Merge 15522cc into 4e55b87

t/test-genome-DBs/collection/core/meta.txt

@@ -1,5 +1,5 @@
 1	\N	schema_type	core
-2	\N	schema_version	100
+2	\N	schema_version	101
 3	\N	patch	patch_88_89_a.sql|schema_version
 4	1	schema.load_started	2017-05-08 19:14:41
 5	1	schema.load_started	2017-05-08 19:14:45
@@ -184,3 +184,5 @@
 556	\N	patch	patch_98_99_a.sql|schema_version
 557	\N	patch	patch_99_100_a.sql|schema_version
 558	\N	patch	patch_99_100_b.sql|alter_externaldb_type_notnull
+559	\N	patch	patch_99_100_c.sql|alter_mapping_session_assembly_length
+560	\N	patch	patch_100_101_a.sql|schema_version

t/test-genome-DBs/collection/core/table.sql

@@ -420,8 +420,8 @@ CREATE TABLE `mapping_session` (
   `new_db_name` varchar(80) NOT NULL DEFAULT '',
   `old_release` varchar(5) NOT NULL DEFAULT '',
   `new_release` varchar(5) NOT NULL DEFAULT '',
-  `old_assembly` varchar(20) NOT NULL DEFAULT '',
-  `new_assembly` varchar(20) NOT NULL DEFAULT '',
+  `old_assembly` varchar(80) NOT NULL DEFAULT '',
+  `new_assembly` varchar(80) NOT NULL DEFAULT '',
   `created` datetime NOT NULL,
   PRIMARY KEY (`mapping_session_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 CHECKSUM=1;
@@ -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=559 DEFAULT CHARSET=latin1 CHECKSUM=1;
+) ENGINE=MyISAM AUTO_INCREMENT=561 DEFAULT CHARSET=latin1 CHECKSUM=1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL,

t/test-genome-DBs/drosophila_melanogaster/core/meta.txt

@@ -1,5 +1,5 @@
 1	\N	schema_type	core
-2	\N	schema_version	100
+2	\N	schema_version	101
 3	\N	patch	patch_76_77_a.sql|schema_version
 4	1	assembly.mapping	chromosome:BDGP6|contig:BDGP6
 5	1	assembly.mapping	contig:BDGP6|chunk:BDGP6
@@ -138,3 +138,5 @@
 228	\N	patch	patch_98_99_a.sql|schema_version
 229	\N	patch	patch_99_100_a.sql|schema_version
 230	\N	patch	patch_99_100_b.sql|alter_externaldb_type_notnull
+231	\N	patch	patch_99_100_c.sql|alter_mapping_session_assembly_length
+232	\N	patch	patch_100_101_a.sql|schema_version

t/test-genome-DBs/drosophila_melanogaster/core/table.sql

@@ -420,8 +420,8 @@ CREATE TABLE `mapping_session` (
   `new_db_name` varchar(80) NOT NULL DEFAULT '',
   `old_release` varchar(5) NOT NULL DEFAULT '',
   `new_release` varchar(5) NOT NULL DEFAULT '',
-  `old_assembly` varchar(20) NOT NULL DEFAULT '',
-  `new_assembly` varchar(20) NOT NULL DEFAULT '',
+  `old_assembly` varchar(80) NOT NULL DEFAULT '',
+  `new_assembly` varchar(80) NOT NULL DEFAULT '',
   `created` datetime NOT NULL,
   PRIMARY KEY (`mapping_session_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 CHECKSUM=1;
@@ -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=231 DEFAULT CHARSET=latin1 CHECKSUM=1;
+) ENGINE=MyISAM AUTO_INCREMENT=233 DEFAULT CHARSET=latin1 CHECKSUM=1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL,

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

@@ -1,5 +1,5 @@
 1	\N	schema_type	core
-2	\N	schema_version	100
+2	\N	schema_version	101
 3	\N	patch	patch_73_74_a.sql|schema_version
 4	\N	patch	patch_73_74_b.sql|remove_dnac
 5	\N	patch	patch_73_74_c.sql|remove_unconventional_transcript_association
@@ -185,3 +185,5 @@
 5884	\N	patch	patch_98_99_a.sql|schema_version
 5885	\N	patch	patch_99_100_a.sql|schema_version
 5886	\N	patch	patch_99_100_b.sql|alter_externaldb_type_notnull
+5887	\N	patch	patch_99_100_c.sql|alter_mapping_session_assembly_length
+5888	\N	patch	patch_100_101_a.sql|schema_version

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

@@ -420,8 +420,8 @@ CREATE TABLE `mapping_session` (
   `new_db_name` varchar(80) NOT NULL DEFAULT '',
   `old_release` varchar(5) NOT NULL DEFAULT '',
   `new_release` varchar(5) NOT NULL DEFAULT '',
-  `old_assembly` varchar(20) NOT NULL DEFAULT '',
-  `new_assembly` varchar(20) NOT NULL DEFAULT '',
+  `old_assembly` varchar(80) NOT NULL DEFAULT '',
+  `new_assembly` varchar(80) NOT NULL DEFAULT '',
   `created` datetime NOT NULL,
   PRIMARY KEY (`mapping_session_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
@@ -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=5887 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=5889 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL,

t/test-genome-DBs/homo_sapiens/funcgen/meta.txt

@@ -1,5 +1,5 @@
 1	1	schema_type	funcgen
-2	\N	schema_version	100
+2	\N	schema_version	101
 3	\N	patch	patch_87_88_a.sql|schema_version
 4	\N	patch	patch_87_88_b.sql|seq_region_name_255
 5	\N	patch	patch_87_88_c.sql|sample_regulatory_feature_id field for regulatory build
@@ -131,3 +131,4 @@
 131	\N	patch	patch_99_100_c.sql|remove default values from text data type
 132	\N	patch	patch_99_100_d.sql|update type column on external_db table
 133	\N	patch	patch_99_100_e.sql|Make some foreign keys not mandatory
+134	\N	patch	patch_100_101_a.sql|schema_version

t/test-genome-DBs/homo_sapiens/funcgen/table.sql

@@ -382,7 +382,7 @@ 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=134 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=135 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL,

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

@@ -1,5 +1,5 @@
 1	\N	schema_type	variation
-2	\N	schema_version	100
+2	\N	schema_version	101
 3	1	species.production_name	homo_sapiens
 4	\N	patch	patch_94_95_a.sql|schema version
 5	\N	patch	patch_94_95_b.sql|create table to store allele synonyms
@@ -20,3 +20,5 @@
 37	\N	patch	patch_99_100_a.sql|schema version
 38	\N	patch	patch_99_100_b.sql|add frequency to structural variation
 39	\N	patch	patch_99_100_c.sql|add class_attrib_id column to phenotype
+40	\N	patch	patch_100_101_a.sql|schema version
+41	\N	patch	patch_100_101_b.sql|Add new data_source_attrib to variation_citation

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

@@ -186,7 +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=40 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=42 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL,
@@ -604,7 +604,7 @@ CREATE TABLE `variation_attrib` (
 CREATE TABLE `variation_citation` (
   `variation_id` int(10) unsigned NOT NULL,
   `publication_id` int(10) unsigned NOT NULL,
-  `data_source_attrib` set('615','616','617') DEFAULT NULL,
+  `data_source_attrib` set('615','616','617','618','619','620') DEFAULT NULL,
   PRIMARY KEY (`variation_id`,`publication_id`),
   KEY `data_source_attrib_idx` (`data_source_attrib`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;