mvdbeek
5cfa818207
Merge branch 'release_21.09' into dev
2021-10-22 22:21:17 +02:00
Marius van den Beek
8762475d57
Merge pull request #12772 from mvdbeek/double_scheduling_21_09_forward
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[21.09] merge 21.05 forward
2021-10-22 22:20:51 +02:00
mvdbeek
2e282b1d4c
Merge branch 'release_21.05' into double_scheduling_21_09_forward
2021-10-22 19:39:14 +02:00
Nate Coraor
947d7cf050
Merge pull request #12763 from mvdbeek/fix_job_double_scheduling
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[21.05] Fix double enqueuing of upload jobs
2021-10-22 13:28:40 -04:00
Sergey Golitsynskiy
c3fa79b039
Merge pull request #12765 from ic4f/dev_mapping_tests2
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Mapping tests: restructure, refactor, decouple session and engine, improve
2021-10-22 12:07:36 -04:00
mvdbeek
2a335c981b
Fix double enqueuing of upload jobs
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The canonical place to call enqueue is in
https://github.com/galaxyproject/galaxy/blob/a5bb3e92667b96ef802b378f17788b253a5c0bc6/lib/galaxy/tools/execute.py#L127 .
In the process of enqueue the db-skip-locked assignment method will set
the handler name to the default tag. If you do this more than once the
job might be picked up by compatible handlers.
Fixes https://github.com/galaxyproject/galaxy/issues/11335
2021-10-22 16:49:00 +02:00
Marius van den Beek
61810c833f
Merge pull request #12760 from davelopez/improve_directory_uri_parameter_validation
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[21.09] Improve error handling in DirectoryUriToolParameter validation
2021-10-22 10:41:42 +02:00
Sergey Golitsynskiy
f497654ef0
Drop unused fixtures
2021-10-22 00:45:32 -04:00
Sergey Golitsynskiy
3418bc7b94
Ignore mypy. Rebinding a reference to a value with a diff type is OK.
2021-10-21 23:40:39 -04:00
Sergey Golitsynskiy
57997a9230
Add comment to session fixture
2021-10-21 22:55:51 -04:00
Sergey Golitsynskiy
649ed292f1
Factor out BaseTest into common
2021-10-21 22:43:56 -04:00
Sergey Golitsynskiy
b0c291cd6d
Do not use Galaxy's session and engine for tests (see note)
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Here we are supposed to be testing mapping; however, by using Galaxy's
session and engine, we also end up testing session and engine setup
(i.e., "testing by coincidence"). Instead, we will use a plain engine
and session, thus limiting these tests to their expected scope.
Applied to model and install_model mapping tests.
2021-10-21 22:31:06 -04:00
Sergey Golitsynskiy
13286b1206
Apply changes from #12714 to model mapping tests
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Disable test verification fixture by default (too expensive!)
Add comment explaining fixture + how to enable it.
2021-10-21 20:45:26 -04:00
Sergey Golitsynskiy
bc55a9373b
Apply changes from #12714 to TS mapping tests
2021-10-21 20:21:11 -04:00
Sergey Golitsynskiy
c005eca8b1
Rename test_test_mapping; fix import
2021-10-21 19:44:18 -04:00
Sergey Golitsynskiy
f622016e75
Drop duplicate stuff, reference common.py from install model test
2021-10-21 19:41:19 -04:00
Sergey Golitsynskiy
afbab2f377
Move test utils out of model test into common.py
2021-10-21 19:38:53 -04:00
Sergey Golitsynskiy
837b1aa1c7
Try out black w/default settings. Because 7K lines is too much.
2021-10-21 19:29:33 -04:00
Sergey Golitsynskiy
43906e014c
Use pkey comparison to compare mapped object collections (see note)
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It is possible (even likely, with a different/better/simpler session
setup) that the objects populating the collection attribute representing
a relationship on a stored object will NOT be the same Python objects
that were initially associated with the object via that relationship.
Thus, Python object identity comparison will fail (when we change the
session setup). Besides, we should be using the database primary key as
the comparison key, because that is the only correct measure of
database-mapped object equality.
