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.
  
  # patch_85_86_e.sql
  #
  # Title: New table with the homology counts of each member
  #
  # Description:
  #   These stats used to be in the gene_member table but are now
  #   moved to a separate table so that we can store stats about
  #   multiple collections
  
  -- MySQL should 'die' on warnings, ensuring data is not truncated
  SET session sql_mode='TRADITIONAL';
  
  CREATE TABLE gene_member_hom_stats (
    gene_member_id              int(10) unsigned NOT NULL, # FK gene_member.gene_member_id
    collection                  varchar(40) NOT NULL,
    `families`                 int(10) unsigned NOT NULL default 0,
    `gene_trees`               tinyint(1) unsigned NOT NULL default 0,
    `gene_gain_loss_trees`     tinyint(1) unsigned NOT NULL default 0,
    `orthologues`              int(10) unsigned NOT NULL default 0,
    `paralogues`               int(10) unsigned NOT NULL default 0,
    `homoeologues`             int(10) unsigned NOT NULL default 0,
  
    FOREIGN KEY (gene_member_id) REFERENCES gene_member(gene_member_id),
  
    PRIMARY KEY (gene_member_id, collection)
  
  ) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
  
  INSERT INTO gene_member_hom_stats
  SELECT gene_member_id, "default", families, gene_trees, gene_gain_loss_trees, orthologues, paralogues, homoeologues
  FROM gene_member;
  
  ALTER TABLE gene_member
  DROP COLUMN families,
  DROP COLUMN gene_trees,
  DROP COLUMN gene_gain_loss_trees,
  DROP COLUMN orthologues,
  DROP COLUMN paralogues,
  DROP COLUMN homoeologues;
  
  # Patch identifier
  INSERT INTO meta (species_id, meta_key, meta_value)
    VALUES (NULL, 'patch', 'patch_85_86_e.sql|gene_member_hom_stats');
  