From 4a64906acf74986c1a0f738aaccdcb517f9b7c04 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Thu, 23 Mar 2017 21:42:30 +0100
Subject: [PATCH] add stoponfail option for protein import
---
.../management/commands/import_v1_data.py | 17 +++++++++++++++--
1 file changed, 15 insertions(+), 2 deletions(-)
diff --git a/ippisite/ippidb/management/commands/import_v1_data.py b/ippisite/ippidb/management/commands/import_v1_data.py
index ee2da525..8820aca4 100644
--- a/ippisite/ippidb/management/commands/import_v1_data.py
+++ b/ippisite/ippidb/management/commands/import_v1_data.py
@@ -1,4 +1,4 @@
-from django.core.management import BaseCommand
+from django.core.management import BaseCommand, CommandError
import mysql.connector
from ippidb.models import Bibliography, Protein, Taxonomy
@@ -22,6 +22,14 @@ class Command(BaseCommand):
default=False,
help='Flush and migrate proteins',
)
+ parser.add_argument(
+ '--stoponfail',
+ action='store_true',
+ dest='stoponfail',
+ default=False,
+ help='Stop on fail',
+ )
+
def handle(self, *args, **options):
conn = mysql.connector.connect(host="localhost",user="root",password="ippidb", database="ippidb")
@@ -57,7 +65,12 @@ class Command(BaseCommand):
p.uniprot_id = row[1]
p.save()
except Exception as e:
- self.stdout.write(self.style.ERROR('Failed inserting {} {}'.format(row[1], row[2])))
+ if options['stoponfail']:
+ import traceback
+ self.stderr.write(traceback.format_exc())
+ raise CommandError('Failed inserting {} {}'.format(row[1], row[2]))
+ else:
+ self.stdout.write(self.style.ERROR('Failed inserting {} {}'.format(row[1], row[2])))
else:
self.stdout.write(self.style.SUCCESS('Successfully inserted {} {}'.format(row[1], row[2])))
--
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