Merge pull request #79 from TheJacksonLaboratory/G3-75-all-geneweaver…

…-packages-need-to-upgrade-pydantic-2-0

G3 75 all geneweaver packages need to upgrade pydantic 2 0

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-api"
-version = "0.7.0a7"
+version = "0.7.0a8"
 description = "The Geneweaver API"
 authors = [
     "Alexander Berger <[email protected]>",
@@ -17,14 +17,15 @@ packages = [
 
 [tool.poetry.dependencies]
 python = "^3.9"
-geneweaver-core = "^0.10.0a2"
-fastapi = {extras = ["all"], version = "^0.99.1"}
-uvicorn = {extras = ["standard"], version = "^0.24.0"}
-geneweaver-db = "0.5.0a11"
+geneweaver-core = "^0.10.0a3"
+fastapi = {extras = ["all"], version = "^0.111.0"}
+uvicorn = {extras = ["standard"], version = "^0.30.0"}
+geneweaver-db = "0.5.0a12"
 psycopg-pool = "^3.1.7"
-requests = "^2.31.0"
+requests = "^2.32.3"
 python-jose = {extras = ["cryptography"], version = "^3.3.0"}
 psycopg-binary = "3.1.18"
+pydantic-settings = "^2.3.4"
 
 [tool.poetry.group.dev.dependencies]
 geneweaver-testing = "^0.1.2"

src/geneweaver/api/controller/genesets.py

@@ -1,13 +1,12 @@
 """Endpoints related to genesets."""
 
 import json
-import os
 import time
 from tempfile import TemporaryDirectory
 from typing import Optional, Set
 
 from fastapi import APIRouter, Depends, HTTPException, Path, Query, Security
-from fastapi.responses import FileResponse
+from fastapi.responses import FileResponse, StreamingResponse
 from geneweaver.api import dependencies as deps
 from geneweaver.api.schemas.apimodels import GeneValueReturn
 from geneweaver.api.schemas.auth import UserInternal
@@ -189,7 +188,7 @@ def get_export_geneset_by_id_type(
     cursor: Optional[deps.Cursor] = Depends(deps.cursor),
     temp_dir: TemporaryDirectory = Depends(deps.get_temp_dir),
     gene_id_type: Optional[GeneIdentifier] = None,
-) -> FileResponse:
+) -> StreamingResponse:
     """Export geneset into JSON file. Search by ID and optional gene identifier type."""
     timestr = time.strftime("%Y%m%d-%H%M%S")
 
@@ -214,15 +213,19 @@ def get_export_geneset_by_id_type(
         geneset_filename = f"geneset_{geneset_id}_{timestr}.json"
 
     # Write the data to temp file
-    temp_file_path = os.path.join(temp_dir, geneset_filename)
-    with open(temp_file_path, "w") as f:
-        json.dump(response, f, default=str)
+    from io import StringIO
+
+    buffer = StringIO()
+
+    json.dump(response, buffer, default=str)
+
+    buffer.seek(0)
 
     # Return as a download
-    return FileResponse(
-        path=temp_file_path,
+    return StreamingResponse(
+        buffer,
         media_type="application/octet-stream",
-        filename=geneset_filename,
+        headers={"Content-Disposition": f"attachment; filename={geneset_filename}"},
     )
 
 

src/geneweaver/api/core/config_class.py

@@ -1,9 +1,11 @@
 """Namespace for the config class for the Geneweaver API."""
 
-from typing import Any, Dict, List, Optional
+from typing import List, Optional
 
 from geneweaver.db.core.settings_class import Settings as DBSettings
-from pydantic import BaseSettings, validator
+from pydantic import model_validator
+from pydantic_settings import BaseSettings, SettingsConfigDict
+from typing_extensions import Self
 
 
 class GeneweaverAPIConfig(BaseSettings):
@@ -20,33 +22,31 @@ class GeneweaverAPIConfig(BaseSettings):
     DB_PORT: int = 5432
     DB: Optional[DBSettings] = None
 
-    @validator("DB", pre=True)
-    def assemble_db_settings(
-        cls, v: Optional[DBSettings], values: Dict[str, Any]  # noqa: N805
-    ) -> DBSettings:
+    @model_validator(mode="after")
+    def assemble_db_settings(self) -> Self:
         """Build the database settings."""
-        if isinstance(v, DBSettings):
-            return v
-        return DBSettings(
-            SERVER=values.get("DB_HOST"),
-            NAME=values.get("DB_NAME"),
-            USERNAME=values.get("DB_USERNAME"),
-            PASSWORD=values.get("DB_PASSWORD"),
-            PORT=values.get("DB_PORT"),
-        )
+        if not isinstance(self.DB, DBSettings):
+            self.DB = DBSettings(
+                SERVER=self.DB_HOST,
+                NAME=self.DB_NAME,
+                USERNAME=self.DB_USERNAME,
+                PASSWORD=self.DB_PASSWORD,
+                PORT=self.DB_PORT,
+            )
+        return self
 
     AUTH_DOMAIN: str = "geneweaver.auth0.com"
     AUTH_AUDIENCE: str = "https://api.geneweaver.org"
     AUTH_ALGORITHMS: List[str] = ["RS256"]
     AUTH_EMAIL_NAMESPACE: str = AUTH_AUDIENCE
-    AUTH_SCOPES = {
+    AUTH_SCOPES: dict = {
         "openid profile email": "read",
     }
     JWT_PERMISSION_PREFIX: str = "approle"
     AUTH_CLIENT_ID: str = "T7bj6wlmtVcAN2O6kzDRwPVFyIj4UQNs"
 
-    class Config:
-        """Configuration for the BaseSettings class."""
-
-        env_file = ".env"
-        case_sensitive = True
+    model_config = SettingsConfigDict(
+        env_file=".env",
+        case_sensitive=False,
+        extra="ignore",
+    )

src/geneweaver/api/schemas/auth.py

@@ -3,7 +3,7 @@
 from enum import Enum
 from typing import List, Optional
 
-from pydantic import BaseModel, Field
+from pydantic import BaseModel, ConfigDict, Field
 
 
 class AppRoles(str, Enum):
@@ -17,8 +17,8 @@ class AppRoles(str, Enum):
 class User(BaseModel):
     """User model."""
 
-    email: Optional[str]
-    name: Optional[str]
+    email: Optional[str] = None
+    name: Optional[str] = None
     sso_id: str = Field(None, alias="sub")
     id: int = Field(None, alias="gw_id")  # noqa: A003
     role: Optional[AppRoles] = AppRoles.user
@@ -29,9 +29,6 @@ class UserInternal(User):
 
     auth_header: dict = {}
     token: str
-    permissions: Optional[List[str]]
+    permissions: Optional[List[str]] = None
 
-    class Config:
-        """Pydantic config."""
-
-        allow_population_by_field_name = True
+    model_config = ConfigDict(populate_by_name=True)

tests/controllers/test_api_standards.py

@@ -17,6 +17,7 @@ def get_openapi_json():
     from unittest.mock import patch
 
     config = GeneweaverAPIConfig(
+        _env_file=None,
         DB_HOST="localhost",
         DB_USERNAME="postgres",
         DB_PASSWORD="postgres",

tests/controllers/test_genesets.py

@@ -66,7 +66,6 @@ def test_export_geneset_w_gene_id_type(mock_service_get_geneset_w_gene_id_type,
     response = client.get("/api/genesets/1234/file?gene_id_type=2")
 
     assert response.headers.get("content-type") == "application/octet-stream"
-    assert int(response.headers.get("content-length")) > 0
     assert response.status_code == 200