[Fix] UI bugs, Registrations Mail, BTRules Popup, Legacy API fixes (#309)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#309

.gitea/actions/setup-envipy/action.yaml

@@ -48,11 +48,6 @@ runs:
       shell: bash
       run: |
         uv run python scripts/pnpm_wrapper.py install
-        cat << 'EOF' > pnpm-workspace.yaml
-        onlyBuiltDependencies:
-          - '@parcel/watcher'
-          - '@tailwindcss/oxide'
-        EOF
         uv run python scripts/pnpm_wrapper.py run build
 
     - name: Wait for Postgres

epdb/legacy_api.py

@@ -212,7 +212,7 @@ def get_user(request, user_uuid):
 
 
 class GroupMember(Schema):
-    id: str = Field(None, alias="url")
+    id: str
     identifier: str
     name: str
 
@@ -228,7 +228,7 @@ class GroupSchema(Schema):
     members: List[GroupMember] = Field([], alias="members")
     name: str = Field(None, alias="name")
     ownerid: str = Field(None, alias="owner.url")
-    ownername: str = Field(None, alias="owner.name")
+    ownername: str = Field(None, alias="owner.get_name")
     packages: List["SimplePackage"] = Field([], alias="packages")
     readers: List[GroupMember] = Field([], alias="readers")
     writers: List[GroupMember] = Field([], alias="writers")
@@ -237,10 +237,10 @@ class GroupSchema(Schema):
     def resolve_members(obj: Group):
         res = []
         for member in obj.user_member.all():
-            res.append(GroupMember(id=member.url, identifier="usermember", name=member.username))
+            res.append(GroupMember(id=member.url, identifier="usermember", name=member.get_name()))
 
         for member in obj.group_member.all():
-            res.append(GroupMember(id=member.url, identifier="groupmember", name=member.name))
+            res.append(GroupMember(id=member.url, identifier="groupmember", name=member.get_name()))
 
         return res
 
@@ -374,7 +374,7 @@ class PackageSchema(Schema):
             ).values_list("user", flat=True)
         ).distinct()
 
-        return [{u.id: u.name} for u in users]
+        return [{u.id: u.get_name()} for u in users]
 
     @staticmethod
     def resolve_writers(obj: Package):
@@ -384,7 +384,7 @@ class PackageSchema(Schema):
             ).values_list("user", flat=True)
         ).distinct()
 
-        return [{u.id: u.name} for u in users]
+        return [{u.id: u.get_name()} for u in users]
 
     @staticmethod
     def resolve_review_comment(obj):
@@ -966,7 +966,12 @@ def create_package_simple_rule(
             raise ValueError("Not yet implemented!")
         else:
             sr = SimpleAmbitRule.create(
-                p, r.name, r.description, r.smirks, r.reactantFilterSmarts, r.productFilterSmarts
+                p,
+                r.name,
+                r.description,
+                r.smirks,
+                r.reactantFilterSmarts,
+                r.productFilterSmarts,
             )
 
         return redirect(sr.url)
@@ -1119,7 +1124,7 @@ class ReactionSchema(Schema):
     name: str = Field(None, alias="name")
     pathways: List["SimplePathway"] = Field([], alias="related_pathways")
     products: List["ReactionCompoundStructure"] = Field([], alias="products")
-    references: List[Dict[str, List[str]]] = Field([], alias="references")
+    references: Dict[str, List[str]] = Field({}, alias="references")
     reviewStatus: str = Field(None, alias="review_status")
     scenarios: List["SimpleScenario"] = Field([], alias="scenarios")
     smirks: str = Field("", alias="smirks")
@@ -1135,8 +1140,12 @@ class ReactionSchema(Schema):
 
     @staticmethod
     def resolve_references(obj: Reaction):
-        # TODO
+        rhea_refs = []
-        return []
+        for rhea in obj.get_rhea_identifiers():
+            rhea_refs.append(f"{rhea.identifier_value}")
+
+        # TODO UniProt
+        return {"rheaReferences": rhea_refs, "uniprotCount": []}
 
     @staticmethod
     def resolve_medline_references(obj: Reaction):
@@ -1715,7 +1724,7 @@ class EdgeSchema(Schema):
     id: str = Field(None, alias="url")
     identifier: str = "edge"
     name: str = Field(None, alias="name")
-    reactionName: str = Field(None, alias="edge_label.name")
+    reactionName: str = Field(None, alias="edge_label.get_name")
     reactionURI: str = Field(None, alias="edge_label.url")
     reviewStatus: str = Field(None, alias="review_status")
     scenarios: List["SimpleScenario"] = Field([], alias="scenarios")
@@ -1764,7 +1773,7 @@ class CreateEdge(Schema):
 
 
 @router.post(
-    "/package/{uuid:package_uuid}/üathway/{uuid:pathway_uuid}/edge",
+    "/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}/edge",
     response={200: str | Any, 403: Error},
 )
 def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
@@ -1783,10 +1792,26 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
 
         if e.edgeAsSmirks:
             for ed in e.edgeAsSmirks.split(">>")[0].split("\\."):
-                educts.append(Node.objects.get(pathway=pw, default_node_label__smiles=ed))
+                stand_ed = FormatConverter.standardize(ed, remove_stereo=True)
+                educts.append(
+                    Node.objects.get(
+                        pathway=pw,
+                        default_node_label=CompoundStructure.objects.get(
+                            compound__package=p, smiles=stand_ed
+                        ).compound.default_structure,
+                    )
+                )
 
             for pr in e.edgeAsSmirks.split(">>")[1].split("\\."):
-                products.append(Node.objects.get(pathway=pw, default_node_label__smiles=pr))
+                stand_pr = FormatConverter.standardize(pr, remove_stereo=True)
+                products.append(
+                    Node.objects.get(
+                        pathway=pw,
+                        default_node_label=CompoundStructure.objects.get(
+                            compound__package=p, smiles=stand_pr
+                        ).compound.default_structure,
+                    )
+                )
         else:
             for ed in e.educts.split(","):
                 educts.append(Node.objects.get(pathway=pw, url=ed.strip()))
@@ -1799,7 +1824,7 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
             start_nodes=educts,
             end_nodes=products,
             rule=None,
-            name=e.name,
+            name=None,
             description=e.edgeReason,
         )
 
