Commit 9d9c94bd authored by Tiago Grego's avatar Tiago Grego
Browse files

update test dbs to match fixed patch

parent 452f7715
......@@ -40,4 +40,8 @@ CREATE INDEX ix_closure_ontology_id ON closure (`ontology_id`);
CREATE INDEX `ix_relation_parent_term_id` ON relation (`parent_term_id`);
CREATE INDEX `ix_relation_relation_type_id` ON relation (`relation_type_id`);
CREATE INDEX `ix_relation_ontology_id` ON relation (`ontology_id`);
\ No newline at end of file
CREATE INDEX `ix_relation_ontology_id` ON relation (`ontology_id`);
-- Patch identifier
INSERT INTO meta (meta_key, meta_value)
VALUES ('patch', 'patch_95_96_b.sql|term_ontology_update');
......@@ -36,6 +36,8 @@ INSERT INTO meta (meta_key, meta_value) VALUES
INSERT INTO meta (meta_key, meta_value)
VALUES ('patch', 'patch_95_96_a.sql|schema_version');
INSERT INTO meta (species_id, meta_key, meta_value)
VALUES (NULL, 'patch', 'patch_95_96_b.sql|term_ontology_update');
CREATE TABLE `ontology` (
`ontology_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
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......@@ -17,3 +17,5 @@
18 Supporting evidence can not be re-mapped to the current assembly
19 Variant maps to more than one genomic location
20 Variant at first base in sequence
21 Reference allele does not match the bases at this genome location
22 Alleles cannot be resolved
......@@ -35,3 +35,7 @@
35 \N patch patch_94_95_a.sql|schema version
36 \N patch patch_94_95_b.sql|create table to store allele synonyms
37 \N patch patch_95_96_a.sql|schema_version
38 \N patch patch_95_96_b.sql|modify index on variation_synonym
39 \N patch patch_95_96_c.sql|add new entries to the failed_description table
40 \N patch patch_95_96_d.sql|create table to store failed variation features
41 \N patch patch_95_96_e.sql|Rename motif_name to binding_matrix_stable_id.
......@@ -113,7 +113,7 @@ CREATE TABLE `failed_description` (
`failed_description_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`description` text NOT NULL,
PRIMARY KEY (`failed_description_id`)
) ENGINE=MyISAM AUTO_INCREMENT=21 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=23 DEFAULT CHARSET=latin1;
CREATE TABLE `failed_structural_variation` (
`failed_structural_variation_id` int(11) NOT NULL AUTO_INCREMENT,
......@@ -131,6 +131,14 @@ CREATE TABLE `failed_variation` (
UNIQUE KEY `variation_idx` (`variation_id`,`failed_description_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `failed_variation_feature` (
`failed_variation_feature_id` int(11) NOT NULL AUTO_INCREMENT,
`variation_feature_id` int(10) unsigned NOT NULL,
`failed_description_id` int(10) unsigned NOT NULL,
PRIMARY KEY (`failed_variation_feature_id`),
UNIQUE KEY `variation_feature_idx` (`variation_feature_id`,`failed_description_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `genotype_code` (
`genotype_code_id` int(11) unsigned NOT NULL,
`allele_code_id` int(11) unsigned NOT NULL,
......@@ -178,7 +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=38 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=42 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL,
......@@ -195,7 +203,7 @@ CREATE TABLE `motif_feature_variation` (
`allele_string` text,
`somatic` tinyint(1) NOT NULL DEFAULT '0',
`consequence_types` set('TF_binding_site_variant','TFBS_ablation','TFBS_fusion','TFBS_amplification','TFBS_translocation') DEFAULT NULL,
`motif_name` varchar(60) DEFAULT NULL,
`binding_matrix_stable_id` varchar(60) DEFAULT NULL,
`motif_start` int(11) unsigned DEFAULT NULL,
`motif_end` int(11) unsigned DEFAULT NULL,
`motif_score_delta` float DEFAULT NULL,
......@@ -675,7 +683,7 @@ CREATE TABLE `variation_synonym` (
