# Source code for pymzml.run

    # -*- coding: utf-8 -*-
    # encoding: utf-8
    """
    The class :py:class:`Reader` has been designed to selectively extract data
    from a mzML file and to expose the data as a python object.
    Necessary information are read in and stored in a fast
    accessible format.
    The reader itself is an iterator, thus looping over all spectra
    follows the classical pythonian syntax.
    Additionally one can random access spectra by their nativeID
    if the file if not truncated by a conversion Program.

    Note:
        The class :py:class:`Writer` is still in development.

    """
    #
    # pymzml
    #
    # Copyright (C) 2016 M. Kösters, C. Fufezan
    #
    #    This program is free software: you can redistribute it and/or modify
    #    it under the terms of the GNU General Public License as published by
    #    the Free Software Foundation, either version 3 of the License, or
    #    (at your option) any later version.
    #
    #    This program is distributed in the hope that it will be useful,
    #    but WITHOUT ANY WARRANTY; without even the implied warranty of
    #    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    #    GNU General Public License for more details.
    #
    #    You should have received a copy of the GNU General Public License
    #    along with this program.  If not, see
    #    <http://www.gnu.org/licenses/>.from __future__ import print_function

    import re
    import os
    from collections import defaultdict as ddict
    import xml.etree.ElementTree as ElementTree
    from pymzml.file_interface import FileInterface
    import pymzml.spec as spec
    import pymzml.obo as obo
    import pymzml.regex_patterns as regex_patterns
    from pymzml.file_classes.standardMzml import StandardMzml

    class Reader(object):
        """
        Initialize Reader object for a given mzML file.

        Arguments:
            path (str): path to the mzml file to parse.

        Keyword Arguments:
            MS_precisions (dict): measured precisions for the different MS levels.
                e.g.::

                    {
                        1 : 5e-6,
                        2 : 20e-6
                    }

            obo_version (str, optional): obo version number as string. If not
                specified the version will be extracted from the mzML file

        Note:
            Setting the precision for MS1 and MSn spectra has changed in version 1.2.
            However, the old syntax as kwargs is still compatible ( e.g. 'MS1_Precision=5e-6').
        """

        def __init__(
            self,
            path,
            MS_precisions = None,
            obo_version   = None,
            build_index_from_scratch=False,
            **kwargs
        ):
            """Initialize and set required attributes."""
            self.build_index_from_scratch = build_index_from_scratch
            if MS_precisions is None:
                MS_precisions = {}
                if 'MS1_Precision' in kwargs.keys():
                    MS_precisions[1] = kwargs['MS1_Precision']
                if 'MSn_Precision' in kwargs.keys():
                    MS_precisions[2] = kwargs['MSn_Precision']

            # Parameters
            self.ms_precisions       = {
                1 : 5e-6,
                2 : 20e-6
            }
            self.ms_precisions.update(MS_precisions)

            # File info
            self.info                = ddict()
            self.info['file_name']   = path
            self.info['encoding']    = self._determine_file_encoding(path)
            self.info['file_object'] = self._open_file(self.info['file_name'])
            # if build_index_from_scratch is True:
            #     print(isinstance(self.info['file_object'], StandardMzml))
            #     print(type(self.info['file_object']))
            #     if isinstance(self.info['file_object'], StandardMzml):
            #         self.info['offset_dict'] = \
            #             self.info['file_object']._build_index_from_scratch()
            #     else:
            #         raise Exception(
            #             'Can only build index from scratch '
            #             'for standard mzML files.'
            #         )
            # else:
            self.info['offset_dict'] = self.info['file_object'].offset_dict
            self.info['obo_version'] = obo_version

            self.iter                = self._init_iter()
            self.OT                  = self._init_obo_translator()

        def __next__(self):
            """
            Iterator for the class :py:class:`Run`.

            Iterates all of the spectra in the file.

            Returns:
                Spectrum (:py:class:`Spectrum`): a spectrum object with interface
                    to the original spectrum element.

            Example:

            >>> for spectrum in Reader:
            ...     print(spectrum.mz, end='\\r')

            """
            has_ref_group = self.info.get('referenceable_param_group_list', False)
            while True:
                event, element = next(self.iter, ('END', 'END'))
                if event == 'end':
                    if element.tag.endswith('}spectrum'):
                        spectrum = spec.Spectrum(element)
                        if has_ref_group:
                            spectrum._set_params_from_reference_group(
                                self.info['referenceable_param_group_list_element']
                            )
                        ms_level = spectrum.ms_level
                        spectrum.measured_precision = self.ms_precisions[ms_level]
                        spectrum.calling_instance = self
                        return spectrum
                elif event == 'END':
                    raise StopIteration

        def __getitem__(self, identifier):
            """
            Access spectrum with native id 'identifier'.

