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

[galaxyproject/galaxy] 676886: Fix non-strict tabular relabel operation
by GitHub 07 Aug '18

07 Aug '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 676886195d1fbe17cdff16af8acad6f5c2115ee1 https://github.com/galaxyproject/galaxy/commit/676886195d1fbe17cdff16af8aca… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-28 (Mon, 28 May 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix non-strict tabular relabel operation Commit: 3b3deb314f4a78684bea9707d2f0d856e306f006 https://github.com/galaxyproject/galaxy/commit/3b3deb314f4a78684bea9707d2f0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/tools/relabel_from_file.xml Log Message: ----------- Use strict mode when testing strict mode ... Commit: 4661b6e8831c2cae86b7d9725431e71bacd22168 https://github.com/galaxyproject/galaxy/commit/4661b6e8831c2cae86b7d9725431… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-02 (Sat, 02 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Allow invalid optional param values for old tools For tools with profile < 18.09 we return None for provided, but illegal default values. This can happen when referencing columns of an optional dataset for instance, as experienced in https://github.com/galaxyproject/tools-iuc/pull/1842. This used to pass prior to 18.05 because we would always return the value if there were no legal values. This was changed in https://github.com/galaxyproject/galaxy/commit/9febc519944dcfb5c8907b8a302f… where we would only allow this in workflow building mode. Commit: 470299a2ce6ef1e5d894a0247bd43f24fd463d41 https://github.com/galaxyproject/galaxy/commit/470299a2ce6ef1e5d894a0247bd4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-18 (Mon, 18 Jun 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/relabel_from_file.xml Log Message: ----------- Merge pull request #6234 from mvdbeek/fix_relabel_non_strict [18.01] Fix non-strict tabular relabel operation Commit: eed703eef8b3884f70019070210633f0e033b39b https://github.com/galaxyproject/galaxy/commit/eed703eef8b3884f700190702106… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-19 (Tue, 19 Jun 2018) Changed paths: M templates/sharing_base.mako Log Message: ----------- Fix share with another user in 18.05 Commit: 48fafa8096fd179e9c74c56bac7be9b042cbade8 https://github.com/galaxyproject/galaxy/commit/48fafa8096fd179e9c74c56bac7b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-19 (Tue, 19 Jun 2018) Changed paths: M templates/sharing_base.mako Log Message: ----------- Merge pull request #6358 from dannon/1805sharingfix [18.01] Fix 'share with another user' Commit: c6403acd0f18196c0453a90fe89ccf861d7a28d6 https://github.com/galaxyproject/galaxy/commit/c6403acd0f18196c0453a90fe89c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Fix logging bug. Commit: d0a0fa8319e5b32e222e261b1b9f0242e210d1c7 https://github.com/galaxyproject/galaxy/commit/d0a0fa8319e5b32e222e261b1b9f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/relabel_from_file.xml M templates/sharing_base.mako Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: 6d5be41b320510d6e2d163399a3a6e30d6f9bda0 https://github.com/galaxyproject/galaxy/commit/6d5be41b320510d6e2d163399a3a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Merge pull request #6366 from jmchilton/job_log_bug [18.05] Fix small bug in logging output name in job finish. Commit: 603b2365b6a261e5603c618c637cf8458e667007 https://github.com/galaxyproject/galaxy/commit/603b2365b6a261e5603c618c637c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-21 (Thu, 21 Jun 2018) Changed paths: M lib/galaxy/app.py M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Force standard HTTPTransport for sentry -- this plays nicer with a wider array of uwsgi configurations Commit: 572f38d1fb47e914ad10766007c855786e1643a2 https://github.com/galaxyproject/galaxy/commit/572f38d1fb47e914ad10766007c8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-21 (Thu, 21 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- move the sanitization to the try/except block as it may fail (and it did, on Main) Commit: f94a073e86be608916ec7ae79285da06ee82483b https://github.com/galaxyproject/galaxy/commit/f94a073e86be608916ec7ae79285… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-21 (Thu, 21 Jun 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Make sure that the workflow step has a proper state available Commit: d28ab2a4f31b363c236a02a535cc43ab049190ca https://github.com/galaxyproject/galaxy/commit/d28ab2a4f31b363c236a02a535cc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-21 (Thu, 21 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- Merge pull request #6377 from martenson/catch-sanitization-faults [18.05] Catch sanitization faults Commit: 9967639bac92eb3f7103794663f41b88f11baa9c https://github.com/galaxyproject/galaxy/commit/9967639bac92eb3f7103794663f4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Comma-separate tool names in missing tools error message Commit: 22d383c39842e0a0198cf2d37ad3832ea1838769 https://github.com/galaxyproject/galaxy/commit/22d383c39842e0a0198cf2d37ad3… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #6378 from guerler/commaseperror [18.05] Comma-separate tool names in missing tools error message Commit: fa2b6baef71984c0559c53ff5750d1fe9b77163e https://github.com/galaxyproject/galaxy/commit/fa2b6baef71984c0559c53ff5750… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/bam_to_bai.xml Log Message: ----------- Revert "Remove bam to bai converter" This reverts commit 7e2727bc0a74868198e7e457f99df3d1e39f1ddb. Commit: 5f24794efdad757b77c75c3aa111da7a11c5bb47 https://github.com/galaxyproject/galaxy/commit/5f24794efdad757b77c75c3aa111… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Add basic .bai datatype Commit: 36706e9eb38728c91c1da2a4cf66ff49f3f44d72 https://github.com/galaxyproject/galaxy/commit/36706e9eb38728c91c1da2a4cf66… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/bam_to_bai.xml Log Message: ----------- Merge pull request #6385 from dannon/revert-baiconverter-removal [18.01] Revert "Remove bam to bai converter" Commit: e0c269291a20ae3a01a24bae930012baba3bb10c https://github.com/galaxyproject/galaxy/commit/e0c269291a20ae3a01a24bae9300… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-23 (Sat, 23 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/bam_to_bai.xml Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: 6654a837527797971b28fd2cbb092d7081c918b9 https://github.com/galaxyproject/galaxy/commit/6654a837527797971b28fd2cbb09… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Hack around #6299. Commit: 39d7cf2eb73177532237ad38a8a75095d1be4428 https://github.com/galaxyproject/galaxy/commit/39d7cf2eb73177532237ad38a8a7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #6433 from jmchilton/hack_6299 [18.05] decode potential encoded id Commit: 0c97d4ff5c83318551319524582619656ae848b8 https://github.com/galaxyproject/galaxy/commit/0c97d4ff5c833185513195245826… Author: thobalose <lose.thoba(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- GIE static url; https://github.com/galaxyproject/galaxy/issues/6459 Commit: 3fe88a9bfe1b010ca30ffac32e5c4e200398c48e https://github.com/galaxyproject/galaxy/commit/3fe88a9bfe1b010ca30ffac32e5c… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Merge pull request #6465 from dannon/backport-gie-static-again [18.05] Backport of IE static url fix (to actual 18.05) Commit: bc95f2563601635cfa1daa686b3d5c4e3ebb51ea https://github.com/galaxyproject/galaxy/commit/bc95f2563601635cfa1daa686b3d… Author: Devon Ryan <dpryan79(a)gmail.com> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Fix the --log-file option in the job handlers (cherry picked from commit 97c344a17a0188a687629103feefcdf03af8e768) Commit: 23666c94a22b816bc5238e4a22c759a11265f7aa https://github.com/galaxyproject/galaxy/commit/23666c94a22b816bc5238e4a22c7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #6477 from natefoo/backport-pr-6351 [18.01] Fix the --log-file option in the job handlers Commit: 93fc3a63507d6cd7c85a99ad62e71b14d4d6265e https://github.com/galaxyproject/galaxy/commit/93fc3a63507d6cd7c85a99ad62e7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Merge pull request #6369 from guerler/pages [18.05] Make sure that the workflow step has a proper state available Commit: 20565a2b8517fbc4c54524fa0ae127c2f6aaefb0 https://github.com/galaxyproject/galaxy/commit/20565a2b8517fbc4c54524fa0ae1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M lib/galaxy/app.py M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Merge pull request #6375 from dannon/sentry_transport_fix [18.05] Specify standard HTTPTransport for Sentry Commit: 4b0ae30a83aeb86a821ec15cfa87e6af7e160a03 https://github.com/galaxyproject/galaxy/commit/4b0ae30a83aeb86a821ec15cfa87… Author: takadonet <philipmabon(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Added fix to ensure that original ftp files that have been uploaded are purged if set in galaxy.yml with flag ftp_upload_purge. Address issue #6492 Commit: dfc996c8d6b8e166ae17fe8502f9e4f9252b6106 https://github.com/galaxyproject/galaxy/commit/dfc996c8d6b8e166ae17fe8502f9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-13 (Fri, 13 Jul 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: fd33c5c6d6aa2478654da74c7e80efdcf31e09a7 https://github.com/galaxyproject/galaxy/commit/fd33c5c6d6aa2478654da74c7e80… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-07-13 (Fri, 13 Jul 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Merge pull request #6497 from martenson/backport-takadonet [18.05] backport ftp purge fix Commit: 7b8e4f9e740725861951535d59e50243e4a0b2e0 https://github.com/galaxyproject/galaxy/commit/7b8e4f9e740725861951535d59e5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-17 (Tue, 17 Jul 2018) Changed paths: M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/empty.txt Log Message: ----------- Fix empty datatypes. Commit: ef702e1458f746299710e9ce5afb7b350b61f91c https://github.com/galaxyproject/galaxy/commit/ef702e1458f746299710e9ce5afb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-17 (Tue, 17 Jul 2018) Changed paths: M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/empty.txt Log Message: ----------- Merge pull request #6510 from nsoranzo/release_18.05_backport_29f8e29b0bf5d50c0b735aa707d2a61623cc805b [18.05] Fix infinite loop in uploads Commit: a8b9899681939286a03badd85c9c71f972958a18 https://github.com/galaxyproject/galaxy/commit/a8b9899681939286a03badd85c9c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml Log Message: ----------- Fix warning in CONVERTER_bam_to_bigwig_0 and CONVERTER_sam_to_bigwig_0 Since v2.27.0 (see https://github.com/arq5x/bedtools2/commit/4d188435777cfbd6ada7394ee78fde37f… ), `bedtools genomecov` emits this warning: ``` ***** *****WARNING: Genome (-g) files are ignored when BAM input is provided. ***** ``` if both `-ibam` and `-g` option are specified, which