def __init__(self, client=None, version=2):
super(SC2BSubmissions, self).__init__(client=client, name="SC2B")
self.version = version
from hpn import HPNAdmin
self.hpn = HPNAdmin(client=self.client)
# download missing file automatically if needed.
from dreamtools import Challenge
c = Challenge('D8C1')
c._download_data('experimental.zip', 'syn1920412')
def __init__(self, client=None, version=2):
super(SC2BSubmissions, self).__init__(client=client, name="SC2B")
self.version = version
from .hpn import HPNAdmin
self.hpn = HPNAdmin(client=self.client)
# download missing file automatically if needed.
from dreamtools import Challenge
c = Challenge('D8C1')
c._download_data('experimental.zip', 'syn1920412')
def _generic_download(name, mode):
c = Challenge(name)
class_inst = c.import_scoring_class()
if mode == 'template':
if len(class_inst.sub_challenges) == 0:
class_inst.download_template()
else:
for subname in class_inst.sub_challenges:
class_inst.download_template(subname)
elif mode == 'gs':
if len(class_inst.sub_challenges) == 0:
class_inst.download_goldstandard()
else:
for subname in class_inst.sub_challenges:
class_inst.download_goldstandard(subname)
def _generic_download(name, mode):
c = Challenge(name)
class_inst = c.import_scoring_class()
if mode == 'template':
if len(class_inst.sub_challenges) == 0:
class_inst.download_template()
else:
for subname in class_inst.sub_challenges:
class_inst.download_template(subname)
elif mode == 'gs':
if len(class_inst.sub_challenges) == 0:
class_inst.download_goldstandard()
else:
for subname in class_inst.sub_challenges:
class_inst.download_goldstandard(subname)
def get_challenge(challenge_name):
"""Test validity of the challenge and returns an instance
:param challenge_name: a valid name e.g. D5C3, D9dot5C1
:return: instance of the challenge
"""
try:
c = Challenge(challenge_name)
except:
txt = "The challenge %s could not be found. " % challenge_name
txt += "See --help for valid names"
print_color(txt, red)
sys.exit()
return c
def scoring(args=None):
"""This function is used by the standalone application called dreamscoring
::
dreamscoring --help
"""
d = DevTools()
if args is None:
args = sys.argv[:]
user_options = Options(prog="dreamtools")
if len(args) == 1:
user_options.parse_args(["prog", "--help"])
else:
options = user_options.parse_args(args[1:])
if options.version is True:
print("%s" % dreamtools.version)
sys.exit()
# Check on the challenge name
if options.challenge is None:
print_color('--challenge must be provided', red)
sys.exit()
else:
options.challenge = options.challenge.upper()
options.challenge = options.challenge.replace('DOT', 'dot')
from dreamtools.admin.download_data import get_challenge_list
if options.challenge not in get_challenge_list():
print_color(
"This challenge %s is not registered in dreamtools." %
options.challenge, red)
print("Here is the list of registered challenges: " +
", ".join(get_challenge_list()))
sys.exit()
# Check that the challenge can be loaded
class_inst = get_challenge(options.challenge)
try:
this = class_inst.import_scoring_class()
except NotImplementedError as err:
print("\n" + str(err))
sys.exit()
else:
