Merge pull request #60 from monarch-initiative/59-cant-make-load-gith…

…ub-obi-or-load-bacdive-field-model_name-has-conflict-with-protected-namespace-model

Add config to each pydantic BaseModel; fix #59

src/curate_gpt/agents/bootstrap_agent.py

@@ -3,14 +3,15 @@
 
 import yaml
 from jinja2 import Template
-from pydantic import BaseModel
+from pydantic import BaseModel, ConfigDict
 
 from curate_gpt.agents.base_agent import BaseAgent
 from curate_gpt.conf.prompts import PROMPTS_DIR
 from curate_gpt.extract import AnnotatedObject
 
 
 class KnowledgeBaseSpecification(BaseModel):
+    model_config = ConfigDict(protected_namespaces=())
     kb_name: str
     description: str
     attributes: str

src/curate_gpt/agents/chat_agent.py

@@ -7,7 +7,7 @@
 
 import yaml
 from llm import Conversation
-from pydantic import BaseModel
+from pydantic import BaseModel, ConfigDict
 
 from curate_gpt.agents.base_agent import BaseAgent
 from curate_gpt.utils.tokens import estimate_num_tokens, max_tokens_by_model
@@ -23,6 +23,8 @@ class ChatResponse(BaseModel):
     TODO: Rename class to indicate that it is provenance-enabled chat
     """
 
+    model_config = ConfigDict(protected_namespaces=())
+
     body: str
     """Text of response."""
 

src/curate_gpt/agents/concept_recognition_agent.py

@@ -5,7 +5,7 @@
 from enum import Enum
 from typing import Dict, List, Optional, Tuple
 
-from pydantic import BaseModel
+from pydantic import BaseModel, ConfigDict
 
 from curate_gpt.agents.base_agent import BaseAgent
 
@@ -18,6 +18,8 @@
 class Span(BaseModel):
     """An individual span of text containing a single concept."""
 
+    model_config = ConfigDict(protected_namespaces=())
+
     text: str
 
     start: Optional[int] = None
@@ -36,6 +38,8 @@ class Span(BaseModel):
 class GroundingResult(BaseModel):
     """Result of grounding text."""
 
+    model_config = ConfigDict(protected_namespaces=())
+
     input_text: str
     """Text that is supplied for grounding, assumed to contain a single context."""
 
@@ -62,6 +66,8 @@ class AnnotationMethod(str, Enum):
 class AnnotatedText(BaseModel):
     """In input text annotated with concept instances."""
 
+    model_config = ConfigDict(protected_namespaces=())
+
     input_text: str
     """Text that is supplied for annotation."""
 

src/curate_gpt/agents/dase_agent.py

@@ -4,7 +4,7 @@
 from dataclasses import dataclass, field
 from typing import Any, ClassVar, Dict, List, Optional, Union
 
-from pydantic import BaseModel
+from pydantic import BaseModel, ConfigDict
 
 from curate_gpt.agents.base_agent import BaseAgent
 from curate_gpt.agents.chat_agent import ChatResponse
@@ -17,6 +17,8 @@
 
 
 class PredictedFieldValue(BaseModel):
+
+    model_config = ConfigDict(protected_namespaces=())
     id: str
     original_id: Optional[str] = None
     predicted_value: Optional[str] = None

src/curate_gpt/agents/dragon_agent.py

@@ -5,7 +5,7 @@
 from typing import Any, ClassVar, Dict, Iterable, List, Optional, Tuple, Union
 
 import yaml
-from pydantic import BaseModel
+from pydantic import BaseModel, ConfigDict
 
 from curate_gpt.agents.base_agent import BaseAgent
 from curate_gpt.extract import AnnotatedObject
@@ -17,6 +17,8 @@
 
 
 class PredictedFieldValue(BaseModel):
+
+    model_config = ConfigDict(protected_namespaces=())
     id: str
     original_id: Optional[str] = None
     predicted_value: Optional[str] = None

src/curate_gpt/agents/mapping_agent.py

@@ -10,7 +10,7 @@
 
 import inflection
 import yaml
-from pydantic import BaseModel
+from pydantic import BaseModel, ConfigDict
 
 from curate_gpt.agents.base_agent import BaseAgent
 from curate_gpt.store.db_adapter import SEARCH_RESULT
@@ -46,12 +46,15 @@ class MappingPredicate(str, Enum):
 class Mapping(BaseModel):
     """Response from chat engine."""
 
