Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 78a8c865a13b98bd3dc93a2b0dade86d2d6e43bf https://github.com/galaxyproject/galaxy/commit/78a8c865a13b98bd3dc93a2b0dade... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/text.py M lib/galaxy/tools/evaluation.py M lib/galaxy/web/framework/webapp.py Log Message: ----------- Revert unnecessary changes Commit: 5bddd24d8b8994f9f59d0f7ba541321c8146a166 https://github.com/galaxyproject/galaxy/commit/5bddd24d8b8994f9f59d0f7ba5413... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M test/api/test_jobs.py Log Message: ----------- Remove unreachable return statement Commit: 4a3ed12f0af3f9b26dc9cb5b66eabb26f9dc542e https://github.com/galaxyproject/galaxy/commit/4a3ed12f0af3f9b26dc9cb5b66eab... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-08-21 (Tue, 21 Aug 2018) Changed paths: M .gitignore Log Message: ----------- Ignore .pytest_cache/ , assets/ and run_integration_tests.html Commit: df8abbe3ef13c0b288becba07af4a05b8f6dc668 https://github.com/galaxyproject/galaxy/commit/df8abbe3ef13c0b288becba07af4a... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-08-21 (Tue, 21 Aug 2018) Changed paths: M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/web/framework/middleware/batch.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/util/encoding_util.py M scripts/secret_decoder_ring.py M test/base/populators.py M test/base/rules_test_data.py M test/integration/test_scripts.py Log Message: ----------- Prefer `unicodify()` for binary-to-text conversion which supports non-utf-8 encodings. Commit: 5d1ced2678737e1ceebb727c3b81d4546ee6588b https://github.com/galaxyproject/galaxy/commit/5d1ced2678737e1ceebb727c3b81d... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-08-21 (Tue, 21 Aug 2018) Changed paths: M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/util/checkers.py Log Message: ----------- Do not open text file in binary mode Commit: f54246e1a1d157ba43783dc2a86f40aeb5c7b7f2 https://github.com/galaxyproject/galaxy/commit/f54246e1a1d157ba43783dc2a86f4... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-08-21 (Tue, 21 Aug 2018) Changed paths: M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml M lib/galaxy/web/framework/middleware/batch.py M test/api/test_authenticate.py Log Message: ----------- Use `encode()` method instead of `bytearray()` to encode a Unicode string to a binary one. Commit: 72f020726593bcd6026cba5a127ff615df49968f https://github.com/galaxyproject/galaxy/commit/72f020726593bcd6026cba5a127ff... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-08-21 (Tue, 21 Aug 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Remove unused `binary_chars` parameter of `smart_str()` Commit: d265b8a88ada5d2e57efbc03740c697ab5c7464f https://github.com/galaxyproject/galaxy/commit/d265b8a88ada5d2e57efbc03740c6... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-08-21 (Tue, 21 Aug 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Raise an exception if `unicodify()` fails the conversion Commit: 61041a7c6b09664b2fa9d8d479de4251647cec87 https://github.com/galaxyproject/galaxy/commit/61041a7c6b09664b2fa9d8d479de4... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-08-21 (Tue, 21 Aug 2018) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Raise `AttributeError` exception in `DatasetCollectionWrapper.__getattr__()` Commit: cd11a8c19ab672d8326cb474d7833cf532ae82cc https://github.com/galaxyproject/galaxy/commit/cd11a8c19ab672d8326cb474d7833... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-08-21 (Tue, 21 Aug 2018) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Use `NamedTemporaryFile` opened in text mode Commit: 670d8b1623b1ba16f2b23cc661e581600556ae61 https://github.com/galaxyproject/galaxy/commit/670d8b1623b1ba16f2b23cc661e58... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-08-21 (Tue, 21 Aug 2018) Changed paths: R test/functional/twilltestcase.py M test/shed_functional/base/twilltestcase.py Log Message: ----------- Merge TwillTestCase in ShedTwillTestCase Commit: ff15f3679818dc8f0ea4610ed28cc5957ac68901 https://github.com/galaxyproject/galaxy/commit/ff15f3679818dc8f0ea4610ed28cc... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-08-21 (Tue, 21 Aug 2018) Changed paths: M .ci/jenkins/api-py3/run_tests.sh M .ci/jenkins/framework-py3/run_tests.sh M .ci/jenkins/integration-py3/run_tests.sh M run_tests.sh Log Message: ----------- Run Py2 API and integration tests with pytest Remove `-api_py3`, `--framework_py3` and `--integration_py3` options of `run_tests.sh`. To run the tests under Python3 it is enough to prepend `GALAXY_VIRTUAL_ENV=.venv3` (or add `--python3` when using `--dockerize`). Commit: c501fb1647b21720dfbaeedb062084813095284e https://github.com/galaxyproject/galaxy/commit/c501fb1647b21720dfbaeedb06208... