Merge pull request #24 from TheJacksonLaboratory/G3-75-all-geneweaver…

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

G3-75: Upgrade pydantic to >=2

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-core"
-version = "0.10.0a2"
+version = "0.10.0a3"
 description = "The core of the Jax-Geneweaver Python library"
 authors = ["Jax Computational Sciences <[email protected]>"]
 readme = "README.md"
@@ -13,11 +13,12 @@ packages = [
 
 [tool.poetry.dependencies]
 python = "^3.9"
-pydantic = { extras = ["dotenv"], version = "^1.10" }
+pydantic = { extras = ["dotenv"], version = "^2.8" }
 openpyxl = "^3.1.2"
 numpy = ">=1.22,<2"
 pandas = ">=1.5,<3"
 requests = "^2.32.0"
+pydantic-settings = "^2.3.4"
 
 [tool.poetry.group.dev.dependencies]
 pylint = "^2.15.4"
@@ -26,6 +27,7 @@ pydocstyle = "^6.1.1"
 pytest-cov = "^4.0.0"
 geneweaver-testing = "^0.1.0"
 
+
 [tool.ruff]
 select = ['F', 'E', 'W', 'A', 'C90', 'N', 'B', 'ANN', 'D', 'I', 'ERA', 'PD', 'NPY', 'PT']
 

src/geneweaver/core/config_class.py

@@ -4,24 +4,23 @@
 https://pydantic-docs.helpmanual.io/usage/settings/
 """
 
-from pydantic import BaseSettings
+from pydantic_settings import BaseSettings, SettingsConfigDict
 
 
 class ExternalServiceSettings(BaseSettings):
     """External Service Config and Settings Configuration."""
 
-    PUBMED_XLM_SVC_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id={0}&retmode=xml"
+    PUBMED_XLM_SVC_URL: str = (
+        "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id={0}&retmode=xml"
+    )
 
 
 class CoreSettings(BaseSettings):
     """Root Config and Settings Configuration."""
 
-    PROJECT_NAME = "jax-geneweaver-core"
-    VERSION = "0.0.2"
+    PROJECT_NAME: str = "jax-geneweaver-core"
+    VERSION: str = "0.0.2"
     LOG_LEVEL: str = "INFO"
     SERVICE_URLS: ExternalServiceSettings = ExternalServiceSettings()
 
-    class Config:
-        """Pydantic Config class."""
-
-        env_prefix = "GW_"
+    model_config = SettingsConfigDict(env_prefix="GW_")

src/geneweaver/core/enum.py

@@ -223,6 +223,8 @@ class Species(_StrToIntMixin, Enum):
     SACCHAROMYCES_CEREVISIAE = "Saccharomyces Cerevisiae"
     GALLUS_GALLUS = "Gallus Gallus"
     CANIS_FAMILIARIS = "Canis Familiaris"
+    XENOPUS_TROPICALIS = "Xenopus Tropicalis"
+    XENOPUS_LAEVIS = "Xenopus Laevis"
 
     @staticmethod
     def _int_class() -> Enum:
@@ -243,6 +245,8 @@ class SpeciesInt(_IntToStrMixin, IntEnum):
     SACCHAROMYCES_CEREVISIAE = 9
     GALLUS_GALLUS = 10
     CANIS_FAMILIARIS = 11
+    XENOPUS_TROPICALIS = 12
+    XENOPUS_LAEVIS = 13
 
     @staticmethod
     def _str_class() -> Enum:

src/geneweaver/core/schema/batch.py

@@ -1,14 +1,15 @@
 """Module for defining schemas for batch endpoints."""
 