@@ -1936,7 +1961,7 @@ def get_model(request, package_uuid, model_uuid, c: Query[Classify]):
                     if pr.rule:
                         res["id"] = pr.rule.url
                         res["identifier"] = pr.rule.get_rule_identifier()
-                        res["name"] = pr.rule.name
+                        res["name"] = pr.rule.get_name()
                         res["reviewStatus"] = (
                             "reviewed" if pr.rule.package.reviewed else "unreviewed"
                         )

epdb/management/commands/bootstrap.py

@@ -8,7 +8,6 @@ from epdb.logic import UserManager, GroupManager, PackageManager, SettingManager
 from epdb.models import (
     UserSettingPermission,
     MLRelativeReasoning,
-    EnviFormer,
     Permission,
     User,
     ExternalDatabase,
@@ -231,7 +230,6 @@ class Command(BaseCommand):
             package=pack,
             rule_packages=[mapping["EAWAG-BBD"]],
             data_packages=[mapping["EAWAG-BBD"]],
-            eval_packages=[],
             threshold=0.5,
             name="ECC - BBD - T0.5",
             description="ML Relative Reasoning",
@@ -239,7 +237,3 @@ class Command(BaseCommand):
 
         ml_model.build_dataset()
         ml_model.build_model()
-
-        # If available, create EnviFormerModel
-        if s.ENVIFORMER_PRESENT:
-            EnviFormer.create(pack, "EnviFormer - T0.5", "EnviFormer Model with Threshold 0.5", 0.5)

epdb/management/commands/dump_enviformer.py

@@ -47,7 +47,7 @@ class Command(BaseCommand):
             "description": model.description,
             "kv": model.kv,
             "data_packages_uuids": [str(p.uuid) for p in model.data_packages.all()],
-            "eval_packages_uuids": [str(p.uuid) for p in model.data_packages.all()],
+            "eval_packages_uuids": [str(p.uuid) for p in model.eval_packages.all()],
             "threshold": model.threshold,
             "eval_results": model.eval_results,
             "multigen_eval": model.multigen_eval,

epdb/models.py

@@ -77,6 +77,9 @@ class User(AbstractUser):
     USERNAME_FIELD = "email"
     REQUIRED_FIELDS = ["username"]
 
+    def get_name(self):
+        return self.username
+
     def save(self, *args, **kwargs):
         if not self.url:
             self.url = self._url()
@@ -208,7 +211,10 @@ class Group(TimeStampedModel):
     )
 
     def __str__(self):
-        return f"{self.name} (pk={self.pk})"
+        return f"{self.get_name()} (pk={self.pk})"
+
+    def get_name(self):
+        return self.name
 
     def save(self, *args, **kwargs):
         if not self.url:
@@ -596,7 +602,7 @@ class EnviPathModel(TimeStampedModel):
         res = {
             "url": self.url,
             "uuid": str(self.uuid),
-            "name": self.name,
+            "name": self.get_name(),
         }
 
         if include_description:
@@ -609,11 +615,14 @@ class EnviPathModel(TimeStampedModel):
             return self.kv.get(k, default)
         return default
 
+    def get_name(self):
+        return self.name
+
     class Meta:
         abstract = True
 
     def __str__(self):
-        return f"{self.name} (pk={self.pk})"
+        return f"{self.get_name()} (pk={self.pk})"
 
 
 class AliasMixin(models.Model):
@@ -624,7 +633,7 @@ class AliasMixin(models.Model):
     @transaction.atomic
     def add_alias(self, new_alias, set_as_default=False):
         if set_as_default:
-            self.aliases.append(self.name)
+            self.aliases.append(self.get_name())
             self.name = new_alias
 
             if new_alias in self.aliases:
@@ -765,15 +774,17 @@ class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin
                 logger.debug(
                     f"#Structures: {num_structs} - #Standardized SMILES: {len(stand_smiles)}"
                 )
-                logger.debug(f"Couldn't infer normalized structure for {self.name} - {self.url}")
+                logger.debug(
+                    f"Couldn't infer normalized structure for {self.get_name()} - {self.url}"
+                )
                 raise ValueError(
-                    f"Couldn't find nor infer normalized structure for {self.name} ({self.url})"
+                    f"Couldn't find nor infer normalized structure for {self.get_name()} ({self.url})"
                 )
             else:
                 cs = CompoundStructure.create(
                     self,
                     stand_smiles.pop(),
-                    name="Normalized structure of {}".format(self.name),
+                    name="Normalized structure of {}".format(self.get_name()),
                     description="{} (in its normalized form)".format(self.description),
                     normalized_structure=True,
                 )
@@ -848,8 +859,10 @@ class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin
         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}"
+
         c.name = name
 
         # We have a default here only set the value if it carries some payload
@@ -978,7 +991,7 @@ class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin
                     cs = CompoundStructure.create(
                         existing_normalized_compound,
                         structure.smiles,
-                        name=structure.name,
+                        name=structure.get_name(),
                         description=structure.description,
                         normalized_structure=structure.normalized_structure,
                     )
@@ -989,13 +1002,13 @@ class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin
 
             else:
                 raise ValueError(
-                    f"Found a CompoundStructure for {default_structure_smiles} but not for {normalized_structure_smiles} in target package {target.name}"
+                    f"Found a CompoundStructure for {default_structure_smiles} but not for {normalized_structure_smiles} in target package {target.get_name()}"
                 )
         else:
             # Here we can safely use Compound.objects.create as we won't end up in a duplicate
             new_compound = Compound.objects.create(
                 package=target,
-                name=self.name,
+                name=self.get_name(),
                 description=self.description,
                 kv=self.kv.copy() if self.kv else {},
             )
@@ -1011,7 +1024,7 @@ class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin
                         canonical_smiles=structure.canonical_smiles,
                         inchikey=structure.inchikey,
                         normalized_structure=structure.normalized_structure,
-                        name=structure.name,
+                        name=structure.get_name(),
                         description=structure.description,
                         kv=structure.kv.copy() if structure.kv else {},
                     )
@@ -1050,11 +1063,8 @@ class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin
     def half_lifes(self):
         hls: Dict[Scenario, List[HalfLife]] = defaultdict(list)
 
-        for n in self.related_nodes:
+        for cs in self.structures:
-            for scen in n.scenarios.all().order_by("name"):
+            hls.update(cs.half_lifes())
-                for ai in scen.get_additional_information():
-                    if isinstance(ai, HalfLife):
-                        hls[scen].append(ai)
 
         return dict(hls)
 
@@ -1104,6 +1114,7 @@ class CompoundStructure(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdenti
         # Clean for potential XSS
         if name is not None:
             cs.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+
         if description is not None:
             cs.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
@@ -1147,6 +1158,21 @@ class CompoundStructure(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdenti
     def is_default_structure(self):
         return self.compound.default_structure == self
 