causes the converters to always fail. Also: - Add `detect_errors="aggressive"` to `<command/>` to prevent future warnings from creating other issues. - Fix input format in `CONVERTER_sam_to_bigwig_0`. Commit: 50b34185394cc38159c33ca98b74e1418a7b1e55 https://github.com/galaxyproject/galaxy/commit/50b34185394cc38159c33ca98b74… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml Log Message: ----------- Merge pull request #6528 from nsoranzo/release_18.05_fix_CONVERTER_bam_to_bigwig_0 [18.05] Fix warning in CONVERTER_bam_to_bigwig_0 and CONVERTER_sam_to_bigwig_0 Commit: 9794d835e507c31d82aa82c79e86998154419980 https://github.com/galaxyproject/galaxy/commit/9794d835e507c31d82aa82c79e86… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-25 (Wed, 25 Jul 2018) Changed paths: M lib/galaxy/tools/parser/output_objects.py M test/api/test_tools.py Log Message: ----------- Fix to_dict with io_details=True for tools with collection outputs. Fixes #6537 and includes a test case. Commit: 5f19b8752dfd940efd156de1a0c1a4e6e914800b https://github.com/galaxyproject/galaxy/commit/5f19b8752dfd940efd156de1a0c1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-26 (Thu, 26 Jul 2018) Changed paths: M lib/galaxy/util/rules_dsl.py M test/unit/test_rule_utils.py Log Message: ----------- Fix empty handling rule. Commit: a88bf0a2bee152c859f229c2a017b8a03d96b8d8 https://github.com/galaxyproject/galaxy/commit/a88bf0a2bee152c859f229c2a017… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-26 (Thu, 26 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #6264 from mvdbeek/allow_optional_and_invalid_parameter_values [18.05] Allow invalid optional param values for tools profile versions < 18.09 Commit: 0a9010156e30a20d730324807c3e238510f44b77 https://github.com/galaxyproject/galaxy/commit/0a9010156e30a20d730324807c3e… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-07-26 (Thu, 26 Jul 2018) Changed paths: M lib/galaxy/tools/parser/output_objects.py M test/api/test_tools.py Log Message: ----------- Merge pull request #6538 from jmchilton/tool_output_io [18.01] Fix to_dict with io_details=True for tools with collection outputs. Commit: 66e74d0e475ef6fd6f6de125b41f9990e274fbfb https://github.com/galaxyproject/galaxy/commit/66e74d0e475ef6fd6f6de125b41f… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M lib/galaxy/util/rules_dsl.py M test/unit/test_rule_utils.py Log Message: ----------- Merge pull request #6542 from jmchilton/1805_fix_empty_handling_rule_on_backend [18.05] Fix "filter empty" rule in Python rule handling framework. Commit: 9630699c21875199fec75bc3f607d5b81a224348 https://github.com/galaxyproject/galaxy/commit/9630699c21875199fec75bc3f607… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-31 (Tue, 31 Jul 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Simpler, more targeted fix for copy datasets dialog tag copies (will refactor in dev) Commit: ba47188f5e896d9f2bd6718796093f05e1c7aa9b https://github.com/galaxyproject/galaxy/commit/ba47188f5e896d9f2bd671879609… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M test/api/test_workflows.py M test/base/workflows_format_2/converter.py Log Message: ----------- Introduce test for auto-labelling subworkflow workflow outputs Commit: 21fd74e640c2ba872d98259ea213e20e99c6ba75 https://github.com/galaxyproject/galaxy/commit/21fd74e640c2ba872d98259ea213… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Use subworkflow index when setting auto-label Previously this would reference the parent workflow index, while the get_data module would use the subworkflow index. This means defining workflows worked fine, but executing would fail when trying to find the output to replace. Using the subworkflow index here seems like the correct thing to do. Fixes https://github.com/galaxyproject/galaxy/issues/6560 Commit: ffdf674c75d49235edee80090fe4235ac9b0d86e https://github.com/galaxyproject/galaxy/commit/ffdf674c75d49235edee80090fe4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix worklfow run link for extracted workflows Commit: 6c7b9a3c7d4459b171fa806f2912d49e44ccd5bd https://github.com/galaxyproject/galaxy/commit/6c7b9a3c7d4459b171fa806f2912… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Merge pull request #6532 from dannon/fix-dataset-copy-tags [18.05] Fix dataset copy tags Commit: 6d9df51f36e293bd1ce20d3bf9e21a5646ff5b94 https://github.com/galaxyproject/galaxy/commit/6d9df51f36e293bd1ce20d3bf9e2… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/base/workflows_format_2/converter.py Log Message: ----------- Merge pull request #6570 from mvdbeek/fix_auto_labelling_and_output_recovery [18.01] Use subworkflow index when setting auto-label Commit: d7959568f85b45f378f6972d971075f7169cffc4 https://github.com/galaxyproject/galaxy/commit/d7959568f85b45f378f6972d9710… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/workflow/modules.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/workflows_format_2/converter.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: ea085b07a0efdd5322aab3bb613fc363b71967b5 https://github.com/galaxyproject/galaxy/commit/ea085b07a0efdd5322aab3bb613f… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #6571 from guerler/fix_link [18.05] Fix workflow run link for extracted workflows Compare: https://github.com/galaxyproject/galaxy/compare/bcf105cbb37a...ea085b07a0ef **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] 4661b6: Allow invalid optional param values for old tools
by GitHub 06 Aug '18

