From 2fe3bd45d0f090e4e7fbfcff76b3eb162117d86d Mon Sep 17 00:00:00 2001
From: Kenzo-Hugo Hillion <kenzo-hugo.hillion1@pasteur.fr>
Date: Mon, 2 Dec 2019 16:17:51 +0100
Subject: [PATCH] add route to retrieve counts of taxonomical annotations per
level
---
.../api/catalog/qparams_validators/gene.py | 9 ++++
backend/metagenedb/api/catalog/views/gene.py | 46 ++++++++++++++++++-
.../metagenedb/api/catalog/views/test_gene.py | 46 ++++++++++++++++++-
.../metagenedb/apps/catalog/factory/gene.py | 4 +-
.../common/utils/mocks/metagenedb.py | 9 ++++
5 files changed, 110 insertions(+), 4 deletions(-)
diff --git a/backend/metagenedb/api/catalog/qparams_validators/gene.py b/backend/metagenedb/api/catalog/qparams_validators/gene.py
index 160adf7..9da2277 100644
--- a/backend/metagenedb/api/catalog/qparams_validators/gene.py
+++ b/backend/metagenedb/api/catalog/qparams_validators/gene.py
@@ -1,7 +1,12 @@
from marshmallow import Schema, fields
+from marshmallow.validate import OneOf
from metagenedb.common.django_default.qparams_validators import PaginatedQueryParams
+TAXA_CHOICES = [
+ 'superkingdom', 'kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species'
+]
+
class GeneLengthQueryParams(Schema):
window_size = fields.Integer()
@@ -11,3 +16,7 @@ class GeneLengthQueryParams(Schema):
class GeneQueryParams(PaginatedQueryParams):
no_taxonomy = fields.Boolean()
no_functions = fields.Boolean()
+
+
+class TaxCountQueryParams(Schema):
+ level = fields.String(validate=OneOf(choices=TAXA_CHOICES))
diff --git a/backend/metagenedb/api/catalog/views/gene.py b/backend/metagenedb/api/catalog/views/gene.py
index dcf485e..65f9b9b 100644
--- a/backend/metagenedb/api/catalog/views/gene.py
+++ b/backend/metagenedb/api/catalog/views/gene.py
@@ -1,3 +1,5 @@
+from collections import defaultdict
+
from django.db.models import Max
from drf_yasg import openapi
from drf_yasg.utils import swagger_auto_schema
@@ -8,7 +10,7 @@ from rest_framework.status import HTTP_204_NO_CONTENT, HTTP_422_UNPROCESSABLE_EN
from metagenedb.apps.catalog.models import Gene
from metagenedb.api.catalog.filters import GeneFilter
-from metagenedb.api.catalog.qparams_validators.gene import GeneLengthQueryParams, GeneQueryParams
+from metagenedb.api.catalog.qparams_validators.gene import GeneLengthQueryParams, GeneQueryParams, TaxCountQueryParams
from metagenedb.apps.catalog.serializers import GeneSerializer
from .bulk_viewset import BulkViewSet
@@ -55,6 +57,8 @@ class GeneViewSet(BulkViewSet):
DEFAULT_WINDOW_SIZE = 1000
DEFAULT_STOP_AT = 10000
+ DEFAULT_LEVEL = 'phylum'
+
def get_permissions(self):
return super(self.__class__, self).get_permissions()
@@ -105,7 +109,6 @@ class GeneViewSet(BulkViewSet):
window_size = query_params.get('window_size', self.DEFAULT_WINDOW_SIZE)
stop_at = query_params.get('stop_at', self.DEFAULT_STOP_AT)
- # df = read_frame(Gene.objects.all(), fieldnames=[self.GENE_LENGTH_COL])
queryset = Gene.objects.all()
if not queryset.exists():
return Response(
@@ -115,3 +118,42 @@ class GeneViewSet(BulkViewSet):
return Response(
{'results': self._count_windows(queryset, window_size=window_size, stop_at=stop_at)}
)
+
+ def _taxonomy_counts(self, queryset, level=DEFAULT_LEVEL):
+ filter_no_annotation = {f"taxonomy__{level}__isnull": True}
+ filter_annotation = {f"taxonomy__{level}__isnull": False}
+ value_to_retrieve = f'taxonomy__{level}__name'
+ taxonomy_counts = {}
+ taxonomy_counts['counts'] = defaultdict(lambda: 0)
+ taxonomy_counts['counts']['No annotation'] = queryset.filter(**filter_no_annotation).values().count()
+ if taxonomy_counts['counts']['No annotation'] == 0:
+ del taxonomy_counts['counts']['No annotation']
+ for value in queryset.filter(**filter_annotation).values(value_to_retrieve):
+ tax_name = value[value_to_retrieve]
+ taxonomy_counts['counts'][tax_name] += 1
+ return taxonomy_counts
+
+ @action(methods=['get'], detail=False)
+ def taxonomy_counts(self, request):
+ try:
+ query_params = TaxCountQueryParams().load(request.query_params)
+ except ValidationError as validation_error:
+ error_message = validation_error.normalized_messages()
+ error_message.update({
