Use pmids instead of pubmeds

src/indra_cogex/client/queries.py

@@ -41,7 +41,7 @@
     "get_evidences_for_stmt_hash",
     "get_evidences_for_stmt_hashes",
     "get_stmts_for_paper",
-    "get_stmts_for_pubmeds",
+    "get_stmts_for_pmids",
     "get_stmts_for_mesh",
     "get_stmts_meta_for_stmt_hashes",
     "get_stmts_for_stmt_hashes",
@@ -955,16 +955,16 @@ def get_stmts_for_paper(
 
 
 @autoclient()
-def get_stmts_for_pubmeds(
-    pubmeds: List[Union[str, int]], *, client: Neo4jClient, **kwargs
+def get_stmts_for_pmids(
+    pmids: List[Union[str, int]], *, client: Neo4jClient, **kwargs
 ) -> List[Statement]:
     """Return the statements with evidence from the given PubMed IDs.
 
     Parameters
     ----------
     client :
         The Neo4j client.
-    pubmeds :
+    pmids :
         The PMIDs to query
 
     Returns
@@ -976,15 +976,15 @@ def get_stmts_for_pubmeds(
     -------
     .. code-block::
 
-        from indra_cogex.client.queries import get_stmts_for_pubmeds
+        from indra_cogex.client.queries import get_stmts_for_pmids
 
-        pubmeds = [20861832, 19503834]
-        stmts = get_stmts_for_pubmeds(pubmeds)
+        pmids = [20861832, 19503834]
+        stmts = get_stmts_for_pmids(pmids)
     """
-    pubmeds = sorted(f"pubmed:{pubmed}" for pubmed in pubmeds)
+    pmids = sorted(f"pubmed:{pmid}" for pmid in pmids)
     hash_query = f"""\
         MATCH (e:Evidence)-[:has_citation]->(p:Publication)
-        WHERE p.id IN {repr(pubmeds)}
+        WHERE p.id IN {repr(pmids)}
         RETURN e.stmt_hash, e.evidence
     """
     result = client.query_tx(hash_query)

tests/test_queries.py

@@ -324,11 +324,11 @@ def test_get_stmts_for_pmid():
 
 
 @pytest.mark.nonpublic
-def test_get_stmts_for_pmid():
+def test_get_stmts_for_pmids():
     # Two queries: first evidences, then the statements
     client = _get_client()
-    pubmeds = ["14898026"]
-    stmts = get_stmts_for_pubmeds(pubmeds, client=client)
+    pmids = ["14898026"]
+    stmts = get_stmts_for_pmids(pmids, client=client)
     assert stmts
     assert isinstance(stmts[0], Statement)