[Fix] Catch Exception for Adding Structures / Show PubChem Substances (#168)

Fixes #163
Fixes #165

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#168

epdb/models.py

@@ -310,7 +310,7 @@ class ExternalDatabase(TimeStampedModel):
                 },
                 {
                     "database": ExternalDatabase.objects.get(name="ChEBI"),
-                    "placeholder": "ChEBI ID without prefix e.g. 12345",
+                    "placeholder": "ChEBI ID without prefix e.g. 10576",
                 },
             ],
             "structure": [
@@ -328,7 +328,7 @@ class ExternalDatabase(TimeStampedModel):
                 },
                 {
                     "database": ExternalDatabase.objects.get(name="ChEBI"),
-                    "placeholder": "ChEBI ID without prefix e.g. 12345",
+                    "placeholder": "ChEBI ID without prefix e.g. 10576",
                 },
             ],
             "reaction": [
@@ -342,7 +342,7 @@ class ExternalDatabase(TimeStampedModel):
                 },
                 {
                     "database": ExternalDatabase.objects.get(name="UniProt"),
-                    "placeholder": "Query ID for UniPro e.g. rhea:12345",
+                    "placeholder": "Query ID for UniProt e.g. rhea:12345",
                 },
             ],
         }
@@ -477,7 +477,7 @@ class ChemicalIdentifierMixin(ExternalIdentifierMixin):
         return self.add_external_identifier("CAS", cas_number)
 
     def get_pubchem_identifiers(self):
-        return self.get_external_identifier("PubChem Compound") or self.get_external_identifier(
+        return self.get_external_identifier("PubChem Compound") | self.get_external_identifier(
             "PubChem Substance"
         )
 
@@ -3043,6 +3043,7 @@ class EnviFormer(PackageBasedModel):
     @cached_property
     def model(self):
         from enviformer import load
+
         ckpt = os.path.join(s.MODEL_DIR, "enviformer", str(self.uuid), f"{self.uuid}.ckpt")
         mod = load(device=s.ENVIFORMER_DEVICE, ckpt_path=ckpt)
         return mod
@@ -3062,7 +3063,9 @@ class EnviFormer(PackageBasedModel):
         start = datetime.now()
         products_list = self.model.predict_batch(canon_smiles)
         end = datetime.now()
-        logger.info(f"Prediction took {(end - start).total_seconds():.2f} seconds. Got results {products_list}")
+        logger.info(
+            f"Prediction took {(end - start).total_seconds():.2f} seconds. Got results {products_list}"
+        )
 
         results = []
         for products in products_list:

epdb/views.py

@@ -1251,7 +1251,16 @@ def package_compound_structures(request, package_uuid, compound_uuid):
         structure_smiles = request.POST.get("structure-smiles")
         structure_description = request.POST.get("structure-description")
 
-        cs = current_compound.add_structure(structure_smiles, structure_name, structure_description)
+        try:
+            cs = current_compound.add_structure(
+                structure_smiles, structure_name, structure_description
+            )
+        except ValueError:
+            return error(
+                request,
+                "Adding structure failed!",
+                "The structure could not be added as normalized structures don't match!",
+            )
 
         return redirect(cs.url)
 

templates/objects/compound.html

@@ -183,7 +183,7 @@
                 </div>
                 <div id="compound-external-identifier" class="panel-collapse collapse in">
                     <div class="panel-body list-group-item">
-                        {% if compound.get_pubchem_identifiers %}
+                        {% if compound.get_pubchem_compound_identifiers %}
                             <div class="panel panel-default panel-heading list-group-item"
                                  style="background-color:silver">
                                 <h4 class="panel-title">
@@ -193,12 +193,28 @@
                                 </h4>
                             </div>
                             <div id="compound-pubchem-identifier" class="panel-collapse collapse in">
-                                {% for eid in compound.get_pubchem_identifiers %}
+                                {% for eid in compound.get_pubchem_compound_identifiers %}
                                     <a class="list-group-item"
                                        href="{{ eid.external_url }}">CID{{ eid.identifier_value }}</a>
                                 {% endfor %}
                             </div>
                         {% endif %}
+                        {% if compound.get_pubchem_substance_identifiers %}
+                            <div class="panel panel-default panel-heading list-group-item"
+                                 style="background-color:silver">
+                                <h4 class="panel-title">
+                                    <a id="compound-pubchem-identifier-link" data-toggle="collapse"
+                                       data-parent="#compound-external-identifier"
+                                       href="#compound-pubchem-identifier">PubChem Substance Identifier</a>
+                                </h4>
+                            </div>
+                            <div id="compound-pubchem-identifier" class="panel-collapse collapse in">
+                                {% for eid in compound.get_pubchem_substance_identifiers %}
+                                    <a class="list-group-item"
+                                       href="{{ eid.external_url }}">SID{{ eid.identifier_value }}</a>
+                                {% endfor %}
+                            </div>
+                        {% endif %}
                         {% if compound.get_chebi_identifiers %}
                             <div class="panel panel-default panel-heading list-group-item"
                                  style="background-color:silver">