# User may just request some information about the challenge.
if options.info is True:
print(this)
sys.exit()
elif options.onweb is True:
this.onweb()
sys.exit()
# Checks name of the sub-challenges
subchallenges = get_subchallenges(options.challenge)
if len(subchallenges) and options.sub_challenge is None:
txt = "This challenge requires a sub challenge name. "
txt += "Please use --sub-challenge followed by one value in %s " % subchallenges
print_color(txt, red)
sys.exit(0)
if options.sub_challenge is not None and len(subchallenges) != 0:
try:
d.check_param_in_list(options.sub_challenge, subchallenges)
except ValueError as err:
txt = "DREAMTools error: unknown sub challenge or not implemented"
txt += "--->" + str(err)
print_color(txt, red)
sys.exit()
# maybe users just need a template
if options.download_template is True:
c = Challenge(options.challenge)
class_inst = c.import_scoring_class()
if options.sub_challenge is None:
print(class_inst.download_template())
else:
print(class_inst.download_template(options.sub_challenge))
return
# similary for the GS
if options.download_goldstandard is True:
c = Challenge(options.challenge)
class_inst = c.import_scoring_class()
if options.sub_challenge is None:
print(class_inst.download_goldstandard())
else:
print(class_inst.download_goldstandard(options.sub_challenge))
return
# finally, we need a submission
if options.filename is None:
txt = "---> filename not provided. You must provide a filename with correct format\n"
txt += "You may get a template using --download-template \n"
txt += "Alternatively, you can user either --info or --onweb option to get information about the challenge.\n"
txt += "https://github.com/dreamtools/dreamtools, or http://dreamchallenges.org\n"
print_color(txt, red)
sys.exit()
# filename
# filename in general is a single string but could be a list of filenames
# Because on the parser, we must convert the string into a single string
# if the list haa a length of 1
for filename in options.filename:
if os.path.exists(filename) is False:
raise IOError("file %s does not seem to exists" % filename)
if len(options.filename) == 1:
options.filename = options.filename[0]
print_color("DREAMTools scoring", purple, underline=True)
print('Challenge %s (sub challenge %s)\n\n' %
(options.challenge, options.sub_challenge))
res = generic_scoring(options.challenge,
options.filename,
subname=options.sub_challenge,
goldstandard=options.goldstandard)
txt = "Solution for %s in challenge %s" % (options.filename,
options.challenge)
if options.sub_challenge is not None:
txt += " (sub-challenge %s)" % options.sub_challenge
txt += " is :\n"
for k in sorted(res.keys()):
txt += darkgreen(" %s:\n %s\n" % (k, res[k]))
print(txt)
def scoring(args=None):
"""This function is used by the standalone application called dreamscoring
::
dreamscoring --help
"""
d = DevTools()
if args is None:
args = sys.argv[:]
user_options = Options(prog="dreamtools")
if len(args) == 1:
user_options.parse_args(["prog", "--help"])
else:
options = user_options.parse_args(args[1:])
if options.version is True:
print("%s" % dreamtools.version)
sys.exit()
# Check on the challenge name
if options.challenge is None:
print_color('--challenge must be provided', red)
sys.exit()
else:
options.challenge = options.challenge.upper()
options.challenge = options.challenge.replace('DOT', 'dot')
from dreamtools.admin.download_data import get_challenge_list
if options.challenge not in get_challenge_list():
print_color("This challenge %s is not registered in dreamtools." %
options.challenge, red)
print("Here is the list of registered challenges: " +
", ".join(get_challenge_list()))
sys.exit()
# Check that the challenge can be loaded
class_inst = get_challenge(options.challenge)
try:
this = class_inst.import_scoring_class()
except NotImplementedError as err:
print("\n"+str(err))
sys.exit()
else:
# User may just request some information about the challenge.
if options.info is True:
print(this)
sys.exit()
elif options.onweb is True:
this.onweb()
sys.exit()
# Checks name of the sub-challenges
subchallenges = get_subchallenges(options.challenge)
if len(subchallenges) and options.sub_challenge is None:
txt = "This challenge requires a sub challenge name. "
txt += "Please use --sub-challenge followed by one value in %s " % subchallenges
print_color(txt, red)
sys.exit(0)
if options.sub_challenge is not None and len(subchallenges) != 0:
try:
d.check_param_in_list(options.sub_challenge, subchallenges)
except ValueError as err:
txt = "DREAMTools error: unknown sub challenge or not implemented"
txt += "--->" + str(err)
print_color(txt, red)
sys.exit()
# maybe users just need a template
if options.download_template is True:
c = Challenge(options.challenge)
class_inst = c.import_scoring_class()
if options.sub_challenge is None:
print(class_inst.download_template())
else:
print(class_inst.download_template(options.sub_challenge))
return
# similary for the GS
if options.download_goldstandard is True:
c = Challenge(options.challenge)
class_inst = c.import_scoring_class()
if options.sub_challenge is None:
