old_contents: # -*- coding: utf-8 -*-
  
  """
  Copyright [2009-2017] 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 luigi
  
  from tasks.config import db
  from .utils.db import cursor
  
  
  SQL = """
  select
      dbid,
      id,
      release_type,
      release_date,
      force_load
  from rnacen.rnc_release
  where status = 'L'
  order by id
  """
  
  CREATE_INDEX = """
  create index if not exists load_rnacentral_all$database
  on rnacen.load_rnacentral_all(database)
  """
  
  
  class StoreRelease(luigi.Task):  # pylint: disable=R0904
      """
      This will store all the loaded data. It will not prepare a new database
      release by itself.
      """
  
      def run(self):
          with cursor(db()) as cur:
              cur.execute(CREATE_INDEX)
              cur.execute("select rnc_update.prepare_releases('F')")
              cur.execute(SQL)
              for result in cur.fetchall():
                  cur.execute('select rnc_update.new_update_release(%s, %s)',
                              (result[0], result[1]))
  
                  # Analyze loaded table
                  cur.execute('VACUUM (VERBOSE,ANALYZE) rnacen.load_rnc_accessions')
  
                  # Compile update procedure? - Probably not needed
                  # psql -d pfmegrnapro -h pgsql-hxvm-038.ebi.ac.uk -U rnacen -f schema/packages/rnc_update/update_rnc_accessions_package.sql
  
                  # run reviewed procedures w/o index creation on
                  # load_rnc_accession (not used in plan) and with work_mem=1GB
                  cur.execute('set work_mem=1GB')
                  cur.execute('select rnc_update.update_rnc_accessions()')
                  cur.execute('select rnc_update.update_literature_references()')
  
new_contents: # -*- coding: utf-8 -*-
  
  """
  Copyright [2009-2017] 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 os
  
  import luigi
  
  from tasks.config import db, output
  from .utils.db import cursor
  
  
  SQL = """
  select
      dbid,
      id,
      release_type,
      release_date,
      force_load
  from rnacen.rnc_release
  where status = 'L'
  order by id
  """
  
  CREATE_INDEX = """
  create index if not exists load_rnacentral_all$database
  on rnacen.load_rnacentral_all(database)
  """
  
  
  class StoreRelease(luigi.Task):  # pylint: disable=R0904
      """
      Import data from the temporary load_* tables into the main tables.
      Create a sentinel file on completion.
      To rerun the import, the sentinel file must be deleted.
      """
  
      def run(self):
          with cursor(db()) as cur:
              cur.execute(CREATE_INDEX)
              cur.execute("select rnc_update.prepare_releases('F')")
              cur.execute(SQL)
              for result in cur.fetchall():
                  cur.execute('select rnc_update.new_update_release(%s, %s)',
                              (result[0], result[1]))
  
                  # Analyze loaded table
                  cur.execute('VACUUM (VERBOSE,ANALYZE) rnacen.load_rnc_accessions')
          with open(self.output().fn , 'w') as sentinel_file:
              sentinel_file.write('Done')
  
                  # Compile update procedure? - Probably not needed
                  # psql -d pfmegrnapro -h pgsql-hxvm-038.ebi.ac.uk -U rnacen -f schema/packages/rnc_update/update_rnc_accessions_package.sql
  
                  # run reviewed procedures w/o index creation on
                  # load_rnc_accession (not used in plan) and with work_mem=1GB
                  cur.execute('set work_mem=1GB')
                  cur.execute('select rnc_update.update_rnc_accessions()')
                  cur.execute('select rnc_update.update_literature_references()')
      def output(self):
          """
          Check that a sentinel file exists.
          """
          return luigi.LocalTarget(os.path.join(output().base, '%s.txt' % self.__class__.__name__))
  
subject: Create a sentinel file after release loading