- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 78a8c8: Revert unnecessary changes
by GitHub 21 Aug '18

21 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 78a8c865a13b98bd3dc93a2b0dade86d2d6e43bf https://github.com/galaxyproject/galaxy/commit/78a8c865a13b98bd3dc93a2b0dad… Author: Nicola Soranzo <nicola.soranzo(a)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/5bddd24d8b8994f9f59d0f7ba541… Author: Nicola Soranzo <nicola.soranzo(a)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/4a3ed12f0af3f9b26dc9cb5b66ea… Author: Nicola Soranzo <nicola.soranzo(a)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/df8abbe3ef13c0b288becba07af4… Author: Nicola Soranzo <nicola.soranzo(a)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/5d1ced2678737e1ceebb727c3b81… Author: Nicola Soranzo <nicola.soranzo(a)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/f54246e1a1d157ba43783dc2a86f… Author: Nicola Soranzo <nicola.soranzo(a)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/72f020726593bcd6026cba5a127f… Author: Nicola Soranzo <nicola.soranzo(a)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/d265b8a88ada5d2e57efbc03740c… Author: Nicola Soranzo <nicola.soranzo(a)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/61041a7c6b09664b2fa9d8d479de… Author: Nicola Soranzo <nicola.soranzo(a)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/cd11a8c19ab672d8326cb474d783… Author: Nicola Soranzo <nicola.soranzo(a)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/670d8b1623b1ba16f2b23cc661e5… Author: Nicola Soranzo <nicola.soranzo(a)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/ff15f3679818dc8f0ea4610ed28c… Author: Nicola Soranzo <nicola.soranzo(a)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/c501fb1647b21720dfbaeedb0620… Author: Nicola Soranzo <nicola.soranzo(a)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/05999f9767b9ad906a719f2e103c… Author: Nicola Soranzo <nicola.soranzo(a)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/ff0d28c35c2c7c5371f2101e72c0… Author: Nicola Soranzo <nicola.soranzo(a)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/99517c6fdf3d07bf98dad6f88946… Author: Marius van den Beek <m.vandenbeek(a)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.

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[galaxyproject/usegalaxy-playbook] 90b047: Keep one plant tribes DM.
by GitHub 20 Aug '18

20 Aug '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 90b047b9ce7fef208e29e2d659f1124aac441660 https://github.com/galaxyproject/usegalaxy-playbook/commit/90b047b9ce7fef20… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M env/test/files/galaxy/var/shed_data_manager_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Keep one plant tribes DM. **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.

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[galaxyproject/usegalaxy-playbook] 395521: Update id_secret
by GitHub 20 Aug '18

20 Aug '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 395521c421db4aa46d6aa61b81cf034c9f55c030 https://github.com/galaxyproject/usegalaxy-playbook/commit/395521c421db4aa4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M env/main/group_vars/galaxyservers/vault.yml Log Message: ----------- Update id_secret Commit: 000bebd7fa4afffaabab1e41507cfb8fa198dc36 https://github.com/galaxyproject/usegalaxy-playbook/commit/000bebd7fa4afffa… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Remove downtime banner Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/241e79e5f057...… **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.

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[galaxyproject/galaxy] 9e07d9: Handle driver shutdown, show all test in pytest
by GitHub 20 Aug '18

