From 49b1731881096e348a421f0ced0ceffb8c167d70 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Mon, 22 May 2017 22:59:37 +0200
Subject: [PATCH] refine MDDR model, and implement MDDR import
fixes #21
---
ippisite/ippidb/admin.py | 4 ++
.../management/commands/import_v1_data.py | 39 ++++++++++++++++++-
.../migrations/0019_auto_20170522_1931.py | 28 +++++++++++++
.../migrations/0020_auto_20170522_1945.py | 20 ++++++++++
.../migrations/0021_auto_20170522_1949.py | 20 ++++++++++
ippisite/ippidb/models.py | 11 +++---
6 files changed, 115 insertions(+), 7 deletions(-)
create mode 100644 ippisite/ippidb/migrations/0019_auto_20170522_1931.py
create mode 100644 ippisite/ippidb/migrations/0020_auto_20170522_1945.py
create mode 100644 ippisite/ippidb/migrations/0021_auto_20170522_1949.py
diff --git a/ippisite/ippidb/admin.py b/ippisite/ippidb/admin.py
index 21a59ca3..18181267 100644
--- a/ippisite/ippidb/admin.py
+++ b/ippisite/ippidb/admin.py
@@ -32,6 +32,10 @@ class ProteinDomainPartnerComplexAdmin(admin.ModelAdmin):
class Symmetry(admin.ModelAdmin):
list_display = ('code', 'description')
+@admin.register(MDDRCompoundImport)
+class MDDRCompoundImport(admin.ModelAdmin):
+ list_display = ('mddr_name', 'dvpmt_phase', 'canonical_smile')
+
for model in apps.get_app_config('ippidb').models.values():
try:
admin.site.register(model)
diff --git a/ippisite/ippidb/management/commands/import_v1_data.py b/ippisite/ippidb/management/commands/import_v1_data.py
index de644fcc..1f6c40e7 100644
--- a/ippisite/ippidb/management/commands/import_v1_data.py
+++ b/ippisite/ippidb/management/commands/import_v1_data.py
@@ -1,9 +1,13 @@
+import glob
+
+from django.utils import timezone
from django.core.management import BaseCommand, CommandError
import mysql.connector
+from pybel import readfile
from ippidb.models import Bibliography, Protein, Taxonomy, MolecularFunction, \
Domain, ProteinDomainBoundComplex, ProteinDomainPartnerComplex, Symmetry, Ppi, PpiComplex, Disease, \
- Compound
+ Compound, MDDRCompoundImport, MDDRActivityClass
class Command(BaseCommand):
@@ -45,6 +49,13 @@ class Command(BaseCommand):
default=False,
help='Flush and migrate ppis and complexes',
)
+ parser.add_argument(
+ '--mddr',
+ action='store_true',
+ dest='mddr',
+ default=False,
+ help='Flush and import MDDR database',
+ )
parser.add_argument(
'--compound',
action='store_true',
@@ -211,6 +222,32 @@ select distinct protein.NumUniprot, domain.PfamNumAccession , complexe.NbCopy,
self.stdout.write(self.style.ERROR('Failed inserting {} {}'.format(row[0], row[1])))
else:
self.stdout.write(self.style.SUCCESS('Successfully inserted {} {}'.format(row[0], row[1])))
+ if options['mddr']:
+ MDDRCompoundImport.objects.all().delete()
+ MDDRActivityClass.objects.all().delete()
+ self.stdout.write(self.style.SUCCESS('Successfully flushed MDDR Compound and Activity class tables'))
+ for sdf_file in glob.glob('/home/hmenager/iPPIDB/mddr20151_2d.sdf/*.sdf'):
+ for item in readfile("sdf", sdf_file):
+ try:
+ m = MDDRCompoundImport()
+ m.mddr_name = item.data['MOLNAME']
+ m.canonical_smile = str(item)
+ m.dvpmt_phase = item.data['PHASE']
+ m.db_import_date = timezone.now()
+ m.save()
+ for activity_class_name in item.data['ACTIV_CLASS'].split(','):
+ activity_class, created = MDDRActivityClass.objects.get_or_create(name=activity_class_name)
+ m.activity_classes.add(activity_class)
+ m.save()
+ except Exception as e:
+ if options['stoponfail']:
+ import traceback
+ self.stderr.write(traceback.format_exc())
+ raise CommandError('Failed inserting {}'.format(str(item)))
+ else:
+ self.stdout.write(self.style.ERROR('Failed inserting {}'.format(str(item))))
+ else:
+ self.stdout.write(self.style.SUCCESS('Successfully inserted {} {}'.format(item.data['MOLNAME'], str(item))))
if options['compound']:
