Added new patch to update current CHARSET and COLLATE for related tables.

misc-scripts/ontology/sql/patch_95_96_b.sql

@@ -21,6 +21,19 @@
 --  Added fields to Term and Ontology tables
 
 -- Added columns
-ALTER TABLE ontology ADD COLUMN `title` varchar(255) COLLATE utf8_unicode_ci DEFAULT NULL;
+ALTER TABLE `ontology` ADD COLUMN `title` varchar(255) DEFAULT NULL;
+
+ALTER TABLE `term` ADD COLUMN `iri` text NULL;
+
+ALTER TABLE `meta` DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
+
+ALTER TABLE `ontology` DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
+
+ALTER TABLE `subset` DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
+
+ALTER TABLE `term` DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
+
+ALTER TABLE `synonym` DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
+
+
 
-ALTER TABLE term ADD COLUMN `iri` text NULL;

misc-scripts/ontology/sql/tables.sql

@@ -20,8 +20,8 @@
 
 CREATE TABLE `meta` (
   `meta_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `meta_key` varchar(64) COLLATE utf8_unicode_ci NOT NULL,
-  `meta_value` varchar(128) COLLATE utf8_unicode_ci DEFAULT NULL,
+  `meta_key` varchar(64) NOT NULL,
+  `meta_value` varchar(128) DEFAULT NULL,
   `species_id` int(10) unsigned DEFAULT NULL,
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `key_value_idx` (`meta_key`,`meta_value`)
@@ -39,10 +39,10 @@ INSERT INTO meta (meta_key, meta_value)
 
 CREATE TABLE `ontology` (
   `ontology_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `name` varchar(64) COLLATE utf8_unicode_ci NOT NULL,
-  `namespace` varchar(64) COLLATE utf8_unicode_ci NOT NULL,
-  `data_version` varchar(64) COLLATE utf8_unicode_ci DEFAULT NULL,
-  `title` varchar(255) COLLATE utf8_unicode_ci DEFAULT NULL,
+  `name` varchar(64) NOT NULL,
+  `namespace` varchar(64) NOT NULL,
+  `data_version` varchar(64) DEFAULT NULL,
+  `title` varchar(255) DEFAULT NULL,
   PRIMARY KEY (`ontology_id`),
   UNIQUE KEY `ontology_name_namespace_idx` (`name`,`namespace`)
 ) ENGINE=MyISAM DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
@@ -50,8 +50,8 @@ CREATE TABLE `ontology` (
 
 CREATE TABLE `subset` (
   `subset_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `name` varchar(64) COLLATE utf8_unicode_ci NOT NULL,
-  `definition` varchar(511) COLLATE utf8_unicode_ci NOT NULL DEFAULT '',
+  `name` varchar(64) NOT NULL,
+  `definition` varchar(511) NOT NULL DEFAULT '',
   PRIMARY KEY (`subset_id`),
   UNIQUE KEY `name` (`name`)
 ) ENGINE=MyISAM DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
@@ -61,23 +61,23 @@ CREATE TABLE `term` (
   `ontology_id` int(10) unsigned NOT NULL,
   `subsets` text,
   `accession` varchar(64) NOT NULL,
-  `name` varchar(255) NOT NULL,
-  `definition` text,
-  `is_root` int(11) NOT NULL DEFAULT '0',
-  `is_obsolete` int(11) NOT NULL DEFAULT '0',
+  `name` varchar(255) COLLATE utf8_general_ci NOT NULL,
+  `definition` text COLLATE utf8_general_ci,
+  `is_root` int(11) NOT NULL DEFAULT 0,
+  `is_obsolete` int(11) NOT NULL DEFAULT 0,
   `iri` text,
   PRIMARY KEY (`term_id`),
   UNIQUE KEY `accession` (`accession`),
   UNIQUE KEY `term_ontology_acc_idx` (`ontology_id`,`accession`),
   KEY `term_name_idx` (`name`(100))
-) ENGINE=MyISAM DEFAULT CHARSET=utf8;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
 
