Unverified Commit 1af1dce3 authored by Ameya Chaubal's avatar Ameya Chaubal Committed by GitHub
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Merge pull request #549 from Ensembl/104_testdbpatch

104 testdb patch for compara.
parents 344c7df4 8eaabcd4
Pipeline #183685 failed with stage
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......@@ -47,7 +47,7 @@ CREATE TABLE "constrained_element" (
"dnafrag_id" bigint NOT NULL,
"dnafrag_start" integer NOT NULL,
"dnafrag_end" integer NOT NULL,
"dnafrag_strand" integer NOT NULL,
"dnafrag_strand" tinyint NOT NULL,
"method_link_species_set_id" integer NOT NULL,
"p_value" double precision NOT NULL DEFAULT 0,
"score" double precision NOT NULL DEFAULT 0
......@@ -69,6 +69,15 @@ CREATE TABLE "dnafrag" (
CREATE UNIQUE INDEX "name" ON "dnafrag" ("genome_db_id", "name");
--
-- Table: "dnafrag_alt_region"
--
CREATE TABLE "dnafrag_alt_region" (
"dnafrag_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
"dnafrag_start" integer NOT NULL,
"dnafrag_end" integer NOT NULL
);
--
-- Table: "dnafrag_region"
--
......@@ -578,10 +587,10 @@ CREATE TABLE "peptide_align_feature" (
"evalue" double precision NOT NULL,
"align_length" integer NOT NULL,
"identical_matches" integer NOT NULL,
"perc_ident" integer NOT NULL,
"perc_ident" tinyint NOT NULL,
"positive_matches" integer NOT NULL,
"perc_pos" integer NOT NULL,
"hit_rank" integer NOT NULL,
"perc_pos" tinyint NOT NULL,
"hit_rank" smallint NOT NULL,
"cigar_line" mediumtext
);
......
......@@ -67,3 +67,5 @@
82 \N patch patch_101_102_c.sql|stn_node_id_bigint
84 \N patch patch_102_103_a.sql|schema_version
86 \N patch patch_103_104_a.sql|schema_version
87 \N patch patch_103_104_b.sql|dnafrag_alt_region
88 \N patch patch_103_104_c.sql|fix_int_types
......@@ -14,7 +14,7 @@ CREATE TABLE `CAFE_gene_family` (
CREATE TABLE `CAFE_species_gene` (
`cafe_gene_family_id` int(10) unsigned NOT NULL,
`node_id` bigint(20) unsigned NOT NULL,
`n_members` int(4) unsigned NOT NULL,
`n_members` int(10) unsigned NOT NULL,
`pvalue` double(5,4) DEFAULT NULL,
PRIMARY KEY (`cafe_gene_family_id`,`node_id`),
KEY `node_id` (`node_id`)
......@@ -32,9 +32,9 @@ CREATE TABLE `conservation_score` (
CREATE TABLE `constrained_element` (
`constrained_element_id` bigint(20) unsigned NOT NULL,
`dnafrag_id` bigint(20) unsigned NOT NULL,
`dnafrag_start` int(12) unsigned NOT NULL,
`dnafrag_end` int(12) unsigned NOT NULL,
`dnafrag_strand` int(2) NOT NULL,
`dnafrag_start` int(10) unsigned NOT NULL,
`dnafrag_end` int(10) unsigned NOT NULL,
`dnafrag_strand` tinyint(4) NOT NULL,
`method_link_species_set_id` int(10) unsigned NOT NULL,
`p_value` double NOT NULL DEFAULT '0',
`score` double NOT NULL DEFAULT '0',
......@@ -51,11 +51,18 @@ CREATE TABLE `dnafrag` (
`coord_system_name` varchar(40) NOT NULL DEFAULT '',
`cellular_component` enum('NUC','MT','PT','OTHER') NOT NULL DEFAULT 'NUC',
`is_reference` tinyint(1) NOT NULL DEFAULT '1',
`codon_table_id` tinyint(2) unsigned NOT NULL DEFAULT '1',
`codon_table_id` tinyint(3) unsigned NOT NULL DEFAULT '1',
PRIMARY KEY (`dnafrag_id`),
UNIQUE KEY `name` (`genome_db_id`,`name`)
) ENGINE=MyISAM AUTO_INCREMENT=14026981 DEFAULT CHARSET=latin1;
CREATE TABLE `dnafrag_alt_region` (
`dnafrag_id` bigint(20) unsigned NOT NULL,
`dnafrag_start` int(10) unsigned NOT NULL,
`dnafrag_end` int(10) unsigned NOT NULL,
PRIMARY KEY (`dnafrag_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `dnafrag_region` (
`synteny_region_id` int(10) unsigned NOT NULL DEFAULT '0',
`dnafrag_id` bigint(20) unsigned NOT NULL DEFAULT '0',
......@@ -69,10 +76,10 @@ CREATE TABLE `dnafrag_region` (
CREATE TABLE `exon_boundaries` (
`gene_member_id` int(10) unsigned NOT NULL,
`seq_member_id` int(10) unsigned NOT NULL,
