Merge pull request #59 from reactome/export-records-lineendings

export_records.py minor fixes & avoiding CSV CRLF

bin/export_records.py

@@ -49,18 +49,24 @@ def main(records_dir: Path):
             cur.execute(query)
             records = cur.fetchall()
 
+    if len(records) == 0:
+        print("No new records found.")
+        return
+
     latest_timestamp: str = max(row[1] for row in records)
 
     record_file = records_dir / f"records_{latest_timestamp}.csv"
 
     with open(record_file, mode="w", newline="") as file:
-        writer = csv.writer(file)
+        writer = csv.writer(file, lineterminator="\n")
         writer.writerow(["threadId", "createdAt", "name", "type", "output"])
         writer.writerows(records)
 
+    print("Wrote", record_file)
+
 
 if __name__ == "__main__":
     parser = ArgumentParser()
-    parser.add_argument("records_dir", type=Path, default=Path("records"))
+    parser.add_argument("records_dir", type=Path, nargs="?", default=Path("records"))
     args = parser.parse_args()
     main(**vars(args))

src/csv_generator/reactome_generator.py

@@ -29,7 +29,7 @@ def generate_csv(
     data: Neo4jDict = data_fetch_func(connector)
     df: pd.DataFrame = pd.DataFrame(data)
     df["url"] = "https://reactome.org/content/detail/" + df["st_id"]
-    df.to_csv(csv_file_path, index=False)
+    df.to_csv(csv_file_path, index=False, lineterminator="\n")
     return str(csv_file_path)