Nicola Soranzo
95c0950ba6
Add type annotations to `JobRunnerMapper` and related code
2024-11-07 15:19:32 +00:00
John Davis
e5635dc2b7
Merge pull request #19073 from jmchilton/pydantic_model_linting
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Integrate Tool Parameter Modeling into Linting (for Planemo)
2024-11-05 17:52:10 -05:00
Nicola Soranzo
1f223d0dc5
Test hash validation also for upload by path
2024-11-05 15:33:40 +00:00
Björn Grüning
a5aaa1c1be
Merge pull request #19077 from davelopez/allow_deferred_as_uri
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Allow deferred datasets to behave as URIs
2024-11-04 23:09:12 +01:00
Nicola Soranzo
ac480e7df5
Drop use of deprecated imghdr standard library module
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which has been removed in the upcoming Python 3.13 .
2024-10-31 12:09:21 +00:00
davelopez
305dd2b181
Add has_deferred_data flag to MockDataset and FakeDatasetAssociation
2024-10-31 11:17:16 +01:00
davelopez
b3a70863fc
Add test for parsing allow_uri_if_protocol
2024-10-31 11:17:16 +01:00
Marius van den Beek
339724e0aa
Merge pull request #19070 from mvdbeek/reuse_trs_import_in_workflow_contents_manager
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Move TRS import into WorkflowContentManager
2024-10-30 15:27:21 -04:00
mvdbeek
48ed0682dc
Move TRS import into WorkflowContentManager
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which fixes missing source metadata when importing a workflow through a
landing page.
2024-10-30 17:32:23 +01:00
John Chilton
5b08e9b9bb
Integrate some new Pydantic models into Planemo lint.
2024-10-30 10:58:35 -04:00
Björn Grüning
d11d8930a3
Merge pull request #19027 from jmchilton/parameter_model_enhancements
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A variety of improvements around tool parameter modeling (second try)
2024-10-29 07:57:12 +01:00
Marius van den Beek
1ebd078043
Merge pull request #18985 from jmchilton/workflow_request
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Allow recovering a normalized version of workflow request state from API
2024-10-28 13:17:08 -04:00
John Chilton
078ad6114b
Fix param models for dynamic options and truevalue/falsevalue
2024-10-22 07:49:37 -04:00
John Chilton
730ea2ee03
Pydantic models for parameter validators.
2024-10-22 07:49:37 -04:00
John Chilton
c198c7cb97
models for tool landing request state...
2024-10-22 07:49:37 -04:00
John Chilton
7ef5cc22e4
Refactor for reuse in galaxy.tool_util.parameters.
2024-10-22 07:49:37 -04:00
John Chilton
f27b202500
Spelling error.
2024-10-22 07:49:37 -04:00
John Chilton
8c10f36dd2
Refactor Tool._populate for reuse of hook checks.
2024-10-22 07:49:37 -04:00
John Chilton
639d3025b3
Merge pull request #18979 from mvdbeek/workflow_landing_improvements
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Workflow landing improvements
2024-10-22 07:47:12 -04:00
mvdbeek
f4a779e45f
Fix unit tests
2024-10-20 18:34:57 -04:00
Nicola Soranzo
4e56b47d5d
Merge branch 'release_24.1' into dev
2024-10-16 11:26:07 +01:00
mvdbeek
67fff6ac73
Allow using TRS ids as workflow id in workflow landing requst
2024-10-15 15:25:38 +02:00
John Chilton
7f7710d392
Implement recovering normalized workflow request from invocation.
2024-10-15 09:12:05 -04:00
John Chilton
edc5bc2a8f
Allow oauth2 file sources with Dropbox initial implementation.
2024-10-14 15:16:41 +02:00
John Chilton
01c42c888b
Expand pre-checking of file source/object store configuration.
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- UI for detailed display of errors.
- UI option to test configuration from management menu.
- API + UI for checking configuration before upgrading to new version of template.
- API + UI for checking configuration before updating current template's settings.
- Add an option during update/upgrade to allow forcing the update even if configuration doesn't validate - I don't allow creation of invalid things, but if there are problems with an existing thing - admins and power users should have recourse. It is their data.
2024-10-14 14:27:05 +02:00
mvdbeek
a42496e8ec
Disable locking when opening h5 files, add missing with
2024-10-12 09:26:54 +02:00
Marius van den Beek
119324f754
Merge pull request #18942 from jdavcs/dev_sharing_fix2
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Fix backend sharing bug
2024-10-08 16:06:00 +02:00
John Chilton
eea3909cb0
Fixes and expansion of webdav unit tests.
2024-10-05 17:23:26 -04:00
John Davis
00bebee7c7
Add test exposing bug
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After user's email has been modified, we can't retrieve sharing roles
for that user
2024-10-04 14:44:41 -04:00
Björn Grüning
d18bc6855d
Merge pull request #18919 from jmchilton/biotools
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Fix commas that shouldn't be in biotools_mappings.tsv
2024-10-04 11:06:06 +02:00
John Chilton
beb4842b8d
Allow multiple xrefs in biotools_mappings.tsv.
