# -*- coding: utf-8 -*-

"""
Copyright [2009-2021] EMBL-European Bioinformatics Institute
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 json
import logging
from pathlib import Path
import typing as ty

from sqlitedict import SqliteDict

from rnacentral_pipeline.databases import data
from rnacentral_pipeline.databases.generic import v1

LOGGER = logging.getLogger(__name__)


def update_entry(context: SqliteDict, entry: ty.Dict[str, ty.Any]) -> ty.Dict[str, ty.Any]:
    taxid = entry['taxonId']
    if taxid not in context:
        raise ValueError(f"Unknown tax id {taxid}")

    tax_info = context[taxid]
    if tax_info.replaced_by:
        pid = entry['primaryId']
        updated = tax_info.replaced_by
        entry['taxonId'] = updated
        LOGGER.info(f"Entry {pid} replaced taxid {taxid} -> {updated}")
    return entry


def parse(context_file: Path, json_file: Path) -> ty.Iterable[data.Entry]:
    context = SqliteDict(filename=context_file)
    with json_file.open('r') as raw:
        ncrnas = json.load(raw)
    ncrnas['data'] = [update_entry(context, e) for e in ncrnas['data']]
    return v1.parse(ncrnas)

# -*- coding: utf-8 -*-

"""
Copyright [2009-2021] EMBL-European Bioinformatics Institute
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 json
import logging
from pathlib import Path
import typing as ty

from sqlitedict import SqliteDict

from rnacentral_pipeline.databases import data
from rnacentral_pipeline.databases.generic import v1

LOGGER = logging.getLogger(__name__)


def update_entry(context: SqliteDict, entry: ty.Dict[str, ty.Any]) -> ty.Dict[str, ty.Any]:
    prefix, raw_taxid = entry['taxonId'].split(":", 1)
    taxid = int(raw_taxid)
    if taxid not in context:
        raise ValueError(f"Unknown tax id {taxid}")

    tax_info = context[taxid]
    if tax_info.replaced_by:
        pid = entry['primaryId']
        updated = tax_info.replaced_by
        entry['taxonId'] = f"{prefix}:{updated}"
        LOGGER.info(f"Entry {pid} replaced taxid {taxid} -> {updated}")
    return entry


def parse(context_file: Path, json_file: Path) -> ty.Iterable[data.Entry]:
    context = SqliteDict(filename=context_file)
    with json_file.open('r') as raw:
        ncrnas = json.load(raw)
    ncrnas['data'] = [update_entry(context, e) for e in ncrnas['data']]
    yield from v1.parse(ncrnas)

Fix taxid parsing