[Feature] Leftovers after Release (#303)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#303

epdb/models.py

@@ -72,6 +72,7 @@ class User(AbstractUser):
         null=True,
         blank=False,
     )
+    is_reviewer = models.BooleanField(default=False)
 
     USERNAME_FIELD = "email"
     REQUIRED_FIELDS = ["username"]
@@ -1828,8 +1829,8 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
                         queue.append(prod)
 
         # We shouldn't lose or make up nodes...
-        assert len(nodes) == len(self.nodes)
-        logger.debug(f"{self.name}: Num Nodes {len(nodes)} vs. DB Nodes {len(self.nodes)}")
+        if len(nodes) != len(self.nodes):
+            logger.debug(f"{self.name}: Num Nodes {len(nodes)} vs. DB Nodes {len(self.nodes)}")
 
         links = [e.d3_json() for e in self.edges]
 
@@ -1880,6 +1881,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
                         "source": pseudo_idx,
                         "target": node_url_to_idx[target],
                         "app_domain": link.get("app_domain", None),
+                        "multi_step": link["multi_step"],
                     }
                     adjusted_links.append(new_link)
 
@@ -2146,6 +2148,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin):
         }
 
     @staticmethod
+    @transaction.atomic
     def create(
         pathway: "Pathway",
         smiles: str,
@@ -2185,8 +2188,11 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin):
         if data:
             rule_ids = defaultdict(list)
             for e in Edge.objects.filter(start_nodes__in=[self]):
-                for r in e.edge_label.rules.all():
-                    rule_ids[str(r.uuid)].append(e.simple_json())
+                # TODO While the Pathway is being predicted we sometimes
+                # TODO receive 'NoneType' object has no attribute 'rules'
+                if e.edge_label:
+                    for r in e.edge_label.rules.all():
+                        rule_ids[str(r.uuid)].append(e.simple_json())
 
             for t in data["assessment"]["transformations"]:
                 if t["rule"]["uuid"] in rule_ids:
@@ -2230,6 +2236,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin):
             "reaction": {"name": self.edge_label.name, "url": self.edge_label.url}
             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()],
@@ -2270,6 +2277,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin):
         return edge_json
 
     @staticmethod
+    @transaction.atomic
     def create(
         pathway,
         start_nodes: List[Node],
@@ -3819,6 +3827,11 @@ class Scenario(EnviPathModel):
 
                 yield inst
 
+    def related_pathways(self):
+        return Pathway.objects.filter(
+            scenarios__in=[self], package__reviewed=True, package=self.package
+        ).distinct()
+
 
 class UserSettingPermission(Permission):
     uuid = models.UUIDField(