Merge github.com:genenetwork/genenetwork2 into acenteno

10 files changed, 228 insertions, 72 deletions

diff --git a/test/__init__.py b/test/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/test/__init__.py
diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index 715f330c..feae6526 100644
--- a/test/requests/link_checker.py
+++ b/test/requests/link_checker.py
@@ -1,4 +1,3 @@
-from __future__ import print_function
 import re
 import requests
 from lxml.html import parse
@@ -23,12 +22,9 @@ def is_in_page_link(link):
     return pattern.match(link)
 
 def get_links(doc):
-    return filter(
-        lambda x: not (
+    return [x for x in [y.get("href") for y in doc.cssselect("a")] if not (
             is_root_link(x)
-            or is_mailto_link(x))
-        , map(lambda y: y.get("href")
-              , doc.cssselect("a")))
+            or is_mailto_link(x))]
 
 def verify_link(link):
     if link[0] == "#":
@@ -52,14 +48,29 @@ def verify_link(link):
         if DO_FAIL:
             raise ex
 
+
+def verify_static_file(link):
+    print("verifying "+link)
+    try:
+        result = requests.get(link, timeout=20, verify=False)
+        if (result.status_code == 200 and
+                result.content.find(bytes("Error: 404 Not Found", "utf-8")) <= 0):
+            print(link+" ==> OK")
+        else:
+            print("ERROR: link {}".format(link))
+            raise Exception("Failed verify")
+    except ConnectionError as ex:
+        print("ERROR: ", link, ex)
+
+
 def check_page(host, start_url):
     print("")
     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) or is_in_page_link(x)), links)
+    in_page_links = list(filter(is_in_page_link, links))
+    internal_links = list(filter(is_internal_link, links))
+    external_links = [x for x in links if not (is_internal_link(x) or is_in_page_link(x))]
 
