migrate TestPKDescription (fix #29)

Former-commit-id: 1acca29b42cdc5370aeb1b0f13eb6a37f82e440f

ippisite/ippidb/management/commands/import_v1_data.py

@@ -7,7 +7,7 @@ import mysql.connector
 from ippidb.models import Bibliography, Protein, Taxonomy, MolecularFunction, \
     Domain, ProteinDomainBoundComplex, ProteinDomainPartnerComplex, Symmetry, Ppi, PpiComplex, Disease, \
     Compound, MDDRCompoundImport, MDDRActivityClass, TestActivityDescription, CellLine, RefCompoundBiblio, \
-    CompoundAction, TestCytotoxDescription
+    CompoundAction, TestCytotoxDescription, TestPKDescription
 
 
 class MyConverter(mysql.connector.conversion.MySQLConverter):
@@ -61,7 +61,7 @@ class Command(BaseCommand):
             action='store_true',
             dest='ppi',
             default=False,
-            help='Flush and migrate ppis and complexes',
+            help='Flush and migrate ppis, complexes, and tests',
         )
         parser.add_argument(
             '--mddr',
@@ -84,13 +84,6 @@ class Command(BaseCommand):
             default=False,
             help='Flush and migrate compounds-bibliography',
         )
-        parser.add_argument(
-            '--test-activity-description',
-            action='store_true',
-            dest='test-activity-description',
-            default=False,
-            help='Flush and migrate test activity descriptions',
-        )
         parser.add_argument(
             '--stoponfail',
             action='store_true',
@@ -392,6 +385,47 @@ select distinct protein.NumUniprot, domain.PfamNumAccession  , complexe.NbCopy,
                 else:
                     self.stdout.write(
                         self.style.SUCCESS('Successfully inserted {}'.format(row[2])))
+            cursor.execute("""SELECT * FROM testPKDescription""")
+            rows = cursor.fetchall()
+            TestPKDescription.objects.all().delete()
+            self.stdout.write(
+                self.style.SUCCESS('Successfully flushed test PK descriptions table'))
+            for row in rows:
+                try:
+                    tpd = TestPKDescription()
+                    cursor.execute(
+                        """select IDSource from biblio where IDBiblio={}""".format(row[1]))
+                    biblio_row = cursor.fetchone()
+                    biblio = Bibliography.objects.get(id_source=biblio_row[0])
+                    tpd.biblio = biblio
+                    tpd.test_name = row[2]
+                    #tcd.compound_concentration = row[4]
+                    try:
+                        taxonomy = Taxonomy.objects.get(taxonomy_id=10090)
+                    except Taxonomy.DoesNotExist:
+                        taxonomy = Taxonomy()
+                        taxonomy.taxonomy_id = 10090 
+                        # dirty hack: all organisms in this table are "mice", 
+                        # hence assuming Mus musculus
+                        taxonomy.save(autofill=True)
+                    tpd.organism = taxonomy
+                    tpd.administration_mode = row[4]
+                    tpd.concentration = row[5]
+                    tpd.dose = round(row[6], 4)
+                    tpd.dose_interval = row[7]  
+                    tpd.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()

ippisite/ippidb/migrations/0029_auto_20180308_1935.py

+# -*- coding: utf-8 -*-
+# Generated by Django 1.11 on 2018-03-08 19:35
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('ippidb', '0028_auto_20180307_1405'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='testpkdescription',
+            name='dose',
+            field=models.DecimalField(blank=True, decimal_places=4, max_digits=9, null=True, verbose_name='Dose in mg/kg'),
+        ),
+    ]

ippisite/ippidb/migrations/0030_testpkdescription_concentration.py

+# -*- coding: utf-8 -*-
+# Generated by Django 1.11 on 2018-03-08 19:45
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('ippidb', '0029_auto_20180308_1935'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='testpkdescription',
+            name='concentration',
+            field=models.DecimalField(blank=True, decimal_places=3, max_digits=7, null=True, verbose_name='Concentration in mg/l'),
+        ),
+    ]

ippisite/ippidb/models.py

@@ -514,8 +514,10 @@ class TestPKDescription(models.Model):
     organism = models.ForeignKey(Taxonomy, models.CASCADE)
     administration_mode = models.CharField(
         'Administration mode', max_length=2, choices=ADMINISTRATION_MODES, blank=True, null=True)
+    concentration = models.DecimalField(
+        'Concentration in mg/l', max_digits=7, decimal_places=3, blank=True, null=True)
     dose = models.DecimalField(
-        'Dose in mg/kg', max_digits=7, decimal_places=4, blank=True, null=True)
+        'Dose in mg/kg', max_digits=9, decimal_places=4, blank=True, null=True)
     dose_interval = models.IntegerField(
         'Dose interval, in hours', blank=True, null=True)