March 2019 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] b089cf: Test data for microarrays data types, Gal and Gpr
by Marius van den Beek 07 Mar '19

07 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b089cfeab52b31bbdff83fd4facf079208fed8f6 https://github.com/galaxyproject/galaxy/commit/b089cfeab52b31bbdff83fd4facf… Author: bensellak <bensellak(a)ensat.ac.ma> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: A lib/galaxy/datatypes/test/test.gal A lib/galaxy/datatypes/test/test.gpr Log Message: ----------- Test data for microarrays data types, Gal and Gpr Commit: 3722b37a4f71e1a84d416b6a785eb38774a76e88 https://github.com/galaxyproject/galaxy/commit/3722b37a4f71e1a84d416b6a785e… Author: bensellak <bensellak(a)ensat.ac.ma> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: A lib/galaxy/datatypes/microarrays.py Log Message: ----------- Added Gpr and Gal classes defintion. Commit: e080098656c5d45189a8f2f2a4f772dc7a23b220 https://github.com/galaxyproject/galaxy/commit/e080098656c5d45189a8f2f2a4f7… Author: bensellak <bensellak(a)ensat.ac.ma> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Added data types Gpr and Gal Gpr and Gal extensions and sniffers Commit: 739be4fdd05df2e19134095cfbdc5fda80ba7494 https://github.com/galaxyproject/galaxy/commit/739be4fdd05df2e19134095cfbdc… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M lib/galaxy/datatypes/microarrays.py Log Message: ----------- Update lib/galaxy/datatypes/microarrays.py Co-Authored-By: bensellak <bensellak(a)ensat.ac.ma> Commit: 2e03231077321103b4d45495c96a6e98a5507039 https://github.com/galaxyproject/galaxy/commit/2e03231077321103b4d45495c96a… Author: bensellak <bensellak(a)ensat.ac.ma> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M lib/galaxy/datatypes/microarrays.py Log Message: ----------- Update microarrays.py Commit: c6d1e5f328f3ca2589dc53869858208a302fe7e9 https://github.com/galaxyproject/galaxy/commit/c6d1e5f328f3ca2589dc53869858… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M lib/galaxy/datatypes/microarrays.py Log Message: ----------- Fix ``get_file_peek`` import Commit: 55edbde1393e7c0caf45d3edd6c4cc202b97af9d https://github.com/galaxyproject/galaxy/commit/55edbde1393e7c0caf45d3edd6c4… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M lib/galaxy/datatypes/microarrays.py Log Message: ----------- Remove ``get_n_first_lines`` function Commit: b3ffbc84e376c1abcad32254310323b131e0e5c9 https://github.com/galaxyproject/galaxy/commit/b3ffbc84e376c1abcad322543103… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M lib/galaxy/datatypes/microarrays.py M lib/galaxy/datatypes/molecules.py Log Message: ----------- Reuse ``count_special_lines`` from ``galaxy.datatypes.util.generic_util`` Commit: eb50086040a358acddeceab14998f11707544d99 https://github.com/galaxyproject/galaxy/commit/eb50086040a358acddeceab14998… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Fix typo Commit: 546e728620b7aa45e7248f98255cf4ee6898a850 https://github.com/galaxyproject/galaxy/commit/546e728620b7aa45e7248f98255c… Author: bensellak <bensellak(a)ensat.ac.ma> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M lib/galaxy/datatypes/microarrays.py Log Message: ----------- Trying to solve the peek issue Commit: aa5a31d7c60cf04b4eee737728cd6dca4f7469c0 https://github.com/galaxyproject/galaxy/commit/aa5a31d7c60cf04b4eee737728cd… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M lib/galaxy/datatypes/test/test.gal Log Message: ----------- dos2unix test.gal Commit: bacd3eeccf974d4f70b5b22db4d17eb7d4418789 https://github.com/galaxyproject/galaxy/commit/bacd3eeccf974d4f70b5b22db4d1… Author: bensellak <bensellak(a)ensat.ac.ma> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M lib/galaxy/datatypes/test/test.gpr Log Message: ----------- dos2unix test.gpr Commit: f5ee004ea57e21e7e292a5a42b73374aebd39afd https://github.com/galaxyproject/galaxy/commit/f5ee004ea57e21e7e292a5a42b73… Author: bensellak <bensellak(a)ensat.ac.ma> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M lib/galaxy/datatypes/test/test.gpr Log Message: ----------- iconv -f ISO-8859-1 -t UTF-8 test.gpr Commit: d3a7f383d9c32646419f378d699207521a6bc348 https://github.com/galaxyproject/galaxy/commit/d3a7f383d9c32646419f378d6992… Author: bensellak <bensellak(a)ensat.ac.ma> Date: 2019-03-06 (Wed, 06 Mar 2019) Changed paths: M lib/galaxy/datatypes/microarrays.py Log Message: ----------- Modified classes definition, metadata and sniffing Commit: f47048bb9cb4af458a00f66389292f552a243aaf https://github.com/galaxyproject/galaxy/commit/f47048bb9cb4af458a00f6638929… Author: bensellak <bensellak(a)ensat.ac.ma> Date: 2019-03-06 (Wed, 06 Mar 2019) Changed paths: M lib/galaxy/datatypes/microarrays.py Log Message: ----------- Update microarrays.py Commit: 7f25bb7874b8a5a3c83e99147189600c15e781db https://github.com/galaxyproject/galaxy/commit/7f25bb7874b8a5a3c83e99147189… Author: bensellak <bensellak(a)ensat.ac.ma> Date: 2019-03-06 (Wed, 06 Mar 2019) Changed paths: M lib/galaxy/datatypes/microarrays.py Log Message: ----------- Add files via upload Commit: cfb854f6c7dc30297a509c5e39fd1387834a0f88 https://github.com/galaxyproject/galaxy/commit/cfb854f6c7dc30297a509c5e39fd… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-06 (Wed, 06 Mar 2019) Changed paths: M lib/galaxy/datatypes/microarrays.py Log Message: ----------- Use ``sniff_prefix()`` Commit: d140178dc67fd937e2006643f2a7309454ce0b7b https://github.com/galaxyproject/galaxy/commit/d140178dc67fd937e2006643f2a7… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-06 (Wed, 06 Mar 2019) Changed paths: M lib/galaxy/datatypes/microarrays.py Log Message: ----------- Use ``enumerate()`` Commit: 9621900512b4178f116d3f0b7ed06f6504b1980d https://github.com/galaxyproject/galaxy/commit/9621900512b4178f116d3f0b7ed0… Author: bensellak <bensellak(a)ensat.ac.ma> Date: 2019-03-06 (Wed, 06 Mar 2019) Changed paths: M lib/galaxy/datatypes/microarrays.py Log Message: ----------- Update microarrays.py Commit: 5f738d95038ccb47ec533b033ba333069b28a6bb https://github.com/galaxyproject/galaxy/commit/5f738d95038ccb47ec533b033ba3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-07 (Thu, 07 Mar 2019) Changed paths: M lib/galaxy/datatypes/microarrays.py Log Message: ----------- Forgot to remove increment to count Introduced in commit d140178dc67fd937e2006643f2a7309454ce0b7b Commit: cf2f192d1b1a5d9b5883c65a433776d93934635d https://github.com/galaxyproject/galaxy/commit/cf2f192d1b1a5d9b5883c65a4337… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-07 (Thu, 07 Mar 2019) Changed paths: M lib/galaxy/datatypes/microarrays.py Log Message: ----------- No need to iterate Commit: a10813a4f8c8c69c84b4d58bd0fb57d124394c97 https://github.com/galaxyproject/galaxy/commit/a10813a4f8c8c69c84b4d58bd0fb… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-03-07 (Thu, 07 Mar 2019) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/microarrays.py M lib/galaxy/datatypes/molecules.py A lib/galaxy/datatypes/test/test.gal A lib/galaxy/datatypes/test/test.gpr Log Message: ----------- Merge pull request #7457 from bensellak/dev Adding microarrays data types Gpr and Gal Compare: https://github.com/galaxyproject/galaxy/compare/3649c01a0c7f...a10813a4f8c8

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[galaxyproject/galaxy] 9d0cf4: added option to pass in individual globs to unit t...
by Dannon 07 Mar '19

07 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9d0cf40fe8989364c47ad75ef8c5631d2bc0887f https://github.com/galaxyproject/galaxy/commit/9d0cf40fe8989364c47ad75ef8c5… Author: Mason <nerdinacan(a)gmail.com> Date: 2019-03-06 (Wed, 06 Mar 2019) Changed paths: M client/karma/karma.config.mocha.js Log Message: ----------- added option to pass in individual globs to unit test watcher Commit: 8a0b1343e55f3be3b6b17315b9ee5a8af21e7fd6 https://github.com/galaxyproject/galaxy/commit/8a0b1343e55f3be3b6b17315b9ee… Author: Mason <nerdinacan(a)gmail.com> Date: 2019-03-06 (Wed, 06 Mar 2019) Changed paths: M client/karma/karma.config.mocha.js Log Message: ----------- Reconfigured args to jive with galaxy arg style Commit: 3649c01a0c7f8ebbdedbb052252157b66a419920 https://github.com/galaxyproject/galaxy/commit/3649c01a0c7f8ebbdedbb0522521… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-03-07 (Thu, 07 Mar 2019) Changed paths: M client/karma/karma.config.mocha.js Log Message: ----------- Merge pull request #7477 from Nerdinacan/watch_individual_karma_tests added option to pass in individual globs to unit test watcher Compare: https://github.com/galaxyproject/galaxy/compare/8bc23e03e020...3649c01a0c7f

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[galaxyproject/galaxy] 53286c: Refactor output discovery toward cohesiveness in j...
by Marius van den Beek 06 Mar '19

