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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.
# -----------------------------------------------------------------------------
__author__ = "Evan Bolyen"
__copyright__ = "Copyright 2011-2013, The BIOM Format Development Team"
__credits__ = [
"Evan Bolyen",
"Jai Ram Rideout",
"Greg Caporaso",
"Daniel McDonald"]
__license__ = "BSD"
__url__ = "http://biom-format.org"
__maintainer__ = "Evan Bolyen"
__email__ = "ebolyen@gmail.com"
from pyqi.core.interfaces.html import (HTMLInputOption, HTMLDownload)
from pyqi.core.command import (make_command_in_collection_lookup_f,
make_command_out_collection_lookup_f)
from pyqi.core.interfaces.html.output_handler import newline_list_of_strings
from biom.interfaces.html.input_handler import load_metadata
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)
inputs = [
HTMLInputOption(Parameter=cmd_in_lookup('table'),
Type='upload_file',
Help='the input table filepath, either in BIOM or classic '
'format'),
HTMLInputOption(Parameter=cmd_in_lookup('to_tsv'),
Type=bool),
HTMLInputOption(Parameter=cmd_in_lookup('to_json'),
Type=bool),
HTMLInputOption(Parameter=cmd_in_lookup('to_hdf5'),
Type=bool),
HTMLInputOption(Parameter=cmd_in_lookup('sample_metadata'),
Type='upload_file',
Handler=load_metadata),
HTMLInputOption(Parameter=cmd_in_lookup('observation_metadata'),
Type='upload_file',
Handler=load_metadata),
HTMLInputOption(Parameter=cmd_in_lookup('header_key')),
HTMLInputOption(Parameter=cmd_in_lookup('output_metadata_id')),
HTMLInputOption(Parameter=cmd_in_lookup('process_obs_metadata'),
Type='multiple_choice',
Choices=['taxonomy', 'naive', 'sc_separated'],
Help='Process metadata associated with observations when '
'converting from a classic table'),
HTMLInputOption(Parameter=cmd_in_lookup('tsv_metadata_formatter'),
Type='multiple_choice',
Choices=['naive', 'sc_separated'],
Help='Format the metadata for TSV output'),
HTMLInputOption(Parameter=None,
Name='download-file',
Required=True,
Help='the download file')
]
outputs = [
HTMLDownload(Parameter=cmd_out_lookup('table'),
Handler=newline_list_of_strings,
FilenameLookup='download-file',
FileExtension='.biom')
]
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