missing contents for commit 3689e89d

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, Ppi, PpiComplex
+    Domain, ProteinDomainBoundComplex, ProteinDomainPartnerComplex, Symmetry, Ppi, PpiComplex, Disease
 
 class Command(BaseCommand):
 
@@ -148,25 +148,29 @@ class Command(BaseCommand):
                     self.stdout.write(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  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) 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  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  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, 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)'''
             cursor.execute(sql_request_string)
             rows = cursor.fetchall()
             ProteinDomainBoundComplex.objects.all().delete()
             ProteinDomainPartnerComplex.objects.all().delete()
+            Disease.objects.all().delete()
             Ppi.objects.all().delete()
             PpiComplex.objects.all().delete()
-            self.stdout.write(self.style.SUCCESS('Successfully flushed protein domain complex tables and Ppi'))
+            self.stdout.write(self.style.SUCCESS('Successfully flushed protein domain complex, PPI, and disease tables'))
             ppi_ids_mapping = {}
             for row in rows:
                 try:
                     # create or retrieve Ppi object
                     if row[5]=='part1':
                         ppi = Ppi()
+                        disease, created = Disease.objects.get_or_create(name=row[7])
                         ppi.pdb_id = row[4]
                         ppi.symmetry = Symmetry.objects.get(code='AS')
                         ppi.save()
+                        ppi.diseases.add(disease)
+                        ppi.save()
                         ppi_ids_mapping[row[6]]=ppi.id
                     else:
                         ppi = Ppi.objects.get(id=ppi_ids_mapping[row[6]])

ippisite/ippidb/models.py

@@ -149,9 +149,17 @@ class Symmetry(models.Model):
     def __str__(self):
         return '{} ({})'.format(self.code, self.description)
 
+
+class Disease(models.Model):
+    name = models.CharField('Disease', max_length=30, unique=True) # is there any database/nomenclature for diseases?
+
+    def __str__(self):
+        return self.name
+
 class Ppi(models.Model):
     pdb_id = models.CharField('PDB ID', max_length=4, null=True)
     symmetry = models.ForeignKey(Symmetry)
+    diseases = models.ManyToManyField(Disease)
 
     def __str__(self):
         return '{} PPI, PDB:{}'.format(self.symmetry.description, self.pdb_id or 'unknown')
@@ -169,6 +177,7 @@ class Ppi(models.Model):
         #this is the less efficient query ever seen, FIXME
         return PpiComplex.objects.filter(ppi=self, complex__in=ProteinDomainBoundComplex.objects.all())
 
+
 class PpiComplex(models.Model):
     ppi = models.ForeignKey(Ppi)
     complex = models.ForeignKey(ProteinDomainComplex)
@@ -180,10 +189,6 @@ class PpiComplex(models.Model):
     def __str__(self):
         return 'PPI {}, Complex {} ({})'.format(self.ppi, self.complex, self.cc_nb)
 
-class Disease(models.Model):
-    ppi = models.ForeignKey(Ppi)
-    disease_name = models.CharField('Disease', max_length=30) # is there any database/nomenclature for diseases?
-
 
 class Compound(models.Model):
     canonical_smile = models.CharField('Canonical Smile', unique=True, max_length=500)