added age <3

core/age.py

@@ -0,0 +1,99 @@
+from contextlib import contextmanager
+from django.db import connections
+from core import models
+
+
+@contextmanager
+def graph_cursor():
+    with connections["default"].cursor() as cursor:
+        cursor.execute("LOAD 'age';")
+        cursor.execute('SET search_path = ag_catalog, "$user", public')
+        yield cursor
+
+
+def create_age_ontology(name: str):
+    with graph_cursor() as cursor:
+        cursor.execute(
+            "SELECT EXISTS(SELECT 1 FROM ag_catalog.ag_graph WHERE name = %s);",
+            [name]
+        )
+        exists = cursor.fetchone()[0]
+        if exists:
+            return exists
+        else:
+            cursor.execute(
+                "SELECT create_graph(%s);",
+                [name]
+            )
+            print(cursor.fetchone())
+
+
+def create_age_entity_kind(graph_name, kind_name):
+    with graph_cursor() as cursor:
+            try:
+                cursor.execute(
+                    "SELECT create_vlabel(%s, %s);",
+                    (graph_name, kind_name)
+                )
+                print(cursor.fetchone())
+            except Exception as e:
+                print(e)
+
+
+def create_age_relation_kind(graph_name, kind_name):
+    with graph_cursor() as cursor:
+            try:
+                cursor.execute(
+                    "SELECT create_elabel(%s, %s);",
+                    (graph_name, kind_name)
+                )
+                print(cursor.fetchone())
+            except Exception as e:
+                print(e)
+
+
+def create_age_entity(graph_name, kind_name, entity_id):
+    with graph_cursor() as cursor:
+        cursor.execute(
+            f"""
+            SELECT * 
+            FROM cypher(%s, $$
+                CREATE (n:{kind_name})
+                RETURN n.id
+            $$) as (id agtype);
+            """,
+            (graph_name,)
+        )
+        print(cursor.fetchone())
+
+
+
+def create_age_relation(relation_kind: models.EntityRelationKind, left_id, right_id):
+    with graph_cursor() as cursor:
+        cursor.execute(
+            f"""
+            SELECT * 
+            FROM cypher(%s, $$
+                MATCH (a:{relation_kind.left_kind.age_name} {{id: %s}})
+                MATCH (b:{relation_kind.right_kind.age_name} {{id: %s}})
+                CREATE (a)-[:{relation_kind.age_name}]->(b)
+            $$) as (id agtype);
+            """,
+            (relation_kind.kind.ontology.age_name, left_id, right_id)
+        )
+        print(cursor.fetchone())
+
+
+def select_all_entities(graph_name):
+    with graph_cursor() as cursor:
+        cursor.execute(
+            f"""
+            SELECT * 
+            FROM cypher(%s, $$
+                MATCH (n)
+                RETURN n.id
+            $$) as (id agtype);
+            """,
+            [graph_name]
+        )
+        print(cursor.fetchall())

core/models.py

@@ -354,6 +354,25 @@ class ProtocolStep(models.Model):
 
 
 
+
+
+
+class Reagent(models.Model):
+    entity_kind = models.ForeignKey("EntityKind", on_delete=models.CASCADE, related_name="reagents", help_text="The associated entity")
+    protocol = models.ForeignKey(
+        Protocol,
+        on_delete=models.CASCADE,
+        null=True,
+        blank=True,
+        related_name="reagents",
+    )
+    volume = models.FloatField(
+        help_text="The volume of the reagent in the protocol",
+        null=True,
+        blank=True,
+    )
+
+
 class Specimen(models.Model):
     entity = models.ForeignKey("Entity", on_delete=models.CASCADE, related_name="specimens", help_text="The associated entity")
     protocol = models.ForeignKey(
@@ -1066,6 +1085,11 @@ class Ontology(models.Model):
 
     def __str__(self) -> str:
         return self.name
+
+
+    @property
+    def age_name(self) -> str:
+        return self.name.replace(" ", "_").lower()
 
 
 
@@ -1093,6 +1117,10 @@ class EntityRelationKind(models.Model):
         help_text="The kind of the relation",
     )
 
+    @property
+    def age_name(self) -> str:
+        return self.kind.label.replace(" ", "_").lower() + "_relation"
+
 
 
 def random_color():
@@ -1155,6 +1183,11 @@ def create_entity(self, group, name: str = None,  instance_kind: str = None, met
     def rgb_color_string(self) -> str:
         return f"rgb({self.color[0]}, {self.color[1]}, {self.color[2]})"
 
+
+    @property
+    def age_name(self) -> str:
+        return self.label.replace(" ", "_").lower()
+
 
 class EntityGroup(models.Model):
     """An EntityGroup is a collection of Entities.

core/mutations/entity.py

@@ -1,6 +1,6 @@
 from kante.types import Info
 import strawberry
-from core import types, models
+from core import types, models, age
 import uuid
 
 
@@ -35,17 +35,22 @@ def create_entity(
     input_kind = models.EntityKind.objects.get(id=input.kind)
 
