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.
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.
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.
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.
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.