migrate TestCytotoxicityDescription (fix #28)

Former-commit-id: 67806cbeb81fdcc7428cb60b69155b7531f002e7

ippisite/ippidb/management/commands/import_v1_data.py

@@ -6,7 +6,8 @@ import mysql.connector
 
 from ippidb.models import Bibliography, Protein, Taxonomy, MolecularFunction, \
     Domain, ProteinDomainBoundComplex, ProteinDomainPartnerComplex, Symmetry, Ppi, PpiComplex, Disease, \
-    Compound, MDDRCompoundImport, MDDRActivityClass, TestActivityDescription, CellLine, RefCompoundBiblio, CompoundAction
+    Compound, MDDRCompoundImport, MDDRActivityClass, TestActivityDescription, CellLine, RefCompoundBiblio, \
+    CompoundAction, TestCytotoxDescription
 
 
 class MyConverter(mysql.connector.conversion.MySQLConverter):
@@ -313,12 +314,14 @@ select distinct protein.NumUniprot, domain.PfamNumAccession  , complexe.NbCopy,
                 else:
                     self.stdout.write(
                         self.style.SUCCESS('Successfully inserted {} {}'.format(row[0], row[1])))
+            CellLine.objects.all().delete()
+            self.stdout.write(
+                self.style.SUCCESS('Successfully flushed cell lines table'))
             cursor.execute("""SELECT * FROM testActivityDescription""")
             rows = cursor.fetchall()
             TestActivityDescription.objects.all().delete()
-            CellLine.objects.all().delete()
             self.stdout.write(
-                self.style.SUCCESS('Successfully flushed test activity descriptions table and cell lines table'))
+                self.style.SUCCESS('Successfully flushed test activity descriptions table'))
             for row in rows:
                 try:
                     tad = TestActivityDescription()
@@ -348,6 +351,37 @@ select distinct protein.NumUniprot, domain.PfamNumAccession  , complexe.NbCopy,
                 else:
                     self.stdout.write(
                         self.style.SUCCESS('Successfully inserted {}'.format(row[2])))
+            cursor.execute("""SELECT * FROM testCytotoxDescription""")
+            rows = cursor.fetchall()
+            TestCytotoxDescription.objects.all().delete()
+            self.stdout.write(
+                self.style.SUCCESS('Successfully flushed test cytotoxicity descriptions table'))
+            for row in rows:
+                try:
+                    tcd = TestCytotoxDescription()
+                    cursor.execute(
+                        """select IDSource from biblio where IDBiblio={}""".format(row[1]))
+                    biblio_row = cursor.fetchone()
+                    biblio = Bibliography.objects.get(id_source=biblio_row[0])
+                    tcd.biblio = biblio
+                    tcd.test_name = row[2]
+                    tcd.compound_concentration = row[4]
+                    if row[3] is not None:
+                        tcd.cell_line, created = CellLine.objects.get_or_create(
+                            name=row[3])
+                    tcd.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[2])))
         if options['mddr']:
             from pybel import readfile
             MDDRCompoundImport.objects.all().delete()