fix: convert/smiles gives 200 response for invalid input - resolves #372

Steinbeck-Lab · Sep 6, 2023 · eea7510 · eea7510
1 parent 981980d
commit eea7510
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Showing 2 changed files with 85 additions and 108 deletions.
diff --git a/app/modules/toolkits/openbabel_wrapper.py b/app/modules/toolkits/openbabel_wrapper.py
@@ -1,5 +1,6 @@
 from openbabel import openbabel as ob
 from openbabel import pybel
+from app.exception_handlers import InvalidInputException
 
 
 def getOBCanonicalSMILES(smiles: str) -> str:
@@ -12,9 +13,7 @@ def getOBCanonicalSMILES(smiles: str) -> str:
     Returns:
         str: Canonical SMILES string.
     """
-
-    if any(char.isspace() for char in smiles):
-        smiles = smiles.replace(" ", "+")
+    smiles = smiles.replace(" ", "+")
 
     # Create an Open Babel molecule object
     mol = ob.OBMol()
@@ -23,9 +22,12 @@ def getOBCanonicalSMILES(smiles: str) -> str:
     conv.SetInAndOutFormats("smi", "can")
     conv.ReadString(mol, smiles)
 
-    canSMILES = conv.WriteString(mol)
-    canSMILES = canSMILES.strip()  # Remove leading/trailing whitespace
-    return canSMILES
+    if mol.NumAtoms() <= 0:
+        raise InvalidInputException(name="smiles", value=smiles)
+    else:
+        canSMILES = conv.WriteString(mol)
+        canSMILES = canSMILES.strip()  # Remove leading/trailing whitespace
+        return canSMILES
 
 
 def getOBInChI(smiles: str, InChIKey: bool = False) -> str:
@@ -40,8 +42,7 @@ def getOBInChI(smiles: str, InChIKey: bool = False) -> str:
         str: InChI string or InChIKey string if InChIKey is True.
     """
 
-    if any(char.isspace() for char in smiles):
-        smiles = smiles.replace(" ", "+")
+    smiles = smiles.replace(" ", "+")
 
     # Create an Open Babel molecule object
     mol = ob.OBMol()
@@ -51,13 +52,16 @@ def getOBInChI(smiles: str, InChIKey: bool = False) -> str:
     conv.SetInAndOutFormats("smi", "inchi")
     conv.ReadString(mol, smiles)
 
-    inchi = conv.WriteString(mol)
-    inchi = inchi.strip()  # Remove leading/trailing whitespace
-    if InChIKey:
-        conv.SetOptions("K", conv.OUTOPTIONS)
-        inchikey_ = conv.WriteString(mol).rstrip()
-        return inchikey_
-    return inchi
+    if mol.NumAtoms() <= 0:
+        raise InvalidInputException(name="smiles", value=smiles)
+    else:
+        inchi = conv.WriteString(mol)
+        inchi = inchi.strip()  # Remove leading/trailing whitespace
+        if InChIKey:
+            conv.SetOptions("K", conv.OUTOPTIONS)
+            inchikey_ = conv.WriteString(mol).rstrip()
+            return inchikey_
+        return inchi
 
 
 def getOBMol(smiles: str, threeD: bool = False, depict: bool = False) -> str:
@@ -72,20 +76,22 @@ def getOBMol(smiles: str, threeD: bool = False, depict: bool = False) -> str:
     Returns:
         str: Mol block (2D/3D).
     """
-    if any(char.isspace() for char in smiles):
-        smiles = smiles.replace(" ", "+")
+    smiles = smiles.replace(" ", "+")
 
     if threeD:
         mol = pybel.readstring("smi", smiles)
-        mol.addh()
-        mol.make3D()
-        gen3d = ob.OBOp.FindType("gen3D")
-        gen3d.Do(mol.OBMol, "--best")
-        if depict:
-            return mol.write("mol")
+        if mol.NumAtoms() <= 0:
+            raise InvalidInputException(name="smiles", value=smiles)
         else:
-            mol.removeh()
-            return mol.write("mol")
+            mol.addh()
+            mol.make3D()
+            gen3d = ob.OBOp.FindType("gen3D")
+            gen3d.Do(mol.OBMol, "--best")
+            if depict:
+                return mol.write("mol")
+            else:
+                mol.removeh()
+                return mol.write("mol")
 
     # Create an Open Babel molecule object
     mol = ob.OBMol()
@@ -94,10 +100,13 @@ def getOBMol(smiles: str, threeD: bool = False, depict: bool = False) -> str:
     conv.SetInAndOutFormats("smi", "mol")
     conv.ReadString(mol, smiles)
 
-    # Generate 2D coordinates
-    obBuilder = ob.OBBuilder()
-    obBuilder.Build(mol)
+    if mol.NumAtoms() <= 0:
+        raise InvalidInputException(name="smiles", value=smiles)
+    else:
+        # Generate 2D coordinates
+        obBuilder = ob.OBBuilder()
+        obBuilder.Build(mol)
 
-    mol_block = conv.WriteString(mol)
-    mol_block = mol_block.strip()  # Remove leading/trailing whitespace
-    return mol_block
+        mol_block = conv.WriteString(mol)
+        mol_block = mol_block.strip()  # Remove leading/trailing whitespace
+        return mol_block
diff --git a/app/routers/converters.py b/app/routers/converters.py
@@ -321,28 +321,15 @@ async def SMILES_canonicalise(
     - ValueError: If an unsupported toolkit option is provided.
 
