text: -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
  -- Copyright [2016-2021] 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.
  
  # patch_65_66_f.sql
  
  # Title: Removal of default options from a number of tables
  #
  # Description:
  # A change in healthchecks has meant the checking of default values which was
  # originally changed back in 2006. Programatically generated from the results
  # of CompareSchema healthcheck for canis e!66 vs. master_schema_66
  
  ALTER TABLE alt_allele 
     ALTER COLUMN gene_id DROP DEFAULT;
  
  ALTER TABLE analysis_description 
     ALTER COLUMN analysis_id DROP DEFAULT;
  
  ALTER TABLE assembly 
     ALTER COLUMN asm_end DROP DEFAULT,
     ALTER COLUMN asm_seq_region_id DROP DEFAULT,
     ALTER COLUMN asm_start DROP DEFAULT,
     ALTER COLUMN cmp_end DROP DEFAULT,
     ALTER COLUMN cmp_seq_region_id DROP DEFAULT,
     ALTER COLUMN cmp_start DROP DEFAULT,
     ALTER COLUMN ori DROP DEFAULT;
  
  ALTER TABLE assembly_exception 
     ALTER COLUMN exc_seq_region_end DROP DEFAULT,
     ALTER COLUMN exc_seq_region_id DROP DEFAULT,
     ALTER COLUMN exc_seq_region_start DROP DEFAULT,
     ALTER COLUMN ori DROP DEFAULT,
     ALTER COLUMN seq_region_end DROP DEFAULT,
     ALTER COLUMN seq_region_id DROP DEFAULT,
     ALTER COLUMN seq_region_start DROP DEFAULT;
  
  ALTER TABLE coord_system 
     ALTER COLUMN name DROP DEFAULT,
     ALTER COLUMN `rank` DROP DEFAULT;
  
  ALTER TABLE density_feature 
     ALTER COLUMN density_type_id DROP DEFAULT,
     ALTER COLUMN density_value DROP DEFAULT,
     ALTER COLUMN seq_region_end DROP DEFAULT,
     ALTER COLUMN seq_region_id DROP DEFAULT,
     ALTER COLUMN seq_region_start DROP DEFAULT;
  
  ALTER TABLE density_type 
     ALTER COLUMN analysis_id DROP DEFAULT,
     ALTER COLUMN block_size DROP DEFAULT,
     ALTER COLUMN region_features DROP DEFAULT,
     ALTER COLUMN value_type DROP DEFAULT;
  
  ALTER TABLE ditag 
     ALTER COLUMN name DROP DEFAULT,
     ALTER COLUMN type DROP DEFAULT;
  
  ALTER TABLE ditag_feature 
     ALTER COLUMN ditag_side DROP DEFAULT;
  
  ALTER TABLE dna 
     ALTER COLUMN seq_region_id DROP DEFAULT;
  
  ALTER TABLE dna_align_feature 
     ALTER COLUMN analysis_id DROP DEFAULT,
     ALTER COLUMN hit_end DROP DEFAULT,
     ALTER COLUMN hit_name DROP DEFAULT,
     ALTER COLUMN hit_start DROP DEFAULT,
     ALTER COLUMN hit_strand DROP DEFAULT,
     ALTER COLUMN seq_region_end DROP DEFAULT,
     ALTER COLUMN seq_region_id DROP DEFAULT,
     ALTER COLUMN seq_region_start DROP DEFAULT,
     ALTER COLUMN seq_region_strand DROP DEFAULT;
  
  ALTER TABLE dnac 
     ALTER COLUMN seq_region_id DROP DEFAULT;
  
  ALTER TABLE exon 
     ALTER COLUMN end_phase DROP DEFAULT,
     ALTER COLUMN phase DROP DEFAULT,
     ALTER COLUMN seq_region_end DROP DEFAULT,
     ALTER COLUMN seq_region_id DROP DEFAULT,
     ALTER COLUMN seq_region_start DROP DEFAULT,
     ALTER COLUMN seq_region_strand DROP DEFAULT;
  
  ALTER TABLE exon_transcript 
     ALTER COLUMN exon_id DROP DEFAULT,
     ALTER COLUMN `rank` DROP DEFAULT,
     ALTER COLUMN transcript_id DROP DEFAULT;
  
  ALTER TABLE external_synonym 
     ALTER COLUMN xref_id DROP DEFAULT;
  
