update test dbs to match fixed patch

misc-scripts/ontology/sql/patch_95_96_b.sql

@@ -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');

misc-scripts/ontology/sql/tables.sql

@@ -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,

modules/t/test-genome-DBs/circ/core/SQLite/table.sql

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Feb 12 10:46:46 2019
+-- Created on Tue Feb 12 11:39:09 2019
 -- 
 
 BEGIN TRANSACTION;

modules/t/test-genome-DBs/homo_sapiens/core/SQLite/table.sql

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Feb 12 10:46:50 2019
+-- Created on Tue Feb 12 11:39:12 2019
 -- 
 
 BEGIN TRANSACTION;

modules/t/test-genome-DBs/homo_sapiens/empty/SQLite/table.sql

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Feb 12 10:46:53 2019
+-- Created on Tue Feb 12 11:39:15 2019
 -- 
 
 BEGIN TRANSACTION;

modules/t/test-genome-DBs/homo_sapiens/patch/SQLite/table.sql

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Feb 12 10:46:56 2019
+-- Created on Tue Feb 12 11:39:18 2019
 -- 
 
 BEGIN TRANSACTION;

modules/t/test-genome-DBs/homo_sapiens/variation/failed_description.txt

@@ -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

modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt

@@ -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.

modules/t/test-genome-DBs/homo_sapiens/variation/table.sql

@@ -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`)

modules/t/test-genome-DBs/homo_sapiens/xref/SQLite/table.sql

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Feb 12 10:46:57 2019
+-- Created on Tue Feb 12 11:39:19 2019
 -- 
 
 BEGIN TRANSACTION;

modules/t/test-genome-DBs/mapping/core/SQLite/table.sql

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Feb 12 10:47:01 2019
+-- Created on Tue Feb 12 11:39:23 2019
 -- 
 
 BEGIN TRANSACTION;

modules/t/test-genome-DBs/multi/compara/SQLite/table.sql

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Feb 12 10:47:03 2019
+-- Created on Tue Feb 12 11:39:25 2019
 -- 
 
 BEGIN TRANSACTION;

modules/t/test-genome-DBs/mus_musculus/core/SQLite/table.sql

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Feb 12 10:47:07 2019
+-- Created on Tue Feb 12 11:39:28 2019
 -- 
 
 BEGIN TRANSACTION;

modules/t/test-genome-DBs/mus_musculus/variation/failed_description.txt

@@ -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

modules/t/test-genome-DBs/mus_musculus/variation/meta.txt

@@ -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.

modules/t/test-genome-DBs/mus_musculus/variation/table.sql

@@ -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`)

modules/t/test-genome-DBs/nameless/core/SQLite/table.sql

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Feb 12 10:47:10 2019
+-- Created on Tue Feb 12 11:39:31 2019
 -- 
 
 BEGIN TRANSACTION;

modules/t/test-genome-DBs/ontology/ontology/SQLite/table.sql

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Feb 12 10:47:11 2019
+-- Created on Tue Feb 12 11:39:33 2019
 -- 
 
 BEGIN TRANSACTION;

modules/t/test-genome-DBs/ontology/ontology/meta.txt

@@ -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

modules/t/test-genome-DBs/polyploidy/core/SQLite/table.sql

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Feb 12 10:47:15 2019
+-- Created on Tue Feb 12 11:39:37 2019
 -- 
 
 BEGIN TRANSACTION;