Merge pull request #5 from fredmanglis/testing

Testing

23 files changed, 1013 insertions, 208 deletions

diff --git a/bin/genenetwork2 b/bin/genenetwork2
index 8886e4bc..2a83a1cd 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -95,6 +95,13 @@ export WQFLASK_OVERRIDES=$overrides   # JSON
 echo WQFLASK_SETTINGS=$settings
 echo WQFLASK_OVERRIDES=$overrides
 
+# This is a temporary hack to inject ES - should have added python2-elasticsearch package to guix instead
+# if [ -z $ELASTICSEARCH_PROFILE ]; then
+#     echo -e "WARNING: Elastic Search profile has not been set - use ELASTICSEARCH_PROFILE";
+# else
+#     PYTHONPATH="$PYTHONPATH${PYTHONPATH:+:}$ELASTICSEARCH_PROFILE/lib/python2.7/site-packages"
+# fi
+
 if [ -z $GN2_PROFILE ] ; then
     echo "WARNING: GN2_PROFILE has not been set - you need the environment, so I hope you know what you are doing!"
     export GN2_PROFILE=$(dirname $(dirname $(which genenetwork2)))
@@ -108,7 +115,7 @@ if [ -z $GN2_PROFILE ]; then
     read -p "PRESS [ENTER] TO CONTINUE..."
 else
     export PATH=$GN2_PROFILE/bin:$PATH
-    export PYTHONPATH=$GN2_PROFILE/lib/python2.7/site-packages
+    export PYTHONPATH="$GN2_PROFILE/lib/python2.7/site-packages${PYTHONPATH:+:}$PYTHONPATH"
     export R_LIBS_SITE=$GN2_PROFILE/site-library
     export GEM_PATH=$GN2_PROFILE/lib/ruby/gems/2.4.0
     export JS_GUIX_PATH=$GN2_PROFILE/share/genenetwork2/javascript
@@ -124,7 +131,11 @@ else
     if [ -z $GEMMA_WRAPPER_COMMAND ]; then
         export GEMMA_WRAPPER_COMMAND="$GN2_PROFILE/bin/gemma-wrapper"
     fi
-    if [ ! -d $PYTHONPATH ] ; then echo "PYTHONPATH not valid "$PYTHONPATH ; exit 1 ; fi
+    while IFS=":" read -ra PPATH; do
+	for PPart in "${PPATH[@]}"; do
+	    if [ ! -d $PPart ] ; then echo "PYTHONPATH not valid "$PYTHONPATH ; exit 1 ; fi
+	done
+    done <<< "$PYTHONPATH"
     if [ ! -d $R_LIBS_SITE ] ; then echo "R_LIBS_SITE not valid "$R_LIBS_SITE ; exit 1 ; fi
     if [ ! -d $GEM_PATH ] ; then echo "GEM_PATH not valid "$GEM_PATH ; exit 1 ; fi
 fi
@@ -157,8 +168,9 @@ if [ "$1" = '-c' ] ; then
     cd $GN2_BASE_DIR/wqflask
     cmd=${2#wqflask/}
     echo PYTHONPATH=$PYTHONPATH
-    echo RUNNING COMMAND $cmd
-    python $cmd
+    shift ; shift
+    echo RUNNING COMMAND $cmd $*
+    python $cmd $*
     exit $?
 fi
 # Now handle command parameter -cli which runs in bash
@@ -167,8 +179,9 @@ if [ "$1" = "-cli" ] ; then
     cd $GN2_BASE_DIR/wqflask
     cmd=$2
     echo PYTHONPATH=$PYTHONPATH
-    echo RUNNING COMMAND $cmd
-    $cmd
+    shift ; shift
+    echo RUNNING COMMAND $cmd $*
+    $cmd $*
     exit $?
 fi
 if [ "$1" = '-gunicorn' ] ; then
diff --git a/bin/mechnical-rob b/bin/mechnical-rob
new file mode 100755
index 00000000..be223d94
--- /dev/null
+++ b/bin/mechnical-rob
@@ -0,0 +1,111 @@
+#!/usr/bin/env ruby
+
+
+USAGE = <<EOT
+This is Mechanical-Rob - an automated web server tester for
+                         Genenetwork.org that uses the brilliant
+                         mechanize gem with minitest.
+
+To use this software you need to install mechanize. Run it from
+the root of the genenetwork2 source tree as, for example,
+
+  ./bin/test-website http://localhost:5003/ (default)
+
+If you are using the small deployment database you can use
+
+  ./bin/test-website --skip -n
+
+To run all tests
+
+  ./bin/test-website --all
+
+To run individual tests on localhost you can do
+
+  ruby -Itest -Itest/lib test/lib/mapping.rb --name="/Mapping/"
+
+For more information see http://genenetwork.org/
+
+EOT
+$stderr.print USAGE
+
+require 'optparse'
+
+options = { database: :small, link_checker: false}
+opts = OptionParser.new do |o|
+  o.banner = "Usage: #{File.basename($0)} [options] URL"
+
+  o.on('-d','--database', String, 'Use database (default db_webqtl_s)') do |s|
+    options[:database] =
+      case s
+      when 'xx'
+        :unknown
+      else
+        :small
+      end
+  end
+
+  o.on('--all', 'Run all tests') do
+    options[:all] = true
+  end
+
+  o.on('-l','--link-checker', 'Check for dead links') do
+    options[:link_checker] = true
+  end
+
+  o.on('--navigation', 'Check for navigation') do
+    options[:navigation] = true
+  end
+
+  o.on('--mapping', 'Check for mapping') do
+    options[:mapping] = true
+  end
+
+  o.on('--skip-broken', 'Skip tests that are known to be broken') do
+    options[:skip_broken] = true
+  end
+
+  o.separator ""
+  o.on_tail('-h', '--help', 'display this help and exit') do
+    options[:show_help] = true
+  end
+end
+
+opts.parse!(ARGV)
+
+if options[:show_help]
+  print opts
+  exit 1
+end
+
+$options = options  # we are using a global here
+$host =
+  if ARGV.size>0
+    ARGV.shift
+  else
+    "http://localhost:5003"
+  end
+
+$stderr.print "Testing <",$host,">\n"
+
+require 'mechanize'
+require 'minitest/spec'
+require 'minitest/autorun'
+
+# These are the actual testing modules
+
+libpath = File.dirname(File.dirname(__FILE__))
+$: << File.join(libpath,'test/lib')
+
+require 'main_web_functionality'
+
+if options[:all] or options[:mapping]
+  require 'mapping'
+end
+
+if options[:all] or options[:link_checker]
+  require 'link_checker'
+end
+
+if options[:all] or options[:navigation]
+  require 'navigation'
+end
diff --git a/bin/test-website b/bin/test-website
index be223d94..5935f016 100755
--- a/bin/test-website
+++ b/bin/test-website
@@ -1,111 +1,7 @@
-#!/usr/bin/env ruby
+#! /bin/bash
 
-
-USAGE = <<EOT
-This is Mechanical-Rob - an automated web server tester for
-                         Genenetwork.org that uses the brilliant
-                         mechanize gem with minitest.
-
-To use this software you need to install mechanize. Run it from
-the root of the genenetwork2 source tree as, for example,
-
-  ./bin/test-website http://localhost:5003/ (default)
-
-If you are using the small deployment database you can use
-
-  ./bin/test-website --skip -n
-
-To run all tests
-
-  ./bin/test-website --all
-
-To run individual tests on localhost you can do
-
-  ruby -Itest -Itest/lib test/lib/mapping.rb --name="/Mapping/"
-
-For more information see http://genenetwork.org/
-
-EOT
-$stderr.print USAGE
-
-require 'optparse'
-
-options = { database: :small, link_checker: false}
-opts = OptionParser.new do |o|
-  o.banner = "Usage: #{File.basename($0)} [options] URL"
-
-  o.on('-d','--database', String, 'Use database (default db_webqtl_s)') do |s|
-    options[:database] =
-      case s
-      when 'xx'
-        :unknown
-      else
-        :small
-      end
-  end
-
-  o.on('--all', 'Run all tests') do
-    options[:all] = true
-  end
-
-  o.on('-l','--link-checker', 'Check for dead links') do
-    options[:link_checker] = true
-  end
-
-  o.on('--navigation', 'Check for navigation') do
-    options[:navigation] = true
-  end
-
-  o.on('--mapping', 'Check for mapping') do
-    options[:mapping] = true
-  end
-
-  o.on('--skip-broken', 'Skip tests that are known to be broken') do
-    options[:skip_broken] = true
-  end
-
-  o.separator ""
-  o.on_tail('-h', '--help', 'display this help and exit') do
-    options[:show_help] = true
-  end
-end
-
-opts.parse!(ARGV)
-
-if options[:show_help]
-  print opts
+if [ -z $GN2_PROFILE ]; then
+  echo "Run request tests with something like"
+  echo env GN2_PROFILE=/home/wrk/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -c ../test/requests/test-website.py http://localhost:5003
   exit 1
-end
-
-$options = options  # we are using a global here
-$host =
-  if ARGV.size>0
-    ARGV.shift
-  else
-    "http://localhost:5003"
-  end
-
-$stderr.print "Testing <",$host,">\n"
-
-require 'mechanize'
-require 'minitest/spec'
-require 'minitest/autorun'
-
-# These are the actual testing modules
-
-libpath = File.dirname(File.dirname(__FILE__))
-$: << File.join(libpath,'test/lib')
-
-require 'main_web_functionality'
-
-if options[:all] or options[:mapping]
-  require 'mapping'
-end
-
-if options[:all] or options[:link_checker]
-  require 'link_checker'
-end
-
-if options[:all] or options[:navigation]
-  require 'navigation'
-end
+fi
diff --git a/etc/default_settings.py b/etc/default_settings.py
index 699d21f1..a70d8aec 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -41,6 +41,24 @@ SECURITY_POST_LOGIN_VIEW = "/thank_you"
 SERVER_PORT = 5003          # running on localhost
 SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a\xbc\xfc\x80:*\xebc'
 
+GITHUB_CLIENT_ID = "UNKNOWN"
+GITHUB_CLIENT_SECRET = "UNKNOWN"
+GITHUB_AUTH_URL = "UNKNOWN"
+GITHUB_API_URL = "UNKNOWN"
+
+ORCID_CLIENT_ID = "UNKNOWN"
+ORCID_CLIENT_SECRET = "UNKNOWN"
+ORCID_AUTH_URL = "UNKNOWN"
+ORCID_TOKEN_URL = "UNKNOWN"
+
+ELASTICSEARCH_HOST = "localhost"
+ELASTICSEARCH_PORT = '9200'
+
+SMTP_CONNECT = "UNKNOWN"
+SMTP_USERNAME = "UNKNOWN"
+SMTP_PASSWORD = "UNKNOWN"
+
+
 # ---- Behavioural settings (defaults) note that logger and log levels can
 #      be overridden at the module level and with enviroment settings
 WEBSERVER_MODE  = 'DEV'     # Python webserver mode (DEBUG|DEV|PROD)
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])
diff --git a/test/unittest/test_registration.py b/test/unittest/test_registration.py
new file mode 100644
index 00000000..98d0cdff
--- /dev/null
+++ b/test/unittest/test_registration.py
@@ -0,0 +1,27 @@
+# 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()
diff --git a/wqflask/mock/__init__.py b/wqflask/mock/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/mock/__init__.py
diff --git a/wqflask/mock/es_double.py b/wqflask/mock/es_double.py
new file mode 100644
index 00000000..6ef8a1b9
--- /dev/null
+++ b/wqflask/mock/es_double.py
@@ -0,0 +1,15 @@
+class ESDouble(object):
+    def __init__(self):
+        self.items = {}
+
+    def ping(self):
+        return true
+
+    def create(self, index, doc_type, body, id):
+        self.items["index"] = {doc_type: {"id": id, "_source": data}}
+
+    def search(self, index, doc_type, body):
+        return {
+            "hits": {
+                "hits": self.items[index][doc_type][body]
+            }}
diff --git a/wqflask/run_gunicorn.py b/wqflask/run_gunicorn.py
index 14a2d689..ebe3add5 100644
--- a/wqflask/run_gunicorn.py
+++ b/wqflask/run_gunicorn.py
@@ -11,6 +11,9 @@ print "Starting up Gunicorn process"
 
 from wqflask import app
 
+app.config['SESSION_TYPE'] = 'filesystem'
+app.config['SECRET_KEY'] = 'super secret key'
+
 @app.route("/gunicorn")
 def hello():
     return "<h1 style='color:blue'>Hello There!</h1>"
diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py
new file mode 100644
index 00000000..2d3d5add
--- /dev/null
+++ b/wqflask/utility/elasticsearch_tools.py
@@ -0,0 +1,54 @@
+from elasticsearch import Elasticsearch, TransportError
+import logging
+
+from utility.logger import getLogger
+logger = getLogger(__name__)
+
+from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT
+
+def get_elasticsearch_connection():
+    logger.info("get_elasticsearch_connection")
+    es = None
+    try:
+        assert(ELASTICSEARCH_HOST)
+        assert(ELASTICSEARCH_PORT)
+        logger.info("ES HOST",ELASTICSEARCH_HOST)
+
+        es = Elasticsearch([{
+            "host": ELASTICSEARCH_HOST
+            , "port": ELASTICSEARCH_PORT
+        }]) if (ELASTICSEARCH_HOST and ELASTICSEARCH_PORT) else None
+
+        es_logger = logging.getLogger("elasticsearch")
+        es_logger.setLevel(logging.INFO)
+        es_logger.addHandler(logging.NullHandler())
+    except:
+        es = None
+
+    return es
+
+def get_user_by_unique_column(es, column_name, column_value, index="users", doc_type="local"):
+    return get_item_by_unique_column(es, column_name, column_value, index=index, doc_type=doc_type)
+
+def save_user(es, user, user_id):
+    es_save_data(es, "users", "local", user, user_id)
+
+def get_item_by_unique_column(es, column_name, column_value, index, doc_type):
+    item_details = None
+    try:
+        response = es.search(
+            index = index
+            , doc_type = doc_type
+            , body = {
+                "query": { "match": { column_name: column_value } }
+            })
+        if len(response["hits"]["hits"]) > 0:
+            item_details = response["hits"]["hits"][0]["_source"]
+    except TransportError as te:
+        pass
+    return item_details
+
+def es_save_data(es, index, doc_type, data_item, data_id,):
+    from time import sleep
+    es.create(index, doc_type, body=data_item, id=data_id)
+    sleep(1) # Delay 1 second to allow indexing
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index d3113302..8c9fed96 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -251,6 +251,26 @@ assert_dir(JS_GUIX_PATH)
 JS_GN_PATH         = get_setting('JS_GN_PATH')
 # assert_dir(JS_GN_PATH)
 
+GITHUB_CLIENT_ID = get_setting('GITHUB_CLIENT_ID')
+GITHUB_CLIENT_SECRET = get_setting('GITHUB_CLIENT_SECRET')
+GITHUB_AUTH_URL = None
+if GITHUB_CLIENT_ID and GITHUB_CLIENT_SECRET:
+    GITHUB_AUTH_URL = "https://github.com/login/oauth/authorize?client_id="+GITHUB_CLIENT_ID+"&client_secret="+GITHUB_CLIENT_SECRET
+GITHUB_API_URL = get_setting('GITHUB_API_URL')
+ORCID_CLIENT_ID = get_setting('ORCID_CLIENT_ID')
+ORCID_CLIENT_SECRET = get_setting('ORCID_CLIENT_SECRET')
+ORCID_AUTH_URL = None
+if ORCID_CLIENT_ID and ORCID_CLIENT_SECRET:
+    ORCID_AUTH_URL = "https://sandbox.orcid.org/oauth/authorize?response_type=code&scope=/authenticate&show_login=true&client_id="+ORCID_CLIENT_ID+"&client_secret="+ORCID_CLIENT_SECRET
+ORCID_TOKEN_URL = get_setting('ORCID_TOKEN_URL')
+
+ELASTICSEARCH_HOST = get_setting('ELASTICSEARCH_HOST')
+ELASTICSEARCH_PORT = get_setting('ELASTICSEARCH_PORT')
+
+SMTP_CONNECT = get_setting('SMTP_CONNECT')
+SMTP_USERNAME = get_setting('SMTP_USERNAME')
+SMTP_PASSWORD = get_setting('SMTP_PASSWORD')
+
 PYLMM_COMMAND      = app_set("PYLMM_COMMAND",pylmm_command())
 GEMMA_COMMAND      = app_set("GEMMA_COMMAND",gemma_command())
 assert(GEMMA_COMMAND is not None)
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 087b95b4..c189fb96 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -114,7 +114,7 @@ class MarkerRegression(object):
         self.num_perm = 0
         self.perm_output = []
         self.bootstrap_results = []
-        self.covariates = start_vars['covariates']
+        self.covariates = start_vars['covariates'] if "covariates" in start_vars else None
 
         #ZS: This is passed to GN1 code for single chr mapping
         self.selected_chr = -1
diff --git a/wqflask/wqflask/templates/new_security/login_user.html b/wqflask/wqflask/templates/new_security/login_user.html
index b9f49a61..0dae3503 100644
--- a/wqflask/wqflask/templates/new_security/login_user.html
+++ b/wqflask/wqflask/templates/new_security/login_user.html
@@ -16,14 +16,39 @@
             <h4>Don't have an account?</h4>
 
 
-            <a href="/n/register" class="btn btn-primary modalize">Create a new account</a>
-
-
-            <hr />
+            {% if es_server: %}
+	    <a href="/n/register" class="btn btn-primary modalize">Create a new account</a>
+	    {% else: %}
+	    <div class="alert alert-warning">
+	      <p>You cannot create an account at this moment.<br />
+		Please try again later.</p>
+	    </div>
+	    {% endif %}
+
+	    <hr />
+	    <h4>Login with external services</h4>
+
+	    {% if external_login: %}
+	    <div>
+	      {% if external_login["github"]: %}
+	      <a href="{{external_login['github']}}" title="Login with GitHub" class="btn btn-info btn-group">Login with Github</a>
+	      {% endif %}
+
+	      {% if external_login["orcid"]: %}
+	      <a href="{{external_login['orcid']}}" title="Login with ORCID" class="btn btn-info btn-group">Login with ORCID</a>
+	      {% endif %}
+	    </div>
+	    {% else: %}
+	    <div class="alert alert-warning">
+	      <p>You cannot login with external services at this time.<br />
+		Please try again later.</p>
+	    </div>
+	    {% endif %}
+	    <hr />
 
             <h4>Already have an account? Sign in here.</h4>
 
-
+	    {% if es_server: %}
             <form class="form-horizontal" action="/n/login" method="POST" name="login_user_form" id="loginUserForm">
                  <fieldset>
                     <div class="form-group">
@@ -61,6 +86,12 @@
               </fieldset>
 
             </form>
+	    {% else: %}
+	    <div class="alert alert-warning">
+	      <p>You cannot login at this moment using your GeneNetwork account.<br />
+		Please try again later.</p>
+	    </div>
+	    {% endif %}
         </div>
     </div>
 
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index f7fcd2d0..c344ea27 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -54,6 +54,9 @@ logger = getLogger(__name__)
 
 from base.data_set import create_datasets_list
 
+import requests
+from utility.elasticsearch_tools import get_elasticsearch_connection, get_user_by_unique_column, save_user
+
 THREE_DAYS = 60 * 60 * 24 * 3
 #THREE_DAYS = 45
 
@@ -119,7 +122,8 @@ class AnonUser(object):
             return collections
 
     def import_traits_to_user(self):
-        collections_list = json.loads(Redis.get(self.key))
+        result = Redis.get(self.key)
+        collections_list = json.loads(result if result else "[]")
         for collection in collections_list:
             uc = model.UserCollection()
             uc.name = collection['name']
@@ -268,16 +272,24 @@ class RegisterUser(object):
         self.thank_you_mode = False
         self.errors = []
         self.user = Bunch()
+        es = kw.get('es_connection', None)
+
+        if not es:
+            self.errors.append("Missing connection object")
 
-        self.user.email_address = kw.get('email_address', '').strip()
+        self.user.email_address = kw.get('email_address', '').encode("utf-8").strip()
         if not (5 <= len(self.user.email_address) <= 50):
             self.errors.append('Email Address needs to be between 5 and 50 characters.')
+        else:
+            email_exists = get_user_by_unique_column(es, "email_address", self.user.email_address)
+            if email_exists:
+                self.errors.append('User already exists with that email')
 
-        self.user.full_name = kw.get('full_name', '').strip()
+        self.user.full_name = kw.get('full_name', '').encode("utf-8").strip()
         if not (5 <= len(self.user.full_name) <= 50):
             self.errors.append('Full Name needs to be between 5 and 50 characters.')
 
-        self.user.organization = kw.get('organization', '').strip()
+        self.user.organization = kw.get('organization', '').encode("utf-8").strip()
         if self.user.organization and not (5 <= len(self.user.organization) <= 50):
             self.errors.append('Organization needs to be empty or between 5 and 50 characters.')
 
@@ -294,28 +306,11 @@ class RegisterUser(object):
         logger.debug("No errors!")
 
         set_password(password, self.user)
+        self.user.user_id = str(uuid.uuid4())
+        self.user.confirmed = 1
 
         self.user.registration_info = json.dumps(basic_info(), sort_keys=True)
-
-        self.new_user = model.User(**self.user.__dict__)
-        db_session.add(self.new_user)
-
-        try:
-            db_session.commit()
-        except sqlalchemy.exc.IntegrityError:
-            # This exception is thrown if the email address is already in the database
-            # To do: Perhaps put a link to sign in using an existing account here
-            self.errors.append("An account with this email address already exists. "
-                               "Click the button above to sign in using an existing account.")
-            return
-
-        logger.debug("Adding verification email to queue")
-        #self.send_email_verification()
-        VerificationEmail(self.new_user)
-        logger.debug("Added verification email to queue")
-
-        self.thank_you_mode = True
-
+        save_user(es, self.user.__dict__, self.user.user_id)
 
 def set_password(password, user):
     pwfields = Bunch()
@@ -361,7 +356,7 @@ class VerificationEmail(object):
         verification_code = str(uuid.uuid4())
         key = self.key_prefix + ":" + verification_code
 
-        data = json.dumps(dict(id=user.id,
+        data = json.dumps(dict(id=user.user_id,
                                timestamp=timestamp())
                           )
 
@@ -378,23 +373,33 @@ class ForgotPasswordEmail(VerificationEmail):
     template_name = "email/forgot_password.txt"
     key_prefix = "forgot_password_code"
     subject = "GeneNetwork password reset"
+    fromaddr = "no-reply@genenetwork.org"
 
-    def __init__(self, user):
+    def __init__(self, toaddr):
+        from email.MIMEMultipart import MIMEMultipart
+        from email.MIMEText import MIMEText
         verification_code = str(uuid.uuid4())
         key = self.key_prefix + ":" + verification_code
 
-        data = json.dumps(dict(id=user.id,
-                               timestamp=timestamp())
-                          )
+        data = {
+            "verification_code": verification_code,
+            "email_address": toaddr,
+            "timestamp": timestamp()
+        }
+        es_save_data(es, self.key_prefix, "local", data, verification_code)
 
-        Redis.set(key, data)
-        #two_days = 60 * 60 * 24 * 2
-        Redis.expire(key, THREE_DAYS)
-        to = user.email_address
         subject = self.subject
-        body = render_template(self.template_name,
-                               verification_code = verification_code)
-        send_email(to, subject, body)
+        body = render_template(
+            self.template_name,
+            verification_code = verification_code)
+
+        msg = MIMEMultipart()
+        msg["To"] = toaddr
+        msg["Subject"] = self.subject
+        msg["From"] = self.fromaddr
+        msg.attach(MIMEText(body, "plain"))
+
+        send_email(toaddr, msg.as_string())
 
 
 class Password(object):
@@ -429,38 +434,61 @@ def verify_email():
     response.set_cookie(UserSession.cookie_name, session_id_signed)
     return response
 
-@app.route("/n/password_reset")
+@app.route("/n/password_reset", methods=['GET'])
 def password_reset():
     logger.debug("in password_reset request.url is:", request.url)
 
     # We do this mainly just to assert that it's in proper form for displaying next page
     # Really not necessary but doesn't hurt
-    user_encode = DecodeUser(ForgotPasswordEmail.key_prefix).reencode_standalone()
-
-    return render_template("new_security/password_reset.html", user_encode=user_encode)
+    # user_encode = DecodeUser(ForgotPasswordEmail.key_prefix).reencode_standalone()
+    verification_code = request.args.get('code')
+    hmac = request.args.get('hm')
+    if verification_code:
+        code_details = get_item_by_unique_column(
+            es
+            , "verification_code"
+            , verification_code
+            , ForgotPasswordEmail.key_prefix
+            , "local")
+        if code_details:
+            user_details = get_user_by_unique_column(
+                es
+                , "email_address"
+                , code_details["email_address"])
+            if user_details:
+                return render_template(
+                    "new_security/password_reset.html", user_encode=user_details["user_id"])
+            else:
+                flash("Invalid code: User no longer exists!", "error")
+        else:
+            flash("Invalid code: Password reset code does not exist or might have expired!", "error")
+        return redirect(url_for("login"))#render_template("new_security/login_user.html", error=error)
 
 @app.route("/n/password_reset_step2", methods=('POST',))
 def password_reset_step2():
+    from utility.elasticsearch_tools import es
     logger.debug("in password_reset request.url is:", request.url)
 
     errors = []
+    user_id = request.form['user_encode']
 
-    user_encode = request.form['user_encode']
-    verification_code, separator, hmac = user_encode.partition(':')
-
-    hmac_verified = actual_hmac_creation(verification_code)
     logger.debug("locals are:", locals())
 
 
-    assert hmac == hmac_verified, "Someone has been naughty"
-
-    user = DecodeUser.actual_get_user(ForgotPasswordEmail.key_prefix, verification_code)
-    logger.debug("user is:", user)
-
+    user = Bunch()
     password = request.form['password']
-
     set_password(password, user)
-    db_session.commit()
+
+    es = get_elasticsearch_connection()
+    es.update(
+        index = "users"
+        , doc_type = "local"
+        , id = user_id
+        , body = {
+            "doc": {
+                "password": user.__dict__.get("password")
+            }
+        })
 
     flash("Password changed successfully. You can now sign in.", "alert-info")
     response = make_response(redirect(url_for('login')))
@@ -492,8 +520,85 @@ class DecodeUser(object):
 @app.route("/n/login", methods=('GET', 'POST'))
 def login():
     lu = LoginUser()
-    return lu.standard_login()
+    login_type = request.args.get("type")
+    if login_type:
+        uid = request.args.get("uid")
+        return lu.oauth2_login(login_type, uid)
+    else:
+        return lu.standard_login()
+
+@app.route("/n/login/github_oauth2", methods=('GET', 'POST'))
+def github_oauth2():
+    from utility.tools import GITHUB_CLIENT_ID, GITHUB_CLIENT_SECRET
+    code = request.args.get("code")
+    data = {
+        "client_id": GITHUB_CLIENT_ID,
+        "client_secret": GITHUB_CLIENT_SECRET,
+        "code": code
+    }
+    result = requests.post("https://github.com/login/oauth/access_token", json=data)
+    result_dict = {arr[0]:arr[1] for arr in [tok.split("=") for tok in [token.encode("utf-8") for token in result.text.split("&")]]}
+
+    github_user = get_github_user_details(result_dict["access_token"])
+    es = get_elasticsearch_connection()
+    user_details = get_user_by_unique_column(es, "github_id", github_user["id"])
+    if user_details == None:
+        user_details = {
+            "user_id": str(uuid.uuid4())
+            , "name": github_user["name"].encode("utf-8")
+            , "github_id": github_user["id"]
+            , "user_url": github_user["html_url"].encode("utf-8")
+            , "login_type": "github"
+            , "organization": ""
+            , "active": 1
+            , "confirmed": 1
+        }
+        save_user(es, user_details, user_details["user_id"])
+    url = "/n/login?type=github&uid="+user_details["user_id"]
+    return redirect(url)
+
+@app.route("/n/login/orcid_oauth2", methods=('GET', 'POST'))
+def orcid_oauth2():
+    from uuid import uuid4
+    from utility.tools import ORCID_CLIENT_ID, ORCID_CLIENT_SECRET, ORCID_TOKEN_URL, ORCID_AUTH_URL
+    code = request.args.get("code")
+    error = request.args.get("error")
+    url = "/n/login"
+    if code:
+        data = {
+            "client_id": ORCID_CLIENT_ID
+            , "client_secret": ORCID_CLIENT_SECRET
+            , "grant_type": "authorization_code"
+            , "code": code
+        }
+        result = requests.post(ORCID_TOKEN_URL, data=data)
+        result_dict = json.loads(result.text.encode("utf-8"))
+
+        es = get_elasticsearch_connection()
+        user_details = get_user_by_unique_column(es, "orcid", result_dict["orcid"])
+        if user_details == None:
+            user_details = {
+                "user_id": str(uuid4())
+                , "name": result_dict["name"]
+                , "orcid": result_dict["orcid"]
+                , "user_url": "%s/%s" % (
+                    "/".join(ORCID_AUTH_URL.split("/")[:-2]),
+                    result_dict["orcid"])
+                , "login_type": "orcid"
+                , "organization": ""
+                , "active": 1
+                , "confirmed": 1
+            }
+            save_user(es, user_details, user_details["user_id"])
+        url = "/n/login?type=orcid&uid="+user_details["user_id"]
+    else:
+        flash("There was an error getting code from ORCID")
+    return redirect(url)
 
+def get_github_user_details(access_token):
+    from utility.tools import GITHUB_API_URL
+    result = requests.get(GITHUB_API_URL, params={"access_token":access_token})
+    return result.json()
 
 class LoginUser(object):
     remember_time = 60 * 60 * 24 * 30 # One month in seconds
@@ -501,27 +606,56 @@ class LoginUser(object):
     def __init__(self):
         self.remember_me = False
 
+    def oauth2_login(self, login_type, user_id):
+        """Login via an OAuth2 provider"""
+        es = get_elasticsearch_connection()
+        user_details = get_user_by_unique_column(es, "user_id", user_id)
+        if user_details:
+            user = model.User()
+            user.id = user_details["user_id"]
+            user.full_name = user_details["name"]
+            user.login_type = user_details["login_type"]
+            return self.actual_login(user)
+        else:
+            flash("Error logging in via OAuth2")
+            return make_response(redirect(url_for('login')))
+
     def standard_login(self):
         """Login through the normal form"""
         params = request.form if request.form else request.args
         logger.debug("in login params are:", params)
+        es = get_elasticsearch_connection()
         if not params:
-            return render_template("new_security/login_user.html")
+            from utility.tools import GITHUB_AUTH_URL, ORCID_AUTH_URL
+            external_login = None
+            if GITHUB_AUTH_URL or ORCID_AUTH_URL:
+                external_login={
+                    "github": GITHUB_AUTH_URL,
+                    "orcid": ORCID_AUTH_URL
+                }
+            assert(es is not None)
+            return render_template(
+                "new_security/login_user.html"
+                , external_login=external_login
+                , es_server=es.ping())
         else:
-            try:
-                user = model.User.query.filter_by(email_address=params['email_address']).one()
-            except sqlalchemy.orm.exc.NoResultFound:
-                logger.debug("No account exists for that email address")
-                valid = False
-                user = None
-            else:
+            user_details = get_user_by_unique_column(es, "email_address", params["email_address"])
+            user = None
+            valid = None
+            if user_details:
+                user = model.User();
+                for key in user_details:
+                    user.__dict__[key] = user_details[key]
+                valid = False;
+
                 submitted_password = params['password']
                 pwfields = Struct(json.loads(user.password))
-                encrypted = Password(submitted_password,
-                                              pwfields.salt,
-                                              pwfields.iterations,
-                                              pwfields.keylength,
-                                              pwfields.hashfunc)
+                encrypted = Password(
+                    submitted_password,
+                    pwfields.salt,
+                    pwfields.iterations,
+                    pwfields.keylength,
+                    pwfields.hashfunc)
                 logger.debug("\n\nComparing:\n{}\n{}\n".format(encrypted.password, pwfields.password))
                 valid = pbkdf2.safe_str_cmp(encrypted.password, pwfields.password)
                 logger.debug("valid is:", valid)
@@ -549,7 +683,7 @@ class LoginUser(object):
         else:
             if user:
                 self.unsuccessful_login(user)
-            flash("Invalid email-address or password. Please try again.", "alert-error")
+            flash("Invalid email-address or password. Please try again.", "alert-danger")
             response = make_response(redirect(url_for('login')))
 
             return response
@@ -558,7 +692,6 @@ class LoginUser(object):
         """The meat of the logging in process"""
         session_id_signed = self.successful_login(user, assumed_by)
         flash("Thank you for logging in {}.".format(user.full_name), "alert-success")
-        print("IMPORT1:", import_collections)
         response = make_response(redirect(url_for('index_page', import_collections=import_collections)))
         if self.remember_me:
             max_age = self.remember_time
@@ -589,8 +722,6 @@ class LoginUser(object):
         else:
             expire_time = THREE_DAYS
         Redis.expire(key, expire_time)
-        db_session.add(login_rec)
-        db_session.commit()
         return session_id_signed
 
     def unsuccessful_login(self, user):
@@ -618,13 +749,16 @@ def forgot_password():
 def forgot_password_submit():
     params = request.form
     email_address = params['email_address']
-    try:
-        user = model.User.query.filter_by(email_address=email_address).one()
-    except orm.exc.NoResultFound:
-        flash("Couldn't find a user associated with the email address {}. Sorry.".format(
-            email_address))
-        return redirect(url_for("login"))
-    ForgotPasswordEmail(user)
+    user_details = get_user_by_unique_column(es, "email_address", email_address)
+    if user_details:
+        ForgotPasswordEmail(user_details["email_address"])
+    # try:
+    #     user = model.User.query.filter_by(email_address=email_address).one()
+    # except orm.exc.NoResultFound:
+    #     flash("Couldn't find a user associated with the email address {}. Sorry.".format(
+    #         email_address))
+    #     return redirect(url_for("login"))
+    # ForgotPasswordEmail(user)
     return render_template("new_security/forgot_password_step2.html",
                             subject=ForgotPasswordEmail.subject)
 
@@ -691,16 +825,18 @@ def register():
 
 
     params = request.form if request.form else request.args
+    params = params.to_dict(flat=True)
+    es = get_elasticsearch_connection()
+    params["es_connection"] = es
 
     if params:
         logger.debug("Attempting to register the user...")
         result = RegisterUser(params)
         errors = result.errors
 
-        if result.thank_you_mode:
-            assert not errors, "Errors while in thank you mode? That seems wrong..."
-            return render_template("new_security/registered.html",
-                                   subject=VerificationEmail.subject)
+        if len(errors) == 0:
+            flash("Registration successful. You may login with your new account", "alert-info")
+            return redirect(url_for("login"))
 
     return render_template("new_security/register_user.html", values=params, errors=errors)
 
@@ -771,13 +907,21 @@ app.jinja_env.globals.update(url_for_hmac=url_for_hmac,
 
 #######################################################################################
 
-def send_email(to, subject, body):
-    msg = json.dumps(dict(From="no-reply@genenetwork.org",
-                     To=to,
-                     Subject=subject,
-                     Body=body))
-    Redis.rpush("mail_queue", msg)
-
+# def send_email(to, subject, body):
+#     msg = json.dumps(dict(From="no-reply@genenetwork.org",
+#                      To=to,
+#                      Subject=subject,
+#                      Body=body))
+#     Redis.rpush("mail_queue", msg)
+
+def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"):
+    from smtplib import SMTP
+    from utility.tools import SMTP_CONNECT, SMTP_USERNAME, SMTP_PASSWORD
+    server = SMTP(SMTP_CONNECT)
+    server.starttls()
+    server.login(SMTP_USERNAME, SMTP_PASSWORD)
+    server.sendmail(fromaddr, toaddr, msg)
+    server.quit()