From 506dcd85a3dca0a62f8a5a9feef809e2aceab5a5 Mon Sep 17 00:00:00 2001
From: Marc Chakiachvili <mchakiachvili@ebi.ac.uk>
Date: Wed, 19 Dec 2018 09:56:52 +0000
Subject: [PATCH] Updated SQL table.sql script for tests
---
.../ontology/ontology/table.sql | 108 +++++++++---------
1 file changed, 56 insertions(+), 52 deletions(-)
diff --git a/modules/t/test-genome-DBs/ontology/ontology/table.sql b/modules/t/test-genome-DBs/ontology/ontology/table.sql
index 8adae562e4..3dbb19df00 100644
--- a/modules/t/test-genome-DBs/ontology/ontology/table.sql
+++ b/modules/t/test-genome-DBs/ontology/ontology/table.sql
@@ -4,120 +4,120 @@ CREATE TABLE `alt_id` (
`accession` varchar(64) NOT NULL,
PRIMARY KEY (`alt_id`),
UNIQUE KEY `term_alt_idx` (`term_id`,`alt_id`),
- KEY `accession_idx` (`accession`(50))
-) ENGINE=MyISAM AUTO_INCREMENT=7 DEFAULT CHARSET=latin1;
+ KEY `ix_alt_id_accession` (`accession`)
+) ENGINE=MyISAM AUTO_INCREMENT=7 DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_Cross_product_review_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_goslim_aspergillus_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_goslim_candida_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_goslim_generic_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_goslim_metagenomics_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_goslim_pir_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_goslim_plant_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_goslim_pombe_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_goslim_yeast_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_gosubset_prok_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_high_level_annotation_qc_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_mf_needs_review_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_virus_checked_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_SO_DBVAR_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_SO_SOFA_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_SO_biosapiens_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `closure` (
`closure_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -126,67 +126,71 @@ CREATE TABLE `closure` (
`subparent_term_id` int(10) unsigned DEFAULT NULL,
`distance` tinyint(3) unsigned NOT NULL,
`ontology_id` int(10) unsigned NOT NULL,
- `confident_relationship` tinyint(1) NOT NULL DEFAULT '0',
+ `confident_relationship` tinyint(1) NOT NULL,
PRIMARY KEY (`closure_id`),
- UNIQUE KEY `child_parent_idx` (`child_term_id`,`parent_term_id`,`subparent_term_id`,`ontology_id`),
+ UNIQUE KEY `closure_child_parent_idx` (`child_term_id`,`parent_term_id`,`subparent_term_id`,`ontology_id`),
+ 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=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=1453438 DEFAULT CHARSET=utf8;
CREATE TABLE `meta` (
`meta_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `meta_key` varchar(64) NOT NULL,
- `meta_value` varchar(128) DEFAULT NULL,
- `species_id` int(1) unsigned DEFAULT NULL,
+ `meta_key` varchar(64) COLLATE utf8_unicode_ci NOT NULL,
+ `meta_value` varchar(128) COLLATE utf8_unicode_ci 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=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=44 DEFAULT CHARSET=utf8;
CREATE TABLE `ontology` (
`ontology_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `name` varchar(64) NOT NULL,
- `namespace` varchar(64) NOT NULL,
- `data_version` varchar(64) DEFAULT NULL,
- `title` varchar(255) DEFAULT NULL,
+ `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,
PRIMARY KEY (`ontology_id`),
- UNIQUE KEY `name_namespace_idx` (`name`,`namespace`)
-) ENGINE=MyISAM AUTO_INCREMENT=8 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `ontology_name_namespace_idx` (`name`,`namespace`)
+) ENGINE=MyISAM AUTO_INCREMENT=8 DEFAULT CHARSET=utf8;
CREATE TABLE `relation` (
`relation_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`child_term_id` int(10) unsigned NOT NULL,
`parent_term_id` int(10) unsigned NOT NULL,
`relation_type_id` int(10) unsigned NOT NULL,
- `intersection_of` tinyint(3) unsigned NOT NULL DEFAULT '0',
+ `intersection_of` tinyint(1) NOT NULL,
`ontology_id` int(10) unsigned NOT NULL,
PRIMARY KEY (`relation_id`),
UNIQUE KEY `child_parent_idx` (`child_term_id`,`parent_term_id`,`relation_type_id`,`intersection_of`,`ontology_id`),
- KEY `parent_idx` (`parent_term_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=68750 DEFAULT CHARSET=latin1;
+ 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;
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_idx` (`name`)
-) ENGINE=MyISAM AUTO_INCREMENT=85 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `name` (`name`)
+) ENGINE=MyISAM AUTO_INCREMENT=85 DEFAULT CHARSET=utf8;
CREATE TABLE `subset` (
`subset_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `name` varchar(64) NOT NULL,
- `definition` varchar(128) NOT NULL,
+ `name` varchar(64) COLLATE utf8_unicode_ci NOT NULL,
+ `definition` varchar(511) COLLATE utf8_unicode_ci NOT NULL DEFAULT '',
PRIMARY KEY (`subset_id`),
- UNIQUE KEY `name_idx` (`name`)
-) ENGINE=MyISAM AUTO_INCREMENT=18 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `name` (`name`)
+) ENGINE=MyISAM AUTO_INCREMENT=18 DEFAULT CHARSET=utf8;
CREATE TABLE `synonym` (
`synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`term_id` int(10) unsigned NOT NULL,
- `name` mediumtext COLLATE utf8_swedish_ci NOT NULL,
- `type` enum('EXACT','BROAD','NARROW','RELATED') COLLATE utf8_swedish_ci DEFAULT NULL,
- `dbxref` varchar(256) COLLATE utf8_swedish_ci 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,
PRIMARY KEY (`synonym_id`),
- UNIQUE KEY `term_synonym_idx` (`term_id`,`synonym_id`),
- KEY `name_idx` (`name`(50))
+ 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;
CREATE TABLE `term` (
@@ -196,12 +200,12 @@ CREATE TABLE `term` (
`accession` varchar(64) NOT NULL,
`name` varchar(255) NOT NULL,
`definition` text,
- `is_root` int(11) DEFAULT NULL,
- `is_obsolete` int(11) DEFAULT NULL,
- `iri` varchar(1000) DEFAULT NULL,
+ `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_idx` (`accession`),
- UNIQUE KEY `ontology_acc_idx` (`ontology_id`,`accession`),
- KEY `name_idx` (`name`)
-) ENGINE=MyISAM AUTO_INCREMENT=45001 DEFAULT CHARSET=latin1;
+ 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;
--
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