Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: ae3b0cfb5585644c34224e82025778fe6978db6e
https://github.com/galaxyproject/galaxy/commit/ae3b0cfb5585644c34224e820257…
Author: pvanheus <pvh(a)sanbi.ac.za>
Date: 2019-03-04 (Mon, 04 Mar 2019)
Changed paths:
M doc/source/admin/framework_dependencies.rst
Log Message:
-----------
Note `cannot import name _remove_dead_weakref` error and solution
Having a different Python version on the Galaxy server vs the compute nodes can cause an error including the message `ImportError: cannot import name _remove_dead_weakref`. This adds text to describe the error and its resolution
Commit: 0a37bb0da0c2f49f281d3e45ca800f729db0aa39
https://github.com/galaxyproject/galaxy/commit/0a37bb0da0c2f49f281d3e45ca80…
Author: Nicola Soranzo <nicola.soranzo(a)gmail.com>
Date: 2019-03-05 (Tue, 05 Mar 2019)
Changed paths:
M doc/source/admin/framework_dependencies.rst
Log Message:
-----------
Merge pull request #7461 from pvanheus/patch-13
Note `cannot import name _remove_dead_weakref` error and solution
Compare: https://github.com/galaxyproject/galaxy/compare/381406e9ec13...0a37bb0da0c2
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: f3898c2136f494a52dc1fec01af379a735ba1842
https://github.com/galaxyproject/galaxy/commit/f3898c2136f494a52dc1fec01af3…
Author: M Bernt <m.bernt(a)ufz.de>
Date: 2019-03-04 (Mon, 04 Mar 2019)
Changed paths:
M lib/galaxy/jobs/output_checker.py
Log Message:
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- check regexp also if FATAL was detected by exit_code
- introduced functions for checking regex against stream
- check regex line by line instead of on the complete stream
(the original behavior is coded in check_output_regex which
could be removed if linewise is OK)
Commit: b458ff54e3585914d3525c4b1f4bcf5ff0dc9f7f
https://github.com/galaxyproject/galaxy/commit/b458ff54e3585914d3525c4b1f4b…
Author: M Bernt <m.bernt(a)ufz.de>
Date: 2019-03-04 (Mon, 04 Mar 2019)
Changed paths:
M lib/galaxy/jobs/output_checker.py
Log Message:
-----------
also check all regexes
Commit: 39b8f7872076508adf35a0b348e4c31a002a9b81
https://github.com/galaxyproject/galaxy/commit/39b8f7872076508adf35a0b348e4…
Author: M Bernt <m.bernt(a)ufz.de>
Date: 2019-03-04 (Mon, 04 Mar 2019)
Changed paths:
M lib/galaxy/jobs/output_checker.py
A test/functional/tools/detect_errors.xml
Log Message:
-----------
added test and changed modification of stdout/err
before stdout and stderr were modified while testing for exit codes and
regexes. this had the potential problem that later tests also checked
this output which might lead to confusions.
furthermore a marker line has been introduces which differentiates
Galaxy and original tool output
Commit: 959af578d07d1eb1372cd4b22055d57b0912a8ca
https://github.com/galaxyproject/galaxy/commit/959af578d07d1eb1372cd4b22055…
Author: M Bernt <m.bernt(a)ufz.de>
Date: 2019-03-04 (Mon, 04 Mar 2019)
Changed paths:
M lib/galaxy/jobs/output_checker.py
M test/functional/tools/detect_errors.xml
Log Message:
-----------
fixed linting and copy paste errors
Commit: b47a8631bbc4fcc9ebbd8b8a62032246effd6f5c
https://github.com/galaxyproject/galaxy/commit/b47a8631bbc4fcc9ebbd8b8a6203…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2019-03-04 (Mon, 04 Mar 2019)
Changed paths:
M lib/galaxy/jobs/output_checker.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
A lib/galaxy/model/migrate/versions/0147_job_messages.py
M lib/galaxy/tools/linters/tests.py
M lib/galaxy/tools/verify/interactor.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M templates/show_params.mako
M test/api/test_jobs.py
M test/functional/tools/samples_tool_conf.xml
M test/unit/tools/test_parsing.py
Log Message:
-----------
Track job failure reasons in a more structured way.
Commit: d6ccc595847a940fe1149c52f27d2786f825dea3
https://github.com/galaxyproject/galaxy/commit/d6ccc595847a940fe1149c52f27d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2019-03-04 (Mon, 04 Mar 2019)
Changed paths:
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/output_checker.py
M test/unit/jobs/test_job_output_checker.py
Log Message:
-----------
Move model/Tool interactions out of galaxy.jobs.output_checker.
This means output_checker can be placed into galaxy-lib without dependency problems, and we can evaluate if a tool passed without access to a job object or a Tool object as long as we have a description of the job outputs and stdio objects (already in galaxy-lib).
This is a prelude to being able to do job output checking in Pulsar without Galaxy internals.
Commit: a910ce08ca1dda188526baae9e8c4a0f631b7f1f
https://github.com/galaxyproject/galaxy/commit/a910ce08ca1dda188526baae9e8c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2019-03-04 (Mon, 04 Mar 2019)
Changed paths:
M lib/galaxy/jobs/output_checker.py
Log Message:
-----------
Simplify, clear up output_checker code a bit.
Based on suggestions from mvdbeek.
Commit: 04f2e87b38bb9a8eec077c11747bde7446d001f6
https://github.com/galaxyproject/galaxy/commit/04f2e87b38bb9a8eec077c11747b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2019-03-04 (Mon, 04 Mar 2019)
Changed paths:
M lib/galaxy/jobs/output_checker.py
Log Message:
-----------
Remove unused code spotted by mvdbeek.
