def test_init(self):
obj = OptparseUsageExample(ShortDesc='a', LongDesc='b', Ex='c')
self.assertEqual(obj.ShortDesc, 'a')
self.assertEqual(obj.LongDesc, 'b')
self.assertEqual(obj.Ex, 'c')
with self.assertRaises(IncompetentDeveloperError):
_ = OptparseUsageExample('a', 'b', Ex=None)
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')
__author__ = "Jai Ram Rideout"
__copyright__ = "Copyright 2011-2013, The BIOM Format Development Team"
__credits__ = ["Jai Ram Rideout", "Greg Caporaso", "Morgan Langille",
"Daniel McDonald"]
__license__ = "BSD"
__url__ = "http://biom-format.org"
__maintainer__ = "Jai Ram Rideout"
__email__ = "*****@*****.**"
cmd_in_lookup = make_command_in_collection_lookup_f(CommandConstructor)
cmd_out_lookup = make_command_out_collection_lookup_f(CommandConstructor)
usage_examples = [
OptparseUsageExample(ShortDesc="Adding sample metadata",
LongDesc="Add sample metadata to a BIOM table",
Ex="%prog -i otu_table.biom -o "
"table_with_sample_metadata.biom -m "
"sample_metadata.txt")
]
inputs = [
OptparseOption(Parameter=cmd_in_lookup('table'),
Type='existing_filepath',
Handler=load_biom_table, ShortName='i',
Name='input-fp'),
OptparseOption(Parameter=cmd_in_lookup('sample_metadata'),
Type='existing_filepath',
Handler=file_reading_handler, ShortName='m',
Name='sample-metadata-fp'),
__copyright__ = "Copyright 2011-2013, The BIOM Format Development Team"
__credits__ = [
"Jai Ram Rideout", "Daniel McDonald", "Jose Antonio Navas Molina"
]
__license__ = "BSD"
__url__ = "http://biom-format.org"
__maintainer__ = "Jai Ram Rideout"
__email__ = "*****@*****.**"
cmd_in_lookup = make_command_in_collection_lookup_f(CommandConstructor)
cmd_out_lookup = make_command_out_collection_lookup_f(CommandConstructor)
usage_examples = [
OptparseUsageExample(ShortDesc="Subsetting a json BIOM table",
LongDesc="Choose a subset of the observations in "
"table.biom and write them to subset.biom",
Ex="%prog -j table.biom -a observations -s "
"observation_ids.txt -o subset.biom"),
OptparseUsageExample(ShortDesc="Subsetting a hdf5 BIOM table",
LongDesc="Choose a subset of the observations in "
"table.biom and write them to subset.biom",
Ex="%prog -i table.biom -a observations -s "
"observation_ids.txt -o subset.biom")
]
inputs = [
OptparseOption(Parameter=cmd_in_lookup('hdf5_table'),
Type='existing_filepath',
Handler=None,
ShortName='i',
Name='input-hdf5-fp',
from pyqi.core.interfaces.optparse import (OptparseOption,
OptparseUsageExample,
OptparseResult)
from pyqi.core.interfaces.optparse.output_handler import write_string
from pyqi.core.command import (make_command_in_collection_lookup_f,
make_command_out_collection_lookup_f)
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')
]
#!/usr/bin/env python
from __future__ import division
__credits__ = ["Daniel McDonald"]
from pyqi.core.interfaces.optparse import (OptparseUsageExample,
OptparseOption, OptparseResult)
from pyqi.core.command import (make_command_in_collection_lookup_f,
make_command_out_collection_lookup_f)
from pyqi.commands.make_release import CommandConstructor
# Convenience function for looking up parameters by name.
cmd_in_lookup = make_command_in_collection_lookup_f(CommandConstructor)
cmd_out_lookup = make_command_out_collection_lookup_f(CommandConstructor)
usage_examples = [
OptparseUsageExample(ShortDesc="Make a release",
LongDesc="Make a release, tag it, update version "
"strings and upload to pypi",
Ex="%prog --package-name=pyqi --real-run")
]
inputs = [
OptparseOption(Parameter=cmd_in_lookup('package_name')),
OptparseOption(Parameter=cmd_in_lookup('real_run'), Action='store_true'),
]
outputs = []
from pyqi.core.interfaces.optparse.output_handler import write_string
from scaling.commands.bench_suite_maker import CommandConstructor
from scaling.interfaces.optparse.input_handler import (get_bench_paths,
load_parameters)
