Fix name lookup

biopragmatics · Apr 11, 2024 · c973e79 · c973e79
1 parent 87a444b
commit c973e79
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Showing 2 changed files with 9 additions and 10 deletions.
diff --git a/src/semra/client.py b/src/semra/client.py
@@ -17,7 +17,6 @@
 
 import semra
 from semra import Evidence, MappingSet, Reference
-from semra.io import _get_name_by_curie
 from semra.rules import RELATIONS
 
 __all__ = [
@@ -42,12 +41,12 @@ def _safe_curie(curie_or_luid: ReferenceHint, prefix: str) -> str:
     return f"{prefix}:{curie_or_luid}"
 
 
-#: A cypher query that if it returns a result signifies that there are concept names in the database
-HAS_NAMES_CYPHER = "MATCH (n:concept) WHERE n.name is not null RETURN n LIMIT 1"
-
 #: A cypher query that gets all of the databases' relation types
 RELATIONS_CYPHER = "CALL db.relationshipTypes() YIELD relationshipType RETURN relationshipType"
 
+#: A cypher query format string for getting the name of a concept
+CONCEPT_NAME_CYPHER = "MATCH (n:concept) WHERE n.curie = $curie RETURN n.name LIMIT 1"
+
 
 class Neo4jClient:
     """A client to Neo4j."""
@@ -76,7 +75,6 @@ def __init__(
         self._rel_q = "|".join(
             f"`{reference.curie}`" for reference in RELATIONS if reference.curie in self._all_relations
         )
-        self._database_has_names = len(self.read_query(HAS_NAMES_CYPHER)) > 1
 
     def __del__(self):
         """Ensure driver is shut down when client is destroyed."""
@@ -330,11 +328,12 @@ def get_concept_name(self, curie: ReferenceHint) -> str | None:
         """Get the name for a CURIE or reference."""
         if isinstance(curie, Reference):
             curie = curie.curie
-        if not self._database_has_names:
-            # return _get_name_by_curie(curie)
+        try:
+            name = self.read_query(CONCEPT_NAME_CYPHER, curie=curie)[0][0]
+        except Exception:
             return None
-        query = "MATCH (n:concept) WHERE n.curie = $curie RETURN n.name"
-        return self.read_query(query)[0][0]
+        else:
+            return name
 
     def sample_mappings_from_set(self, curie: ReferenceHint, n: int = 10) -> t.List:
         """Get n mappings from a given set (by CURIE)."""

diff --git a/src/semra/templates/concept.html b/src/semra/templates/concept.html
@@ -78,7 +78,7 @@
         <div class="card">
             <div class="card-body">
                 <h5 class="card-title">
-                    {{ name }} <a class="badge badge-info" href="https://bioregistry.io/{{ curie }}">{{ curie }}</a>
+                    {{ name }} <a class="badge badge-info" href="https://bioregistry.io/{{ curie }}"><code>{{ curie }}</code></a>
                 </h5>
                 <h6>Exact Matches</h6>
             </div>