adjusted migration

Initial bayer app

Show Pack Classification

Adjusted docker compose to bayer specifics

Adjusted Dockerfile for Bayer

Adding secret flags to group, add secret pools to packages

Adjusted View for Package creation

Prep configs, added Package Create Modal

wip

More on PES

wip

wip

Wip

minor

PW interactions

API PES

wip

Make Select Widget reflect required

make required generallay available

Update UI if pathway mode is set to build

Added ais

circle adjustments

Initial Zoom, fix AD Creation

wip

auth log, bb4g fix

missing import

Added viz hint if PES is part of reaction

Add Edge check for pes

flip boolean

...

pes

Added extra

...

In / Out Edges Viz, Submitting Button Text

...

Make PES Link clickable

Return proper http response instead of error

Fixed error return, removed unused options

Fix PES Link HTML for other entities

Fixed molfile assignment, adjusted Export

Package Export/Import cycle

highlight Description links

implemented non persistent

Harmonised proposed field in Json output

Added pesLink field to PW Api output

PES Fields in API Output

removed debug

Fix Classification import, Fix PES Deserialization

underline pes link in templates

Fix alter name/desc for node, make /node /edge funcitonal

provide setting link and copy button

Implemented Compound Names / Reaction Names View Option

Unconnected Nodes

Make links thicker, reduce timeout trigger time

Show proposed info in popover

Pathway Build no stereo removal

Include probs in reaction name option viz

Detect clicks outside nodes/edges

epdb/models.py

@@ -205,6 +205,7 @@ class Group(TimeStampedModel):
     name = models.TextField(blank=False, null=False, verbose_name="Group name")
     owner = models.ForeignKey("User", verbose_name="Group Owner", on_delete=models.CASCADE)
     public = models.BooleanField(verbose_name="Public Group", default=False)
+    secret = models.BooleanField(verbose_name="Secret Group", default=False)
     description = models.TextField(
         blank=False, null=False, verbose_name="Descriptions", default="no description"
     )
@@ -576,6 +577,10 @@ class ReactionIdentifierMixin(ExternalIdentifierMixin):
     def get_uniprot_identifiers(self):
         return self.get_external_identifier("UniProt")
 
+    def contains_pes(self):
+        from bayer.models import PESStructure
+        return any([isinstance(o, PESStructure) for o in self.educts.all()]) or any(
+            [isinstance(o, PESStructure) for o in self.products.all()])
 
 ##############
 # EP Objects #
@@ -868,29 +873,51 @@ 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)
 
+        subclasses = CompoundStructure.__subclasses__()
+
+        qs = CompoundStructure.objects.filter(smiles=smiles, compound__package=package)
+        if subclasses:
+            qs = qs.not_instance_of(*subclasses)
+
         # 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)
+        if subclasses:
+            qs = qs.not_instance_of(*subclasses)
 
         # Check if we can find the standardized one
-        if CompoundStructure.objects.filter(
-            smiles=standardized_smiles, compound__package=package
-        ).exists():
+        if qs.exists():
             # TODO should we add a structure?
-            return CompoundStructure.objects.get(
-                smiles=standardized_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
 
         # 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}"
 
@@ -1141,18 +1168,27 @@ 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:
+            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()
@@ -1160,6 +1196,10 @@ 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"]
 
@@ -1376,6 +1416,9 @@ 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() != "":
@@ -1387,14 +1430,17 @@ 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}"
 
@@ -1642,6 +1688,11 @@ 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 = []
 
@@ -1696,14 +1747,19 @@ 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()
@@ -1939,6 +1995,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                 # add links start -> pseudo
                 new_link = {
                     "name": link["name"],
+                    "plain_name": link["plain_name"],
                     "id": link["id"],
                     "url": link["url"],
                     "image": link["image"],
@@ -1948,6 +2005,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                     "source": node_url_to_idx[link["start_node_urls"][0]],
                     "target": pseudo_idx,
                     "app_domain": link.get("app_domain", None),
+                    "to_pseudo": True,
                 }
                 adjusted_links.append(new_link)
 
