#!/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__ = "Greg Caporaso"
__copyright__ = "Copyright 2011-2013, The BIOM Format Development Team"
__credits__ = ["Greg Caporaso", "Jai Ram Rideout"]
__license__ = "BSD"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"

import json
from biom.util import biom_open
from biom.parse import MetadataMap, parse_biom_table
from pyqi.core.interfaces.optparse.input_handler import load_file_contents


def biom_load_file_contents(fp):
    if fp is None:
        return fp
    return load_file_contents(fp)


def load_hdf5_or_json(fp):
    """Return a parsed JSON object or an HDF5 object"""
    with biom_open(fp) as f:
        if hasattr(f, 'seek'):
            return json.load(f)
        else:
            return f


def load_biom_table(biom_fp):
    """Return a parsed BIOM table."""
    with biom_open(biom_fp, 'U') as table_f:
        return parse_biom_table(table_f)


def load_biom_table_with_file_contents(biom_fp):
    """Return a BIOM table and the original open filehandle as a tuple.

    Useful when additional computation needs to be performed on the file
    contents, such as an MD5 sum.

    WARNING: this function does not close the open filehandle that it returns.
    Users of this function are responsible for closing the filehandle when done
    using it!
    """
    with biom_open(biom_fp, 'U') as biom_f:
        table = parse_biom_table(biom_f)

        if hasattr(biom_f, 'seek'):
            biom_f.seek(0)

        return table, biom_f


def load_json_document(fp):
    """Return a parsed JSON object."""
    with biom_open(fp, 'U') as f:
        return json.load(f)


def load_metadata(fp):
    """Parse a sample/observation metadata file, return a ``MetadataMap``.

    If ``fp`` is ``None``, this function will return ``None``.
    """
    if fp is None:
        return None
    else:
        with open(fp, 'U') as f:
            return MetadataMap.from_file(f)