...

docker-compose.dev.yml

@@ -29,7 +29,7 @@ services:
     container_name: epbiotransformer3
 
   celery_worker:
-    image: git.envipath.com/envipath/envipy-bayer:1.0
+    image: git.envipath.com/envipath/envipy-bayer:1.2
     container_name: epcelery
     env_file:
       - .env

epdb/models.py

@@ -860,7 +860,7 @@ class Compound(
     @staticmethod
     @transaction.atomic
     def create(
-        package: "Package", smiles: str, name: str = None, description: str = None, *args, **kwargs
+        package: "Package", smiles: str, name: str = None, description: str = None, molfile: str = None, *args, **kwargs
     ) -> "Compound":
         if smiles is None or smiles.strip() == "":
             raise InvalidSMILESException("SMILES is required")
@@ -885,9 +885,11 @@ class Compound(
 
         # Check if we find a direct match for a given SMILES
         if qs.exists():
-            found_compound = qs.first().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
@@ -900,9 +902,11 @@ class Compound(
         # Check if we can find the standardized one
         if qs.exists():
             # TODO should we add a structure?
-            found_compound = qs.first().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
@@ -1161,7 +1165,7 @@ class CompoundStructure(
     @staticmethod
     @transaction.atomic
     def create(
-        compound: Compound, smiles: str, name: str = None, description: str = None, *args, **kwargs
+        compound: Compound, smiles: str, name: str = None, description: str = None, molfile: str = None, *args, **kwargs
     ):
         # Clean for potential XSS
         if name is not None:
@@ -1189,6 +1193,10 @@ class CompoundStructure(
         cs.smiles = smiles
         cs.compound = compound
 
+        # Check if molfile is present and valid
+        if molfile is not None and FormatConverter.from_molfile(molfile) is not None:
+            cs.molfile = molfile
+
         if "normalized_structure" in kwargs:
             cs.normalized_structure = kwargs["normalized_structure"]
 
@@ -1206,6 +1214,8 @@ class CompoundStructure(
 
     @property
     def as_svg(self, width: int = 800, height: int = 400):
+        if self.molfile is not None and self.molfile.strip() != "":
+            return IndigoUtils.mol_to_svg(self.molfile, width=width, height=height)
         return IndigoUtils.mol_to_svg(self.smiles, width=width, height=height)
 
     @property
@@ -2341,7 +2351,8 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             "node_label_id": self.default_node_label.url,
             "image": f"{self.url}?image=svg",
             "image_svg": IndigoUtils.mol_to_svg(
-                self.default_node_label.smiles, width=40, height=40
+                self.default_node_label.molfile if self.default_node_label.molfile is not None and self.default_node_label.molfile.strip() else self.default_node_label.smiles,
+                width=40, height=40
             ),
             "image_type": "svg",
             "name": self.get_name(),
@@ -2395,6 +2406,8 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
 
     @property
     def as_svg(self):
+        if self.default_node_label.molfile is not None and self.default_node_label.molfile.strip() != "":
+            return IndigoUtils.mol_to_svg(self.default_node_label.molfile)
         return IndigoUtils.mol_to_svg(self.default_node_label.smiles)
 
     def get_timeseries_data(self):

epdb/views.py

@@ -1124,6 +1124,9 @@ def package_model(request, package_uuid, model_uuid):
                             }
                         )
 
+                # Sort data by prob desc
+                res["pred"] = sorted(res["pred"], key=lambda x: x["probability"], reverse=True)
+
                 return JsonResponse(res, safe=False)
 
             elif half_life:

static/css/input.css

@@ -34,3 +34,8 @@
 }
 
 @import "./daisyui-theme.css";
+
+select.select[multiple] {
+  display: block;
+  white-space: normal;
+}