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authorzsloan2018-03-29 10:36:12 -0500
committerGitHub2018-03-29 10:36:12 -0500
commitb215b5fe5c6d13f0ed445106230e1e38db71c918 (patch)
tree97f1f47b092bef38856ac34c1bd745e471c38311
parente67e3a76fca0bad4796853eb58140a412922bc9c (diff)
parente0c706c51c834caa836ecffd27a5d18fc23178ff (diff)
downloadgenenetwork2-b215b5fe5c6d13f0ed445106230e1e38db71c918.tar.gz
Merge pull request #297 from pjotrp/testing
Testing
-rw-r--r--RELEASE-NOTES.md17
-rwxr-xr-xbin/genenetwork256
-rwxr-xr-xbin/mechnical-rob111
-rwxr-xr-xbin/test-website114
-rw-r--r--etc/default_settings.py18
-rw-r--r--test/requests/link_checker.py63
-rw-r--r--test/requests/main_web_functionality.py40
-rw-r--r--test/requests/mapping_tests.py43
-rw-r--r--test/requests/parametrized_test.py27
-rw-r--r--test/requests/run-integration-tests.py34
-rwxr-xr-xtest/requests/test-website.py71
-rw-r--r--test/requests/test_login_github.py47
-rw-r--r--test/requests/test_login_local.py60
-rw-r--r--test/requests/test_login_orcid.py47
-rw-r--r--test/requests/test_registration.py41
-rw-r--r--test/unittest/test_registration.py27
-rw-r--r--wqflask/flask_security/__init__.py25
-rw-r--r--wqflask/flask_security/changeable.py45
-rw-r--r--wqflask/flask_security/confirmable.py83
-rw-r--r--wqflask/flask_security/core.py382
-rw-r--r--wqflask/flask_security/datastore.py261
-rw-r--r--wqflask/flask_security/decorators.py207
-rw-r--r--wqflask/flask_security/forms.py286
-rw-r--r--wqflask/flask_security/passwordless.py59
-rw-r--r--wqflask/flask_security/recoverable.py80
-rw-r--r--wqflask/flask_security/registerable.py44
-rw-r--r--wqflask/flask_security/script.py130
-rw-r--r--wqflask/flask_security/signals.py29
-rw-r--r--wqflask/flask_security/templates/.DS_Storebin6148 -> 0 bytes
-rw-r--r--wqflask/flask_security/templates/security/.DS_Storebin6148 -> 0 bytes
-rw-r--r--wqflask/flask_security/templates/security/_macros.html16
-rw-r--r--wqflask/flask_security/templates/security/_menu.html15
-rw-r--r--wqflask/flask_security/templates/security/_messages.html9
-rw-r--r--wqflask/flask_security/templates/security/change_password.html11
-rw-r--r--wqflask/flask_security/templates/security/email/change_notice.html4
-rw-r--r--wqflask/flask_security/templates/security/email/change_notice.txt5
-rw-r--r--wqflask/flask_security/templates/security/email/confirmation_instructions.html3
-rw-r--r--wqflask/flask_security/templates/security/email/confirmation_instructions.txt3
-rw-r--r--wqflask/flask_security/templates/security/email/login_instructions.html5
-rw-r--r--wqflask/flask_security/templates/security/email/login_instructions.txt5
-rw-r--r--wqflask/flask_security/templates/security/email/reset_instructions.html1
-rw-r--r--wqflask/flask_security/templates/security/email/reset_instructions.txt3
-rw-r--r--wqflask/flask_security/templates/security/email/reset_notice.html1
-rw-r--r--wqflask/flask_security/templates/security/email/reset_notice.txt1
-rw-r--r--wqflask/flask_security/templates/security/email/welcome.html7
-rw-r--r--wqflask/flask_security/templates/security/email/welcome.txt7
-rw-r--r--wqflask/flask_security/templates/security/forgot_password.html9
-rw-r--r--wqflask/flask_security/templates/security/login_user.html12
-rw-r--r--wqflask/flask_security/templates/security/register_user.html13
-rw-r--r--wqflask/flask_security/templates/security/reset_password.html10
-rw-r--r--wqflask/flask_security/templates/security/send_confirmation.html9
-rw-r--r--wqflask/flask_security/templates/security/send_login.html9
-rw-r--r--wqflask/flask_security/utils.py379
-rw-r--r--wqflask/flask_security/views.py359
-rw-r--r--wqflask/mock/__init__.py0
-rw-r--r--wqflask/mock/es_double.py15
-rw-r--r--wqflask/run_gunicorn.py5
-rw-r--r--wqflask/runserver.py17
-rw-r--r--wqflask/utility/elasticsearch_tools.py59
-rw-r--r--wqflask/utility/startup_config.py39
-rw-r--r--wqflask/utility/tools.py42
-rw-r--r--wqflask/utility/type_checking.py42
-rw-r--r--wqflask/wqflask/__init__.py4
-rw-r--r--wqflask/wqflask/correlation/show_corr_results.py42
-rw-r--r--wqflask/wqflask/gsearch.py6
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression.py2
-rw-r--r--wqflask/wqflask/search_results.py23
-rw-r--r--wqflask/wqflask/templates/new_security/login_user.html49
-rw-r--r--wqflask/wqflask/user_manager.py317
-rw-r--r--wqflask/wqflask/views.py71
70 files changed, 1211 insertions, 2865 deletions
diff --git a/RELEASE-NOTES.md b/RELEASE-NOTES.md
new file mode 100644
index 00000000..d15cad1a
--- /dev/null
+++ b/RELEASE-NOTES.md
@@ -0,0 +1,17 @@
+## ChangeLog v2.11 (date unknown)
+
+This is a massive bug fix release with many improvements. For contributions
+see
+[contributors](https://github.com/genenetwork/genenetwork2/contributors)
+and
+[commits](https://github.com/genenetwork/genenetwork2/commits/master).
+
+### Added GEMMA support
+
+* Front-end support
+
+### Added test framework and unit tests
+
+* Added python integration and unit tests
+
+
diff --git a/bin/genenetwork2 b/bin/genenetwork2
index 8886e4bc..3f06e7f9 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -68,32 +68,36 @@ if [ "$1" = "-c" -o "$1" = "-gunicorn" ]; then
echo "Can not use $1 switch without default settings file"
exit 1
fi
-# Handle settings parameter (can be .py or .json)
-if [ ! -z $1 ]; then
- settings=$(realpath "$1")
- if [ ! -e $settings ]; then
- settings=$GN2_BASE_DIR/etc/default_settings.py
- else
- shift
- fi
-fi
-ext="${settings##*.}"
-if [ "$ext" = "json" -o "$ext" = "JSON" ]; then
- overrides=$settings
+settings=$1
+if [ -z $settings ]; then
+ settings=$GN2_BASE_DIR/etc/default_settings.py
else
- echo $settings
+ shift
fi
+settings=$(realpath $settings)
+
+# ext="${settings##*.}"
+# if [ "$ext" = "json" -o "$ext" = "JSON" ]; then
+# overrides=$settings
+# else
+# echo $settings
+# fi
if [ ! -e $settings ]; then
echo "ERROR: can not locate settings file - pass it in the command line"
exit 1
fi
-export WQFLASK_SETTINGS=$settings # Python
-export WQFLASK_OVERRIDES=$overrides # JSON
-echo WQFLASK_SETTINGS=$settings
-echo WQFLASK_OVERRIDES=$overrides
+export GN2_SETTINGS=$settings # Python
+echo GN2_SETTINGS=$settings
+
+# 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!"
@@ -108,7 +112,7 @@ 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="$GN2_PROFILE/lib/python2.7/site-packages" # never inject another PYTHONPATH!!
export R_LIBS_SITE=$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 +128,11 @@ 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 $PPART ] ; then echo "$PPART in 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 +165,9 @@ 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 +176,9 @@ 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/flask_security/__init__.py b/wqflask/flask_security/__init__.py
deleted file mode 100644
index 81e6c89e..00000000
--- a/wqflask/flask_security/__init__.py
+++ /dev/null
@@ -1,25 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
- flask.ext.security
- ~~~~~~~~~~~~~~~~~~
-
- Flask-Security is a Flask extension that aims to add quick and simple
- security via Flask-Login, Flask-Principal, Flask-WTF, and passlib.
-
- :copyright: (c) 2012 by Matt Wright.
- :license: MIT, see LICENSE for more details.
-"""
-
-__version__ = '1.6.0'
-
-from .core import Security, RoleMixin, UserMixin, AnonymousUser, current_user
-from .datastore import SQLAlchemyUserDatastore, MongoEngineUserDatastore, PeeweeUserDatastore
-from .decorators import auth_token_required, http_auth_required, \
- login_required, roles_accepted, roles_required
-from .forms import ForgotPasswordForm, LoginForm, RegisterForm, \
- ResetPasswordForm, PasswordlessLoginForm, ConfirmRegisterForm
-from .signals import confirm_instructions_sent, password_reset, \
- reset_password_instructions_sent, user_confirmed, user_registered
-from .utils import login_user, logout_user, url_for_security
-
-print "Using our own flask.ext.security" \ No newline at end of file
diff --git a/wqflask/flask_security/changeable.py b/wqflask/flask_security/changeable.py
deleted file mode 100644
index 4447b655..00000000
--- a/wqflask/flask_security/changeable.py
+++ /dev/null
@@ -1,45 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
- flask.ext.security.changeable
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Flask-Security recoverable module
-
- :copyright: (c) 2012 by Matt Wright.
- :author: Eskil Heyn Olsen
- :license: MIT, see LICENSE for more details.
-"""
-
-from flask import current_app as app, request
-from werkzeug.local import LocalProxy
-
-from .signals import password_changed
-from .utils import send_mail, encrypt_password, url_for_security, \
- config_value
-
-
-# Convenient references
-_security = LocalProxy(lambda: app.extensions['security'])
-
-_datastore = LocalProxy(lambda: _security.datastore)
-
-
-def send_password_changed_notice(user):
- """Sends the password changed notice email for the specified user.
-
- :param user: The user to send the notice to
- """
- send_mail(config_value('EMAIL_SUBJECT_PASSWORD_CHANGE_NOTICE'), user.email,
- 'change_notice', user=user)
-
-
-def change_user_password(user, password):
- """Change the specified user's password
-
- :param user: The user to change_password
- :param password: The unencrypted new password
- """
- user.password = encrypt_password(password)
- _datastore.put(user)
- send_password_changed_notice(user)
- password_changed.send(user, app=app._get_current_object())
diff --git a/wqflask/flask_security/confirmable.py b/wqflask/flask_security/confirmable.py
deleted file mode 100644
index a7caf6cd..00000000
--- a/wqflask/flask_security/confirmable.py
+++ /dev/null
@@ -1,83 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
- flask.ext.security.confirmable
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Flask-Security confirmable module
-
- :copyright: (c) 2012 by Matt Wright.
- :license: MIT, see LICENSE for more details.
-"""
-
-from datetime import datetime
-
-from flask import current_app as app, request
-from werkzeug.local import LocalProxy
-
-from .utils import send_mail, md5, url_for_security, get_token_status,\
- config_value
-from .signals import user_confirmed, confirm_instructions_sent
-
-
-# Convenient references
-_security = LocalProxy(lambda: app.extensions['security'])
-
-_datastore = LocalProxy(lambda: _security.datastore)
-
-
-def generate_confirmation_link(user):
- token = generate_confirmation_token(user)
- url = url_for_security('confirm_email', token=token)
- return request.url_root[:-1] + url, token
-
-
-def send_confirmation_instructions(user):
- """Sends the confirmation instructions email for the specified user.
-
- :param user: The user to send the instructions to
- :param token: The confirmation token
- """
-
- confirmation_link, token = generate_confirmation_link(user)
-
- send_mail(config_value('EMAIL_SUBJECT_CONFIRM'), user.email,
- 'confirmation_instructions', user=user,
- confirmation_link=confirmation_link)
-
- confirm_instructions_sent.send(user, app=app._get_current_object())
- return token
-
-
-def generate_confirmation_token(user):
- """Generates a unique confirmation token for the specified user.
-
- :param user: The user to work with
- """
- data = [str(user.id), md5(user.email)]
- return _security.confirm_serializer.dumps(data)
-
-
-def requires_confirmation(user):
- """Returns `True` if the user requires confirmation."""
- return _security.confirmable and user.confirmed_at == None
-
-
-def confirm_email_token_status(token):
- """Returns the expired status, invalid status, and user of a confirmation
- token. For example::
-
- expired, invalid, user = confirm_email_token_status('...')
-
- :param token: The confirmation token
- """
- return get_token_status(token, 'confirm', 'CONFIRM_EMAIL')
-
-
-def confirm_user(user):
- """Confirms the specified user
-
- :param user: The user to confirm
- """
- user.confirmed_at = datetime.utcnow()
- _datastore.put(user)
- user_confirmed.send(user, app=app._get_current_object())
diff --git a/wqflask/flask_security/core.py b/wqflask/flask_security/core.py
deleted file mode 100644
index 0f3a231f..00000000
--- a/wqflask/flask_security/core.py
+++ /dev/null
@@ -1,382 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
- flask.ext.security.core
- ~~~~~~~~~~~~~~~~~~~~~~~
-
- Flask-Security core module
-
- :copyright: (c) 2012 by Matt Wright.
- :license: MIT, see LICENSE for more details.
