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Commit 2b98d982 authored by Aflitos, Saulo Alves's avatar Aflitos, Saulo Alves
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ssl and login separated

parent 4814150f
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.gitignore
View file @ 2b98d982
......@@ -31,3 +31,4 @@ config.keylen
config.secret
flask_sslify.py
templates/*.pem
README.md
View file @ 2b98d982
Introgression Viewer
Saulo Aflitos - 2013-2014
Saulo Aflitos - 2013-2015
sauloalves.aflitos@wur.nl
Cluster Bioinformatics
Plant Research International - PRI
......
behaviour.py
View file @ 2b98d982
......@@ -3,6 +3,7 @@ import sys
import io
import base64
import subprocess
import shutil
import ssl
from Crypto.PublicKey import RSA
......@@ -16,8 +17,9 @@ librepoints = [
IDEBUG = False
USE_SQL = True
MAX_CONTENT_LENGTH = 128*1024*1024
SSL_KEY_LENGTH = 2048
DEFAULT_SSL_KEY_SIZE = 2048
DEFAULT_SERVER_PORT = 10000
DEFAULT_SERVER_IP = '127.0.0.1'
print "IMPORTING FUNCTIONS"
sys.path.insert(0, os.path.dirname(os.path.abspath( __file__ )))
......@@ -59,6 +61,7 @@ else:
# return Response(content, mimetype=mimetype)
def add_default_users():
if not check_user_exists("admin"):
print "admin user does not exists. CREATING admin user with default password admin"
......@@ -74,31 +77,42 @@ def add_default_users():
raise
class encryption(object):
def __init__(self, data_folder):
self.data_folder = data_folder
self.keylen_file = os.path.join( data_folder, "config.keylen" )
if not os.path.exists( self.keylen_file ):
print "keylen file %s does not exists. CREATING with default %d" % ( self.keylen_file, 2048 )
open(self.keylen_file, 'w').write(str(2048))
class encryption(object):
def __init__(self, data_folder, config):
self.data_folder = data_folder
self.data_folder_bn = data_folder.replace('/','').replace('\\','').replace('.','').replace(' ','')
self.key_bn = os.path.join( data_folder, self.data_folder_bn )
self.RSA_KEY_SIZE = int(open(self.keylen_file , 'r' ).read())
self.RSA_KEY_SIZE = config['SSL_KEY_LENGTH']
print "RSA_KEY_SIZE", self.RSA_KEY_SIZE
self.rsa_private_key_file_name = 'rsa_%d_priv.pem' % self.RSA_KEY_SIZE
#self.rsa_private_key_file_name = os.path.join( "templates", 'rsa_%d_priv.pem' % self.RSA_KEY_SIZE )
self.rsa_public_key_file_name = os.path.join( "templates", 'rsa_%d_pub.pem' % self.RSA_KEY_SIZE )
self.rsa_private_key_file_name = '%s_rsa_%d_priv.pem' % (self.key_bn , self.RSA_KEY_SIZE)
self.rsa_public_key_file_name2 = '%s_rsa_%d_pub.pem' % (self.key_bn , self.RSA_KEY_SIZE)
self.rsa_public_key_file_name3 = os.path.join( dir_path , "templates", '%s_rsa_%d_pub.pem' % (self.data_folder_bn, self.RSA_KEY_SIZE) )
self.rsa_public_key_file_name = '%s_rsa_%d_pub.pem' % (self.data_folder_bn, self.RSA_KEY_SIZE)
if ( not os.path.exists( self.rsa_private_key_file_name ) ) or ( not os.path.exists( self.rsa_public_key_file_name ) ):
print "rsa private key file name ", self.rsa_private_key_file_name
print "rsa public key file name full", self.rsa_public_key_file_name2
print "rsa public key file name bkp ", self.rsa_public_key_file_name3
print "rsa public key file name temp", self.rsa_public_key_file_name