# Convenience function for looking up parameters by name.
cmd_in_lookup = make_command_in_collection_lookup_f(CommandConstructor)
cmd_out_lookup = make_command_out_collection_lookup_f(CommandConstructor)
# Examples of how the command can be used from the command line using an
# optparse interface.
usage_examples = [
OptparseUsageExample(ShortDesc="Parameters example usage",
LongDesc="Test the command \"pick_otus.py\" using "
"different similarity values. The file parameters.txt"
" should follow these structure\nsimilarity<tab>"
"val1,val2,val3",
Ex="%prog -c \"pick_otus.py -i seqs.fna\" -p "
"parameters.txt -o pick_otus_bench_suite.sh"),
OptparseUsageExample(ShortDesc="Input files example usage",
LongDesc="Test the command \"pick_otus.py\" using "
"different input files. The folder bench_files should"
" include only the input files used by the command",
Ex="%prog -c \"pick_otus.py\" -i bench_files -o "
"pick_otus_bench_suite.sh"),
OptparseUsageExample(ShortDesc="Multiple input files example usage",
LongDesc="Test the command \"split_librarires_fastq."
"py\" using different input files. These command "
"takes the input file in pairs so we provide the "
"input files in two different folders",
Ex="%prog -c \"split_librarires_fastq.py -m "
OptparseOption, OptparseResult)
from pyqi.core.command import (make_command_in_collection_lookup_f,
make_command_out_collection_lookup_f)
from readgood.commands.readgooder import CommandConstructor
from readgood.interfaces.optparse.input_handler import driver
from readgood.interfaces.optparse.output_handler import box_writer
# Convenience function for looking up parameters by name.
cmd_in_lookup = make_command_in_collection_lookup_f(CommandConstructor)
cmd_out_lookup = make_command_out_collection_lookup_f(CommandConstructor)
# Examples of how the command can be used from the command line using an
# optparse interface.
usage_examples = [
OptparseUsageExample(ShortDesc="Write all the text",
LongDesc="Read gooder",
Ex="%prog --text=some_file")
]
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'),
OptparseOption, OptparseResult)
from pyqi.core.command import (make_command_in_collection_lookup_f,
make_command_out_collection_lookup_f)
from pyqi.core.interfaces.optparse.input_handler import string_list_handler
from scaling.commands.bench_results_comparator import CommandConstructor
from scaling.interfaces.optparse.output_handler import write_matplotlib_figure
# Convenience function for looking up parameters by name.
cmd_in_lookup = make_command_in_collection_lookup_f(CommandConstructor)
cmd_out_lookup = make_command_out_collection_lookup_f(CommandConstructor)
# Examples of how the command can be used from the command line using an
# optparse interface.
usage_examples = [
OptparseUsageExample(
ShortDesc="A short single sentence description of the example",
LongDesc="A longer, more detailed description",
Ex="%prog --foo --bar some_file")
]
# inputs map command line arguments and values onto Parameters. It is possible
# to define options here that do not exist as parameters, e.g., an output file.
inputs = [
OptparseOption(
Parameter=cmd_in_lookup('input_dirs'),
Type='existing_dirpaths',
Action='store', # default is 'store', change if desired
Handler=None, # must be defined if desired
ShortName='i', # must be defined if desired
# Name='input_dirs', # implied by Parameter
# Required=True, # implied by Parameter
# Help='List with the path to the directories with the time results of different runs of the same bench suite', # implied by Parameter
def _get_usage_examples(self):
return [OptparseUsageExample('a', 'b', 'c')]
cmd_in_lookup = make_command_in_collection_lookup_f(CommandConstructor)
cmd_out_lookup = make_command_out_collection_lookup_f(CommandConstructor)
def report_table_validity(result_key, data, option_value=None):
if data:
print "The input file is a valid BIOM-formatted file."
sys.exit(0)
else:
print "The input file is not a valid BIOM-formatted file."
