migrate compound-bibliography data

Former-commit-id: b315278b18e80d3ccb5947e6bb6ad27f96c7a241

ippisite/ippidb/management/commands/import_v1_data.py

@@ -3,11 +3,10 @@ import glob
 from django.utils import timezone
 from django.core.management import BaseCommand, CommandError
 import mysql.connector
-from pybel import readfile
 
 from ippidb.models import Bibliography, Protein, Taxonomy, MolecularFunction, \
     Domain, ProteinDomainBoundComplex, ProteinDomainPartnerComplex, Symmetry, Ppi, PpiComplex, Disease, \
-    Compound, MDDRCompoundImport, MDDRActivityClass, TestActivityDescription, CellLine
+    Compound, MDDRCompoundImport, MDDRActivityClass, TestActivityDescription, CellLine, RefCompoundBiblio
 
 
 class MyConverter(mysql.connector.conversion.MySQLConverter):
@@ -77,6 +76,13 @@ class Command(BaseCommand):
             default=False,
             help='Flush and migrate compounds',
         )
+        parser.add_argument(
+            '--compound-biblio',
+            action='store_true',
+            dest='compoundbiblio',
+            default=False,
+            help='Flush and migrate compounds-bibliography',
+        )
         parser.add_argument(
             '--test-activity-description',
             action='store_true',
@@ -301,6 +307,7 @@ select distinct protein.NumUniprot, domain.PfamNumAccession  , complexe.NbCopy,
                     self.stdout.write(
                         self.style.SUCCESS('Successfully inserted {}'.format(row[2])))
         if options['mddr']:
+            from pybel import readfile
             MDDRCompoundImport.objects.all().delete()
             MDDRActivityClass.objects.all().delete()
             self.stdout.write(
@@ -409,3 +416,30 @@ select distinct protein.NumUniprot, domain.PfamNumAccession  , complexe.NbCopy,
                 else:
                     self.stdout.write(
                         self.style.SUCCESS('Successfully inserted {} {}'.format(row[1], row[2])))
+        if options['compoundbiblio']:
+            cursor.execute("""select r.CmpdNameInBiblio, c.CanonicalSmile, b.IDSource from refCmpdBiblio as r inner join compound as c on r.IDCompound=c.IDCompound inner join biblio as b on r.IDBiblio=b.IDBiblio;""")
+            rows = cursor.fetchall()
+            RefCompoundBiblio.objects.all().delete()
+            self.stdout.write(
+                self.style.SUCCESS('Successfully flushed compound-biblio table'))
+            for row in rows:
+                try:
+                    c = Compound.objects.get(canonical_smile=row[1])
+                    b = Bibliography.objects.get(id_source=row[2])
+                    r = RefCompoundBiblio()
+                    r.compound_id = c.id
+                    r.bibliography_id = b.id
+                    r.compound_name = row[0]
+                    r.save()
+                except Exception as e:
+                    if options['stoponfail']:
+                        import traceback
+                        self.stderr.write(traceback.format_exc())
+                        raise CommandError(
+                            'Failed inserting {} {}'.format(row[1], row[2]))
+                    else:
+                        self.stdout.write(
+                            self.style.ERROR('Failed inserting {} {}'.format(row[1], row[2])))
+                else:
+                    self.stdout.write(
+                        self.style.SUCCESS('Successfully inserted {} {}'.format(row[1], row[2])))