Commit 082c2055 authored by Marek Szuba's avatar Marek Szuba
Browse files

Patch test databases

Source: release/98 branch of ols-ensembl-loader and master branches
of all other relevant Ensembl repositories, pulled a few minutes ago.
Compara, Variation and ontology schemas all have already been bumped to
version 98.
parent 4291dddf
......@@ -263,7 +263,6 @@ CREATE TABLE `gene_tree_root_attr` (
`taxonomic_coverage` float DEFAULT NULL,
`ratio_species_genes` float DEFAULT NULL,
`model_name` varchar(40) DEFAULT NULL,
`division` varchar(10) DEFAULT NULL,
PRIMARY KEY (`root_id`),
KEY `lca_node_id` (`lca_node_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
......@@ -429,7 +428,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`(255)),
KEY `species_value_idx` (`species_id`,`meta_value`(255))
) ENGINE=MyISAM AUTO_INCREMENT=65 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=66 DEFAULT CHARSET=latin1;
CREATE TABLE `method_link` (
`method_link_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Tue Apr 2 16:04:10 2019
-- Created on Mon Jun 17 16:51:53 2019
--
BEGIN TRANSACTION;
......
1 \N schema_type core
2 \N schema_version 97
2 \N schema_version 98
3 \N patch patch_65_66_a.sql|schema_version
4 \N patch patch_65_66_b.sql|fix_external_db_id
5 \N patch patch_65_66_c.sql|reorder_unmapped_obj_index
......@@ -188,3 +188,4 @@
1700 \N patch patch_96_97_c.sql|rnaproduct_tables
1701 \N patch patch_96_97_d.sql|add_object_type_rnaproduct
1702 \N patch patch_96_97_e.sql|add_stable_id_event_type_rnaproduct
1703 \N patch patch_97_98_a.sql|schema_version
......@@ -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=1703 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=1704 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
......
1 \N schema_type variation
2 \N schema_version 97
2 \N schema_version 98
6 1 species.production_name mus_musculus
15 1 web_config sv_study#Keane 2011 (DGVa study estd118)#Keane 2011#estd118
14 1 web_config set#All failed variants#All failed variants#variation_set_fail_all#failed
......@@ -69,3 +69,4 @@
75 \N patch patch_96_97_a.sql|schema version
76 \N patch patch_96_97_b.sql|move ancestral allele column to variation_feature
77 \N patch patch_96_97_c.sql|add an unique index on the name column
78 \N patch patch_97_98_a.sql|schema version
......@@ -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=78 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=79 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL,
......
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Tue Apr 2 16:04:13 2019
-- Created on Mon Jun 17 16:51:56 2019
--
BEGIN TRANSACTION;
......
1 \N schema_version 97
1 \N schema_version 98
2 1 assembly.default NCBI34
3 1 species.taxonomy_id 9606
26 1 species.classification Homo sapiens
......@@ -109,3 +109,4 @@
163 \N patch patch_96_97_c.sql|rnaproduct_tables
164 \N patch patch_96_97_d.sql|add_object_type_rnaproduct
165 \N patch patch_96_97_e.sql|add_stable_id_event_type_rnaproduct
166 \N patch patch_97_98_a.sql|schema_version
......@@ -480,7 +480,7 @@ 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=166 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=167 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
......
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Tue Apr 2 16:04:14 2019
-- Created on Mon Jun 17 16:51:58 2019
--
BEGIN TRANSACTION;
......@@ -262,7 +262,7 @@ CREATE UNIQUE INDEX "name" ON "relation_type" ("name");
CREATE TABLE "subset" (
"subset_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
"name" varchar(64) NOT NULL,
"definition" varchar(511) NOT NULL DEFAULT ''
"definition" varchar(1023) NOT NULL DEFAULT ''
);
CREATE UNIQUE INDEX "name02" ON "subset" ("name");
......
