ENSCORESW-2967: update schema to 96

misc-scripts/ontology/sql/patch_95_96_a.sql

+-- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+-- Copyright [2016-2018] 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_95_96_a.sql
+#
+# Title: Update schema version.
+#
+# Description:
+#   Update schema_version in meta table to 96.
+
+UPDATE meta SET meta_value='96' WHERE meta_key='schema_version';
+
+# Patch identifier
+INSERT INTO meta (species_id, meta_key, meta_value)
+  VALUES (NULL, 'patch', 'patch_95_96_a.sql|schema_version');

misc-scripts/ontology/sql/tables.sql

@@ -31,11 +31,11 @@ CREATE TABLE meta (
 # Add schema type and schema version to the meta table
 INSERT INTO meta (meta_key, meta_value) VALUES
   ('schema_type', 'ontology'),
-  ('schema_version', '95');
+  ('schema_version', '96');
 
 # Patches included in this schema file
 INSERT INTO meta (meta_key, meta_value)
-  VALUES ('patch', 'patch_94_95_a.sql|schema_version');
+  VALUES ('patch', 'patch_95_96_a.sql|schema_version');
 
 
 CREATE TABLE ontology (

modules/Bio/EnsEMBL/ApiVersion.pm

@@ -56,7 +56,7 @@ use base qw( Exporter );
 
 our @EXPORT = qw( software_version );
 
-my $API_VERSION = 95;
+my $API_VERSION = 96;
 
 sub software_version { return $API_VERSION }
 

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

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Wed Sep 26 16:18:37 2018
+-- Created on Thu Dec  6 13:49:32 2018
 -- 
 
 BEGIN TRANSACTION;
@@ -620,7 +620,7 @@ CREATE TABLE "object_xref" (
   "analysis_id" smallint
 );
 
-CREATE UNIQUE INDEX "xref_idx" ON "object_xref" ("xref_id", "ensembl_object_type", "ensembl_id", "analysis_id");
+CREATE UNIQUE INDEX "xref_idx" ON "object_xref" ("xref_id", "ensembl_object_type", "ensembl_id");
 
 --
 -- Table: "ontology_xref"

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

@@ -39,7 +39,7 @@
 95	\N	patch	patch_83_84_c.sql|protein_feature_unique
 96	\N	patch	patch_83_84_d.sql|longer_synonym
 1	\N	schema_type	core
-2	\N	schema_version	95
+2	\N	schema_version	96
 8	1	assembly.accession	GCA_000292705.1
 10	1	assembly.date	2012-08
 7	1	assembly.default	GCA_000292705.1
@@ -124,3 +124,5 @@
 124	\N	patch	patch_93_94_c.sql|default_aln_type
 125	\N	patch	patch_94_95_a.sql|schema_version
 126	\N	patch	patch_94_95_b.sql|vertebrate_division_rename
+127	\N	patch	patch_94_95_c.sql|ox_key_update
+128	\N	patch	patch_95_96_a.sql|schema_version

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

@@ -489,7 +489,7 @@ 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=127 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=129 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
@@ -543,7 +543,7 @@ CREATE TABLE `object_xref` (
   `linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   `analysis_id` smallint(5) unsigned DEFAULT NULL,
   PRIMARY KEY (`object_xref_id`),
-  UNIQUE KEY `xref_idx` (`xref_id`,`ensembl_object_type`,`ensembl_id`,`analysis_id`),
+  UNIQUE KEY `xref_idx` (`xref_id`,`ensembl_object_type`,`ensembl_id`),
   KEY `ensembl_idx` (`ensembl_object_type`,`ensembl_id`),
   KEY `analysis_idx` (`analysis_id`)
 ) ENGINE=MyISAM AUTO_INCREMENT=81424 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;

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

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Wed Sep 26 16:18:44 2018
+-- Created on Thu Dec  6 13:49:43 2018
 -- 
 
 BEGIN TRANSACTION;
@@ -620,7 +620,7 @@ CREATE TABLE "object_xref" (
   "analysis_id" smallint
 );
 