20 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9e07d9cc062bf8a21bfab72c2505191e1d3c86e4 https://github.com/galaxyproject/galaxy/commit/9e07d9cc062bf8a21bfab72c2505… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: A test/functional/conftest.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py M test/functional/test_toolbox_pytest.py Log Message: ----------- Handle driver shutdown, show all test in pytest This is pretty hackish as fixtures can't be used during test discovery. To properly shut down the driver I've added a conftest.py file that will be called when quitting pytest. We might be able to handle this a little better if we wrote a full plugin, but for now this works. Also now reports all test indexes, so you can select e.g test 2 of a tool. Commit: 2b275b7df033c323cec93c34a8089a4820fce768 https://github.com/galaxyproject/galaxy/commit/2b275b7df033c323cec93c34a808… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M test/functional/test_toolbox_pytest.py Log Message: ----------- Start counting test numbers at 1 and use _test_n That allows for nicer select syntax like ```` pytest test/functional/test_toolbox_pytest.py -k '(random_lines1 or Cut1) and _test_1' ``` Commit: e07cc9a96009bafb47c27199cc231213ce2c3514 https://github.com/galaxyproject/galaxy/commit/e07cc9a96009bafb47c27199cc23… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: A test/functional/conftest.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py M test/functional/test_toolbox_pytest.py Log Message: ----------- Merge pull request #6608 from mvdbeek/more_pytest_improvements Handle driver shutdown, show all tests in pytest Compare: https://github.com/galaxyproject/galaxy/compare/3c7eeecee52d...e07cc9a96009 **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.

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[galaxyproject/galaxy] 899353: add dcd datatype
by GitHub 20 Aug '18

20 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 899353d631b1a3fa0b38730009f9dfc6e97b761f https://github.com/galaxyproject/galaxy/commit/899353d631b1a3fa0b38730009f9… Author: Chris Barnett <chris.barnett(a)uct.ac.za> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- add dcd datatype Commit: c63e4fde41c4c72a45a8d2999833804481c9c9a2 https://github.com/galaxyproject/galaxy/commit/c63e4fde41c4c72a45a8d2999833… Author: Chris Barnett <chris.barnett(a)uct.ac.za> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- register dcd datatype Commit: 98e4dab4ef48617bd8e03590d19d009c730284ab https://github.com/galaxyproject/galaxy/commit/98e4dab4ef48617bd8e03590d19d… Author: Chris Barnett <chris.barnett(a)uct.ac.za> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: A lib/galaxy/datatypes/test/test_glucose_vacuum.dcd Log Message: ----------- add dcd example file Commit: f8833cc4b34784a033e8d0910ae09eeddab5105c https://github.com/galaxyproject/galaxy/commit/f8833cc4b34784a033e8d0910ae0… Author: Chris Barnett <chris.barnett(a)uct.ac.za> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- PEP corrections Commit: d05e8e0cb10cd75310c59a903eed8f4e0cab7fa2 https://github.com/galaxyproject/galaxy/commit/d05e8e0cb10cd75310c59a903eed… Author: Chris Barnett <chris.barnett(a)uct.ac.za> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- file open fix Commit: 3fc40c16a3fc9cda2284cf9e5cca91373797a52c https://github.com/galaxyproject/galaxy/commit/3fc40c16a3fc9cda2284cf9e5cca… Author: Chris Barnett <chris.barnett(a)uct.ac.za> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- use seek. logic improved. Commit: 33794fa318e49b8eeef2e65ce59a8a5bf361db3a https://github.com/galaxyproject/galaxy/commit/33794fa318e49b8eeef2e65ce59a… Author: Chris Barnett <chris.barnett(a)uct.ac.za> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/test_charmm.vel Log Message: ----------- add vel datatype,register and example Commit: f8b797c06092695c5e5431be49d806b94e900780 https://github.com/galaxyproject/galaxy/commit/f8b797c06092695c5e5431be49d8… Author: Chris Barnett <chris.barnett(a)uct.ac.za> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- no edam format yet. soon. Commit: e9846ae9766e29bbbb8b16ff8e5b6b654333e168 https://github.com/galaxyproject/galaxy/commit/e9846ae9766e29bbbb8b16ff8e5b… Author: Chris Barnett <chris.barnett(a)uct.ac.za> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- edam data Commit: 3c7eeecee52d5babf8039fd48ab161555086f84f https://github.com/galaxyproject/galaxy/commit/3c7eeecee52d5babf8039fd48ab1… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/test_charmm.vel A lib/galaxy/datatypes/test/test_glucose_vacuum.dcd Log Message: ----------- Merge pull request #6613 from chrisbarnettster/cbb_md_dcd add dcd datatype for molecular dynamics Compare: https://github.com/galaxyproject/galaxy/compare/85f347e1c659...3c7eeecee52d **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.

