[Chore] Leftovers (#426)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#426

epdb/legacy_api.py

@@ -1620,7 +1620,7 @@ class PathwayNode(Schema):
     image: str = Field(None, alias="image")
     imageSize: int = Field(None, alias="image_size")
     name: str = Field(None, alias="name")
-    proposed: List[Dict[str, str]] = Field([], alias="proposed_intermediate")
+    proposed: List[Dict[str, str]] = []
     smiles: str = Field(None, alias="smiles")
     pseudo: bool = Field(False, alias="pseudo")
 
@@ -1910,7 +1910,7 @@ def add_pathway_node(request, package_uuid, pathway_uuid, n: Form[CreateNode]):
         else:
             node_depth = -1
 
-        n = Node.create(
+        node = Node.create(
             pw,
             n.nodeAsSmiles,
             node_depth,
@@ -1919,7 +1919,7 @@ def add_pathway_node(request, package_uuid, pathway_uuid, n: Form[CreateNode]):
             description=n.nodeReason,
         )
 
-        return redirect(n.url)
+        return redirect(node.url)
     except ValueError:
         return 403, {"message": "Adding node failed!"}
 

epdb/logic.py

@@ -1008,8 +1008,6 @@ class PackageManager(object):
         data: Dict[str, Any],
         owner: User,
         preserve_uuids=False,
-        add_import_timestamp=True,
-        trust_reviewed=False,
     ) -> Package:
         importer = PackageImporter(data, preserve_uuids)
         imported_package = importer.do_import()
@@ -1830,6 +1828,7 @@ class SPathway(object):
 
             if edge.rule:
                 e["rule"] = edge.rule.simple_json()
+
             if edge.probability:
                 e["probability"] = edge.probability
 

epdb/models.py

@@ -894,34 +894,46 @@ class Compound(
         if parsed is None:
             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)
 
+        qs = CompoundStructure.objects.filter(smiles=smiles, compound__package=package)
+
         # Check if we find a direct match for a given SMILES
-        if CompoundStructure.objects.filter(smiles=smiles, compound__package=package).exists():
+        if qs.exists():
-            return CompoundStructure.objects.get(smiles=smiles, compound__package=package).compound
+            found_structure = qs.first()
+            found_compound = found_structure.compound
+
+            if name:
+                found_structure.add_alias(name)
+                found_compound.add_alias(name)
+
+            return found_compound
+
+        qs = CompoundStructure.objects.filter(smiles=standardized_smiles, compound__package=package)
 
         # Check if we can find the standardized one
-        if CompoundStructure.objects.filter(
+        if qs.exists():
-            smiles=standardized_smiles, compound__package=package
+            found_structure = qs.first()
-        ).exists():
+            found_compound = found_structure.compound
-            found_c = CompoundStructure.objects.get(
-                smiles=standardized_smiles, compound__package=package
-            ).compound
 
-            # As a direct match wasn't found add a new structure
+            # We've only found the standardized one, create the very structure
-            # TODO return newly created structure
+            _ = found_compound.add_structure(
-            _ = found_c.add_structure(smiles, molfile=molfile, name=name, description=description)
+                smiles, molfile=molfile, name=name, description=description
+            )
 
-            return found_c
+            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}"
 
@@ -1218,8 +1230,15 @@ class CompoundStructure(
                 # Overwrite SMILES from molfile
                 smiles = FormatConverter.to_smiles(mol)
 
+        # 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():
-            found_cs = CompoundStructure.objects.get(smiles=smiles, compound=compound)
+            found_cs = CompoundStructure.objects.get(compound=compound, smiles=smiles)
+
+            if name:
+                found_cs.add_alias(name)
 
             if found_cs.molfile is None and (molfile is not None and molfile.strip() != ""):
                 logger.info(
@@ -1236,16 +1255,17 @@ class CompoundStructure(
         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:
+        # We have a default here only set the value if it carries some payload
+        if description is not None and description.strip() != "":
             cs.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
         cs.compound = compound
         cs.smiles = smiles
 
-        # Check if molfile is present and valid
+        # If molfile is not None, it hase to be a valid Molfile as we've survived the parsing check
-        if molfile is not None and molfile.strip() != "":
+        if molfile is not None:
             cs.molfile = molfile
 
         if "normalized_structure" in kwargs:
@@ -1464,6 +1484,9 @@ 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() != "":
@@ -1475,14 +1498,17 @@ 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}"
 
@@ -1615,6 +1641,9 @@ class ParallelRule(Rule):
                     f"Simple rule {sr.uuid} does not belong to package {package.uuid}!"
                 )
 