`dnafrag_start` int(11) NOT NULL,
`dnafrag_end` int(11) NOT NULL,
`dnafrag_start` int(10) unsigned NOT NULL,
`dnafrag_end` int(10) unsigned NOT NULL,
`sequence_length` int(10) unsigned NOT NULL,
`left_over` tinyint(1) NOT NULL DEFAULT '0',
`left_over` tinyint(3) unsigned NOT NULL DEFAULT '0',
KEY `seq_member_id` (`seq_member_id`),
KEY `gene_member_id` (`gene_member_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
......@@ -117,7 +124,7 @@ CREATE TABLE `gene_align` (
`gene_align_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`seq_type` varchar(40) DEFAULT NULL,
`aln_method` varchar(40) NOT NULL DEFAULT '',
`aln_length` int(10) NOT NULL DEFAULT '0',
`aln_length` int(10) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`gene_align_id`)
) ENGINE=MyISAM AUTO_INCREMENT=100000189 DEFAULT CHARSET=latin1;
......@@ -132,7 +139,7 @@ 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,
`version` int(10) DEFAULT '0',
`version` int(10) unsigned DEFAULT '0',
`source_name` enum('ENSEMBLGENE','EXTERNALGENE') NOT NULL,
`taxon_id` int(10) unsigned NOT NULL,
`genome_db_id` int(10) unsigned DEFAULT NULL,
......@@ -140,8 +147,8 @@ CREATE TABLE `gene_member` (
`canonical_member_id` int(10) unsigned DEFAULT NULL,
`description` text,
`dnafrag_id` bigint(20) unsigned DEFAULT NULL,
`dnafrag_start` int(10) DEFAULT NULL,
`dnafrag_end` int(10) DEFAULT NULL,
`dnafrag_start` int(10) unsigned DEFAULT NULL,
`dnafrag_end` int(10) unsigned DEFAULT NULL,
`dnafrag_strand` tinyint(4) DEFAULT NULL,
`display_label` varchar(128) DEFAULT NULL,
PRIMARY KEY (`gene_member_id`),
......@@ -184,8 +191,8 @@ CREATE TABLE `gene_tree_node` (
`node_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`parent_id` int(10) unsigned DEFAULT NULL,
`root_id` int(10) unsigned DEFAULT NULL,
`left_index` int(10) NOT NULL DEFAULT '0',
`right_index` int(10) NOT NULL DEFAULT '0',
`left_index` int(10) unsigned NOT NULL DEFAULT '0',
`right_index` int(10) unsigned NOT NULL DEFAULT '0',
`distance_to_parent` double NOT NULL DEFAULT '1',
`seq_member_id` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`node_id`),
......@@ -299,11 +306,11 @@ CREATE TABLE `genomic_align` (
`genomic_align_block_id` bigint(20) unsigned NOT NULL,
`method_link_species_set_id` int(10) unsigned NOT NULL DEFAULT '0',
`dnafrag_id` bigint(20) unsigned NOT NULL DEFAULT '0',
`dnafrag_start` int(10) NOT NULL DEFAULT '0',
`dnafrag_end` int(10) NOT NULL DEFAULT '0',
`dnafrag_start` int(10) unsigned NOT NULL DEFAULT '0',
`dnafrag_end` int(10) unsigned NOT NULL DEFAULT '0',
`dnafrag_strand` tinyint(4) NOT NULL DEFAULT '0',
`cigar_line` mediumtext NOT NULL,
`visible` tinyint(2) unsigned NOT NULL DEFAULT '1',
`visible` tinyint(3) unsigned NOT NULL DEFAULT '1',
`node_id` bigint(20) unsigned DEFAULT NULL,
PRIMARY KEY (`genomic_align_id`),
KEY `genomic_align_block_id` (`genomic_align_block_id`),
......@@ -317,10 +324,10 @@ CREATE TABLE `genomic_align_block` (
`method_link_species_set_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`perc_id` tinyint(3) unsigned DEFAULT NULL,
`length` int(10) NOT NULL,
`length` int(10) unsigned NOT NULL,
`group_id` bigint(20) unsigned DEFAULT NULL,
`level_id` tinyint(2) unsigned NOT NULL DEFAULT '0',
`direction` tinyint(1) unsigned DEFAULT NULL,
`level_id` tinyint(3) unsigned NOT NULL DEFAULT '0',
`direction` tinyint(3) unsigned DEFAULT NULL,
PRIMARY KEY (`genomic_align_block_id`),
KEY `method_link_species_set_id` (`method_link_species_set_id`)
) ENGINE=MyISAM AUTO_INCREMENT=6770001148336 DEFAULT CHARSET=latin1;
......@@ -329,8 +336,8 @@ CREATE TABLE `genomic_align_tree` (
`node_id` bigint(20) unsigned NOT NULL AUTO_INCREMENT,
`parent_id` bigint(20) unsigned DEFAULT NULL,