2024-10-02 00:10:44 -04:00
Marius van den Beek
2ead0c41e9
Merge pull request #18807 from jmchilton/landing
2024-10-01 21:44:50 +02:00
Marius van den Beek
8db5a7682c
Merge pull request #18834 from jmchilton/data_fetch_fixes
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Fixes and tests for data fetch models.
2024-10-01 19:15:00 +02:00
Nicola Soranzo
136747e766
Type annotations and fixes
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- Use `galaxy.util.path.StrPath` everywhere
2024-09-30 21:33:44 +01:00
John Chilton
93f2af6a44
Allow dataset and source checksum validation during materialization.
2024-09-30 13:25:02 -04:00
John Chilton
660f78fe37
Implement workflow landings.
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Includes a lot of plumbing for tools but not the APIs - they are not ready to go yet.
2024-09-30 13:25:02 -04:00
John Chilton
80aaff8d23
Plumbing for dereferencing URLs into datasets.
2024-09-30 13:25:02 -04:00
John Chilton
ad73e9e838
Tool Request models.
2024-09-30 13:25:02 -04:00
John Chilton
dc4b59d6f5
Fixes and tests for data fetch models.
2024-09-30 13:25:02 -04:00
John Chilton
813ed02d53
Merge pull request #18886 from jdavcs/dev_db_test_update
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Refactor migration testing setup code
2024-09-25 10:49:27 -04:00
Matthias Bernt
7dd606a6b2
Merge branch 'release_24.1' into dev
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# Conflicts:
# lib/galaxy/version.py
# packages/app/HISTORY.rst
# packages/app/setup.cfg
# packages/auth/HISTORY.rst
# packages/auth/setup.cfg
# packages/config/HISTORY.rst
# packages/config/setup.cfg
# packages/data/HISTORY.rst
# packages/data/setup.cfg
# packages/files/HISTORY.rst
# packages/files/setup.cfg
# packages/job_execution/HISTORY.rst
# packages/job_execution/setup.cfg
# packages/job_metrics/HISTORY.rst
# packages/job_metrics/setup.cfg
# packages/navigation/HISTORY.rst
# packages/navigation/setup.cfg
# packages/objectstore/HISTORY.rst
# packages/objectstore/setup.cfg
# packages/schema/HISTORY.rst
# packages/schema/setup.cfg
# packages/selenium/HISTORY.rst
# packages/selenium/setup.cfg
# packages/test_api/HISTORY.rst
# packages/test_api/setup.cfg
# packages/test_base/HISTORY.rst
# packages/test_base/setup.cfg
# packages/test_driver/HISTORY.rst
# packages/test_driver/setup.cfg
# packages/tool_shed/HISTORY.rst
# packages/tool_shed/setup.cfg
# packages/tool_util/HISTORY.rst
# packages/tool_util/setup.cfg
# packages/tours/HISTORY.rst
# packages/tours/setup.cfg
# packages/util/HISTORY.rst
# packages/util/setup.cfg
# packages/web_apps/HISTORY.rst
# packages/web_apps/setup.cfg
# packages/web_framework/HISTORY.rst
# packages/web_framework/setup.cfg
# packages/web_stack/HISTORY.rst
# packages/web_stack/setup.cfg
2024-09-25 14:29:37 +02:00
Marius van den Beek
3c924147f1
Merge pull request #18884 from jmchilton/test_format
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Implement Pydantic model for workflow test format.
2024-09-25 12:07:06 +02:00
John Davis
b57ec18991
Refactor migration testing setup code
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- Do not explicitly import fixtures (a little duplication is safer/cleaner)
- Move dangerous fixture into module to prevent accidental usage from other modules
- Ensure only one database is used for all tests in module
2024-09-24 20:47:09 -04:00
John Davis
03641a98fa
Fix migration data fixes tests
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When upgrading back to a valid revision, upgrade to head, not the
revision under test: we need the latest version of the model definition
in the database for the test to cleanup correctly.
2024-09-24 16:16:05 -04:00
John Chilton
675c9670e2
Models for YAML test format.
2024-09-24 12:47:07 -04:00
John Davis
5524ea77a7
Add tests for migration fixes
2024-09-23 23:52:05 -04:00
John Davis
2fc21f9962
Do not pass unnecessary arguments
2024-09-23 17:05:15 -04:00
John Davis
6c4ddeb91d
Test that private roles are not assignable
2024-09-23 17:05:15 -04:00
John Davis
8c4a90010a
Add tests for user and history default permissions
2024-09-23 17:05:15 -04:00
John Davis
19d76e9580
Fix mypy: statements are reachable
2024-09-23 17:05:15 -04:00
Nicola Soranzo