxy/workflow/modules.py

Log Message: ----------- Merge pull request #4396 from jmchilton/workflow_warnings

Slightly improve workflow warnings/errors logging.

Commit: 4e75635d629f654f7b9d203fa6b6c1bc61495aa6 https://github.com/galaxyproject/galaxy/commit/4e75635d629f654f7b9d203fa6b6c... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-08-18 (Fri, 18 Aug 2017)

Changed paths: M lib/galaxy/config.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/tools/execute.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/users.py M scripts/communication/communication_server.py M scripts/secret_decoder_ring.py

Log Message: ----------- Use log.warning() instead of deprecated warn()

Commit: e32ad2864f6b4ea05a347602b19202b94ae0ea81 https://github.com/galaxyproject/galaxy/commit/e32ad2864f6b4ea05a347602b1920... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-08-18 (Fri, 18 Aug 2017)

Changed paths: M lib/galaxy/containers/__init__.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py

Log Message: ----------- Remove container config log message from cleanup scripts logs

Commit: bd88524a109e6695a68f57e55ace64c21f907089 https://github.com/galaxyproject/galaxy/commit/bd88524a109e6695a68f57e55ace6... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-08-18 (Fri, 18 Aug 2017)

Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/containers/__init__.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/users.py M scripts/communication/communication_server.py M scripts/secret_decoder_ring.py

Log Message: ----------- Fix import order and Python3 compatibility

Commit: b459399edebbeada2be6254a8567de85b43dabc4 https://github.com/galaxyproject/galaxy/commit/b459399edebbeada2be6254a8567d... Author: Eric Rasche hxr@hx42.org Date: 2017-08-18 (Fri, 18 Aug 2017)

Changed paths: M lib/galaxy/web/base/interactive_environments.py

Log Message: ----------- Merge pull request #4454 from xgaia/interactive_environment

Interactive Environment: possibility to don't uppercase env variables

Commit: 8d132b2bca0dab22f7e028773dd31aa553cae668 https://github.com/galaxyproject/galaxy/commit/8d132b2bca0dab22f7e028773dd31... Author: E Rasche hxr@hx42.org Date: 2017-08-18 (Fri, 18 Aug 2017)

Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py

Log Message: ----------- More detailed sentry reports

Commit: dd89a9c65f7297d4da5f0c0f7b6fea884a9698e6 https://github.com/galaxyproject/galaxy/commit/dd89a9c65f7297d4da5f0c0f7b6fe... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2017-08-18 (Fri, 18 Aug 2017)

Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/collection_creates_dynamic_nested_from_json.xml A test/functional/tools/collection_creates_dynamic_nested_from_json_elements.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/tool_provided_metadata_1.xml M test/functional/tools/tool_provided_metadata_2.xml M test/functional/tools/tool_provided_metadata_3.xml A test/functional/tools/tool_provided_metadata_4.xml A test/functional/tools/tool_provided_metadata_5.xml A test/functional/tools/tool_provided_metadata_6.xml A test/functional/tools/tool_provided_metadata_7.xml A test/functional/tools/tool_provided_metadata_8.xml A test/functional/tools/tool_provided_metadata_9.xml M test/unit/tools/test_collect_primary_datasets.py

Log Message: ----------- Merge pull request #4437 from jmchilton/galaxy_json_rev

Enhanced tool options for dataset discovery

Commit: e987b9b9e48bfa2f5ee69c013f991eb8bec70a2d https://github.com/galaxyproject/galaxy/commit/e987b9b9e48bfa2f5ee69c013f991... Author: E Rasche hxr@hx42.org Date: 2017-08-18 (Fri, 18 Aug 2017)

Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py

Log Message: ----------- swap id to username

Commit: 30562c09c54e112f141a91635e91aa942ff4ece7 https://github.com/galaxyproject/galaxy/commit/30562c09c54e112f141a91635e91a... Author: xgaia xgaia@gmx.com Date: 2017-08-18 (Fri, 18 Aug 2017)

Changed paths: M lib/galaxy/web/base/interactive_environments.py

Log Message: ----------- don't uppercase envoverride

Commit: e4924942825c6ea2d472d8ccff45222f165fa6bf https://github.com/galaxyproject/galaxy/commit/e4924942825c6ea2d472d8ccff452... Author: John Chilton jmchilton@gmail.com Date: 2017-08-18 (Fri, 18 Aug 2017)

Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/config.py M lib/galaxy/containers/__init__.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/tools/execute.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/users.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/communication/communication_server.py M scripts/secret_decoder_ring.py

Log Message: ----------- Merge pull request #4456 from nsoranzo/logging_fixes

Logging fixes

Commit: 9c6fd670cf201b9b3fed67cd5f100d75a24cb5f6 https://github.com/galaxyproject/galaxy/commit/9c6fd670cf201b9b3fed67cd5f100... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-08-18 (Fri, 18 Aug 2017)

Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/pastescript/serve.py

Log Message: ----------- Merge pull request #4455 from nsoranzo/multiline_if_conditionals

Uniform indentation of multiline if conditionals

Commit: cd22de114c2098ecbf2ab2108f3526abe70f00e6 https://github.com/galaxyproject/galaxy/commit/cd22de114c2098ecbf2ab2108f352... Author: John Chilton jmchilton@gmail.com Date: 2017-08-18 (Fri, 18 Aug 2017)

Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py

Log Message: ----------- Merge pull request #4457 from erasche/sentry-extra-info

More detailed sentry reports

Commit: d883fc162e4d0a6606b9e4408337e5c564fd1840 https://github.com/galaxyproject/galaxy/commit/d883fc162e4d0a6606b9e4408337e... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-18 (Fri, 18 Aug 2017)

Changed paths: M lib/galaxy/managers/workflows.py

Log Message: ----------- add ommitted conflict resolution

Commit: 7f50a8a29f53c7fa86e5b0c7a57d2d898c6c4650 https://github.com/galaxyproject/galaxy/commit/7f50a8a29f53c7fa86e5b0c7a57d2... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-08-18 (Fri, 18 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/style/less/ui.less M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js M static/style/blue/base.css

Log Message: ----------- Merge pull request #4438 from guerler/improve_form_modules

Augment form module separation

Commit: dd27c1edccb06b54ef5d503749ce51f79abcfcf0 https://github.com/galaxyproject/galaxy/commit/dd27c1edccb06b54ef5d503749ce5... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-08-18 (Fri, 18 Aug 2017)

Changed paths: M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map

Log Message: ----------- Client rebuild, @guerler and I were trying to figure out what changed in the recently merged #4438 but don't see anything obvious.

Commit: 263018326895c3f6e36288dcdeb242a056580892 https://github.com/galaxyproject/galaxy/commit/263018326895c3f6e36288dcdeb24... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-18 (Fri, 18 Aug 2017)

Changed paths: M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map

Log Message: ----------- Merge pull request #4464 from dannon/rebuild_000

Client rebuild, @guerler and I were trying to figure out what changed…

Commit: 1342c2bd706b353038871a73992ae1a19878a694 https://github.com/galaxyproject/galaxy/commit/1342c2bd706b353038871a73992ae... Author: Nuwan Goonasekera nuwan.ag@gmail.com Date: 2017-08-19 (Sat, 19 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js A client/galaxy/scripts/mvc/tool/tool-genomespace.js A client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/style/less/ui.less M config/tool_conf.xml.main M config/tool_conf.xml.sample M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/form_builder.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_file_browser.py R tools/genomespace/genomespace_file_browser_dev.xml R tools/genomespace/genomespace_file_browser_prod.xml R tools/genomespace/genomespace_file_browser_test.xml M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_importer.xml

Log Message: ----------- Integrated File Browsing and Workflow support for GenomeSpace

Commit: e39901ef0695d6e7828d81ce3d1a9a230fda1569 https://github.com/galaxyproject/galaxy/commit/e39901ef0695d6e7828d81ce3d1a9... Author: Nuwan Goonasekera nuwan.ag@gmail.com Date: 2017-08-19 (Sat, 19 Aug 2017)

Changed paths: M client/galaxy/style/less/ui.less M lib/galaxy/dependencies/pinned-requirements.txt M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_importer.xml

Log Message: ----------- Moved back some code to wrapper and added back data type sniffing.

Commit: ad1b61344557b53af10fae91011ec4a7be5d4a67 https://github.com/galaxyproject/galaxy/commit/ad1b61344557b53af10fae91011ec... Author: Nuwan Goonasekera nuwan.ag@gmail.com Date: 2017-08-19 (Sat, 19 Aug 2017)

Changed paths: M config/tool_conf.xml.main M config/tool_conf.xml.sample M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_importer.xml A tools/genomespace/genomespace_push.xml

Log Message: ----------- Added support for pushing multiple files from GenomeSpace to Galaxy.

Commit: b04ccbe55b33ffca1aa09668885bceea61951dfe https://github.com/galaxyproject/galaxy/commit/b04ccbe55b33ffca1aa09668885bc... Author: slugger70 slugger70@gmail.com Date: 2017-08-19 (Sat, 19 Aug 2017)

Changed paths: M tools/genomespace/genomespace_importer.xml

Log Message: ----------- Fixed genomespace_importer.xml command block

Commit: cb1b086324b1625d4f5ac0087e00971f3048afd4 https://github.com/galaxyproject/galaxy/commit/cb1b086324b1625d4f5ac0087e009... Author: Nuwan Goonasekera nuwan.ag@gmail.com Date: 2017-08-19 (Sat, 19 Aug 2017)

Changed paths: M lib/galaxy/tools/parameters/basic.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_importer.py

Log Message: ----------- Fixed pylint errors

Commit: 46c04dcbd4eb47a2f3a2ff559c9ba4e280621750 https://github.com/galaxyproject/galaxy/commit/46c04dcbd4eb47a2f3a2ff559c9ba... Author: Nuwan Goonasekera nuwan.ag@gmail.com Date: 2017-08-19 (Sat, 19 Aug 2017)

Changed paths: M tools/genomespace/genomespace_importer.py

Log Message: ----------- Fix incorrect reference when determining file type through file ext

Commit: 678d575a7ae2cf7056564b525971396dc16d9b39 https://github.com/galaxyproject/galaxy/commit/678d575a7ae2cf7056564b5259713... Author: Nuwan Goonasekera nuwan.ag@gmail.com Date: 2017-08-19 (Sat, 19 Aug 2017)

Changed paths: M tools/genomespace/genomespace_importer.py

Log Message: ----------- Improved recognition of compressed files

Commit: ae6ae8ffe2c1558513737b5fab77840a22cea0a8 https://github.com/galaxyproject/galaxy/commit/ae6ae8ffe2c1558513737b5fab778... Author: Nuwan Goonasekera nuwan.ag@gmail.com Date: 2017-08-19 (Sat, 19 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-genomespace.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/managers/configuration.py

Log Message: ----------- Added new config setting for GenomeSpace UI URL

Commit: 517fd23fc8cd84c5277ccadc33222fa913230cc8 https://github.com/galaxyproject/galaxy/commit/517fd23fc8cd84c5277ccadc33222... Author: Nuwan Goonasekera nuwan.ag@gmail.com Date: 2017-08-19 (Sat, 19 Aug 2017)

Changed paths: M tools/genomespace/genomespace_exporter.xml

Log Message: ----------- Fixed typo in exporter help text

Commit: b73e21b584dc13716460f550ed80108634adca37 https://github.com/galaxyproject/galaxy/commit/b73e21b584dc13716460f550ed801... Author: Nuwan Goonasekera nuwan.ag@gmail.com Date: 2017-08-19 (Sat, 19 Aug 2017)

Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/form_builder.py M tools/genomespace/genomespace_importer.py

Log Message: ----------- Formatting and linting fixes for GenomeSpace tool

Commit: b995e551d408bd192322de530db89ddd08d35db2 https://github.com/galaxyproject/galaxy/commit/b995e551d408bd192322de530db89... Author: Nuwan Goonasekera nuwan.ag@gmail.com Date: 2017-08-19 (Sat, 19 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/style/less/ui.less

Log Message: ----------- Fixed alignment of buttons in Genomespace Importer

Commit: 46dc4a252cf6144672053864b16e52a85c810e34 https://github.com/galaxyproject/galaxy/commit/46dc4a252cf6144672053864b16e5... Author: Nuwan Goonasekera nuwan.ag@gmail.com Date: 2017-08-19 (Sat, 19 Aug 2017)

Changed paths: M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml

Log Message: ----------- Fixed template formatting according to review comments

Commit: 3e8bf3c4e72ca035f98142b3dc153de0a8e9d6a1 https://github.com/galaxyproject/galaxy/commit/3e8bf3c4e72ca035f98142b3dc153... Author: Nuwan Goonasekera nuwan.ag@gmail.com Date: 2017-08-19 (Sat, 19 Aug 2017)

Changed paths: M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_push.xml

Log Message: ----------- Moved genomespace token to environment variable

Commit: 52b26f45a2bd3bcb0155553bf6e3e765d3bd4b2c https://github.com/galaxyproject/galaxy/commit/52b26f45a2bd3bcb0155553bf6e3e... Author: Nuwan Goonasekera nuwan.ag@gmail.com Date: 2017-08-19 (Sat, 19 Aug 2017)

Changed paths: M lib/galaxy/tools/__init__.py M tools/genomespace/genomespace_importer.xml

Log Message: ----------- Registered genomespace_importer as a tool needing Galaxy's python env

Commit: 32401978234c46aeef80bc0ee144a478820468dc https://github.com/galaxyproject/galaxy/commit/32401978234c46aeef80bc0ee144a... Author: Nuwan Goonasekera nuwan.ag@gmail.com Date: 2017-08-19 (Sat, 19 Aug 2017)

Changed paths: M static/maps/mvc/form/form-parameters.js.map A static/maps/mvc/tool/tool-genomespace.js.map A static/maps/mvc/ui/ui-select-genomespace.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-parameters.js A static/scripts/mvc/tool/tool-genomespace.js A static/scripts/mvc/ui/ui-select-genomespace.js M static/style/blue/base.css

Log Message: ----------- Rebuilt galaxy client files

Commit: ac5be429e70a8533aae3583fed9cd29cb17fc13f https://github.com/galaxyproject/galaxy/commit/ac5be429e70a8533aae3583fed9cd... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-18 (Fri, 18 Aug 2017)

Changed paths: 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-librarytoolbar-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-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-librarytoolbar-view.js

Log Message: ----------- repack

Commit: f5ac8ce30d369c3661a8e1e4ea8424a540a41f66 https://github.com/galaxyproject/galaxy/commit/f5ac8ce30d369c3661a8e1e4ea842... Author: Björn Grüning bjoern@gruenings.eu Date: 2017-08-18 (Fri, 18 Aug 2017)

Changed paths: M config/datatypes_conf.xml.sample

Log Message: ----------- add mz5 datatype

Commit: fd51a61d014c4d3affe146b69fc3ed097037d2a1 https://github.com/galaxyproject/galaxy/commit/fd51a61d014c4d3affe146b69fc3e... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-18 (Fri, 18 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js A client/galaxy/scripts/mvc/tool/tool-genomespace.js A client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/style/less/ui.less M config/galaxy.ini.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M lib/galaxy/config.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/managers/configuration.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/form_builder.py M static/maps/mvc/form/form-parameters.js.map A static/maps/mvc/tool/tool-genomespace.js.map A static/maps/mvc/ui/ui-select-genomespace.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-parameters.js A static/scripts/mvc/tool/tool-genomespace.js A static/scripts/mvc/ui/ui-select-genomespace.js M static/style/blue/base.css M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_file_browser.py R tools/genomespace/genomespace_file_browser_dev.xml R tools/genomespace/genomespace_file_browser_prod.xml R tools/genomespace/genomespace_file_browser_test.xml M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_importer.xml A tools/genomespace/genomespace_push.xml

Log Message: ----------- Merge pull request #1814 from gvlproject/genomespace_workflows

Galaxy Workflow support for GenomeSpace

Commit: 912da2f3b93e7ae655725b6619febf0dbbcc4455 https://github.com/galaxyproject/galaxy/commit/912da2f3b93e7ae655725b6619feb... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-19 (Sat, 19 Aug 2017)

Changed paths: M lib/galaxy/managers/workflows.py M test/api/test_workflows.py

Log Message: ----------- Fix checking WorkflowInvocation for published workflows

Commit: 413233eec3ce9b3f930db8e40413856831dfc0cb https://github.com/galaxyproject/galaxy/commit/413233eec3ce9b3f930db8e404138... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-19 (Sat, 19 Aug 2017)

Changed paths: M lib/galaxy/managers/workflows.py

Log Message: ----------- Correctly raise Exception if invocation not found

Commit: 0a4203ed92acb795a2f32c5ca095146b388a2ec2 https://github.com/galaxyproject/galaxy/commit/0a4203ed92acb795a2f32c5ca0951... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-19 (Sat, 19 Aug 2017)

Changed paths: M test/api/test_workflows.py

Log Message: ----------- Fix test to use invocation_id instead of history_id

Commit: 80e264d35ffbf9eecacf37918fab7f7dbfa27cc7 https://github.com/galaxyproject/galaxy/commit/80e264d35ffbf9eecacf37918fab7... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-19 (Sat, 19 Aug 2017)

Changed paths: M lib/galaxy/managers/workflows.py

Log Message: ----------- Check ownership of invocation, instead of stored_workflow

Commit: 2d16470132b86fb04bd67665bbdaf20e55874170 https://github.com/galaxyproject/galaxy/commit/2d16470132b86fb04bd67665bbdaf... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-20 (Sun, 20 Aug 2017)

Changed paths: M lib/galaxy/managers/workflows.py

Log Message: ----------- Allow admin user to view workflow invocation (thx @nsoranzo)

Commit: cff306b86bc6368b4489805b96f92da04761c013 https://github.com/galaxyproject/galaxy/commit/cff306b86bc6368b4489805b96f92... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-20 (Sun, 20 Aug 2017)

Changed paths: M lib/galaxy/managers/workflows.py

Log Message: ----------- Only skip check_security checks if check_ownership and check_accessible are false

Commit: 64f8e74adeb5f46e781fb3cf54294097c6301880 https://github.com/galaxyproject/galaxy/commit/64f8e74adeb5f46e781fb3cf54294... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-20 (Sun, 20 Aug 2017)

Changed paths: M test/unit/workflows/workflow_support.py

Log Message: ----------- Fix subworkflow tests

Commit: 0e46888eed5412a85439f82907f58f540d9963d9 https://github.com/galaxyproject/galaxy/commit/0e46888eed5412a85439f82907f58... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-20 (Sun, 20 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py

Log Message: ----------- Show up to 15 histories by default in saved histories menu

Commit: a9d5c7c59c6b1bf2b656ec58d6ae3cea5a94d6ca https://github.com/galaxyproject/galaxy/commit/a9d5c7c59c6b1bf2b656ec58d6ae3... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-20 (Sun, 20 Aug 2017)

Changed paths: M templates/tagging_common.mako

Log Message: ----------- Show tag if < 3 tags on history

Commit: 2346c0aa7e66580792b4cd2d0bd48656421c5352 https://github.com/galaxyproject/galaxy/commit/2346c0aa7e66580792b4cd2d0bd48... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-20 (Sun, 20 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py M templates/tagging_common.mako

Log Message: ----------- Merge pull request #4467 from mvdbeek/saved_history_tags

More items per page in saved history and directly show tags

Commit: e3b3457b1fbeac31e1837be18f96a2e4d795902f https://github.com/galaxyproject/galaxy/commit/e3b3457b1fbeac31e1837be18f96a... Author: John Chilton jmchilton@gmail.com Date: 2017-08-21 (Mon, 21 Aug 2017)

Changed paths: M lib/galaxy/managers/workflows.py M test/api/test_workflows.py M test/unit/workflows/workflow_support.py

Log Message: ----------- Merge pull request #4465 from mvdbeek/workflow_invocation_security_check

Fix checking WorkflowInvocation for published workflows

Commit: 092ad6d67fe63a8b8895c003e2ad6ce54a612878 https://github.com/galaxyproject/galaxy/commit/092ad6d67fe63a8b8895c003e2ad6... Author: guerler aysam.guerler@gmail.com Date: 2017-08-21 (Mon, 21 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/api/quotas.py

Log Message: ----------- Fix quota function name

Commit: ae48774f54f317c2417b7677f1ef6cfde662a5f4 https://github.com/galaxyproject/galaxy/commit/ae48774f54f317c2417b7677f1ef6... Author: E Rasche hxr@hx42.org Date: 2017-08-21 (Mon, 21 Aug 2017)

Changed paths: M lib/galaxy/webapps/reports/config.py

Log Message: ----------- needed for sentry functionality in reports webapp

Commit: 63d1d428a1d98f3f607381c84e501030481eadbf https://github.com/galaxyproject/galaxy/commit/63d1d428a1d98f3f607381c84e501... Author: Nicola Soranzo nsoranzo@tiscali.it Date: 2017-08-21 (Mon, 21 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/api/quotas.py

Log Message: ----------- Merge pull request #4469 from guerler/fix_quota_api

Fix quota function name

Commit: da5b72a030d8d07c663566527fc64560e067eb54 https://github.com/galaxyproject/galaxy/commit/da5b72a030d8d07c663566527fc64... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-08-22 (Tue, 22 Aug 2017)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml R lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py R lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml A lib/galaxy/datatypes/converters/bcf_to_bcf_uncompressed_converter.xml A lib/galaxy/datatypes/converters/bcf_uncompressed_to_bcf_converter.xml A lib/galaxy/datatypes/test/1.bcf A lib/galaxy/datatypes/test/1.bcf_uncompressed

Log Message: ----------- Alias `bcf_bgzip` datatype to `bcf`. Add `bcf_uncompressed` and converters

Since https://bitbucket.org/galaxy/galaxy-central/pull-requests/353 (only) compressed BCF files have been sniffed as `bcf`, so the `bcf_bgzip` datatype (introduced 2 years later in https://github.com/galaxyproject/galaxy/pull/1148 ) is an unused duplicate.

This adds also a distinct `bcf_uncompressed` datatype (and converters) for the rare cases when it may be useful.

Commit: 8dc0e697d3f8841270f6d934d19b271cf23b219e https://github.com/galaxyproject/galaxy/commit/8dc0e697d3f8841270f6d934d19b2... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-08-22 (Tue, 22 Aug 2017)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/tabular.py M test/functional/tools/sample_datatypes_conf.xml

Log Message: ----------- Fix `vcf_bgzip` datatype

In https://github.com/galaxyproject/galaxy/pull/4254 `vcf_bgzip` was made a proper datatype with the introduction of the `VcfGz` class, but was still described as a subclass in `datatypes_conf.xml` .

Also fix `file_ext` attribute in `BaseVcf` and subclasses.

Commit: a63af63b41e81a104dc177cb13dc2f6f3b4e9e6d https://github.com/galaxyproject/galaxy/commit/a63af63b41e81a104dc177cb13dc2... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-08-22 (Tue, 22 Aug 2017)

Changed paths: M lib/galaxy/datatypes/set_metadata_tool.xml

Log Message: ----------- Add requirement for bcftools to set_metadata tool

The `bcftools` binary is used by the `set_meta()` method of the `Bcf` datatype class. Having a `<requirement>` for it in the set_metadata tool makes it possible to use conda to resolve the dependency instead of forcing the admin to install `bcftools` on the PATH of the Galaxy user.

This will also fix errors like https://travis-ci.org/galaxyproject/tools-iuc/jobs/266923024#L1994 when running ``` planemo test --conda_dependency_resolution --conda_auto_install ```

Commit: d3ae7351f734b4e841c91495c1e41c77fe4e01b1 https://github.com/galaxyproject/galaxy/commit/d3ae7351f734b4e841c91495c1e41... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-08-22 (Tue, 22 Aug 2017)

Changed paths: M lib/galaxy/tools/verify/__init__.py

Log Message: ----------- Use pysam instead of samtools binary

This will make it possible to remove the requirement of having `samtools` installed when testing tools, e.g. in the tools-iuc TravisCI setup: https://github.com/galaxyproject/tools-iuc/blob/master/.travis.yml#L59

Commit: eefc268eae2961186a84dc396921326549ea4822 https://github.com/galaxyproject/galaxy/commit/eefc268eae2961186a84dc3969213... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2017-08-23 (Wed, 23 Aug 2017)

Changed paths: A test/selenium_tests/test_published_history_grid.py

Log Message: ----------- add the first test: history grid

Commit: 946d64b8f7dc08b92ebb03f34a91cab8aa7ecfbb https://github.com/galaxyproject/galaxy/commit/946d64b8f7dc08b92ebb03f34a91c... Author: Aurélien Bernard aurelien.bernard.bioinfo63@gmail.com Date: 2017-08-23 (Wed, 23 Aug 2017)

Changed paths: A lib/galaxy/tools/deps/resolvers/lmod.py

Log Message: ----------- LMOD Dependency resolver - Initial commit (lib lmod.py)

Initial commit of a prototype dependency resolver based on the LMOD environment modules system.

Commit: 4d143479d5998531cc4803af11579e12d160c87b https://github.com/galaxyproject/galaxy/commit/4d143479d5998531cc4803af11579... Author: Aurélien Bernard aurelien.bernard.bioinfo63@gmail.com Date: 2017-08-23 (Wed, 23 Aug 2017)

Changed paths: M config/dependency_resolvers_conf.xml.sample

Log Message: ----------- Update of the dependency_resolvers_conf.xml.sample file

Addition of the LMOD Dependency resolver to the appropriate sample configuration file (dependency_resolvers_conf.xml.sample). Comment lines have also been added to describe the possible attributes of the resolver as well as their default values.

Commit: e84284c477182b3c03e785b79f93dd88d63e6ebd https://github.com/galaxyproject/galaxy/commit/e84284c477182b3c03e785b79f93d... Author: Aurélien Bernard aurelien.bernard.bioinfo63@gmail.com Date: 2017-08-23 (Wed, 23 Aug 2017)

Changed paths: M config/dependency_resolvers_conf.xml.sample A config/lmod_modules_mapping.yml.sample M lib/galaxy/tools/deps/resolvers/lmod.py

Log Message: ----------- LMOD Dependency resolver - Default mapping file

If a lmod_modules_mapping.yml file exists in the config folder then it will be taken into consideration automatically to map Galaxy requirements to LMOD modules.

Commit: a6632f31338911176052db99257aa8f825286008 https://github.com/galaxyproject/galaxy/commit/a6632f31338911176052db99257aa... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-23 (Wed, 23 Aug 2017)

Changed paths: M client/galaxy/style/less/dataset.less M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/style/blue/base.css

Log Message: ----------- replace exclamation with a clock icon

Commit: 27bd71332a66195f66536825d6da05ed505330f1 https://github.com/galaxyproject/galaxy/commit/27bd71332a66195f66536825d6da0... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-08-23 (Wed, 23 Aug 2017)

Changed paths: M client/galaxy/style/less/dataset.less M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/style/blue/base.css

Log Message: ----------- Merge pull request #4485 from martenson/remove-exclamation

replace exclamation with a clock icon

Commit: 89c811b790d7ef3508f361195ca4333903e5b955 https://github.com/galaxyproject/galaxy/commit/89c811b790d7ef3508f361195ca43... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-08-23 (Wed, 23 Aug 2017)

Changed paths: M templates/webapps/galaxy/dataset/copy_view.mako

Log Message: ----------- Move 'Copy History Items' to the bottom of the second column in the old copy histories page.

Commit: b664f26aa0d7a3ad151f236ba569efecb09a5526 https://github.com/galaxyproject/galaxy/commit/b664f26aa0d7a3ad151f236ba569e... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2017-08-23 (Wed, 23 Aug 2017)

Changed paths: M test/selenium_tests/test_published_history_grid.py

Log Message: ----------- add standard search test

Commit: a83438159c2aa8d92b9c9f53ec64f9188ec94a8f https://github.com/galaxyproject/galaxy/commit/a83438159c2aa8d92b9c9f53ec64f... Author: Eric Rasche hxr@hx42.org Date: 2017-08-23 (Wed, 23 Aug 2017)

Changed paths: M lib/galaxy/web/base/interactive_environments.py

Log Message: ----------- Merge pull request #4458 from xgaia/interactive_environment

don't uppercase envoverride

Commit: 0e1cbc09f8a604c1b45127faf30170ba1b67bb1b https://github.com/galaxyproject/galaxy/commit/0e1cbc09f8a604c1b45127faf3017... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2017-08-23 (Wed, 23 Aug 2017)

Changed paths: M test/selenium_tests/test_published_history_grid.py

Log Message: ----------- add 'sort by name/owner' tests

Commit: fed3206a87e4ae4ede380c90cfa3409220847cf7 https://github.com/galaxyproject/galaxy/commit/fed3206a87e4ae4ede380c90cfa34... Author: Aurélien Bernard aurelien.bernard.bioinfo63@gmail.com Date: 2017-08-24 (Thu, 24 Aug 2017)

Changed paths: M lib/galaxy/tools/deps/resolvers/lmod.py

Log Message: ----------- Fix errors reported by the initial Travis tests

Fix incorrect numbers of blank lines. Fix deprecated syntax.

Commit: 09887529765ba88adb70e739d1b9d8896cb86229 https://github.com/galaxyproject/galaxy/commit/09887529765ba88adb70e739d1b9d... Author: Aurélien Bernard aurelien.bernard.bioinfo63@gmail.com Date: 2017-08-24 (Thu, 24 Aug 2017)

Changed paths: M lib/galaxy/tools/deps/resolvers/lmod.py

Log Message: ----------- Syntax fix in the shell_commands method

The built command now reflect more directly the command that is really executed by the the LMOD "module" bash function when a user execute "module load package_name/package_version".

Commit: 574e697a4d66a53f298f37f4987d31db96ff8e14 https://github.com/galaxyproject/galaxy/commit/574e697a4d66a53f298f37f4987d3... Author: Aurélien Bernard aurelien.bernard.bioinfo63@gmail.com Date: 2017-08-24 (Thu, 24 Aug 2017)

Changed paths: M config/dependency_resolvers_conf.xml.sample

Log Message: ----------- Dependency_resolvers_conf.xml - More explanations

Some more explanations about the versionless mode have been added.

Commit: db5efdaa7cbc197eaf6a777d4d390de24b212e88 https://github.com/galaxyproject/galaxy/commit/db5efdaa7cbc197eaf6a777d4d390... Author: Aurélien Bernard aurelien.bernard.bioinfo63@gmail.com Date: 2017-08-24 (Thu, 24 Aug 2017)

Changed paths: M lib/galaxy/tools/deps/resolvers/lmod.py

Log Message: ----------- Clearer comment lines in the has_module method

A comment of the has_module method of the AvailModuleChecker class has been modified to be clearer and more explicit.

Commit: eda36ffb99a1abec8f878c0b7ae194938781c8d6 https://github.com/galaxyproject/galaxy/commit/eda36ffb99a1abec8f878c0b7ae19... Author: Aurélien Bernard aurelien.bernard.bioinfo63@gmail.com Date: 2017-08-24 (Thu, 24 Aug 2017)

Changed paths: M test/unit/tools/test_tool_deps.py

Log Message: ----------- LMOD Dependency resolver - Unit tests added

The unit/tools/tests_tool_deps.py script has been updated to includ unit tests for the LMOD dependency resolver.

Commit: bbec357bbd744b9e0d760e8d0903adfa43d1b7e2 https://github.com/galaxyproject/galaxy/commit/bbec357bbd744b9e0d760e8d0903a... Author: Aurélien Bernard aurelien.bernard.bioinfo63@gmail.com Date: 2017-08-24 (Thu, 24 Aug 2017)

Changed paths: M test/unit/tools/test_tool_deps.py

Log Message: ----------- Fix the import order error raised by Travis

The order of the import statements in the test_tool_deps script was incorrect (as stated by travis). That should no longer be the case.

Commit: 9822f5f2a91fae7e3420a06c58f2621a2cf084ac https://github.com/galaxyproject/galaxy/commit/9822f5f2a91fae7e3420a06c58f26... Author: Aurélien Bernard aurelien.bernard.bioinfo63@gmail.com Date: 2017-08-24 (Thu, 24 Aug 2017)

Changed paths: M test/unit/tools/test_tool_deps.py

Log Message: ----------- Fix attempt for the modulepath issue in unit tests

On a computer where LMOD is not installed, the MODULEPATH variable is not defined and the modulepath attributes of the LMOD dependency resolver must be used.

Commit: 001d94ae4ea0af1ed16c809a6e8e26c356549396 https://github.com/galaxyproject/galaxy/commit/001d94ae4ea0af1ed16c809a6e8e2... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-08-24 (Thu, 24 Aug 2017)

Changed paths: M lib/galaxy/tools/verify/__init__.py

Log Message: ----------- Merge pull request #4479 from nsoranzo/use_pysam_in_verify

Use pysam instead of samtools binary

Commit: 5d04c593b637146c69eed1b6909a74c67ab4de1a https://github.com/galaxyproject/galaxy/commit/5d04c593b637146c69eed1b6909a7... Author: guerler aysam.guerler@gmail.com Date: 2017-08-24 (Thu, 24 Aug 2017)

Changed paths: M lib/galaxy/workflow/modules.py

Log Message: ----------- Removes unused comma from subworkflow populator

Commit: 5ae1446970ec43e578ab400f529bd753cd81d052 https://github.com/galaxyproject/galaxy/commit/5ae1446970ec43e578ab400f529bd... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-08-24 (Thu, 24 Aug 2017)

Changed paths: M lib/galaxy/workflow/modules.py

Log Message: ----------- Merge pull request #4492 from guerler/fix_subworkflow_comma

Remove unused comma from subworkflow populator

Commit: b80ee79b4302bd208ce5aa1fb86fb58e2b89a0c7 https://github.com/galaxyproject/galaxy/commit/b80ee79b4302bd208ce5aa1fb86fb... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-08-24 (Thu, 24 Aug 2017)

Changed paths: R lib/galaxy/webapps/galaxy/controllers/mobile.py 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

Log Message: ----------- Remove /mobile and associated templates. It has been deactivated for almost three years now.

Commit: e542c47872881964c9c5fd0220904caee16f868a https://github.com/galaxyproject/galaxy/commit/e542c47872881964c9c5fd0220904... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-08-24 (Thu, 24 Aug 2017)

Changed paths: R client/galaxy/style/less/iphone.less M client/grunt-tasks/style.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map R static/style/blue/iphone.css

Log Message: ----------- Remove ancient 'iphone' styling that is unused (and missing assets)

Commit: 4c14de6955a6c2fef489fd9603aec4e88df65539 https://github.com/galaxyproject/galaxy/commit/4c14de6955a6c2fef489fd9603aec... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-08-24 (Thu, 24 Aug 2017)

Changed paths: M client/bower.json R client/galaxy/scripts/libs/jquery/jqtouch.js M client/grunt-tasks/install-libs.js 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

Log Message: ----------- strip jqtouch

Commit: 1426225a78d0adc7a024d33f314bdfa613eabe5d https://github.com/galaxyproject/galaxy/commit/1426225a78d0adc7a024d33f314bd... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-24 (Thu, 24 Aug 2017)

Changed paths: M client/bower.json R client/galaxy/scripts/libs/jquery/jqtouch.js R client/galaxy/style/less/iphone.less M client/grunt-tasks/install-libs.js M client/grunt-tasks/style.js R lib/galaxy/webapps/galaxy/controllers/mobile.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/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map R static/style/blue/iphone.css 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

Log Message: ----------- Merge pull request #4494 from dannon/no_mobile

Remove /mobile and associated templates

Commit: c89233c7cbbe263d3670fd5d4066a83f537ee173 https://github.com/galaxyproject/galaxy/commit/c89233c7cbbe263d3670fd5d4066a... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-08-24 (Thu, 24 Aug 2017)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml R lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py R lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml A 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/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 test/functional/tools/sample_datatypes_conf.xml

Log Message: ----------- Merge pull request #4477 from nsoranzo/vcf_bcf_fixes

Fixes for VCF/BCF datatypes

Commit: 0e467b73bcb1c6493bda6997bb133c19b72a275d https://github.com/galaxyproject/galaxy/commit/0e467b73bcb1c6493bda6997bb133... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-08-24 (Thu, 24 Aug 2017)

Changed paths: M lib/galaxy/webapps/reports/config.py

Log Message: ----------- Fixes for reports sentry dsn (lint and missing import).

Commit: f09b5c5b9de02d66fbca836bbe5a19a8f1e66dfb https://github.com/galaxyproject/galaxy/commit/f09b5c5b9de02d66fbca836bbe5a1... Author: Eric Rasche hxr@hx42.org Date: 2017-08-25 (Fri, 25 Aug 2017)

Changed paths: M lib/galaxy/webapps/reports/config.py

Log Message: ----------- Merge pull request #19 from dannon/reports-sentry-dsn

Fixes for reports sentry dsn (lint and missing import).