-# ruff: noqa: N805, ANN001, ANN101
-from typing import List, Optional, Union
+# ruff: noqa: N805, ANN001, ANN101, ANN401
+from typing import Any, List, Optional, Type, Union
 
 from geneweaver.core.enum import GeneIdentifierInt, MicroarrayInt, SpeciesInt
 from geneweaver.core.parse.score import parse_score
 from geneweaver.core.schema.gene import GeneValue
 from geneweaver.core.schema.messages import MessageResponse
 from geneweaver.core.schema.score import GenesetScoreType
-from pydantic import BaseModel, validator
+from pydantic import BaseModel, field_validator, model_validator
+from typing_extensions import Self
 
 # Header characters which DO NOT need to be space separated.
 HEADER_CHARACTERS = {
@@ -86,17 +87,21 @@ class BatchUploadGeneset(BaseModel):
     description: str = ""
     values: List[GeneValue]
 
-    @validator("species", pre=True)
-    def initialize_species(cls, v) -> SpeciesInt:
+    @field_validator("species", mode="before")
+    @classmethod
+    def initialize_species(cls: Type["BatchUploadGeneset"], v: Any) -> SpeciesInt:
         """Initialize species."""
         if isinstance(v, SpeciesInt):
             return v
         elif isinstance(v, str):
             return SpeciesInt[v.replace(" ", "_").upper()]
         return SpeciesInt(v)
 
-    @validator("gene_id_type", pre=True)
-    def initialize_gene_id_type(cls, v) -> Union[GeneIdentifierInt, MicroarrayInt]:
+    @field_validator("gene_id_type", mode="before")
+    @classmethod
+    def initialize_gene_id_type(
+        cls: Type["BatchUploadGeneset"], v: Any
+    ) -> Union[GeneIdentifierInt, MicroarrayInt]:
         """Initialize gene id type."""
         if isinstance(v, GeneIdentifierInt) or isinstance(v, MicroarrayInt):
             return v
@@ -111,29 +116,31 @@ def initialize_gene_id_type(cls, v) -> Union[GeneIdentifierInt, MicroarrayInt]:
                 ]
             return MicroarrayInt(v)
 
-    @validator("score", pre=True)
-    def initialize_score(cls, v) -> GenesetScoreType:
+    @field_validator("score", mode="before")
+    @classmethod
+    def initialize_score(cls: Type["BatchUploadGeneset"], v: Any) -> GenesetScoreType:
         """Initialize score type."""
         if isinstance(v, GenesetScoreType):
             return v
         elif isinstance(v, dict):
             return GenesetScoreType(**v)
         return parse_score(v)
 
-    @validator("private", pre=True)
-    def private_to_bool(cls, v) -> bool:
+    @field_validator("private", mode="before")
+    @classmethod
+    def private_to_bool(cls: Type["BatchUploadGeneset"], v: Any) -> bool:
         """Convert private str to bool."""
         if isinstance(v, bool):
             return v
         return v.lower() != "public"
 
-    @validator("curation_id", pre=True)
-    def curation_id_to_int(cls, v, values) -> int:
+    @model_validator(mode="after")
+    def curation_id_to_int(self) -> Self:
         """Initialize curation id based on `private` value."""
-        if not v:
+        if not self.curation_id:
             # If the geneset is private, it should be set to have
             # curation tier 5, otherwise it should be set to have
             # curation tier 4.
             # It should default to private if not specified.
-            return 5 if values.get("private", True) else 4
-        return v
+            self.curation_id = 5 if self.private else 4
+        return self

src/geneweaver/core/schema/gene.py

@@ -4,7 +4,7 @@
 from typing import Any, List, Optional
 
 from geneweaver.core.enum import GeneIdentifier, Species
-from pydantic import BaseModel
+from pydantic import BaseModel, ConfigDict
 
 
 class Gene(BaseModel):
@@ -26,20 +26,16 @@ class GeneRow(BaseModel):
     gdb_id: int
     sp_id: int
     ode_pref: bool
-    ode_date: Optional[str]
-    old_ode_gene_ids: Optional[List[int]]
+    ode_date: Optional[str] = None
+    old_ode_gene_ids: Optional[List[int]] = None
 
 
 class GeneValue(BaseModel):
     """A gene value."""
 
