From d31a21c68b1d08c100862ff4f91a114771bfd06b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Thu, 16 Mar 2017 22:34:31 +0100
Subject: [PATCH] migrate proteins and choose migrated models with arguments
# Please enter the commit message for your changes. Lines starting
---
.../management/commands/import_v1_data.py | 67 ++++++++++++++-----
1 file changed, 50 insertions(+), 17 deletions(-)
diff --git a/ippisite/ippidb/management/commands/import_v1_data.py b/ippisite/ippidb/management/commands/import_v1_data.py
index c49cf75e..22a073ef 100644
--- a/ippisite/ippidb/management/commands/import_v1_data.py
+++ b/ippisite/ippidb/management/commands/import_v1_data.py
@@ -1,27 +1,60 @@
from django.core.management import BaseCommand
import mysql.connector
-from ippidb.models import Bibliography
+from ippidb.models import Bibliography, Protein
class Command(BaseCommand):
+
help = "Import data from the local v1 database"
+ def add_arguments(self, parser):
+ parser.add_argument(
+ '--bibliographies',
+ action='store_true',
+ dest='bibliographies',
+ default=False,
+ help='Flush and migrate bibliographies',
+ )
+ parser.add_argument(
+ '--proteins',
+ action='store_true',
+ dest='proteins',
+ default=False,
+ help='Flush and migrate proteins',
+ )
+
def handle(self, *args, **options):
conn = mysql.connector.connect(host="localhost",user="root",password="ippidb", database="ippidb")
cursor = conn.cursor()
- cursor.execute("""SELECT * FROM biblio""")
- rows = cursor.fetchall()
- Bibliography.objects.all().delete()
- self.stdout.write(self.style.SUCCESS('Successfully flushed bibliography table'))
- for row in rows:
- try:
- b = Bibliography()
- if row[1]=='article':
- b.source = 'PM'
+ if options['bibliographies']:
+ cursor.execute("""SELECT * FROM biblio""")
+ rows = cursor.fetchall()
+ Bibliography.objects.all().delete()
+ self.stdout.write(self.style.SUCCESS('Successfully flushed bibliography table'))
+ for row in rows:
+ try:
+ b = Bibliography()
+ if row[1]=='article':
+ b.source = 'PM'
+ else:
+ b.source = 'PT'
+ b.id_source = row[2]
+ b.save()
+ except Exception as e:
+ self.stdout.write(self.style.ERROR('Failed inserting {}'.format(row[2])))
+ else:
+ self.stdout.write(self.style.SUCCESS('Successfully inserted {}'.format(row[2])))
+ if options['proteins']:
+ cursor.execute("""SELECT * FROM protein""")
+ rows = cursor.fetchall()
+ Protein.objects.all().delete()
+ self.stdout.write(self.style.SUCCESS('Successfully flushed protein table'))
+ for row in rows:
+ try:
+ p = Protein()
+ p.uniprot_id = row[1]
+ p.save()
+ except Exception as e:
+ self.stdout.write(self.style.ERROR('Failed inserting {} {}'.format(row[1], row[2])))
else:
- b.source = 'PT'
- b.id_source = row[2]
- b.save()
- except Exception as e:
- self.stdout.write(self.style.ERROR('Failed inserting {}'.format(row[2])))
- else:
- self.stdout.write(self.style.SUCCESS('Successfully inserted {}'.format(row[2])))
+ self.stdout.write(self.style.SUCCESS('Successfully inserted {} {}'.format(row[1], row[2])))
+
--
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