Feature/sckan 284 (#262)

* SCKAN-284 chore: Update tests

* SCKAN-284 feat: Replace placeholder data for Origin widget

* SCKAN-284 fix: Update journey calculation to work with implicit from_entities

backend/composer/services/graph_service.py

@@ -45,14 +45,14 @@ def create_paths_from_origin(origin, vias, destinations, current_path, destinati
         # This checks if the last node in the current path is one of the nodes that can lead to the current via.
         # In other words, it checks if there is a valid connection
         # from the last node in the current path to the current via.
-        if current_path[-1][0] in list(
-                a.name for a in current_via.from_entities.all()) or not current_via.from_entities.exists():
+        if (current_path[-1][0] in list(a.name for a in current_via.from_entities.all())
+                or (not current_via.from_entities.exists() and current_path[-1][1] == via_layer - 1)):
             for entity in current_via.anatomical_entities.all():
                 # Build new sub-paths including the current via entity
                 new_sub_path = current_path + [(entity.name, via_layer)]
                 # Recursively call to build paths from the next vias
-                new_paths.extend(
-                    create_paths_from_origin(origin, vias[idx + 1:], destinations, new_sub_path, destination_layer))
+                new_paths.extend(create_paths_from_origin(origin, vias[idx + 1:], destinations,
+                                                          new_sub_path, destination_layer))
 
                 # Check for direct connections to destinations from the current via
                 for dest in destinations:

backend/tests/models/test_vias.py

@@ -1,5 +1,6 @@
 from django.test import TestCase
-from composer.models import ConnectivityStatement, Via, Sentence, AnatomicalEntity
+from composer.models import ConnectivityStatement, Via, Sentence, AnatomicalEntity, AnatomicalEntityMeta
+
 
 class ViaModelTestCase(TestCase):
 
@@ -44,7 +45,8 @@ def test_via_deletion_updates_order(self):
 
     def test_via_order_change_clears_from_entities(self):
         statement, initial_vias = self.create_initial_state()
-        anatomical_entity = AnatomicalEntity.objects.create(name="Test Entity")
+        anatomical_entity_meta = AnatomicalEntityMeta.objects.create(name="Test Entity")
+        anatomical_entity = AnatomicalEntity.objects.create(simple_entity=anatomical_entity_meta)
 
         for via in initial_vias:
             via.from_entities.add(anatomical_entity)

backend/tests/test_journey.py

@@ -1,22 +1,32 @@
 from django.db import connection
 from django.test import TestCase, override_settings
 
-from composer.models import Sentence, ConnectivityStatement, AnatomicalEntity, Via, Destination
+from composer.models import Sentence, ConnectivityStatement, AnatomicalEntity, AnatomicalEntityMeta, Via, Destination
 from composer.services.graph_service import generate_paths, consolidate_paths
 
 
 @override_settings(DEBUG=True)
 class JourneyTestCase(TestCase):
 
+    def setUp(self):
+        self.created_entities = {}
+
+    def create_or_get_anatomical_entity(self, name):
+        if name not in self.created_entities:
+            meta, _ = AnatomicalEntityMeta.objects.get_or_create(name=name, ontology_uri=name)
+            entity, _ = AnatomicalEntity.objects.get_or_create(simple_entity=meta)
+            self.created_entities[name] = entity
+        return self.created_entities[name]
+
     def test_journey_simple_graph_with_jump(self):
         # Test setup
         sentence = Sentence.objects.create()
         cs = ConnectivityStatement.objects.create(sentence=sentence)
 
-        origin1 = AnatomicalEntity.objects.create(name='Oa')
-        origin2 = AnatomicalEntity.objects.create(name='Ob')
-        via1 = AnatomicalEntity.objects.create(name='V1a')
-        destination1 = AnatomicalEntity.objects.create(name='Da')
+        origin1 = self.create_or_get_anatomical_entity("Oa")
+        origin2 = self.create_or_get_anatomical_entity("Ob")
+        via1 = self.create_or_get_anatomical_entity('V1a')
+        destination1 = self.create_or_get_anatomical_entity('Da')
 
         cs.origins.add(origin1, origin2)
 
@@ -42,10 +52,7 @@ def test_journey_simple_graph_with_jump(self):
             [('Ob', 0), ('Da', 2)]
         ]
 
-        initial_query_count = len(connection.queries)
         all_paths = generate_paths(origins, vias, destinations)
-        new_query_count = len(connection.queries) - initial_query_count
-        self.assertTrue(new_query_count == 0)
 
         all_paths.sort()
         expected_paths.sort()
@@ -70,9 +77,9 @@ def test_journey_simple_direct_graph(self):
         cs = ConnectivityStatement.objects.create(sentence=sentence)
 