     for link in internal_links:
         verify_link(host+link)
@@ -79,3 +90,66 @@ def check_links(args_obj, parser):
     check_page(
         host,
         host+"/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P")
+
+
+def check_packaged_js_files(args_obj, parser):
+    host = args_obj.host
+    js_files = [
+        # Datatables Extensions:
+        "/css/DataTablesExtensions/buttonsBootstrap/css/buttons.bootstrap.css",
+        "/js/DataTablesExtensions/buttons/js/dataTables.buttons.min.js",
+        "/css/DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css",
+        "/js/DataTablesExtensions/buttons/js/dataTables.buttons.min.js",
+        "/js/DataTablesExtensions/colResize/dataTables.colResize.js",
+        "/js/DataTablesExtensions/colReorder/js/dataTables.colReorder.js",
+        "/js/DataTablesExtensions/buttons/js/buttons.colVis.min.js",
+        "/js/DataTablesExtensions/scroller/js/dataTables.scroller.min.js",
+        "/js/DataTables/js/jquery.dataTables.js",
+        "/js/DataTablesExtensions/scrollerStyle/css/scroller.dataTables.min.css",
+        # Datatables plugins:
+        "/js/DataTablesExtensions/plugins/sorting/natural.js",
+        "/js/DataTablesExtensions/plugins/sorting/scientific.js",
+        # Other js libraries
+        "/js/chroma/chroma.min.js",
+        "/js/d3-tip/d3-tip.js",
+        "/js/d3js/d3.min.js",
+        "/js/js_alt/underscore.min.js",
+        "/js/nvd3/nv.d3.min.css",
+        "/js/qtip2/jquery.qtip.min.js",
+        "/js/js_alt/md5.min.js",
+        "/js/bootstrap/js/bootstrap.min.js",
+        "/css/bootstrap/css/bootstrap.css",
+        "/js/jquery-ui/jquery-ui.min.js",
+        "/js/jquery-cookie/jquery.cookie.js",
+        "/js/jquery/jquery.min.js",
+        "/js/typeahead/typeahead.bundle.js",
+        "/js/underscore-string/underscore.string.min.js",
+        "/js/js_alt/jstat.min.js",
+        "/js/js_alt/parsley.min.js",
+        "/js/js_alt/timeago.min.js",
+        "/js/plotly/plotly.min.js",
+        "/js/ckeditor/ckeditor.js",
+        "/js/jszip/jszip.min.js",
+        "/js/jscolor/jscolor.js",
+        "/js/DataTables/js/jquery.js",
+        "/css/DataTables/css/jquery.dataTables.css",
+        "/js/colorbox/jquery.colorbox-min.js",
+        "/css/nouislider/nouislider.min.css",
+        "/js/nouislider/nouislider.js",
+        "/js/purescript-genome-browser/js/purescript-genetics-browser.js",
+        "/js/purescript-genome-browser/css/purescript-genetics-browser.css",
+        "/js/cytoscape/cytoscape.min.js",
+        "/js/cytoscape-panzoom/cytoscape-panzoom.js",
+        "/js/cytoscape-panzoom/cytoscape.js-panzoom.css",
+        "/js/cytoscape-qtip/cytoscape-qtip.js",
+        "/css/d3-tip/d3-tip.css",
+        "/js/zxcvbn/zxcvbn.js",
+        "/js/javascript-twitter-post-fetcher/js/twitterFetcher_min.js",
+        "/js/DataTables/images/sort_asc_disabled.png",
+        "/js/DataTables/images/sort_desc_disabled.png",
+        "/js/shapiro-wilk/shapiro-wilk.js",
+    ]
+
+    print("Checking links")
+    for link in js_files:
+        verify_static_file(host+link)
diff --git a/test/requests/links_scraper/genelinks.py b/test/requests/links_scraper/genelinks.py
new file mode 100644
index 00000000..52c13489
--- /dev/null
+++ b/test/requests/links_scraper/genelinks.py
@@ -0,0 +1,121 @@
+import re
+import requests
+import urllib3
+import os
+
+from urllib.request import urlopen as uReq
+from bs4 import BeautifulSoup as soup
+from urllib.parse import urljoin
+from urllib.parse import urlparse
+
+
+PORT = os.environ.get("PORT", "5004")
+TEMPLATE_PATH = "../wqflask/wqflask/templates"
+
+BROKEN_LINKS = set()
+
+
+def search_templates():
+    """searches for broken links in templates"""
+    html_parsed_pages = []
+    for subdir, dirs, files in os.walk(TEMPLATE_PATH):
+        for file in files:
+            file_path = os.path.join(subdir, file)
+            if file_path.endswith(".html"):
+                parsed_page = soup(
+                    open(file_path, encoding="utf8"), "html.parser")
+                html_parsed_pages.append(parsed_page)
+    return html_parsed_pages
+
+
+def is_valid_link(url_link):
+    try:
+        result = urlparse(url_link)
+        return all([result.scheme, result.netloc, result.path])
+    except Exception:
+        return False
+
+
+def test_link(link):
+    print(f'Checking -->{link}')
+    results = None
+    try:
+        results = requests.get(link, verify=False, timeout=10)
+        status_code = results.status_code
+    except Exception:
+        status_code = 408
+    return int(status_code) > 403
+
+
+def fetch_css_links(parsed_page):
+    print("fetching css links")
+    for link in parsed_page.findAll("link"):
+        full_path = None
+        link_url = link.attrs.get("href")
+        if is_valid_link(link_url):
+            full_path = link_url
+        elif re.match(r"^/css", link_url) or re.match(r"^/js", link_url):
+            full_path = urljoin('http://localhost:5004/', link_url)
+        if full_path is not None:
+            if test_link(full_path):
+                BROKEN_LINKS.add(full_path)
+
+
+def fetch_html_links(parsed_page):
+    print("fetching a tags ")
+    for link in parsed_page.findAll("a"):
+        full_path = None
+        link_url = link.attrs.get("href")
+        if re.match(r"^/", link_url):
+            full_path = urljoin('http://localhost:5004/', link_url)
+        elif is_valid_link(link_url):
+            full_path = link_url
+        if full_path is not None:
+            if test_link(full_path):
+                BROKEN_LINKS.add(full_path)
+
+
+def fetch_script_tags(parsed_page):
+    print("--->fetching js links")
+    for link in parsed_page.findAll("script"):
+        js_link = link.attrs.get("src")
+        if js_link is not None:
+            if is_valid_link(js_link):
+                raise SystemExit("Failed,the library should be "
+                                 "packaged in guix. "
+                                 "Please contact, "
+                                 "http://genenetwork.org/ "
+                                 "for more details")
+
+            elif re.match(r"^/css", js_link) or re.match(r"^/js", js_link):
+                full_path = urljoin('http://localhost:5004/', js_link)
+                if test_link(full_path):
+                    BROKEN_LINKS.add(full_path)
+
+
+def fetch_page_links(page_url):
+    urllib3.disable_warnings(urllib3.exceptions.InsecureRequestWarning)
+    html_page = uReq(page_url)
+    parsed_page = soup(html_page, "html.parser")
+    fetch_script_tags(parsed_page=parsed_page)
+    fetch_css_links(parsed_page=parsed_page)
+    fetch_html_links(parsed_page=parsed_page)
+
+
+def webpages_to_check():
+    pages = [f"http://localhost:{PORT}/"]
+    return pages
+
+
+if __name__ == '__main__':
+    for page in webpages_to_check():
+        fetch_page_links(page)
+        if len(BROKEN_LINKS) > 0:
+            print("THE LINKS BELOW ARE BROKEN>>>>>>>>>>>>>")
+            for link in BROKEN_LINKS:
+                print(link)
+
+    if len(BROKEN_LINKS) > 0:
+        raise SystemExit(
+            "The links Above are broken. "
+            "Please contact genenetwork.org<<<<<<<<")
diff --git a/test/requests/main_web_functionality.py b/test/requests/main_web_functionality.py
index 7b89b833..28033ad5 100644
--- a/test/requests/main_web_functionality.py
+++ b/test/requests/main_web_functionality.py
@@ -1,9 +1,7 @@
-from __future__ import print_function
-import re
 import requests
 from lxml.html import parse
 from link_checker import check_page
-from requests.exceptions import ConnectionError
+
 
