* Add mapping tests. Fix link-checker tests.

* Add tests for the R/qtl and CIM mapping tools.
* Fix tests for in-page links.

2 files changed, 34 insertions, 17 deletions

diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index 256bf6ef..a75327f0 100644
--- a/test/requests/link_checker.py
+++ b/test/requests/link_checker.py
@@ -16,6 +16,10 @@ def is_internal_link(link):
     pattern = re.compile("^/.*")
     return pattern.match(link)
 
+def is_in_page_link(link):
+    pattern = re.compile("^#.*")
+    return pattern.match(link)
+
 def get_links(doc):
     return filter(
         lambda x: not (
@@ -32,17 +36,21 @@ def verify_link(link):
         else:
             print("ERROR: link `"+link+"` failed with status "
                   , result.status_code)
-    except ConnectionError as ex:
-        print("ERROR: ", link, ex)
+    except Exception as ex:
+        print("ERROR: ("+link+")", ex)
 
 def check_page(host, start_url):
     print("")
     print("Checking links in page `"+start_url+"`")
     doc = parse(start_url).getroot()
     links = get_links(doc)
+    in_page_links = filter(is_in_page_link, links)
     internal_links = filter(is_internal_link, links)
-    external_links = filter(lambda x: not is_internal_link(x), links)
-    external_links.append("http://somenon-existentsite.brr")
+    external_links = filter(lambda x: not (is_internal_link(x) or is_in_page_link(x)), links)
+
+    for link in in_page_links:
+        verify_link(start_url+link)
+
     for link in internal_links:
         verify_link(host+link)
 
diff --git a/test/requests/mapping_tests.py b/test/requests/mapping_tests.py
index fd20df11..8eb19de7 100644
--- a/test/requests/mapping_tests.py
+++ b/test/requests/mapping_tests.py
@@ -1,17 +1,10 @@
 from __future__ import print_function
 import re
+import copy
 import json
 import requests
 from lxml.html import fromstring
 
-def get_data(list_item):
-    try:
-        value = list_item[1]
-    except:
-        value = None
-    #print("list_item:", list_item, "==>", value)
-    return value
-
 def load_data_from_file():
     filename = "../test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json"
     file_handle = open(filename, "r")
@@ -19,6 +12,8 @@ def load_data_from_file():
     return file_data
 
 def check_pylmm_tool_selection(host, data):
+    print("")
+    print("pylmm mapping tool selection")
     data["method"] = "pylmm"
     page = requests.post(host+"/marker_regression", data=data)
     doc = fromstring(page.text)
@@ -27,10 +22,24 @@ def check_pylmm_tool_selection(host, data):
     assert form.fields["value:BXD1"] == "15.034" # Check value in the file
 
 def check_R_qtl_tool_selection(host, data):
-    pass
+    print("")
+    print("R/qtl mapping tool selection")
+    headers = {"Content-Type": "application/x-www-form-urlencoded"}
+    page = requests.post(host+"/marker_regression", data=data, headers=headers)
+    doc = fromstring(page.text)
+    form = doc.forms[1]
+    assert form.fields["dataset"] == "HC_M2_0606_P"
+    assert form.fields["value:BXD1"] == "15.034"
 
 def check_CIM_tool_selection(host, data):
-    pass
+    print("")
+    print("CIM mapping tool selection (using reaper)")
+    data["method"] = "reaper"
+    page = requests.post(host+"/marker_regression", data=data)
+    doc = fromstring(page.text)
+    form = doc.forms[1]
+    assert form.fields["dataset"] == "HC_M2_0606_P"
+    assert form.fields["value:BXD1"] == "15.034"
 
 def check_mapping(args_obj, parser):
     print("")
@@ -38,6 +47,6 @@ def check_mapping(args_obj, parser):
 
     host = args_obj.host
     data = load_data_from_file()
-    check_pylmm_tool_selection(host, data)
-    check_R_qtl_tool_selection(host, data)
-    check_CIM_tool_selection(host, data)
+    check_pylmm_tool_selection(host, copy.deepcopy(data))
+    check_R_qtl_tool_selection(host, copy.deepcopy(data)) ## Why does this fail?
+    check_CIM_tool_selection(host, copy.deepcopy(data))