diff --git a/t/test-genome-DBs/collection/core/meta.txt b/t/test-genome-DBs/collection/core/meta.txt index 6d13bb50..5da61b68 100644 --- a/t/test-genome-DBs/collection/core/meta.txt +++ b/t/test-genome-DBs/collection/core/meta.txt @@ -1,5 +1,5 @@ 1 \N schema_type core -2 \N schema_version 107 +2 \N schema_version 108 3 \N patch patch_88_89_a.sql|schema_version 4 1 schema.load_started 2017-05-08 19:14:41 5 1 schema.load_started 2017-05-08 19:14:45 @@ -193,3 +193,4 @@ 565 \N patch patch_105_106_a.sql|schema_version 566 \N patch patch_106_107_a.sql|schema_version 567 \N patch patch_106_107_b.sql|Added index for seq_region_mapping +568 \N patch patch_107_108_a.sql|schema_version diff --git a/t/test-genome-DBs/collection/core/table.sql b/t/test-genome-DBs/collection/core/table.sql index 7f8f534f..014aafba 100644 --- a/t/test-genome-DBs/collection/core/table.sql +++ b/t/test-genome-DBs/collection/core/table.sql @@ -490,7 +490,7 @@ CREATE TABLE `meta` ( PRIMARY KEY (`meta_id`), UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`), KEY `species_value_idx` (`species_id`,`meta_value`) -) ENGINE=MyISAM AUTO_INCREMENT=568 DEFAULT CHARSET=latin1 CHECKSUM=1; +) ENGINE=MyISAM AUTO_INCREMENT=569 DEFAULT CHARSET=latin1 CHECKSUM=1; CREATE TABLE `meta_coord` ( `table_name` varchar(40) NOT NULL, diff --git a/t/test-genome-DBs/drosophila_melanogaster/core/meta.txt b/t/test-genome-DBs/drosophila_melanogaster/core/meta.txt index 5dcf73da..2609871a 100644 --- a/t/test-genome-DBs/drosophila_melanogaster/core/meta.txt +++ b/t/test-genome-DBs/drosophila_melanogaster/core/meta.txt @@ -1,5 +1,5 @@ 1 \N schema_type core -2 \N schema_version 107 +2 \N schema_version 108 3 \N patch patch_76_77_a.sql|schema_version 4 1 assembly.mapping chromosome:BDGP6|contig:BDGP6 5 1 assembly.mapping contig:BDGP6|chunk:BDGP6 @@ -147,3 +147,4 @@ 237 \N patch patch_105_106_a.sql|schema_version 238 \N patch patch_106_107_a.sql|schema_version 239 \N patch patch_106_107_b.sql|Added index for seq_region_mapping +240 \N patch patch_107_108_a.sql|schema_version diff --git a/t/test-genome-DBs/drosophila_melanogaster/core/table.sql b/t/test-genome-DBs/drosophila_melanogaster/core/table.sql index 2571f98b..c0c3a93d 100644 --- a/t/test-genome-DBs/drosophila_melanogaster/core/table.sql +++ b/t/test-genome-DBs/drosophila_melanogaster/core/table.sql @@ -490,7 +490,7 @@ CREATE TABLE `meta` ( PRIMARY KEY (`meta_id`), UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`), KEY `species_value_idx` (`species_id`,`meta_value`) -) ENGINE=MyISAM AUTO_INCREMENT=240 DEFAULT CHARSET=latin1 CHECKSUM=1; +) ENGINE=MyISAM AUTO_INCREMENT=241 DEFAULT CHARSET=latin1 CHECKSUM=1; CREATE TABLE `meta_coord` ( `table_name` varchar(40) NOT NULL, diff --git a/t/test-genome-DBs/homo_sapiens/core/meta.txt b/t/test-genome-DBs/homo_sapiens/core/meta.txt index de4f7fd8..6328fe25 100644 --- a/t/test-genome-DBs/homo_sapiens/core/meta.txt +++ b/t/test-genome-DBs/homo_sapiens/core/meta.txt @@ -1,5 +1,5 @@ 1 \N schema_type core -2 \N schema_version 107 +2 \N schema_version 108 3 \N patch patch_73_74_a.sql|schema_version 4 \N patch patch_73_74_b.sql|remove_dnac 5 \N patch patch_73_74_c.sql|remove_unconventional_transcript_association @@ -194,3 +194,4 @@ 5893 \N patch patch_105_106_a.sql|schema_version 5894 \N patch patch_106_107_a.sql|schema_version 5895 \N patch patch_106_107_b.sql|Added index for seq_region_mapping +5896 \N patch patch_107_108_a.sql|schema_version diff --git a/t/test-genome-DBs/homo_sapiens/core/table.sql b/t/test-genome-DBs/homo_sapiens/core/table.sql index 9a09bbc2..391adbd6 100644 --- a/t/test-genome-DBs/homo_sapiens/core/table.sql +++ b/t/test-genome-DBs/homo_sapiens/core/table.sql @@ -490,7 +490,7 @@ CREATE TABLE `meta` ( PRIMARY KEY (`meta_id`), UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`), KEY `species_value_idx` (`species_id`,`meta_value`) -) ENGINE=MyISAM AUTO_INCREMENT=5896 DEFAULT CHARSET=latin1; +) ENGINE=MyISAM