Fix tests

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

@@ -5,6 +5,7 @@ from drf_yasg import openapi
 from drf_yasg.utils import swagger_auto_schema
 from marshmallow.exceptions import ValidationError
 from rest_framework.decorators import action
+from rest_framework.permissions import AllowAny
 from rest_framework.response import Response
 from rest_framework.status import HTTP_204_NO_CONTENT, HTTP_422_UNPROCESSABLE_ENTITY
 
@@ -60,6 +61,8 @@ class GeneViewSet(BulkViewSet):
     DEFAULT_LEVEL = 'phylum'
 
     def get_permissions(self):
+        if self.action in ['gene_length', 'taxonomy_counts']:
+            return [AllowAny()]
         return super(self.__class__, self).get_permissions()
 
     def _count_windows(self, queryset, window_size=DEFAULT_WINDOW_SIZE, window_col=GENE_LENGTH_COL,

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

+from django.contrib.auth.models import User
 from requests.exceptions import HTTPError
 from rest_framework.test import APITestCase
+from rest_framework_jwt.settings import api_settings
 
 from metagenedb.apps.catalog.factory import FunctionFactory
 from metagenedb.common.utils.mocks.metagenedb import MetageneDBCatalogFunctionAPIMock
 
 
+class TestOperationsBulkViewSetNoCredentials(APITestCase):
+
+    def setUp(self):
+        self.function_api = MetageneDBCatalogFunctionAPIMock(self.client)
+
+    def test_create_function(self):
+        data = {
+            "function_id": 'k_test1',
+            "source": "kegg",
+            "name": "Kegg Test 1"
+        }
+        with self.assertRaises(HTTPError):
+            self.function_api.post(data)
+
+    def test_update_existing_function(self):
+        function = FunctionFactory()
+        data = {
+            "function_id": function.function_id,
+            "source": function.source,
+            "name": "Kegg Test 1"
+        }
+        with self.assertRaises(HTTPError):
+            self.function_api.put(data, function.function_id)
+
+
 class TestOperationsBulkViewSet(APITestCase):
     """
     We are testing the different functions through the API directly through the mock redirecting
@@ -14,7 +41,15 @@ class TestOperationsBulkViewSet(APITestCase):
     """
 
     def setUp(self):
-        self.function_api = MetageneDBCatalogFunctionAPIMock(self.client)
+        jwt_payload_handler = api_settings.JWT_PAYLOAD_HANDLER
+        jwt_encode_handler = api_settings.JWT_ENCODE_HANDLER
+        user = User.objects.create_user(username='user_admin', email='user@admin.com', password='pass')
+        user.is_active = True
+        user.is_staff = True
+        user.save()
+        payload = jwt_payload_handler(user)
+        jwt_token = jwt_encode_handler(payload)
+        self.function_api = MetageneDBCatalogFunctionAPIMock(self.client, jwt_token=jwt_token)
 
     def test_create_function(self):
         data = {

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

@@ -14,33 +14,43 @@ class MetageneDBAPIMock(MetageneDBCatalogGeneAPI):
     REVERSE_PATH = ''
     BAD_REQUESTS = range(400, 452)
 
-    def __init__(self, client):
+    def __init__(self, client, jwt_token=None):
         self.client = client
         self.reverse_path = ':'.join([self.BASE_REVERSE, self.REVERSE_PATH])
+        self.headers = {}
+        if jwt_token is not None:
+            self.headers.update({
+                'HTTP_AUTHORIZATION': f"JWT {jwt_token}",
+            })
 
     def get_all(self, params=None):
-        response = self.client.get(reverse(f'{self.reverse_path}-list'), params)
+        response = self.client.get(reverse(f'{self.reverse_path}-list'), params, **self.headers)
         if response.status_code in self.BAD_REQUESTS:
             raise HTTPError
         return response.json()
 
