def main(argv):
# Setup logging
setup_log()
logging.debug('Hello!')
# Print usage
if len(argv) <= 1:
abort('USAGE: jm module [module args]')
# Parse the arguments
args = Args.Args(argv[1:])
parse_global_config(args.args)
# Load the module
module = args.margs[0]
job = JobBinary(module)
# Remove JM arguments when passing to the module
margv = args.margs
# Wrapper to include job module
def run_wrapper(argv):
return run(argv, job)
# Run the module
logging.info('Running module')
r = job.spits_main(margv, run_wrapper)
# Finalize
logging.debug('Bye!')
def main(argv):
# Print usage
if len(argv) <= 1:
abort('USAGE: jm module [module args]')
# Parse the arguments
args = Args.Args(argv[1:])
parse_global_config(args.args)
# Setup logging
setup_log()
logging.debug('Hello!')
# Enable memory debugging
if jm_memstat == 1:
memstat.enable()
memstat.stats()
# Load the module
module = args.margs[0]
job = JobBinary(module)
# Remove JM arguments when passing to the module
margv = args.margs
# Keep a run identifier
runid = [0]
# Wrapper to include job module
def run_wrapper(argv, jobinfo):
runid[0] = runid[0] + 1
return run(argv, jobinfo, job, runid[0])
# Wrapper for the heartbeat
finished = [False]
def heartbeat_wrapper():
heartbeat(finished)
# Start the heartbeat
threading.Thread(target=heartbeat_wrapper).start()
# Run the module
logging.info('Running module')
memstat.stats()
r = job.spits_main(margv, run_wrapper)
memstat.stats()
# Stop the heartbeat thread
finished[0] = True
# Kill the workers
if jm_killtms:
killtms()
# Print final memory report
memstat.stats()
# Finalize
logging.debug('Bye!')
def main(argv):
if len(argv) <= 1:
abort('USAGE: tm [args] module [module args]')
args = Args.Args(argv[1:])
parse_global_config(args.args)
setup_log()
logging.debug('Hello!')
App(args).run()
logging.debug('Bye!')
def main():
from Args import Args
print("OutcomeStats.main()")
# print(type(self.outcomeFormats()))
args = Args('occurrence_qc.json', 'outcomeStats.xlsx', 'stats.ini')
workbook = xlsxwriter.Workbook(args.getOutfile())
worksheet = workbook.add_worksheet()
origin1 = [0, 0]
origin2 = [5, 0]
stats = OutcomeStats(workbook, worksheet, args, origin1, origin2)
def _cli_callable_from_params(params: List[str] = None) -> callable:
args: Args = Args(params)
if args.version:
return api.version_method
if args.clear_log:
return api.clear_log_method
if args.dump_log:
return partial(api.dump_log_method, args.dump_log)
return lambda: None
def test_non_existing_dir_raises_argument_type_error(self, tmp_path_as_cwd):
with pytest.raises(SystemExit), pytest.raises(argparse.ArgumentTypeError), mock.patch('sys.stderr'):
params = ['--dump-log', 'non_existing_dir']
Args(params)
def test_args_dump_log_defaults_to_cwd(self):
cwd: Path = Path()
params = ['--dump-log']
assert Args(params).dump_log == cwd
def test_args_dump_log_is_not_none_when_dump_log_dir_in_args_list(self):
params = ['--dump-log', '.']
assert Args(params).dump_log is not None
def test_unrecognized_arguments_raises_system_exit(self):
with pytest.raises(SystemExit), mock.patch('sys.stderr'):
Args(['--foo'])
def test_args_param_property_is_true_when_param_in_args_list(self, params, param_property):
args: Any = Args(params)
assert param_property.getter(args)
def test_expected_params(self, params):
assert Args(params)
for f in os.listdir(kron_dir):
filename = os.fsdecode(f)
if filename.endswith(".txt"):
txt_files.append(filename)
elif filename.endswith(".dat"):
return utils.load_graph_list(os.path.join(kron_dir, filename))
G_list = []
for filename in txt_files:
G_list.append(
utils.snap_txt_output_to_nx(os.path.join(kron_dir, filename)))
return G_list
if __name__ == "__main__":
args = Args()
args_evaluate = Args_evaluate()
parser = argparse.ArgumentParser(description="Evaluation arguments.")