`source_id` int(10) unsigned NOT NULL,
`name` varchar(255) DEFAULT NULL,
PRIMARY KEY (`variation_synonym_id`),
UNIQUE KEY `name` (`name`,`source_id`),
UNIQUE KEY `name_idx` (`name`,`source_id`,`variation_id`),
KEY `variation_idx` (`variation_id`),
KEY `subsnp_idx` (`subsnp_id`),
KEY `source_idx` (`source_id`)
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......@@ -17,3 +17,5 @@
18 Supporting evidence can not be re-mapped to the current assembly
19 Variant maps to more than one genomic location
20 Variant at first base in sequence
21 Reference allele does not match the bases at this genome location
22 Alleles cannot be resolved
......@@ -62,3 +62,7 @@
68 \N patch patch_94_95_a.sql|schema version
69 \N patch patch_94_95_b.sql|create table to store allele synonyms
70 \N patch patch_95_96_a.sql|schema_version
71 \N patch patch_95_96_b.sql|modify index on variation_synonym
72 \N patch patch_95_96_c.sql|add new entries to the failed_description table
73 \N patch patch_95_96_d.sql|create table to store failed variation features
74 \N patch patch_95_96_e.sql|Rename motif_name to binding_matrix_stable_id.
......@@ -113,7 +113,7 @@ CREATE TABLE `failed_description` (
`failed_description_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`description` text NOT NULL,
PRIMARY KEY (`failed_description_id`)
) ENGINE=MyISAM AUTO_INCREMENT=21 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=23 DEFAULT CHARSET=latin1;
CREATE TABLE `failed_structural_variation` (
`failed_structural_variation_id` int(11) NOT NULL AUTO_INCREMENT,
......@@ -131,6 +131,14 @@ CREATE TABLE `failed_variation` (
UNIQUE KEY `variation_idx` (`variation_id`,`failed_description_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `failed_variation_feature` (
`failed_variation_feature_id` int(11) NOT NULL AUTO_INCREMENT,
`variation_feature_id` int(10) unsigned NOT NULL,
`failed_description_id` int(10) unsigned NOT NULL,
PRIMARY KEY (`failed_variation_feature_id`),
UNIQUE KEY `variation_feature_idx` (`variation_feature_id`,`failed_description_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `genotype_code` (
`genotype_code_id` int(11) unsigned NOT NULL,
`allele_code_id` int(11) unsigned NOT NULL,
......@@ -178,7 +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=71 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=75 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL,
......@@ -195,7 +203,7 @@ CREATE TABLE `motif_feature_variation` (
`allele_string` text,
`somatic` tinyint(1) NOT NULL DEFAULT '0',
`consequence_types` set('TF_binding_site_variant','TFBS_ablation','TFBS_fusion','TFBS_amplification','TFBS_translocation') DEFAULT NULL,
`motif_name` varchar(60) DEFAULT NULL,
`binding_matrix_stable_id` varchar(60) DEFAULT NULL,
`motif_start` int(11) unsigned DEFAULT NULL,
`motif_end` int(11) unsigned DEFAULT NULL,
`motif_score_delta` float DEFAULT NULL,
......@@ -681,7 +689,7 @@ CREATE TABLE `variation_synonym` (
`source_id` int(10) unsigned NOT NULL,
`name` varchar(255) DEFAULT NULL,
PRIMARY KEY (`variation_synonym_id`),
UNIQUE KEY `name` (`name`,`source_id`),
UNIQUE KEY `name_idx` (`name`,`source_id`,`variation_id`),
KEY `variation_idx` (`variation_id`),
KEY `subsnp_idx` (`subsnp_id`),
KEY `source_idx` (`source_id`)
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-- Created on Tue Feb 12 10:47:10 2019
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......@@ -38,3 +38,4 @@
41 patch patch_93_94_a.sql|schema_version \N
42 patch patch_94_95_a.sql|schema_version \N
43 patch patch_95_96_a.sql|schema_version \N
44 patch patch_95_96_b.sql|term_ontology_update \N
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