Merge pull request #389 from Steinbeck-Lab/dev-chandu

fix: resolves #387, #388

app/modules/tools/sugar_removal.py

@@ -130,10 +130,10 @@ def remove_linear_and_circular_sugar(molecule: any):
             molecule, True
         )
         try:
+            print(MoleculeWithoutSugars)
             S_SMILES = SmilesGenerator.create(MoleculeWithoutSugars)
+            return str(S_SMILES)
         except Exception as e:
-            print(e)
-            return "Error generating SMILES"
-        return str(S_SMILES)
+            raise Exception(f"{str(e)}")
     else:
         return "No Linear or Circular sugars found"

app/modules/tools/surge.py

@@ -70,8 +70,8 @@ def generate_structures_SURGE(molecular_formula: str) -> Union[list, str]:
                 smiles = [line.strip() for line in output_lines]
                 return smiles
             else:
-                return f"Error running surge: {stderr.decode('utf-8')}"
-        except Exception as e:
-            return f"An error occurred: {str(e)}"
+                raise Exception(f"Error running surge: {stderr.decode('utf-8')}")
+        except Exception:
+            raise Exception(f"Error running surge: {stderr.decode('utf-8')}")
     else:
         return "The molecular formula contains more heavy atoms than allowed (10 Heavy Atoms max)."

app/routers/ocsr.py

@@ -3,12 +3,12 @@
 from fastapi.responses import JSONResponse
 from urllib.request import urlopen
 from urllib.parse import urlsplit
-from fastapi import Body, APIRouter, status, HTTPException
+from fastapi import Body, APIRouter, status, HTTPException, File, UploadFile
 from app.modules.decimer import get_predicted_segments_from_file
 from app.schemas import HealthCheck
 from app.schemas.error import ErrorResponse, BadRequestModel, NotFoundModel
 from app.schemas.ocsr_schema import ExtractChemicalInfoResponse
-from fastapi import UploadFile
+from typing import Annotated
 
 router = APIRouter(
     prefix="/ocsr",
@@ -63,7 +63,7 @@ async def Extract_ChemicalInfo_From_File(
     path: str = Body(
         None,
         embed=True,
-        description="URL or local file path to the chemical structure depiction image.",
+        description="Local or Remote path to the image file",
         openapi_examples={
             "example1": {
                 "summary": "Cheminformatics - Article example image",
@@ -75,20 +75,24 @@ async def Extract_ChemicalInfo_From_File(
             },
         },
     ),
-    reference: str = Body(None, embed=True, description="Reference information."),
+    reference: str = Body(
+        None,
+        embed=True,
+        description="User defined reference information for tracking",
+    ),
     img: str = Body(
         None,
         embed=True,
-        description="Bytes content of the chemical structure depiction image.",
+        description="Image: Bytes content of the chemical structure depiction image",
     ),
 ):
     """
     Detect, segment and convert a chemical structure depiction into a SMILES string using the DECIMER modules.
 
     Parameters:
-    - **path**: optional if img is provided (str): URL or local file path to the chemical structure depiction image.
-    - **reference**: optional (str): URL or local file path to the chemical structure depiction image.
-    - **img**: optional if a valid path is provided (str): URL or local file path to the chemical structure depiction image.
+    - **path**: optional if img is provided (str): Local or Remote path to the image file.
+    - **reference**: optional (str): User defined reference information for tracking.
+    - **img**: optional if a valid path is provided (str): Image: Bytes content of the chemical structure depiction image.
 
     Returns:
     - JSONResponse: A JSON response containing the extracted SMILES and the reference (if provided).
@@ -139,12 +143,14 @@ async def Extract_ChemicalInfo_From_File(
         422: {"description": "Unprocessable Entity", "model": ErrorResponse},
     },
 )
-async def extract_chemicalinfo_from_upload(file: UploadFile):
+async def extract_chemicalinfo_from_upload(
+    file: Annotated[UploadFile, File(description="Chemical structure depiction image")],
+):
     """
     Detect, segment and convert a chemical structure depiction in the uploaded image file into a SMILES string using the DECIMER modules.
 
     Parameters:
-    - **file**: required (File):
+    - **file**: required (File): Chemical structure depiction image
 
     Returns:
     - JSONResponse: A JSON response containing the extracted SMILES and the reference (if provided).

app/routers/tools.py

@@ -211,8 +211,8 @@ async def remove_linear_sugars(
     - str: The modified SMILES string with linear sugars removed.
 
     """
+    mol = parse_input(smiles, "cdk", False)
     try:
-        mol = parse_input(smiles, "cdk", False)
         removed_smiles = remove_linear_sugar(mol)
         if removed_smiles:
             return removed_smiles

docs/index.md

@@ -2,7 +2,7 @@
 layout: home
 
 hero:
-  name: "Cheminformatics Microservice (CM)"
+  name: "Cheminformatics Microservice"
   text: ""
   tagline: Effortlessly integrate cheminformatics tools into your web application or workflows.
   actions:
@@ -17,7 +17,7 @@ features:
   - title: Multi-Tool Kit Support (Portability)
     details: Seamlessly incorporate and utilize various toolkits, such as RDKit, CDK, and OpenBabel, to improve your cheminformatics and computational chemistry tasks without the need for complex setup. Maximize the benefits of different frameworks available.
   - title: Consistent and Reproducible Environments (Reproducibility)
-    details: CM packages toolkits and all their dependencies, libraries, and system tools, into a single container (including the entire runtime ensuring consistency across different deployments).
+    details: Cheminformatics Microservice packages toolkits and all their dependencies, libraries, and system tools, into a single container (including the entire runtime ensuring consistency across different deployments).
   - title: Advanced logging (Metrics)
-    details: Prometheus and Grafana provide a powerful monitoring solution for CM that collects and visualizes metrics in real time, enabling efficient tracking of system health, performance, and behaviour.
+    details: Prometheus and Grafana provide a powerful monitoring solution for Cheminformatics Microservice that collects and visualizes metrics in real time, enabling efficient tracking of system health, performance, and behaviour.
 ---

tests/test_tools.py

@@ -50,7 +50,7 @@ def test_sugars_info(input, response_text, response_code):
     "input,response_text, response_code",
     [
         ("OCC(O)C(O)C(O)C(O)C1OC(CO)C(O)C(O)C1O", '"C(C1C(C(C(CO1)O)O)O)O"', 200),
-        ("INVALID_INPUT", "", 500),
+        ("INVALID_INPUT", "", 422),
     ],
 )
 def test_remove_linear_sugars(input, response_text, response_code):