Fix ingest post dependency upgrade #1428
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Using the `pydantic.v1` `root_validator` failed to properly populate the `annotations` column of our annotated models.
It doesn't seem like `mypy` was picking up on the relationship between `BaseModel` and our defined models.
jeffbaumes
reviewed
Oct 21, 2024
marySalvi
reviewed
Oct 21, 2024
danlamanna
reviewed
Oct 21, 2024
marySalvi
approved these changes
Oct 22, 2024
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Fix #1423
Caused by #1420
Changes
After merging #1420 into dev, ingest stopped working. The initial reason reported by the failed ingest job was related to the use of
pydanticinnmdc-server. After addressing that issue, I noticed there were more issues preventing ingest from running successfully.PydanticUserError:
Studyis not fully defined; you should defineList, then callStudy.model_rebuild().This was the original issue, which can be seen in the logs for the failed ingest jobs. I followed the instructions given in the message to resolve this.
Type mismatch between data and postgres tables
Several columns on
MetagenomeAssemblyandMetatranscriptomeAssemblywere mistyped asBigInteger, where the most recentnmdc-schemadocumentation reports them as having a range ofFloat. The columns have had their types changed and a migration is included in this PR. The analogous pydantic model properties and faker properties have been changed as well. I'm not sure what the relationship between the changes in #1420 and this error being discovered is, but it was not reported before.Failure to populate
annotationscolumnAs suggested in the issue, #1423, the json column,
annotationson a few of our tables was empty. This caused an ingest failure because the annotations are used to populate themultiomicscolumn for biosamples. This was fixed here by using Pydantic v2model_validators instead of v1root_validators. Some feature of Pydantic v1 can still be imported an used, but in this case those weren't working, while the v2 equivalent did.