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Migrate models to pydantic 2 #17262

Merged
merged 182 commits into from Jan 11, 2024
Merged

Migrate models to pydantic 2 #17262

merged 182 commits into from Jan 11, 2024

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mvdbeek
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@mvdbeek mvdbeek commented Jan 10, 2024

Continuation of #16527 ... sorry for the huge PR, but there's not much one can do incrementally.

How to test the changes?

(Select all options that apply)

  • I've included appropriate automated tests.
  • This is a refactoring of components with existing test coverage.
  • Instructions for manual testing are as follows:
    1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

  • I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

@mvdbeek
Temp
aae0376
@mvdbeek
Port OffsetNaiveDatetime to pydantic2
5673cbc
@mvdbeek
Fix up remaining pydantic issues
181c5e1
@mvdbeek
Remove DecodedDatabaseIdField instance check
c6a25b8
@mvdbeek
Replace DecodedDatabaseIdField.encode with Security.security.encode_id
1593570
@mvdbeek
Fix example -> examples
0fc981c
@mvdbeek
Fix valid_id validator
396206a
@mvdbeek
Fix validation error transform
e25553d
@mvdbeek
Drop explicit json encoder
b1e05c3
@mvdbeek
Fix ValidationError import
0c3c760
@mvdbeek
Adapt as_form decorator
8117f02
@mvdbeek
Drop more Required
727b21b
@mvdbeek
Fix one more ValidationError import
87a7b77
@mvdbeek
Also override validation schema
8987752
@mvdbeek
Revert me: drop custom schema generation
f49a399
@mvdbeek
Use model_construct and model_dump
82e1301
@mvdbeek
Field fixes
b55f335
@mvdbeek
Validation error fix
7f38e1c
@mvdbeek
Fix use of HistoryIDPathParam
76f17ab
@mvdbeek
Re-use more path params
e2475fd
@mvdbeek
Update user api path param
22ca53a
@mvdbeek
Fix double encoding of user ids
c2fa422
@mvdbeek
Rename id to workflow_id parameter
1472463
@mvdbeek
Fix one more case of __root__ in pydantic RootModel
49c5a9d
@mvdbeek
Optional attributes are still required
3fcc810
@mvdbeek
Don't double-encode user id
60d477c
@mvdbeek
Fix collection type optionality in collection payload
fbe3070
@mvdbeek
Create new type from annotated types
6cf2316 
That's needed so that the new type will be picked up from the default
value assignment, as in:

```
def needs_id(id: DecodedDatabaseId =Path(...))
```
@mvdbeek
Use model_rebuild instead of update_forward_refs
970bbf4
@mvdbeek
Fix fetch_data schema unit tests
ed1c30a
@mvdbeek mvdbeek added kind/refactoring cleanup or refactoring of existing code, no functional changes and removed area/dependencies area/libraries Data libraries area/objectstore area/testing/api area/client area/packaging labels Jan 10, 2024
@github-actions github-actions bot added this to the 24.0 milestone Jan 10, 2024
@mvdbeek mvdbeek requested review from a team and davelopez January 10, 2024 09:39
nsoranzo
nsoranzo reviewed Jan 10, 2024
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lib/galaxy/schema/drs/openapi.yaml Outdated
@@ -0,0 +1,1731 @@
openapi: 3.0.3
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Does this file need to be included in the repo?

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Yeah - expanded diff for the same question 😆.

nsoranzo
nsoranzo reviewed Jan 10, 2024
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packages/schema/setup.cfg Outdated
@@ -31,7 +31,8 @@ version = 23.1.0.dev0
include_package_data = True
install_requires =
galaxy-util
pydantic[email]<2
pydantic[email]>=2
pycryptodome
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I cannot find where this is used?

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It's used for id encoding and decoding via IdEncodingHelper

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which I could make a type-only import

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which I could make a type-only import

That's probably better, otherwise you'd need to require galaxy-data .

nsoranzo
nsoranzo reviewed Jan 10, 2024
View reviewed changes
packages/web_apps/setup.cfg Outdated
@@ -9,6 +9,7 @@ classifiers =
Natural Language :: English
Operating System :: POSIX
Programming Language :: Python :: 3
Programming Language :: Python :: 3.7
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There seems to be a number of merge issues with this file, can you please double-check?

nsoranzo
nsoranzo reviewed Jan 10, 2024
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scripts/dump_openapi_schema.py Outdated
AnyUrl,
url_regex,
)
from pydantic.networks import AnyUrl # url_regex,
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Can the commented-out code be removed?

lib/tool_shed/webapp/api2/repositories.py Outdated
Comment on lines 511 to 512
def _hack_fastapi_4428(as_dict) -> RepositoryMetadata:
return RepositoryMetadata(root=as_dict)
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This can probably just be dropped since it's called only in one place?

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Good call, thank you!

jmchilton
jmchilton approved these changes Jan 10, 2024
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This is wildly ambitious and I am grateful for our test coverage. Really, really impressive @mvdbeek.

@mvdbeek mvdbeek merged commit e341ced into galaxyproject:dev Jan 11, 2024
56 checks passed
@mvdbeek mvdbeek deleted the pydantic_v2_2024 branch January 11, 2024 08:36
This was referenced Jan 11, 2024
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nsoranzo added a commit to nsoranzo/galaxy that referenced this pull request Jan 15, 2024
@nsoranzo
Update missed pydantic version pin
69d197e 
Forgotten in galaxyproject#17262 .

Fix broken Update dependencies CI build:
https://github.com/galaxyproject/galaxy/actions/runs/7509887325/job/20447594708
nsoranzo added a commit that referenced this pull request Jan 15, 2024
@nsoranzo
Merge pull request #17302 from nsoranzo/17274_followup
7af682d 
Follow-up on #17274 and #17262
@nsoranzo nsoranzo mentioned this pull request Jan 16, 2024
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@davelopez
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Amazing indeed! Thank you so much for taking care of all this 🙏

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@nsoranzo nsoranzo nsoranzo left review comments

@jmchilton jmchilton jmchilton approved these changes

@davelopez davelopez Awaiting requested review from davelopez

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@mvdbeek @davelopez @jmchilton @nsoranzo