John Chilton
4bd80ce6ef
Flush out documentation and service-info for DRS API a bit.
2022-12-08 10:08:01 -05:00
Uwe Winter
f24e55aa9f
Implement access_id method to resolve object with expensive url generation schema. See https://ga4gh.github.io/data-repository-service-schemas/preview/develop/docs/#tag/AccessMethodModel
2022-12-08 10:08:01 -05:00
John Chilton
8ff9fe2610
Implement initial GA4GH DRS Support.
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- Implement APIs for serving Galaxy's public datasets as DRS objects.
- Implement support in galaxy.files.uris for DRS URIs so that upload, etc... can use DRS URIs from other data repositories.
The ways this can be improved are endless:
- New object ID patterns can be implemented to allow access to composite data, metadata files from a bundle view of datasets.
- New object ID patterns can be implemented to allow access to collections as bundles of datasets.
- More auth types and AccessMethods could be implemented for loading datasets from clients.
- Some sort of scheme for providing authenticated URLs to non-public data could be implemented to provide access to more of Galaxy's data if user's can implement.
Despite all these limitations - I think having the guts in like this provide useful points for interested parties to go and add functionality to enable their desired usecases.
2022-12-08 10:07:11 -05:00
Marius van den Beek
2a6f9c2a29
Merge pull request #15017 from natefoo/gravity-1.0
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Update Gravity version to 1.0.0 pre-release
2022-12-07 07:37:59 +01:00
Nicola Soranzo
f9daab77c3
Install involucro when resolvers are instantiated
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i.e. at Galaxy startup.
Also:
- Type annotations
- Code refactorings
2022-12-07 02:26:51 +00:00
Nicola Soranzo
f882d387d9
Fix resolved default value of `tool_dependency_dir and involucro_path` config options
2022-12-06 19:50:06 +00:00
Nate Coraor
fad0453e72
Update gravity section of sample config
2022-12-06 10:53:21 -05:00
Aysam Guerler
be46794aa0
Merge pull request #14985 from itisAliRH/vuetify_published_histories
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Vuetify published histories
2022-12-06 10:16:59 -05:00
Dannon
6f836720c7
Merge pull request #15106 from mvdbeek/typescript_api_client
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Add autogenerated typescript API client & use it
2022-12-06 09:07:51 -05:00
Marius van den Beek
d689b79169
Merge pull request #15090 from davelopez/fix_task_history_export_ftp
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Fix export history to FTP using tasks
2022-12-06 14:51:49 +01:00
mvdbeek
b7c62d0ac8
Add script that can dump openapi schema without a running galaxy
2022-12-06 12:59:01 +01:00
Marius van den Beek
1986e73841
Merge pull request #15105 from mvdbeek/model_class_fix
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Fix ``model_class`` field annotations
2022-12-06 11:50:42 +01:00
Dannon Baker
1a04b0f396
Merge remote-tracking branch 'upstream/release_22.05' into dev
2022-12-05 14:52:14 -05:00
Dannon Baker
1482c2be37
Merge remote-tracking branch 'upstream/release_22.01' into release_22.05
2022-12-05 14:36:31 -05:00
Dannon Baker
e5e6bda4f0
Contain directory traversal for static files to host static root.
2022-12-05 14:35:56 -05:00
mvdbeek
c797ae2df1
Use model class string literals instead of enum
2022-12-05 19:03:16 +01:00
Nate Coraor
9976d9b42e
Set gravity log dir for tests
2022-12-05 12:52:12 -05:00
Nate Coraor
36f6e39011
Update gravity section of sample config for 1.0
2022-12-05 12:52:12 -05:00
Nate Coraor
f329c71a97
Update gravity launch test for 1.0
2022-12-05 12:52:12 -05:00
Nate Coraor
0b9c30779d
Document setting env vars on static handlers
2022-12-05 12:52:11 -05:00
Nate Coraor
619c6ae47e
Use Gravity 1.0.0 pre-release
2022-12-05 12:52:11 -05:00
mvdbeek
d707507f46
Use a fixed example date
2022-12-05 18:51:18 +01:00
mvdbeek
47ff70af8e
Fix model_class schema annotations
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They would previously be marked as optional constants with a default
value, but I think literal is correct here. Coincidentally fixes a
typescript client generation issue.
