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-rw-r--r--test/requests/link_checker.py10
-rw-r--r--test/requests/mapping_tests.py35
-rw-r--r--test/requests/navigation_tests.py15
-rwxr-xr-xtest/requests/test-website.py2
-rw-r--r--wqflask/base/anon_collection.py3
-rw-r--r--wqflask/utility/elasticsearch_tools.py2
-rw-r--r--wqflask/utility/svg.py2
7 files changed, 51 insertions, 18 deletions
diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index 64553ed8..715f330c 100644
--- a/test/requests/link_checker.py
+++ b/test/requests/link_checker.py
@@ -18,6 +18,10 @@ 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 (
@@ -40,6 +44,7 @@ def verify_link(link):
         else:
             print("ERROR: link `"+link+"` failed with status "
                   , result.status_code)
+
             if DO_FAIL:
                 raise Exception("Failed verify")
     except ConnectionError as ex:
@@ -52,9 +57,10 @@ def check_page(host, start_url):
     print("Checking links host "+host+" 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 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))
diff --git a/test/requests/navigation_tests.py b/test/requests/navigation_tests.py
new file mode 100644
index 00000000..eda27324
--- /dev/null
+++ b/test/requests/navigation_tests.py
@@ -0,0 +1,15 @@
+from __future__ import print_function
+import re
+import requests
+from lxml.html import parse
+
+def check_navigation(args_obj, parser):
+    print("")
+    print("Checking navigation.")
+
+    host = args_obj.host
+    url = host + "/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P"
+    print("URL: ", url)
+    page = requests.get(url)
+    # Page is built by the javascript, hence using requests fails for this.
+    # Investigate use of selenium maybe?
diff --git a/test/requests/test-website.py b/test/requests/test-website.py
index 118c9df1..a33fe708 100755
--- a/test/requests/test-website.py
+++ b/test/requests/test-website.py
@@ -7,6 +7,7 @@ from __future__ import print_function
 import argparse
 from link_checker import check_links
 from mapping_tests import check_mapping
+from navigation_tests import check_navigation
 from main_web_functionality import check_main_web_functionality
 import link_checker
 import sys
@@ -63,6 +64,7 @@ parser.add_argument("-m", "--mapping", dest="accumulate"
                     , action="store_const", const=check_mapping, default=print_help
                     , help="Checks for mapping.")
 
+# Navigation tests deactivated since system relies on Javascript
 # parser.add_argument("-n", "--navigation", dest="accumulate"
 #                     , action="store_const", const=check_navigation, default=print_help
 #                     , help="Checks for navigation.")
diff --git a/wqflask/base/anon_collection.py b/wqflask/base/anon_collection.py
index 8ee73296..dd1aa27f 100644
--- a/wqflask/base/anon_collection.py
+++ b/wqflask/base/anon_collection.py
@@ -1,6 +1,6 @@
 class AnonCollection(TraitCollection):

     

-    def __init__(self, anon_id)

+    def __init__(self, anon_id):

         self.anon_id = anon_id

         self.collection_members = Redis.smembers(self.anon_id)

         print("self.collection_members is:", self.collection_members)

@@ -12,6 +12,7 @@ class AnonCollection(TraitCollection):
         print("traits_to_remove:", traits_to_remove)

         for trait in traits_to_remove:

             Redis.srem(self.anon_id, trait)

+

         members_now = self.collection_members - traits_to_remove

         print("members_now:", members_now)

         print("Went from {} to {} members in set.".format(len(self.collection_members), len(members_now)))

diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py
index 734379f7..075a8f65 100644
--- a/wqflask/utility/elasticsearch_tools.py
+++ b/wqflask/utility/elasticsearch_tools.py
@@ -7,7 +7,7 @@ logger = getLogger(__name__)
 from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT
 
 def test_elasticsearch_connection():
-    es = Elasticsearch(['http://'+ELASTICSEARCH_HOST+":"+ELASTICSEARCH_PORT+'/'], verify_certs=True)
+    es = Elasticsearch(['http://'+ELASTICSEARCH_HOST+":"+str(ELASTICSEARCH_PORT)+'/'], verify_certs=True)
     if not es.ping():
         logger.warning("Elasticsearch is DOWN")
 
diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py
index 512bc9e6..db13b9d1 100644
--- a/wqflask/utility/svg.py
+++ b/wqflask/utility/svg.py
@@ -1029,7 +1029,7 @@ class drawing:
         try:
             xv.feed(svg)
         except:
-            raise "SVG is not well formed, see messages above"
+            raise Exception("SVG is not well formed, see messages above")
         else:
             print "SVG well formed"
 if __name__=='__main__':
generated by cgit-pink 1.4.1 (git 2.36.1) at 2025-10-06 16:01:30 +0000