`root_id` bigint(20) unsigned NOT NULL DEFAULT '0',
`left_index` int(10) NOT NULL DEFAULT '0',
`right_index` int(10) NOT NULL DEFAULT '0',
`left_index` int(10) unsigned NOT NULL DEFAULT '0',
`right_index` int(10) unsigned NOT NULL DEFAULT '0',
`left_node_id` bigint(20) unsigned DEFAULT NULL,
`right_node_id` bigint(20) unsigned DEFAULT NULL,
`distance_to_parent` double NOT NULL DEFAULT '1',
......@@ -429,7 +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=87 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=89 DEFAULT CHARSET=latin1;
CREATE TABLE `method_link` (
`method_link_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -504,7 +511,7 @@ CREATE TABLE `ncbi_taxa_node` (
CREATE TABLE `other_member_sequence` (
`seq_member_id` int(10) unsigned NOT NULL,
`seq_type` varchar(40) NOT NULL,
`length` int(10) NOT NULL,
`length` int(10) unsigned NOT NULL,
`sequence` mediumtext NOT NULL,
PRIMARY KEY (`seq_member_id`,`seq_type`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=10000000 AVG_ROW_LENGTH=60000;
......@@ -515,18 +522,18 @@ CREATE TABLE `peptide_align_feature` (
`hmember_id` int(10) unsigned NOT NULL,
`qgenome_db_id` int(10) unsigned DEFAULT NULL,
`hgenome_db_id` int(10) unsigned DEFAULT NULL,
`qstart` int(10) NOT NULL DEFAULT '0',
`qend` int(10) NOT NULL DEFAULT '0',
`qstart` int(10) unsigned NOT NULL DEFAULT '0',
`qend` int(10) unsigned NOT NULL DEFAULT '0',
`hstart` int(10) unsigned NOT NULL DEFAULT '0',
`hend` int(10) unsigned NOT NULL DEFAULT '0',
`score` double(16,4) NOT NULL DEFAULT '0.0000',
`evalue` double NOT NULL,
`align_length` int(10) NOT NULL,
`identical_matches` int(10) NOT NULL,
`perc_ident` int(10) NOT NULL,
`positive_matches` int(10) NOT NULL,
`perc_pos` int(10) NOT NULL,
`hit_rank` int(10) NOT NULL,
`align_length` int(10) unsigned NOT NULL,
`identical_matches` int(10) unsigned NOT NULL,
`perc_ident` tinyint(3) unsigned NOT NULL,
`positive_matches` int(10) unsigned NOT NULL,
`perc_pos` tinyint(3) unsigned NOT NULL,
`hit_rank` smallint(5) unsigned NOT NULL,
`cigar_line` mediumtext,
PRIMARY KEY (`peptide_align_feature_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=133;
......@@ -534,7 +541,7 @@ 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,
`version` int(10) DEFAULT '0',
`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,
`genome_db_id` int(10) unsigned DEFAULT NULL,
......@@ -544,8 +551,8 @@ CREATE TABLE `seq_member` (
`has_translation_edits` tinyint(1) NOT NULL DEFAULT '0',
`description` text,
`dnafrag_id` bigint(20) unsigned DEFAULT NULL,
`dnafrag_start` int(10) DEFAULT NULL,
`dnafrag_end` int(10) DEFAULT NULL,
`dnafrag_start` int(10) unsigned DEFAULT NULL,
`dnafrag_end` int(10) unsigned DEFAULT NULL,
`dnafrag_strand` tinyint(4) DEFAULT NULL,
`display_label` varchar(128) DEFAULT NULL,
PRIMARY KEY (`seq_member_id`),
......@@ -577,7 +584,7 @@ CREATE TABLE `seq_member_projection_stable_id` (
CREATE TABLE `sequence` (
`sequence_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`length` int(10) NOT NULL,
`length` int(10) unsigned NOT NULL,
`md5sum` char(32) NOT NULL,
`sequence` longtext NOT NULL,
PRIMARY KEY (`sequence_id`),
......@@ -612,8 +619,8 @@ CREATE TABLE `species_tree_node` (
`node_id` bigint(20) unsigned NOT NULL AUTO_INCREMENT,
`parent_id` bigint(20) unsigned DEFAULT NULL,
`root_id` bigint(20) unsigned DEFAULT NULL,
`left_index` int(10) NOT NULL DEFAULT '0',
`right_index` int(10) NOT NULL DEFAULT '0',
`left_index` int(10) unsigned NOT NULL DEFAULT '0',
`right_index` int(10) unsigned NOT NULL DEFAULT '0',
`distance_to_parent` double DEFAULT '1',
`taxon_id` int(10) unsigned DEFAULT NULL,
`genome_db_id` int(10) unsigned DEFAULT NULL,
......
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