diff --git a/ippisite/ippidb/management/commands/import_v1_data.py b/ippisite/ippidb/management/commands/import_v1_data.py
index c14585e2f37096a0fdb676baa204aa38fffd7062..d2fe65cc676fe3f892c12ba57555ba457832227a 100644
--- a/ippisite/ippidb/management/commands/import_v1_data.py
+++ b/ippisite/ippidb/management/commands/import_v1_data.py
@@ -7,7 +7,8 @@ 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, TestCytotoxDescription
+ CompoundAction, TestCytotoxDescription, TestPKDescription, CompoundActivityResult, \
+ CompoundCytotoxicityResult, CompoundPKResult
class MyConverter(mysql.connector.conversion.MySQLConverter):
@@ -61,7 +62,7 @@ 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 +85,6 @@ 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',
@@ -326,6 +320,7 @@ select distinct protein.NumUniprot, domain.PfamNumAccession , complexe.NbCopy,
TestActivityDescription.objects.all().delete()
self.stdout.write(
self.style.SUCCESS('Successfully flushed test activity descriptions table'))
+ tad_id_mapping = {}
for row in rows:
try:
tad = TestActivityDescription()
@@ -349,6 +344,7 @@ select distinct protein.NumUniprot, domain.PfamNumAccession , complexe.NbCopy,
tad.cell_line, created = CellLine.objects.get_or_create(
name=row[16])
tad.save()
+ tad_id_mapping[row[0]] = tad.id
except Exception as e:
if options['stoponfail']:
import traceback
@@ -361,11 +357,39 @@ select distinct protein.NumUniprot, domain.PfamNumAccession , complexe.NbCopy,
else:
self.stdout.write(
self.style.SUCCESS('Successfully inserted {}'.format(row[2])))
+ cursor.execute("""select c.CanonicalSmile, r.IDTestActivity, r.ActivityType, r.Activity, r.PourcentInhib from cmpdActiveResult as r inner join compound as c on r.IDCompound = c.IDCompound;""")
+ rows = cursor.fetchall()
+ CompoundActivityResult.objects.all().delete()
+ self.stdout.write(
+ self.style.SUCCESS('Successfully flushed compound activity result table'))
+ for row in rows:
+ try:
+ car = CompoundActivityResult()
+ car.test_activity_description = TestActivityDescription.objects.get(id=tad_id_mapping[row[1]])
+ car.compound = Compound.objects.get(canonical_smile=row[0])
+ car.activity_type = row[2]
+ car.activity = row[3]
+ car.inhibition_percentage = row[4]
+ car.modulation_type = 'I' # because previous DB is only about inhibitors
+ car.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(str(car))))
cursor.execute("""SELECT * FROM testCytotoxDescription""")
rows = cursor.fetchall()
TestCytotoxDescription.objects.all().delete()
self.stdout.write(
self.style.SUCCESS('Successfully flushed test cytotoxicity descriptions table'))
+ tcd_id_mapping = {}
for row in rows:
try:
tcd = TestCytotoxDescription()
@@ -380,6 +404,74 @@ select distinct protein.NumUniprot, domain.PfamNumAccession , complexe.NbCopy,
tcd.cell_line, created = CellLine.objects.get_or_create(
name=row[3])
tcd.save()
+ tcd_id_mapping[row[0]] = tcd.id
+ 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])))
+ cursor.execute("""select c.CanonicalSmile, r.IDTestCytotox, r.IDTestCytotox from cmpdCytotoxResult as r inner join compound as c on r.IDCompound = c.IDCompound;""")
+ rows = cursor.fetchall()
+ CompoundCytotoxicityResult.objects.all().delete()
+ self.stdout.write(
+ self.style.SUCCESS('Successfully flushed compound cytotoxicity result table'))
+ for row in rows:
+ try:
+ ccr = CompoundCytotoxicityResult()
+ ccr.test_cytotoxicity_description = TestCytotoxDescription.objects.get(id=tcd_id_mapping[row[1]])
+ ccr.compound = Compound.objects.get(canonical_smile=row[0])