......@@ -9,7 +9,7 @@
10 patch patch_72_73_b.sql|meta \N
12 patch patch_73_74_a.sql|schema_version \N
14 patch patch_74_75_a.sql|schema_version \N
15 schema_version 97 \N
15 schema_version 98 \N
16 patch patch_75_76_a.sql|schema_version \N
17 patch patch_76_77_a.sql|schema_version \N
18 patch patch_77_78_a.sql|schema_version \N
......@@ -40,3 +40,4 @@
43 patch patch_95_96_a.sql|schema_version \N
44 patch patch_95_96_b.sql|term_ontology_update \N
45 patch patch_96_97_a.sql|schema_version \N
46 patch patch_97_98_a.sql|schema_version \N
......@@ -141,7 +141,7 @@ CREATE TABLE `meta` (
`species_id` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`meta_id`),
UNIQUE KEY `key_value_idx` (`meta_key`,`meta_value`)
) ENGINE=MyISAM AUTO_INCREMENT=46 DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
) ENGINE=MyISAM AUTO_INCREMENT=47 DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
CREATE TABLE `ontology` (
`ontology_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -177,7 +177,7 @@ CREATE TABLE `relation_type` (
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 '',
`definition` varchar(1023) COLLATE utf8_unicode_ci NOT NULL DEFAULT '',
PRIMARY KEY (`subset_id`),
UNIQUE KEY `name` (`name`)
) ENGINE=MyISAM AUTO_INCREMENT=18 DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
......@@ -196,13 +196,13 @@ CREATE TABLE `synonym` (
CREATE TABLE `term` (
`term_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`ontology_id` int(10) unsigned NOT NULL,
`subsets` text COLLATE utf8_unicode_ci,
`subsets` text COLLATE utf8_unicode_ci DEFAULT NULL,
`accession` varchar(64) COLLATE utf8_unicode_ci NOT NULL,
`name` varchar(255) CHARACTER SET utf8 NOT NULL,
`definition` text CHARACTER SET utf8,
`is_root` int(11) NOT NULL DEFAULT '0',
`is_obsolete` int(11) NOT NULL DEFAULT '0',
`iri` text COLLATE utf8_unicode_ci,
`definition` text CHARACTER SET utf8 DEFAULT NULL,
`is_root` int(11) NOT NULL DEFAULT 0,
`is_obsolete` int(11) NOT NULL DEFAULT 0,
`iri` text COLLATE utf8_unicode_ci DEFAULT NULL,
PRIMARY KEY (`term_id`),
UNIQUE KEY `accession` (`accession`),
UNIQUE KEY `term_ontology_acc_idx` (`ontology_id`,`accession`),
......
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Tue Apr 2 16:04:17 2019
-- Created on Mon Jun 17 16:52:01 2019
--
BEGIN TRANSACTION;
......
1 \N schema_type core
2 \N schema_version 97
2 \N schema_version 98
3 \N patch patch_68_69_a.sql|schema_version
4 1 species.taxonomy_id 4565
6 1 species.alias bread wheat
......@@ -164,3 +164,4 @@
244 \N patch patch_96_97_c.sql|rnaproduct_tables
245 \N patch patch_96_97_d.sql|add_object_type_rnaproduct
246 \N patch patch_96_97_e.sql|add_stable_id_event_type_rnaproduct
247 \N patch patch_97_98_a.sql|schema_version
......@@ -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=247 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=248 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
......
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Tue Apr 2 16:04:19 2019
-- Created on Mon Jun 17 16:52:04 2019
--
BEGIN TRANSACTION;
......
......@@ -39,7 +39,7 @@
190 \N patch patch_83_84_c.sql|protein_feature_unique
191 \N patch patch_83_84_d.sql|longer_synonym
1 \N schema_type core
2 \N schema_version 97
2 \N schema_version 98
8 1 assembly.accession GCA_000292705.1
10 1 assembly.date 2012-08
7 1 assembly.default GCA_000292705.1
......@@ -184,3 +184,4 @@
226 \N patch patch_96_97_c.sql|rnaproduct_tables
227 \N patch patch_96_97_d.sql|add_object_type_rnaproduct
228 \N patch patch_96_97_e.sql|add_stable_id_event_type_rnaproduct
229 \N patch patch_97_98_a.sql|schema_version
......@@ -480,7 +480,7 @@ 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=229 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=230 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
......
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