06 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4661b6e8831c2cae86b7d9725431e71bacd22168 https://github.com/galaxyproject/galaxy/commit/4661b6e8831c2cae86b7d9725431… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-02 (Sat, 02 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Allow invalid optional param values for old tools For tools with profile < 18.09 we return None for provided, but illegal default values. This can happen when referencing columns of an optional dataset for instance, as experienced in https://github.com/galaxyproject/tools-iuc/pull/1842. This used to pass prior to 18.05 because we would always return the value if there were no legal values. This was changed in https://github.com/galaxyproject/galaxy/commit/9febc519944dcfb5c8907b8a302f… where we would only allow this in workflow building mode. Commit: 9794d835e507c31d82aa82c79e86998154419980 https://github.com/galaxyproject/galaxy/commit/9794d835e507c31d82aa82c79e86… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-25 (Wed, 25 Jul 2018) Changed paths: M lib/galaxy/tools/parser/output_objects.py M test/api/test_tools.py Log Message: ----------- Fix to_dict with io_details=True for tools with collection outputs. Fixes #6537 and includes a test case. Commit: 5f19b8752dfd940efd156de1a0c1a4e6e914800b https://github.com/galaxyproject/galaxy/commit/5f19b8752dfd940efd156de1a0c1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-26 (Thu, 26 Jul 2018) Changed paths: M lib/galaxy/util/rules_dsl.py M test/unit/test_rule_utils.py Log Message: ----------- Fix empty handling rule. Commit: a88bf0a2bee152c859f229c2a017b8a03d96b8d8 https://github.com/galaxyproject/galaxy/commit/a88bf0a2bee152c859f229c2a017… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-26 (Thu, 26 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #6264 from mvdbeek/allow_optional_and_invalid_parameter_values [18.05] Allow invalid optional param values for tools profile versions < 18.09 Commit: 0a9010156e30a20d730324807c3e238510f44b77 https://github.com/galaxyproject/galaxy/commit/0a9010156e30a20d730324807c3e… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-07-26 (Thu, 26 Jul 2018) Changed paths: M lib/galaxy/tools/parser/output_objects.py M test/api/test_tools.py Log Message: ----------- Merge pull request #6538 from jmchilton/tool_output_io [18.01] Fix to_dict with io_details=True for tools with collection outputs. Commit: 66e74d0e475ef6fd6f6de125b41f9990e274fbfb https://github.com/galaxyproject/galaxy/commit/66e74d0e475ef6fd6f6de125b41f… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M lib/galaxy/util/rules_dsl.py M test/unit/test_rule_utils.py Log Message: ----------- Merge pull request #6542 from jmchilton/1805_fix_empty_handling_rule_on_backend [18.05] Fix "filter empty" rule in Python rule handling framework. Commit: 9630699c21875199fec75bc3f607d5b81a224348 https://github.com/galaxyproject/galaxy/commit/9630699c21875199fec75bc3f607… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-31 (Tue, 31 Jul 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Simpler, more targeted fix for copy datasets dialog tag copies (will refactor in dev) Commit: ba47188f5e896d9f2bd6718796093f05e1c7aa9b https://github.com/galaxyproject/galaxy/commit/ba47188f5e896d9f2bd671879609… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M test/api/test_workflows.py M test/base/workflows_format_2/converter.py Log Message: ----------- Introduce test for auto-labelling subworkflow workflow outputs Commit: 21fd74e640c2ba872d98259ea213e20e99c6ba75 https://github.com/galaxyproject/galaxy/commit/21fd74e640c2ba872d98259ea213… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Use subworkflow index when setting auto-label Previously this would reference the parent workflow index, while the get_data module would use the subworkflow index. This means defining workflows worked fine, but executing would fail when trying to find the output to replace. Using the subworkflow index here seems like the correct thing to do. Fixes https://github.com/galaxyproject/galaxy/issues/6560 Commit: ffdf674c75d49235edee80090fe4235ac9b0d86e https://github.com/galaxyproject/galaxy/commit/ffdf674c75d49235edee80090fe4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix worklfow run link for extracted workflows Commit: 6c7b9a3c7d4459b171fa806f2912d49e44ccd5bd https://github.com/galaxyproject/galaxy/commit/6c7b9a3c7d4459b171fa806f2912… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Merge pull request #6532 from dannon/fix-dataset-copy-tags [18.05] Fix dataset copy tags Commit: 6d9df51f36e293bd1ce20d3bf9e21a5646ff5b94 https://github.com/galaxyproject/galaxy/commit/6d9df51f36e293bd1ce20d3bf9e2… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/base/workflows_format_2/converter.py Log Message: ----------- Merge pull request #6570 from mvdbeek/fix_auto_labelling_and_output_recovery [18.01] Use subworkflow index when setting auto-label Commit: d7959568f85b45f378f6972d971075f7169cffc4 https://github.com/galaxyproject/galaxy/commit/d7959568f85b45f378f6972d9710… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/workflow/modules.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/workflows_format_2/converter.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: ea085b07a0efdd5322aab3bb613fc363b71967b5 https://github.com/galaxyproject/galaxy/commit/ea085b07a0efdd5322aab3bb613f… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #6571 from guerler/fix_link [18.05] Fix workflow run link for extracted workflows Commit: d1423b6e18cbf054799027d6c6700b1b1186d6a9 https://github.com/galaxyproject/galaxy/commit/d1423b6e18cbf054799027d6c670… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/util/rules_dsl.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/workflows_format_2/converter.py M test/unit/test_rule_utils.py Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/561e0099bc22...d1423b6e18cb **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] ffdf67: Fix worklfow run link for extracted workflows
by GitHub 06 Aug '18

