fix flake

BioDataFuse · Oct 14, 2024 · 615bbf5 · 615bbf5
1 parent a1b74d4
commit 615bbf5
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Showing 2 changed files with 1 addition and 6 deletions.
diff --git a/src/pyBiodatafuse/annotators/wikipathways.py b/src/pyBiodatafuse/annotators/wikipathways.py
@@ -113,11 +113,6 @@ def get_gene_wikipathways(bridgedb_df: pd.DataFrame):
     intermediate_df = pd.DataFrame()
 
     for gene_list_str in tqdm(query_gene_lists, desc="Querying WikiPathways"):
-        if query_count > 10:
-            print("Sleeping for 5 seconds to avoid overloading the server.")
-            time.sleep(5)
-            query_count = 0
-
         sparql_query_template = Template(sparql_query)
         substit_dict = dict(gene_list=gene_list_str)
         sparql_query_template_sub = sparql_query_template.substitute(substit_dict)

diff --git a/src/pyBiodatafuse/graph/generator.py b/src/pyBiodatafuse/graph/generator.py
@@ -954,7 +954,7 @@ def save_graph(
 
     # Save the graph
     g = build_networkx_graph(combined_df, disease_compound)
-    logger.warning(f"Graph is built successfully")
+    logger.warning("Graph is built successfully")
 
     with open(graph_path_pickle, "wb") as f:
         pickle.dump(g, f)