feature_parser = parser.add_mutually_exclusive_group(required=False)
feature_parser.add_argument("--export-real",
dest="export",
action="store_true")
feature_parser.add_argument("--no-export-real",
dest="export",
action="store_false")
feature_parser.add_argument(
"--kron-dir",
dest="kron_dir",
help="Directory where graphs generated by kronecker method is stored.",
)
tf = item[1]
dl = file[item[0]][1]
TF = ((k1 + 1) * tf) / (k1 * (0.25 + 0.75 * dl / avdl) + tf)
### Add into Rank List
if item[0] not in rank: rank[item[0]] = [0] * len(term)
rank[item[0]][indx] = float(DF * TF * QF)
### Add into Vect List
vect.append(time)
indx += 1
return vect, rank
args = Args.Args()
vocb = Parse.ParseVocb(args.m)
file, avdl = Parse.ParseFile(args.m, args.d)
invt = Parse.ParseInvt(args.m)
qury = Parse.ParseQury(args.i)
print("")
N = len(file)
text = "query_id,retrieved_docs\n"
for temp in qury:
accm = {}
### Consider label k
for k in range(1, 5):
def test_parse_global_config(self):
args = Args.Args(['--timeout=10'])
tm.parse_global_config(args.args)
self.assertEqual(tm.tm_timeout, 10)
def test_args(self):
args = Args.Args(['--timeout=10', 'module', 'arg1', 'arg2'])
self.assertIn('timeout', args.args)
self.assertEqual(args.args['timeout'], '10')
self.assertSequenceEqual(['module', 'arg1', 'arg2'], args.margs)
def test_args_version_is_false_when_version_is_not_in_args_list(self):
assert not Args([]).version
import xlsxwriter
#import OutcomeFormats
from OutcomeStats import *
from OutcomeFormats import *
from Args import *
import argparse
#import unittest
#parser = argparse.ArgumentParser()
#parser.add_argument('--i',default='occurrence_qc.json', help="Defaults to occurrence_qc.json if '--i' absent")
#parser.add_argument('--o',default='outcomeStats.xlsx', help="Defaults to outcomeStats.xlsx if '--o' absent")
#parser.add_argument('--c',default='stats.ini', help="Defaults to stats.ini if --c absent")
#args = parser.parse_args()
#outfile = args.o
#args = parser.parse_args()
args=Args('occurrence_qc.json', 'outcomeStats.xlsx', 'stats.ini')
#Supply your favorite JSON output of FP-Akka as input. Do python3 statstest.py --help for help
#tested against FP-Akka 1.5.2 JSON output with python3
if __name__=="__main__":
###################################################
############# First initialize resources ##########
###################################################
# set input jason file from FPAkka or elsewhere
# set output xlsx file
# set stats.ini configurations
args=Args('occurrence_qc.json', 'outcomeStats.xlsx', 'stats.ini')
#load entire jason file. (Note: syntactically it is a Dictionary !!! )
with open(args.getInfile()) as data_file:
fpAkkaOutput=json.load(data_file)
-xyz (if at least x,y have defaults)
abreviations allowed (arguments = 'name', 'territorial') (acceptable, -na -ter) etc... unless ambiguious
group = argparse.add_mutually_exclusive_group()
group.add_argument...
any arguments added, only 1 can be used or error
.set_defaults(**kwargs) --> will become default arguments even if the arguments were not created with .add_argument
.get_default('key') --> return the default of the key
--- useage ---
(above class saved in Args.py modual)
import Args
arg_parser = Args.Args()
inputArgs = arg_parser.parse()
inputArgs.ARGNAME #ie inputArgs.sample
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Looping
for x,y in zip(l1,l2): --> loop through two items at once
for k,v in dictionary.iteriteritems(): --> loop through keys and values in a dictionary
xrange(0,10,2) --> range of 0 to 10, by 2s
