Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 27dd8362154b2f26850f05b0b8b558757b8ffa20 https://github.com/galaxyproject/galaxy/commit/27dd8362154b2f26850f05b0b8b55... Author: Nate Coraor <nate@bx.psu.edu> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- WIP load shed tools w/o install DB Commit: 1e7d8087d26829326edfde02b2a38119893aa8de https://github.com/galaxyproject/galaxy/commit/1e7d8087d26829326edfde02b2a38... Author: Nate Coraor <nate@bx.psu.edu> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix "show in toolshed" link Commit: d4e88636067733a4a5c9bf579692ba3968b5c9b0 https://github.com/galaxyproject/galaxy/commit/d4e88636067733a4a5c9bf579692b... Author: Nate Coraor <nate@bx.psu.edu> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/buildapp.py A lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- WIP broken support tool help w/out repository_id and start de-hackifying Commit: 90d61af69a7afd798a515164aec6aa760d39ed4b https://github.com/galaxyproject/galaxy/commit/90d61af69a7afd798a515164aec6a... Author: Nate Coraor <nate@bx.psu.edu> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix generation of repo_path Commit: 9f27ae897ffc877db21b247e25ab2eafced1fb30 https://github.com/galaxyproject/galaxy/commit/9f27ae897ffc877db21b247e25ab2... Author: Nate Coraor <nate@bx.psu.edu> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py Log Message: ----------- Got tool help images working Commit: 8bc3f93b26963bf9d6043dfd90b339bea4850b4a https://github.com/galaxyproject/galaxy/commit/8bc3f93b26963bf9d6043dfd90b33... Author: Nate Coraor <nate@bx.psu.edu> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py Log Message: ----------- Better condition handling for populating a tool's shed info Commit: 4627546831224fcf0b85479a4c39893a4edaea8a https://github.com/galaxyproject/galaxy/commit/4627546831224fcf0b85479a4c398... Author: Nate Coraor <nate@bx.psu.edu> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/tool_shed/tools/tool_validator.py Log Message: ----------- Fix silent failure when installing tools. Commit: 2e04301d6b4f1d18a2e1ad6b328001789c86a140 https://github.com/galaxyproject/galaxy/commit/2e04301d6b4f1d18a2e1ad6b32800... Author: Nate Coraor <nate@bx.psu.edu> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/galaxy/tools/__init__.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Fix installing TS tools Commit: 767c8497a5e0ca167a395ff56b3bd00c906068cd https://github.com/galaxyproject/galaxy/commit/767c8497a5e0ca167a395ff56b3bd... Author: Nate Coraor <nate@bx.psu.edu> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py Log Message: ----------- Lint Commit: 1673d645ced97cb37fd4f5efb36b59de2ae7eba8 https://github.com/galaxyproject/galaxy/commit/1673d645ced97cb37fd4f5efb36b5... Author: Nate Coraor <nate@bx.psu.edu> Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Add unnecessary column Commit: 037202c3010aefb361b582127dc7d5b3b575a773 https://github.com/galaxyproject/galaxy/commit/037202c3010aefb361b582127dc7d... Author: Nate Coraor <nate@bx.psu.edu> Date: 2019-02-08 (Fri, 08 Feb 2019) Changed paths: M lib/tool_shed/tools/tool_validator.py Log Message: ----------- Log exceptions instead of raising. Commit: e1001d3754c7b469dd3d5e7a9989d13b89fa5d2f https://github.com/galaxyproject/galaxy/commit/e1001d3754c7b469dd3d5e7a9989d... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cache.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Some small fixes and improvements Most notably only use tool_shed_repository while constructing a Tool, this avoids stale references to sqlalchemy objects. Commit: 6678a6baf0c61c7538425c7c82d0fadb6f27a3ea https://github.com/galaxyproject/galaxy/commit/6678a6baf0c61c7538425c7c82d0f... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py Log Message: ----------- Fix display of images in static/images Commit: 99447a9d299e8e8e52ff0367144bb9665627ccf3 https://github.com/galaxyproject/galaxy/commit/99447a9d299e8e8e52ff0367144bb... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/tools/repositories.py Log Message: ----------- Add dummy tool shed registry Commit: 0d6f4b13837e52371ddf12881375639cb198ef33 https://github.com/galaxyproject/galaxy/commit/0d6f4b13837e52371ddf128813756... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/tool_shed/util/readme_util.py Log Message: ----------- Remove useless lock Commit: 0b6e9cfd7c55f9eedde9a37719fa477ac8839fd8 https://github.com/galaxyproject/galaxy/commit/0b6e9cfd7c55f9eedde9a37719fa4... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Mock the mock shed registry Commit: 694dde1b07099fdf4a1b400eb5054fee59335ae7 https://github.com/galaxyproject/galaxy/commit/694dde1b07099fdf4a1b400eb5054... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix set_image_path for tools in tool shed Commit: 8b9239172acc43969946b00c8f3fb94e403803d9 https://github.com/galaxyproject/galaxy/commit/8b9239172acc43969946b00c8f3fb... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Simplify getting changeset revision from path Commit: 2e57760086bba24df25b1c0e2650be3c90e90ecb https://github.com/galaxyproject/galaxy/commit/2e57760086bba24df25b1c0e2650b... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Simplify some more Commit: 063a4a4e394dea128f4f2b9820ac08c97e6eaeef https://github.com/galaxyproject/galaxy/commit/063a4a4e394dea128f4f2b9820ac0... Author: Nate Coraor <nate@bx.psu.edu> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cache.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/repositories.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py M lib/tool_shed/util/readme_util.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge pull request #10 from mvdbeek/natefoo-installdbless-shed-tools Simplify loading repositories and fix tests Commit: 0a39badc798160ec4978e9f60a7f4b8275b5c299 https://github.com/galaxyproject/galaxy/commit/0a39badc798160ec4978e9f60a7f4... Author: John Chilton <jmchilton@gmail.com> Date: 2019-02-27 (Wed, 27 Feb 2019) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cache.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/repositories.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/buildapp.py A lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge pull request #7316 from natefoo/installdbless-shed-tools Support loading/using tools that are not in the install database Compare: https://github.com/galaxyproject/galaxy/compare/25aa54e28b18...0a39badc7981