fixing mongomodel

backend/app/models/authorization.py

@@ -4,8 +4,6 @@
 from beanie import Document
 from charset_normalizer.md import List
 from pydantic import BaseModel, EmailStr, Field
-
-from app.models.mongomodel import MongoModel
 from app.models.pyobjectid import PyObjectId
 
 

backend/app/models/datasets.py

@@ -98,7 +98,7 @@ class GroupAndRole(BaseModel):
     role: RoleType
 
 
-class DatasetRoles(MongoModel):
+class DatasetRoles(BaseModel):
     dataset_id: str
     user_roles: List[UserAndRole] = []
     group_roles: List[GroupAndRole] = []

backend/app/models/errors.py

@@ -1,8 +1,8 @@
 from datetime import datetime
 from typing import Optional
-from pydantic import Field
+from pydantic import Field, BaseModel
 
-from app.models.mongomodel import MongoModel, MongoDBRef
+from app.models.mongomodel import MongoDBRef
 
 
 class ServiceUnreachable(Exception):
@@ -16,7 +16,7 @@ def __str__(self):
         return f"{self.service} could not be reached."
 
 
-class Error(MongoModel):
+class Error(BaseModel):
     message: str  # Shorthand message of the error
     trace: str  # Full stack trace of the error
     resource: Optional[MongoDBRef] = None

backend/app/models/files.py

@@ -4,7 +4,6 @@
 from beanie import Document, PydanticObjectId
 from pydantic import Field, BaseModel
 
-from app.models.mongomodel import MongoModel
 from app.models.pyobjectid import PyObjectId
 from app.models.users import UserOut
 
@@ -20,7 +19,7 @@ class FileContentType(BaseModel):
     main_type: str = "N/A"
 
 
-class FileVersion(MongoModel):
+class FileVersion(BaseModel):
     file_id: PyObjectId
     creator: UserOut
     created: datetime = Field(default_factory=datetime.utcnow)
@@ -36,7 +35,7 @@ class Settings:
         name = "file_versions"
 
 
-class FileBase(MongoModel):
+class FileBase(BaseModel):
     name: str = "N/A"
 
 

backend/app/models/folders.py

@@ -2,14 +2,13 @@
 from typing import Optional
 
 from beanie import Document, PydanticObjectId
-from pydantic import Field
+from pydantic import Field, BaseModel
 
-from app.models.mongomodel import MongoModel
 from app.models.pyobjectid import PyObjectId
 from app.models.users import UserOut
 
 
-class FolderBase(MongoModel):
+class FolderBase(BaseModel):
     name: str = "N/A"
 
 

backend/app/models/groups.py

@@ -3,7 +3,6 @@
 
 from pydantic import Field, BaseModel
 from beanie import Document, View, PydanticObjectId
-from app.models.mongomodel import OID, MongoModel
 from app.models.users import UserOut
 from app.models.authorization import Provenance, RoleType
 

backend/app/models/mongomodel.py

@@ -23,47 +23,6 @@ def __modify_schema__(cls, field_schema):
         field_schema.update(type="string")
 
 
-class MongoModel(BaseModel):
-    id: PyObjectId = Field(default_factory=PyObjectId)
-
-    def __init__(self, **pydict):
-        super().__init__(**pydict)
-        if "_id" in pydict.keys():
-            self.id = pydict.pop("_id", None)
-
-    class Config(BaseConfig):
-        allow_population_by_field_name = True
-        json_encoders = {
-            datetime: lambda dt: dt.isoformat(),
-            ObjectId: lambda oid: str(oid),
-        }
-
-    @classmethod
-    def from_mongo(cls, data: dict):
-        """We must convert _id into "id"."""
-        if not data:
-            return data
-        id = data.pop("_id", None)
-        return cls(**dict(data, id=id))
-
-    def to_mongo(self, **kwargs):
-        # include all key/value pairs by default. Is this the correct default behaviour?
-        exclude_unset = kwargs.pop("exclude_unset", False)
-        by_alias = kwargs.pop("by_alias", True)
-
-        parsed = self.dict(
-            exclude_unset=exclude_unset,
-            by_alias=by_alias,
-            **kwargs,
-        )
-
-        # Mongo uses `_id` as default key. We should stick to that as well.
-        if "_id" not in parsed and "id" in parsed:
-            parsed["_id"] = parsed.pop("id")
-
-        return parsed
-
-
 class MongoDBRef(BaseModel):
     collection: str
     resource_id: PyObjectId

backend/app/models/users.py

@@ -6,12 +6,10 @@
 from pymongo import MongoClient
 from beanie import Document, View, PydanticObjectId
 
-from app.models.mongomodel import MongoModel
-
 pwd_context = CryptContext(schemes=["bcrypt"], deprecated="auto")
 
 
-class UserBase(MongoModel):
+class UserBase(BaseModel):
     email: EmailStr
 
 
@@ -57,7 +55,7 @@ class Settings:
         name = "user_keys"
 
 
-class UserAPIKeyOut(MongoModel):
+class UserAPIKeyOut(BaseModel):
     # don't show the raw key
     name: str
     user: EmailStr