Samples: Hook-up external async script to upload the samples.

1 files changed, 7 insertions, 5 deletions

diff --git a/scripts/insert_samples.py b/scripts/insert_samples.py
index 43c6a38..6b6faf1 100644
--- a/scripts/insert_samples.py
+++ b/scripts/insert_samples.py
@@ -42,21 +42,25 @@ def insert_samples(conn: mdb.Connection,# pylint: disable=[too-many-arguments]
                    firstlineheading: bool,
                    quotechar: str):
     """Insert the samples into the database."""
+    print("Checking for errors:")
     species = species_by_id(conn, speciesid)
     if not bool(species):
         logging.error("Species with id '%s' does not exist.", str(speciesid))
         return 1
+    print(f"\tSpecies with ID '{speciesid}' found")
     population = population_by_id(conn, populationid)
     if not bool(population):
         logging.error("Population with id '%s' does not exist.",
                       str(populationid))
         return 1
-    logging.info("Inserting samples ...")
+    print(f"\tPopulations with ID '{populationid}' found")
+    print("No errors found. Continuing...")
+    print("\nInserting samples ...")
     save_samples_data(
         conn,
         speciesid,
         read_samples_file(samplesfile, separator, firstlineheading))
-    logging.info("Cross-referencing samples with their populations.")
+    print("Cross-referencing samples with their populations.")
     cross_reference_samples(
         conn,
         speciesid,
@@ -66,7 +70,7 @@ def insert_samples(conn: mdb.Connection,# pylint: disable=[too-many-arguments]
                            separator,
                            firstlineheading,
                            quotechar=quotechar)))
-
+    print("Samples upload successfully completed.")
     return 0
 
 if __name__ == "__main__":
@@ -133,8 +137,6 @@ if __name__ == "__main__":
 
         with (Redis.from_url(args.redisuri, decode_responses=True) as rconn,
               database_connection(args.databaseuri) as dbconn):
-            print("We got here...")
-            print(args)
             return insert_samples(dbconn,
                                   rconn,
                                   args.speciesid,