change table to contain version of eggnog

backend/metagenedb/api/catalog/urls.py

@@ -54,7 +54,7 @@ class CustomRouter(DefaultRouter):
 api_router = CustomRouter()
 api_router.register(r'functions', views.FunctionViewSet, basename='functions')
 api_router.register(r'kegg-orthologies', views.KeggOrthologyViewSet, basename='kegg-orthologies')
-api_router.register(r'eggnogs', views.EggNogViewSet, basename='eggnogs')
+api_router.register(r'eggnogs', views.EggNOGv5ViewSet, basename='eggnogs')
 api_router.register(r'genes', views.GeneViewSet, basename='genes')
 api_router.register(r'taxonomy', views.TaxonomyViewSet, basename='taxonomy')
 

backend/metagenedb/api/catalog/views/__init__.py

-from .function import EggNogViewSet, KeggOrthologyViewSet, FunctionViewSet  # noqa
+from .function import EggNOGv5ViewSet, KeggOrthologyViewSet, FunctionViewSet  # noqa
 from .gene import GeneViewSet  # noqa
 from .taxonomy import TaxonomyViewSet  # noqa

backend/metagenedb/api/catalog/views/function.py

@@ -7,8 +7,8 @@ from rest_framework.viewsets import ModelViewSet
 
 from metagenedb.api.catalog.filters import FunctionFilter
 from metagenedb.api.catalog.qparams_validators.function import FunctionQueryParams
-from metagenedb.apps.catalog.models import EggNog, Function, KeggOrthology
-from metagenedb.apps.catalog.serializers import EggNogSerializer, FunctionSerializer, KeggOrthologySerializer
+from metagenedb.apps.catalog.models import EggNOGv5, Function, KeggOrthology
+from metagenedb.apps.catalog.serializers import EggNOGSerializer, FunctionSerializer, KeggOrthologySerializer
 from metagenedb.common.utils.external_api.togows import GetFunctionExternalInfo
 
 from .bulk_viewset import BulkViewSet
@@ -57,7 +57,7 @@ class KeggOrthologyViewSet(ModelViewSet):
         return Response(returned_data)
 
 
-class EggNogViewSet(ModelViewSet):
-    queryset = EggNog.objects.all()
-    serializer_class = EggNogSerializer
+class EggNOGv5ViewSet(ModelViewSet):
+    queryset = EggNOGv5.objects.all()
+    serializer_class = EggNOGSerializer
     lookup_field = 'function_id'

backend/metagenedb/api/catalog/views/test_function.py

@@ -2,7 +2,7 @@ from rest_framework.test import APITestCase
 
 import mock
 
-from metagenedb.apps.catalog.factory import EggNogFactory, KeggOrthologyFactory
+from metagenedb.apps.catalog.factory import EggNOGv5Factory, KeggOrthologyFactory
 from metagenedb.common.utils.mocks.metagenedb import (
     MetageneDBCatalogFunctionAPIMock, MetageneDBCatalogKeggOrthologyAPIMock
 )
@@ -14,7 +14,7 @@ class TestKeggOrthologyViewSet(APITestCase):
         self.function_api = MetageneDBCatalogFunctionAPIMock(self.client)
         self.kegg_ortho_api = MetageneDBCatalogKeggOrthologyAPIMock(self.client)
         self.kegg_function = KeggOrthologyFactory.create()
-        self.eggnog_function = EggNogFactory.create()
+        self.eggnog_function = EggNOGv5Factory.create()
 
     def test_retrieve(self):
         for function in [self.kegg_function, self.eggnog_function]:

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

 from django.contrib import admin
 
-from metagenedb.apps.catalog.models import EggNog, EggNogFunctionalCategory, Function, KeggOrthology
+from metagenedb.apps.catalog.models import EggNOGv5, EggNOGFunctionalCategory, Function, KeggOrthology
 
 
 @admin.register(KeggOrthology)
@@ -17,8 +17,8 @@ class FunctionAdmin(admin.ModelAdmin):
     search_fields = ('function_id',)
 
 
-@admin.register(EggNog)
-class EggNogAdmin(admin.ModelAdmin):
+@admin.register(EggNOGv5)
+class EggNOGv5Admin(admin.ModelAdmin):
 
     list_display = ('function_id', 'name', 'get_functional_categories')
     search_fields = ('function_id', 'name')
@@ -30,8 +30,8 @@ class EggNogAdmin(admin.ModelAdmin):
     get_functional_categories.short_description = 'Functional categories'
 
 
-@admin.register(EggNogFunctionalCategory)
-class EggNogFunctionalCategoryAdmin(admin.ModelAdmin):
+@admin.register(EggNOGFunctionalCategory)
+class EggNOGFunctionalCategoryAdmin(admin.ModelAdmin):
 
     list_display = ('category_id', 'name', 'group')
     search_fields = ('category_id', 'name')

