update master schema to release 79

modules/Bio/EnsEMBL/ApiVersion.pm

@@ -55,7 +55,7 @@ use base qw( Exporter );
 
 our @EXPORT = qw( software_version );
 
-my $API_VERSION = 78;
+my $API_VERSION = 79;
 
 sub software_version { return $API_VERSION }
 

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

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Oct 28 16:45:25 2014
+-- Created on Fri Dec  5 13:10:29 2014
 -- 
 
 BEGIN TRANSACTION;

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

@@ -23,8 +23,9 @@
 79	\N	patch	patch_77_78_a.sql|schema_version
 80	\N	patch	patch_77_78_b.sql|source_column_increase
 81	\N	patch	patch_77_78_c.sql|Change unmapped_reason_id from smallint to int
+82	\N	patch	patch_78_79_a.sql|schema_version
 1	\N	schema_type	core
-2	\N	schema_version	78
+2	\N	schema_version	79
 8	1	assembly.accession	GCA_000292705.1
 10	1	assembly.date	2012-08
 7	1	assembly.default	GCA_000292705.1

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

@@ -469,7 +469,7 @@ 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=InnoDB AUTO_INCREMENT=82 DEFAULT CHARSET=latin1;
+) ENGINE=InnoDB AUTO_INCREMENT=83 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL,

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

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Oct 28 16:45:34 2014
+-- Created on Fri Dec  5 13:10:39 2014
 -- 
 
 BEGIN TRANSACTION;

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

-1	\N	schema_version	78
+1	\N	schema_version	79
 2	1	assembly.default	NCBI34
 3	1	species.taxonomy_id	9606
 26	1	species.classification	Homo sapiens
@@ -58,3 +58,4 @@
 118	\N	patch	patch_77_78_a.sql|schema_version
 119	\N	patch	patch_77_78_b.sql|source_column_increase
 120	\N	patch	patch_77_78_c.sql|Change unmapped_reason_id from smallint to int
+121	\N	patch	patch_78_79_a.sql|schema_version

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

@@ -468,7 +468,7 @@ 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=121 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=122 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL,

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

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Oct 28 16:45:41 2014
+-- Created on Fri Dec  5 13:10:45 2014
 -- 
 
 BEGIN TRANSACTION;

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

-1	\N	schema_version	78
+1	\N	schema_version	79
 2	1	assembly.default	NCBI34
 33	1	species.classification	Chordata
 32	1	species.classification	Vertebrata
@@ -58,3 +58,4 @@
 107	\N	patch	patch_77_78_a.sql|schema_version
 108	\N	patch	patch_77_78_b.sql|source_column_increase
 109	\N	patch	patch_77_78_c.sql|Change unmapped_reason_id from smallint to int
+110	\N	patch	patch_78_79_a.sql|schema_version

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

@@ -463,7 +463,7 @@ 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=110 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=111 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL DEFAULT '',

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

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Oct 28 16:45:49 2014
+-- Created on Fri Dec  5 13:10:53 2014
 -- 
 
 BEGIN TRANSACTION;

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

-1	\N	schema_version	78
+1	\N	schema_version	79
 2014	1	species.classification	Haplorrhini
 40	1	assembly.default	GRCh37
 41	1	assembly.date	2009-02
@@ -62,3 +62,4 @@
 2069	\N	patch	patch_77_78_a.sql|schema_version
 2070	\N	patch	patch_77_78_b.sql|source_column_increase
 2071	\N	patch	patch_77_78_c.sql|Change unmapped_reason_id from smallint to int
+2072	\N	patch	patch_78_79_a.sql|schema_version

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

@@ -462,7 +462,7 @@ 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=2072 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=2073 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 May 30 13:08:11 2014
+-- Created on Fri Dec  5 13:11:00 2014
 -- 
 
 BEGIN TRANSACTION;

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

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Oct 28 16:45:58 2014
+-- Created on Fri Dec  5 13:11:06 2014
 -- 
 
 BEGIN TRANSACTION;

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

-1	\N	schema_version	78
+1	\N	schema_version	79
 2	1	assembly.default	NCBI34
 3	1	species.taxonomy_id	9606
 26	1	species.classification	Homo sapiens
@@ -57,3 +57,4 @@
 111	\N	patch	patch_77_78_a.sql|schema_version
 112	\N	patch	patch_77_78_b.sql|source_column_increase
 113	\N	patch	patch_77_78_c.sql|Change unmapped_reason_id from smallint to int
+114	\N	patch	patch_78_79_a.sql|schema_version

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

@@ -468,7 +468,7 @@ 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=114 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=115 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL,

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

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Oct 28 16:46:06 2014
+-- Created on Fri Dec  5 13:11:12 2014
 -- 
 
 BEGIN TRANSACTION;
@@ -270,7 +270,8 @@ CREATE UNIQUE INDEX name_idx02 ON subset (name);
 CREATE TABLE synonym (
   synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   term_id integer NOT NULL,
-  name text NOT NULL
+  name text NOT NULL,
+  type enum
 );
 
 CREATE UNIQUE INDEX term_synonym_idx ON synonym (term_id, synonym_id);

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

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Oct 28 16:46:13 2014
+-- Created on Fri Dec  5 13:11:19 2014
 -- 
 
 BEGIN TRANSACTION;

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

@@ -23,8 +23,9 @@
 174	\N	patch	patch_77_78_a.sql|schema_version
 175	\N	patch	patch_77_78_b.sql|source_column_increase
 176	\N	patch	patch_77_78_c.sql|Change unmapped_reason_id from smallint to int
+177	\N	patch	patch_78_79_a.sql|schema_version
 1	\N	schema_type	core
-2	\N	schema_version	78
+2	\N	schema_version	79
 8	1	assembly.accession	GCA_000292705.1
 10	1	assembly.date	2012-08
 7	1	assembly.default	GCA_000292705.1