def main(belversion, species, pathways):
"""Process Reactome into BEL
Example: ./processReactome.py -b 1 -s "H**o sapiens" -s "Mus musculus" -p Metabolism
Example: ./processReactome.py -b 2 -s "H**o sapiens" -p Metabolism -p "Transmembrane transport of small molecules"
Result: reactome.bels
"""
setBelVersion(belversion)
# quit and show help if no arguments are set
if not species:
click.help_option()
print('Here')
if 'all' in species:
species = speciesList
# Collect reactions
reactionList = []
for specie in species:
reactionList.extend(getReactions(specie, pathways=pathways))
# import json
# with open('reactionlist.json', 'w') as f:
# json.dump(reactionList, f, indent=4)
# quit()
# human, mouse and rat share rxnIds
reactionList = set(reactionList)
buildBelEvidences(reactionList, belversion, pathways=pathways)
def main(belversion, species, pathways):
"""Process Reactome into BEL
Example: ./processReactome.py -b 1 -s "H**o sapiens" -s "Mus musculus" -p Metabolism
Example: ./processReactome.py -b 2 -s "H**o sapiens" -p Metabolism -p "Transmembrane transport of small molecules"
Result: reactome.bels
"""
setBelVersion(belversion)
# quit and show help if no arguments are set
if not species:
click.help_option()
print('Here')
if 'all' in species:
species = speciesList
# Collect reactions
reactionList = []
for specie in species:
reactionList.extend(getReactions(specie, pathways=pathways))
# import json
# with open('reactionlist.json', 'w') as f:
# json.dump(reactionList, f, indent=4)
# quit()
# human, mouse and rat share rxnIds
reactionList = set(reactionList)
buildBelEvidences(reactionList, belversion, pathways=pathways)
def get_command(self, ctx, name):
ns = {}
fn = os.path.join(command_folder, name + '.py')
try:
with open(fn) as f:
code = compile(f.read(), fn, 'exec')
eval(code, ns, ns)
return ns[name]
except IOError:
click.help_option()
def common_options(f):
f = click.option("-i",
"--input-dir",
required=False,
default='.',
show_default=True,
type=click.Path(exists=True,
dir_okay=True,
file_okay=False),
help="base directory of the dataset")(f)
f = click.option("-o",
"--output-dir",
required=False,
default='.',
show_default=True,
type=click.Path(exists=True,
dir_okay=True,
file_okay=False),
help="output directory for the created bag file")(f)
f = click.option("--compression",
required=False,
type=click.Choice(compression_choices),
default=rosbag.Compression.NONE,
show_default=True,
help="which compression to use for the created bag")(f)
f = click.help_option('-h', '--help')(f)
return f
def define_command(descriptor, wizard):
callback = descriptor['callback']
command = click.command(name=descriptor['name'], short_help=descriptor['help'], cls=DeprecatedOptionsCommand)(click.pass_context(callback))
if 'arguments' in descriptor:
for key, value in descriptor['arguments'].items():
command = click.argument(key, **value)(command)
if 'options' in descriptor:
for key, value in descriptor['options'].items():
if not wizard:
value.pop('prompt', None)
callbacks = [check_empty_values]
if 'validators' in value:
callbacks = callbacks + value.pop('validators')
value['callback'] = partial(multiple_option_callback, callbacks)
if type(key) == tuple:
click_option = click.option(*key, **value)
else:
click_option = click.option(key, **value)
command = click_option(command)
command = click.help_option(hidden=True)(command)
verbose_option = click.option('--verbose', is_flag=True, expose_value=False, callback=set_verbose_mode,
help=help_msg.VERBOSE_OPTION)
command = verbose_option(command)
for group in descriptor['groups']:
command_copy = copy.deepcopy(command)
if '%s' in descriptor['help']:
command_copy.help = descriptor['help'] % group.name
else:
command_copy.help = descriptor['help']
group.add_command(command_copy)
def define_command(descriptor):
callback = descriptor['callback']
command = click.command(name=descriptor['name'],
help=descriptor['help'],
cls=DeprecatedOptionsCommand)(
click.pass_context(callback))
if 'arguments' in descriptor:
for key, value in descriptor['arguments'].items():
command = click.argument(key, **value)(command)
if 'options' in descriptor:
for key, value in descriptor['options'].items():
if type(key) == tuple:
click_option = click.option(*key, **value)
else:
click_option = click.option(key, **value)
command = click_option(command)
command = click.help_option(hidden=True)(command)
verbose_option = click.option('--verbose',
is_flag=True,
expose_value=False,
callback=set_verbose_mode,
help='Debug mode')
command = verbose_option(command)
for group in descriptor['groups']:
command_copy = copy.deepcopy(command)
if '%s' in descriptor['help']:
command_copy.help = descriptor['help'] % group.name
group.add_command(command_copy)
def common_options(f):
"""
Global/shared options decorator.
"""
f = click.help_option("-h", "--help")(f)
f = click.version_option(__version__, "-v", "--version")(f)
f = debug_option(f)
return f
def common_options(f):
"""
Global/shared options decorator.
:param f:
:return:
"""
f = click.help_option('-h', '--help')(f)
f = click.version_option(__version__, '-v', '--version')(f)
f = debug_option(f)
return f
def common_options(command):
"""
Mark ``cli`` commands with common flags.
Used to mark ``cli`` commands with the flags that add the option
flags that we want to include in all of them.
"""
options = [
click.version_option(
changelog_gen.VERSION, "-v", "--version", prog_name="changelog-gen",
),
click.help_option("--help", help="Show this message and exit."),
]
for option in options:
command = option(command)
return command
def decorate(f, **kwargs):
"""
Work of actually decorating a function -- wrapped in here because we
want to dispatch depending on how `common_options` is invoked
"""
f = version_option(f)
f = debug_option(f)
f = verbose_option(f)
f = click.help_option("-h", "--help")(f)
# if the format option is being allowed, it needs to be applied to `f`
if not kwargs.get("no_format_option"):
f = format_option(f)
# if the --map-http-status option is being allowed, ...
if not kwargs.get("no_map_http_status_option"):
f = map_http_status_option(f)
return f
def decorate(f, **kwargs):
"""
Work of actually decorating a function -- wrapped in here because we
want to dispatch depending on how `common_options` is invoked
"""
f = version_option(f)
f = debug_option(f)
f = verbose_option(f)
f = click.help_option('-h', '--help')(f)
# if the format option is being allowed, it needs to be applied to `f`
if not kwargs.get('no_format_option'):
f = format_option(f)
# if the --map-http-status option is being allowed, ...
if not kwargs.get('no_map_http_status_option'):
f = map_http_status_option(f)
return f
def help_options(f):
f = click.help_option(
help='Show help message for this command and exit.')(f)
f = all_help_option(f)
return f
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""
Click options used for multiple scommands.
"""
from __future__ import absolute_import, print_function
import click
help_option = [ # pylint: disable=invalid-name
click.help_option('-h', '--help', help=u'Show this help message.')]
quiet_option = [ # pylint: disable=invalid-name
click.option('-q', '--quiet', is_flag=True, default=False,
help=u'Print no messages.')]
def add_options(options):
"""
Decorator that adds multiple Click options.
The list is reversed because of the way Click processes options
Parameters:
options: list of click.option definitions
self.fail(
'%s "%s" is a file.' %
(self.path_type, filename_to_ui(value)), param, ctx)
if not self.dir_okay and stat.S_ISDIR(st.st_mode):
self.fail(
'%s "%s" is a directory.' %
(self.path_type, filename_to_ui(value)), param, ctx)
if self.writable and not os.access(value, os.W_OK):
self.fail(
'%s "%s" is not writable.' %
(self.path_type, filename_to_ui(value)), param, ctx)
if self.readable and not os.access(value, os.R_OK):
self.fail(
'%s "%s" is not readable.' %
(self.path_type, filename_to_ui(value)), param, ctx)
return self.coerce_path_result(rv)
def noncontext_callback(f):
@wraps(f)
def fake_callback(ctx, param, value):
return f(value)
return fake_callback
option_of_common_help = click.help_option(help="show usages details")
option_of_not_implement_help = click.help_option(
help="Sorry, this command is not implemented now!")
def add_help_option(self):
"""Add a help option to the command."""
click.help_option(*('--help', '-h'))(self)
def add_help_option(self):
"""Add a help option to the command."""
click.help_option(*('--help', '-h'))(self)
def common_options(f):
# any shared/common options for all commands
return click.help_option("-h", "--help")(f)
"""
Grab value of --monokrom option and set global state of _show_colors
"""
global _show_colors
_show_colors = not value
_default_options = [
click.option(
"-m",
"--monokrom",
is_flag=True,
callback=_set_monochrome,
help="Vis ikke farver i terminalen",
),
click.help_option(help="Vis denne hjælp tekst"),
]
def default_options():
def _add_options(func):
for option in reversed(_default_options):
func = option(func)
return func
return _add_options
def print(*args, **kwargs):
"""
Custom print function based on click.secho.
def add_help_option(self):
"""Add a help option to the command."""
click.help_option(*("--help", "-h"))(self)