Commit: df0507e494208018ff19c71d17afb9f5c4b3b6ce https://github.com/galaxyproject/galaxy/commit/df0507e494208018ff19c71d17afb... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-08-25 (Fri, 25 Aug 2017)

Changed paths: M lib/galaxy/webapps/reports/config.py

Log Message: ----------- Merge pull request #4471 from erasche/reports-sentry-dsn

needed for sentry functionality in reports webapp

Commit: a904df604ef6962628916635d42068ece1368d01 https://github.com/galaxyproject/galaxy/commit/a904df604ef6962628916635d4206... Author: E Rasche hxr@hx42.org Date: 2017-08-25 (Fri, 25 Aug 2017)

Changed paths: M lib/tool_shed/galaxy_install/installed_repository_manager.py

Log Message: ----------- Only parse once

Commit: cbe6970a4cf5c5a3b7bb55c97d7190fef4019388 https://github.com/galaxyproject/galaxy/commit/cbe6970a4cf5c5a3b7bb55c97d719... Author: E Rasche hxr@hx42.org Date: 2017-08-25 (Fri, 25 Aug 2017)

Changed paths: M lib/tool_shed/galaxy_install/installed_repository_manager.py

Log Message: ----------- per @nsoranzo, only log error message when it is there

Commit: 2ff4292cd6171fc128e91ddbb66f5124368c25ee https://github.com/galaxyproject/galaxy/commit/2ff4292cd6171fc128e91ddbb66f5... Author: E Rasche hxr@hx42.org Date: 2017-08-25 (Fri, 25 Aug 2017)

Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/galaxy_bootstrap/variables.less

Log Message: ----------- move to somewhere it can be overridden

Commit: 68f9c6905ef56ce9b82e2889a48b4185370e83b4 https://github.com/galaxyproject/galaxy/commit/68f9c6905ef56ce9b82e2889a48b4... Author: E Rasche hxr@hx42.org Date: 2017-08-25 (Fri, 25 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/style/less/base.less

Log Message: ----------- Large click target for tools

Commit: cd6cc88ac19b5d7c218e31fb14c74382d2439a1f https://github.com/galaxyproject/galaxy/commit/cd6cc88ac19b5d7c218e31fb14c74... Author: E Rasche hxr@hx42.org Date: 2017-08-25 (Fri, 25 Aug 2017)

Changed paths: M client/galaxy/style/less/galaxy_variables.less A client/galaxy/style/less/theme/plain.less M static/maps/mvc/tool/tools.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

Log Message: ----------- Plain theme

Commit: 0010f6c0d8ab7ad128ba4bfefd406dccc9bc5e9f https://github.com/galaxyproject/galaxy/commit/0010f6c0d8ab7ad128ba4bfefd406... Author: Eric Rasche hxr@hx42.org Date: 2017-08-25 (Fri, 25 Aug 2017)

Changed paths: M config/datatypes_conf.xml.sample

Log Message: ----------- Merge pull request #4466 from bgruening/mz5

add mz5 datatype

Commit: 97ee0f1fcdd7d059d5c37e1bb25a8c3389559698 https://github.com/galaxyproject/galaxy/commit/97ee0f1fcdd7d059d5c37e1bb25a8... Author: E Rasche hxr@hx42.org Date: 2017-08-25 (Fri, 25 Aug 2017)

Changed paths: M static/style/blue/base.css

Log Message: ----------- rebuild style

Commit: 426aa310fd21f320767b575dcd209ae63ad88b24 https://github.com/galaxyproject/galaxy/commit/426aa310fd21f320767b575dcd209... Author: Eric Rasche hxr@hx42.org Date: 2017-08-25 (Fri, 25 Aug 2017)

Changed paths: M templates/webapps/galaxy/dataset/copy_view.mako

Log Message: ----------- Merge pull request #4486 from dannon/copy_history_minor_improvement

Minor copy datasets dialog improvement.

Commit: 72195e14baa5e5f3131f2364858e71c4e4fb960c https://github.com/galaxyproject/galaxy/commit/72195e14baa5e5f3131f2364858e7... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2017-08-25 (Fri, 25 Aug 2017)

Changed paths: M test/selenium_tests/test_published_history_grid.py

Log Message: ----------- [WIP]: add advanced search tests

Commit: 2403916c7b6a29810e74cb3485d3634ef904dde6 https://github.com/galaxyproject/galaxy/commit/2403916c7b6a29810e74cb3485d36... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2017-08-26 (Sat, 26 Aug 2017)

Changed paths: M test/selenium_tests/test_published_history_grid.py

Log Message: ----------- test clicking tags

Commit: 2f547b09737d6711e44de7d9c7600384aa97038e https://github.com/galaxyproject/galaxy/commit/2f547b09737d6711e44de7d9c7600... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2017-08-26 (Sat, 26 Aug 2017)

Changed paths: M test/selenium_tests/test_published_history_grid.py

Log Message: ----------- small improvements

Commit: da1518db48265617cb2e2a00f9b738058c648f4b https://github.com/galaxyproject/galaxy/commit/da1518db48265617cb2e2a00f9b73... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2017-08-26 (Sat, 26 Aug 2017)

Changed paths: M test/selenium_tests/test_published_history_grid.py

Log Message: ----------- set annotations

Commit: 2dda34a00240a9af990a23c14cd73abb87db4268 https://github.com/galaxyproject/galaxy/commit/2dda34a00240a9af990a23c14cd73... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2017-08-26 (Sat, 26 Aug 2017)

Changed paths: A test/selenium_tests/test_published_histories_grid.py R test/selenium_tests/test_published_history_grid.py

Log Message: ----------- rename the file

Commit: a0bd78034defb11adf2140f7c6dd90e63bc7da43 https://github.com/galaxyproject/galaxy/commit/a0bd78034defb11adf2140f7c6dd9... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-27 (Sun, 27 Aug 2017)

Changed paths: M lib/galaxy/managers/workflows.py

Log Message: ----------- Optimize loading of StoredWorkflow attributes

WorkflowsManager.get_stored_workflow is used when exporting or editing workflows. In these cases we iterate over the related workflow objects steps as well as the related tags and annotation objects. Each iteration will emit a new SQL statement. Joinedloading these relations here speeds up the workflow run form and the editor. With sqlite as backend this speeds up exporting a workflow for the workflow editor by about 5X.

Commit: 62204de0aeb4a833e43e5a1f81657293853ffb03 https://github.com/galaxyproject/galaxy/commit/62204de0aeb4a833e43e5a1f81657... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-27 (Sun, 27 Aug 2017)

Changed paths: M lib/galaxy/model/item_attrs.py

Log Message: ----------- Use pre-existing annotations object if possible

This avoids additional requests to the database.

Commit: db04f295d34e8ca03b151f462e7ffd1d613a1321 https://github.com/galaxyproject/galaxy/commit/db04f295d34e8ca03b151f462e7ff... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-27 (Sun, 27 Aug 2017)

Changed paths: M lib/galaxy/tools/__init__.py

Log Message: ----------- Do not provide a history in workflow_building_mode

Commit: cb1392fd2d707587859bcbbb3e1744fb472ebf22 https://github.com/galaxyproject/galaxy/commit/cb1392fd2d707587859bcbbb3e174... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-27 (Sun, 27 Aug 2017)

Changed paths: M lib/galaxy/web/base/controller.py

Log Message: ----------- Use WorkflowManager to get StoredWorkflow in workflow web controller

Commit: 83bb7b108e90086ae0f421d63107c3870dea5d73 https://github.com/galaxyproject/galaxy/commit/83bb7b108e90086ae0f421d63107c... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-27 (Sun, 27 Aug 2017)

Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py

Log Message: ----------- Avoid ToolShedRepository attributes where possible

Commit: d5eee194252270ebf4be008c6cf0492d5c6c3340 https://github.com/galaxyproject/galaxy/commit/d5eee194252270ebf4be008c6cf04... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-27 (Sun, 27 Aug 2017)

Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/controllers/workflow.py

Log Message: ----------- Use workflow_building_modes.ENABLED instead of True

Commit: e4f4dc91eebe7d5e4fbf8667bff52079498d88ea https://github.com/galaxyproject/galaxy/commit/e4f4dc91eebe7d5e4fbf8667bff52... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-27 (Sun, 27 Aug 2017)

Changed paths: M lib/galaxy/datatypes/registry.py

Log Message: ----------- Cache edam_data and edam_formats

Commit: 17246225d962f4d1494b4b718440f42631fd6210 https://github.com/galaxyproject/galaxy/commit/17246225d962f4d1494b4b718440f... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-27 (Sun, 27 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py

Log Message: ----------- Use joinedload for latest_workflow.steps when building workflow editor config

Commit: 1a1232e11dd31b96284d2842292d13f9b67ee22e https://github.com/galaxyproject/galaxy/commit/1a1232e11dd31b96284d2842292d1... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-27 (Sun, 27 Aug 2017)

Changed paths: M lib/galaxy/managers/workflows.py

Log Message: ----------- Use get_item_annotation_str instead of get_item_annotation_obj

Commit: e6155367e61d8b4e66883992db6af88444f346a0 https://github.com/galaxyproject/galaxy/commit/e6155367e61d8b4e66883992db6af... Author: E Rasche hxr@hx42.org Date: 2017-08-28 (Mon, 28 Aug 2017)

Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/web/framework/base.py

Log Message: ----------- 2017-08 Security Patch

Commit: 773029bd364037943a810506a79cebca85f2a260 https://github.com/galaxyproject/galaxy/commit/773029bd364037943a810506a79ce... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2017-08-28 (Mon, 28 Aug 2017)

Changed paths: M test/selenium_tests/test_published_histories_grid.py

Log Message: ----------- fix flake8 issues

Commit: e130b55b04c8bc7c30b85ac7e2688890b890c71c https://github.com/galaxyproject/galaxy/commit/e130b55b04c8bc7c30b85ac7e2688... Author: E Rasche hxr@hx42.org Date: 2017-08-28 (Mon, 28 Aug 2017)

Changed paths: M lib/tool_shed/util/xml_util.py

Log Message: ----------- log error if does not exist

Commit: 0159162c9e7b3463b2f667fec820d3ae83bfd3dc https://github.com/galaxyproject/galaxy/commit/0159162c9e7b3463b2f667fec820d... Author: E Rasche hxr@hx42.org Date: 2017-08-28 (Mon, 28 Aug 2017)

Changed paths: M lib/tool_shed/galaxy_install/installed_repository_manager.py

Log Message: ----------- Merge branch 'parse-once' of github.com:erasche/galaxy into parse-once

Commit: 4b9b14979a7137f4aca90e1e1e7869e88ae1bb6e https://github.com/galaxyproject/galaxy/commit/4b9b14979a7137f4aca90e1e1e786... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-08-28 (Mon, 28 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/style/less/base.less M client/galaxy/style/less/galaxy_bootstrap/variables.less M client/galaxy/style/less/galaxy_variables.less A client/galaxy/style/less/theme/plain.less M static/maps/mvc/tool/tools.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/style/blue/base.css

Log Message: ----------- Merge pull request #4470 from erasche/retheme

Nicer tool click targets for base + "plain" theme

Commit: f159df391ea4eeaac01779426cfad00e38b5f907 https://github.com/galaxyproject/galaxy/commit/f159df391ea4eeaac01779426cfad... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-28 (Mon, 28 Aug 2017)

Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/web/framework/base.py

Log Message: ----------- Merge pull request #4501 from erasche/2017-08-security

2017-08 Security Patch

Commit: 9337c9fdc118f7c4883a6c7b4cada483b09461c7 https://github.com/galaxyproject/galaxy/commit/9337c9fdc118f7c4883a6c7b4cada... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-28 (Mon, 28 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M lib/galaxy/datatypes/data.py M lib/galaxy/workflow/modules.py M static/maps/mvc/ui/ui-select-content.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/ui/ui-select-content.js

Log Message: ----------- Merge branch 'release_17.05' into merge-release1705

Commit: 8aefa9d49535b7592bd7398541f9cbeaba9146ce https://github.com/galaxyproject/galaxy/commit/8aefa9d49535b7592bd7398541f9c... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-28 (Mon, 28 Aug 2017)

Changed paths: 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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js

Log Message: ----------- repack client

Commit: 15b1a41df83940961d8f516e4023cd410b38964b https://github.com/galaxyproject/galaxy/commit/15b1a41df83940961d8f516e4023c... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-08-28 (Mon, 28 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M lib/galaxy/datatypes/data.py M lib/galaxy/workflow/modules.py 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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js

Log Message: ----------- Merge pull request #4506 from martenson/merge-release1705

Merge release_17.05 to dev

Commit: 6613df5b7a826e8147b2a46c8e87391b230f4315 https://github.com/galaxyproject/galaxy/commit/6613df5b7a826e8147b2a46c8e873... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-28 (Mon, 28 Aug 2017)

Changed paths: M lib/galaxy/managers/library_datasets.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/buildapp.py

Log Message: ----------- add methods for vlidating and updating ld's attributes

Commit: a394faf3be18eceae72ca68dae67596123c89ff6 https://github.com/galaxyproject/galaxy/commit/a394faf3be18eceae72ca68dae675... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-28 (Mon, 28 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/api/library_datasets.py

Log Message: ----------- fix refactoring error

Commit: c060bbb5fa54c7062a8daf8df7192d793e354e6e https://github.com/galaxyproject/galaxy/commit/c060bbb5fa54c7062a8daf8df7192... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-28 (Mon, 28 Aug 2017)

Changed paths: M lib/galaxy/managers/library_datasets.py

Log Message: ----------- fix wrongly called exceptions

Commit: 2ede34659b688089ed549ea24416f7610be0a698 https://github.com/galaxyproject/galaxy/commit/2ede34659b688089ed549ea24416f... Author: John Chilton jmchilton@gmail.com Date: 2017-08-28 (Mon, 28 Aug 2017)

Changed paths: M lib/galaxy/datatypes/data.py

Log Message: ----------- Fix bad merge of security patch from 17.05 into dev.

Commit: d56fcf6777d93c83db5ebbc4af7968cb9889e524 https://github.com/galaxyproject/galaxy/commit/d56fcf6777d93c83db5ebbc4af796... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-08-28 (Mon, 28 Aug 2017)

Changed paths: M lib/galaxy/datatypes/data.py

Log Message: ----------- Merge pull request #4508 from jmchilton/dev_merge_fix

Fix bad merge of security patch from 17.05 into dev.

Commit: 5ab28634cabc1df2aa14e9db303247e41b9ea311 https://github.com/galaxyproject/galaxy/commit/5ab28634cabc1df2aa14e9db30324... Author: John Chilton jmchilton@gmail.com Date: 2017-08-29 (Tue, 29 Aug 2017)

Changed paths: M test/api/test_jobs.py

Log Message: ----------- Prevent transient job state test failures from failing the build.

A precondition to the real meat of the test is failing to be met sometimes in production - this failure is indicating a problem with the test and not with Galaxy. I previously tried to address this with https://github.com/galaxyproject/galaxy/pull/3988 but that didn't work. Now if the trainsient ok occurs the test will be skipped. Most of the time it won't skip and the rest of the test will execute and ensure there aren't regressions in behaviors related to cleaning up datasets after job completion. I'm placing the skips a couple different places so hopefully we can get a stack trace at somepoint - knowing where the code is when the job state is changing from running to ok will help puzzle out what is handing for the two minutes the job is running in the test framework.

Commit: 6deff3f9e518a1c7b51cea584ced1e4755ba9254 https://github.com/galaxyproject/galaxy/commit/6deff3f9e518a1c7b51cea584ced1... Author: Frederic Sapet frederic.sapet@biogemma.com Date: 2017-08-29 (Tue, 29 Aug 2017)

Changed paths: M lib/galaxy/tools/imp_exp/__init__.py

Log Message: ----------- import of history works even if we use symlink in database directory

Commit: 82687795413520b5a23e86b17bc3198df3803e39 https://github.com/galaxyproject/galaxy/commit/82687795413520b5a23e86b17bc31... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-29 (Tue, 29 Aug 2017)

Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/rsh.py

Log Message: ----------- Allow paramiko runner to recover from ssh timeout

Commit: d76e304d9bec3d09867c2c264af3f73eabcd17dc https://github.com/galaxyproject/galaxy/commit/d76e304d9bec3d09867c2c264af3f... Author: Frederic Sapet frederic.sapet@biogemma.com Date: 2017-08-29 (Tue, 29 Aug 2017)

Changed paths: M lib/galaxy/tools/imp_exp/__init__.py

Log Message: ----------- remove the redundant call to os.path.abspath(), which is called internally by os.path.realpath()

Commit: a464fe9db6ab993e282feb1ba9ec4eea78ada376 https://github.com/galaxyproject/galaxy/commit/a464fe9db6ab993e282feb1ba9ec4... Author: John Chilton jmchilton@gmail.com Date: 2017-08-29 (Tue, 29 Aug 2017)

Changed paths: M test/selenium_tests/test_published_histories_grid.py

Log Message: ----------- Rework published histories selenium test a bit.

- Wait for elements to be clickable before clicking them. - Allow individual tests to be run on their own and out of order. - Use randomly generated emails - the tests still can't really be applied to an external Galaxy test server but this gets us closer.

Commit: 2faa56eefe7a8b029ed62b9b4402894c2a26248f https://github.com/galaxyproject/galaxy/commit/2faa56eefe7a8b029ed62b9b44028... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-08-29 (Tue, 29 Aug 2017)

Changed paths: M lib/galaxy/tools/__init__.py

Log Message: ----------- Rework if statement to be more explicit

Commit: b096155637e922ab87bab9b86c606e08ef82fea1 https://github.com/galaxyproject/galaxy/commit/b096155637e922ab87bab9b86c606... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-29 (Tue, 29 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M lib/galaxy/managers/library_datasets.py M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/mvc/library/library-dataset-view.js

Log Message: ----------- add functionality to the UI for updating library dataset

Commit: b75f793ea4c58786747da3a9571ba3bd938cd181 https://github.com/galaxyproject/galaxy/commit/b75f793ea4c58786747da3a9571ba... Author: John Chilton jmchilton@gmail.com Date: 2017-08-29 (Tue, 29 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py

Log Message: ----------- Load tools with collection type source attributes into the workflow editor.

Should allow using filter failed and merge collection tools within workflows.

Commit: ba8a7f0e3a540c99b3d8e7be3ea67008e2e76ff2 https://github.com/galaxyproject/galaxy/commit/ba8a7f0e3a540c99b3d8e7be3ea67... Author: John Chilton jmchilton@gmail.com Date: 2017-08-29 (Tue, 29 Aug 2017)

Changed paths: M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view-terminals.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-terminals.js

Log Message: ----------- Pack client.

Commit: 2d9ae75cae83969b3a708c0921ca33841ad08ef5 https://github.com/galaxyproject/galaxy/commit/2d9ae75cae83969b3a708c0921ca3... Author: John Chilton jmchilton@gmail.com Date: 2017-08-29 (Tue, 29 Aug 2017)

Changed paths: M lib/galaxy/datatypes/data.py

Log Message: ----------- Fix another bad merge issue?

Commit: 80c9763757a626355a70e360fd9aedffd8f8dac3 https://github.com/galaxyproject/galaxy/commit/80c9763757a626355a70e360fd9ae... Author: shiltemann zazkia@gmail.com Date: 2017-08-30 (Wed, 30 Aug 2017)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py

Log Message: ----------- add biom2 datatype

Commit: 86902068268903292d1caf003a2274e0a5438f7d https://github.com/galaxyproject/galaxy/commit/86902068268903292d1caf003a227... Author: shiltemann zazkia@gmail.com Date: 2017-08-30 (Wed, 30 Aug 2017)

Changed paths: A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom

Log Message: ----------- add test biom2 file

Commit: b9fb935be594db1224c524bfd03c22b8b90f4bea https://github.com/galaxyproject/galaxy/commit/b9fb935be594db1224c524bfd03c2... Author: shiltemann zazkia@gmail.com Date: 2017-08-30 (Wed, 30 Aug 2017)

Changed paths: M lib/galaxy/datatypes/text.py

Log Message: ----------- add edam format to biom1 datatype

Commit: 8314867ecb57b58caceb4843c021f300dc39472e https://github.com/galaxyproject/galaxy/commit/8314867ecb57b58caceb4843c021f... Author: shiltemann zazkia@gmail.com Date: 2017-08-30 (Wed, 30 Aug 2017)

Changed paths: M config/datatypes_conf.xml.sample

Log Message: ----------- fix sniffer order

Commit: 6feb3e22d19c2cb162adc0b5d80655540305a805 https://github.com/galaxyproject/galaxy/commit/6feb3e22d19c2cb162adc0b5d8065... Author: shiltemann zazkia@gmail.com Date: 2017-08-30 (Wed, 30 Aug 2017)

Changed paths: M lib/galaxy/datatypes/binary.py

Log Message: ----------- order matters

Commit: 07ef9b4f4b2a38259ae55f382ebee36e43743a9d https://github.com/galaxyproject/galaxy/commit/07ef9b4f4b2a38259ae55f382ebee... Author: shiltemann zazkia@gmail.com Date: 2017-08-30 (Wed, 30 Aug 2017)

Changed paths: M lib/galaxy/datatypes/binary.py

Log Message: ----------- use h5py to parse hdf5 header

Commit: ca1ebf97c02e7261fc36352206834de5ab74a0fd https://github.com/galaxyproject/galaxy/commit/ca1ebf97c02e7261fc36352206834... Author: Saskia Hiltemann zazkia@gmail.com Date: 2017-08-30 (Wed, 30 Aug 2017)

Changed paths: M lib/galaxy/datatypes/binary.py

Log Message: ----------- set metadata

Commit: ac61072452cd345d45e87d3548e6564858589029 https://github.com/galaxyproject/galaxy/commit/ac61072452cd345d45e87d3548e65... Author: Saskia Hiltemann zazkia@gmail.com Date: 2017-08-30 (Wed, 30 Aug 2017)

Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt

Log Message: ----------- add h5py requirement for extracting metadata from biom2/hdf5 datatypes

Commit: 92e25158410238bfbc80a931fedb80a55b570e2d https://github.com/galaxyproject/galaxy/commit/92e25158410238bfbc80a931fedb8... Author: Saskia Hiltemann zazkia@gmail.com Date: 2017-08-30 (Wed, 30 Aug 2017)

Changed paths: M lib/galaxy/datatypes/binary.py

Log Message: ----------- fix import order

Commit: 4119caf9b7fbd1fc9c374403e7f7836b8d9397c1 https://github.com/galaxyproject/galaxy/commit/4119caf9b7fbd1fc9c374403e7f78... Author: Saskia Hiltemann zazkia@gmail.com Date: 2017-08-30 (Wed, 30 Aug 2017)

Changed paths: M lib/galaxy/datatypes/data.py

Log Message: ----------- remove unused variable

Commit: 062c88a3cce66df350dc0da7aed14542fe6ad65b https://github.com/galaxyproject/galaxy/commit/062c88a3cce66df350dc0da7aed14... Author: shiltemann zazkia@gmail.com Date: 2017-08-30 (Wed, 30 Aug 2017)

Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/biom1_to_biom2.xml A lib/galaxy/datatypes/converters/biom2_to_biom1.xml

Log Message: ----------- add converters

Commit: a3b316031c5aa1565d7255eab5aa92ff4a749f4d https://github.com/galaxyproject/galaxy/commit/a3b316031c5aa1565d7255eab5aa9... Author: shiltemann zazkia@gmail.com Date: 2017-08-30 (Wed, 30 Aug 2017)

Changed paths: M lib/galaxy/datatypes/binary.py

Log Message: ----------- simplify

Commit: 995f2cee4a2914c157420467829ff647a2e8c7d6 https://github.com/galaxyproject/galaxy/commit/995f2cee4a2914c157420467829ff... Author: shiltemann zazkia@gmail.com Date: 2017-08-30 (Wed, 30 Aug 2017)

Changed paths: M lib/galaxy/datatypes/sniff.py

Log Message: ----------- add guess_ext test

Commit: 21eac0d445cbf8523cd48402d0992dc7ff1720c6 https://github.com/galaxyproject/galaxy/commit/21eac0d445cbf8523cd48402d0992... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-08-30 (Wed, 30 Aug 2017)

Changed paths: M lib/galaxy/datatypes/data.py

Log Message: ----------- Merge pull request #4515 from jmchilton/another_merge_issue

Fix subdirectory listing for extra files

Commit: f3b8a121b7d9d5535381aa8cae7887bd978f9678 https://github.com/galaxyproject/galaxy/commit/f3b8a121b7d9d5535381aa8cae788... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-08-30 (Wed, 30 Aug 2017)

Changed paths: A test/selenium_tests/test_published_histories_grid.py

Log Message: ----------- Merge pull request #4502 from anatskiy/published_history_test

Published History Grid tests

Commit: 95aacc010e730ce24e2e10557bac8395c538d2af https://github.com/galaxyproject/galaxy/commit/95aacc010e730ce24e2e10557bac8... Author: shiltemann zazkia@gmail.com Date: 2017-08-30 (Wed, 30 Aug 2017)

Changed paths: M lib/galaxy/datatypes/binary.py

Log Message: ----------- add metadata to peek

Commit: 907e931fa8f62856fa846d2b9a9bc6392f26952a https://github.com/galaxyproject/galaxy/commit/907e931fa8f62856fa846d2b9a9bc... Author: shiltemann zazkia@gmail.com Date: 2017-08-30 (Wed, 30 Aug 2017)

Changed paths: M lib/galaxy/datatypes/binary.py

Log Message: ----------- don't cast to string

Commit: e8de89afd56b5e125e1e879855d7168a7d2c79b5 https://github.com/galaxyproject/galaxy/commit/e8de89afd56b5e125e1e879855d71... Author: guerler aysam.guerler@gmail.com Date: 2017-08-30 (Wed, 30 Aug 2017)

Changed paths: M config/datatypes_conf.xml.sample

Log Message: ----------- Display d3 hierarchy files in uploader

Commit: 3ac0c7ced7224e63bc55cde9fad3679b390d9628 https://github.com/galaxyproject/galaxy/commit/3ac0c7ced7224e63bc55cde9fad36... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-30 (Wed, 30 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js

Log Message: ----------- improve UX of importing from history to folder

fixes #4151

Commit: 48bb43b8b04b1bdcfb636277c9a595c6a8cbbbb6 https://github.com/galaxyproject/galaxy/commit/48bb43b8b04b1bdcfb636277c9a59... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-30 (Wed, 30 Aug 2017)

Changed paths: M lib/galaxy/managers/library_datasets.py M lib/galaxy/webapps/galaxy/api/library_datasets.py

Log Message: ----------- fix travis issues - whitespace, imports

Commit: 43fd81df59c1862c745813e3b340e93976ef1e2b https://github.com/galaxyproject/galaxy/commit/43fd81df59c1862c745813e3b340e... Author: John Chilton jmchilton@gmail.com Date: 2017-08-30 (Wed, 30 Aug 2017)

Changed paths: M test/galaxy_selenium/driver_factory.py M test/selenium_tests/framework.py

Log Message: ----------- More logging for selenium tests.

Dumb the browser log and the driver log out as JSON to the test error directory for that test.

Commit: f35fed29356d1f55af803f2f24cd2e54634cc8a6 https://github.com/galaxyproject/galaxy/commit/f35fed29356d1f55af803f2f24cd2... Author: John Chilton jmchilton@gmail.com Date: 2017-08-30 (Wed, 30 Aug 2017)

Changed paths: M test/galaxy_selenium/sizzle.py A test/selenium_tests/test_sizzle_loading.py

Log Message: ----------- Improve setting up Sizzle for Selenium tests.

Something releated to AMD broke our way of injecting Sizzle into Galaxy for Selenium tests. This is a much better way that seems to work - just use jQuery ($) as Sizzle if it is available. Avoids an external dependency and another page fetch per test as well as fixing the problem.

Add a test case that just tests the sizzle stuff works on its own. It will be a clear indiciation what is broken if there are related regressions in the future.

Commit: f79eba25b532e42e38fec5f6df25229ea6085a03 https://github.com/galaxyproject/galaxy/commit/f79eba25b532e42e38fec5f6df252... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-30 (Wed, 30 Aug 2017)

Changed paths: M lib/galaxy/managers/library_datasets.py M test/api/test_libraries.py

Log Message: ----------- fix small regressions and add tests for the new API

Commit: 2f9cd0ee491cc99af4a64416e21ce95e6e7dbb33 https://github.com/galaxyproject/galaxy/commit/2f9cd0ee491cc99af4a64416e21ce... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-30 (Wed, 30 Aug 2017)

Changed paths: M test/api/test_jobs.py

Log Message: ----------- Merge pull request #4510 from jmchilton/job_test_fix

Prevent transient job state test failures from failing the build.

Commit: bd13cadbddbbd991460095ad94d9c974cc2a40c9 https://github.com/galaxyproject/galaxy/commit/bd13cadbddbbd991460095ad94d9c... Author: Nicola Soranzo nsoranzo@tiscali.it Date: 2017-08-30 (Wed, 30 Aug 2017)

Changed paths: M config/datatypes_conf.xml.sample

Log Message: ----------- Merge pull request #4522 from guerler/d3_hierarchy_in_uploader

Display d3 hierarchy datatype in upload interface

Commit: 4071fb65c3a8ee83dad2d45fa33c76a787ed3842 https://github.com/galaxyproject/galaxy/commit/4071fb65c3a8ee83dad2d45fa33c7... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-30 (Wed, 30 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js

Log Message: ----------- allow linking, posix and spaces conversions

closes #2977

Commit: 65185f5e435a733c0f6b4639ac91f607b12eb844 https://github.com/galaxyproject/galaxy/commit/65185f5e435a733c0f6b4639ac91f... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-30 (Wed, 30 Aug 2017)

Changed paths: M lib/galaxy/webapps/galaxy/api/library_datasets.py

Log Message: ----------- lint imports

Commit: 5142509f131591b978ecadebbaefc1bb6f608f47 https://github.com/galaxyproject/galaxy/commit/5142509f131591b978ecadebbaefc... Author: John Chilton jmchilton@gmail.com Date: 2017-08-31 (Thu, 31 Aug 2017)

Changed paths: M test/api/test_workflows.py

Log Message: ----------- Make a couple workflow invocation tests more robust.

Less random sleeping, wait for actual invocation. I think this is likely the cause this transient failure (https://jenkins.galaxyproject.org/job/docker-api/8215/testReport/junit/api.t...) picking up the input as the last dataset in the history instead of the output - I bet the workflow just hadn't been invoked yet.

Commit: a85d65c6a2ce3fd0a166e130f8a89dc198c3e0c7 https://github.com/galaxyproject/galaxy/commit/a85d65c6a2ce3fd0a166e130f8a89... Author: John Chilton jmchilton@gmail.com Date: 2017-08-31 (Thu, 31 Aug 2017)

Changed paths: M test/selenium_tests/test_workflow_run.py

Log Message: ----------- Another fix for Selenium worklow tests.

This time for the workflow upgrade message test, mirrors the fix in #4524 - the content we are searching for in on this page is no longer in the iframe.

Commit: 01d16358efa5a71f7030c48c302129cca515e6c6 https://github.com/galaxyproject/galaxy/commit/01d16358efa5a71f7030c48c30212... Author: John Chilton jmchilton@gmail.com Date: 2017-08-31 (Thu, 31 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map

Log Message: ----------- Adjust JS styling for workflow-terminal.js.

Commit: 326477d957bda9c32f63497b5fc911e8c2a9731d https://github.com/galaxyproject/galaxy/commit/326477d957bda9c32f63497b5fc91... Author: E Rasche hxr@hx42.org Date: 2017-08-31 (Thu, 31 Aug 2017)

Changed paths: M config/error_report.yml.sample M doc/source/admin/special_topics/bug_reports.rst A lib/galaxy/tools/error_reports/plugins/influxdb.py

Log Message: ----------- implement influxdb error reporter

Commit: f67fa22dd9bd05d72df859065a3e126af0161d62 https://github.com/galaxyproject/galaxy/commit/f67fa22dd9bd05d72df859065a3e1... Author: E Rasche hxr@hx42.org Date: 2017-08-31 (Thu, 31 Aug 2017)

Changed paths: M lib/galaxy/tools/error_reports/plugins/influxdb.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py

Log Message: ----------- also add destination id everywhere

Commit: 823eb1d4ec84f17f92e4bbf2a12194b2bc0ea9d0 https://github.com/galaxyproject/galaxy/commit/823eb1d4ec84f17f92e4bbf2a1219... Author: Björn Grüning bjoern@gruenings.eu Date: 2017-08-31 (Thu, 31 Aug 2017)

Changed paths: M test/api/test_workflows.py

Log Message: ----------- Merge pull request #4530 from jmchilton/api_test_fixes

More robust workflow invocation testing.

Commit: d09ced249d729b5c0a2098a9d5e81472c91f62b6 https://github.com/galaxyproject/galaxy/commit/d09ced249d729b5c0a2098a9d5e81... Author: Björn Grüning bjoern@gruenings.eu Date: 2017-08-31 (Thu, 31 Aug 2017)

Changed paths: M test/galaxy_selenium/driver_factory.py M test/galaxy_selenium/sizzle.py M test/selenium_tests/framework.py A test/selenium_tests/test_sizzle_loading.py

Log Message: ----------- Merge pull request #4523 from jmchilton/selenium_fixes_15

Selenium test fixes and improvements.

Commit: 49f2438622075f3e9cbe9097ad31b177c97f532a https://github.com/galaxyproject/galaxy/commit/49f2438622075f3e9cbe9097ad31b... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2017-08-31 (Thu, 31 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view-terminals.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-terminals.js

Log Message: ----------- Merge pull request #4514 from jmchilton/collection_operations

Load tools with collection type source attributes into the workflow editor

Commit: cd1c38c527e54b8f7b0817eda5ac9aa0c68dc349 https://github.com/galaxyproject/galaxy/commit/cd1c38c527e54b8f7b0817eda5ac9... Author: John Chilton jmchilton@gmail.com Date: 2017-08-31 (Thu, 31 Aug 2017)

Changed paths: M test/base/populators.py

Log Message: ----------- Break up populator methods for greater composibility and reuse.

All of these changes are needed for various downstream enhancements I'm working on for things like CWL support and extra file testing - but I think they should all be okay refactorings on their own.

Commit: 5a7a15d161bececf0a3cd93714e15768b329d95f https://github.com/galaxyproject/galaxy/commit/5a7a15d161bececf0a3cd93714e15... Author: John Chilton jmchilton@gmail.com Date: 2017-08-31 (Thu, 31 Aug 2017)

Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd M test/api/test_tools.py M test/base/interactor.py M test/base/populators.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 M tools/sr_assembly/velvetg.xml

Log Message: ----------- Test and clarifications for composite uploads.

- Add an API test for datatype-defined composite uploads - including exercising newline conversion and the space_to_tab parameter. - Add a test decorator skip_without_datatype to mirror skip_without_tool for this test, improve both decorators. - The ftype parameter in the composite test tools does nothing - drop it and drop it from the XSD spec. - Slightly improve the documentation for these composite_data elements in the XSD.

Commit: cfefeebdd713552c9e0776b932fca59fe65961a3 https://github.com/galaxyproject/galaxy/commit/cfefeebdd713552c9e0776b932fca... Author: John Chilton jmchilton@gmail.com Date: 2017-08-31 (Thu, 31 Aug 2017)

Changed paths: M test/api/test_histories.py

Log Message: ----------- Refactor history import/export tests to allow collection testing (not yet implemented).

xref #4345, #4532

Commit: 7db1a3fb3e6f61540f1354a899fce1c55e834775 https://github.com/galaxyproject/galaxy/commit/7db1a3fb3e6f61540f1354a899fce... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-31 (Thu, 31 Aug 2017)

Changed paths: M config/error_report.yml.sample M doc/source/admin/special_topics/bug_reports.rst A lib/galaxy/tools/error_reports/plugins/influxdb.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py

Log Message: ----------- Merge pull request #4533 from erasche/influxdb-error-reporter

Implement influxdb error reporter

Commit: de624b48b14f491841921363e4ef7d1ba72db3f3 https://github.com/galaxyproject/galaxy/commit/de624b48b14f491841921363e4ef7... Author: John Chilton jmchilton@gmail.com Date: 2017-08-31 (Thu, 31 Aug 2017)

Changed paths: M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/linters/help.py M lib/galaxy/util/__init__.py

Log Message: ----------- Sync non-CWL galaxy-lib changes.

Covers https://github.com/galaxyproject/galaxy-lib/pull/71 and https://github.com/galaxyproject/galaxy-lib/pull/69.

