aboutsummaryrefslogtreecommitdiff
path: root/test/requests
diff options
context:
space:
mode:
Diffstat (limited to 'test/requests')
-rw-r--r--test/requests/link_checker.py63
-rw-r--r--test/requests/main_web_functionality.py40
-rw-r--r--test/requests/mapping_tests.py43
-rw-r--r--test/requests/parametrized_test.py27
-rw-r--r--test/requests/run-integration-tests.py34
-rwxr-xr-xtest/requests/test-website.py71
-rw-r--r--test/requests/test_login_github.py47
-rw-r--r--test/requests/test_login_local.py60
-rw-r--r--test/requests/test_login_orcid.py47
-rw-r--r--test/requests/test_registration.py41
10 files changed, 473 insertions, 0 deletions
diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
new file mode 100644
index 00000000..256bf6ef
--- /dev/null
+++ b/test/requests/link_checker.py
@@ -0,0 +1,63 @@
+from __future__ import print_function
+import re
+import requests
+from lxml.html import parse
+from requests.exceptions import ConnectionError
+
+def is_root_link(link):
+ pattern = re.compile("^/$")
+ return pattern.match(link)
+
+def is_mailto_link(link):
+ pattern = re.compile("^mailto:.*")
+ return pattern.match(link)
+
+def is_internal_link(link):
+ pattern = re.compile("^/.*")
+ return pattern.match(link)
+
+def get_links(doc):
+ return filter(
+ lambda x: not (
+ is_root_link(x)
+ or is_mailto_link(x))
+ , map(lambda y: y.get("href")
+ , doc.cssselect("a")))
+
+def verify_link(link):
+ try:
+ result = requests.get(link, timeout=20)
+ if result.status_code == 200:
+ print(link+" ==> OK")
+ else:
+ print("ERROR: link `"+link+"` failed with status "
+ , result.status_code)
+ except ConnectionError 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)
+ 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")
+ for link in internal_links:
+ verify_link(host+link)
+
+ for link in external_links:
+ verify_link(link)
+
+def check_links(args_obj, parser):
+ print("")
+ print("Checking links")
+ host = args_obj.host
+
+ # Check the home page
+ check_page(host, host)
+
+ # Check traits page
+ check_page(
+ host,
+ host+"/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P")
diff --git a/test/requests/main_web_functionality.py b/test/requests/main_web_functionality.py
new file mode 100644
index 00000000..7b89b833
--- /dev/null
+++ b/test/requests/main_web_functionality.py
@@ -0,0 +1,40 @@
+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()
+ search_button = doc.cssselect("#btsearch")
+ assert(search_button[0].value == "Search")
+ print("OK")
+
+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)")
+ result = requests.get(host+"/search", params=data)
+ found = result.text.find("/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P")
+ assert(found >= 0)
+ print("OK")
+ 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()
+ traits_form = doc.forms[1]
+ assert(traits_form.fields["corr_dataset"] == "HC_M2_0606_P")
+ print("OK")
+ check_page(host, host+traits_url)
+
+def check_main_web_functionality(args_obj, parser):
+ print("")
+ print("Checking main web functionality...")
