[Chore] Leftovers (#426)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch> Reviewed-on: enviPath/enviPy#426
2026-07-16 21:33:12 +12:00
parent 72a63b4876
commit 3566571b42
6 changed files with 109 additions and 46 deletions
--- a/epdb/legacy_api.py
+++ b/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!"}

--- a/epdb/logic.py
+++ b/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

--- a/epdb/models.py
+++ b/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():
-            return CompoundStructure.objects.get(smiles=smiles, compound__package=package).compound
+        if qs.exists():
+            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(
-            smiles=standardized_smiles, compound__package=package
-        ).exists():
-            found_c = CompoundStructure.objects.get(
-                smiles=standardized_smiles, compound__package=package
-            ).compound
+        if qs.exists():
+            found_structure = qs.first()
+            found_compound = found_structure.compound

-            # As a direct match wasn't found add a new structure
-            # TODO return newly created structure
-            _ = found_c.add_structure(smiles, molfile=molfile, name=name, description=description)
+            # We've only found the standardized one, create the very structure
+            _ = found_compound.add_structure(
+                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 and molfile.strip() != "":
+        # If molfile is not None, it hase to be a valid Molfile as we've survived the parsing check
+        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}")
-            return existing_rule_qs.first()
+                logger.error(
+                    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 not None and name.strip() != "":
-            r.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+        if name is None or name == "":
+            name = f"Reaction {Reaction.objects.filter(package=package).count() + 1}"
+
+        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"],
--- a/templates/objects/compound.html
+++ b/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>
--- a/templates/objects/compound_structure.html
+++ b/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">
--- a/tests/test_reaction_model.py
+++ b/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):