         # Create Anatomical Entities
-        origin1 = AnatomicalEntity.objects.create(name='Oa')
-        origin2 = AnatomicalEntity.objects.create(name='Ob')
-        destination1 = AnatomicalEntity.objects.create(name='Da')
+        origin1 = self.create_or_get_anatomical_entity("Oa")
+        origin2 = self.create_or_get_anatomical_entity("Ob")
+        destination1 = self.create_or_get_anatomical_entity('Da')
 
         # Add origins
         cs.origins.add(origin1, origin2)
@@ -115,10 +122,10 @@ def test_journey_simple_graph_no_jumps(self):
         cs = ConnectivityStatement.objects.create(sentence=sentence)
 
         # Create Anatomical Entities
-        origin1 = AnatomicalEntity.objects.create(name='Oa')
-        origin2 = AnatomicalEntity.objects.create(name='Ob')
-        via1 = AnatomicalEntity.objects.create(name='V1a')
-        destination1 = AnatomicalEntity.objects.create(name='Da')
+        origin1 = self.create_or_get_anatomical_entity("Oa")
+        origin2 = self.create_or_get_anatomical_entity("Ob")
+        via1 = self.create_or_get_anatomical_entity('V1a')
+        destination1 = self.create_or_get_anatomical_entity('Da')
 
         # Add origins
         cs.origins.add(origin1, origin2)
@@ -170,11 +177,11 @@ def test_journey_multiple_vias_no_jumps(self):
         cs = ConnectivityStatement.objects.create(sentence=sentence)
 
         # Create Anatomical Entities
-        origin1 = AnatomicalEntity.objects.create(name='Oa')
-        origin2 = AnatomicalEntity.objects.create(name='Ob')
-        via1 = AnatomicalEntity.objects.create(name='V1a')
-        via2 = AnatomicalEntity.objects.create(name='V1b')
-        destination1 = AnatomicalEntity.objects.create(name='Da')
+        origin1 = self.create_or_get_anatomical_entity("Oa")
+        origin2 = self.create_or_get_anatomical_entity("Ob")
+        via1 = self.create_or_get_anatomical_entity('V1a')
+        via2 = self.create_or_get_anatomical_entity('V1b')
+        destination1 = self.create_or_get_anatomical_entity('Da')
 
         # Add origins
         cs.origins.add(origin1, origin2)
@@ -232,15 +239,14 @@ def test_journey_complex_graph(self):
         sentence = Sentence.objects.create()
         cs = ConnectivityStatement.objects.create(sentence=sentence)
 
-        # Create Anatomical Entities
-        origin_a = AnatomicalEntity.objects.create(name='Oa')
-        origin_b = AnatomicalEntity.objects.create(name='Ob')
-        via1_a = AnatomicalEntity.objects.create(name='V1a')
-        via2_a = AnatomicalEntity.objects.create(name='V2a')
-        via2_b = AnatomicalEntity.objects.create(name='V2b')
-        via3_a = AnatomicalEntity.objects.create(name='V3a')
-        via4_a = AnatomicalEntity.objects.create(name='V4a')
-        destination_a = AnatomicalEntity.objects.create(name='Da')
+        origin_a = self.create_or_get_anatomical_entity("Oa")
+        origin_b = self.create_or_get_anatomical_entity("Ob")
+        via1_a = self.create_or_get_anatomical_entity('V1a')
+        via2_a = self.create_or_get_anatomical_entity('V2a')
+        via2_b = self.create_or_get_anatomical_entity('V2b')
+        via3_a = self.create_or_get_anatomical_entity('V3a')
+        via4_a = self.create_or_get_anatomical_entity('V4a')
+        destination_a = self.create_or_get_anatomical_entity('Da')
 
         # Add origins
         cs.origins.add(origin_a, origin_b)
@@ -304,18 +310,17 @@ def test_journey_complex_graph_2(self):
         sentence = Sentence.objects.create()
         cs = ConnectivityStatement.objects.create(sentence=sentence)
 
-        # Create Anatomical Entities
-        origin_a = AnatomicalEntity.objects.create(name='Oa')
-        origin_b = AnatomicalEntity.objects.create(name='Ob')
-        via1_a = AnatomicalEntity.objects.create(name='V1a')
-        via2_a = AnatomicalEntity.objects.create(name='V2a')
-        via2_b = AnatomicalEntity.objects.create(name='V2b')
-        via3_a = AnatomicalEntity.objects.create(name='V3a')
-        via4_a = AnatomicalEntity.objects.create(name='V4a')
-        via5_a = AnatomicalEntity.objects.create(name='V5a')
-        via5_b = AnatomicalEntity.objects.create(name='V5b')
-        via6_a = AnatomicalEntity.objects.create(name='V6a')
-        destination_a = AnatomicalEntity.objects.create(name='Da')
+        origin_a = self.create_or_get_anatomical_entity("Oa")
+        origin_b = self.create_or_get_anatomical_entity("Ob")
+        via1_a = self.create_or_get_anatomical_entity('V1a')
+        via2_a = self.create_or_get_anatomical_entity('V2a')
+        via2_b = self.create_or_get_anatomical_entity('V2b')
+        via3_a = self.create_or_get_anatomical_entity('V3a')
+        via4_a = self.create_or_get_anatomical_entity('V4a')
+        via5_a = self.create_or_get_anatomical_entity('V5a')
+        via5_b = self.create_or_get_anatomical_entity('V5b')
+        via6_a = self.create_or_get_anatomical_entity('V6a')
+        destination_a = self.create_or_get_anatomical_entity('Da')
 