-"""
-
-from flask import current_app
-from flask.ext.login import AnonymousUser as AnonymousUserBase, \
- UserMixin as BaseUserMixin, LoginManager, current_user
-from flask.ext.principal import Principal, RoleNeed, UserNeed, Identity, \
- identity_loaded
-from itsdangerous import URLSafeTimedSerializer
-from passlib.context import CryptContext
-from werkzeug.datastructures import ImmutableList
-from werkzeug.local import LocalProxy
-
-from .utils import config_value as cv, get_config, md5, url_for_security
-from .views import create_blueprint
-from .forms import LoginForm, ConfirmRegisterForm, RegisterForm, \
- ForgotPasswordForm, ChangePasswordForm, ResetPasswordForm, \
- SendConfirmationForm, PasswordlessLoginForm
-
-# Convenient references
-_security = LocalProxy(lambda: current_app.extensions['security'])
-
-
-#: Default Flask-Security configuration
-_default_config = {
- 'BLUEPRINT_NAME': 'security',
- 'URL_PREFIX': None,
- 'SUBDOMAIN': None,
- 'FLASH_MESSAGES': True,
- 'PASSWORD_HASH': 'plaintext',
- 'PASSWORD_SALT': None,
- 'LOGIN_URL': '/login',
- 'LOGOUT_URL': '/logout',
- 'REGISTER_URL': '/register',
- 'RESET_URL': '/reset',
- 'CHANGE_URL': '/change',
- 'CONFIRM_URL': '/confirm',
- 'POST_LOGIN_VIEW': '/',
- 'POST_LOGOUT_VIEW': '/',
- 'CONFIRM_ERROR_VIEW': None,
- 'POST_REGISTER_VIEW': None,
- 'POST_CONFIRM_VIEW': None,
- 'POST_RESET_VIEW': None,
- 'POST_CHANGE_VIEW': None,
- 'UNAUTHORIZED_VIEW': None,
- 'FORGOT_PASSWORD_TEMPLATE': 'security/forgot_password.html',
- 'LOGIN_USER_TEMPLATE': 'security/login_user.html',
- 'REGISTER_USER_TEMPLATE': 'security/register_user.html',
- 'RESET_PASSWORD_TEMPLATE': 'security/reset_password.html',
- 'SEND_CONFIRMATION_TEMPLATE': 'security/send_confirmation.html',
- 'SEND_LOGIN_TEMPLATE': 'security/send_login.html',
- 'CONFIRMABLE': False,
- 'REGISTERABLE': False,
- 'RECOVERABLE': False,
- 'TRACKABLE': False,
- 'PASSWORDLESS': False,
- 'CHANGEABLE': False,
- 'SEND_REGISTER_EMAIL': True,
- 'LOGIN_WITHIN': '1 days',
- 'CONFIRM_EMAIL_WITHIN': '5 days',
- 'RESET_PASSWORD_WITHIN': '5 days',
- 'LOGIN_WITHOUT_CONFIRMATION': False,
- 'EMAIL_SENDER': 'no-reply@localhost',
- 'TOKEN_AUTHENTICATION_KEY': 'auth_token',
- 'TOKEN_AUTHENTICATION_HEADER': 'Authentication-Token',
- 'CONFIRM_SALT': 'confirm-salt',
- 'RESET_SALT': 'reset-salt',
- 'LOGIN_SALT': 'login-salt',
- 'CHANGE_SALT': 'change-salt',
- 'REMEMBER_SALT': 'remember-salt',
- 'DEFAULT_HTTP_AUTH_REALM': 'Login Required',
- 'EMAIL_SUBJECT_REGISTER': 'Welcome',
- 'EMAIL_SUBJECT_CONFIRM': 'Please confirm your email',
- 'EMAIL_SUBJECT_PASSWORDLESS': 'Login instructions',
- 'EMAIL_SUBJECT_PASSWORD_NOTICE': 'Your password has been reset',
- 'EMAIL_SUBJECT_PASSWORD_CHANGE_NOTICE': 'Your password has been changed',
- 'EMAIL_SUBJECT_PASSWORD_RESET': 'Password reset instructions'
-}
-
-#: Default Flask-Security messages
-_default_messages = {
- 'UNAUTHORIZED': ('You do not have permission to view this resource.', 'error'),
- 'CONFIRM_REGISTRATION': ('Thank you. Confirmation instructions have been sent to %(email)s.', 'success'),
- 'EMAIL_CONFIRMED': ('Thank you. Your email has been confirmed.', 'success'),
- 'ALREADY_CONFIRMED': ('Your email has already been confirmed.', 'info'),
- 'INVALID_CONFIRMATION_TOKEN': ('Invalid confirmation token.', 'error'),
- 'EMAIL_ALREADY_ASSOCIATED': ('%(email)s is already associated with an account.', 'error'),
- 'PASSWORD_MISMATCH': ('Password does not match', 'error'),
- 'RETYPE_PASSWORD_MISMATCH': ('Passwords do not match', 'error'),
- 'INVALID_REDIRECT': ('Redirections outside the domain are forbidden', 'error'),
- 'PASSWORD_RESET_REQUEST': ('Instructions to reset your password have been sent to %(email)s.', 'info'),
- 'PASSWORD_RESET_EXPIRED': ('You did not reset your password within %(within)s. New instructions have been sent to %(email)s.', 'error'),
- 'INVALID_RESET_PASSWORD_TOKEN': ('Invalid reset password token.', 'error'),
- 'CONFIRMATION_REQUIRED': ('Email requires confirmation.', 'error'),
- 'CONFIRMATION_REQUEST': ('Confirmation instructions have been sent to %(email)s.', 'info'),
- 'CONFIRMATION_EXPIRED': ('You did not confirm your email within %(within)s. New instructions to confirm your email have been sent to %(email)s.', 'error'),
- 'LOGIN_EXPIRED': ('You did not login within %(within)s. New instructions to login have been sent to %(email)s.', 'error'),
- 'LOGIN_EMAIL_SENT': ('Instructions to login have been sent to %(email)s.', 'success'),
- 'INVALID_LOGIN_TOKEN': ('Invalid login token.', 'error'),
- 'DISABLED_ACCOUNT': ('Account is disabled.', 'error'),
- 'EMAIL_NOT_PROVIDED': ('Email not provided', 'error'),
- 'INVALID_EMAIL_ADDRESS': ('Invalid email address', 'error'),
- 'PASSWORD_NOT_PROVIDED': ('Password not provided', 'error'),
- 'USER_DOES_NOT_EXIST': ('Specified user does not exist', 'error'),
- 'INVALID_PASSWORD': ('Invalid password', 'error'),
- 'PASSWORDLESS_LOGIN_SUCCESSFUL': ('You have successfuly logged in.', 'success'),
- 'PASSWORD_RESET': ('You successfully reset your password and you have been logged in automatically.', 'success'),
- 'PASSWORD_CHANGE': ('You successfully changed your password.', 'success'),
- 'LOGIN': ('Please log in to access this page.', 'info'),
- 'REFRESH': ('Please reauthenticate to access this page.', 'info'),
-}
-
-_allowed_password_hash_schemes = [
- 'bcrypt',
- 'des_crypt',
- 'pbkdf2_sha256',
- 'pbkdf2_sha512',
- 'sha256_crypt',
- 'sha512_crypt',
- # And always last one...
- 'plaintext'
-]
-
-_default_forms = {
- 'login_form': LoginForm,
- 'confirm_register_form': ConfirmRegisterForm,
- 'register_form': RegisterForm,
- 'forgot_password_form': ForgotPasswordForm,
- 'reset_password_form': ResetPasswordForm,
- 'change_password_form': ChangePasswordForm,
- 'send_confirmation_form': SendConfirmationForm,
- 'passwordless_login_form': PasswordlessLoginForm,
-}
-
-
-def _user_loader(user_id):
- return _security.datastore.find_user(id=user_id)
-
-
-def _token_loader(token):
- try:
- data = _security.remember_token_serializer.loads(token)
- user = _security.datastore.find_user(id=data[0])
- if user and md5(user.password) == data[1]:
- return user
- except:
- pass
-
- return None
-
-
-def _identity_loader():
- if not isinstance(current_user._get_current_object(), AnonymousUser):
- identity = Identity(current_user.id)
- return identity
-
-
-def _on_identity_loaded(sender, identity):
- if hasattr(current_user, 'id'):
- identity.provides.add(UserNeed(current_user.id))
-
- for role in current_user.roles:
- identity.provides.add(RoleNeed(role.name))
-
- identity.user = current_user
-
-
-def _get_login_manager(app):
- lm = LoginManager()
- lm.anonymous_user = AnonymousUser
- lm.login_view = '%s.login' % cv('BLUEPRINT_NAME', app=app)
- lm.user_loader(_user_loader)
- lm.token_loader(_token_loader)
- lm.login_message, lm.login_message_category = cv('MSG_LOGIN', app=app)
- lm.needs_refresh_message, lm.needs_refresh_message_category = cv('MSG_REFRESH', app=app)
- lm.init_app(app)
- return lm
-
-
-def _get_principal(app):
- p = Principal(app, use_sessions=False)
- p.identity_loader(_identity_loader)
- return p
-
-
-def _get_pwd_context(app):
- pw_hash = cv('PASSWORD_HASH', app=app)
- if pw_hash not in _allowed_password_hash_schemes:
- allowed = ', '.join(_allowed_password_hash_schemes[:-1]) + ' and ' + _allowed_password_hash_schemes[-1]
- raise ValueError("Invalid hash scheme %r. Allowed values are %s" % (pw_hash, allowed))
- return CryptContext(schemes=_allowed_password_hash_schemes, default=pw_hash)
-
-
-def _get_serializer(app, name):
- secret_key = app.config.get('SECRET_KEY')
- salt = app.config.get('SECURITY_%s_SALT' % name.upper())
- return URLSafeTimedSerializer(secret_key=secret_key, salt=salt)
-
-
-def _get_state(app, datastore, **kwargs):
- for key, value in get_config(app).items():
- print "in _get_state [{}]: {}".format(key, value)
- kwargs[key.lower()] = value
-
- kwargs.update(dict(
- app=app,
- datastore=datastore,
- login_manager=_get_login_manager(app),
- principal=_get_principal(app),
- pwd_context=_get_pwd_context(app),
- remember_token_serializer=_get_serializer(app, 'remember'),
- login_serializer=_get_serializer(app, 'login'),
- reset_serializer=_get_serializer(app, 'reset'),
- confirm_serializer=_get_serializer(app, 'confirm'),
- _context_processors={},
- _send_mail_task=None
- ))
-
- for key, value in _default_forms.items():
- if key not in kwargs or not kwargs[key]:
- kwargs[key] = value
-
- return _SecurityState(**kwargs)
-
-
-def _context_processor():
- return dict(url_for_security=url_for_security, security=_security)
-
-
-class RoleMixin(object):
- """Mixin for `Role` model definitions"""
- def __eq__(self, other):
- return (self.name == other or \
- self.name == getattr(other, 'name', None))
-
- def __ne__(self, other):
- return (self.name != other and
- self.name != getattr(other, 'name', None))
-
-
-class UserMixin(BaseUserMixin):
- """Mixin for `User` model definitions"""
-
- def is_active(self):
- """Returns `True` if the user is active."""
- return self.active
-
- def get_auth_token(self):
- """Returns the user's authentication token."""
- data = [str(self.id), md5(self.password)]
- return _security.remember_token_serializer.dumps(data)
-
- def has_role(self, role):
- """Returns `True` if the user identifies with the specified role.
-
- :param role: A role name or `Role` instance"""
- return role in self.roles
-
-
-class AnonymousUser(AnonymousUserBase):
- """AnonymousUser definition"""
-
- def __init__(self):
- super(AnonymousUser, self).__init__()
- self.roles = ImmutableList()
-
- def has_role(self, *args):
- """Returns `False`"""
- return False
-
-
-class _SecurityState(object):
-
- def __init__(self, **kwargs):
- for key, value in kwargs.items():
- setattr(self, key.lower(), value)
-
- def _add_ctx_processor(self, endpoint, fn):
- group = self._context_processors.setdefault(endpoint, [])
- fn not in group and group.append(fn)
-
- def _run_ctx_processor(self, endpoint):
- rv, fns = {}, []
- for g in [None, endpoint]:
- for fn in self._context_processors.setdefault(g, []):
- rv.update(fn())
- return rv
-
- def context_processor(self, fn):
- self._add_ctx_processor(None, fn)
-
- def forgot_password_context_processor(self, fn):
- self._add_ctx_processor('forgot_password', fn)
-
- def login_context_processor(self, fn):
- self._add_ctx_processor('login', fn)
-
- def register_context_processor(self, fn):
- self._add_ctx_processor('register', fn)
-
- def reset_password_context_processor(self, fn):
- self._add_ctx_processor('reset_password', fn)
-
- def change_password_context_processor(self, fn):
- self._add_ctx_processor('change_password', fn)
-
- def send_confirmation_context_processor(self, fn):
- self._add_ctx_processor('send_confirmation', fn)
-
- def send_login_context_processor(self, fn):
- self._add_ctx_processor('send_login', fn)
-
- def mail_context_processor(self, fn):
- self._add_ctx_processor('mail', fn)
-
- def send_mail_task(self, fn):
- self._send_mail_task = fn
-
-
-class Security(object):
- """The :class:`Security` class initializes the Flask-Security extension.
-
- :param app: The application.
- :param datastore: An instance of a user datastore.
- """
- def __init__(self, app=None, datastore=None, **kwargs):
- self.app = app
- self.datastore = datastore
-
- if app is not None and datastore is not None:
- self._state = self.init_app(app, datastore, **kwargs)
-
- def init_app(self, app, datastore=None, register_blueprint=True,
- login_form=None, confirm_register_form=None,
- register_form=None, forgot_password_form=None,
- reset_password_form=None, change_password_form=None,
- send_confirmation_form=None, passwordless_login_form=None):
- """Initializes the Flask-Security extension for the specified
- application and datastore implentation.
-
- :param app: The application.
- :param datastore: An instance of a user datastore.
- :param register_blueprint: to register the Security blueprint or not.
- """
- datastore = datastore or self.datastore
-
- for key, value in _default_config.items():
- app.config.setdefault('SECURITY_' + key, value)
-
- for key, value in _default_messages.items():
- app.config.setdefault('SECURITY_MSG_' + key, value)
-
- identity_loaded.connect_via(app)(_on_identity_loaded)
-
- state = _get_state(app, datastore,
- login_form=login_form,
- confirm_register_form=confirm_register_form,
- register_form=register_form,
- forgot_password_form=forgot_password_form,
- reset_password_form=reset_password_form,
- change_password_form=change_password_form,
- send_confirmation_form=send_confirmation_form,
- passwordless_login_form=passwordless_login_form)
-
- if register_blueprint:
- app.register_blueprint(create_blueprint(state, __name__))
- app.context_processor(_context_processor)
-
- app.extensions['security'] = state
-
- return state
-
- def __getattr__(self, name):
- return getattr(self._state, name, None)
diff --git a/wqflask/flask_security/datastore.py b/wqflask/flask_security/datastore.py
deleted file mode 100644
index 634399d9..00000000
--- a/wqflask/flask_security/datastore.py
+++ /dev/null
@@ -1,261 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
- flask.ext.security.datastore
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- This module contains an user datastore classes.
-
- :copyright: (c) 2012 by Matt Wright.
- :license: MIT, see LICENSE for more details.
-"""
-
-class Datastore(object):
- def __init__(self, db):
- self.db = db
-
- def commit(self):
- pass
-
- def put(self, model):
- raise NotImplementedError
-
- def delete(self, model):
- raise NotImplementedError
-
-
-class SQLAlchemyDatastore(Datastore):
- def commit(self):
- self.db.session.commit()
-
- def put(self, model):
- self.db.session.add(model)
- return model
-
- def delete(self, model):
- self.db.session.delete(model)
-
-
-class MongoEngineDatastore(Datastore):
- def put(self, model):
- model.save()
- return model
-
- def delete(self, model):
- model.delete()
-
-
-class PeeweeDatastore(Datastore):
- def put(self, model):
- model.save()
- return model
-
- def delete(self, model):
- model.delete_instance()
-
-
-class UserDatastore(object):
- """Abstracted user datastore.
