From 1808807bb13cee8d658c7dc3fc43c56052cf3480 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Thu, 18 May 2017 22:38:54 +0200
Subject: [PATCH] start script options for migration of Compound
(start working on #18)
---
.../management/commands/import_v1_data.py | 34 +++++++++++++++++--
1 file changed, 32 insertions(+), 2 deletions(-)
diff --git a/ippisite/ippidb/management/commands/import_v1_data.py b/ippisite/ippidb/management/commands/import_v1_data.py
index 704eed48..acbf3758 100644
--- a/ippisite/ippidb/management/commands/import_v1_data.py
+++ b/ippisite/ippidb/management/commands/import_v1_data.py
@@ -2,7 +2,8 @@ from django.core.management import BaseCommand, CommandError
import mysql.connector
from ippidb.models import Bibliography, Protein, Taxonomy, MolecularFunction, \
- Domain, ProteinDomainBoundComplex, ProteinDomainPartnerComplex, Symmetry, Ppi, PpiComplex, Disease
+ Domain, ProteinDomainBoundComplex, ProteinDomainPartnerComplex, Symmetry, Ppi, PpiComplex, Disease, \
+ Compound
class Command(BaseCommand):
@@ -44,6 +45,13 @@ class Command(BaseCommand):
default=False,
help='Flush and migrate ppis and complexes',
)
+ parser.add_argument(
+ '--compound',
+ action='store_true',
+ dest='compound',
+ default=False,
+ help='Flush and migrate compounds',
+ )
parser.add_argument(
'--stoponfail',
action='store_true',
@@ -203,4 +211,26 @@ select distinct protein.NumUniprot, domain.PfamNumAccession , complexe.NbCopy,
self.stdout.write(self.style.ERROR('Failed inserting {} {}'.format(row[0], row[1])))
else:
self.stdout.write(self.style.SUCCESS('Successfully inserted {} {}'.format(row[0], row[1])))
-
+ if options['compound']:
+ cursor.execute("""SELECT * FROM compound""")
+ rows = cursor.fetchall()
+ Compound.objects.all().delete()
+ self.stdout.write(self.style.SUCCESS('Successfully flushed compound table'))
+ for row in rows:
+ try:
+ compound = Compound()
+ compound.canonical_smile = row[1]
+ compound.is_macrocycle = (row[4]=='Y')
+ compound.aromatic_ratio = row[5]
+ compound.balaban_index = row[6]
+ compound.balaban_index = row[6]
+ compound.save()
+ except Exception as e:
+ 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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