patched test databases with patch_92_93_b.sql

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

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Fri Jan 12 13:37:14 2018
+-- Created on Fri Feb 16 15:28:14 2018
 -- 
 
 BEGIN TRANSACTION;
@@ -131,6 +131,22 @@ CREATE TABLE attrib_type (
 
 CREATE UNIQUE INDEX code_idx ON attrib_type (code);
 
+--
+-- Table: biotype
+--
+CREATE TABLE biotype (
+  biotype_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  name varchar(64) NOT NULL,
+  object_type enum NOT NULL DEFAULT 'gene',
+  db_type varchar NOT NULL DEFAULT 'core',
+  attrib_type_id integer,
+  description text,
+  biotype_group enum,
+  so_acc varchar(64)
+);
+
+CREATE UNIQUE INDEX name_type_idx ON biotype (name, object_type);
+
 --
 -- Table: coord_system
 --

modules/t/test-genome-DBs/circ/core/meta.txt

@@ -117,3 +117,4 @@
 117	\N	patch	patch_91_92_a.sql|schema_version
 118	\N	patch	patch_91_92_b.sql|add_cigar_line_align_type
 119	\N	patch	patch_92_93_a.sql|schema_version
+120	\N	patch	patch_92_93_b.sql|biotype_table

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

@@ -105,6 +105,19 @@ CREATE TABLE `attrib_type` (
   UNIQUE KEY `code_idx` (`code`)
 ) ENGINE=MyISAM AUTO_INCREMENT=391 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
+CREATE TABLE `biotype` (
+  `biotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `name` varchar(64) NOT NULL,
+  `object_type` enum('gene','transcript') NOT NULL DEFAULT 'gene',
+  `db_type` set('cdna','core','coreexpressionatlas','coreexpressionest','coreexpressiongnf','funcgen','otherfeatures','rnaseq','variation','vega','presite','sangervega') NOT NULL DEFAULT 'core',
+  `attrib_type_id` int(11) DEFAULT NULL,
+  `description` text,
+  `biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group') DEFAULT NULL,
+  `so_acc` varchar(64) DEFAULT NULL,
+  PRIMARY KEY (`biotype_id`),
+  UNIQUE KEY `name_type_idx` (`name`,`object_type`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
 CREATE TABLE `coord_system` (
   `coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `species_id` int(10) unsigned NOT NULL DEFAULT '1',
@@ -476,7 +489,7 @@ 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=120 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=121 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',

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

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Fri Jan 12 13:37:26 2018
+-- Created on Fri Feb 16 15:28:17 2018
 -- 
 
 BEGIN TRANSACTION;
@@ -131,6 +131,22 @@ CREATE TABLE attrib_type (
 
 CREATE UNIQUE INDEX code_idx ON attrib_type (code);
 
+--
+-- Table: biotype
+--
+CREATE TABLE biotype (
+  biotype_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  name varchar(64) NOT NULL,
+  object_type enum NOT NULL DEFAULT 'gene',
+  db_type varchar NOT NULL DEFAULT 'core',
+  attrib_type_id integer,
+  description text,
+  biotype_group enum,
+  so_acc varchar(64)
+);
+
+CREATE UNIQUE INDEX name_type_idx ON biotype (name, object_type);
+
 --
 -- Table: coord_system
 --

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

@@ -96,3 +96,4 @@
 163	\N	patch	patch_91_92_a.sql|schema_version
 164	\N	patch	patch_91_92_b.sql|add_cigar_line_align_type
 165	\N	patch	patch_92_93_a.sql|schema_version
+166	\N	patch	patch_92_93_b.sql|biotype_table

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

@@ -105,6 +105,19 @@ CREATE TABLE `attrib_type` (
   UNIQUE KEY `code_idx` (`code`)
 ) ENGINE=MyISAM AUTO_INCREMENT=392 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
+CREATE TABLE `biotype` (
+  `biotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `name` varchar(64) NOT NULL,
+  `object_type` enum('gene','transcript') NOT NULL DEFAULT 'gene',
+  `db_type` set('cdna','core','coreexpressionatlas','coreexpressionest','coreexpressiongnf','funcgen','otherfeatures','rnaseq','variation','vega','presite','sangervega') NOT NULL DEFAULT 'core',
+  `attrib_type_id` int(11) DEFAULT NULL,
+  `description` text,
+  `biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group') DEFAULT NULL,
+  `so_acc` varchar(64) DEFAULT NULL,
+  PRIMARY KEY (`biotype_id`),
+  UNIQUE KEY `name_type_idx` (`name`,`object_type`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
 CREATE TABLE `coord_system` (
   `coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `species_id` int(10) unsigned NOT NULL DEFAULT '1',
@@ -476,7 +489,7 @@ 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=166 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=167 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',

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

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Fri Jan 12 13:37:38 2018
+-- Created on Fri Feb 16 15:28:20 2018
 -- 
 
 BEGIN TRANSACTION;
@@ -131,6 +131,22 @@ CREATE TABLE attrib_type (
 
 CREATE UNIQUE INDEX code_idx ON attrib_type (code);
 