-
- :param user_model: A user model class definition
- :param role_model: A role model class definition
- """
-
- def __init__(self, user_model, role_model):
- self.user_model = user_model
- self.role_model = role_model
-
- def _prepare_role_modify_args(self, user, role):
- if isinstance(user, basestring):
- user = self.find_user(email=user)
- if isinstance(role, basestring):
- role = self.find_role(role)
- return user, role
-
- def _prepare_create_user_args(self, **kwargs):
- kwargs.setdefault('active', True)
- roles = kwargs.get('roles', [])
- for i, role in enumerate(roles):
- rn = role.name if isinstance(role, self.role_model) else role
- # see if the role exists
- roles[i] = self.find_role(rn)
- kwargs['roles'] = roles
- return kwargs
-
- def find_user(self, *args, **kwargs):
- """Returns a user matching the provided parameters."""
- raise NotImplementedError
-
- def find_role(self, *args, **kwargs):
- """Returns a role matching the provided name."""
- raise NotImplementedError
-
- def add_role_to_user(self, user, role):
- """Adds a role tp a user
-
- :param user: The user to manipulate
- :param role: The role to add to the user
- """
- rv = False
- user, role = self._prepare_role_modify_args(user, role)
- if role not in user.roles:
- rv = True
- user.roles.append(role)
- return rv
-
- def remove_role_from_user(self, user, role):
- """Removes a role from a user
-
- :param user: The user to manipulate
- :param role: The role to remove from the user
- """
- rv = False
- user, role = self._prepare_role_modify_args(user, role)
- if role in user.roles:
- rv = True
- user.roles.remove(role)
- return rv
-
- def toggle_active(self, user):
- """Toggles a user's active status. Always returns True."""
- user.active = not user.active
- return True
-
- def deactivate_user(self, user):
- """Deactivates a specified user. Returns `True` if a change was made.
-
- :param user: The user to deactivate
- """
- if user.active:
- user.active = False
- return True
- return False
-
- def activate_user(self, user):
- """Activates a specified user. Returns `True` if a change was made.
-
- :param user: The user to activate
- """
- if not user.active:
- user.active = True
- return True
- return False
-
- def create_role(self, **kwargs):
- """Creates and returns a new role from the given parameters."""
-
- role = self.role_model(**kwargs)
- return self.put(role)
-
- def find_or_create_role(self, name, **kwargs):
- """Returns a role matching the given name or creates it with any
- additionally provided parameters
- """
- kwargs["name"] = name
- return self.find_role(name) or self.create_role(**kwargs)
-
- def create_user(self, **kwargs):
- """Creates and returns a new user from the given parameters."""
-
- user = self.user_model(**self._prepare_create_user_args(**kwargs))
- print "in abstraced create_user, user is:", user
- return self.put(user)
-
- def delete_user(self, user):
- """Delete the specified user
-
- :param user: The user to delete
- """
- self.delete(user)
-
-
-class SQLAlchemyUserDatastore(SQLAlchemyDatastore, UserDatastore):
- """A SQLAlchemy datastore implementation for Flask-Security that assumes the
- use of the Flask-SQLAlchemy extension.
- """
- def __init__(self, db, user_model, role_model):
- SQLAlchemyDatastore.__init__(self, db)
- UserDatastore.__init__(self, user_model, role_model)
-
- def find_user(self, **kwargs):
- return self.user_model.query.filter_by(**kwargs).first()
-
- def find_role(self, role):
- return self.role_model.query.filter_by(name=role).first()
-
-
-class MongoEngineUserDatastore(MongoEngineDatastore, UserDatastore):
- """A MongoEngine datastore implementation for Flask-Security that assumes
- the use of the Flask-MongoEngine extension.
- """
- def __init__(self, db, user_model, role_model):
- MongoEngineDatastore.__init__(self, db)
- UserDatastore.__init__(self, user_model, role_model)
-
- def find_user(self, **kwargs):
- return self.user_model.objects(**kwargs).first()
-
- def find_role(self, role):
- return self.role_model.objects(name=role).first()
-
-
-class PeeweeUserDatastore(PeeweeDatastore, UserDatastore):
- """A PeeweeD datastore implementation for Flask-Security that assumes
- the use of the Flask-Peewee extension.
-
- :param user_model: A user model class definition
- :param role_model: A role model class definition
- :param role_link: A model implementing the many-to-many user-role relation
- """
- def __init__(self, db, user_model, role_model, role_link):
- PeeweeDatastore.__init__(self, db)
- UserDatastore.__init__(self, user_model, role_model)
- self.UserRole = role_link
-
- def find_user(self, **kwargs):
- try:
- return self.user_model.filter(**kwargs).get()
- except self.user_model.DoesNotExist:
- return None
-
- def find_role(self, role):
- try:
- return self.role_model.filter(name=role).get()
- except self.role_model.DoesNotExist:
- return None
-
- def create_user(self, **kwargs):
- """Creates and returns a new user from the given parameters."""
- roles = kwargs.pop('roles', [])
- user = self.user_model(**self._prepare_create_user_args(**kwargs))
- user = self.put(user)
- for role in roles:
- self.add_role_to_user(user, role)
- return user
-
-
- def add_role_to_user(self, user, role):
- """Adds a role tp a user
-
- :param user: The user to manipulate
- :param role: The role to add to the user
- """
- user, role = self._prepare_role_modify_args(user, role)
- if self.UserRole.select().where(self.UserRole.user==user, self.UserRole.role==role).count():
- return False
- else:
- self.UserRole.create(user=user, role=role)
- return True
-
- def remove_role_from_user(self, user, role):
- """Removes a role from a user
-
- :param user: The user to manipulate
- :param role: The role to remove from the user
- """
- user, role = self._prepare_role_modify_args(user, role)
- if self.UserRole.select().where(self.UserRole.user==user, self.UserRole.role==role).count():
- self.UserRole.delete().where(self.UserRole.user==user, self.UserRole.role==role)
- return True
- else:
- return False
-
diff --git a/wqflask/flask_security/decorators.py b/wqflask/flask_security/decorators.py
deleted file mode 100644
index 0ea1105c..00000000
--- a/wqflask/flask_security/decorators.py
+++ /dev/null
@@ -1,207 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
- flask.ext.security.decorators
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Flask-Security decorators module
-
- :copyright: (c) 2012 by Matt Wright.
- :license: MIT, see LICENSE for more details.
-"""
-
-from functools import wraps
-
-from flask import current_app, Response, request, redirect, _request_ctx_stack
-from flask.ext.login import current_user, login_required
-from flask.ext.principal import RoleNeed, Permission, Identity, identity_changed
-from werkzeug.local import LocalProxy
-
-from . import utils
-
-
-# Convenient references
-_security = LocalProxy(lambda: current_app.extensions['security'])
-
-
-_default_unauthorized_html = """
- <h1>Unauthorized</h1>
- <p>The server could not verify that you are authorized to access the URL
- requested. You either supplied the wrong credentials (e.g. a bad password),
- or your browser doesn't understand how to supply the credentials required.</p>
- """
-
-
-def _get_unauthorized_response(text=None, headers=None):
- text = text or _default_unauthorized_html
- headers = headers or {}
- return Response(text, 401, headers)
-
-
-def _get_unauthorized_view():
- cv = utils.get_url(utils.config_value('UNAUTHORIZED_VIEW'))
- utils.do_flash(*utils.get_message('UNAUTHORIZED'))
- return redirect(cv or request.referrer or '/')
-
-
-def _check_token():
- header_key = _security.token_authentication_header
- args_key = _security.token_authentication_key
- header_token = request.headers.get(header_key, None)
- token = request.args.get(args_key, header_token)
- if request.json:
- token = request.json.get(args_key, token)
- serializer = _security.remember_token_serializer
-
- try:
- data = serializer.loads(token)
- except:
- return False
-
- user = _security.datastore.find_user(id=data[0])
-
- if utils.md5(user.password) == data[1]:
- app = current_app._get_current_object()
- _request_ctx_stack.top.user = user
- identity_changed.send(app, identity=Identity(user.id))
- return True
-
-
-def _check_http_auth():
- auth = request.authorization or dict(username=None, password=None)
- user = _security.datastore.find_user(email=auth.username)
-
- if user and utils.verify_and_update_password(auth.password, user):
- _security.datastore.commit()
- app = current_app._get_current_object()
- _request_ctx_stack.top.user = user
- identity_changed.send(app, identity=Identity(user.id))
- return True
-
- return False
-
-
-def http_auth_required(realm):
- """Decorator that protects endpoints using Basic HTTP authentication.
- The username should be set to the user's email address.
-
- :param realm: optional realm name"""
-
- def decorator(fn):
- @wraps(fn)
- def wrapper(*args, **kwargs):
- if _check_http_auth():
- return fn(*args, **kwargs)
- r = _security.default_http_auth_realm if callable(realm) else realm
- h = {'WWW-Authenticate': 'Basic realm="%s"' % r}
- return _get_unauthorized_response(headers=h)
- return wrapper
-
- if callable(realm):
- return decorator(realm)
- return decorator
-
-
-def auth_token_required(fn):
- """Decorator that protects endpoints using token authentication. The token
- should be added to the request by the client by using a query string
- variable with a name equal to the configuration value of
- `SECURITY_TOKEN_AUTHENTICATION_KEY` or in a request header named that of
- the configuration value of `SECURITY_TOKEN_AUTHENTICATION_HEADER`
- """
-
- @wraps(fn)
- def decorated(*args, **kwargs):
- if _check_token():
- return fn(*args, **kwargs)
- return _get_unauthorized_response()
- return decorated
-
-
-def auth_required(*auth_methods):
- """
- Decorator that protects enpoints through multiple mechanisms
- Example::
-
- @app.route('/dashboard')
- @auth_required('token', 'session')
- def dashboard():
- return 'Dashboard'
-
- :param auth_methods: Specified mechanisms.
- """
- login_mechanisms = {
- 'token': lambda: _check_token(),
- 'basic': lambda: _check_http_auth(),
- 'session': lambda: current_user.is_authenticated()
- }
-
- def wrapper(fn):
- @wraps(fn)
- def decorated_view(*args, **kwargs):
- mechanisms = [login_mechanisms.get(method) for method in auth_methods]
- for mechanism in mechanisms:
- if mechanism and mechanism():
- return fn(*args, **kwargs)
- return _get_unauthorized_response()
- return decorated_view
- return wrapper
-
-
-def roles_required(*roles):
- """Decorator which specifies that a user must have all the specified roles.
- Example::
-
- @app.route('/dashboard')
- @roles_required('admin', 'editor')
- def dashboard():
- return 'Dashboard'
-
- The current user must have both the `admin` role and `editor` role in order
- to view the page.
-
- :param args: The required roles.
- """
- def wrapper(fn):
- @wraps(fn)
- def decorated_view(*args, **kwargs):
- perms = [Permission(RoleNeed(role)) for role in roles]
- for perm in perms:
- if not perm.can():
- return _get_unauthorized_view()
- return fn(*args, **kwargs)
- return decorated_view
- return wrapper
-
-
-def roles_accepted(*roles):
- """Decorator which specifies that a user must have at least one of the
- specified roles. Example::
-
- @app.route('/create_post')
- @roles_accepted('editor', 'author')
- def create_post():
- return 'Create Post'
-
- The current user must have either the `editor` role or `author` role in
- order to view the page.
-
- :param args: The possible roles.
- """
- def wrapper(fn):
- @wraps(fn)
- def decorated_view(*args, **kwargs):
- perm = Permission(*[RoleNeed(role) for role in roles])
- if perm.can():
- return fn(*args, **kwargs)
- return _get_unauthorized_view()
- return decorated_view
- return wrapper
-
-
-def anonymous_user_required(f):
- @wraps(f)
- def wrapper(*args, **kwargs):
- if current_user.is_authenticated():
- return redirect(utils.get_url(_security.post_login_view))
- return f(*args, **kwargs)
- return wrapper
diff --git a/wqflask/flask_security/forms.py b/wqflask/flask_security/forms.py
deleted file mode 100644
index 54677e77..00000000
--- a/wqflask/flask_security/forms.py
+++ /dev/null
@@ -1,286 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
- flask.ext.security.forms
- ~~~~~~~~~~~~~~~~~~~~~~~~
-
- Flask-Security forms module
-
- :copyright: (c) 2012 by Matt Wright.
- :license: MIT, see LICENSE for more details.