 def check_home(url):
     doc = parse(url).getroot()
@@ -13,17 +11,20 @@ def check_home(url):
 
 def check_search_page(host):
     data = dict(
-        species="mouse"
-        , group="BXD"
-        , type="Hippocampus mRNA"
-        , dataset="HC_M2_0606_P"
-        , search_terms_or=""
-        , search_terms_and="MEAN=(15 16) LRS=(23 46)")
+        species="mouse",
+        group="BXD",
+        type="Hippocampus mRNA",
+        dataset="HC_M2_0606_P",
+        search_terms_or="",
+        search_terms_and="MEAN=(15 16) LRS=(23 46)")
     result = requests.get(host+"/search", params=data)
-    found = result.text.find("/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P")
+    found = result.text.find("records were found")
     assert(found >= 0)
+    assert(result.status_code == 200)
     print("OK")
-    check_traits_page(host, "/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P")
+    check_traits_page(host, ("/show_trait?trait_id=1435395_"
+                             "s_at&dataset=HC_M2_0606_P"))
+
 
 def check_traits_page(host, traits_url):
     doc = parse(host+traits_url).getroot()
@@ -32,6 +33,7 @@ def check_traits_page(host, traits_url):
     print("OK")
     check_page(host, host+traits_url)
 
+
 def check_main_web_functionality(args_obj, parser):
     print("")
     print("Checking main web functionality...")
diff --git a/test/requests/mapping_tests.py b/test/requests/mapping_tests.py
index 6de81bfe..19b22c21 100644
--- a/test/requests/mapping_tests.py
+++ b/test/requests/mapping_tests.py
@@ -1,4 +1,3 @@
-from __future__ import print_function
 import re
 import copy
 import json
@@ -15,9 +14,9 @@ def check_R_qtl_tool_selection(host, data):
     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)
+    page = requests.post(host+"/loading", data=data, headers=headers)
     doc = fromstring(page.text)
-    form = doc.forms[1]
+    form = doc.forms[0]
     assert form.fields["dataset"] == "HC_M2_0606_P"
     assert form.fields["value:BXD1"] == "15.034"
 
@@ -25,9 +24,9 @@ def check_CIM_tool_selection(host, data):
     print("")
     print("CIM mapping tool selection (using reaper)")
     data["method"] = "reaper"
-    page = requests.post(host+"/marker_regression", data=data)
+    page = requests.post(host+"/loading", data=data)
     doc = fromstring(page.text)
-    form = doc.forms[1]
+    form = doc.forms[0]
     assert form.fields["dataset"] == "HC_M2_0606_P"
     assert form.fields["value:BXD1"] == "15.034"
 
