From 276b0126b610018f036083d8246c44ba45129673 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Wed, 17 May 2017 22:00:55 +0200
Subject: [PATCH] start adding code for migrating data to the new Ppi model
further progress requires to answer question asked in #36
---
ippisite/ippidb/management/commands/import_v1_data.py | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/ippisite/ippidb/management/commands/import_v1_data.py b/ippisite/ippidb/management/commands/import_v1_data.py
index e2dfc077..67b83282 100644
--- a/ippisite/ippidb/management/commands/import_v1_data.py
+++ b/ippisite/ippidb/management/commands/import_v1_data.py
@@ -2,7 +2,7 @@ from django.core.management import BaseCommand, CommandError
import mysql.connector
from ippidb.models import Bibliography, Protein, Taxonomy, MolecularFunction, \
- Domain, ProteinDomainBoundComplex, ProteinDomainPartnerComplex, Symmetry
+ Domain, ProteinDomainBoundComplex, ProteinDomainPartnerComplex, Symmetry, Ppi
class Command(BaseCommand):
@@ -119,12 +119,13 @@ class Command(BaseCommand):
self.stdout.write(self.style.SUCCESS('Successfully inserted {} {}'.format(row[1], row[2])))
if options['complexes']:
sql_request_string = '''
- select distinct protein.NumUniprot, domain.PfamNumAccession , complexe.NbCopy, cmpdAction.IDComplexeBound from bindingSite inner join ppi on (bindingSite.IDBindingSite=ppi.IDBindingSite1) inner join complexe on (ppi.IDComplexe1=complexe.IDComplexe) left outer join cmpdAction on (complexe.IDComplexe=cmpdAction.IDComplexeBound) inner join protein on (bindingSite.IDProtein=protein.IDProtein) inner join domain on (bindingSite.IDDomain=domain.IDDomain) union select distinct protein.NumUniprot, domain.PfamNumAccession , complexe.NbCopy, cmpdAction.IDComplexeBound from bindingSite inner join ppi on (bindingSite.IDBindingSite=ppi.IDBindingSite2) inner join complexe on (ppi.IDComplexe2=complexe.IDComplexe) left outer join cmpdAction on (complexe.IDComplexe=cmpdAction.IDComplexeBound) inner join protein on (bindingSite.IDProtein=protein.IDProtein) inner join domain on (bindingSite.IDDomain=domain.IDDomain)'''
+ select distinct protein.NumUniprot, domain.PfamNumAccession , complexe.NbCopy, cmpdAction.IDComplexeBound, bindingSiteEvidence.CodePDB from bindingSite inner join ppi on (bindingSite.IDBindingSite=ppi.IDBindingSite1) inner join complexe on (ppi.IDComplexe1=complexe.IDComplexe) left outer join cmpdAction on (complexe.IDComplexe=cmpdAction.IDComplexeBound) inner join protein on (bindingSite.IDProtein=protein.IDProtein) inner join domain on (bindingSite.IDDomain=domain.IDDomain) union select distinct protein.NumUniprot, domain.PfamNumAccession , complexe.NbCopy, cmpdAction.IDComplexeBound from bindingSite inner join ppi on (bindingSite.IDBindingSite=ppi.IDBindingSite2) inner join complexe on (ppi.IDComplexe2=complexe.IDComplexe) left outer join cmpdAction on (complexe.IDComplexe=cmpdAction.IDComplexeBound) inner join protein on (bindingSite.IDProtein=protein.IDProtein) inner join domain on (bindingSite.IDDomain=domain.IDDomain) left outer join bindingSiteEvidence on (ppi.IDPPI=bindingSiteEvidence.IDPPI)'''
cursor.execute(sql_request_string)
rows = cursor.fetchall()
ProteinDomainBoundComplex.objects.all().delete()
ProteinDomainPartnerComplex.objects.all().delete()
- self.stdout.write(self.style.SUCCESS('Successfully flushed protein domain complex tables'))
+ Ppi.objects.all().delete()
+ self.stdout.write(self.style.SUCCESS('Successfully flushed protein domain complex tables and Ppi'))
for row in rows:
try:
if row[3]=="null":
--
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