Merge pull request #59 from TheJacksonLaboratory/G3-75-all-geneweaver…

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

G3-75: Updating dependencies

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-db"
-version = "0.5.0a11"
+version = "0.5.0a12"
 description = "Database Interaction Services for GeneWeaver"
 authors = ["Jax Computational Sciences <[email protected]>"]
 readme = "README.md"
@@ -13,7 +13,7 @@ packages = [
 
 [tool.poetry.dependencies]
 python = "^3.9"
-geneweaver-core = ">=0.10.0a0,<1.0.0"
+geneweaver-core = ">=0.10.0a3,<1.0.0"
 psycopg = {version = "3.1.18", extras = ["binary"]}
 
 [tool.poetry.group.dev.dependencies]

src/geneweaver/db/aio/project.py

@@ -80,7 +80,7 @@ async def add(
     :return: The ID of the added project
     """
     await cursor.execute(
-        *project_query.add(user_id=user_id, starred=starred, **project.dict())
+        *project_query.add(user_id=user_id, starred=starred, **project.model_dump())
     )
 
     return await cursor.fetchone()

src/geneweaver/db/aio/publication.py

@@ -66,7 +66,7 @@ async def add(cursor: AsyncCursor, publication: PublicationInfo) -> Optional[row
 
     :return: optional row using `.fetchone()`
     """
-    await cursor.execute(*publication_query.add(**publication.dict()))
+    await cursor.execute(*publication_query.add(**publication.model_dump()))
     return await cursor.fetchone()
 
 

src/geneweaver/db/core/settings_class.py

@@ -10,15 +10,17 @@
 """
 
 # ruff: noqa: N805, ANN101, ANN401
-from typing import Any, Dict, Optional
+from typing import Optional
 
-from pydantic import BaseSettings, PostgresDsn, validator
+from pydantic import PostgresDsn, field_validator, model_validator
+from pydantic_settings import BaseSettings, SettingsConfigDict
+from typing_extensions import Self, Type
 
 
 class Settings(BaseSettings):
     """Settings class for the GeneWeaver Database module."""
 
-    DEBUG_MODE = False
+    DEBUG_MODE: bool = False
 
     CONNECTION_SCHEME: str = "postgresql"
 
@@ -29,32 +31,32 @@ class Settings(BaseSettings):
     PORT: int = 5432
     URI: Optional[str] = None
 
-    @validator("SERVER", pre=True)
-    def replace_localhost(cls, v: str) -> str:
-        """Replace localhost with 127.0.0.1."""
+    @field_validator("SERVER", mode="after")
+    @classmethod
+    def name_must_contain_space(cls: Type["Settings"], v: str) -> str:
+        """Ensure that the server name is not 'localhost'."""
         if v == "localhost":
             return "127.0.0.1"
         return v
 
-    @validator("URI", pre=True)
-    def assemble_db_connection(cls, v: Optional[str], values: Dict[str, Any]) -> str:
-        """Build the database connection string, unless one is provided."""
-        if isinstance(v, str):
-            return v
-        return str(
-            PostgresDsn.build(
-                scheme=values.get("CONNECTION_SCHEME"),
-                user=values.get("USERNAME"),
-                password=values.get("PASSWORD"),
-                host=values.get("SERVER"),
-                port=str(values.get("PORT")),
-                path=f"/{values.get('NAME') or ''}",
+    @model_validator(mode="after")
+    def assemble_db_connection(self) -> Self:
+        """Build the database connection string."""
+        if isinstance(self.URI, str):
+            self.URI = str(PostgresDsn(self.URI))
+        else:
+            self.URI = str(
+                PostgresDsn.build(
+                    scheme=self.CONNECTION_SCHEME,
+                    username=self.USERNAME,
+                    password=self.PASSWORD,
+                    host=self.SERVER,
+                    port=self.PORT,
+                    path=f"{self.NAME or ''}",
+                )
             )
-        )
+        return self
 
-    class Config:
-        """Configuration for the BaseSettings class."""
-
-        env_prefix = "GWDB_"
-        env_file = ".env"
-        case_sensitive = True
+    model_config = SettingsConfigDict(
+        env_prefix="GWDB_", env_file=".env", case_sensitive=True
+    )

src/geneweaver/db/project.py

@@ -85,7 +85,7 @@ def add(
 
     """
     cursor.execute(
-        *project_query.add(user_id=user_id, starred=starred, **project.dict())
+        *project_query.add(user_id=user_id, starred=starred, **project.model_dump())
     )
 
     return cursor.fetchone()

src/geneweaver/db/publication.py

@@ -64,7 +64,7 @@ def add(cursor: Cursor, publication: PublicationInfo) -> Optional[rows.Row]:
 
