old_contents: # -*- coding: utf-8 -*-
  
  """
  Copyright [2009-2018] 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 click
  
  from . import ensembl
  from . import europepmc
  from . import external
  from . import fetch
  from . import ftp_export
  from . import genes
  from . import genome_mapping
  from . import lookup
  from . import misc
  from . import ncbi
  from . import ols
  from . import precompute
  from . import qa
  from . import r2dt
  from . import rfam
  from . import search_export
  from . import text_mining
  
  
  @click.group()
  def cli():
      """
      This script contains commands for dealing with the RNAcentral import
      pipeline. This handles individual python parts, and the overall pipeline is
      coordinated by nextflow.
      """
      pass
  
  
  cli.add_command(ensembl.cli)
  cli.add_command(europepmc.cli)
  cli.add_command(external.cli)
  cli.add_command(fetch.cli)
  cli.add_command(ftp_export.cli)
  cli.add_command(genes.cli)
  cli.add_command(genome_mapping.cli)
  cli.add_command(lookup.cli)
  cli.add_command(misc.check_release)
  cli.add_command(misc.crs_data)
  cli.add_command(misc.find_upi_ranges)
  cli.add_command(misc.run_release)
  cli.add_command(misc.validate_pgloader)
  cli.add_command(ncbi.cli)
  cli.add_command(ols.cli)
  cli.add_command(precompute.cli)
  cli.add_command(qa.cli)
  cli.add_command(r2dt.cli)
  cli.add_command(rfam.cli)
  cli.add_command(search_export.cli)
  cli.add_command(text_mining.cli)
  
new_contents: # -*- coding: utf-8 -*-
  
  """
  Copyright [2009-2018] 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 logging
  
  import click
  
  from . import (ensembl, europepmc, external, fetch, ftp_export, genes,
                 genome_mapping, lookup, misc, ncbi, ols, precompute, qa, r2dt,
                 rfam, search_export, text_mining)
  
  
  @click.group()
  @click.option(
      "--log-level",
      default="warn",
      type=click.Choice(
          ["critical", "error", "warn", "info", "debug"], case_sensitive=False
      ),
  )
  def cli(log_level):
      """
      This script contains commands for dealing with the RNAcentral import
      pipeline. This handles individual python parts, and the overall pipeline is
      coordinated by nextflow.
      """
      level = getattr(logging, log_level.upper())
      logger = logging.getLogger()
      logger.setLevel(level=level)
      pass
  
  
  cli.add_command(ensembl.cli)
  cli.add_command(europepmc.cli)
  cli.add_command(external.cli)
  cli.add_command(fetch.cli)
  cli.add_command(ftp_export.cli)
  cli.add_command(genes.cli)
  cli.add_command(genome_mapping.cli)
  cli.add_command(lookup.cli)
  cli.add_command(misc.check_release)
  cli.add_command(misc.crs_data)
  cli.add_command(misc.find_upi_ranges)
  cli.add_command(misc.run_release)
  cli.add_command(misc.validate_pgloader)
  cli.add_command(ncbi.cli)
  cli.add_command(ols.cli)
  cli.add_command(precompute.cli)
  cli.add_command(qa.cli)
  cli.add_command(r2dt.cli)
  cli.add_command(rfam.cli)
  cli.add_command(search_export.cli)
  cli.add_command(text_mining.cli)
  
subject: Add some logging config