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[galaxyproject/usegalaxy-playbook] 241e79: Updated plant tribes scaffold downloader.
by GitHub 20 Aug '18

20 Aug '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 241e79e5f0570da937b888956aaba8943d3b5ad4 https://github.com/galaxyproject/usegalaxy-playbook/commit/241e79e5f0570da9… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M env/test/files/galaxy/var/shed_data_manager_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Updated plant tribes scaffold downloader. **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.

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[galaxyproject/galaxy] bf206c: Reorder inputs before multiplications
by GitHub 20 Aug '18

20 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bf206c870b793edda71aaa5655baeca070e3729a https://github.com/galaxyproject/galaxy/commit/bf206c870b793edda71aaa5655ba… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M lib/galaxy/tools/parameters/meta.py M lib/galaxy/util/permutations.py Log Message: ----------- Reorder inputs before multiplications This should be a stable order. Ideally this would be configurable to the user or tool auther, but for now this is based on the order within which data paramaters appear in tool.inputs, which depends on the order in the XML/YML. If this isn't stable the order of the input combinations may change, and elements will jump in the collection structure. For instance the reverse:forward output for a pair:pair in inputA multiplied by pair:pair in input B may end up in forward:reverse if re-run. Commit: 9138651bdd92e0eb1fe2ea2b2099b5b2f04f655d https://github.com/galaxyproject/galaxy/commit/9138651bdd92e0eb1fe2ea2b2099… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M lib/galaxy/managers/jobs.py M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Serialize JobParamters with sort_keys=True This wasn't a bigger issue on python 2 for the same reason that the input ordering in the previous commit didn't matter. I hope it'll make the test_workflow_rerun_with_use_cached_job test that is marked as flakey stable as well. Commit: 2d60d9af0132c4975ae636d161097140b72e6fbc https://github.com/galaxyproject/galaxy/commit/2d60d9af0132c4975ae636d16109… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Wait for first workflow when testing cache That should make the test less flakey. While in theory we should be able to replace scheduled workflow jobs with cached jobs, this is not what we're testing here, and I assume it doesn't work for now. Commit: 7160b7f4e48e0c611758aea890771fea07a059ec https://github.com/galaxyproject/galaxy/commit/7160b7f4e48e0c611758aea89077… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M lib/galaxy/tools/parameters/meta.py Log Message: ----------- No kwargs for rsplit on python 2 Commit: 85f347e1c6597523b0e8718d7a93d4dc27cac2f9 https://github.com/galaxyproject/galaxy/commit/85f347e1c6597523b0e8718d7a93… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M lib/galaxy/managers/jobs.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/util/permutations.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #6609 from mvdbeek/fix_random_implicit_collection_order Order data parameters before unlinked multiplication Compare: https://github.com/galaxyproject/galaxy/compare/f5bd245faaaa...85f347e1c659 **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.

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[galaxyproject/galaxy] 283947: Update ucsc genome-test server URL.
by GitHub 17 Aug '18

