Unverified Commit 6b64a71c authored by Marek Szuba's avatar Marek Szuba Committed by GitHub
Browse files

Merge pull request #396 from Ensembl/e98_version_bump

Release-98 version bump
parents 1d07af8d 082c2055
...@@ -51,3 +51,4 @@ ...@@ -51,3 +51,4 @@
61 \N patch patch_94_95_d.sql|node_type_within_species_speciation 61 \N patch patch_94_95_d.sql|node_type_within_species_speciation
62 \N patch patch_95_96_a.sql|schema_version 62 \N patch patch_95_96_a.sql|schema_version
64 \N patch patch_96_97_a.sql|schema_version 64 \N patch patch_96_97_a.sql|schema_version
65 \N patch patch_97_98_b.sql|division_name
...@@ -263,7 +263,6 @@ CREATE TABLE `gene_tree_root_attr` ( ...@@ -263,7 +263,6 @@ CREATE TABLE `gene_tree_root_attr` (
`taxonomic_coverage` float DEFAULT NULL, `taxonomic_coverage` float DEFAULT NULL,
`ratio_species_genes` float DEFAULT NULL, `ratio_species_genes` float DEFAULT NULL,
`model_name` varchar(40) DEFAULT NULL, `model_name` varchar(40) DEFAULT NULL,
`division` varchar(10) DEFAULT NULL,
PRIMARY KEY (`root_id`), PRIMARY KEY (`root_id`),
KEY `lca_node_id` (`lca_node_id`) KEY `lca_node_id` (`lca_node_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1; ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
...@@ -429,7 +428,7 @@ CREATE TABLE `meta` ( ...@@ -429,7 +428,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`), PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`(255)), UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`(255)),
KEY `species_value_idx` (`species_id`,`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` ( CREATE TABLE `method_link` (
`method_link_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `method_link_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......
-- --
-- Created by SQL::Translator::Producer::SQLite -- 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; BEGIN TRANSACTION;
......
1 \N schema_type core 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 3 \N patch patch_65_66_a.sql|schema_version
4 \N patch patch_65_66_b.sql|fix_external_db_id 4 \N patch patch_65_66_b.sql|fix_external_db_id
5 \N patch patch_65_66_c.sql|reorder_unmapped_obj_index 5 \N patch patch_65_66_c.sql|reorder_unmapped_obj_index
...@@ -188,3 +188,4 @@ ...@@ -188,3 +188,4 @@
1700 \N patch patch_96_97_c.sql|rnaproduct_tables 1700 \N patch patch_96_97_c.sql|rnaproduct_tables
1701 \N patch patch_96_97_d.sql|add_object_type_rnaproduct 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 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` ( ...@@ -490,7 +490,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`), PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`), UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`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` ( CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '', `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
......
1 \N schema_type variation 1 \N schema_type variation
2 \N schema_version 97 2 \N schema_version 98
6 1 species.production_name mus_musculus 6 1 species.production_name mus_musculus
15 1 web_config sv_study#Keane 2011 (DGVa study estd118)#Keane 2011#estd118 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 14 1 web_config set#All failed variants#All failed variants#variation_set_fail_all#failed
...@@ -69,3 +69,4 @@ ...@@ -69,3 +69,4 @@
75 \N patch patch_96_97_a.sql|schema version 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 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 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` ( ...@@ -186,7 +186,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`), PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`), UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`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` ( CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL, `table_name` varchar(40) NOT NULL,
......
-- --
-- Created by SQL::Translator::Producer::SQLite -- 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; BEGIN TRANSACTION;
......
1 \N schema_version 97 1 \N schema_version 98
2 1 assembly.default NCBI34 2 1 assembly.default NCBI34
3 1 species.taxonomy_id 9606 3 1 species.taxonomy_id 9606
26 1 species.classification Homo sapiens 26 1 species.classification Homo sapiens
...@@ -109,3 +109,4 @@ ...@@ -109,3 +109,4 @@
163 \N patch patch_96_97_c.sql|rnaproduct_tables 163 \N patch patch_96_97_c.sql|rnaproduct_tables
164 \N patch patch_96_97_d.sql|add_object_type_rnaproduct 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 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` ( ...@@ -480,7 +480,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`), PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`), UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`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` ( CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '', `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
......
-- --
-- Created by SQL::Translator::Producer::SQLite -- 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; BEGIN TRANSACTION;
...@@ -262,7 +262,7 @@ CREATE UNIQUE INDEX "name" ON "relation_type" ("name"); ...@@ -262,7 +262,7 @@ CREATE UNIQUE INDEX "name" ON "relation_type" ("name");
CREATE TABLE "subset" ( CREATE TABLE "subset" (
"subset_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL, "subset_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
"name" varchar(64) 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"); CREATE UNIQUE INDEX "name02" ON "subset" ("name");
......