-"""
-
-import inspect
-import urlparse
-
-import flask_wtf as wtf
-
-from flask import request, current_app
-from flask_wtf import Form as BaseForm, TextField, PasswordField, \
- SubmitField, HiddenField, BooleanField, ValidationError, Field
-from flask_login import current_user
-from werkzeug.local import LocalProxy
-
-from .confirmable import requires_confirmation
-from .utils import verify_and_update_password, get_message
-
-# Convenient reference
-_datastore = LocalProxy(lambda: current_app.extensions['security'].datastore)
-
-_default_field_labels = {
- 'email': 'Email Address',
- 'password': 'Password',
- 'remember_me': 'Remember Me',
- 'login': 'Login',
- 'retype_password': 'Retype Password',
- 'register': 'Register',
- 'send_confirmation': 'Resend Confirmation Instructions',
- 'recover_password': 'Recover Password',
- 'reset_password': 'Reset Password',
- 'retype_password': 'Retype Password',
- 'new_password': 'New Password',
- 'change_password': 'Change Password',
- 'send_login_link': 'Send Login Link'
-}
-
-
-class ValidatorMixin(object):
- def __call__(self, form, field):
- if self.message and self.message.isupper():
- self.message = get_message(self.message)[0]
- return super(ValidatorMixin, self).__call__(form, field)
-
-
-class EqualTo(ValidatorMixin, wtf.EqualTo):
- pass
-
-
-class Required(ValidatorMixin, wtf.Required):
- pass
-
-
-class Email(ValidatorMixin, wtf.Email):
- pass
-
-
-class Length(ValidatorMixin, wtf.Length):
- pass
-
-
-email_required = Required(message='EMAIL_NOT_PROVIDED')
-email_validator = Email(message='INVALID_EMAIL_ADDRESS')
-password_required = Required(message='PASSWORD_NOT_PROVIDED')
-
-
-def get_form_field_label(key):
- return _default_field_labels.get(key, '')
-
-
-def unique_user_email(form, field):
- if _datastore.find_user(email=field.data) is not None:
- msg = get_message('EMAIL_ALREADY_ASSOCIATED', email=field.data)[0]
- raise ValidationError(msg)
-
-
-def valid_user_email(form, field):
- form.user = _datastore.find_user(email=field.data)
- if form.user is None:
- raise ValidationError(get_message('USER_DOES_NOT_EXIST')[0])
-
-
-class Form(BaseForm):
- def __init__(self, *args, **kwargs):
- #print "importing tracer"
- #from wqflask import tracer
- #tracer.turn_on()
- #print "imported tracer"
- print "in Form, args:", args
- print "in Form, kwargs:", kwargs
- if current_app.testing:
- self.TIME_LIMIT = None
- super(Form, self).__init__(*args, **kwargs)
-
-
-class EmailFormMixin():
- email = TextField(get_form_field_label('email'),
- validators=[email_required,
- email_validator])
-
-
-class UserEmailFormMixin():
- user = None
- email = TextField(get_form_field_label('email'),
- validators=[email_required,
- email_validator,
- valid_user_email])
-
-
-class UniqueEmailFormMixin():
- email = TextField(get_form_field_label('email'),
- validators=[email_required,
- email_validator,
- unique_user_email])
-
-
-class PasswordFormMixin():
- password = PasswordField(get_form_field_label('password'),
- validators=[password_required])
-
-
-class NewPasswordFormMixin():
- password = PasswordField(get_form_field_label('password'),
- validators=[password_required,
- Length(min=6, max=128)])
-
-
-class PasswordConfirmFormMixin():
- password_confirm = PasswordField(
- get_form_field_label('retype_password'),
- validators=[EqualTo('password', message='RETYPE_PASSWORD_MISMATCH')])
-
-
-class NextFormMixin():
- next = HiddenField()
-
- def validate_next(self, field):
- url_next = urlparse.urlsplit(field.data)
- url_base = urlparse.urlsplit(request.host_url)
- if url_next.netloc and url_next.netloc != url_base.netloc:
- field.data = ''
- raise ValidationError(get_message('INVALID_REDIRECT')[0])
-
-
-class RegisterFormMixin():
- submit = SubmitField(get_form_field_label('register'))
-
- def to_dict(form):
- def is_field_and_user_attr(member):
- print "in ifaua:", member
- return isinstance(member, Field) and \
- hasattr(_datastore.user_model, member.name)
-
- print("green:", vars(form))
- fields = inspect.getmembers(form, is_field_and_user_attr)
- print("fields:" ,vars(form))
- return dict((key, value.data) for key, value in fields)
-
-
-class SendConfirmationForm(Form, UserEmailFormMixin):
- """The default forgot password form"""
-
- submit = SubmitField(get_form_field_label('send_confirmation'))
-
- def __init__(self, *args, **kwargs):
- super(SendConfirmationForm, self).__init__(*args, **kwargs)
- if request.method == 'GET':
- self.email.data = request.args.get('email', None)
-
- def validate(self):
- if not super(SendConfirmationForm, self).validate():
- return False
- if self.user.confirmed_at is not None:
- self.email.errors.append(get_message('ALREADY_CONFIRMED')[0])
- return False
- return True
-
-
-class ForgotPasswordForm(Form, UserEmailFormMixin):
- """The default forgot password form"""
-
- submit = SubmitField(get_form_field_label('recover_password'))
-
-
-class PasswordlessLoginForm(Form, UserEmailFormMixin):
- """The passwordless login form"""
-
- submit = SubmitField(get_form_field_label('send_login_link'))
-
- def __init__(self, *args, **kwargs):
- super(PasswordlessLoginForm, self).__init__(*args, **kwargs)
-
- def validate(self):
- if not super(PasswordlessLoginForm, self).validate():
- return False
- if not self.user.is_active():
- self.email.errors.append(get_message('DISABLED_ACCOUNT')[0])
- return False
- return True
-
-
-class LoginForm(Form, NextFormMixin):
- """The default login form"""
-
- email = TextField(get_form_field_label('email'))
- password = PasswordField(get_form_field_label('password'))
- remember = BooleanField(get_form_field_label('remember_me'))
- submit = SubmitField(get_form_field_label('login'))
-
- def __init__(self, *args, **kwargs):
- super(LoginForm, self).__init__(*args, **kwargs)
-
- def validate(self):
- if not super(LoginForm, self).validate():
- return False
-
- if self.email.data.strip() == '':
- self.email.errors.append(get_message('EMAIL_NOT_PROVIDED')[0])
- return False
-
- if self.password.data.strip() == '':
- self.password.errors.append(get_message('PASSWORD_NOT_PROVIDED')[0])
- return False
-
- self.user = _datastore.find_user(email=self.email.data)
-
- if self.user is None:
- self.email.errors.append(get_message('USER_DOES_NOT_EXIST')[0])
- return False
- if not verify_and_update_password(self.password.data, self.user):
- self.password.errors.append(get_message('INVALID_PASSWORD')[0])
- return False
- if requires_confirmation(self.user):
- self.email.errors.append(get_message('CONFIRMATION_REQUIRED')[0])
- return False
- if not self.user.is_active():
- self.email.errors.append(get_message('DISABLED_ACCOUNT')[0])
- return False
- return True
-
-
-class ConfirmRegisterForm(Form, RegisterFormMixin,
- UniqueEmailFormMixin, NewPasswordFormMixin):
- pass
-
-
-class RegisterForm(ConfirmRegisterForm, PasswordConfirmFormMixin):
- pass
-
-
-class ResetPasswordForm(Form, NewPasswordFormMixin, PasswordConfirmFormMixin):
- """The default reset password form"""
-
- submit = SubmitField(get_form_field_label('reset_password'))
-
-
-class ChangePasswordForm(Form, PasswordFormMixin):
- """The default change password form"""
-
- new_password = PasswordField(get_form_field_label('new_password'),
- validators=[password_required,
- Length(min=6, max=128)])
-
- new_password_confirm = PasswordField(get_form_field_label('retype_password'),
- validators=[EqualTo('new_password', message='RETYPE_PASSWORD_MISMATCH')])
-
- submit = SubmitField(get_form_field_label('change_password'))
-
- def validate(self):
- if not super(ChangePasswordForm, self).validate():
- return False
-
- if self.password.data.strip() == '':
- self.password.errors.append(get_message('PASSWORD_NOT_PROVIDED')[0])
- return False
- if not verify_and_update_password(self.password.data, current_user):
- self.password.errors.append(get_message('INVALID_PASSWORD')[0])
- return False
- return True
diff --git a/wqflask/flask_security/passwordless.py b/wqflask/flask_security/passwordless.py
deleted file mode 100644
index b0accb2c..00000000
--- a/wqflask/flask_security/passwordless.py
+++ /dev/null
@@ -1,59 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
- flask.ext.security.passwordless
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Flask-Security passwordless module
-
- :copyright: (c) 2012 by Matt Wright.
- :license: MIT, see LICENSE for more details.
-"""
-
-from flask import request, current_app as app
-from werkzeug.local import LocalProxy
-
-from .signals import login_instructions_sent
-from .utils import send_mail, url_for_security, get_token_status, \
- config_value
-
-
-# Convenient references
-_security = LocalProxy(lambda: app.extensions['security'])
-
-_datastore = LocalProxy(lambda: _security.datastore)
-
-
-def send_login_instructions(user):
- """Sends the login instructions email for the specified user.
-
- :param user: The user to send the instructions to
- :param token: The login token
- """
- token = generate_login_token(user)
- url = url_for_security('token_login', token=token)
- login_link = request.url_root[:-1] + url
-
- send_mail(config_value('EMAIL_SUBJECT_PASSWORDLESS'), user.email,
- 'login_instructions', user=user, login_link=login_link)
-
- login_instructions_sent.send(dict(user=user, login_token=token),
- app=app._get_current_object())
-
-
-def generate_login_token(user):
- """Generates a unique login token for the specified user.
-
- :param user: The user the token belongs to
- """
- return _security.login_serializer.dumps([str(user.id)])
-
-
-def login_token_status(token):
- """Returns the expired status, invalid status, and user of a login token.
- For example::
-
- expired, invalid, user = login_token_status('...')
-
- :param token: The login token
- """
- return get_token_status(token, 'login', 'LOGIN')
diff --git a/wqflask/flask_security/recoverable.py b/wqflask/flask_security/recoverable.py
deleted file mode 100644
index 6aafc111..00000000
--- a/wqflask/flask_security/recoverable.py
+++ /dev/null
@@ -1,80 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
- flask.ext.security.recoverable
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Flask-Security recoverable module
-
- :copyright: (c) 2012 by Matt Wright.
- :license: MIT, see LICENSE for more details.
-"""
-
-from flask import current_app as app, request
-from werkzeug.local import LocalProxy
-
-from .signals import password_reset, reset_password_instructions_sent
-from .utils import send_mail, md5, encrypt_password, url_for_security, \
- get_token_status, config_value
-
-
-# Convenient references
-_security = LocalProxy(lambda: app.extensions['security'])
-
-_datastore = LocalProxy(lambda: _security.datastore)
-
-
-def send_reset_password_instructions(user):
- """Sends the reset password instructions email for the specified user.
-
- :param user: The user to send the instructions to
- """
- token = generate_reset_password_token(user)
- url = url_for_security('reset_password', token=token)
- reset_link = request.url_root[:-1] + url
-
- send_mail(config_value('EMAIL_SUBJECT_PASSWORD_RESET'), user.email,
- 'reset_instructions',
- user=user, reset_link=reset_link)
-
- reset_password_instructions_sent.send(dict(user=user, token=token),
- app=app._get_current_object())
-
-
-def send_password_reset_notice(user):
- """Sends the password reset notice email for the specified user.
-
- :param user: The user to send the notice to
- """
- send_mail(config_value('EMAIL_SUBJECT_PASSWORD_NOTICE'), user.email,
- 'reset_notice', user=user)
-
-
-def generate_reset_password_token(user):
- """Generates a unique reset password token for the specified user.
-
- :param user: The user to work with
- """
- data = [str(user.id), md5(user.password)]
- return _security.reset_serializer.dumps(data)
-
-
-def reset_password_token_status(token):
- """Returns the expired status, invalid status, and user of a password reset
- token. For example::
-
- expired, invalid, user = reset_password_token_status('...')
-
- :param token: The password reset token
- """
- return get_token_status(token, 'reset', 'RESET_PASSWORD')
-
-def update_password(user, password):
- """Update the specified user's password
-
- :param user: The user to update_password
- :param password: The unencrypted new password
- """
- user.password = encrypt_password(password)
- _datastore.put(user)
- send_password_reset_notice(user)
- password_reset.send(user, app=app._get_current_object())
diff --git a/wqflask/flask_security/registerable.py b/wqflask/flask_security/registerable.py
deleted file mode 100644
index 4606c7c6..00000000
--- a/wqflask/flask_security/registerable.py
+++ /dev/null
@@ -1,44 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
- flask.ext.security.registerable
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Flask-Security registerable module
-
- :copyright: (c) 2012 by Matt Wright.
- :license: MIT, see LICENSE for more details.
-"""
-
-from flask import current_app as app
-from werkzeug.local import LocalProxy
-
-from .confirmable import generate_confirmation_link
-from .signals import user_registered
-from .utils import do_flash, get_message, send_mail, encrypt_password, \
- config_value
-
-# Convenient references
-_security = LocalProxy(lambda: app.extensions['security'])
-
-_datastore = LocalProxy(lambda: _security.datastore)
-
-
-def register_user(**kwargs):
- print "in register_user kwargs:", kwargs
- confirmation_link, token = None, None
- kwargs['password'] = encrypt_password(kwargs['password'])
- user = _datastore.create_user(**kwargs)
- _datastore.commit()
-
- if _security.confirmable:
- confirmation_link, token = generate_confirmation_link(user)
- do_flash(*get_message('CONFIRM_REGISTRATION', email=user.email))
-
- user_registered.send(dict(user=user, confirm_token=token),
- app=app._get_current_object())
-
- if config_value('SEND_REGISTER_EMAIL'):
- send_mail(config_value('EMAIL_SUBJECT_REGISTER'), user.email, 'welcome',
- user=user, confirmation_link=confirmation_link)
-
- return user
diff --git a/wqflask/flask_security/script.py b/wqflask/flask_security/script.py
deleted file mode 100644
index 9c9a2469..00000000
--- a/wqflask/flask_security/script.py
+++ /dev/null
@@ -1,130 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
- flask.ext.security.script
- ~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Flask-Security script module
-
- :copyright: (c) 2012 by Matt Wright.
- :license: MIT, see LICENSE for more details.
-"""
-try:
- import simplejson as json
-except ImportError:
- import json
-
-import re
-
-from flask import current_app
-from flask.ext.script import Command, Option
-from werkzeug.local import LocalProxy
-
-from .utils import encrypt_password
-
-
-_datastore = LocalProxy(lambda: current_app.extensions['security'].datastore)
-
-
-def pprint(obj):
- print json.dumps(obj, sort_keys=True, indent=4)
-
-
-def commit(fn):
- def wrapper(*args, **kwargs):
- fn(*args, **kwargs)
- _datastore.commit()
- return wrapper
-
-
-class CreateUserCommand(Command):
- """Create a user"""
-
- option_list = (
- Option('-e', '--email', dest='email', default=None),
- Option('-p', '--password', dest='password', default=None),
- Option('-a', '--active', dest='active', default=''),
- )
-
- @commit
- def run(self, **kwargs):
- # sanitize active input
- ai = re.sub(r'\s', '', str(kwargs['active']))
- kwargs['active'] = ai.lower() in ['', 'y', 'yes', '1', 'active']
-
- from flask_security.forms import ConfirmRegisterForm
- from werkzeug.datastructures import MultiDict
-
- form = ConfirmRegisterForm(MultiDict(kwargs), csrf_enabled=False)
-
- if form.validate():
- kwargs['password'] = encrypt_password(kwargs['password'])
- _datastore.create_user(**kwargs)
- print 'User created successfully.'
- kwargs['password'] = '****'
- pprint(kwargs)
- else:
- print 'Error creating user'
- pprint(form.errors)
-
-
-class CreateRoleCommand(Command):
- """Create a role"""
-
- option_list = (
- Option('-n', '--name', dest='name', default=None),
- Option('-d', '--desc', dest='description', default=None),
- )
-
- @commit
- def run(self, **kwargs):
- _datastore.create_role(**kwargs)
- print 'Role "%(name)s" created successfully.' % kwargs
-
-
-class _RoleCommand(Command):
- option_list = (
- Option('-u', '--user', dest='user_identifier'),
- Option('-r', '--role', dest='role_name'),
- )
-
-
-class AddRoleCommand(_RoleCommand):
- """Add a role to a user"""
-
- @commit
- def run(self, user_identifier, role_name):
- _datastore.add_role_to_user(user_identifier, role_name)
- print "Role '%s' added to user '%s' successfully" % (role_name, user_identifier)
-
-
-class RemoveRoleCommand(_RoleCommand):
- """Add a role to a user"""
-
- @commit
- def run(self, user_identifier, role_name):
- _datastore.remove_role_from_user(user_identifier, role_name)
- print "Role '%s' removed from user '%s' successfully" % (role_name, user_identifier)
-
-
-class _ToggleActiveCommand(Command):
- option_list = (
- Option('-u', '--user', dest='user_identifier'),
- )
-
-
-class DeactivateUserCommand(_ToggleActiveCommand):
- """Deactive a user"""
-
- @commit
- def run(self, user_identifier):
- _datastore.deactivate_user(user_identifier)
- print "User '%s' has been deactivated" % user_identifier
-
-
-class ActivateUserCommand(_ToggleActiveCommand):
- """Deactive a user"""
-
- @commit
- def run(self, user_identifier):
- _datastore.activate_user(user_identifier)
- print "User '%s' has been activated" % user_identifier
diff --git a/wqflask/flask_security/signals.py b/wqflask/flask_security/signals.py
deleted file mode 100644
index e1c29548..00000000
--- a/wqflask/flask_security/signals.py
+++ /dev/null
@@ -1,29 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
- flask.ext.security.signals
- ~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Flask-Security signals module
-
- :copyright: (c) 2012 by Matt Wright.
