From ead2f1828d5732b3d858d0cc9173d02405ae1071 Mon Sep 17 00:00:00 2001
From: Kenzo-Hugo Hillion <kenzo-hugo.hillion1@pasteur.fr>
Date: Mon, 4 Nov 2019 18:06:28 +0100
Subject: [PATCH] Optimise to not have to build hierarchy everytime
---
.../metagenedb/api/catalog/views/taxonomy.py | 2 +-
.../apps/catalog/models/taxonomy.py | 26 +++++++++++++++++--
.../apps/catalog/models/test_taxonomy.py | 5 +++-
3 files changed, 29 insertions(+), 4 deletions(-)
diff --git a/backend/metagenedb/api/catalog/views/taxonomy.py b/backend/metagenedb/api/catalog/views/taxonomy.py
index 9b6f92e..2f9b484 100644
--- a/backend/metagenedb/api/catalog/views/taxonomy.py
+++ b/backend/metagenedb/api/catalog/views/taxonomy.py
@@ -15,6 +15,6 @@ class TaxonomyViewSet(BulkViewSet):
def retrieve(self, request, *args, **kwargs):
instance = self.get_object()
- instance.build_parental_hierarchy()
+ hierarchy = instance.parental_hierarchy # noqa
serializer = self.get_serializer(instance)
return Response(serializer.data)
diff --git a/backend/metagenedb/apps/catalog/models/taxonomy.py b/backend/metagenedb/apps/catalog/models/taxonomy.py
index bc3498d..13c5c01 100644
--- a/backend/metagenedb/apps/catalog/models/taxonomy.py
+++ b/backend/metagenedb/apps/catalog/models/taxonomy.py
@@ -97,11 +97,33 @@ class Taxonomy(models.Model):
def __str__(self):
return f"{self.name}"
- def build_parental_hierarchy(self):
+ @property
+ def parental_hierarchy(self):
+ if self.kingdom is None and self.superkingdom is None:
+ return self._build_parental_hierarchy()
+ return self._dict_parental_hierarchy()
+
+ def _dict_parental_hierarchy(self):
+ """
+ Return parental hierarchy from
+ """
+ ranks = [
+ "superkingdom", "kingdom", "phylum", "class_rank", "order", "family", "genus", "species"
+ ]
+ hierarchy = {}
+ for rank in ranks:
+ if getattr(self, rank, None) is not None:
+ hierarchy[rank] = getattr(self, rank)
+ return hierarchy
+
+ def _build_parental_hierarchy(self):
+ """
+ Build and save parental hierarchy for an entry
+ """
hierarchy = {}
if self.name != 'root' and self.parent is not None:
hierarchy[self.rank] = self
- hierarchy = {**hierarchy, **self.parent.build_parental_hierarchy()}
+ hierarchy = {**hierarchy, **self.parent.parental_hierarchy}
for level, value in hierarchy.items():
setattr(self, level, value)
self.save()
diff --git a/backend/metagenedb/apps/catalog/models/test_taxonomy.py b/backend/metagenedb/apps/catalog/models/test_taxonomy.py
index a9e8cad..3263bd6 100644
--- a/backend/metagenedb/apps/catalog/models/test_taxonomy.py
+++ b/backend/metagenedb/apps/catalog/models/test_taxonomy.py
@@ -33,6 +33,9 @@ class TestBuildHierarchy(APITestCase):
'kingdom': self.kingdom
}
self.assertNotEqual(getattr(self.phylum, 'kingdom', None), self.kingdom)
- test_dict = self.phylum.build_parental_hierarchy()
+ test_dict = self.phylum.parental_hierarchy
self.assertDictEqual(test_dict, expected_dict)
self.assertEqual(getattr(self.phylum, 'kingdom', None), self.kingdom)
+ # Now try a second time from saved information
+ test_dict = self.phylum.parental_hierarchy
+ self.assertDictEqual(test_dict, expected_dict)
--
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