2021-10-21 19:28:17 -04:00
Sergey Golitsynskiy
e66454734a
Move mapping tests into own dir; start refactoring
2021-10-21 18:50:25 -04:00
Sergey Golitsynskiy
a834b54039
Replace old function w/improved version; adjust calls
2021-10-21 18:42:23 -04:00
Sergey Golitsynskiy
518cc517fc
Add better function+test for testing collection equality
2021-10-21 18:37:53 -04:00
M Bernt
00dbdf3963
Merge pull request #12762 from dannon/to-to
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[21.09] 'to to' typos (minor)
2021-10-21 21:06:31 +02:00
Dannon
5dc9111f45
Merge pull request #12739 from assuntad23/bugfix/removing-end-punctuation-from-pair-name/12154
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Removing last character of pair name for Paired List Collections if it's a . or _
2021-10-21 13:11:19 -04:00
davelopez
2fd861bf89
Improve error handling in DirectoryUriToolParameter validation
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Avoids 500 status code if the parameter has a wrong value
2021-10-21 19:07:58 +02:00
Dannon Baker
2dd0eed46b
Fix several 'to to' redundant word typos.
2021-10-21 12:28:45 -04:00
Marius van den Beek
cf08f3a11f
Merge pull request #12755 from bernt-matthias/topic/getfullargspec
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Remove `galaxy.util.getfullargspec`
2021-10-21 15:38:46 +02:00
Marius van den Beek
31e6b32221
Merge pull request #12758 from dannon/fix_history_sort
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[21.09] Prefer model class when it exists in grid sorting
2021-10-21 15:36:34 +02:00
Dannon Baker
29e0901794
Prefer model class when it exists (assuming it is more correct/refined logic) over column. This fixes history sort to work correctly in grids.
2021-10-21 07:37:54 -04:00
Marius van den Beek
f302a2def7
Merge pull request #12756 from ic4f/dev_install_model_declarative
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Convert install_model to declarative mapping
2021-10-21 10:26:26 +02:00
Matthias Bernt
dc34550610
remove util.getargspec
2021-10-21 10:23:19 +02:00
Sergey Golitsynskiy
404bac3903
Fix .metadata_ in tool_shed dir
2021-10-20 20:58:54 -04:00
Sergey Golitsynskiy
bd765b0b24
Replace all remaining instances of TSR.metadata
2021-10-20 18:51:46 -04:00
Sergey Golitsynskiy
5acbb140b1
Remove refs to ToolShedRepository.metadata in scripts/
2021-10-20 17:15:39 -04:00
Sergey Golitsynskiy
691a3f6599
Remove refs to ToolShedRepository.metadata in test/
2021-10-20 17:15:39 -04:00
Sergey Golitsynskiy
d870278f7c
Map ToolShedRepository declaratively (see note)
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Rename metadata to metadata_. This will break things.
(we are only renaming the model attribute, not the table column)
Next step: rename all instances of [ToolShedRepository].metadata in code base.
2021-10-20 17:15:38 -04:00
Sergey Golitsynskiy
638f9a7a1c
Fix import error
2021-10-20 15:12:20 -04:00
Sergey Golitsynskiy
3738c1a281
Add missing delete-from-db statement
2021-10-20 15:09:23 -04:00
Sergey Golitsynskiy
353ce421cf
Drop redundant model constructors
2021-10-20 14:54:39 -04:00
Sergey Golitsynskiy
b0446b1750
Drop redundant datatypes from fkeys
2021-10-20 14:51:01 -04:00
Sergey Golitsynskiy
a8e3c843f2
Fix SAWarning: add back_populates args
2021-10-20 14:48:16 -04:00
Sergey Golitsynskiy
cf964678b9
Remove unnecessary primary_join attr
2021-10-20 14:38:17 -04:00
Sergey Golitsynskiy
f99a3972cd
Remove backref from ToolShedRepository.tool_dependencies
2021-10-20 14:36:22 -04:00
Sergey Golitsynskiy
19dc5c9092
Remove backref from ToolShedRepository.tool_version
2021-10-20 14:33:20 -04:00
Marius van den Beek
a5bb3e9266
Merge pull request #12754 from mvdbeek/dev
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Merge 21.09 forward again
2021-10-20 20:03:07 +02:00
Dannon
b7a61d972c
Merge pull request #12752 from scholtalbers/patch-2
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Update CONTRIBUTORS.md
2021-10-20 13:32:33 -04:00
Sergey Golitsynskiy
191464f2fc
Map ToolVersionAssociation declaratively
2021-10-20 13:31:10 -04:00
Sergey Golitsynskiy
1fe5e6dfc8
Map ToolVersion declaratively
2021-10-20 13:22:13 -04:00
Sergey Golitsynskiy
92b32bab81
Map ToolDependency declaratively
2021-10-20 13:17:02 -04:00
Sergey Golitsynskiy
a3d7a37c8e
Map RepositoryDependency declaratively
2021-10-20 13:09:47 -04:00
mvdbeek