subsequence limit and trunc512 flag added in mockserver

tests/conftest.py

@@ -32,6 +32,10 @@ def pytest_addoption(parser):
         "--redir",
         action="store_true",
         default="False", help="success queries redirection")
+    parser.addoption(
+        "--trunc512",
+        action="store_true",
+        default="False", help="trunc512 support")
 
 
 @pytest.fixture(scope='session')
@@ -47,7 +51,8 @@ def server(request):
         return 'http://' + option.server
     circular_support = request.config.getoption("--cir")
     redirection = request.config.getoption("--redir")
+    trunc512 = request.config.getoption("--trunc512")
     port = get_free_port()
-    start_mock_server(port, circular_support, redirection)
+    start_mock_server(port, circular_support, redirection, trunc512=trunc512)
     server_base_url = 'http://localhost:' + str(port)
     return server_base_url

tests/mockserver.py

@@ -13,6 +13,8 @@
 DATA = []
 CIRCULAR_CHROMOSOME_SUPPORT = True
 REDIRECTION = False
+SUBSEQUENCE_LIMIT = 400000
+TRUNC512 = True
 
 
 class MockServerRequestHandler(BaseHTTPRequestHandler):
@@ -150,7 +152,9 @@ def get_seq_obj(self):
 
         seq_id = self.get_seq_id()
         for seq in DATA:
-            if seq.md5 == seq_id or seq.sha512 == seq_id:
+            if seq.md5 == seq_id:
+                return seq
+            if TRUNC512 is True and seq.sha512 == seq_id:
                 return seq
         return None
 
@@ -173,6 +177,9 @@ def send(self, status_code, content="".encode("ascii"), headers={}):
         such as do_GET, handle_subsequence_query_range and
         handle_subsequence_query_start_end
         '''
+        if len(content) > SUBSEQUENCE_LIMIT:
+            self.send(416)
+            return
 
         self.send_response(status_code)
         for key in headers:
@@ -342,7 +349,7 @@ def get_free_port():
     return port
 
 
-def start_mock_server(port, circular_support, redirection, daemon=True):
+def start_mock_server(port, circular_support, redirection, daemon=True, trunc512=True):
     ''' start_mock_server used by test suite's conftest.py file to run the server
     on the fly. It gets circular_support (a boolean variable) from conftest.py
     to set the global variable CIRCULAR_CHROMOSOME_SUPPORT in the server.
@@ -351,9 +358,10 @@ def start_mock_server(port, circular_support, redirection, daemon=True):
     running all the tests.
     '''
 
-    global CIRCULAR_CHROMOSOME_SUPPORT, REDIRECTION
+    global CIRCULAR_CHROMOSOME_SUPPORT, REDIRECTION, TRUNC512
     CIRCULAR_CHROMOSOME_SUPPORT = circular_support
     REDIRECTION = redirection
+    TRUNC512 = trunc512
     set_data()
     mock_server = HTTPServer(('localhost', port), MockServerRequestHandler)
     mock_server_thread = Thread(target=mock_server.serve_forever)