- :license: MIT, see LICENSE for more details.
-"""
-
-import blinker
-
-
-signals = blinker.Namespace()
-
-user_registered = signals.signal("user-registered")
-
-user_confirmed = signals.signal("user-confirmed")
-
-confirm_instructions_sent = signals.signal("confirm-instructions-sent")
-
-login_instructions_sent = signals.signal("login-instructions-sent")
-
-password_reset = signals.signal("password-reset")
-
-password_changed = signals.signal("password-changed")
-
-reset_password_instructions_sent = signals.signal("password-reset-instructions-sent")
diff --git a/wqflask/flask_security/templates/.DS_Store b/wqflask/flask_security/templates/.DS_Store
deleted file mode 100644
index b72f1d98..00000000
--- a/wqflask/flask_security/templates/.DS_Store
+++ /dev/null
Binary files differ
diff --git a/wqflask/flask_security/templates/security/.DS_Store b/wqflask/flask_security/templates/security/.DS_Store
deleted file mode 100644
index 5008ddfc..00000000
--- a/wqflask/flask_security/templates/security/.DS_Store
+++ /dev/null
Binary files differ
diff --git a/wqflask/flask_security/templates/security/_macros.html b/wqflask/flask_security/templates/security/_macros.html
deleted file mode 100644
index 8575f3db..00000000
--- a/wqflask/flask_security/templates/security/_macros.html
+++ /dev/null
@@ -1,16 +0,0 @@
-{% macro render_field_with_errors(field) %}
- <p>
- {{ field.label }} {{ field(**kwargs)|safe }}
- {% if field.errors %}
- <ul>
- {% for error in field.errors %}
- <li>{{ error }}</li>
- {% endfor %}
- </ul>
- {% endif %}
- </p>
-{% endmacro %}
-
-{% macro render_field(field) %}
- <p>{{ field(**kwargs)|safe }}</p>
-{% endmacro %} \ No newline at end of file
diff --git a/wqflask/flask_security/templates/security/_menu.html b/wqflask/flask_security/templates/security/_menu.html
deleted file mode 100644
index 5291f809..00000000
--- a/wqflask/flask_security/templates/security/_menu.html
+++ /dev/null
@@ -1,15 +0,0 @@
-{% if security.registerable or security.recoverable or security.confirmabled %}
-<h2>Menu</h2>
-<ul>
- <li><a href="{{ url_for_security('login') }}">Login</a></li>
- {% if security.registerable %}
- <li><a href="{{ url_for_security('register') }}">Register</a><br/></li>
- {% endif %}
- {% if security.recoverable %}
- <li><a href="{{ url_for_security('forgot_password') }}">Forgot password</a><br/></li>
- {% endif %}
- {% if security.confirmable %}
- <li><a href="{{ url_for_security('send_confirmation') }}">Confirm account</a></li>
- {% endif %}
-</ul>
-{% endif %}
diff --git a/wqflask/flask_security/templates/security/_messages.html b/wqflask/flask_security/templates/security/_messages.html
deleted file mode 100644
index 179d0636..00000000
--- a/wqflask/flask_security/templates/security/_messages.html
+++ /dev/null
@@ -1,9 +0,0 @@
-{%- with messages = get_flashed_messages(with_categories=true) -%}
- {% if messages %}
- <ul class="flashes">
- {% for category, message in messages %}
- <li class="{{ category }}">{{ message }}</li>
- {% endfor %}
- </ul>
- {% endif %}
-{%- endwith %} \ No newline at end of file
diff --git a/wqflask/flask_security/templates/security/change_password.html b/wqflask/flask_security/templates/security/change_password.html
deleted file mode 100644
index 8ee3eb73..00000000
--- a/wqflask/flask_security/templates/security/change_password.html
+++ /dev/null
@@ -1,11 +0,0 @@
-{% from "security/_macros.html" import render_field_with_errors, render_field %}
-{% include "security/_messages.html" %}
-<h1>Change password</h1>
-<form action="{{ url_for_security('change_password') }}" method="POST" name="change_password_form">
- {{ change_password_form.hidden_tag() }}
- {{ render_field_with_errors(change_password_form.password) }}
- {{ render_field_with_errors(change_password_form.new_password) }}
- {{ render_field_with_errors(change_password_form.new_password_confirm) }}
- {{ render_field(change_password_form.submit) }}
-</form>
-
diff --git a/wqflask/flask_security/templates/security/email/change_notice.html b/wqflask/flask_security/templates/security/email/change_notice.html
deleted file mode 100644
index d1224cf5..00000000
--- a/wqflask/flask_security/templates/security/email/change_notice.html
+++ /dev/null
@@ -1,4 +0,0 @@
-<p>Your password has been changed.</p>
-{% if security.recoverable %}
-<p>If you did not change your password, <a href="{{ url_for_security('forgot_password', _external=True) }}">click here to reset it</a>.</p>
-{% endif %}
diff --git a/wqflask/flask_security/templates/security/email/change_notice.txt b/wqflask/flask_security/templates/security/email/change_notice.txt
deleted file mode 100644
index e74bd80d..00000000
--- a/wqflask/flask_security/templates/security/email/change_notice.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-Your password has been changed
-{% if security.recoverable %}
-If you did not change your password, click the link below to reset it.
-{{ url_for_security('forgot_password', _external=True) }}
-{% endif %}
diff --git a/wqflask/flask_security/templates/security/email/confirmation_instructions.html b/wqflask/flask_security/templates/security/email/confirmation_instructions.html
deleted file mode 100644
index 5082a9a8..00000000
--- a/wqflask/flask_security/templates/security/email/confirmation_instructions.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<p>Please confirm your email through the link below:</p>
-
-<p><a href="{{ confirmation_link }}">Confirm my account</a></p> \ No newline at end of file
diff --git a/wqflask/flask_security/templates/security/email/confirmation_instructions.txt b/wqflask/flask_security/templates/security/email/confirmation_instructions.txt
deleted file mode 100644
index fb435b55..00000000
--- a/wqflask/flask_security/templates/security/email/confirmation_instructions.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-Please confirm your email through the link below:
-
-{{ confirmation_link }} \ No newline at end of file
diff --git a/wqflask/flask_security/templates/security/email/login_instructions.html b/wqflask/flask_security/templates/security/email/login_instructions.html
deleted file mode 100644
index 45a7cb57..00000000
--- a/wqflask/flask_security/templates/security/email/login_instructions.html
+++ /dev/null
@@ -1,5 +0,0 @@
-<p>Welcome {{ user.email }}!</p>
-
-<p>You can log into your through the link below:</p>
-
-<p><a href="{{ login_link }}">Login now</a></p> \ No newline at end of file
diff --git a/wqflask/flask_security/templates/security/email/login_instructions.txt b/wqflask/flask_security/templates/security/email/login_instructions.txt
deleted file mode 100644
index 1364ed65..00000000
--- a/wqflask/flask_security/templates/security/email/login_instructions.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-Welcome {{ user.email }}!
-
-You can log into your through the link below:
-
-{{ login_link }} \ No newline at end of file
diff --git a/wqflask/flask_security/templates/security/email/reset_instructions.html b/wqflask/flask_security/templates/security/email/reset_instructions.html
deleted file mode 100644
index fd0b48d8..00000000
--- a/wqflask/flask_security/templates/security/email/reset_instructions.html
+++ /dev/null
@@ -1 +0,0 @@
-<p><a href="{{ reset_link }}">Click here to reset your password</a></p> \ No newline at end of file
diff --git a/wqflask/flask_security/templates/security/email/reset_instructions.txt b/wqflask/flask_security/templates/security/email/reset_instructions.txt
deleted file mode 100644
index 91ac288e..00000000
--- a/wqflask/flask_security/templates/security/email/reset_instructions.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-Click the link below to reset your password:
-
-{{ reset_link }} \ No newline at end of file
diff --git a/wqflask/flask_security/templates/security/email/reset_notice.html b/wqflask/flask_security/templates/security/email/reset_notice.html
deleted file mode 100644
index 536e2961..00000000
--- a/wqflask/flask_security/templates/security/email/reset_notice.html
+++ /dev/null
@@ -1 +0,0 @@
-<p>Your password has been reset</p> \ No newline at end of file
diff --git a/wqflask/flask_security/templates/security/email/reset_notice.txt b/wqflask/flask_security/templates/security/email/reset_notice.txt
deleted file mode 100644
index a3fa0b4b..00000000
--- a/wqflask/flask_security/templates/security/email/reset_notice.txt
+++ /dev/null
@@ -1 +0,0 @@
-Your password has been reset \ No newline at end of file
diff --git a/wqflask/flask_security/templates/security/email/welcome.html b/wqflask/flask_security/templates/security/email/welcome.html
deleted file mode 100644
index 55eaed61..00000000
--- a/wqflask/flask_security/templates/security/email/welcome.html
+++ /dev/null
@@ -1,7 +0,0 @@
-<p>Welcome {{ user.email }}!</p>
-
-{% if security.confirmable %}
-<p>You can confirm your email through the link below:</p>
-
-<p><a href="{{ confirmation_link }}">Confirm my account</a></p>
-{% endif %} \ No newline at end of file
diff --git a/wqflask/flask_security/templates/security/email/welcome.txt b/wqflask/flask_security/templates/security/email/welcome.txt
deleted file mode 100644
index fb6ee5b5..00000000
--- a/wqflask/flask_security/templates/security/email/welcome.txt
+++ /dev/null
@@ -1,7 +0,0 @@
-Welcome {{ user.email }}!
-
-{% if security.confirmable %}
-You can confirm your email through the link below:
-
-{{ confirmation_link }}
-{% endif %} \ No newline at end of file
diff --git a/wqflask/flask_security/templates/security/forgot_password.html b/wqflask/flask_security/templates/security/forgot_password.html
deleted file mode 100644
index 90fcaf66..00000000
--- a/wqflask/flask_security/templates/security/forgot_password.html
+++ /dev/null
@@ -1,9 +0,0 @@
-{% from "security/_macros.html" import render_field_with_errors, render_field %}
-{% include "security/_messages.html" %}
-<h1>Send password reset instructions</h1>
-<form action="{{ url_for_security('forgot_password') }}" method="POST" name="forgot_password_form">
- {{ forgot_password_form.hidden_tag() }}
- {{ render_field_with_errors(forgot_password_form.email) }}
- {{ render_field(forgot_password_form.submit) }}
-</form>
-{% include "security/_menu.html" %} \ No newline at end of file
diff --git a/wqflask/flask_security/templates/security/login_user.html b/wqflask/flask_security/templates/security/login_user.html
deleted file mode 100644
index d781ce08..00000000
--- a/wqflask/flask_security/templates/security/login_user.html
+++ /dev/null
@@ -1,12 +0,0 @@
-{% from "security/_macros.html" import render_field_with_errors, render_field %}
-{% include "security/_messages.html" %}
-<h1>Login</h1>
-<form action="{{ url_for_security('login') }}" method="POST" name="login_user_form">
- {{ login_user_form.hidden_tag() }}
- {{ render_field_with_errors(login_user_form.email) }}
- {{ render_field_with_errors(login_user_form.password) }}
- {{ render_field_with_errors(login_user_form.remember) }}
- {{ render_field(login_user_form.next) }}
- {{ render_field(login_user_form.submit) }}
-</form>
-{% include "security/_menu.html" %} \ No newline at end of file
diff --git a/wqflask/flask_security/templates/security/register_user.html b/wqflask/flask_security/templates/security/register_user.html
deleted file mode 100644
index 87cf9b1d..00000000
--- a/wqflask/flask_security/templates/security/register_user.html
+++ /dev/null
@@ -1,13 +0,0 @@
-{% from "security/_macros.html" import render_field_with_errors, render_field %}
-{% include "security/_messages.html" %}
-<h1>Register</h1>
-<form action="{{ url_for_security('register') }}" method="POST" name="register_user_form">
- {{ register_user_form.hidden_tag() }}
- {{ render_field_with_errors(register_user_form.email) }}
- {{ render_field_with_errors(register_user_form.password) }}
- {% if register_user_form.password_confirm %}
- {{ render_field_with_errors(register_user_form.password_confirm) }}
- {% endif %}
- {{ render_field(register_user_form.submit) }}
-</form>
-{% include "security/_menu.html" %} \ No newline at end of file
diff --git a/wqflask/flask_security/templates/security/reset_password.html b/wqflask/flask_security/templates/security/reset_password.html
deleted file mode 100644
index e6fc3f58..00000000
--- a/wqflask/flask_security/templates/security/reset_password.html
+++ /dev/null
@@ -1,10 +0,0 @@
-{% from "security/_macros.html" import render_field_with_errors, render_field %}
-{% include "security/_messages.html" %}
-<h1>Reset password</h1>
-<form action="{{ url_for_security('reset_password', token=reset_password_token) }}" method="POST" name="reset_password_form">
- {{ reset_password_form.hidden_tag() }}
- {{ render_field_with_errors(reset_password_form.password) }}
- {{ render_field_with_errors(reset_password_form.password_confirm) }}
- {{ render_field(reset_password_form.submit) }}
-</form>
-{% include "security/_menu.html" %} \ No newline at end of file
diff --git a/wqflask/flask_security/templates/security/send_confirmation.html b/wqflask/flask_security/templates/security/send_confirmation.html
deleted file mode 100644
index 3e828407..00000000
--- a/wqflask/flask_security/templates/security/send_confirmation.html
+++ /dev/null
@@ -1,9 +0,0 @@
-{% from "security/_macros.html" import render_field_with_errors, render_field %}
-{% include "security/_messages.html" %}
-<h1>Resend confirmation instructions</h1>
-<form action="{{ url_for_security('send_confirmation') }}" method="POST" name="send_confirmation_form">
- {{ send_confirmation_form.hidden_tag() }}
- {{ render_field_with_errors(send_confirmation_form.email) }}
- {{ render_field(send_confirmation_form.submit) }}
-</form>
-{% include "security/_menu.html" %} \ No newline at end of file
diff --git a/wqflask/flask_security/templates/security/send_login.html b/wqflask/flask_security/templates/security/send_login.html
deleted file mode 100644
index 15611c57..00000000
--- a/wqflask/flask_security/templates/security/send_login.html
+++ /dev/null
@@ -1,9 +0,0 @@
-{% from "security/_macros.html" import render_field_with_errors, render_field %}
-{% include "security/_messages.html" %}
-<h1>Login</h1>
-<form action="{{ url_for_security('login') }}" method="POST" name="send_login_form">
- {{ send_login_form.hidden_tag() }}
- {{ render_field_with_errors(send_login_form.email) }}
- {{ render_field(send_login_form.submit) }}
-</form>
-{% include "security/_menu.html" %} \ No newline at end of file
diff --git a/wqflask/flask_security/utils.py b/wqflask/flask_security/utils.py
deleted file mode 100644
index 7397ab4f..00000000
--- a/wqflask/flask_security/utils.py
+++ /dev/null
@@ -1,379 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
- flask.ext.security.utils
- ~~~~~~~~~~~~~~~~~~~~~~~~
-
- Flask-Security utils module
-
- :copyright: (c) 2012 by Matt Wright.
