diff --git a/.gitignore b/.gitignore
index 96540b91b86f34830090127c634a32325544c05e..543740071faae3ece06627c568d09b220f1c357f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,7 +1,7 @@
.DS_Store
__pycache__/
*.egg-info/
-.env
+*.env
.env_dev
.idea/
.vscode
@@ -19,3 +19,4 @@ notebooks/
# Tests files
.coverage
+.pytest_cache
diff --git a/backend/metagenedb/apps/catalog/factory/__init__.py b/backend/metagenedb/apps/catalog/factory/__init__.py
index 0bc64025b63e8f1466eb10721d165ec95de7c7b9..2621779eb9c22b7571e0b1dc3f0393e2eb058c39 100644
--- a/backend/metagenedb/apps/catalog/factory/__init__.py
+++ b/backend/metagenedb/apps/catalog/factory/__init__.py
@@ -1,2 +1,3 @@
from .function import FunctionFactory # noqa
+from .gene import GeneFactory # noqa
from .taxonomy import TaxonomyFactory # noqa
diff --git a/backend/metagenedb/apps/catalog/factory/gene.py b/backend/metagenedb/apps/catalog/factory/gene.py
new file mode 100644
index 0000000000000000000000000000000000000000..ba0ca0faece9ed9d0680b30f0bdd4ffd964dbbf4
--- /dev/null
+++ b/backend/metagenedb/apps/catalog/factory/gene.py
@@ -0,0 +1,21 @@
+from factory import DjangoModelFactory, lazy_attribute
+from faker import Factory
+
+from metagenedb.apps.catalog import models
+
+faker = Factory.create()
+
+SELECTED_SOURCE = [i[0] for i in models.Function.SOURCE_CHOICES]
+
+
+class GeneFactory(DjangoModelFactory):
+ class Meta:
+ model = models.Gene
+
+ @lazy_attribute
+ def gene_id(self):
+ return str(faker.pyint())
+
+ @lazy_attribute
+ def length(self):
+ return str(faker.pyint())
diff --git a/backend/metagenedb/apps/catalog/models/__init__.py b/backend/metagenedb/apps/catalog/models/__init__.py
index 696898934e377dce77652053d8169a7c5aa8a77b..c80511a6f0f86e7711a7e6e9ded4a9f1a043b602 100644
--- a/backend/metagenedb/apps/catalog/models/__init__.py
+++ b/backend/metagenedb/apps/catalog/models/__init__.py
@@ -1,3 +1,3 @@
from .function import Function, KeggOrthology # noqa
-from .gene import Gene # noqa
+from .gene import Gene, GeneFunction # noqa
from .taxonomy import Taxonomy # noqa
diff --git a/backend/metagenedb/apps/catalog/serializers/gene.py b/backend/metagenedb/apps/catalog/serializers/gene.py
index 22e6094c8cfad37ce59b0f23a596a4cbfb8214bf..131c47edfe79a9dce774dd2599442b8e6406020c 100644
--- a/backend/metagenedb/apps/catalog/serializers/gene.py
+++ b/backend/metagenedb/apps/catalog/serializers/gene.py
@@ -3,8 +3,7 @@ import traceback
from rest_framework import serializers
from rest_framework.utils import model_meta
-from metagenedb.apps.catalog.models import Function, Gene, Taxonomy
-from metagenedb.apps.catalog.serializers import FunctionSerializer
+from metagenedb.apps.catalog.models import Function, Gene, GeneFunction, Taxonomy
from .bulk_list import BulkListSerializer
@@ -16,15 +15,45 @@ class GeneListSerializer(BulkListSerializer):
class Meta:
model = Gene
+ def _generate_gene_function_mapping(self, values, genes):
+ """
+ Generate a list of GeneFunction pair to create relation between them
+ """
+ genes_dict = {gene.gene_id: gene for gene in genes}
+ mapping = []
+ for value in values:
+ for function in value['functions']:
+ mapping.append(GeneFunction(gene=genes_dict[value['gene_id']],
+ function=function))
+ return mapping
+
+ def _handle_functions(self, values):
+ """
+ :param values: each dictionnary has the 'functions' and 'gene_id' keys
+ :type values: LIST of DICT
+ """
+ # Get all Gene objects
+ gene_ids = [item['gene_id'] for item in values]
+ # Get all link with corresponding genes & Delete them
+ genes = Gene.objects.filter(gene_id__in=gene_ids)
+ GeneFunction.objects.filter(gene__in=genes).delete()
+ # Generate table for bulk_create of function <-> gene and create it
+ GeneFunction.objects.bulk_create(
+ self._generate_gene_function_mapping(values, genes)
+ )
+ print("hi")
+
def create(self, validated_data):
instances = super().create(validated_data)
return instances
class GeneSerializer(serializers.ModelSerializer):
- functions = FunctionSerializer(
+ functions = serializers.SlugRelatedField(
+ queryset=Function.objects.all(),
+ slug_field='function_id',
many=True,
- required=False
+ required=False,
)
taxonomy = serializers.SlugRelatedField(
queryset=Taxonomy.objects.all(),
@@ -47,12 +76,12 @@ class GeneSerializer(serializers.ModelSerializer):
def _handle_functions(self, functions, instance):
for function in functions:
try:
- function = Function.objects.get(function_id=function.get('function_id'))
+ function = Function.objects.get(function_id=function)
instance.functions.add(function)
instance.full_clean()
instance.save()
except Function.DoesNotExist:
- _LOGGER.warning(f"{function.get('function_id')} not found for {instance.gene_id}. Function ignored")