+ 'allowed_query_params': ', '.join(GeneLengthQueryParams().declared_fields.keys())
+ })
+ return Response(error_message, status=HTTP_422_UNPROCESSABLE_ENTITY)
+
+ level = query_params.get('level', self.DEFAULT_LEVEL)
+ level = 'class_rank' if level == 'class' else level # deal with class exception @TODO fix cleaner way
+ queryset = Gene.objects.all().select_related(f'taxonomy__{level}')
+ if not queryset.exists():
+ return Response(
+ {},
+ status=HTTP_204_NO_CONTENT
+ )
+ counts = self._taxonomy_counts(queryset, level=level)
+ counts['level'] = query_params.get('level', self.DEFAULT_LEVEL)
+ return Response(
+ {'results': counts}
+ )
diff --git a/backend/metagenedb/api/catalog/views/test_gene.py b/backend/metagenedb/api/catalog/views/test_gene.py
index 24e2ee2..e2e4421 100644
--- a/backend/metagenedb/api/catalog/views/test_gene.py
+++ b/backend/metagenedb/api/catalog/views/test_gene.py
@@ -5,7 +5,7 @@ from rest_framework import status
from rest_framework.test import APITestCase
from rest_framework_jwt.settings import api_settings
-from metagenedb.apps.catalog.factory import GeneFactory
+from metagenedb.apps.catalog.factory import GeneFactory, TaxonomyFactory
from metagenedb.common.utils.mocks.metagenedb import MetageneDBCatalogGeneAPIMock
@@ -71,3 +71,47 @@ class TestCountWindowsAPI(APITestCase):
'stop_at': 2000
}
self.assertDictEqual(self.gene_api.get_gene_length(params=query_params), expected_dict)
+
+
+class TestTaxonomyCountsAPI(APITestCase):
+
+ def setUp(self):
+ self.gene_api = MetageneDBCatalogGeneAPIMock(self.client)
+
+ def test_taxonomy_counts_no_content(self):
+ self.assertFalse(self.gene_api.get_tax_counts())
+
+ def test_taxonomy_counts_api(self):
+ tax_name = "TaxTest"
+ taxonomy = TaxonomyFactory(rank='phylum', name=tax_name)
+ taxonomy.phylum = taxonomy # link taxonomy to itself as phylum
+ taxonomy.save()
+ gene = GeneFactory.create(taxonomy=taxonomy) # noqa
+ expected_dict = {
+ 'results': {
+ 'level': 'phylum',
+ 'counts': {
+ tax_name: 1
+ }
+ }
+ }
+ self.assertDictEqual(self.gene_api.get_tax_counts(), expected_dict)
+
+ def test_taxonomy_counts_api_class_level(self):
+ tax_name = "TaxTest"
+ taxonomy = TaxonomyFactory(rank='class_rank', name=tax_name)
+ taxonomy.class_rank = taxonomy # link taxonomy to itself as phylum
+ taxonomy.save()
+ gene = GeneFactory.create(taxonomy=taxonomy) # noqa
+ expected_dict = {
+ 'results': {
+ 'level': 'class',
+ 'counts': {
+ tax_name: 1
+ }
+ }
+ }
+ query_params = {
+ 'level': 'class'
+ }
+ self.assertDictEqual(self.gene_api.get_tax_counts(params=query_params), expected_dict)
diff --git a/backend/metagenedb/apps/catalog/factory/gene.py b/backend/metagenedb/apps/catalog/factory/gene.py
index ec337ea..7423229 100644
--- a/backend/metagenedb/apps/catalog/factory/gene.py
+++ b/backend/metagenedb/apps/catalog/factory/gene.py
@@ -1,9 +1,10 @@
-from factory import DjangoModelFactory, fuzzy
+from factory import DjangoModelFactory, SubFactory, fuzzy
from faker import Factory
from metagenedb.apps.catalog import models
from .fuzzy_base import FuzzyLowerText
+from .taxonomy import TaxonomyFactory
faker = Factory.create()
@@ -17,3 +18,4 @@ class GeneFactory(DjangoModelFactory):
gene_id = FuzzyLowerText(prefix='gene-', length=15)
gene_name = fuzzy.FuzzyText(prefix='name-', length=15)
length = fuzzy.FuzzyInteger(200, 10000)
+ taxonomy = SubFactory(TaxonomyFactory)
diff --git a/backend/metagenedb/common/utils/mocks/metagenedb.py b/backend/metagenedb/common/utils/mocks/metagenedb.py
index 8f39b15..01f65ed 100644
--- a/backend/metagenedb/common/utils/mocks/metagenedb.py
+++ b/backend/metagenedb/common/utils/mocks/metagenedb.py
@@ -56,6 +56,15 @@ class MetageneDBCatalogGeneAPIMock(MetageneDBAPIMock):
return {}
return response.json()
+ def get_tax_counts(self, params=None):
+ reverse_path = f"{self.reverse_path}-taxonomy-counts"
+ response = self.client.get(reverse(reverse_path), params)
+ if response.status_code in self.BAD_REQUESTS:
+ raise HTTPError
+ if response.status_code == 204: # no content
+ return {}
+ return response.json()
+
class MetageneDBCatalogTaxonomyAPIMock(MetageneDBAPIMock):
KEY_ID = 'gene_id'
--
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