Feature/sckan-324 - journey computation

backend/composer/api/views.py

@@ -252,20 +252,23 @@ class ModelRetrieveViewSet(
     # mixins.DestroyModelMixin,
     # mixins.ListModelMixin,
     viewsets.GenericViewSet,
-): ...
+):
+    ...
 
 
 class ModelCreateRetrieveViewSet(
     ModelRetrieveViewSet,
     mixins.CreateModelMixin,
     mixins.ListModelMixin,
-): ...
+):
+    ...
 
 
 class ModelNoDeleteViewSet(
     ModelCreateRetrieveViewSet,
     mixins.UpdateModelMixin,
-): ...
+):
+    ...
 
 
 class AnatomicalEntityViewSet(viewsets.ReadOnlyModelViewSet):
@@ -506,7 +509,8 @@ def my(self, request, *args, **kwargs):
             msg = "User not logged in."
             raise ValidationError(msg, code="authorization")
 
-        profile, created = Profile.objects.get_or_create(user=self.request.user)
+        profile, created = Profile.objects.get_or_create(
+            user=self.request.user)
         return Response(self.get_serializer(profile).data)
 
 
@@ -547,6 +551,7 @@ class StatementAlertViewSet(viewsets.ModelViewSet):
     serializer_class = StatementAlertSerializer
     permission_classes = [IsOwnerOfConnectivityStatementOrReadOnly]
 
+
 @extend_schema(
     responses=OpenApiTypes.OBJECT,
 )

backend/composer/migrations/0066_connectivitystatement_journey_path.py

@@ -0,0 +1,18 @@
+# Generated by Django 4.1.4 on 2024-12-18 08:25
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("composer", "0065_alter_statementalert_text"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="connectivitystatement",
+            name="journey_path",
+            field=models.JSONField(blank=True, null=True),
+        ),
+    ]

backend/composer/migrations/0067_auto_20241218_0928.py

@@ -0,0 +1,23 @@
+# Generated by Django 4.1.4 on 2024-12-18 08:28
+
+from django.db import migrations
+from django.db import migrations
+from composer.services.graph_service import compile_journey
+
+
+def update_journey_fields(apps, schema_editor):
+    ConnectivityStatement = apps.get_model('composer', 'ConnectivityStatement')
+    for cs in ConnectivityStatement.objects.all():
+        cs.journey_path = compile_journey(cs)
+        cs.save(update_fields=["journey_path"])
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("composer", "0066_connectivitystatement_journey_path"),
+    ]
+
+    operations = [
+        migrations.RunPython(update_journey_fields),
+    ]

backend/composer/models.py

@@ -4,6 +4,7 @@
 from django.db.models.expressions import F
 from django.forms.widgets import Input as InputWidget
 from django_fsm import FSMField, transition
+from composer.services.graph_service import build_journey_description, build_journey_entities
 
 from composer.services.layers_service import update_from_entities_on_deletion
 from composer.services.state_services import (
@@ -21,7 +22,6 @@
     ViaType,
     Projection,
 )
-from .services.graph_service import compile_journey
 from .utils import doi_uri, pmcid_uri, pmid_uri, create_reference_uri
 
 
@@ -567,6 +567,7 @@ class ConnectivityStatement(models.Model):
     )
     created_date = models.DateTimeField(auto_now_add=True, db_index=True)
     modified_date = models.DateTimeField(auto_now=True, db_index=True)
+    journey_path = models.JSONField(null=True, blank=True)
 
     def __str__(self):
         suffix = ""
@@ -683,11 +684,10 @@ def get_previous_layer_entities(self, via_order):
             return set(self.via_set.get(order=via_order - 1).anatomical_entities.all())
 
     def get_journey(self):
-        return compile_journey(self)['journey']
+        return build_journey_description(self.journey_path, self)
 
     def get_entities_journey(self):
-        entities_journey = compile_journey(self)['entities']
-        return entities_journey
+        return build_journey_entities(self.journey_path, self)
 
     def get_laterality_description(self):
         laterality_map = {
@@ -716,7 +716,6 @@ def save(self, *args, **kwargs):
             self.reference_uri = create_reference_uri(self.pk)
             self.save(update_fields=["reference_uri"])
 
-
     def set_origins(self, origin_ids):
         self.origins.set(origin_ids, clear=True)
         self.save()

backend/composer/services/graph_service.py

@@ -88,9 +88,7 @@ def consolidate_paths(paths):
 
         paths = consolidated + [paths[i] for i in range(len(paths)) if i not in used_indices]
 
-    return paths, [[((node[1].replace(JOURNEY_DELIMITER, ' or '), node[2]) if (
-            node[2] == 0 or path.index(node) == len(path) - 1) else (
-        node[1].replace(JOURNEY_DELIMITER, ', '), node[2])) for node in path] for path in paths]
+    return paths
 
 
 def can_merge(path1, path2):
@@ -144,7 +142,7 @@ def merge_paths(path1, path2):
     return merged_path
 
 
-def compile_journey(connectivity_statement) -> dict:
+def compile_journey(connectivity_statement) -> List[str]:
     """
    Generates a string of descriptions of journey paths for a given connectivity statement.
 