if ( not os.path.exists( self.rsa_private_key_file_name ) ) or ( not os.path.exists( self.rsa_public_key_file_name2 ) ):
print "one of the ssl keys is missing. deleting"
if ( os.path.exists( self.rsa_private_key_file_name ) ):
print "ssl key % exists. deleting" % self.rsa_private_key_file_name
os.remove(self.rsa_private_key_file_name)
if ( os.path.exists( self.rsa_public_key_file_name ) ):
os.remove(self.rsa_public_key_file_name)
if ( os.path.exists( self.rsa_public_key_file_name2 ) ):
print "ssl key % exists. deleting" % self.rsa_public_key_file_name2
os.remove(self.rsa_public_key_file_name2)
if ( os.path.exists( self.rsa_public_key_file_name3 ) ):
print "ssl key % exists. deleting" % self.rsa_public_key_file_name3
os.remove(self.rsa_public_key_file_name3)
print "PUBLIC KEY %s OR PRIVATE KEY %s DOES NOT EXISTS. CREATING" % (self.rsa_private_key_file_name, self.rsa_public_key_file_name)
print "PUBLIC KEY %s OR PRIVATE KEY %s DOES NOT EXISTS. CREATING" % (self.rsa_private_key_file_name, self.rsa_public_key_file_name2)
#(pubkey, privkey) = rsa.newkeys(RSA_KEY_SIZE, accurate=True, poolsize=1)
#open(rsa_public_key_file_name , 'w').write( pubkey.save_pkcs1() )
#open(rsa_private_key_file_name, 'w').write( privkey.save_pkcs1() )
......@@ -107,14 +121,22 @@ class encryption(object):
self.privkey = RSA.generate(self.RSA_KEY_SIZE)
self.pubkey = self.privkey.publickey()
open(self.rsa_public_key_file_name , 'w').write( self.pubkey.exportKey('PEM') )
open(self.rsa_public_key_file_name2, 'w').write( self.pubkey.exportKey( 'PEM') )
open(self.rsa_private_key_file_name, 'w').write( self.privkey.exportKey('PEM') )
print "saved public and private keys"
if os.path.exists(self.rsa_public_key_file_name3):
print "temporary rsa pub key %s exists. deleting" % ( self.rsa_public_key_file_name3 )
os.remove(self.rsa_public_key_file_name3)
shutil.copy2(self.rsa_public_key_file_name2, self.rsa_public_key_file_name3)
self.rsa_private_key = RSA.importKey(open(self.rsa_private_key_file_name, 'r').read())
self.rsa_public_key = RSA.importKey(open(self.rsa_public_key_file_name , 'r').read())
self.rsa_public_key = RSA.importKey(open(self.rsa_public_key_file_name2, 'r').read())
self.enc_cipher = PKCS1_v1_5.new(self.rsa_public_key )
self.dec_cipher = PKCS1_v1_5.new(self.rsa_private_key)
......@@ -161,23 +183,45 @@ class encryption(object):
def create_self_signed_cert(cert_dir=".", cert_name="server"):
def create_self_signed_cert(cert_dir=".", cert_name="server", key_size=DEFAULT_SSL_KEY_SIZE):
print "generating self signed certificate"
C_F = os.path.join(os.path.abspath(cert_dir), cert_name + ".crt")
K_F = os.path.join(os.path.abspath(cert_dir), cert_name + ".key")
if not os.path.exists(C_F) or not os.path.exists(K_F):
print " certificates do not exists. creating"
cmdline = "openssl req -nodes -new -newkey rsa:%(key_length)d -x509 -batch -days 365 -extensions v3_req -keyout %(key_file)s -out %(cert_file)s" % {"key_length": SSL_KEY_LENGTH, "key_file": K_F, "cert_file": C_F }
cmdline = "openssl req -nodes -new -newkey rsa:%(key_length)d -x509 -batch -days 365 -extensions v3_req -keyout %(key_file)s -out %(cert_file)s" % {"key_length": key_size, "key_file": K_F, "cert_file": C_F }