-CREATE UNIQUE INDEX "xref_idx" ON "object_xref" ("xref_id", "ensembl_object_type", "ensembl_id", "analysis_id");
+CREATE UNIQUE INDEX "xref_idx" ON "object_xref" ("xref_id", "ensembl_object_type", "ensembl_id");
 
 --
 -- Table: "ontology_xref"

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

-1	\N	schema_version	95
+1	\N	schema_version	96
 2	1	assembly.default	NCBI34
 3	1	species.taxonomy_id	9606
 26	1	species.classification	Homo sapiens
@@ -103,3 +103,5 @@
 170	\N	patch	patch_93_94_c.sql|default_aln_type
 171	\N	patch	patch_94_95_a.sql|schema_version
 172	\N	patch	patch_94_95_b.sql|vertebrate_division_rename
+173	\N	patch	patch_94_95_c.sql|ox_key_update
+174	\N	patch	patch_95_96_a.sql|schema_version

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

@@ -489,7 +489,7 @@ 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=173 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=175 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
@@ -543,7 +543,7 @@ CREATE TABLE `object_xref` (
   `linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   `analysis_id` smallint(5) unsigned DEFAULT NULL,
   PRIMARY KEY (`object_xref_id`),
-  UNIQUE KEY `xref_idx` (`xref_id`,`ensembl_object_type`,`ensembl_id`,`analysis_id`),
+  UNIQUE KEY `xref_idx` (`xref_id`,`ensembl_object_type`,`ensembl_id`),
   KEY `ensembl_idx` (`ensembl_object_type`,`ensembl_id`),
   KEY `analysis_idx` (`analysis_id`)
 ) ENGINE=MyISAM AUTO_INCREMENT=253694 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;

modules/t/test-genome-DBs/homo_sapiens/empty/SQLite/table.sql

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Wed Sep 26 16:18:52 2018
+-- Created on Thu Dec  6 13:49:54 2018
 -- 
 
 BEGIN TRANSACTION;
@@ -620,7 +620,7 @@ CREATE TABLE "object_xref" (
   "analysis_id" smallint
 );
 
-CREATE UNIQUE INDEX "xref_idx" ON "object_xref" ("xref_id", "ensembl_object_type", "ensembl_id", "analysis_id");
+CREATE UNIQUE INDEX "xref_idx" ON "object_xref" ("xref_id", "ensembl_object_type", "ensembl_id");
 
 --
 -- Table: "ontology_xref"

modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt

-1	\N	schema_version	95
+1	\N	schema_version	96
 2	1	assembly.default	NCBI34
 33	1	species.classification	Chordata
 32	1	species.classification	Vertebrata
@@ -103,3 +103,5 @@
 152	\N	patch	patch_93_94_c.sql|default_aln_type
 153	\N	patch	patch_94_95_a.sql|schema_version
 154	\N	patch	patch_94_95_b.sql|vertebrate_division_rename
+155	\N	patch	patch_94_95_c.sql|ox_key_update
+156	\N	patch	patch_95_96_a.sql|schema_version

modules/t/test-genome-DBs/homo_sapiens/empty/table.sql

@@ -489,7 +489,7 @@ 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=155 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=157 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
@@ -543,7 +543,7 @@ CREATE TABLE `object_xref` (
   `linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   `analysis_id` smallint(5) unsigned DEFAULT NULL,
   PRIMARY KEY (`object_xref_id`),
-  UNIQUE KEY `xref_idx` (`xref_id`,`ensembl_object_type`,`ensembl_id`,`analysis_id`),
+  UNIQUE KEY `xref_idx` (`xref_id`,`ensembl_object_type`,`ensembl_id`),
   KEY `ensembl_idx` (`ensembl_object_type`,`ensembl_id`),
   KEY `analysis_idx` (`analysis_id`)
 ) ENGINE=MyISAM AUTO_INCREMENT=81424 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;

modules/t/test-genome-DBs/homo_sapiens/patch/SQLite/table.sql

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Wed Sep 26 16:18:59 2018
+-- Created on Thu Dec  6 13:50:04 2018
 -- 
 
 BEGIN TRANSACTION;
@@ -620,7 +620,7 @@ CREATE TABLE "object_xref" (
   "analysis_id" smallint
 );
 
