diff --git a/ippisite/ippidb/management/commands/import_v1_data.py b/ippisite/ippidb/management/commands/import_v1_data.py index e2dfc077facdae6823dacb688b6649ad46c84030..67b83282921858fab32d01476f8e4dbd584c8eb4 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":