@@ -37,6 +36,6 @@ def check_mapping(args_obj, parser):
 
     host = args_obj.host
     data = load_data_from_file()
-    check_pylmm_tool_selection(host, copy.deepcopy(data))
-    check_R_qtl_tool_selection(host, copy.deepcopy(data)) ## Why does this fail?
+    # check_pylmm_tool_selection(host, copy.deepcopy(data)) ## Not defined
+    check_R_qtl_tool_selection(host, copy.deepcopy(data))
     check_CIM_tool_selection(host, copy.deepcopy(data))
diff --git a/test/requests/navigation_tests.py b/test/requests/navigation_tests.py
index eda27324..6b91c1fd 100644
--- a/test/requests/navigation_tests.py
+++ b/test/requests/navigation_tests.py
@@ -1,4 +1,3 @@
-from __future__ import print_function
 import re
 import requests
 from lxml.html import parse
diff --git a/test/requests/test-website.py b/test/requests/test-website.py
index b2e09bc4..8bfb47c2 100755
--- a/test/requests/test-website.py
+++ b/test/requests/test-website.py
@@ -3,9 +3,10 @@
 #   env GN2_PROFILE=/home/wrk/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -c ../test/requests/test-website.py http://localhost:5003
 #
 # Mostly to pick up the Guix GN2_PROFILE and python modules
-from __future__ import print_function
+
 import argparse
 from link_checker import check_links
+from link_checker import check_packaged_js_files
 from mapping_tests import check_mapping
 from navigation_tests import check_navigation
 from main_web_functionality import check_main_web_functionality
@@ -30,6 +31,7 @@ def run_all(args_obj, parser):
     link_checker.DO_FAIL = args_obj.fail
     check_main_web_functionality(args_obj, parser)
     check_links(args_obj, parser)
+    check_packaged_js_files(args_obj, parser)
     check_mapping(args_obj, parser)
     # TODO: Add other functions as they are created.
 
@@ -104,16 +106,7 @@ parser.add_argument("-i", "--integration-tests", dest="accumulate"
                     , action="store_const", const=integration_tests, default=print_help
                     , help="Runs integration tests.")
 
-# 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.")
-
-# parser.add_argument("-s", "--skip-broken", dest="accumulate"
-#                     , action="store_const", const=dummy, default=print_help
-#                     , help="Skip tests that are known to be broken.")
-
 args = parser.parse_args()
-# print("The arguments object: ", args)
+
 
 args.accumulate(args, parser)
diff --git a/test/requests/test_forgot_password.py b/test/requests/test_forgot_password.py
index 2bf34c5c..346524bc 100644
--- a/test/requests/test_forgot_password.py
+++ b/test/requests/test_forgot_password.py
@@ -1,5 +1,4 @@
 import requests
-from wqflask import user_manager
 from utility.elasticsearch_tools import get_user_by_unique_column
 from parameterized import parameterized
 from parametrized_test import ParametrizedTest
@@ -27,8 +26,7 @@ class TestForgotPassword(ParametrizedTest):
             "password": "test_password",
             "password_confirm": "test_password"
         }
-        user_manager.basic_info = lambda : { "basic_info": "basic" }
-        user_manager.RegisterUser(data)
+
 
     def testWithoutEmail(self):
         data = {"email_address": ""}
diff --git a/test/requests/test_login_local.py b/test/requests/test_login_local.py
index 808649ca..6691d135 100644
--- a/test/requests/test_login_local.py
+++ b/test/requests/test_login_local.py
@@ -1,5 +1,4 @@
 import requests
-from wqflask import user_manager
 from parameterized import parameterized
 from parametrized_test import ParametrizedTest
 
@@ -19,8 +18,6 @@ class TestLoginLocal(ParametrizedTest):
             "password": "test_password",
             "password_confirm": "test_password"
         }
-        user_manager.basic_info = lambda : { "basic_info": "basic" }
-        user_manager.RegisterUser(data)
 
     
     @parameterized.expand([
diff --git a/test/unittest/test_registration.py b/test/unittest/test_registration.py
deleted file mode 100644
index 98d0cdff..00000000
--- a/test/unittest/test_registration.py
+++ /dev/null
@@ -1,27 +0,0 @@
-# Run test with something like
-#
-# env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=$HOME/gn2_data ./bin/genenetwork2 ./etc/default_settings.py -c ../test/unittest/test_registration.py
-#
-
-import unittest
-import mock.es_double as es
-from wqflask.user_manager import RegisterUser
-
-class TestRegisterUser(unittest.TestCase):
-    def setUp(self):
-        self.es = es.ESDouble()
-
-    def testRegisterUserWithCorrectData(self):
-        data = {
-            "email_address": "user@example.com"
-            , "full_name": "A.N. Other"
-            , "organization": "Some Organisation"
-            , "password": "testing"
-            , "password_confirm": "testing"
-            , "es_connection": self.es
-        }
-        result = RegisterUser(data)
-        self.assertEqual(len(result.errors), 0, "Errors were not expected")
-
-if __name__ == "__main__":
-    unittest.main()