python3
cpanse opened this issue · comments
- replace suds with zeep
https://github.com/mvantellingen/python-zeep
cp@fgcz-113:~/bin > diff bfabric-suds.py bfabric-zeep.py
1c1
< #!/usr/bin/env python2.7
---
> #!/usr/bin/env python3
32,33c32
< from suds.client import Client
< from suds.client import WebFault
---
> from zeep import Client
44,48d42
< # fixes bfabric8 wsdl problems
< import httplib
< httplib.HTTPConnection._http_vsn = 10
< httplib.HTTPConnection._http_vsn_str = 'HTTP/1.0'
<
135,136c129
< except WebFault, e:
< print (e)
---
> except:
166a160
>
172c166
< print ("{}\t{}\t{}\t{}".format(x._id, x.createdby, x.modified, x.name))
---
> print ("{}\t{}\t{}\t{}".format(x.id, x.createdby, x.modified, x.name))
cp@fgcz-113:~/bin >
cp@fgcz-113:~/bin > cat bfabric-*.py
#!/usr/bin/env python2.7
# -*- coding: latin1 -*-
"""
B-Fabric Appliaction Interface using WSDL
The code contains classes for wrapper_creator and submitter.
Ensure that this file is available on the bfabric exec host.
Copyright (C) 2014, 2015, 2016, 2017 Functional Genomics Center Zurich ETHZ|UZH. All rights reserved.
Authors:
Marco Schmidt <marco.schmidt@fgcz.ethz.ch>
Christian Panse <cp@fgcz.ethz.ch>
Licensed under GPL version 3
$Id: bfabric.py 3000 2017-08-18 14:18:30Z cpanse $
$HeadURL: http://fgcz-svn.uzh.ch/repos/scripts/trunk/linux/bfabric/apps/python/bfabric/bfabric.py $
$Date: 2017-08-18 16:18:30 +0200 (Fri, 18 Aug 2017) $
$Revision: 3000 $
"""
import yaml
import sys
from pprint import pprint
try:
from suds.client import Client
from suds.client import WebFault
except:
raise
import hashlib
import os
import base64
import datetime
import re
import unittest
# fixes bfabric8 wsdl problems
import httplib
httplib.HTTPConnection._http_vsn = 10
httplib.HTTPConnection._http_vsn_str = 'HTTP/1.0'
class Bfabric(object):
"""
Implements read and save object methods for BFabric wsdl interface
"""
__version__ = "0.9.10"
verbose = False
bflogin = None
bfpassword = None
webbase = 'https://fgcz-bfabric.uzh.ch/bfabric'
bfabricrc = dict()
query_counter = 0
bfabricfilename = os.path.normpath("{0}/{1}"
.format(os.path.expanduser("~"), ".bfabricrc.py"))
def warning(self, msg):
sys.stderr.write("\033[93m{}\033[0m\n".format(msg))
def _read_bfabric(self):
if self.verbose:
print ("self.bfabricfilename='{}'".format(self.bfabricfilename))
if not os.path.isfile(self.bfabricfilename):
self.warning("could not find '.bfabricrc.py' file in home directory.")
return
try:
with open(self.bfabricfilename) as myfile:
for line in myfile:
if not re.match("^#", line):
A = line.strip().replace("\"", "").replace("'", "").partition('=')
if not A[0] in ['_PASSWD', '_LOGIN', '_WEBBASE']:
continue
if not A[0] in self.bfabricrc:
self.bfabricrc[A[0]] = A[2]
else:
self.warning("while reading {0}. '{1}' is already set."
.format(self.bfabricfilename, A[0]))
except:
raise
def __init__(self, login=None, password=None, webbase=None, externaljobid=None, bfabricrc=None, verbose=False):
if bfabricrc:
self.bfabricfilename = bfabricrc
self.verbose = verbose
self._read_bfabric()
if '_PASSWD' in self.bfabricrc.keys() and password is None:
password = self.bfabricrc['_PASSWD']
if '_LOGIN' in self.bfabricrc.keys() and login is None:
login = self.bfabricrc['_LOGIN']
if '_WEBBASE' in self.bfabricrc.keys() and webbase is None:
self.webbase = self.bfabricrc['_WEBBASE']
if not login is None:
self.bflogin = login
if not password is None:
self.bfpassword = password
if not webbase is None:
self.webbase = webbase
if not password or not login:
print ("login or password missing")
raise
if self.verbose:
pprint(self.bfabricrc)
def get_para(self):
return {'bflogin': self.bflogin, 'webbase': self.webbase}
def read_object(self, endpoint, obj):
"""
A generic methode which can connect to any endpoint, e.g., workunit, project,
externaljob, etc, and returns the object with the requested id.
obj is a python dictionary which contains all the attributes of the endpoint
for the "query".
"""
self.query_counter = self.query_counter + 1
QUERY = dict(login=self.bflogin, page='', password=self.bfpassword, query=obj)
try:
client = Client("".join((self.webbase, '/', endpoint, "?wsdl")))
except WebFault, e:
print (e)
raise
QUERYRES = getattr(client.service.read(QUERY), endpoint, None)
if self.verbose:
pprint (QUERYRES)
return QUERYRES
if __name__ == "__main__":
bfapp = Bfabric()
endpoints = ['access', 'annotation', 'application',
'attachement', 'comment', 'dataset', 'executable',
'externaljob', 'groupingvar', 'importresource', 'mail',
'parameter', 'project', 'resource', 'sample',
'storage', 'user', 'workunit', 'order', 'instrument']
query_obj = {}
print (len(sys.argv))
endpoint = sys.argv[1]
if len(sys.argv) == 4:
attribute = sys.argv[2]
name = sys.argv[3]
query_obj[attribute] = name
if endpoint in endpoints:
res = bfapp.read_object(endpoint=endpoint, obj=query_obj)
if len(res) == 1:
for i in res:
print (i)
try:
for x in res:
print ("{}\t{}\t{}\t{}".format(x._id, x.createdby, x.modified, x.name))
except:
print (res)
else:
raise "1st argument must be a valid endpoint."