+ host = args_obj.host
+ check_home(host)
+ check_search_page(host)
diff --git a/test/requests/mapping_tests.py b/test/requests/mapping_tests.py
new file mode 100644
index 00000000..fd20df11
--- /dev/null
+++ b/test/requests/mapping_tests.py
@@ -0,0 +1,43 @@
+from __future__ import print_function
+import re
+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")
+ file_data = json.loads(file_handle.read().encode("utf-8"))
+ return file_data
+
+def check_pylmm_tool_selection(host, data):
+ data["method"] = "pylmm"
+ 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" # Check value in the file
+
+def check_R_qtl_tool_selection(host, data):
+ pass
+
+def check_CIM_tool_selection(host, data):
+ pass
+
+def check_mapping(args_obj, parser):
+ print("")
+ print("Checking mapping")
+
+ 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)
diff --git a/test/requests/parametrized_test.py b/test/requests/parametrized_test.py
new file mode 100644
index 00000000..abf98fce
--- /dev/null
+++ b/test/requests/parametrized_test.py
@@ -0,0 +1,27 @@
+import logging
+import unittest
+from elasticsearch import Elasticsearch, TransportError
+
+class ParametrizedTest(unittest.TestCase):
+
+ def __init__(self, methodName='runTest', gn2_url="http://localhost:5003", es_url="localhost:9200"):
+ super(ParametrizedTest, self).__init__(methodName=methodName)
+ self.gn2_url = gn2_url
+ self.es_url = es_url
+
+ def setUp(self):
+ self.es = Elasticsearch([self.es_url])
+ self.es_cleanup = []
+
+ es_logger = logging.getLogger("elasticsearch")
+ es_logger.addHandler(
+ logging.FileHandler("/tmp/es_TestRegistrationInfo.log"))
+ es_trace_logger = logging.getLogger("elasticsearch.trace")
+ es_trace_logger.addHandler(
+ logging.FileHandler("/tmp/es_TestRegistrationTrace.log"))
+
+ def tearDown(self):
+ self.es.delete_by_query(
+ index="users"
+ , doc_type="local"
+ , body={"query":{"match":{"email_address":"test@user.com"}}})
diff --git a/test/requests/run-integration-tests.py b/test/requests/run-integration-tests.py
new file mode 100644
index 00000000..5e816549
--- /dev/null
+++ b/test/requests/run-integration-tests.py
@@ -0,0 +1,34 @@
+import sys
+from test_login_local import TestLoginLocal
+from test_login_orcid import TestLoginOrcid
+from test_login_github import TestLoginGithub
+from test_registration import TestRegistration
+from unittest import TestSuite, TextTestRunner, TestLoader
+
+test_cases = [
+ TestRegistration
+ , TestLoginLocal
+ , TestLoginGithub
+ , TestLoginOrcid
+]
+
+def suite(gn2_url, es_url):
+ the_suite = TestSuite()
+ for case in test_cases:
+ the_suite.addTests(initTest(case, gn2_url, es_url))
+ return the_suite
+
+def initTest(klass, gn2_url, es_url):
+ loader = TestLoader()
+ methodNames = loader.getTestCaseNames(klass)
+ return [klass(mname, gn2_url, es_url) for mname in methodNames]
+
+def main(gn2_url, es_url):
+ runner = TextTestRunner()
+ runner.run(suite(gn2_url, es_url))
+
+if __name__ == "__main__":
+ if len(sys.argv) < 3:
+ raise Exception("Required arguments missing:\n\tTry running `run-integration-test.py <gn2-url> <es-url>`")
+ else:
+ main(sys.argv[1], sys.argv[2])
diff --git a/test/requests/test-website.py b/test/requests/test-website.py
new file mode 100755
index 00000000..2bef6eb1
--- /dev/null
+++ b/test/requests/test-website.py
@@ -0,0 +1,71 @@
+# Run with something like
+#
+# 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 mapping_tests import check_mapping
+from main_web_functionality import check_main_web_functionality
+
+print("Mechanical Rob firing up...")
+
+def run_all(args_obj, parser):
+ print("")
+ print("Running all tests.")
+ check_main_web_functionality(args_obj, parser)
+ check_links(args_obj, parser)
+ check_mapping(args_obj, parser)
+ # TODO: Add other functions as they are created.
+
+def print_help(args_obj, parser):
+ print(parser.format_help())
+
+def dummy(args_obj, parser):
+ print("Not implemented yet.")
+
+
+desc = """
+This is Mechanical-Rob - an automated web server tester for
+ Genenetwork.org
+"""
+parser = argparse.ArgumentParser(description=desc)
+
+parser.add_argument("-d", "--database", metavar="DB", type=str
+ , default="db_webqtl_s"
+ , help="Use database (default db_webqtl_s)")
+
+parser.add_argument("host", metavar="HOST", type=str
+ , default="http://localhost:5003"
+ , help="The url to the web server")
+
+parser.add_argument("-a", "--all", dest="accumulate", action="store_const"
+ , const=run_all, default=print_help
+ , help="Runs all tests.")
+
+parser.add_argument("-l", "--link-checker", dest="accumulate"
+ , action='store_const', const=check_links, default=print_help
+ , help="Checks for dead links.")
+
+parser.add_argument("-f", "--main-functionality", dest="accumulate"
+ , action='store_const', const=check_main_web_functionality
+ , default=print_help
+ , help="Checks for main web functionality.")
+
+parser.add_argument("-m", "--mapping", dest="accumulate"
+ , action="store_const", const=check_mapping, default=print_help
+ , help="Checks for mapping.")
