Merge branch 'schema_version_update' into feature/biotype

misc-scripts/ontology/sql/patch_92_93_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_92_93_a.sql
+#
+# Title: Update schema version.
+#
+# Description:
+#   Update schema_version in meta table to 93.
+
+UPDATE meta SET meta_value='93' WHERE meta_key='schema_version';
+
+# Patch identifier
+INSERT INTO meta (species_id, meta_key, meta_value)
+  VALUES (NULL, 'patch', 'patch_92_93_a.sql|schema_version');

misc-scripts/ontology/sql/tables.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.
@@ -29,13 +29,13 @@ CREATE TABLE meta (
 ) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
 
 # Add schema type and schema version to the meta table
-INSERT INTO meta (meta_key, meta_value) VALUES 
+INSERT INTO meta (meta_key, meta_value) VALUES
   ('schema_type', 'ontology'),
-  ('schema_version', '92');
+  ('schema_version', '93');
 
 # Patches included in this schema file
 INSERT INTO meta (meta_key, meta_value)
-  VALUES ('patch', 'patch_91_92_a.sql|schema_version');
+  VALUES ('patch', 'patch_92_93_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 = 92;
+my $API_VERSION = 93;
 
 sub software_version { return $API_VERSION }
 

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	92
+2	\N	schema_version	93
 8	1	assembly.accession	GCA_000292705.1
 10	1	assembly.date	2012-08
 7	1	assembly.default	GCA_000292705.1
@@ -116,3 +116,4 @@
 116	\N	patch	patch_90_91_d.sql|remove_external_data
 117	\N	patch	patch_91_92_a.sql|schema_version
 118	\N	patch	patch_91_92_b.sql|add_cigar_line_align_type
+119	\N	patch	patch_92_93_a.sql|schema_version

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

@@ -476,7 +476,7 @@ 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=119 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=120 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',

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

-1	\N	schema_version	92
+1	\N	schema_version	93
 2	1	assembly.default	NCBI34
 3	1	species.taxonomy_id	9606
 26	1	species.classification	Homo sapiens
@@ -95,3 +95,4 @@
 162	\N	patch	patch_90_91_d.sql|remove_external_data
 163	\N	patch	patch_91_92_a.sql|schema_version
 164	\N	patch	patch_91_92_b.sql|add_cigar_line_align_type
+165	\N	patch	patch_92_93_a.sql|schema_version

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

@@ -476,7 +476,7 @@ 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=165 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=166 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',

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

-1	\N	schema_version	92
+1	\N	schema_version	93
 2	1	assembly.default	NCBI34
 33	1	species.classification	Chordata
 32	1	species.classification	Vertebrata
@@ -95,3 +95,4 @@
 144	\N	patch	patch_90_91_d.sql|remove_external_data
 145	\N	patch	patch_91_92_a.sql|schema_version
 146	\N	patch	patch_91_92_b.sql|add_cigar_line_align_type
+147	\N	patch	patch_92_93_a.sql|schema_version

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

@@ -476,7 +476,7 @@ 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=147 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=148 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',

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

-1	\N	schema_version	92
+1	\N	schema_version	93
 2014	1	species.classification	Haplorrhini
 40	1	assembly.default	GRCh37
 41	1	assembly.date	2009-02
@@ -100,3 +100,4 @@
 2107	\N	patch	patch_90_91_d.sql|remove_external_data
 2108	\N	patch	patch_91_92_a.sql|schema_version
 2109	\N	patch	patch_91_92_b.sql|add_cigar_line_align_type
+2110	\N	patch	patch_92_93_a.sql|schema_version

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

@@ -476,7 +476,7 @@ 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=2110 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=2111 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',

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

-1	\N	schema_version	92
+1	\N	schema_version	93
 2	1	assembly.default	MULTIMAP
 3	1	species.taxonomy_id	1
 4	1	assembly.mapping	chromosome:MULTIMAP#contig
@@ -56,3 +56,4 @@
 149	\N	patch	patch_90_91_d.sql|remove_external_data
 150	\N	patch	patch_91_92_a.sql|schema_version
 151	\N	patch	patch_91_92_b.sql|add_cigar_line_align_type
+152	\N	patch	patch_92_93_a.sql|schema_version

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

@@ -476,7 +476,7 @@ 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=152 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=153 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',

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

 1	\N	schema_type	core
-2	\N	schema_version	92
+2	\N	schema_version	93
 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
@@ -173,3 +173,4 @@
 1685	\N	patch	patch_90_91_d.sql|remove_external_data
 1686	\N	patch	patch_91_92_a.sql|schema_version
 1687	\N	patch	patch_91_92_b.sql|add_cigar_line_align_type
+1688	\N	patch	patch_92_93_a.sql|schema_version

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

@@ -476,7 +476,7 @@ 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=1688 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=1689 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',

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

-1	\N	schema_version	92
+1	\N	schema_version	93
 2	1	assembly.default	NCBI34
 3	1	species.taxonomy_id	9606
 26	1	species.classification	Homo sapiens
@@ -94,3 +94,4 @@
 148	\N	patch	patch_90_91_d.sql|remove_external_data
 149	\N	patch	patch_91_92_a.sql|schema_version
 150	\N	patch	patch_91_92_b.sql|add_cigar_line_align_type
+151	\N	patch	patch_92_93_a.sql|schema_version

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

@@ -466,7 +466,7 @@ 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=151 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=152 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',

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	92	\N
+15	schema_version	93	\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
@@ -34,3 +34,4 @@
 37	patch	patch_89_90_a.sql|schema_version	\N
 38	patch	patch_90_91_a.sql|schema_version	\N
 39	patch	patch_91_92_a.sql|schema_version	\N
+40	patch	patch_92_93_a.sql|schema_version	\N

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

@@ -139,7 +139,7 @@ CREATE TABLE `meta` (
   `species_id` int(1) unsigned DEFAULT NULL,
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `key_value_idx` (`meta_key`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=40 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=41 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `ontology` (
   `ontology_id` int(10) unsigned NOT NULL AUTO_INCREMENT,

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

 1	\N	schema_type	core
-2	\N	schema_version	92
+2	\N	schema_version	93
 3	\N	patch	patch_68_69_a.sql|schema_version
 4	1	species.taxonomy_id	4565
 6	1	species.alias	bread wheat
@@ -149,3 +149,4 @@
 229	\N	patch	patch_90_91_d.sql|remove_external_data
 230	\N	patch	patch_91_92_a.sql|schema_version
 231	\N	patch	patch_91_92_b.sql|add_cigar_line_align_type
+232	\N	patch	patch_92_93_a.sql|schema_version