17 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2839475967320b7d95ade125e542625c6d54c1b9 https://github.com/galaxyproject/galaxy/commit/2839475967320b7d95ade125e542… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M cron/build_chrom_db.py M cron/parse_builds_3_sites.py M tools/data_source/ucsc_tablebrowser_test.xml Log Message: ----------- Update ucsc genome-test server URL. Commit: 1cd36e3f815b6ad06da7a1aa1ee2c56d67edc36c https://github.com/galaxyproject/galaxy/commit/1cd36e3f815b6ad06da7a1aa1ee2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M tools/data_source/ucsc_tablebrowser_test.xml Log Message: ----------- Bump version; 'patch' since it should be the exact same, as much as anything over the net ever could be\? Commit: 6cbb574553a882b7573d86f25bede17e7293cc76 https://github.com/galaxyproject/galaxy/commit/6cbb574553a882b7573d86f25bed… Author: Matthew Spelchak <mrs11teen(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M doc/source/admin/special_topics/interactive_environments.rst Log Message: ----------- Fix Location of Plugin Static Content Commit: 7e445be502a64213c96cb233200aa0f53a2821f4 https://github.com/galaxyproject/galaxy/commit/7e445be502a64213c96cb233200a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M doc/source/admin/special_topics/interactive_environments.rst Log Message: ----------- Merge pull request #6602 from phac-nml/ie_documentation_fix [18.05] Fix Location of Plugin Static Content In Documentation for 18.05 Commit: 709e49f104e2cba5d180bffb0ed0fee175f5ffba https://github.com/galaxyproject/galaxy/commit/709e49f104e2cba5d180bffb0ed0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M cron/build_chrom_db.py M cron/parse_builds_3_sites.py M tools/data_source/ucsc_tablebrowser_test.xml Log Message: ----------- Merge pull request #6591 from dannon/ucsc-test-server-domain [18.05] Update UCSC genome-test server URLs Commit: f5bd245faaaa90693d8a5739f60bc863f545762f https://github.com/galaxyproject/galaxy/commit/f5bd245faaaa90693d8a5739f60b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: M cron/build_chrom_db.py M cron/parse_builds_3_sites.py M doc/source/admin/special_topics/interactive_environments.rst M tools/data_source/ucsc_tablebrowser_test.xml Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/2c6900930c24...f5bd245faaaa **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.

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[galaxyproject/galaxy] dac763: Keep unicode tags
by GitHub 17 Aug '18

17 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dac763a665703e84bd7cd29f63de60dd75fd305c https://github.com/galaxyproject/galaxy/commit/dac763a665703e84bd7cd29f63de… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Keep unicode tags Should fix ``` selenium.webdriver.remote.remote_connection DEBUG 2018-08-16 19:17:13,852 Finished Request galaxy.web.framework.decorators ERROR 2018-08-16 19:17:13,858 Uncaught exception in exposed API method: Traceback (most recent call last): File "/galaxy/lib/galaxy/web/framework/decorators.py", line 157, in decorator rval = func(self, trans, *args, **kwargs) File "/galaxy/lib/galaxy/web/framework/decorators.py", line 77, in decorator return func(self, trans, *args, **kwargs) File "/galaxy/lib/galaxy/webapps/galaxy/controllers/history.py", line 317, in list return self.stored_list_grid(trans, **kwargs) File "/galaxy/lib/galaxy/web/framework/helpers/grids.py", line 139, in __call__ query = column.filter(trans, trans.user, query, column_filter) File "/galaxy/lib/galaxy/web/framework/helpers/grids.py", line 664, in filter query = query.filter(self.get_filter(trans, user, column_filter)) File "/galaxy/lib/galaxy/web/framework/helpers/grids.py", line 703, in get_filter raw_tags = trans.app.tag_handler.parse_tags(column_filter.encode("utf-8")) File "/galaxy/lib/galaxy/managers/tags.py", line 260, in parse_tags raw_tags = reg_exp.split(tag_str) TypeError: cannot use a string pattern on a bytes-like object ``` Commit: 85f76945777b09958488672ef1a7c456d2bc5980 https://github.com/galaxyproject/galaxy/commit/85f76945777b09958488672ef1a7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/tag.py Log Message: ----------- Fix one more case of tag encoding Commit: 2c6900930c2454979fcc96e9159bdbbe44bafc3b https://github.com/galaxyproject/galaxy/commit/2c6900930c2454979fcc96e9159b… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/tag.py Log Message: ----------- Merge pull request #6610 from mvdbeek/fix_selenium_py3_tests Fix remaining selenium py3 test failures Compare: https://github.com/galaxyproject/galaxy/compare/d9f394793897...2c6900930c24 **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.

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[galaxyproject/usegalaxy-playbook] 868a32: Downtime banner
by GitHub 16 Aug '18

16 Aug '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 868a321bc326741adaafb1e8e2e08176d56078bf https://github.com/galaxyproject/usegalaxy-playbook/commit/868a321bc326741a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Downtime banner **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.

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