2022-12-04 22:24:03 +01:00
galaxybot
bbd0e64474
Update Python dependencies
2022-12-03 16:32:25 +00:00
Aysam Guerler
4c40fe8071
Merge pull request #15082 from guerler/composition_bar
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Use Galaxy logo instead of Logo/Text combo, refactor masthead to composition api
2022-12-03 10:41:09 -05:00
Björn Grüning
6a5608bcd6
Merge pull request #15031 from jmchilton/structured_test_decorators
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Infrastructure for indicating Galaxy features being used by tests.
2022-12-03 10:34:49 +01:00
Alireza Heidari
bbabe3dedf
add get_published_history_names_from_server to histories published test
2022-12-02 14:47:23 +01:00
davelopez
48c9d6f7c8
Relax file source access requirements in tests
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By default the user must have the required role and groups. To simplify the setup of other tests, by default `PosixFileSourceSetup` will not require groups unless explicitly specified in the test.
This way we are always testing the default `test user` access through the role.
2022-12-02 13:12:28 +01:00
davelopez
ab4d24e26c
Fix ftp import export using tasks
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The FTP file source needs the user's context to access the ftp folder. It will also be required in case there are access restrictions on the target file source.
2022-12-02 10:04:06 +01:00
davelopez
a8dd40e0ab
Fix typing in test populator
2022-12-02 09:57:29 +01:00
davelopez
f98da7349c
Fix UUID serialization in Celery
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Most objects at `lib/galaxy/web/short_term_storage/__init__.py` are declared as `dataclass` (and not Pydantic models), so the UUID won't be automatically serialized.
2022-12-02 09:57:29 +01:00
davelopez
99166d0863
Make short_term_storage_request_id an UUID instead of str
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This provides correct typing and validation directly in the API
2022-12-02 09:57:29 +01:00
davelopez
efcf76e3b5
Return 404 when target expires or doesn't exists
2022-12-02 09:57:29 +01:00
davelopez and Nicola Soranzo
4566b59c01
Make sure there is no ambiguity ordering by type
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Co-authored-by: Nicola Soranzo <nicola.soranzo@earlham.ac.uk >
2022-12-01 19:11:02 +01:00
davelopez
464368ebf3
Sort always folders by name
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If the folder cannot be sorted by the specified column
2022-12-01 18:48:11 +01:00
Alireza Heidari
4306414cef
fix selenium error
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get all published histories from server to make sure all of them are included in assertions
2022-12-01 16:46:36 +01:00
Alireza Heidari
98f8eda622
delete unused imports from history controller
2022-12-01 10:58:55 +01:00
Alireza Heidari
f1a733f432
delete HistoryAllPublishedGrid class and related lines from history controller
2022-12-01 10:58:55 +01:00
Alireza Heidari
04477d6472
add selenium tests for published histories: test_histories_published
2022-12-01 10:58:54 +01:00
Alireza Heidari
cfbc66d452
delete test_published_histories_grid selenium test
2022-12-01 10:58:54 +01:00
John Davis
0aa0feb610
Merge pull request #15004 from jdavcs/dev_mypy_workflow
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Run mypy on a fully loaded galaxy venv for stricter type checking
2022-11-30 22:30:37 -05:00
Nicola Soranzo
303f1a04af
Revert "Add type annotation to `config attribute of MinimalToolApp` protocol"
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This reverts commit b1c35bfc6a
2022-12-01 01:52:25 +00:00
Dannon
4c7018caba
Merge pull request #15095 from nsoranzo/test_pkce
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Add ``pkce`` to dev/test requirements
2022-11-30 19:42:54 -05:00
guerler
72fd52f087
Deprecate brand title text option, logo now contains text
2022-11-30 17:19:07 -05:00
John Davis
b8f2aec155
Combine update lint/typecheck reqs scripts
2022-11-30 14:44:30 -05:00
Martin Cech
0b53cf510a
Merge pull request #13815 from bernt-matthias/topic/expect_test_failure
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expect_test_failure: also test if no failure was found
2022-11-30 20:14:50 +01:00
Martin Cech
02ff6ff7b4
Merge pull request #14984 from davelopez/22.05_fix_invalid_quota_amount
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[22.05] Fix invalid quota amount
2022-11-30 20:09:31 +01:00
Martin Cech
e4becc21a0
Merge pull request #14959 from bernt-matthias/topic/lint-expect_failure_num_outputs
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lint for coexisting expect_num_outputs and expect_failure
2022-11-30 20:06:29 +01:00
Nicola Soranzo
b1c35bfc6a
Add type annotation to `config attribute of MinimalToolApp` protocol
2022-11-30 17:57:29 +00:00
Nicola Soranzo
139d14e952
Fix `object_store type in MinimalToolApp` protocol
2022-11-30 17:55:04 +00:00
John Chilton