update model of eggnog for different versions

backend/Pipfile

@@ -59,6 +59,7 @@ python-slugify = "*"
 marshmallow = "*"
 django-pandas = "*"
 bioapi = {git = "https://github.com/khillion/bioapi.git"}
+django-admin-list-filter-dropdown = "*"
 
 [requires]
 python_version = "3.7"

backend/Pipfile.lock

 {
     "_meta": {
         "hash": {
-            "sha256": "c448dca73004a15b2c0d65f4ff1e2b2da1aac4d1439a0be2adf97531783af899"
+            "sha256": "57d6d564aa9c1a9f750c89666f2191d1c5036bfa413119cb26f92719fbe48a6e"
         },
         "pipfile-spec": 6,
         "requires": {
@@ -65,6 +65,14 @@
             "index": "pypi",
             "version": "==3.0"
         },
+        "django-admin-list-filter-dropdown": {
+            "hashes": [
+                "sha256:07cd37b6a9be1b08f11d4a92957c69b67bc70b1f87a2a7d4ae886c93ea51eb53",
+                "sha256:bf1b48bab9772dad79db71efef17e78782d4f2421444d5e49bb10e0da71cd6bb"
+            ],
+            "index": "pypi",
+            "version": "==1.0.3"
+        },
         "django-cors-headers": {
             "hashes": [
                 "sha256:84933651fbbde8f2bc084bef2f077b79db1ec1389432f21dd661eaae6b3d6a95",
@@ -403,7 +411,7 @@
                 "sha256:5b26757dc6f79a3b7dc9fab95359328d5747fcb2409d331ea66d0272b90ab2a0",
                 "sha256:8b995ffe925347a2138d7ac0fe77155e4311a0ea6d6da4f5128fe4b3cbe5ed71"
             ],
-            "markers": "sys_platform == 'darwin'",
+            "markers": "platform_system == 'Darwin'",
             "version": "==0.1.0"
         },
         "astroid": {

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.EggNOGv5ViewSet, basename='eggnogs')
+api_router.register(r'eggnogs', views.EggNOGViewSet, 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 EggNOGv5ViewSet, KeggOrthologyViewSet, FunctionViewSet  # noqa
+from .function import EggNOGViewSet, KeggOrthologyViewSet, FunctionViewSet  # noqa
 from .gene import GeneViewSet  # noqa
 from .taxonomy import TaxonomyViewSet  # noqa

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

@@ -7,7 +7,7 @@ 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 EggNOGv5, Function, KeggOrthology
+from metagenedb.apps.catalog.models import EggNOG, Function, KeggOrthology
 from metagenedb.apps.catalog.serializers import EggNOGSerializer, FunctionSerializer, KeggOrthologySerializer
 from metagenedb.common.utils.external_api.togows import GetFunctionExternalInfo
 
@@ -57,7 +57,7 @@ class KeggOrthologyViewSet(ModelViewSet):
         return Response(returned_data)
 
 
-class EggNOGv5ViewSet(ModelViewSet):
-    queryset = EggNOGv5.objects.all()
+class EggNOGViewSet(ModelViewSet):
+    queryset = EggNOG.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 EggNOGv5Factory, KeggOrthologyFactory
+from metagenedb.apps.catalog.factory import EggNOGFactory, 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 = EggNOGv5Factory.create()
+        self.eggnog_function = EggNOGFactory.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 EggNOGv5, EggNOGFunctionalCategory, Function, KeggOrthology
+from metagenedb.apps.catalog.models import EggNOG, EggNOGFunctionalCategory, Function, KeggOrthology
 
 
 @admin.register(KeggOrthology)
@@ -17,10 +17,11 @@ class FunctionAdmin(admin.ModelAdmin):
     search_fields = ('function_id',)
 
 
-@admin.register(EggNOGv5)
-class EggNOGv5Admin(admin.ModelAdmin):
+@admin.register(EggNOG)
+class EggNOGAdmin(admin.ModelAdmin):
 