- :license: MIT, see LICENSE for more details.
-"""
-
-import base64
-import blinker
-import functools
-import hashlib
-import hmac
-from contextlib import contextmanager
-from datetime import datetime, timedelta
-
-from flask import url_for, flash, current_app, request, session, render_template
-from flask.ext.login import login_user as _login_user, \
- logout_user as _logout_user
-from flask.ext.mail import Message
-from flask.ext.principal import Identity, AnonymousIdentity, identity_changed
-from itsdangerous import BadSignature, SignatureExpired
-from werkzeug.local import LocalProxy
-
-from .signals import user_registered, user_confirmed, \
- confirm_instructions_sent, login_instructions_sent, \
- password_reset, password_changed, reset_password_instructions_sent
-
-# Convenient references
-_security = LocalProxy(lambda: current_app.extensions['security'])
-
-_datastore = LocalProxy(lambda: _security.datastore)
-
-_pwd_context = LocalProxy(lambda: _security.pwd_context)
-
-
-def login_user(user, remember=True):
- """Performs the login and sends the appropriate signal."""
-
- if not _login_user(user, remember):
- return False
-
- if _security.trackable:
- old_current_login, new_current_login = user.current_login_at, datetime.utcnow()
- remote_addr = request.remote_addr or 'untrackable'
- old_current_ip, new_current_ip = user.current_login_ip, remote_addr
-
- user.last_login_at = old_current_login or new_current_login
- user.current_login_at = new_current_login
- user.last_login_ip = old_current_ip or new_current_ip
- user.current_login_ip = new_current_ip
- user.login_count = user.login_count + 1 if user.login_count else 1
-
- _datastore.put(user)
-
- identity_changed.send(current_app._get_current_object(),
- identity=Identity(user.id))
- return True
-
-
-def logout_user():
- for key in ('identity.name', 'identity.auth_type'):
- session.pop(key, None)
- identity_changed.send(current_app._get_current_object(),
- identity=AnonymousIdentity())
- _logout_user()
-
-
-def get_hmac(password):
- if _security.password_hash == 'plaintext':
- return password
-
- if _security.password_salt is None:
- raise RuntimeError('The configuration value `SECURITY_PASSWORD_SALT` '
- 'must not be None when the value of `SECURITY_PASSWORD_HASH` is '
- 'set to "%s"' % _security.password_hash)
-
- h = hmac.new(_security.password_salt, password.encode('utf-8'), hashlib.sha512)
- return base64.b64encode(h.digest())
-
-
-def verify_password(password, password_hash):
- return _pwd_context.verify(get_hmac(password), password_hash)
-
-
-def verify_and_update_password(password, user):
- verified, new_password = _pwd_context.verify_and_update(get_hmac(password), user.password)
- if verified and new_password:
- user.password = new_password
- _datastore.put(user)
- return verified
-
-
-def encrypt_password(password):
- return _pwd_context.encrypt(get_hmac(password))
-
-
-def md5(data):
- return hashlib.md5(data).hexdigest()
-
-
-def do_flash(message, category=None):
- """Flash a message depending on if the `FLASH_MESSAGES` configuration
- value is set.
-
- :param message: The flash message
- :param category: The flash message category
- """
- if config_value('FLASH_MESSAGES'):
- flash(message, category)
-
-
-def get_url(endpoint_or_url):
- """Returns a URL if a valid endpoint is found. Otherwise, returns the
- provided value.
-
- :param endpoint_or_url: The endpoint name or URL to default to
- """
- try:
- return url_for(endpoint_or_url)
- except:
- return endpoint_or_url
-
-
-def get_security_endpoint_name(endpoint):
- return '%s.%s' % (_security.blueprint_name, endpoint)
-
-
-def url_for_security(endpoint, **values):
- """Return a URL for the security blueprint
-
- :param endpoint: the endpoint of the URL (name of the function)
- :param values: the variable arguments of the URL rule
- :param _external: if set to `True`, an absolute URL is generated. Server
- address can be changed via `SERVER_NAME` configuration variable which
- defaults to `localhost`.
- :param _anchor: if provided this is added as anchor to the URL.
- :param _method: if provided this explicitly specifies an HTTP method.
- """
- endpoint = get_security_endpoint_name(endpoint)
- return url_for(endpoint, **values)
-
-
-def get_post_login_redirect():
- """Returns the URL to redirect to after a user logs in successfully."""
- return (get_url(request.args.get('next')) or
- get_url(request.form.get('next')) or
- find_redirect('SECURITY_POST_LOGIN_VIEW'))
-
-
-def find_redirect(key):
- """Returns the URL to redirect to after a user logs in successfully.
-
- :param key: The session or application configuration key to search for
- """
- rv = (get_url(session.pop(key.lower(), None)) or
- get_url(current_app.config[key.upper()] or None) or '/')
- return rv
-
-
-def get_config(app):
- """Conveniently get the security configuration for the specified
- application without the annoying 'SECURITY_' prefix.
-
- :param app: The application to inspect
- """
- items = app.config.items()
- prefix = 'SECURITY_'
-
- def strip_prefix(tup):
- return (tup[0].replace('SECURITY_', ''), tup[1])
-
- return dict([strip_prefix(i) for i in items if i[0].startswith(prefix)])
-
-
-def get_message(key, **kwargs):
- rv = config_value('MSG_' + key)
- return rv[0] % kwargs, rv[1]
-
-
-def config_value(key, app=None, default=None):
- """Get a Flask-Security configuration value.
-
- :param key: The configuration key without the prefix `SECURITY_`
- :param app: An optional specific application to inspect. Defaults to Flask's
- `current_app`
- :param default: An optional default value if the value is not set
- """
- app = app or current_app
- return get_config(app).get(key.upper(), default)
-
-
-def get_max_age(key, app=None):
- now = datetime.utcnow()
- expires = now + get_within_delta(key + '_WITHIN', app)
- td = (expires - now)
- return (td.microseconds + (td.seconds + td.days * 24 * 3600) * 1e6) / 1e6
-
-
-def get_within_delta(key, app=None):
- """Get a timedelta object from the application configuration following
- the internal convention of::
-
- <Amount of Units> <Type of Units>
-
- Examples of valid config values::
-
- 5 days
- 10 minutes
-
- :param key: The config value key without the 'SECURITY_' prefix
- :param app: Optional application to inspect. Defaults to Flask's
- `current_app`
- """
- txt = config_value(key, app=app)
- values = txt.split()
- return timedelta(**{values[1]: int(values[0])})
-
-
-def send_mail(subject, recipient, template, **context):
- """Send an email via the Flask-Mail extension.
-
- :param subject: Email subject
- :param recipient: Email recipient
- :param template: The name of the email template
- :param context: The context to render the template with
- """
-
- context.setdefault('security', _security)
- context.update(_security._run_ctx_processor('mail'))
-
- msg = Message(subject,
- sender=_security.email_sender,
- recipients=[recipient])
-
- ctx = ('security/email', template)
- msg.body = render_template('%s/%s.txt' % ctx, **context)
- msg.html = render_template('%s/%s.html' % ctx, **context)
-
- if _security._send_mail_task:
- _security._send_mail_task(msg)
- return
-
- mail = current_app.extensions.get('mail')
- mail.send(msg)
-
-
-def get_token_status(token, serializer, max_age=None):
- serializer = getattr(_security, serializer + '_serializer')
- max_age = get_max_age(max_age)
- user, data = None, None
- expired, invalid = False, False
-
- try:
- data = serializer.loads(token, max_age=max_age)
- except SignatureExpired:
- d, data = serializer.loads_unsafe(token)
- expired = True
- except BadSignature:
- invalid = True
-
- if data:
- user = _datastore.find_user(id=data[0])
-
- expired = expired and (user is not None)
- return expired, invalid, user
-
-
-@contextmanager
-def capture_passwordless_login_requests():
- login_requests = []
-
- def _on(data, app):
- login_requests.append(data)
-
- login_instructions_sent.connect(_on)
-
- try:
- yield login_requests
- finally:
- login_instructions_sent.disconnect(_on)
-
-
-@contextmanager
-def capture_registrations():
- """Testing utility for capturing registrations.
-
- :param confirmation_sent_at: An optional datetime object to set the
- user's `confirmation_sent_at` to
- """
- registrations = []
-
- def _on(data, app):
- registrations.append(data)
-
- user_registered.connect(_on)
-
- try:
- yield registrations
- finally:
- user_registered.disconnect(_on)
-
-
-@contextmanager
-def capture_reset_password_requests(reset_password_sent_at=None):
- """Testing utility for capturing password reset requests.
-
- :param reset_password_sent_at: An optional datetime object to set the
- user's `reset_password_sent_at` to
- """
- reset_requests = []
-
- def _on(request, app):
- reset_requests.append(request)
-
- reset_password_instructions_sent.connect(_on)
-
- try:
- yield reset_requests
- finally:
- reset_password_instructions_sent.disconnect(_on)
-
-
-class CaptureSignals(object):
- """Testing utility for capturing blinker signals.
-
- Context manager which mocks out selected signals and registers which are `sent` on and what
- arguments were sent. Instantiate with a list of blinker `NamedSignals` to patch. Each signal
- has it's `send` mocked out.
- """
- def __init__(self, signals):
- """Patch all given signals and make them available as attributes.
-
- :param signals: list of signals
- """
- self._records = {}
- self._receivers = {}
- for signal in signals:
- self._records[signal] = []
- self._receivers[signal] = functools.partial(self._record, signal)
-
- def __getitem__(self, signal):
- """All captured signals are available via `ctxt[signal]`.
- """
- if isinstance(signal, blinker.base.NamedSignal):
- return self._records[signal]
- else:
- super(CaptureSignals, self).__setitem__(signal)
-
- def _record(self, signal, *args, **kwargs):
- self._records[signal].append((args, kwargs))
-
- def __enter__(self):
- for signal, receiver in self._receivers.iteritems():
- signal.connect(receiver)
- return self
-
- def __exit__(self, type, value, traceback):
- for signal, receiver in self._receivers.iteritems():
- signal.disconnect(receiver)
-
- def signals_sent(self):
- """Return a set of the signals sent.
- :rtype: list of blinker `NamedSignals`.
- """
- return set([signal for signal, _ in self._records.iteritems() if self._records[signal]])
-
-
-def capture_signals():
- """Factory method that creates a `CaptureSignals` with all the flask_security signals."""
- return CaptureSignals([user_registered, user_confirmed,
- confirm_instructions_sent, login_instructions_sent,
- password_reset, password_changed,
- reset_password_instructions_sent])
-
-
diff --git a/wqflask/flask_security/views.py b/wqflask/flask_security/views.py
deleted file mode 100644
index 1b8488d8..00000000
--- a/wqflask/flask_security/views.py
+++ /dev/null
@@ -1,359 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
- flask.ext.security.views
- ~~~~~~~~~~~~~~~~~~~~~~~~
-
- Flask-Security views module
-
- :copyright: (c) 2012 by Matt Wright.
- :license: MIT, see LICENSE for more details.
-"""
-
-from flask import current_app, redirect, request, render_template, jsonify, \
- after_this_request, Blueprint
-from flask_login import current_user
-from werkzeug.datastructures import MultiDict
-from werkzeug.local import LocalProxy
-
-from .confirmable import send_confirmation_instructions, \
- confirm_user, confirm_email_token_status
-from .decorators import login_required, anonymous_user_required
-from .passwordless import send_login_instructions, \
- login_token_status
-from .recoverable import reset_password_token_status, \
- send_reset_password_instructions, update_password
-from .changeable import change_user_password
-from .registerable import register_user
-from .utils import get_url, get_post_login_redirect, do_flash, \
- get_message, login_user, logout_user, url_for_security as url_for, \
- config_value
-
-
-# Convenient references
-_security = LocalProxy(lambda: current_app.extensions['security'])
-
-_datastore = LocalProxy(lambda: _security.datastore)
-
-
-def _render_json(form, include_auth_token=False):
- has_errors = len(form.errors) > 0
-
- if has_errors:
- code = 400
- response = dict(errors=form.errors)
- else:
- code = 200
- response = dict(user=dict(id=str(form.user.id)))
- if include_auth_token:
- token = form.user.get_auth_token()
- response['user']['authentication_token'] = token
-
- return jsonify(dict(meta=dict(code=code), response=response))
-
-
-def _commit(response=None):
- _datastore.commit()
- return response
-
-
-def _ctx(endpoint):
- return _security._run_ctx_processor(endpoint)
-
-
-@anonymous_user_required
-def login():
- """View function for login view"""
-
- form_class = _security.login_form
-
- if request.json:
- form = form_class(MultiDict(request.json))
- else:
- form = form_class()
-
- if form.validate_on_submit():
- login_user(form.user, remember=form.remember.data)
- after_this_request(_commit)
-
- if not request.json:
- return redirect(get_post_login_redirect())
-
- form.next.data = get_url(request.args.get('next')) \
- or get_url(request.form.get('next')) or ''
-
- if request.json:
- return _render_json(form, True)
-
- return render_template(config_value('LOGIN_USER_TEMPLATE'),
- login_user_form=form,
- **_ctx('login'))
-
-
-@login_required
-def logout():
- """View function which handles a logout request."""
-
- logout_user()
-
- return redirect(request.args.get('next', None) or
- get_url(_security.post_logout_view))
-
-
-def register():
- """View function which handles a registration request."""
-
- if _security.confirmable or request.json:
- form_class = _security.confirm_register_form
- else:
- form_class = _security.register_form
-
- if request.json:
- form_data = MultiDict(request.json)
- else:
- form_data = request.form
-
- form = form_class(form_data)
-
- if form.validate_on_submit():
- user = register_user(**form.to_dict())
- form.user = user
-
- if not _security.confirmable or _security.login_without_confirmation:
- after_this_request(_commit)
- login_user(user)
-
- if not request.json:
- post_register_url = get_url(_security.post_register_view)
- post_login_url = get_url(_security.post_login_view)
- return redirect(post_register_url or post_login_url)
-
- if request.json:
- return _render_json(form)
-
- return render_template(config_value('REGISTER_USER_TEMPLATE'),
- register_user_form=form,
- **_ctx('register'))
-
-
-def send_login():
- """View function that sends login instructions for passwordless login"""
-
- form_class = _security.passwordless_login_form
-
- if request.json:
- form = form_class(MultiDict(request.json))
- else:
- form = form_class()
-
- if form.validate_on_submit():
- send_login_instructions(form.user)
- if request.json is None:
- do_flash(*get_message('LOGIN_EMAIL_SENT', email=form.user.email))
-
- if request.json:
- return _render_json(form)
-
- return render_template(config_value('SEND_LOGIN_TEMPLATE'),
- send_login_form=form,
- **_ctx('send_login'))
-
-
-@anonymous_user_required
-def token_login(token):
- """View function that handles passwordless login via a token"""
-
- expired, invalid, user = login_token_status(token)
-
- if invalid:
- do_flash(*get_message('INVALID_LOGIN_TOKEN'))
- if expired:
- send_login_instructions(user)
- do_flash(*get_message('LOGIN_EXPIRED', email=user.email,
- within=_security.login_within))
- if invalid or expired:
- return redirect(url_for('login'))
-
- login_user(user, True)
- after_this_request(_commit)
- do_flash(*get_message('PASSWORDLESS_LOGIN_SUCCESSFUL'))
-
- return redirect(get_post_login_redirect())
-
-
-def send_confirmation():
- """View function which sends confirmation instructions."""