 CREATE TABLE `synonym` (
   `synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `term_id` int(10) unsigned NOT NULL,
-  `name` text CHARACTER SET utf8 NOT NULL,
-  `type` enum('EXACT','BROAD','NARROW','RELATED') COLLATE utf8_unicode_ci DEFAULT NULL,
-  `dbxref` varchar(500) COLLATE utf8_unicode_ci DEFAULT NULL,
+  `name` text COLLATE utf8_general_ci NOT NULL,
+  `type` enum('EXACT','BROAD','NARROW','RELATED') DEFAULT NULL,
+  `dbxref` varchar(500) DEFAULT NULL,
   PRIMARY KEY (`synonym_id`),
   UNIQUE KEY `synonym_term_idx` (`term_id`,`synonym_id`),
   KEY `synonym_name_idx` (`name`(100))
@@ -90,14 +90,14 @@ CREATE TABLE `alt_id` (
   PRIMARY KEY (`alt_id`),
   UNIQUE KEY `term_alt_idx` (`term_id`,`alt_id`),
   KEY `ix_alt_id_accession` (`accession`)
-) ENGINE=MyISAM DEFAULT CHARSET=utf8;
+) ENGINE=MyISAM;
 
 CREATE TABLE `relation_type` (
   `relation_type_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `name` varchar(64) NOT NULL,
   PRIMARY KEY (`relation_type_id`),
   UNIQUE KEY `name` (`name`)
-) ENGINE=MyISAM DEFAULT CHARSET=utf8;
+) ENGINE=MyISAM;
 
 
 CREATE TABLE `relation` (
@@ -112,7 +112,7 @@ CREATE TABLE `relation` (
   KEY `ix_relation_parent_term_id` (`parent_term_id`),
   KEY `ix_relation_relation_type_id` (`relation_type_id`),
   KEY `ix_relation_ontology_id` (`ontology_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=utf8;
+) ENGINE=MyISAM;
 
 
 CREATE TABLE `closure` (
@@ -128,7 +128,7 @@ CREATE TABLE `closure` (
   KEY `ix_closure_subparent_term_id` (`subparent_term_id`),
   KEY `ix_closure_ontology_id` (`ontology_id`),
   KEY `parent_subparent_idx` (`parent_term_id`,`subparent_term_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=utf8;
+) ENGINE=MyISAM;
 
 -- There are additional tables in the released databases called
 -- "aux_XX_YY_map".  These are created by the "add_subset_maps.pl"

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

@@ -5,7 +5,7 @@ CREATE TABLE `alt_id` (
   PRIMARY KEY (`alt_id`),
   UNIQUE KEY `term_alt_idx` (`term_id`,`alt_id`),
   KEY `ix_alt_id_accession` (`accession`)
-) ENGINE=MyISAM AUTO_INCREMENT=7 DEFAULT CHARSET=utf8;
+) ENGINE=MyISAM AUTO_INCREMENT=7;
 
 CREATE TABLE `aux_GO_Cross_product_review_map` (
   `term_id` int(10) unsigned NOT NULL,
@@ -132,26 +132,26 @@ CREATE TABLE `closure` (
   KEY `ix_closure_subparent_term_id` (`subparent_term_id`),
   KEY `ix_closure_ontology_id` (`ontology_id`),
   KEY `parent_subparent_idx` (`parent_term_id`,`subparent_term_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=1453438 DEFAULT CHARSET=utf8;
+) ENGINE=MyISAM AUTO_INCREMENT=1453438;
 
 CREATE TABLE `meta` (
   `meta_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `meta_key` varchar(64) COLLATE utf8_unicode_ci NOT NULL,
-  `meta_value` varchar(128) COLLATE utf8_unicode_ci DEFAULT NULL,
+  `meta_key` varchar(64) NOT NULL,
+  `meta_value` varchar(128) DEFAULT NULL,
   `species_id` int(10) unsigned DEFAULT NULL,
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `key_value_idx` (`meta_key`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=44 DEFAULT CHARSET=utf8;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci AUTO_INCREMENT=44;
 
