From 3b7850f2908f0c70433d8381ea350f671058a2f2 Mon Sep 17 00:00:00 2001
From: Marc Chakiachvili <mchakiachvili@ebi.ac.uk>
Date: Wed, 19 Dec 2018 13:08:56 +0000
Subject: [PATCH] Added new patch to update current CHARSET and COLLATE for
related tables.
---
misc-scripts/ontology/sql/patch_95_96_b.sql | 17 ++++++-
misc-scripts/ontology/sql/tables.sql | 40 ++++++++--------
.../ontology/ontology/table.sql | 48 +++++++++----------
3 files changed, 59 insertions(+), 46 deletions(-)
diff --git a/misc-scripts/ontology/sql/patch_95_96_b.sql b/misc-scripts/ontology/sql/patch_95_96_b.sql
index 92934a805d..8e71a9dd9b 100644
--- a/misc-scripts/ontology/sql/patch_95_96_b.sql
+++ b/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;
diff --git a/misc-scripts/ontology/sql/tables.sql b/misc-scripts/ontology/sql/tables.sql
index 00a7d783d7..51798881e0 100644
--- a/misc-scripts/ontology/sql/tables.sql
+++ b/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"
diff --git a/modules/t/test-genome-DBs/ontology/ontology/table.sql b/modules/t/test-genome-DBs/ontology/ontology/table.sql
index 3dbb19df00..cca2a18dd0 100644
--- a/modules/t/test-genome-DBs/ontology/ontology/table.sql
+++ b/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;
--
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