Update code to be compatible with Pydantic2

.github/workflows/tests.yml

@@ -22,7 +22,7 @@ jobs:
           pip install "tox<4.0.0"
       - name: Test with pytest
         run: |
-          export MIRA_REST_URL=http://34.230.33.149:8771
+          export MIRA_REST_URL=http://mira-epi-dkg-lb-c7b58edea41524e6.elb.us-east-1.amazonaws.com:8771
           tox -e py
 #      - name: Upload coverage report to codecov
 #        uses: codecov/codecov-action@v1

mira/dkg/api.py

@@ -25,18 +25,18 @@
 class RelationQuery(BaseModel):
     """A query for relations in the domain knowledge graph."""
 
-    source_type: Optional[str] = Field(description="The source type (i.e., prefix)", example="vo")
+    source_type: Optional[str] = Field(None, description="The source type (i.e., prefix)", examples=["vo"])
     source_curie: Optional[str] = Field(
-        description="The source compact URI (CURIE)", example="doid:946"
+        None, description="The source compact URI (CURIE)", examples=["doid:946"]
     )
     target_type: Optional[str] = Field(
-        description="The target type (i.e., prefix)", example="ncbitaxon"
+        None, description="The target type (i.e., prefix)", examples=["ncbitaxon"]
     )
     target_curie: Optional[str] = Field(
-        description="The target compact URI (CURIE)", example="ncbitaxon:10090"
+        None, description="The target compact URI (CURIE)", examples=["ncbitaxon:10090"]
     )
     relations: Union[None, str, List[str]] = Field(
-        description="A relation string or list of relation strings", example="vo:0001243"
+        None, description="A relation string or list of relation strings", examples=["vo:0001243"]
     )
     relation_direction: Literal["right", "left", "both"] = Field(
         "right", description="The direction of the relationship"
@@ -50,7 +50,7 @@ class RelationQuery(BaseModel):
         ge=0,
     )
     limit: Optional[int] = Field(
-        description="A limit on the number of records returned", example=50, ge=0
+        None, description="A limit on the number of records returned", examples=[50], ge=0
     )
     full: bool = Field(
         False,
@@ -178,12 +178,12 @@ def get_transitive_closure(
 class RelationResponse(BaseModel):
     """A triple (or multi-predicate triple) with abbreviated data."""
 
-    subject: str = Field(description="The CURIE of the subject of the triple", example="doid:96")
+    subject: str = Field(description="The CURIE of the subject of the triple", examples=["doid:96"])
     predicate: Union[str, List[str]] = Field(
         description="A predicate or list of predicates as CURIEs",
-        example="ro:0002452",
+        examples=["ro:0002452"],
     )
-    object: str = Field(description="The CURIE of the object of the triple", example="symp:0000001")
+    object: str = Field(description="The CURIE of the object of the triple", examples=["symp:0000001"])
 
 
 class FullRelationResponse(BaseModel):
@@ -396,10 +396,10 @@ class IsOntChildResult(BaseModel):
     """Result of a query to /is_ontological_child"""
 
     child_curie: str = Field(...,
-                             example="vo:0001113",
+                             examples=["vo:0001113"],
                              description="The child CURIE")
     parent_curie: str = Field(...,
-                              example="obi:0000047",
+                              examples=["obi:0000047"],
                               description="The parent CURIE")
     is_child: bool = Field(
         ...,

mira/dkg/client.py

@@ -14,7 +14,7 @@
 import pystow
 import requests
 from neo4j import GraphDatabase, Transaction, unit_of_work
-from pydantic import BaseModel, Field, validator
+from pydantic import BaseModel, Field, field_validator
 from tqdm import tqdm
 from typing_extensions import Literal, TypeAlias
 
@@ -44,82 +44,82 @@
 class Relation(BaseModel):
     """A relationship between two entities in the DKG"""
     source_curie: str = Field(
-        description="The curie of the source node", example="probonto:k0000000"
+        description="The curie of the source node", examples=["probonto:k0000000"]
     )
     target_curie: str = Field(
-        description="The curie of the target node", example="probonto:k0000007"
+        description="The curie of the target node", examples=["probonto:k0000007"]
     )
     type: str = Field(
-        description="The type of the relation", example="has_parameter"
+        description="The type of the relation", examples=["has_parameter"]
     )
     pred: str = Field(
         description="The curie of the relation type",
-        example="probonto:c0000062"
+        examples=["probonto:c0000062"]
     )
     source: str = Field(
-        description="The prefix of the relation curie", example="probonto"
+        description="The prefix of the relation curie", examples=["probonto"]
     )
     graph: str = Field(
         description="The URI of the relation",
-        example="https://raw.githubusercontent.com/probonto"
-                "/ontology/master/probonto4ols.owl"
+        examples=["https://raw.githubusercontent.com/probonto"
+                "/ontology/master/probonto4ols.owl"]
     )
     version: str = Field(
-        description="The version number", example="2.5"
+        description="The version number", examples=["2.5"]
     )
 
 
 class Entity(BaseModel):
     """An entity in the domain knowledge graph."""
 