     def get(self, entry_id, params=None):
-        response = self.client.get(reverse(f'{self.reverse_path}-detail', kwargs={self.KEY_ID: entry_id}), params)
+        response = self.client.get(reverse(f'{self.reverse_path}-detail', kwargs={self.KEY_ID: entry_id}),
+                                   params, **self.headers)
         if response.status_code in self.BAD_REQUESTS:
             raise HTTPError
         return response.json()
 
     def post(self, data):
-        response = self.client.post(reverse(f'{self.reverse_path}-list'), data, format='json')
+        response = self.client.post(reverse(f'{self.reverse_path}-list'), data, format='json', **self.headers)
         if response.status_code in self.BAD_REQUESTS:
             raise HTTPError
         return response.json()
 
     def put(self, data, entry_id=None):
         if entry_id:
-            return self.client.put(reverse(f'{self.reverse_path}-detail', kwargs={self.KEY_ID: entry_id}),
-                                   data, format='json').json()
-        return self.client.put(reverse(f'{self.reverse_path}-list'), data, format='json').json()
+            response = self.client.put(reverse(f'{self.reverse_path}-detail', kwargs={self.KEY_ID: entry_id}),
+                                       data, format='json', **self.headers)
+        else:
+            response = self.client.put(reverse(f'{self.reverse_path}-list'), data, format='json', **self.headers)
+        if response.status_code in self.BAD_REQUESTS:
+            raise HTTPError
+        return response.json()
 
 
 class MetageneDBCatalogGeneAPIMock(MetageneDBAPIMock):

backend/scripts/populate_db/test_import_igc_data.py

@@ -27,7 +27,7 @@ class TestParseGene(TestCase):
             'cohort_assembled'
         ]
         self.raw_line = "\t".join(raw_data)
-        self.import_igc_genes = ImportIGCGenes('test', 'test')
+        self.import_igc_genes = ImportIGCGenes('test', 'test_url', 'test_token')
 
     def test_parse_gene_default_selected_keys(self):
         """
@@ -71,7 +71,7 @@ class TestParseGene(TestCase):
 class TestCleanGene(TestCase):
 
     def setUp(self):
-        self.import_igc_genes = ImportIGCGenes('test', 'test')
+        self.import_igc_genes = ImportIGCGenes('test', 'test_url', 'test_token')
         self.import_igc_genes._select_taxonomy = lambda x: x  # Mock to return same dict
         self.import_igc_genes._clean_functions = lambda x: x
         self.gene_dict = {
@@ -123,7 +123,7 @@ class TestSelectTaxonomy(TestCase):
         self.genus_name = 'Genus1'
         self.phylum_id = 'phylum_1'
         self.phylum_name = 'Phylum1'
-        self.import_igc_genes = ImportIGCGenes('test', 'test')
+        self.import_igc_genes = ImportIGCGenes('test', 'test_url', 'test_token')
         self.import_igc_genes.phylum_mapping = {
             self.phylum_name: self.phylum_id
         }
@@ -227,7 +227,7 @@ class TestBuildTaxoMapping(APITestCase):
         cls.phylum_items = TaxonomyFactory.create_batch(20, rank='phylum')
 
     def setUp(self):
-        self.import_igc_genes = ImportIGCGenes('test', 'test')
+        self.import_igc_genes = ImportIGCGenes('test', 'test_url', 'test_token')
         self.api_mock = MetageneDBCatalogTaxonomyAPIMock(self.client)
         self.import_igc_genes.metagenedb_taxonomy_api = self.api_mock
 
@@ -250,7 +250,7 @@ class TestBuildBuildFunctionCatalog(APITestCase):
         cls.functions = FunctionFactory.create_batch(100)
 
     def setUp(self):
-        self.import_igc_genes = ImportIGCGenes('test', 'test')
+        self.import_igc_genes = ImportIGCGenes('test', 'test_url', 'test_token')
         self.api_mock = MetageneDBCatalogFunctionAPIMock(self.client)
         self.import_igc_genes.metagenedb_function_api = self.api_mock