 
+    id = uuid.uuid4().hex
 
     item, _ = models.Entity.objects.get_or_create(
-        name=input.name or uuid.uuid4().hex,
+        name=id,
         group=group,
         kind=input_kind,
         defaults=dict(
-            name=input.name or uuid.uuid4().hex,
+            name=id,
             instance_kind=input.instance_kind,
         )
     )
 
+    age.create_age_entity(input_kind.ontology.age_name, input_kind.age_name, id)
+
+
+
 
 
     assert item.kind.id == input_kind.id, f"Entity kind mismatch {item.kind} vs {input_kind}"

core/mutations/entity_kind.py

@@ -1,6 +1,7 @@
 from kante.types import Info
 import strawberry
 from core import types, models
+from core import age
 
 
 @strawberry.input
@@ -35,6 +36,10 @@ def create_entity_kind(
             description="Default ontology for {}".format(user.username),)
         )
 
+        age.create_age_ontology(ontology.age_name)
+
+
+
     if input.color:
         assert len(input.color) == 3 or len(input.color) == 4, "Color must be a list of 3 or 4 values RGBA"
 
@@ -46,6 +51,13 @@ def create_entity_kind(
         color=input.color or models.random_color(),
         )
     )
+
+    age.create_age_entity_kind(ontology.age_name, item.age_name)
+
+
+
+
+
     return item
 
 

core/mutations/entity_relation.py

@@ -1,6 +1,6 @@
 from kante.types import Info
 import strawberry
-from core import types, models
+from core import types, models, age
 
 
 @strawberry.input
@@ -32,6 +32,12 @@ def create_entity_relation_kind(
         right_kind=models.EntityKind.objects.get(id=input.right_kind),
         kind=models.EntityKind.objects.get(id=input.kind),
     )
+
+
+    age.create_age_relation_kind(item.kind.ontology.age_name, item.age_name)
+
+
+
     return item
 
 
@@ -40,11 +46,19 @@ def create_entity_relation(
     info: Info,
     input: EntityRelationInput,
 ) -> types.EntityRelation:
+
+    kind = models.EntityRelationKind.objects.get(id=input.kind)
     item, _ = models.EntityRelation.objects.get_or_create(
         left=models.Entity.objects.get(id=input.left),
         right=models.Entity.objects.get(id=input.right),
-        kind=models.EntityRelationKind.objects.get(id=input.kind),
+        kind=kind
     )
+
+    age.create_age_relation(kind, input.left, input.right)
+
+
+
+
     return item
 
 

core/mutations/ontology.py

@@ -1,6 +1,9 @@
 from kante.types import Info
 import strawberry
-from core import types, models
+from core import types, models, age
+from django.db import connections
+from contextlib import contextmanager
+
 
 
 @strawberry.input
@@ -15,18 +18,23 @@ class DeleteOntologyInput:
     id: strawberry.ID
 
 
+def to_snake_case(string):
+    return string.replace(" ", "_").lower()
+
 
 def create_ontology(
     info: Info,
     input: OntologyInput,
 ) -> types.Ontology:
 
     item, _ = models.Ontology.objects.update_or_create(
-        name=input.name,
+        name=to_snake_case(input.name),
         defaults=dict(
         description=input.description or "",
         purl=input.purl)
     )
+
+    age.create_age_ontology(item.name)
 
     return item
 
@@ -35,7 +43,17 @@ def delete_ontology(
     info: Info,
     input: DeleteOntologyInput,
 ) -> strawberry.ID:
-    item = models.Entity.objects.get(id=input.id)
+    item = models.Ontology.objects.get(id=input.id)
+
+
+    with graph_cursor() as cursor:
+        cursor.execute(
+            "SELECT delete_graph(%s);",
+            [item.name]
+        )
+        print(cursor.fetchone())
+
     item.delete()
+
     return input.id
 

core/queries/entity_graph.py

@@ -1,5 +1,5 @@
 import strawberry
-from core import models
+from core import models, age
 
 
 @strawberry.type
@@ -52,6 +52,11 @@ def entity_graph(id: strawberry.ID) -> EntityGraph:
     entity = models.Entity.objects.get(id=id)
 
 
+    print(age.select_all_entities(entity.kind.ontology.age_name))
+
+
+
+
     def parse_entity(entity: models.Entity, is_root=False):
 
         node = EntityNode(id=entity.id, subtitle=entity.name, metrics=[], label=entity.kind.label, is_root=is_root, color=entity.kind.rgb_color_string)

mikro_server/settings.py

@@ -148,6 +148,14 @@
         "PASSWORD": conf.db.password,
         "HOST": conf.db.host,
         "PORT": conf.db.port,
+    },
+    "graph": {
+        "ENGINE": conf.db.engine,
+        "NAME": "mikro_graph",
+        "USER": conf.db.username,
+        "PASSWORD": conf.db.password,
+        "HOST": "age",
+        "PORT": conf.db.port,
     }
 }