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#!/usr/bin/env python
# ----------------------------------------------------------------------------
# Copyright (c) 2011-2013, The BIOM Format Development Team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# ----------------------------------------------------------------------------
import sys
from pyqi.core.interfaces.optparse import (OptparseOption,
OptparseUsageExample,
OptparseResult)
from pyqi.core.command import (make_command_in_collection_lookup_f,
make_command_out_collection_lookup_f)
from pyqi.core.interfaces.optparse.output_handler import print_list_of_strings
from biom.commands.table_validator import CommandConstructor
from biom.interfaces.optparse.input_handler import load_hdf5_or_json
__author__ = "Jai Ram Rideout"
__copyright__ = "Copyright 2011-2013, The BIOM Format Development Team"
__credits__ = ["Jai Ram Rideout", "Daniel McDonald"]
__license__ = "BSD"
__url__ = "http://biom-format.org"
__maintainer__ = "Jai Ram Rideout"
__email__ = "jai.rideout@gmail.com"
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'),
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)
]
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