  ALTER TABLE gene 
     ALTER COLUMN analysis_id DROP DEFAULT,
     ALTER COLUMN biotype DROP DEFAULT,
     ALTER COLUMN seq_region_end DROP DEFAULT,
     ALTER COLUMN seq_region_id DROP DEFAULT,
     ALTER COLUMN seq_region_start DROP DEFAULT,
     ALTER COLUMN seq_region_strand DROP DEFAULT,
     ALTER COLUMN source DROP DEFAULT;
  
  ALTER TABLE gene_archive 
     ALTER COLUMN gene_stable_id DROP DEFAULT,
     ALTER COLUMN mapping_session_id DROP DEFAULT,
     ALTER COLUMN transcript_stable_id DROP DEFAULT;
  
  ALTER TABLE identity_xref 
     ALTER COLUMN object_xref_id DROP DEFAULT;
  
  ALTER TABLE interpro 
     ALTER COLUMN id DROP DEFAULT,
     ALTER COLUMN interpro_ac DROP DEFAULT;
  
  ALTER TABLE karyotype 
     ALTER COLUMN band DROP DEFAULT,
     ALTER COLUMN seq_region_id DROP DEFAULT,
     ALTER COLUMN stain DROP DEFAULT;
  
  ALTER TABLE map 
     ALTER COLUMN map_name DROP DEFAULT;
  
  ALTER TABLE mapping_session 
     ALTER COLUMN created DROP DEFAULT;
  
  ALTER TABLE marker 
     ALTER COLUMN left_primer DROP DEFAULT,
     ALTER COLUMN max_primer_dist DROP DEFAULT,
     ALTER COLUMN min_primer_dist DROP DEFAULT,
     ALTER COLUMN right_primer DROP DEFAULT;
  
  ALTER TABLE marker_feature 
     ALTER COLUMN analysis_id DROP DEFAULT,
     ALTER COLUMN marker_id DROP DEFAULT,
     ALTER COLUMN seq_region_end DROP DEFAULT,
     ALTER COLUMN seq_region_id DROP DEFAULT,
     ALTER COLUMN seq_region_start DROP DEFAULT;
  
  ALTER TABLE marker_map_location 
     ALTER COLUMN chromosome_name DROP DEFAULT,
     ALTER COLUMN map_id DROP DEFAULT,
     ALTER COLUMN marker_id DROP DEFAULT,
     ALTER COLUMN marker_synonym_id DROP DEFAULT,
     ALTER COLUMN position DROP DEFAULT;
  
  ALTER TABLE marker_synonym 
     ALTER COLUMN marker_id DROP DEFAULT;
  
  ALTER TABLE meta 
     ALTER COLUMN meta_key DROP DEFAULT;
  
  ALTER TABLE meta_coord 
     ALTER COLUMN coord_system_id DROP DEFAULT,
     ALTER COLUMN table_name DROP DEFAULT;
  
  ALTER TABLE object_xref 
     ALTER COLUMN ensembl_id DROP DEFAULT,
     ALTER COLUMN xref_id DROP DEFAULT;
  
  ALTER TABLE prediction_exon 
     ALTER COLUMN exon_rank DROP DEFAULT,
     ALTER COLUMN prediction_transcript_id DROP DEFAULT,
     ALTER COLUMN seq_region_end DROP DEFAULT,
     ALTER COLUMN seq_region_id DROP DEFAULT,
     ALTER COLUMN seq_region_start DROP DEFAULT,
     ALTER COLUMN seq_region_strand DROP DEFAULT,
     ALTER COLUMN start_phase DROP DEFAULT;
  
  ALTER TABLE prediction_transcript 
     ALTER COLUMN analysis_id DROP DEFAULT,
     ALTER COLUMN seq_region_end DROP DEFAULT,
     ALTER COLUMN seq_region_id DROP DEFAULT,
     ALTER COLUMN seq_region_start DROP DEFAULT,
     ALTER COLUMN seq_region_strand DROP DEFAULT;
  
  ALTER TABLE protein_align_feature 
     ALTER COLUMN analysis_id DROP DEFAULT,
     ALTER COLUMN hit_end DROP DEFAULT,
     ALTER COLUMN hit_name DROP DEFAULT,
     ALTER COLUMN hit_start DROP DEFAULT,
     ALTER COLUMN seq_region_end DROP DEFAULT,
     ALTER COLUMN seq_region_id DROP DEFAULT,
     ALTER COLUMN seq_region_start DROP DEFAULT;
  