+        if name is not None:
+            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+
         # Deduplication check
         query = ParallelRule.objects.annotate(
             srs_count=Count("simple_rules", filter=Q(simple_rules__in=simple_rules), distinct=True)
@@ -1626,15 +1655,19 @@ class ParallelRule(Rule):
 
         if existing_rule_qs.exists():
             if existing_rule_qs.count() > 1:
-                logger.error(f"Found more than one reaction for given input! {existing_rule_qs}")
+                logger.error(
-            return existing_rule_qs.first()
+                    f"Found more than one ParallelRule for given input! {existing_rule_qs}"
+                )
+
+            found_rule = existing_rule_qs.first()
+            if name:
+                found_rule.add_alias(name)
+
+            return found_rule
 
         r = ParallelRule()
         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}"
 
@@ -1730,6 +1763,10 @@ class Reaction(
         rules: Union[Rule | List[Rule]] = None,
         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 = []
 
@@ -1784,14 +1821,21 @@ 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 None or name == "":
-        if name is not None and name.strip() != "":
+            name = f"Reaction {Reaction.objects.filter(package=package).count() + 1}"
-            r.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+
+        r.name = name
 
         if description is not None and description.strip() != "":
             r.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
@@ -2420,6 +2464,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             },
             "predicted_properties": predicted_properties,
             "is_engineered_intermediate": self.kv.get("is_engineered_intermediate", False),
+            "proposed": self.get_proposed_info(),
             "timeseries": self.get_timeseries_data(),
             **structure_data,
         }
@@ -2516,7 +2561,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
 
         return res
 
-    def is_proposed_intermediate(self):
+    def get_proposed_info(self):
         collected = defaultdict(dict)
         for ai in self.additional_information.filter(
             type__in=["ProposedIntermediate", "TransformationProductImportance", "Confidence"],

templates/objects/compound.html

@@ -134,7 +134,7 @@
     <!-- Reactions -->
     {% if compound.related_reactions %}
       <div class="collapse-arrow bg-base-200 collapse">
-        <input type="checkbox" checked />
+        <input type="checkbox" />
         <div class="collapse-title text-xl font-medium">Reactions</div>
         <div class="collapse-content">
           <ul class="menu bg-base-100 rounded-box">
@@ -153,7 +153,7 @@
     <!-- Pathways -->
     {% if compound.related_pathways %}
       <div class="collapse-arrow bg-base-200 collapse">
-        <input type="checkbox" checked />
+        <input type="checkbox" />
         <div class="collapse-title text-xl font-medium">Pathways</div>
         <div class="collapse-content">
           <ul class="menu bg-base-100 rounded-box">
@@ -172,7 +172,7 @@
     <!-- Scenarios -->
     {% if compound.scenarios.all %}
       <div class="collapse-arrow bg-base-200 collapse">
-        <input type="checkbox" checked />
+        <input type="checkbox" />
         <div class="collapse-title text-xl font-medium">Scenarios</div>
         <div class="collapse-content">
           <ul class="menu bg-base-100 rounded-box">
@@ -240,7 +240,7 @@
     <!-- External Identifiers -->
     {% if compound.get_external_identifiers %}
       <div class="collapse-arrow bg-base-200 collapse">
-        <input type="checkbox" checked />
+        <input type="checkbox" />
         <div class="collapse-title text-xl font-medium">
           External Identifier
         </div>

templates/objects/compound_structure.html

@@ -92,6 +92,25 @@
       </div>
     {% endif %}
 
+    <!-- Pathways -->
+    {% if compound.related_pathways %}
+      <div class="collapse-arrow bg-base-200 collapse">
+        <input type="checkbox" />
+        <div class="collapse-title text-xl font-medium">Pathways</div>
+        <div class="collapse-content">
+          <ul class="menu bg-base-100 rounded-box">
+            {% for r in compound.related_pathways %}
+              <li>
+                <a href="{{ r.url }}" class="hover:bg-base-200"
+                  >{{ r.name }} <i>({{ r.package.name }})</i></a
+                >
+              </li>
+            {% endfor %}
+          </ul>
+        </div>
+      </div>
+    {% endif %}
+
     {% if compound_structure.half_lifes %}
       <div class="collapse-arrow bg-base-200 collapse">
         <input type="checkbox" />
@@ -144,7 +163,7 @@
     {% if compound_structure.scenarios.all %}
       <!-- Scenarios -->
       <div class="collapse-arrow bg-base-200 collapse">
-        <input type="checkbox" checked />
+        <input type="checkbox" />
         <div class="collapse-title text-xl font-medium">Scenarios</div>
         <div class="collapse-content">
           <ul class="menu bg-base-100 rounded-box">

tests/test_reaction_model.py

@@ -106,7 +106,7 @@ class ReactionTest(TestCase):
             multi_step=False,
         )
 
-        self.assertEqual(r.name, "no name")
+        self.assertEqual(r.name, "Reaction 1")
         self.assertEqual(r.description, "no description")
 
     def test_deduplication(self):