Merge pull request #259 from CanDIG/daisieh/allele_form

CanDIG · May 3, 2023 · 10a3e40 · 10a3e40
2 parents 182237a + b6aeb8d
commit 10a3e40
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Showing 3 changed files with 16 additions and 9 deletions.
diff --git a/htsget_server/authz.py b/htsget_server/authz.py
@@ -11,7 +11,7 @@
 def is_authed(id_, request):
     if request is None:
         return 401
-    if request.headers.get("Test_Key") == TEST_KEY:
+    if request.headers.get("Authorization") == f"Bearer {TEST_KEY}":
         print("WARNING: TEST MODE, AUTHORIZATION IS DISABLED")
         app.logger.warning("WARNING: TEST MODE, AUTHORIZATION IS DISABLED")
         return 200 # no auth
@@ -30,7 +30,7 @@ def is_authed(id_, request):
 
 
 def is_testing(request):
-    if request.headers.get("Test_Key") == TEST_KEY:
+    if request.headers.get("Authorization") == f"Bearer {TEST_KEY}":
         print("WARNING: TEST MODE, AUTHORIZATION IS DISABLED")
         app.logger.warning("WARNING: TEST MODE, AUTHORIZATION IS DISABLED")
         return True
@@ -49,7 +49,7 @@ def is_site_admin(request):
     """
     Is the user associated with the token a site admin?
     """
-    if request.headers.get("Test_Key") == TEST_KEY:
+    if request.headers.get("Authorization") == f"Bearer {TEST_KEY}":
         print("WARNING: TEST MODE, AUTHORIZATION IS DISABLED")
         app.logger.warning("WARNING: TEST MODE, AUTHORIZATION IS DISABLED")
         return True # no auth

diff --git a/htsget_server/beacon_operations.py b/htsget_server/beacon_operations.py
@@ -7,6 +7,7 @@
 import json
 import re
 import connexion
+from functools import reduce
 
 
 app = Flask(__name__)
@@ -126,6 +127,12 @@ def post_search():
     if 'requestedGranularity' not in req:
         req['requestedGranularity'] = 'record'
 
+    params = list(req['query']['requestParameters'].keys())
+    for param in params:
+        # change all names of parameters to snake case from camel case
+        new_param = reduce(lambda x, y: x + ('_' if y.isupper() else '') + y, param).lower()
+        req['query']['requestParameters'][new_param] = req['query']['requestParameters'].pop(param)
+
     try:
         result = search(req)
         return result, 200

diff --git a/tests/test_htsget_server.py b/tests/test_htsget_server.py
@@ -24,12 +24,12 @@
 
 
 def get_headers(username=USERNAME, password=PASSWORD):
-    headers={"Test_Key": TEST_KEY}
+    headers = {}
     try:
         token = get_access_token(username=username, password=password)
         headers["Authorization"] = f"Bearer {token}"
     except Exception as e:
-        headers["Authorization"] = "Bearer testtest"
+        headers["Authorization"] = f"Bearer {TEST_KEY}"
     return headers
 
 
@@ -354,7 +354,7 @@ def test_beacon_get_search():
 
     # for an unauthorized user, the request should not contain a full response, just a count
     headers = get_headers(username="test", password="test")
-    headers.pop("Test_Key")
+    headers["Authorization"] = "Bearer unauthorized"
     response = requests.get(url, headers=headers)
     print(response.text)
     assert 'response' not in response.json()
@@ -371,8 +371,8 @@ def get_beacon_post_search():
                         "requestParameters": {
                             "start": [5030000],
                             "end": [5030847],
-                            "assembly_id": "hg37",
-                            "reference_name": "21"
+                            "assemblyId": "hg37",
+                            "referenceName": "21"
                         }
                     },
                     "meta": {
@@ -388,7 +388,7 @@ def get_beacon_post_search():
                         "requestParameters": {
                             "start": [16562322],
                             "end": [16613564],
-                            "reference_name": "1"
+                            "referenceName": "1"
                         }
                     },
                     "meta": {