Commit: 8f3bb497e7d4453104546743eccb18c3b24c1a53
https://github.com/galaxyproject/galaxy/commit/8f3bb497e7d4453104546743eccb…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2019-03-04 (Mon, 04 Mar 2019)
Changed paths:
M lib/galaxy/jobs/runners/__init__.py
Log Message:
-----------
Don't determine job failure from stderr, that makes no sense anymore.
Commit: 06f66524563f0dab134aaef950f9be16cc156394
https://github.com/galaxyproject/galaxy/commit/06f66524563f0dab134aaef950f9…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2019-03-04 (Mon, 04 Mar 2019)
Changed paths:
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/local.py
Log Message:
-----------
More consistent exit_code handling across runners.
Commit: cc7cde8ce09113690e05587e3bcd72e172956729
https://github.com/galaxyproject/galaxy/commit/cc7cde8ce09113690e05587e3bcd…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2019-03-04 (Mon, 04 Mar 2019)
Changed paths:
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/local.py
Log Message:
-----------
More consistent job finish/resubmit handling across local and async runners.
Commit: 7e5f3d83e8cfd80ecb9a301a5f72050af15bc319
https://github.com/galaxyproject/galaxy/commit/7e5f3d83e8cfd80ecb9a301a5f72…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2019-03-04 (Mon, 04 Mar 2019)
Changed paths:
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/local.py
Log Message:
-----------
De-duplicate constants and parameters for shrink_stream in jobs code.
Commit: 0fe13b7e5af60b1bf7417a1a5ff981dd21cb026f
https://github.com/galaxyproject/galaxy/commit/0fe13b7e5af60b1bf7417a1a5ff9…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2019-03-04 (Mon, 04 Mar 2019)
Changed paths:
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/migrate/versions/0147_job_messages.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/verify/interactor.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M test/functional/tools/job_environment_default.xml
A test/integration/io_injection_job_conf.xml
M test/integration/test_job_environments.py
M test/unit/jobs/test_command_factory.py
M test/unit/tools/test_history_imp_exp.py
Log Message:
-----------
Seperate tool and job script standard I/O.
This should allow Galaxy to reason about what the tool reports vs. what dependency resolution and metadata reports, allow us to enable logging during metadata collection, and allow us to reason about the tool's I/O from inside the job script during cleanup/metadata collection at the end.
Commit: 381406e9ec13c386fe6041585ebfab7664529917
https://github.com/galaxyproject/galaxy/commit/381406e9ec13c386fe6041585ebf…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2019-03-05 (Tue, 05 Mar 2019)
Changed paths:
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/output_checker.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
A lib/galaxy/model/migrate/versions/0147_job_messages.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/linters/tests.py
M lib/galaxy/tools/verify/interactor.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M templates/show_params.mako
M test/api/test_jobs.py
A test/functional/tools/detect_errors.xml
M test/functional/tools/job_environment_default.xml
M test/functional/tools/samples_tool_conf.xml
A test/integration/io_injection_job_conf.xml
M test/integration/test_job_environments.py
M test/unit/jobs/test_command_factory.py
M test/unit/jobs/test_job_output_checker.py
M test/unit/tools/test_history_imp_exp.py
M test/unit/tools/test_parsing.py
Log Message:
-----------
Merge pull request #7095 from jmchilton/structured_job_outputs
More Structured Job I/O Tracking
Compare: https://github.com/galaxyproject/galaxy/compare/503e9fd58469...381406e9ec13
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: d36d1a25e67206a161cd524405ec258290b710f8
https://github.com/galaxyproject/galaxy/commit/d36d1a25e67206a161cd524405ec…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2019-03-05 (Tue, 05 Mar 2019)
Changed paths:
M lib/galaxy/workflow/modules.py
M test/unit/workflows/test_modules.py
Log Message:
-----------
Simple filter_output
This obviously doesn't work (yet) with filters that work
on the input dataset, but this already removes a lot of
outputs that arent' going to be produced based on static
options. Since exceptions default to priduing the dataset
this isn't much harm.
Commit: 0bed6455d45fbcc57fb3c04f1354717c9c81085d
https://github.com/galaxyproject/galaxy/commit/0bed6455d45fbcc57fb3c04f1354…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2019-03-05 (Tue, 05 Mar 2019)
Changed paths:
M test/unit/tools/test_toolbox.py
Log Message:
-----------
Bump up retries
Commit: 35caf355a7976f9aa8969f8713faecc07f4ae911
https://github.com/galaxyproject/galaxy/commit/35caf355a7976f9aa8969f8713fa…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2019-03-05 (Tue, 05 Mar 2019)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
Use workflow building mode when building module
Otherwise state inputs contain history datasets.
This is a bug that might result in non-deterministic tool module
behavior.
Commit: 5c521e1ba867f353e484e28e24adc78bb61b3e11
https://github.com/galaxyproject/galaxy/commit/5c521e1ba867f353e484e28e24ad…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2019-03-05 (Tue, 05 Mar 2019)
Changed paths:
M test/api/test_workflows.py
M test/functional/tools/output_filter_with_input.xml
Log Message:
-----------
Test that switching parameters results in filtered outputs
Commit: 503e9fd584692e85275966f87dbdb4249e8a3fe8
https://github.com/galaxyproject/galaxy/commit/503e9fd584692e85275966f87dbd…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2019-03-05 (Tue, 05 Mar 2019)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/workflow/modules.py
M test/api/test_workflows.py
M test/functional/tools/output_filter_with_input.xml
M test/unit/tools/test_toolbox.py
M test/unit/workflows/test_modules.py
Log Message:
-----------
Merge pull request #7466 from mvdbeek/filter_outputs_in_wf_editor
Simple filter_output
Compare: https://github.com/galaxyproject/galaxy/compare/abf3070292fd...503e9fd58469