continue update method for bulklist

backend/metagenedb/apps/catalog/factory/__init__.py

+from .function import FunctionFactory  # noqa
 from .taxonomy import TaxonomyFactory  # noqa

backend/metagenedb/apps/catalog/factory/function.py

+from factory import fuzzy
+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 FunctionFactory(DjangoModelFactory):
+    class Meta:
+        model = models.Function
+
+    source = fuzzy.FuzzyChoice(SELECTED_SOURCE)
+
+    @lazy_attribute
+    def function_id(self):
+        return str(faker.pyint())

backend/metagenedb/apps/catalog/factory/taxonomy.py

@@ -17,4 +17,4 @@ class TaxonomyFactory(DjangoModelFactory):
 
     @lazy_attribute
     def tax_id(self):
-        return faker.pyint()
+        return str(faker.pyint())

backend/metagenedb/apps/catalog/migrations/0009_meta_taxonomy_functions.py → backend/metagenedb/apps/catalog/migrations/0009_meta_unique.py

-# Generated by Django 2.2.4 on 2019-08-29 09:23
+# Generated by Django 2.2.4 on 2019-08-29 13:18
 
-from django.db import migrations
+from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
@@ -18,4 +18,9 @@ class Migration(migrations.Migration):
             name='taxonomy',
             options={'ordering': ['-tax_id'], 'verbose_name_plural': 'Taxonomy'},
         ),
+        migrations.AlterField(
+            model_name='function',
+            name='function_id',
+            field=models.CharField(db_index=True, max_length=100, unique=True),
+        ),
     ]

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

@@ -11,7 +11,7 @@ class Function(models.Model):
         (EGGNOG, 'EggNOG')
     ]
 
-    function_id = models.CharField(max_length=100, db_index=True)
+    function_id = models.CharField(max_length=100, db_index=True, unique=True)
     name = models.CharField(max_length=100)
     source = models.CharField(max_length=10, choices=SOURCE_CHOICES, default=UNDEFINED)
 

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

@@ -5,7 +5,7 @@ from .function import Function
 
 class Gene(models.Model):
     gene_name = models.CharField(max_length=100, unique=True)
-    gene_id = models.SlugField(max_length=100, unique=True)
+    gene_id = models.SlugField(max_length=100, db_index=True, unique=True)
     length = models.PositiveIntegerField()
     functions = models.ManyToManyField(Function)
     taxonomy = models.ForeignKey(

backend/metagenedb/apps/catalog/serializers/bulk_list.py

@@ -9,14 +9,17 @@ class BulkListSerializer(serializers.ListSerializer):
         for field_name, relation_info in info.relations.items():
             if relation_info.to_many:
                 for data_item, many_to_many_item in zip(validated_data, many_to_many):
-                    print(many_to_many_item, data_item)
                     if field_name in data_item:
                         many_to_many_item[field_name] = data_item.pop(field_name)
-                    else:
-                        print("missing key")
-                    print(many_to_many_item, data_item)
         return many_to_many
 
+    def _get_db_index_fields(self, info):
+        db_index_keys = []
+        for field_name, field in info.fields.items():
+            if field.db_index:
+                db_index_keys.append(field_name)
+        return db_index_keys
+
     def create(self, validated_data):
         ModelClass = self.Meta.model
         instances = ModelClass.objects.bulk_create(
@@ -24,5 +27,16 @@ class BulkListSerializer(serializers.ListSerializer):
         )
         return instances
 
+    def update(self, instances, validated_data):
+        ModelClass = self.Meta.model
+        info = model_meta.get_field_info(ModelClass)
+        db_index_fields = self._get_db_index_fields(info)
+        id_list = [data.pop(db_index_fields[0]) for data in validated_data]  # noqa
+        instances = ModelClass.objects.bulk_update(
+            instances,
+            ['name']
+        )
+        return instances
+
     class Meta:
         model = NotImplemented

backend/metagenedb/apps/catalog/serializers/test_bulk_list.py

@@ -4,9 +4,10 @@ from unittest.mock import Mock
 
 from rest_framework.test import APITestCase
 
-from metagenedb.common.utils.mocks.metagenedb import MetageneDBCatalogFunctionAPIMock
 from metagenedb.apps.catalog.serializers import FunctionSerializer
 from metagenedb.apps.catalog.serializers.bulk_list import BulkListSerializer
+from metagenedb.apps.catalog.factory import FunctionFactory
+from metagenedb.common.utils.mocks.metagenedb import MetageneDBCatalogFunctionAPIMock
 
 
 class BulkListSerializerTestExtractManyToMany(BulkListSerializer):
@@ -18,7 +19,7 @@ class BulkListSerializerTestExtractManyToMany(BulkListSerializer):
         pass
 
 
-class TestExtractManyToMany(TestCase):
+class BaseTestBulkListSerializerMethods(TestCase):
 
     def setUp(self):
         self.data = [
@@ -28,6 +29,9 @@ class TestExtractManyToMany(TestCase):
         self.bulk_list_serializer = BulkListSerializerTestExtractManyToMany()
         self.info = Mock()
 
+
+class TestExtractManyToMany(BaseTestBulkListSerializerMethods):
+
     def test_extract_many_to_many(self):
         self.info.relations = {
             'field1': Mock(to_many=True),
@@ -57,6 +61,27 @@ class TestExtractManyToMany(TestCase):
         self.assertListEqual(ori_list, self.data)
 
 
+class TestGetDbIndexFields(BaseTestBulkListSerializerMethods):
+
+    def test_get_db_index_fields(self):
+        self.info.fields = {
+            'field1': Mock(db_index=True),
+            'field2': Mock(db_index=False)
+        }
+        expected_keys = ['field1']
+        tested_keys = self.bulk_list_serializer._get_db_index_fields(self.info)
+        self.assertListEqual(tested_keys, expected_keys)
+
+    def test_get_db_index_fields_no_keys(self):
+        self.info.fields = {
+            'field1': Mock(db_index=False),
+            'field2': Mock(db_index=False)
+        }
+        expected_keys = []
+        tested_keys = self.bulk_list_serializer._get_db_index_fields(self.info)
+        self.assertListEqual(tested_keys, expected_keys)
+
+
 class TestCreateBulk(APITestCase):
     """
     We are going to use an Serializer based on a real model since there are interactions with the DB.
@@ -83,3 +108,22 @@ class TestCreateBulk(APITestCase):
         tested_instances = serializer.create(validated_data)
         self.assertEqual(self.function_api.get_all()['count'], 2)
         self.assertEqual(len(tested_instances), len(validated_data))
+
+    def test_update_existing_functions(self):
+        functions = FunctionFactory.create_batch(2)
+        validated_data = [
+            {
+                "function_id": functions[0].function_id,
+                "source": functions[0].source,
+                "name": "Test 1"
+            },
+            {
+                "function_id": functions[1].function_id,
+                "source": functions[1].source,
+                "name": "Test 2"
+            }
+        ]
+        serializer = FunctionSerializer(many=True)
+        serializer.update(functions, validated_data)
+        self.assertEqual(self.function_api.get_all()['count'], 2)
+        print(self.function_api.get_all())