  ALTER TABLE protein_feature 
     ALTER COLUMN analysis_id DROP DEFAULT,
     ALTER COLUMN hit_end DROP DEFAULT,
     ALTER COLUMN hit_start DROP DEFAULT,
     ALTER COLUMN seq_end DROP DEFAULT,
     ALTER COLUMN seq_start DROP DEFAULT,
     ALTER COLUMN translation_id DROP DEFAULT;
  
  ALTER TABLE qtl 
     ALTER COLUMN trait DROP DEFAULT;
  
  ALTER TABLE qtl_feature 
     ALTER COLUMN analysis_id DROP DEFAULT,
     ALTER COLUMN qtl_id DROP DEFAULT,
     ALTER COLUMN seq_region_end DROP DEFAULT,
     ALTER COLUMN seq_region_id DROP DEFAULT,
     ALTER COLUMN seq_region_start DROP DEFAULT;
  
  ALTER TABLE qtl_synonym 
     ALTER COLUMN qtl_id DROP DEFAULT,
     ALTER COLUMN source_database DROP DEFAULT,
     ALTER COLUMN source_primary_id DROP DEFAULT;
  
  ALTER TABLE repeat_consensus 
     ALTER COLUMN repeat_class DROP DEFAULT,
     ALTER COLUMN repeat_name DROP DEFAULT,
     ALTER COLUMN repeat_type DROP DEFAULT;
  
  ALTER TABLE repeat_feature 
     ALTER COLUMN analysis_id DROP DEFAULT,
     ALTER COLUMN repeat_consensus_id DROP DEFAULT,
     ALTER COLUMN repeat_end DROP DEFAULT,
     ALTER COLUMN repeat_start DROP DEFAULT,
     ALTER COLUMN seq_region_end DROP DEFAULT,
     ALTER COLUMN seq_region_id DROP DEFAULT,
     ALTER COLUMN seq_region_start DROP DEFAULT;
  
  ALTER TABLE seq_region 
     ALTER COLUMN coord_system_id DROP DEFAULT,
     ALTER COLUMN name DROP DEFAULT;
  
  ALTER TABLE simple_feature 
     ALTER COLUMN analysis_id DROP DEFAULT,
     ALTER COLUMN seq_region_end DROP DEFAULT,
     ALTER COLUMN seq_region_id DROP DEFAULT,
     ALTER COLUMN seq_region_start DROP DEFAULT,
     ALTER COLUMN seq_region_strand DROP DEFAULT;
  
  ALTER TABLE stable_id_event 
     ALTER COLUMN type DROP DEFAULT;
  
  ALTER TABLE transcript 
     ALTER COLUMN analysis_id DROP DEFAULT,
     ALTER COLUMN biotype DROP DEFAULT,
     ALTER COLUMN seq_region_end DROP DEFAULT,
     ALTER COLUMN seq_region_id DROP DEFAULT,
     ALTER COLUMN seq_region_start DROP DEFAULT,
     ALTER COLUMN seq_region_strand DROP DEFAULT;
  
  ALTER TABLE translation 
     ALTER COLUMN end_exon_id DROP DEFAULT,
     ALTER COLUMN seq_end DROP DEFAULT,
     ALTER COLUMN seq_start DROP DEFAULT,
     ALTER COLUMN start_exon_id DROP DEFAULT,
     ALTER COLUMN transcript_id DROP DEFAULT;
  
  ALTER TABLE unconventional_transcript_association 
     ALTER COLUMN gene_id DROP DEFAULT,
     ALTER COLUMN transcript_id DROP DEFAULT;
  
  ALTER TABLE unmapped_object 
     ALTER COLUMN analysis_id DROP DEFAULT,
     ALTER COLUMN identifier DROP DEFAULT,
     ALTER COLUMN unmapped_reason_id DROP DEFAULT;
  
  ALTER TABLE xref 
     ALTER COLUMN dbprimary_acc DROP DEFAULT,
     ALTER COLUMN display_label DROP DEFAULT;
  
  # Patch identifier:
  INSERT INTO meta (species_id, meta_key, meta_value)
    VALUES (NULL, 'patch', 'patch_65_66_f.sql|drop_default_values');
  