06 Aug '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: ffdf674c75d49235edee80090fe4235ac9b0d86e https://github.com/galaxyproject/galaxy/commit/ffdf674c75d49235edee80090fe4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix worklfow run link for extracted workflows Commit: ea085b07a0efdd5322aab3bb613fc363b71967b5 https://github.com/galaxyproject/galaxy/commit/ea085b07a0efdd5322aab3bb613f… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #6571 from guerler/fix_link [18.05] Fix workflow run link for extracted workflows Compare: https://github.com/galaxyproject/galaxy/compare/d7959568f85b...ea085b07a0ef **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.

1 0

[galaxyproject/galaxy] 9794d8: Fix to_dict with io_details=True for tools with co...
by GitHub 06 Aug '18

06 Aug '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 9794d835e507c31d82aa82c79e86998154419980 https://github.com/galaxyproject/galaxy/commit/9794d835e507c31d82aa82c79e86… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-25 (Wed, 25 Jul 2018) Changed paths: M lib/galaxy/tools/parser/output_objects.py M test/api/test_tools.py Log Message: ----------- Fix to_dict with io_details=True for tools with collection outputs. Fixes #6537 and includes a test case. Commit: 0a9010156e30a20d730324807c3e238510f44b77 https://github.com/galaxyproject/galaxy/commit/0a9010156e30a20d730324807c3e… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-07-26 (Thu, 26 Jul 2018) Changed paths: M lib/galaxy/tools/parser/output_objects.py M test/api/test_tools.py Log Message: ----------- Merge pull request #6538 from jmchilton/tool_output_io [18.01] Fix to_dict with io_details=True for tools with collection outputs. Commit: ba47188f5e896d9f2bd6718796093f05e1c7aa9b https://github.com/galaxyproject/galaxy/commit/ba47188f5e896d9f2bd671879609… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M test/api/test_workflows.py M test/base/workflows_format_2/converter.py Log Message: ----------- Introduce test for auto-labelling subworkflow workflow outputs Commit: 21fd74e640c2ba872d98259ea213e20e99c6ba75 https://github.com/galaxyproject/galaxy/commit/21fd74e640c2ba872d98259ea213… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Use subworkflow index when setting auto-label Previously this would reference the parent workflow index, while the get_data module would use the subworkflow index. This means defining workflows worked fine, but executing would fail when trying to find the output to replace. Using the subworkflow index here seems like the correct thing to do. Fixes https://github.com/galaxyproject/galaxy/issues/6560 Commit: 6d9df51f36e293bd1ce20d3bf9e21a5646ff5b94 https://github.com/galaxyproject/galaxy/commit/6d9df51f36e293bd1ce20d3bf9e2… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/base/workflows_format_2/converter.py Log Message: ----------- Merge pull request #6570 from mvdbeek/fix_auto_labelling_and_output_recovery [18.01] Use subworkflow index when setting auto-label Commit: d7959568f85b45f378f6972d971075f7169cffc4 https://github.com/galaxyproject/galaxy/commit/d7959568f85b45f378f6972d9710… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/workflow/modules.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/workflows_format_2/converter.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Compare: https://github.com/galaxyproject/galaxy/compare/6c7b9a3c7d44...d7959568f85b **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.

1 0

[galaxyproject/galaxy] ba4718: Introduce test for auto-labelling subworkflow work...
by GitHub 06 Aug '18

06 Aug '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: ba47188f5e896d9f2bd6718796093f05e1c7aa9b https://github.com/galaxyproject/galaxy/commit/ba47188f5e896d9f2bd671879609… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M test/api/test_workflows.py M test/base/workflows_format_2/converter.py Log Message: ----------- Introduce test for auto-labelling subworkflow workflow outputs Commit: 21fd74e640c2ba872d98259ea213e20e99c6ba75 https://github.com/galaxyproject/galaxy/commit/21fd74e640c2ba872d98259ea213… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Use subworkflow index when setting auto-label Previously this would reference the parent workflow index, while the get_data module would use the subworkflow index. This means defining workflows worked fine, but executing would fail when trying to find the output to replace. Using the subworkflow index here seems like the correct thing to do. Fixes https://github.com/galaxyproject/galaxy/issues/6560 Commit: 6d9df51f36e293bd1ce20d3bf9e21a5646ff5b94 https://github.com/galaxyproject/galaxy/commit/6d9df51f36e293bd1ce20d3bf9e2… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/base/workflows_format_2/converter.py Log Message: ----------- Merge pull request #6570 from mvdbeek/fix_auto_labelling_and_output_recovery [18.01] Use subworkflow index when setting auto-label Compare: https://github.com/galaxyproject/galaxy/compare/0a9010156e30...6d9df51f36e2 **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.

1 0

[galaxyproject/galaxy] 963069: Simpler, more targeted fix for copy datasets dialo...
by GitHub 06 Aug '18

06 Aug '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 9630699c21875199fec75bc3f607d5b81a224348 https://github.com/galaxyproject/galaxy/commit/9630699c21875199fec75bc3f607… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-31 (Tue, 31 Jul 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Simpler, more targeted fix for copy datasets dialog tag copies (will refactor in dev) Commit: 6c7b9a3c7d4459b171fa806f2912d49e44ccd5bd https://github.com/galaxyproject/galaxy/commit/6c7b9a3c7d4459b171fa806f2912… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Merge pull request #6532 from dannon/fix-dataset-copy-tags [18.05] Fix dataset copy tags Compare: https://github.com/galaxyproject/galaxy/compare/66e74d0e475e...6c7b9a3c7d44 **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.