Commit: 9fb78b1010f8e106d34bf0b44888265b980521fd https://github.com/galaxyproject/galaxy/commit/9fb78b1010f8e106d34bf0b448882... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-31 (Thu, 31 Aug 2017)

Changed paths: M test/selenium_tests/test_workflow_run.py

Log Message: ----------- Merge pull request #4531 from jmchilton/selenium_fixes_17

Another fix for Selenium worklow tests.

Commit: 354ce19677bae15d5cf976386ca988586a0c3eff https://github.com/galaxyproject/galaxy/commit/354ce19677bae15d5cf976386ca98... Author: John Chilton jmchilton@gmail.com Date: 2017-08-31 (Thu, 31 Aug 2017)

Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_workflow_run.py

Log Message: ----------- Fix workflow run Selenium test and make it more robust.

This test went from transiently broken to always broken during this release cycle. This PR makes two changes to try to fix both of those conditions. It correct the frame and button Selector for the new workflow run UX for the newer error and this allows explicitly refreshing the browser when waiting for datasets to appear to deal with the transient problems.

Commit: edd3b07c3dcace5263dafafef72b8564c8b7ce06 https://github.com/galaxyproject/galaxy/commit/edd3b07c3dcace5263dafafef72b8... Author: John Chilton jmchilton@gmail.com Date: 2017-08-31 (Thu, 31 Aug 2017)

Changed paths: M test/galaxy_selenium/driver_factory.py

Log Message: ----------- Fix "all" vs. "ALL" in Selenium logging configuration.

The previous value broke all the tests on Jenkins.

Commit: dd9c757a15e929be2ab6d138fb181f0ed543c156 https://github.com/galaxyproject/galaxy/commit/dd9c757a15e929be2ab6d138fb181... Author: John Chilton jmchilton@gmail.com Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/item_attrs.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py

Log Message: ----------- Merge pull request #4500 from mvdbeek/workflow_loading_speedup

Workflow loading speedup

Commit: f5b29b82d29548a05da911b03d1b3e0dce5dc6e7 https://github.com/galaxyproject/galaxy/commit/f5b29b82d29548a05da911b03d1b3... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/tag.js A client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/mvc/workflow/workflow.js

Log Message: ----------- WIP - show/add/remove workflow tags

Commit: 5e667a7d54eba623bbf6cb42865507e063bdb4a5 https://github.com/galaxyproject/galaxy/commit/5e667a7d54eba623bbf6cb4286550... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/mvc/workflow/workflow.js

Log Message: ----------- Allow editing tags in workflow overview page

Commit: b57b2de7dac8c2fb36e4f3a626d6d33c57da6064 https://github.com/galaxyproject/galaxy/commit/b57b2de7dac8c2fb36e4f3a626d6d... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py

Log Message: ----------- Allow exporting and importing workflow tags

Commit: e1b5a459dcfd183327d8ea1d3485fb5f509b6d82 https://github.com/galaxyproject/galaxy/commit/e1b5a459dcfd183327d8ea1d3485f... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py

Log Message: ----------- Allow updating workflows from partial information

The workflow overview page gets workflow information from the /api/workflows, which returns a reduced amount of information, most notably the steps are not being returned. This commit skips updating the actual workflow steps if the steps are not included in the workflow payload. We can now update name, tags and whether a workflow should be shown in the tool panel. We also return owner and number of steps in the response to importing workflows.

Commit: e2d1fabf58f813c2d722849ad9bf5d1d46517665 https://github.com/galaxyproject/galaxy/commit/e2d1fabf58f813c2d722849ad9bf5... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-model.js

Log Message: ----------- Remove unncessary boilerplate from workflow model

Commit: 17be825cdf3714d2f335ba20ad2b6f51ad10c622 https://github.com/galaxyproject/galaxy/commit/17be825cdf3714d2f335ba20ad2b6... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js

Log Message: ----------- Allow renaming, downloading, dropping workflow files to import

Commit: 5dfe36deceb6d4e38a82c0130a011956c29c06df https://github.com/galaxyproject/galaxy/commit/5dfe36deceb6d4e38a82c0130a011... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: M lib/galaxy/managers/workflows.py

Log Message: ----------- Only access tags if workflow exists

Commit: 060952fa88dd84af04bc1e879e67726596cbc7ff https://github.com/galaxyproject/galaxy/commit/060952fa88dd84af04bc1e879e677... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/webapps/galaxy/api/workflows.py

Log Message: ----------- Allow downloading .ga workflows via the UI

Commit: 1a4effa70e9ad8088e19ae334753b7a898d286aa https://github.com/galaxyproject/galaxy/commit/1a4effa70e9ad8088e19ae334753b... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py

Log Message: ----------- Remove downloading workflows through controller

Commit: 1015b510f81723b927866546390d179abef796f9 https://github.com/galaxyproject/galaxy/commit/1015b510f81723b927866546390d1... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: M lib/galaxy/workflow/modules.py

Log Message: ----------- Properly raise Exception if tool not found

Commit: 70c889435892ebfd1fb88edaab187cb84ba1dccf https://github.com/galaxyproject/galaxy/commit/70c889435892ebfd1fb88edaab187... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/mvc/workflow/workflow.js

Log Message: ----------- Copy workflows without reloading page

Commit: 1dcfe56bb9f1c81567efe68f5ebe4c2f4c6bfb7f https://github.com/galaxyproject/galaxy/commit/1dcfe56bb9f1c81567efe68f5ebe4... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/workflow/workflow.js

Log Message: ----------- Merge WorkflowTagsEditor with TagsEditor

Commit: f1f412ff298a3d859da1f4fe8b7640d722827a1f https://github.com/galaxyproject/galaxy/commit/f1f412ff298a3d859da1f4fe8b764... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js

Log Message: ----------- Make tag_editor local variable

Commit: 911c969631a1dcfb7eee2f2499f81d662b617800 https://github.com/galaxyproject/galaxy/commit/911c969631a1dcfb7eee2f2499f81... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js

Log Message: ----------- Fix logic for determining whether username should be mentioned

Commit: e54b1d1c379f56f2b45ef129a9863be77c379ae7 https://github.com/galaxyproject/galaxy/commit/e54b1d1c379f56f2b45ef129a9863... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js

Log Message: ----------- Fix adjusting dropdown menu

Commit: 0aa4e5463d410df448f484c13174b0e8d6ba87f8 https://github.com/galaxyproject/galaxy/commit/0aa4e5463d410df448f484c13174b... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js

Log Message: ----------- Use toastr for informing user about success/failure

Commit: 61ac1d77a4679938c98e43f54bea9e52073ae32e https://github.com/galaxyproject/galaxy/commit/61ac1d77a4679938c98e43f54bea9... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less

Log Message: ----------- Highlight workflow dropzone

Commit: 09f66a6394303a70b279a34c8f63458b059febc5 https://github.com/galaxyproject/galaxy/commit/09f66a6394303a70b279a34c8f634... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js

Log Message: ----------- Remove unused $el_wf_link variable

Commit: 1de485d3f70165ca1860fbc388a30f40d1a21888 https://github.com/galaxyproject/galaxy/commit/1de485d3f70165ca1860fbc388a30... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js

Log Message: ----------- camelCase functions and variables

Commit: bbaf59a05a7ff6bb048f93fe1eb192157301d6db https://github.com/galaxyproject/galaxy/commit/bbaf59a05a7ff6bb048f93fe1eb19... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js

Log Message: ----------- Display errors to user

Commit: 2968e0e588e35da24caecd0cc4223f694332673b https://github.com/galaxyproject/galaxy/commit/2968e0e588e35da24caecd0cc4223... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js

Log Message: ----------- Show toast at the top-right (which is the default setting)

Commit: 268a895d2b787d9c77a5b87d04ec772382615a8b https://github.com/galaxyproject/galaxy/commit/268a895d2b787d9c77a5b87d04ec7... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-model.js

Log Message: ----------- Describe workflow model and collection (thx @martenson)

Commit: aa49c0053a278d40dcc0affaf894b0e60b3d3949 https://github.com/galaxyproject/galaxy/commit/aa49c0053a278d40dcc0affaf894b... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/mvc/workflow/workflow.js

Log Message: ----------- Move fetching out of WorkflowCollection

thx for the hint @martenson.

Commit: 9a331363cb51733b446aa44eca71f3439152d4ab https://github.com/galaxyproject/galaxy/commit/9a331363cb51733b446aa44eca71f... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js

Log Message: ----------- Improve error reporting to user

Commit: ede8c200f944a9cc21d894654fb6ec0027747333 https://github.com/galaxyproject/galaxy/commit/ede8c200f944a9cc21d894654fb6e... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: M static/maps/mvc/tag.js.map A static/maps/mvc/workflow/workflow-model.js.map M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tag.js A static/scripts/mvc/workflow/workflow-model.js M static/scripts/mvc/workflow/workflow.js M static/style/blue/base.css

Log Message: ----------- Add static JS

Commit: d0df3886fa7acaa3d5f63360e2af78aab2deaaaa https://github.com/galaxyproject/galaxy/commit/d0df3886fa7acaa3d5f63360e2af7... Author: John Chilton jmchilton@gmail.com Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/framework.py M test/selenium_tests/test_workflow_management.py

Log Message: ----------- More workflow index page Selenium tests.

- Fix rename test for recent change to using alert. - Test basic adding a tag. - Outline of a test for downloading workflows. - Add test for publishing display on index. - Add test for using the search box on the workflow index page.

Commit: 259e12d760c721badf9a6f65da90a9bb5bcb0983 https://github.com/galaxyproject/galaxy/commit/259e12d760c721badf9a6f65da90a... Author: John Chilton jmchilton@gmail.com Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: M test/base/api.py A test/base/testcase.py M test/base/twilltestcase.py M test/functional/test_toolbox.py M test/selenium_tests/framework.py

Log Message: ----------- Continue separation of FunctionalTestCase from TwillTestCase.

Move non-twill stuff out into its own module including FunctionalTestCase.

Commit: 6e17ff57ea62320e8764b390e50135d95aaa242d https://github.com/galaxyproject/galaxy/commit/6e17ff57ea62320e8764b390e5013... Author: John Chilton jmchilton@gmail.com Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: R test/functional/test_library_templates.py

Log Message: ----------- Remove test/functional/test_library_templates.py.

Hasn't been run in forever and it seems like we are deprecating these features.

Commit: 6d7c8b3136e24ff3e752efecb14f57574cd53174 https://github.com/galaxyproject/galaxy/commit/6d7c8b3136e24ff3e752efecb14f5... Author: John Chilton jmchilton@gmail.com Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: M test/base/tool_shed_util.py

Log Message: ----------- Cleanup sys.path hacking in test/base/tool_shed_util.py.

Commit: 7343463daca00ef60836e99faecdf90f85c9fd2a https://github.com/galaxyproject/galaxy/commit/7343463daca00ef60836e99faecdf... Author: John Chilton jmchilton@gmail.com Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: M test/base/driver_util.py R test/base/test_db_util.py R test/functional/database_contexts.py M test/shed_functional/base/test_db_util.py

Log Message: ----------- Rework hack to inject database contexts into Tool Shed tests.

Rather than depend on something in ``functional`` test module from ``base.driver_util``, just set these global hacks up in ``driver_util`` itself. This eliminates a dependency of ``functional`` on ``base`` - ideally ``base`` would not depend on any other test modules.

Commit: aba726a89f69fe1dbd4b4147e725c7ce0a7a3a33 https://github.com/galaxyproject/galaxy/commit/aba726a89f69fe1dbd4b4147e725c... Author: John Chilton jmchilton@gmail.com Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: R test/base/twilltestcase.py M test/functional/test_toolbox.py A test/functional/twilltestcase.py M test/shed_functional/base/twilltestcase.py

Log Message: ----------- Move twilltestcase from ``base`` to ``functional`` module.

This way nothing in ``base`` has any dependencies on Twill anymore.

Commit: 558e22a49cbd9a1622a6b7db77ad6f66f17b5229 https://github.com/galaxyproject/galaxy/commit/558e22a49cbd9a1622a6b7db77ad6... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/linters/help.py M lib/galaxy/util/__init__.py

Log Message: ----------- Merge pull request #4535 from jmchilton/galaxy-lib

Sync non-CWL galaxy-lib changes.

Commit: 47efd8089c5b1dfc67af7cf3887ce5b8b907e057 https://github.com/galaxyproject/galaxy/commit/47efd8089c5b1dfc67af7cf3887ce... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/tag.js A client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tag.js.map A static/maps/mvc/workflow/workflow-model.js.map M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tag.js A static/scripts/mvc/workflow/workflow-model.js M static/scripts/mvc/workflow/workflow.js M static/style/blue/base.css M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/framework.py M test/selenium_tests/test_workflow_management.py

Log Message: ----------- Merge pull request #4476 from mvdbeek/workflow_view_tags

Show tags, import by drag-and-drop and avoid refreshed in workflow page

Commit: 5358db58231482312850351d3d1dded25797dec8 https://github.com/galaxyproject/galaxy/commit/5358db58231482312850351d3d1dd... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-01 (Fri, 01 Sep 2017)

Changed paths: M test/base/tool_shed_util.py

Log Message: ----------- fix lint order

Commit: 14497719ba6d3a9727563d15dbeacf2b537551f3 https://github.com/galaxyproject/galaxy/commit/14497719ba6d3a9727563d15dbeac... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-03 (Sun, 03 Sep 2017)

Changed paths: M lib/galaxy/tools/actions/upload_common.py M tools/data_source/upload.py

Log Message: ----------- Prevent in-place editing if purge_source is false

When importing files from the FTP folder the admin can choose to prevent purging of imported files. In this case the source file should not be modified in-place by galaxy.

This also modifies relevant bare `except:` statements and modifies the meaning of `in_place` in upload.py from no external chown script to do not edit files in place if we keep the source file.

This fixes https://github.com/galaxyproject/galaxy/issues/4527.

Commit: 62ef8b52aedb9b9b34403db83703083a0cddbaf9 https://github.com/galaxyproject/galaxy/commit/62ef8b52aedb9b9b34403db837030... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-03 (Sun, 03 Sep 2017)

Changed paths: M tools/data_source/upload.py

Log Message: ----------- Fix sniffing for non-binary files

Commit: 06db29413e838fd88a2ec84ede347f097be161e2 https://github.com/galaxyproject/galaxy/commit/06db29413e838fd88a2ec84ede347... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-03 (Sun, 03 Sep 2017)

Changed paths: M tools/data_source/upload.py

Log Message: ----------- Move instead of copying converted datasets when possible

shutil.move tries to move files by renaming them. If that fails with OSError (due to permission or cross-filesystem rename) it falls back to copying files followed by removing them (https://github.com/python/cpython/blob/2.7/Lib/shutil.py#L279). By using shutil.move and catching permission problems we avoid an unnecessary copy if source and destination are on the same filesystem.

Also avoids shutil.move if the upload tool is run as real-user which should fix https://github.com/galaxyproject/galaxy/issues/4300.

Commit: 471707bd7dfa048a412aad9cdcc1d0b4aea70bc7 https://github.com/galaxyproject/galaxy/commit/471707bd7dfa048a412aad9cdcc1d... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-03 (Sun, 03 Sep 2017)

Changed paths: M lib/galaxy/datatypes/registry.py

Log Message: ----------- Build converters_by_datatype only once per registry lifetime

Commit: ea9f5f7eb2536765a175f7e411f8d64cb8c34cad https://github.com/galaxyproject/galaxy/commit/ea9f5f7eb2536765a175f7e411f8d... Author: Björn Grüning bjoern@gruenings.eu Date: 2017-09-03 (Sun, 03 Sep 2017)

Changed paths: M test/galaxy_selenium/driver_factory.py M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_workflow_run.py

Log Message: ----------- Merge pull request #4524 from jmchilton/selenium_fixes_16

Fix workflow run Selenium test and make it more robust.

Commit: d1a2007275f128fea051ead55fb47d2c2686abf5 https://github.com/galaxyproject/galaxy/commit/d1a2007275f128fea051ead55fb47... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-03 (Sun, 03 Sep 2017)

Changed paths: M lib/galaxy/work/context.py

Log Message: ----------- Cache user roles during WorkRequestContext lifetime

This speeds up building the tool module by a factor of 5.

Commit: 2d8b242e697a08775879fc873578b5f244d4d5cb https://github.com/galaxyproject/galaxy/commit/2d8b242e697a08775879fc873578b... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-03 (Sun, 03 Sep 2017)

Changed paths: M lib/galaxy/datatypes/registry.py

Log Message: ----------- Fix caching of `get_converters_by_datatype` result

Commit: ae7e1f97f0b71f90968abd09dd2f88387d0dc2e4 https://github.com/galaxyproject/galaxy/commit/ae7e1f97f0b71f90968abd09dd2f8... Author: Aysam Guerler aysam.guerler@gmail.com Date: 2017-09-03 (Sun, 03 Sep 2017)

Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/work/context.py

Log Message: ----------- Merge pull request #4541 from mvdbeek/build_module_speedup

Speedup toolform building

Commit: a1e79b13e1471f73a9ef192c0b7762ec6322fa93 https://github.com/galaxyproject/galaxy/commit/a1e79b13e1471f73a9ef192c0b776... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2017-09-03 (Sun, 03 Sep 2017)

Changed paths: A test/selenium_tests/test_saved_histories.py

Log Message: ----------- add the first test

Commit: 634f7dcd3917eef17994a29c1f63f91c4b22a4b9 https://github.com/galaxyproject/galaxy/commit/634f7dcd3917eef17994a29c1f63f... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-03 (Sun, 03 Sep 2017)

Changed paths: A doc/source/dev/finding_and_improving_slow_code.rst

Log Message: ----------- Add a small howto on profiling galaxy code

Commit: 2e5bbad353ca76f25bff9588fea2958cd6d5596a https://github.com/galaxyproject/galaxy/commit/2e5bbad353ca76f25bff9588fea29... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-03 (Sun, 03 Sep 2017)

Changed paths: M doc/source/dev/finding_and_improving_slow_code.rst

Log Message: ----------- Clarify the last section

Commit: b2ceef5b6c258b0d6bc90240549299dbcc3d6ee4 https://github.com/galaxyproject/galaxy/commit/b2ceef5b6c258b0d6bc9024054929... Author: Björn Grüning bjoern@gruenings.eu Date: 2017-09-03 (Sun, 03 Sep 2017)

Changed paths: M test/base/api.py M test/base/driver_util.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 A test/functional/twilltestcase.py M test/selenium_tests/framework.py M test/shed_functional/base/test_db_util.py M test/shed_functional/base/twilltestcase.py

Log Message: ----------- Merge pull request #4536 from jmchilton/test_refactoring

Refactor test modules toward cleaner dependencies

Commit: f6fa7c39f104d390f4a7df62d0b227ab1823c838 https://github.com/galaxyproject/galaxy/commit/f6fa7c39f104d390f4a7df62d0b22... Author: John Chilton jmchilton@gmail.com Date: 2017-09-03 (Sun, 03 Sep 2017)

Changed paths: A doc/source/dev/finding_and_improving_slow_code.rst

Log Message: ----------- Merge pull request #4542 from mvdbeek/build_module_speedup

Add a small howto on profiling galaxy code

Commit: 8f1303217eea29e4973cbbbd13c4b3f8b47f8d5c https://github.com/galaxyproject/galaxy/commit/8f1303217eea29e4973cbbbd13c4b... Author: John Chilton jmchilton@gmail.com Date: 2017-09-03 (Sun, 03 Sep 2017)

Changed paths: M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/util/xml_util.py

Log Message: ----------- Merge pull request #4495 from erasche/parse-once

41% reduction in freiburg galaxy startup time

Commit: 3d9809a50d942e51c8afc7dd4cbae8e775b33147 https://github.com/galaxyproject/galaxy/commit/3d9809a50d942e51c8afc7dd4cbae... Author: John Chilton jmchilton@gmail.com Date: 2017-09-04 (Mon, 04 Sep 2017)

Changed paths: M .ci/flake8_lint_include_list.txt 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-librarytoolbar-view.js M lib/galaxy/managers/libraries.py A lib/galaxy/managers/library_datasets.py M lib/galaxy/managers/workflows.py R lib/galaxy/webapps/galaxy/api/lda_datasets.py A lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/buildapp.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-librarytoolbar-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-librarytoolbar-view.js M test/api/test_libraries.py

Log Message: ----------- Merge pull request #4512 from martenson/improving-datalibraries

A round of data libraries improvements.

Commit: 9556c467e3a4c9947939f8444873530b53b39c20 https://github.com/galaxyproject/galaxy/commit/9556c467e3a4c9947939f84448735... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-04 (Mon, 04 Sep 2017)

Changed paths: M lib/galaxy/work/context.py

Log Message: ----------- Check user roles only once if user has no roles

The previous implementation in #4541 would check user roles multiple times if a user has no roles.

Noticed by @nsoranzo, many thanks!

Commit: 003344ac2f0e6ebd13d78aa8222b958f93bfcf93 https://github.com/galaxyproject/galaxy/commit/003344ac2f0e6ebd13d78aa8222b9... Author: Nicola Soranzo nsoranzo@tiscali.it Date: 2017-09-04 (Mon, 04 Sep 2017)

Changed paths: M lib/galaxy/work/context.py

Log Message: ----------- Merge pull request #4546 from mvdbeek/tool_form_followup

Check user roles only once if user has no roles

Commit: 9b4cd096e1e9cbbd86aafb384e5b7773abf585ab https://github.com/galaxyproject/galaxy/commit/9b4cd096e1e9cbbd86aafb384e5b7... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-04 (Mon, 04 Sep 2017)

Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd M test/api/test_tools.py M test/base/interactor.py M test/base/populators.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 M tools/sr_assembly/velvetg.xml

Log Message: ----------- Merge pull request #4505 from jmchilton/composite_upload_refine

Tests and clarifications for composite uploads.

Commit: 4d3452c09e67be62812a13ea7ad803f62ce76fbb https://github.com/galaxyproject/galaxy/commit/4d3452c09e67be62812a13ea7ad80... Author: John Chilton jmchilton@gmail.com Date: 2017-09-04 (Mon, 04 Sep 2017)

Changed paths: M .ci/jenkins/selenium/docker-compose.yml

Log Message: ----------- Update the default testing Selenium Chrome Docker target.

Some recent changes was incompatible with some bug in the older version (possibly this bug https://bugs.chromium.org/p/chromedriver/issues/detail?id=1552), the result is a huge number of failures in Jenkins as some persistent session error occurs. For example the older (https://jenkins.galaxyproject.org/job/selenium/209/testReport/) but with me hacking the Jenkins job to make this change only two tests fail (https://jenkins.galaxyproject.org/job/selenium/210/testReport/).

Commit: ebcb4aa623dce9f92b904bf1f2ad58f59f07dbaf https://github.com/galaxyproject/galaxy/commit/ebcb4aa623dce9f92b904bf1f2ad5... Author: John Chilton jmchilton@gmail.com Date: 2017-09-04 (Mon, 04 Sep 2017)

Changed paths: M test/selenium_tests/test_published_histories_grid.py

Log Message: ----------- Possible fix for a transient failure in the published histories grid tests.

See failure here (https://jenkins.galaxyproject.org/job/selenium/210/testReport/selenium_tests...).

Uses technique to retry atomic assertions that may not be immediately true but will settle as the DOM is updated in response to changes to be true (added in https://github.com/galaxyproject/galaxy/commit/d0df3886fa7acaa3d5f63360e2af7...).

Commit: a91c03d4403ad57336ce5cc235b22cf4be5ebd6d https://github.com/galaxyproject/galaxy/commit/a91c03d4403ad57336ce5cc235b22... Author: John Chilton jmchilton@gmail.com Date: 2017-09-04 (Mon, 04 Sep 2017)

Changed paths: M test/selenium_tests/test_workflow_editor.py

Log Message: ----------- Remove Selenium test that is broken because Galaxy is broken.

See (https://github.com/galaxyproject/galaxy/issues/4548) for more information on the underlying issue.

Commit: 686cb48c716912212effc3d584d194ead54f216e https://github.com/galaxyproject/galaxy/commit/686cb48c716912212effc3d584d19... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-05 (Tue, 05 Sep 2017)

Changed paths: M lib/galaxy/managers/workflows.py

Log Message: ----------- Alternative fix for workflow editor hang with missing tools

Commit: 33defd130772a0c7a3b63594aad27307e108ead9 https://github.com/galaxyproject/galaxy/commit/33defd130772a0c7a3b63594aad27... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-05 (Tue, 05 Sep 2017)

Changed paths: M lib/galaxy/workflow/modules.py

Log Message: ----------- Revert "Properly raise Exception if tool not found"

This reverts commit 1015b510f81723b927866546390d179abef796f9.

Commit: 09c96dace2f6eb84ae33c856183fcf25175b65bf https://github.com/galaxyproject/galaxy/commit/09c96dace2f6eb84ae33c856183fc... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-05 (Tue, 05 Sep 2017)

Changed paths: M lib/galaxy/managers/workflows.py

Log Message: ----------- Fix extra-space (thx @nsoranzo)

Commit: 40c9ca5ee9e3ab6eee8396218a8467a311225d37 https://github.com/galaxyproject/galaxy/commit/40c9ca5ee9e3ab6eee8396218a846... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-05 (Tue, 05 Sep 2017)

Changed paths: M lib/galaxy/workflow/modules.py

Log Message: ----------- Log warning for missing tools when building workflow modules

Commit: af9173d7cfa85156babca323e1a93d98f53acffd https://github.com/galaxyproject/galaxy/commit/af9173d7cfa85156babca323e1a93... Author: John Chilton jmchilton@gmail.com Date: 2017-09-05 (Tue, 05 Sep 2017)

Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py

Log Message: ----------- Merge pull request #4552 from mvdbeek/fix_missing_tools_wf_editor_alternative

Fix missing tools wf editor alternative

Commit: bff6b58a1ba356f904af7ec17735a88be4b348de https://github.com/galaxyproject/galaxy/commit/bff6b58a1ba356f904af7ec17735a... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-05 (Tue, 05 Sep 2017)

Changed paths: M lib/galaxy/managers/workflows.py

Log Message: ----------- Allow exporting workflows when tool is uninstalled

Commit: 6e6845b4987ab2de5608e216b1f537ad9b1f0fd5 https://github.com/galaxyproject/galaxy/commit/6e6845b4987ab2de5608e216b1f53... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-05 (Tue, 05 Sep 2017)

Changed paths: M test/api/test_histories.py

Log Message: ----------- Merge pull request #4534 from jmchilton/collection_import_export_test_case

Refactor history import/export tests to allow collection testing.

Commit: 96cf1b94f14b7c92c767943fa4595e638eb322e3 https://github.com/galaxyproject/galaxy/commit/96cf1b94f14b7c92c767943fa4595... Author: John Chilton jmchilton@gmail.com Date: 2017-09-05 (Tue, 05 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js 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/collection/list-of-pairs-collection-creator.js

Log Message: ----------- Lower threshold for auto-matching dataset pairs in the collection builder.

Thanks to @mvdbeek for originally testing this and verifying it works.

Fixes #4349.

Commit: 1e3bd2d4e831331b8e3b314bac287288fa4533fc https://github.com/galaxyproject/galaxy/commit/1e3bd2d4e831331b8e3b314bac287... Author: John Chilton jmchilton@gmail.com Date: 2017-09-05 (Tue, 05 Sep 2017)

Changed paths: M config/dependency_resolvers_conf.xml.sample A config/lmod_modules_mapping.yml.sample A lib/galaxy/tools/deps/resolvers/lmod.py M test/unit/tools/test_tool_deps.py

Log Message: ----------- Merge pull request #4489 from arbernard/LMOD_Dependency_resolver

New Dependency resolver for the LMOD environment modules system

Commit: 63392a61071b89d699f26f06d036d7b42a235ff7 https://github.com/galaxyproject/galaxy/commit/63392a61071b89d699f26f06d036d... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-05 (Tue, 05 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js

Log Message: ----------- fix copypasta

Commit: a13bd06f48eb1eda43c034e3fe0a3d9363d8cda4 https://github.com/galaxyproject/galaxy/commit/a13bd06f48eb1eda43c034e3fe0a3... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-05 (Tue, 05 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js 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/collection/list-of-pairs-collection-creator.js

Log Message: ----------- Merge pull request #4555 from jmchilton/lower_matching_threshold

Lower threshold for auto-matching dataset pairs in the collection builder

Commit: 932a3aa3be3327938b619b6c7f97d837264a12a6 https://github.com/galaxyproject/galaxy/commit/932a3aa3be3327938b619b6c7f97d... Author: John Chilton jmchilton@gmail.com Date: 2017-09-05 (Tue, 05 Sep 2017)

Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt

Log Message: ----------- Make chronos dependency conditional.

Fixes #4085.

Commit: c6715819006256e429bf4e589dd456835b8d349c https://github.com/galaxyproject/galaxy/commit/c6715819006256e429bf4e589dd45... Author: John Chilton jmchilton@gmail.com Date: 2017-09-05 (Tue, 05 Sep 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py

Log Message: ----------- Prevent unbound variable error history controller.

Fixes #4423 I suppose - thanks @erasche.

Commit: 338b0c994cf8f249ac2f4cd7dce2ced811e3a58a https://github.com/galaxyproject/galaxy/commit/338b0c994cf8f249ac2f4cd7dce2c... Author: John Chilton jmchilton@gmail.com Date: 2017-09-05 (Tue, 05 Sep 2017)

Changed paths: M lib/galaxy/tools/imp_exp/__init__.py

Log Message: ----------- Merge pull request #4511 from FredericBGA/import_history_and_symlink

import of history works even if we use symlink in database directory

Commit: 46c85ffa986ec2211bbda7be4f90ab579d3fff69 https://github.com/galaxyproject/galaxy/commit/46c85ffa986ec2211bbda7be4f90a... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-05 (Tue, 05 Sep 2017)

Changed paths: M lib/galaxy/datatypes/sniff.py M lib/galaxy/util/checkers.py M lib/galaxy/util/compression_utils.py M lib/tool_shed/util/commit_util.py M tools/data_source/upload.py

Log Message: ----------- Allow working with pbzip2 compressed files

This adds supprt for uploading and uncompressing pbzip2 compressed files by exchanging the bz2 module with bz2file (recommended as workaround in https://docs.python.org/2/library/bz2.html). The problem was reported by @alpapan in #4538 and this commit should fix #4538.

Depends on https://github.com/galaxyproject/starforge/pull/147 for the bz2file wheel.

Commit: 65b86e3eb0152f872a4d30b3be6741972f2fe7f7 https://github.com/galaxyproject/galaxy/commit/65b86e3eb0152f872a4d30b3be674... Author: John Chilton jmchilton@gmail.com Date: 2017-09-05 (Tue, 05 Sep 2017)

Changed paths: M lib/galaxy/managers/workflows.py

Log Message: ----------- Merge pull request #4553 from mvdbeek/allow_exporting_workflow_with_uninstalled_tools

Allow exporting workflows when tool is uninstalled

Commit: b12d29d14b64ce9aa267f1e1a9dd7a452ecf6270 https://github.com/galaxyproject/galaxy/commit/b12d29d14b64ce9aa267f1e1a9dd7... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-05 (Tue, 05 Sep 2017)

Changed paths: M lib/galaxy/managers/library_datasets.py M lib/galaxy/webapps/galaxy/api/library_datasets.py

Log Message: ----------- improve docs and access checks

thanks @nsoranzo

Commit: 4de0ec59f396868c5b56fb139929672c5ac8c3cd https://github.com/galaxyproject/galaxy/commit/4de0ec59f396868c5b56fb1399296... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-05 (Tue, 05 Sep 2017)

Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt

Log Message: ----------- Add bz2file to list of requirements

Commit: 87b798d40a5acb78ddf428d82639f2d5a7f40098 https://github.com/galaxyproject/galaxy/commit/87b798d40a5acb78ddf428d82639f... Author: jvolkening jdv@base2bio.com Date: 2017-09-05 (Tue, 05 Sep 2017)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py

Log Message: ----------- FAST5 archive support

Commit: 235bdca1eb942605eadedf719190de54559fde3a https://github.com/galaxyproject/galaxy/commit/235bdca1eb942605eadedf719190d... Author: Nicola Soranzo nsoranzo@tiscali.it Date: 2017-09-05 (Tue, 05 Sep 2017)

Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt

Log Message: ----------- Merge pull request #4556 from jmchilton/conditional_chronos

Make chronos dependency conditional.

Commit: cccf79ac5f1d4ef8dcd6d66585b5cc7966847bca https://github.com/galaxyproject/galaxy/commit/cccf79ac5f1d4ef8dcd6d66585b5c... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-05 (Tue, 05 Sep 2017)

Changed paths: M lib/galaxy/datatypes/sniff.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/util/checkers.py M lib/galaxy/util/compression_utils.py M lib/tool_shed/util/commit_util.py M tools/data_source/upload.py

Log Message: ----------- Make bz2file dependency conditional on python being below version 3.3

Commit: 3962ba94d756defce37b49375d77e221890904d7 https://github.com/galaxyproject/galaxy/commit/3962ba94d756defce37b49375d77e... Author: Björn Grüning bjoern@gruenings.eu Date: 2017-09-05 (Tue, 05 Sep 2017)

Changed paths: M .ci/jenkins/selenium/docker-compose.yml M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_workflow_editor.py

Log Message: ----------- Merge pull request #4549 from jmchilton/selenium_fixes_18

Assorted Selenium test fixes

Commit: 2541928855159504caf049dd58ffca9570b8bde1 https://github.com/galaxyproject/galaxy/commit/2541928855159504caf049dd58ffc... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-05 (Tue, 05 Sep 2017)

Changed paths: M test/selenium_tests/test_workflow_editor.py

Log Message: ----------- Revert "Remove Selenium test that is broken because Galaxy is broken."

This reverts commit a91c03d4403ad57336ce5cc235b22cf4be5ebd6d.

Commit: b734581495f4bf39da16013ce8ae5536d0cc4437 https://github.com/galaxyproject/galaxy/commit/b734581495f4bf39da16013ce8ae5... Author: John Chilton jmchilton@gmail.com Date: 2017-09-05 (Tue, 05 Sep 2017)

Changed paths: M test/selenium_tests/test_workflow_editor.py

Log Message: ----------- Merge pull request #4561 from mvdbeek/reintroduce_missing_tool_test

Revert "Remove Selenium test that is broken because Galaxy is broken."

Commit: 7db47e7e3c012d34fd27cfb7aadfca17469b2480 https://github.com/galaxyproject/galaxy/commit/7db47e7e3c012d34fd27cfb7aadfc... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-05 (Tue, 05 Sep 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py

Log Message: ----------- Merge pull request #4557 from jmchilton/shared_histories_unbound

Prevent unbound variable error history controller.

Commit: 8c4716e71d600711021041fc31bc8b02972c24c4 https://github.com/galaxyproject/galaxy/commit/8c4716e71d600711021041fc31bc8... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-05 (Tue, 05 Sep 2017)

Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt

Log Message: ----------- Use environment markers to select bz2file when python is < 3.3

Commit: f78eca89126f8f35062541d201af4a85c602808e https://github.com/galaxyproject/galaxy/commit/f78eca89126f8f35062541d201af4... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-05 (Tue, 05 Sep 2017)

Changed paths: M lib/galaxy/managers/library_datasets.py

Log Message: ----------- remove unused import

Commit: 580811d7405f4566bfb8cb62e3bff5c7cc0e80a7 https://github.com/galaxyproject/galaxy/commit/580811d7405f4566bfb8cb62e3bff... Author: John Chilton jmchilton@gmail.com Date: 2017-09-05 (Tue, 05 Sep 2017)

Changed paths: M test/selenium_tests/test_published_histories_grid.py

Log Message: ----------- Potential fix for transiently failing Selenium published histories test.

The the [latest Selenium test execution](https://jenkins.galaxyproject.org/job/selenium/212/testReport/) most of the published histories tests failed. It looks like this is because of the three histories that were supposed to be published, only 2 were actually published. My best guess for what happeend was that the click of the button to publish the history occurred but the next Selenium command happened so quickly that the page had not gotten a chance to respond to the click. This tweaked approach to publishing histories ensures we stay on the page until the "unpublish" link appears - this will either fix the problem or rule this theory out as the explanation.

