#!/usr/bin/env python
# Dan Blankenberg
# Very simple example of using the API to run Data Managers
# Script makes the naive assumption that dbkey==sequence id, which in many cases is not true nor desired
# *** This script is not recommended for use as-is on a production server ***
from __future__ import print_function

import optparse
import time

from six.moves.urllib.parse import urljoin

from common import get, post  # noqa: I100,I202

DEFAULT_SLEEP_TIME = 3
FETCH_GENOME_TOOL_ID = 'testtoolshed.g2.bx.psu.edu/repos/blankenberg/data_manager_fetch_genome_all_fasta/data_manager_fetch_genome_all_fasta/0.0.1'
BUILD_INDEX_TOOLS_ID = ['testtoolshed.g2.bx.psu.edu/repos/blankenberg/data_manager_bwa_index_builder/bwa_index_builder_data_manager/0.0.1',
                        'testtoolshed.g2.bx.psu.edu/repos/blankenberg/data_manager_bwa_index_builder/bwa_color_space_index_builder_data_manager/0.0.1']


def run_tool(tool_id, history_id, params, api_key, galaxy_url, wait=True, sleep_time=None, **kwargs):
    sleep_time = sleep_time or DEFAULT_SLEEP_TIME
    tools_url = urljoin(galaxy_url, 'api/tools')
    payload = {
        'tool_id': tool_id,
    }
    if history_id:
        payload['history_id'] = history_id
    payload['inputs'] = params
    rval = post(api_key, tools_url, payload)
    if wait:
        outputs = list(rval['outputs'])
        while outputs:
            finished_datasets = []
            for i, dataset_dict in enumerate(outputs):
                if dataset_is_terminal(dataset_dict['id'], api_key=api_key, galaxy_url=galaxy_url):
                    finished_datasets.append(i)
            for i in reversed(finished_datasets):
                outputs.pop(0)
            if wait and outputs:
                time.sleep(sleep_time)

    return rval


def get_dataset_state(hda_id, api_key, galaxy_url):
    datasets_url = urljoin(galaxy_url, 'api/datasets/%s' % hda_id)
    dataset_info = get(api_key, datasets_url)
    return dataset_info['state']


def dataset_is_terminal(hda_id, api_key, galaxy_url):
    dataset_state = get_dataset_state(hda_id, api_key, galaxy_url)
    return dataset_state in ['ok', 'error']


if __name__ == '__main__':
    parser = optparse.OptionParser()
    parser.add_option('-k', '--key', dest='api_key', action='store', type="string", default=None, help='API Key.')
    parser.add_option('-u', '--url', dest='base_url', action='store', type="string", default='http://localhost:8080', help='Base URL of Galaxy Server')
    parser.add_option('-d', '--dbkey', dest='dbkeys', action='append', type="string", default=[], help='List of dbkeys to download and Index')
    parser.add_option('-s', '--sleep_time', dest='sleep_time', action='store', type="int", default=DEFAULT_SLEEP_TIME, help='How long to sleep between check loops')
    (options, args) = parser.parse_args()

    # check options
    assert options.api_key is not None, ValueError('You must specify an API key.')
    assert options.dbkeys, ValueError('You must specify at least one dbkey to use.')

    # check user is admin
    configuration_options = get(options.api_key, urljoin(options.base_url, 'api/configuration'))
    if 'library_import_dir' not in configuration_options:  # hack to check if is admin user
        print("Warning: Data Managers are only available to admin users. The API Key provided does not appear to belong to an admin user. Will attempt to run anyway.")

    # Fetch Genomes
    dbkeys = {}
    for dbkey in options.dbkeys:
        if dbkey not in dbkeys:
            dbkeys[dbkey] = run_tool(FETCH_GENOME_TOOL_ID, None, {'dbkey': dbkey, 'reference_source|reference_source_selector': 'ucsc', 'reference_source|requested_dbkey': dbkey}, options.api_key, options.base_url, wait=False)
        else:
            "dbkey (%s) was specified more than once, skipping additional specification." % (dbkey)

    print('Genomes Queued for downloading.')

    # Start indexers
    indexing_tools = []
    while dbkeys:
        for dbkey, value in dbkeys.items():
            if dataset_is_terminal(value['outputs'][0]['id'], options.api_key, options.base_url):
                del dbkeys[dbkey]
                for tool_id in BUILD_INDEX_TOOLS_ID:
                    indexing_tools.append(run_tool(tool_id, None, {'all_fasta_source': dbkey}, options.api_key, options.base_url, wait=False))
        if dbkeys:
            time.sleep(options.sleep_time)

    print('All genomes downloaded and indexers now queued.')

    # Wait for indexers to finish
    while indexing_tools:
        for i, indexing_tool_value in enumerate(indexing_tools):
            if dataset_is_terminal(indexing_tool_value['outputs'][0]['id'], options.api_key, options.base_url):
                print('Finished:', indexing_tool_value)
                del indexing_tools[i]
                break
        if indexing_tools:
            time.sleep(options.sleep_time)

    print('All indexers have been run, please check results.')