@@ -157,17 +155,55 @@ def compile_journey(connectivity_statement) -> dict:
     # Extract origins, vias, and destinations from the connectivity statement
     Via = apps.get_model('composer', 'Via')
     Destination = apps.get_model('composer', 'Destination')
+    Origin = apps.get_model('composer', 'AnatomicalEntity')
 
-    origins = list(connectivity_statement.origins.all())
-
-    vias = list(Via.objects.filter(connectivity_statement=connectivity_statement))
-    destinations = list(Destination.objects.filter(connectivity_statement=connectivity_statement))
+    vias = list(Via.objects.filter(connectivity_statement__id=connectivity_statement.id))
+    destinations = list(Destination.objects.filter(connectivity_statement__id=connectivity_statement.id))
+    origins = list(Origin.objects.filter(origins_relations__id=connectivity_statement.id).distinct())
+    # origins = list(connectivity_statement.origins.all())
 
     # Generate all paths and then consolidate them
     all_paths2 = generate_paths(origins, vias, destinations)
-    consolidated_paths, journey_paths = consolidate_paths(all_paths2)
+    consolidated_paths = consolidate_paths(all_paths2)
+    return consolidated_paths
+
+
+def get_journey_path_from_consolidated_paths(consolidated_paths):
+    journey_paths = [[((node[1].replace(JOURNEY_DELIMITER, ' or '), node[2]) if (
+        node[2] == 0 or path.index(node) == len(path) - 1) else (
+        node[1].replace(JOURNEY_DELIMITER, ', '), node[2])) for node in path] for path in consolidated_paths]
+    return journey_paths
+
+
+def build_journey_description(consolidated_paths, connectivity_statement):
+    journey_paths = get_journey_path_from_consolidated_paths(
+        consolidated_paths)
+    Via = apps.get_model('composer', 'Via')
+    vias = list(Via.objects.filter(
+        connectivity_statement=connectivity_statement))
+
+    # Create sentences for each journey path
+    journey_descriptions = []
+    for path in journey_paths:
+        origin_names = path[0][0]
+        destination_names = path[-1][0]
+        via_names = ' via '.join([node for node, layer in path if 0 < layer < len(vias) + 1])
+
+        if via_names:
+            sentence = f"from {origin_names} to {destination_names} via {via_names}"
+        else:
+            sentence = f"from {origin_names} to {destination_names}"
 
+        journey_descriptions.append(sentence)
+    return journey_descriptions
+
+
+def build_journey_entities(consolidated_paths, connectivity_statement):
     entities = []
+    Via = apps.get_model('composer', 'Via')
+    vias = list(Via.objects.filter(
+        connectivity_statement=connectivity_statement))
+
     for path in consolidated_paths:
         origin_splits = path[0][0].split(JOURNEY_DELIMITER)
         destination_splits = path[-1][0].split(JOURNEY_DELIMITER)
@@ -181,22 +217,9 @@ def compile_journey(connectivity_statement) -> dict:
             'vias': [{'label': node, 'id': node_id} for node_id, node, layer in path if 0 < layer < len(vias) + 1]
         }
         entities.append(entity)
+    return entities
 
-    # Create sentences for each journey path
-    journey_descriptions = []
-    for path in journey_paths:
-        origin_names = path[0][0]
-        destination_names = path[-1][0]
-        via_names = ' via '.join([node for node, layer in path if 0 < layer < len(vias) + 1])
-
-        if via_names:
-            sentence = f"from {origin_names} to {destination_names} via {via_names}"
-        else:
-            sentence = f"from {origin_names} to {destination_names}"
-
-        journey_descriptions.append(sentence)
 
-    return {
-        'journey': journey_descriptions,
-        'entities': entities
-    }
+def recompile_journey_path(instance):
+    instance.journey_path = compile_journey(instance)
+    instance.save(update_fields=["journey_path"])

backend/composer/signals.py

@@ -19,6 +19,8 @@
     Via,
 )
 from .services.export_services import compute_metrics, ConnectivityStatementStateService
+from .services.graph_service import recompile_journey_path
+
 
 
 @receiver(post_save, sender=ExportBatch)
@@ -101,6 +103,8 @@ def connectivity_statement_origins_changed(sender, instance, action, pk_set, **k
             pass
         except ValueError:
             pass
+        recompile_journey_path(instance)
+
 
     # Call `update_from_entities_on_deletion` for each removed entity
     if action == "post_remove" and pk_set:
@@ -118,6 +122,7 @@ def via_anatomical_entities_changed(sender, instance, action, pk_set, **kwargs):
             pass
         except ValueError:
             pass
+        recompile_journey_path(instance.connectivity_statement)
 
     # Call `update_from_entities_on_deletion` for each removed entity
     if action == "post_remove" and pk_set:
@@ -135,6 +140,8 @@ def via_from_entities_changed(sender, instance, action, **kwargs):
             pass
         except ValueError:
             pass
+        recompile_journey_path(instance.connectivity_statement)
+
 
 
 # Signals for Destination anatomical_entities
@@ -147,6 +154,8 @@ def destination_anatomical_entities_changed(sender, instance, action, **kwargs):
             pass
         except ValueError:
             pass
+        recompile_journey_path(instance.connectivity_statement)
+
 
 
 # Signals for Destination from_entities
@@ -159,6 +168,8 @@ def destination_from_entities_changed(sender, instance, action, **kwargs):
             pass
         except ValueError:
             pass
+        recompile_journey_path(instance.connectivity_statement)
+
 
 
 # Signals for Via model changes