+    @property
+    def related_nodes(self):
+        return Node.objects.filter(node_labels__in=[self], pathway__package=self.compound.package)
+
+    def half_lifes(self):
+        hls: Dict[Scenario, List[HalfLife]] = defaultdict(list)
+
+        for n in self.related_nodes:
+            for scen in n.scenarios.all().order_by("name"):
+                for ai in scen.get_additional_information():
+                    if isinstance(ai, HalfLife):
+                        hls[scen].append(ai)
+
+        return dict(hls)
+
 
 class EnzymeLink(EnviPathModel, KEGGIdentifierMixin):
     rule = models.ForeignKey("Rule", on_delete=models.CASCADE, db_index=True)
@@ -1218,7 +1244,7 @@ class Rule(PolymorphicModel, EnviPathModel, AliasMixin, ScenarioMixin):
         if rule_type == SimpleAmbitRule:
             new_rule = SimpleAmbitRule.create(
                 package=target,
-                name=self.name,
+                name=self.get_name(),
                 description=self.description,
                 smirks=self.smirks,
                 reactant_filter_smarts=self.reactant_filter_smarts,
@@ -1232,7 +1258,7 @@ class Rule(PolymorphicModel, EnviPathModel, AliasMixin, ScenarioMixin):
         elif rule_type == SimpleRDKitRule:
             new_rule = SimpleRDKitRule.create(
                 package=target,
-                name=self.name,
+                name=self.get_name(),
                 description=self.description,
                 reaction_smarts=self.reaction_smarts,
             )
@@ -1250,7 +1276,7 @@ class Rule(PolymorphicModel, EnviPathModel, AliasMixin, ScenarioMixin):
             new_rule = ParallelRule.create(
                 package=target,
                 simple_rules=new_srs,
-                name=self.name,
+                name=self.get_name(),
                 description=self.description,
             )
 
@@ -1624,9 +1650,11 @@ class Reaction(EnviPathModel, AliasMixin, ScenarioMixin, ReactionIdentifierMixin
 
         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 description is not None and name.strip() != "":
             r.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
@@ -1674,7 +1702,7 @@ class Reaction(EnviPathModel, AliasMixin, ScenarioMixin, ReactionIdentifierMixin
 
         new_reaction = Reaction.create(
             package=target,
-            name=self.name,
+            name=self.get_name(),
             description=self.description,
             educts=copied_reaction_educts,
             products=copied_reaction_products,
@@ -1830,7 +1858,9 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
 
         # We shouldn't lose or make up nodes...
         if len(nodes) != len(self.nodes):
-            logger.debug(f"{self.name}: Num Nodes {len(nodes)} vs. DB Nodes {len(self.nodes)}")
+            logger.debug(
+                f"{self.get_name()}: Num Nodes {len(nodes)} vs. DB Nodes {len(self.nodes)}"
+            )
 
         links = [e.d3_json() for e in self.edges]
 
@@ -1898,7 +1928,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
             "isIncremental": self.kv.get("mode") == "incremental",
             "isPredicted": self.kv.get("mode") == "predicted",
             "lastModified": self.modified.strftime("%Y-%m-%d %H:%M:%S"),
-            "pathwayName": self.name,
+            "pathwayName": self.get_name(),
             "reviewStatus": "reviewed" if self.package.reviewed else "unreviewed",
             "scenarios": [],
             "upToDate": True,
@@ -1941,14 +1971,14 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
             if include_pathway_url:
                 row.append(n.pathway.url)
 
-            row += [cs.smiles, cs.name, n.depth]
+            row += [cs.smiles, cs.get_name(), n.depth]
 
             edges = self.edges.filter(end_nodes__in=[n])
             if len(edges):
                 for e in edges:
                     _row = row.copy()
                     _row.append(e.kv.get("probability"))
-                    _row.append(",".join([r.name for r in e.edge_label.rules.all()]))
+                    _row.append(",".join([r.get_name() for r in e.edge_label.rules.all()]))
                     _row.append(",".join([r.url for r in e.edge_label.rules.all()]))
                     _row.append(e.start_nodes.all()[0].default_node_label.smiles)
                     rows.append(_row)
@@ -1979,12 +2009,14 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
         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"Pathway {Pathway.objects.filter(package=package).count() + 1}"
 
         pw.name = name
         if description is not None and description.strip() != "":
             pw.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
+
         pw.predicted = predicted
 
         pw.save()
@@ -2009,7 +2041,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
         # deduplicated
         new_pathway = Pathway.objects.create(
             package=target,
-            name=self.name,
+            name=self.get_name(),
             description=self.description,
             setting=self.setting,  # TODO copy settings?
             kv=self.kv.copy() if self.kv else {},
@@ -2039,7 +2071,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
                 pathway=new_pathway,
                 default_node_label=copied_structure,
                 depth=node.depth,
-                name=node.name,
+                name=node.get_name(),
                 description=node.description,
                 kv=node.kv.copy() if node.kv else {},
             )
@@ -2063,7 +2095,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
             new_edge = Edge.objects.create(
                 pathway=new_pathway,
                 edge_label=copied_reaction,
-                name=edge.name,
+                name=edge.get_name(),
                 description=edge.description,
                 kv=edge.kv.copy() if edge.kv else {},
             )
@@ -2123,6 +2155,18 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin):
     def _url(self):
         return "{}/node/{}".format(self.pathway.url, self.uuid)
 
+    def get_name(self):
+        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)"
+        )
+
     def d3_json(self):
         app_domain_data = self.get_app_domain_assessment_data()
 
@@ -2135,9 +2179,9 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin):
             "image_svg": IndigoUtils.mol_to_svg(
                 self.default_node_label.smiles, width=40, height=40
             ),
-            "name": self.default_node_label.name,
+            "name": self.get_name(),
             "smiles": self.default_node_label.smiles,
-            "scenarios": [{"name": s.name, "url": s.url} for s in self.scenarios.all()],
+            "scenarios": [{"name": s.get_name(), "url": s.url} for s in self.scenarios.all()],
             "app_domain": {
                 "inside_app_domain": app_domain_data["assessment"]["inside_app_domain"]
                 if app_domain_data
@@ -2205,7 +2249,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin):
         res = super().simple_json()
         name = res.get("name", None)
         if name == "no name":
-            res["name"] = self.default_node_label.name
+            res["name"] = self.default_node_label.get_name()
 
         return res
 
@@ -2229,18 +2273,24 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin):
 
     def d3_json(self):
         edge_json = {
-            "name": self.name,
+            "name": self.get_name(),
             "id": self.url,
             "url": self.url,
             "image": self.url + "?image=svg",
-            "reaction": {"name": self.edge_label.name, "url": self.edge_label.url}
+            "reaction": {
+                "name": self.edge_label.get_name(),
+                "url": self.edge_label.url,
+                "rules": [
+                    {"name": r.get_name(), "url": r.url} for r in self.edge_label.rules.all()
+                ],
+            }
             if self.edge_label
             else None,
             "multi_step": self.edge_label.multi_step if self.edge_label else False,
             "reaction_probability": self.kv.get("probability"),
             "start_node_urls": [x.url for x in self.start_nodes.all()],
             "end_node_urls": [x.url for x in self.end_nodes.all()],
-            "scenarios": [{"name": s.name, "url": s.url} for s in self.scenarios.all()],
+            "scenarios": [{"name": s.get_name(), "url": s.url} for s in self.scenarios.all()],
         }
 
         for n in self.start_nodes.all():
@@ -2329,10 +2379,22 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin):
         res = super().simple_json()
         name = res.get("name", None)
         if name == "no name":
-            res["name"] = self.edge_label.name
+            res["name"] = self.edge_label.get_name()
 
         return res
 
+    def get_name(self):
+        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)"
+        )
+
 
 class EPModel(PolymorphicModel, EnviPathModel):
     package = models.ForeignKey(
@@ -2613,7 +2675,7 @@ class PackageBasedModel(EPModel):
                     root_compounds.append(pw.root_nodes[0].default_node_label)
                 else:
                     logger.info(
-                        f"Skipping MG Eval of Pathway {pw.name} ({pw.uuid}) as it has no root compounds!"
+                        f"Skipping MG Eval of Pathway {pw.get_name()} ({pw.uuid}) as it has no root compounds!"
                     )
 
