def setUp(self):
self.obj = optparse_factory(
ghetto, [OptparseUsageExample('a', 'b', 'c')], [
OptparseOption(
Type=str, Parameter=ghetto.CommandIns['c'], ShortName='n')
], [
OptparseResult(Type=str,
Parameter=ghetto.CommandOuts['itsaresult'],
Handler=oh)
], '2.0-dev')
ShortName='i',
Name='input_dir',
Required=True,
Help='Path to the directory with the time results',
),
OptparseOption(Parameter=cmd_in_lookup('job_ids'),
Type='str',
Action='store',
Handler=string_list_handler,
ShortName='w',
Name='wait_on',
Required=False,
Help='Comma-separated list of job ids to wait for before '
'processing the results'),
OptparseOption(Parameter=None,
Type='new_dirpath',
ShortName='o',
Name='output-dir',
Required=True,
Help='The output directory')
]
# outputs map result keys to output options and handlers. It is not necessary
# to supply an associated option, but if you do, it must be an option from the
# inputs list (above).
outputs = [
OptparseResult(Parameter=cmd_out_lookup('bench_data'),
Handler=write_bench_results,
InputName='output-dir'),
]
),
OptparseOption(
Parameter=cmd_in_lookup('labels'),
Type='str',
Action='store', # default is 'store', change if desired
Handler=string_list_handler, # must be defined if desired
ShortName='l', # must be defined if desired
# Name='labels', # implied by Parameter
# Required=True, # implied by Parameter
# Help='List of strings to label each data series on the plot', # implied by Parameter
),
OptparseOption(Parameter=None,
Type='new_dirpath',
ShortName='o',
Name='output-dir',
Required=True,
Help='The output directory')
]
# outputs map result keys to output options and handlers. It is not necessary
# to supply an associated option, but if you do, it must be an option from the
# inputs list (above).
outputs = [
OptparseResult(Parameter=cmd_out_lookup('mem_fig'),
Handler=write_matplotlib_figure,
InputName='output-dir'),
OptparseResult(Parameter=cmd_out_lookup('time_fig'),
Handler=write_matplotlib_figure,
InputName='output-dir'),
]
# normalization to relative_abundance
OptparseOption(Parameter=cmd_in_lookup('relative_abund'),
ShortName='r',
Action='store_true',
Help='convert table to relative abundance'),
# conversion to presensce/absence
OptparseOption(Parameter=cmd_in_lookup('presence_absence'),
ShortName='p',
Action='store_true',
Help='convert table to presence/absence'),
# if relative abundance then normalize by sample or by observation
OptparseOption(Parameter=cmd_in_lookup('axis'),
ShortName='a',
Default='sample'),
OptparseOption(Parameter=None,
Type='new_filepath',
ShortName='o',
Name='output-fp',
Required=True,
Help='the output filepath')
]
outputs = [
OptparseResult(Parameter=cmd_out_lookup('table'),
Handler=write_biom_table,
InputName='output-fp')
]
from pyqi.commands.make_bash_completion import CommandConstructor
cmd_in_lookup = make_command_in_collection_lookup_f(CommandConstructor)
cmd_out_lookup = make_command_out_collection_lookup_f(CommandConstructor)
usage_examples = [
OptparseUsageExample(
ShortDesc="Create a bash completion script",
LongDesc="Create a bash completion script for use with a pyqi driver",
Ex=
"%prog --command-config-module pyqi.interfaces.optparse.config --driver-name pyqi -o ~/.bash_completion.d/pyqi"
)
]
inputs = [
OptparseOption(Parameter=cmd_in_lookup('command_config_module')),
OptparseOption(Parameter=cmd_in_lookup('driver_name')),
OptparseOption(Parameter=None,
Type='new_filepath',
ShortName='o',
Name='output-fp',
Required=True,
Help='output filepath')
]
outputs = [
OptparseResult(Parameter=cmd_out_lookup('result'),
Handler=write_string,
InputName='output-fp')
]
usage_examples = [
OptparseUsageExample(ShortDesc="Basic script usage",