 CREATE TABLE `ontology` (
   `ontology_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `name` varchar(64) COLLATE utf8_unicode_ci NOT NULL,
-  `namespace` varchar(64) COLLATE utf8_unicode_ci NOT NULL,
-  `data_version` varchar(64) COLLATE utf8_unicode_ci DEFAULT NULL,
-  `title` varchar(255) COLLATE utf8_unicode_ci DEFAULT NULL,
+  `name` varchar(64) NOT NULL,
+  `namespace` varchar(64) NOT NULL,
+  `data_version` varchar(64) DEFAULT NULL,
+  `title` varchar(255) DEFAULT NULL,
   PRIMARY KEY (`ontology_id`),
   UNIQUE KEY `ontology_name_namespace_idx` (`name`,`namespace`)
-) ENGINE=MyISAM AUTO_INCREMENT=8 DEFAULT CHARSET=utf8;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci AUTO_INCREMENT=8;
 
 CREATE TABLE `relation` (
   `relation_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -165,47 +165,47 @@ CREATE TABLE `relation` (
   KEY `ix_relation_parent_term_id` (`parent_term_id`),
   KEY `ix_relation_relation_type_id` (`relation_type_id`),
   KEY `ix_relation_ontology_id` (`ontology_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=68750 DEFAULT CHARSET=utf8;
+) ENGINE=MyISAM AUTO_INCREMENT=68750;
 
 CREATE TABLE `relation_type` (
   `relation_type_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `name` varchar(64) NOT NULL,
   PRIMARY KEY (`relation_type_id`),
   UNIQUE KEY `name` (`name`)
-) ENGINE=MyISAM AUTO_INCREMENT=85 DEFAULT CHARSET=utf8;
+) ENGINE=MyISAM AUTO_INCREMENT=85;
 
 CREATE TABLE `subset` (
   `subset_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `name` varchar(64) COLLATE utf8_unicode_ci NOT NULL,
-  `definition` varchar(511) COLLATE utf8_unicode_ci NOT NULL DEFAULT '',
+  `name` varchar(64) NOT NULL,
+  `definition` varchar(511) NOT NULL DEFAULT '',
   PRIMARY KEY (`subset_id`),
   UNIQUE KEY `name` (`name`)
-) ENGINE=MyISAM AUTO_INCREMENT=18 DEFAULT CHARSET=utf8;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci AUTO_INCREMENT=18;
 
 CREATE TABLE `synonym` (
   `synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `term_id` int(10) unsigned NOT NULL,
-  `name` text CHARACTER SET utf8 NOT NULL,
-  `type` enum('EXACT','BROAD','NARROW','RELATED') COLLATE utf8_unicode_ci DEFAULT NULL,
-  `dbxref` varchar(500) COLLATE utf8_unicode_ci DEFAULT NULL,
+  `name` text COLLATE utf8_general_ci NOT NULL,
+  `type` enum('EXACT','BROAD','NARROW','RELATED') DEFAULT NULL,
+  `dbxref` varchar(500) DEFAULT NULL,
   PRIMARY KEY (`synonym_id`),
   UNIQUE KEY `synonym_term_idx` (`term_id`,`synonym_id`),
   KEY `synonym_name_idx` (`name`(100))
-) ENGINE=MyISAM AUTO_INCREMENT=104283 DEFAULT CHARSET=utf8 COLLATE=utf8_swedish_ci;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci AUTO_INCREMENT=104283;
 
 CREATE TABLE `term` (
   `term_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `ontology_id` int(10) unsigned NOT NULL,
   `subsets` text,
   `accession` varchar(64) NOT NULL,
-  `name` varchar(255) NOT NULL,
-  `definition` text,
-  `is_root` int(11) NOT NULL DEFAULT '0',
-  `is_obsolete` int(11) NOT NULL DEFAULT '0',
+  `name` varchar(255) COLLATE utf8_general_ci NOT NULL,
+  `definition` text COLLATE utf8_general_ci,
+  `is_root` int(11) NOT NULL DEFAULT 0,
+  `is_obsolete` int(11) NOT NULL DEFAULT 0,
   `iri` text,
   PRIMARY KEY (`term_id`),
   UNIQUE KEY `accession` (`accession`),
   UNIQUE KEY `term_ontology_acc_idx` (`ontology_id`,`accession`),
   KEY `term_name_idx` (`name`(100))
-) ENGINE=MyISAM AUTO_INCREMENT=45001 DEFAULT CHARSET=utf8;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci AUTO_INCREMENT=45001;