             # As we need a Model Instance in our setting, get a fresh copy from db, overwrite the serialized mode and
@@ -2739,7 +2801,7 @@ class PackageBasedModel(EPModel):
                         pathways.append(pathway)
                     else:
                         logging.warning(
-                            f"No root compound in pathway {pathway.name}, excluding from multigen evaluation"
+                            f"No root compound in pathway {pathway.get_name()}, excluding from multigen evaluation"
                         )
 
                 # build lookup reaction -> {uuid1, uuid2} for overlap check
@@ -3071,7 +3133,7 @@ class ApplicabilityDomain(EnviPathModel):
         ad = ApplicabilityDomain()
         ad.model = mlrr
         # ad.uuid = mlrr.uuid
-        ad.name = f"AD for {mlrr.name}"
+        ad.name = f"AD for {mlrr.get_name()}"
         ad.num_neighbours = num_neighbours
         ad.reliability_threshold = reliability_threshold
         ad.local_compatibilty_threshold = local_compatibility_threshold
@@ -3355,7 +3417,7 @@ class EnviFormer(PackageBasedModel):
             )
             for smiles in smiles_list
         ]
-        logger.info(f"Submitting {canon_smiles} to {self.name}")
+        logger.info(f"Submitting {canon_smiles} to {self.get_name()}")
         start = datetime.now()
         products_list = self.model.predict_batch(canon_smiles)
         end = datetime.now()
@@ -3512,7 +3574,7 @@ class EnviFormer(PackageBasedModel):
                 root_node = p.root_nodes
                 if len(root_node) > 1:
                     logging.warning(
-                        f"Pathway {p.name} has more than one root compound, only {root_node[0]} will be used"
+                        f"Pathway {p.get_name()} has more than one root compound, only {root_node[0]} will be used"
                     )
                 root_node = ".".join(
                     [
@@ -3632,7 +3694,7 @@ class EnviFormer(PackageBasedModel):
                         pathways.append(pathway)
                     else:
                         logging.warning(
-                            f"No root compound in pathway {pathway.name}, excluding from multigen evaluation"
+                            f"No root compound in pathway {pathway.get_name()}, excluding from multigen evaluation"
                         )
 
                 # build lookup reaction -> {uuid1, uuid2} for overlap check
@@ -4038,6 +4100,6 @@ class JobLog(TimeStampedModel):
         return self.task_result
 
     def is_result_downloadable(self):
-        downloadable = ["batch_predict"]
+        downloadable = ["batch_predict", "identify_missing_rules"]
 
         return self.job_name in downloadable

epdb/tasks.py

@@ -7,6 +7,7 @@ from uuid import uuid4
 from celery import shared_task
 from celery.utils.functional import LRUCache
 from django.conf import settings as s
+from django.core.mail import EmailMultiAlternatives
 from django.utils import timezone
 
 from epdb.logic import SPathway
@@ -73,7 +74,31 @@ def predict_simple(model_pk: int, smiles: str):
 
 @shared_task(queue="background")
 def send_registration_mail(user_pk: int):
-    pass
+    u = User.objects.get(id=user_pk)
+
+    tpl = """Welcome {username}!,
+
+Thank you for your interest in enviPath.
+
+The public system is intended for non-commercial use only.
+We will review your account details and usually activate your account within 24 hours.
+Once activated, you will be notified by email.
+
+If we have any questions, we will contact you at this email address.
+
+Best regards,
+
+enviPath team"""
+
+    msg = EmailMultiAlternatives(
+        "Your enviPath account",
+        tpl.format(username=u.username),
+        "admin@envipath.org",
+        [u.email],
+        bcc=["admin@envipath.org"],
+    )
+
+    msg.send(fail_silently=False)
 
 
 @shared_task(bind=True, queue="model")

epdb/views.py

@@ -1,7 +1,7 @@
 import json
 import logging
-from typing import Any, Dict, List
 from datetime import datetime
+from typing import Any, Dict, List
 
 import nh3
 from django.conf import settings as s
@@ -13,6 +13,7 @@ from django.urls import reverse
 from django.views.decorators.csrf import csrf_exempt
 from envipy_additional_information import NAME_MAPPING
 from oauth2_provider.decorators import protected_resource
+from sentry_sdk import capture_exception
 
 from utilities.chem import FormatConverter, IndigoUtils
 from utilities.decorators import package_permission_required
@@ -34,6 +35,7 @@ from .models import (
     EnviFormer,
     EnzymeLink,
     EPModel,
+    ExpansionSchemeChoice,
     ExternalDatabase,
     ExternalIdentifier,
     Group,
@@ -51,7 +53,6 @@ from .models import (
     SimpleAmbitRule,
     User,
     UserPackagePermission,
-    ExpansionSchemeChoice,
 )
 
 logger = logging.getLogger(__name__)
@@ -238,6 +239,15 @@ def register(request):
         try:
             u = UserManager.create_user(username, email, password)
             logger.info(f"Created user {u.username} ({u.pk})")
+
+            try:
+                from .tasks import send_registration_mail
+
+                send_registration_mail.delay(u.pk)
+            except Exception as e:
+                logger.error(f"Failed to send registration mail to {u.email}: {e}")
+                capture_exception(e)
+
         except Exception:
             context["message"] = "Registration failed! Couldn't create User Account."
             return render(request, "static/login.html", context)
@@ -339,7 +349,7 @@ def breadcrumbs(
         {"Package": s.SERVER_URL + "/package"},
     ]
     if first_level_object is not None:
-        bread.append({first_level_object.name: first_level_object.url})
+        bread.append({first_level_object.get_name(): first_level_object.url})
 
     if second_level_namespace is not None:
         bread.append(
@@ -350,7 +360,7 @@ def breadcrumbs(
         )
 
     if second_level_object is not None:
-        bread.append({second_level_object.name: second_level_object.url})
+        bread.append({second_level_object.get_name(): second_level_object.url})
 
     if third_level_namespace is not None:
         bread.append(
@@ -361,7 +371,7 @@ def breadcrumbs(
         )
 
     if third_level_object is not None:
-        bread.append({third_level_object.name: third_level_object.url})
+        bread.append({third_level_object.get_name(): third_level_object.url})
 
     return bread
 
@@ -462,7 +472,7 @@ def package_predict_pathway(request, package_uuid):
     current_package = PackageManager.get_package_by_id(current_user, package_uuid)
 
     context = get_base_context(request)
-    context["title"] = f"enviPath - {current_package.name} - Predict Pathway"
+    context["title"] = f"enviPath - {current_package.get_name()} - Predict Pathway"
     context["meta"]["current_package"] = current_package
 
     return render(request, "predict_pathway.html", context)
@@ -475,6 +485,10 @@ def packages(request):
         context = get_base_context(request)
         context["title"] = "enviPath - Packages"
         context["meta"]["current_package"] = context["meta"]["user"].default_package
+        context["breadcrumbs"] = [
+            {"Home": s.SERVER_URL},
+            {"Package": s.SERVER_URL + "/package"},
+        ]
 
