Merge branch 'main' of https://github.com/Clinical-Genomics/schug int…

…o version_1.5

CHANGELOG.md

@@ -5,6 +5,8 @@
 - Updated version of external images used in GitHub actions
 - Updated Python version to v3.11 in tests GitHub action
 - Removed pytest from the package dependencies
+### Fixed
+- Converted deprecated Pydantic validators and Config into Pydantic 2 format
 
 ## [1.4]
 ### Changed

schug/config.py

@@ -1,6 +1,6 @@
 from pathlib import Path
 
-from pydantic_settings import BaseSettings
+from pydantic_settings import BaseSettings, SettingsConfigDict
 
 DEMO_DB: str = "sqlite://"
 SCHUG_PACKAGE = Path(__file__).parent
@@ -11,12 +11,10 @@
 class Settings(BaseSettings):
     """Settings for serving the schug app"""
 
+    model_config = SettingsConfigDict(env_file=str(ENV_FILE))
     db_uri: str = DEMO_DB
     host: str = "localhost"
     port: int = 8000
 
-    class Config:
-        from_file = str(ENV_FILE)
-
 
 settings = Settings()

schug/models/common.py

@@ -1,7 +1,7 @@
 from enum import Enum
 from typing import Literal, Optional
 
-from pydantic import validator
+from pydantic import field_validator
 from sqlmodel import SQLModel
 
 
@@ -26,7 +26,7 @@ class CoordBase(SQLModel):
     resource_id: str
     genome_build: str
 
-    @validator("genome_build", pre=True)
+    @field_validator("genome_build", mode="before")
     def correct_build(cls, v):
         if v != "37" and v != "38":
             raise ValueError(f"genome build: {v} must be either 37 or 38")

schug/models/gene.py

@@ -2,7 +2,7 @@
 
 from pydantic import BaseModel
 from pydantic import Field as PydanticField
-from pydantic import validator
+from pydantic import field_validator
 from sqlmodel import Field, Relationship
 
 from .common import CoordBase
@@ -44,21 +44,21 @@ class EnsemblGene(BaseModel):
     hgnc_symbol: Optional[str] = PydanticField(None, alias="HGNC symbol")
     hgnc_id: Optional[int] = PydanticField(None, alias="HGNC ID")
 
-    @validator("*", pre=True)
+    @field_validator("*", mode="before")
     def convert_to_none(cls, v):
         if v == "":
             return None
         return v
 
-    @validator("hgnc_id", pre=True)
+    @field_validator("hgnc_id", mode="before")
     def modify_id(cls, v):
         if type(v) != int:
             return v.replace("HGNC:", "")
         return v
 
 
 class HgncGene(BaseModel):
-    gene_id: str = PydanticField(..., alias="Gene stable ID")
+    gene_id: str = PydanticField(..., alias="Gene stable ID", validate_default=True)
     ensembl_gene_id: str
     entrez_id: int
     hgnc_symbol: str = PydanticField(None, alias="HGNC symbol")
@@ -69,7 +69,7 @@ class HgncGene(BaseModel):
 
     aliases: List[str] = []
 
-    @validator("gene_id", always=True)
+    @field_validator("gene_id")
     def set_alias_symbols(cls, _, values: dict):
         return values["alias_symbols"].split("|")
 
@@ -86,42 +86,3 @@ def into_gene(ensembl_gene: EnsemblGene) -> Gene:
         resource_id=ensembl_gene.resource_id,
         resource=ensembl_gene.resource,
     )
-
-
-"""
-{
-    "hgnc_id": "HGNC:15766",
-    "homeodb": "8666",
-    "horde_id": None,
-    "imgt": None,
-    "intermediate_filament_db": None,
-    "iuphar": None,
-    "kznf_gene_catalog": None,
-    "lncrnadb": None,
-    "location": "20q13.13",
-    "location_sortable": "20q13.13",
-    "locus_group": "protein-coding gene",
-    "locus_type": "gene with protein product",
-    "lsdb": "",
-    "mamit-trnadb": None,
-    "merops": None,
-    "mgd_id": "MGI:1338758",
-    "mirbase": "",
-    "name": "activity dependent neuroprotector homeobox",
-    "omim_id": "611386",
-    "orphanet": "406010",
-    "prev_name": "activity-dependent neuroprotector",
-    "prev_symbol": "",
-    "pseudogene.org": None,
-    "pubmed_id": "9872452|11013255",
-    "refseq_accession": "NM_181442",
-    "rgd_id": "RGD:71030",
-    "rna_central_ids": None,
-    "snornabase": "",
-    "status": "Approved",
-    "symbol": "ADNP",
-    "ucsc_id": "uc002xvt.3",
-    "uniprot_ids": "Q9H2P0",
-    "vega_id": "OTTHUMG00000032737",
-}
-"""

schug/models/transcript.py

@@ -2,7 +2,7 @@
 
 from pydantic import BaseModel
 from pydantic import Field as PydanticField
-from pydantic import validator
+from pydantic import field_validator
 from schug.models.exon import ExonRead
 from sqlmodel import Field, Relationship, SQLModel
 
@@ -53,9 +53,9 @@ class EnsemblTranscript(BaseModel):
     refseq_mrna: str = PydanticField(None, alias="RefSeq mRNA ID")
     refseq_mrna_predicted: str = PydanticField(None, alias="RefSeq mRNA predicted ID")
     refseq_ncrna_predicted: str = PydanticField(None, alias="RefSeq ncRNA ID")
-    refseq_id: Optional[str] = None
+    refseq_id: Optional[str] = PydanticField(None, validate_default=True)
 
-    @validator("refseq_id", always=True)
+    @field_validator("refseq_id")
     def set_refseq_id(cls, _, values: dict) -> Optional[str]:
         order: List[str] = [
             "refseq_mrna",