+
+# 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_login_github.py b/test/requests/test_login_github.py
new file mode 100644
index 00000000..1bf4f695
--- /dev/null
+++ b/test/requests/test_login_github.py
@@ -0,0 +1,47 @@
+import uuid
+import requests
+from time import sleep
+from wqflask import app
+from parameterized import parameterized
+from parametrized_test import ParametrizedTest
+
+login_link_text = '<a id="login_in" href="/n/login">Sign in</a>'
+logout_link_text = '<a id="login_out" title="Signed in as ." href="/n/logout">Sign out</a>'
+uid = str(uuid.uuid4())
+
+class TestLoginGithub(ParametrizedTest):
+
+ def setUp(self):
+ super(TestLoginGithub, self).setUp()
+ data = {
+ "user_id": uid
+ , "name": "A. T. Est User"
+ , "github_id": 693024
+ , "user_url": "https://fake-github.com/atestuser"
+ , "login_type": "github"
+ , "organization": ""
+ , "active": 1
+ , "confirmed": 1
+ }
+ self.es.create(index="users", doc_type="local", body=data, id=uid)
+ sleep(1)
+
+ def tearDown(self):
+ super(TestLoginGithub, self).tearDown()
+ self.es.delete(index="users", doc_type="local", id=uid)
+
+ def testLoginUrl(self):
+ login_button_text = '<a href="https://github.com/login/oauth/authorize?client_id=' + app.config.get("GITHUB_CLIENT_ID") + '&amp;client_secret=' + app.config.get("GITHUB_CLIENT_SECRET") + '" title="Login with GitHub" class="btn btn-info btn-group">Login with Github</a>'
+ result = requests.get(self.gn2_url+"/n/login")
+ index = result.content.find(login_button_text)
+ self.assertTrue(index >= 0, "Should have found `Login with Github` button")
+
+ @parameterized.expand([
+ ("1234", login_link_text, "Login should have failed with non-existing user")
+ , (uid, logout_link_text, "Login should have been successful with existing user")
+ ])
+ def testLogin(self, test_uid, expected, message):
+ url = self.gn2_url+"/n/login?type=github&uid="+test_uid
+ result = requests.get(url)
+ index = result.content.find(expected)
+ self.assertTrue(index >= 0, message)
diff --git a/test/requests/test_login_local.py b/test/requests/test_login_local.py
new file mode 100644
index 00000000..808649ca
--- /dev/null
+++ b/test/requests/test_login_local.py
@@ -0,0 +1,60 @@
+import requests
+from wqflask import user_manager
+from parameterized import parameterized
+from parametrized_test import ParametrizedTest
+
+login_link_text = '<a id="login_in" href="/n/login">Sign in</a>'
+logout_link_text = '<a id="login_out" title="Signed in as ." href="/n/logout">Sign out</a>'
+
+class TestLoginLocal(ParametrizedTest):
+
+ def setUp(self):
+ super(TestLoginLocal, self).setUp()
+ self.login_url = self.gn2_url +"/n/login"
+ data = {
+ "es_connection": self.es,
+ "email_address": "test@user.com",
+ "full_name": "Test User",
+ "organization": "Test Organisation",
+ "password": "test_password",
+ "password_confirm": "test_password"
+ }
+ user_manager.basic_info = lambda : { "basic_info": "basic" }
+ user_manager.RegisterUser(data)
+
+
+ @parameterized.expand([
+ (
+ {
+ "email_address": "non@existent.email",
+ "password": "doesitmatter?"
