From 81e4e2ebb0533f6969f1ae686782290d87454ece Mon Sep 17 00:00:00 2001
From: Kenzo-Hugo Hillion <kenzo-hugo.hillion1@pasteur.fr>
Date: Thu, 12 Sep 2019 15:44:50 +0200
Subject: [PATCH] add table for gene to function m2m
---
.../catalog/migrations/0010_genefunction.py | 37 +++++++++++++++++++
.../0011_change_through_genefunction.py | 23 ++++++++++++
.../metagenedb/apps/catalog/models/gene.py | 14 ++++++-
3 files changed, 73 insertions(+), 1 deletion(-)
create mode 100644 backend/metagenedb/apps/catalog/migrations/0010_genefunction.py
create mode 100644 backend/metagenedb/apps/catalog/migrations/0011_change_through_genefunction.py
diff --git a/backend/metagenedb/apps/catalog/migrations/0010_genefunction.py b/backend/metagenedb/apps/catalog/migrations/0010_genefunction.py
new file mode 100644
index 0000000..1f44bec
--- /dev/null
+++ b/backend/metagenedb/apps/catalog/migrations/0010_genefunction.py
@@ -0,0 +1,37 @@
+# Generated by Django 2.2.5 on 2019-09-12 13:08
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+from metagenedb.common.utils.chunks import generate_chunks
+
+
+def copy_gene_functions(apps, schema_editor):
+ Gene = apps.get_model('catalog', 'Gene')
+ GeneFunction = apps.get_model('catalog', 'GeneFunction')
+ OldGeneFunctions = Gene.functions.through
+ for chunk in generate_chunks(OldGeneFunctions.objects.all(), 500):
+ new_objs = [GeneFunction(gene=item.gene, function=item.function) for item in chunk]
+ GeneFunction.objects.bulk_create(new_objs)
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('catalog', '0009_meta_unique'),
+ ]
+
+ operations = [
+ migrations.CreateModel(
+ name='GeneFunction',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('function', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='catalog.Function')),
+ ('gene', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='catalog.Gene')),
+ ],
+ options={
+ 'unique_together': {('gene', 'function')},
+ },
+ ),
+ migrations.RunPython(copy_gene_functions)
+ ]
diff --git a/backend/metagenedb/apps/catalog/migrations/0011_change_through_genefunction.py b/backend/metagenedb/apps/catalog/migrations/0011_change_through_genefunction.py
new file mode 100644
index 0000000..82fb137
--- /dev/null
+++ b/backend/metagenedb/apps/catalog/migrations/0011_change_through_genefunction.py
@@ -0,0 +1,23 @@
+# Generated by Django 2.2.5 on 2019-09-12 13:43
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('catalog', '0010_genefunction'),
+ ]
+
+ operations = [
+ migrations.RemoveField(
+ model_name='gene',
+ name='functions',
+ field=models.ManyToManyField(to='catalog.Function'),
+ ),
+ migrations.AddField(
+ model_name='gene',
+ name='functions',
+ field=models.ManyToManyField(through='catalog.GeneFunction', to='catalog.Function'),
+ ),
+ ]
diff --git a/backend/metagenedb/apps/catalog/models/gene.py b/backend/metagenedb/apps/catalog/models/gene.py
index 802ef9f..453910d 100644
--- a/backend/metagenedb/apps/catalog/models/gene.py
+++ b/backend/metagenedb/apps/catalog/models/gene.py
@@ -7,7 +7,7 @@ class Gene(models.Model):
gene_name = models.CharField(max_length=100, unique=True)
gene_id = models.SlugField(max_length=100, db_index=True, unique=True)
length = models.PositiveIntegerField()
- functions = models.ManyToManyField(Function)
+ functions = models.ManyToManyField(Function, through='GeneFunction')
taxonomy = models.ForeignKey(
'Taxonomy', related_name='genes',
on_delete=models.SET_NULL,
@@ -19,3 +19,15 @@ class Gene(models.Model):
class Meta:
ordering = ['-gene_id']
+
+class GeneFunction(models.Model):
+ gene = models.ForeignKey(Gene, on_delete=models.CASCADE)
+ function = models.ForeignKey(Function, on_delete=models.CASCADE)
+
+ def __str__(self):
+ return f"{self.gene.gene_id} <-> {self.function.function_id}"
+
+ class Meta:
+ unique_together = [
+ 'gene', 'function'
+ ]
--
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