Adding in a patch which synchronises the state of default values between core...

Adding in a patch which synchronises the state of default values between core like DBs and their master DBs

sql/patch_65_66_f.sql

+# 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');