+ ccr.toxicity = row[2] == 'Y'
+ ccr.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:
+ import traceback
+ self.stderr.write(traceback.format_exc())
+ self.stdout.write(
+ self.style.ERROR('Failed inserting {} {}'.format(row[1], row[2])))
+ else:
+ self.stdout.write(
+ self.style.SUCCESS('Successfully inserted {}'.format(str(ccr))))
+ 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
diff --git a/ippisite/ippidb/migrations/0029_auto_20180308_1935.py b/ippisite/ippidb/migrations/0029_auto_20180308_1935.py
new file mode 100644
index 0000000000000000000000000000000000000000..7e2c9f63d1ea437868a3ba0fcfc0f9dd447772c2
--- /dev/null
+++ b/ippisite/ippidb/migrations/0029_auto_20180308_1935.py
@@ -0,0 +1,20 @@
+# -*- 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'),
+ ),
+ ]
diff --git a/ippisite/ippidb/migrations/0030_testpkdescription_concentration.py b/ippisite/ippidb/migrations/0030_testpkdescription_concentration.py
new file mode 100644
index 0000000000000000000000000000000000000000..3522e6e9a652babd407d09456834ed536a57e330
--- /dev/null
+++ b/ippisite/ippidb/migrations/0030_testpkdescription_concentration.py
@@ -0,0 +1,20 @@
+# -*- 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'),
+ ),
+ ]
diff --git a/ippisite/ippidb/migrations/0031_compoundactivityresult_inhibition_percentage.py b/ippisite/ippidb/migrations/0031_compoundactivityresult_inhibition_percentage.py
new file mode 100644
index 0000000000000000000000000000000000000000..00e3279a98dea166a7857238fed7942c04563dd2
--- /dev/null
+++ b/ippisite/ippidb/migrations/0031_compoundactivityresult_inhibition_percentage.py
@@ -0,0 +1,20 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11 on 2018-03-08 21:12
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0030_testpkdescription_concentration'),
+ ]
+
+ operations = [
+ migrations.AddField(
+ model_name='compoundactivityresult',
+ name='inhibition_percentage',
+ field=models.DecimalField(decimal_places=0, max_digits=3, null=True, verbose_name='Inhibition percentage'),
+ ),
+ ]
diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index 55e9612ffd1e4930d6fadaf1cfa5fb187c46a721..76a635dfef5f76086205c601d4c766104e82653d 100644
--- a/ippisite/ippidb/models.py
+++ b/ippisite/ippidb/models.py
@@ -477,6 +477,8 @@ class CompoundActivityResult(models.Model):
'Activity type', max_length=5, choices=ACTIVITY_TYPES)
activity = models.DecimalField(
'Activity', max_digits=12, decimal_places=10)
+ inhibition_percentage = models.DecimalField(
+ 'Inhibition percentage', max_digits=3, decimal_places=0, null=True)
modulation_type = models.CharField(
'Modulation type', max_length=1, choices=MODULATION_TYPES)
@@ -484,6 +486,8 @@ class CompoundActivityResult(models.Model):
unique_together = (
('compound', 'test_activity_description', 'activity_type'),)
+ def __str__(self):
+ return 'Compound activity result for {} test {} on {}'.format(self.activity_type, self.test_activity_description.id, self.compound.id)
class TestCytotoxDescription(models.Model):
biblio = models.ForeignKey(Bibliography, models.CASCADE)
@@ -501,6 +505,9 @@ class CompoundCytotoxicityResult(models.Model):
class Meta:
unique_together = (('compound', 'test_cytotoxicity_description'),)
+ def __str__(self):
+ return 'Compound cytotoxicity result for test {} on {}'.format(self.test_cytotoxicity_description.id, self.compound.id)
+
class TestPKDescription(models.Model):
ADMINISTRATION_MODES = (
@@ -514,8 +521,10 @@ 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)