         # Context for paginated template
         context["entity_type"] = "package"
@@ -529,6 +543,10 @@ def compounds(request):
         context = get_base_context(request)
         context["title"] = "enviPath - Compounds"
         context["meta"]["current_package"] = context["meta"]["user"].default_package
+        context["breadcrumbs"] = [
+            {"Home": s.SERVER_URL},
+            {"Compound": s.SERVER_URL + "/compound"},
+        ]
 
         # Context for paginated template
         context["entity_type"] = "compound"
@@ -759,7 +777,7 @@ def package_models(request, package_uuid):
 
     if request.method == "GET":
         context = get_base_context(request)
-        context["title"] = f"enviPath - {current_package.name} - Models"
+        context["title"] = f"enviPath - {current_package.get_name()} - Models"
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "model"
@@ -781,7 +799,7 @@ def package_models(request, package_uuid):
             return JsonResponse(
                 {
                     "objects": [
-                        {"name": pw.name, "url": pw.url, "reviewed": current_package.reviewed}
+                        {"name": pw.get_name(), "url": pw.url, "reviewed": current_package.reviewed}
                         for pw in (
                             reviewed_model_qs if current_package.reviewed else unreviewed_model_qs
                         )
@@ -931,7 +949,7 @@ def package_model(request, package_uuid, model_uuid):
                 return JsonResponse(app_domain_assessment, safe=False)
 
         context = get_base_context(request)
-        context["title"] = f"enviPath - {current_package.name} - {current_model.name}"
+        context["title"] = f"enviPath - {current_package.get_name()} - {current_model.get_name()}"
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "model"
@@ -1009,7 +1027,7 @@ def package(request, package_uuid):
 
     if request.method == "GET":
         if request.GET.get("export", False) == "true":
-            filename = f"{current_package.name.replace(' ', '_')}_{current_package.uuid}.json"
+            filename = f"{current_package.get_name().replace(' ', '_')}_{current_package.uuid}.json"
             pack_json = PackageManager.export_package(
                 current_package, include_models=False, include_external_identifiers=False
             )
@@ -1019,7 +1037,7 @@ def package(request, package_uuid):
             return response
 
         context = get_base_context(request)
-        context["title"] = f"enviPath - {current_package.name}"
+        context["title"] = f"enviPath - {current_package.get_name()}"
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "package"
@@ -1056,7 +1074,7 @@ def package(request, package_uuid):
                 if current_user.default_package == current_package:
                     return error(
                         request,
-                        f'Package "{current_package.name}" is the default and cannot be deleted!',
+                        f'Package "{current_package.get_name()}" is the default and cannot be deleted!',
                         "You cannot delete the default package. If you want to delete this package you have to set another default package first.",
                     )
 
@@ -1154,7 +1172,7 @@ def package_compounds(request, package_uuid):
 
     if request.method == "GET":
         context = get_base_context(request)
-        context["title"] = f"enviPath - {current_package.name} - Compounds"
+        context["title"] = f"enviPath - {current_package.get_name()} - Compounds"
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "compound"
@@ -1179,7 +1197,7 @@ def package_compounds(request, package_uuid):
             return JsonResponse(
                 {
                     "objects": [
-                        {"name": pw.name, "url": pw.url, "reviewed": current_package.reviewed}
+                        {"name": pw.get_name(), "url": pw.url, "reviewed": current_package.reviewed}
                         for pw in (
                             reviewed_compound_qs
                             if current_package.reviewed
@@ -1216,7 +1234,9 @@ def package_compound(request, package_uuid, compound_uuid):
 
     if request.method == "GET":
         context = get_base_context(request)
-        context["title"] = f"enviPath - {current_package.name} - {current_compound.name}"
+        context["title"] = (
+            f"enviPath - {current_package.get_name()} - {current_compound.get_name()}"
+        )
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "compound"
@@ -1300,7 +1320,7 @@ def package_compound_structures(request, package_uuid, compound_uuid):
     if request.method == "GET":
         context = get_base_context(request)
         context["title"] = (
-            f"enviPath - {current_package.name} - {current_compound.name} - Structures"
+            f"enviPath - {current_package.get_name()} - {current_compound.get_name()} - Structures"
         )
 
         context["meta"]["current_package"] = current_package
@@ -1309,7 +1329,7 @@ def package_compound_structures(request, package_uuid, compound_uuid):
             current_package, "compound", current_compound, "structure"
         )
         context["entity_type"] = "structure"
-        context["page_title"] = f"{current_compound.name} - Structures"
+        context["page_title"] = f"{current_compound.get_name()} - Structures"
         context["api_endpoint"] = (
             f"/api/v1/package/{current_package.uuid}/compound/{current_compound.uuid}/structure/"
         )
@@ -1362,7 +1382,7 @@ def package_compound_structure(request, package_uuid, compound_uuid, structure_u
 
         context = get_base_context(request)
         context["title"] = (
-            f"enviPath - {current_package.name} - {current_compound.name} - {current_structure.name}"
+            f"enviPath - {current_package.get_name()} - {current_compound.get_name()} - {current_structure.get_name()}"
         )
 
         context["meta"]["current_package"] = current_package
@@ -1468,7 +1488,7 @@ def package_rules(request, package_uuid):
 
     if request.method == "GET":
         context = get_base_context(request)
-        context["title"] = f"enviPath - {current_package.name} - Rules"
+        context["title"] = f"enviPath - {current_package.get_name()} - Rules"
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "rule"
@@ -1490,7 +1510,7 @@ def package_rules(request, package_uuid):
             return JsonResponse(
                 {
                     "objects": [
-                        {"name": pw.name, "url": pw.url, "reviewed": current_package.reviewed}
+                        {"name": pw.get_name(), "url": pw.url, "reviewed": current_package.reviewed}
                         for pw in (
                             reviewed_rule_qs if current_package.reviewed else unreviewed_rule_qs
                         )
@@ -1580,7 +1600,7 @@ def package_rule(request, package_uuid, rule_uuid):
                 content_type="image/svg+xml",
             )
 
