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.utils.pgloader import PGLoader
  
  from tasks.ontologies import Ontologies
  
  from .quickgo_data import QuickGoData
  
  
  CONTROL_FILE = """
  LOAD CSV
  FROM '{filename}'
  WITH ENCODING ISO-8859-14
  
  HAVING FIELDS ({fields})
  INTO {db_url}
  TARGET COLUMNS ({columns})
  
  SET
      search_path = '{search_path}'
  
  WITH
      fields escaped by double-quote,
      fields terminated by ','
  
  BEFORE LOAD DO
  $$
  create table if not exists {load_table} (
      rna_id varchar(50),
      qualifier varchar(30),
      assigned_by varchar(50),
      extensions jsonb,
      ontology_term_id varchar(15),
      evidence_code varchar(15)
  );
  $$,
  $$
  truncate table {load_table};
  $$
  
  AFTER LOAD DO
  $$
  INSERT INTO {final_table} (
      rna_id,
      qualifier,
      assigned_by,
      extensions,
      ontology_term_id,
      evidence_code
  ) (
  SELECT (
      rna_id,
      qualifier,
      assigned_by,
      extensions,
      ontology_term_id,
      evidence_code
  )
  FROM {load_table}
  )
  ON CONFLICT (rna_id, qualifier, assigned_by, ontology_term_id, evidence_code)
  DO UPDATE
  SET
      rna_id = excluded.rna_id,
      qualifier = excluded.qualifier,
      assigned_by = excluded.assigned_by,
      extensions = excluded.extensions,
      ontology_term_id = excluded.ontology_term_id,
      evidence_code = excluded.evidence_code
  ;
  $$,
  $$
  DROP TABLE {load_table};
  $$
  ;
  """
  
  
  class QuickGoLoadAnnotations(PGLoader):
      def requires(self):
          return [
              QuickGoData(),
              Ontologies(),
          ]
  
      def control_file(self):
          output = self.requires()[0].output()
          table = 'go_term_annotations'
          load_table = 'load_' + table
          fields = ', '.join(output.annotations.headers)
  
          return CONTROL_FILE.format(
              filename=output.annotations.filename,
              fields=fields,
              columns=fields,
              final_table=table,
              load_table=load_table,
              db_url=self.db_url(table=load_table),
              search_path=self.db_search_path(),
          )
  
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.utils.pgloader import PGLoader
  
  from tasks.ontologies import Ontologies
  
  from .quickgo_data import QuickGoData
  
  
  CONTROL_FILE = """
  LOAD CSV
  FROM '{filename}'
  WITH ENCODING ISO-8859-14
  
  HAVING FIELDS ({fields})
  INTO {db_url}
  TARGET COLUMNS ({columns})
  
  SET
      search_path = '{search_path}'
  
  WITH
      fields escaped by double-quote,
      fields terminated by ','
  
  BEFORE LOAD DO
  $$
  create table if not exists {load_table} (
      rna_id varchar(50),
      qualifier varchar(30),
      assigned_by varchar(50),
      extensions jsonb,
      ontology_term_id varchar(15),
      evidence_code varchar(15)
  );
  $$,
  $$
  truncate table {load_table};
  $$
  
  AFTER LOAD DO
  $$
  INSERT INTO {final_table} (
      rna_id,
      qualifier,
      assigned_by,
      extensions,
      ontology_term_id,
      evidence_code
  ) (
  SELECT
      rna_id,
      qualifier,
      assigned_by,
      extensions,
      ontology_term_id,
      evidence_code
  FROM {load_table}
  )
  ON CONFLICT (rna_id, qualifier, assigned_by, ontology_term_id, evidence_code)
  DO UPDATE
  SET
      rna_id = excluded.rna_id,
      qualifier = excluded.qualifier,
      assigned_by = excluded.assigned_by,
      extensions = excluded.extensions,
      ontology_term_id = excluded.ontology_term_id,
      evidence_code = excluded.evidence_code
  ;
  $$,
  $$
  DROP TABLE {load_table};
  $$
  ;
  """
  
  
  class QuickGoLoadAnnotations(PGLoader):
      def requires(self):
          return [
              QuickGoData(),
              Ontologies(),
          ]
  
      def control_file(self):
          output = self.requires()[0].output()
          table = 'go_term_annotations'
          load_table = 'load_' + table
          fields = ', '.join(output.annotations.headers)
  
          return CONTROL_FILE.format(
              filename=output.annotations.filename,
              fields=fields,
              columns=fields,
              final_table=table,
              load_table=load_table,
              db_url=self.db_url(table=load_table),
              search_path=self.db_search_path(),
          )
  
subject: Remove extra parens