sys.exit(1)
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'),
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 write_list_of_strings
from pyqi.core.command import (make_command_in_collection_lookup_f,
make_command_out_collection_lookup_f)
from pyqi.commands.make_command 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="Basic Command",
LongDesc="Create a basic Command with appropriate attribution",
Ex=
'%prog -n example -a "some author" -c "Copyright 2013, The pyqi project" -e "*****@*****.**" -l BSD --command-version "0.1" --credits "someone else","and another person" -o example.py'
)
]
inputs = [
OptparseOption(Parameter=cmd_in_lookup('name'), ShortName='n'),
OptparseOption(Parameter=cmd_in_lookup('author'), ShortName='a'),
OptparseOption(Parameter=cmd_in_lookup('email'), ShortName='e'),
OptparseOption(Parameter=cmd_in_lookup('license'), ShortName='l'),
OptparseOption(Parameter=cmd_in_lookup('copyright'), ShortName='c'),
OptparseOption(Parameter=cmd_in_lookup('version'), Name='command-version'),
OptparseOption(Parameter=cmd_in_lookup('credits'),
Handler=string_list_handler,
Help='comma-separated list of other authors'),
OptparseOption(Parameter=cmd_in_lookup('test_code'),
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)
]
OptparseResult)
from pyqi.core.interfaces.optparse.input_handler import (command_handler,
string_list_handler)
from pyqi.core.interfaces.optparse.output_handler import write_list_of_strings
from pyqi.core.command import (make_command_in_collection_lookup_f,
make_command_out_collection_lookup_f)
from pyqi.commands.make_optparse import CommandConstructor
cmdin_lookup = make_command_in_collection_lookup_f(CommandConstructor)
cmdout_lookup = make_command_out_collection_lookup_f(CommandConstructor)
usage_examples = [
OptparseUsageExample(
ShortDesc="Create an optparse config template",
LongDesc=
"Construct the beginning of an optparse configuration file based on the Parameters required by the Command.",
Ex=
'%prog -c pyqi.commands.make_optparse.MakeOptparse -m pyqi.commands.make_optparse -a "some author" --copyright "Copyright 2013, The pyqi project" -e "*****@*****.**" -l BSD --config-version "0.1" --credits "someone else","and another person" -o pyqi/interfaces/optparse/config/make_optparse.py'
),
OptparseUsageExample(
ShortDesc="Create a different optparse config template",
LongDesc=
"Construct the beginning of an optparse configuration file based on the Parameters required by the Command. This command corresponds to the pyqi tutorial example where a sequence_collection_summarizer command line interface is created for a SequenceCollectionSummarizer Command.",
Ex=
'%prog -c sequence_collection_summarizer.SequenceCollectionSummarizer -m sequence_collection_summarizer -a "Greg Caporaso" --copyright "Copyright 2013, Greg Caporaso" -e "*****@*****.**" -l BSD --config-version 0.0.1 -o summarize_sequence_collection.py'
)
]
inputs = [
OptparseOption(Parameter=cmdin_lookup('command'),
ShortName='c',
__author__ = "Michael Shaffer"
__copyright__ = "Copyright 2011-2013, The BIOM Format Development Team"
__credits__ = ["Michael Shaffer"]
__license__ = "BSD"
__url__ = "http://biom-format.org"
__maintainer__ = "Michael Shaffer"
__email__ = "*****@*****.**"
cmd_in_lookup = make_command_in_collection_lookup_f(CommandConstructor)
cmd_out_lookup = make_command_out_collection_lookup_f(CommandConstructor)
usage_examples = [
OptparseUsageExample(ShortDesc="Normalizing a BIOM table to relative"
"abundnace",
LongDesc="Take a BIOM table and replace all values "
"with their relative abundance in relation "
"to the sample",
Ex="%prog -i table.biom -r -o "
"normalized_table.biom"),
OptparseUsageExample(ShortDesc="Converting a BIOM table to a "
"presence/absence table",
LongDesc="Take a BIOM table and convert the values "
"to 0's and 1's based on presensce or "
"absence of observations",
Ex="%prog -i table.biom -p -o converted_table.biom")
]
inputs = [
# table input
OptparseOption(Parameter=cmd_in_lookup('biom_table'),
Type='existing_filepath',
from pyqi.core.interfaces.optparse import (OptparseUsageExample,
OptparseOption, OptparseResult)
from pyqi.core.command import (make_command_in_collection_lookup_f,
make_command_out_collection_lookup_f)
from biom.interfaces.optparse.input_handler import (load_biom_table,
load_metadata)
from biom.interfaces.optparse.output_handler import write_biom_table
from biom.commands.table_converter 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="Converting from classic to BIOM format",
LongDesc="Convert the classic file table.txt to a "
"sparse BIOM format OTU table",
Ex='%prog -i table.txt -o table.biom '
'--table-type "otu table"')
]
inputs = [
OptparseOption(Parameter=cmd_in_lookup('table'),
Type='existing_filepath',
Handler=load_biom_table,
ShortName='i',
Name='input-fp',
Help='the input table filepath, either in BIOM or classic '
'format'),
OptparseOption(Parameter=cmd_in_lookup('sample_metadata'),
Type='existing_filepath',
Handler=load_metadata,
from scaling.commands.bench_results_comparator import CommandConstructor
from scaling.interfaces.optparse.input_handler import (
load_summarized_results_list)