Commit: 29622bba69422389f7bae7dfa2b6f7c9a6542acb https://github.com/galaxyproject/galaxy/commit/29622bba69422389f7bae7dfa2b6f... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2017-09-05 (Tue, 05 Sep 2017)

Changed paths: M test/selenium_tests/test_saved_histories.py

Log Message: ----------- add history rename test

Commit: 3aacbdffd63c4e6a0570b3144082edffdcad175a https://github.com/galaxyproject/galaxy/commit/3aacbdffd63c4e6a0570b3144082e... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-05 (Tue, 05 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js

Log Message: ----------- Merge pull request #4547 from martenson/library-import-conversions

allow linking, posix and spaces conversions in datalib imports

Commit: 486f436e76b0d3c67514a0d676a85002e5b82f1e https://github.com/galaxyproject/galaxy/commit/486f436e76b0d3c67514a0d676a85... Author: Nicola Soranzo nsoranzo@tiscali.it Date: 2017-09-06 (Wed, 06 Sep 2017)

Changed paths: M lib/galaxy/datatypes/sniff.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/util/checkers.py M lib/galaxy/util/compression_utils.py M lib/tool_shed/util/commit_util.py M tools/data_source/upload.py

Log Message: ----------- Merge pull request #4559 from mvdbeek/use_bzip2file

Allow working with pbzip2 compressed files

Commit: 49eadb682ac5b2662dbe603cea4f0ba68cf59eec https://github.com/galaxyproject/galaxy/commit/49eadb682ac5b2662dbe603cea4f0... Author: John Chilton jmchilton@gmail.com Date: 2017-09-05 (Tue, 05 Sep 2017)

Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_workflow_management.py

Log Message: ----------- Increase the robustness of Selenium workflow management tests.

Next Selenium build encountered a few different problems with importing workflows from URL:

- https://jenkins.galaxyproject.org/job/selenium/213/artifact/213-test-errors/... - https://jenkins.galaxyproject.org/job/selenium/213/artifact/213-test-errors/... - https://jenkins.galaxyproject.org/job/selenium/213/artifact/213-test-errors/...

On full test retry, only one of these actually caused a test error but we shouldn't have to depend on the test re-running stuff.

Commit: 37802abee2b545a2524ef10b8ebaa628a03681fa https://github.com/galaxyproject/galaxy/commit/37802abee2b545a2524ef10b8ebaa... Author: Nicola Soranzo nsoranzo@tiscali.it Date: 2017-09-06 (Wed, 06 Sep 2017)

Changed paths: M lib/galaxy/managers/library_datasets.py M lib/galaxy/webapps/galaxy/api/library_datasets.py

Log Message: ----------- Merge pull request #4560 from martenson/improving-datalibraries

improve docs and access checks in datalibs manager/api

Commit: c57b993b456d226da3896633a576013b977eab1b https://github.com/galaxyproject/galaxy/commit/c57b993b456d226da3896633a5760... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2017-09-06 (Wed, 06 Sep 2017)

Changed paths: M test/selenium_tests/test_saved_histories.py

Log Message: ----------- quick fix

Commit: 7824fdab6b0001570001b60bc76e3a77da402877 https://github.com/galaxyproject/galaxy/commit/7824fdab6b0001570001b60bc76e3... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2017-09-06 (Wed, 06 Sep 2017)

Changed paths: M test/selenium_tests/test_saved_histories.py

Log Message: ----------- add delete/undelete test

Commit: a95566b36c18667cca73286f463b89fabeb8fbf8 https://github.com/galaxyproject/galaxy/commit/a95566b36c18667cca73286f463b8... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-06 (Wed, 06 Sep 2017)

Changed paths: M test/selenium_tests/test_published_histories_grid.py

Log Message: ----------- Merge pull request #4562 from jmchilton/selenium_fixes_19

Potential fix for transiently failing Selenium published histories test.

Commit: eb799267ee35da3b5b9dbef8a58ed8107aeb16ae https://github.com/galaxyproject/galaxy/commit/eb799267ee35da3b5b9dbef8a58ed... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-09-06 (Wed, 06 Sep 2017)

Log Message: ----------- Merge branch 'release_17.05' into dev

Commit: 095c1045b6605756934ef9524907d6cb73c4baf9 https://github.com/galaxyproject/galaxy/commit/095c1045b6605756934ef9524907d... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-06 (Wed, 06 Sep 2017)

Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py

Log Message: ----------- add logging to ts index building

Commit: e8ee2741f9093496aa68c2afe435aa9fc7dd8fcc https://github.com/galaxyproject/galaxy/commit/e8ee2741f9093496aa68c2afe435a... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-06 (Wed, 06 Sep 2017)

Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py

Log Message: ----------- Merge pull request #4567 from martenson/index-refresh-logging

add logging to ts index building

Commit: 30b97f1f1ea9987f967e9774f65ed2e3d8450a3b https://github.com/galaxyproject/galaxy/commit/30b97f1f1ea9987f967e9774f65ed... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-06 (Wed, 06 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js

Log Message: ----------- refactor callback hell to use promises

Commit: cf09a25fdc742998d5bd71deca32527a947c6812 https://github.com/galaxyproject/galaxy/commit/cf09a25fdc742998d5bd71deca325... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-06 (Wed, 06 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js

Log Message: ----------- fix import of collections to datalibs

I swear I fixed this before

Commit: 8f7d2374cac0fcf44b2f878490d912e9bb98a8ec https://github.com/galaxyproject/galaxy/commit/8f7d2374cac0fcf44b2f878490d91... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-06 (Wed, 06 Sep 2017)

Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_workflow_management.py

Log Message: ----------- Merge pull request #4564 from jmchilton/selenium_fixes_20

Increase the robustness of Selenium workflow management tests.

Commit: 20b935639670d171eadb96b3406d00174d978ae6 https://github.com/galaxyproject/galaxy/commit/20b935639670d171eadb96b3406d0... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-06 (Wed, 06 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js

Log Message: ----------- Merge pull request #4568 from martenson/fix-collection-import

Fix datalib collection import

Commit: 9e6cb13e314d451cba7e0eaf841f05410ac19750 https://github.com/galaxyproject/galaxy/commit/9e6cb13e314d451cba7e0eaf841f0... Author: jvolkening jdv@base2bio.com Date: 2017-09-06 (Wed, 06 Sep 2017)

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client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js A client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.js R client/galaxy/scripts/libs/jquery/jqtouch.js M client/galaxy/scripts/mvc/citation/citation-view.js A client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js A client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js A client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M 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test/shed_functional/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py M test/shed_functional/functional/test_1300_reset_all_metadata.py M test/shed_functional/functional/test_1400_review_migration_stages.py M test/shed_functional/functional/test_1410_update_manager.py M test/shed_functional/functional/test_1420_tool_dependency_environment_inheritance.py M test/shed_functional/functional/test_1430_repair_installed_repository.py M test/shed_functional/functional/test_1440_missing_env_sh_files.py M test/shed_functional/functional/test_1450_installing_datatypes_sniffers.py M test/shed_functional/functional/test_1460_data_managers.py M test/shed_functional/functional/test_1470_updating_installed_repositories.py M test/shed_functional/functional_tests.py A test/unit/config/1607_root_filters/config/galaxy.ini A test/unit/config/1607_root_filters/config/tool_shed.ini A test/unit/config/1607_root_samples/config/galaxy.ini A test/unit/config/1607_root_samples/config/reports.ini A test/unit/config/1607_root_samples/config/tool_shed.ini A test/unit/config/test_config_manage.py M test/unit/dataset_collections/test_matching.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/datatypes/test_data.py A test/unit/jobs/conditional_runners_job_conf.xml M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_datasets.py M test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_rule_helper.py M test/unit/jobs/test_rules/10_site.py M test/unit/jobs/test_runner_local.py M test/unit/jobs/test_runner_params.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_fabric_util.py A test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_td_common_util.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_galaxy_mapping.py M test/unit/test_galaxy_transactions.py A test/unit/test_remote_shell.py M test/unit/test_routes.py M test/unit/test_security_helper.py M test/unit/test_sqlite_utils.py M test/unit/test_topsort.py M test/unit/tools/filter_modules/filtermod.py M test/unit/tools/test_actions.py M test/unit/tools/test_citations.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_panel.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/tools/test_watcher.py M test/unit/tools/test_wrappers.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/unittest_utils/utility.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_extract_summary.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py M tool-data/shared/ucsc/builds.txt.sample M tool-data/shared/ucsc/ucsc_build_sites.txt.sample M tool_list.py M tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/hbvar_filter.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/data_source/upload.xml M tools/evolution/add_scores.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/axt_to_lav_code.py M tools/filters/bed_to_gff_converter.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_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/secure_hash_message_digest.py M tools/filters/sorter.py M tools/filters/trimmer.py M tools/filters/trimmer.xml 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/filters/wc_gnu.xml M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_file_browser.py R tools/genomespace/genomespace_file_browser_dev.xml R tools/genomespace/genomespace_file_browser_prod.xml R tools/genomespace/genomespace_file_browser_test.xml M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_importer.xml A tools/genomespace/genomespace_push.xml M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.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_split_by_species.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/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/meme/fimo_wrapper.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/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.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_assembly/velvetg.xml M tools/sr_assembly/velvetg_wrapper.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_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 M tools/visualization/LAJ.py M tools/visualization/LAJ_code.py M tox.ini

Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into fast5

Commit: d887cb17f0e330bed43d80073801568165746454 https://github.com/galaxyproject/galaxy/commit/d887cb17f0e330bed43d800738015... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-06 (Wed, 06 Sep 2017)

Changed paths: 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 tools/filters/join.py M tools/filters/joiner.xml

Log Message: ----------- Merge join_header into dev.

Commit: 696a1eda3ca5695f9c0631c3f2f357c83b4a8995 https://github.com/galaxyproject/galaxy/commit/696a1eda3ca5695f9c0631c3f2f35... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-06 (Wed, 06 Sep 2017)

Changed paths: 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 tools/filters/join.py M tools/filters/joiner.xml

Log Message: ----------- Merge integration branch of 'header_join' into dev

Commit: bca6dfefb6946aa5497819a5d80c74f3d2a7210f https://github.com/galaxyproject/galaxy/commit/bca6dfefb6946aa5497819a5d80c7... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2017-09-07 (Thu, 07 Sep 2017)

Changed paths: M test/selenium_tests/test_saved_histories.py

Log Message: ----------- add history switch test

Commit: da42c16ae7014723012dccdc17c0d39a32ab5713 https://github.com/galaxyproject/galaxy/commit/da42c16ae7014723012dccdc17c0d... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2017-09-07 (Thu, 07 Sep 2017)

Changed paths: M test/selenium_tests/test_saved_histories.py

Log Message: ----------- add history view test

Commit: ff769da9287ddc7f6ad598799a9773d6a2d77c30 https://github.com/galaxyproject/galaxy/commit/ff769da9287ddc7f6ad598799a977... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2017-09-07 (Thu, 07 Sep 2017)

Changed paths: M test/selenium_tests/test_saved_histories.py

Log Message: ----------- add history publish test

Commit: 29ed1bec66ddfb5b1a8559a0a6a8f34aeb928c14 https://github.com/galaxyproject/galaxy/commit/29ed1bec66ddfb5b1a8559a0a6a8f... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2017-09-07 (Thu, 07 Sep 2017)

Changed paths: M test/selenium_tests/test_saved_histories.py

Log Message: ----------- add multiple histories delete/undelete test

Commit: 2fc60430a187cc4a95e2d935b89b65f52acd86b8 https://github.com/galaxyproject/galaxy/commit/2fc60430a187cc4a95e2d935b89b6... Author: jvolkening jdv@base2bio.com Date: 2017-09-07 (Thu, 07 Sep 2017)

Changed paths: M lib/galaxy/datatypes/binary.py

Log Message: ----------- fix formatting to make tox happy

Commit: 5dedd397718166723cdc0bb054565b69e7435d23 https://github.com/galaxyproject/galaxy/commit/5dedd397718166723cdc0bb054565... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2017-09-07 (Thu, 07 Sep 2017)

Changed paths: M test/selenium_tests/test_saved_histories.py

Log Message: ----------- add sort by name test

Commit: e6ebc9e022dd184109374f7f30dec3505b9a2c6e https://github.com/galaxyproject/galaxy/commit/e6ebc9e022dd184109374f7f30dec... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2017-09-07 (Thu, 07 Sep 2017)

Changed paths: M test/selenium_tests/test_saved_histories.py

Log Message: ----------- add standard search test

Commit: 90f0dfc8bcf04309873e8cd8771840c2c7e9fa8d https://github.com/galaxyproject/galaxy/commit/90f0dfc8bcf04309873e8cd877184... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2017-09-07 (Thu, 07 Sep 2017)

Changed paths: M test/selenium_tests/test_saved_histories.py

Log Message: ----------- add advanced search test

Commit: 57ff68edd0627a58c1bdce645d666ad3243df8d2 https://github.com/galaxyproject/galaxy/commit/57ff68edd0627a58c1bdce645d666... Author: John Chilton jmchilton@gmail.com Date: 2017-09-07 (Thu, 07 Sep 2017)

Changed paths: M lib/galaxy/tools/actions/upload_common.py M tools/data_source/upload.py

Log Message: ----------- Merge pull request #4539 from mvdbeek/purge_source

Prevent in-place editing of uploaded files if files are imported from the FTP folder

Commit: 74f7181eafa93eec8fb2bd21ccab5c1373e73c07 https://github.com/galaxyproject/galaxy/commit/74f7181eafa93eec8fb2bd21ccab5... Author: Nate Coraor nate@bx.psu.edu Date: 2017-09-07 (Thu, 07 Sep 2017)

Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/rsh.py

Log Message: ----------- Merge pull request #4503 from mvdbeek/paramiko_long_running

Allow paramiko cli to recover from ssh timeout

Commit: 316eb330bb21b4bd54c340b389217de9f91f0097 https://github.com/galaxyproject/galaxy/commit/316eb330bb21b4bd54c340b389217... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2017-09-07 (Thu, 07 Sep 2017)

Changed paths: M test/selenium_tests/test_saved_histories.py

Log Message: ----------- add permanently delete history test

Commit: e50e7239b58ef80f62c537096bdf642198aaa9cb https://github.com/galaxyproject/galaxy/commit/e50e7239b58ef80f62c537096bdf6... Author: E Rasche hxr@hx42.org Date: 2017-09-07 (Thu, 07 Sep 2017)

Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/webapps/galaxy/controllers/library_common.py

Log Message: ----------- Implement IP address whitelisting

Commit: 569bd6bedf17b1b1f73c964345dd41b3d29cf104 https://github.com/galaxyproject/galaxy/commit/569bd6bedf17b1b1f73c964345dd4... Author: E Rasche hxr@hx42.org Date: 2017-09-07 (Thu, 07 Sep 2017)

Changed paths: M client/galaxy/scripts/utils/uploadbox.js M static/maps/utils/uploadbox.js.map M static/scripts/utils/uploadbox.js

Log Message: ----------- Show a more useful error when one is available

Commit: d1892fc4446474b14da33b6862002a7d54fd9fd2 https://github.com/galaxyproject/galaxy/commit/d1892fc4446474b14da33b6862002... Author: E Rasche hxr@hx42.org Date: 2017-09-07 (Thu, 07 Sep 2017)

Changed paths: M lib/galaxy/config.py M lib/galaxy/tools/actions/upload_common.py

Log Message: ----------- the library prefers unicode stuff

Commit: 36758478d590664615f7fe8e32ef9f7879eb2284 https://github.com/galaxyproject/galaxy/commit/36758478d590664615f7fe8e32ef9... Author: E Rasche hxr@hx42.org Date: 2017-09-07 (Thu, 07 Sep 2017)

Changed paths: M lib/galaxy/tools/actions/upload_common.py

Log Message: ----------- non-URL things get passed to this function

Commit: b620536dc25af3b68a28aade5682b6b7a92af15d https://github.com/galaxyproject/galaxy/commit/b620536dc25af3b68a28aade5682b... Author: E Rasche hxr@hx42.org Date: 2017-09-07 (Thu, 07 Sep 2017)

Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map

Log Message: ----------- rebuild client

Commit: cb416390781e546ce77b94f56cca73e48faed070 https://github.com/galaxyproject/galaxy/commit/cb416390781e546ce77b94f56cca7... Author: E Rasche hxr@hx42.org Date: 2017-09-07 (Thu, 07 Sep 2017)

Changed paths: M lib/galaxy/config.py

Log Message: ----------- flake8

Commit: e8ea1104a7ec1775350d881d3f5eed9fb420b38e https://github.com/galaxyproject/galaxy/commit/e8ea1104a7ec1775350d881d3f5ee... Author: E Rasche hxr@hx42.org Date: 2017-09-07 (Thu, 07 Sep 2017)

Changed paths: M test/integration/test_upload_configuration_options.py

Log Message: ----------- add a test expecting failure

Commit: 618d89b972258db5d2dafcb127ed3a6b473402ae https://github.com/galaxyproject/galaxy/commit/618d89b972258db5d2dafcb127ed3... Author: E Rasche hxr@hx42.org Date: 2017-09-07 (Thu, 07 Sep 2017)

Changed paths: M lib/galaxy/config.py

Log Message: ----------- lint-import-order

Commit: 4e2cd5fea628884d1dddd305e28f3ec81b509982 https://github.com/galaxyproject/galaxy/commit/4e2cd5fea628884d1dddd305e28f3... Author: E Rasche hxr@hx42.org Date: 2017-09-07 (Thu, 07 Sep 2017)

Changed paths: M static/maps/mvc/library/library-foldertoolbar-view.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/library/library-foldertoolbar-view.js

Log Message: ----------- rebuild client

Commit: 2aeb4590d1c9c7bb86bb21b42d6fe20ffc8d59f8 https://github.com/galaxyproject/galaxy/commit/2aeb4590d1c9c7bb86bb21b42d6fe... Author: John Chilton jmchilton@gmail.com Date: 2017-09-07 (Thu, 07 Sep 2017)

Changed paths: M client/galaxy/scripts/utils/uploadbox.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/utils/uploadbox.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/library/library-foldertoolbar-view.js M static/scripts/utils/uploadbox.js M test/integration/test_upload_configuration_options.py

Log Message: ----------- Merge pull request #4289 from erasche/local-network

Local network access restrictions

Commit: 8f3c65c59efe623c325f54e2407c383688ffeedb https://github.com/galaxyproject/galaxy/commit/8f3c65c59efe623c325f54e2407c3... Author: Saskia Hiltemann shiltemann@users.noreply.github.com Date: 2017-09-07 (Thu, 07 Sep 2017)

Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt

Log Message: ----------- use version 2.7.1 of h5py

Commit: d4cf4bff4f249c5e100fde8a31315c92acbe4fc8 https://github.com/galaxyproject/galaxy/commit/d4cf4bff4f249c5e100fde8a31315... Author: shiltemann zazkia@gmail.com Date: 2017-09-07 (Thu, 07 Sep 2017)

Changed paths: M lib/galaxy/datatypes/binary.py

Log Message: ----------- PEP8 fix

Commit: 2615094597ff6bdb0b03e496ea075c2a16f561b9 https://github.com/galaxyproject/galaxy/commit/2615094597ff6bdb0b03e496ea075... Author: shiltemann zazkia@gmail.com Date: 2017-09-07 (Thu, 07 Sep 2017)

Changed paths: M lib/galaxy/datatypes/data.py

Log Message: ----------- Revert "remove unused variable"

This reverts commit 4119caf9b7fbd1fc9c374403e7f7836b8d9397c1.

Commit: f07c6a98431f1a4c2a2d81f99d3b54a23f0a901e https://github.com/galaxyproject/galaxy/commit/f07c6a98431f1a4c2a2d81f99d3b5... Author: jvolkening jdv@base2bio.com Date: 2017-09-07 (Thu, 07 Sep 2017)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py

Log Message: ----------- optimized sniffing, subclassed different tarball types

Commit: 65b2fe8a4aa48ec0fefa36b4f30aeab1627ff33d https://github.com/galaxyproject/galaxy/commit/65b2fe8a4aa48ec0fefa36b4f30ae... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-07 (Thu, 07 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/options-menu.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/history/options-menu.js

Log Message: ----------- Fix delete option in history menu.

Commit: 31043698d0a8a20294c9964d93a0e726b0ff91ca https://github.com/galaxyproject/galaxy/commit/31043698d0a8a20294c9964d93a0e... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-07 (Thu, 07 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/options-menu.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/history/options-menu.js

Log Message: ----------- Fix purge option in history menu. Now delete&purge use modern models/handling.

Commit: 297d2353ce594b3325d029fb72c3ffd825c07f57 https://github.com/galaxyproject/galaxy/commit/297d2353ce594b3325d029fb72c3f... Author: jvolkening jdv@base2bio.com Date: 2017-09-07 (Thu, 07 Sep 2017)

Changed paths: M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/test.fast5.tar A lib/galaxy/datatypes/test/test.fast5.tar.bz2 A lib/galaxy/datatypes/test/test.fast5.tar.gz

Log Message: ----------- add datatype tests

Commit: b3f0f36c89a09056e6a49e4e5c65779a676fc1c5 https://github.com/galaxyproject/galaxy/commit/b3f0f36c89a09056e6a49e4e5c657... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2017-09-07 (Thu, 07 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/options-menu.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/history/options-menu.js

Log Message: ----------- Merge pull request #4574 from dannon/history_options_fixes

Fix delete option in history menu

Commit: a8df8729b8670e23c4f77616cd775aed98463ca7 https://github.com/galaxyproject/galaxy/commit/a8df8729b8670e23c4f77616cd775... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-07 (Thu, 07 Sep 2017)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/biom1_to_biom2.xml A lib/galaxy/datatypes/converters/biom2_to_biom1.xml M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom M lib/galaxy/datatypes/text.py M lib/galaxy/dependencies/pinned-requirements.txt

Log Message: ----------- Merge pull request #4519 from shiltemann/biom2_datatype

add biom2 datatype

Commit: 46b799dfbb56a25df10b3e85368db372ce97f8be https://github.com/galaxyproject/galaxy/commit/46b799dfbb56a25df10b3e85368db... Author: John Chilton jmchilton@gmail.com Date: 2017-09-07 (Thu, 07 Sep 2017)

Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_login.py

Log Message: ----------- Make submitting logins for Selenium tests a bit more robust.

There are a few different transiently failing tests on Jenkins that seem to fail because the test thinks Galaxy is logged in but it is not. So now after we click the login button in Selenium - we will wait for to see the "Register or Login" button turn into the "User" button.

This is a similar problem and fix to what was done in #4562 - which seemed to help.

Commit: 5e179df2a852aa956ce3bd48d4c365d646c2d035 https://github.com/galaxyproject/galaxy/commit/5e179df2a852aa956ce3bd48d4c36... Author: John Chilton jmchilton@gmail.com Date: 2017-09-07 (Thu, 07 Sep 2017)

Changed paths: M test/selenium_tests/test_published_histories_grid.py

Log Message: ----------- Fix logic error in new published histories sort by owner test.

I switched to randomly generated usernames without actually ensure the random usernames would be generated in the same lexiographic order - that wasn't super bright of me. That sort by owner test should pass as frequently as the other tests in that test case class now.

Commit: f623613a392ca21b23b5278530f95257e8d2f365 https://github.com/galaxyproject/galaxy/commit/f623613a392ca21b23b5278530f95... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-07 (Thu, 07 Sep 2017)

Changed paths: M test/selenium_tests/test_published_histories_grid.py

Log Message: ----------- Merge pull request #4577 from jmchilton/selenium_fixes_22

Fix logic error in new published histories sort by owner test.

Commit: 508fdb9d2b4766668e3d1b962216db7e4e7b3e48 https://github.com/galaxyproject/galaxy/commit/508fdb9d2b4766668e3d1b962216d... Author: Eric Rasche hxr@hx42.org Date: 2017-09-08 (Fri, 08 Sep 2017)

Changed paths: A config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.ini.sample A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.xml A config/plugins/interactive_environments/hicbrowser/static/js/hicbrowser.js A config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako

Log Message: ----------- Merge pull request #3330 from bgruening/hicbrowser

HiCBrowser as Galaxy IE

Commit: 49258a7df8bb0f8c489c06dc2a77c27b2244b5f9 https://github.com/galaxyproject/galaxy/commit/49258a7df8bb0f8c489c06dc2a77c... Author: jvolkening jdv@base2bio.com Date: 2017-09-08 (Fri, 08 Sep 2017)

Changed paths: M lib/galaxy/datatypes/binary.py

Log Message: ----------- fixed sniff order and misc linting errors

Commit: 08b5a47c396d38d288d54806edb87e9e717b799d https://github.com/galaxyproject/galaxy/commit/08b5a47c396d38d288d54806edb87... Author: jvolkening jdv@base2bio.com Date: 2017-09-08 (Fri, 08 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/utils/uploadbox.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample A config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.ini.sample A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.xml A config/plugins/interactive_environments/hicbrowser/static/js/hicbrowser.js A config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/biom1_to_biom2.xml A lib/galaxy/datatypes/converters/biom2_to_biom1.xml M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom M lib/galaxy/datatypes/text.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/utils/uploadbox.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/history/options-menu.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/utils/uploadbox.js 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/integration/test_upload_configuration_options.py M test/selenium_tests/test_published_histories_grid.py M tools/data_source/upload.py M tools/filters/join.py M tools/filters/joiner.xml

Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into fast5

Commit: 82267855ed3bc6d3f8911acf6e7e388023f6693d https://github.com/galaxyproject/galaxy/commit/82267855ed3bc6d3f8911acf6e7e3... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-08 (Fri, 08 Sep 2017)

Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/workflow/workflow.js M static/maps/layout/page.js.map M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js M static/scripts/mvc/workflow/workflow.js

Log Message: ----------- Support for applying window title on display() of views.

Commit: 9a66adb4fe7a3be6e07baaec6cef8f553d6b486d https://github.com/galaxyproject/galaxy/commit/9a66adb4fe7a3be6e07baaec6cef8... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-08 (Fri, 08 Sep 2017)

Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js.map

Log Message: ----------- Standard (for now) paren spacing.

Commit: 0a54a313b77b7c47cf57d5f7365cd37231b879ea https://github.com/galaxyproject/galaxy/commit/0a54a313b77b7c47cf57d5f7365cd... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-08 (Fri, 08 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/style/less/library.less M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js M static/style/blue/base.css M static/style/blue/library.css

Log Message: ----------- remove unneeded property, fix import from history targets

some refactoring

Commit: 5b87754ab77dbba1aab632345517e404bc421295 https://github.com/galaxyproject/galaxy/commit/5b87754ab77dbba1aab632345517e... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-08 (Fri, 08 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js

Log Message: ----------- refactor traversing to use latest() instead

Commit: 84de84294c95110f0ee3059ad8a5e9924daf6a9d https://github.com/galaxyproject/galaxy/commit/84de84294c95110f0ee3059ad8a5e... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-08 (Fri, 08 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/history/history-list.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-list.js M static/scripts/mvc/tours.js M static/scripts/mvc/user/user-preferences.js

Log Message: ----------- History List, Tours, and User Preferences titles

Commit: 6b2277e37dd0520de26442701407badcf792cfab https://github.com/galaxyproject/galaxy/commit/6b2277e37dd0520de26442701407b... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-08 (Fri, 08 Sep 2017)

Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow.js

Log Message: ----------- Automatically append 'Galaxy | ' to title instead of requiring it for all view titles.

Commit: 2cb8a28f7be2ff8b7076ef04a6d575d276e3bca6 https://github.com/galaxyproject/galaxy/commit/2cb8a28f7be2ff8b7076ef04a6d57... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-08 (Fri, 08 Sep 2017)

Changed paths: M static/maps/layout/page.js.map M static/maps/mvc/history/history-list.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/tours.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow.js

Log Message: ----------- Rebuild.

Commit: 9a0506c5c0832c93dcd7844ea9de92b619c00773 https://github.com/galaxyproject/galaxy/commit/9a0506c5c0832c93dcd7844ea9de9... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-08 (Fri, 08 Sep 2017)

Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js

Log Message: ----------- Include Galaxy brand in titles.

Commit: 8adbf03f565b1d60fb42ca986d184387e19e94af https://github.com/galaxyproject/galaxy/commit/8adbf03f565b1d60fb42ca986d184... Author: chambm matt.chambers42@gmail.com Date: 2017-09-08 (Fri, 08 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js

Log Message: ----------- Add show/hide deleted/hidden links when history is filtered by find box; addresses #4103

Commit: 91eb849500faec57bebb35228a5a2e2638be70aa https://github.com/galaxyproject/galaxy/commit/91eb849500faec57bebb35228a5a2... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-08 (Fri, 08 Sep 2017)

Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js

Log Message: ----------- Use 'Galaxy / Brand' consistent styling instead of 'Galaxy | Brand'

Commit: 2259c7d41380f6a2aa23ea1bc13169d1d7a5fb54 https://github.com/galaxyproject/galaxy/commit/2259c7d41380f6a2aa23ea1bc1316... Author: John Chilton jmchilton@gmail.com Date: 2017-09-08 (Fri, 08 Sep 2017)

Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_panel.py

Log Message: ----------- Retry failed clicks more aggressively for Selenium tests.

Would have prevented from this (https://jenkins.galaxyproject.org/job/selenium/238/testReport/junit/selenium...) failure in retrospect. Also refactor that common pattern into a helper and use throughout. Add missing @selenium_test decorator on that test also - it would have retried if this had been there and we would have a screenshot.

Commit: 28fd37be40f09ac7054043eed7ef5fdbc10333ef https://github.com/galaxyproject/galaxy/commit/28fd37be40f09ac7054043eed7ef5... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-08 (Fri, 08 Sep 2017)

Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_login.py

Log Message: ----------- Merge pull request #4576 from jmchilton/selenium_fixes_21

Make submitting logins for Selenium tests a bit more robust.

Commit: 935f25aa32b3a22a53de02d5bfe4b5f7de819a0b https://github.com/galaxyproject/galaxy/commit/935f25aa32b3a22a53de02d5bfe4b... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-08 (Fri, 08 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/grid/grid-shared.js M static/maps/mvc/grid/grid-shared.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/grid/grid-shared.js

Log Message: ----------- Titles for abstract grids w/ plural set.

Commit: f83188e7f3c19a5686a623d9bb30f683cd04ff27 https://github.com/galaxyproject/galaxy/commit/f83188e7f3c19a5686a623d9bb30f... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-08 (Fri, 08 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/mvc/grid/grid-view.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/grid/grid-view.js

Log Message: ----------- Normal grid title propagation.

Commit: 97264e3de8d9ea8cd0b4cec9bbe91b1b3d81636d https://github.com/galaxyproject/galaxy/commit/97264e3de8d9ea8cd0b4cec9bbe91... Author: chambm matt.chambers42@gmail.com Date: 2017-09-08 (Fri, 08 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js

Log Message: ----------- Try to start personal CI build

Commit: 900699037da5db8528a51a2f0dd7bc287e346301 https://github.com/galaxyproject/galaxy/commit/900699037da5db8528a51a2f0dd7b... Author: John Chilton jmchilton@gmail.com Date: 2017-09-09 (Sat, 09 Sep 2017)

Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_panel.py

Log Message: ----------- Retry failed clicks more aggressively for Selenium tests.

Would have prevented from this (https://jenkins.galaxyproject.org/job/selenium/238/testReport/junit/selenium...) failure in retrospect. Also refactor that common pattern into a helper and use throughout. Add missing @selenium_test decorator on that test also - it would have retried if this had been there and we would have a screenshot.

Commit: b9cff7ad91f4e157fc2f65e28d00969a4434c09a https://github.com/galaxyproject/galaxy/commit/b9cff7ad91f4e157fc2f65e28d009... Author: John Chilton jmchilton@gmail.com Date: 2017-09-09 (Sat, 09 Sep 2017)

Changed paths: M test/selenium_tests/test_published_histories_grid.py

Log Message: ----------- Fix another issue with sorting by owner for published histories Selenium test.

Locally this never happens, but remotely sometimes when sorting by owner the histories are sorted by owner but not in the same order as the test was asserting. I would assume this is likely a postgres vs. sqlite difference - perhaps the former doesn't sort the rows by the order they were created within equal sort classifications (i.e. same owner) but the latter does. I've fixed this - the test should not have been asserting such a strong condition I don't think.

Commit: 928ad294936c4f6ca4ebc007963578527886af02 https://github.com/galaxyproject/galaxy/commit/928ad294936c4f6ca4ebc00796357... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-09 (Sat, 09 Sep 2017)

Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js

Log Message: ----------- Localize displayed titles.

Commit: a2ef2cc4b95b1a5fd6f5be9d6ceb6cd1c8ed0e7d https://github.com/galaxyproject/galaxy/commit/a2ef2cc4b95b1a5fd6f5be9d6ceb6... Author: Björn Grüning bjoern@gruenings.eu Date: 2017-09-10 (Sun, 10 Sep 2017)

Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_panel.py

Log Message: ----------- Merge pull request #4582 from jmchilton/selenium_fixes_23

Retry failed clicks more aggressively for Selenium tests.

Commit: a21f05d9a8aa457c7b73398caf946b5428ee24a9 https://github.com/galaxyproject/galaxy/commit/a21f05d9a8aa457c7b73398caf946... Author: Björn Grüning bjoern@gruenings.eu Date: 2017-09-10 (Sun, 10 Sep 2017)

Changed paths: M test/selenium_tests/test_published_histories_grid.py

Log Message: ----------- Merge pull request #4586 from jmchilton/selenium_fixes_24

Fix another issue with sorting by owner for published histories Selenium test.

Commit: ca59aaeda017d605f05f6a22b8c6dc09a6f3be3c https://github.com/galaxyproject/galaxy/commit/ca59aaeda017d605f05f6a22b8c6d... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2017-09-10 (Sun, 10 Sep 2017)

Changed paths: M test/selenium_tests/test_saved_histories.py

Log Message: ----------- add the tags test

Commit: d78e60186b6138efe45c1b4107254e624d7424f2 https://github.com/galaxyproject/galaxy/commit/d78e60186b6138efe45c1b4107254... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2017-09-10 (Sun, 10 Sep 2017)

Changed paths: M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/docker-compose.yml M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.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-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/utils/uploadbox.js M config/datatypes_conf.xml.sample M config/dependency_resolvers_conf.xml.sample M config/galaxy.ini.sample A config/lmod_modules_mapping.yml.sample A config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.ini.sample A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.xml A config/plugins/interactive_environments/hicbrowser/static/js/hicbrowser.js A config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako A doc/source/dev/finding_and_improving_slow_code.rst M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/biom1_to_biom2.xml A lib/galaxy/datatypes/converters/biom2_to_biom1.xml M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom M lib/galaxy/datatypes/text.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/managers/libraries.py A lib/galaxy/managers/library_datasets.py M lib/galaxy/managers/workflows.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py A lib/galaxy/tools/deps/resolvers/lmod.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/checkers.py M lib/galaxy/util/compression_utils.py R lib/galaxy/webapps/galaxy/api/lda_datasets.py A lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/work/context.py M lib/galaxy/workflow/modules.py M lib/tool_shed/galaxy_install/installed_repository_manager.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/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-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/utils/uploadbox.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/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/history/options-menu.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-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/utils/uploadbox.js 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/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/navigates_galaxy.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_login.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_workflow_management.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 saved_histories_tests

Commit: 8533c717879f7505b8f293c1ba945f3db63addcb https://github.com/galaxyproject/galaxy/commit/8533c717879f7505b8f293c1ba945... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2017-09-10 (Sun, 10 Sep 2017)

Changed paths: M test/selenium_tests/test_saved_histories.py

Log Message: ----------- use the wait_for_and_click_selector function

Commit: b61ca47c99da6661dee64d6612f8aa30daa464f8 https://github.com/galaxyproject/galaxy/commit/b61ca47c99da6661dee64d6612f8a... Author: John Chilton jmchilton@gmail.com Date: 2017-09-10 (Sun, 10 Sep 2017)

Changed paths: M test/selenium_tests/test_history_sharing.py

Log Message: ----------- Make history sharing tests more robust and informative.

- Be sure when sharing a history with a user we wait to actually see that user's e-mail address appear in the history's sharing list after submission. - Print something for the failed history sharing assertions (I'm pretty sure they are 403 errors because some aspect of the sharing or login didn't work - but might as well verify).

Commit: e2730ca7143f71758d6cd18f129c566447423302 https://github.com/galaxyproject/galaxy/commit/e2730ca7143f71758d6cd18f129c5... Author: John Chilton jmchilton@gmail.com Date: 2017-09-10 (Sun, 10 Sep 2017)

Changed paths: M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_panel.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py

Log Message: ----------- Reduce duplication, increase robustness in Selenium history tests.

- set_tags() appeared in both published and saved history tests, refactored into navigates_galaxy with function name history_panel_add_tags - is_displayed() appeared in both published and saved history tests, refactored into has_driver as selector_is_displayed - Introduced history_panel_rename to reduce duplication across history panel tests and newer published and saved history tests. - Removed custom history click option helper in saved and published history tests and just used the variant in navigates_galaxy. - use wait_for_and_click a couple more places...

Commit: 1e832733db6c6d3e7e191886d836f05708a84440 https://github.com/galaxyproject/galaxy/commit/1e832733db6c6d3e7e191886d836f... Author: John Chilton jmchilton@gmail.com Date: 2017-09-10 (Sun, 10 Sep 2017)

Changed paths: M test/galaxy_selenium/navigates_galaxy.py

Log Message: ----------- Improve error reporting in Selenium tests when ``wait_for_logged_in`` fails.

