old_contents: # -*- 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 csv
  
  import psycopg2
  from pypika import Query, Table, Field
  from pypika import functions as fn
  
  
  def upi_taxid_ranges(ranges, tablename, db_url):
      table = Table(tablename)
      with psycopg2.connect(db_url) as conn:
          with conn.cursor() as cur:
              for (start, stop) in ranges:
                  query = Query.from_(table).\
                      select(fn.Min(table.id),
                              fn.Max(table.id)).\
                      where(table.precompute_urs_id.isin([start, stop]))
  
                  cur.execute(str(query), ((start, stop),))
                  results = cur.fetchall()
                  assert len(results) == 1
                  (upi_start, upi_max) = results[0]
                  yield (start, upi_start, upi_max)
  
  
  def write(handle, output, tablename=None, db_url=None):
      reader = csv.reader(handle)
      ranges = [(start, stop) for (_tablename, start, stop) in reader]
      writer = csv.writer(output)
      writer.writerows(upi_taxid_ranges(ranges, tablename, db_url))
  
new_contents: # -*- 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 csv
  
  import psycopg2
  from pypika import Query, Table, Field
  from pypika import functions as fn
  
  
  def upi_taxid_ranges(ranges, tablename, db_url):
      table = Table(tablename)
      with psycopg2.connect(db_url) as conn:
          with conn.cursor() as cur:
              for (start, stop) in ranges:
                  query = Query.from_(table).\
                      select(fn.Min(table.id),
                             fn.Max(table.id)).\
                      where(table.precompute_urs_id.isin([start, stop]))
  
                  cur.execute(str(query), ((start, stop),))
                  results = cur.fetchall()
                  assert len(results) == 1
                  (upi_start, upi_max) = results[0]
                  yield (start, upi_start, upi_max)
  
  
  def write(handle, output, tablename='precompute_urs_taxid', db_url=None):
      reader = csv.reader(handle)
      ranges = [(start, stop) for (_tablename, start, stop) in reader]
      writer = csv.writer(output)
      writer.writerows(upi_taxid_ranges(ranges, tablename, db_url))
  
subject: Format and add default tablename