     :return: optional row using `.fetchone()`
     """
-    cursor.execute(*publication_query.add(**publication.dict()))
+    cursor.execute(*publication_query.add(**publication.model_dump()))
     return cursor.fetchone()
 
 

tests/unit/core/test_settings_class.py

@@ -2,6 +2,7 @@
 
 from geneweaver.db.core.settings_class import Settings
 from pydantic import BaseModel, PostgresDsn
+from pydantic.networks import MultiHostUrl
 
 
 class PostgresDsnExample(BaseModel):
@@ -42,7 +43,9 @@ def test_settings_class_has_expected_attributes():
     parsed = PostgresDsnExample(db=settings.URI)
     assert parsed is not None, "URI should be parsable as a PostgresDsn"
     assert parsed.db is not None, "URI should be parsable as a PostgresDsn"
-    assert isinstance(parsed.db, PostgresDsn), "URI should be parsable as a PostgresDsn"
+    assert isinstance(
+        parsed.db, MultiHostUrl
+    ), "URI should be parsable as a PostgresDsn"
 
     # "localhost" should be replaced with 127.0.0.1
     assert (
@@ -81,7 +84,9 @@ def test_settings_class_can_directly_set_database_uri():
     parsed = PostgresDsnExample(db=settings.URI)
     assert parsed is not None, "URI should be parsable as a PostgresDsn"
     assert parsed.db is not None, "URI should be parsable as a PostgresDsn"
-    assert isinstance(parsed.db, PostgresDsn), "URI should be parsable as a PostgresDsn"
+    assert isinstance(
+        parsed.db, MultiHostUrl
+    ), "URI should be parsable as a PostgresDsn"
 
     assert (
         str(settings.URI) == "postgresql://other_admin@non_localhost/"

tests/unit/publication/test_add.py

@@ -17,7 +17,7 @@
     abstract="Abstract 1",
     journal="Journal 1",
     pubmed_id="12345678",
-    pages=1,
+    pages="1",
     month="Dec",
     year=2021,
 )

tests/unit/query/threshold/test_set_geneset_threshold.py

@@ -33,6 +33,14 @@
 )
 def test_set_geneset_threshold(geneset_id, score_type, threshold):
     """Test the set_geneset_threshold function for both async and sync."""
+    # Threshold_low values are not allowed for score types other than correlation and
+    # effect
+    if (
+        score_type not in [ScoreType.CORRELATION, ScoreType.EFFECT]
+        and "threshold_low" in threshold
+    ):
+        del threshold["threshold_low"]
+
     geneset_score_type = GenesetScoreType(score_type=score_type, **threshold)
     sql, params = set_geneset_threshold(geneset_id, geneset_score_type)
 
@@ -105,11 +113,15 @@ def test_set_geneset_threshold_error(geneset_id, score_type, threshold):
     """Test the set_geneset_threshold function for an error."""
     geneset_id = 0
     geneset_score_type = GenesetScoreType(
-        score_type=score_type,
-        threshold_low=threshold["threshold_low"],
+        score_type=ScoreType.CORRELATION,
         threshold=threshold["threshold"],
     )
 
+    # We patch the values back to their invalid state since pydantic will now
+    # complain on initialization. We still want to check that this is caught.
+    geneset_score_type.score_type = score_type
+    geneset_score_type.threshold_low = threshold["threshold_low"]
+
     error_str = (
         "geneset_score_type.threshold must be larger "
         "than geneset_score_type.threshold_low"

tests/unit/query/threshold/test_set_geneset_value_threshold.py

@@ -35,6 +35,14 @@
 )
 def test_set_geneset_threshold(geneset_id, score_type, threshold):
     """Test the set_geneset_threshold function for both async and sync."""
+    # Threshold_low values are not allowed for score types other than correlation and
+    # effect
+    if (
+        score_type not in [ScoreType.CORRELATION, ScoreType.EFFECT]
+        and "threshold_low" in threshold
+    ):
+        del threshold["threshold_low"]
+
     geneset_score_type = GenesetScoreType(score_type=score_type, **threshold)
     sql, params = set_geneset_value_threshold(geneset_id, geneset_score_type)
 
@@ -103,11 +111,15 @@ def test_set_geneset_threshold_error(geneset_id, score_type, threshold):
     """Test the set_geneset_threshold function for an error."""
     geneset_id = 0
     geneset_score_type = GenesetScoreType(
-        score_type=score_type,
-        threshold_low=threshold["threshold_low"],
+        score_type=ScoreType.CORRELATION,
         threshold=threshold["threshold"],
     )
 
+    # We patch the values back to their invalid state since pydantic will now
+    # complain on initialization. We still want to check that this is caught.
+    geneset_score_type.score_type = score_type
+    geneset_score_type.threshold_low = threshold["threshold_low"]
+
     error_str = (
         "geneset_score_type.threshold must be larger "
         "than geneset_score_type.threshold_low"