1 0

[galaxyproject/galaxy] 5a3e28: Better encapsulation when queueing jobs.
by GitHub 06 Aug '18

06 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5a3e28db774a51197e7000b0cb493a5741b24474 https://github.com/galaxyproject/galaxy/commit/5a3e28db774a51197e7000b0cb49… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Better encapsulation when queueing jobs. No need for the runner to know all these internals of the JobWrapper when it is just taking attributes on the job or job wrapper and calling job wrapper methods with them. Provides nice symmetry between queue/finish now also. Commit: 1b5dff11a738c8d01b457dedda80e5f533ad1127 https://github.com/galaxyproject/galaxy/commit/1b5dff11a738c8d01b457dedda80… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/webapps/galaxy/config_schema.yml M test/unit/jobs/test_job_wrapper.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Setup objectstore for datasets in job handler instead of web thread. This is good for a few reasons * It speeds up the bottleneck that is the job creation code in the web thread (the job handler is much easier to parallelize). Skipping the flush for all those datasets and skipping the disk write per dataset should really speed things up nicely when submitting large numbers of jobs and jobs with a large number of inputs. * This prevents a disk slow down from grinding the web response to a halt. We don't want the handler to freeze up either - but if something is going to freeze it is a better user experience and easier to recover from the job handler freezing while their are disk problems. * This allows per-job-handler object store configurations - simply configure different job handlers with different object store configurations. This is cool and important and I can imagine some awesome applications but I will wait for them to materialize. Commit: 36019f93085d4c5c51c14b3eafa936d779096513 https://github.com/galaxyproject/galaxy/commit/36019f93085d4c5c51c14b3eafa9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Restructure JobWrapper/TaskWrapper for more unified initialization... ... especially after changes to set object store id in the job handler. This fixes the parallelism tests for those changes. Commit: c9d17545d843df5e3989185433b8419036fe8208 https://github.com/galaxyproject/galaxy/commit/c9d17545d843df5e3989185433b8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Config rebuild, and a few typos. Commit: 561e0099bc22ce5593a3ca2b363cceb8a05fd6c6 https://github.com/galaxyproject/galaxy/commit/561e0099bc22ce5593a3ca2b363c… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/webapps/galaxy/config_schema.yml M test/unit/jobs/test_job_wrapper.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge pull request #6550 from jmchilton/objectstore_setup Configure object store for datasets in job handler instead of web thread. Compare: https://github.com/galaxyproject/galaxy/compare/1f35d13db561...561e0099bc22 **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] d53366: Move back to paste's FileApp
by GitHub 04 Aug '18

04 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d53366c2f01be1c1648a061f978e8a2f73383117 https://github.com/galaxyproject/galaxy/commit/d53366c2f01be1c1648a061f978e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M lib/galaxy/web/framework/middleware/static.py Log Message: ----------- Move back to paste's FileApp I didn't figure out how to set the the max_age header using webob's FileApp. Fixes https://github.com/galaxyproject/galaxy/pull/6561#issuecomment-409973637 Commit: 4b89a73f224fe0d6e1d9010d5d5313683fb16d69 https://github.com/galaxyproject/galaxy/commit/4b89a73f224fe0d6e1d9010d5d53… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M lib/galaxy/web/framework/middleware/static.py Log Message: ----------- Fix import order for I100 lint error Commit: da94441400e991aaac91daab6bd0ec07ffe382a8 https://github.com/galaxyproject/galaxy/commit/da94441400e991aaac91daab6bd0… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-08-04 (Sat, 04 Aug 2018) Changed paths: M lib/galaxy/web/framework/middleware/static.py Log Message: ----------- Merge pull request #7 from dannon/fix_fileapp_max_age_cache Fix import order for I100 lint error Commit: 1f35d13db5615e8167e187f729bbc4aa3a7da5b0 https://github.com/galaxyproject/galaxy/commit/1f35d13db5615e8167e187f729bb… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-04 (Sat, 04 Aug 2018) Changed paths: M lib/galaxy/web/framework/middleware/static.py Log Message: ----------- Merge pull request #6567 from mvdbeek/fix_fileapp_max_age_cache Move back to paste's FileApp Compare: https://github.com/galaxyproject/galaxy/compare/feb4e2933baa...1f35d13db561 **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.

1 0

[galaxyproject/galaxy] 876fb1: Fix formatting in repo information display (spacin...
by GitHub 02 Aug '18

02 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 876fb17ab03716fe5c0ad8fe38f50264e7cbb9c8 https://github.com/galaxyproject/galaxy/commit/876fb17ab03716fe5c0ad8fe38f5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-view.js Log Message: ----------- Fix formatting in repo information display (spacing) Commit: a0dd200026ab6d57ffb6478634918451d11e56fd https://github.com/galaxyproject/galaxy/commit/a0dd200026ab6d57ffb647863491… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js Log Message: ----------- Simplify navigation/state management in toolshed admin app. Discard and recreate views always -- simpler, safer, and basically the same speed since many of these did a full re-initialization anyway. Commit: b26ab71ce1282659d4390d4ad90e55250f6840f7 https://github.com/galaxyproject/galaxy/commit/b26ab71ce1282659d4390d4ad90e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-view.js Log Message: ----------- Minor formatting. Commit: feb4e2933baa6ffcd906fdbef4ac1575716b4748 https://github.com/galaxyproject/galaxy/commit/feb4e2933baa6ffcd906fdbef4ac… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js Log Message: ----------- Merge pull request #6564 from dannon/ts-admin-fixes Misc Admin TS Panel Fixes Compare: https://github.com/galaxyproject/galaxy/compare/389a1d6563f0...feb4e2933baa **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] 632cde: Replace paste.httpexception with webob.exc classes
by GitHub 02 Aug '18

