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.
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.
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.
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.
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.
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
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