fix: flake8 errors fix

app/routers/chem.py

@@ -1,9 +1,11 @@
 from typing import Annotated
 from psycopg2.errors import UniqueViolation
 from app.modules.cdkmodules import getCDKHOSECodes
-from fastapi import APIRouter, HTTPException, status, Query
+from fastapi import APIRouter, HTTPException, status, Query, Body
 from app.modules.rdkitmodules import getRDKitHOSECodes
 from app.schemas import HealthCheck
+from app.schemas.alatis import AlatisModel
+import requests
 
 router = APIRouter(
     prefix="/chem",
@@ -76,3 +78,36 @@ async def HOSE_Codes(
             detail="Error paring the structure " + e.message,
             headers={"X-Error": "RDKit molecule input parse error"},
         )
+
+
+@router.post(
+    "/label-atoms",
+    tags=["chem"],
+    summary="Label atoms using ALATIS naming system",
+    response_model=AlatisModel,
+    response_description="",
+    status_code=status.HTTP_200_OK,
+)
+async def label_atoms(
+    data: Annotated[
+        str,
+        Body(embed=False, media_type="text/plain"),
+    ]
+):
+    """
+    ## Generates atom labels for a given molecule
+
+    Returns:
+        JSON with various representations
+    """
+    try:
+        url = "http://alatis.nmrfam.wisc.edu/upload"
+        payload = {"input_text": data, "format": "format_", "response_type": "json"}
+        response = requests.request("POST", url, data=payload)
+        return response.json()
+    except Exception as e:
+        raise HTTPException(
+            status_code=422,
+            detail="Error paring the structure " + e.message,
+            headers={"X-Error": "RDKit molecule input parse error"},
+        )

app/routers/spectra.py

@@ -1,9 +1,6 @@
-from typing import Annotated
-from fastapi import APIRouter, HTTPException, status, FastAPI, File, UploadFile
-from fastapi.responses import Response
+from fastapi import APIRouter, HTTPException, status, UploadFile
 from app.schemas import HealthCheck
 import subprocess
-import json
 
 router = APIRouter(
     prefix="/spectra",
@@ -12,6 +9,7 @@
     responses={404: {"description": "Not found"}},
 )
 
+
 @router.get("/", include_in_schema=False)
 @router.get(
     "/health",
@@ -41,7 +39,6 @@ def get_health() -> HealthCheck:
     summary="Parse the input spectra format and extract metadata",
     response_description="",
     status_code=status.HTTP_200_OK,
-    
 )
 async def parse_spectra(file: UploadFile):
     """
@@ -54,17 +51,24 @@ async def parse_spectra(file: UploadFile):
     try:
         contents = file.file.read()
         file_path = "/tmp/" + file.filename
-        with open(file_path, 'wb') as f:
+        with open(file_path, "wb") as f:
             f.write(contents)
-        p = subprocess.Popen("npx nmr-cli -p " + file_path, stdout=subprocess.PIPE, shell=True)
+        p = subprocess.Popen(
+            "npx nmr-cli -p " + file_path, stdout=subprocess.PIPE, shell=True
+        )
         (output, err) = p.communicate()
         p_status = p.wait()
         return output
     except Exception as e:
         raise HTTPException(
             status_code=422,
-            detail="Error paring the structure " + e.message + ". Error: " + err + ". Status:" + p_status,
+            detail="Error paring the structure "
+            + e.message
+            + ". Error: "
+            + err
+            + ". Status:"
+            + p_status,
             headers={"X-Error": "RDKit molecule input parse error"},
         )
     finally:
-        file.file.close()
+        file.file.close()

app/schemas/alatis.py

@@ -0,0 +1,11 @@
+from __future__ import annotations
+
+from pydantic import BaseModel
+
+
+class AlatisModel(BaseModel):
+    html_url: str
+    inchi: str
+    key: str
+    status: str
+    structure: str