- galaxy-commits - lists.galaxyproject.org

[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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[galaxyproject/galaxy] 1a636c: Fix HiddenParameter use
by Dannon 05 Mar '19

05 Mar '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 1a636c376fe7fbdaa0ead866989ddfbf0ed7e943 https://github.com/galaxyproject/galaxy/commit/1a636c376fe7fbdaa0ead866989d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix HiddenParameter use Broken in https://github.com/galaxyproject/galaxy/commit/dd8d74f364770a1272555a3753f5… Fixes https://github.com/galaxyproject/galaxy/issues/7454 Commit: 76be1263cac3ed5f7954e451693352d7276e69a7 https://github.com/galaxyproject/galaxy/commit/76be1263cac3ed5f7954e4516933… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M test/api/test_workflows.py A test/functional/tools/hidden_param.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Test that workflows with hidden params can be run Commit: b5bbdfd89fc64796a2049ffd2f3f4d568afbd7f3 https://github.com/galaxyproject/galaxy/commit/b5bbdfd89fc64796a2049ffd2f3f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M run_tests.sh Log Message: ----------- Also use correct image Commit: 9c711e7efabafbd13c0f35f6ec348a32c3a115dd https://github.com/galaxyproject/galaxy/commit/9c711e7efabafbd13c0f35f6ec34… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M lib/galaxy/workflow/modules.py M run_tests.sh M test/api/test_workflows.py A test/functional/tools/hidden_param.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #7458 from mvdbeek/fix_broken_hidden_parameter [19.01] Fix hidden parameter use in workflows Compare: https://github.com/galaxyproject/galaxy/compare/91e49acf374f...9c711e7efaba

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[galaxyproject/galaxy] d27dce: fix syntax of xsd tool schema
by John Chilton 05 Mar '19

05 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d27dceb73df27e7f761fa8119c33b48d62176691 https://github.com/galaxyproject/galaxy/commit/d27dceb73df27e7f761fa8119c33… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- fix syntax of xsd tool schema Commit: abf3070292fd45ee14606dbb76066e86612a76c7 https://github.com/galaxyproject/galaxy/commit/abf3070292fd45ee14606dbb7606… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #7462 from martenson/tool-schema fix syntax of xsd tool schema Compare: https://github.com/galaxyproject/galaxy/compare/b990a77a8c2e...abf3070292fd

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[galaxyproject/ansible-galaxy] bbe5eb: Add spinning fifo plugin
by Helena Rasche 05 Mar '19

05 Mar '19

Branch: refs/heads/fifo Home: https://github.com/galaxyproject/ansible-galaxy Commit: bbe5eb6b2d42c237a46ee9188e82c7dbacbe94f9 https://github.com/galaxyproject/ansible-galaxy/commit/bbe5eb6b2d42c237a46e… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M defaults/main.yml A files/spinningfifo.c A tasks/fifo.yml M tasks/main.yml Log Message: ----------- Add spinning fifo plugin

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[galaxyproject/galaxy] 30d391: set_metadata "unit" test.
by Martin Cech 04 Mar '19

04 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 30d391760def83685935d6dd9ec3a874cc0b4701 https://github.com/galaxyproject/galaxy/commit/30d391760def83685935d6dd9ec3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: A test/unit/tools/test_metadata.py M test/unit/tools_support.py Log Message: ----------- set_metadata "unit" test. Commit: b990a77a8c2e901e60a93f37b749ce1dcab43ddf https://github.com/galaxyproject/galaxy/commit/b990a77a8c2e901e60a93f37b749… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: A test/unit/tools/test_metadata.py M test/unit/tools_support.py Log Message: ----------- Merge pull request #7459 from jmchilton/set_meta_unit set_metadata "unit" tests Compare: https://github.com/galaxyproject/galaxy/compare/f9df69d5f2d5...b990a77a8c2e

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[galaxyproject/usegalaxy-playbook] bfbd76: Installed new version of Fabio's BloomTree tools.
by Dave B. 04 Mar '19

04 Mar '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bfbd76de539139266d11b2bfeec4749574a2e3ec https://github.com/galaxyproject/usegalaxy-playbook/commit/bfbd76de53913926… Author: Dave B <dave(a)bx.psu.edu> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Installed new version of Fabio's BloomTree tools.

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[galaxyproject/infrastructure-playbook] 1a2ab9: Disable biostar backups
by Nate Coraor 04 Mar '19

04 Mar '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 1a2ab92f647582a5a0e8a0e992db31b5046a9753 https://github.com/galaxyproject/infrastructure-playbook/commit/1a2ab92f647… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M env/galaxy/host_vars/westvleteren.galaxyproject.org/vars.yml Log Message: ----------- Disable biostar backups

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