+    model_config = ConfigDict(protected_namespaces=())
     subject_id: str
     object_id: str
     predicate_id: Optional[MappingPredicate] = None
 
 
 class MappingSet(BaseModel):
+
+    model_config = ConfigDict(protected_namespaces=())
     mappings: List[Mapping]
     prompt: str = None
     response_text: str = None

src/curate_gpt/app/cart.py

@@ -1,13 +1,14 @@
 from typing import Dict, List, Optional, Union
 
-from pydantic import BaseModel
+from pydantic import BaseModel, ConfigDict
 
 
 class CartItem(BaseModel):
     """
     A cart item is a single item in a cart
     """
 
+    model_config = ConfigDict(protected_namespaces=())
     object: Union[Dict, BaseModel]
     object_type: Optional[str] = None
     source: Optional[str] = None
@@ -19,6 +20,7 @@ class Cart(BaseModel):
     A cart is a list of items that can be added to or removed from
     """
 
+    model_config = ConfigDict(protected_namespaces=())
     items: List[CartItem] = []
 
     @property

src/curate_gpt/evaluation/evaluation_datamodel.py

@@ -2,14 +2,15 @@
 from pathlib import Path
 from typing import Dict, List, Optional, Union
 
-from pydantic import BaseModel
+from pydantic import BaseModel, ConfigDict
 
 
 class StratifiedCollection(BaseModel):
     """
     A collection of objects that have been split into training, test, and validation sets.
     """
 
+    model_config = ConfigDict(protected_namespaces=())
     source: str = None
     training_set: List[Dict] = None
     testing_set: List[Dict] = None
@@ -33,6 +34,8 @@ class AggregationMethod(str, Enum):
 
 
 class ClassificationMetrics(BaseModel):
+
+    model_config = ConfigDict(protected_namespaces=())
     precision: float
     recall: float
     f1_score: float
@@ -49,6 +52,7 @@ class Task(BaseModel):
     A task to be run by the evaluation runner.
     """
 
+    model_config = ConfigDict(protected_namespaces=())
     model_name: str = "gpt-3.5-turbo"
     embedding_model_name: str = "openai:"
     generate_background: bool = False

src/curate_gpt/extract/extractor.py

@@ -9,6 +9,7 @@
 import llm
 from linkml_runtime import SchemaView
 from pydantic import BaseModel as BaseModel
+from pydantic import ConfigDict
 
 from curate_gpt.store.schema_proxy import SchemaProxy
 
@@ -20,6 +21,8 @@ class AnnotatedObject(BaseModel):
     Annotated object shadows a basic dictionary object
     """
 
+    model_config = ConfigDict(protected_namespaces=())
+
     # object: Union[Dict[str, Any], List[Dict[str, Any]]] = {} - TODO: pydantic bug?
     object: Any = {}
     annotations: Dict[str, Any] = {}

src/curate_gpt/store/db_metadata.py

@@ -1,10 +1,13 @@
 from pathlib import Path
 
 import yaml
-from pydantic import BaseModel
+from pydantic import BaseModel, ConfigDict
 
 
 class DBSettings(BaseModel):
+
+    model_config = ConfigDict(protected_namespaces=())
+
     name: str = "duckdb"
     """Name of the database."""
 

src/curate_gpt/store/duckdb_result.py

@@ -1,11 +1,14 @@
 from typing import Any, Dict, Iterator, List, Optional, Set, Tuple
 
-from pydantic import BaseModel
+from pydantic import BaseModel, ConfigDict
 
 SEARCH_RESULT = Tuple[Dict[str, Any], Dict, float, Optional[Dict]]
 
 
 class DuckDBSearchResult(BaseModel):
+
+    model_config = ConfigDict(protected_namespaces=())
+
     ids: Optional[str] = None
     metadatas: Optional[Dict[str, Any]] = None
     embeddings: Optional[List[float]] = None

src/curate_gpt/store/in_memory_adapter.py

@@ -4,7 +4,7 @@
 from dataclasses import dataclass, field
 from typing import ClassVar, Dict, Iterable, Iterator, List, Optional, Union
 
-from pydantic import BaseModel
+from pydantic import BaseModel, ConfigDict
 
 from curate_gpt import DBAdapter
 from curate_gpt.store.db_adapter import OBJECT, PROJECTION, QUERY, SEARCH_RESULT
@@ -14,6 +14,9 @@
 
 
 class Collection(BaseModel):
+
+    model_config = ConfigDict(protected_namespaces=())
+
     objects: List[Dict] = []
     metadata: Dict = {}
 
