August 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 84597a: Lists-as-tuples collection operations.
by GitHub 26 Aug '18

26 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 84597a12356aaa5b5d59ba95c30691739fed2300 https://github.com/galaxyproject/galaxy/commit/84597a12356aaa5b5d59ba95c306… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/build_list.xml A lib/galaxy/tools/extract_dataset.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools/test_parsing.py Log Message: ----------- Lists-as-tuples collection operations. Commit: a3fc0b9f324f3aa2a4824b260f3057a36471857a https://github.com/galaxyproject/galaxy/commit/a3fc0b9f324f3aa2a4824b260f30… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/build_list.xml A lib/galaxy/tools/extract_dataset.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools/test_parsing.py Log Message: ----------- Merge pull request #6312 from jmchilton/tuple_operations Lists-as-tuples collection operations Compare: https://github.com/galaxyproject/galaxy/compare/2560919bd04d...a3fc0b9f324f **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] 626195: Integration test for job recovery (before and afte...
by GitHub 25 Aug '18

25 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 626195335ee70dbc2d0568603e0627744d07d529 https://github.com/galaxyproject/galaxy/commit/626195335ee70dbc2d0568603e06… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-21 (Tue, 21 Aug 2018) Changed paths: M test/base/driver_util.py M test/base/integration_util.py A test/integration/delay_job_conf.xml A test/integration/delay_rules/__init__.py A test/integration/delay_rules/rules.py A test/integration/test_job_recovery.py M test/integration/test_job_resubmission.py Log Message: ----------- Integration test for job recovery (before and after handler has picked it up). Commit: ded2311799a772914ddb9c732d59ba2f4de572b4 https://github.com/galaxyproject/galaxy/commit/ded2311799a772914ddb9c732d59… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Handle job_wrapper.working_directory correctly during job recovery. Commit: 2560919bd04d6f27e14fcf9f580aea66244afa30 https://github.com/galaxyproject/galaxy/commit/2560919bd04d6f27e14fcf9f580a… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M lib/galaxy/jobs/__init__.py M test/base/driver_util.py M test/base/integration_util.py A test/integration/delay_job_conf.xml A test/integration/delay_rules/__init__.py A test/integration/delay_rules/rules.py A test/integration/test_job_recovery.py M test/integration/test_job_resubmission.py Log Message: ----------- Merge pull request #6620 from jmchilton/job_recovery_test Integration test for job recovery. Compare: https://github.com/galaxyproject/galaxy/compare/107c89a0a994...2560919bd04d **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] ead33c: Installed PlantTribes tools.
by GitHub 24 Aug '18

24 Aug '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ead33c95c90d7b1ae0490616fac0ac2c7be81aa1 https://github.com/galaxyproject/usegalaxy-playbook/commit/ead33c95c90d7b1a… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Installed PlantTribes tools. **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] 2d4b71: Test case to clarify workflow API a bit in simple ...
by GitHub 24 Aug '18

24 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2d4b717aaff3fc8a76852af8a16744f1085fa8cc https://github.com/galaxyproject/galaxy/commit/2d4b717aaff3fc8a76852af8a167… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-22 (Wed, 22 Aug 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test case to clarify workflow API a bit in simple cases. Commit: c593bd1772dc6d8780153115641d556bea347bc9 https://github.com/galaxyproject/galaxy/commit/c593bd1772dc6d8780153115641d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-22 (Wed, 22 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Allow uniform access to job state for WorkflowInvocationSteps. Use the concept of job_source_type and job_source_id used by IDs to summarize the state and list out individual jobs in the response as a shortcut. This information used to be readily accessible before 18.01. Commit: 35ebdc5b1029bbe782c2852b5f6b094d97dbd7ea https://github.com/galaxyproject/galaxy/commit/35ebdc5b1029bbe782c2852b5f6b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-22 (Wed, 22 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py Log Message: ----------- Add a legacy_job_state mode to restore 17.09 workflow invocation behavior. Commit: 3879a019490a05f9e26e3651e6de52d0586d5963 https://github.com/galaxyproject/galaxy/commit/3879a019490a05f9e26e3651e6de… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M test/api/test_workflows.py Log Message: ----------- Add API endpoint to index all invocations for a user or history. Refactor toward managers to allow unified serialization of invocations and such. Add test case. Commit: 107c89a0a994a50fd37589fbd2b4d104064c7336 https://github.com/galaxyproject/galaxy/commit/107c89a0a994a50fd37589fbd2b4… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #6580 from jmchilton/wf_invocation_update Add API endpoint to fetch a history's workflow invocations. Compare: https://github.com/galaxyproject/galaxy/compare/dfdf3dd5eac4...107c89a0a994 **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] ac29ab: Fix metadata elements reset when creating Metadata...
by GitHub 24 Aug '18

