ESCKAN-65 - get entities in the journey as part of serializer export

backend/composer/api/serializers.py

@@ -516,6 +516,7 @@ class ConnectivityStatementSerializer(BaseConnectivityStatementSerializer):
     )
     available_transitions = serializers.SerializerMethodField()
     journey = serializers.SerializerMethodField()
+    entities_journey = serializers.SerializerMethodField()    
     statement_preview = serializers.SerializerMethodField()
     errors = serializers.SerializerMethodField()
 
@@ -528,6 +529,10 @@ def get_journey(self, instance):
         if 'journey' not in self.context:
             self.context['journey'] = instance.get_journey()
         return self.context['journey']
+
+    def get_entities_journey(self, instance):
+        self.context['entities_journey'] = instance.get_entities_journey()
+        return self.context['entities_journey']
 
     def get_statement_preview(self, instance):
         if 'journey' not in self.context:
@@ -630,6 +635,7 @@ class Meta(BaseConnectivityStatementSerializer.Meta):
             "projection_phenotype",
             "projection_phenotype_id",
             "journey",
+            "entities_journey",
             "laterality",
             "projection",
             "circuit_type",
@@ -722,6 +728,7 @@ class Meta(ConnectivityStatementSerializer.Meta):
             "provenances",
             "knowledge_statement",
             "journey",
+            "entities_journey",
             "laterality",
             "projection",
             "circuit_type",

backend/composer/models.py

@@ -21,7 +21,7 @@
     ViaType,
     Projection,
 )
-from .services.graph_service import compile_journey
+from .services.graph_service import compile_journey, compile_entities_name
 from .utils import doi_uri, pmcid_uri, pmid_uri, create_reference_uri
 
 
@@ -663,7 +663,11 @@ 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)
+        return compile_journey(self)['journey']
+
+    def get_entities_journey(self):
+        entities_journey = compile_journey(self)['entities']
+        return entities_journey
 
     def get_laterality_description(self):
         laterality_map = {

backend/composer/services/graph_service.py

@@ -88,7 +88,7 @@ def consolidate_paths(paths):
 
         paths = consolidated + [paths[i] for i in range(len(paths)) if i not in used_indices]
 
-    return [[((node[0].replace(JOURNEY_DELIMITER, ' or '), node[1]) if (
+    return paths, [[((node[0].replace(JOURNEY_DELIMITER, ' or '), node[1]) if (
             node[1] == 0 or path.index(node) == len(path) - 1) else (
         node[0].replace(JOURNEY_DELIMITER, ', '), node[1])) for node in path] for path in paths]
 
@@ -132,7 +132,7 @@ def merge_paths(path1, path2):
     return merged_path
 
 
-def compile_journey(connectivity_statement) -> List[str]:
+def compile_journey(connectivity_statement) -> dict:
     """
    Generates a string of descriptions of journey paths for a given connectivity statement.
 
@@ -153,7 +153,16 @@ def compile_journey(connectivity_statement) -> List[str]:
 
     # Generate all paths and then consolidate them
     all_paths = generate_paths(origins, vias, destinations)
-    journey_paths = consolidate_paths(all_paths)
+    consolidated_paths, journey_paths = consolidate_paths(all_paths)
+
+    entities = []
+    for path in consolidated_paths:
+        entity = {
+            'origins': path[0][0].split(JOURNEY_DELIMITER),
+            'destinations': path[-1][0].split(JOURNEY_DELIMITER),
+            'vias': [node for node, layer in path if 0 < layer < len(vias) + 1]
+        }
+        entities.append(entity)
 
     # Create sentences for each journey path
     journey_descriptions = []
@@ -169,4 +178,7 @@ def compile_journey(connectivity_statement) -> List[str]:
 
         journey_descriptions.append(sentence)
 
-    return journey_descriptions
+    return {
+        'journey': journey_descriptions,
+        'entities': entities
+    }