From cf66a659ea7bf4aa79a5bc54339093289785ee20 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Thu, 8 Mar 2018 22:46:36 +0100
Subject: [PATCH] migrate Compound activity results (fix #15)
Former-commit-id: 5a5f698c25d82c03c96cb49900bd47282946fe9c
---
.../management/commands/import_v1_data.py | 31 ++++++++++++++++++-
...undactivityresult_inhibition_percentage.py | 20 ++++++++++++
ippisite/ippidb/models.py | 4 +++
3 files changed, 54 insertions(+), 1 deletion(-)
create mode 100644 ippisite/ippidb/migrations/0031_compoundactivityresult_inhibition_percentage.py
diff --git a/ippisite/ippidb/management/commands/import_v1_data.py b/ippisite/ippidb/management/commands/import_v1_data.py
index 42c45eb7..8800e291 100644
--- a/ippisite/ippidb/management/commands/import_v1_data.py
+++ b/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, TestPKDescription
+ CompoundAction, TestCytotoxDescription, TestPKDescription, CompoundActivityResult
class MyConverter(mysql.connector.conversion.MySQLConverter):
@@ -319,6 +319,7 @@ 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()
@@ -342,6 +343,7 @@ 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
@@ -354,6 +356,33 @@ 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()
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 00000000..00e3279a
--- /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 f9d77052..4b1ec02e 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)
--
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