+--
+-- Table: biotype
+--
+CREATE TABLE biotype (
+  biotype_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  name varchar(64) NOT NULL,
+  object_type enum NOT NULL DEFAULT 'gene',
+  db_type varchar NOT NULL DEFAULT 'core',
+  attrib_type_id integer,
+  description text,
+  biotype_group enum,
+  so_acc varchar(64)
+);
+
+CREATE UNIQUE INDEX name_type_idx ON biotype (name, object_type);
+
 --
 -- Table: coord_system
 --

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

@@ -96,3 +96,4 @@
 145	\N	patch	patch_91_92_a.sql|schema_version
 146	\N	patch	patch_91_92_b.sql|add_cigar_line_align_type
 147	\N	patch	patch_92_93_a.sql|schema_version
+148	\N	patch	patch_92_93_b.sql|biotype_table

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

@@ -105,6 +105,19 @@ CREATE TABLE `attrib_type` (
   UNIQUE KEY `code_idx` (`code`)
 ) ENGINE=MyISAM AUTO_INCREMENT=391 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
+CREATE TABLE `biotype` (
+  `biotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `name` varchar(64) NOT NULL,
+  `object_type` enum('gene','transcript') NOT NULL DEFAULT 'gene',
+  `db_type` set('cdna','core','coreexpressionatlas','coreexpressionest','coreexpressiongnf','funcgen','otherfeatures','rnaseq','variation','vega','presite','sangervega') NOT NULL DEFAULT 'core',
+  `attrib_type_id` int(11) DEFAULT NULL,
+  `description` text,
+  `biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group') DEFAULT NULL,
+  `so_acc` varchar(64) DEFAULT NULL,
+  PRIMARY KEY (`biotype_id`),
+  UNIQUE KEY `name_type_idx` (`name`,`object_type`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
 CREATE TABLE `coord_system` (
   `coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `species_id` int(10) unsigned NOT NULL DEFAULT '1',
@@ -476,7 +489,7 @@ 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=148 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=149 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',

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

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Fri Jan 12 13:37:50 2018
+-- Created on Fri Feb 16 15:28:23 2018
 -- 
 
 BEGIN TRANSACTION;
@@ -131,6 +131,22 @@ CREATE TABLE attrib_type (
 
 CREATE UNIQUE INDEX code_idx ON attrib_type (code);
 
+--
+-- Table: biotype
+--
+CREATE TABLE biotype (
+  biotype_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  name varchar(64) NOT NULL,
+  object_type enum NOT NULL DEFAULT 'gene',
+  db_type varchar NOT NULL DEFAULT 'core',
+  attrib_type_id integer,
+  description text,
+  biotype_group enum,
+  so_acc varchar(64)
+);
+
+CREATE UNIQUE INDEX name_type_idx ON biotype (name, object_type);
+
 --
 -- Table: coord_system
 --

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

@@ -101,3 +101,4 @@
 2108	\N	patch	patch_91_92_a.sql|schema_version
 2109	\N	patch	patch_91_92_b.sql|add_cigar_line_align_type
 2110	\N	patch	patch_92_93_a.sql|schema_version
+2111	\N	patch	patch_92_93_b.sql|biotype_table

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

@@ -105,6 +105,19 @@ CREATE TABLE `attrib_type` (
   UNIQUE KEY `code_idx` (`code`)
 ) ENGINE=MyISAM AUTO_INCREMENT=407 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
+CREATE TABLE `biotype` (
+  `biotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `name` varchar(64) NOT NULL,
+  `object_type` enum('gene','transcript') NOT NULL DEFAULT 'gene',
+  `db_type` set('cdna','core','coreexpressionatlas','coreexpressionest','coreexpressiongnf','funcgen','otherfeatures','rnaseq','variation','vega','presite','sangervega') NOT NULL DEFAULT 'core',
+  `attrib_type_id` int(11) DEFAULT NULL,
+  `description` text,
+  `biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group') DEFAULT NULL,
+  `so_acc` varchar(64) DEFAULT NULL,
+  PRIMARY KEY (`biotype_id`),
+  UNIQUE KEY `name_type_idx` (`name`,`object_type`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
 CREATE TABLE `coord_system` (
   `coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `species_id` int(10) unsigned NOT NULL DEFAULT '1',
@@ -476,7 +489,7 @@ 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=2111 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=2112 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',

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

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Fri Jan 12 13:38:03 2018
+-- Created on Fri Feb 16 15:28:26 2018
 -- 
 
 BEGIN TRANSACTION;
@@ -131,6 +131,22 @@ CREATE TABLE attrib_type (
 
 CREATE UNIQUE INDEX code_idx ON attrib_type (code);
 
