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-rw-r--r--test/requests/link_checker.py92
-rw-r--r--test/requests/links_scraper/genelinks.py121
-rw-r--r--test/requests/main_web_functionality.py24
-rw-r--r--test/requests/mapping_tests.py13
-rw-r--r--test/requests/navigation_tests.py1
-rwxr-xr-xtest/requests/test-website.py15
-rw-r--r--test/requests/test_forgot_password.py4
-rw-r--r--test/requests/test_login_local.py3
8 files changed, 228 insertions, 45 deletions
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([
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-25 18:12:15 +0000