kemal
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End-to-end variant interpretation platform for rare genetic disease research: SvelteKit UI, FastAPI + PostgreSQL API, Nextflow/Ensembl VEP pipeline, LightGBM pathogenicity scoring with MLflow, K8s/ArgoCD/GCP infrastructure. Public test data only; no clinical claims.
64 lines
1.1 KiB
Python
64 lines
1.1 KiB
Python
from datetime import datetime
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import uuid
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from pydantic import BaseModel, ConfigDict, Field
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from app.models import JobStatus
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class ORMModel(BaseModel):
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model_config = ConfigDict(from_attributes=True)
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class SampleCreate(BaseModel):
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name: str = Field(min_length=1, max_length=120)
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vcf_uri: str
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assembly: str = "GRCh38"
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class SampleOut(ORMModel):
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id: uuid.UUID
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name: str
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vcf_uri: str
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assembly: str
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created_at: datetime
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class JobOut(ORMModel):
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id: uuid.UUID
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sample_id: uuid.UUID
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status: JobStatus
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workflow_ref: str | None
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vep_version: str | None
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created_at: datetime
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finished_at: datetime | None
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class PredictionOut(ORMModel):
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model_name: str
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model_version: str
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score: float
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class VariantOut(ORMModel):
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id: int
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chrom: str
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pos: int
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ref: str
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alt: str
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gene: str | None
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consequence: str | None
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impact: str | None
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hgvsc: str | None
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hgvsp: str | None
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gnomad_af: float | None
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clinvar_sig: str | None
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prediction: PredictionOut | None = None
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class VariantPage(BaseModel):
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items: list[VariantOut]
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total: int
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limit: int
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offset: int
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