     symbol: str
     value: float
-
-    class Config:
-        """Pydantic config."""
-
-        allow_mutation = False
+    model_config = ConfigDict(frozen=True)
 
     def __str__(self: "GeneValue") -> str:
         """Return the gene symbol."""
@@ -76,4 +72,4 @@ class GeneDatabaseRow(BaseModel):
     gdb_shortname: str
     gdb_date: str
     gdb_precision: int
-    gdb_linkout_url: Optional[str]
+    gdb_linkout_url: Optional[str] = None

src/geneweaver/core/schema/legacy_api.py

@@ -3,20 +3,20 @@
 from typing import List, Optional
 
 from geneweaver.core.enum import GenesetAccess, ScoreType
-from pydantic import BaseModel, HttpUrl
+from pydantic import BaseModel, ConfigDict, HttpUrl
 
 
 class AddGenesetByUserPublication(BaseModel):
     """Publication schema for adding genesets by user."""
 
-    pub_abstract: Optional[str]
-    pub_authors: Optional[str]
-    pub_journal: Optional[str]
-    pub_pages: Optional[str]
-    pub_pubmed: Optional[str]
-    pub_title: Optional[str]
-    pub_volume: Optional[str]
-    pub_year: Optional[str]
+    pub_abstract: Optional[str] = None
+    pub_authors: Optional[str] = None
+    pub_journal: Optional[str] = None
+    pub_pages: Optional[str] = None
+    pub_pubmed: Optional[str] = None
+    pub_title: Optional[str] = None
+    pub_volume: Optional[str] = None
+    pub_year: Optional[str] = None
 
 
 class AddGenesetByUserBase(BaseModel):
@@ -28,14 +28,10 @@ class AddGenesetByUserBase(BaseModel):
     gs_name: str
     gs_threshold_type: ScoreType
     permissions: GenesetAccess
-    publication: Optional[AddGenesetByUserPublication]
+    publication: Optional[AddGenesetByUserPublication] = None
     select_groups: List[str]
     sp_id: str
-
-    class Config:
-        """Pydantic config."""
-
-        use_enum_values = True
+    model_config = ConfigDict(use_enum_values=True)
 
 
 class AddGenesetByUser(AddGenesetByUserBase):

src/geneweaver/core/schema/score.py

@@ -5,7 +5,8 @@
 from typing import Optional
 
 from geneweaver.core.enum import ScoreType
-from pydantic import BaseModel, validator
+from pydantic import BaseModel, model_validator
+from typing_extensions import Self
 
 
 class GenesetScoreType(BaseModel):
@@ -29,26 +30,22 @@ def threshold_as_db_string(self) -> str:
         else:
             return str(self.threshold)
 
-    @validator("threshold_low")
-    def threshold_low_must_be_less_than_threshold(
-        cls, v: Optional[float], values: dict
-    ) -> Optional[float]:
+    @model_validator(mode="after")
+    def threshold_low_must_be_less_than_threshold(self) -> Self:
         """Threshold low must be less than threshold."""
-        if v is not None and v > values.get("threshold"):
+        if self.threshold_low is not None and self.threshold_low > self.threshold:
             raise ValueError("threshold_low must be less than threshold")
-        return v
+        return self
 
