Add building of hierarchy from direct parent

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')

backend/metagenedb/apps/catalog/migrations/0003_auto_20190717_1551.py

+# 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'),
+        ),
+    ]

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"

backend/metagenedb/apps/catalog/models/test_taxonomy.py

+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)

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',
+        )

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__":