-
- form_class = _security.send_confirmation_form
-
- if request.json:
- form = form_class(MultiDict(request.json))
- else:
- form = form_class()
-
- if form.validate_on_submit():
- send_confirmation_instructions(form.user)
- if request.json is None:
- do_flash(*get_message('CONFIRMATION_REQUEST', email=form.user.email))
-
- if request.json:
- return _render_json(form)
-
- return render_template(config_value('SEND_CONFIRMATION_TEMPLATE'),
- send_confirmation_form=form,
- **_ctx('send_confirmation'))
-
-
-@anonymous_user_required
-def confirm_email(token):
- """View function which handles a email confirmation request."""
-
- expired, invalid, user = confirm_email_token_status(token)
-
- if not user or invalid:
- invalid = True
- do_flash(*get_message('INVALID_CONFIRMATION_TOKEN'))
- if expired:
- send_confirmation_instructions(user)
- do_flash(*get_message('CONFIRMATION_EXPIRED', email=user.email,
- within=_security.confirm_email_within))
- if invalid or expired:
- return redirect(get_url(_security.confirm_error_view) or
- url_for('send_confirmation'))
-
- confirm_user(user)
- login_user(user, True)
- after_this_request(_commit)
- do_flash(*get_message('EMAIL_CONFIRMED'))
-
- return redirect(get_url(_security.post_confirm_view) or
- get_url(_security.post_login_view))
-
-
-def forgot_password():
- """View function that handles a forgotten password request."""
-
- form_class = _security.forgot_password_form
-
- if request.json:
- form = form_class(MultiDict(request.json))
- else:
- form = form_class()
-
- if form.validate_on_submit():
- send_reset_password_instructions(form.user)
- if request.json is None:
- do_flash(*get_message('PASSWORD_RESET_REQUEST', email=form.user.email))
-
- if request.json:
- return _render_json(form)
-
- return render_template(config_value('FORGOT_PASSWORD_TEMPLATE'),
- forgot_password_form=form,
- **_ctx('forgot_password'))
-
-
-@anonymous_user_required
-def reset_password(token):
- """View function that handles a reset password request."""
-
- expired, invalid, user = reset_password_token_status(token)
-
- if invalid:
- do_flash(*get_message('INVALID_RESET_PASSWORD_TOKEN'))
- if expired:
- do_flash(*get_message('PASSWORD_RESET_EXPIRED', email=user.email,
- within=_security.reset_password_within))
- if invalid or expired:
- return redirect(url_for('forgot_password'))
-
- form = _security.reset_password_form()
-
- if form.validate_on_submit():
- after_this_request(_commit)
- update_password(user, form.password.data)
- do_flash(*get_message('PASSWORD_RESET'))
- login_user(user, True)
- return redirect(get_url(_security.post_reset_view) or
- get_url(_security.post_login_view))
-
- return render_template(config_value('RESET_PASSWORD_TEMPLATE'),
- reset_password_form=form,
- reset_password_token=token,
- **_ctx('reset_password'))
-
-
-@login_required
-def change_password():
- """View function which handles a change password request."""
-
- form_class = _security.change_password_form
-
- if request.json:
- form = form_class(MultiDict(request.json))
- else:
- form = form_class()
-
- if form.validate_on_submit():
- after_this_request(_commit)
- change_user_password(current_user, form.new_password.data)
- if request.json is None:
- do_flash(*get_message('PASSWORD_CHANGE'))
- return redirect(get_url(_security.post_change_view) or
- get_url(_security.post_login_view))
-
- if request.json:
- return _render_json(form)
-
- return render_template('security/change_password.html',
- change_password_form=form,
- **_ctx('change_password'))
-
-
-def create_blueprint(state, import_name):
- """Creates the security extension blueprint"""
-
- bp = Blueprint(state.blueprint_name, import_name,
- url_prefix=state.url_prefix,
- subdomain=state.subdomain,
- template_folder='templates')
-
- bp.route(state.logout_url, endpoint='logout')(logout)
-
- if state.passwordless:
- bp.route(state.login_url,
- methods=['GET', 'POST'],
- endpoint='login')(send_login)
- bp.route(state.login_url + '/<token>',
- endpoint='token_login')(token_login)
- else:
- bp.route(state.login_url,
- methods=['GET', 'POST'],
- endpoint='login')(login)
-
- if state.registerable:
- bp.route(state.register_url,
- methods=['GET', 'POST'],
- endpoint='register')(register)
-
- if state.recoverable:
- bp.route(state.reset_url,
- methods=['GET', 'POST'],
- endpoint='forgot_password')(forgot_password)
- bp.route(state.reset_url + '/<token>',
- methods=['GET', 'POST'],
- endpoint='reset_password')(reset_password)
-
- if state.changeable:
- bp.route(state.change_url,
- methods=['GET', 'POST'],
- endpoint='change_password')(change_password)
-
- if state.confirmable:
- bp.route(state.confirm_url,
- methods=['GET', 'POST'],
- endpoint='send_confirmation')(send_confirmation)
- bp.route(state.confirm_url + '/<token>',
- methods=['GET', 'POST'],
- endpoint='confirm_email')(confirm_email)
-
- return bp
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..adffdca3 100644
--- a/wqflask/run_gunicorn.py
+++ b/wqflask/run_gunicorn.py
@@ -7,9 +7,12 @@
# from flask import Flask
# application = Flask(__name__)
-print "Starting up Gunicorn process"
+print "===> Starting up Gunicorn process"
from wqflask import app
+from utility.startup_config import app_config
+
+app_config()
@app.route("/gunicorn")
def hello():
diff --git a/wqflask/runserver.py b/wqflask/runserver.py
index a0c76e51..5f41d04d 100644
--- a/wqflask/runserver.py
+++ b/wqflask/runserver.py
@@ -21,22 +21,9 @@ GREEN = '\033[92m'
BOLD = '\033[1m'
ENDC = '\033[0m'
-import os
-app.config['SECRET_KEY'] = os.urandom(24)
+from utility.startup_config import app_config
-from utility.tools import WEBSERVER_MODE,get_setting_int,get_setting,get_setting_bool
-
-port = get_setting_int("SERVER_PORT")
-
-print("GN2 API server URL is ["+BLUE+get_setting("GN_SERVER_URL")+ENDC+"]")
-
-if get_setting_bool("USE_GN_SERVER"):
- import requests
- page = requests.get(get_setting("GN_SERVER_URL"))
- if page.status_code != 200:
- raise Exception("API server not found!")
-
-print("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" % (BLUE,str(port),ENDC,get_setting("WEBSERVER_URL")))
+app_config()
werkzeug_logger = logging.getLogger('werkzeug')
diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py
new file mode 100644
index 00000000..734379f7
--- /dev/null
+++ b/wqflask/utility/elasticsearch_tools.py
@@ -0,0 +1,59 @@
+from elasticsearch import Elasticsearch, TransportError
+import logging
+
+from utility.logger import getLogger
+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)
+ if not es.ping():
+ logger.warning("Elasticsearch is DOWN")
+
+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/startup_config.py b/wqflask/utility/startup_config.py
new file mode 100644
index 00000000..5a62cc50
--- /dev/null
+++ b/wqflask/utility/startup_config.py
@@ -0,0 +1,39 @@
+
+from wqflask import app
+from utility.tools import WEBSERVER_MODE, show_settings, get_setting_int, get_setting, get_setting_bool
+
+import utility.logger
+logger = utility.logger.getLogger(__name__ )
+
+BLUE = '\033[94m'
+GREEN = '\033[92m'
+BOLD = '\033[1m'
+ENDC = '\033[0m'
+
+def app_config():
+ app.config['SESSION_TYPE'] = 'filesystem'
+ if not app.config.get('SECRET_KEY'):
+ import os
+ app.config['SECRET_KEY'] = str(os.urandom(24))
+
+ mode = WEBSERVER_MODE
+ if mode == "DEV" or mode == "DEBUG":
+ app.config['TEMPLATES_AUTO_RELOAD'] = True
+ # if mode == "DEBUG":
+ # app.config['EXPLAIN_TEMPLATE_LOADING'] = True <--- use overriding app param instead
+ print("==========================================")
+ show_settings()
+
+ port = get_setting_int("SERVER_PORT")
+
+ if get_setting_bool("USE_GN_SERVER"):
+ print("GN2 API server URL is ["+BLUE+get_setting("GN_SERVER_URL")+ENDC+"]")
+ import requests
+ page = requests.get(get_setting("GN_SERVER_URL"))
+ if page.status_code != 200:
+ raise Exception("API server not found!")
+
+ import utility.elasticsearch_tools as es
+ es.test_elasticsearch_connection()
+
+ print("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" % (BLUE,str(port),ENDC,get_setting("WEBSERVER_URL")))
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index d3113302..59bb49d8 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -54,7 +54,7 @@ def get_setting(command_id,guess=None):
# print("Looking for "+command_id+"\n")
command = value(os.environ.get(command_id))
if command is None or command == "":
- command = OVERRIDES.get(command_id)
+ command = OVERRIDES.get(command_id) # currently not in use
if command is None:
# ---- Check whether setting exists in app
command = value(app.config.get(command_id))
@@ -220,7 +220,7 @@ def show_settings():
logger.info(OVERRIDES)
logger.info(BLUE+"Mr. Mojo Risin 2"+ENDC)
- print "runserver.py: ****** Webserver configuration ******"
+ print "runserver.py: ****** Webserver configuration - k,v pairs from app.config ******"
keylist = app.config.keys()
keylist.sort()
for k in keylist:
@@ -251,6 +251,31 @@ 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 != 'UNKNOWN' 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 != 'UNKNOWN' 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')
+import utility.elasticsearch_tools as es
+es.test_elasticsearch_connection()
+
+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)
@@ -265,18 +290,5 @@ assert_dir(JS_TWITTER_POST_FETCHER_PATH)
from six import string_types
-if os.environ.get('WQFLASK_OVERRIDES'):
- jsonfn = get_setting('WQFLASK_OVERRIDES')
- logger.info("WQFLASK_OVERRIDES: %s" % jsonfn)
- with open(jsonfn) as data_file:
- overrides = json.load(data_file)
- for k in overrides:
- cmd = overrides[k]
- if isinstance(cmd, string_types):
- OVERRIDES[k] = eval(cmd)
- else:
- OVERRIDES[k] = cmd
- logger.debug(OVERRIDES)
-
# assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData")
assert_file(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js")
diff --git a/wqflask/utility/type_checking.py b/wqflask/utility/type_checking.py
new file mode 100644
index 00000000..220e5f62
--- /dev/null
+++ b/wqflask/utility/type_checking.py
@@ -0,0 +1,42 @@
+# Type checking functions
+
+def is_float(value):
+ try:
+ float(value)
+ return True
+ except:
+ return False
+
+def is_int(value):
+ try:
+ int(value)
+ return True
+ except:
+ return False
+
+def is_str(value):
+ if value is None:
+ return False
+ try:
+ str(value)
+ return True
+ except:
+ return False
+
+def get_float(vars,name,default=None):
+ if name in vars:
+ if is_float(vars[name]):
+ return float(vars[name])
+ return None
+
+def get_int(vars,name,default=None):
+ if name in vars:
+ if is_int(vars[name]):
+ return float(vars[name])
+ return default
+
+def get_string(vars,name,default=None):
+ if name in vars:
+ if not vars[name] is None:
+ return str(vars[name])
+ return default
diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py
index 2188ce17..bc8e9900 100644
--- a/wqflask/wqflask/__init__.py
+++ b/wqflask/wqflask/__init__.py
@@ -13,8 +13,8 @@ logging.basicConfig(level=logging.INFO)
app = Flask(__name__)
app.config.from_object('cfg.default_settings') # Get the defaults from cfg.default_settings
-app.config.from_envvar('WQFLASK_SETTINGS') # See http://flask.pocoo.org/docs/config/#configuring-from-files
-# Note we also use WQFLASK_OVERRIDES
+app.config.from_envvar('GN2_SETTINGS') # See http://flask.pocoo.org/docs/config/#configuring-from-files
+# Note no longer use the badly named WQFLASK_OVERRIDES (nyi)
app.jinja_env.globals.update(
undefined = jinja2.StrictUndefined,
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 9b048346..2c6c3a14 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -52,6 +52,7 @@ import utility.webqtlUtil #this is for parallel computing only.
from wqflask.correlation import correlation_functions
from utility.benchmark import Bench
import utility.webqtlUtil
+from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string
from wqflask import user_manager
from MySQLdb import escape_string as escape
@@ -77,47 +78,6 @@ def print_mem(stage=""):
mem = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss
#print("{}: {}".format(stage, mem/1024))
-def is_float(value):
- try:
- float(value)
- return True
- except:
- return False
-
-def is_int(value):
- try:
- int(value)
- return True
- except:
- return False
-
-def is_str(value):
- if value is None:
- return False
- try:
- str(value)
- return True
- except:
- return False
-
-def get_float(vars,name,default=None):
- if name in vars:
- if is_float(vars[name]):
- return float(vars[name])
- return None
-
-def get_int(vars,name,default=None):
- if name in vars:
- if is_int(vars[name]):
- return float(vars[name])
- return default
-
-def get_string(vars,name,default=None):
- if name in vars:
- if not vars[name] is None:
- return str(vars[name])
- return default
-
class AuthException(Exception):
pass
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index e33e04e1..fe1e17d2 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -5,6 +5,7 @@ from base.data_set import create_dataset
from base.trait import GeneralTrait
from db import webqtlDatabaseFunction
+from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string
from utility.benchmark import Bench
from utility.logger import getLogger
@@ -13,8 +14,13 @@ logger = getLogger(__name__)
class GSearch(object):
def __init__(self, kw):
+ assert('type' in kw)
+ assert('terms' in kw)
+
self.type = kw['type']
self.terms = kw['terms']
+ assert(is_str(self.type))
+
if self.type == "gene":
sql = """
SELECT
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index db4f8f46..3ec61e55 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/search_results.py b/wqflask/wqflask/search_results.py
index 59e100d8..53c96591 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -10,6 +10,7 @@ import time
import math
import datetime
import collections
+import re
from pprint import pformat as pf
@@ -25,6 +26,7 @@ from db import webqtlDatabaseFunction
from flask import render_template
from utility import formatting
+from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string
from utility.logger import getLogger
logger = getLogger(__name__ )
@@ -64,14 +66,26 @@ views.py).