-    list_display = ('function_id', 'name', 'get_functional_categories')
+    list_display = ('function_id', 'name', 'get_functional_categories', 'version')
+    list_filter = ('version',)
     search_fields = ('function_id', 'name')
 
     def get_functional_categories(self, obj):

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

 from django.contrib import admin
+from django_admin_listfilter_dropdown.filters import DropdownFilter
 
 from metagenedb.apps.catalog.models import Taxonomy
 
@@ -10,4 +11,5 @@ class TaxonomyAdmin(admin.ModelAdmin):
         'tax_id', 'name', 'rank', 'superkingdom',
         'kingdom', 'phylum', 'class_rank', 'order', 'family', 'genus', 'species',
     )
+    list_filter = (('rank', DropdownFilter),)
     search_fields = ('tax_id', 'name')

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

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

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

@@ -8,6 +8,7 @@ from .fuzzy_base import FuzzyLowerText
 faker = Factory.create()
 
 SELECTED_SOURCE = [i[0] for i in models.Function.SOURCE_CHOICES]
+EGGNOG_VERSIONS = [i[0] for i in models.EggNOG.VERSION_CHOICES]
 
 
 class BaseFunctionFactory(DjangoModelFactory):
@@ -22,9 +23,11 @@ class FunctionFactory(BaseFunctionFactory):
     function_id = FuzzyLowerText(prefix='function-', length=15)
 
 
-class EggNOGv5Factory(BaseFunctionFactory):
+class EggNOGFactory(BaseFunctionFactory):
     class Meta:
-        model = models.EggNOGv5
+        model = models.EggNOG
+
+    version = fuzzy.FuzzyChoice(EGGNOG_VERSIONS)
 
 
 class KeggOrthologyFactory(BaseFunctionFactory):

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 EggNOGv5, EggNOGFunctionalCategory
+from metagenedb.apps.catalog.models import EggNOG, EggNOGFunctionalCategory
 from metagenedb.common.utils.chunks import file_len
 from metagenedb.common.utils.parsers import EggNOGAnnotationLineParser
 
@@ -43,14 +43,14 @@ class ImportEggNOG(object):
                 payload = {k: v for k, v in eggnog_dict.items() if v != ""}
                 eggnog = None
                 try:
-                    eggnog = EggNOGv5(**payload)
+                    eggnog = EggNOG(**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 = EggNOGv5.objects.get(function_id=payload.get('function_id'))
+                            eggnog = EggNOG.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_add_eggnog_version.py

+# Generated by Django 3.0 on 2019-12-12 10:46
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('catalog', '0015_m2m_func_cat_eggnog'),
+    ]
+
+    operations = [
+        migrations.AlterModelOptions(
+            name='eggnog',
+            options={},
+        ),
+        migrations.AddField(
+            model_name='eggnog',
+            name='version',
+            field=models.CharField(choices=[('3.0', '3.0'), ('5.0', '5.0')], default=5.0, max_length=5),
+            preserve_default=False,
+        ),
+        migrations.AlterField(
+            model_name='eggnog',
+            name='functional_categories',
+            field=models.ManyToManyField(to='catalog.EggNOGFunctionalCategory'),
+        ),
+    ]

backend/metagenedb/apps/catalog/migrations/0016_rename_eggnog.py → backend/metagenedb/apps/catalog/migrations/0017_rename_meta_eggnog.py

-# Generated by Django 3.0 on 2019-12-11 22:07
+# Generated by Django 3.0 on 2019-12-12 11:12
 
 from django.db import migrations, models
 
@@ -6,16 +6,16 @@ from django.db import migrations, models
 class Migration(migrations.Migration):
 
     dependencies = [
-        ('catalog', '0015_m2m_func_cat_eggnog'),
+        ('catalog', '0016_add_eggnog_version'),
     ]
 
     operations = [
-        migrations.RenameModel(
-            old_name='EggNog',
-            new_name='EggNOGv5',
+        migrations.AlterModelOptions(
+            name='eggnog',
+            options={'verbose_name': 'EggNOG', 'verbose_name_plural': 'EggNOGs'},
         ),
         migrations.AlterField(
-            model_name='eggnogv5',
+            model_name='eggnog',
             name='functional_categories',
             field=models.ManyToManyField(to='catalog.EggNOGFunctionalCategory'),
         ),

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

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

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

@@ -56,14 +56,19 @@ class EggNOGFunctionalCategory(models.Model):
         verbose_name_plural = "EggNOG functional categories"
 
 
-class EggNOGv5(Function):
+class EggNOG(Function):
     SOURCE = 'eggnog'
+    VERSION_CHOICES = [
+        ('3.0', '3.0'),
+        ('5.0', '5.0')
+    ]
 
     functional_categories = models.ManyToManyField(EggNOGFunctionalCategory)
+    version = models.CharField(max_length=5, choices=VERSION_CHOICES)
 
     def __init__(self, *args, **kwargs):
-        super(EggNOGv5, self).__init__(source=self.SOURCE, *args, **kwargs)
+        super(EggNOG, self).__init__(source=self.SOURCE, *args, **kwargs)
 
     class Meta:
-        verbose_name = "EggNOG v5.0"
-        verbose_name_plural = "EggNOGs v5.0"
+        verbose_name = "EggNOG"
+        verbose_name_plural = "EggNOGs"

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

 from rest_framework import serializers
-from metagenedb.apps.catalog.models import EggNOGv5, Function, KeggOrthology
+from metagenedb.apps.catalog.models import EggNOG, Function, KeggOrthology
 
 from .bulk_list import BulkListSerializer
 
@@ -21,15 +21,15 @@ class FunctionSerializer(serializers.ModelSerializer):
 class EggNOGListSerializer(BulkListSerializer):
 
     class Meta:
-        model = EggNOGv5
+        model = EggNOG
 
 
 class EggNOGSerializer(serializers.ModelSerializer):
 
     class Meta:
-        model = EggNOGv5
+        model = EggNOG
         list_serializer_class = EggNOGListSerializer
-        fields = ('function_id', 'name', 'functional_categories')
+        fields = ('function_id', 'name', 'functional_categories', 'version')
 
 
 class KeggOrthologyListSerializer(BulkListSerializer):

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

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

backend/metagenedb/settings/django.py

@@ -21,6 +21,7 @@ INSTALLED_APPS = [
     'django_filters',
     'corsheaders',
     'drf_yasg',
+    'django_admin_listfilter_dropdown',
 ]
 
 MIDDLEWARE = [

backend/scripts/populate_db/import_igc_data.py

@@ -10,7 +10,7 @@ from bioapi import (
     MetageneDBCatalogGeneAPI,
     MetageneDBCatalogTaxonomyAPI,
     MetageneDBCatalogKeggOrthologyAPI,
-    MetageneDBCatalogEggNogAPI
+    MetageneDBCatalogEggNogAPI,
 )
 from requests.exceptions import HTTPError
 from slugify import slugify

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,
-    MetageneDBCatalogEggNOGv5APIMock,
+    MetageneDBCatalogEggNOGAPIMock,
     MetageneDBCatalogKeggOrthologyAPIMock
 )
 from metagenedb.apps.catalog.factory import (
     TaxonomyFactory,
     KeggOrthologyFactory,
-    EggNOGv5Factory
+    EggNOGFactory
 )
 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 = EggNOGv5Factory.create_batch(100)
+        cls.eggnogs = EggNOGFactory.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 = MetageneDBCatalogEggNOGv5APIMock(self.client)
+        self.eggnog_api_mock = MetageneDBCatalogEggNOGAPIMock(self.client)
         self.import_igc_genes.metagenedb_kegg_api = self.kegg_api_mock
         self.import_igc_genes.metagenedb_eggnog_api = self.eggnog_api_mock