@@ -1955,6 +2013,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                 for target in link["end_node_urls"]:
                     new_link = {
                         "name": link["name"],
+                        "plain_name": link["plain_name"],
                         "id": link["id"],
                         "url": link["url"],
                         "image": link["image"],
@@ -1965,6 +2024,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                         "target": node_url_to_idx[target],
                         "app_domain": link.get("app_domain", None),
                         "multi_step": link["multi_step"],
+                        "from_pseudo": True,
                     }
                     adjusted_links.append(new_link)
 
@@ -2274,17 +2334,19 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
     def _url(self):
         return "{}/node/{}".format(self.pathway.url, self.uuid)
 
-    def get_name(self):
+    def get_name(self, include_suffix=True):
         non_generic_name = True
 
         if self.name == "no name":
             non_generic_name = False
 
-        return (
-            self.name
-            if non_generic_name
-            else f"{self.default_node_label.name} (taken from underlying structure)"
-        )
+        if non_generic_name:
+            return self.name
+        else:
+            if include_suffix:
+                f"{self.default_node_label.name} (taken from underlying structure)"
+            else:
+                return self.default_node_label.name
 
     def d3_json(self):
         app_domain_data = self.get_app_domain_assessment_data()
@@ -2314,6 +2376,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             ),
             "image_type": "svg",
             "name": self.get_name(),
+            "plain_name": self.get_name(include_suffix=False),
             "smiles": self.default_node_label.smiles,
             "scenarios": [{"name": s.get_name(), "url": s.url} for s in self.scenarios.all()],
             "app_domain": {
@@ -2324,6 +2387,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             },
             "predicted_properties": predicted_properties,
             "is_engineered_intermediate": self.kv.get("is_engineered_intermediate", False),
+            "proposed": self.is_proposed_intermediate(),
             "timeseries": self.get_timeseries_data(),
             **structure_data,
         }
@@ -2397,6 +2461,26 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
 
         return data
 
+    def is_proposed_intermediate(self):
+        collected = defaultdict(dict)
+        for ai in self.additional_information.filter(
+                type__in=["ProposedIntermediate", "TransformationProductImportance", "Confidence"]
+                , scenario__isnull=False
+        ):
+            collected[str(ai.scenario.uuid)]["scenarioId"] = ai.scenario.url
+            collected[str(ai.scenario.uuid)]["scenarioName"] = ai.scenario.name
+
+            if ai.type == "ProposedIntermediate":
+                collected[str(ai.scenario.uuid)]["proposed"] = True
+
+            if ai.type == "Confidence":
+                collected[str(ai.scenario.uuid)]["Confidence"] = ai.get().level
+
+            if ai.type == "TransformationProductImportance":
+                collected[str(ai.scenario.uuid)]["Transformation product importance"] = ai.get().importance.value
+
+        return list(collected.values())
+
     def simple_json(self, include_description=False):
         res = super().simple_json()
         name = res.get("name", None)
@@ -2426,6 +2510,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
     def d3_json(self):
         edge_json = {
             "name": self.get_name(),
+            "plain_name": self.get_name(include_suffix=False),
             "id": self.url,
             "url": self.url,
             "image": self.url + "?image=svg",
@@ -2540,17 +2625,19 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
 
         return res
 
-    def get_name(self):
+    def get_name(self, include_suffix=True):
         non_generic_name = True
 
         if self.name == "no name":
             non_generic_name = False
 
-        return (
-            self.name
-            if non_generic_name
-            else f"{self.edge_label.name} (taken from underlying reaction)"
-        )
+        if non_generic_name:
+            return self.name
+        else:
+            if include_suffix:
+                return f"{self.edge_label.name} (taken from underlying reaction)"
+            else:
+                return self.edge_label.name
 
 
 class EPModel(PolymorphicModel, EnviPathModel, AdditionalInformationMixin):