LongDesc="Write a summary of table.biom to "
"table_summary.txt",
Ex="%prog -i table.biom -o table_summary.txt")
]
inputs = [
OptparseOption(Parameter=cmd_in_lookup('table'),
Type="existing_filepath",
Handler=load_biom_table_with_file_contents,
ShortName='i',
Name='input-fp'),
OptparseOption(Parameter=cmd_in_lookup('qualitative'),
Type=None,
Action="store_true"),
OptparseOption(Parameter=None,
Type='new_filepath',
ShortName='o',
Name='output-fp',
Required=False,
Default=None,
Help='the output filepath')
]
outputs = [
OptparseResult(Parameter=cmd_out_lookup('biom_summary'),
Handler=write_or_print_list_of_strings,
InputName='output-fp')
]
def _get_outputs(self):
return [
OptparseResult(Parameter=ghetto.CommandOuts['itsaresult'],
Handler=oh)
]
usage_examples = [
OptparseUsageExample(ShortDesc="Validating a BIOM file",
LongDesc="Validate the contents of table.biom for "
"adherence to the BIOM format specification",
Ex="%prog -i table.biom")
]
inputs = [
OptparseOption(Parameter=cmd_in_lookup('table'),
Type='existing_filepath',
Handler=None,
ShortName='i',
Name='input-fp',
Help='the input filepath to validate against the BIOM '
'format specification'),
OptparseOption(Parameter=cmd_in_lookup('is_json'),
Type=None,
Action='store_true'),
OptparseOption(Parameter=cmd_in_lookup('format_version'), ShortName='f'),
OptparseOption(Parameter=cmd_in_lookup('detailed_report'),
Type=None,
Action='store_true')
]
outputs = [
OptparseResult(Parameter=cmd_out_lookup('report_lines'),
Handler=print_list_of_strings),
OptparseResult(Parameter=cmd_out_lookup('valid_table'),
Handler=report_table_validity)
]
# Help='Path to the directory with the time results', # implied by Parameter
),
OptparseOption(Parameter=None,
Type='new_dirpath',
ShortName='o',
Name='output-dir',
Required=True,
Help='The output directory')
]
# outputs map result keys to output options and handlers. It is not necessary
# to supply an associated option, but if you do, it must be an option from the
# inputs list (above).
outputs = [
OptparseResult(Parameter=cmd_out_lookup('bench_data'),
Handler=write_summarized_results,
InputName='output-dir'),
OptparseResult(Parameter=cmd_out_lookup('mem_fig'),
Handler=write_matplotlib_figure,
InputName='output-dir'),
OptparseResult(Parameter=cmd_out_lookup('mem_str'),
Handler=write_string_to_dir,
InputName='output-dir'),
OptparseResult(Parameter=cmd_out_lookup('time_fig'),
Handler=write_matplotlib_figure,
InputName='output-dir'),
OptparseResult(Parameter=cmd_out_lookup('time_str'),
Handler=write_string_to_dir,
InputName='output-dir'),
]
from pyqi.core.interfaces.optparse import (OptparseUsageExample,
OptparseResult)
from pyqi.core.command import make_command_out_collection_lookup_f
from pyqi.core.interfaces.optparse.output_handler import print_list_of_strings
from biom.commands.installation_informer import CommandConstructor
__author__ = "Jai Ram Rideout"
__copyright__ = "Copyright 2011-2013, The BIOM Format Development Team"
__credits__ = ["Jai Ram Rideout", "Greg Caporaso", "Daniel McDonald"]
__license__ = "BSD"
__url__ = "http://biom-format.org"
__maintainer__ = "Jai Ram Rideout"
__email__ = "*****@*****.**"
cmd_out_lookup = make_command_out_collection_lookup_f(CommandConstructor)
usage_examples = [
OptparseUsageExample(ShortDesc="Displaying installation info",
LongDesc="Display biom-format installation "
"information",
Ex="%prog")
]
inputs = []
outputs = [
OptparseResult(Parameter=cmd_out_lookup('install_info_lines'),
Handler=print_list_of_strings)
]
inputs = [
OptparseOption(Parameter=cmdin_lookup('command'),
ShortName='c',
Handler=command_handler),
OptparseOption(Parameter=cmdin_lookup('command_module'), ShortName='m'),
