diff --git a/backend/metagenedb/apps/catalog/admin/taxonomy.py b/backend/metagenedb/apps/catalog/admin/taxonomy.py
index cb5857ef338bda64c56f8b4d4f2f0956a0a9f3de..79090d33522e6487f19714f3f769881205ca9d2b 100644
--- a/backend/metagenedb/apps/catalog/admin/taxonomy.py
+++ b/backend/metagenedb/apps/catalog/admin/taxonomy.py
@@ -6,5 +6,8 @@ from metagenedb.apps.catalog.models import Taxonomy
@admin.register(Taxonomy)
class TaxonomyAdmin(admin.ModelAdmin):
- list_display = ('tax_id', 'name', 'rank', 'parent')
+ list_display = (
+ 'tax_id', 'name', 'rank',
+ 'kingdom', 'phylum', 'class_rank', 'order', 'family', 'genus', 'species',
+ )
search_fields = ('tax_id', 'name')
diff --git a/backend/metagenedb/apps/catalog/migrations/0003_auto_20190717_1551.py b/backend/metagenedb/apps/catalog/migrations/0003_auto_20190717_1551.py
new file mode 100644
index 0000000000000000000000000000000000000000..d54074d3fc529e3dcdcce3e8d8185431ab73e9c8
--- /dev/null
+++ b/backend/metagenedb/apps/catalog/migrations/0003_auto_20190717_1551.py
@@ -0,0 +1,54 @@
+# Generated by Django 2.2.1 on 2019-07-17 13:51
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('catalog', '0002_taxonomy'),
+ ]
+
+ operations = [
+ migrations.AddField(
+ model_name='taxonomy',
+ name='class_rank',
+ field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='class_children', to='catalog.Taxonomy', verbose_name='class'),
+ ),
+ migrations.AddField(
+ model_name='taxonomy',
+ name='family',
+ field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='family_children', to='catalog.Taxonomy'),
+ ),
+ migrations.AddField(
+ model_name='taxonomy',
+ name='genus',
+ field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='genus_children', to='catalog.Taxonomy'),
+ ),
+ migrations.AddField(
+ model_name='taxonomy',
+ name='kingdom',
+ field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='kingdom_children', to='catalog.Taxonomy'),
+ ),
+ migrations.AddField(
+ model_name='taxonomy',
+ name='order',
+ field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='order_children', to='catalog.Taxonomy'),
+ ),
+ migrations.AddField(
+ model_name='taxonomy',
+ name='phylum',
+ field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='phylum_children', to='catalog.Taxonomy'),
+ ),
+ migrations.AddField(
+ model_name='taxonomy',
+ name='species',
+ field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='species_children', to='catalog.Taxonomy'),
+ ),
+ migrations.AlterField(
+ model_name='taxonomy',
+ name='parent',
+ field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='direct_children', to='catalog.Taxonomy'),
+ ),
+ ]
diff --git a/backend/metagenedb/apps/catalog/models/taxonomy.py b/backend/metagenedb/apps/catalog/models/taxonomy.py
index 3f6fc43a62dc37fbaf0025639af3cb2dda9dac2c..ccd113596bbfcbcd3c3068331afe3d54ebd933ab 100644
--- a/backend/metagenedb/apps/catalog/models/taxonomy.py
+++ b/backend/metagenedb/apps/catalog/models/taxonomy.py
@@ -47,8 +47,44 @@ class Taxonomy(models.Model):
name = models.CharField(max_length=200, default=NAME_DEFAULT)
rank = models.CharField(max_length=20, choices=RANK_CHOICES)
