aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorzsloan2018-04-16 10:46:56 -0500
committerGitHub2018-04-16 10:46:56 -0500
commita58a4c3b8ee4f7256a18c99542ff6a9f355c0a2e (patch)
tree1e7677fa1fa210a2a957855578cd3ac3a47b720b
parent270f86c41f7c90cc4ca51bca0aec789a09a36a0e (diff)
parentebbc8c67c13b44df98ea3c2b355e86f77572543b (diff)
downloadgenenetwork2-a58a4c3b8ee4f7256a18c99542ff6a9f355c0a2e.tar.gz
Merge pull request #317 from pjotrp/testing
Testing
-rw-r--r--README.md24
-rwxr-xr-xbin/test-website2
-rw-r--r--test/requests/link_checker.py10
-rw-r--r--test/requests/mapping_tests.py35
-rw-r--r--test/requests/navigation_tests.py15
-rw-r--r--test/requests/parametrized_test.py7
-rw-r--r--test/requests/run-integration-tests.py34
-rwxr-xr-xtest/requests/test-website.py42
-rw-r--r--test/requests/test_forgot_password.py52
-rw-r--r--wqflask/base/anon_collection.py3
-rw-r--r--wqflask/utility/elasticsearch_tools.py61
-rw-r--r--wqflask/utility/svg.py2
-rw-r--r--wqflask/wqflask/templates/new_security/login_user.html7
-rw-r--r--wqflask/wqflask/user_manager.py35
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):