else:
self.and_or = "and"
self.search_terms = kw['search_terms_and']
- self.search_term_exists = True
+ search = self.search_terms
+ # check for dodgy search terms
+ rx = re.compile(r'.*\W(href|http|sql|select|update)\W.*',re.IGNORECASE)
+ if rx.match(search):
+ logger.info("Regex failed search")
+ self.search_term_exists = False
+ return
+ else:
+ self.search_term_exists = True
+
self.results = []
- if kw['type'] == "Phenotypes": # split datatype on type field
+ type = kw.get('type')
+ if type == "Phenotypes": # split datatype on type field
dataset_type = "Publish"
- elif kw['type'] == "Genotypes":
+ elif type == "Genotypes":
dataset_type = "Geno"
else:
dataset_type = "ProbeSet" # ProbeSet is default
+
+ assert(is_str(kw.get('dataset')))
self.dataset = create_dataset(kw['dataset'], dataset_type)
logger.debug("search_terms:", self.search_terms)
self.search()
@@ -145,6 +159,7 @@ statement and executes
else:
combined_where_clause += "OR"
else:
+ logger.debug("Search failed 1")
self.search_term_exists = False
if self.search_term_exists:
combined_where_clause = "(" + combined_where_clause + ")"
@@ -155,6 +170,7 @@ statement and executes
else:
logger.debug("len(search_terms)<=1")
if self.search_terms == []:
+ logger.debug("Search failed 2")
self.search_term_exists = False
else:
for a_search in self.search_terms:
@@ -162,6 +178,7 @@ statement and executes
if the_search != None:
self.results.extend(the_search.run())
else:
+ logger.debug("Search failed 3")
self.search_term_exists = False
if self.search_term_exists:
diff --git a/wqflask/wqflask/templates/new_security/login_user.html b/wqflask/wqflask/templates/new_security/login_user.html
index b9f49a61..949760b6 100644
--- a/wqflask/wqflask/templates/new_security/login_user.html
+++ b/wqflask/wqflask/templates/new_security/login_user.html
@@ -15,15 +15,39 @@
<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 +85,19 @@
</fieldset>
</form>
+ {% else: %}
+ <div class="alert alert-warning">
+ <p>You cannot login at this moment using your GeneNetwork account (the authentication service is down).<br />
+ Please try again later.</p>
+ </div>
+ {% endif %}
+ {% if not es_server and not external_login: %}
+ <hr>
+ <div class="alert alert-warning">
+ Note: it is safe to use GeneNetwork without a login. Login is only required for keeping track of
+ collections and getting access to some types of restricted data.
+ </div>
+ {% endif %}
</div>
</div>
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index f7fcd2d0..c55649f3 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 +606,55 @@ 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, GITHUB_CLIENT_ID, ORCID_AUTH_URL, ORCID_CLIENT_ID
+ external_login = {}
+ if GITHUB_AUTH_URL and GITHUB_CLIENT_ID != 'UNKNOWN':
+ external_login["github"] = GITHUB_AUTH_URL
+ if ORCID_AUTH_URL and ORCID_CLIENT_ID != 'UNKNOWN':
+ external_login["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 +682,7 @@ 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 +691,6 @@ 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 +721,6 @@ 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 +748,16 @@ 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 +824,18 @@ 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 +906,21 @@ 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()
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 17a2d762..a65924d8 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -123,7 +123,7 @@ def handle_bad_request(e):
@app.route("/")
def index_page():
logger.info("Sending index_page")
- logger.error(request.url)
+ logger.info(request.url)
params = request.args
if 'import_collections' in params:
import_collections = params['import_collections']
@@ -141,7 +141,7 @@ def index_page():
def tmp_page(img_path):
logger.info("In tmp_page")
logger.info("img_path:", img_path)
- logger.error(request.url)
+ logger.info(request.url)
initial_start_vars = request.form
logger.info("initial_start_vars:", initial_start_vars)
imgfile = open(GENERATED_IMAGE_DIR + img_path, 'rb')
@@ -174,7 +174,7 @@ def twitter(filename):
@app.route("/search", methods=('GET',))
def search_page():
logger.info("in search_page")
- logger.error(request.url)
+ logger.info(request.url)
if 'info_database' in request.args:
logger.info("Going to sharing_info_page")
template_vars = sharing_info_page()
@@ -199,21 +199,22 @@ def search_page():
logger.info("request.args is", request.args)
the_search = search_results.SearchResultPage(request.args)
result = the_search.__dict__
+ valid_search = result['search_term_exists']
logger.debugf("result", result)
- if USE_REDIS:
+ if USE_REDIS and valid_search:
Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL))
Redis.expire(key, 60*60)
- if result['search_term_exists']:
+ if valid_search:
return render_template("search_result_page.html", **result)
else:
return render_template("search_error.html")
@app.route("/gsearch", methods=('GET',))
def gsearchact():
- logger.error(request.url)
+ logger.info(request.url)
result = gsearch.GSearch(request.args).__dict__
type = request.args['type']
if type == "gene":
@@ -224,7 +225,7 @@ def gsearchact():
@app.route("/gsearch_updating", methods=('POST',))
def gsearch_updating():
logger.info("REQUEST ARGS:", request.values)
- logger.error(request.url)
+ logger.info(request.url)
result = update_search_results.GSearch(request.args).__dict__
return result['results']
# type = request.args['type']
@@ -235,31 +236,31 @@ def gsearch_updating():
@app.route("/docedit")
def docedit():
- logger.error(request.url)
+ logger.info(request.url)
doc = docs.Docs(request.args['entry'])
return render_template("docedit.html", **doc.__dict__)
@app.route('/generated/<filename>')
def generated_file(filename):
- logger.error(request.url)
+ logger.info(request.url)
return send_from_directory(GENERATED_IMAGE_DIR,filename)
@app.route("/help")
def help():
- logger.error(request.url)
+ logger.info(request.url)
doc = docs.Docs("help")
return render_template("docs.html", **doc.__dict__)
@app.route("/wgcna_setup", methods=('POST',))
def wcgna_setup():
logger.info("In wgcna, request.form is:", request.form) # We are going to get additional user input for the analysis
- logger.error(request.url)
+ logger.info(request.url)
return render_template("wgcna_setup.html", **request.form) # Display them using the template
@app.route("/wgcna_results", methods=('POST',))
def wcgna_results():
logger.info("In wgcna, request.form is:", request.form)
- logger.error(request.url)
+ logger.info(request.url)
wgcna = wgcna_analysis.WGCNA() # Start R, load the package and pointers and create the analysis
wgcnaA = wgcna.run_analysis(request.form) # Start the analysis, a wgcnaA object should be a separate long running thread
result = wgcna.process_results(wgcnaA) # After the analysis is finished store the result
@@ -268,13 +269,13 @@ def wcgna_results():
@app.route("/ctl_setup", methods=('POST',))
def ctl_setup():
logger.info("In ctl, request.form is:", request.form) # We are going to get additional user input for the analysis
- logger.error(request.url)
+ logger.info(request.url)
return render_template("ctl_setup.html", **request.form) # Display them using the template
@app.route("/ctl_results", methods=('POST',))
def ctl_results():
logger.info("In ctl, request.form is:", request.form)
- logger.error(request.url)
+ logger.info(request.url)
ctl = ctl_analysis.CTL() # Start R, load the package and pointers and create the analysis
ctlA = ctl.run_analysis(request.form) # Start the analysis, a ctlA object should be a separate long running thread
result = ctl.process_results(ctlA) # After the analysis is finished store the result
@@ -313,13 +314,13 @@ def environments():
@app.route("/submit_trait")
def submit_trait_form():
- logger.error(request.url)
+ logger.info(request.url)
species_and_groups = get_species_groups()
return render_template("submit_trait.html", **{'species_and_groups' : species_and_groups, 'gn_server_url' : GN_SERVER_URL, 'version' : GN_VERSION})
@app.route("/create_temp_trait", methods=('POST',))
def create_temp_trait():
- logger.error(request.url)
+ logger.info(request.url)
print("REQUEST.FORM:", request.form)
#template_vars = submit_trait.SubmitTrait(request.form)
@@ -332,7 +333,7 @@ def export_trait_excel():
"""Excel file consisting of the sample data from the trait data and analysis page"""
logger.info("In export_trait_excel")
logger.info("request.form:", request.form)
- logger.error(request.url)
+ logger.info(request.url)
sample_data = export_trait_data.export_sample_table(request.form)
logger.info("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data)))
@@ -358,7 +359,7 @@ def export_trait_csv():
"""CSV file consisting of the sample data from the trait data and analysis page"""
logger.info("In export_trait_csv")
logger.info("request.form:", request.form)
- logger.error(request.url)
+ logger.info(request.url)
sample_data = export_trait_data.export_sample_table(request.form)
logger.info("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data)))
@@ -379,7 +380,7 @@ def export_traits_csv():
"""CSV file consisting of the traits from the search result page"""
logger.info("In export_traits_csv")
logger.info("request.form:", request.form)
- logger.error(request.url)
+ logger.info(request.url)
csv_data = export_traits.export_search_results_csv(request.form)
return Response(csv_data,
@@ -389,7 +390,7 @@ def export_traits_csv():
@app.route('/export_perm_data', methods=('POST',))
def export_perm_data():
"""CSV file consisting of the permutation data for the mapping results"""
- logger.error(request.url)
+ logger.info(request.url)
num_perm = float(request.form['num_perm'])
perm_data = json.loads(request.form['perm_results'])
@@ -412,7 +413,7 @@ def export_perm_data():
@app.route("/show_temp_trait", methods=('POST',))
def show_temp_trait_page():
- logger.error(request.url)
+ logger.info(request.url)
template_vars = show_trait.ShowTrait(request.form)
#logger.info("js_data before dump:", template_vars.js_data)
template_vars.js_data = json.dumps(template_vars.js_data,
@@ -427,7 +428,7 @@ def show_temp_trait_page():
@app.route("/show_trait")
def show_trait_page():
- logger.error(request.url)
+ logger.info(request.url)
template_vars = show_trait.ShowTrait(request.args)
#logger.info("js_data before dump:", template_vars.js_data)
template_vars.js_data = json.dumps(template_vars.js_data,
@@ -443,7 +444,7 @@ def show_trait_page():
@app.route("/heatmap", methods=('POST',))
def heatmap_page():
logger.info("In heatmap, request.form is:", pf(request.form))
- logger.error(request.url)
+ logger.info(request.url)
start_vars = request.form
temp_uuid = uuid.uuid4()
@@ -493,7 +494,7 @@ def mapping_results_container_page():
@app.route("/loading", methods=('POST',))
def loading_page():
- logger.error(request.url)
+ logger.info(request.url)
initial_start_vars = request.form
logger.debug("Marker regression called with initial_start_vars:", initial_start_vars.items())
#temp_uuid = initial_start_vars['temp_uuid']
@@ -552,7 +553,7 @@ def loading_page():
def marker_regression_page():
initial_start_vars = request.form
logger.debug("Marker regression called with initial_start_vars:", initial_start_vars.items())
- logger.error(request.url)
+ logger.info(request.url)
temp_uuid = initial_start_vars['temp_uuid']
wanted = (
'trait_id',
@@ -678,7 +679,7 @@ def marker_regression_page():
@app.route("/export_mapping_results", methods = ('POST',))
def export_mapping_results():
logger.info("request.form:", request.form)
- logger.error(request.url)
+ logger.info(request.url)
file_path = request.form.get("results_path")
results_csv = open(file_path, "r").read()
response = Response(results_csv,
@@ -691,7 +692,7 @@ def export_mapping_results():
@app.route("/export", methods = ('POST',))
def export():
logger.info("request.form:", request.form)
- logger.error(request.url)
+ logger.info(request.url)
svg_xml = request.form.get("data", "Invalid data")
filename = request.form.get("filename", "manhattan_plot_snp")
response = Response(svg_xml, mimetype="image/svg+xml")
@@ -702,7 +703,7 @@ def export():
def export_pdf():
import cairosvg
logger.info("request.form:", request.form)
- logger.error(request.url)
+ logger.info(request.url)
svg_xml = request.form.get("data", "Invalid data")
logger.info("svg_xml:", svg_xml)
filename = request.form.get("filename", "interval_map_pdf")
@@ -715,7 +716,7 @@ def export_pdf():
@app.route("/network_graph", methods=('POST',))
def network_graph_page():
logger.info("In network_graph, request.form is:", pf(request.form))
- logger.error(request.url)
+ logger.info(request.url)
start_vars = request.form
traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
if traits[0] != "":
@@ -731,7 +732,7 @@ def network_graph_page():
@app.route("/corr_compute", methods=('POST',))
def corr_compute_page():
logger.info("In corr_compute, request.form is:", pf(request.form))
- logger.error(request.url)
+ logger.info(request.url)
#fd = webqtlFormData.webqtlFormData(request.form)
template_vars = show_corr_results.CorrelationResults(request.form)
return render_template("correlation_page.html", **template_vars.__dict__)
@@ -739,7 +740,7 @@ def corr_compute_page():
@app.route("/corr_matrix", methods=('POST',))
def corr_matrix_page():
logger.info("In corr_matrix, request.form is:", pf(request.form))
- logger.error(request.url)
+ logger.info(request.url)
start_vars = request.form
traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
@@ -755,7 +756,7 @@ def corr_matrix_page():
@app.route("/corr_scatter_plot")
def corr_scatter_plot_page():
- logger.error(request.url)
+ logger.info(request.url)
template_vars = corr_scatter_plot.CorrScatterPlot(request.args)
template_vars.js_data = json.dumps(template_vars.js_data,
default=json_default_handler,
@@ -764,7 +765,7 @@ def corr_scatter_plot_page():
@app.route("/submit_bnw", methods=('POST',))
def submit_bnw():
- logger.error(request.url)
+ logger.info(request.url)
template_vars = get_bnw_input(request.form)
return render_template("empty_collection.html", **{'tool':'Correlation Matrix'})
@@ -772,7 +773,7 @@ def submit_bnw():
def sharing_info_page():
"""Info page displayed when the user clicks the "Info" button next to the dataset selection"""
logger.info("In sharing_info_page")
- logger.error(request.url)
+ logger.info(request.url)
fd = webqtlFormData.webqtlFormData(request.args)
template_vars = SharingInfoPage.SharingInfoPage(fd)
return template_vars
@@ -780,7 +781,7 @@ def sharing_info_page():
# Take this out or secure it before putting into production
@app.route("/get_temp_data")
def get_temp_data():
- logger.error(request.url)
+ logger.info(request.url)
temp_uuid = request.args['key']
return flask.jsonify(temp_data.TempData(temp_uuid).get_all())