02 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 632cdeae86c70d8ca66e78643c82c130501e0ca6 https://github.com/galaxyproject/galaxy/commit/632cdeae86c70d8ca66e78643c82… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/tools/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/static.py M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Replace paste.httpexception with webob.exc classes Commit: 27a354f97ec40e99343caa1f1f1e7da94a721c53 https://github.com/galaxyproject/galaxy/commit/27a354f97ec40e99343caa1f1f1e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Fix make_file method of patched cgi_FieldStorage This copies the behavior from webob.compat.cgi_FieldStorage, except we use a NamedTemporaryFile instead of TemporaryFile. Commit: deba605e7eaaa418fe9fed3f1e0f6a9e15223718 https://github.com/galaxyproject/galaxy/commit/deba605e7eaaa418fe9fed3f1e0f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Pass bytestring to hash function Commit: 6b86ed56f35e1b51e27053169e80c5b4b7b9ddf2 https://github.com/galaxyproject/galaxy/commit/6b86ed56f35e1b51e27053169e80… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py Log Message: ----------- Fix binary file check Commit: cb7ebd73494153b1950ec87a39d12e874c183a13 https://github.com/galaxyproject/galaxy/commit/cb7ebd73494153b1950ec87a39d1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/web/base/controller.py M test/unit/tools/test_history_imp_exp.py Log Message: ----------- py3: Fix history import/export tool - Open history tarfile in binary mode - Fix base64 encoding in history import tool - test history export more extensively Commit: 1dc4cf224108db9756a96b9d50a71f9f099a00f2 https://github.com/galaxyproject/galaxy/commit/1dc4cf224108db9756a96b9d50a7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Fix cgi_FieldStorage monkey patch self.__file is defined in cgi.FieldStorage, so that is the class that needs to be patched. Followup to a65cd29c366035fb8b26e2274046e8c96e3cab33 Commit: 8093d6b61046f7b09381c520d5c95dda54f7ed71 https://github.com/galaxyproject/galaxy/commit/8093d6b61046f7b09381c520d5c9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M test/api/test_dataset_collections.py Log Message: ----------- py3: Fix dataset collection test Commit: a88ce7cfd21646f3dbd04ef41f8e1755da793713 https://github.com/galaxyproject/galaxy/commit/a88ce7cfd21646f3dbd04ef41f8e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/util/checkers.py Log Message: ----------- py3: fix check_html Commit: dc9e5c5a83877599991274298fca3316263a4b36 https://github.com/galaxyproject/galaxy/commit/dc9e5c5a83877599991274298fca… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/authenticate.py M test/api/test_authenticate.py Log Message: ----------- py3: Fix authenticate api test Commit: a760ecdaf0e56a9eee9a02ace9dc7a97906dda02 https://github.com/galaxyproject/galaxy/commit/a760ecdaf0e56a9eee9a02ace9dc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Cast to bytestring for is_binary check Commit: 02d9415ece13452e5c23ee8078d644c34a6b40cd https://github.com/galaxyproject/galaxy/commit/02d9415ece13452e5c23ee8078d6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/datasets.py Log Message: ----------- py3: Fix raw dataset display Commit: 330aaf8683587484efdbd02f93ba04e82c568859 https://github.com/galaxyproject/galaxy/commit/330aaf8683587484efdbd02f93ba… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/web/framework/decorators.py Log Message: ----------- py3: Fix catching malformed IDs Commit: bbf739a3dfb28a9d0a5350f4d640c1113b2e977a https://github.com/galaxyproject/galaxy/commit/bbf739a3dfb28a9d0a5350f4d640… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/tools/data/__init__.py M lib/galaxy/webapps/galaxy/api/tool_data.py M test/api/test_tool_data.py Log Message: ----------- py3: Fix tool_data API Commit: 8f7363549987536748c4a7e88dd88a60280b9089 https://github.com/galaxyproject/galaxy/commit/8f7363549987536748c4a7e88dd8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M test/api/test_jobs.py Log Message: ----------- py3: Fix upload jobs API tests Commit: 27a30b762d8663b0d1c6a6c0b21d44f35791884d https://github.com/galaxyproject/galaxy/commit/27a30b762d8663b0d1c6a6c0b21d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M test/api/test_libraries.py Log Message: ----------- py3: Fix library tests Commit: 33c0b58ae0db139aa9b0f0c619e01a40eba06c03 https://github.com/galaxyproject/galaxy/commit/33c0b58ae0db139aa9b0f0c619e0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py Log Message: ----------- py3: Send bytestring in various datatatypes' display_data methods Commit: c2c2117e497365ab59483aad660d82bdd8c714e8 https://github.com/galaxyproject/galaxy/commit/c2c2117e497365ab59483aad660d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- py3: Cast map objects to lists when serializing tools to json Commit: 057938c30d57da3afce259a08d064e837e0d5ede https://github.com/galaxyproject/galaxy/commit/057938c30d57da3afce259a08d06… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/webhooks.py Log Message: ----------- py3: Fix getting first webhook Commit: 187457a461a7d28878e1ece803a843c868f7c174 https://github.com/galaxyproject/galaxy/commit/187457a461a7d28878e1ece803a8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- py3: Don't rely on order of outputs, instead match by output name Commit: f3bc18c85a8d450f2b3bed3e28c03ed5ea65576b https://github.com/galaxyproject/galaxy/commit/f3bc18c85a8d450f2b3bed3e28c0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M test/base/populators.py Log Message: ----------- py3: Use reponse.text instead of reponse.content for decoded text Commit: 9ea589d5e737bcca173040682513b2e913675da4 https://github.com/galaxyproject/galaxy/commit/9ea589d5e737bcca173040682513… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M