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

-from .function import EggNogFactory, FunctionFactory, KeggOrthologyFactory  # noqa
+from .function import EggNOGv5Factory, FunctionFactory, KeggOrthologyFactory  # noqa
 from .gene import GeneFactory  # noqa
 from .taxonomy import TaxonomyFactory  # noqa

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

@@ -22,9 +22,9 @@ class FunctionFactory(BaseFunctionFactory):
     function_id = FuzzyLowerText(prefix='function-', length=15)
 
 
-class EggNogFactory(BaseFunctionFactory):
+class EggNOGv5Factory(BaseFunctionFactory):
     class Meta:
-        model = models.EggNog
+        model = models.EggNOGv5
 
 
 class KeggOrthologyFactory(BaseFunctionFactory):

backend/metagenedb/apps/catalog/management/commands/create_eggnog_functional_cat.py

@@ -3,7 +3,7 @@ import logging
 from django.core.management.base import BaseCommand
 from django.core.exceptions import ValidationError
 
-from metagenedb.apps.catalog.models import EggNogFunctionalCategory
+from metagenedb.apps.catalog.models import EggNOGFunctionalCategory
 from metagenedb.common.utils.parsers.eggnog import EggNOGFunctionalCategoriesParser
 
 logging.basicConfig(format='[%(asctime)s] %(levelname)s:%(name)s:%(message)s')
@@ -12,7 +12,7 @@ logger = logging.getLogger(__name__)
 
 class ImportEggNOGFunctionalCategories(object):
     LOOKUP_FIELD = 'category_id'
-    MODEL = EggNogFunctionalCategory
+    MODEL = EggNOGFunctionalCategory
     GROUP_MAPPING = {
         'Information storage and processing': 'info_storage_processing',
         'Cellular processes and signaling': 'cellular_processes_signaling',

backend/metagenedb/apps/catalog/management/commands/create_update_eggnog.py

@@ -3,7 +3,7 @@ import logging
 from django.core.management.base import BaseCommand
 from django.core.exceptions import ValidationError
 
-from metagenedb.apps.catalog.models import EggNog, EggNogFunctionalCategory
+from metagenedb.apps.catalog.models import EggNOGv5, EggNOGFunctionalCategory
 from metagenedb.common.utils.chunks import file_len
 from metagenedb.common.utils.parsers import EggNOGAnnotationLineParser
 
@@ -24,7 +24,7 @@ class ImportEggNOG(object):
         self.skipped_errors = []
 
     def _build_functional_category_dict(self):
-        all_categories = EggNogFunctionalCategory.objects.all()
+        all_categories = EggNOGFunctionalCategory.objects.all()
         if not all_categories:
             raise Exception("You need to create Functional categories first.")
         self.functional_cat_instances = {cat.category_id: cat for cat in all_categories}
@@ -43,14 +43,14 @@ class ImportEggNOG(object):
                 payload = {k: v for k, v in eggnog_dict.items() if v != ""}
                 eggnog = None
                 try:
-                    eggnog = EggNog(**payload)
+                    eggnog = EggNOGv5(**payload)
                     eggnog.full_clean()
                     eggnog.save()
                     self.created_count += 1
                 except ValidationError as validation_error:
                     if 'function_id' in validation_error.error_dict.keys():
                         try:
-                            eggnog = EggNog.objects.get(function_id=payload.get('function_id'))
+                            eggnog = EggNOGv5.objects.get(function_id=payload.get('function_id'))
                             for k, v in payload.items():
                                 setattr(eggnog, k, v)
                             eggnog.full_clean()

backend/metagenedb/apps/catalog/migrations/0016_rename_eggnog.py

+# Generated by Django 3.0 on 2019-12-11 22:07
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('catalog', '0015_m2m_func_cat_eggnog'),
+    ]
+
+    operations = [
+        migrations.RenameModel(
+            old_name='EggNog',
+            new_name='EggNOGv5',
+        ),
+        migrations.AlterField(
+            model_name='eggnogv5',
+            name='functional_categories',
+            field=models.ManyToManyField(to='catalog.EggNOGFunctionalCategory'),
+        ),
+    ]

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

-from .function import EggNog, EggNogFunctionalCategory, Function, KeggOrthology  # noqa
+from .function import EggNOGv5, EggNOGFunctionalCategory, Function, KeggOrthology  # noqa
 from .gene import Gene, GeneFunction  # noqa
 from .taxonomy import Taxonomy  # noqa

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

@@ -36,7 +36,7 @@ class KeggOrthology(Function):
         verbose_name_plural = "KEGG orthologies"
 
