...

bb4g/__init__.py

@@ -89,14 +89,13 @@ class BB4G(Classifier):
         }
 
         started = False
-        retries = 0
-        while not started and retries < 5:
+
+        while not started:
             res = requests.post(f"{self.url}/start", headers=header, data={}, proxies=s.PROXIES or None)
             logger.info(f"Starting BB4G: {res.status_code}")
             if res.status_code == 200:
                 started = True
             elif res.status_code in [500, 502]:
-                retries += 1
                 import time
                 time.sleep(5)
             else:
@@ -171,7 +170,7 @@ class BB4G(Classifier):
             }
 
             retries = 0
-            while retries < 5:
+            while retries < 100:
                 resp = requests.post(f"{self.url}/compute", headers=header, data=json.dumps(data),
                                      proxies=s.PROXIES or None)
 
@@ -179,7 +178,7 @@ class BB4G(Classifier):
                     retries += 1
                     logger.info(f"BB4G predict hit a 418, retrying in 60 seconds")
                     import time
-                    time.sleep(60)
+                    time.sleep(3)
                     continue
 
                 resp.raise_for_status()

epdb/exceptions.py

@@ -0,0 +1,2 @@
+class InvalidSMILESException(Exception):
+    pass

epdb/models.py

@@ -31,6 +31,7 @@ from sklearn.model_selection import ShuffleSplit
 
 from bridge.contracts import Property
 from bridge.dto import RunResult, PropertyPrediction
+from epdb.exceptions import InvalidSMILESException
 from utilities.chem import FormatConverter, IndigoUtils, PredictionResult, ProductSet
 from utilities.ml import (
     ApplicabilityDomainPCA,
@@ -785,7 +786,7 @@ class Compound(
         "CompoundStructure",
         verbose_name="Default Structure",
         related_name="compound_default_structure",
-        on_delete=models.CASCADE,
+        on_delete=models.SET_NULL,
         null=True,
     )
 
@@ -862,13 +863,17 @@ class Compound(
         package: "Package", smiles: str, name: str = None, description: str = None, *args, **kwargs
     ) -> "Compound":
         if smiles is None or smiles.strip() == "":
-            raise ValueError("SMILES is required")
+            raise InvalidSMILESException("SMILES is required")
 
         smiles = smiles.strip()
 
         parsed = FormatConverter.from_smiles(smiles)
         if parsed is None:
-            raise ValueError("Given SMILES is invalid")
+            raise InvalidSMILESException("Given SMILES is invalid")
+
+        if name is not None:
+            # Clean for potential XSS
+            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
 
         standardized_smiles = FormatConverter.standardize(smiles, remove_stereo=True)
 
@@ -880,7 +885,12 @@ class Compound(
 
         # Check if we find a direct match for a given SMILES
         if qs.exists():
-            return qs.first().compound
+            found_compound = qs.first().compound
+
+            if name:
+                found_compound.add_alias(name)
+
+            return found_compound
 
 
         qs = CompoundStructure.objects.filter(smiles=standardized_smiles, compound__package=package)
@@ -890,16 +900,17 @@ class Compound(
         # Check if we can find the standardized one
         if qs.exists():
             # TODO should we add a structure?
-            return qs.first().compound
+            found_compound = qs.first().compound
+
+            if name:
+                found_compound.add_alias(name)
+
+            return found_compound
 
         # Generate Compound
         c = Compound()
         c.package = package
 
-        if name is not None:
-            # Clean for potential XSS
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-
         if name is None or name == "":
             name = f"Compound {Compound.objects.filter(package=package).count() + 1}"
 
@@ -1152,16 +1163,25 @@ class CompoundStructure(
     def create(
         compound: Compound, smiles: str, name: str = None, description: str = None, *args, **kwargs
     ):
+        # Clean for potential XSS
+        if name is not None:
+            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+
         if CompoundStructure.objects.filter(compound=compound, smiles=smiles).exists():
-            return CompoundStructure.objects.get(compound=compound, smiles=smiles)
+            found_cs = CompoundStructure.objects.get(compound=compound, smiles=smiles)
+
+            if name:
+                found_cs.add_alias(name)
+
+            return found_cs
 
         if compound.pk is None:
             raise ValueError("Unpersisted Compound! Persist compound first!")
 
         cs = CompoundStructure()
-        # Clean for potential XSS
+
         if name is not None:
-            cs.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+            cs.name = name
 
         if description is not None:
             cs.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
@@ -1383,6 +1403,9 @@ class SimpleAmbitRule(SimpleRule):
         if not FormatConverter.is_valid_smirks(smirks):
             raise ValueError(f'SMIRKS "{smirks}" is invalid!')
 
+        if name is not None:
+            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+
         query = SimpleAmbitRule.objects.filter(package=package, smirks=smirks)
 
         if reactant_filter_smarts is not None and reactant_filter_smarts.strip() != "":
@@ -1394,14 +1417,17 @@ class SimpleAmbitRule(SimpleRule):
         if query.exists():
             if query.count() > 1:
                 logger.error(f"More than one rule matched this one! {query}")
-            return query.first()
+
+            found_rule = query.first()
+
+            if name:
+                found_rule.add_alias(name)
+
+            return found_rule
 
         r = SimpleAmbitRule()
         r.package = package
 
-        if name is not None:
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-
         if name is None or name == "":
             name = f"Rule {Rule.objects.filter(package=package).count() + 1}"
 
@@ -1642,8 +1668,13 @@ class Reaction(
         educts: Union[List[str], List[CompoundStructure]] = None,
         products: Union[List[str], List[CompoundStructure]] = None,
         rules: Union[Rule | List[Rule]] = None,
-        multi_step: bool = True,
+        multi_step: bool = False,
     ):
+
+        # Clean for potential XSS
+        if name is not None and name.strip() != "":
+            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+
         _educts = []
         _products = []
 
@@ -1698,14 +1729,19 @@ class Reaction(
                 logger.error(
                     f"Found more than one reaction for given input! {existing_reaction_qs}"
                 )
-            return existing_reaction_qs.first()
+
+            found_reaction = existing_reaction_qs.first()
+
+            if name:
+                found_reaction.add_alias(name)
+
+            return found_reaction
 
         r = Reaction()
         r.package = package
 
-        # Clean for potential XSS
-        if name is not None and name.strip() != "":
-            r.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+        if r is not None:
+            r.name = name
 
         if description is not None and description.strip() != "":
             r.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()

epdb/views.py

@@ -19,6 +19,7 @@ from sentry_sdk import capture_exception
 
 from utilities.chem import FormatConverter, IndigoUtils
 from utilities.decorators import package_permission_required
+from .exceptions import InvalidSMILESException
 
 from .logic import (
     EPDBURLParser,
@@ -2364,7 +2365,10 @@ def package_pathway_nodes(request, package_uuid, pathway_uuid):
         node_description = request.POST.get("node-description")
 
         node_smiles = request.POST.get("node-smiles").strip()
+        try:
             current_pathway.add_node(node_smiles, name=node_name, description=node_description)
+        except InvalidSMILESException as e:
+            return error(request, "Node creation failed!", f"Given SMILES ({node_smiles}) is invalid")
 
         return redirect(current_pathway.url)