06 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 53286c51dcd0aff38ade2f33d1aa8252953ddfb5 https://github.com/galaxyproject/galaxy/commit/53286c51dcd0aff38ade2f33d1aa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Refactor output discovery toward cohesiveness in job wrapper. Commit: 0967412e3f66b5d89307a7e98849d4b3445f40d9 https://github.com/galaxyproject/galaxy/commit/0967412e3f66b5d89307a7e98849… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M test/unit/tools/test_collect_primary_datasets.py Log Message: ----------- Refactor output discovery toward cohesiveness in Tool class. Commit: df0e58ba11154cad2629ed252d84a151b6be0995 https://github.com/galaxyproject/galaxy/commit/df0e58ba11154cad2629ed252d84… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Relocate job param code for clarity. Commit: 2841a3dc260753ede5ed6aeae3971f3fa6b45b77 https://github.com/galaxyproject/galaxy/commit/2841a3dc260753ede5ed6aeae397… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Refactor output_collect to use app less. Commit: 3077895b22cfcedfce272c07ef8a8db3794fa26c https://github.com/galaxyproject/galaxy/commit/3077895b22cfcedfce272c07ef8a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Relocate dynamic output metadata source code for clarity. Commit: 8bc23e03e020a4199e9fa1c405b5f2fd50c39f09 https://github.com/galaxyproject/galaxy/commit/8bc23e03e020a4199e9fa1c405b5… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-03-06 (Wed, 06 Mar 2019) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/output_collect.py M test/unit/tools/test_collect_primary_datasets.py Log Message: ----------- Merge pull request #7471 from jmchilton/model_free_job_refactor_0 Collected Refactoring of Job Output Handling Code Compare: https://github.com/galaxyproject/galaxy/compare/492ee286969e...8bc23e03e020

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[galaxyproject/galaxy] 557407: correct virtualenv download with no wget/curl
by Dannon 06 Mar '19

06 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 557407c384d065a6c37e8f4c8466d6a53d9fbacd https://github.com/galaxyproject/galaxy/commit/557407c384d065a6c37e8f4c8466… Author: Hervé Ménager <herve.menager(a)gmail.com> Date: 2019-03-06 (Wed, 06 Mar 2019) Changed paths: M scripts/common_startup.sh Log Message: ----------- correct virtualenv download with no wget/curl the embedded python code needs a small correction to work in the no curl/wget available case. Commit: 492ee286969e7fa4d716945a8ffc06181b310e5f https://github.com/galaxyproject/galaxy/commit/492ee286969e7fa4d716945a8ffc… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-03-06 (Wed, 06 Mar 2019) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #7476 from hmenager/patch-1 correct virtualenv download with no wget/curl Compare: https://github.com/galaxyproject/galaxy/compare/67aac7b2c598...492ee286969e

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[galaxyproject/galaxy] 9d4f85: Fix workflow_building_mode typo
by Martin Cech 05 Mar '19

05 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9d4f857378a782d0782ef7cd7584f33d1a38686b https://github.com/galaxyproject/galaxy/commit/9d4f857378a782d0782ef7cd7584… 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: ----------- Fix workflow_building_mode typo Commit: 05dbbe5b6eb427e03f49ab5f04f6d5188db6fb36 https://github.com/galaxyproject/galaxy/commit/05dbbe5b6eb427e03f49ab5f04f6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M test/api/test_workflows.py Log Message: ----------- Use correct tools in skip_without_tool decorator Commit: 67aac7b2c598fba7bd559a7fe95a2b66d3f0a483 https://github.com/galaxyproject/galaxy/commit/67aac7b2c598fba7bd559a7fe95a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #7472 from mvdbeek/fix_workflow_building_typo Fix workflow building typo Compare: https://github.com/galaxyproject/galaxy/compare/0a37bb0da0c2...67aac7b2c598

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[galaxyproject/infrastructure-playbook] 5dc8b5: Mount Postorius at / and Hyperkitty at /archives
by Nate Coraor 05 Mar '19

05 Mar '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 5dc8b56bad0eef2cdd1251125482dc6c612f2534 https://github.com/galaxyproject/infrastructure-playbook/commit/5dc8b56bad0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M env/mailman/group_vars/listservers/vars.yml Log Message: ----------- Mount Postorius at / and Hyperkitty at /archives Commit: a950a46bf881324a8519ea5742f5e88b94768f5e https://github.com/galaxyproject/infrastructure-playbook/commit/a950a46bf88… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M env/mailman/group_vars/listservers/vars.yml M env/mailman/listservers.yml Log Message: ----------- Use xapian for Hyperkitty indexes Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/6ec3e53029…

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[galaxyproject/infrastructure-playbook] 6ec3e5: Correct instructions for archive import
by Nate Coraor 05 Mar '19

05 Mar '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 6ec3e5302969e69918d93efffb368e7a432922d4 https://github.com/galaxyproject/infrastructure-playbook/commit/6ec3e530296… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M env/mailman/TODO.txt Log Message: ----------- Correct instructions for archive import

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[galaxyproject/galaxy] ae3b0c: Note `cannot import name _remove_dead_weakref` err...
by Nicola Soranzo 05 Mar '19

05 Mar '19

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

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[galaxyproject/galaxy] f3898c: - check regexp also if FATAL was detected by exit_...
by Marius van den Beek 05 Mar '19

05 Mar '19

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: ----------- - 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

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[galaxyproject/galaxy] d36d1a: Simple filter_output
by John Chilton 05 Mar '19

05 Mar '19

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

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