add new fields in migration of TestActivityDescription

fix #27


Former-commit-id: c85e9128b02978d2510d64a04393529fa81ee39e

ippisite/ippidb/management/commands/import_v1_data.py

@@ -227,9 +227,9 @@ class Command(BaseCommand):
                         self.style.SUCCESS('Successfully inserted {} {}'.format(row[0], row[1])))
         if options['ppi']:
             sql_request_string = '''
-select distinct protein.NumUniprot, domain.PfamNumAccession, complexe.NbCopy, cmpdAction.IDComplexeBound, bindingSiteEvidence.CodePDB, 'part1', ppi.IDPPI, disease.Disease  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) inner join disease on (disease.IDPPI=ppi.IDPPI) left outer join bindingSiteEvidence on (ppi.IDPPI=bindingSiteEvidence.IDPPI)
+select distinct protein.NumUniprot, domain.PfamNumAccession, complexe.NbCopy, cmpdAction.IDComplexeBound, bindingSiteEvidence.CodePDB, 'part1', ppi.IDPPI, disease.Disease, complexe.IDComplexe  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) inner join disease on (disease.IDPPI=ppi.IDPPI) left outer join bindingSiteEvidence on (ppi.IDPPI=bindingSiteEvidence.IDPPI)
 union
-select distinct protein.NumUniprot, domain.PfamNumAccession  , complexe.NbCopy, cmpdAction.IDComplexeBound, null, 'part2', ppi.IDPPI, disease.Disease  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) inner join disease on (disease.IDPPI=ppi.IDPPI)'''
+select distinct protein.NumUniprot, domain.PfamNumAccession  , complexe.NbCopy, cmpdAction.IDComplexeBound, null, 'part2', ppi.IDPPI, disease.Disease, complexe.IDComplexe  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) inner join disease on (disease.IDPPI=ppi.IDPPI)'''
             cursor.execute(sql_request_string)
             rows = cursor.fetchall()
             ProteinDomainBoundComplex.objects.all().delete()
@@ -241,6 +241,7 @@ select distinct protein.NumUniprot, domain.PfamNumAccession  , complexe.NbCopy,
             self.stdout.write(
                 self.style.SUCCESS('Successfully flushed protein domain complex, PPI, compound actions, and disease tables'))
             ppi_ids_mapping = {}
+            protein_domain_bound_complexes_mapping = {}
             for row in rows:
                 try:
                     # create or retrieve Ppi object
@@ -270,6 +271,9 @@ select distinct protein.NumUniprot, domain.PfamNumAccession  , complexe.NbCopy,
                     if isinstance(c, ProteinDomainBoundComplex):
                         c.ppp_copy_nb_per_p = 1
                     c.save()
+                    # save ProteinDomainBoundComplex/source ID in 'complexe' table
+                    if row[3] is not None: 
+                        protein_domain_bound_complexes_mapping[row[8]] = c
                     # create the PpiComplex object
                     ppi_complex = PpiComplex()
                     ppi_complex.ppi = ppi
@@ -330,8 +334,14 @@ select distinct protein.NumUniprot, domain.PfamNumAccession  , complexe.NbCopy,
                     biblio_row = cursor.fetchone()
                     biblio = Bibliography.objects.get(id_source=biblio_row[0])
                     tad.biblio = biblio
+                    tad.protein_domain_bound_complex = protein_domain_bound_complexes_mapping[row[1]]
                     tad.ppi = Ppi.objects.get(id=ppi_ids_mapping[row[3]])
                     tad.test_name = row[4]
+                    tad.is_primary = row[5]=='Y'
+                    if row[6]=='Unspecified':
+                        tad.protein_bound_construct = 'U'
+                    elif row[6]=='Full length':
+                        tad.protein_bound_construct = 'F'
                     tad.test_type = row[7].upper()
                     tad.test_modulation_type = row[8][0]
                     tad.nb_active_compounds = row[9]