Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 632cdeae86c70d8ca66e78643c82c130501e0ca6 https://github.com/galaxyproject/galaxy/commit/632cdeae86c70d8ca66e78643c82c... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/tools/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/static.py M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Replace paste.httpexception with webob.exc classes Commit: 27a354f97ec40e99343caa1f1f1e7da94a721c53 https://github.com/galaxyproject/galaxy/commit/27a354f97ec40e99343caa1f1f1e7... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Fix make_file method of patched cgi_FieldStorage This copies the behavior from webob.compat.cgi_FieldStorage, except we use a NamedTemporaryFile instead of TemporaryFile. Commit: deba605e7eaaa418fe9fed3f1e0f6a9e15223718 https://github.com/galaxyproject/galaxy/commit/deba605e7eaaa418fe9fed3f1e0f6... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Pass bytestring to hash function Commit: 6b86ed56f35e1b51e27053169e80c5b4b7b9ddf2 https://github.com/galaxyproject/galaxy/commit/6b86ed56f35e1b51e27053169e80c... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py Log Message: ----------- Fix binary file check Commit: cb7ebd73494153b1950ec87a39d12e874c183a13 https://github.com/galaxyproject/galaxy/commit/cb7ebd73494153b1950ec87a39d12... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/web/base/controller.py M test/unit/tools/test_history_imp_exp.py Log Message: ----------- py3: Fix history import/export tool - Open history tarfile in binary mode - Fix base64 encoding in history import tool - test history export more extensively Commit: 1dc4cf224108db9756a96b9d50a71f9f099a00f2 https://github.com/galaxyproject/galaxy/commit/1dc4cf224108db9756a96b9d50a71... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Fix cgi_FieldStorage monkey patch self.__file is defined in cgi.FieldStorage, so that is the class that needs to be patched. Followup to a65cd29c366035fb8b26e2274046e8c96e3cab33 Commit: 8093d6b61046f7b09381c520d5c95dda54f7ed71 https://github.com/galaxyproject/galaxy/commit/8093d6b61046f7b09381c520d5c95... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M test/api/test_dataset_collections.py Log Message: ----------- py3: Fix dataset collection test Commit: a88ce7cfd21646f3dbd04ef41f8e1755da793713 https://github.com/galaxyproject/galaxy/commit/a88ce7cfd21646f3dbd04ef41f8e1... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/util/checkers.py Log Message: ----------- py3: fix check_html Commit: dc9e5c5a83877599991274298fca3316263a4b36 https://github.com/galaxyproject/galaxy/commit/dc9e5c5a83877599991274298fca3... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/authenticate.py M test/api/test_authenticate.py Log Message: ----------- py3: Fix authenticate api test Commit: a760ecdaf0e56a9eee9a02ace9dc7a97906dda02 https://github.com/galaxyproject/galaxy/commit/a760ecdaf0e56a9eee9a02ace9dc7... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Cast to bytestring for is_binary check Commit: 02d9415ece13452e5c23ee8078d644c34a6b40cd https://github.com/galaxyproject/galaxy/commit/02d9415ece13452e5c23ee8078d64... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/datasets.py Log Message: ----------- py3: Fix raw dataset display Commit: 330aaf8683587484efdbd02f93ba04e82c568859 https://github.com/galaxyproject/galaxy/commit/330aaf8683587484efdbd02f93ba0... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/web/framework/decorators.py Log Message: ----------- py3: Fix catching malformed IDs Commit: bbf739a3dfb28a9d0a5350f4d640c1113b2e977a https://github.com/galaxyproject/galaxy/commit/bbf739a3dfb28a9d0a5350f4d640c... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/tools/data/__init__.py M lib/galaxy/webapps/galaxy/api/tool_data.py M test/api/test_tool_data.py Log Message: ----------- py3: Fix tool_data API Commit: 8f7363549987536748c4a7e88dd88a60280b9089 https://github.com/galaxyproject/galaxy/commit/8f7363549987536748c4a7e88dd88... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M test/api/test_jobs.py Log Message: ----------- py3: Fix upload jobs API tests Commit: 27a30b762d8663b0d1c6a6c0b21d44f35791884d https://github.com/galaxyproject/galaxy/commit/27a30b762d8663b0d1c6a6c0b21d4... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M test/api/test_libraries.py Log Message: ----------- py3: Fix library tests Commit: 33c0b58ae0db139aa9b0f0c619e01a40eba06c03 https://github.com/galaxyproject/galaxy/commit/33c0b58ae0db139aa9b0f0c619e01... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py Log Message: ----------- py3: Send bytestring in various datatatypes' display_data methods Commit: c2c2117e497365ab59483aad660d82bdd8c714e8 https://github.com/galaxyproject/galaxy/commit/c2c2117e497365ab59483aad660d8... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- py3: Cast map objects to lists when serializing tools to json Commit: 057938c30d57da3afce259a08d064e837e0d5ede https://github.com/galaxyproject/galaxy/commit/057938c30d57da3afce259a08d064... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/webhooks.py Log Message: ----------- py3: Fix getting first webhook Commit: 187457a461a7d28878e1ece803a843c868f7c174 https://github.com/galaxyproject/galaxy/commit/187457a461a7d28878e1ece803a84... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- py3: Don't rely on order of outputs, instead match by output name Commit: f3bc18c85a8d450f2b3bed3e28c03ed5ea65576b https://github.com/galaxyproject/galaxy/commit/f3bc18c85a8d450f2b3bed3e28c03... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M test/base/populators.py Log Message: ----------- py3: Use reponse.text instead of reponse.content for decoded text Commit: 9ea589d5e737bcca173040682513b2e913675da4 https://github.com/galaxyproject/galaxy/commit/9ea589d5e737bcca173040682513b... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M tools/filters/random_lines_two_pass.py Log Message: ----------- Make random_lines reproducible between py2 and py3 random.seed has changed in python 3, and while there's backwards compatibility using `version=1`, random.randint and random.sample have also changed. The most striaghtforward change without adding additional dependencies then was to copy those methods from the python 2.7 source code. Commit: 7fe1079a52822d99e687d9cd966ee4d5e5f828b9 https://github.com/galaxyproject/galaxy/commit/7fe1079a52822d99e687d9cd966ee... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/web/framework/webapp.py M templates/tagging_common.mako Log Message: ----------- py3: Fix the remaining mako issues Commit: 11f92221223fe191cf2c4141e6dfc3b3630affa7 https://github.com/galaxyproject/galaxy/commit/11f92221223fe191cf2c4141e6dfc... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M test/unit/tools/test_execution.py Log Message: ----------- Fix redirection unit test Commit: fab5d69d58e70ab85ce160a4b963a1d0bd4f3677 https://github.com/galaxyproject/galaxy/commit/fab5d69d58e70ab85ce160a4b963a... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- fix is_binary Commit: a2a155777dadda2fc576d078e5f9c8a488931e56 https://github.com/galaxyproject/galaxy/commit/a2a155777dadda2fc576d078e5f9c... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- py3: Fix redirection Commit: 4a9faf78c198ad92430a2e0666dcb92f0469fcb8 https://github.com/galaxyproject/galaxy/commit/4a9faf78c198ad92430a2e0666dcb... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Fix webob.compat make_file patching for py2 Commit: 418f1220c8f6b21bcf3b4ddcf9d19f29bdb2c373 https://github.com/galaxyproject/galaxy/commit/418f1220c8f6b21bcf3b4ddcf9d19... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/tools/test.py Log Message: ----------- py3: Fix DataParameter test data upload Commit: bb26a3a7ac361b2bc094285184775990de99f7ee https://github.com/galaxyproject/galaxy/commit/bb26a3a7ac361b2bc094285184775... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/jobs/runners/state_handlers/_safe_eval.py Log Message: ----------- py3: fix safe_eval Commit: d13697b66b5dfb6a38221036fa777f477f2d1dca https://github.com/galaxyproject/galaxy/commit/d13697b66b5dfb6a38221036fa777... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py Log Message: ----------- py3: Fix mulled resolver Commit: e91d892a9bb3bec5b16389ff1435cd90195cea7a https://github.com/galaxyproject/galaxy/commit/e91d892a9bb3bec5b16389ff1435c... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/util/hash_util.py Log Message: ----------- py3: fix sha1 hashing Commit: 63da35889d45459de83a8c66e4fbb7060d92e72c https://github.com/galaxyproject/galaxy/commit/63da35889d45459de83a8c66e4fbb... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M test/base/populators.py Log Message: ----------- py3: Fix exception handling in wait_on method Commit: fd5e8cdd288846a375c34ae6ca83f051cfdea45b https://github.com/galaxyproject/galaxy/commit/fd5e8cdd288846a375c34ae6ca83f... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- py3: fix test_scripts integration test Commit: 8ccd5ed137797e31ed2fac34fa68244f770c6514 https://github.com/galaxyproject/galaxy/commit/8ccd5ed137797e31ed2fac34fa682... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M test/integration/test_upload_configuration_options.py Log Message: ----------- py3: Fix upload_configuration_options integration test Commit: 049e4d0fa37c66c41961d609337649791271c883 https://github.com/galaxyproject/galaxy/commit/049e4d0fa37c66c41961d60933764... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M test/api/test_libraries.py Log Message: ----------- py3: Fix test_fetch_zip_to_folder test Commit: b7163c0597fac16a34b53d607ae7e8485869022a https://github.com/galaxyproject/galaxy/commit/b7163c0597fac16a34b53d607ae7e... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/workflow/steps.py M test/base/data/test_workflow_topoambigouity.ga M test/base/data/test_workflow_topoambigouity_auto_laidout.ga Log Message: ----------- Explicitly sort workflow step edges This seems to be necessary so that the workflow_stability test passes under python 2 and python3, but does change the result under python 2, hence the updated workflows (produced by uploading and downloading the workflow to an instance running with this commit). Commit: 389a1d6563f06fc5b8b4ae42fa1824053f3897d4 https://github.com/galaxyproject/galaxy/commit/389a1d6563f06fc5b8b4ae42fa182... Author: John Chilton <jmchilton@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/runners/state_handlers/_safe_eval.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/test.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/hash_util.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/static.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/authenticate.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/tool_data.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/workflow/steps.py M templates/tagging_common.mako M test/api/test_authenticate.py M test/api/test_dataset_collections.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_tool_data.py M test/api/test_tools.py M test/base/data/test_workflow_topoambigouity.ga M test/base/data/test_workflow_topoambigouity_auto_laidout.ga M test/base/populators.py M test/integration/test_scripts.py M test/integration/test_upload_configuration_options.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M tools/filters/random_lines_two_pass.py Log Message: ----------- Merge pull request #6561 from mvdbeek/start_py3_api_tests Fix all py3 api tests Compare: https://github.com/galaxyproject/galaxy/compare/b7dba0b82d49...389a1d6563f0 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.