+ }, login_link_text, "Login should have failed with the wrong user details."),
+ (
+ {
+ "email_address": "test@user.com",
+ "password": "test_password"
+ }, logout_link_text, "Login should have been successful with correct user details and neither import_collections nor remember_me set"),
+ (
+ {
+ "email_address": "test@user.com",
+ "password": "test_password",
+ "import_collections": "y"
+ }, logout_link_text, "Login should have been successful with correct user details and only import_collections set"),
+ (
+ {
+ "email_address": "test@user.com",
+ "password": "test_password",
+ "remember_me": "y"
+ }, logout_link_text, "Login should have been successful with correct user details and only remember_me set"),
+ (
+ {
+ "email_address": "test@user.com",
+ "password": "test_password",
+ "remember_me": "y",
+ "import_collections": "y"
+ }, logout_link_text, "Login should have been successful with correct user details, and both remember_me, and import_collections set")
+ ])
+ def testLogin(self, data, expected, message):
+ result = requests.post(self.login_url, data=data)
+ index = result.content.find(expected)
+ self.assertTrue(index >= 0, message)
diff --git a/test/requests/test_login_orcid.py b/test/requests/test_login_orcid.py
new file mode 100644
index 00000000..ea15642e
--- /dev/null
+++ b/test/requests/test_login_orcid.py
@@ -0,0 +1,47 @@
+import uuid
+import requests
+from time import sleep
+from wqflask import app
+from parameterized import parameterized
+from parametrized_test import ParametrizedTest
+
+login_link_text = '<a id="login_in" href="/n/login">Sign in</a>'
+logout_link_text = '<a id="login_out" title="Signed in as ." href="/n/logout">Sign out</a>'
+uid = str(uuid.uuid4())
+
+class TestLoginOrcid(ParametrizedTest):
+
+ def setUp(self):
+ super(TestLoginOrcid, self).setUp()
+ data = {
+ "user_id": uid
+ , "name": "A. T. Est User"
+ , "orcid": 345872
+ , "user_url": "https://fake-orcid.org/atestuser"
+ , "login_type": "orcid"
+ , "organization": ""
+ , "active": 1
+ , "confirmed": 1
+ }
+ self.es.create(index="users", doc_type="local", body=data, id=uid)
+ sleep(1)
+
+ def tearDown(self):
+ super(TestLoginOrcid, self).tearDown()
+ self.es.delete(index="users", doc_type="local", id=uid)
+
+ def testLoginUrl(self):
+ login_button_text = 'a href="https://sandbox.orcid.org/oauth/authorize?response_type=code&amp;scope=/authenticate&amp;show_login=true&amp;client_id=' + app.config.get("ORCID_CLIENT_ID") + '&amp;client_secret=' + app.config.get("ORCID_CLIENT_SECRET") + '" title="Login with ORCID" class="btn btn-info btn-group">Login with ORCID</a>'
+ result = requests.get(self.gn2_url+"/n/login")
+ index = result.content.find(login_button_text)
+ self.assertTrue(index >= 0, "Should have found `Login with ORCID` button")
+
+ @parameterized.expand([
+ ("1234", login_link_text, "Login should have failed with non-existing user")
+ , (uid, logout_link_text, "Login should have been successful with existing user")
+ ])
+ def testLogin(self, test_uid, expected, message):
+ url = self.gn2_url+"/n/login?type=orcid&uid="+test_uid
+ result = requests.get(url)
+ index = result.content.find(expected)
+ self.assertTrue(index >= 0, message)
diff --git a/test/requests/test_registration.py b/test/requests/test_registration.py
new file mode 100644
index 00000000..0047e8a6
--- /dev/null
+++ b/test/requests/test_registration.py
@@ -0,0 +1,41 @@
+import sys
+import requests
+from parametrized_test import ParametrizedTest
+
+class TestRegistration(ParametrizedTest):
+
+ def tearDown(self):
+ for item in self.es_cleanup:
+ self.es.delete(index="users", doc_type="local", id=item["_id"])
+
+ def testRegistrationPage(self):
+ if self.es.ping():
+ data = {
+ "email_address": "test@user.com",
+ "full_name": "Test User",
+ "organization": "Test Organisation",
+ "password": "test_password",
+ "password_confirm": "test_password"
+ }
+ requests.post(self.gn2_url+"/n/register", data)
+ response = self.es.search(
+ index="users"
+ , doc_type="local"
+ , body={
+ "query": {"match": {"email_address": "test@user.com"}}})
+ self.assertEqual(len(response["hits"]["hits"]), 1)
+ else:
+ self.skipTest("The elasticsearch server is down")
+
+def main(gn2, es):
+ import unittest
+ suite = unittest.TestSuite()
+ suite.addTest(TestRegistration(methodName="testRegistrationPage", gn2_url=gn2, es_url=es))
+ runner = unittest.TextTestRunner()
+ runner.run(suite)
+
+if __name__ == "__main__":
+ if len(sys.argv) < 3:
+ raise Exception("Required arguments missing")
+ else:
+ main(sys.argv[1], sys.argv[2])
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 15:51:26 +0000