Previously just a notification about waiting for ``a.loggedin-only`` failed would show up. This doesn't indicate if the login failed completely or the masthead just failed to update. I suspect the login failed completely, but just in case I've updated the error handling to actually ping the API and check and print a better error message with this information.

New messages look like:

``` TimeoutException: Message: Failed waiting for masthead to update for login, but user API response indicates [test0ol61vs8fo] is logged in. This seems to be a bug in Galaxy. API response was [{u'username': u'test0ol61vs8fo', u'quota_percent': None, u'preferences': {}, u'total_disk_usage': 0.0, u'deleted': False, u'id': u'adb5f5c93f827949', u'nice_total_disk_usage': u'0 bytes', u'quota': None, u'email': u'test0ol61vs8fo@test.test', u'is_admin': False, u'tags_used': [], u'purged': False}].Timeout waiting on CSS selector [a.loggedin-only-x] to become visible. ```

and

``` TimeoutException: Message: Failed waiting for masthead to update for login, API indicates no user is logged in - there is a problem with this test. API response was [{u'quota_percent': None, u'nice_total_disk_usage': u'0 bytes', u'total_disk_usage': 0}]. Timeout waiting on CSS selector [a.loggedin-only] to become visible. ```

Commit: dcbe30515f02c3a9f7332f2f3a043132c6cf1fe5 https://github.com/galaxyproject/galaxy/commit/dcbe30515f02c3a9f7332f2f3a043... Author: John Chilton jmchilton@gmail.com Date: 2017-09-10 (Sun, 10 Sep 2017)

Changed paths: M test/galaxy_selenium/navigates_galaxy.py

Log Message: ----------- More robust rename for histories.

I think the wait_for_and_click_selector method will prevent errors like this one https://jenkins.galaxyproject.org/job/selenium/249/testReport/selenium_tests....

Commit: 6b14dda216d103da518a906f4eda018eb58bafbe https://github.com/galaxyproject/galaxy/commit/6b14dda216d103da518a906f4eda0... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-11 (Mon, 11 Sep 2017)

Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/layout/page.js.map M static/maps/mvc/grid/grid-view.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js M static/scripts/mvc/grid/grid-view.js

Log Message: ----------- Grids do a late initialization and the title isn't available until this happens (after display()), so provide a way to allow views to set title late if necessary.

Commit: dcc18134e79bcae7fb055162ba9f8d5f74e66b65 https://github.com/galaxyproject/galaxy/commit/dcc18134e79bcae7fb055162ba9f8... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2017-09-11 (Mon, 11 Sep 2017)

Changed paths: M test/selenium_tests/test_saved_histories.py

Log Message: ----------- generate random history names

Commit: 59d0e297f7217faed3d7c6d30e88678f1eaef600 https://github.com/galaxyproject/galaxy/commit/59d0e297f7217faed3d7c6d30e886... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-11 (Mon, 11 Sep 2017)

Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js

Log Message: ----------- When title isn't set, revert to the default -- otherwise display()'d contents without titles show up with the previous and incorrect titles.

Commit: 2c40efb6c236220ccaffd7893fafa1b8969f1ad2 https://github.com/galaxyproject/galaxy/commit/2c40efb6c236220ccaffd7893fafa... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-11 (Mon, 11 Sep 2017)

Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/utils/utils.js 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

Log Message: ----------- Minor refactor, use a single Utils.setWindowTitle() method.

Commit: a5dbf29e13e1d558ac1c6798e7952963b0599e6e https://github.com/galaxyproject/galaxy/commit/a5dbf29e13e1d558ac1c6798e7952... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-11 (Mon, 11 Sep 2017)

Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js.map

Log Message: ----------- Use standard naming for Utils import.

Commit: 51464551647635e5a1859b3d42ddf281a4f89ad8 https://github.com/galaxyproject/galaxy/commit/51464551647635e5a1859b3d42ddf... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2017-09-11 (Mon, 11 Sep 2017)

Changed paths: M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py

Log Message: ----------- generate random history names for the published history grid tests

Commit: 1359965a992f3a5f3a33276e6d1e1ea6afca0bd8 https://github.com/galaxyproject/galaxy/commit/1359965a992f3a5f3a33276e6d1e1... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-11 (Mon, 11 Sep 2017)

Changed paths: M test/galaxy_selenium/navigates_galaxy.py

Log Message: ----------- Merge pull request #4589 from jmchilton/selenium_fixes_26

Improve error reporting in Selenium tests when ``wait_for_logged_in`` fails.

Commit: 31f2168c3d7f321927a20f21baaddcbfec496389 https://github.com/galaxyproject/galaxy/commit/31f2168c3d7f321927a20f21baadd... Author: John Chilton jmchilton@gmail.com Date: 2017-09-11 (Mon, 11 Sep 2017)

Changed paths: M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_panel.py M test/selenium_tests/test_published_histories_grid.py A test/selenium_tests/test_saved_histories.py

Log Message: ----------- Merge pull request #4587 from anatskiy/saved_histories_tests

Add Selenium tests for the Saved Histories

Commit: a190903bd031ff78f286977cdb7eaca04884de4c https://github.com/galaxyproject/galaxy/commit/a190903bd031ff78f286977cdb7ea... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-11 (Mon, 11 Sep 2017)

Changed paths: M test/selenium_tests/test_history_sharing.py

Log Message: ----------- Merge pull request #4588 from jmchilton/selenium_fixes_25

Make history sharing Selenium tests more robust and informative.

Commit: 79a37830bb75ccd4d8c18236f7938a50a83f87c2 https://github.com/galaxyproject/galaxy/commit/79a37830bb75ccd4d8c18236f7938... Author: John Chilton jmchilton@gmail.com Date: 2017-09-11 (Mon, 11 Sep 2017)

Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_workflow_editor.py

Log Message: ----------- Small improvements to workflow editor Selenium tests.

I saw a failed test earlier that would have been fixed by a switch to wait_for_and_click in workflow_editor_click_options. This makes that switch and moves some of these workflow editor helper functions into navigates_galaxy.py for reuse by other test cases and by library users.

Commit: 1aadd7866f6b94460a5703a8aa35949f7632adcf https://github.com/galaxyproject/galaxy/commit/1aadd7866f6b94460a5703a8aa359... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-11 (Mon, 11 Sep 2017)

Changed paths: M static/maps/mvc/history/history-view-edit.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/history/history-view-edit.js

Log Message: ----------- Make client.

Commit: fd1926767996a161cd2fc8bd184e6835fd688765 https://github.com/galaxyproject/galaxy/commit/fd1926767996a161cd2fc8bd184e6... Author: Matt Chambers matt.chambers42@gmail.com Date: 2017-09-11 (Mon, 11 Sep 2017)

Changed paths: M static/maps/mvc/history/history-view-edit.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/history/history-view-edit.js

Log Message: ----------- Merge pull request #2 from dannon/chambmdev

Make client

Commit: ecb4e06799fb61c4577e1a52276359149670cdf7 https://github.com/galaxyproject/galaxy/commit/ecb4e06799fb61c4577e1a5227635... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-11 (Mon, 11 Sep 2017)

Changed paths: M client/galaxy/scripts/utils/utils.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/utils.js

Log Message: ----------- We apparently always use '|' in the title, even though masthead uses '/'. It does look better.

Commit: ae1c68c7dbb9214def95e97a2f6714c68e23927b https://github.com/galaxyproject/galaxy/commit/ae1c68c7dbb9214def95e97a2f671... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-11 (Mon, 11 Sep 2017)

Changed paths: M client/galaxy/scripts/apps/admin.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map

Log Message: ----------- Set title on base admin page.

Commit: ff5b430319196a61e2a593b04a4bc60859062e3c https://github.com/galaxyproject/galaxy/commit/ff5b430319196a61e2a593b04a4bc... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-11 (Mon, 11 Sep 2017)

Changed paths: M templates/webapps/galaxy/workflow/editor.mako

Log Message: ----------- Workflow editor title fix (not new-style, to keep it simple and use the approach consistent with the .mako layout used.

Commit: 74a486084bcb5d0aef50bebe499b9b39b8a68a74 https://github.com/galaxyproject/galaxy/commit/74a486084bcb5d0aef50bebe499b9... Author: John Chilton jmchilton@gmail.com Date: 2017-09-11 (Mon, 11 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/style/less/library.less M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/style/blue/base.css M static/style/blue/library.css

Log Message: ----------- Merge pull request #4579 from martenson/fix-reload-error

datalibs: fix two bugs, refactor

Commit: c71d3035ab7bbcdfb682a39e4e9e3cb49417289d https://github.com/galaxyproject/galaxy/commit/c71d3035ab7bbcdfb682a39e4e9e3... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-11 (Mon, 11 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/style/less/library.less A config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.ini.sample A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.xml A config/plugins/interactive_environments/hicbrowser/static/js/hicbrowser.js A config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/style/blue/base.css M static/style/blue/library.css M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.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

Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into titles_in_views

Commit: 5da62ca264826bca0318a08f10d9d5e0ab6a3cc8 https://github.com/galaxyproject/galaxy/commit/5da62ca264826bca0318a08f10d9d... Author: John Chilton jmchilton@gmail.com Date: 2017-09-11 (Mon, 11 Sep 2017)

Changed paths: M lib/galaxy/workflow/run.py M test/api/test_workflows.py

Log Message: ----------- Cancel workflow invocations when histories are deleted.

With test case, rebased with spelling fixes thanks to @nsoranzo.

xref #3555 (third point)

Commit: 7efe561867b7c5a3a16e873c215889c58d225277 https://github.com/galaxyproject/galaxy/commit/7efe561867b7c5a3a16e873c21588... Author: John Chilton jmchilton@gmail.com Date: 2017-09-11 (Mon, 11 Sep 2017)

Changed paths: M test/api/test_workflows.py

Log Message: ----------- Rework invocation state tracking in API tests.

At the insistence of @nsoranzo, be more explicit about waiting for workflow test in API tests. While I was in there I also setup new abstractions for waiting on state and updated various workflow cancelling tests to use test_history context for better error reporting.

Commit: e1cdb740cb431104439dbbd63c2f1c0472d2c16b https://github.com/galaxyproject/galaxy/commit/e1cdb740cb431104439dbbd63c2f1... Author: Nicola Soranzo nsoranzo@tiscali.it Date: 2017-09-12 (Tue, 12 Sep 2017)

Changed paths: M lib/galaxy/workflow/run.py M test/api/test_workflows.py

Log Message: ----------- Merge pull request #4580 from jmchilton/deleted_history

Cancel workflow invocations when histories are deleted.

Commit: 7e2727bc0a74868198e7e457f99df3d1e39f1ddb https://github.com/galaxyproject/galaxy/commit/7e2727bc0a74868198e7e457f99df... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-12 (Tue, 12 Sep 2017)

Changed paths: M config/datatypes_conf.xml.sample R lib/galaxy/datatypes/converters/bam_to_bai.xml

Log Message: ----------- Remove bam to bai converter

This converter served no real purpose (you can download bam index files by clicking on the floppy icon, and we never had a bai datatype).

Commit: c5a08186b7ff8090b5ec7191ed149c3e13c9aa90 https://github.com/galaxyproject/galaxy/commit/c5a08186b7ff8090b5ec7191ed149... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-12 (Tue, 12 Sep 2017)