     """
-    try:
-        if toolkit == "cdk":
-            mol = parseInput(smiles, "cdk", False)
-            return str(getCanonSMILES(mol))
-        elif toolkit == "rdkit":
-            mol = parseInput(smiles, "rdkit", False)
-            if mol:
-                return str(Chem.MolToSmiles(mol, kekuleSmiles=True))
-            else:
-                raise HTTPException(
-                    status_code=400,
-                    detail="Error reading input text, please check again.",
-                )
-        elif toolkit == "openbabel":
-            return str(getOBCanonicalSMILES(smiles))
-        else:
-            raise HTTPException(
-                status_code=422,
-                detail="Error reading input text, please check again.",
-            )
-    except Exception as e:
-        raise HTTPException(status_code=422, detail=str(e))
+    if toolkit == "cdk":
+        mol = parseInput(smiles, "cdk", False)
+        return str(getCanonSMILES(mol))
+    elif toolkit == "rdkit":
+        mol = parseInput(smiles, "rdkit", False)
+        return str(Chem.MolToSmiles(mol, kekuleSmiles=True))
+    elif toolkit == "openbabel":
+        smiles = getOBCanonicalSMILES(smiles)
+        return smiles
 
 
 @router.get(
@@ -396,19 +383,16 @@ async def SMILES_to_CXSMILES(
     Note:
     - CXSMILES is a Chemaxon Extended SMILES which is used for storing special features of the molecules after the SMILES string.
     """
-    try:
-        if toolkit == "cdk":
-            mol = parseInput(smiles, "cdk", False)
-            cxsmiles = getCXSMILES(mol)
-            if cxsmiles:
-                return str(cxsmiles)
-        else:
-            mol = parseInput(smiles, "rdkit", False)
-            cxsmiles = getRDKitCXSMILES(mol)
-            if cxsmiles:
-                return str(cxsmiles)
-    except Exception as e:
-        raise HTTPException(status_code=422, detail=str(e))
+    if toolkit == "cdk":
+        mol = parseInput(smiles, "cdk", False)
+        cxsmiles = getCXSMILES(mol)
+        if cxsmiles:
+            return str(cxsmiles)
+    else:
+        mol = parseInput(smiles, "rdkit", False)
+        cxsmiles = getRDKitCXSMILES(mol)
+        if cxsmiles:
+            return str(cxsmiles)
 
 
 @router.get(
@@ -459,29 +443,21 @@ async def SMILES_to_InChI(
     - ValueError: If an unsupported toolkit option is provided.
 
     """
-    try:
-        if toolkit == "cdk":
-            mol = parseInput(smiles, "cdk", False)
-            inchi = getInChI(mol)
-            if inchi:
-                return str(inchi)
-        elif toolkit == "rdkit":
-            mol = parseInput(smiles, "rdkit", False)
-            if mol:
-                inchi = Chem.inchi.MolToInchi(mol)
-                if inchi:
-                    return str(inchi)
-        elif toolkit == "openbabel":
-            inchi = getOBInChI(smiles)
+    if toolkit == "cdk":
+        mol = parseInput(smiles, "cdk", False)
+        inchi = getInChI(mol)
+        if inchi:
+            return str(inchi)
+    elif toolkit == "rdkit":
+        mol = parseInput(smiles, "rdkit", False)
+        if mol:
+            inchi = Chem.inchi.MolToInchi(mol)
             if inchi:
                 return str(inchi)
-        else:
-            raise HTTPException(
-                status_code=422,
-                detail="Error reading input text, please check again.",
-            )
-    except Exception as e:
-        raise HTTPException(status_code=422, detail=str(e))
+    elif toolkit == "openbabel":
+        inchi = getOBInChI(smiles)
+        if inchi:
+            return str(inchi)
 
 
 @router.get(
@@ -532,30 +508,22 @@ async def SMILES_to_InChIKey(
     - ValueError: If an unsupported toolkit option is provided.
 
     """
-    try:
-        if toolkit == "cdk":
-            mol = parseInput(smiles, "cdk", False)
-            inchikey = getInChI(mol, InChIKey=True)
-            if inchikey:
-                return str(inchikey)
+    if toolkit == "cdk":
+        mol = parseInput(smiles, "cdk", False)
+        inchikey = getInChI(mol, InChIKey=True)
+        if inchikey:
+            return str(inchikey)
 
-        elif toolkit == "rdkit":
-            mol = parseInput(smiles, "rdkit", False)
-            if mol:
-                inchikey = Chem.inchi.MolToInchiKey(mol)
-                if inchikey:
-                    return str(inchikey)
-        elif toolkit == "openbabel":
-            inchikey = getOBInChI(smiles, InChIKey=True)
+    elif toolkit == "rdkit":
+        mol = parseInput(smiles, "rdkit", False)
+        if mol:
+            inchikey = Chem.inchi.MolToInchiKey(mol)
             if inchikey:
                 return str(inchikey)
-        else:
-            raise HTTPException(
-                status_code=422,
-                detail="Error reading input text, please check again.",
-            )
-    except Exception as e:
-        raise HTTPException(status_code=422, detail=str(e))
+    elif toolkit == "openbabel":
+        inchikey = getOBInChI(smiles, InChIKey=True)
+        if inchikey:
+            return str(inchikey)
 
 
 @router.get(