24 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ac29abb6266fb9b83c985b27804db607c503ef51 https://github.com/galaxyproject/galaxy/commit/ac29abb6266fb9b83c985b27804d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-23 (Thu, 23 Aug 2018) Changed paths: M lib/galaxy/model/metadata.py Log Message: ----------- Fix metadata elements reset when creating Metadata files This is a fallout out from 9780d069c8646fb4f02de848d62159680d95ae79 Commit: dfdf3dd5eac4f6ae182ddf3d50490dc73a4dd614 https://github.com/galaxyproject/galaxy/commit/dfdf3dd5eac4f6ae182ddf3d5049… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M lib/galaxy/model/metadata.py Log Message: ----------- Merge pull request #6631 from mvdbeek/fix_metadata_element_rest Fix metadata elements reset when creating Metadata files Compare: https://github.com/galaxyproject/galaxy/compare/6220a557f766...dfdf3dd5eac4 **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] a2d99e: Update all dependencies
by GitHub 23 Aug '18

23 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a2d99e30c727e7050c1fd6218603b7b2941c8c4d https://github.com/galaxyproject/galaxy/commit/a2d99e30c727e7050c1fd6218603… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-08-23 (Thu, 23 Aug 2018) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/Pipfile A lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt R lib/galaxy/dependencies/pipfiles/develop/Pipfile R lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh Log Message: ----------- Update all dependencies Also merge dev dependencies in default Pipfile. Commit: ea42956c6c3a02435a9a0f6f43ae653cb9d9bd00 https://github.com/galaxyproject/galaxy/commit/ea42956c6c3a02435a9a0f6f43ae… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-08-23 (Thu, 23 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/roles.py Log Message: ----------- Catch all exception types when decoding an id Under Python 3 `codecs.decode()` raises a `binascii.Error` exception instead of a `TypeError`. Fix the following traceback produced by the `test/api/test_roles.py::RolesApiTestCase::test_show_error_codes` API test under Python 3: ``` galaxy.web.framework.decorators ERROR 2018-08-22 22:17:47,960 Uncaught exception in exposed API method: Traceback (most recent call last): File "/galaxy_venv3/lib/python3.5/encodings/hex_codec.py", line 19, in hex_decode return (binascii.a2b_hex(input), len(input)) binascii.Error: Odd-length string The above exception was the direct cause of the following exception: 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/webapps/galaxy/api/roles.py", line 39, in show decoded_role_id = trans.security.decode_id(role_id) File "/galaxy/lib/galaxy/web/security/__init__.py", line 84, in decode_id return int(unicodify(id_cipher.decrypt(codecs.decode(obj_id, 'hex'))).lstrip("!")) binascii.Error: decoding with 'hex' codec failed (Error: Odd-length string) ``` See https://jenkins.galaxyproject.org/job/docker-api-py3/140/testReport/junit/t… Commit: 6220a557f7661a3f658450530bf485914b657f5e https://github.com/galaxyproject/galaxy/commit/6220a557f7661a3f658450530bf4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-08-23 (Thu, 23 Aug 2018) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/Pipfile A lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt R lib/galaxy/dependencies/pipfiles/develop/Pipfile R lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh M lib/galaxy/webapps/galaxy/api/roles.py Log Message: ----------- Merge pull request #6628 from nsoranzo/update_deps Update all dependencies Compare: https://github.com/galaxyproject/galaxy/compare/6ad304976ecb...6220a557f766 **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] f6a55e: Tweak conda_* setting in test driver
by GitHub 23 Aug '18

23 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f6a55ee2eef2fe85cc8d7ed198c1610be5607165 https://github.com/galaxyproject/galaxy/commit/f6a55ee2eef2fe85cc8d7ed198c1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-23 (Thu, 23 Aug 2018) Changed paths: M test/base/driver_util.py Log Message: ----------- Tweak conda_* setting in test driver Thanks @nsoranzo! Commit: 6ad304976ecb41d428e55a7a33614dd5e76edb2d https://github.com/galaxyproject/galaxy/commit/6ad304976ecb41d428e55a7a3361… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-23 (Thu, 23 Aug 2018) Changed paths: M test/base/driver_util.py Log Message: ----------- Merge pull request #6633 from mvdbeek/testing_framework_followup Tweak conda_* setting in test driver Compare: https://github.com/galaxyproject/galaxy/compare/43dbfdc7b129...6ad304976ecb **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] e824fb: Sort local test data if output is sort="true"
by GitHub 23 Aug '18

23 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e824fbeec16c68b144a3f1dcddcdae2609619ac7 https://github.com/galaxyproject/galaxy/commit/e824fbeec16c68b144a3f1dcddcd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-23 (Thu, 23 Aug 2018) Changed paths: M lib/galaxy/tools/verify/__init__.py Log Message: ----------- Sort local test data if output is sort="true" This means if you run planemo test --update_test_data, your test will actually work, instead of needing to sort it manually. The other benefit is that you can see the expected test data without sorting, e.g sorted HTML files are most likely not valid after sorting. Commit: 23cfb4600115ad9d6c2fee239b73aa7dc72ea92b https://github.com/galaxyproject/galaxy/commit/23cfb4600115ad9d6c2fee239b73… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-23 (Thu, 23 Aug 2018) Changed paths: M test/base/driver_util.py M test/integration/uses_shed.py Log Message: ----------- Allow setting CONDA_PREFIX using GALAXY_TEST_CONDA_PREFIX in testing Commit: 0d85a6c5c089934df6cfc8c0d5ae9af31678aa81 https://github.com/galaxyproject/galaxy/commit/0d85a6c5c089934df6cfc8c0d5ae… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-23 (Thu, 23 Aug 2018) Changed paths: M lib/galaxy/tools/verify/test_data.py Log Message: ----------- Use first resolved test data file Commit: 000026a46a620607defde16fa518cace953b1ca9 https://github.com/galaxyproject/galaxy/commit/000026a46a620607defde16fa518… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-23 (Thu, 23 Aug 2018) Changed paths: M lib/galaxy/jobs/output_checker.py Log Message: ----------- Report stderr whenever a job fails, and report more The 250 character level is usually not enough to figure out what's going on, and I think if we want to see the stderr if a job fails because of stderr problems, we probably also want to see a peek of the stderr if a job fails because of the exit code. Commit: 43dbfdc7b1290f493584901ae00dd08ea1b0396a https://github.com/galaxyproject/galaxy/commit/43dbfdc7b1290f493584901ae00d… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-23 (Thu, 23 Aug 2018) Changed paths: M lib/galaxy/jobs/output_checker.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/tools/verify/test_data.py M test/base/driver_util.py M test/integration/uses_shed.py Log Message: ----------- Merge pull request #6632 from mvdbeek/testing_framework_improvements Testing framework improvements Compare: https://github.com/galaxyproject/galaxy/compare/5c889cd5e18e...43dbfdc7b129 **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] 7360a9: Remove check_python_dependencies job from Travis
by GitHub 23 Aug '18

23 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7360a90695db121008acc7df51c9bcab7824a4c2 https://github.com/galaxyproject/galaxy/commit/7360a90695db121008acc7df51c9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-08-22 (Wed, 22 Aug 2018) Changed paths: M .travis.yml Log Message: ----------- Remove check_python_dependencies job from Travis No need to run it on every pull request and merge. It can be run locally via: ``` $ tox -e check_python_dependencies ``` Commit: 5c889cd5e18e60818a922816884f56cb35262a2e https://github.com/galaxyproject/galaxy/commit/5c889cd5e18e60818a922816884f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-23 (Thu, 23 Aug 2018) Changed paths: M .travis.yml Log Message: ----------- Merge pull request #6630 from nsoranzo/remove_check_python_dependencies_from_travis Remove check_python_dependencies job from Travis Compare: https://github.com/galaxyproject/galaxy/compare/636e8c66785c...5c889cd5e18e **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] 5f4dd9: Update some run_tests.sh docs for recent changes.
by GitHub 23 Aug '18

23 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5f4dd9be92e3d9446d25b34fd83e7e8cc61e8c67 https://github.com/galaxyproject/galaxy/commit/5f4dd9be92e3d9446d25b34fd83e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-22 (Wed, 22 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Update some run_tests.sh docs for recent changes. Commit: 636e8c66785cf4757b502d7fab2e80607612d324 https://github.com/galaxyproject/galaxy/commit/636e8c66785cf4757b502d7fab2e… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-08-23 (Thu, 23 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #6629 from jmchilton/run_test_update Update some run_tests.sh docs for recent changes. Compare: https://github.com/galaxyproject/galaxy/compare/89f237216d7d...636e8c66785c **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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