Changed paths: M lib/galaxy/jobs/runners/cli.py

Log Message: ----------- Retry job submissions in ShellJobRunner

If I submit a large amount of jobs in a very short time I sometimes see

``` galaxy.jobs.runners.cli ERROR 2017-09-11 05:03:02,404 (17633) submission failed (stderr): qsub: submit error (Invalid credential) ```

in my logs for a minor subset of jobs (2 out of 120 in the last instance that this happened). In this case waiting a little while and trying again solves the problem. By default we will try submitting the job 3 times, and sleep 10 seconds before trying again.

Commit: c0e2db2d98ead7f9d532ad0f5106d644019d5265 https://github.com/galaxyproject/galaxy/commit/c0e2db2d98ead7f9d532ad0f5106d... Author: Nicola Soranzo nsoranzo@tiscali.it Date: 2017-09-12 (Tue, 12 Sep 2017)

Changed paths: M config/datatypes_conf.xml.sample R lib/galaxy/datatypes/converters/bam_to_bai.xml

Log Message: ----------- Merge pull request #4598 from mvdbeek/remove_bai_converter

Remove bam to bai converter

Commit: 36a3a6b3d9c0b00c26ae861649983a441f725ae8 https://github.com/galaxyproject/galaxy/commit/36a3a6b3d9c0b00c26ae861649983... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2017-09-12 (Tue, 12 Sep 2017)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/test.fast5.tar A lib/galaxy/datatypes/test/test.fast5.tar.bz2 A lib/galaxy/datatypes/test/test.fast5.tar.gz

Log Message: ----------- Merge pull request #4569 from jvolkening/fast5

fast5_archive datatype

Commit: 2e160935d9ceb3ca8441e3b51107594b9539573d https://github.com/galaxyproject/galaxy/commit/2e160935d9ceb3ca8441e3b511075... Author: Aysam Guerler aysam.guerler@gmail.com Date: 2017-09-12 (Tue, 12 Sep 2017)

Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/layout/page.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/tours.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/utils/utils.js 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/tours.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow.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/bundled/login.bundled.js.map M static/scripts/layout/page.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/tours.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow.js M static/scripts/utils/utils.js M templates/webapps/galaxy/workflow/editor.mako

Log Message: ----------- Merge pull request #4578 from dannon/titles_in_views

Delegate displaying of page titles to Layout.display()

Commit: 9468bef057f6372f75ceaee832457386c79e39cc https://github.com/galaxyproject/galaxy/commit/9468bef057f6372f75ceaee832457... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-12 (Tue, 12 Sep 2017)

Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_workflow_editor.py

Log Message: ----------- Merge pull request #4592 from jmchilton/workflow_click_fix

Small improvements to workflow editor Selenium tests.

Commit: b3b71343c101ce7ca39ced3308bd2540dcccc59c https://github.com/galaxyproject/galaxy/commit/b3b71343c101ce7ca39ced3308bd2... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-12 (Tue, 12 Sep 2017)

Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/evaluation.py

Log Message: ----------- Write out registry once per job

Commit: 51f2ecf857dbbdd0e2fd3c78d7f515a87b0ff7e5 https://github.com/galaxyproject/galaxy/commit/51f2ecf857dbbdd0e2fd3c78d7f51... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-12 (Tue, 12 Sep 2017)

Changed paths: M lib/galaxy/datatypes/registry.py

Log Message: ----------- Use a string template to write registry xml

Commit: 49884cdfa3d9cc06192d204c3cc0d727449987d5 https://github.com/galaxyproject/galaxy/commit/49884cdfa3d9cc06192d204c3cc0d... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-12 (Tue, 12 Sep 2017)

Changed paths: M lib/galaxy/app.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/actions/metadata.py

Log Message: ----------- Remove references to integrated_datatypes_config

Commit: 26c7abb130bade73b64284956f0077f35067095f https://github.com/galaxyproject/galaxy/commit/26c7abb130bade73b64284956f007... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-12 (Tue, 12 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M static/maps/mvc/history/history-view-edit.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/history/history-view-edit.js

Log Message: ----------- Merge remote-tracking branch 'chambm/dev' into dev

Commit: 194b249e1d53a480a38910d51e24e267d3164a46 https://github.com/galaxyproject/galaxy/commit/194b249e1d53a480a38910d51e24e... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-12 (Tue, 12 Sep 2017)

Changed paths: M lib/galaxy/datatypes/registry.py

Log Message: ----------- Fix import order

Commit: 60dd7306d04c47aa4a9b2efed149cb3c4d259a10 https://github.com/galaxyproject/galaxy/commit/60dd7306d04c47aa4a9b2efed149c... Author: E Rasche hxr@hx42.org Date: 2017-09-13 (Wed, 13 Sep 2017)

Changed paths: M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/jobs/runners/state_handlers/_safe_eval.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/model/metadata.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/pulsar.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/grids/repository_grids.py

Log Message: ----------- Remove unreachable statements

Commit: 61e05670c26cb75b9a76e3660e049a6f9383a644 https://github.com/galaxyproject/galaxy/commit/61e05670c26cb75b9a76e3660e049... Author: E Rasche hxr@hx42.org Date: 2017-09-13 (Wed, 13 Sep 2017)

Changed paths: M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/jobs/runners/state_handlers/_safe_eval.py

Log Message: ----------- now unused imports

Commit: e33b35def3453d6158bf6ed4109c3ec2dbffbc37 https://github.com/galaxyproject/galaxy/commit/e33b35def3453d6158bf6ed4109c3... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2017-09-13 (Wed, 13 Sep 2017)

Changed paths: M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/jobs/runners/state_handlers/_safe_eval.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/model/metadata.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/pulsar.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/grids/repository_grids.py

Log Message: ----------- Merge pull request #4603 from erasche/dead-code

Remove unreachable statements

Commit: ecd8b90e44decbef60db4359bf4837ef5b12ed1f https://github.com/galaxyproject/galaxy/commit/ecd8b90e44decbef60db4359bf483... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-13 (Wed, 13 Sep 2017)

Changed paths: M lib/galaxy/jobs/runners/cli.py

Log Message: ----------- Decrease log-level for resubmission msg

and specifiy log level directly in if/else clause. Thx @erasche.

Commit: 11d4380d2b40b4e18806f6b2d1e07f4a6eec1f8b https://github.com/galaxyproject/galaxy/commit/11d4380d2b40b4e18806f6b2d1e07... Author: Eric Rasche hxr@hx42.org Date: 2017-09-13 (Wed, 13 Sep 2017)

Changed paths: M lib/galaxy/jobs/runners/cli.py

Log Message: ----------- Merge pull request #4599 from mvdbeek/make_qsub_submissions_more_robust

Retry job submissions in ShellJobRunner

Commit: 38add849710c4e7bb8d350dfae2d7b86b7c8b50b https://github.com/galaxyproject/galaxy/commit/38add849710c4e7bb8d350dfae2d7... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-13 (Wed, 13 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/toolshed/scripts/mvc/groups/group-list-view.js M static/maps/mvc/library/library-librarylist-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-librarylist-view.js

Log Message: ----------- remove unused cruft

Commit: 2daf4317f1f22a683ae29f44e566ad9c2bf4883e https://github.com/galaxyproject/galaxy/commit/2daf4317f1f22a683ae29f44e566a... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-13 (Wed, 13 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-librarylist-view.js M static/maps/mvc/library/library-librarylist-view.js.map M static/scripts/mvc/library/library-librarylist-view.js

Log Message: ----------- show the first page of search results

insted of the current selected (would hide short resutls)

Commit: bf8940071372d0244314795723a24118b3c622bf https://github.com/galaxyproject/galaxy/commit/bf8940071372d0244314795723a24... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-13 (Wed, 13 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-librarylist-view.js M static/maps/mvc/library/library-librarylist-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-librarylist-view.js

Log Message: ----------- remove unused requirements

thanks @anuprulez

Commit: 191d11c4a096df44e3e469328197358d6200dd20 https://github.com/galaxyproject/galaxy/commit/191d11c4a096df44e3e4693281973... Author: Nate Coraor nate@bx.psu.edu Date: 2017-09-13 (Wed, 13 Sep 2017)

Changed paths: M lib/galaxy_ext/metadata/set_metadata.py

Log Message: ----------- Python 3 fixes for set_metadata.py

Commit: cdca22b33e84053df4c6aa6eae7b2d9f5157d9a7 https://github.com/galaxyproject/galaxy/commit/cdca22b33e84053df4c6aa6eae7b2... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-13 (Wed, 13 Sep 2017)

Changed paths: M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map

Log Message: ----------- rebuild client

Commit: e7696027e489c0438fda83293b0efb04a494e465 https://github.com/galaxyproject/galaxy/commit/e7696027e489c0438fda83293b0ef... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-13 (Wed, 13 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-library-view.js 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-library-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-library-view.js

Log Message: ----------- remove cruft

Commit: 1f69ae5d5bc58a31963a91df2e74807c5746d76b https://github.com/galaxyproject/galaxy/commit/1f69ae5d5bc58a31963a91df2e748... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-13 (Wed, 13 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js

Log Message: ----------- refactor few functionas and rename variables

Commit: d63601eacf2ae5de703a24efb470255ee8baf535 https://github.com/galaxyproject/galaxy/commit/d63601eacf2ae5de703a24efb4702... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-13 (Wed, 13 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js

Log Message: ----------- fix the bug with accessing length instead of the variable itself

Commit: ba3ffd82d3a56d9ae66e462d0fe82979e5e70a66 https://github.com/galaxyproject/galaxy/commit/ba3ffd82d3a56d9ae66e462d0fe82... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-13 (Wed, 13 Sep 2017)

Changed paths: M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map

Log Message: ----------- rebuild client

Commit: b442113e76fde691577bf14bfd0717fcca166539 https://github.com/galaxyproject/galaxy/commit/b442113e76fde691577bf14bfd071... Author: Nate Coraor nate@bx.psu.edu Date: 2017-09-13 (Wed, 13 Sep 2017)

Changed paths: M lib/galaxy_ext/metadata/set_metadata.py

Log Message: ----------- Don't use + on iterators.

Commit: 52436aa4f93d13a5d2345deaed7a8f0a343a0074 https://github.com/galaxyproject/galaxy/commit/52436aa4f93d13a5d2345deaed7a8... Author: John Chilton jmchilton@gmail.com Date: 2017-09-13 (Wed, 13 Sep 2017)

Changed paths: 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

Log Message: ----------- Merge pull request #4600 from mvdbeek/datatypes_registroy_in_working_directory

Write datatypes registry xml to working directory

Commit: 4f93f88f0a2df07c5a8c3fa7c62fd4bda40fb3c1 https://github.com/galaxyproject/galaxy/commit/4f93f88f0a2df07c5a8c3fa7c62fd... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-13 (Wed, 13 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M static/maps/mvc/base/controlled-fetch-collection.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/base/controlled-fetch-collection.js

Log Message: ----------- Allow fetchMore to actually specify a 0 offset when intentional. This should fix the mysterious missing history in multiview bug.

Commit: 1502e0067552b72b87853834d3f857a409ead379 https://github.com/galaxyproject/galaxy/commit/1502e0067552b72b87853834d3f85... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-13 (Wed, 13 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-model.js M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-model.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/base/controlled-fetch-collection.js

Log Message: ----------- Some cruft fixing and configuring of Galaxy.debug output instead of commented out console.logs -- should help immensely for troubleshooting

Commit: a6acf116cd50aec61fbf9d670145e30f2273a5fc https://github.com/galaxyproject/galaxy/commit/a6acf116cd50aec61fbf9d670145e... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-13 (Wed, 13 Sep 2017)

Changed paths: M lib/galaxy_ext/metadata/set_metadata.py

Log Message: ----------- Merge pull request #4607 from natefoo/py3-set-meta

Python 3 fixes for set_metadata.py

Commit: a9bfb04caa41129ffb524b1caf880f1ce90544b5 https://github.com/galaxyproject/galaxy/commit/a9bfb04caa41129ffb524b1caf880... Author: Eric Rasche hxr@hx42.org 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 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/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js

Log Message: ----------- Merge pull request #4595 from martenson/datalib-various-fixes

Datalibs various fixes

Commit: cdb95d6045739175e440e68e643e0f4cebadfe50 https://github.com/galaxyproject/galaxy/commit/cdb95d6045739175e440e68e643e0... Author: Eric Rasche hxr@hx42.org Date: 2017-09-14 (Thu, 14 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/toolshed/scripts/mvc/groups/group-list-view.js M static/maps/mvc/library/library-librarylist-view.js.map M static/scripts/mvc/library/library-librarylist-view.js

Log Message: ----------- Merge pull request #4594 from martenson/fix-search-pagination

Fix datalib search pagination

Commit: 62e73a37d3736063113f2118b3e997449e54c75e https://github.com/galaxyproject/galaxy/commit/62e73a37d3736063113f2118b3e99... Author: Dannon Baker dannon.baker@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 remote-tracking branch 'upstream/dev' into fix_missing_histories

Commit: 95969267c226193152e62b537824e6567144c1db https://github.com/galaxyproject/galaxy/commit/95969267c226193152e62b537824e... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2017-09-14 (Thu, 14 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-model.js M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-model.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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js

Log Message: ----------- Merge pull request #4610 from dannon/fix_missing_histories

Multiview missing histories fix

Commit: d8dfbe56c427e73f359595609c932105114950eb https://github.com/galaxyproject/galaxy/commit/d8dfbe56c427e73f359595609c932... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-14 (Thu, 14 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js

Log Message: ----------- unify library dataset permission frontend for all users

also refactor

Commit: 028aac0a3dabe31a5392feaf35a93900ac7eb8b7 https://github.com/galaxyproject/galaxy/commit/028aac0a3dabe31a5392feaf35a93... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-14 (Thu, 14 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/api/library_datasets.py

Log Message: ----------- respect expose_user_email when offering roles to datalib permissions

Commit: a1cd3bd1e41d4da17d116c1a8cde1eedb6143ab9 https://github.com/galaxyproject/galaxy/commit/a1cd3bd1e41d4da17d116c1a8cde1... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-14 (Thu, 14 Sep 2017)

Changed paths: M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js

Log Message: ----------- rebuild client

Commit: 1b2221cd5600823285737fae5d7819c3f2670cfb https://github.com/galaxyproject/galaxy/commit/1b2221cd5600823285737fae5d781... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-14 (Thu, 14 Sep 2017)

Changed paths: M lib/galaxy/security/__init__.py

Log Message: ----------- fix indent

Commit: 2c128b097a07057f4d5a6f9c622eab0f5dabcf3b https://github.com/galaxyproject/galaxy/commit/2c128b097a07057f4d5a6f9c622ea... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2017-09-14 (Thu, 14 Sep 2017)

Changed paths: A test/selenium_tests/test_custom_builds.py

Log Message: ----------- add custom builds tests

Commit: 9084edd8200cc7c7387d62ae969921daf3feec86 https://github.com/galaxyproject/galaxy/commit/9084edd8200cc7c7387d62ae96992... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-14 (Thu, 14 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/mvc/library/library-dataset-view.js

Log Message: ----------- fix typo

thanks @dannon

Commit: e1be66312b536a419383746b8e702b6148edeeec https://github.com/galaxyproject/galaxy/commit/e1be66312b536a419383746b8e702... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-09-14 (Thu, 14 Sep 2017)

Changed paths: M create_db.sh M extract_dataset_parts.sh M manage_db.sh M manage_tools.sh

Log Message: ----------- Fix virtualenv activation for some scripts

In particular add virtualenv activation to extract_dataset_parts.sh to fix the following error when running tools which use `<parallelism>`: ``` Fatal error: /tmp/tmpOoQ01k/job_working_directory/000/12/task_0: Traceback (most recent call last): File "./scripts/extract_dataset_part.py", line 17, in <module> import galaxy.model.mapping # need to load this before we unpickle, in order to setup properties assigned by the mappers File "/opt/galaxyproject_galaxy_release_17.05/lib/galaxy/model/__init__.py", line 20, in <module> from six import string_types ModuleNotFoundError: No module named 'six' ```

Commit: 8b9e91310fd98c9e21bc3511df940b0cba5720b7 https://github.com/galaxyproject/galaxy/commit/8b9e91310fd98c9e21bc3511df940... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-14 (Thu, 14 Sep 2017)

Changed paths: M lib/galaxy/webhooks/__init__.py

Log Message: ----------- Merge branch 'release_17.05' into dev

Commit: 3f38e81cb7bb2246cc3c79dd10dc5992685f1337 https://github.com/galaxyproject/galaxy/commit/3f38e81cb7bb2246cc3c79dd10dc5... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-14 (Thu, 14 Sep 2017)

Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/config_watchers.py A test/integration/test_data_manager_table_reload.py

Log Message: ----------- Update tables to watch when installing new data manager

Commit: 843d2e420011cde58e3742cacc58d3c6f1ab6255 https://github.com/galaxyproject/galaxy/commit/843d2e420011cde58e3742cacc58d... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-14 (Thu, 14 Sep 2017)

Changed paths: M lib/galaxy/tools/toolbox/base.py

Log Message: ----------- Assign correct guids to DM tools after TS install

Commit: d6ae9127ebb7c654ea93f98b1de18ccb92705713 https://github.com/galaxyproject/galaxy/commit/d6ae9127ebb7c654ea93f98b1de18... Author: guerler aysam.guerler@gmail.com Date: 2017-09-14 (Thu, 14 Sep 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Fix group creation label in admin panel

Commit: d247d698a29e3e24816068624061411be97d6ad1 https://github.com/galaxyproject/galaxy/commit/d247d698a29e3e248160686240614... Author: guerler aysam.guerler@gmail.com Date: 2017-09-14 (Thu, 14 Sep 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Fix auto create checkbox name

Commit: 90eed104f0d80fed13ac6b5cfc13f96d28d01771 https://github.com/galaxyproject/galaxy/commit/90eed104f0d80fed13ac6b5cfc13f... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2017-09-15 (Fri, 15 Sep 2017)

Changed paths: M create_db.sh M extract_dataset_parts.sh M manage_db.sh M manage_tools.sh

Log Message: ----------- Merge pull request #4616 from nsoranzo/fix_scripts

Fix virtualenv activation for some scripts

Commit: c677621481abf7823f2d77a506c8aa6908070022 https://github.com/galaxyproject/galaxy/commit/c677621481abf7823f2d77a506c8a... Author: Eric Rasche hxr@hx42.org Date: 2017-09-15 (Fri, 15 Sep 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Merge pull request #4619 from guerler/fix_group_label

Fix group creation label in admin panel and checkbox name

Commit: d06fb09f4bb93906ef36faf0c947eb5625c457e9 https://github.com/galaxyproject/galaxy/commit/d06fb09f4bb93906ef36faf0c947e... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-15 (Fri, 15 Sep 2017)

Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py M lib/tool_shed/tools/tool_validator.py A test/integration/tool_sheds_conf.xml

Log Message: ----------- Make DynamicOptions use updated tool_data_tables

Otherwise a restart would be necessary after adding items to a data table.

Commit: 2e6654b18bd2a38f39d202e35ee5d24562122b3a https://github.com/galaxyproject/galaxy/commit/2e6654b18bd2a38f39d202e35ee5d... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-15 (Fri, 15 Sep 2017)

Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py M test/integration/test_data_manager_table_reload.py

Log Message: ----------- Linting fixes

Commit: a4c4d826dca64b2d85bd8c38cccf9cf6f7762008 https://github.com/galaxyproject/galaxy/commit/a4c4d826dca64b2d85bd8c38cccf9... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-15 (Fri, 15 Sep 2017)

Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt

Log Message: ----------- Make watchdog a conditional dependency

Commit: c5ff555ec4ef32e0d12020c4ea4e0f52f214e31e https://github.com/galaxyproject/galaxy/commit/c5ff555ec4ef32e0d12020c4ea4e0... Author: Eric Rasche hxr@hx42.org Date: 2017-09-15 (Fri, 15 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js

Log Message: ----------- Merge pull request #4611 from martenson/respect-email-exposure

respect expose_user_email configuration in datalibraries permissions list

Commit: 4b403008270bf26e29f037ae902526641dea8e3e https://github.com/galaxyproject/galaxy/commit/4b403008270bf26e29f037ae90252... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-15 (Fri, 15 Sep 2017)

Changed paths: M lib/galaxy/config.py M lib/tool_shed/tool_shed_registry.py

Log Message: ----------- Remove unused root_dir argument

Commit: 2d844a86e7b1534c4211d4a3de7de6e367b5fd44 https://github.com/galaxyproject/galaxy/commit/2d844a86e7b1534c4211d4a3de7de... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-15 (Fri, 15 Sep 2017)

Changed paths: M lib/galaxy/dependencies/dev-requirements.txt

Log Message: ----------- Add watchdog to dev-requirements so it is available for integration tests

Commit: ac084495978a8e5b607d90cf45dfb36c853aaf79 https://github.com/galaxyproject/galaxy/commit/ac084495978a8e5b607d90cf45dfb... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-15 (Fri, 15 Sep 2017)

Changed paths: M templates/webapps/galaxy/admin/sanitize_whitelist.mako

Log Message: ----------- Swap sanitize whitelist form to use a post.

Commit: 1c1ca9bd91298e2265cb4a9e6982f18c3e4ae39d https://github.com/galaxyproject/galaxy/commit/1c1ca9bd91298e2265cb4a9e6982f... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-15 (Fri, 15 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js

Log Message: ----------- Fix loose->lose in help text for library dataset view.

Commit: d5aba7da15f5a05821e7659828bd701fd438769e https://github.com/galaxyproject/galaxy/commit/d5aba7da15f5a05821e7659828bd7... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-15 (Fri, 15 Sep 2017)

Changed paths: M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/util/maf_utilities.py

Log Message: ----------- Three more looses.

Commit: 7831b9889897e1d51ba2004cc8fcc5df079c0594 https://github.com/galaxyproject/galaxy/commit/7831b9889897e1d51ba2004cc8fcc... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-15 (Fri, 15 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/mvc/library/library-dataset-view.js

Log Message: ----------- Occurred, spelling.

Commit: 0ea6272f5d35a769bc63a4706c503793fa903fe2 https://github.com/galaxyproject/galaxy/commit/0ea6272f5d35a769bc63a4706c503... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-15 (Fri, 15 Sep 2017)

Changed paths: 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/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-list-view.js 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/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/toolshed/scripts/mvc/groups/group-detail-view.js M static/toolshed/scripts/mvc/groups/group-list-view.js

Log Message: ----------- More spelling.

Commit: 64af1bd9e96265cbd6b21faadbad5adea4a2d613 https://github.com/galaxyproject/galaxy/commit/64af1bd9e96265cbd6b21faadbad5... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-09-15 (Fri, 15 Sep 2017)

Log Message: ----------- Merge branch 'release_17.05' into dev

Commit: 540322e38856cc86a4a3d91aa3ac670418378d90 https://github.com/galaxyproject/galaxy/commit/540322e38856cc86a4a3d91aa3ac6... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-15 (Fri, 15 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-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/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-list-view.js M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/util/maf_utilities.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-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/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-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/toolshed/scripts/mvc/groups/group-detail-view.js M static/toolshed/scripts/mvc/groups/group-list-view.js

Log Message: ----------- Merge pull request #4626 from dannon/loose_use

Misc. spelling/grammatical error fixes.

Commit: 7d2cd2272299b94b01c8d22c0c1f7f5cbfb2b91a https://github.com/galaxyproject/galaxy/commit/7d2cd2272299b94b01c8d22c0c1f7... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-15 (Fri, 15 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/mvc/library/library-dataset-view.js

Log Message: ----------- replace colon and comma in role names since they are also separators

Commit: 3b4bd3bb6fa922c9e2156fe87660de409acf3367 https://github.com/galaxyproject/galaxy/commit/3b4bd3bb6fa922c9e2156fe87660d... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-15 (Fri, 15 Sep 2017)

Changed paths: M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js

Log Message: ----------- make client

Commit: 69af37f653569117371413bfadd06e5428486526 https://github.com/galaxyproject/galaxy/commit/69af37f653569117371413bfadd06... Author: Vahid VJalili@users.noreply.github.com Date: 2017-09-15 (Fri, 15 Sep 2017)

Changed paths: M lib/galaxy/objectstore/__init__.py

Log Message: ----------- Typo fix

Commit: fe88dab79b0b47245c079ebc372563392c917f30 https://github.com/galaxyproject/galaxy/commit/fe88dab79b0b47245c079ebc37256... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-15 (Fri, 15 Sep 2017)

Changed paths: M lib/galaxy/objectstore/__init__.py

Log Message: ----------- Merge pull request #4628 from VJalili/patch-3

Typo fix

Commit: 2c77d386def0dc21b8aa40d5d7cf5f8934c16a74 https://github.com/galaxyproject/galaxy/commit/2c77d386def0dc21b8aa40d5d7cf5... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-15 (Fri, 15 Sep 2017)

Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/evaluation.py

Log Message: ----------- Write out registry once per job

Commit: 860f0ab6ba6c45c98b5c9f3f002096cc9ef0c7b6 https://github.com/galaxyproject/galaxy/commit/860f0ab6ba6c45c98b5c9f3f00209... Author: Vahid VJalili@users.noreply.github.com Date: 2017-09-15 (Fri, 15 Sep 2017)

Changed paths: M lib/galaxy/model/__init__.py

Log Message: ----------- Some function description updates

Commit: e3e26ae202369876eb1523562b2582f2a15495cb https://github.com/galaxyproject/galaxy/commit/e3e26ae202369876eb1523562b258... Author: Vahid VJalili@users.noreply.github.com Date: 2017-09-15 (Fri, 15 Sep 2017)

Changed paths: M lib/galaxy/model/__init__.py

Log Message: ----------- Updated a comment

Commit: 3cca06a153253f65f752d1f80aae2fd2e3cf221e https://github.com/galaxyproject/galaxy/commit/3cca06a153253f65f752d1f80aae2... Author: Vahid VJalili@users.noreply.github.com Date: 2017-09-15 (Fri, 15 Sep 2017)

Changed paths: M lib/galaxy/model/__init__.py

Log Message: ----------- updated a comment.

Commit: 604fdde4248dc2d7f261e63449ab5530463058a3 https://github.com/galaxyproject/galaxy/commit/604fdde4248dc2d7f261e63449ab5... Author: Vahid VJalili@users.noreply.github.com Date: 2017-09-15 (Fri, 15 Sep 2017)

Changed paths: M lib/galaxy/jobs/__init__.py

Log Message: ----------- typo

Commit: 2897992ab56b69164a916ec400a2ed92b9c72d20 https://github.com/galaxyproject/galaxy/commit/2897992ab56b69164a916ec400a2e... Author: Vahid VJalili@users.noreply.github.com Date: 2017-09-15 (Fri, 15 Sep 2017)

Changed paths: M lib/galaxy/jobs/__init__.py

Log Message: ----------- Refactored a dataset variable to hda

Commit: ea7b27443715730597e273b315dce875910738ce https://github.com/galaxyproject/galaxy/commit/ea7b27443715730597e273b315dce... Author: Nicola Soranzo nsoranzo@tiscali.it Date: 2017-09-15 (Fri, 15 Sep 2017)

Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py

Log Message: ----------- Merge pull request #4629 from VJalili/patch-3

Updated function description and fix some typos

Commit: 153dfaa68080481607a90731c5a0825754cf713d https://github.com/galaxyproject/galaxy/commit/153dfaa68080481607a90731c5a08... Author: Eric Rasche hxr@hx42.org Date: 2017-09-16 (Sat, 16 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js

Log Message: ----------- Merge pull request #4621 from martenson/library-sharing-roles

replace separators in library sharing role names

Commit: 0624a043a73f1a16fc36621b1c61a5cf52c67ba4 https://github.com/galaxyproject/galaxy/commit/0624a043a73f1a16fc36621b1c61a... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-15 (Fri, 15 Sep 2017)

Changed paths: M .travis.yml

Log Message: ----------- remove macos testing

Commit: 432d7f44053a7c7d1fde1504e3f382edf2a539ec https://github.com/galaxyproject/galaxy/commit/432d7f44053a7c7d1fde1504e3f38... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-16 (Sat, 16 Sep 2017)

Changed paths: M lib/galaxy/jobs/__init__.py

Log Message: ----------- Restore correct metadata path in setup_external_metdata

This is a change I shouldn't have touched in https://github.com/galaxyproject/galaxy/pull/4600

Commit: 9d3af63660461c8738782f0a3903e8112e1e5c93 https://github.com/galaxyproject/galaxy/commit/9d3af63660461c8738782f0a3903e... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-16 (Sat, 16 Sep 2017)

Changed paths: M test/integration/test_data_manager_table_reload.py

Log Message: ----------- Skip DataManagerIntegrationTestCase when watchdog unavailable

Commit: e03ee53f3c398fe429ba1fe8693782a06b20cd73 https://github.com/galaxyproject/galaxy/commit/e03ee53f3c398fe429ba1fe869378... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-16 (Sat, 16 Sep 2017)

Changed paths: M lib/galaxy/app.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/actions/metadata.py

Log Message: ----------- Remove references to integrated_datatypes_config

Commit: 22b0542d0bb7a2f88b1503b53a8950d236be0f25 https://github.com/galaxyproject/galaxy/commit/22b0542d0bb7a2f88b1503b53a895... Author: John Chilton jmchilton@gmail.com Date: 2017-09-16 (Sat, 16 Sep 2017)

Changed paths: M .travis.yml

Log Message: ----------- Merge pull request #4631 from martenson/disable-macos-travis

disable MacOS CI on travis

Commit: 6dbd47e661971969c734a46938a06c42b85eea8f https://github.com/galaxyproject/galaxy/commit/6dbd47e661971969c734a46938a06... Author: John Chilton jmchilton@gmail.com Date: 2017-09-16 (Sat, 16 Sep 2017)

Changed paths: M lib/galaxy/jobs/__init__.py

Log Message: ----------- Merge pull request #4632 from mvdbeek/fix_unintended_change

[BUG] Restore tool provided metadata path in setup_external_metdata

Commit: 4c9cc67a8f107887f341b1e386b2ac994acc2ba5 https://github.com/galaxyproject/galaxy/commit/4c9cc67a8f107887f341b1e386b2a... Author: John Chilton jmchilton@gmail.com Date: 2017-09-16 (Sat, 16 Sep 2017)

Changed paths: M lib/galaxy/jobs/__init__.py

Log Message: ----------- Merge pull request #4630 from VJalili/patch-4

Refactored a dataset variable to hda

Commit: 13881bd264eb647bff4019ebbbf52aabf134f92b https://github.com/galaxyproject/galaxy/commit/13881bd264eb647bff4019ebbbf52... Author: John Chilton jmchilton@gmail.com Date: 2017-09-16 (Sat, 16 Sep 2017)

Changed paths: M templates/webapps/galaxy/admin/sanitize_whitelist.mako

Log Message: ----------- Merge pull request #4625 from dannon/sanitize_whitelist_post

Swap sanitize whitelist form to use a post.

Commit: 03d9a9c6fba0e26fae080a7ebb65fd6f0676477e https://github.com/galaxyproject/galaxy/commit/03d9a9c6fba0e26fae080a7ebb65f... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-16 (Sat, 16 Sep 2017)

Changed paths: 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

Log Message: ----------- Merge pull request #4633 from mvdbeek/backport_registry_to_working_dir

[17.05] Backport #4600: Write datatypes registry xml to working directory

Commit: 706434da41e70922f3d723b8cc390f3d0e5d984a https://github.com/galaxyproject/galaxy/commit/706434da41e70922f3d723b8cc390... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-16 (Sat, 16 Sep 2017)

Changed paths: M test/integration/test_data_manager_table_reload.py M test/integration/test_resolvers.py

Log Message: ----------- Append temp dirs to test_driver list of temp dirs

Thanks for the hint @jmchilton.

Commit: 642aaa811bb99a0ef3b532eac3fd5d245972994a https://github.com/galaxyproject/galaxy/commit/642aaa811bb99a0ef3b532eac3fd5... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-16 (Sat, 16 Sep 2017)

Changed paths: M test/base/driver_util.py

Log Message: ----------- Do cleanup if skip_cleanup is not set

Commit: f3c593fc59f0c1a43ddc992feed582cc7668caee https://github.com/galaxyproject/galaxy/commit/f3c593fc59f0c1a43ddc992feed58... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2017-09-16 (Sat, 16 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js

Log Message: ----------- fix column order in Custom Builds

Commit: 8f337f692f2aa2a5aef766bc525929c51cad7324 https://github.com/galaxyproject/galaxy/commit/8f337f692f2aa2a5aef766bc52592... Author: Björn Grüning bjoern@gruenings.eu Date: 2017-09-17 (Sun, 17 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js

Log Message: ----------- Merge pull request #4634 from anatskiy/custom_builds_fix

Fix data order in Custom Builds

Commit: 5f635bda100d7d8f93564c442c5f2d354ae453d0 https://github.com/galaxyproject/galaxy/commit/5f635bda100d7d8f93564c442c5f2... Author: Björn Grüning bjoern@gruenings.eu Date: 2017-09-17 (Sun, 17 Sep 2017)

Changed paths: M lib/galaxy/tools/loader_directory.py

Log Message: ----------- remove .git and .hg from recursive file search

Commit: cfb0d06575dc7523a8f7496e930b6c530e341a5c https://github.com/galaxyproject/galaxy/commit/cfb0d06575dc7523a8f7496e930b6... Author: Eric Rasche hxr@hx42.org Date: 2017-09-18 (Mon, 18 Sep 2017)

Changed paths: M lib/galaxy/tools/loader_directory.py

Log Message: ----------- Exclude venv

Commit: ef602e1d1a1e2b4f90d4d4ac58fb6968424b5bf6 https://github.com/galaxyproject/galaxy/commit/ef602e1d1a1e2b4f90d4d4ac58fb6... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-09-18 (Mon, 18 Sep 2017)

Changed paths: M lib/galaxy/tools/actions/metadata.py

Log Message: ----------- Merge branch 'release_17.05' into dev

Conflicts: lib/galaxy/datatypes/registry.py lib/galaxy/jobs/__init__.py lib/galaxy/jobs/command_factory.py lib/galaxy/tools/actions/metadata.py lib/galaxy/tools/evaluation.py

Commit: d9a805536840f9e606caee9abc0f4e2a64ffe8ea https://github.com/galaxyproject/galaxy/commit/d9a805536840f9e606caee9abc0f4... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2017-09-18 (Mon, 18 Sep 2017)

Changed paths: M lib/galaxy/tools/loader_directory.py

Log Message: ----------- Merge pull request #4636 from bgruening/find_file

remove .git and .hg from recursive file search

Commit: 0df4db5175bec7653aaa855a5d873b3e6de14fcb https://github.com/galaxyproject/galaxy/commit/0df4db5175bec7653aaa855a5d873... Author: guerler aysam.guerler@gmail.com Date: 2017-09-18 (Mon, 18 Sep 2017)

Changed paths: M lib/galaxy/tools/parameters/grouping.py

Log Message: ----------- Replace spaces with newlines in multi url upload requests

Commit: 2bcd46c7234aba06a871b6a824e49f5e39057239 https://github.com/galaxyproject/galaxy/commit/2bcd46c7234aba06a871b6a824e49... Author: guerler aysam.guerler@gmail.com Date: 2017-09-18 (Mon, 18 Sep 2017)

Changed paths: M lib/galaxy/tools/parameters/grouping.py

Log Message: ----------- Split by space instead of newline

Commit: 6af7661fb181a90b31f50e055ac99b9113d1b287 https://github.com/galaxyproject/galaxy/commit/6af7661fb181a90b31f50e055ac99... Author: guerler aysam.guerler@gmail.com Date: 2017-09-18 (Mon, 18 Sep 2017)

Changed paths: M lib/galaxy/tools/parameters/grouping.py

Log Message: ----------- Drop manual string replacements, rely on split without parameters

Commit: 8a4c63738897a7324e31683076f4e77253ef3408 https://github.com/galaxyproject/galaxy/commit/8a4c63738897a7324e31683076f4e... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-18 (Mon, 18 Sep 2017)

Changed paths: M lib/galaxy/managers/libraries.py M lib/galaxy/webapps/galaxy/api/libraries.py

Log Message: ----------- optimize the process of identifying public libraries

this aims to speed up the library loading considerably

Commit: 260a8346197e4a8997f7033f1d99be7acdf302c6 https://github.com/galaxyproject/galaxy/commit/260a8346197e4a8997f7033f1d99b... Author: Evgeny Anatskiy evgeny.anatskiy@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/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map 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 custom_builds_tests

Commit: db67d254ed02f628254464f8b60d2043b871f282 https://github.com/galaxyproject/galaxy/commit/db67d254ed02f628254464f8b60d2... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2017-09-18 (Mon, 18 Sep 2017)

Changed paths: M test/selenium_tests/test_custom_builds.py

Log Message: ----------- don't test the uploading of fasta files

Commit: 8b517e7a036f0df3666e6d89f1aa0e885835225c https://github.com/galaxyproject/galaxy/commit/8b517e7a036f0df3666e6d89f1aa0... Author: guerler aysam.guerler@gmail.com Date: 2017-09-18 (Mon, 18 Sep 2017)

Changed paths: M lib/galaxy/tools/parameters/grouping.py

Log Message: ----------- Restore previous behavior

Commit: 403cd3ffca23fc91c6f8976e1734fcf96af26a78 https://github.com/galaxyproject/galaxy/commit/403cd3ffca23fc91c6f8976e1734f... Author: guerler aysam.guerler@gmail.com Date: 2017-09-18 (Mon, 18 Sep 2017)

Changed paths: M client/galaxy/style/less/upload.less M static/style/blue/base.css

Log Message: ----------- Remove line wrap

Commit: e01b57da58d55763870ad7943a3c04b0e6a34c5b https://github.com/galaxyproject/galaxy/commit/e01b57da58d55763870ad7943a3c0... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2017-09-18 (Mon, 18 Sep 2017)

Changed paths: M test/selenium_tests/test_custom_builds.py

Log Message: ----------- small improvement

Commit: a3ff1297435721d3f687052382b75a2a2f2f9b25 https://github.com/galaxyproject/galaxy/commit/a3ff1297435721d3f687052382b75... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-19 (Tue, 19 Sep 2017)

Changed paths: M lib/galaxy/jobs/__init__.py

Log Message: ----------- Explicitly write registry.xml when creating a job for the upload tool

Commit: a17ae7b90cda7c6c71875f0a7b332410dab15a43 https://github.com/galaxyproject/galaxy/commit/a17ae7b90cda7c6c71875f0a7b332... Author: John Chilton jmchilton@gmail.com Date: 2017-09-19 (Tue, 19 Sep 2017)

Changed paths: 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/queue_worker.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/toolbox/base.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 test/base/driver_util.py A test/integration/test_data_manager_table_reload.py M test/integration/test_resolvers.py A test/integration/tool_sheds_conf.xml

Log Message: ----------- Merge pull request #4617 from mvdbeek/data_manager_watch_new_tables

Allow adding new data tables without restart

Commit: 844f083c7b8c9d29d95a4bca3817db3f918273a4 https://github.com/galaxyproject/galaxy/commit/844f083c7b8c9d29d95a4bca3817d... Author: John Chilton jmchilton@gmail.com Date: 2017-09-19 (Tue, 19 Sep 2017)

Changed paths: A test/selenium_tests/test_custom_builds.py

Log Message: ----------- Merge pull request #4641 from anatskiy/custom_builds_tests

Custom Builds tests

Commit: d980dfa162b340423ffd8822ac9dcdf6f1997e80 https://github.com/galaxyproject/galaxy/commit/d980dfa162b340423ffd8822ac9dc... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-19 (Tue, 19 Sep 2017)

Changed paths: M lib/galaxy/jobs/__init__.py

Log Message: ----------- Write registry.xml for all tools that require galaxy's python env

This should cover the upload and data_source tools.

Commit: 87bb576c39dadadbf119167dee581a6801a54cea https://github.com/galaxyproject/galaxy/commit/87bb576c39dadadbf119167dee581... Author: John Chilton jmchilton@gmail.com Date: 2017-09-19 (Tue, 19 Sep 2017)

Changed paths: M test/selenium_tests/framework.py M test/selenium_tests/test_custom_builds.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py

Log Message: ----------- Improved state handling for @anatskiy-style Selenium tests.

These tests aren't idealized unittest.TestCase because they initialize class level data in instance level methods. While this isn't ideal, it is seems an entirely fair workaround given that SeleniumTestCase setups up the Selenium connection itself in an instance method - so class-level initializers would not be able to setup Galaxy data. Since I think we will continue using this pattern then, probably best to formalize it a bit and improve error handling.

This provides a formal super class for these test cases that provides a uniform method for setting up the class level data and tracks whether this is successful or not. This serves a couple purposes beyond simple uniformity. First, it tracks if the state has actually been setup or not and will skip subsequent tests if it hasn't. Some of these tests aren't passing very consistently on Jenkins and so we get a bunch of extra noise for tests that are attempting to run without their preconditions met - this will fix that and make the original errors much more clear. Moving the "hacky" part of this into the framework itself also means the tests themselves don't have to repeat hacks like seeing if variables are set with ``getattr`` and such - I always prefer one framework hack to a dozen application hacks.

Commit: c5d29be0a2c2c2d16be13d0fa528ad01e5022e1d https://github.com/galaxyproject/galaxy/commit/c5d29be0a2c2c2d16be13d0fa528a... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-19 (Tue, 19 Sep 2017)

Changed paths: M lib/galaxy/managers/libraries.py

Log Message: ----------- avoid mutable default, improve docs

switch to set comprehension

Commit: 3f51e7dc1ef99a68aa8694cfe6858a70e9482e50 https://github.com/galaxyproject/galaxy/commit/3f51e7dc1ef99a68aa8694cfe6858... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-19 (Tue, 19 Sep 2017)

Changed paths: M test/selenium_tests/framework.py M test/selenium_tests/test_custom_builds.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py

Log Message: ----------- Merge pull request #4647 from jmchilton/selenium_fixes_28

Improved state handling for @anatskiy-style Selenium tests.

Commit: 7d394f202d84200e9b4a3c63ce42bf7baf53ccc8 https://github.com/galaxyproject/galaxy/commit/7d394f202d84200e9b4a3c63ce42b... Author: John Chilton jmchilton@gmail.com Date: 2017-09-19 (Tue, 19 Sep 2017)

Changed paths: M lib/galaxy/managers/libraries.py M lib/galaxy/webapps/galaxy/api/libraries.py

Log Message: ----------- Merge pull request #4640 from martenson/datalibs-optimize-access-checks

optimize the process of identifying public libraries

Commit: f1540587760184b0f622c94802d0c8f84b885833 https://github.com/galaxyproject/galaxy/commit/f1540587760184b0f622c94802d0c... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-19 (Tue, 19 Sep 2017)

Changed paths: M client/galaxy/style/less/upload.less M static/style/blue/base.css

Log Message: ----------- Merge pull request #4639 from guerler/replace_spaces_url

do not wrap lines in the upload url fetch

Commit: eee4a17a4cb45b6d79e610c00cbdf37df0988993 https://github.com/galaxyproject/galaxy/commit/eee4a17a4cb45b6d79e610c00cbdf... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-19 (Tue, 19 Sep 2017)

Changed paths: M lib/galaxy/version.py

Log Message: ----------- Update version to 17.09.rc1

Commit: b7b3ffb1813f31b7811bdbb35602743294356f66 https://github.com/galaxyproject/galaxy/commit/b7b3ffb1813f31b7811bdbb356027... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-19 (Tue, 19 Sep 2017)

Changed paths: M test/unit/jobs/test_job_wrapper.py

Log Message: ----------- Fix unit test failure

Commit: 7fd6813dd7fcf373cc09a3da6fd6f4bf5c8b0863 https://github.com/galaxyproject/galaxy/commit/7fd6813dd7fcf373cc09a3da6fd6f... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-19 (Tue, 19 Sep 2017)

Changed paths: M tox.ini

Log Message: ----------- pin flake8 deps for release

Commit: a25b6e5b0eb5ed97e789e1b4b8643be775a55e05 https://github.com/galaxyproject/galaxy/commit/a25b6e5b0eb5ed97e789e1b4b8643... Author: John Chilton jmchilton@gmail.com Date: 2017-09-19 (Tue, 19 Sep 2017)

Changed paths: M lib/galaxy/version.py

Log Message: ----------- Merge pull request #4648 from martenson/version-17.09

[17.09]Update version to 17.09.rc1

Commit: f46a5c1797fb4c1f3fc663addf83ce9a411beac6 https://github.com/galaxyproject/galaxy/commit/f46a5c1797fb4c1f3fc663addf83c... Author: John Chilton jmchilton@gmail.com Date: 2017-09-19 (Tue, 19 Sep 2017)

Changed paths: M tox.ini

Log Message: ----------- Merge pull request #4650 from martenson/release_17.09

[17.09] pin flake8 deps for release

Commit: ee6b8b1af8c997d874a9ad7213231582b69cf82c https://github.com/galaxyproject/galaxy/commit/ee6b8b1af8c997d874a9ad7213231... Author: Martin Cech marten@bx.psu.edu Date: 2017-09-19 (Tue, 19 Sep 2017)

Changed paths: M tox.ini

Log Message: ----------- pin the last flake8

thanks @nsoranzo :eagle: :eyes:

Commit: 0e89935460a54fa846dff53041fcfe3b8e7e9ecd https://github.com/galaxyproject/galaxy/commit/0e89935460a54fa846dff53041fcf... Author: Nicola Soranzo nsoranzo@tiscali.it Date: 2017-09-20 (Wed, 20 Sep 2017)

Changed paths: M tox.ini

Log Message: ----------- Merge pull request #4652 from martenson/release_17.09

[17.09] pin the last missing flake8

Commit: 5404f7cda7ca4f3b9a2c423bdd29898fb7d8c911 https://github.com/galaxyproject/galaxy/commit/5404f7cda7ca4f3b9a2c423bdd298... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-20 (Wed, 20 Sep 2017)

Changed paths: M templates/display_base.mako M templates/display_common.mako

Log Message: ----------- Small (temporary, mako is going away) layer to support modern routes in old display_base pages (workflow, history, etc).

Commit: 69a87003f70e3925554fcc88fd2080edab619ed1 https://github.com/galaxyproject/galaxy/commit/69a87003f70e3925554fcc88fd208... Author: Nate Coraor nate@bx.psu.edu Date: 2017-09-20 (Wed, 20 Sep 2017)

Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py

Log Message: ----------- Fix modules resolver (addition of the resolver_msg property on the base class references name and version attributes that were not defined in the ModuleDependecy).

Commit: c9aead91d75a1e0e636cf08ba725a8c2f8ff300a https://github.com/galaxyproject/galaxy/commit/c9aead91d75a1e0e636cf08ba725a... Author: John Chilton jmchilton@gmail.com Date: 2017-09-21 (Thu, 21 Sep 2017)

Changed paths: M templates/display_base.mako M templates/display_common.mako

Log Message: ----------- Merge pull request #4656 from dannon/display_link_fixes

[17.09] Fix links on workflow, history items.

Commit: 5d7b524b5785fcb483dbc7381c871595a070b1b0 https://github.com/galaxyproject/galaxy/commit/5d7b524b5785fcb483dbc7381c871... Author: Nate Coraor nate@bx.psu.edu Date: 2017-09-21 (Thu, 21 Sep 2017)

Changed paths: M lib/galaxy/jobs/__init__.py M test/unit/jobs/test_job_wrapper.py

Log Message: ----------- Merge pull request #4644 from mvdbeek/upload_tool_registry_xml_failure

[17.05] BUG: Explicitly write registry.xml when creating a job for the upload tool

Commit: 2ffeedfa723cae9252bda2098918df82daf9cf41 https://github.com/galaxyproject/galaxy/commit/2ffeedfa723cae9252bda2098918d... Author: Nicola Soranzo nsoranzo@tiscali.it Date: 2017-09-21 (Thu, 21 Sep 2017)

Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py

Log Message: ----------- Merge pull request #4663 from natefoo/fix-modules-resolver

[16.07] Fix modules resolver

Commit: 2495ceae267da873813d2dc1aae145b686d18672 https://github.com/galaxyproject/galaxy/commit/2495ceae267da873813d2dc1aae14... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-21 (Thu, 21 Sep 2017)

Changed paths: M lib/galaxy/jobs/actions/post.py

Log Message: ----------- Remove overly chatty debug statement in workflow output cleanup -- this happens pretty often and much of the time is not a problem at all. If we have to track down any new issues with workflow output cleanup, it's easy enough to temporarily add this logging.

Commit: e178879c0f9f4351bf0270f1602a60d660a4da04 https://github.com/galaxyproject/galaxy/commit/e178879c0f9f4351bf0270f1602a6... Author: Nate Coraor nate@bx.psu.edu Date: 2017-09-21 (Thu, 21 Sep 2017)

Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py

Log Message: ----------- Merge branch 'release_16.07' into release_16.10

Commit: 706a5b2cd2bdac4c30a5b4d86aaf73a9e4ffa291 https://github.com/galaxyproject/galaxy/commit/706a5b2cd2bdac4c30a5b4d86aaf7... Author: Nate Coraor nate@bx.psu.edu Date: 2017-09-21 (Thu, 21 Sep 2017)

Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py

Log Message: ----------- Merge branch 'release_16.10' into release_17.01

Commit: cfabe37d69549e919d3fce15cbcca108fdcf1597 https://github.com/galaxyproject/galaxy/commit/cfabe37d69549e919d3fce15cbcca... Author: Nate Coraor nate@bx.psu.edu Date: 2017-09-21 (Thu, 21 Sep 2017)

Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py

Log Message: ----------- Merge branch 'release_17.01' into release_17.05

Commit: 4dbadc26e4bb4e40ca04ef746247abc504e98ca2 https://github.com/galaxyproject/galaxy/commit/4dbadc26e4bb4e40ca04ef746247a... Author: Nate Coraor nate@bx.psu.edu Date: 2017-09-21 (Thu, 21 Sep 2017)

Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/deps/resolvers/modules.py M test/unit/jobs/test_job_wrapper.py

Log Message: ----------- Merge branch 'release_17.05' into release_17.09

Commit: 244fc834cd4dd3980cc3edb755d22ca5a9372421 https://github.com/galaxyproject/galaxy/commit/244fc834cd4dd3980cc3edb755d22... Author: Nate Coraor nate@bx.psu.edu Date: 2017-09-21 (Thu, 21 Sep 2017)

Changed paths: M scripts/common_startup.sh

Log Message: ----------- Explicitly include PyPI as an --extra-index-url to pip so we can install from PyPI even when a package exists (but the correct version or architecture does not exist) on wheels.galaxyproject.org. Previously, PyPI was only checked after wheels.galaxyproject.org because pypiserver performs an automatic redirect to PyPI for any packages that do not exist in its index.

Commit: 832da6ca66cba8fe155adccd4d327289c9e04430 https://github.com/galaxyproject/galaxy/commit/832da6ca66cba8fe155adccd4d327... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-21 (Thu, 21 Sep 2017)

Changed paths: M scripts/common_startup.sh

Log Message: ----------- Merge pull request #4674 from natefoo/use-pypi

[17.09] Explicitly include PyPI as an --extra-index-url to pip

Commit: 74ad0acb52031355c7efe28b00d1d9b0205174f2 https://github.com/galaxyproject/galaxy/commit/74ad0acb52031355c7efe28b00d1d... Author: Nate Coraor nate@bx.psu.edu Date: 2017-09-21 (Thu, 21 Sep 2017)

Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh

Log Message: ----------- Remove repetition in Galaxy env setup in the job script and fix issues with remote metadata on Pulsar.

Commit: 276af4db2ab5e81f4af8f35b7d09f48d9fed8dcd https://github.com/galaxyproject/galaxy/commit/276af4db2ab5e81f4af8f35b7d09f... Author: Nate Coraor nate@bx.psu.edu Date: 2017-09-21 (Thu, 21 Sep 2017)

Changed paths: M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh

Log Message: ----------- Job script enhancements based on feedback.

Commit: 53095d688be81a36c31b9721caebf58b383cfe72 https://github.com/galaxyproject/galaxy/commit/53095d688be81a36c31b9721caebf... Author: Nate Coraor nate@bx.psu.edu Date: 2017-09-21 (Thu, 21 Sep 2017)

Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/model/metadata.py

Log Message: ----------- Fix remote datatypes_conf.xml and registry.xml param rewriting with Pulsar

Commit: db5185cca0bb9b5f59d8fcf218eb4c5d81cb5911 https://github.com/galaxyproject/galaxy/commit/db5185cca0bb9b5f59d8fcf218eb4... Author: Nate Coraor nate@bx.psu.edu Date: 2017-09-21 (Thu, 21 Sep 2017)

Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/runners/pulsar.py

Log Message: ----------- Pulsar release was 0.8.0 not 0.7.5

Commit: 2669ab022ed2f90faac54c510014f87783efeaa0 https://github.com/galaxyproject/galaxy/commit/2669ab022ed2f90faac54c510014f... Author: Nate Coraor nate@bx.psu.edu Date: 2017-09-21 (Thu, 21 Sep 2017)

Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py

Log Message: ----------- Pass job output file unqualified names to Pulsar so that it can create them before running the job.

Commit: 3344c77a188cd92ffb2e7150a4f4a2f4f7facedb https://github.com/galaxyproject/galaxy/commit/3344c77a188cd92ffb2e7150a4f4a... Author: Nate Coraor nate@bx.psu.edu Date: 2017-09-21 (Thu, 21 Sep 2017)

Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt

Log Message: ----------- Bump pulsar lib version to 0.8.0 for output touch support.

Commit: c7699cd3a0e16b9522af334cf2ea1a107fbe5f57 https://github.com/galaxyproject/galaxy/commit/c7699cd3a0e16b9522af334cf2ea1... Author: Nate Coraor nate@bx.psu.edu Date: 2017-09-21 (Thu, 21 Sep 2017)

Changed paths: M lib/galaxy/jobs/runners/pulsar.py

Log Message: ----------- Fix lint error

Commit: 27a28e2c406d274e396cf3cb095576ebae9cd38c https://github.com/galaxyproject/galaxy/commit/27a28e2c406d274e396cf3cb09557... Author: John Chilton jmchilton@gmail.com Date: 2017-09-22 (Fri, 22 Sep 2017)

Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py

Log Message: ----------- Merge pull request #4662 from natefoo/pulsar-touch-outputs

[17.09] Pass job output file unqualified names to Pulsar so that it can create them before running the job

Commit: d1be9e6a8fa1a383b3f75d1ea5f1b0d486b69258 https://github.com/galaxyproject/galaxy/commit/d1be9e6a8fa1a383b3f75d1ea5f1b... Author: John Chilton jmchilton@gmail.com Date: 2017-09-22 (Fri, 22 Sep 2017)

Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/model/metadata.py

Log Message: ----------- Merge pull request #4622 from natefoo/pulsar-remote-metadata-fixes

[17.09] Pulsar remote metadata fixes

Commit: 4f9d5df34fb84e2547a280ab7536491a66e1da28 https://github.com/galaxyproject/galaxy/commit/4f9d5df34fb84e2547a280ab75364... Author: Nate Coraor nate@bx.psu.edu Date: 2017-09-22 (Fri, 22 Sep 2017)

Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/interactive_environments/jupyter/templates/jupyter.mako

Log Message: ----------- WIP a bunch of GIE javascript that probabaly won't work

Commit: 04b03b28530455ff850f41215c2cfa15b597ef19 https://github.com/galaxyproject/galaxy/commit/04b03b28530455ff850f41215c2cf... Author: Nate Coraor nate@bx.psu.edu Date: 2017-09-22 (Fri, 22 Sep 2017)

Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M config/plugins/interactive_environments/jupyter/static/js/jupyter.js

Log Message: ----------- Make the URL spinner actually work.

Commit: 7896413b2b6a55ea99958504134ab6027baefbe8 https://github.com/galaxyproject/galaxy/commit/7896413b2b6a55ea99958504134ab... Author: John Chilton jmchilton@gmail.com Date: 2017-09-23 (Sat, 23 Sep 2017)

Changed paths: M lib/galaxy/jobs/actions/post.py

Log Message: ----------- Merge pull request #4671 from dannon/remove_debug

[17.09] Remove chatty debug statement

Commit: 41013563e5e15745fd2bf796340578f6d758fbe8 https://github.com/galaxyproject/galaxy/commit/41013563e5e15745fd2bf79634057... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-24 (Sun, 24 Sep 2017)

Changed paths: M CITATION

Log Message: ----------- Update CITATION file with 2016 paper

Commit: 3ae6318b02e61fcf997b6d2726f12851f51aa802 https://github.com/galaxyproject/galaxy/commit/3ae6318b02e61fcf997b6d2726f12... Author: Eric Rasche hxr@hx42.org Date: 2017-09-25 (Mon, 25 Sep 2017)

Changed paths: M CITATION

Log Message: ----------- Merge pull request #4686 from mvdbeek/citation_update

Update CITATION file with 2016 paper

Commit: 744ea8289ee29572775d2d606ab31a15e2cf4b12 https://github.com/galaxyproject/galaxy/commit/744ea8289ee29572775d2d606ab31... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-09-26 (Tue, 26 Sep 2017)

Changed paths: M lib/galaxy/tools/deps/conda_util.py

Log Message: ----------- Update versions of conda and conda-build

Creating environments for (some) Python packages now requires conda 4.3 due to the conda-forge `python`:

``` $ conda create -n __crossmap@0.2.2 crossmap=0.2.2 Fetching package metadata ............... ... Linking packages ... Installing conda-forge::wheel-0.30.0-py_1 requires a minimum conda version of 4.3. ```

Commit: 7edeedd7fe123ad8740f830e4c7b5e8478552137 https://github.com/galaxyproject/galaxy/commit/7edeedd7fe123ad8740f830e4c7b5... Author: Nate Coraor nate@bx.psu.edu Date: 2017-09-26 (Tue, 26 Sep 2017)

Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M config/plugins/interactive_environments/jupyter/static/js/jupyter.js

Log Message: ----------- Additional GIE spinning fixes for when the error condition is not a timeout.

Commit: 180bfe718485bdfd05233402d4720f67f114d88f https://github.com/galaxyproject/galaxy/commit/180bfe718485bdfd05233402d4720... Author: Nate Coraor nate@bx.psu.edu Date: 2017-09-26 (Tue, 26 Sep 2017)

Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M config/plugins/interactive_environments/jupyter/static/js/jupyter.js

Log Message: ----------- Treat timeouts and errors the same, except that timeouts step the ajax timeout of the next request. Also fixes for toastr messages.

Commit: 9075976669be95c4ee1b505fb952d246660a6f2c https://github.com/galaxyproject/galaxy/commit/9075976669be95c4ee1b505fb952d... Author: Nate Coraor nate@bx.psu.edu Date: 2017-09-26 (Tue, 26 Sep 2017)

Changed paths: M lib/galaxy/tools/deps/conda_util.py

Log Message: ----------- Support conda create --offline for Conda >= 4.3.18.

Commit: 40900d76a96bb76542653e2c2bf886c7d88e9552 https://github.com/galaxyproject/galaxy/commit/40900d76a96bb76542653e2c2bf88... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-27 (Wed, 27 Sep 2017)

Changed paths: M config/plugins/interactive_environments/jupyter/templates/jupyter.mako M static/maps/galaxy.interactive_environments.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/galaxy.interactive_environments.js

Log Message: ----------- Re-enable keepalive, build client.

Commit: c235382ceefb09e28c987621164f9f40450f1ed1 https://github.com/galaxyproject/galaxy/commit/c235382ceefb09e28c987621164f9... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-27 (Wed, 27 Sep 2017)

Changed paths: M config/plugins/interactive_environments/jupyter/templates/jupyter.mako

Log Message: ----------- No need for this keep_alive invocation after all; removes the commented out code.

Commit: 1c5c046a63d6afd160d6cb7dcafd4ec273ec029a https://github.com/galaxyproject/galaxy/commit/1c5c046a63d6afd160d6cb7dcafd4... Author: John Chilton jmchilton@gmail.com Date: 2017-09-27 (Wed, 27 Sep 2017)

Changed paths: M lib/galaxy/tools/deps/conda_util.py

Log Message: ----------- Merge pull request #4701 from nsoranzo/release_17.09_update_conda_version

[17.09] Update versions of conda and conda-build

Commit: 242755ee9f6a267e416a525bbf69ef513c35a2f4 https://github.com/galaxyproject/galaxy/commit/242755ee9f6a267e416a525bbf69e... Author: Nate Coraor nate@bx.psu.edu Date: 2017-09-27 (Wed, 27 Sep 2017)

Changed paths: M config/plugins/interactive_environments/jupyter/templates/jupyter.mako M static/maps/galaxy.interactive_environments.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/galaxy.interactive_environments.js

Log Message: ----------- Merge pull request #7 from dannon/gie_fixes

Re-enable keepalive, build client.

Commit: 8230d14fad3765585517e02a6b74126835f46fce https://github.com/galaxyproject/galaxy/commit/8230d14fad3765585517e02a6b741... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-27 (Wed, 27 Sep 2017)

Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/interactive_environments/jupyter/templates/jupyter.mako M static/maps/galaxy.interactive_environments.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/galaxy.interactive_environments.js

Log Message: ----------- Merge pull request #4680 from natefoo/gie-client

[17.09] Client side fixes for GIEs

Commit: 1676434ab58d35da37b3f9327d31e763eb4e9cc8 https://github.com/galaxyproject/galaxy/commit/1676434ab58d35da37b3f9327d31e... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-27 (Wed, 27 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-model.js M static/maps/mvc/workflow/workflow-model.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/workflow/workflow-model.js

Log Message: ----------- Correct base route for workflows, allowing proxy-prefix to work.