from scaling.interfaces.optparse.output_handler import write_comp_results
# Convenience function for looking up parameters by name.
cmd_in_lookup = make_command_in_collection_lookup_f(CommandConstructor)
cmd_out_lookup = make_command_out_collection_lookup_f(CommandConstructor)
# Examples of how the command can be used from the command line using an
# optparse interface.
usage_examples = [
OptparseUsageExample(ShortDesc="Compare different runs results of the same"
" bench suite",
LongDesc="Takes a comma-separated list with paths to "
"directories with benchmark results and generates a "
"plot with the wall time and a plot with the memory "
"consumption of the different runs, allowing "
"performance comparison between them.",
Ex="%prog -i timing1,timing2 -l run1,run2 -o plots")
]
# inputs map command line arguments and values onto Parameters. It is possible
# to define options here that do not exist as parameters, e.g., an output file.
inputs = [
OptparseOption(Parameter=cmd_in_lookup('bench_results'),
Type='existing_filepaths',
Action='store',
Handler=load_summarized_results_list,
ShortName='i',
Name='input_dirs',
Required=True,
make_command_out_collection_lookup_f)
from pyqi.core.interfaces.optparse import (OptparseOption,
OptparseUsageExample,
OptparseResult)
from pyqi.core.interfaces.optparse.output_handler import (
write_or_print_list_of_strings)
from biom.commands.table_summarizer import CommandConstructor
from biom.interfaces.optparse.input_handler import (
load_biom_table_with_file_contents)
cmd_in_lookup = make_command_in_collection_lookup_f(CommandConstructor)
cmd_out_lookup = make_command_out_collection_lookup_f(CommandConstructor)
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',
from pyqi.core.interfaces.optparse.input_handler import string_list_handler
from scaling.commands.bench_results_processer import CommandConstructor
from scaling.interfaces.optparse.output_handler import write_bench_results
from scaling.interfaces.optparse.input_handler import parse_timing_directory
# Convenience function for looking up parameters by name.
cmd_in_lookup = make_command_in_collection_lookup_f(CommandConstructor)
cmd_out_lookup = make_command_out_collection_lookup_f(CommandConstructor)
# Examples of how the command can be used from the command line using an
# optparse interface.
usage_examples = [
OptparseUsageExample(ShortDesc="Processes the benchmark suite results",
LongDesc="Takes the benchmark suite output directory "
"and processes the benchmark measurements, creating "
"plots and collapsing results in a usable form.",
Ex="%prog -i timing -o plots"),
OptparseUsageExample(ShortDesc="Wait for a set of PBS jobs to complete and"
" process the benchmark suite results",
LongDesc="Takes a list of PBS job ids, wait for its "
"completion and then takes the benchmark suite output"
" directory and processes the benchmark measurements,"
" creating plots and collapsing results in a usable "
"form.",
Ex="%prog -i timing -o plots -w 124311,124312,124313")
]
# inputs map command line arguments and values onto Parameters. It is possible
# to define options here that do not exist as parameters, e.g., an output file.
inputs = [
__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)
]