         # Add origins
         cs.origins.add(origin_a, origin_b)
@@ -405,9 +410,9 @@ def test_journey_cycles(self):
         cs = ConnectivityStatement.objects.create(sentence=sentence)
 
         # Create Anatomical Entities
-        origin1 = AnatomicalEntity.objects.create(name='Oa')
-        origin2 = AnatomicalEntity.objects.create(name='Ob')
-        destination1 = AnatomicalEntity.objects.create(name='Da')
+        origin1 = self.create_or_get_anatomical_entity("Oa")
+        origin2 = self.create_or_get_anatomical_entity("Ob")
+        destination1 = self.create_or_get_anatomical_entity('Da')
 
         # Add origins
         cs.origins.add(origin1, origin2)
@@ -459,10 +464,10 @@ def test_journey_nonconsecutive_vias(self):
         sentence = Sentence.objects.create()
         cs = ConnectivityStatement.objects.create(sentence=sentence)
 
-        origin1 = AnatomicalEntity.objects.create(name='Oa')
-        via1 = AnatomicalEntity.objects.create(name='V1a')
-        via2 = AnatomicalEntity.objects.create(name='V2a')
-        destination1 = AnatomicalEntity.objects.create(name='Da')
+        origin1 = self.create_or_get_anatomical_entity("Oa")
+        via1 = self.create_or_get_anatomical_entity('V1a')
+        via2 = self.create_or_get_anatomical_entity("V2a")
+        destination1 = self.create_or_get_anatomical_entity('Da')
 
         cs.origins.add(origin1)
 
@@ -508,3 +513,55 @@ def test_journey_nonconsecutive_vias(self):
         expected_journey.sort()
         self.assertTrue(journey_paths == expected_journey,
                         f"Expected journey {expected_journey}, but found {journey_paths}")
+
+    def test_journey_implicit_from_entities(self):
+        # Test setup
+        sentence = Sentence.objects.create()
+        cs = ConnectivityStatement.objects.create(sentence=sentence)
+
+        origin1 = self.create_or_get_anatomical_entity("Myenteric")
+        via1 = self.create_or_get_anatomical_entity('Longitudinal')
+        via2 = self.create_or_get_anatomical_entity("Serosa")
+        via3 = self.create_or_get_anatomical_entity("lumbar")
+        destination1 = self.create_or_get_anatomical_entity('inferior')
+
+        cs.origins.add(origin1)
+
+        via_a = Via.objects.create(connectivity_statement=cs)
+        via_a.anatomical_entities.add(via1)
+
+        via_b = Via.objects.create(connectivity_statement=cs)
+        via_b.anatomical_entities.add(via2)
+
+        via_c = Via.objects.create(connectivity_statement=cs)
+        via_c.anatomical_entities.add(via3)
+
+        destination = Destination.objects.create(connectivity_statement=cs)
+        destination.anatomical_entities.add(destination1)
+
+        # Prefetch related data
+        origins = list(cs.origins.all())
+        vias = list(
+            Via.objects.filter(connectivity_statement=cs).prefetch_related('anatomical_entities', 'from_entities'))
+        destinations = list(
+            Destination.objects.filter(connectivity_statement=cs).prefetch_related('anatomical_entities',
+                                                                                   'from_entities'))
+
+        expected_paths = [
+            [('Myenteric', 0), ('Longitudinal', 1), ('Serosa', 2), ('lumbar', 3), ('inferior', 4)],
+        ]
+
+        all_paths = generate_paths(origins, vias, destinations)
+
+        all_paths.sort()
+        expected_paths.sort()
+        self.assertTrue(all_paths == expected_paths, f"Expected paths {expected_paths}, but found {all_paths}")
+
+        journey_paths = consolidate_paths(all_paths)
+        expected_journey = [
+            [('Myenteric', 0), ('Longitudinal', 1), ('Serosa', 2), ('lumbar', 3), ('inferior', 4)],
+        ]
+        journey_paths.sort()
+        expected_journey.sort()
+        self.assertTrue(journey_paths == expected_journey,
+                        f"Expected journey {expected_journey}, but found {journey_paths}")

frontend/src/components/ProofingTab/GraphDiagram/Widgets/OriginNodeWidget.tsx

@@ -92,7 +92,7 @@ export const OriginNodeWidget: React.FC<OriginNodeProps> = ({
                                 lineHeight: "1.25rem",
                             }}
                         >
-                            Intermediolateral nucleus of eleventh thoracic segment
+                            {model.name}
                         </Typography>
                         <Typography
                             sx={{