def test_argparse(self):
"""
Same as above but setting up options using ruffus.cmdline.get_argparse
--verbose on its own increases the verbosity by one
--verbose NNN (re)sets the verbosity to NNN whatever the previous state
--verbose NNN:MMM sets the verbose_abbreviated_path to MMM
"""
parser = cmdline.get_argparse(
description='WHAT DOES THIS PIPELINE DO?')
import sys
sys.argv = ["test", "--verbose", "--verbose=2"]
options = parser.parse_args()
handle_verbose(options)
self.assertTrue(options.verbose == 2)
self.assertTrue(options.verbose_abbreviated_path == None)
sys.argv = ["test", "--verbose", "--verbose=3", "--verbose"]
options = parser.parse_args()
handle_verbose(options)
self.assertTrue(options.verbose == 4)
self.assertTrue(options.verbose_abbreviated_path == None)
sys.argv = ["test", "--verbose", "--verbose=5:3", "--verbose"]
options = parser.parse_args()
handle_verbose(options)
self.assertTrue(options.verbose == 6)
self.assertTrue(options.verbose_abbreviated_path == 3)
sys.argv = [
"test", "--verbose", "--verbose=5:3", "--verbose", "--verbose=7",
"--verbose"
]
options = parser.parse_args()
handle_verbose(options)
self.assertTrue(options.verbose == 8)
self.assertTrue(options.verbose_abbreviated_path == 3)
sys.argv = [
"test", "--verbose", "--verbose=5:3", "--verbose", "--verbose=7:5",
"--verbose"
]
options = parser.parse_args()
handle_verbose(options)
self.assertTrue(options.verbose == 8)
self.assertTrue(options.verbose_abbreviated_path == 5)
def test_argparse(self):
"""
Same as above but setting up options using ruffus.cmdline.get_argparse
--verbose on its own increases the verbosity by one
--verbose NNN (re)sets the verbosity to NNN whatever the previous state
--verbose NNN:MMM sets the verbose_abbreviated_path to MMM
"""
parser = cmdline.get_argparse(description='WHAT DOES THIS PIPELINE DO?')
import sys
sys.argv = ["test", "--verbose", "--verbose=2"]
options = parser.parse_args()
handle_verbose(options)
self.assertTrue(options.verbose==2)
self.assertTrue(options.verbose_abbreviated_path==None)
sys.argv = ["test", "--verbose", "--verbose=3", "--verbose"]
options = parser.parse_args()
handle_verbose(options)
self.assertTrue(options.verbose==4)
self.assertTrue(options.verbose_abbreviated_path==None)
sys.argv = ["test", "--verbose", "--verbose=5:3", "--verbose"]
options = parser.parse_args()
handle_verbose(options)
self.assertTrue(options.verbose==6)
self.assertTrue(options.verbose_abbreviated_path==3)
sys.argv = ["test", "--verbose", "--verbose=5:3", "--verbose", "--verbose=7", "--verbose"]
options = parser.parse_args()
handle_verbose(options)
self.assertTrue(options.verbose==8)
self.assertTrue(options.verbose_abbreviated_path==3)
sys.argv = ["test", "--verbose", "--verbose=5:3", "--verbose", "--verbose=7:5", "--verbose"]
options = parser.parse_args()
handle_verbose(options)
self.assertTrue(options.verbose==8)
self.assertTrue(options.verbose_abbreviated_path==5)
def test_verbose_abbreviated_path (self):
"""
--verbose NNN:MMM sets the verbose_abbreviated_path to MMM
"""
#
# do not override users' verbose_abbreviated_path
#
options = t_options()
# take verbose_abbreviated_path
setattr(options, "verbose", ["+", "5", "+", "4:3"])
handle_verbose(options)
self.assertTrue(options.verbose==4)
self.assertTrue(options.verbose_abbreviated_path==3)
# do not override users' verbose_abbreviated_path
setattr(options, "verbose", ["+", "5", "+", "7:5"])
handle_verbose(options)
self.assertTrue(options.verbose==7)
self.assertTrue(options.verbose_abbreviated_path==3)
options = t_options()
# take verbose_abbreviated_path
setattr(options, "verbose", ["+", "5:3", "+", "7:5", "+"])
handle_verbose(options)
self.assertTrue(options.verbose==8)
self.assertTrue(options.verbose_abbreviated_path==5)
def test_verbose (self):
"""
--verbose on its own increases the verbosity by one
--verbose NNN (re)sets the verbosity to NNN whatever the previous state
"""
# options.verbose defined by user to be None
options = t_options()
setattr(options, "verbose", None)
handle_verbose(options)
self.assertTrue(options.verbose==None)
self.assertTrue(options.verbose_abbreviated_path is None)
# options.verbose defined by user to be 0
options = t_options()
setattr(options, "verbose", 0)
handle_verbose(options)
self.assertTrue(options.verbose==0)
self.assertTrue(options.verbose_abbreviated_path is None)
# options.verbose defined by user to be "6"
options = t_options()
setattr(options, "verbose", "6")
handle_verbose(options)
self.assertTrue(options.verbose==6)
self.assertTrue(options.verbose_abbreviated_path==None)
# options.verbose defined by user to be 6
options = t_options()
setattr(options, "verbose", 6)
handle_verbose(options)
self.assertTrue(options.verbose==6)
self.assertTrue(options.verbose_abbreviated_path==None)
# options.verbose defined by user to "+"
options = t_options()
setattr(options, "verbose", "+")
handle_verbose(options)
self.assertTrue(options.verbose==1)
self.assertTrue(options.verbose_abbreviated_path==None)
# --verbose not set
options = t_options()
setattr(options, "verbose", [])
handle_verbose(options)
self.assertTrue(options.verbose==0)
self.assertTrue(options.verbose_abbreviated_path==None)
# --verbose
options = t_options()
setattr(options, "verbose", ["+"])
handle_verbose(options)
self.assertTrue(options.verbose==1)
self.assertTrue(options.verbose_abbreviated_path==None)
# --verbose --verbose 5 --verbose
options = t_options()
setattr(options, "verbose", ["+", "5", "+"])
handle_verbose(options)
self.assertTrue(options.verbose==6)
self.assertTrue(options.verbose_abbreviated_path==None)
# --verbose --verbose 5 --verbose --verbose 4
# last value overrides the 5
options = t_options()
setattr(options, "verbose", ["+", "5", "+", "4"])
handle_verbose(options)
self.assertTrue(options.verbose==4)
self.assertTrue(options.verbose_abbreviated_path==None)
#crocodile.reptiles.animal
# -> reptiles.results
#
#pufferfish.fish.animal
# -> fish.results
"""
for grouping in species_list:
assert (open(tempdir + grouping + ".results").read() == "".join(
s + "\n" for s in sorted(species_list[grouping])))
#
# Necessary to protect the "entry point" of the program under windows.
# see: http://docs.python.org/library/multiprocessing.html#multiprocessing-programming
#
if __name__ == '__main__':
if options.debug:
import os
os.system("rm -rf %s" % tempdir)
options = cmdline.handle_verbose(options)
pipeline_run(target_tasks=options.target_tasks,
forcedtorun_tasks=options.forced_tasks,
multiprocess=options.jobs,
verbose=options.verbose)
check_species_correct()
#os.system("rm -rf %s" % tempdir)
print("OK")
else:
cmdline.run(options)