OptparseOption(Parameter=cmdin_lookup('author'), ShortName='a'),
OptparseOption(Parameter=cmdin_lookup('email'), ShortName='e'),
OptparseOption(Parameter=cmdin_lookup('license'), ShortName='l'),
OptparseOption(Parameter=cmdin_lookup('copyright')),
OptparseOption(Parameter=cmdin_lookup('version'), Name='config-version'),
OptparseOption(Parameter=cmdin_lookup('credits'),
Handler=string_list_handler,
Help='comma-separated list of other authors'),
OptparseOption(
Parameter=None,
Type='new_filepath',
ShortName='o',
Name='output-fp',
Required=True,
Help=
'output filepath to store generated optparse Python configuration file'
)
]
outputs = [
OptparseResult(Parameter=cmdout_lookup('result'),
Handler=write_list_of_strings,
InputName='output-fp')
]
]
inputs = [
OptparseOption(Parameter=cmd_in_lookup('tickmark_in_box_index'),
Type=int,
Action='store', # default is 'store', change if desired
ShortName=None, # must be defined if desired
),
OptparseOption(Parameter=cmd_in_lookup('text'),
Type=str,
Action='store',
Handler=driver
),
OptparseOption(Parameter=cmd_in_lookup('box_width'),
Type=int,
Action='store', # default is 'store', change if desired
ShortName=None, # must be defined if desired
),
OptparseOption(Parameter=cmd_in_lookup('buffer_size'),
Type=int,
Action='store', # default is 'store', change if desired
ShortName=None, # must be defined if desired
)
]
outputs = [
OptparseResult(Parameter=cmd_out_lookup('orp_word'),
Handler=box_writer, # must be defined
InputName=None), # define if tying to an OptparseOption
]
__credits__ = ["Evan Bolyen"]
from pyqi.core.interfaces.optparse import (OptparseOption, OptparseResult,
OptparseUsageExample)
from pyqi.core.interfaces.optparse.input_handler import string_list_handler
from pyqi.core.interfaces.optparse.output_handler import print_string
from pyqi.core.command import make_command_in_collection_lookup_f, make_command_out_collection_lookup_f
from pyqi.commands.serve_html_interface import CommandConstructor
cmdin_lookup = make_command_in_collection_lookup_f(CommandConstructor)
cmdout_lookup = make_command_out_collection_lookup_f(CommandConstructor)
usage_examples = [
OptparseUsageExample(
ShortDesc="Start html interface",
LongDesc=
"Starts an html interface server on the specified --port and --interface-module",
Ex='%prog -p 8080 -m pyqi.interfaces.html.config')
]
inputs = [
OptparseOption(Parameter=cmdin_lookup('port'), ShortName='p', Type=int),
OptparseOption(Parameter=cmdin_lookup('interface_module'),
ShortName='m',
Required=True)
]
outputs = [
OptparseResult(Parameter=cmdout_lookup('result'), Handler=print_string)
]
),
OptparseOption(Parameter=None,
Type='new_filepath',
ShortName='o',
Name='output-fp',
Required=True,
Help='the output filepath')
]
# outputs map result keys to output options and handlers. It is not necessary
# to supply an associated option, but if you do, it must be an option from the
# inputs list (above).
outputs = [
# An example option that maps to a CommandIn.
# OptparseResult(Parameter=cmd_out_lookup('name_of_a_command_out'),
# Handler=write_string, # a function applied to the output of the Command
# # the name of the option (defined in inputs, above), whose
# # value will be made available to Handler. This name
# # can be either an underscored or dashed version of the
# # option name (e.g., 'output_fp' or 'output-fp')
# InputName='output-fp'),
#
# An example option that does not map to a CommandIn.
# OptparseResult(Parameter=cmd_out_lookup('some_other_result'),
# Handler=print_string)
OptparseResult(
Parameter=cmd_out_lookup('bench_suite'),
Handler=write_string, # must be defined
InputName='output-fp'), # define if tying to an OptparseOption
]