print " running:", cmdline
os.system(cmdline)
else:
print " certificates exists. skipping"
return (C_F, K_F)
##VARIABLES
#hasLogin = False
#SERVER_PORT = 10000
#librepaths = [
# '/api',
# '/favicon.ico'
#]
#DEBUG = True
#USE_SSL = False
#
#MAX_NUMBER_OF_COLUMNS = 300
#MAX_CONTENT_LENGTH = 128 * 1024 * 1024
#USE_SQL = True
#INFOLDER = None
#
#
#SECRET_KEY = None
#USER_DATABASE_FILE = None
#SECRET_FILE = None
#ENCRYPTION_INST = None
def load_config( args ):
if len(args) == 0:
print "no config file or command given"
......@@ -185,7 +229,10 @@ def load_config( args ):
variables = {
'HAS_LOGIN' : False,
'SERVER_PORT' : 10000,
'USE_SSL' : False,
'SSL_KEY_LENGTH' : DEFAULT_SSL_KEY_SIZE,
'SERVER_PORT' : DEFAULT_SERVER_PORT,
'SERVER_IP' : DEFAULT_SERVER_IP,
'DEBUG' : True,
......@@ -195,35 +242,9 @@ def load_config( args ):
'/api',
'/favicon.ico'
],
'IDEBUG' : IDEBUG,
'getManager' : getManager,
'INTERFACE' : interface
}
##VARIABLES
#hasLogin = False
#SERVER_PORT = 10000
#librepaths = [
# '/api',
# '/favicon.ico'
#]
#DEBUG = True
#USE_SSL = False
#
#MAX_NUMBER_OF_COLUMNS = 300
#MAX_CONTENT_LENGTH = 128 * 1024 * 1024
#USE_SQL = True
#INFOLDER = None
#
#
#SECRET_KEY = None
#USER_DATABASE_FILE = None
#SECRET_FILE = None
#ENCRYPTION_INST = None
INFOLDER = os.path.abspath( args[0] )
if not os.path.exists( INFOLDER ):
print "data folder %s does not exists" % INFOLDER
......@@ -242,7 +263,7 @@ def load_config( args ):
secret = os.urandom(24)
open(SECRET_FILE, 'wb').write(secret)
SECRET_KEY = open(SECRET_FILE , 'rb').read().strip()
SECRET_KEY = open(SECRET_FILE , 'rb').read().strip()
print "SECRET KEY ", repr(SECRET_KEY)
variables['SECRET_FILE'] = SECRET_FILE
variables['SECRET_KEY' ] = SECRET_KEY
......@@ -251,8 +272,10 @@ def load_config( args ):
config_file = os.path.join( INFOLDER, 'config.py' )
if not os.path.exists( config_file ):
print "config file %s does not exists" % config_file
sys.exit( 1 )
print "config file %s does not exists. COPYING DEFAULT" % config_file
config_template = os.path.join(dir_path, 'config.template')
shutil.copy2(config_template, config_file)
print "loading config", config_file
lcl = {}
......@@ -265,6 +288,10 @@ def load_config( args ):
variables['IDEBUG' ] = IDEBUG
variables['getManager'] = getManager
variables['INTERFACE' ] = interface
app.before_first_request(init_db)
app.secret_key = variables['SECRET_KEY']
......@@ -281,9 +308,10 @@ def load_config( args ):
if variables['HAS_LOGIN']:
print "LOGIN ENABLED"
print "INITIALIZING DB"
USER_DATABASE_FILE = os.path.join( INFOLDER, 'users.sqlite' )
variables['USER_DATABASE_FILE'] = USER_DATABASE_FILE
variables[ 'USER_DATABASE_FILE' ] = USER_DATABASE_FILE
app.config['DATABASE_FILE' ] = USER_DATABASE_FILE
app.config['SQLALCHEMY_DATABASE_URI'] = 'sqlite:///' + app.config['DATABASE_FILE']
app.config['SQLALCHEMY_ECHO' ] = False
......@@ -294,34 +322,37 @@ def load_config( args ):
print "INITIALIZING ENCRYPTION"
app.config["ENCRYPTION_INST"] = encryption( INFOLDER )
print "INITIALIZING ENCRYPTION"
app.config["ENCRYPTION_INST"] = encryption( INFOLDER, app.config )
