Merge pull request #1428 from microbiomedata/1423-fix-ingest

Fix ingest post dependency upgrade

nmdc_server/fakes.py

@@ -222,25 +222,25 @@ class Meta:
         model = models.MetagenomeAssembly
         sqlalchemy_session = db
 
-    scaffolds: int = Faker("pyint")
-    contigs: int = Faker("pyint")
-    scaf_bp: int = Faker("pyint")
-    contig_bp: int = Faker("pyint")
-    scaf_n50: int = Faker("pyint")
-    scaf_l50: int = Faker("pyint")
-    ctg_n50: int = Faker("pyint")
-    ctg_l50: int = Faker("pyint")
-    scaf_n90: int = Faker("pyint")
-    scaf_l90: int = Faker("pyint")
-    ctg_n90: int = Faker("pyint")
-    ctg_l90: int = Faker("pyint")
-    scaf_max: int = Faker("pyint")
-    ctg_max: int = Faker("pyint")
-    scaf_n_gt50k: int = Faker("pyint")
-    scaf_l_gt50k: int = Faker("pyint")
-    scaf_pct_gt50k: int = Faker("pyint")
-    num_input_reads: int = Faker("pyint")
-    num_aligned_reads: int = Faker("pyint")
+    scaffolds: float = Faker("pyfloat")
+    contigs: float = Faker("pyfloat")
+    scaf_bp: float = Faker("pyfloat")
+    contig_bp: float = Faker("pyfloat")
+    scaf_n50: float = Faker("pyfloat")
+    scaf_l50: float = Faker("pyfloat")
+    ctg_n50: float = Faker("pyfloat")
+    ctg_l50: float = Faker("pyfloat")
+    scaf_n90: float = Faker("pyfloat")
+    scaf_l90: float = Faker("pyfloat")
+    ctg_n90: float = Faker("pyfloat")
+    ctg_l90: float = Faker("pyfloat")
+    scaf_max: float = Faker("pyfloat")
+    ctg_max: float = Faker("pyfloat")
+    scaf_n_gt50k: float = Faker("pyfloat")
+    scaf_l_gt50k: float = Faker("pyfloat")
+    scaf_pct_gt50k: float = Faker("pyfloat")
+    num_input_reads: float = Faker("pyfloat")
+    num_aligned_reads: float = Faker("pyfloat")
     scaf_logsum: float = Faker("pyfloat")
     scaf_powsum: float = Faker("pyfloat")
     ctg_logsum: float = Faker("pyfloat")

nmdc_server/ingest/biosample.py

@@ -3,8 +3,8 @@
 from datetime import datetime
 from typing import Any, Dict
 
-from pydantic import field_validator
-from pydantic.v1 import root_validator, validator
+from pydantic import field_validator, model_validator
+from pydantic.v1 import validator
 from pymongo.cursor import Cursor
 from sqlalchemy.orm import Session
 
@@ -21,7 +21,7 @@
 class Biosample(BiosampleCreate):
     _extract_value = validator("*", pre=True, allow_reuse=True)(extract_value)
 
-    @root_validator(pre=True)
+    @model_validator(mode="before")
     def extract_extras(cls, values):
         if "lat_lon" in values:
             if "latitude" in values["lat_lon"] and "longitude" in values["lat_lon"]:
@@ -31,7 +31,7 @@ def extract_extras(cls, values):
                 lat, lon = values.pop("lat_lon")["has_raw_value"].split(" ")
                 values["latitude"] = float(lat)
                 values["longitude"] = float(lon)
-        return extract_extras(cls, values)
+        return extract_extras(cls, values)  # type: ignore
 
     @field_validator("depth", mode="before")
     @classmethod

nmdc_server/ingest/common.py

@@ -48,7 +48,7 @@ def extract_extras(
     cls: BaseModel, values: Dict[str, Any], exclude: Optional[Set[str]] = None
 ) -> Dict[str, Any]:
     # Move unknown attributes into values['annotations']
-    fields = set(cls.__fields__.keys())
+    fields = set(cls.model_fields.keys())
     exclude = (exclude or set()).union(EXCLUDED_FIELDS)
     values.setdefault("annotations", {})
     for key, value in values.items():

nmdc_server/ingest/omics_processing.py

@@ -3,8 +3,8 @@
 from datetime import datetime
 from typing import Any, Dict, Optional
 
-from pydantic import field_validator
-from pydantic.v1 import root_validator, validator
+from pydantic import field_validator, model_validator
+from pydantic.v1 import validator
 from pymongo.collection import Collection
 from pymongo.cursor import Cursor
 from pymongo.database import Database
@@ -36,9 +36,9 @@
 class OmicsProcessing(OmicsProcessingCreate):
     _extract_value = validator("*", pre=True, allow_reuse=True)(extract_value)
 
-    @root_validator(pre=True)
+    @model_validator(mode="before")
     def extract_extras(cls, values):
-        return extract_extras(cls, values)
+        return extract_extras(cls, values)  # type: ignore
 
     @field_validator("add_date", "mod_date", mode="before")
     @classmethod

nmdc_server/ingest/study.py

@@ -1,8 +1,9 @@
 import re
-from typing import Optional
+from typing import List, Optional
 
 import requests
-from pydantic.v1 import root_validator, validator
+from pydantic import model_validator
+from pydantic.v1 import validator
 from pymongo.cursor import Cursor
 from sqlalchemy.orm import Session
 
@@ -41,17 +42,17 @@ def get_or_create_pi(db: Session, name: str, url: Optional[str], orcid: Optional
 class Study(StudyCreate):
     _extract_value = validator("*", pre=True, allow_reuse=True)(extract_value)
 
-    @root_validator(pre=True)
+    @model_validator(mode="before")
     def extract_extras(cls, values):
-        return extract_extras(cls, values)
+        return extract_extras(cls, values)  # type: ignore
 
 
 def transform_doi(doi: str) -> str:
     matches = re.findall(r"10.\d{4,9}/[-._;()/:a-zA-Z0-9]+$", doi)
     return matches[0]
 
 
-def get_study_image_data(image_urls: list[dict[str, str]]) -> Optional[bytes]:
+def get_study_image_data(image_urls: List[dict[str, str]]) -> Optional[bytes]:
     if image_urls:
         r = requests.get(image_urls[0]["url"])
         if r.ok: