diff --git a/backend/Pipfile b/backend/Pipfile
index 248e6dc4c15e1c8e5da1d32337170c2d43d9e115..99a30ee4ce4816f746a0e2aa645834f25efb1622 100644
--- a/backend/Pipfile
+++ b/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"
diff --git a/backend/Pipfile.lock b/backend/Pipfile.lock
index 86dcc9a13d99385894ebfe846e4901d1eeafab72..57d51111b69cb596f26167047a8e0003193c4d85 100644
--- a/backend/Pipfile.lock
+++ b/backend/Pipfile.lock
@@ -1,7 +1,7 @@
{
"_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": {
diff --git a/backend/metagenedb/api/catalog/urls.py b/backend/metagenedb/api/catalog/urls.py
index e4f6b6f387a0ca42a4cc53dc3553c9074b317226..49c88b3f60ed8d01d742f69fa11a20d97a965bde 100644
--- a/backend/metagenedb/api/catalog/urls.py
+++ b/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')
diff --git a/backend/metagenedb/api/catalog/views/__init__.py b/backend/metagenedb/api/catalog/views/__init__.py
index 07491013b0382a900af3e1ac28fa1a640ec929dd..03229a3b12067d04e43c6fd59407a8ccff6e529a 100644
--- a/backend/metagenedb/api/catalog/views/__init__.py
+++ b/backend/metagenedb/api/catalog/views/__init__.py
@@ -1,3 +1,3 @@
-from .function import EggNOGv5ViewSet, KeggOrthologyViewSet, FunctionViewSet # noqa
+from .function import EggNOGViewSet, KeggOrthologyViewSet, FunctionViewSet # noqa
from .gene import GeneViewSet # noqa
from .taxonomy import TaxonomyViewSet # noqa
diff --git a/backend/metagenedb/api/catalog/views/function.py b/backend/metagenedb/api/catalog/views/function.py
index 9d1dc4cc0edfcbd32b5465e30407f9115f2e4dbd..3dcb685f5a07bc7b5a6455ff4dafd09679656d60 100644
--- a/backend/metagenedb/api/catalog/views/function.py
+++ b/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'
diff --git a/backend/metagenedb/api/catalog/views/test_function.py b/backend/metagenedb/api/catalog/views/test_function.py
index 5734445f2733c4d83789726d5034e03ce638a241..217e7b54edb52fc8385b41149f4e43a4d949293c 100644
--- a/backend/metagenedb/api/catalog/views/test_function.py
+++ b/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]:
diff --git a/backend/metagenedb/apps/catalog/admin/function.py b/backend/metagenedb/apps/catalog/admin/function.py
index c6a675b86f0dc41253a569199480f9c73a79e7d7..a3df9e83f991656586796ab707c607e92d1bdc22 100644
--- a/backend/metagenedb/apps/catalog/admin/function.py
+++ b/backend/metagenedb/apps/catalog/admin/function.py
@@ -1,6 +1,6 @@
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):
diff --git a/backend/metagenedb/apps/catalog/admin/taxonomy.py b/backend/metagenedb/apps/catalog/admin/taxonomy.py
index 633f57b0c94b4556ae0e747b57a16c6479356ef0..445228df8d00eb61d4d43397a05ffa7ab323fa09 100644
--- a/backend/metagenedb/apps/catalog/admin/taxonomy.py
+++ b/backend/metagenedb/apps/catalog/admin/taxonomy.py
@@ -1,4 +1,5 @@
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')
diff --git a/backend/metagenedb/apps/catalog/factory/__init__.py b/backend/metagenedb/apps/catalog/factory/__init__.py
index a02fda04be86dd90dfc5a3b11c5fd37e61c4ac16..d7b5b1431f8ae24bc153ae78122bafacc3a015d5 100644
--- a/backend/metagenedb/apps/catalog/factory/__init__.py
+++ b/backend/metagenedb/apps/catalog/factory/__init__.py
@@ -1,3 +1,3 @@
-from .function import EggNOGv5Factory, FunctionFactory, KeggOrthologyFactory # noqa
+from .function import EggNOGFactory, FunctionFactory, KeggOrthologyFactory # noqa
from .gene import GeneFactory # noqa
from .taxonomy import TaxonomyFactory # noqa
diff --git a/backend/metagenedb/apps/catalog/factory/function.py b/backend/metagenedb/apps/catalog/factory/function.py
index fc523e88f98bffc587b0e9c481985503af8ea39d..1ab878bd9d42815cbf8ce6da17db64a18674804d 100644
--- a/backend/metagenedb/apps/catalog/factory/function.py
+++ b/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):
diff --git a/backend/metagenedb/apps/catalog/management/commands/create_update_eggnog.py b/backend/metagenedb/apps/catalog/management/commands/create_update_eggnog.py
index 3c6750f5de090491cb06b6937b31b3a35b8ecc17..91fcbfb1a1b29de1b3644f0d60c5737981cb24d1 100644
--- a/backend/metagenedb/apps/catalog/management/commands/create_update_eggnog.py
+++ b/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()
diff --git a/backend/metagenedb/apps/catalog/migrations/0016_add_eggnog_version.py b/backend/metagenedb/apps/catalog/migrations/0016_add_eggnog_version.py
new file mode 100644
index 0000000000000000000000000000000000000000..b92f5b5b55b286d284f94cdf564eb7cc2fbb0864
--- /dev/null
+++ b/backend/metagenedb/apps/catalog/migrations/0016_add_eggnog_version.py
@@ -0,0 +1,28 @@
+# 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'),
+ ),
+ ]
diff --git a/backend/metagenedb/apps/catalog/migrations/0016_rename_eggnog.py b/backend/metagenedb/apps/catalog/migrations/0017_rename_meta_eggnog.py
similarity index 53%
rename from backend/metagenedb/apps/catalog/migrations/0016_rename_eggnog.py
rename to backend/metagenedb/apps/catalog/migrations/0017_rename_meta_eggnog.py
index bc77106a2c864d227a5ae5b663e3d2d605a68948..ad200e61e6557020089e7b835bd0c37ab5afc8ff 100644
--- a/backend/metagenedb/apps/catalog/migrations/0016_rename_eggnog.py
+++ b/backend/metagenedb/apps/catalog/migrations/0017_rename_meta_eggnog.py
@@ -1,4 +1,4 @@
-# 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'),
),
diff --git a/backend/metagenedb/apps/catalog/models/__init__.py b/backend/metagenedb/apps/catalog/models/__init__.py
index 50aa3ddeabf0f49892c9db59f9b5f152e4fb89f4..795bdebd8f5b8a28cccea5a2319dd1a4474b9da8 100644
--- a/backend/metagenedb/apps/catalog/models/__init__.py
+++ b/backend/metagenedb/apps/catalog/models/__init__.py
@@ -1,3 +1,3 @@
-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
diff --git a/backend/metagenedb/apps/catalog/models/function.py b/backend/metagenedb/apps/catalog/models/function.py
index aa10577c604720186651e7a133c333c9fa69ff9e..45b6fe9a294b60360085b968a52017f73f3d4b13 100644
--- a/backend/metagenedb/apps/catalog/models/function.py
+++ b/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"
diff --git a/backend/metagenedb/apps/catalog/serializers/function.py b/backend/metagenedb/apps/catalog/serializers/function.py
index f937dd327c1c1d39fa288f89b1b8e80b137d227a..15cbe30400d9378c1ff3c46ed383858dd9815349 100644
--- a/backend/metagenedb/apps/catalog/serializers/function.py
+++ b/backend/metagenedb/apps/catalog/serializers/function.py
@@ -1,5 +1,5 @@
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):
diff --git a/backend/metagenedb/common/utils/mocks/metagenedb.py b/backend/metagenedb/common/utils/mocks/metagenedb.py
index ec8baee2d0d52780db568d687cee75b806d04843..c8e0185ff457f23f4c968f80b429bf427046f83c 100644
--- a/backend/metagenedb/common/utils/mocks/metagenedb.py
+++ b/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'
diff --git a/backend/metagenedb/settings/django.py b/backend/metagenedb/settings/django.py
index 02ddd749b22c50635e6a69de4b1ee9792d2d904a..fd14467b70c5ee664e00feee19801f6d1778afe4 100644
--- a/backend/metagenedb/settings/django.py
+++ b/backend/metagenedb/settings/django.py
@@ -21,6 +21,7 @@ INSTALLED_APPS = [
'django_filters',
'corsheaders',
'drf_yasg',
+ 'django_admin_listfilter_dropdown',
]
MIDDLEWARE = [
diff --git a/backend/scripts/populate_db/import_igc_data.py b/backend/scripts/populate_db/import_igc_data.py
index a0d9d685d007852814d3268d1b2b7fe9a0c1a97f..c95c40975524597e0ae03b7207abca2a7dfcbc10 100755
--- a/backend/scripts/populate_db/import_igc_data.py
+++ b/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
diff --git a/backend/scripts/populate_db/test_import_igc_data.py b/backend/scripts/populate_db/test_import_igc_data.py
index 9960d0216530f4a72ad4349ea5a00c708b01d764..ba76a096564c3ef44cd6fcf4f8eda4c20f281346 100644
--- a/backend/scripts/populate_db/test_import_igc_data.py
+++ b/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