From 85b910083d329fced347812b1a5810e8a4cd68a7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Sun, 29 Jul 2018 13:44:10 +0200
Subject: [PATCH] denormalize ppi name to improve compound query performance
Former-commit-id: efe273eac847d110d0b8791fa2eb89191d212ffa
---
ippisite/db.sqlite3.REMOVED.git-id | 2 +-
ippisite/ippidb/migrations/0009_ppi_name.py | 20 ++++++++++++++++++++
ippisite/ippidb/models.py | 18 ++++++++----------
3 files changed, 29 insertions(+), 11 deletions(-)
create mode 100644 ippisite/ippidb/migrations/0009_ppi_name.py
diff --git a/ippisite/db.sqlite3.REMOVED.git-id b/ippisite/db.sqlite3.REMOVED.git-id
index 5e73a6d9..c97e351a 100644
--- a/ippisite/db.sqlite3.REMOVED.git-id
+++ b/ippisite/db.sqlite3.REMOVED.git-id
@@ -1 +1 @@
-a95c9b99cc69a1cae8a8fa13dfa234ef88d45f4e
\ No newline at end of file
+487393aa0af165ca4ce78c99486b57039379f535
\ No newline at end of file
diff --git a/ippisite/ippidb/migrations/0009_ppi_name.py b/ippisite/ippidb/migrations/0009_ppi_name.py
new file mode 100644
index 00000000..d052b637
--- /dev/null
+++ b/ippisite/ippidb/migrations/0009_ppi_name.py
@@ -0,0 +1,20 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11 on 2018-07-29 10:13
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0008_auto_20180727_0845'),
+ ]
+
+ operations = [
+ migrations.AddField(
+ model_name='ppi',
+ name='name',
+ field=models.TextField(blank=True, null=True, verbose_name='PPI name'),
+ ),
+ ]
diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index 6ccd9d07..d6eb9bf9 100644
--- a/ippisite/ippidb/models.py
+++ b/ippisite/ippidb/models.py
@@ -211,22 +211,21 @@ class PpiFamily(models.Model):
return self.name
-class Ppi(models.Model):
+class Ppi(AutoFillableModel):
pdb_id = models.CharField('PDB ID', max_length=4, null=True, blank=True)
pockets_nb = models.IntegerField(
'Total number of pockets in the complex', default=1)
symmetry = models.ForeignKey(Symmetry, models.CASCADE)
diseases = models.ManyToManyField(Disease)
family = models.ForeignKey(PpiFamily, models.CASCADE, null=True, blank=True)
+ name = models.TextField('PPI name', null=True, blank=True)
def __str__(self):
return '{} PPI, PDB:{}'.format(self.symmetry.description, self.pdb_id or 'unknown')
- def get_ppi_complexes(self):
- """
- return all ppi complexes belonging to this ppi
- """
- return PpiComplex.objects.filter(ppi=self)
+ def autofill(self):
+ # name is denormalized and stored in the database to reduce SQL queries in query mode
+ self.name = self.compute_name_from_protein_names()
def get_ppi_bound_complexes(self):
"""
@@ -235,10 +234,9 @@ class Ppi(models.Model):
# this is the less efficient query ever seen, FIXME
return PpiComplex.objects.filter(ppi=self, complex__in=ProteinDomainBoundComplex.objects.all())
- @property
- def name(self):
+ def compute_name_from_protein_names(self):
all_protein_names = set(
- [ppi_complex.complex.protein.short_name for ppi_complex in self.get_ppi_complexes()])
+ [ppi_complex.complex.protein.short_name for ppi_complex in self.ppicomplex_set.all()])
bound_protein_names = set(
[ppi_complex.complex.protein.short_name for ppi_complex in self.get_ppi_bound_complexes()])
partner_protein_names = all_protein_names - bound_protein_names
@@ -614,7 +612,7 @@ class TestActivityDescription(models.Model):
depends on the modulation type
"""
if self.test_modulation_type == 'I':
- return self.ppi.get_ppi_complexes()
+ return self.ppi.ppicomplex_set.all()
else:
return self.ppi.get_ppi_bound_complexes()
--
GitLab