minor

epdb/admin.py

@@ -11,6 +11,7 @@ from .models import (
     CompoundStructure,
     Edge,
     EnviFormer,
+    EnzymeLink,
     ExternalDatabase,
     ExternalIdentifier,
     Group,
@@ -212,6 +213,10 @@ class CompoundStructureAdmin(EPAdmin):
     pass
 
 
+class EnzymeLinkAdmin(EPAdmin):
+    pass
+
+
 class SimpleAmbitRuleAdmin(EPAdmin):
     pass
 
@@ -266,6 +271,7 @@ admin.site.register(License, LicenseAdmin)
 admin.site.register(ClassifierPluginModel, ClassifierPluginModelAdmin)
 admin.site.register(Compound, CompoundAdmin)
 admin.site.register(CompoundStructure, CompoundStructureAdmin)
+admin.site.register(EnzymeLink, EnzymeLinkAdmin)
 admin.site.register(SimpleAmbitRule, SimpleAmbitRuleAdmin)
 admin.site.register(ParallelRule, ParallelRuleAdmin)
 admin.site.register(Reaction, ReactionAdmin)

epdb/logic.py

@@ -665,11 +665,11 @@ class PackageManager(object):
         # EDIT START
         if data.get("classification"):
             if data["classification"] == "INTERNAL":
-                pack.classification = Package.Classification.RESTRICTED
+                pack.classification_level = Package.Classification.RESTRICTED
             elif data["classification"] == "RESTRICTED":
-                pack.classification = Package.Classification.RESTRICTED
+                pack.classification_level = Package.Classification.RESTRICTED
             elif data["classification"] == "SECRET":
-                pack.classification = Package.Classification.SECRET
+                pack.classification_level = Package.Classification.SECRET
 
                 if not "datapool" in data:
                     raise ValueError("Missing datapool in package")

utilities/misc.py

@@ -21,6 +21,8 @@ from epdb.models import (
     Compound,
     CompoundStructure,
     Edge,
+    EnzymeLink,
+    Group,
     License,
     Node,
     ParallelRule,
@@ -150,6 +152,8 @@ class ReactionExportSchema(RefReactionExportSchema):
 # Rules #
 #########
 class EnzymeExportSchema(RefEnzymeExportSchema):
+    name: str
+    description: str
     ec_number: str
     classification_level: int
     linking_method: str
@@ -162,12 +166,12 @@ class EnzymeRuleExportSchema(RefRuleExportSchema):
 
     @staticmethod
     def resolve_enzymes(obj):
-        if isinstance(obj, dict):
-            res = []
-            for e in obj.get("enzymes", []):
-                res.append(EnzymeExportSchema.model_validate(e))
-            return res
-        return obj.enzymelink_set.all()
+        if isinstance(obj, EnzymeRuleExportSchema):
+            return obj.enzymes
+        elif isinstance(obj, dict):
+            return obj.get("enzymes", [])
+        else:
+            return obj.enzymelink_set.all()
 
 
 class RuleExportSchema(EnzymeRuleExportSchema):
@@ -679,6 +683,27 @@ class PackageImporter:
                 for scen in elem.scenarios:
                     elem_obj.scenarios.add(self._cache[scen.uuid])
 
+    def _import_enzyme(self, rule: Rule, enzyme: EnzymeExportSchema):
+        e = EnzymeLink()
+        e.uuid = str(uuid.uuid4()) if not self.preserve_uuids else enzyme.uuid
+        e.rule = rule
+        e.name = enzyme.name
+        e.description = enzyme.description
+        e.ec_number = enzyme.ec_number
+        e.classification_level = enzyme.classification_level
+        e.linking_method = enzyme.linking_method
+        e.save()
+        for reaction in enzyme.reaction_evidence:
+            e.reaction_evidence.add(self._cache[reaction.uuid])
+        for edge in enzyme.edge_evidence:
+            e.edge_evidence.add(self._cache[edge.uuid])
+        self._cache[enzyme.uuid] = e
+
+    def _import_and_link_enzymes(self, data: PackageExportSchema):
+        for rule in data.composite_rules:
+            for enzyme in rule.enzymes:
+                self._import_enzyme(self._cache[rule.uuid], enzyme)
+
     def _import_package_from_json(
         self,
     ) -> Package:
@@ -717,6 +742,7 @@ class PackageImporter:
         self._import_scenarios(package, parsed.scenarios)
         self._import_additional_information(package, parsed.additional_information)
         self._link_scenarios_after_import(parsed)
+        self._import_and_link_enzymes(parsed)
 
         return package