cursor.execute("""SELECT * FROM compound""")
rows = cursor.fetchall()
diff --git a/ippisite/ippidb/migrations/0019_auto_20170522_1931.py b/ippisite/ippidb/migrations/0019_auto_20170522_1931.py
new file mode 100644
index 00000000..4b1fb044
--- /dev/null
+++ b/ippisite/ippidb/migrations/0019_auto_20170522_1931.py
@@ -0,0 +1,28 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.1 on 2017-05-22 19:31
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0018_auto_20170522_1501'),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name='mddrcompoundimport',
+ name='db_import_date',
+ field=models.DateTimeField(verbose_name='MDDR release year/month'),
+ ),
+ migrations.AlterUniqueTogether(
+ name='mddrcompoundimport',
+ unique_together=set([('mddr_name', 'dvpmt_phase', 'canonical_smile')]),
+ ),
+ migrations.RemoveField(
+ model_name='mddrcompoundimport',
+ name='mddr_compound_id',
+ ),
+ ]
diff --git a/ippisite/ippidb/migrations/0020_auto_20170522_1945.py b/ippisite/ippidb/migrations/0020_auto_20170522_1945.py
new file mode 100644
index 00000000..1aee4b10
--- /dev/null
+++ b/ippisite/ippidb/migrations/0020_auto_20170522_1945.py
@@ -0,0 +1,20 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.1 on 2017-05-22 19:45
+from __future__ import unicode_literals
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0019_auto_20170522_1931'),
+ ]
+
+ operations = [
+ migrations.RenameField(
+ model_name='mddractivityclass',
+ old_name='activity_class',
+ new_name='name',
+ ),
+ ]
diff --git a/ippisite/ippidb/migrations/0021_auto_20170522_1949.py b/ippisite/ippidb/migrations/0021_auto_20170522_1949.py
new file mode 100644
index 00000000..fcb415f2
--- /dev/null
+++ b/ippisite/ippidb/migrations/0021_auto_20170522_1949.py
@@ -0,0 +1,20 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.1 on 2017-05-22 19:49
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0020_auto_20170522_1945'),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name='mddrcompoundimport',
+ name='canonical_smile',
+ field=models.CharField(blank=True, max_length=500, null=True, verbose_name='Canonical Smile'),
+ ),
+ ]
diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index 48fb10e3..377f692a 100644
--- a/ippisite/ippidb/models.py
+++ b/ippisite/ippidb/models.py
@@ -244,27 +244,26 @@ class Compound(models.Model):
class MDDRActivityClass(models.Model):
- activity_class = models.CharField('Activity Class', max_length=100, unique=True)
+ name = models.CharField('Activity Class', max_length=100, unique=True)
class Meta:
verbose_name_plural = "MDDR activity classes"
def __str__(self):
- return self.activity_class
+ return self.name
class MDDRCompoundImport(models.Model):
- mddr_compound_id = models.IntegerField('MDDR compound ID')
mddr_name = models.CharField('MDDR name', max_length=40)
dvpmt_phase = models.CharField('Development phase', max_length=20)
- canonical_smile = models.CharField('Canonical Smile', max_length=500, unique=True, blank=True, null=True)
+ canonical_smile = models.CharField('Canonical Smile', max_length=500, blank=True, null=True)
#TODO index this table on canonical_smile
- db_import_date = models.DecimalField('MDDR release year/month', max_digits=6, decimal_places=0)
+ db_import_date = models.DateTimeField('MDDR release year/month')
activity_classes = models.ManyToManyField(MDDRActivityClass)
class Meta:
# over multiple releases of the MDDR database, the same compound can evolve in its development phase
# the same compound can have different names and development phases in the same MDDR release
- unique_together = (('mddr_compound_id', 'mddr_name', 'dvpmt_phase'),)
+ unique_together = (('mddr_name', 'dvpmt_phase', 'canonical_smile'),)
verbose_name_plural = "MDDR compound imports"
class MDDRSimilarity(models.Model):
--
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