Commit: d214ccc0e4884edd8234de8758400d08b8dda64d https://github.com/galaxyproject/galaxy/commit/d214ccc0e4884edd8234de8758400... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-27 (Wed, 27 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-model.js M static/maps/mvc/workflow/workflow-model.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/workflow/workflow-model.js

Log Message: ----------- Leading slash not required here

Commit: 146010fcbf215f21e9f232467aabac1f095fe2d5 https://github.com/galaxyproject/galaxy/commit/146010fcbf215f21e9f232467aaba... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-27 (Wed, 27 Sep 2017)

Changed paths: M client/galaxy/scripts/onload.js M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/onload.js

Log Message: ----------- Fix onload webhook call w/ Galaxy.root

Commit: 42c81293f6cccbb26c4466bd5f5f3d702943fa93 https://github.com/galaxyproject/galaxy/commit/42c81293f6cccbb26c4466bd5f5f3... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-27 (Wed, 27 Sep 2017)

Changed paths: M client/toolshed/scripts/mvc/groups/group-model.js M static/toolshed/maps/mvc/groups/group-detail-view.js.map M static/toolshed/maps/mvc/groups/group-list-view.js.map M static/toolshed/maps/mvc/groups/group-listrow-view.js.map M static/toolshed/maps/mvc/groups/group-model.js.map M static/toolshed/scripts/mvc/groups/group-detail-view.js M static/toolshed/scripts/mvc/groups/group-list-view.js M static/toolshed/scripts/mvc/groups/group-listrow-view.js M static/toolshed/scripts/mvc/groups/group-model.js

Log Message: ----------- Galaxy.root (proxy prefix) support for toolshed's Group model.

Commit: 89ce44803ea5cf38b778e61bb7eedfc7b952ce12 https://github.com/galaxyproject/galaxy/commit/89ce44803ea5cf38b778e61bb7eed... Author: John Chilton jmchilton@gmail.com Date: 2017-09-27 (Wed, 27 Sep 2017)

Changed paths: M lib/galaxy/web/framework/webapp.py

Log Message: ----------- Append fewer characters to id_secret by default for encrypting csrf tokens.

Seems there is a maximum length and main hit it. It never did for job files - so this should be fine. If you have a secret that is near the maximum lenght one just needs to set ``per_kind_id_secret_base`` to something shorter than id_secret.

Commit: 7775d429b6b06397b5ab90d7bea1671a7aa4b424 https://github.com/galaxyproject/galaxy/commit/7775d429b6b06397b5ab90d7bea16... Author: John Chilton jmchilton@gmail.com Date: 2017-09-27 (Wed, 27 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/onload.js M client/toolshed/scripts/mvc/groups/group-model.js M static/maps/mvc/workflow/workflow-model.js.map M static/maps/onload.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/workflow/workflow-model.js M static/scripts/onload.js M static/toolshed/maps/mvc/groups/group-detail-view.js.map M static/toolshed/maps/mvc/groups/group-list-view.js.map M static/toolshed/maps/mvc/groups/group-listrow-view.js.map M static/toolshed/maps/mvc/groups/group-model.js.map M static/toolshed/scripts/mvc/groups/group-detail-view.js M static/toolshed/scripts/mvc/groups/group-list-view.js M static/toolshed/scripts/mvc/groups/group-listrow-view.js M static/toolshed/scripts/mvc/groups/group-model.js

Log Message: ----------- Merge pull request #4705 from dannon/proxy_prefix_model_fixes

[17.09] Correct base route for workflows, allowing proxy-prefix to work.

Commit: d41f4ce0ec8996677dba6b12be49f0c94f7d4f24 https://github.com/galaxyproject/galaxy/commit/d41f4ce0ec8996677dba6b12be49f... Author: Nate Coraor nate@bx.psu.edu Date: 2017-09-27 (Wed, 27 Sep 2017)

Changed paths: M lib/galaxy/web/framework/webapp.py

Log Message: ----------- Merge pull request #4710 from jmchilton/id_secret_fix

[17.09] Append fewer characters to id_secret by default for encrypting csrf tokens.

Commit: f709ddcfe6b6bad0ca03ff208195f68d4e65fdc4 https://github.com/galaxyproject/galaxy/commit/f709ddcfe6b6bad0ca03ff208195f... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-27 (Wed, 27 Sep 2017)

Changed paths: M config/plugins/interactive_environments/common/templates/ie.mako

Log Message: ----------- Add requirejs config to cachebust IE require'd files.

Commit: 03394d44c92d2bec790c37b59e50872c072f99e6 https://github.com/galaxyproject/galaxy/commit/03394d44c92d2bec790c37b59e508... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-27 (Wed, 27 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M static/maps/mvc/workflow/workflow.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/mvc/workflow/workflow.js

Log Message: ----------- Support workflow list messaging

Commit: fa4c1b5da7aa2c035bb5685d150b3cb8f952dd6a https://github.com/galaxyproject/galaxy/commit/fa4c1b5da7aa2c035bb5685d150b3... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-27 (Wed, 27 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow.js

Log Message: ----------- More fixes for the workflow list page, and some general cleanup.

Commit: 63022e6718f2e9206e7a94b63949a8e97d08d352 https://github.com/galaxyproject/galaxy/commit/63022e6718f2e9206e7a94b63949a... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-27 (Wed, 27 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js

Log Message: ----------- Drop stray debugging statement.

Commit: 8820e3bc583ea140f1c154bd35c2ccc905ab4fb8 https://github.com/galaxyproject/galaxy/commit/8820e3bc583ea140f1c154bd35c2c... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-27 (Wed, 27 Sep 2017)

Changed paths: M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow.js

Log Message: ----------- Rebuild client.

Commit: 266361d1517b60177889e7a34a2f32cc0a6a938f https://github.com/galaxyproject/galaxy/commit/266361d1517b60177889e7a34a2f3... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-27 (Wed, 27 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/analysis.bundled.js.map

Log Message: ----------- Minor formatting.

Commit: 958d917cb51c2ade15d69279d893489d37c8d976 https://github.com/galaxyproject/galaxy/commit/958d917cb51c2ade15d69279d8934... Author: guerler aysam.guerler@gmail.com Date: 2017-09-27 (Wed, 27 Sep 2017)

Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map

Log Message: ----------- Display error message when workflow loading fails

Commit: 407da92f88ac859d3f9b259be83640516159fe15 https://github.com/galaxyproject/galaxy/commit/407da92f88ac859d3f9b259be8364... Author: Aysam Guerler aysam.guerler@gmail.com Date: 2017-09-27 (Wed, 27 Sep 2017)

Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/workflow/workflow.js M static/maps/mvc/workflow/workflow.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/mvc/workflow/workflow.js

Log Message: ----------- Merge pull request #4716 from dannon/workflow_list_messaging

[17.09] Add message (error and info) display to workflows display list.

Commit: 7167c0434b713562293267f7c8adebff3920d6cc https://github.com/galaxyproject/galaxy/commit/7167c0434b713562293267f7c8ade... Author: John Chilton jmchilton@gmail.com Date: 2017-09-28 (Thu, 28 Sep 2017)

Changed paths: M config/plugins/interactive_environments/common/templates/ie.mako

Log Message: ----------- Merge pull request #4714 from dannon/cachebust_ies

[17.09] Cachebust IE require'd files (jupyter.js, etc).

Commit: d49c49d0eebc4390a0dda7d5e830ae464284b7b9 https://github.com/galaxyproject/galaxy/commit/d49c49d0eebc4390a0dda7d5e830a... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-09-28 (Thu, 28 Sep 2017)

Changed paths: M client/galaxy/scripts/onload.js M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/onload.js

Log Message: ----------- Pull a minor cosmetic fix out of the urlFor refactoring. Might as well be consistent in the release.

Commit: 38b19d4c47d227c7eeccb33fa8bfa64f0b0ec297 https://github.com/galaxyproject/galaxy/commit/38b19d4c47d227c7eeccb33fa8bfa... Author: Björn Grüning bjoern@gruenings.eu Date: 2017-09-28 (Thu, 28 Sep 2017)

Changed paths: M client/galaxy/scripts/onload.js M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/onload.js

Log Message: ----------- Merge pull request #4715 from dannon/proxy_prefix_model_fixes

[17.09] Pull a minor tweak out of the JS-side urlFor refactoring

Commit: 18977d4132556a0c2bd0348db510cf765d434e6a https://github.com/galaxyproject/galaxy/commit/18977d4132556a0c2bd0348db510c... Author: Nate Coraor nate@bx.psu.edu Date: 2017-09-29 (Fri, 29 Sep 2017)

Changed paths: M lib/galaxy/tools/toolbox/base.py

Log Message: ----------- Don't load hidden tools into the tool panel at all.

Commit: 54357f38e9929f3f3a084f298bd644395976a91a https://github.com/galaxyproject/galaxy/commit/54357f38e9929f3f3a084f298bd64... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-09-29 (Fri, 29 Sep 2017)

Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy_ext/metadata/set_metadata.py

Log Message: ----------- Write out registry.xml file in case jobs are missing this file

Commit: 94540adda48fbc0c75ffd6b7caa56864b387b721 https://github.com/galaxyproject/galaxy/commit/94540adda48fbc0c75ffd6b7caa56... Author: John Chilton jmchilton@gmail.com Date: 2017-09-29 (Fri, 29 Sep 2017)

Changed paths: M lib/galaxy/jobs/handler.py

Log Message: ----------- Clarify previous commit.

Commit: 2eed478545857ab2c3b4c958bc3e2c360656af42 https://github.com/galaxyproject/galaxy/commit/2eed478545857ab2c3b4c958bc3e2... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-10-02 (Mon, 02 Oct 2017)

Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/resolvers/conda.py

Log Message: ----------- Update conda channel order to sync with Bioconda

Commit: a5b7dce09fb690f09d25f1b806d3339bdf2171c9 https://github.com/galaxyproject/galaxy/commit/a5b7dce09fb690f09d25f1b806d33... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-10-02 (Mon, 02 Oct 2017)

Changed paths: M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py

Log Message: ----------- Remove _ensure_conda_context() function

and make conda_context argument mandatory in functions/methods. This should help making sure the correct context (e.g. channels) is used for all Conda operations.

Also remove unused is_target_available() function.

Conflicts: lib/galaxy/tools/deps/conda_util.py

Commit: 3551386a1ac667e0d2f7c6e82256d180aa5100f7 https://github.com/galaxyproject/galaxy/commit/3551386a1ac667e0d2f7c6e82256d... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-10-02 (Mon, 02 Oct 2017)

Changed paths: M lib/galaxy/tools/deps/conda_util.py

Log Message: ----------- Override channel list on the command line instead of modifying condarc

The way we were modifying condarc in the ensure_channels_configured() method was broken because we were appending the missing channels at the end, so the final order may not be the one specified in conda_ensure_channels .

Also: - not modifying the user condarc is a much better approach - overriding the channel list on the command line will make debugging easier

Commit: 04a572e509e875414b07e73c295f1c4bb37c1e0c https://github.com/galaxyproject/galaxy/commit/04a572e509e875414b07e73c295f1... Author: John Chilton jmchilton@gmail.com Date: 2017-10-02 (Mon, 02 Oct 2017)

Changed paths: M lib/galaxy/tools/toolbox/base.py

Log Message: ----------- Merge pull request #4726 from natefoo/panel-hidden-fix

[17.09] If the newest version of a tool is hidden, load the newest older version, if any, into the tool panel

Commit: 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071 https://github.com/galaxyproject/galaxy/commit/81ece2551cea27cbd0e718ef5b7a2... Author: John Chilton jmchilton@gmail.com Date: 2017-10-02 (Mon, 02 Oct 2017)

Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py

Log Message: ----------- Merge pull request #4731 from nsoranzo/release_17.05_backport_4409

[17.05] Backport #4409

Commit: 280dc48c386f41c850ae3bbf9971979296b5abbc https://github.com/galaxyproject/galaxy/commit/280dc48c386f41c850ae3bbf99719... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-02 (Mon, 02 Oct 2017)

Log Message: ----------- Merge branch 'release_17.05' into release_17.09

Commit: a8aea10dfb609fbd0790b6df22b49a60192966e3 https://github.com/galaxyproject/galaxy/commit/a8aea10dfb609fbd0790b6df22b49... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-03 (Tue, 03 Oct 2017)

Changed paths: M lib/galaxy/web/base/interactive_environments.py

Log Message: ----------- Fix missing support for command_inject when using containers lib in GIEs

Commit: fa2d80d7ecddb780e29835869b94a2e3e16d12a1 https://github.com/galaxyproject/galaxy/commit/fa2d80d7ecddb780e29835869b94a... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-10-03 (Tue, 03 Oct 2017)

Changed paths: M lib/galaxy/model/__init__.py

Log Message: ----------- Fix t, a, g, s return value for tags

Commit: 0827b23bd504208b51956be67f5bebf75b8fb4b0 https://github.com/galaxyproject/galaxy/commit/0827b23bd504208b51956be67f5be... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-10-03 (Tue, 03 Oct 2017)

Changed paths: M lib/galaxy/model/__init__.py

Log Message: ----------- Merge pull request #4742 from mvdbeek/tags_fix

[17.09] Fix t, a, g, s returned in to_dict() method

Commit: fbf3cf30d7df5673ebbc098a2561e26a5486a18a https://github.com/galaxyproject/galaxy/commit/fbf3cf30d7df5673ebbc098a2561e... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-10-03 (Tue, 03 Oct 2017)

Changed paths: M tools/filters/joiner.xml

Log Message: ----------- Fix joiner tool to inherit datatype, restoring previous behavior.

Commit: 7ce0d87a597353d7915a29708a440939e73bb7a3 https://github.com/galaxyproject/galaxy/commit/7ce0d87a597353d7915a29708a440... Author: Nicola Soranzo nsoranzo@tiscali.it Date: 2017-10-03 (Tue, 03 Oct 2017)

Changed paths: M tools/filters/joiner.xml

Log Message: ----------- Merge pull request #4745 from dannon/joiner_fix

[17.09] Fix joiner tool to inherit datatype from the input format

Commit: 096b387f8e97a3620855793cb0d257dd3a56883f https://github.com/galaxyproject/galaxy/commit/096b387f8e97a3620855793cb0d25... Author: Anthony Bretaudeau anthony.bretaudeau@inria.fr Date: 2017-10-04 (Wed, 04 Oct 2017)

Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt

Log Message: ----------- update python-ldap with fix for ldaps

Commit: d788bfb80ae1140ecb7757eea2d192de0a7e4045 https://github.com/galaxyproject/galaxy/commit/d788bfb80ae1140ecb7757eea2d19... Author: John Chilton jmchilton@gmail.com Date: 2017-10-04 (Wed, 04 Oct 2017)

Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt

Log Message: ----------- Merge pull request #4748 from abretaud/ldap

[17.09] Fix auth with ldaps://

Commit: fb0586398d81a39734ee1f2031375d547b2da6c1 https://github.com/galaxyproject/galaxy/commit/fb0586398d81a39734ee1f2031375... Author: John Chilton jmchilton@gmail.com Date: 2017-10-04 (Wed, 04 Oct 2017)

Changed paths: M config/galaxy.ini.sample M lib/galaxy/web/security/__init__.py M test/unit/test_security_helper.py

Log Message: ----------- Better hanlding of long id secrets when generating per-kind encryption keys.

Generally more validation and more testing as well. Test cases layout the reasons for some of these changes.

Thanks to @nsoranzo for the Python 3 fix.

Commit: 59e5b17ac704e1c45cf693187174225d3eefe994 https://github.com/galaxyproject/galaxy/commit/59e5b17ac704e1c45cf6931871742... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-10-04 (Wed, 04 Oct 2017)

Changed paths: M config/local_conda_mapping.yml.sample

Log Message: ----------- Fix path to example conda mapping

Commit: bf5c8248b340a0f60519f3c40afb05b8020ddcf3 https://github.com/galaxyproject/galaxy/commit/bf5c8248b340a0f60519f3c40afb0... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-10-04 (Wed, 04 Oct 2017)

Changed paths: M client/galaxy/scripts/onload.js M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/onload.js

Log Message: ----------- Force onload webhooks to wait for Galaxy object (and root) resolution.

Commit: 95d5ffc71d5c373b92252e1ea1ec4d119ebbf636 https://github.com/galaxyproject/galaxy/commit/95d5ffc71d5c373b92252e1ea1ec4... Author: John Chilton jmchilton@gmail.com Date: 2017-10-04 (Wed, 04 Oct 2017)

Changed paths: M client/galaxy/scripts/onload.js M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/onload.js

Log Message: ----------- Merge pull request #4750 from dannon/onloadjs_webhooks_fix

[17.09] Force onload webhooks to wait for Galaxy object (and root) resolution.

Commit: c3f7f391cbca37624566ca99fa1c8e0e5c525a83 https://github.com/galaxyproject/galaxy/commit/c3f7f391cbca37624566ca99fa1c8... Author: Martin Cech marten@bx.psu.edu Date: 2017-10-04 (Wed, 04 Oct 2017)

Changed paths: M config/galaxy.ini.sample M lib/galaxy/web/security/__init__.py M test/unit/test_security_helper.py

Log Message: ----------- Merge pull request #4713 from jmchilton/id_secret_fix

[17.09] Better handling of long id secrets when generating per-kind encryption keys.

Commit: a9c23f0ba97b1a5560642b6106aa9236c7645682 https://github.com/galaxyproject/galaxy/commit/a9c23f0ba97b1a5560642b6106aa9... Author: Martin Cech marten@bx.psu.edu Date: 2017-10-04 (Wed, 04 Oct 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js

Log Message: ----------- replace selector for selecting selected rows

muhaha

Commit: f118fc32c0d7222b2ef2aad3146ef66b4247825f https://github.com/galaxyproject/galaxy/commit/f118fc32c0d7222b2ef2aad3146ef... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-04 (Wed, 04 Oct 2017)

Changed paths: M lib/galaxy/web/base/interactive_environments.py

Log Message: ----------- Fix linting error

Commit: 9a954ca3432e3da8f002bc901bfd723f8caa3aef https://github.com/galaxyproject/galaxy/commit/9a954ca3432e3da8f002bc901bfd7... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-10-04 (Wed, 04 Oct 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js

Log Message: ----------- Merge pull request #4752 from martenson/fix-library-allselect

[17.09] replace selector for selecting selected rows

Commit: 8c769b2e29d0503d76b6cc35c734871a3216ef4a https://github.com/galaxyproject/galaxy/commit/8c769b2e29d0503d76b6cc35c7348... Author: John Chilton jmchilton@gmail.com Date: 2017-10-05 (Thu, 05 Oct 2017)

Changed paths: M lib/galaxy/web/base/interactive_environments.py

Log Message: ----------- Merge pull request #4740 from natefoo/containers-env

[17.09] Fix missing support for command_inject when using containers lib in GIEs

Commit: 1b7b4da9a266fac29486aef3b3a290e1c9749199 https://github.com/galaxyproject/galaxy/commit/1b7b4da9a266fac29486aef3b3a29... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-05 (Thu, 05 Oct 2017)

Changed paths: M lib/galaxy/web/base/interactive_environments.py

Log Message: ----------- GIEs: Grandfather automatic uppercasing of some env_override variables.

Commit: f9eae90944790530274a9079d7eb76fc10ce68eb https://github.com/galaxyproject/galaxy/commit/f9eae90944790530274a9079d7eb7... Author: Martin Cech marten@bx.psu.edu Date: 2017-10-05 (Thu, 05 Oct 2017)

Changed paths: M lib/galaxy/web/base/interactive_environments.py

Log Message: ----------- Merge pull request #4760 from natefoo/gie-upper-grandfather

[17.09] GIEs: Grandfather automatic uppercasing of some env_override variables

Commit: 4dcba21d838bd2bad806687d7c212d7da0b8e85e https://github.com/galaxyproject/galaxy/commit/4dcba21d838bd2bad806687d7c212... Author: Martin Cech marten@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: 1c9ff98b81a803de48eafa5deb6f9d5e95733c9d https://github.com/galaxyproject/galaxy/commit/1c9ff98b81a803de48eafa5deb6f9... Author: guerler aysam.guerler@gmail.com Date: 2017-10-09 (Mon, 09 Oct 2017)

Changed paths: M client/galaxy/scripts/layout/router.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/layout/router.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/router.js M static/scripts/mvc/dataset/dataset-li-edit.js

Log Message: ----------- Load dataset edit attributes without page refresh

Commit: dcad663cee2ce50f7b35871e51e50554b0d9b727 https://github.com/galaxyproject/galaxy/commit/dcad663cee2ce50f7b35871e51e50... Author: guerler aysam.guerler@gmail.com Date: 2017-10-09 (Mon, 09 Oct 2017)

Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li-edit.js

Log Message: ----------- Load dataset errors without page refresh

Commit: ecd0dc4244cff688491dec7f2404ef65d1e1d861 https://github.com/galaxyproject/galaxy/commit/ecd0dc4244cff688491dec7f2404e... Author: John Chilton jmchilton@gmail.com Date: 2017-10-09 (Mon, 09 Oct 2017)

Changed paths: M tox.ini

Log Message: ----------- Pin pydocstyles for stable release.

Commit: 012aaf832027ba905b492645ebdeea9d903b6726 https://github.com/galaxyproject/galaxy/commit/012aaf832027ba905b492645ebdee... Author: John Chilton jmchilton@gmail.com Date: 2017-10-09 (Mon, 09 Oct 2017)

Changed paths: M tox.ini

Log Message: ----------- Pin pydocstyle...

Commit: 220fdccd57cda5268d2beb482c1d4469cb8b5d94 https://github.com/galaxyproject/galaxy/commit/220fdccd57cda5268d2beb482c1d4... Author: guerler aysam.guerler@gmail.com Date: 2017-10-09 (Mon, 09 Oct 2017)

Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li-edit.js

Log Message: ----------- Do not rely on the existence of the analysis app router

Commit: a0f63b671f29f41d078c23b0421b981b3ac0bcdd https://github.com/galaxyproject/galaxy/commit/a0f63b671f29f41d078c23b0421b9... Author: Martin Cech marten@bx.psu.edu Date: 2017-10-10 (Tue, 10 Oct 2017)

Changed paths: M tox.ini

Log Message: ----------- Merge pull request #4775 from jmchilton/pin_pydocstyle

[17.09] Pin pydocstyles for stable release.

Commit: f64b7fcfb124756ed8dc65bbfdfbe6b2f0cb66e0 https://github.com/galaxyproject/galaxy/commit/f64b7fcfb124756ed8dc65bbfdfbe... Author: Martin Cech marten@bx.psu.edu Date: 2017-10-10 (Tue, 10 Oct 2017)

Changed paths: M tox.ini

Log Message: ----------- Merge pull request #4777 from jmchilton/release_17.01_pydocstyle_ping

[17.01] Pin linting functions in tox.ini.

Commit: 1635f46430b176f03b7c3982f4d02287e7d4a5e1 https://github.com/galaxyproject/galaxy/commit/1635f46430b176f03b7c3982f4d02... Author: Martin Cech marten@bx.psu.edu Date: 2017-10-10 (Tue, 10 Oct 2017)

Changed paths: M tox.ini

Log Message: ----------- Merge branch 'release_17.01' into release_17.05

Commit: 27e3e724cded1b5c99cc902dc478653feb84e505 https://github.com/galaxyproject/galaxy/commit/27e3e724cded1b5c99cc902dc4786... Author: Martin Cech marten@bx.psu.edu Date: 2017-10-10 (Tue, 10 Oct 2017)

Changed paths: M tox.ini

Log Message: ----------- Merge branch 'release_17.05' into release_17.09

Commit: 2b18a0b8d5f7316e8a5e5fbc84e9c1062e519fa2 https://github.com/galaxyproject/galaxy/commit/2b18a0b8d5f7316e8a5e5fbc84e9c... Author: Martin Cech marten@bx.psu.edu Date: 2017-10-10 (Tue, 10 Oct 2017)

Changed paths: M client/galaxy/scripts/layout/router.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/layout/router.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/router.js M static/scripts/mvc/dataset/dataset-li-edit.js

Log Message: ----------- Merge pull request #4773 from guerler/fix_edit_reload.000

[17.09] Load dataset attribute editing and errors without page refresh

Commit: fb7015bf70aaf3468b34f9d5a464df18edcae7ac https://github.com/galaxyproject/galaxy/commit/fb7015bf70aaf3468b34f9d5a464d... Author: John Chilton jmchilton@gmail.com Date: 2017-10-10 (Tue, 10 Oct 2017)

Changed paths: M lib/galaxy/tools/parser/xml.py

Log Message: ----------- Bug fix for XML warning during tool loads.

Commit: fd8e2e1927f0c6248e6d7ae4c5338015328bf9a0 https://github.com/galaxyproject/galaxy/commit/fd8e2e1927f0c6248e6d7ae4c5338... Author: Nicola Soranzo nsoranzo@tiscali.it Date: 2017-10-10 (Tue, 10 Oct 2017)

Changed paths: M lib/galaxy/tools/parser/xml.py

Log Message: ----------- Merge pull request #4784 from jmchilton/tool_xml_warning

[17.09] Bug fix for XML warning during tool loads.

Commit: 24308fb6053dcecbf20d6e7a8a8e9b7d96fe07db https://github.com/galaxyproject/galaxy/commit/24308fb6053dcecbf20d6e7a8a8e9... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-10-12 (Thu, 12 Oct 2017)

Changed paths: M templates/show_params.mako

Log Message: ----------- Fix listify import in show_params.mako

This fixes a problem reported on the [mailing list](http://dev.list.galaxyproject.org/Show-history-structure-Error-Undefined-obj...). I am not sure why importing at the top of the file is not enough though.

Commit: a83123ef5e384f95778a1293f293e4b9a919054b https://github.com/galaxyproject/galaxy/commit/a83123ef5e384f95778a1293f293e... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-10-12 (Thu, 12 Oct 2017)

Changed paths: M templates/show_params.mako

Log Message: ----------- Merge pull request #4794 from mvdbeek/fix_listify_import_in_show_params

[17.05][BUG] Fix listify import in show params

Commit: ebdadb68ad7caaa4afbde544e46ad57b4ab49dba https://github.com/galaxyproject/galaxy/commit/ebdadb68ad7caaa4afbde544e46ad... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-10-12 (Thu, 12 Oct 2017)

Changed paths: M templates/show_params.mako

Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.05' into release_17.09

Commit: a474822f3cbe232b82d23c48507e48f65b6f16c0 https://github.com/galaxyproject/galaxy/commit/a474822f3cbe232b82d23c48507e4... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-12 (Thu, 12 Oct 2017)

Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy_ext/metadata/set_metadata.py

Log Message: ----------- Merge pull request #4728 from mvdbeek/fix_registry_missing

[17.05] Fix metadata for deleted registry by Galaxy shutdown.

Commit: e4518ff3e3d628f2cd47ea48217da6352ef11e30 https://github.com/galaxyproject/galaxy/commit/e4518ff3e3d628f2cd47ea48217da... Author: E Rasche hxr@hx42.org Date: 2017-10-12 (Thu, 12 Oct 2017)

Changed paths: M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_coverage.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/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/citations.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/capsule/capsule_manager.py M scripts/data_libraries/build_lucene_index.py M scripts/edam_mapping.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py M scripts/transfer.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/unit/workflows/workflow_support.py

Log Message: ----------- Rebase hardening commits from dev

Commit: b5ded00eb50181f17b3c003e1b7c895098b85d25 https://github.com/galaxyproject/galaxy/commit/b5ded00eb50181f17b3c003e1b7c8... Author: John Chilton jmchilton@gmail.com Date: 2017-10-13 (Fri, 13 Oct 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py

Log Message: ----------- Fix invalid requests imports introduced in #4604.

Even when we remove the requests controller the pyc files will stick around - so probably best to keep these absolute imports for these controllers indefinitely. This broke workflow import from URL coming through the GUI and so it broke a bunch of Selenium tests.

Commit: 545d5556588dfe28c8a9857333366ba62dbcd2fd https://github.com/galaxyproject/galaxy/commit/545d5556588dfe28c8a9857333366... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-13 (Fri, 13 Oct 2017)

Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py

Log Message: ----------- Fix additional uses of subprocess shell=True

Commit: 2f79351e3cdb1fe9705f00590038b11cba4b428e https://github.com/galaxyproject/galaxy/commit/2f79351e3cdb1fe9705f00590038b... Author: E Rasche hxr@hx42.org Date: 2017-10-13 (Fri, 13 Oct 2017)

Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py

Log Message: ----------- Rebase script integrity check improvements (#4720) from dev

Commit: 9fa9d42c5093ddd8f70193cc6a07ae0af0394f8c https://github.com/galaxyproject/galaxy/commit/9fa9d42c5093ddd8f70193cc6a07a... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-13 (Fri, 13 Oct 2017)

Changed paths: M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/web/proxy/__init__.py M lib/tool_shed/capsule/capsule_manager.py

Log Message: ----------- Fix backport issues

Commit: f925ffe4b743d080585bc6d151dc8ca98cc4f171 https://github.com/galaxyproject/galaxy/commit/f925ffe4b743d080585bc6d151dc8... Author: Nicola Soranzo nsoranzo@tiscali.it Date: 2017-10-13 (Fri, 13 Oct 2017)

Changed paths: M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_coverage.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/converters/sam_to_bam.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/citations.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/capsule/capsule_manager.py M scripts/data_libraries/build_lucene_index.py M scripts/edam_mapping.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py M scripts/transfer.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/unit/workflows/workflow_support.py

Log Message: ----------- Merge pull request #4801 from natefoo/backport-hardening-16.07

[16.07] Various bits of hardening from #4604

Commit: e60f324b66676cc5020aa74bfa011f886eaeca68 https://github.com/galaxyproject/galaxy/commit/e60f324b66676cc5020aa74bfa011... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-13 (Fri, 13 Oct 2017)

Changed paths: M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_coverage.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/converters/sam_to_bam.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/citations.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/capsule/capsule_manager.py M scripts/data_libraries/build_lucene_index.py M scripts/edam_mapping.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py M scripts/transfer.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/unit/workflows/workflow_support.py

Log Message: ----------- Merge remote-tracking branch 'origin/release_16.07' into backport-hardening-16.10

Commit: ef268027191b526b8c8dfe69c3d8352c0412ce1d https://github.com/galaxyproject/galaxy/commit/ef268027191b526b8c8dfe69c3d83... Author: E Rasche hxr@hx42.org Date: 2017-10-13 (Fri, 13 Oct 2017)

Changed paths: M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/webhooks/__init__.py

Log Message: ----------- Hardening backport differences from dev present in 16.10 but not 16.07

Commit: d70713d07a3c4d98b71df9247bbd8644ab6b2b40 https://github.com/galaxyproject/galaxy/commit/d70713d07a3c4d98b71df9247bbd8... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-10-13 (Fri, 13 Oct 2017)

Changed paths: M tox.ini

Log Message: ----------- Pin flake8 and plugins in tox.ini

For all tox environments used in .travis.yml except the ones allowed to fail.

Commit: fe9839bf7ca720061548ff3bcebdc79062e7adf5 https://github.com/galaxyproject/galaxy/commit/fe9839bf7ca720061548ff3bcebdc... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-10-13 (Fri, 13 Oct 2017)

Changed paths: M setup.cfg M tox.ini

Log Message: ----------- Update pin for flake8-docstrings

Similar to commit 2586df45637d794c63252838573b2d1e6d692243 .

Commit: 36b974c90514332c6cb732f9c376a66767100944 https://github.com/galaxyproject/galaxy/commit/36b974c90514332c6cb732f9c376a... Author: John Chilton jmchilton@gmail.com Date: 2017-10-13 (Fri, 13 Oct 2017)

Changed paths: M tox.ini

Log Message: ----------- Pin pydocstyle...

Commit: 3bb5d825c13ae2dbd366f24dc316bcdaa7171eb9 https://github.com/galaxyproject/galaxy/commit/3bb5d825c13ae2dbd366f24dc316b... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-13 (Fri, 13 Oct 2017)

Changed paths: M setup.cfg

Log Message: ----------- Ignore I201 errors in 16.10

Commit: 8d573db729a92344ad9115b7657ace07a4718a21 https://github.com/galaxyproject/galaxy/commit/8d573db729a92344ad9115b7657ac... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-10-13 (Fri, 13 Oct 2017)

Changed paths: M .travis.yml

Log Message: ----------- Use container-based infrastructure (sudo: false) in TravisCI

Commit: 6d8f8ecb466ae75ca7d586496512cb70206a08f6 https://github.com/galaxyproject/galaxy/commit/6d8f8ecb466ae75ca7d586496512c... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-13 (Fri, 13 Oct 2017)

Changed paths: M scripts/grt.py

Log Message: ----------- Add missing backport of hardening to scripts/grt.py

Commit: b04aafa8e871f4d2f3bf7a636ccf0ef432fda875 https://github.com/galaxyproject/galaxy/commit/b04aafa8e871f4d2f3bf7a636ccf0... Author: Nicola Soranzo nsoranzo@tiscali.it Date: 2017-10-14 (Sat, 14 Oct 2017)

Changed paths: M .travis.yml M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_coverage.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/converters/sam_to_bam.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/citations.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webhooks/__init__.py M lib/tool_shed/capsule/capsule_manager.py M scripts/data_libraries/build_lucene_index.py M scripts/edam_mapping.py M scripts/grt.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py M scripts/transfer.py M setup.cfg M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/unit/workflows/workflow_support.py M tox.ini

Log Message: ----------- Merge pull request #4804 from natefoo/backport-hardening-16.10

[16.10] Various bits of hardening from #4604

Commit: 139ba7c13e38a98a090a91167e0538f259baa7c2 https://github.com/galaxyproject/galaxy/commit/139ba7c13e38a98a090a91167e053... Author: John Chilton jmchilton@gmail.com Date: 2017-10-14 (Sat, 14 Oct 2017)

Changed paths: M tox.ini

Log Message: ----------- Pin pydocstyle...

Commit: 03087e5ee77701e410e7d9336a74cedf3206e3f3 https://github.com/galaxyproject/galaxy/commit/03087e5ee77701e410e7d9336a74c... Author: E Rasche hxr@hx42.org Date: 2017-10-14 (Sat, 14 Oct 2017)

Changed paths: M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_coverage.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/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/citations.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webhooks/__init__.py M lib/tool_shed/capsule/capsule_manager.py M scripts/data_libraries/build_lucene_index.py M scripts/edam_mapping.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py M scripts/transfer.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/workflows_format_2/converter.py M test/base/workflows_format_2/main.py M test/galaxy_selenium/data.py M test/galaxy_selenium/navigates_galaxy.py M test/unit/workflows/workflow_support.py

Log Message: ----------- Rebase hardening commits from dev

Commit: f9213b16f5bb26b2b7176d50602d852ea4e08562 https://github.com/galaxyproject/galaxy/commit/f9213b16f5bb26b2b7176d50602d8... Author: John Chilton jmchilton@gmail.com Date: 2017-10-14 (Sat, 14 Oct 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py

Log Message: ----------- Fix invalid requests imports introduced in #4604.

Even when we remove the requests controller the pyc files will stick around - so probably best to keep these absolute imports for these controllers indefinitely. This broke workflow import from URL coming through the GUI and so it broke a bunch of Selenium tests.

