Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into production

7 files changed, 145 insertions, 50 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/parametrized_test.py b/test/requests/parametrized_test.py
index abf98fce..50003850 100644
--- a/test/requests/parametrized_test.py
+++ b/test/requests/parametrized_test.py
@@ -1,5 +1,7 @@
 import logging
 import unittest
+from wqflask import app
+from utility.elasticsearch_tools import get_elasticsearch_connection, get_user_by_unique_column
 from elasticsearch import Elasticsearch, TransportError
 
 class ParametrizedTest(unittest.TestCase):
@@ -10,10 +12,11 @@ class ParametrizedTest(unittest.TestCase):
         self.es_url = es_url
 
     def setUp(self):
-        self.es = Elasticsearch([self.es_url])
+        self.es = get_elasticsearch_connection()
         self.es_cleanup = []
 
         es_logger = logging.getLogger("elasticsearch")
+        es_logger.setLevel(app.config.get("LOG_LEVEL"))
         es_logger.addHandler(
             logging.FileHandler("/tmp/es_TestRegistrationInfo.log"))
         es_trace_logger = logging.getLogger("elasticsearch.trace")
@@ -21,7 +24,9 @@ class ParametrizedTest(unittest.TestCase):
             logging.FileHandler("/tmp/es_TestRegistrationTrace.log"))
 
     def tearDown(self):
+        from time import sleep
         self.es.delete_by_query(
             index="users"
             , doc_type="local"
             , body={"query":{"match":{"email_address":"test@user.com"}}})
+        sleep(1)
diff --git a/test/requests/run-integration-tests.py b/test/requests/run-integration-tests.py
deleted file mode 100644
index 5e816549..00000000
--- a/test/requests/run-integration-tests.py
+++ /dev/null
@@ -1,34 +0,0 @@
-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
index 118c9df1..b2e09bc4 100755
--- a/test/requests/test-website.py
+++ b/test/requests/test-website.py
@@ -7,10 +7,20 @@ 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
 
+# Imports for integration tests
+from wqflask import app
+from test_login_local import TestLoginLocal
+from test_login_orcid import TestLoginOrcid
+from test_login_github import TestLoginGithub
+from test_registration import TestRegistration
+from test_forgot_password import TestForgotPassword
+from unittest import TestSuite, TextTestRunner, TestLoader
+
 print("Mechanical Rob firing up...")
 
 def run_all(args_obj, parser):
@@ -29,6 +39,33 @@ def print_help(args_obj, parser):
 def dummy(args_obj, parser):
     print("Not implemented yet.")
 
+def integration_tests(args_obj, parser):
+    gn2_url = args_obj.host
+    es_url = app.config.get("ELASTICSEARCH_HOST")+":"+str(app.config.get("ELASTICSEARCH_PORT"))
+    run_integration_tests(gn2_url, es_url)
+
+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 integration_suite(gn2_url, es_url):
+    test_cases = [
+        TestRegistration
+        , TestLoginLocal
+        , TestLoginGithub
+        , TestLoginOrcid
+        , TestForgotPassword
+    ]
+    the_suite = TestSuite()
+    for case in test_cases:
+        the_suite.addTests(initTest(case, gn2_url, es_url))
+    return the_suite
+
+def run_integration_tests(gn2_url, es_url):
+    runner = TextTestRunner()
+    runner.run(integration_suite(gn2_url, es_url))
+
 
 desc = """
 This is Mechanical-Rob - an automated web server tester for
@@ -63,6 +100,11 @@ parser.add_argument("-m", "--mapping", dest="accumulate"
                     , action="store_const", const=check_mapping, default=print_help
                     , help="Checks for mapping.")
 
+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.")
diff --git a/test/requests/test_forgot_password.py b/test/requests/test_forgot_password.py
new file mode 100644
index 00000000..2bf34c5c
--- /dev/null
+++ b/test/requests/test_forgot_password.py
@@ -0,0 +1,52 @@
+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
+
+passwork_reset_link = ''
+forgot_password_page = None
+
+class TestForgotPassword(ParametrizedTest):
+
+    def setUp(self):
+        super(TestForgotPassword, self).setUp()
+        self.forgot_password_url = self.gn2_url+"/n/forgot_password_submit"
+        def send_email(to_addr, msg, fromaddr="no-reply@genenetwork.org"):
+            print("CALLING: send_email_mock()")
+            email_data = {
+                "to_addr": to_addr
+                , "msg": msg
+                , "fromaddr": from_addr}
+
+        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)
+
+    def testWithoutEmail(self):
+        data = {"email_address": ""}
+        error_notification = '<div class="alert alert-danger">You MUST provide an email</div>'
+        result = requests.post(self.forgot_password_url, data=data)
+        self.assertEqual(result.url, self.gn2_url+"/n/forgot_password")
+        self.assertTrue(
+            result.content.find(error_notification) >= 0
+            , "Error message should be displayed but was not")
+
+    def testWithNonExistingEmail(self):
+        # Monkey patching doesn't work, so simply test that getting by email
+        # returns the correct data
+        user = get_user_by_unique_column(self.es, "email_address", "non-existent@domain.com")
+        self.assertTrue(user is None, "Should not find non-existent user")
+
+    def testWithExistingEmail(self):
+        # Monkey patching doesn't work, so simply test that getting by email
+        # returns the correct data
+        user = get_user_by_unique_column(self.es, "email_address", "test@user.com")
+        self.assertTrue(user is not None, "Should find user")