print "ENCRYPTION KEY SIZE", app.config["ENCRYPTION_INST"].RSA_KEY_SIZE
#jsonpickle.set_preferred_backend('simplejson')
#jsonpickle.set_encoder_options('simplejson', ensure_ascii=True, sort_keys=True, indent=1)
print "ENCRYPTION KEY SIZE", app.config["ENCRYPTION_INST"].RSA_KEY_SIZE
#jsonpickle.set_preferred_backend('simplejson')
#jsonpickle.set_encoder_options('simplejson', ensure_ascii=True, sort_keys=True, indent=1)
app.jinja_env.globals['encbitsize' ] = str( app.config["ENCRYPTION_INST"].RSA_KEY_SIZE )
app.jinja_env.globals['encbitsize' ] = str( app.config["ENCRYPTION_INST"].RSA_KEY_SIZE )
app.jinja_env.globals['rsa_public_key_file_name'] = str( app.config["ENCRYPTION_INST"].rsa_public_key_file_name )
#http://stackoverflow.com/questions/9767585/insert-static-files-literally-into-jinja-templates-without-parsing-them
def include_file(name):
return Markup(app.jinja_loader.get_source(app.jinja_env, name)[0])
#http://stackoverflow.com/questions/9767585/insert-static-files-literally-into-jinja-templates-without-parsing-them
def include_file(name):
return Markup(app.jinja_loader.get_source(app.jinja_env, name)[0])
def include_file_multiline(name):
lines = app.jinja_loader.get_source(app.jinja_env, name)[0]
#lines.replace("RSA PUBLIC KEY", "PUBLIC KEY")
lines = lines.split("\n")
lines = [ "'" + l + "\\n' +" for l in lines ]
lines[-1] = lines[-1].strip(" +")
return Markup("\n".join( lines ))
def include_file_multiline(name):
lines = app.jinja_loader.get_source(app.jinja_env, name)[0]
#lines.replace("RSA PUBLIC KEY", "PUBLIC KEY")
lines = lines.split("\n")
lines = [ "'" + l + "\\n' +" for l in lines ]
lines[-1] = lines[-1].strip(" +")
return Markup("\n".join( lines ))
app.jinja_env.globals['include_file' ] = include_file
app.jinja_env.globals['include_file_multiline'] = include_file_multiline
app.jinja_env.globals['include_file' ] = include_file
app.jinja_env.globals['include_file_multiline'] = include_file_multiline
if variables['USE_SSL']:
print "INITIALIZING SSL"
ssl_cert, ssl_key = create_self_signed_cert(cert_dir=dir_path, cert_name="server")
ssl_cert, ssl_key = create_self_signed_cert(cert_dir=INFOLDER, cert_name=app.config["ENCRYPTION_INST"].key_bn, key_size=app.config["ENCRYPTION_INST"].RSA_KEY_SIZE)
app.config["SSL_CERT" ] = ssl_cert
app.config["SSL_KEY" ] = ssl_key
......@@ -362,7 +393,7 @@ def run_action(args):
if ( action not in ("init") ) and ( not app.config['HAS_LOGIN'] ):
print "no login, no add/gen user"
print "login not enabled, therefore, no possible to add/gen/list user"
sys.exit(1)
......@@ -486,4 +517,3 @@ def run_action(args):
# open(C_F, "wt").write(crypto.dump_certificate(crypto.FILETYPE_PEM, cert))
# open(K_F, "wt").write(crypto.dump_privatekey( crypto.FILETYPE_PEM, k ))
# return (C_F, K_F)
config.template
View file @ 2b98d982
#decide whether to have user control or not
HAS_LOGIN = False
#decide whether to have ssl or not
USE_SSL = False
SSL_KEY_LENGTH = 2048
#define port to server webpage
SERVER_PORT = 10000
SERVER_PORT = 10000
#defined ip to serve. 127.0.0.1 for local computer, 0.0.0.0 for any computer
SERVER_IP = '127.0.0.1'
# pages which can be seen without login
LIBRE_PATHS = [
......
