From 8b3c9e274fe6b374f4ad14dfdb6d49e154910457 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Wed, 29 Mar 2017 17:03:32 +0200
Subject: [PATCH] finish last model classes and update db.
---
ippisite/db.sqlite3 | Bin 520192 -> 536576 bytes
.../migrations/0008_auto_20170329_1441.py | 66 ++++++++++++++++++
ippisite/ippidb/models.py | 50 +++++--------
3 files changed, 85 insertions(+), 31 deletions(-)
create mode 100644 ippisite/ippidb/migrations/0008_auto_20170329_1441.py
diff --git a/ippisite/db.sqlite3 b/ippisite/db.sqlite3
index 4322d387f7390adb118f06d2b776199986ca1340..47ec17349e4b67ca860f635c93619456554a9e2f 100644
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diff --git a/ippisite/ippidb/migrations/0008_auto_20170329_1441.py b/ippisite/ippidb/migrations/0008_auto_20170329_1441.py
new file mode 100644
index 00000000..a4226179
--- /dev/null
+++ b/ippisite/ippidb/migrations/0008_auto_20170329_1441.py
@@ -0,0 +1,66 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.10.5 on 2017-03-29 14:41
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0007_auto_20170328_2045'),
+ ]
+
+ operations = [
+ migrations.CreateModel(
+ name='RefCompoundBiblio',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('compound_name', models.CharField(max_length=50, verbose_name='Compound name in the publication')),
+ ('bibliography_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Bibliography')),
+ ('compound_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Compound')),
+ ],
+ ),
+ migrations.AddField(
+ model_name='cmpdaction',
+ name='nb_copy_compounds',
+ field=models.IntegerField(default=1, verbose_name='Number of copies for the compound'),
+ preserve_default=False,
+ ),
+ migrations.AddField(
+ model_name='cmpdaction',
+ name='pdb_id',
+ field=models.CharField(default='NA', max_length=4, verbose_name='PDB ID'),
+ preserve_default=False,
+ ),
+ migrations.AddField(
+ model_name='cmpdaction',
+ name='ppi_id',
+ field=models.ForeignKey(default=1, on_delete=django.db.models.deletion.CASCADE, to='ippidb.Ppi'),
+ preserve_default=False,
+ ),
+ migrations.AddField(
+ model_name='compoundactivityresult',
+ name='modulation_type',
+ field=models.CharField(choices=[('B', 'Binding'), ('I', 'Inhibition'), ('S', 'Stabilization')], default='B', max_length=1, verbose_name='Modulation type'),
+ preserve_default=False,
+ ),
+ migrations.AlterField(
+ model_name='cmpdaction',
+ name='activation_mode',
+ field=models.CharField(choices=[('O', 'Orthosteric'), ('A', 'Allosteric')], max_length=1, verbose_name='Activation mode'),
+ ),
+ migrations.RemoveField(
+ model_name='cmpdaction',
+ name='modulation_type',
+ ),
+ migrations.AlterUniqueTogether(
+ name='cmpdaction',
+ unique_together=set([('complex_id', 'compound_id', 'pdb_id')]),
+ ),
+ migrations.AlterUniqueTogether(
+ name='refcompoundbiblio',
+ unique_together=set([('compound_id', 'bibliography_id')]),
+ ),
+ ]
diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index 325a849e..73de8458 100644
--- a/ippisite/ippidb/models.py
+++ b/ippisite/ippidb/models.py
@@ -119,6 +119,9 @@ class Domain(models.Model):
self.pfam_description = info['description']
super(Domain, self).save(*args, **kwargs)
+ def __str__(self):
+ return '{} ({}-{})'.format(self.pfam_acc, self.pfam_id, self.pfam_description)
+
class ProteinDomainComplex(models.Model):
protein_id = models.ForeignKey('Protein')
domain_id = models.ForeignKey('Domain')
@@ -277,10 +280,16 @@ class ActivityType(models.Model):
name = models.CharField('Name', max_length=50, unique=True)
class CompoundActivityResult(models.Model):
+ MODULATION_TYPES = (
+ ('B', 'Binding'),
+ ('I', 'Inhibition'),
+ ('S', 'Stabilization')
+ )
compound_id = models.ForeignKey(Compound)
test_activity_description_id = models.ForeignKey(TestActivityDescription)
activity_type_id = models.ForeignKey(ActivityType)
activity = models.DecimalField('Activity', max_digits=12, decimal_places=10)
+ modulation_type = models.CharField('Modulation type', max_length=1, choices=MODULATION_TYPES)
class Meta:
unique_together = (('compound_id', 'test_activity_description_id', 'activity_type_id'),)
@@ -329,43 +338,22 @@ class CompoundPKResult(models.Model):
class CmpdAction(models.Model):
ACTIVATION_MODES = (
('O', 'Orthosteric'),
- ('A', 'Allosteric'),
- ('U', 'Unspecified')
- )
- MODULATION_TYPES = (
- ('I', 'Inhibition'),
- ('S', 'Stabilization')
+ ('A', 'Allosteric')
)
complex_id = models.ForeignKey(ProteinDomainBoundComplex)
compound_id = models.ForeignKey(Compound)
activation_mode = models.CharField('Activation mode', max_length=1, choices=ACTIVATION_MODES)
- modulation_type = models.CharField('Modulation type', max_length=1, choices=MODULATION_TYPES)
-
-""""
-class Actionevidencetest(models.Model):
- idcmpdaction = models.ForeignKey('Cmpdaction', models.DO_NOTHING, ='IDCmpdAction')
- idtestactivity = models.ForeignKey('Testactivitydescription', models.DO_NOTHING, ='IDTestActivity')
- nbcopycompound = models.IntegerField(='NbCopyCompound', blank=True, null=True)
+ ppi_id = models.ForeignKey(Ppi)
+ pdb_id = models.CharField('PDB ID', max_length=4)
+ nb_copy_compounds = models.IntegerField('Number of copies for the compound')
class Meta:
-# managed = False
- db_table = 'actionEvidenceTest'
- unique_together = (('idcmpdaction', 'idtestactivity'),)
-
-
+ unique_together = (('complex_id', 'compound_id', 'pdb_id'),)
-
-
-
-
-class Refcmpdbiblio(models.Model):
- idcompound = models.ForeignKey(Compound, models.DO_NOTHING, ='IDCompound')
- idbiblio = models.ForeignKey(Biblio, models.DO_NOTHING, ='IDBiblio')
- cmpdnameinbiblio = models.CharField(='CmpdNameInBiblio', max_length=20, blank=True, null=True)
+class RefCompoundBiblio(models.Model):
+ compound_id = models.ForeignKey(Compound)
+ bibliography_id = models.ForeignKey(Bibliography)
+ compound_name = models.CharField('Compound name in the publication', max_length=50)
class Meta:
-# managed = False
- db_table = 'refCmpdBiblio'
- unique_together = (('idcompound', 'idbiblio'),)
-
-"""
+ unique_together = (('compound_id', 'bibliography_id'),)
--
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