tools/filters/random_lines_two_pass.py Log Message: ----------- Make random_lines reproducible between py2 and py3 random.seed has changed in python 3, and while there's backwards compatibility using `version=1`, random.randint and random.sample have also changed. The most striaghtforward change without adding additional dependencies then was to copy those methods from the python 2.7 source code. Commit: 7fe1079a52822d99e687d9cd966ee4d5e5f828b9 https://github.com/galaxyproject/galaxy/commit/7fe1079a52822d99e687d9cd966e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/web/framework/webapp.py M templates/tagging_common.mako Log Message: ----------- py3: Fix the remaining mako issues Commit: 11f92221223fe191cf2c4141e6dfc3b3630affa7 https://github.com/galaxyproject/galaxy/commit/11f92221223fe191cf2c4141e6df… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M test/unit/tools/test_execution.py Log Message: ----------- Fix redirection unit test Commit: fab5d69d58e70ab85ce160a4b963a1d0bd4f3677 https://github.com/galaxyproject/galaxy/commit/fab5d69d58e70ab85ce160a4b963… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- fix is_binary Commit: a2a155777dadda2fc576d078e5f9c8a488931e56 https://github.com/galaxyproject/galaxy/commit/a2a155777dadda2fc576d078e5f9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- py3: Fix redirection Commit: 4a9faf78c198ad92430a2e0666dcb92f0469fcb8 https://github.com/galaxyproject/galaxy/commit/4a9faf78c198ad92430a2e0666dc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Fix webob.compat make_file patching for py2 Commit: 418f1220c8f6b21bcf3b4ddcf9d19f29bdb2c373 https://github.com/galaxyproject/galaxy/commit/418f1220c8f6b21bcf3b4ddcf9d1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/tools/test.py Log Message: ----------- py3: Fix DataParameter test data upload Commit: bb26a3a7ac361b2bc094285184775990de99f7ee https://github.com/galaxyproject/galaxy/commit/bb26a3a7ac361b2bc09428518477… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/jobs/runners/state_handlers/_safe_eval.py Log Message: ----------- py3: fix safe_eval Commit: d13697b66b5dfb6a38221036fa777f477f2d1dca https://github.com/galaxyproject/galaxy/commit/d13697b66b5dfb6a38221036fa77… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py Log Message: ----------- py3: Fix mulled resolver Commit: e91d892a9bb3bec5b16389ff1435cd90195cea7a https://github.com/galaxyproject/galaxy/commit/e91d892a9bb3bec5b16389ff1435… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/util/hash_util.py Log Message: ----------- py3: fix sha1 hashing Commit: 63da35889d45459de83a8c66e4fbb7060d92e72c https://github.com/galaxyproject/galaxy/commit/63da35889d45459de83a8c66e4fb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M test/base/populators.py Log Message: ----------- py3: Fix exception handling in wait_on method Commit: fd5e8cdd288846a375c34ae6ca83f051cfdea45b https://github.com/galaxyproject/galaxy/commit/fd5e8cdd288846a375c34ae6ca83… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- py3: fix test_scripts integration test Commit: 8ccd5ed137797e31ed2fac34fa68244f770c6514 https://github.com/galaxyproject/galaxy/commit/8ccd5ed137797e31ed2fac34fa68… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M test/integration/test_upload_configuration_options.py Log Message: ----------- py3: Fix upload_configuration_options integration test Commit: 049e4d0fa37c66c41961d609337649791271c883 https://github.com/galaxyproject/galaxy/commit/049e4d0fa37c66c41961d6093376… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M test/api/test_libraries.py Log Message: ----------- py3: Fix test_fetch_zip_to_folder test Commit: b7163c0597fac16a34b53d607ae7e8485869022a https://github.com/galaxyproject/galaxy/commit/b7163c0597fac16a34b53d607ae7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/workflow/steps.py M test/base/data/test_workflow_topoambigouity.ga M test/base/data/test_workflow_topoambigouity_auto_laidout.ga Log Message: ----------- Explicitly sort workflow step edges This seems to be necessary so that the workflow_stability test passes under python 2 and python3, but does change the result under python 2, hence the updated workflows (produced by uploading and downloading the workflow to an instance running with this commit). Commit: 389a1d6563f06fc5b8b4ae42fa1824053f3897d4 https://github.com/galaxyproject/galaxy/commit/389a1d6563f06fc5b8b4ae42fa18… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/runners/state_handlers/_safe_eval.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/test.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/hash_util.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/static.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/authenticate.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/tool_data.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/workflow/steps.py M templates/tagging_common.mako M test/api/test_authenticate.py M test/api/test_dataset_collections.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_tool_data.py M test/api/test_tools.py M test/base/data/test_workflow_topoambigouity.ga M test/base/data/test_workflow_topoambigouity_auto_laidout.ga M test/base/populators.py M test/integration/test_scripts.py M test/integration/test_upload_configuration_options.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M tools/filters/random_lines_two_pass.py Log Message: ----------- Merge pull request #6561 from mvdbeek/start_py3_api_tests Fix all py3 api tests Compare: https://github.com/galaxyproject/galaxy/compare/b7dba0b82d49...389a1d6563f0 **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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