[Feature] EnzymeLink Annotations (#152)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#152

epdb/models.py

@@ -494,6 +494,20 @@ class ChemicalIdentifierMixin(ExternalIdentifierMixin):
         return self.get_external_identifier("CAS")
 
 
+class KEGGIdentifierMixin(ExternalIdentifierMixin):
+    @property
+    def kegg_reaction_links(self):
+        return self.get_external_identifier("KEGG Reaction")
+
+    def add_kegg_reaction_id(self, kegg_id):
+        return self.add_external_identifier(
+            "KEGG Reaction", kegg_id, f"https://www.genome.jp/entry/{kegg_id}"
+        )
+
+    class Meta:
+        abstract = True
+
+
 class ReactionIdentifierMixin(ExternalIdentifierMixin):
     class Meta:
         abstract = True
@@ -1014,6 +1028,26 @@ class CompoundStructure(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdenti
         return self.compound.default_structure == self
 
 
+class EnzymeLink(EnviPathModel, KEGGIdentifierMixin):
+    rule = models.ForeignKey("Rule", on_delete=models.CASCADE, db_index=True)
+    ec_number = models.TextField(blank=False, null=False, verbose_name="EC Number")
+    classification_level = models.IntegerField(
+        blank=False, null=False, verbose_name="Classification Level"
+    )
+    linking_method = models.TextField(blank=False, null=False, verbose_name="Linking Method")
+
+    reaction_evidence = models.ManyToManyField("epdb.Reaction")
+    edge_evidence = models.ManyToManyField("epdb.Edge")
+
+    external_identifiers = GenericRelation("ExternalIdentifier")
+
+    def _url(self):
+        return "{}/enzymelink/{}".format(self.rule.url, self.uuid)
+
+    def get_group(self) -> str:
+        return ".".join(self.ec_number.split(".")[:3]) + ".-"
+
+
 class Rule(PolymorphicModel, EnviPathModel, AliasMixin, ScenarioMixin):
     package = models.ForeignKey(
         "epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
@@ -1095,6 +1129,18 @@ class Rule(PolymorphicModel, EnviPathModel, AliasMixin, ScenarioMixin):
 
         return new_rule
 
+    def enzymelinks(self):
+        return self.enzymelink_set.all()
+
+    def get_grouped_enzymelinks(self):
+        res = defaultdict(list)
+
+        for el in self.enzymelinks():
+            key = ".".join(el.ec_number.split(".")[:3]) + ".-"
+            res[key].append(el)
+
+        return dict(res)
+
 
 class SimpleRule(Rule):
     pass
@@ -1437,6 +1483,16 @@ class Reaction(EnviPathModel, AliasMixin, ScenarioMixin, ReactionIdentifierMixin
             id__in=Edge.objects.filter(edge_label=self).values("pathway_id")
         ).order_by("name")
 
+    def get_related_enzymes(self):
+        res = []
+        edges = Edge.objects.filter(edge_label=self)
+        for e in edges:
+            for scen in e.scenarios.all():
+                for ai in scen.additional_information.keys():
+                    if ai == "Enzyme":
+                        res.extend(scen.additional_information[ai])
+        return res
+
 
 class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
     package = models.ForeignKey(