text: -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
  -- Copyright [2016-2018] 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.
  
  
  # Updating the schema version
  
  DELETE FROM meta WHERE meta_key="schema_version";
  INSERT INTO meta (meta_key,meta_value) VALUES ("schema_version",37);
  
  # Renaming the old schema tables
  
  RENAME TABLE synteny_region TO synteny_region_old, dnafrag_region TO dnafrag_region_old;
  
  # Creating the new schema tables
  
  CREATE TABLE synteny_region (
    synteny_region_id           int(10) unsigned NOT NULL auto_increment,
    method_link_species_set_id  int(10) unsigned NOT NULL,
  
    PRIMARY KEY (synteny_region_id),
    KEY (method_link_species_set_id)
  ) COLLATE=latin1_swedish_ci;
  
  
  CREATE TABLE dnafrag_region (
    synteny_region_id           int(10) unsigned DEFAULT '0' NOT NULL,
    dnafrag_id                  int(10) unsigned DEFAULT '0' NOT NULL,
    dnafrag_start               int(10) unsigned DEFAULT '0' NOT NULL,
    dnafrag_end                 int(10) unsigned DEFAULT '0' NOT NULL,
    dnafrag_strand              tinyint(4) DEFAULT '0' NOT NULL,
    
    FOREIGN KEY (dnafrag_id) REFERENCES dnafrag(dnafrag_id),
  
    UNIQUE unique_synteny (synteny_region_id,dnafrag_id),
    UNIQUE unique_synteny_reversed (dnafrag_id,synteny_region_id)
  ) COLLATE=latin1_swedish_ci;
  
  # Transferring the data from the old schema tables to the new schema tables
  
  INSERT INTO dnafrag_region SELECT dfr1.*,"1" FROM synteny_region_old sr, dnafrag_region_old dfr1, dnafrag_region_old dfr2 WHERE sr.synteny_region_id=dfr1.synteny_region_id AND sr.synteny_region_id=dfr2.synteny_region_id AND dfr1.dnafrag_id<dfr2.dnafrag_id;
  
  INSERT INTO dnafrag_region SELECT dfr2.*,sr.rel_orientation FROM synteny_region_old sr, dnafrag_region_old dfr1, dnafrag_region_old dfr2 WHERE sr.synteny_region_id=dfr1.synteny_region_id AND sr.synteny_region_id=dfr2.synteny_region_id AND dfr1.dnafrag_id<dfr2.dnafrag_id;
  
  INSERT INTO synteny_region SELECT synteny_region_id,method_link_species_set_id from synteny_region_old;
  
  # Dropping the old schema tables
  
  DROP TABLE synteny_region_old;
  DROP TABLE dnafrag_region_old;
  
  