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-08-21 (Tue, 21 Aug 2018) Changed paths: M lib/galaxy/util/bunch.py M lib/galaxy/util/expressions.py M lib/galaxy/util/none_like.py Log Message: ----------- Alias `__nonzero__` to `__bool__` Commit: 05999f9767b9ad906a719f2e103c96e64e1b41a7 https://github.com/galaxyproject/galaxy/commit/05999f9767b9ad906a719f2e103c9... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-08-21 (Tue, 21 Aug 2018) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Unicodify all farm elements Commit: ff0d28c35c2c7c5371f2101e72c00259ebd4950b https://github.com/galaxyproject/galaxy/commit/ff0d28c35c2c7c5371f2101e72c00... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-08-21 (Tue, 21 Aug 2018) Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/util/template.py M test/functional/tools/unicode_stream.xml Log Message: ----------- Fix unicode_stream framework tests on Docker This fixes the following traceback: ``` ( unicode_stream ) > Test-1 ... galaxy.tools DEBUG 2018-08-21 09:40:59,052 Validated and populated state for tool request (0.098 ms) galaxy.tools.actions INFO 2018-08-21 09:40:59,076 Handled output named out_file1 for tool unicode_stream (1.337 ms) galaxy.tools.actions INFO 2018-08-21 09:40:59,080 Added output datasets to history (4.399 ms) galaxy.tools.actions INFO 2018-08-21 09:40:59,084 Verified access to datasets for Job[unflushed,tool_id=unicode_stream] (0.058 ms) galaxy.tools.actions INFO 2018-08-21 09:40:59,086 Setup for job Job[unflushed,tool_id=unicode_stream] complete, ready to flush (5.220 ms) galaxy.tools.actions INFO 2018-08-21 09:40:59,127 Flushed transaction for job Job[id=354,tool_id=unicode_stream] (40.627 ms) galaxy.tools.execute DEBUG 2018-08-21 09:40:59,127 Tool [unicode_stream] created job [354] (56.506 ms) galaxy.tools.execute DEBUG 2018-08-21 09:40:59,132 Executed 1 job(s) for tool unicode_stream request: (79.434 ms) galaxy.jobs.mapper DEBUG 2018-08-21 09:40:59,556 (354) Mapped job to destination id: local galaxy.jobs.handler DEBUG 2018-08-21 09:40:59,561 (354) Dispatching to local runner galaxy.jobs DEBUG 2018-08-21 09:40:59,571 (354) Working directory for job is: /tmp/tmp3drfmr6x/tmp_ywd33ar/tmpbzo4a1d9/database/job_working_directory_azry9a1y/000/354 galaxy.jobs DEBUG 2018-08-21 09:40:59,574 (354) Persisting job destination (destination id: local) galaxy.jobs.runners DEBUG 2018-08-21 09:40:59,589 Job [354] queued (27.361 ms) galaxy.jobs.handler INFO 2018-08-21 09:40:59,604 (354) Job dispatched galaxy.jobs.runners ERROR 2018-08-21 09:40:59,715 (354) Failure preparing job Traceback (most recent call last): File "/galaxy/lib/galaxy/jobs/runners/__init__.py", line 187, in prepare_job job_wrapper.prepare() File "/galaxy/lib/galaxy/jobs/__init__.py", line 874, in prepare self.command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build() File "/galaxy/lib/galaxy/tools/evaluation.py", line 435, in build raise e File "/galaxy/lib/galaxy/tools/evaluation.py", line 431, in build self.__build_config_files() File "/galaxy/lib/galaxy/tools/evaluation.py", line 504, in __build_config_files self.__write_workdir_file(config_filename, config_text, param_dict, is_template=is_template) File "/galaxy/lib/galaxy/tools/evaluation.py", line 578, in __write_workdir_file f.write(value) UnicodeEncodeError: 'ascii' codec can't encode characters in position 0-5: ordinal not in range(128) galaxy.tools.error_reports DEBUG 2018-08-21 09:40:59,869 Bug report plugin <galaxy.tools.error_reports.plugins.sentry.SentryPlugin object at 0x7f92efb81668> generated response None FAIL ``` which is due to the fact that the default encoding in the Docker image is `ANSI_X3.4-1968`. Also update `unicode_stream` test tool to IUC best practices. Commit: 99517c6fdf3d07bf98dad6f88946bca4fb82fea1 https://github.com/galaxyproject/galaxy/commit/99517c6fdf3d07bf98dad6f88946b... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2018-08-21 (Tue, 21 Aug 2018) Changed paths: M .ci/jenkins/api-py3/run_tests.sh M .ci/jenkins/framework-py3/run_tests.sh M .ci/jenkins/integration-py3/run_tests.sh M .gitignore M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/text.py M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/evaluation.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/wrappers.py M lib/galaxy/util/__init__.py M lib/galaxy/util/bunch.py M lib/galaxy/util/checkers.py M lib/galaxy/util/expressions.py M lib/galaxy/util/none_like.py M lib/galaxy/util/template.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/stack/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/util/encoding_util.py M run_tests.sh M scripts/secret_decoder_ring.py M test/api/test_authenticate.py M test/api/test_jobs.py M test/base/populators.py M test/base/rules_test_data.py M test/functional/tools/unicode_stream.xml R test/functional/twilltestcase.py M test/integration/test_scripts.py M test/shed_functional/base/twilltestcase.py Log Message: ----------- Merge pull request #6616 from nsoranzo/followup_on_6561 Py3 testing cleanups Compare: https://github.com/galaxyproject/galaxy/compare/e07cc9a96009...99517c6fdf3d **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.