 
-class EggNogFunctionalCategory(models.Model):
+class EggNOGFunctionalCategory(models.Model):
     GROUP_CHOICES = [
         ('info_storage_processing', 'Information Storage and Processing'),
         ('cellular_processes_signaling', 'Cellular Processes and Signaling'),
@@ -56,14 +56,14 @@ class EggNogFunctionalCategory(models.Model):
         verbose_name_plural = "EggNOG functional categories"
 
 
-class EggNog(Function):
+class EggNOGv5(Function):
     SOURCE = 'eggnog'
 
-    functional_categories = models.ManyToManyField(EggNogFunctionalCategory)
+    functional_categories = models.ManyToManyField(EggNOGFunctionalCategory)
 
     def __init__(self, *args, **kwargs):
-        super(EggNog, self).__init__(source=self.SOURCE, *args, **kwargs)
+        super(EggNOGv5, self).__init__(source=self.SOURCE, *args, **kwargs)
 
     class Meta:
-        verbose_name = "EggNOG"
-        verbose_name_plural = "EggNOGs"
+        verbose_name = "EggNOG v5.0"
+        verbose_name_plural = "EggNOGs v5.0"

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

-from .function import EggNogSerializer, FunctionSerializer, KeggOrthologySerializer  # noqa
+from .function import EggNOGSerializer, FunctionSerializer, KeggOrthologySerializer  # noqa
 from .gene import GeneSerializer  # noqa
 from .taxonomy import TaxonomySerializer  # noqa

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

 from rest_framework import serializers
-from metagenedb.apps.catalog.models import EggNog, Function, KeggOrthology
+from metagenedb.apps.catalog.models import EggNOGv5, Function, KeggOrthology
 
 from .bulk_list import BulkListSerializer
 
@@ -18,17 +18,17 @@ class FunctionSerializer(serializers.ModelSerializer):
         fields = ('function_id', 'source', 'name')
 
 
-class EggNogListSerializer(BulkListSerializer):
+class EggNOGListSerializer(BulkListSerializer):
 
     class Meta:
-        model = EggNog
+        model = EggNOGv5
 
 
-class EggNogSerializer(serializers.ModelSerializer):
+class EggNOGSerializer(serializers.ModelSerializer):
 
     class Meta:
-        model = EggNog
-        list_serializer_class = EggNogListSerializer
+        model = EggNOGv5
+        list_serializer_class = EggNOGListSerializer
         fields = ('function_id', 'name', 'functional_categories')
 
 

backend/metagenedb/common/utils/mocks/metagenedb.py

@@ -90,5 +90,5 @@ class MetageneDBCatalogKeggOrthologyAPIMock(MetageneDBCatalogFunctionAPIMock):
     REVERSE_PATH = 'catalog:v1:kegg-orthologies'
 
 
-class MetageneDBCatalogEggNogAPIMock(MetageneDBCatalogFunctionAPIMock):
+class MetageneDBCatalogEggNOGv5APIMock(MetageneDBCatalogFunctionAPIMock):
     REVERSE_PATH = 'catalog:v1:eggnogs'

backend/scripts/populate_db/test_import_igc_data.py

@@ -4,13 +4,13 @@ from rest_framework.test import APITestCase
 
 from metagenedb.common.utils.mocks.metagenedb import (
     MetageneDBCatalogTaxonomyAPIMock,
-    MetageneDBCatalogEggNogAPIMock,
+    MetageneDBCatalogEggNOGv5APIMock,
     MetageneDBCatalogKeggOrthologyAPIMock
 )
 from metagenedb.apps.catalog.factory import (
     TaxonomyFactory,
     KeggOrthologyFactory,
-    EggNogFactory
+    EggNOGv5Factory
 )
 from scripts.populate_db.import_igc_data import ImportIGCGenes
 
@@ -302,12 +302,12 @@ class TestBuildBuildFunctionCatalog(APITestCase):
     @classmethod
     def setUpTestData(cls):
         cls.keggs = KeggOrthologyFactory.create_batch(100)
-        cls.eggnogs = EggNogFactory.create_batch(100)
+        cls.eggnogs = EggNOGv5Factory.create_batch(100)
 
     def setUp(self):
         self.import_igc_genes = ImportIGCGenes('test', 'test_url', 'test_token')
         self.kegg_api_mock = MetageneDBCatalogKeggOrthologyAPIMock(self.client)
-        self.eggnog_api_mock = MetageneDBCatalogEggNogAPIMock(self.client)
+        self.eggnog_api_mock = MetageneDBCatalogEggNOGv5APIMock(self.client)
         self.import_igc_genes.metagenedb_kegg_api = self.kegg_api_mock
         self.import_igc_genes.metagenedb_eggnog_api = self.eggnog_api_mock