parent = models.ForeignKey(
- 'Taxonomy',
- related_name='children',
+ 'Taxonomy', related_name='direct_children',
+ on_delete=models.SET_NULL,
+ null=True, blank=True,
+ )
+
+ kingdom = models.ForeignKey(
+ 'Taxonomy', related_name='kingdom_children',
+ on_delete=models.SET_NULL,
+ null=True, blank=True,
+ )
+ phylum = models.ForeignKey(
+ 'Taxonomy', related_name='phylum_children',
+ on_delete=models.SET_NULL,
+ null=True, blank=True,
+ )
+ class_rank = models.ForeignKey(
+ 'Taxonomy', related_name='class_children',
+ on_delete=models.SET_NULL,
+ null=True, blank=True,
+ verbose_name="class"
+ )
+ order = models.ForeignKey(
+ 'Taxonomy', related_name='order_children',
+ on_delete=models.SET_NULL,
+ null=True, blank=True,
+ )
+ family = models.ForeignKey(
+ 'Taxonomy', related_name='familyphy_children',
+ on_delete=models.SET_NULL,
+ null=True, blank=True,
+ )
+ genus = models.ForeignKey(
+ 'Taxonomy', related_name='genus_children',
+ on_delete=models.SET_NULL,
+ null=True, blank=True,
+ )
+ species = models.ForeignKey(
+ 'Taxonomy', related_name='species_children',
on_delete=models.SET_NULL,
null=True, blank=True,
)
@@ -56,5 +92,13 @@ class Taxonomy(models.Model):
def __str__(self):
return f"{self.name}"
+ def build_parental_hierarchy(self):
+ hierarchy = {}
+ if self.name != 'root' and self.parent is not None:
+ hierarchy[self.rank] = self.tax_id
+ hierarchy = {**hierarchy, **self.parent.build_parental_hierarchy()}
+ hierarchy['tax_id'] = self.tax_id
+ return hierarchy
+
class Meta:
verbose_name_plural = "Taxonomy"
diff --git a/backend/metagenedb/apps/catalog/models/test_taxonomy.py b/backend/metagenedb/apps/catalog/models/test_taxonomy.py
new file mode 100644
index 0000000000000000000000000000000000000000..141485119c0b315d64d856c17bd9e52c88a46f3a
--- /dev/null
+++ b/backend/metagenedb/apps/catalog/models/test_taxonomy.py
@@ -0,0 +1,38 @@
+from unittest import TestCase
+
+from .taxonomy import Taxonomy
+
+
+class TestBuildHierarchy(TestCase):
+
+ @classmethod
+ def setUpClass(cls):
+ """
+ Build some test data for different tests
+ """
+ cls.root = Taxonomy(
+ tax_id="1",
+ name="root",
+ rank="no_rank",
+ )
+ cls.kingdom = Taxonomy(
+ tax_id="2",
+ name="KINGDOM",
+ rank="kingdom",
+ parent=cls.root
+ )
+ cls.phylum = Taxonomy(
+ tax_id="3",
+ name="PHYLUM",
+ rank="phylum",
+ parent=cls.kingdom
+ )
+
+ def test_build_hierarchy(self):
+ expected_dict = {
+ 'tax_id': '3',
+ 'phylum': '3',
+ 'kingdom': '2'
+ }
+ test_dict = self.phylum.build_parental_hierarchy()
+ self.assertDictEqual(test_dict, expected_dict)
diff --git a/backend/metagenedb/apps/catalog/serializers/taxonomy.py b/backend/metagenedb/apps/catalog/serializers/taxonomy.py
index 6c6b4e22d38fb218d17edd250851c5640c3689ee..87816c32c8b34c1ad5b90c524830e91799efe8e4 100644
--- a/backend/metagenedb/apps/catalog/serializers/taxonomy.py
+++ b/backend/metagenedb/apps/catalog/serializers/taxonomy.py
@@ -3,13 +3,52 @@ from metagenedb.apps.catalog.models import Taxonomy
class TaxonomySerializer(serializers.ModelSerializer):
+ rank = serializers.CharField(required=False)