@@ -25,6 +28,9 @@ def delete(self, key_value: str, key: str) -> None:
 
 
 class CollectionIndex(BaseModel):
+
+    model_config = ConfigDict(protected_namespaces=())
+
     collections: Dict[str, Collection] = {}
 
     def get_collection(self, name: str) -> Collection:

src/curate_gpt/store/metadata.py

@@ -1,6 +1,6 @@
 from typing import Dict, Optional
 
-from pydantic import BaseModel
+from pydantic import BaseModel, ConfigDict
 
 
 class CollectionMetadata(BaseModel):
@@ -10,6 +10,8 @@ class CollectionMetadata(BaseModel):
     This is an open class, so additional metadata can be added.
     """
 
+    model_config = ConfigDict(protected_namespaces=())
+
     name: Optional[str] = None
     """Name of the collection"""
 

src/curate_gpt/store/schema_proxy.py

@@ -4,7 +4,7 @@
 
 from linkml_runtime import SchemaView
 from linkml_runtime.linkml_model import SchemaDefinition
-from pydantic import BaseModel
+from pydantic import BaseModel, ConfigDict
 
 
 @dataclass
@@ -13,6 +13,8 @@ class SchemaProxy:
     Manage connection to a schema
     """
 
+    model_config = ConfigDict(protected_namespaces=())
+
     schema_source: Union[str, Path, SchemaDefinition] = None
     _pydantic_root_model: BaseModel = None
     _schemaview: SchemaView = None

src/curate_gpt/utils/eval_utils.py

@@ -3,10 +3,13 @@
 from copy import copy
 from typing import Any, Dict, List, Optional, Union
 
-from pydantic import BaseModel
+from pydantic import BaseModel, ConfigDict
 
 
 class Outcome(BaseModel):
+
+    model_config = ConfigDict(protected_namespaces=())
+
     prediction: Union[Dict[str, Any], List[Dict[str, Any]]] = {}
     expected: Union[Dict[str, Any], List[Dict[str, Any]]] = {}
     parameters: Dict[str, Any] = {}

src/curate_gpt/wrappers/general/github_wrapper.py

@@ -1,4 +1,4 @@
-"""Chat with a Google Drive."""
+"""Chat with issues from a GitHub repository."""
 
 import logging
 import os
@@ -8,20 +8,22 @@
 
 import requests
 import requests_cache
-from pydantic import BaseModel
+from pydantic import BaseModel, ConfigDict
 
 from curate_gpt.wrappers.base_wrapper import BaseWrapper
 
 logger = logging.getLogger(__name__)
 
 
 class Comment(BaseModel):
+    model_config = ConfigDict(protected_namespaces=())
     id: str
     user: str = None
     body: str = None
 
 
 class Issue(BaseModel):
+    model_config = ConfigDict(protected_namespaces=())
     id: str
     number: int = None
     type: str = None

src/curate_gpt/wrappers/ontology/ontology.py

@@ -1,6 +1,6 @@
 from typing import List
 
-from pydantic import BaseModel, Extra
+from pydantic import BaseModel, ConfigDict, Extra
 
 
 class Relationship(BaseModel):
@@ -10,6 +10,7 @@ class Relationship(BaseModel):
     Corresponds to an edge in an OBO graph.
     """
 
+    model_config = ConfigDict(protected_namespaces=())
     predicate: str
     target: str
 
@@ -21,6 +22,7 @@ class OntologyClass(BaseModel, extra=Extra.allow):
     Corresponds to a node in an OBO graph.
     """
 
+    model_config = ConfigDict(protected_namespaces=())
     id: str
     label: str = None
     definition: str = None
@@ -37,4 +39,5 @@ class Ontology(BaseModel):
     Corresponds to an OBO graph.
     """
 
+    model_config = ConfigDict(protected_namespaces=())
     elements: List[OntologyClass] = None

tests/extract/test_extractor.py

@@ -2,7 +2,7 @@
 
 import pytest
 from linkml_runtime.utils.schema_builder import SchemaBuilder
-from pydantic import BaseModel
+from pydantic import BaseModel, ConfigDict
 
 from curate_gpt.extract.basic_extractor import BasicExtractor
 from curate_gpt.extract.extractor import AnnotatedObject
@@ -12,11 +12,13 @@
 
 
 class Occupation(BaseModel):
+    model_config = ConfigDict(protected_namespaces=())
     category: str
     current: bool
 
 
 class Person(BaseModel):
+    model_config = ConfigDict(protected_namespaces=())
     name: str
     age: int
     occupations: List[Occupation]