ngs_models.py

from pydantic import BaseModel, Field
from typing import List, Optional
from datetime import date

class Variant(BaseModel):
    """
    A class to represent a single genetic variant found in an NGS report.
    """
    gene_name: str = Field(..., description="The name of the gene with the variant, e.g., 'ESR1'.")
    variant_type: str = Field(..., description="Type of genetic variation, e.g., 'Missense'.")
    chromosome_location: str = Field(..., description="The chromosomal location of the variant.")
    exon_intron: Optional[str] = Field(None, description="The specific exon or intron number.")
    protein_change: Optional[str] = Field(None, description="The change in the protein sequence, e.g., 'p.Arg538Gly'.")
    clinical_significance: Optional[str] = Field(None, description="Clinical significance of the variant, e.g., 'PATHOGENIC'.")
    drug_comment: Optional[str] = Field(None, description="Comments related to drugs.")
    mutant_allele_evidence: Optional[str] = Field(None, description="Evidence for the mutant allele.")
    reference_id: Optional[str] = Field(None, description="A reference ID for the variant, e.g., 'rs5823449'.")
    therapy_drugs: Optional[List[str]] = Field(None, description="Associated therapy drugs.")
    final_suggested_drugs: Optional[List[str]] = Field(None, description="Final suggested drugs based on the finding.")
    pathways_involved: Optional[List[str]] = Field(None, description="Biological pathways involved with this variant.")


class NGSReport(BaseModel):
    """
    A Pydantic model to represent a patient's Next-Generation Sequencing (NGS) report.
    """
    patient_name: str = Field(..., description="Name of the patient.")
    date_of_test: date = Field(..., description="Date the test was performed.")
    assay_method: str = Field(..., description="The name of the NGS assay used, e.g., 'TARGET V(2)IENCE'.")
    variants: List[Variant] = Field(..., description="A list of genetic variants identified in the report.")
    tmb_value: Optional[str] = Field(None, description="Tumor Mutational Burden (TMB) value.")
    tmb_percentile: Optional[int] = Field(None, description="TMB percentile.")
    tmb_score: Optional[str] = Field(None, description="TMB score, e.g., 'Low'.")
    tmb_unit: Optional[str] = Field(None, description="The unit of measurement for the TMB value.")
    hospital_name: str = Field(..., description="Name of the hospital or laboratory.")
    hospital_location: str = Field(..., description="Location of the hospital or laboratory.")