-        context["title"] = f"enviPath - {current_package.name} - {current_rule.name}"
+        context["title"] = f"enviPath - {current_package.get_name()} - {current_rule.get_name()}"
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "rule"
@@ -1653,7 +1673,7 @@ def package_rule_enzymelink(request, package_uuid, rule_uuid, enzymelink_uuid):
     if request.method == "GET":
         context = get_base_context(request)
 
-        context["title"] = f"enviPath - {current_package.name} - {current_rule.name}"
+        context["title"] = f"enviPath - {current_package.get_name()} - {current_rule.get_name()}"
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "enzyme"
@@ -1676,7 +1696,7 @@ def package_reactions(request, package_uuid):
 
     if request.method == "GET":
         context = get_base_context(request)
-        context["title"] = f"enviPath - {current_package.name} - Reactions"
+        context["title"] = f"enviPath - {current_package.get_name()} - Reactions"
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "reaction"
@@ -1700,7 +1720,7 @@ def package_reactions(request, package_uuid):
             return JsonResponse(
                 {
                     "objects": [
-                        {"name": pw.name, "url": pw.url, "reviewed": current_package.reviewed}
+                        {"name": pw.get_name(), "url": pw.url, "reviewed": current_package.reviewed}
                         for pw in (
                             reviewed_reaction_qs
                             if current_package.reviewed
@@ -1741,7 +1761,9 @@ def package_reaction(request, package_uuid, reaction_uuid):
 
     if request.method == "GET":
         context = get_base_context(request)
-        context["title"] = f"enviPath - {current_package.name} - {current_reaction.name}"
+        context["title"] = (
+            f"enviPath - {current_package.get_name()} - {current_reaction.get_name()}"
+        )
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "reaction"
@@ -1824,7 +1846,7 @@ def package_pathways(request, package_uuid):
 
     if request.method == "GET":
         context = get_base_context(request)
-        context["title"] = f"enviPath - {current_package.name} - Pathways"
+        context["title"] = f"enviPath - {current_package.get_name()} - Pathways"
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "pathway"
@@ -1846,7 +1868,7 @@ def package_pathways(request, package_uuid):
             return JsonResponse(
                 {
                     "objects": [
-                        {"name": pw.name, "url": pw.url, "reviewed": current_package.reviewed}
+                        {"name": pw.get_name(), "url": pw.url, "reviewed": current_package.reviewed}
                         for pw in (
                             reviewed_pathway_qs
                             if current_package.reviewed
@@ -1953,7 +1975,7 @@ def package_pathway(request, package_uuid, pathway_uuid):
             )
 
         if request.GET.get("download", False) == "true":
-            filename = f"{current_pathway.name.replace(' ', '_')}_{current_pathway.uuid}.csv"
+            filename = f"{current_pathway.get_name().replace(' ', '_')}_{current_pathway.uuid}.csv"
             csv_pw = current_pathway.to_csv()
             response = HttpResponse(csv_pw, content_type="text/csv")
             response["Content-Disposition"] = f'attachment; filename="{filename}"'
@@ -1973,7 +1995,7 @@ def package_pathway(request, package_uuid, pathway_uuid):
                 current_user, identify_missing_rules, [current_pathway.pk], rule_package.pk
             )
 
-            filename = f"{current_pathway.name.replace(' ', '_')}_{current_pathway.uuid}.csv"
+            filename = f"{current_pathway.get_name().replace(' ', '_')}_{current_pathway.uuid}.csv"
             response = HttpResponse(res, content_type="text/csv")
             response["Content-Disposition"] = f'attachment; filename="{filename}"'
 
@@ -1996,7 +2018,7 @@ def package_pathway(request, package_uuid, pathway_uuid):
         ).get(uuid=pathway_uuid)
 
         context = get_base_context(request)
-        context["title"] = f"enviPath - {current_package.name} - {current_pathway.name}"
+        context["title"] = f"enviPath - {current_package.get_name()} - {current_pathway.get_name()}"
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "pathway"
@@ -2008,9 +2030,9 @@ def package_pathway(request, package_uuid, pathway_uuid):
         context["breadcrumbs"] = [
             {"Home": s.SERVER_URL},
             {"Package": s.SERVER_URL + "/package"},
-            {current_package.name: current_package.url},
+            {current_package.get_name(): current_package.url},
             {"Pathway": current_package.url + "/pathway"},
-            {current_pathway.name: current_pathway.url},
+            {current_pathway.get_name(): current_pathway.url},
         ]
 
         return render(request, "objects/pathway.html", context)
@@ -2097,16 +2119,18 @@ def package_pathway_nodes(request, package_uuid, pathway_uuid):
 
     if request.method == "GET":
         context = get_base_context(request)
-        context["title"] = f"enviPath - {current_package.name} - {current_pathway.name} - Nodes"
+        context["title"] = (
+            f"enviPath - {current_package.get_name()} - {current_pathway.get_name()} - Nodes"
+        )
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "node"
         context["breadcrumbs"] = [
             {"Home": s.SERVER_URL},
             {"Package": s.SERVER_URL + "/package"},
-            {current_package.name: current_package.url},
+            {current_package.get_name(): current_package.url},
             {"Pathway": current_package.url + "/pathway"},
-            {current_pathway.name: current_pathway.url},
+            {current_pathway.get_name(): current_pathway.url},
             {"Node": current_pathway.url + "/node"},
         ]
 
@@ -2122,7 +2146,7 @@ def package_pathway_nodes(request, package_uuid, pathway_uuid):
             return JsonResponse(
                 {
                     "objects": [
-                        {"name": pw.name, "url": pw.url, "reviewed": current_package.reviewed}
+                        {"name": pw.get_name(), "url": pw.url, "reviewed": current_package.reviewed}
                         for pw in (
                             reviewed_node_qs if current_package.reviewed else unreviewed_node_qs
                         )
@@ -2196,7 +2220,7 @@ def package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
                 return HttpResponse(svg_data, content_type="image/svg+xml")
 
         context = get_base_context(request)
-        context["title"] = f"enviPath - {current_package.name} - {current_pathway.name}"
+        context["title"] = f"enviPath - {current_package.get_name()} - {current_pathway.get_name()}"
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "pathway"
@@ -2204,11 +2228,11 @@ def package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
         context["breadcrumbs"] = [
             {"Home": s.SERVER_URL},
             {"Package": s.SERVER_URL + "/package"},
-            {current_package.name: current_package.url},
+            {current_package.get_name(): current_package.url},
             {"Pathway": current_package.url + "/pathway"},
-            {current_pathway.name: current_pathway.url},
+            {current_pathway.get_name(): current_pathway.url},
             {"Node": current_pathway.url + "/node"},
-            {current_node.name: current_node.url},
+            {current_node.get_name(): current_node.url},
         ]
 
         context["node"] = current_node
@@ -2261,16 +2285,18 @@ def package_pathway_edges(request, package_uuid, pathway_uuid):
 
     if request.method == "GET":
         context = get_base_context(request)
-        context["title"] = f"enviPath - {current_package.name} - {current_pathway.name} - Edges"
+        context["title"] = (
+            f"enviPath - {current_package.get_name()} - {current_pathway.get_name()} - Edges"
+        )
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "edge"
         context["breadcrumbs"] = [
             {"Home": s.SERVER_URL},
             {"Package": s.SERVER_URL + "/package"},
-            {current_package.name: current_package.url},
+            {current_package.get_name(): current_package.url},
             {"Pathway": current_package.url + "/pathway"},
-            {current_pathway.name: current_pathway.url},
+            {current_pathway.get_name(): current_pathway.url},
             {"Edge": current_pathway.url + "/edge"},
         ]
 
