#
# readGet.py
#
#
# Copyright 2017 EMBL-EBI, Hinxton outstation
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#   http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#

import os
import sys
import argparse

import utils

def check_read_format(output_format):
    if output_format not in [utils.SUBMITTED_FORMAT, utils.FASTQ_FORMAT, utils.SRA_FORMAT]:
        sys.stderr.write(
            'ERROR: Invalid format. Please select a valid format for this accession: {0}\n'.format(
            [utils.SUBMITTED_FORMAT, utils.FASTQ_FORMAT, utils.SRA_FORMAT])
        )
        sys.exit(1)

def check_analysis_format(output_format):
    if output_format != utils.SUBMITTED_FORMAT:
        sys.stderr.write(
            'ERROR: Invalid format. Please select a valid format for this accession: {0}\n'.format(
            utils.SUBMITTED_FORMAT)
        )
        sys.exit(1)

def attempt_file_download(file_url, dest_dir, md5, aspera):
    if md5 is not None:
        print 'Downloading file with md5 check:' + file_url
        if aspera:
            return utils.get_aspera_file_with_md5_check(file_url, dest_dir, md5)
        else:
            return utils.get_ftp_file_with_md5_check('ftp://' + file_url, dest_dir, md5)
    print 'Downloading file:' + file_url
    if aspera:
        return utils.get_aspera_file(file_url, dest_dir)
    return utils.get_ftp_file('ftp://' + file_url, dest_dir)

def download_file(file_url, dest_dir, md5, aspera):
    if utils.file_exists(file_url, dest_dir, md5):
        return
    success = attempt_file_download(file_url, dest_dir, md5, aspera)
    if not success:
        success = attempt_file_download(file_url, dest_dir, md5, aspera)
    if not success:
        print 'Failed to download file after two attempts'

def download_meta(accession, dest_dir):
    utils.download_record(dest_dir, accession, utils.XML_FORMAT)

def download_experiment_meta(run_accession, dest_dir):
    search_url = utils.get_experiment_search_query(run_accession)
    response = utils.get_report_from_portal(search_url)
    header = True
    for line in response:
        if header:
            header = False
            continue
        experiment_accession = line.strip().split('\t')[-1]
        break
    download_meta(experiment_accession, dest_dir)

def download_files(accession, output_format, dest_dir, fetch_index, fetch_meta, aspera):
    accession_dir = os.path.join(dest_dir, accession)
    utils.create_dir(accession_dir)
    # download experiment xml
    is_experiment = utils.is_experiment(accession)
    if fetch_meta and is_experiment:
        download_meta(accession, accession_dir)
    if fetch_meta and utils.is_run(accession):
        download_experiment_meta(accession, accession_dir)
    # download data files
    search_url = utils.get_file_search_query(accession, aspera)
    temp_file = os.path.join(dest_dir, 'temp.txt')
    utils.download_report_from_portal(search_url, temp_file)
    f = open(temp_file)
    lines = f.readlines()
    f.close()
    os.remove(temp_file)
    for line in lines[1:]:
        data_accession, filelist, md5list, indexlist = utils.parse_file_search_result_line(
            line, accession, output_format)
        # create run directory if downloading all data for an experiment
        if is_experiment:
            run_dir = os.path.join(accession_dir, data_accession)
            utils.create_dir(run_dir)
            target_dir = run_dir
        else:
            target_dir = accession_dir
        # download run/analysis XML
        if fetch_meta:
            download_meta(data_accession, target_dir)
        if len(filelist) == 0:
            if output_format is None:
                print 'No files available for {0}'.format(data_accession)
            else:
                print 'No files of format {0} available for {1}'.format(
                    output_format, data_accession)
            continue
        for i in range(len(filelist)):
            file_url = filelist[i]
            md5 = md5list[i]
            if file_url != '':
                download_file(file_url, target_dir, md5, aspera)
        if fetch_index:
            for index_file in indexlist:
                if index_file != '':
                    download_file(index_file, target_dir, None, aspera)
        if utils.is_empty_dir(target_dir):
            print 'Deleting directory ' + os.path.basename(target_dir)
            os.rmdir(target_dir)