Merge pull request #52 from BackofenLab/workNico

correct issues happend by rebasing master onto workNico

backend/src/enrichment.py

@@ -83,6 +83,7 @@ def functional_enrichment(driver: neo4j.Driver, in_genes, species_id: Any):
     csv.field_size_limit(sys.maxsize)
 
     # Read Terms and put into Dataframe
+    df_terms = pd.DataFrame(queries.get_enrichment_terms(driver, species_id))
     tot_tests = len(df_terms)
 
     stopwatch.round("setup_enrichment")
@@ -134,4 +135,4 @@ def functional_enrichment(driver: neo4j.Driver, in_genes, species_id: Any):
 
     stopwatch.round("fdr_enrichment")
     stopwatch.total("functional_enrichment")
-    return df_terms
+    return df_terms

backend/src/main.py

@@ -19,7 +19,6 @@
 import queries
 import signal
 from util.stopwatch import Stopwatch
-import g4f, asyncio
 
 app = Flask(__name__)
 
@@ -74,6 +73,7 @@ def proteins_enrichment():
     json_str = json.dumps(list_enrichment.to_dict("records"), ensure_ascii=False, separators=(",", ":"))
     return Response(json_str, mimetype="application/json")
 
+
 # ====================== Subgraph API ======================
 # request comes from home.js
 # TODO Refactor this
@@ -110,7 +110,6 @@ def proteins_subgraph_api():
         pd.DataFrame(proteins).rename(columns={"ENSEMBL_PROTEIN": "external_id"}).drop_duplicates(subset="external_id")
     )
 
-
     edges = pd.DataFrame({"source": source, "target": target, "score": score})
     edges = edges.drop_duplicates(subset=["source", "target"])
 
@@ -253,4 +252,4 @@ def run_flask():
 if __name__ == "__main__":
     signal.signal(signal.SIGINT, signal_handler)
     flask_process = Process(target=run_flask)
-    flask_process.start()
+    flask_process.start()

backend/src/queries.py

@@ -111,6 +111,7 @@ def get_protein_associations(
         result = session.run(query)
         return _convert_to_connection_info_score(result=result, _int=True, protein=True)
 
+
 def get_enrichment_terms(driver: neo4j.Driver, species_id: int) -> list[dict[str, Any]]:
     if species_id == 10090:
         species = "Mus_Musculus"
@@ -185,4 +186,4 @@ def _convert_to_connection_info_score(
         else:
             score.append(float(row["score"]))
 
-    return nodes, source, target, score
+    return nodes, source, target, score