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#!/usr/bin/env python3
"""MedGenesis – **data schemas** powered by `pydantic`.
This module formalises the JSON objects exchanged between the backend
(orchestrator) and the Streamlit UI. It now aligns with the *enhanced*
pipeline that returns live genes, trials, and Open Targets edges.
"""
from __future__ import annotations
from typing import List, Optional
from pydantic import BaseModel, Field, HttpUrl
# ----------------------------------------------------------------------
# Literature & concepts
# ----------------------------------------------------------------------
class Paper(BaseModel):
title : str
authors : str
summary : str
link : HttpUrl
published : str = Field(description="ISO date string")
source : str = Field(description="'arxiv' | 'pubmed' | other")
class UMLSConcept(BaseModel):
term : str
cui : Optional[str]
name : Optional[str]
rootSource : Optional[str]
# ----------------------------------------------------------------------
# Safety & biomedical enrichers
# ----------------------------------------------------------------------
class DrugSafety(BaseModel):
safety_report_id : Optional[str]
serious : Optional[str]
reactions : Optional[List[str]]
receivedate : Optional[str]
class GeneInfo(BaseModel):
symbol : str
name : Optional[str]
summary : Optional[str]
entrezgene : Optional[int]
clinvar : Optional[dict]
class MeshDefinition(BaseModel):
term : str
definition : str
class GeneDiseaseLink(BaseModel):
gene_symbol : str
disease_id : str
score : float
class ClinicalTrial(BaseModel):
nct_id : str = Field(alias="nctId")
brief_title: str = Field(alias="briefTitle")
phase : Optional[str]
status : Optional[str]
start_date : Optional[str]
class OTAssociation(BaseModel):
score : float
datatypeId : str
datasourceId: str
disease : dict # {id, name}
target : dict # {id, symbol}
# ----------------------------------------------------------------------
# Search I/O
# ----------------------------------------------------------------------
class UnifiedSearchInput(BaseModel):
query: str
class UnifiedSearchResult(BaseModel):
papers : List[Paper]
umls : List[UMLSConcept]
drug_safety : List[DrugSafety]
genes : List[GeneInfo]
mesh_defs : List[MeshDefinition]
gene_disease : List[GeneDiseaseLink]
clinical_trials : List[ClinicalTrial]
ot_associations : Optional[List[OTAssociation]] = []
ai_summary : str
llm_used : str
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