@@ -2286,7 +2312,7 @@ def package_pathway_edges(request, package_uuid, pathway_uuid):
             return JsonResponse(
                 {
                     "objects": [
-                        {"name": pw.name, "url": pw.url, "reviewed": current_package.reviewed}
+                        {"name": pw.get_name(), "url": pw.url, "reviewed": current_package.reviewed}
                         for pw in (
                             reviewed_edge_qs if current_package.reviewed else unreviewed_edge_qs
                         )
@@ -2338,7 +2364,7 @@ def package_pathway_edge(request, package_uuid, pathway_uuid, edge_uuid):
 
         context = get_base_context(request)
         context["title"] = (
-            f"enviPath - {current_package.name} - {current_pathway.name} - {current_edge.edge_label.name}"
+            f"enviPath - {current_package.get_name()} - {current_pathway.get_name()} - {current_edge.edge_label.get_name()}"
         )
 
         context["meta"]["current_package"] = current_package
@@ -2391,11 +2417,11 @@ def package_scenarios(request, package_uuid):
             "all", False
         ):
             scens = Scenario.objects.filter(package=current_package).order_by("name")
-            res = [{"name": s_.name, "url": s_.url, "uuid": s_.uuid} for s_ in scens]
+            res = [{"name": s_.get_name(), "url": s_.url, "uuid": s_.uuid} for s_ in scens]
             return JsonResponse(res, safe=False)
 
         context = get_base_context(request)
-        context["title"] = f"enviPath - {current_package.name} - Scenarios"
+        context["title"] = f"enviPath - {current_package.get_name()} - Scenarios"
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "scenario"
@@ -2419,7 +2445,7 @@ def package_scenarios(request, package_uuid):
             return JsonResponse(
                 {
                     "objects": [
-                        {"name": pw.name, "url": pw.url, "reviewed": current_package.reviewed}
+                        {"name": pw.get_name(), "url": pw.url, "reviewed": current_package.reviewed}
                         for pw in (
                             reviewed_scenario_qs
                             if current_package.reviewed
@@ -2511,7 +2537,9 @@ def package_scenario(request, package_uuid, scenario_uuid):
 
     if request.method == "GET":
         context = get_base_context(request)
-        context["title"] = f"enviPath - {current_package.name} - {current_scenario.name}"
+        context["title"] = (
+            f"enviPath - {current_package.get_name()} - {current_scenario.get_name()}"
+        )
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "scenario"
@@ -2748,13 +2776,13 @@ def group(request, group_uuid):
 
     if request.method == "GET":
         context = get_base_context(request)
-        context["title"] = f"enviPath - {current_group.name}"
+        context["title"] = f"enviPath - {current_group.get_name()}"
 
         context["object_type"] = "group"
         context["breadcrumbs"] = [
             {"Home": s.SERVER_URL},
             {"Group": s.SERVER_URL + "/group"},
-            {current_group.name: current_group.url},
+            {current_group.get_name(): current_group.url},
         ]
 
         context["group"] = current_group
@@ -2909,13 +2937,13 @@ def setting(request, setting_uuid):
 
     if request.method == "GET":
         context = get_base_context(request)
-        context["title"] = f"enviPath - {current_setting.name}"
+        context["title"] = f"enviPath - {current_setting.get_name()}"
 
         context["object_type"] = "setting"
         context["breadcrumbs"] = [
             {"Home": s.SERVER_URL},
             {"Setting": s.SERVER_URL + "/setting"},
-            {f"{current_setting.name}": current_setting.url},
+            {f"{current_setting.get_name()}": current_setting.url},
         ]
 
         context["setting"] = current_setting
@@ -2964,8 +2992,8 @@ def jobs(request):
 
             target_package = PackageManager.create_package(
                 current_user,
-                f"Autogenerated Package for Pathway Engineering of {pathway_to_engineer.name}",
+                f"Autogenerated Package for Pathway Engineering of {pathway_to_engineer.get_name()}",
-                f"This Package was generated automatically for the engineering Task of {pathway_to_engineer.name}.",
+                f"This Package was generated automatically for the engineering Task of {pathway_to_engineer.get_name()}.",
             )
 
             from .tasks import dispatch, engineer_pathways
@@ -3019,7 +3047,7 @@ def jobs(request):
                 "This Package was generated automatically for the batch prediction task.",
             )
 
-            from .tasks import dispatch, batch_predict
+            from .tasks import batch_predict, dispatch
 
             res = dispatch(
                 current_user,
@@ -3057,6 +3085,8 @@ def job(request, job_uuid):
 
             if job.job_name == "batch_predict":
                 filename = f"{job.job_name.replace(' ', '_')}_{job.task_id}.csv"
+            elif job.job_name == "identify_missing_rules":
+                filename = f"{job.job_name.replace(' ', '_')}_{job.task_id}.csv"
             else:
                 raise BadRequest("Result is not downloadable!")
 

pnpm-workspace.yaml

@@ -0,0 +1,3 @@
+onlyBuiltDependencies:
+  - '@parcel/watcher'
+  - '@tailwindcss/oxide'

static/js/pw.js

@@ -393,7 +393,14 @@ function draw(pathway, elem) {
     }
 
     function edge_popup(e) {
-        popupContent = "<a href='" + e.url + "'>" + e.name + "</a><br>";
+        popupContent = "<a href='" + e.url + "'>" + e.name + "</a><br><br>";
+
+        if (e.reaction.rules) {
+            console.log(e.reaction.rules);
+            for (var rule of e.reaction.rules) {
+                popupContent += "Rule <a href='" + rule.url + "'>" + rule.name + "</a><br>";
+            }
+        }
 
         if (e.app_domain) {
             adcontent = "<p>";

templates/index/index.html

@@ -176,8 +176,8 @@
                       href="#"
                       class="example-link hover:text-primary cursor-pointer"
                       title="load example"
-                      @click.prevent="loadExample('CC(C)CC1=CC=C(C=C1)C(C)C(=O)O', $el)"
+                      @click.prevent="loadExample('COC(=O)[C@H](CC1=CC=CC=C1)NC(=O)[C@H](CC(=O)O)N', $el)"
-                      >Ibuprofen</a
+                      >Aspartame</a
                     >
                   </div>
                   <a

