CompoundAction migration, WIP

Former-commit-id: e5b8790a83d03bd6d01fa8925caf0bb10e2caaa3

ippisite/ippidb/management/commands/import_v1_data.py

@@ -6,7 +6,7 @@ import mysql.connector
 
 from ippidb.models import Bibliography, Protein, Taxonomy, MolecularFunction, \
     Domain, ProteinDomainBoundComplex, ProteinDomainPartnerComplex, Symmetry, Ppi, PpiComplex, Disease, \
-    Compound, MDDRCompoundImport, MDDRActivityClass, TestActivityDescription, CellLine, RefCompoundBiblio
+    Compound, MDDRCompoundImport, MDDRActivityClass, TestActivityDescription, CellLine, RefCompoundBiblio, CompoundAction
 
 
 class MyConverter(mysql.connector.conversion.MySQLConverter):
@@ -102,6 +102,8 @@ class Command(BaseCommand):
         conn = mysql.connector.connect(
             converter_class=MyConverter, host="localhost", user="root", password="ippidb", database="ippidb")
         cursor = conn.cursor()
+        cursor_aux = conn.cursor(buffered=True)
+        cursor_aux2 = conn.cursor(buffered=True)
         if options['bibliographies']:
             cursor.execute("""SELECT * FROM biblio""")
             rows = cursor.fetchall()
@@ -234,8 +236,9 @@ select distinct protein.NumUniprot, domain.PfamNumAccession  , complexe.NbCopy,
             Disease.objects.all().delete()
             Ppi.objects.all().delete()
             PpiComplex.objects.all().delete()
+            CompoundAction.objects.all().delete()
             self.stdout.write(
-                self.style.SUCCESS('Successfully flushed protein domain complex, PPI, and disease tables'))
+                self.style.SUCCESS('Successfully flushed protein domain complex, PPI, compound actions, and disease tables'))
             ppi_ids_mapping = {}
             for row in rows:
                 try:
@@ -272,6 +275,32 @@ select distinct protein.NumUniprot, domain.PfamNumAccession  , complexe.NbCopy,
                     ppi_complex.complex = c
                     ppi_complex.cc_nb = 1
                     ppi_complex.save()
+                    if row[3] is not None:
+                        sql_ca_string = '''select distinct c.CanonicalSmile from cmpdAction as ca 
+                                                           inner join compound as c on ca.IDCompound=c.IDCompound where ca.IDComplexeBound='''\
+                                                         + str(row[3])
+                        cursor_aux.execute(sql_ca_string)
+                        rows_aux = cursor_aux.fetchall()
+                        for row_aux in rows_aux:
+                            if row_aux is None:
+                                self.stdout.write(sql_ca_string)
+                                continue
+                            canonical_smile = row_aux[0]
+                            sql_bse_string = '''select CodePDB from bindingSiteEvidence where IDPPI=''' + str(ppi.id)
+                            cursor_aux.execute(sql_bse_string)
+                            row_aux2 = cursor_aux2.fetchone()
+                            if row_aux2 is None:
+                                pdb_id_ca = None
+                            else:
+                                pdb_id_ca = row_aux2[0]
+                            c = Compound.objects.get(canonical_smile=canonical_smile)
+                            ca = CompoundAction()
+                            ca.compound = c
+                            ca.ppi = ppi
+                            ca.activation_mode = 'U'
+                            ca.nb_copy_compounds = 1
+                            ca.pdb_id = pdb_id_ca
+                            ca.save()
                 except Exception as e:
                     if options['stoponfail']:
                         import traceback