Resolved conflicts for pulling from testing branch

10 files changed, 491 insertions, 0 deletions

diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
new file mode 100644
index 00000000..64553ed8
--- /dev/null
+++ b/test/requests/link_checker.py
@@ -0,0 +1,75 @@
+from __future__ import print_function
+import re
+import requests
+from lxml.html import parse
+from requests.exceptions import ConnectionError
+
+DO_FAIL=False  # fail on error
+
+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):
+    if link[0] == "#":
+        # local link on page
+        return
+    print("verifying "+link)
+    try:
+        result = requests.get(link, timeout=20, verify=False)
+        if result.status_code == 200:
+            print(link+" ==> OK")
+        elif result.status_code == 307:
+            print(link+" ==> REDIRECT")
+        else:
+            print("ERROR: link `"+link+"` failed with status "
+                  , result.status_code)
+            if DO_FAIL:
+                raise Exception("Failed verify")
+    except ConnectionError as ex:
+        print("ERROR: ", link, ex)
+        if DO_FAIL:
+            raise 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)
+    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..118c9df1
--- /dev/null
+++ b/test/requests/test-website.py
@@ -0,0 +1,77 @@
+# 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
+import link_checker
+import sys
+
+print("Mechanical Rob firing up...")
+
+def run_all(args_obj, parser):
+    print("")
+    print("Running all tests.")
+    print(args_obj)
+    link_checker.DO_FAIL = args_obj.fail
+    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("--fail", help="Fail and stop on any error", action="store_true")
+
+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])