ibrowser.py
View file @ 2b98d982
......@@ -36,14 +36,37 @@ def init( args ):
load_config( args )
def start():
if app.config['HAS_LOGIN']:
print "SSL ENABLED: access by https://127.0.0.1:%d" % app.config["SERVER_PORT" ]
proto = 'http'
if app.config['USE_SSL']:
proto = 'https'
URL = "%s://%s:%d" % ( proto, app.config["SERVER_IP" ], app.config["SERVER_PORT" ] )
cfg = {
'port': app.config["SERVER_PORT"],
'host': app.config["SERVER_IP" ]
}
app.run(port=app.config["SERVER_PORT" ], host='0.0.0.0', ssl_context=(app.config["SSL_CERT"], app.config["SSL_KEY"]))
if app.config['USE_SSL']:
cfg['ssl_context'] = (app.config["SSL_CERT"], app.config["SSL_KEY"])
#app.run(port=app.config["SERVER_PORT" ], host='0.0.0.0', ssl_context=app.config["SSL_CONTEXT"])
if app.config['HAS_LOGIN']:
print 'USING LOGIN',
else:
print "SSL DISABLED: access by http://127.0.0.1:%d" % app.config["SERVER_PORT" ]
app.run(port=app.config["SERVER_PORT" ], host='0.0.0.0')
print 'NOT USING LOGIN',
if app.config['USE_SSL']:
print ": USING SSL ::",
else:
print ": NOT USING SSL ::",
print "ACCESS AT %s" % URL
app.run(**cfg)
if __name__ == '__main__':
......@@ -57,8 +80,10 @@ if __name__ == '__main__':
add_default_users()
load_database()
start()
else:
load_database()
application = app
routes.py
View file @ 2b98d982
......@@ -1275,8 +1275,7 @@ def init_db():
"""
If no database defined in config.py. quit
"""
print 'no databases given. please edit config.py'
sys.exit(1)
print '!!!!!!!!! NO DATABASES GIVEN. PLEASE ADD DATABASES !!!!!!!!!'
else:
with app.app_context():
......
run.bat
View file @ 2b98d982
python vcf_walk_server.py walk_out
python ibrowser.py data/
static/index.html
View file @ 2b98d982
......@@ -238,11 +238,9 @@
<a href="https://www.linkedin.com/in/sauloaflitos" title="LinkedIn Profile"><img src="static/images/LinkedIn_Logo60px.png" alt="LinkedIn Profile" class="srcicon"></a>
<a href="http://www.ab.wur.nl/ab/" title="Applied Bioinformatics">AB</a>
<a href="http://www.ab.wur.nl/ab/" title="Applied Bioinformatics">Applied Bioinformatics</a>
<a href="http://www.wageningenur.nl/en.htm" title="Wageningen University"><img src="static/images/wur.png" alt="Wageningen University" class="srcicon"></a>
2012-2014
</b>
<i class="glyphicon glyphicon-question-sign" title="Help" data-ng-click="showHelp()"></i>
......
templates/crypto.html
View file @ 2b98d982
......@@ -16,12 +16,12 @@
<script type="text/javascript">
var encbitsize = {{ encbitsize }};
var encrypter = new JSEncrypt(default_key_size=encbitsize);
var pubkey = {{ include_file_multiline('rsa_'+encbitsize+'_pub.pem') }};
encrypter.setPublicKey( pubkey );
var encrypted = encrypter.encrypt( "test" );
console.log( "encrypted ", encrypted );
var encbitsize = {{ encbitsize }};
var pubkey = {{ include_file_multiline(rsa_public_key_file_name) }};
var encrypter = new JSEncrypt(default_key_size=encbitsize);
encrypter.setPublicKey( pubkey );
var encrypted = encrypter.encrypt( "test" );
console.log( "encrypted ", encrypted );
</script>
<!--{- include 'decrypto.html' -}-->
templates/login.html
View file @ 2b98d982
......@@ -41,11 +41,9 @@
<a href="https://www.linkedin.com/in/sauloaflitos" title="LinkedIn Profile" target="_blank">LinkedIn profile</a> //
<a href="http://www.ab.wur.nl/ab/" title="Applied Bioinformatics" target="_blank">Aplied Bioinformatics</a> //
<a href="http://www.ab.wur.nl/ab/" title="Applied Bioinformatics" target="_blank">Applied Bioinformatics</a> //
<a href="http://www.wageningenur.nl/en.htm" title="Wageningen University" target="_blank">Wageningen University</a>
2012-2014
</b>
</div>
</body>
......
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