Don't send so many synonyms

strider/compatibility.py

@@ -110,8 +110,6 @@ async def fetch(
             self,
             kp_id: str,
             request: dict,
-            input_prefixes: dict = None,
-            output_prefixes: dict = None,
     ):
         """Wrap fetch with CURIE mapping(s)."""
         request = remove_null_values(request)
@@ -242,44 +240,48 @@ def map_curie(
         data: dict[str, Entity],
         prefixes: dict[str, list[str]],
         logger: logging.Logger = None,
-    ):
-        """Map single CURIE."""
+    ) -> str:
+        """Map a single CURIE to the list of preferred equivalent CURIES.
+
+        1. Find the most-preferred prefix for which the provided CURIE has synonyms.
+        2. Return all synonymous CURIEs that have that prefix.
+        """
         try:
             categories, identifiers = data[curie]
         except KeyError:
             return [curie]
-        prefixes = {
+        # Gather the preferred prefixes for each category, deduplicating while retaining order
+        prefixes = list(dict.fromkeys(
             prefix
             for category in categories
             for prefix in prefixes.get(category, [])
-        }
+        ))
         if not prefixes:
-            # no preferred prefixes for these categories
+            # There are no preferred prefixes for these categories - use the prefixes that Biolink prefers
             logger.debug(
                 "[{}] Cannot not find preferred prefixes for at least one of: {}".format(
                     getattr(logger, "context", ""),
                     categories,
                 )
             )
-            return identifiers
+            prefixes = identifiers[0].split(":")[0]
 
-        # Find CURIEs beginning with any of prefixes
-        prefix_identifiers = [
-            curie
-            for curie in identifiers
-            if any(
-                curie.startswith(prefix)
-                for prefix in prefixes
-            )
-        ]
-        if not prefix_identifiers:
-            # no preferred curie with these prefixes
-            logger.debug(
-                "[{}] Cannot find identifier in {} with a preferred prefix in {}".format(
-                    getattr(logger, "context", ""),
-                    identifiers,
-                    prefixes,
-                ),
-            )
-            return [curie]
-        return prefix_identifiers
+        # Find CURIEs beginning with the most-preferred prefix
+        for prefix in prefixes:
+            curies = [
+                _curie
+                for _curie in identifiers
+                if _curie.startswith(prefix)
+            ]
+            if curies:
+                return curies
+
+        # There is no equivalent CURIE with any of the acceptable prefixes - return the original CURIE
+        logger.debug(
+            "[{}] Cannot find identifier in {} with a preferred prefix in {}".format(
+                getattr(logger, "context", ""),
+                identifiers,
+                prefixes,
+            ),
+        )
+        return [curie]

strider/fetcher.py

@@ -405,8 +405,6 @@ async def setup(
                 details,
                 self.portal,
                 kp_id,
-                self.kp_preferred_prefixes[kp_id],
-                self.preferred_prefixes,
             )
             for kp_id, details in kps.items()
         }

strider/util.py

@@ -193,22 +193,18 @@ async def post_json(url, request, logger, log_name):
 
 class KnowledgeProvider():
     """Knowledge provider."""
-    def __init__(self, details, portal, id, in_prefixes, out_prefixes, *args, **kwargs):
+    def __init__(self, details, portal, id, *args, **kwargs):
         """Initialize."""
         self.details = details
         self.portal = portal
         # self.portal: KnowledgePortal = portal
         self.id = id
-        self.in_prefixes = in_prefixes
-        self.out_prefixes = out_prefixes
 
     async def solve_onehop(self, request):
         """Solve one-hop query."""
         return await self.portal.fetch(
             self.id,
             {"message": {"query_graph": request}},
-            self.in_prefixes,
-            self.out_prefixes,
         )
 
 

tests/helpers/utils.py

@@ -53,7 +53,7 @@ def generate_kps(qty):
         )
     )
 
-    return {str(i): kp for i, kp in enumerate(kp_generator) if i < qty}
+    return {str(i): kp for i, kp in zip(range(qty), kp_generator)}
 
 
 def query_graph_from_string(s):

tests/test_compatibility.py

@@ -306,8 +306,6 @@ async def test_fetch():
         response = await portal.fetch(
             kp_id="ctd",
             request={"message": {"query_graph": query_graph}},
-            input_prefixes=CTD_PREFIXES,
-            output_prefixes=preferred_prefixes,
         )
 
     allowed_response_prefixes = [