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

@@ -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":