# ----------------------------------------------------------------------------
# Copyright (c) 2022, Bokulich Laboratories.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------

import qiime2 as q2

import pandas as pd
import threading

from q2_fondue.utils import handle_threaded_exception
from qiime2 import Artifact


threading.excepthook = handle_threaded_exception


def get_all(
        ctx, accession_ids, email, n_jobs=1, retries=2, log_level='INFO',
        linked_doi=None):

    # get required methods
    get_metadata = ctx.get_action('fondue', 'get_metadata')
    get_sequences = ctx.get_action('fondue', 'get_sequences')

    # fetch metadata
    metadata, failed_ids = get_metadata(
        accession_ids, email, n_jobs, log_level, linked_doi
    )
    failed_ids_df = failed_ids.view(pd.DataFrame)

    # fetch sequences - use metadata to get run ids, regardless if
    # runs or projects were requested
    run_ids = q2.Artifact.import_data(
        'NCBIAccessionIDs', pd.Series(metadata.view(pd.DataFrame).index)
    )
    seq_single, seq_paired, failed_ids, = get_sequences(
        run_ids, email, retries, n_jobs, log_level
    )
    failed_ids_df = pd.concat(
        [failed_ids_df, failed_ids.view(pd.DataFrame)])
    if failed_ids_df.shape[0] > 0:
        failed_ids = Artifact.import_data('SRAFailedIDs', failed_ids_df)

    return metadata, seq_single, seq_paired, failed_ids