-CREATE UNIQUE INDEX "xref_idx" ON "object_xref" ("xref_id", "ensembl_object_type", "ensembl_id", "analysis_id");
+CREATE UNIQUE INDEX "xref_idx" ON "object_xref" ("xref_id", "ensembl_object_type", "ensembl_id");
 
 --
 -- Table: "ontology_xref"

modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt

-1	\N	schema_version	95
+1	\N	schema_version	96
 2014	1	species.classification	Haplorrhini
 40	1	assembly.default	GRCh37
 41	1	assembly.date	2009-02
@@ -108,3 +108,5 @@
 2115	\N	patch	patch_93_94_c.sql|default_aln_type
 2116	\N	patch	patch_94_95_a.sql|schema_version
 2117	\N	patch	patch_94_95_b.sql|vertebrate_division_rename
+2118	\N	patch	patch_94_95_c.sql|ox_key_update
+2119	\N	patch	patch_95_96_a.sql|schema_version

modules/t/test-genome-DBs/homo_sapiens/patch/table.sql

@@ -489,7 +489,7 @@ 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=2118 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=2120 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
@@ -543,7 +543,7 @@ CREATE TABLE `object_xref` (
   `linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   `analysis_id` smallint(5) unsigned DEFAULT NULL,
   PRIMARY KEY (`object_xref_id`),
-  UNIQUE KEY `xref_idx` (`xref_id`,`ensembl_object_type`,`ensembl_id`,`analysis_id`),
+  UNIQUE KEY `xref_idx` (`xref_id`,`ensembl_object_type`,`ensembl_id`),
   KEY `ensembl_idx` (`ensembl_object_type`,`ensembl_id`),
   KEY `analysis_idx` (`analysis_id`)
 ) ENGINE=MyISAM AUTO_INCREMENT=17375428 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;

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

 1	\N	schema_type	variation
-2	\N	schema_version	95
+2	\N	schema_version	96
 3	\N	patch	patch_84_85_a.sql|schema version
 4	\N	patch	patch_84_85_b.sql|create sample_synonym
 5	\N	patch	patch_84_85_c.sql|drop column moltype from variation_synonym
@@ -34,3 +34,4 @@
 34	\N	patch	patch_93_94_a.sql|schema version
 35	\N	patch	patch_94_95_a.sql|schema version
 36	\N	patch	patch_94_95_b.sql|create table to store allele synonyms
+37	\N	patch	patch_95_96_a.sql|schema_version

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

@@ -178,7 +178,7 @@ 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=37 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=38 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL,

modules/t/test-genome-DBs/homo_sapiens/xref/SQLite/table.sql

+-- 
+-- Created by SQL::Translator::Producer::SQLite
+-- Created on Thu Dec  6 13:50:07 2018
+-- 
+
+BEGIN TRANSACTION;
+
+COMMIT;

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

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Wed Sep 26 16:19:07 2018
+-- Created on Thu Dec  6 13:50:17 2018
 -- 
 
 BEGIN TRANSACTION;
@@ -620,7 +620,7 @@ CREATE TABLE "object_xref" (
   "analysis_id" smallint
 );
 
-CREATE UNIQUE INDEX "xref_idx" ON "object_xref" ("xref_id", "ensembl_object_type", "ensembl_id", "analysis_id");
+CREATE UNIQUE INDEX "xref_idx" ON "object_xref" ("xref_id", "ensembl_object_type", "ensembl_id");
 
 --
 -- Table: "ontology_xref"

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

-1	\N	schema_version	95
+1	\N	schema_version	96
 2	1	assembly.default	MULTIMAP
 3	1	species.taxonomy_id	1
 4	1	assembly.mapping	chromosome:MULTIMAP#contig
@@ -64,3 +64,5 @@
 157	\N	patch	patch_93_94_c.sql|default_aln_type
 158	\N	patch	patch_94_95_a.sql|schema_version
 159	\N	patch	patch_94_95_b.sql|vertebrate_division_rename
+160	\N	patch	patch_94_95_c.sql|ox_key_update
+161	\N	patch	patch_95_96_a.sql|schema_version