            Arguments:
                identifier (str or int): last number in the id tag of the spectrum
                    element

            Returns:
                spectrum (Spectrum or Chromatogram): spectrum/chromatogram object
                with native id 'identifier'
            """
            try:
                if int(identifier) > self.get_spectrum_count():
                    raise Exception('Requested identifier is out of range')
            except:
                pass
            spectrum = self.info['file_object'][identifier]
            spectrum.calling_instance = self
            if isinstance(spectrum, spec.Spectrum):
                spectrum.measured_precision = self.ms_precisions[spectrum.ms_level]
            return spectrum

        @property
        def file_class(self):
            """Return file object in use."""
            return type(self.info['file_object'].file_handler)

        def _open_file(self, path):
            """
            Open the path using the FileInterface class as a wrapper.

            Arguments:
                path (str): path to the file to parse

            Returns:
                (FileInterface): Wrapper class for compressed and uncompressed
                    mzml files
            """
            return FileInterface(
                path,
                self.info['encoding'],
                build_index_from_scratch=self.build_index_from_scratch
            )

        def _determine_file_encoding(self, path):
            """
            Determine the encoding used for the file in path.

            Arguments:
                path (str): path to the mzml files

            Returns:
                mzml_encoding (str): encoding type of the file
            """
            mzml_encoding = 'utf-8'
            if os.path.exists(path):
                sniffer = open(path, 'rb')
                header = sniffer.readline()
                encoding_pattern = regex_patterns.FILE_ENCODING_PATTERN
                match = encoding_pattern.search(header)
                if match:
                    mzml_encoding = bytes.decode(
                        match.group('encoding')
                    )
                sniffer.close()
            return mzml_encoding

        def _init_obo_translator(self):
            """
            Initialize the obo translator with the minimum requirement
            and extra Accessions.

            Returns:
                obo_translator (OboTranslator): translator class to translate
                    accessions to names
            """
            # parse obo, check MS tags and if they are ok in minimum.py (minimum
            # required) ...
            if self.info.get('obo_version', None) is None:
                self.info['obo_version'] = '1.1.0'
            obo_translator = obo.OboTranslator(version=self.info['obo_version'])

            return obo_translator

        def _init_iter(self):
            """
            Initalize the iterator for the spectra and sets it to the start
            of the spectrumList element.

            Returns:
                mzml_iter (xml.etree.ElementTree._IterParseIterator): Iterator over
                    all element in the file starting with the first spectrum
            """
            mzml_iter = iter(ElementTree.iterparse(
                self.info['file_object'],
                events=('end', 'start')
            ))  # NOTE: end might be sufficient
            _, self.root = next(mzml_iter)
            while True:
                event, element = next(mzml_iter, ('END', 'END'))
                if element.tag.endswith('}mzML'):
                    if 'version' in element.attrib \
                            and len(element.attrib['version']) > 0:
                        self.info['mzml_version'] = element.attrib['version']
                    else:
                        s = element.attrib[
                            '{http://www.w3.org/2001/XMLSchema-instance}'
                            'schemaLocation'
                        ]
                        self.info['mzml_version'] = re.search(
                            r'[0-9]*\.[0-9]*\.[0-9]*', s).group()
                elif element.tag.endswith('}cv'):
                    if not self.info['obo_version'] \
                            and element.attrib.get('id', None) == 'MS':
                        self.info['obo_version'] = element.attrib.get(
                            'version',
                            '1.1.0'
                        )
                elif element.tag.endswith('}referenceableParamGroupList'):
                    self.info['referenceable_param_group_list'] = True
                    self.info['referenceable_param_group_list_element'] = element
                elif element.tag.endswith('}spectrumList'):
                    spec_cnt = element.attrib.get('count')
                    self.info['spectrum_count'] = int(spec_cnt) if spec_cnt else None
                    break
                elif element.tag.endswith('}chromatogramList'):
                    chrom_cnt = element.attrib.get('count', None)
                    if chrom_cnt is None:
                        self.info['chromatogram_count'] = None
                    else:
                        self.info['chromatogram_count'] = int(chrom_cnt)
                    break
                elif element.tag.endswith('}run'):
                    run_id = element.attrib.get('id')
                    start_time = element.attrib.get('startTimeStamp')
                    self.info['run_id'] = run_id
                    self.info['start_time'] = start_time
                else:
                    pass
            self.root.clear()
            return mzml_iter

        def __iter__(self):
            """Return self."""
            return self

        def next(self):
            """Function to return the next Spectrum element."""
            return self.__next__()

        def get_spectrum_count(self):
            """
            Number of spectra in file.

            Returns:
                spectrum count (int): Number of spectra in file.
            """
            return self.info['spectrum_count']

        def get_chromatogram_count(self):
            """
            Number of chromatograms in file.

            Returns:
                chromatogram count (int): Number of chromatograms in file.
            """
            return self.info['chromatogram_count']

    if __name__ == '__main__':
        print(__doc__)