parent_tax_id = serializers.SlugRelatedField(
queryset=Taxonomy.objects.all(),
slug_field='tax_id',
source='parent',
+ required=False,
+ )
+ kingdom = serializers.SlugRelatedField(
+ queryset=Taxonomy.objects.all(),
+ slug_field='tax_id',
+ required=False
+ )
+ phylum = serializers.SlugRelatedField(
+ queryset=Taxonomy.objects.all(),
+ slug_field='tax_id',
+ required=False
+ )
+ class_rank = serializers.SlugRelatedField(
+ queryset=Taxonomy.objects.all(),
+ slug_field='tax_id',
+ required=False
+ )
+ order = serializers.SlugRelatedField(
+ queryset=Taxonomy.objects.all(),
+ slug_field='tax_id',
+ required=False
+ )
+ family = serializers.SlugRelatedField(
+ queryset=Taxonomy.objects.all(),
+ slug_field='tax_id',
+ required=False
+ )
+ genus = serializers.SlugRelatedField(
+ queryset=Taxonomy.objects.all(),
+ slug_field='tax_id',
+ required=False
+ )
+ species = serializers.SlugRelatedField(
+ queryset=Taxonomy.objects.all(),
+ slug_field='tax_id',
required=False
- )
+ )
class Meta:
model = Taxonomy
- fields = ('tax_id', 'name', 'rank', 'parent_tax_id')
+ fields = (
+ 'tax_id', 'name', 'rank', 'parent_tax_id',
+ 'kingdom', 'phylum', 'class_rank', 'order', 'family', 'genus', 'species',
+ )
diff --git a/backend/scripts/populate_db/import_ncbi_taxonomy.py b/backend/scripts/populate_db/import_ncbi_taxonomy.py
index 351b87e761f41fb86671e825829c908d472bbc11..3206c02fd85e41e39435f261de36e4852e25ab37 100755
--- a/backend/scripts/populate_db/import_ncbi_taxonomy.py
+++ b/backend/scripts/populate_db/import_ncbi_taxonomy.py
@@ -50,7 +50,7 @@ def create_taxo_nodes(taxonomy_nodes_file, taxo_name_dict):
def update_taxo_nodes(taxonomy_nodes_file):
- _LOGGER.info(f"Linking taxonomy objects to parental nodes from {taxonomy_nodes_file}...")
+ _LOGGER.info(f"Linking taxonomy objects to direct parental node from {taxonomy_nodes_file}...")
with open(taxonomy_nodes_file, "r") as file:
for i in file:
node = NCBITaxonomyLineParser.node(i)
@@ -59,7 +59,24 @@ def update_taxo_nodes(taxonomy_nodes_file):
if serializer.is_valid():
serializer.save()
else:
- _LOGGER.warning(f"Invalid data: {serializer.errors}. Insertion skipped. Data: {serializer.data}")
+ _LOGGER.warning(f"Invalid data: {serializer.errors}. Link to parent skipped. Data: {serializer.data}")
+
+
+def build_hierarchy():
+ """
+ Uses class method from Taxonomy model to retrieve the parental hierarchy and
+ assign corresponding attribute to each entry.
+ """
+ _LOGGER.info(f"Linking taxonomy objects to parental nodes from direct parental nodes...")
+ for taxo in Taxonomy.objects.all():
+ hierarchy = taxo.build_parental_hierarchy()
+ if 'class' in hierarchy.keys():
+ hierarchy['class_rank'] = hierarchy.pop('class')
+ serializer = TaxonomySerializer(taxo, hierarchy)
+ if serializer.is_valid():
+ serializer.save()
+ else:
+ _LOGGER.warning(f"Invalid data: {serializer.errors}. Building hierarchy skipped. Data: {serializer.data}")
def parse_arguments():
@@ -82,6 +99,7 @@ def run():
taxonomy_names = import_names(args.names)
create_taxo_nodes(args.nodes, taxonomy_names)
update_taxo_nodes(args.nodes)
+ build_hierarchy()
if __name__ == "__main__":