Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 58ed0308faa7fa94f1b36dc2e62b866ac6f49bdd https://github.com/galaxyproject/galaxy/commit/58ed0308faa7fa94f1b36dc2e62b8... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/app.py M lib/galaxy/tools/__init__.py Log Message: ----------- Create fewer objects when instantiating tools. Commit: 5e6c1c9f517ad7d6353db777e82c8e48f4769f06 https://github.com/galaxyproject/galaxy/commit/5e6c1c9f517ad7d6353db777e82c8... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M config/plugins/webhooks/demo/tour_generator/__init__.py M lib/galaxy/app.py M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M test/base/driver_util.py M test/base/interactor.py M test/base/testcase.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py Log Message: ----------- New abstraction to obtain tool test data paths. Can be shared between tests and TDTs. A step toward not requiring one to load the tool to test the tool (important for external testing of tools). Commit: 210d5cbd7a52ecc3bbbef24c1bee4362fbcb9770 https://github.com/galaxyproject/galaxy/commit/210d5cbd7a52ecc3bbbef24c1bee4... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M test/base/driver_util.py M test/base/testcase.py Log Message: ----------- Eliminate shed tools dict no longer used. Commit: 58ac3b6eff5f2158d5690d684a143716c4471ba4 https://github.com/galaxyproject/galaxy/commit/58ac3b6eff5f2158d5690d684a143... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: R test/base/tool_shed_util.py M test/shed_functional/base/twilltestcase.py Log Message: ----------- Eliminate tool shed test helper no longer used. Commit: 7e372c5dd217fdb4c19f4da6a49d86d65d205f76 https://github.com/galaxyproject/galaxy/commit/7e372c5dd217fdb4c19f4da6a49d8... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/tools/verify/__init__.py M test/base/interactor.py M test/base/testcase.py Log Message: ----------- Refactor more tool test verification code into galaxy-lib. Should enable greater reuse from outside the test framework (e.g. standalone scripts and Planemo). Commit: 70e76cae9f1f354540a3b97020323be1caba9817 https://github.com/galaxyproject/galaxy/commit/70e76cae9f1f354540a3b97020323... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M test/base/interactor.py M test/base/testcase.py Log Message: ----------- Refactor polling code from testcase into more standalone interactor. Working toward making interactor stand-alone and independent of the test framework. Commit: 289937506bc97b7c8783975316e0a236a6ebf76b https://github.com/galaxyproject/galaxy/commit/289937506bc97b7c8783975316e0a... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/tools/verify/__init__.py A lib/galaxy/tools/verify/interactor.py M test/base/api.py M test/base/driver_util.py M test/base/interactor.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py M test/functional/twilltestcase.py Log Message: ----------- Refactor much more tool testing code into galaxy-lib. Commit: 508047f00ece58c98ba0f9bb093d2ae7506ade77 https://github.com/galaxyproject/galaxy/commit/508047f00ece58c98ba0f9bb093d2... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/tools/test.py M lib/galaxy/tools/verify/interactor.py M test/functional/test_toolbox.py Log Message: ----------- Refactor ToolTestBuilder to not require an in-memory Tool object. This gets us a lot closer to being able to construct a ToolTestBuilder from simple dictionaries generated from the API for instance or from any tool really. Commit: c3af6c8feae90bc2d4b6328559fb79e3d7d35a5c https://github.com/galaxyproject/galaxy/commit/c3af6c8feae90bc2d4b6328559fb7... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/test.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M test/api/test_tools.py M test/base/driver_util.py M test/base/testcase.py M test/functional/test_toolbox.py Log Message: ----------- Serialize tool test descriptions through the API. Use this is in tool testing. Prevents needing to load / have tools in memory to run tool tests - should allow external tool testing. Commit: b1779e1a46564d976a7c024084c48c94df2db8e5 https://github.com/galaxyproject/galaxy/commit/b1779e1a46564d976a7c024084c48... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py A lib/galaxy/tools/verify/script.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M test/base/driver_util.py M test/functional/test_toolbox.py Log Message: ----------- Refactor tool test outline construction to allow more reuse. Commit: cd002615ee8a1f251eac9c0a5ae3cc12c45d2bde https://github.com/galaxyproject/galaxy/commit/cd002615ee8a1f251eac9c0a5ae3c... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/tools/verify/test_data.py Log Message: ----------- Setup a default GALAXY_TEST_FILE_DIR in case unset in the Galaxy itself. Previously this was set in the test framework but that doesn't help running Galaxies. Commit: 6f908a76c5db474725c2e45b51ad6ee9c27487cc https://github.com/galaxyproject/galaxy/commit/6f908a76c5db474725c2e45b51ad6... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M test/integration/test_data_manager_table_reload.py A test/integration/uses_shed.py Log Message: ----------- Refactor data manager test to allow more integration tests with tool shed. Commit: 662f29fda271454a9976fbf4fdad273300a89bfa https://github.com/galaxyproject/galaxy/commit/662f29fda271454a9976fbf4fdad2... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: A test/integration/test_shed_tool_tests.py Log Message: ----------- Integration test case for running tool tests against shed installed tools. Commit: db6dafac07b92a06cac1da728f8fffb979d81d87 https://github.com/galaxyproject/galaxy/commit/db6dafac07b92a06cac1da728f8ff... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Revise repository directory calculation in tool class. Based on conversations with @mvdbeek on https://github.com/galaxyproject/galaxy/pull/5545/files. Commit: e7f7759cc22aac8ace05eaeab5b706634322a80b https://github.com/galaxyproject/galaxy/commit/e7f7759cc22aac8ace05eaeab5b70... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Better default configuration of Galaxy test data directory. Commit: dc080b926ec3c0ecb967224ffa3b505e0128f783 https://github.com/galaxyproject/galaxy/commit/dc080b926ec3c0ecb967224ffa3b5... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/tools/verify/script.py Log Message: ----------- Add structured output json example to galaxy.tools.verify.script. Capture more information about the test. Commit: 52b6bf2486b08aa8bbe621961baed42bd27c1ddd https://github.com/galaxyproject/galaxy/commit/52b6bf2486b08aa8bbe621961baed... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py Log Message: ----------- Stronger security around test data path resolution, now with tests. Commit: bb7de2c0db60d6a69d84401279830fa87e8d9000 https://github.com/galaxyproject/galaxy/commit/bb7de2c0db60d6a69d84401279830... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/test.py M lib/galaxy/tools/verify/interactor.py M test/unit/tools/test_parsing.py Log Message: ----------- Improved tool test API. Cleanup up internal representations used to bridge the tool parser and the tool testing modules to produce more sensible dictified representations when exported via the API. This is mostly replacing tuples (which get converted to JSON lists) to dicts but there are some other small cleanups. Commit: 28ba0279d90dfae7603cdb06bed69235bf4f6f06 https://github.com/galaxyproject/galaxy/commit/28ba0279d90dfae7603cdb06bed69... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Bug fix for exclude mercurial repo from test data search. Thanks to :eagle::eyes:. Commit: 227bf4ad045fcecc1aaab77a9b04f0ad0daa1e19 https://github.com/galaxyproject/galaxy/commit/227bf4ad045fcecc1aaab77a9b04f... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/app.py M lib/galaxy/tools/verify/interactor.py M test/base/driver_util.py Log Message: ----------- Cleanup external tool testing based on @nsoranzo's comments. Commit: f741ab142adc2411397fb6ef28710b850e02db78 https://github.com/galaxyproject/galaxy/commit/f741ab142adc2411397fb6ef28710... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py Log Message: ----------- Switch default tool test dbkey to '?'. This makes a lot more sense, since the target Galaxy may not be configured with this dbkey. Thanks to @mvdbeek for the catch (https://github.com/galaxyproject/galaxy/pull/5628#pullrequestreview-10146158...). Restore the legacy behavior with "export GALAXY_TEST_DEFAULT_DBKEY=hg17". Commit: 3afb4abad3a387997c0cb1c9398f8644219b0298 https://github.com/galaxyproject/galaxy/commit/3afb4abad3a387997c0cb1c9398f8... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M config/galaxy.yml.sample M config/plugins/webhooks/demo/tour_generator/__init__.py M doc/source/admin/galaxy_options.rst M lib/galaxy/app.py M lib/galaxy/config.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/parser/yaml.py M lib/galaxy/tools/test.py A lib/galaxy/tools/verify/interactor.py A lib/galaxy/tools/verify/script.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml 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/testcase.py R test/base/tool_shed_util.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py M test/functional/twilltestcase.py M test/integration/test_data_manager_table_reload.py A test/integration/test_shed_tool_tests.py A test/integration/uses_shed.py M test/shed_functional/base/twilltestcase.py M test/unit/tools/test_parsing.py Log Message: ----------- Merge pull request #5628 from jmchilton/external_tool_tests_better_api Externally Executable Tool Tests 2 (with better API) Compare: https://github.com/galaxyproject/galaxy/compare/7ceb24601822...3afb4abad3a3