#!/usr/bin/env python3
# -*- coding: latin1 -*-
"""
B-Fabric Appliaction Interface using WSDL
The code contains classes for wrapper_creator and submitter.
Ensure that this file is available on the bfabric exec host.
Copyright (C) 2014, 2015, 2016, 2017 Functional Genomics Center Zurich ETHZ|UZH. All rights reserved.
Authors:
Marco Schmidt <marco.schmidt@fgcz.ethz.ch>
Christian Panse <cp@fgcz.ethz.ch>
Licensed under GPL version 3
$Id: bfabric.py 3000 2017-08-18 14:18:30Z cpanse $
$HeadURL: http://fgcz-svn.uzh.ch/repos/scripts/trunk/linux/bfabric/apps/python/bfabric/bfabric.py $
$Date: 2017-08-18 16:18:30 +0200 (Fri, 18 Aug 2017) $
$Revision: 3000 $
"""
import yaml
import sys
from pprint import pprint
try:
from zeep import Client
except:
raise
import hashlib
import os
import base64
import datetime
import re
import unittest
class Bfabric(object):
"""
Implements read and save object methods for BFabric wsdl interface
"""
__version__ = "0.9.10"
verbose = False
bflogin = None
bfpassword = None
webbase = 'https://fgcz-bfabric.uzh.ch/bfabric'
bfabricrc = dict()
query_counter = 0
bfabricfilename = os.path.normpath("{0}/{1}"
.format(os.path.expanduser("~"), ".bfabricrc.py"))
def warning(self, msg):
sys.stderr.write("\033[93m{}\033[0m\n".format(msg))
def _read_bfabric(self):
if self.verbose:
print ("self.bfabricfilename='{}'".format(self.bfabricfilename))
if not os.path.isfile(self.bfabricfilename):
self.warning("could not find '.bfabricrc.py' file in home directory.")
return
try:
with open(self.bfabricfilename) as myfile:
for line in myfile:
if not re.match("^#", line):
A = line.strip().replace("\"", "").replace("'", "").partition('=')
if not A[0] in ['_PASSWD', '_LOGIN', '_WEBBASE']:
continue
if not A[0] in self.bfabricrc:
self.bfabricrc[A[0]] = A[2]
else:
self.warning("while reading {0}. '{1}' is already set."
.format(self.bfabricfilename, A[0]))
except:
raise
def __init__(self, login=None, password=None, webbase=None, externaljobid=None, bfabricrc=None, verbose=False):
if bfabricrc:
self.bfabricfilename = bfabricrc
self.verbose = verbose
self._read_bfabric()
if '_PASSWD' in self.bfabricrc.keys() and password is None:
password = self.bfabricrc['_PASSWD']
if '_LOGIN' in self.bfabricrc.keys() and login is None:
login = self.bfabricrc['_LOGIN']
if '_WEBBASE' in self.bfabricrc.keys() and webbase is None:
self.webbase = self.bfabricrc['_WEBBASE']
if not login is None:
self.bflogin = login
if not password is None:
self.bfpassword = password
if not webbase is None:
self.webbase = webbase
if not password or not login:
print ("login or password missing")
raise
if self.verbose:
pprint(self.bfabricrc)
def get_para(self):
return {'bflogin': self.bflogin, 'webbase': self.webbase}
def read_object(self, endpoint, obj):
"""
A generic methode which can connect to any endpoint, e.g., workunit, project,
externaljob, etc, and returns the object with the requested id.
obj is a python dictionary which contains all the attributes of the endpoint
for the "query".
"""
self.query_counter = self.query_counter + 1
QUERY = dict(login=self.bflogin, page='', password=self.bfpassword, query=obj)
try:
client = Client("".join((self.webbase, '/', endpoint, "?wsdl")))
except:
raise
QUERYRES = getattr(client.service.read(QUERY), endpoint, None)
if self.verbose:
pprint (QUERYRES)
return QUERYRES
if __name__ == "__main__":
bfapp = Bfabric()
endpoints = ['access', 'annotation', 'application',
'attachement', 'comment', 'dataset', 'executable',
'externaljob', 'groupingvar', 'importresource', 'mail',
'parameter', 'project', 'resource', 'sample',
'storage', 'user', 'workunit', 'order', 'instrument']
query_obj = {}
print (len(sys.argv))
endpoint = sys.argv[1]
if len(sys.argv) == 4:
attribute = sys.argv[2]
name = sys.argv[3]
query_obj[attribute] = name
if endpoint in endpoints:
res = bfapp.read_object(endpoint=endpoint, obj=query_obj)
if len(res) == 1:
for i in res:
print (i)
try:
for x in res:
print ("{}\t{}\t{}\t{}".format(x.id, x.createdby, x.modified, x.name))
except:
print (res)
else:
raise "1st argument must be a valid endpoint."
replacing suds with suds-py3