templates/objects/compound_structure.html

@@ -85,6 +85,55 @@
       </div>
     {% endif %}
 
+    {% if compound_structure.half_lifes %}
+      <div class="collapse-arrow bg-base-200 collapse">
+        <input type="checkbox" />
+        <div class="collapse-title text-xl font-medium">Half-lives</div>
+        <div class="collapse-content">
+          <div class="overflow-x-auto">
+            <table class="table-zebra table">
+              <thead>
+                <tr>
+                  <th>Scenario</th>
+                  <th>Values</th>
+                </tr>
+              </thead>
+              <tbody>
+                {% for scenario, half_lifes in compound_structure.half_lifes.items %}
+                  <tr>
+                    <td>
+                      <a href="{{ scenario.url }}" class="hover:bg-base-200"
+                        >{{ scenario.name }}
+                        <i>({{ scenario.package.name }})</i></a
+                      >
+                    </td>
+                    <td>
+                      <table class="table-zebra table">
+                        <tbody>
+                          <tr>
+                            <td>Scenario Type</td>
+                            <td>{{ scenario.scenario_type }}</td>
+                          </tr>
+                          <tr>
+                            <td>Half-life (days)</td>
+                            <td>{{ half_lifes.0.dt50 }}</td>
+                          </tr>
+                          <tr>
+                            <td>Model</td>
+                            <td>{{ half_lifes.0.model }}</td>
+                          </tr>
+                        </tbody>
+                      </table>
+                    </td>
+                  </tr>
+                {% endfor %}
+              </tbody>
+            </table>
+          </div>
+        </div>
+      </div>
+    {% endif %}
+
     {% if compound_structure.scenarios.all %}
       <!-- Scenarios -->
       <div class="collapse-arrow bg-base-200 collapse">

templates/objects/edge.html

@@ -14,7 +14,7 @@
     <div class="card bg-base-100">
       <div class="card-body">
         <div class="flex items-center justify-between">
-          <h2 class="card-title text-2xl">{{ edge.edge_label.name }}</h2>
+          <h2 class="card-title text-2xl">{{ edge.get_name }}</h2>
           <div id="actionsButton" class="dropdown dropdown-end hidden">
             <div tabindex="0" role="button" class="btn btn-ghost btn-sm">
               <svg
@@ -45,6 +45,11 @@
             </ul>
           </div>
         </div>
+        <p class="mt-2">
+          The underlying reaction can be found
+          <a href="{{ edge.edge_label.url }}" class="link link-primary">here</a
+          >.
+        </p>
       </div>
     </div>
 

templates/objects/joblog.html

@@ -103,7 +103,7 @@
                 </ul>
               </div>
             </div>
-          {% elif job.job_name == 'batch_predict' %}
+          {% elif job.job_name == 'batch_predict' or job.job_name == 'identify_missing_rules' %}
             <div
               id="table-container"
               class="overflow-x-auto overflow-y-auto max-h-96 border rounded-lg"

templates/objects/node.html

@@ -14,7 +14,7 @@
     <div class="card bg-base-100">
       <div class="card-body">
         <div class="flex items-center justify-between">
-          <h2 class="card-title text-2xl">{{ node.name }}</h2>
+          <h2 class="card-title text-2xl">{{ node.get_name }}</h2>
           <div id="actionsButton" class="dropdown dropdown-end hidden">
             <div tabindex="0" role="button" class="btn btn-ghost btn-sm">
               <svg
@@ -54,28 +54,6 @@
       </div>
     </div>
 
-    <!-- Description -->
-    <div class="collapse-arrow bg-base-200 collapse">
-      <input type="checkbox" checked />
-      <div class="collapse-title text-xl font-medium">Description</div>
-      <div class="collapse-content">{{ node.description }}</div>
-    </div>
-
-    {% if node.aliases %}
-      <!-- Aliases -->
-      <div class="collapse-arrow bg-base-200 collapse">
-        <input type="checkbox" checked />
-        <div class="collapse-title text-xl font-medium">Aliases</div>
-        <div class="collapse-content">
-          <ul class="menu bg-base-100 rounded-box">
-            {% for alias in node.aliases %}
-              <li><a class="hover:bg-base-200">{{ alias }}</a></li>
-            {% endfor %}
-          </ul>
-        </div>
-      </div>
-    {% endif %}
-
     <!-- Image Representation -->
     <div class="collapse-arrow bg-base-200 collapse">
       <input type="checkbox" checked />
@@ -96,6 +74,70 @@
       <div class="collapse-content">{{ node.default_node_label.smiles }}</div>
     </div>
 
+    {% if node.default_node_label.aliases %}
+      <!-- Aliases -->
+      <div class="collapse-arrow bg-base-200 collapse">
+        <input type="checkbox" checked />
+        <div class="collapse-title text-xl font-medium">Aliases</div>
+        <div class="collapse-content">
+          <ul class="menu bg-base-100 rounded-box">
+            {% for alias in node.default_node_label.aliases %}
+              <li><a class="hover:bg-base-200">{{ alias }}</a></li>
+            {% endfor %}
+          </ul>
+        </div>
+      </div>
+    {% endif %}
+
+    {% if node.default_node_label.half_lifes %}
+      <div class="collapse-arrow bg-base-200 collapse">
+        <input type="checkbox" />
+        <div class="collapse-title text-xl font-medium">Half-lives</div>
+        <div class="collapse-content">
+          <div class="overflow-x-auto">
+            <table class="table-zebra table">
+              <thead>
+                <tr>
+                  <th>Scenario</th>
+                  <th>Values</th>
+                </tr>
+              </thead>
+              <tbody>
+                {% for scenario, half_lifes in node.default_node_label.half_lifes.items %}
+                  <tr>
+                    <td>
+                      <a href="{{ scenario.url }}" class="hover:bg-base-200"
+                        >{{ scenario.name }}
+                        <i>({{ scenario.package.name }})</i></a
+                      >
+                    </td>
+                    <td>
+                      <table class="table-zebra table">
+                        <tbody>
+                          <tr>
+                            <td>Scenario Type</td>
+                            <td>{{ scenario.scenario_type }}</td>
+                          </tr>
+                          <tr>
+                            <td>Half-life (days)</td>
+                            <td>{{ half_lifes.0.dt50 }}</td>
+                          </tr>
+                          <tr>
+                            <td>Model</td>
+                            <td>{{ half_lifes.0.model }}</td>
+                          </tr>
+                        </tbody>
+                      </table>
+                    </td>
+                  </tr>
+                {% endfor %}
+              </tbody>
+            </table>
+          </div>
+        </div>
+      </div>
+    {% endif %}
+
     {% if node.scenarios.all %}
       <!-- Scenarios -->
       <div class="collapse-arrow bg-base-200 collapse">