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.
  """
  
  from tasks.config import ontologies
  
  from tasks.utils.pgloader import PGLoader
  
  from tasks.rfam.go_terms import RfamGoTerms
  from tasks.quickgo.quickgo_data import QuickGoData
  
  
  CONTROL_FILE = """
  LOAD CSV
  FROM ALL FILENAMES MATCHING ~<{pattern}> WITH ENCODING ISO-8859-14
  HAVING FIELDS
  (
      ontology_term_id,
      ontology,
      name,
      definition
  )
  INTO {db_url}
  TARGET COLUMNS
  (
      ontology_term_id,
      ontology,
      name,
      definition
  )
  SET
      search_path = '{search_path}'
  
  WITH
      skip header = 1,
      fields escaped by double-quote,
      fields terminated by ','
  
  BEFORE LOAD DO
  $$
  evidence
  create table if not exists {load_table} (
      ontology_term_id varchar(15),
      ontology varchar(5),
      name text,
      definition text
  );
  $$,
  $$
  truncate table {load_table};
  $$
  
  AFTER LOAD DO
  $$ insert into {final_table} (
      ontology_term_id,
      ontology,
      name,
      definition
  ) (
  select
      ontology_term_id,
      ontology,
      name,
      definition
  from load_go_terms
  )
  ON CONFLICT (ontology_term_id) DO UPDATE SET
      ontology_term_id = excluded.ontology_term_id,
      ontology = excluded.ontology,
      name = excluded.name,
      definition = excluded.definition
  ;
  $$,
  $$
  drop table {load_table};
  $$
  ;
  """
  
  
  class Ontologies(PGLoader):  # pylint: disable=R0904
      """
      Load all Ontology data into the database.
      """
  
      def requires(self):
          return [
              QuickGoData(),
              RfamGoTerms(),
          ]
  
      def control_file(self):
          table = 'ontology_terms'
          load_table = 'load_' + table
          return CONTROL_FILE.format(
              pattern=ontologies().to_load('*'),
              final_table=table,
              load_table=load_table,
              search_path=self.db_search_path(),
              db_url=self.db_url(table=load_table),
          )
  
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.
  """
  
  from tasks.config import ontologies
  
  from tasks.utils.pgloader import PGLoader
  
  from tasks.rfam.go_terms import RfamGoTerms
  from tasks.quickgo.quickgo_data import QuickGoData
  
  
  CONTROL_FILE = """
  LOAD CSV
  FROM ALL FILENAMES MATCHING ~<{pattern}> WITH ENCODING ISO-8859-14
  HAVING FIELDS
  (
      ontology_term_id,
      ontology,
      name,
      definition
  )
  INTO {db_url}
  TARGET COLUMNS
  (
      ontology_term_id,
      ontology,
      name,
      definition
  )
  SET
      search_path = '{search_path}'
  
  WITH
      skip header = 1,
      fields escaped by double-quote,
      fields terminated by ','
  
  BEFORE LOAD DO
  $$
  create table if not exists {load_table} (
      ontology_term_id varchar(15),
      ontology varchar(5),
      name text,
      definition text
  );
  $$,
  $$
  truncate table {load_table};
  $$
  
  AFTER LOAD DO
  $$ insert into {final_table} (
      ontology_term_id,
      ontology,
      name,
      definition
  ) (
  select
      ontology_term_id,
      ontology,
      name,
      definition
  from load_go_terms
  )
  ON CONFLICT (ontology_term_id) DO UPDATE SET
      ontology_term_id = excluded.ontology_term_id,
      ontology = excluded.ontology,
      name = excluded.name,
      definition = excluded.definition
  ;
  $$,
  $$
  drop table {load_table};
  $$
  ;
  """
  
  
  class Ontologies(PGLoader):  # pylint: disable=R0904
      """
      Load all Ontology data into the database.
      """
  
      def requires(self):
          return [
              QuickGoData(),
              RfamGoTerms(),
          ]
  
      def control_file(self):
          table = 'ontology_terms'
          load_table = 'load_' + table
          return CONTROL_FILE.format(
              pattern=ontologies().to_load('*'),
              final_table=table,
              load_table=load_table,
              search_path=self.db_search_path(),
              db_url=self.db_url(table=load_table),
          )
  
subject: Delete strange word