guerler
fbabcf178d
Remove legacy admin router and bundle entry point (for now)
2022-08-25 10:28:16 -04:00
guerler
58901c9036
Redirect admin client routes
2022-08-25 10:28:14 -04:00
Marius van den Beek
4c41d3e5d5
Merge pull request #14506 from dannon/rxjs-cleanup
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RxJS cleanup; removing cruft we no longer use
2022-08-25 15:58:25 +02:00
Marius van den Beek
eed63201e5
Merge pull request #14461 from dannon/about-this-galaxy
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Add "About this Galaxy" page.
2022-08-25 12:54:46 +02:00
Dannon Baker
f33c65cf4e
No longer need a barrel here, and we don't want to encourage proliferation.
2022-08-24 16:45:17 -04:00
Dannon Baker
3237fac798
Cleanup of rxjs; removing cruft we no longer use (most was associated with the 'beta' history implementation)
2022-08-24 16:41:23 -04:00
John Chilton
9a8260ce26
Merge pull request #14472 from qiagu/dynamic_destination
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Refactor dynamic destination mapper
2022-08-24 15:01:00 -04:00
John Chilton
be79f5ad3a
Merge pull request #14436 from davelopez/refactor_pydantic_id_handling
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Refactor pydantic id handling
2022-08-24 14:50:31 -04:00
Marius van den Beek
ef81872614
Merge pull request #14441 from ElectronicBlueberry/fix-currentuser-duplicate-request
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Fix duplicate Request to CurrentUser
2022-08-24 17:05:47 +02:00
Dannon Baker
03193ae425
Swap license container to span (inline by default, anywhere that needs it in a separate block can do that); link whole name.
2022-08-24 10:57:56 -04:00
mvdbeek
68d07cb890
Merge branch 'release_22.05' into dev
2022-08-24 15:24:04 +02:00
Dannon Baker
60d83063c0
Dump table display, list simple key/val
2022-08-24 08:17:33 -04:00
Dannon
e1561ad665
Merge pull request #14494 from mvdbeek/fix_refactor_action
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[22.05] Fix refactor action dropping outputs on subworkflow connection
2022-08-24 07:07:06 -04:00
davelopez
4f0f0fccb5
Refactor configuration API decode_id
2022-08-24 12:05:50 +02:00
davelopez
968fc9b961
Refactor create page
2022-08-24 12:05:50 +02:00
davelopez
a3c48dc6d1
Remove decoding from libraries import store
2022-08-24 12:05:50 +02:00
davelopez
a4dd876020
Fix get_library_folder in output_collect
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The destination is not handled by a pydantic model and might require decoding
2022-08-24 12:05:50 +02:00
davelopez
8ad117e7ff
Fix history archive export
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- Use pydantic model construct to avoid revalidation
- Keep JobIdResponse ID as EncodedDatabaseIdField so it gets automatically encoded back
2022-08-24 12:05:50 +02:00
davelopez
2db10b5278
Fix materialize history contents
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Use pydantic model construct to avoid revalidation
2022-08-24 12:05:49 +02:00
davelopez
f4521542b9
Fix library folder create content
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Remove unused parameters and duplicated ID decode
2022-08-24 12:05:49 +02:00
davelopez
389cdfd09c
Remove ID encoding in recalculate_user_disk_usage
2022-08-24 12:05:49 +02:00
davelopez
9ddde05dc1
Fix run_as in get_api_user
2022-08-24 12:05:49 +02:00
mvdbeek
27f4b54df1
Drop response_model_exclude_unset=True
...
It's a nice option, but all clients need to be aware of this change, and
we don't have a way to ensure this right now. I think we can work with
media types in the future to enable this for clients that expect certain
fields to no be present.
Fixes:
```
____________ HistoryContentsApiTestCase.test_index_hda_detail_by_id ____________
self = <galaxy_test.api.test_history_contents.HistoryContentsApiTestCase testMethod=test_index_hda_detail_by_id>
def test_index_hda_detail_by_id(self):
hda1 = self.dataset_populator.new_dataset(self.history_id)
contents_response = self._get(f"histories/{self.history_id}/contents?details={hda1['id']}")
hda_details = self.__check_for_hda(contents_response, hda1)
> self.__assert_hda_has_full_details(hda_details)
lib/galaxy_test/api/test_history_contents.py:159:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
lib/galaxy_test/api/test_history_contents.py:633: in __assert_hda_has_full_details
self._assert_has_keys(hda_details, "display_types", "display_apps")
lib/galaxy_test/base/api.py:117: in _assert_has_keys
assert_has_keys(response, *keys)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
response = {'create_time': '2022-03-25T09:54:23.655522', 'dataset_id': '3492b5c7510432ff', 'deleted': False, 'extension': 'txt', ...}
keys = ('display_types', 'display_apps'), key = 'display_types'
def assert_has_keys(response: dict, *keys: str):
"""Assert that the supplied response (dict) has the supplied keys."""