AUTO_INCREMENT=5897 DEFAULT CHARSET=latin1; CREATE TABLE `meta_coord` ( `table_name` varchar(40) NOT NULL, diff --git a/t/test-genome-DBs/homo_sapiens/funcgen/meta.txt b/t/test-genome-DBs/homo_sapiens/funcgen/meta.txt index 111f2e16..851f46be 100644 --- a/t/test-genome-DBs/homo_sapiens/funcgen/meta.txt +++ b/t/test-genome-DBs/homo_sapiens/funcgen/meta.txt @@ -1,5 +1,5 @@ 1 1 schema_type funcgen -2 \N schema_version 107 +2 \N schema_version 108 3 \N patch patch_87_88_a.sql|schema_version 4 \N patch patch_87_88_b.sql|seq_region_name_255 5 \N patch patch_87_88_c.sql|sample_regulatory_feature_id field for regulatory build @@ -140,3 +140,4 @@ 140 \N patch patch_104_105_b.sql|New indices 141 \N patch patch_105_106_a.sql|schema_version 142 \N patch patch_106_107_a.sql|schema_version +143 \N patch patch_107_108_a.sql|schema_version diff --git a/t/test-genome-DBs/homo_sapiens/funcgen/table.sql b/t/test-genome-DBs/homo_sapiens/funcgen/table.sql index 42879cf9..d21ac5e3 100644 --- a/t/test-genome-DBs/homo_sapiens/funcgen/table.sql +++ b/t/test-genome-DBs/homo_sapiens/funcgen/table.sql @@ -382,7 +382,7 @@ CREATE TABLE `meta` ( PRIMARY KEY (`meta_id`), UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`), KEY `species_value_idx` (`species_id`,`meta_value`) -) ENGINE=MyISAM AUTO_INCREMENT=143 DEFAULT CHARSET=latin1; +) ENGINE=MyISAM AUTO_INCREMENT=144 DEFAULT CHARSET=latin1; CREATE TABLE `meta_coord` ( `table_name` varchar(40) NOT NULL, diff --git a/t/test-genome-DBs/homo_sapiens/variation/meta.txt b/t/test-genome-DBs/homo_sapiens/variation/meta.txt index 3a2ebba4..e23ed0fb 100644 --- a/t/test-genome-DBs/homo_sapiens/variation/meta.txt +++ b/t/test-genome-DBs/homo_sapiens/variation/meta.txt @@ -1,5 +1,5 @@ 1 \N schema_type variation -2 \N schema_version 107 +2 \N schema_version 108 3 1 species.production_name homo_sapiens 4 \N patch patch_94_95_a.sql|schema version 5 \N patch patch_94_95_b.sql|create table to store allele synonyms @@ -30,3 +30,6 @@ 47 \N patch patch_105_106_a.sql|schema version 48 \N patch patch_106_107_a.sql|schema version 49 \N patch patch_106_107_b.sql|consequences update +50 \N patch patch_106_107_c.sql|remove regulatory and TFBS consequences from consequence_types in transcript_variation +51 \N patch patch_107_108_a.sql|schema version +52 \N patch patch_107_108_b.sql|fix SAS population description diff --git a/t/test-genome-DBs/homo_sapiens/variation/table.sql b/t/test-genome-DBs/homo_sapiens/variation/table.sql index 1d1d1b37..c616f833 100644 --- a/t/test-genome-DBs/homo_sapiens/variation/table.sql +++ b/t/test-genome-DBs/homo_sapiens/variation/table.sql @@ -186,7 +186,7 @@ CREATE TABLE `meta` ( PRIMARY KEY (`meta_id`), UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`), KEY `species_value_idx` (`species_id`,`meta_value`) -) ENGINE=MyISAM AUTO_INCREMENT=50 DEFAULT CHARSET=latin1; +) ENGINE=MyISAM AUTO_INCREMENT=53 DEFAULT CHARSET=latin1; CREATE TABLE `meta_coord` ( `table_name` varchar(40) NOT NULL, @@ -544,7 +544,7 @@ CREATE TABLE `transcript_variation` ( `feature_stable_id` varchar(128) DEFAULT NULL, `allele_string` text, `somatic` tinyint(1) NOT NULL DEFAULT '0', - `consequence_types` set('splice_acceptor_variant','splice_donor_variant','stop_lost','coding_sequence_variant','missense_variant','stop_gained','synonymous_variant','frameshift_variant','non_coding_transcript_variant','non_coding_transcript_exon_variant','mature_miRNA_variant','NMD_transcript_variant','5_prime_UTR_variant','3_prime_UTR_variant','incomplete_terminal_codon_variant','intron_variant','splice_region_variant','downstream_gene_variant','upstream_gene_variant','start_lost','stop_retained_variant','inframe_insertion','inframe_deletion','transcript_ablation','transcript_fusion','transcript_amplification','transcript_translocation','TFBS_ablation','TFBS_fusion','TFBS_amplification','TFBS_translocation','regulatory_region_ablation','regulatory_region_fusion','regulatory_region_amplification','regulatory_region_translocation','feature_elongation','feature_truncation','protein_altering_variant','start_retained_variant','splice_donor_5th_base_variant','splice_donor_region_variant','splice_polypyrimidine_tract_variant') DEFAULT