+ _LOGGER.warning("%s not found for %s. Function ignored", function, instance.gene_id)
def create(self, validated_data):
ModelClass = self.Meta.model
diff --git a/backend/metagenedb/apps/catalog/serializers/test_bulk_list.py b/backend/metagenedb/apps/catalog/serializers/test_bulk_list.py
index 10b0ec3f2b977b9eac18474c752da39e844f7969..b5e73770ee680d44f88a5e3c24109c98a2ce3b97 100644
--- a/backend/metagenedb/apps/catalog/serializers/test_bulk_list.py
+++ b/backend/metagenedb/apps/catalog/serializers/test_bulk_list.py
@@ -52,6 +52,29 @@ class TestExtractManyToMany(BaseTestBulkListSerializerMethods):
self.assertDictEqual(tested_dict, expected_dict)
self.assertNotEqual(ori_list, self.data)
+ def test_extract_many_to_many_two_fields(self):
+ self.info.relations = {
+ 'field1': Mock(to_many=True),
+ 'field2': Mock(to_many=True)
+ }
+ ori_list = deepcopy(self.data)
+ expected_dict = {
+ 'keys': {'field1', 'field2'},
+ 'values': {
+ 'field1': [
+ {'field1': 'value1', 'id': 'entry_1'},
+ {'field1': 'value3', 'id': 'entry_2'}
+ ],
+ 'field2': [
+ {'field2': 'value2', 'id': 'entry_1'},
+ {'field2': 'value4', 'id': 'entry_2'}
+ ]
+ }
+ }
+ tested_dict = self.bulk_list_serializer._extract_many_to_many(self.data, self.info, 'id')
+ self.assertDictEqual(tested_dict, expected_dict)
+ self.assertNotEqual(ori_list, self.data)
+
def test_extract_no_many_to_many(self):
self.info.relations = {
'field1': Mock(to_many=False),
@@ -67,18 +90,18 @@ class TestExtractManyToMany(BaseTestBulkListSerializerMethods):
self.assertListEqual(ori_list, self.data)
-class TestGetDbIndexFields(BaseTestBulkListSerializerMethods):
+class TestGetAllKeyFields(BaseTestBulkListSerializerMethods):
- def test_get_db_index_fields(self):
+ def test_get_all_key_fields(self):
expected_keys = ['field1', 'field2']
tested_keys = self.bulk_list_serializer._get_all_key_fields(self.data)
for key in expected_keys:
self.assertIn(key, tested_keys)
-class TestGetKeyFields(BaseTestBulkListSerializerMethods):
+class TestGetDbIndexFields(BaseTestBulkListSerializerMethods):
- def test_get_all_key_fields(self):
+ def test_get_db_index_fields(self):
self.info.fields = {
'field1': Mock(db_index=True),
'field2': Mock(db_index=False)
@@ -87,7 +110,7 @@ class TestGetKeyFields(BaseTestBulkListSerializerMethods):
tested_keys = self.bulk_list_serializer._get_db_index_fields(self.info)
self.assertListEqual(tested_keys, expected_keys)
- def test_get_all_key_fields_no_keys(self):
+ def test_get_db_index_fields_no_keys(self):
self.info.fields = {
'field1': Mock(db_index=False),
'field2': Mock(db_index=False)
diff --git a/backend/metagenedb/apps/catalog/serializers/test_gene.py b/backend/metagenedb/apps/catalog/serializers/test_gene.py
new file mode 100644
index 0000000000000000000000000000000000000000..10e99b878e9d608749e926c2cb4e278e2fc6e013
--- /dev/null
+++ b/backend/metagenedb/apps/catalog/serializers/test_gene.py
@@ -0,0 +1,53 @@
+from unittest import TestCase
+
+from rest_framework.test import APITestCase
+
+from metagenedb.apps.catalog.factory import FunctionFactory, GeneFactory
+from metagenedb.apps.catalog.models import GeneFunction
+from metagenedb.apps.catalog.serializers.gene import GeneListSerializer
+
+
+class GeneListSerializerTest(GeneListSerializer):
+ """
+ overload to skip __init__() and just test the _extract_many_to_many method.
+ """
+
+ def __init__(self):
+ pass
+
+
+class TestGenerateGeneFunctionMapping(TestCase):
+
+ def test_generate_gene_function_mapping(self):
+ genes = [GeneFactory.build(gene_id='gene_1')]
+ values = [{
+ 'gene_id': 'gene_1',
+ 'functions': [FunctionFactory.build()]
+ }]
+ expected_object = GeneFunction(gene=genes[0], function=values[0]['functions'][0])
+ serializer = GeneListSerializerTest()
+ tested_object = serializer._generate_gene_function_mapping(values, genes)[0]
+ self.assertEqual(tested_object.gene, expected_object.gene)
+ self.assertEqual(tested_object.function, expected_object.function)
+
+
+class TestHandleFunctions(APITestCase):
+
+ def test_handle_functions(self):
+ """
+ @TODO function in the gene object is not found but the link is created
+ """
+ gene = GeneFactory.create()
+ function = FunctionFactory.create()
+ values = [{
+ 'gene_id': gene.gene_id,
+ 'functions': [function]
+ }]
+ self.assertNotEqual(gene.functions, [function])
+ self.assertEqual(GeneFunction.objects.all().count(), 0)
+ serializer = GeneListSerializerTest()
+ serializer._handle_functions(values)
+ link = GeneFunction.objects.all()
+ self.assertEqual(link.count(), 1)
+ self.assertEqual(link[0].gene.gene_id, gene.gene_id)
+ self.assertEqual(link[0].function.function_id, function.function_id)