[Feature] EnzymeLink Annotations (#152)

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

epdb/logic.py

@@ -26,6 +26,7 @@ from epdb.models import (
     Compound,
     Reaction,
     CompoundStructure,
+    EnzymeLink,
 )
 from utilities.chem import FormatConverter
 from utilities.misc import PackageImporter, PackageExporter
@@ -617,6 +618,8 @@ class PackageManager(object):
         parent_mapping = {}
         # Mapping old scen_id to old_obj_id
         scen_mapping = defaultdict(list)
+        # Enzymelink Mapping rule_id to enzymelink objects
+        enzyme_mapping = defaultdict(list)
 
         # Store Scenarios
         for scenario in data["scenarios"]:
@@ -648,9 +651,7 @@ class PackageManager(object):
                 # Broken eP Data
                 if name == "initialmasssediment" and addinf_data == "missing data":
                     continue
-
-                # TODO Enzymes arent ready yet
-                if name == "enzyme":
+                if name == "columnheight" and addinf_data == "(2)-(2.5);(6)-(8)":
                     continue
 
                 try:
@@ -740,6 +741,9 @@ class PackageManager(object):
             for scen in rule["scenarios"]:
                 scen_mapping[scen["id"]].append(r)
 
+            for enzyme_link in rule.get("enzymeLinks", []):
+                enzyme_mapping[r.uuid].append(enzyme_link)
+
         print("Par: ", len(par_rules))
         print("Seq: ", len(seq_rules))
 
@@ -757,6 +761,9 @@ class PackageManager(object):
             for scen in par_rule["scenarios"]:
                 scen_mapping[scen["id"]].append(r)
 
+            for enzyme_link in par_rule.get("enzymeLinks", []):
+                enzyme_mapping[r.uuid].append(enzyme_link)
+
             for simple_rule in par_rule["simpleRules"]:
                 if simple_rule["id"] in mapping:
                     r.simple_rules.add(SimpleRule.objects.get(uuid=mapping[simple_rule["id"]]))
@@ -777,6 +784,9 @@ class PackageManager(object):
             for scen in seq_rule["scenarios"]:
                 scen_mapping[scen["id"]].append(r)
 
+            for enzyme_link in seq_rule.get("enzymeLinks", []):
+                enzyme_mapping[r.uuid].append(enzyme_link)
+
             for i, simple_rule in enumerate(seq_rule["simpleRules"]):
                 sro = SequentialRuleOrdering()
                 sro.simple_rule = simple_rule
@@ -910,6 +920,39 @@ class PackageManager(object):
 
         print("Scenarios linked...")
 
+        # Import Enzyme Links
+        for rule_uuid, enzyme_links in enzyme_mapping.items():
+            r = Rule.objects.get(uuid=rule_uuid)
+            for enzyme in enzyme_links:
+                e = EnzymeLink()
+                e.uuid = UUID(enzyme["id"].split("/")[-1]) if keep_ids else uuid4()
+                e.rule = r
+                e.name = enzyme["name"]
+                e.ec_number = enzyme["ecNumber"]
+                e.classification_level = enzyme["classificationLevel"]
+                e.linking_method = enzyme["linkingMethod"]
+                e.save()
+
+                for reaction in enzyme["reactionLinkEvidence"]:
+                    reaction = Reaction.objects.get(uuid=mapping[reaction["id"]])
+                    e.reaction_evidence.add(reaction)
+
+                for edge in enzyme["edgeLinkEvidence"]:
+                    edge = Edge.objects.get(uuid=mapping[edge["id"]])
+                    e.reaction_evidence.add(edge)
+
+                for evidence in enzyme["linkEvidence"]:
+                    matches = re.findall(r">(R[0-9]+)<", evidence["evidence"])
+                    if not matches or len(matches) != 1:
+                        logger.warning(f"Could not find reaction id in {evidence['evidence']}")
+                        continue
+
+                    e.add_kegg_reaction_id(matches[0])
+
+                e.save()
+
+        print("Enzyme links imported...")
+
         print("Import statistics:")
         print("Package {} stored".format(pack.url))
         print("Imported {} compounds".format(Compound.objects.filter(package=pack).count()))