Commit: 7ad6182ef4952480354e4737b72c062fc75be93e https://github.com/galaxyproject/galaxy/commit/7ad6182ef4952480354e4737b72c0... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-14 (Sat, 14 Oct 2017)

Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py

Log Message: ----------- Fix additional uses of subprocess shell=True

Commit: b13f5d7f943106cf27670c7153e6c8967a749bcf https://github.com/galaxyproject/galaxy/commit/b13f5d7f943106cf27670c7153e6c... Author: E Rasche hxr@hx42.org Date: 2017-10-14 (Sat, 14 Oct 2017)

Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py

Log Message: ----------- Rebase script integrity check improvements (#4720) from dev

Commit: 24c8a26852aecdcc5d8d23300e551f282b90c628 https://github.com/galaxyproject/galaxy/commit/24c8a26852aecdcc5d8d23300e551... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-14 (Sat, 14 Oct 2017)

Changed paths: M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/web/proxy/__init__.py

Log Message: ----------- Fix backport issues

Commit: 9955c4d24bff197b01f2ff6227fdfb06224d9ab9 https://github.com/galaxyproject/galaxy/commit/9955c4d24bff197b01f2ff6227fdf... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-14 (Sat, 14 Oct 2017)

Changed paths: M setup.cfg

Log Message: ----------- Ignore I201 errors in 16.10

Commit: 950f92627176068609fc5191c72f681e3e16fb22 https://github.com/galaxyproject/galaxy/commit/950f92627176068609fc5191c72f6... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-14 (Sat, 14 Oct 2017)

Changed paths: M scripts/grt.py

Log Message: ----------- Add missing backport of hardening to scripts/grt.py

Commit: d8ee1a9a8d42f1287262a25fa282799d44d4f583 https://github.com/galaxyproject/galaxy/commit/d8ee1a9a8d42f1287262a25fa2827... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-14 (Sat, 14 Oct 2017)

Changed paths: M setup.cfg

Log Message: ----------- Revert ignoring I201 from 16.10 in 17.01

Commit: 25fc0982b75243e9c95a5312b56359f83bc72e87 https://github.com/galaxyproject/galaxy/commit/25fc0982b75243e9c95a5312b5635... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-16 (Mon, 16 Oct 2017)

Log Message: ----------- Merge branch 'release_16.10' into backport-hardening-17.01

Commit: 86929ff9f01201f0ef50429b96d4ab83a3887e8f https://github.com/galaxyproject/galaxy/commit/86929ff9f01201f0ef50429b96d4a... Author: Anthony Bretaudeau anthony.bretaudeau@inria.fr Date: 2017-10-16 (Mon, 16 Oct 2017)

Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/annotation.py

Log Message: ----------- add augustus and snap datatypes

Commit: 272ed6217d4662f7bdc6b385206a7f301295a033 https://github.com/galaxyproject/galaxy/commit/272ed6217d4662f7bdc6b385206a7... Author: Martin Cech marten@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/06d3f4051543e7c319e775884ea3a... Author: Martin Cech marten@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/eab76b9ae014c4fa2dd3a1ba09199... Author: Martin Cech marten@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/812b04d14eb1c3d3ec016efb6aa8f... Author: Martin Cech marten@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/5bde1d1c3a0239ef37369f59e90ce... Author: John Chilton jmchilton@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: 54d3994131f28963a1c3c4beccaf029a121d15b1 https://github.com/galaxyproject/galaxy/commit/54d3994131f28963a1c3c4beccaf0... Author: Nicola Soranzo nsoranzo@tiscali.it Date: 2017-10-17 (Tue, 17 Oct 2017)

Changed paths: M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_coverage.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/converters/sam_to_bam.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/citations.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webhooks/__init__.py M lib/tool_shed/capsule/capsule_manager.py M scripts/data_libraries/build_lucene_index.py M scripts/edam_mapping.py M scripts/grt.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py M scripts/transfer.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/workflows_format_2/converter.py M test/base/workflows_format_2/main.py M test/galaxy_selenium/data.py M test/galaxy_selenium/navigates_galaxy.py M test/unit/workflows/workflow_support.py

Log Message: ----------- Merge pull request #4807 from natefoo/backport-hardening-17.01

[17.01] Various bits of hardening from #4604

Commit: 8fa7cc8a1dcc1ced376912692aa0162ea133de12 https://github.com/galaxyproject/galaxy/commit/8fa7cc8a1dcc1ced376912692aa01... Author: Anthony Bretaudeau anthony.bretaudeau@inria.fr Date: 2017-10-17 (Tue, 17 Oct 2017)

Changed paths: M config/datatypes_conf.xml.sample

Log Message: ----------- sniff snaphmm too

Commit: deedb17caf66760855b4749771fa0e1655618dc0 https://github.com/galaxyproject/galaxy/commit/deedb17caf66760855b4749771fa0... Author: Anthony Bretaudeau anthony.bretaudeau@inria.fr Date: 2017-10-17 (Tue, 17 Oct 2017)

Changed paths: M lib/galaxy/datatypes/annotation.py

Log Message: ----------- edam terms

Commit: 66820a46eba8f8adc0a573a8c2727e28e0de23e8 https://github.com/galaxyproject/galaxy/commit/66820a46eba8f8adc0a573a8c2727... Author: E Rasche hxr@hx42.org Date: 2017-10-17 (Tue, 17 Oct 2017)

Changed paths: M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/containers/__init__.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_coverage.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/converters/sam_to_bam.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/citations.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/locations/dockstore.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webhooks/__init__.py M lib/tool_shed/capsule/capsule_manager.py M scripts/data_libraries/build_lucene_index.py M scripts/edam_mapping.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py M scripts/transfer.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/workflows_format_2/converter.py M test/base/workflows_format_2/main.py M test/functional/webhooks/phdcomics/helper/__init__.py M test/galaxy_selenium/data.py M test/galaxy_selenium/navigates_galaxy.py M test/unit/workflows/workflow_support.py

Log Message: ----------- Backport of hardening fixes to 17.05

Commit: 60b5abfa3e85502631fc922b231f51f63b118234 https://github.com/galaxyproject/galaxy/commit/60b5abfa3e85502631fc922b231f5... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2017-10-17 (Tue, 17 Oct 2017)

Changed paths: M config/plugins/webhooks/demo/tour_generator/static/script.js

Log Message: ----------- fix TDT's dependency

Commit: 9241c9e3dbf67bb3f55fa89181c80a13e5466e0e https://github.com/galaxyproject/galaxy/commit/9241c9e3dbf67bb3f55fa89181c80... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-17 (Tue, 17 Oct 2017)

Changed paths: M scripts/grt.py

Log Message: ----------- Merge remote-tracking branch 'origin/release_17.01' into backport-hardening-17.05

Commit: 7906a946f110ef8f55524121e3addb320982979c https://github.com/galaxyproject/galaxy/commit/7906a946f110ef8f55524121e3add... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-10-17 (Tue, 17 Oct 2017)

Changed paths: M config/plugins/webhooks/demo/tour_generator/static/script.js

Log Message: ----------- Merge pull request #4815 from anatskiy/release_17.09_tdt_fix

Fix TDT's dependency

Commit: c96e9945a613a27f4826baf3c0e61edda2dfa0bb https://github.com/galaxyproject/galaxy/commit/c96e9945a613a27f4826baf3c0e61... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-10-17 (Tue, 17 Oct 2017)

Changed paths: M lib/galaxy/util/biostar.py M lib/galaxy/util/handlers.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/image_util.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/util/streamball.py M lib/galaxy/util/submodules.py

Log Message: ----------- Force absolute import in much of galaxy.util

Commit: b15f5a74957ec154e7cd501f0a65936d11206aa0 https://github.com/galaxyproject/galaxy/commit/b15f5a74957ec154e7cd501f0a659... Author: Martin Cech marten@bx.psu.edu Date: 2017-10-17 (Tue, 17 Oct 2017)

Changed paths: M lib/galaxy/util/biostar.py M lib/galaxy/util/handlers.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/image_util.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/util/streamball.py M lib/galaxy/util/submodules.py

Log Message: ----------- Merge pull request #4817 from dannon/backport_abs_import

[17.09] Backport abs-import changes from util.

Commit: ef203a69e95facee788086fc507b062528cbb638 https://github.com/galaxyproject/galaxy/commit/ef203a69e95facee788086fc507b0... Author: Nicola Soranzo nsoranzo@tiscali.it Date: 2017-10-17 (Tue, 17 Oct 2017)

Changed paths: M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/containers/__init__.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_coverage.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/converters/sam_to_bam.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/citations.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/locations/dockstore.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webhooks/__init__.py M lib/tool_shed/capsule/capsule_manager.py M scripts/data_libraries/build_lucene_index.py M scripts/edam_mapping.py M scripts/grt.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py M scripts/transfer.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/workflows_format_2/converter.py M test/base/workflows_format_2/main.py M test/functional/webhooks/phdcomics/helper/__init__.py M test/galaxy_selenium/data.py M test/galaxy_selenium/navigates_galaxy.py M test/unit/workflows/workflow_support.py

Log Message: ----------- Merge pull request #4816 from natefoo/backport-hardening-17.05

[17.05] Various bits of hardening from #4604

Commit: 136925087e08eaef706e38b35299d1daa1ca2266 https://github.com/galaxyproject/galaxy/commit/136925087e08eaef706e38b35299d... Author: Martin Cech marten@bx.psu.edu Date: 2017-10-17 (Tue, 17 Oct 2017)

Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/annotation.py

Log Message: ----------- Merge pull request #4808 from abretaud/augsnaptypes

[17.09] Add augustus and snap datatypes

Commit: 6d8948217b0a106304ec4fe0f35bc9c4e73d9310 https://github.com/galaxyproject/galaxy/commit/6d8948217b0a106304ec4fe0f35bc... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-18 (Wed, 18 Oct 2017)

Changed paths: M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py

Log Message: ----------- Additional hardening for older releases

Commit: 7fc354f11806208a074595455342e941f632fd00 https://github.com/galaxyproject/galaxy/commit/7fc354f11806208a074595455342e... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-10-18 (Wed, 18 Oct 2017)

Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy_ext/metadata/set_metadata.py

Log Message: ----------- Write out registry.xml file in case jobs are missing this file

Commit: 7a2b7f27c51a883f89eed8ef4022d638d6acde1f https://github.com/galaxyproject/galaxy/commit/7a2b7f27c51a883f89eed8ef4022d... Author: John Chilton jmchilton@gmail.com Date: 2017-10-18 (Wed, 18 Oct 2017)

Changed paths: M lib/galaxy/jobs/handler.py

Log Message: ----------- Clarify previous commit.

Commit: 0f311470d9c2ce0a2de869b32c84143cd56acc6e https://github.com/galaxyproject/galaxy/commit/0f311470d9c2ce0a2de869b32c841... Author: E Rasche hxr@hx42.org Date: 2017-10-18 (Wed, 18 Oct 2017)

Changed paths: M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/containers/__init__.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_coverage.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/converters/sam_to_bam.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/citations.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/locations/dockstore.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/util/properties.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webhooks/__init__.py M lib/tool_shed/capsule/capsule_manager.py M scripts/data_libraries/build_lucene_index.py M scripts/edam_mapping.py M scripts/grt/export.py M scripts/grt/upload.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py M scripts/transfer.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/workflows_format_2/converter.py M test/base/workflows_format_2/main.py M test/functional/webhooks/phdcomics/helper/__init__.py M test/galaxy_selenium/data.py M test/galaxy_selenium/navigates_galaxy.py M test/unit/workflows/workflow_support.py

Log Message: ----------- Backport of hardening fixes to 17.09

Commit: a3daa338b8941a1676d0e0f36b854c3c93f73fbe https://github.com/galaxyproject/galaxy/commit/a3daa338b8941a1676d0e0f36b854... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-18 (Wed, 18 Oct 2017)

Log Message: ----------- Merge remote-tracking branch 'origin/release_17.05' into backport-hardening-17.09

Commit: 07e58a1cdf181bb277ef322ce51af4b2cdc86d00 https://github.com/galaxyproject/galaxy/commit/07e58a1cdf181bb277ef322ce51af... Author: Nicola Soranzo nsoranzo@tiscali.it Date: 2017-10-18 (Wed, 18 Oct 2017)

Changed paths: M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/containers/__init__.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_coverage.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/converters/sam_to_bam.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/citations.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/locations/dockstore.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/util/properties.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webhooks/__init__.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/capsule/capsule_manager.py M scripts/data_libraries/build_lucene_index.py M scripts/edam_mapping.py M scripts/grt/export.py M scripts/grt/upload.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py M scripts/transfer.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/workflows_format_2/converter.py M test/base/workflows_format_2/main.py M test/functional/webhooks/phdcomics/helper/__init__.py M test/galaxy_selenium/data.py M test/galaxy_selenium/navigates_galaxy.py M test/unit/workflows/workflow_support.py

Log Message: ----------- Merge pull request #4824 from natefoo/backport-hardening-17.09

[17.09] Various bits of hardening from #4604

Commit: 8e199a33cf2564f72cfb9e12ca71e48c873c6d5a https://github.com/galaxyproject/galaxy/commit/8e199a33cf2564f72cfb9e12ca71e... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2017-10-19 (Thu, 19 Oct 2017)

Changed paths: M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py

Log Message: ----------- Merge pull request #4812 from natefoo/hardening-extras-16.07

[16.07] Additional hardening for older releases

Commit: 34344a7563a3859c5171c65c3544ab8f7773fe2b https://github.com/galaxyproject/galaxy/commit/34344a7563a3859c5171c65c3544a... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-19 (Thu, 19 Oct 2017)

Changed paths: M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py

Log Message: ----------- Merge remote-tracking branch 'origin/release_16.07' into release_16.10

Commit: ae140949a8696a3b12aee83a9176e8091787a85d https://github.com/galaxyproject/galaxy/commit/ae140949a8696a3b12aee83a9176e... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-19 (Thu, 19 Oct 2017)

Changed paths: M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py

Log Message: ----------- Merge remote-tracking branch 'origin/release_16.10' into release_17.01

Commit: f0e9767912f91932d3541a3e824ebe026648cbf6 https://github.com/galaxyproject/galaxy/commit/f0e9767912f91932d3541a3e824eb... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-19 (Thu, 19 Oct 2017)

Changed paths: M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py

Log Message: ----------- Merge remote-tracking branch 'origin/release_17.01' into release_17.05

Commit: acc59e4d5db43ae9f3430529605988a9743a8a6d https://github.com/galaxyproject/galaxy/commit/acc59e4d5db43ae9f343052960598... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-19 (Thu, 19 Oct 2017)

Changed paths: M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py

Log Message: ----------- Merge remote-tracking branch 'origin/release_17.05' into release_17.09

Commit: 93a8bfc7cb5e9c3395c5057910ec39d68ad787b4 https://github.com/galaxyproject/galaxy/commit/93a8bfc7cb5e9c3395c5057910ec3... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-19 (Thu, 19 Oct 2017)

Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.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/webapps/galaxy/api/lda_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/user.py M lib/tool_shed/managers/groups.py

Log Message: ----------- Security: Fix issues with path handling in libraries and in general.

Commit: 0e698813a96f1ad61d797255686f69cf5e6b1280 https://github.com/galaxyproject/galaxy/commit/0e698813a96f1ad61d797255686f6... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-19 (Thu, 19 Oct 2017)

Changed paths: M tools/data_source/data_source.py

Log Message: ----------- [GX-2017-0003]: Fix for the reported issue, only allow http, https, and ftp schemes in the data_source tool.

Commit: ed045cd570cf6b2198fb496852458194c8e28d6f https://github.com/galaxyproject/galaxy/commit/ed045cd570cf6b2198fb496852458... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-19 (Thu, 19 Oct 2017)

Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.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/webapps/galaxy/api/lda_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/user.py M lib/tool_shed/managers/groups.py

Log Message: ----------- Security: Fix issues with path handling in libraries and in general.

Commit: 9e672f94588b8eeecee745665162fc92f0158e27 https://github.com/galaxyproject/galaxy/commit/9e672f94588b8eeecee745665162f... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-19 (Thu, 19 Oct 2017)

Changed paths: M tools/data_source/data_source.py

Log Message: ----------- [GX-2017-0003]: Fix for the reported issue, only allow http, https, and ftp schemes in the data_source tool.

Commit: 1bccbefbffc02803e93913b145f4214b8eb78d54 https://github.com/galaxyproject/galaxy/commit/1bccbefbffc02803e93913b145f42... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-19 (Thu, 19 Oct 2017)

Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.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/webapps/galaxy/api/lda_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/user.py M lib/tool_shed/managers/groups.py

Log Message: ----------- Security: Fix issues with path handling in libraries and in general.

Commit: 658f126e7a387c11df9b5f0a01e0b75e4d84410b https://github.com/galaxyproject/galaxy/commit/658f126e7a387c11df9b5f0a01e0b... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-19 (Thu, 19 Oct 2017)

Changed paths: M tools/data_source/data_source.py

Log Message: ----------- [GX-2017-0003]: Fix for the reported issue, only allow http, https, and ftp schemes in the data_source tool.

Commit: e8a72252effa5fdd888abd0e3462dde3b5c70f6e https://github.com/galaxyproject/galaxy/commit/e8a72252effa5fdd888abd0e3462d... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-19 (Thu, 19 Oct 2017)

Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.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/webapps/galaxy/api/lda_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/user.py M lib/tool_shed/managers/groups.py

Log Message: ----------- Security: Fix issues with path handling in libraries and in general.

Commit: 9f8d3ee444ad10038add204ed1c1dc11e636dd9d https://github.com/galaxyproject/galaxy/commit/9f8d3ee444ad10038add204ed1c1d... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-19 (Thu, 19 Oct 2017)

Changed paths: M lib/galaxy/web/base/interactive_environments.py

Log Message: ----------- Security: Switch GIE Popen() calls to run without shell=True to fix an ACE vulnerability.

Commit: cded49354e5fba4b93432294a4518c93b51f259f https://github.com/galaxyproject/galaxy/commit/cded49354e5fba4b93432294a4518... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-19 (Thu, 19 Oct 2017)

Changed paths: M tools/data_source/data_source.py

Log Message: ----------- [GX-2017-0003]: Fix for the reported issue, only allow http, https, and ftp schemes in the data_source tool.

Commit: 3b03b5b6cca75fb93c114d93c97e29b8157869b8 https://github.com/galaxyproject/galaxy/commit/3b03b5b6cca75fb93c114d93c97e2... Author: Daniel Blankenberg dan.blankenberg@gmail.com Date: 2017-10-19 (Thu, 19 Oct 2017)

Changed paths: M lib/galaxy/tools/parameters/basic.py

Log Message: ----------- Fix for single select list initial value when multiple options are selected by default.

Commit: 1f6df5580bc27d89a93755502f792c711d07b4b5 https://github.com/galaxyproject/galaxy/commit/1f6df5580bc27d89a93755502f792... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-19 (Thu, 19 Oct 2017)

Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M static/maps/galaxy.interactive_environments.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/galaxy.interactive_environments.js

Log Message: ----------- Fix the spinner for the GIE container readiness check.

Commit: 9475e9aac1068538131bce8c047f89c3c4546bb8 https://github.com/galaxyproject/galaxy/commit/9475e9aac1068538131bce8c047f8... Author: Nicola Soranzo nsoranzo@tiscali.it Date: 2017-10-19 (Thu, 19 Oct 2017)

Changed paths: M lib/galaxy/tools/parameters/basic.py

Log Message: ----------- Merge pull request #4834 from blankenberg/multiple-initial-single-select-param

[17.09] Fix for single select list initial value when multiple options are selected by default.

Commit: 42dc7b361756b096f9d3b17c06e2db1a5cefbe61 https://github.com/galaxyproject/galaxy/commit/42dc7b361756b096f9d3b17c06e2d... Author: guerler aysam.guerler@gmail.com Date: 2017-10-20 (Fri, 20 Oct 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py

Log Message: ----------- Filter histories for visualization grids by user

Commit: 30b9e5e4afa2c646a36213fa10d31fd1bc848c3e https://github.com/galaxyproject/galaxy/commit/30b9e5e4afa2c646a36213fa10d31... Author: Martin Cech marten@bx.psu.edu Date: 2017-10-20 (Fri, 20 Oct 2017)

Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M static/maps/galaxy.interactive_environments.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/galaxy.interactive_environments.js

Log Message: ----------- Merge pull request #4835 from natefoo/gie-spinner-fix

[17.09] Fix the spinner for the GIE container readiness check

Commit: 799fda61dbf3ddaad1b386d9d32602ef2b1c8a83 https://github.com/galaxyproject/galaxy/commit/799fda61dbf3ddaad1b386d9d3260... Author: guerler aysam.guerler@gmail.com Date: 2017-10-20 (Fri, 20 Oct 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py

Log Message: ----------- Filter library dataset by user

Commit: 646a8d1092541c797238e540d071c4346cc5885b https://github.com/galaxyproject/galaxy/commit/646a8d1092541c797238e540d071c... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-20 (Fri, 20 Oct 2017)

Changed paths: M scripts/cleanup_datasets/pgcleanup.py

Log Message: ----------- Support a log directory argument for pgcleanup.py

Commit: 5016a2d5251f42c87c22f1ad9d2bf164436f9ffd https://github.com/galaxyproject/galaxy/commit/5016a2d5251f42c87c22f1ad9d2bf... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-20 (Fri, 20 Oct 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py

Log Message: ----------- Merge pull request #4836 from guerler/filter_visualization_grid

[17.09] Add filter to visualization dataset queries

Commit: 1af06ce6fe2a3e20a240d7159391dd8a3e237b72 https://github.com/galaxyproject/galaxy/commit/1af06ce6fe2a3e20a240d7159391d... Author: John Chilton jmchilton@gmail.com Date: 2017-10-23 (Mon, 23 Oct 2017)

Changed paths: M scripts/cleanup_datasets/pgcleanup.py

Log Message: ----------- Merge pull request #4837 from natefoo/pgcleanup-log-dir

[17.09] Support a log directory argument for pgcleanup.py

Commit: f02cd7ddb6cc5ae3c9fe5d1b78abcff471ffc461 https://github.com/galaxyproject/galaxy/commit/f02cd7ddb6cc5ae3c9fe5d1b78abc... Author: Nate Coraor nate@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/managers/folders.py M lib/galaxy/managers/libraries.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/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/tool_shed/managers/groups.py

Log Message: ----------- Security: Fix issues with path handling in libraries and in general.

Commit: c3fd90a36dfa0468447b20a63affbd7a6853f0f7 https://github.com/galaxyproject/galaxy/commit/c3fd90a36dfa0468447b20a63affb... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-23 (Mon, 23 Oct 2017)

Changed paths: M lib/galaxy/web/base/interactive_environments.py

Log Message: ----------- Security: Switch GIE Popen() calls to run without shell=True to fix an ACE vulnerability.

Commit: 391586ba01fc1a01443962d137e9df3fce707434 https://github.com/galaxyproject/galaxy/commit/391586ba01fc1a01443962d137e9d... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-23 (Mon, 23 Oct 2017)

Changed paths: M tools/data_source/data_source.py

Log Message: ----------- [GX-2017-0003]: Fix for the reported issue, only allow http, https, and ftp schemes in the data_source tool.

Commit: dda175dbf088bb4ba014fbea70b610cb7e2c2ed6 https://github.com/galaxyproject/galaxy/commit/dda175dbf088bb4ba014fbea70b61... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-23 (Mon, 23 Oct 2017)

Log Message: ----------- Merge branch 'release_16.07' into release_16.10

Commit: c4855af7d516b0a955e508cc7e5bc8716028b670 https://github.com/galaxyproject/galaxy/commit/c4855af7d516b0a955e508cc7e5bc... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-23 (Mon, 23 Oct 2017)

Log Message: ----------- Merge branch 'release_16.10' into release_17.01

Commit: b35fe934d4246ae0b4c1b6aa3a446fd5672d55c6 https://github.com/galaxyproject/galaxy/commit/b35fe934d4246ae0b4c1b6aa3a446... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-23 (Mon, 23 Oct 2017)

Log Message: ----------- Merge branch 'release_17.01' into release_17.05

Commit: cfe3dfc6eb93c65f55dd794b742b08762edd5d02 https://github.com/galaxyproject/galaxy/commit/cfe3dfc6eb93c65f55dd794b742b0... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-23 (Mon, 23 Oct 2017)

Log Message: ----------- Merge branch 'release_17.05' into release_17.09

Commit: dd609265a20a820da4313e21204075836ba51567 https://github.com/galaxyproject/galaxy/commit/dd609265a20a820da4313e2120407... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-10-23 (Mon, 23 Oct 2017)

Changed paths: M lib/galaxy/managers/workflows.py

Log Message: ----------- Only subqueryload latest_workflow instead of all workflows

Commit: ee27188b59d174f4db16d2ce4b7cd2181ea93517 https://github.com/galaxyproject/galaxy/commit/ee27188b59d174f4db16d2ce4b7cd... Author: Martin Cech marten@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/180472a3d8ceb40f6d015c0bfe5ef... Author: Dave Clements clements@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/c8efbb3327cb4e2805c0099975c5a... Author: Dave Clements clements@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/4252f4f813c3d5a390ead3d86c4ee... Author: John Chilton jmchilton@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/199ec6dd4c70c733edd200e61d647... Author: John Chilton jmchilton@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/3e8bf27fca44f5b70ac9e7e1f66ac... Author: John Chilton jmchilton@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/1b5421c1df5392ce83a66de22dceb... Author: Martin Cech marten@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/00bc7a51f9c780e15041b465e0245... Author: John Chilton jmchilton@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/d1190bb067146d76bc16ec403562d... Author: Martin Cech marten@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/fe440d27367ef00b663057bf8ebe3... Author: Martin Cech marten@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/6bbf345c282782efac6a026d36f60... Author: Martin Cech marten@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/73b31ce3199ac73a0208dd7844208... Author: John Chilton jmchilton@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/f5981e6ef381d5c4be33e0725cdb6... Author: Martin Cech marten@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/add3a97bb014392d773c7a5bb8243... Author: Martin Cech marten@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/cfb61e069659fa43b4ad290b4cc4a... Author: John Chilton jmchilton@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/01b244a810434a1184d3e72ff9476... Author: John Chilton jmchilton@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/9791dd22d4d9084989cafa3498ae3... Author: Nicola Soranzo nicola.soranzo@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/a4a8f155376119277df2cfebd1337... Author: John Chilton jmchilton@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/899b0d806808d29291bf132a8c9e4... Author: John Chilton jmchilton@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/4b5dc399b934542092bfe66c3c4e0... Author: John Chilton jmchilton@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/fcb23eb8f878700bfd77384ef679a... Author: John Chilton jmchilton@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/95f8f48416c5a4d2590120e965cf9... Author: John Chilton jmchilton@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/7e08ba6f19346668350d358ee4eb0... Author: John Chilton jmchilton@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/e3e28ddc2dac1c4faaa45a9764abc... Author: Nicola Soranzo nsoranzo@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/90289b6116c6a6ba1f6f0b4cbdee0... Author: Nicola Soranzo nicola.soranzo@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/a7bf1601a1ad34e5896978e1bce9c... Author: Nicola Soranzo nicola.soranzo@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/20621b7d09443fc80c8326d91bdd2... Author: Nicola Soranzo nicola.soranzo@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/986031bf190b82317cf687ed7e82e... Author: Nicola Soranzo nicola.soranzo@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/1baed58e1e7c813e6a87b5a83883c... Author: Nicola Soranzo nicola.soranzo@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: b9adcc81e866a949601f815dd778b62bef631461 https://github.com/galaxyproject/galaxy/commit/b9adcc81e866a949601f815dd778b... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-26 (Thu, 26 Oct 2017)

Changed paths: M lib/galaxy/managers/workflows.py

Log Message: ----------- Merge pull request #4844 from mvdbeek/workflow_performance_issues

[17.09] Only subqueryload latest_workflow instead of all workflows

Commit: aef5f4fa95c56362029dba6cf636103cf235fd13 https://github.com/galaxyproject/galaxy/commit/aef5f4fa95c56362029dba6cf6361... Author: John Chilton jmchilton@gmail.com Date: 2017-10-26 (Thu, 26 Oct 2017)

Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt

Log Message: ----------- [16.10] Fix test fixtures dependency.

It should have never been in the pinned requirements and has disappeared from PyPI.

Commit: 7bf2bbfa405029898a65f1ea092d8cacd2903483 https://github.com/galaxyproject/galaxy/commit/7bf2bbfa405029898a65f1ea092d8... Author: John Chilton jmchilton@gmail.com Date: 2017-10-27 (Fri, 27 Oct 2017)

Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt

Log Message: ----------- Merge pull request #4873 from jmchilton/fix_test_fixtures

[16.10] Fix test fixtures dependency.

Commit: 676f6a5960a185c80d7400b9cb8c92d5217bfae4 https://github.com/galaxyproject/galaxy/commit/676f6a5960a185c80d7400b9cb8c9... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-10-30 (Mon, 30 Oct 2017)

Changed paths: M client/galaxy/style/less/upload.less M static/style/blue/base.css

Log Message: ----------- Fix uploadbox text content formatting.

Commit: 09fdac513d59ca6dad440616a53daa97751ff905 https://github.com/galaxyproject/galaxy/commit/09fdac513d59ca6dad440616a53da... Author: John Chilton jmchilton@gmail.com Date: 2017-10-30 (Mon, 30 Oct 2017)

Changed paths: M scripts/common_startup.sh

Log Message: ----------- Fix extra index URL call in common startup.

- Use it for dev requirements also. - Use more correct API target that supports older versions of dependencies on PyPI.

xref https://gist.github.com/jmchilton/ad8f180f5ac1eb5f689f815b04f603fa

Commit: 45d4fefe63d59627063cbacaf6cdd797ee81d158 https://github.com/galaxyproject/galaxy/commit/45d4fefe63d59627063cbacaf6cdd... Author: Nicola Soranzo nsoranzo@tiscali.it Date: 2017-10-30 (Mon, 30 Oct 2017)

Changed paths: M scripts/common_startup.sh

Log Message: ----------- Merge pull request #4898 from jmchilton/fix_extra_index

[17.09] Fix extra index URL call in common startup.

Commit: a537aa4ca4f7622bafe20da7339d5652e263d78f https://github.com/galaxyproject/galaxy/commit/a537aa4ca4f7622bafe20da7339d5... Author: Nicola Soranzo nsoranzo@tiscali.it Date: 2017-10-30 (Mon, 30 Oct 2017)

Changed paths: M config/local_conda_mapping.yml.sample

Log Message: ----------- Merge pull request #4749 from mvdbeek/conda_mapping_path_fix

[17.05] Fix path to example conda mapping

Commit: 1664a2c7e644ee12a3bd599bfd08c5a618443ef0 https://github.com/galaxyproject/galaxy/commit/1664a2c7e644ee12a3bd599bfd08c... Author: Martin Cech marten@bx.psu.edu Date: 2017-10-30 (Mon, 30 Oct 2017)

Changed paths: M client/galaxy/style/less/upload.less M static/style/blue/base.css

Log Message: ----------- Merge pull request #4897 from dannon/uploadbox_wrap_fix

[17.09] Fix uploadbox text content formatting.

Commit: ee5774a887fbbc86b99e266d476de170935025b2 https://github.com/galaxyproject/galaxy/commit/ee5774a887fbbc86b99e266d476de... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-10-30 (Mon, 30 Oct 2017)

Changed paths: M client/galaxy/style/less/upload.less M static/style/blue/base.css

Log Message: ----------- Swap from overflow:scroll to overflow:auto on text.

Commit: c7b09f870d31b93dab87a2eaaa95ace7f6f503b4 https://github.com/galaxyproject/galaxy/commit/c7b09f870d31b93dab87a2eaaa95a... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-10-30 (Mon, 30 Oct 2017)

Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt

Log Message: ----------- Merge branch 'release_16.10' into release_17.01

Conflicts: lib/galaxy/dependencies/pinned-requirements.txt

Commit: 7688b057e604f4e6e38a21fca3e47ce65c16c413 https://github.com/galaxyproject/galaxy/commit/7688b057e604f4e6e38a21fca3e47... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-10-30 (Mon, 30 Oct 2017)

Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt

Log Message: ----------- Merge branch 'release_17.01' into release_17.05

Commit: be30d6824d4975f6cb15fdd9519f4edf3e9e3079 https://github.com/galaxyproject/galaxy/commit/be30d6824d4975f6cb15fdd9519f4... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-10-30 (Mon, 30 Oct 2017)

Changed paths: M config/local_conda_mapping.yml.sample M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt

Log Message: ----------- Merge branch 'release_17.05' into release_17.09

Commit: fca1d0c3e8d180a6607b2adb35c9b6486a6e66e5 https://github.com/galaxyproject/galaxy/commit/fca1d0c3e8d180a6607b2adb35c9b... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-10-30 (Mon, 30 Oct 2017)

Changed paths: M client/galaxy/style/less/upload.less M static/style/blue/base.css

Log Message: ----------- Bump active upload box size

Commit: c96e1386a8749b0e6f706bf945bc6751a5d89467 https://github.com/galaxyproject/galaxy/commit/c96e1386a8749b0e6f706bf945bc6... Author: Martin Cech marten@bx.psu.edu Date: 2017-10-30 (Mon, 30 Oct 2017)

Changed paths: M doc/source/releases/17.09_announce.rst

Log Message: ----------- announce complete removal of sample tracking

Commit: 68c5ebcf824b5a4302184ae3e2ca8231fe633e21 https://github.com/galaxyproject/galaxy/commit/68c5ebcf824b5a4302184ae3e2ca8... Author: John Chilton jmchilton@gmail.com Date: 2017-10-31 (Tue, 31 Oct 2017)

Changed paths: M lib/galaxy/app.py M lib/galaxy/webapps/galaxy/config_watchers.py

Log Message: ----------- Shutdown watchers during app shutdown.

Commit: e747bcbaa24e6eb3b0c1542007b5bc0a3e77d47e https://github.com/galaxyproject/galaxy/commit/e747bcbaa24e6eb3b0c1542007b5b... Author: Martin Cech marten@bx.psu.edu Date: 2017-10-31 (Tue, 31 Oct 2017)

Changed paths: M lib/galaxy/app.py M lib/galaxy/webapps/galaxy/config_watchers.py

Log Message: ----------- Merge pull request #4904 from jmchilton/clean_watchers

[17.09] Shutdown watchers during app shutdown.

Commit: 2784ef5a04d4878e2e67b39da1e9670a481ab0d0 https://github.com/galaxyproject/galaxy/commit/2784ef5a04d4878e2e67b39da1e96... Author: Martin Cech marten@bx.psu.edu Date: 2017-10-31 (Tue, 31 Oct 2017)

Changed paths: M client/galaxy/style/less/upload.less M static/style/blue/base.css

Log Message: ----------- Merge pull request #4899 from dannon/uploadbox_wrap_fix

[17.09] One more uploadbox regression fix

Commit: 7b6df3074a0d3377b8428cc3917238332a5aaab2 https://github.com/galaxyproject/galaxy/commit/7b6df3074a0d3377b8428cc391723... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-10-31 (Tue, 31 Oct 2017)

Changed paths: M doc/source/releases/17.09_announce.rst

Log Message: ----------- Merge pull request #4902 from martenson/deprecate-tracking

[17.09] deprecate and announce complete removal of sample tracking

Commit: 61361e7c1cf205f5877bcd973e4740e450523bb5 https://github.com/galaxyproject/galaxy/commit/61361e7c1cf205f5877bcd973e474... Author: Martin Cech marten@bx.psu.edu Date: 2017-10-31 (Tue, 31 Oct 2017)

Changed paths: M doc/source/releases/17.09_announce.rst

Log Message: ----------- deprecate configuration/toolbox endpoint

Commit: 76a02eb9b5e5701bae0afb38fa1169ef36cb37d2 https://github.com/galaxyproject/galaxy/commit/76a02eb9b5e5701bae0afb38fa116... Author: John Chilton jmchilton@gmail.com Date: 2017-10-31 (Tue, 31 Oct 2017)

Changed paths: M doc/source/releases/17.09_announce.rst

Log Message: ----------- Merge pull request #4905 from martenson/deprecate-reload

[17.09] Deprecate tool reload endpoint

Commit: 24da84a52501a45debb8e88744040901767cb004 https://github.com/galaxyproject/galaxy/commit/24da84a52501a45debb8e88744040... Author: Martin Cech marten@bx.psu.edu Date: 2017-10-31 (Tue, 31 Oct 2017)

Changed paths: M lib/galaxy/version.py

Log Message: ----------- Update version to 17.09

Commit: 15372f7369137b964534e9ddb8e81fb150dc2677 https://github.com/galaxyproject/galaxy/commit/15372f7369137b964534e9ddb8e81... Author: Martin Cech marten@bx.psu.edu Date: 2017-10-31 (Tue, 31 Oct 2017)

Changed paths: A .ci/autopep8.sh M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/docker-compose.yml M .ci/py3_sources.txt M .gitignore M .travis.yml M CITATION M CONTRIBUTING.md M Makefile M README.rst A SECURITY_POLICY.md M client/bower.json A client/galaxy/scripts/admin.toolshed.js A client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js R client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/apps/login.js A client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/apps/panels/history-panel.js A client/galaxy/scripts/apps/panels/tool-panel.js R client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js A client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.js R client/galaxy/scripts/libs/jquery/jqtouch.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js A client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js A client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-view.js A client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-model.js A client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M 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config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml A config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/static/script.js A config/plugins/webhooks/demo/tour_generator/static/styles.css R config/reports.ini.sample A config/reports.yml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample R config/tool_shed.ini.sample A config/tool_shed.yml.sample A config/user_preferences_extra_conf.yml.sample M contrib/galaxy.debian-init M contrib/galaxy_supervisor.conf M contrib/nagios/check_galaxy.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M cron/updateucsc.sh.sample M doc/Makefile R doc/patch.py M doc/source/admin/authentication.md M doc/source/admin/dependency_resolvers.rst A doc/source/admin/reports.rst A doc/source/admin/reports_options.rst A doc/source/admin/special_topics/bug_reports.rst M 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tools/genomespace/genomespace_file_browser_test.xml M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_importer.xml A tools/genomespace/genomespace_push.xml M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.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_split_by_species.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/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/meme/fimo_wrapper.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/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.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_assembly/velvetg.xml M tools/sr_assembly/velvetg_wrapper.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_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 M tools/visualization/LAJ.py M tools/visualization/LAJ_code.py M tox.ini

Log Message: ----------- Merge branch 'release_17.09'

Compare: https://github.com/galaxyproject/galaxy/compare/0a39bfcbf7dc...15372f736913