-    @validator("threshold_low")
-    def threshold_low_correlation_and_effect_only(
-        cls, v: Optional[float], values: dict
-    ) -> Optional[float]:
+    @model_validator(mode="after")
+    def threshold_low_correlation_and_effect_only(self) -> Self:
         """Threshold low should only be set for correlation and effect score types."""
-        if v is not None and values.get("score_type") not in [
+        if self.threshold_low is not None and self.score_type not in [
             ScoreType.CORRELATION,
             ScoreType.EFFECT,
         ]:
             raise ValueError(
                 "threshold_low should only be set for "
                 "correlation and effect score types"
             )
-        return v
+        return self

src/geneweaver/core/schema/species.py

@@ -13,7 +13,7 @@ class Species(BaseModel):
     id: int  # noqa: A003
     name: str
     taxonomic_id: int
-    reference_gene_identifier: Optional[GeneIdentifier]
+    reference_gene_identifier: Optional[GeneIdentifier] = None
 
 
 class SpeciesRow(BaseModel):
@@ -22,7 +22,7 @@ class SpeciesRow(BaseModel):
     sp_id: int
     sp_name: str
     sp_taxid: int
-    sp_ref_gdb_id: Optional[int]
+    sp_ref_gdb_id: Optional[int] = None
     sp_date: datetime.date
-    sp_biomart_info: Optional[str]
+    sp_biomart_info: Optional[str] = None
     sp_source_data: Json[Any]

tests/unit/conftest.py

@@ -13,18 +13,22 @@
 @pytest.fixture(scope="session")
 def core_settings_fields() -> List[str]:
     """Return a list of the pydantic Settings class fields."""
-    return [field.name for field in CoreSettings.__fields__.values()]
+    return [name for name in CoreSettings.model_fields.keys()]
 
 
 @pytest.fixture(scope="session")
 def core_settings_required_fields() -> List[str]:
     """Return a list of the pydantic Settings class fields."""
-    return [field.name for field in CoreSettings.__fields__.values() if field.required]
+    return [
+        name for name, field in CoreSettings.model_fields.items() if field.is_required()
+    ]
 
 
 @pytest.fixture(scope="session")
 def core_settings_optional_fields() -> Dict[str, Any]:
     """Return a dict of the optional pydantic Settings class fields."""
     return {
-        f.name: f.default for f in CoreSettings.__fields__.values() if not f.required
+        name: field.default
+        for name, field in CoreSettings.model_fields.items()
+        if not field.is_required()
     }

tests/unit/publication/pubmed/test_get_publication.py

@@ -128,7 +128,7 @@ def test_get_publication(
 
     result = get_publication(pubmed_id)
 
-    assert result.dict() == expected.dict()
+    assert result.model_dump() == expected.model_dump()
 
     mock_get_xml_for_pubmed_id.assert_called_once_with(pubmed_id)
     mock_extract_fields.assert_called_once()

tests/unit/render/batch/test_format_genest_metadata.py

@@ -11,6 +11,6 @@ def test_format_geneset_metadata_standard(mock_batch_upload_geneset_all_combinat
     # Assert that the output is a string and has the expected structure
     assert isinstance(formatted_metadata, str)
     # Additional assertions can be made based on the specific format of the metadata
-    assert formatted_metadata.count("\n") == 8
+    assert formatted_metadata.count("\n") == 9
     for char in ["!", "@", "%", "A", ":", "=", "+"]:
         assert char in formatted_metadata

tests/unit/schema/legacy/test_legacy_schema_create.py

@@ -6,6 +6,7 @@
     AddGenesetByUserFile,
     AddGenesetByUserPublication,
 )
+from pydantic.networks import AnyUrl
 
 
 def test_add_gs_by_user_pub_schema(add_geneset_by_user_publication_data: dict) -> None:
@@ -44,4 +45,5 @@ def test_add_gs_by_user_file_schema(add_geneset_by_user_file_data: dict) -> None
     """Test the AddGenesetByUserFile class."""
     gs = AddGenesetByUserFile(**add_geneset_by_user_file_data)
     _shared_add_gs_by_user_asserts(gs, add_geneset_by_user_file_data)
-    assert gs.file_url == add_geneset_by_user_file_data["file_url"]
+    assert gs.file_url == AnyUrl(add_geneset_by_user_file_data["file_url"])
+    assert str(gs.file_url) == add_geneset_by_user_file_data["file_url"] + "/"