...@@ -9,7 +9,7 @@ ...@@ -9,7 +9,7 @@
10 patch patch_72_73_b.sql|meta \N 10 patch patch_72_73_b.sql|meta \N
12 patch patch_73_74_a.sql|schema_version \N 12 patch patch_73_74_a.sql|schema_version \N
14 patch patch_74_75_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 16 patch patch_75_76_a.sql|schema_version \N
17 patch patch_76_77_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 18 patch patch_77_78_a.sql|schema_version \N
...@@ -40,3 +40,4 @@ ...@@ -40,3 +40,4 @@
43 patch patch_95_96_a.sql|schema_version \N 43 patch patch_95_96_a.sql|schema_version \N
44 patch patch_95_96_b.sql|term_ontology_update \N 44 patch patch_95_96_b.sql|term_ontology_update \N
45 patch patch_96_97_a.sql|schema_version \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` ( ...@@ -141,7 +141,7 @@ CREATE TABLE `meta` (
`species_id` int(10) unsigned DEFAULT NULL, `species_id` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`meta_id`), PRIMARY KEY (`meta_id`),
UNIQUE KEY `key_value_idx` (`meta_key`,`meta_value`) 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` ( CREATE TABLE `ontology` (
`ontology_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `ontology_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
...@@ -177,7 +177,7 @@ CREATE TABLE `relation_type` ( ...@@ -177,7 +177,7 @@ CREATE TABLE `relation_type` (
CREATE TABLE `subset` ( CREATE TABLE `subset` (
`subset_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `subset_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(64) COLLATE utf8_unicode_ci NOT NULL, `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`), PRIMARY KEY (`subset_id`),
UNIQUE KEY `name` (`name`) UNIQUE KEY `name` (`name`)
) ENGINE=MyISAM AUTO_INCREMENT=18 DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci; ) ENGINE=MyISAM AUTO_INCREMENT=18 DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
...@@ -196,13 +196,13 @@ CREATE TABLE `synonym` ( ...@@ -196,13 +196,13 @@ CREATE TABLE `synonym` (
CREATE TABLE `term` ( CREATE TABLE `term` (
`term_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `term_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`ontology_id` int(10) unsigned NOT NULL, `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, `accession` varchar(64) COLLATE utf8_unicode_ci NOT NULL,
`name` varchar(255) CHARACTER SET utf8 NOT NULL, `name` varchar(255) CHARACTER SET utf8 NOT NULL,
`definition` text CHARACTER SET utf8, `definition` text CHARACTER SET utf8 DEFAULT NULL,
`is_root` int(11) NOT NULL DEFAULT '0', `is_root` int(11) NOT NULL DEFAULT 0,
`is_obsolete` int(11) NOT NULL DEFAULT '0', `is_obsolete` int(11) NOT NULL DEFAULT 0,
`iri` text COLLATE utf8_unicode_ci, `iri` text COLLATE utf8_unicode_ci DEFAULT NULL,
PRIMARY KEY (`term_id`), PRIMARY KEY (`term_id`),
UNIQUE KEY `accession` (`accession`), UNIQUE KEY `accession` (`accession`),
UNIQUE KEY `term_ontology_acc_idx` (`ontology_id`,`accession`), UNIQUE KEY `term_ontology_acc_idx` (`ontology_id`,`accession`),
......
-- --
-- Created by SQL::Translator::Producer::SQLite -- 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; BEGIN TRANSACTION;
......
1 \N schema_type core 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 3 \N patch patch_68_69_a.sql|schema_version
4 1 species.taxonomy_id 4565 4 1 species.taxonomy_id 4565
6 1 species.alias bread wheat 6 1 species.alias bread wheat
...@@ -164,3 +164,4 @@ ...@@ -164,3 +164,4 @@
244 \N patch patch_96_97_c.sql|rnaproduct_tables 244 \N patch patch_96_97_c.sql|rnaproduct_tables
245 \N patch patch_96_97_d.sql|add_object_type_rnaproduct 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 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` ( ...@@ -490,7 +490,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`), PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`), UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`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` ( CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '', `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
......
-- --
-- Created by SQL::Translator::Producer::SQLite -- 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; BEGIN TRANSACTION;
......
...@@ -39,7 +39,7 @@ ...@@ -39,7 +39,7 @@
190 \N patch patch_83_84_c.sql|protein_feature_unique 190 \N patch patch_83_84_c.sql|protein_feature_unique
191 \N patch patch_83_84_d.sql|longer_synonym 191 \N patch patch_83_84_d.sql|longer_synonym
1 \N schema_type core 1 \N schema_type core
2 \N schema_version 97 2 \N schema_version 98
8 1 assembly.accession GCA_000292705.1 8 1 assembly.accession GCA_000292705.1
10 1 assembly.date 2012-08 10 1 assembly.date 2012-08
7 1 assembly.default GCA_000292705.1 7 1 assembly.default GCA_000292705.1
...@@ -184,3 +184,4 @@ ...@@ -184,3 +184,4 @@
226 \N patch patch_96_97_c.sql|rnaproduct_tables 226 \N patch patch_96_97_c.sql|rnaproduct_tables
227 \N patch patch_96_97_d.sql|add_object_type_rnaproduct 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 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` ( ...@@ -480,7 +480,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`), PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`), UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`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` ( CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '', `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
......
-- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-- Copyright [2016-2019] EMBL-European Bioinformatics Institute
--
-- Licensed under the Apache License, Version 2.0 (the "License");
-- you may not use this file except in compliance with the License.
-- You may obtain a copy of the License at
--
-- http://www.apache.org/licenses/LICENSE-2.0
--
-- Unless required by applicable law or agreed to in writing, software
-- distributed under the License is distributed on an "AS IS" BASIS,
-- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-- See the License for the specific language governing permissions and
-- limitations under the License.
# patch_97_98_a.sql
#
# Title: Update schema version.
#
# Description:
# Update schema_version in meta table to 98.
UPDATE meta SET meta_value='98' WHERE meta_key='schema_version';
# Patch identifier
INSERT INTO meta (species_id, meta_key, meta_value)
VALUES (NULL, 'patch', 'patch_97_98_a.sql|schema_version');
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