From 9b275b48d1e9928fe7248943f730bf30c158d981 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= <herve.menager@pasteur.fr>
Date: Mon, 29 Jun 2020 20:03:13 +0200
Subject: [PATCH] Use django-polymorphic to manage ProteinDomainComplex
subclasses
WIP on #225
---
..._proteindomaincomplex_polymorphic_ctype.py | 34 +++++++++++++++++++
ippisite/ippidb/models.py | 11 +++++-
ippisite/ippisite/settings.py | 1 +
ippisite/ippisite/settings.template.py | 1 +
ippisite/requirements-core.txt | 1 +
5 files changed, 47 insertions(+), 1 deletion(-)
create mode 100644 ippisite/ippidb/migrations/0064_proteindomaincomplex_polymorphic_ctype.py
diff --git a/ippisite/ippidb/migrations/0064_proteindomaincomplex_polymorphic_ctype.py b/ippisite/ippidb/migrations/0064_proteindomaincomplex_polymorphic_ctype.py
new file mode 100644
index 00000000..aa4370a4
--- /dev/null
+++ b/ippisite/ippidb/migrations/0064_proteindomaincomplex_polymorphic_ctype.py
@@ -0,0 +1,34 @@
+# Generated by Django 2.2.1 on 2020-06-29 06:51
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+
+def forwards_func(apps, schema_editor):
+ # add the content type to the classes using django-polymorphic
+ # i.e. ProteinDomainBoundComplex and ProteinDomainPartnerComplex
+ # code is adapted from https://django-polymorphic.readthedocs.io/en/stable/migrating.html
+ ProteinDomainBoundComplex = apps.get_model('ippidb', 'ProteinDomainBoundComplex')
+ ProteinDomainPartnerComplex = apps.get_model('ippidb', 'ProteinDomainPartnerComplex')
+ ContentType = apps.get_model('contenttypes', 'ContentType')
+ pdbc_ct = ContentType.objects.get_for_model(ProteinDomainBoundComplex)
+ ProteinDomainBoundComplex.objects.filter(polymorphic_ctype__isnull=True).update(polymorphic_ctype=pdbc_ct)
+ pdpc_ct = ContentType.objects.get_for_model(ProteinDomainPartnerComplex)
+ ProteinDomainPartnerComplex.objects.filter(polymorphic_ctype__isnull=True).update(polymorphic_ctype=pdpc_ct)
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('contenttypes', '0002_remove_content_type_name'),
+ ('ippidb', '0063_fill_drugbank_links'),
+ ]
+
+ operations = [
+ migrations.AddField(
+ model_name='proteindomaincomplex',
+ name='polymorphic_ctype',
+ field=models.ForeignKey(editable=False, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='polymorphic_ippidb.proteindomaincomplex_set+', to='contenttypes.ContentType'),
+ ),
+ migrations.RunPython(forwards_func, migrations.RunPython.noop),
+ ]
diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index fd6d9bde..aa3ce3de 100644
--- a/ippisite/ippidb/models.py
+++ b/ippisite/ippidb/models.py
@@ -20,6 +20,7 @@ from django.utils.translation import ugettext_lazy as _
from django_celery_results.models import TaskResult
from django.dispatch import receiver
from django.db.models.signals import post_save
+from polymorphic.models import PolymorphicModel
from .utils import FingerPrinter, smi2inchi, smi2inchikey
from .ws import (
@@ -363,7 +364,7 @@ class ProteinDomainComplexGroup(models.Model):
return str(self)
-class ProteinDomainComplex(models.Model):
+class ProteinDomainComplex(PolymorphicModel):
"""
Protein-Domain association
"""
@@ -405,6 +406,10 @@ class ProteinDomainBoundComplex(ProteinDomainComplex):
ppp_copy_nb_per_p = models.IntegerField(_("ppp_copy_nb_per_p"))
+ @property
+ def complex_type(self):
+ return "Bound"
+
class Meta:
verbose_name_plural = "bound complexes"
@@ -427,6 +432,10 @@ class ProteinDomainPartnerComplex(ProteinDomainComplex):
Protein-Domain association with a "partner complex" role
"""
+ @property
+ def complex_type(self):
+ return "Partner"
+
class Meta:
verbose_name_plural = "partner complexes"
diff --git a/ippisite/ippisite/settings.py b/ippisite/ippisite/settings.py
index eae1293b..1cd64c66 100644
--- a/ippisite/ippisite/settings.py
+++ b/ippisite/ippisite/settings.py
@@ -57,6 +57,7 @@ INSTALLED_APPS = [
"allauth.socialaccount",
# "allauth.socialaccount.providers.github",
"allauth.socialaccount.providers.orcid",
+ "polymorphic",
]
MIDDLEWARE = [
diff --git a/ippisite/ippisite/settings.template.py b/ippisite/ippisite/settings.template.py
index cc738033..8991371a 100644
--- a/ippisite/ippisite/settings.template.py
+++ b/ippisite/ippisite/settings.template.py
@@ -60,6 +60,7 @@ INSTALLED_APPS = [
"allauth.socialaccount",
# "allauth.socialaccount.providers.github",
"allauth.socialaccount.providers.orcid",
+ "polymorphic",
]
MIDDLEWARE = [
diff --git a/ippisite/requirements-core.txt b/ippisite/requirements-core.txt
index f1744c72..3cde9a19 100644
--- a/ippisite/requirements-core.txt
+++ b/ippisite/requirements-core.txt
@@ -28,3 +28,4 @@ git+https://gitlab.pasteur.fr/hmenager/django-diu.git#egg=django_diu
#openbabel
django-crispy-forms
celery
+django-polymorphic
\ No newline at end of file
--
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