def exec_before_job( app, inp_data, out_data, param_dict, tool=None):
"""Build a temp file with errors in it"""
errors = []
for name, data in inp_data.items():
validation_errors = data.validation_errors
for error in validation_errors:
# build dummy class
try:
temp = eval(error.err_type)()
except:
temp = object()
# stuff attributes
temp.__dict__ = util.string_to_object( error.attributes )
errors.append(temp)
# There *should* only be 1 input, so we assume there is and continue
# base64 pickel
errors_str = util.object_to_string( errors )
# write
database_tmp = "./database/tmp" # globaly visible path
error_file = tempfile.NamedTemporaryFile(mode="w", dir=database_tmp, suffix=".b64")
error_file_name = error_file.name
error_file.close()
error_file = open(error_file_name, "w")
error_file.write(errors_str)
error_file.close()
param_dict["errorsfile"] = error_file_name
def index(self, trans, init=False, **kwd):
base_url = None
params = dict(kwd)
try:
store = params.get("__GALAXY__", None)
if store:
store = json.loads(util.string_to_object(store))
else:
store = {}
UCSC_URL = 'UCSC_URL'
base_url = store.get(UCSC_URL,
"http://genome.ucsc.edu/cgi-bin/hgTables?")
params = dict(kwd)
params['init'] = init
if not init:
for key, value in kwd.items():
store[key] = value
try:
del store["__GALAXY__"]
except:
pass
else:
store = {}
if init == "1":
base_url = "http://genome.ucsc.edu/cgi-bin/hgTables?"
params['db'] = 'hg17'
if init == "2":
base_url = "http://genome-test.cse.ucsc.edu/cgi-bin/hgTables?"
params['db'] = 'hg17'
if init == "3":
base_url = "http://archaea.ucsc.edu/cgi-bin/hgTables?"
store[UCSC_URL] = base_url
try:
del params["__GALAXY__"]
except:
pass
url = base_url + urllib.urlencode(params)
page = urllib.urlopen(url)
content = page.info().get('Content-type', '')
except Exception, exc:
trans.log_event("Proxy Error -> %s" % str(exc))
msg = 'There has been a problem connecting to <i>%s</i> <p> <b>%s<b>' % (
base_url, exc)
return msg
def index(self, trans, init=False, **kwd):
base_url = None
params = dict(kwd)
try:
store = params.get("__GALAXY__", None)
if store:
store = json.loads(util.string_to_object(store))
else:
store = {}
UCSC_URL = 'UCSC_URL'
base_url = store.get(UCSC_URL, "http://genome.ucsc.edu/cgi-bin/hgTables?")
params = dict(kwd)
params['init'] = init
if not init:
for key, value in kwd.items():
store[key] = value
try:
del store["__GALAXY__"]
except:
pass
else:
store = {}
if init == "1":
base_url = "http://genome.ucsc.edu/cgi-bin/hgTables?"
params['db'] = 'hg17'
if init == "2":
base_url = "http://genome-test.cse.ucsc.edu/cgi-bin/hgTables?"
params['db'] = 'hg17'
if init == "3":
base_url = "http://archaea.ucsc.edu/cgi-bin/hgTables?"
store[UCSC_URL] = base_url
try:
del params["__GALAXY__"]
except:
pass
url = base_url + urllib.urlencode(params)
page = urllib.urlopen(url)
content = page.info().get('Content-type', '')
except Exception, exc:
trans.log_event( "Proxy Error -> %s" % str(exc) )
msg = 'There has been a problem connecting to <i>%s</i> <p> <b>%s<b>' % (base_url, exc)
return msg
def main():
options, args = doc_optparse.parse( __doc__ )
try:
extension = options.ext
except:
doc_optparse.exception()
# create datatype
data = model.Dataset( extension=extension, id=int( args[0] ) )
data.file_path = "/home/ian/trunk/database/files/"
if options.metadata:
data.metadata = util.string_to_object( options.metadata )
errors = data.datatype.validate( data )
print util.object_to_string(errors)
def main():
options, args = doc_optparse.parse(__doc__)
methods = []
try:
if options.methods: methods = options.methods.split(",")
except:
pass
ext = options.ext
in_file = open(args[0], "r")
error_file = open(args[1], "r")
out_file = open(args[2], "w")
# string_to_object errors
error_list = util.string_to_object(error_file.read())
# index by error type and then by line number
error_lines = {}
error_types = {}
for error in error_list:
if error.linenum:
if error.linenum in error_lines:
error_lines[error.linenum].append(error)
else:
error_lines[error.linenum] = [error]
error_type = error.__class__.__name__
if error_type in error_types:
error_types[error_type].append(error)
else:
error_types[error_type] = [error]
linenum = 0
for line in in_file:
linenum += 1
# write unless
if "lines" in methods:
if linenum in error_lines:
line = None
# other processing here?
if line:
out_file.write(line)
def main():
options, args = doc_optparse.parse( __doc__ )
methods = []
try:
if options.methods: methods = options.methods.split(",")
except:
pass
ext = options.ext
in_file = open(args[0], "r")
error_file = open(args[1], "r")
out_file = open(args[2], "w")
# string_to_object errors
error_list = util.string_to_object(error_file.read())
# index by error type and then by line number
error_lines = {}
error_types = {}
for error in error_list:
if error.linenum:
if error.linenum in error_lines:
error_lines[error.linenum].append(error)
else:
error_lines[error.linenum] = [error]
error_type = error.__class__.__name__
if error_type in error_types:
error_types[error_type].append(error)
else:
error_types[error_type] = [error]
linenum = 0
for line in in_file:
linenum += 1
# write unless
if "lines" in methods:
if linenum in error_lines:
line = None
# other processing here?
if line:
out_file.write(line)
def __string_to_state(self, state_string):
encoded_state = string_to_object(state_string)
state = DefaultToolState()
state.decode(encoded_state, self.tool, self.app)
return state
def __string_to_state( self, state_string ):
encoded_state = string_to_object( state_string )
state = DefaultToolState()
state.decode( encoded_state, self.tool, self.app )
return state
