def main():
endpoint = None
ver = -99
mol = None
vtype = None
background = None
refname = None
refver = None
try:
opts, args = getopt.getopt(
sys.argv[1:], 'e:f:v:h',
['type=', 'background', 'refname=', 'refver='])
except getopt.GetoptError:
writeError('Error. Arguments not recognized')
usage()
sys.exit(1)
if args:
writeError('Error. Arguments not recognized')
usage()
sys.exit(1)
if len(opts) > 0:
for opt, arg in opts:
if opt in '-e':
endpoint = arg
elif opt in '-f':
mol = arg
elif opt in '-v':
if 'last' in arg:
ver = -1
else:
try:
ver = int(arg)
except ValueError:
ver = -99
elif opt in '-h':
usage()
sys.exit(0)
elif opt in '--type':
vtype = arg
elif opt in '--background':
background = True
elif opt in '--refname':
refname = arg
elif opt in '--refver':
try:
refver = int(arg)
except:
refver = 0
if not mol and ver == -99:
usage()
sys.exit(1)
if not endpoint:
usage()
sys.exit(1)
if vtype not in [None, 'pca', 'property', 'project', 'model']:
print '+', property, '+'
usage()
sys.exit(1)
if vtype == 'project' and (refname == None and mol == None):
print 'project view type requires to define the reference endpoint name'
usage()
sys.exit(1)
if vtype == 'project' and refver == None:
refver = 0
## print vtype, background, refname, refver
result = view(endpoint, mol, ver, vtype, background, refname, refver)
presentResults(result)
def main ():
endpoint = None
ver = -99
loc = -99
api = 0
mol = None
progress = False
detail = False
extvalid = False
try:
opts, args = getopt.getopt(sys.argv[1:], 'abcge:f:v:s:hqx')
except getopt.GetoptError:
writeError('Error. Arguments not recognized')
usage()
sys.exit(1)
if args:
writeError('Error. Arguments not recognized')
usage()
sys.exit(1)
if len( opts ) > 0:
for opt, arg in opts:
if opt in '-e':
endpoint = arg
elif opt in '-f':
mol = arg
elif opt in '-v':
if 'last' in arg:
ver = -1
else:
try:
ver = int(arg)
except ValueError:
ver = -99
elif opt in '-x': ### run external validation using embeeded activity values
extvalid = True
##################################################################
### Internal prediction calls
###
### modifier API use
### none 0 interactive, command mode use
### -a 1 web service v1 (deprecated)
### -b 2 web service v2
### -c 6 web service v3
### -s 3 local model (followed by local ID)
### -g 4 eTOX GUI
### -q 5 internal from hierarchical model
###
### Not for use in command mode. Do not document with -h !
###
##################################################################
elif opt in '-a': ### web service call. API v1 (deprecated)
api = 1
elif opt in '-b': ### web service call. API v2
api = 2
elif opt in '-c': ### web service call. API v3
api = 6
elif opt in '-s': ### call for local models (like HERG4)
api = 3
loc = int(arg)
elif opt in '-g': ### eTOXlab GUI calls
api = 4
elif opt in '-q': ### internal call from hierarchical models (like LQT)
api = 5
elif opt in '-h':
usage()
sys.exit(0)
if ver == -99:
if api in (1,2,5): # web services API v1 and v2 or hierarchical models do not define versions
pass
else:
usage()
sys.exit (1)
if api in (1,2,3,4,5,6):
sys.path.append ('/opt/RDKit/')
sys.path.append ('/opt/standardiser/standardise20140206/')
if api in (2,6):
progress = True
if not mol:
if api==0: # for interactive use the definition of mol is compulsory
usage()
sys.exit (1)
else: # for non-interactive calls, input_file.sdf is the default
mol = './input_file.sdf'
if not endpoint:
usage()
sys.exit (1)
# make sure imodel has not been copied to eTOXlab/src. If this were true, this version will
# be used, instead of those on the versions folder producing hard to track errors and severe
# misfunction
testimodel()
result=predict (endpoint,mol,ver,api,loc,
detail, progress, extvalid)
presentPrediction (result, api)
sys.exit(0)
def reportError(e):
try:
writeError(e)
waterLogClient.addSystemEvent(waterLogClient.ERROR_SYSTEM_EVENT)
except:
pass