for key in keys:
> assert key in response, f"Response [{response}] does not contain key [{key}]"
E AssertionError: Response [{'state': 'queued', 'url': '/api/histories/763817bba969bb3b/contents/111726bf3c6a45d3', 'history_id': '763817bba969bb3b', 'type': 'file', 'create_time': '2022-03-25T09:54:23.655522', 'history_content_type': 'dataset', 'hid': 1, 'purged': False, 'deleted': False, 'visible': True, 'type_id': 'dataset-111726bf3c6a45d3', 'dataset_id': '3492b5c7510432ff', 'name': 'Test_Dataset', 'id': '111726bf3c6a45d3', 'extension': 'txt', 'tags': [], 'update_time': '2022-03-25T09:54:23.742463'}] does not contain key [display_types]
```
2022-08-24 12:05:49 +02:00
mvdbeek
ad1e5d96a7
Fix page manager usage in controller
2022-08-24 12:05:49 +02:00
mvdbeek
c5945a82f5
Drop library code path that has been broken since 18.01
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since _check_modify was never ported from the legacy mako interface.
I also don't see any use of `replace_id`, so I don't think this is used.
2022-08-24 12:05:49 +02:00
mvdbeek
7bfb9740ad
Fix library stuff
2022-08-24 12:05:48 +02:00
mvdbeek
826f1c9931
Fix id handling in library API
2022-08-24 12:05:48 +02:00
mvdbeek
8835c1bef9
Fix run_as functionality
2022-08-24 12:05:48 +02:00
mvdbeek
a5cf5df385
Fix test_hda_security test
2022-08-24 12:05:48 +02:00
mvdbeek
07530572a0
Fix invocations filter
2022-08-24 12:05:48 +02:00
mvdbeek
0e4e3f5c33
Fix ShareableService._get_user
2022-08-24 12:05:48 +02:00
davelopez
a7303e219e
Fix API unit tests with ID encodings
2022-08-24 12:05:47 +02:00
davelopez
a840696b93
Remove encoding in CreatesCollectionsMixin
2022-08-24 12:05:47 +02:00
davelopez
9beeb4f1ea
Fix whoami endpoint
2022-08-24 12:05:47 +02:00
davelopez
e21c665053
Fix import format
2022-08-24 12:05:47 +02:00
davelopez
5d119e781a
Fix create history item from copy content model
2022-08-24 12:05:47 +02:00
davelopez
64da2b22aa
Refactor library folders API
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- Use DecodedDatabaseIdField
- Build response models with `construct` to avoid validation before serialization
2022-08-24 12:05:47 +02:00
davelopez
f8ea65ac63
Refactor libraries API
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- Use DecodedDatabaseIdField
- Build response models with `construct` to avoid validation before serialization
2022-08-24 12:05:47 +02:00
davelopez
f87e4152a6
Refactor fetch
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- Use DecodedDatabaseIdField
2022-08-24 12:05:46 +02:00
davelopez
12f014d4c6
Refactor datasets API
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- Use DecodedDatabaseIdField
- Build response models with `construct` to avoid validation before serialization
2022-08-24 12:05:46 +02:00
davelopez
cf735e12bd
Add some type hints to user manager
2022-08-24 12:05:46 +02:00
davelopez
841452b506
Refactor tool_data API
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- Use DecodedDatabaseIdField
- Build response models with `construct` to avoid validation before serialization
2022-08-24 12:05:46 +02:00
davelopez
7903174ecf
Refactor workflows API (partially)
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- Use DecodedDatabaseIdField where possible
- Build response models with `construct` to avoid validation before serialization
2022-08-24 12:05:46 +02:00
davelopez
c742932bb2
Refactor pages API
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- Build response models with `construct` to avoid validation before serialization
2022-08-24 12:05:45 +02:00
davelopez
7d2693ccad
Use different slugs in pages API tests
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I'm surprised this didn't fail before when running both tests `test_index_show_shared_with_me` and `test_index_show_shared_with_me_deleted` in the same batch since the slugs must be unique.
2022-08-24 12:05:45 +02:00
davelopez
a224bea462
Refactor pages API
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- Use DecodedDatabaseIdField
- Build response models with `construct` to avoid validation before serialization
2022-08-24 12:05:45 +02:00
davelopez
ed12c221c9
Refactor history_contents API
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- Use DecodedDatabaseIdField
- Build response models with `construct` to avoid validation before serialization
2022-08-24 12:05:45 +02:00
davelopez
462f0c3fbf
Refactor histories API
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- Use DecodedDatabaseIdField
- Build response models with `construct` to avoid validation before serialization
2022-08-24 12:05:45 +02:00
davelopez
a3d67ff958
Refactor tags manager
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- Use DecodedDatabaseIdField
- Reduce use of trans
2022-08-24 12:05:44 +02:00
davelopez
b181e8e400
Refactor dataset_collections API
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- Use DecodedDatabaseIdField
- Build response models with `construct` to avoid validation before serialization
2022-08-24 12:05:44 +02:00
guerler