Fix/query bug (#73)

compose.yaml

@@ -122,7 +122,7 @@ services:
       dockerfile: build/Dockerfile
     command: --host=0.0.0.0 --port=5734
   external_data_query:
-    image: 'ghcr.io/basedlabs/external-data-query:1.0.0'
+    image: 'ghcr.io/basedlabs/external-data-query:1.0.1'
     network_mode: host
     build:
       context: microservices/external_data_query

microservices/external_data_query/external_data_query/chembl/api_models.py

@@ -1,12 +1,12 @@
 from __future__ import annotations
 
-import dataclasses
+from pydantic.dataclasses import dataclass
 from typing import List, Optional, Dict, Union
 
 from external_data_query.mixins import BaseModelMixin
 
 
-@dataclasses.dataclass
+@dataclass
 class Molecule:
     chembl_id: str
     molecule_type: str
@@ -16,33 +16,33 @@ class Molecule:
     pref_name: str = None
 
 
-@dataclasses.dataclass
+@dataclass
 class ChEMBLMoleculeRequest(BaseModelMixin):
     filters: Dict[str, Union[str, bool, int]] = None
     order_by: str = None
     limit: int = 20
     job_id: Optional[str] = None
 
 
-@dataclasses.dataclass
+@dataclass
 class ChEMBLMoleculeResponse(BaseModelMixin):
     molecules: List[Molecule]
 
 
-@dataclasses.dataclass
+@dataclass
 class IsJobRunningResponse:
     is_running: bool
 
 
-@dataclasses.dataclass
+@dataclass
 class DrugIndicationRequest(BaseModelMixin):
     filters: Dict[str, Union[str, bool, int]] = None
     order_by: str = None
     limit: int = 20  # Default page size
     job_id: Optional[str] = None
 
 
-@dataclasses.dataclass
+@dataclass
 class DrugIndicationResponse(BaseModelMixin):
     drugs: List[Molecule]  # Assuming Molecule can also represent a drug in this context
     total_count: int

microservices/external_data_query/external_data_query/pubmed/api_models.py

@@ -1,29 +1,29 @@
 from __future__ import annotations
 
-import dataclasses
+from pydantic.dataclasses import dataclass
 from typing import List, Optional
 
 from external_data_query.mixins import BaseModelMixin
 
-@dataclasses.dataclass
+@dataclass
 class FetchedArticle:
     title: str
     summary: str
     link: str
 
 
-@dataclasses.dataclass
+@dataclass
 class PubMedSearchRequest(BaseModelMixin):
     search_terms: str
     max_results: int
     api_key: Optional[str] = None
     job_id: Optional[str] = None
 
-@dataclasses.dataclass
+@dataclass
 class PubMedSearchResponse(BaseModelMixin):
     articles: List[FetchedArticle]
 
 
-@dataclasses.dataclass
+@dataclass
 class IsJobRunningResponse:
     is_running: bool

microservices/external_data_query/external_data_query/rcsb_pdb/api_models.py

@@ -37,7 +37,6 @@ class SequenceType(str, Enum):
     DNA = "dna"
     RNA = "rna"
 
-@dataclass
 class SequenceQueryRequest(BaseModel):
     sequence: str
     sequence_type: SequenceType