API

Makefile

@@ -11,7 +11,8 @@ help:
 	@echo "  format          Format source code"
 	@echo "  lint            Run lint checks"
 	@echo "  example_run     Run example"
-	@echo "  run			 Run the application"
+	@echo "  run			 Run the CLI application"
+	@echo "  serve		 Run the API application"
 	@echo "  test-remote     Run remote tests"
 	@echo "  test            Run tests"
 	@echo "  test-all        Run all tests"
@@ -91,6 +92,10 @@ else
 	pipenv run python -m src.cli "$(VAR)"
 endif
 
+.PHONY: serve
+serve:
+	pipenv run uvicorn src.main:app --host 0.0.0.0 --port 8080 --reload --workers 8
+
 .PHONY: test-remote
 test-remote:
 	pipenv run pytest \

Pipfile

@@ -15,6 +15,8 @@ seqrepo = "*"
 pytabix = "*"
 httpx = "*"
 yoyo-migrations = "*"
+fastapi = "*"
+uvicorn = "*"
 
 [dev-packages]
 mypy = "*"

src/api/internal/__init__.py

@@ -0,0 +1,3 @@
+from .api import router as internal_router
+
+__all__ = ["internal_router"]

src/api/internal/api.py

@@ -0,0 +1,79 @@
+from fastapi import APIRouter, HTTPException, Query
+
+from src.auto_acmg import AutoACMG
+from src.core.config import settings
+from src.defs.api import (
+    ApiAutoACMGSeqVarData,
+    ApiAutoACMGSeqVarResult,
+    SeqVarPredictionResponse,
+    StrucVarPredictionResponse,
+)
+from src.defs.auto_acmg import AutoACMGSeqVarResult, AutoACMGStrucVarResult
+from src.defs.exceptions import AutoAcmgBaseException
+from src.defs.genome_builds import GenomeRelease
+
+router = APIRouter()
+
+
+@router.post("/predict/seqvar", response_model=SeqVarPredictionResponse)
+async def predict_seqvar(
+    variant_name: str = Query(..., description="The name or identifier of the sequence variant"),
+    genome_release: str = Query(default="GRCh38", description="The genome release version"),
+):
+    try:
+        genome_release_enum = GenomeRelease.from_string(genome_release)
+        if not genome_release_enum:
+            raise HTTPException(status_code=400, detail="Invalid genome release")
+
+        auto_acmg = AutoACMG(variant_name, genome_release_enum)
+        prediction = auto_acmg.predict()
+
+        if (
+            prediction is None
+            or not isinstance(prediction, AutoACMGSeqVarResult)
+            or prediction.seqvar is None
+        ):
+            raise HTTPException(
+                status_code=400, detail="No valid sequence variant prediction was made"
+            )
+
+        # Convert AutoACMGSeqVarResult to ApiAutoACMGSeqVarResult
+        api_prediction = ApiAutoACMGSeqVarResult(
+            seqvar=prediction.seqvar,
+            data=ApiAutoACMGSeqVarData(**prediction.data.model_dump()),
+            criteria=prediction.criteria,
+        )
+
+        return SeqVarPredictionResponse(prediction=api_prediction)
+    except AutoAcmgBaseException as e:
+        raise HTTPException(status_code=400, detail=str(e))
+
+
+@router.post("/predict/strucvar", response_model=StrucVarPredictionResponse)
+async def predict_strucvar(
+    variant_name: str = Query(..., description="The name or identifier of the structural variant"),
+    genome_release: str = Query(default="GRCh38", description="The genome release version"),
+    duplication_tandem: bool = Query(
+        default=False,
+        description="The duplication is in tandem and disrupts reading frame and undergoes NMD",
+    ),
+):
+    try:
+        # Set default duplication tandem if provided
+        settings.DUPLICATION_TANDEM = duplication_tandem
+
+        genome_release_enum = GenomeRelease.from_string(genome_release)
+        if not genome_release_enum:
+            raise HTTPException(status_code=400, detail="Invalid genome release")
+
+        auto_acmg = AutoACMG(variant_name, genome_release_enum)
+        prediction = auto_acmg.predict()
+
+        if prediction is None or not isinstance(prediction, AutoACMGStrucVarResult):
+            raise HTTPException(
+                status_code=400, detail="No valid structural variant prediction was made"
+            )
+
+        return StrucVarPredictionResponse(prediction=prediction)
+    except AutoAcmgBaseException as e:
+        raise HTTPException(status_code=400, detail=str(e))