+--
+-- Table: biotype
+--
+CREATE TABLE biotype (
+  biotype_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  name varchar(64) NOT NULL,
+  object_type enum NOT NULL DEFAULT 'gene',
+  db_type varchar NOT NULL DEFAULT 'core',
+  attrib_type_id integer,
+  description text,
+  biotype_group enum,
+  so_acc varchar(64)
+);
+
+CREATE UNIQUE INDEX name_type_idx ON biotype (name, object_type);
+
 --
 -- Table: coord_system
 --

modules/t/test-genome-DBs/mapping/core/meta.txt

@@ -57,3 +57,4 @@
 150	\N	patch	patch_91_92_a.sql|schema_version
 151	\N	patch	patch_91_92_b.sql|add_cigar_line_align_type
 152	\N	patch	patch_92_93_a.sql|schema_version
+153	\N	patch	patch_92_93_b.sql|biotype_table

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

@@ -105,6 +105,19 @@ CREATE TABLE `attrib_type` (
   UNIQUE KEY `code_idx` (`code`)
 ) ENGINE=MyISAM AUTO_INCREMENT=391 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
+CREATE TABLE `biotype` (
+  `biotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `name` varchar(64) NOT NULL,
+  `object_type` enum('gene','transcript') NOT NULL DEFAULT 'gene',
+  `db_type` set('cdna','core','coreexpressionatlas','coreexpressionest','coreexpressiongnf','funcgen','otherfeatures','rnaseq','variation','vega','presite','sangervega') NOT NULL DEFAULT 'core',
+  `attrib_type_id` int(11) DEFAULT NULL,
+  `description` text,
+  `biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group') DEFAULT NULL,
+  `so_acc` varchar(64) DEFAULT NULL,
+  PRIMARY KEY (`biotype_id`),
+  UNIQUE KEY `name_type_idx` (`name`,`object_type`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
 CREATE TABLE `coord_system` (
   `coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `species_id` int(10) unsigned NOT NULL DEFAULT '1',
@@ -476,7 +489,7 @@ 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=153 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=154 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',

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

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Fri Jan 12 13:38:11 2018
+-- Created on Fri Feb 16 15:28:28 2018
 -- 
 
 BEGIN TRANSACTION;

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

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Fri Jan 12 13:38:22 2018
+-- Created on Fri Feb 16 15:28:31 2018
 -- 
 
 BEGIN TRANSACTION;
@@ -131,6 +131,22 @@ CREATE TABLE attrib_type (
 
 CREATE UNIQUE INDEX code_idx ON attrib_type (code);
 
+--
+-- Table: biotype
+--
+CREATE TABLE biotype (
+  biotype_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  name varchar(64) NOT NULL,
+  object_type enum NOT NULL DEFAULT 'gene',
+  db_type varchar NOT NULL DEFAULT 'core',
+  attrib_type_id integer,
+  description text,
+  biotype_group enum,
+  so_acc varchar(64)
+);
+
+CREATE UNIQUE INDEX name_type_idx ON biotype (name, object_type);
+
 --
 -- Table: coord_system
 --

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

@@ -174,3 +174,4 @@
 1686	\N	patch	patch_91_92_a.sql|schema_version
 1687	\N	patch	patch_91_92_b.sql|add_cigar_line_align_type
 1688	\N	patch	patch_92_93_a.sql|schema_version
+1689	\N	patch	patch_92_93_b.sql|biotype_table

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

@@ -105,6 +105,19 @@ CREATE TABLE `attrib_type` (
   UNIQUE KEY `code_idx` (`code`)
 ) ENGINE=MyISAM AUTO_INCREMENT=508 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
+CREATE TABLE `biotype` (
+  `biotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `name` varchar(64) NOT NULL,
+  `object_type` enum('gene','transcript') NOT NULL DEFAULT 'gene',
+  `db_type` set('cdna','core','coreexpressionatlas','coreexpressionest','coreexpressiongnf','funcgen','otherfeatures','rnaseq','variation','vega','presite','sangervega') NOT NULL DEFAULT 'core',
+  `attrib_type_id` int(11) DEFAULT NULL,
+  `description` text,
+  `biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group') DEFAULT NULL,
+  `so_acc` varchar(64) DEFAULT NULL,
+  PRIMARY KEY (`biotype_id`),
+  UNIQUE KEY `name_type_idx` (`name`,`object_type`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
 CREATE TABLE `coord_system` (
   `coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `species_id` int(10) unsigned NOT NULL DEFAULT '1',
@@ -476,7 +489,7 @@ 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=1689 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=1690 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',

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

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Fri Jan 12 13:38:33 2018
+-- Created on Fri Feb 16 15:28:34 2018
 -- 
 
 BEGIN TRANSACTION;
@@ -131,6 +131,22 @@ CREATE TABLE attrib_type (
 
 CREATE UNIQUE INDEX code_idx ON attrib_type (code);
 
+--
+-- Table: biotype
+--
+CREATE TABLE biotype (
+  biotype_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  name varchar(64) NOT NULL,
+  object_type enum NOT NULL DEFAULT 'gene',
+  db_type varchar NOT NULL DEFAULT 'core',
+  attrib_type_id integer,
+  description text,
+  biotype_group enum,
+  so_acc varchar(64)
+);
+
+CREATE UNIQUE INDEX name_type_idx ON biotype (name, object_type);
+
 --
 -- Table: coord_system
 --