Merge pull request #64 from Ensembl/task/test-db-patches

Patching test databases for 107

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

-1	\N	schema_version	106
+1	\N	schema_version	107
 2	1	assembly.default	NCBI34
 3	1	species.taxonomy_id	9606
 26	1	species.classification	Homo sapiens
@@ -121,3 +121,5 @@
 195	\N	patch	patch_103_104_a.sql|schema_version
 196	\N	patch	patch_104_105_a.sql|schema_version
 197	\N	patch	patch_105_106_a.sql|schema_version
+198	\N	patch	patch_106_107_a.sql|schema_version
+199	\N	patch	patch_106_107_b.sql|Added index for seq_region_mapping

modules/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=198 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=200 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
@@ -776,6 +776,7 @@ CREATE TABLE `seq_region_mapping` (
   `external_seq_region_id` int(10) unsigned NOT NULL,
   `internal_seq_region_id` int(10) unsigned NOT NULL,
   `mapping_set_id` int(10) unsigned NOT NULL,
+  UNIQUE KEY `seq_region_mapping_uindex` (`external_seq_region_id`,`internal_seq_region_id`,`mapping_set_id`),
   KEY `mapping_set_idx` (`mapping_set_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 

modules/t/test-genome-DBs/multi/compara/meta.txt

-92	\N	schema_version	106
+95	\N	schema_version	107
 2	\N	schema_type	compara
 3	\N	patch	patch_84_85_a.sql|schema_version
 4	\N	patch	patch_84_85_b.sql|gene_tree_root_attr
@@ -72,3 +72,5 @@
 90	\N	patch	patch_104_105_a.sql|schema_version
 91	\N	patch	patch_104_105_b.sql|genebuild_varchar255
 93	\N	patch	patch_105_106_a.sql|schema_version
+94	\N	patch	patch_105_106_b.sql|clusterset_id_varchar50
+96	\N	patch	patch_106_107_a.sql|schema_version

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

@@ -230,7 +230,7 @@ CREATE TABLE `gene_tree_root` (
   `root_id` int(10) unsigned NOT NULL,
   `member_type` enum('protein','ncrna') NOT NULL,
   `tree_type` enum('clusterset','supertree','tree') NOT NULL,
-  `clusterset_id` varchar(20) NOT NULL DEFAULT 'default',
+  `clusterset_id` varchar(50) NOT NULL DEFAULT 'default',
   `method_link_species_set_id` int(10) unsigned NOT NULL,
   `species_tree_root_id` bigint(20) unsigned DEFAULT NULL,
   `gene_align_id` int(10) unsigned 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=94 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=97 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `method_link` (
   `method_link_id` int(10) unsigned NOT NULL AUTO_INCREMENT,

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

 1	\N	schema_type	core
-2	\N	schema_version	106
+2	\N	schema_version	107
 3	\N	patch	patch_65_66_a.sql|schema_version
 4	\N	patch	patch_65_66_b.sql|fix_external_db_id
 5	\N	patch	patch_65_66_c.sql|reorder_unmapped_obj_index
@@ -199,3 +199,5 @@
 1711	\N	patch	patch_103_104_a.sql|schema_version
 1712	\N	patch	patch_104_105_a.sql|schema_version
 1713	\N	patch	patch_105_106_a.sql|schema_version
+1714	\N	patch	patch_106_107_a.sql|schema_version
+1715	\N	patch	patch_106_107_b.sql|Added index for seq_region_mapping

modules/t/test-genome-DBs/mus_musculus/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=1714 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=1716 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
@@ -776,6 +776,7 @@ CREATE TABLE `seq_region_mapping` (
   `external_seq_region_id` int(10) unsigned NOT NULL,
   `internal_seq_region_id` int(10) unsigned NOT NULL,
   `mapping_set_id` int(10) unsigned NOT NULL,
+  UNIQUE KEY `seq_region_mapping_uindex` (`external_seq_region_id`,`internal_seq_region_id`,`mapping_set_id`),
   KEY `mapping_set_idx` (`mapping_set_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;