Merge pull request #396 from Ensembl/e98_version_bump

Release-98 version bump

modules/t/test-genome-DBs/multi/compara/meta.txt

@@ -51,3 +51,4 @@
 61	\N	patch	patch_94_95_d.sql|node_type_within_species_speciation
 62	\N	patch	patch_95_96_a.sql|schema_version
 64	\N	patch	patch_96_97_a.sql|schema_version
+65	\N	patch	patch_97_98_b.sql|division_name

modules/t/test-genome-DBs/multi/compara/table.sql

@@ -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,

modules/t/test-genome-DBs/mus_musculus/core/SQLite/table.sql

 -- 
 -- 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;

modules/t/test-genome-DBs/mus_musculus/core/meta.txt

 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

modules/t/test-genome-DBs/mus_musculus/core/table.sql

@@ -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 '',

modules/t/test-genome-DBs/mus_musculus/variation/meta.txt

 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

modules/t/test-genome-DBs/mus_musculus/variation/table.sql

@@ -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,

modules/t/test-genome-DBs/nameless/core/SQLite/table.sql

 -- 
 -- 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;

modules/t/test-genome-DBs/nameless/core/meta.txt

-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

modules/t/test-genome-DBs/nameless/core/table.sql

@@ -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 '',

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

 -- 
 -- 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");

modules/t/test-genome-DBs/ontology/ontology/meta.txt

@@ -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

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

@@ -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`),

modules/t/test-genome-DBs/polyploidy/core/SQLite/table.sql

 -- 
 -- 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;

modules/t/test-genome-DBs/polyploidy/core/meta.txt

 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

modules/t/test-genome-DBs/polyploidy/core/table.sql

@@ -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 '',

modules/t/test-genome-DBs/test_collection/core/SQLite/table.sql

 -- 
 -- 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;

modules/t/test-genome-DBs/test_collection/core/meta.txt

@@ -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

modules/t/test-genome-DBs/test_collection/core/table.sql

@@ -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 '',

sql/patch_97_98_a.sql

+-- 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');