NULL, + `consequence_types` set('splice_acceptor_variant','splice_donor_variant','stop_lost','coding_sequence_variant','missense_variant','stop_gained','synonymous_variant','frameshift_variant','non_coding_transcript_variant','non_coding_transcript_exon_variant','mature_miRNA_variant','NMD_transcript_variant','5_prime_UTR_variant','3_prime_UTR_variant','incomplete_terminal_codon_variant','intron_variant','splice_region_variant','downstream_gene_variant','upstream_gene_variant','start_lost','stop_retained_variant','inframe_insertion','inframe_deletion','transcript_ablation','transcript_fusion','transcript_amplification','transcript_translocation','feature_elongation','feature_truncation','protein_altering_variant','start_retained_variant','splice_donor_5th_base_variant','splice_donor_region_variant','splice_polypyrimidine_tract_variant') DEFAULT NULL, `cds_start` int(11) unsigned DEFAULT NULL, `cds_end` int(11) unsigned DEFAULT NULL, `cdna_start` int(11) unsigned DEFAULT NULL, diff --git a/t/test-genome-DBs/multi/compara/meta.txt b/t/test-genome-DBs/multi/compara/meta.txt index 20dd7093..7f88b671 100644 --- a/t/test-genome-DBs/multi/compara/meta.txt +++ b/t/test-genome-DBs/multi/compara/meta.txt @@ -1,6 +1,6 @@ 2 \N schema_type compara 3 \N division vertebrates -158 \N schema_version 107 +161 \N schema_version 108 5 \N patch patch_70_71_a.sql|other_member_sequence_keys 6 \N patch patch_70_71_b.sql|member_xref 8 \N patch patch_70_71_c.sql|schema_version @@ -120,3 +120,5 @@ 156 \N patch patch_105_106_a.sql|schema_version 157 \N patch patch_105_106_b.sql|clusterset_id_varchar50 159 \N patch patch_106_107_a.sql|schema_version +160 \N patch patch_106_107_b.sql|case_sensitive_stable_id +162 \N patch patch_107_108_a.sql|schema_version diff --git a/t/test-genome-DBs/multi/compara/table.sql b/t/test-genome-DBs/multi/compara/table.sql index 3592f5e1..b191176c 100644 --- a/t/test-genome-DBs/multi/compara/table.sql +++ b/t/test-genome-DBs/multi/compara/table.sql @@ -138,7 +138,7 @@ CREATE TABLE `gene_align_member` ( CREATE TABLE `gene_member` ( `gene_member_id` int(10) unsigned NOT NULL AUTO_INCREMENT, - `stable_id` varchar(128) NOT NULL, + `stable_id` varchar(128) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL, `version` int(10) unsigned DEFAULT '0', `source_name` enum('ENSEMBLGENE','EXTERNALGENE') NOT NULL, `taxon_id` int(10) unsigned NOT NULL, @@ -176,7 +176,7 @@ CREATE TABLE `gene_member_hom_stats` ( ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `gene_member_qc` ( - `gene_member_stable_id` varchar(128) NOT NULL, + `gene_member_stable_id` varchar(128) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL, `genome_db_id` int(10) unsigned NOT NULL, `seq_member_id` int(10) unsigned DEFAULT NULL, `n_species` int(11) DEFAULT NULL, @@ -436,7 +436,7 @@ CREATE TABLE `meta` ( PRIMARY KEY (`meta_id`), UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`(255)), KEY `species_value_idx` (`species_id`,`meta_value`(255)) -) ENGINE=MyISAM AUTO_INCREMENT=160 DEFAULT CHARSET=latin1; +) ENGINE=MyISAM AUTO_INCREMENT=163 DEFAULT CHARSET=latin1; CREATE TABLE `method_link` ( `method_link_id` int(10) unsigned NOT NULL AUTO_INCREMENT, @@ -540,7 +540,7 @@ CREATE TABLE `peptide_align_feature` ( CREATE TABLE `seq_member` ( `seq_member_id` int(10) unsigned NOT NULL AUTO_INCREMENT, - `stable_id` varchar(128) NOT NULL, + `stable_id` varchar(128) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL, `version` int(10) unsigned DEFAULT '0', `source_name` enum('ENSEMBLPEP','ENSEMBLTRANS','Uniprot/SPTREMBL','Uniprot/SWISSPROT','EXTERNALPEP','EXTERNALTRANS','EXTERNALCDS') NOT NULL, `taxon_id` int(10) unsigned NOT NULL,