     id: str = Field(
-        ..., title="Compact URI", description="The CURIE of the entity", example="ido:0000511"
+        ..., title="Compact URI", description="The CURIE of the entity", examples=["ido:0000511"]
     )
-    name: Optional[str] = Field(description="The name of the entity", example="infected population")
-    type: EntityType = Field(..., description="The type of the entity", example="class")
-    obsolete: bool = Field(..., description="Is the entity marked obsolete?", example=False)
+    name: Optional[str] = Field(None, description="The name of the entity", examples=["infected population"])
+    type: EntityType = Field(..., description="The type of the entity", examples=["class"])
+    obsolete: bool = Field(..., description="Is the entity marked obsolete?", examples=[False])
     description: Optional[str] = Field(
-        description="The description of the entity.",
-        example="An organism population whose members have an infection.",
+        None, description="The description of the entity.",
+        examples=["An organism population whose members have an infection."],
     )
     synonyms: List[Synonym] = Field(
-        default_factory=list, description="A list of string synonyms", example=[]
+        default_factory=list, description="A list of string synonyms", examples=[[]]
     )
     alts: List[str] = Field(
         title="Alternative Identifiers",
         default_factory=list,
-        example=[],
+        examples=[[]],
         description="A list of alternative identifiers, given as CURIE strings.",
     )
     xrefs: List[Xref] = Field(
         title="Database Cross-references",
         default_factory=list,
-        example=[],
+        examples=[[]],
         description="A list of database cross-references, given as CURIE strings.",
     )
     labels: List[str] = Field(
         default_factory=list,
-        example=["ido"],
+        examples=[["ido"]],
         description="A list of Neo4j labels assigned to the entity.",
     )
     properties: Dict[str, List[str]] = Field(
         default_factory=dict,
         description="A mapping of properties to their values",
-        example={},
+        examples=[{}],
     )
     # Gets auto-populated
     link: Optional[str] = None
 
-    @validator("link")
-    def set_link(cls, value, values):
+    @field_validator("link")
+    def set_link(cls, value, validation_info):
         """
         Set the value of the ``link`` field based on the value of the ``id``
         field. This gets run as a post-init hook by Pydantic
 
         See also:
         https://stackoverflow.com/questions/54023782/pydantic-make-field-none-in-validator-based-on-other-fields-value
         """
-        curie = values["id"]
+        curie = validation_info.data["id"]
         return f"{METAREGISTRY_BASE}/{curie}"
 
     @property
@@ -235,12 +235,12 @@ class AskemEntity(Entity):
     """An extended entity with more ASKEM stuff loaded in."""
 
     # TODO @ben please write descriptions for these
-    physical_min: Optional[float] = Field(description="")
-    physical_max: Optional[float] = Field(description="")
-    suggested_data_type: Optional[str] = Field(description="")
-    suggested_unit: Optional[str] = Field(description="")
-    typical_min: Optional[float] = Field(description="")
-    typical_max: Optional[float] = Field(description="")
+    physical_min: Optional[float] = Field(None, description="")
+    physical_max: Optional[float] = Field(None, description="")
+    suggested_data_type: Optional[str] = Field(None, description="")
+    suggested_unit: Optional[str] = Field(None, description="")
+    typical_min: Optional[float] = Field(None, description="")
+    typical_max: Optional[float] = Field(None, description="")
 
 
 class Neo4jClient:

mira/dkg/grounding.py

@@ -18,16 +18,16 @@
 class GroundRequest(BaseModel):
     """A model representing the parameters to be passed to :func:`gilda.ground` for grounding."""
 
-    text: str = Field(..., description="The text to be grounded", example="Infected Population")
+    text: str = Field(..., description="The text to be grounded", examples=["Infected Population"])
     context: Optional[str] = Field(
         None,
         description="Context around the text to be grounded",
-        example="The infected population increased over the past month",
+        examples=["The infected population increased over the past month"],
     )
     namespaces: Optional[List[str]] = Field(
         None,
         description="A list of namespaces to filter groundings to.",
-        example=["do", "mondo", "ido"],
+        examples=[["do", "mondo", "ido"]],
     )
 
 
@@ -37,30 +37,30 @@ class GroundResult(BaseModel):
     url: str = Field(
         ...,
         description="A URL that resolves the term to an external web service",
-        example=f"{BR_BASE}/ido:0000511",
+        examples=[f"{BR_BASE}/ido:0000511"],
     )
     score: float = Field(
-        ..., description="The matching score calculated by Gilda", ge=0.0, le=1.0, example=0.78
+        ..., description="The matching score calculated by Gilda", ge=0.0, le=1.0, examples=[0.78]
     )
     prefix: str = Field(
         ...,
         description="The prefix corresponding to the ontology/database from which the term comes",
-        example="ido",
+        examples=["ido"],
     )
     identifier: str = Field(
         ...,
         description="The local unique identifier for the term in the ontology/database denoted by the prefix",
-        example="0000511",
+        examples=["0000511"],
     )
     curie: str = Field(
         ...,
         description="The compact URI that combines the prefix and local identifier.",
-        example="ido:0000511",
+        examples=["ido:0000511"],
     )
     name: str = Field(
-        ..., description="The standard entity name for the term", example="infected population"
+        ..., description="The standard entity name for the term", examples=["infected population"]
     )
-    status: str = Field(..., description="The match status, e.g., name, synonym", example="name")
+    status: str = Field(..., description="The match status, e.g., name, synonym", examples=["name"])
 
     @classmethod
     def from_scored_match(cls, scored_match: ScoredMatch) -> "GroundResult":