Log info about dryrun

NBISweden · Mar 5, 2019 · 3b8f11a · 3b8f11a
1 parent c9e5af5
commit 3b8f11a
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Showing 2 changed files with 6 additions and 3 deletions.
diff --git a/scripts/importer/data_importer/raw_data_importer.py b/scripts/importer/data_importer/raw_data_importer.py
@@ -258,13 +258,14 @@ def _insert_coverage(self):
                 db.Coverage.insert_many(batch)
         if self.counter['coverage'] != None:
             self._tick(True)
-        logging.info("Inserted {} coverage records in {}".format(counter, self._time_since(start)))
+        if not self.settings.dry_run:
+            logging.info("Inserted {} coverage records in {}".format(counter, self._time_since(start)))
 
     def _insert_variants(self):
         """
         Insert variants from a VCF file
         """
-        logging.info("Inserting variants")
+        logging.info("Inserting variants%s", " (dry run)" if self.settings.dry_run else "")
         header = [("chrom", str), ("pos", int), ("rsid", str), ("ref", str),
                   ("alt", str), ("site_quality", float), ("filter_string", str)]
         start = time.time()
@@ -440,7 +441,8 @@ def _insert_variants(self):
         self.dataset_version.save()
         if self.counter['variants'] != None:
             self._tick(True)
-        logging.info("Inserted {} variant records in {}".format(counter, self._time_since(start)))
+        if not self.settings.dry_run:
+            logging.info("Inserted {} variant records in {}".format(counter, self._time_since(start)))
 
     def count_entries(self):
         start = time.time()

diff --git a/scripts/importer/importer.py b/scripts/importer/importer.py
@@ -141,6 +141,7 @@
         importer.start_import()
 
     if args.add_raw_data:
+        logging.info("Adding raw data %s", "(dry run)" if args.dry_run else '')
         importer = RawDataImporter(args)
         importer.prepare_data()
         if not args.disable_progress: