Merge pull request #317 from pjotrp/testing

Testing

14 files changed, 248 insertions, 81 deletions

diff --git a/README.md b/README.md
index 3e7e64d0..59645994 100644
--- a/README.md
+++ b/README.md
@@ -17,25 +17,35 @@ deploy GN2 and dependencies as a self contained unit on any machine.
 The database can be run separately as well as the source tree (for
 developers).  See the [installation docs](doc/README.org).
 
-## Test
+## Run
 
 Once installed GN2 can be run online through a browser interface
 
 ```sh
-./bin/genenetwork2
+genenetwork2
 ```
 
-(default is http://localhost:5003/). For more examples, including running scripts and a Python REPL
-see the startup script [./bin/genenetwork2](https://github.com/genenetwork/genenetwork2/blob/testing/bin/genenetwork2).
+(default is http://localhost:5003/). For full examples (you'll need to
+set a number of environment variables), including running scripts and
+a Python REPL, see the startup script
+[./bin/genenetwork2](https://github.com/genenetwork/genenetwork2/blob/testing/bin/genenetwork2).
 
+## Testing
 
-We are building up automated
-testing using [mechanize](https://github.com/genenetwork/genenetwork2/tree/master/test/lib) which can be run with
+We are building 'Mechanical Rob' automated testing using Python
+[requests](https://github.com/genenetwork/genenetwork2/tree/master/test/lib)
+which can be run with something like
 
 ```sh
-./bin/test-website
+env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -c ../test/requests/test-website.py -a http://localhost:5003
 ```
 
+The GN2_PROFILE is the Guix profile that contains all
+dependencies. The ./bin/genenetwork2 script sets up the environment
+and executes test-website.py in a Python interpreter. The -a switch
+says to run all tests and the URL points to the running GN2 http
+server.
+
 ## Documentation
 
 User documentation can be found
diff --git a/bin/test-website b/bin/test-website
index 5935f016..7fbcfd2f 100755
--- a/bin/test-website
+++ b/bin/test-website
@@ -2,6 +2,6 @@
 
 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
+  echo env GN2_PROFILE=/home/wrk/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -c ../test/requests/test-website.py -a http://localhost:5003
   exit 1
 fi
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")
diff --git a/wqflask/base/anon_collection.py b/wqflask/base/anon_collection.py
index 8ee73296..dd1aa27f 100644
--- a/wqflask/base/anon_collection.py
+++ b/wqflask/base/anon_collection.py
@@ -1,6 +1,6 @@
 class AnonCollection(TraitCollection):

     

-    def __init__(self, anon_id)

+    def __init__(self, anon_id):

         self.anon_id = anon_id

         self.collection_members = Redis.smembers(self.anon_id)

         print("self.collection_members is:", self.collection_members)

@@ -12,6 +12,7 @@ class AnonCollection(TraitCollection):
         print("traits_to_remove:", traits_to_remove)

         for trait in traits_to_remove:

             Redis.srem(self.anon_id, trait)

+

         members_now = self.collection_members - traits_to_remove

         print("members_now:", members_now)

         print("Went from {} to {} members in set.".format(len(self.collection_members), len(members_now)))

diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py
index 1dba357d..76dcaebf 100644
--- a/wqflask/utility/elasticsearch_tools.py
+++ b/wqflask/utility/elasticsearch_tools.py
@@ -1,3 +1,44 @@
+# Elasticsearch support
+#
+# Some helpful commands to view the database:
+#
+# You can test the server being up with
+#
+#   curl -H 'Content-Type: application/json' http://localhost:9200
+#
+# List all indices
+#
+#   curl -H 'Content-Type: application/json' 'localhost:9200/_cat/indices?v'
+#
+# To see the users index 'table'
+#
+#   curl http://localhost:9200/users
+#
+# To list all user ids
+#
+# curl -H 'Content-Type: application/json' http://localhost:9200/users/local/_search?pretty=true -d '
+# {
+#     "query" : {
+#         "match_all" : {}
+#     },
+#     "stored_fields": []
+# }'
+#
+# To view a record
+#
+#   curl -H 'Content-Type: application/json' http://localhost:9200/users/local/_search?pretty=true -d '
+#   {
+#     "query" : {
+#       "match" : { "email_address": "pjotr2017@thebird.nl"}
+#     }
+#   }'
+#
+#
+# To delete the users index and data (dangerous!)
+#
+#   curl -XDELETE -H 'Content-Type: application/json' 'localhost:9200/users'
+
+
 from elasticsearch import Elasticsearch, TransportError
 import logging
 
@@ -7,7 +48,7 @@ logger = getLogger(__name__)
 from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT
 
 def test_elasticsearch_connection():
-    es = Elasticsearch(['http://'+ELASTICSEARCH_HOST+":"+ELASTICSEARCH_PORT+'/'], verify_certs=True)
+    es = Elasticsearch(['http://'+ELASTICSEARCH_HOST+":"+str(ELASTICSEARCH_PORT)+'/'], verify_certs=True)
     if not es.ping():
         logger.warning("Elasticsearch is DOWN")
 
@@ -24,15 +65,29 @@ def get_elasticsearch_connection():
             "host": ELASTICSEARCH_HOST, "port": ELASTICSEARCH_PORT
         }]) if (ELASTICSEARCH_HOST and ELASTICSEARCH_PORT) else None
 
+        setup_users_index(es)
+
         es_logger = logging.getLogger("elasticsearch")
         es_logger.setLevel(logging.INFO)
         es_logger.addHandler(logging.NullHandler())
-    except:
-        logger.error("Failed to get elasticsearch connection")
+    except Exception as e:
+        logger.error("Failed to get elasticsearch connection", e)
         es = None
 
     return es
 
+def setup_users_index(es_connection):
+    if es_connection:
+        index_settings = {
+            "properties": {
+                "email_address": {
+                    "type": "keyword"}}}
+
+        es_connection.indices.create(index='users', ignore=400)
+        es_connection.indices.close(index="users")
+        es_connection.indices.put_mapping(body=index_settings, index="users", doc_type="local")
+        es_connection.indices.open(index="users")
+
 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)
 
diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py
index 512bc9e6..db13b9d1 100644
--- a/wqflask/utility/svg.py
+++ b/wqflask/utility/svg.py
@@ -1029,7 +1029,7 @@ class drawing:
         try:
             xv.feed(svg)
         except:
-            raise "SVG is not well formed, see messages above"
+            raise Exception("SVG is not well formed, see messages above")
         else:
             print "SVG well formed"
 if __name__=='__main__':
diff --git a/wqflask/wqflask/templates/new_security/login_user.html b/wqflask/wqflask/templates/new_security/login_user.html
index 4a857c60..27b20ebf 100644
--- a/wqflask/wqflask/templates/new_security/login_user.html
+++ b/wqflask/wqflask/templates/new_security/login_user.html
@@ -31,16 +31,19 @@
 	    <div>
 	      {% if external_login["github"]: %}
 	      <a href="{{external_login['github']}}" title="Login with GitHub" class="btn btn-info btn-group">Login with Github</a>
+              {% else %}
+              <p>Github login is not available right now</p>
 	      {% endif %}
 
 	      {% if external_login["orcid"]: %}
 	      <a href="{{external_login['orcid']}}" title="Login with ORCID" class="btn btn-info btn-group">Login with ORCID</a>
+              {% else %}
+              <p>ORCID login is not available right now</p>
 	      {% endif %}
 	    </div>
 	    {% else: %}
 	    <div class="alert alert-warning">
-	      <p>You cannot login with external services at this time.<br />
-		Please try again later.</p>
+	      <p>Sorry, you cannot login with Github or ORCID at this time.</p>
 	    </div>
 	    {% endif %}
 	    <hr />
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index 5f6c818e..d652f2e9 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -727,30 +727,33 @@ def logout():
     return response
 
 
-@app.route("/n/forgot_password")
+@app.route("/n/forgot_password", methods=['GET'])
 def forgot_password():
     """Entry point for forgotten password"""
-    return render_template("new_security/forgot_password.html")
+    print("ARGS: ", request.args)
+    errors = {"no-email": request.args.get("no-email")}
+    print("ERRORS: ", errors)
+    return render_template("new_security/forgot_password.html", errors=errors)
 
 @app.route("/n/forgot_password_submit", methods=('POST',))
 def forgot_password_submit():
     """When a forgotten password form is submitted we get here"""
     params = request.form
     email_address = params['email_address']
-    logger.debug("Wants to send password E-mail to ",email_address)
-    es = get_elasticsearch_connection()
-    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)
+    next_page = None
+    if email_address != "":
+        logger.debug("Wants to send password E-mail to ",email_address)
+        es = get_elasticsearch_connection()
+        user_details = get_user_by_unique_column(es, "email_address", email_address)
+        if user_details:
+            ForgotPasswordEmail(user_details["email_address"])
+
+        return render_template("new_security/forgot_password_step2.html",
+                               subject=ForgotPasswordEmail.subject)
+
+    else:
+        flash("You MUST provide an email", "alert-danger")
+        return redirect(url_for("forgot_password"))
 
 @app.errorhandler(401)
 def unauthorized(error):