print(class_inst.download_goldstandard())
else:
print(class_inst.download_goldstandard(options.sub_challenge))
return
# finally, we need a submission
if options.filename is None:
txt = "---> filename not provided. You must provide a filename with correct format\n"
txt += "You may get a template using --download-template \n"
txt += "Alternatively, you can user either --info or --onweb option to get information about the challenge.\n"
txt += "https://github.com/dreamtools/dreamtools, or http://dreamchallenges.org\n"
print_color(txt, red)
sys.exit()
# filename
# filename in general is a single string but could be a list of filenames
# Because on the parser, we must convert the string into a single string
# if the list haa a length of 1
for filename in options.filename:
if os.path.exists(filename) is False:
raise IOError("file %s does not seem to exists" % filename)
if len(options.filename) == 1:
options.filename = options.filename[0]
print_color("DREAMTools scoring", purple, underline=True)
print('Challenge %s (sub challenge %s)\n\n' % (options.challenge,
options.sub_challenge))
res = generic_scoring(options.challenge,
options.filename,
subname=options.sub_challenge,
goldstandard=options.goldstandard)
txt = "Solution for %s in challenge %s" % (options.filename,
options.challenge)
if options.sub_challenge is not None:
txt += " (sub-challenge %s)" % options.sub_challenge
txt += " is :\n"
for k in sorted(res.keys()):
txt += darkgreen(" %s:\n %s\n" %(k, res[k]))
print(txt)
def scoring(args=None):
"""This function is used by the standalone application called dreamscoring
::
dreamscoring --help
"""
d = DevTools()
if args == None:
args = sys.argv[:]
user_options = Options(prog="dreamtools")
if len(args) == 1:
user_options.parse_args(["prog", "--help"])
else:
options = user_options.parse_args(args[1:])
# Check on the challenge name
if options.challenge is None:
print_color("--challenge and --sub-challenge must be provided", red)
sys.exit()
else:
options.challenge = options.challenge.upper()
options.challenge = options.challenge.replace("DOT", "dot")
# Check that the challenge can be loaded
class_inst = get_challenge(options.challenge)
try:
class_inst.import_scoring_class()
except NotImplementedError as err:
print("\n" + err.message)
sys.exit()
# Checks name of the sub-challenges
subchallenges = get_subchallenges(options.challenge)
if len(subchallenges) and options.sub_challenge is None:
txt = "This challenge requires a sub challenge name."
txt += "Please provide one amongst %s " % subchallenges
print_color(txt, red)
sys.exit(0)
if options.sub_challenge is not None and len(subchallenges) != 0:
try:
d.check_param_in_list(options.sub_challenge, subchallenges)
except ValueError as err:
txt = "DreamTools error: unknown sub challenge or not implemented"
txt += "--->" + err.message
print_color(txt, red)
sys.exit()
if options.download_template is True:
c = Challenge(options.challenge)
class_inst = c.import_scoring_class()
if options.sub_challenge is None:
print(class_inst.download_template())
else:
print(class_inst.download_template(options.sub_challenge))
return
# similary for the GS
if options.download_goldstandard is True:
c = Challenge(options.challenge)
class_inst = c.import_scoring_class()
if options.sub_challenge is None:
print(class_inst.download_goldstandard())
else:
print(class_inst.download_goldstandard(options.sub_challenge))
return
if options.filename is None:
txt = "---> filename not provided. You must provide a filename with correct format\n"
txt += "You may get a template using --download-template option\n"
txt += "https://github.com/dreamtools/dreamtools, or http://dreamchallenges.org\n"
print_color(txt, red)
sys.exit()
# filename
# filename in general is a single string but could be a list of filenames
# Because on the parser, we must convert the string into a single string
# if the list haa a length of 1
for filename in options.filename:
if os.path.exists(filename) is False:
raise IOError("file %s does not seem to exists" % filename)
if len(options.filename) == 1:
options.filename = options.filename[0]
print_color("Dreamtools scoring", purple, underline=True)
print("Challenge %s (sub challenge %s)\n\n" % (options.challenge, options.sub_challenge))
res = "??"
if options.challenge == "D8C1":
if options.sub_challenge == "sc1a":
res = d8c1_sc1a(options.filename, verbose=options.verbose)
elif options.sub_challenge == "sc1b":
res = d8c1_sc1b(options.filename, verbose=options.verbose)
elif options.sub_challenge == "sc2a":
res = d8c1_sc2a(options.filename, verbose=options.verbose)
elif options.sub_challenge == "sc2b":
res = d8c1_sc2b(options.filename, verbose=options.verbose)
else:
res = generic_scoring(
options.challenge, options.filename, subname=options.sub_challenge, goldstandard=options.goldstandard
)
txt = "Solution for %s in challenge %s" % (options.filename, options.challenge)
if options.sub_challenge is not None:
txt += " (sub-challenge %s)" % options.sub_challenge
txt += " is :\n"
for k in sorted(res.keys()):
txt += darkgreen(" %s:\n %s\n" % (k, res[k]))
print(txt)
def test_challenge():
c = Challenge("D0C0")
