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updated to version 94
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Magali Ruffier committed Apr 24, 2018
1 parent 6f882c1 commit 53e6da4
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Showing 36 changed files with 100 additions and 41 deletions.
27 changes: 27 additions & 0 deletions misc-scripts/ontology/sql/patch_93_94_a.sql
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-- 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_93_94_a.sql
#
# Title: Update schema version.
#
# Description:
# Update schema_version in meta table to 94.

UPDATE meta SET meta_value='94' WHERE meta_key='schema_version';

# Patch identifier
INSERT INTO meta (species_id, meta_key, meta_value)
VALUES (NULL, 'patch', 'patch_93_94_a.sql|schema_version');
4 changes: 2 additions & 2 deletions misc-scripts/ontology/sql/tables.sql
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Expand Up @@ -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', '93');
('schema_version', '94');

# Patches included in this schema file
INSERT INTO meta (meta_key, meta_value)
VALUES ('patch', 'patch_92_93_a.sql|schema_version');
VALUES ('patch', 'patch_93_94_a.sql|schema_version');


CREATE TABLE ontology (
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/ApiVersion.pm
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Expand Up @@ -56,7 +56,7 @@ use base qw( Exporter );

our @EXPORT = qw( software_version );

my $API_VERSION = 93;
my $API_VERSION = 94;

sub software_version { return $API_VERSION }

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2 changes: 1 addition & 1 deletion modules/t/test-genome-DBs/circ/core/SQLite/table.sql
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--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Fri Apr 6 15:15:57 2018
-- Created on Tue Apr 24 11:41:38 2018
--

BEGIN TRANSACTION;
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3 changes: 2 additions & 1 deletion modules/t/test-genome-DBs/circ/core/meta.txt
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Expand Up @@ -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 93
2 \N schema_version 94
8 1 assembly.accession GCA_000292705.1
10 1 assembly.date 2012-08
7 1 assembly.default GCA_000292705.1
Expand Down Expand Up @@ -119,3 +119,4 @@
119 \N patch patch_92_93_a.sql|schema_version
120 \N patch patch_92_93_b.sql|biotype_table
121 \N patch patch_92_93_c.sql|collate_index_interpro
122 \N patch patch_93_94_a.sql|schema_version
2 changes: 1 addition & 1 deletion modules/t/test-genome-DBs/circ/core/table.sql
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Expand Up @@ -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=122 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=123 DEFAULT CHARSET=latin1;

CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
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2 changes: 1 addition & 1 deletion modules/t/test-genome-DBs/homo_sapiens/core/SQLite/table.sql
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@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Fri Apr 6 15:16:01 2018
-- Created on Tue Apr 24 11:41:49 2018
--

BEGIN TRANSACTION;
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3 changes: 2 additions & 1 deletion modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
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@@ -1,4 +1,4 @@
1 \N schema_version 93
1 \N schema_version 94
2 1 assembly.default NCBI34
3 1 species.taxonomy_id 9606
26 1 species.classification Homo sapiens
Expand Down Expand Up @@ -98,3 +98,4 @@
165 \N patch patch_92_93_a.sql|schema_version
166 \N patch patch_92_93_b.sql|biotype_table
167 \N patch patch_92_93_c.sql|collate_index_interpro
168 \N patch patch_93_94_a.sql|schema_version
2 changes: 1 addition & 1 deletion modules/t/test-genome-DBs/homo_sapiens/core/table.sql
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Expand Up @@ -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=168 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=169 DEFAULT CHARSET=latin1;

CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
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2 changes: 1 addition & 1 deletion modules/t/test-genome-DBs/homo_sapiens/empty/SQLite/table.sql
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@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Fri Apr 6 15:16:04 2018
-- Created on Tue Apr 24 11:42:00 2018
--

BEGIN TRANSACTION;
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3 changes: 2 additions & 1 deletion modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
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@@ -1,4 +1,4 @@
1 \N schema_version 93
1 \N schema_version 94
2 1 assembly.default NCBI34
33 1 species.classification Chordata
32 1 species.classification Vertebrata
Expand Down Expand Up @@ -98,3 +98,4 @@
147 \N patch patch_92_93_a.sql|schema_version
148 \N patch patch_92_93_b.sql|biotype_table
149 \N patch patch_92_93_c.sql|collate_index_interpro
150 \N patch patch_93_94_a.sql|schema_version
2 changes: 1 addition & 1 deletion modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
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Expand Up @@ -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=150 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=151 DEFAULT CHARSET=latin1;

CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
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2 changes: 1 addition & 1 deletion modules/t/test-genome-DBs/homo_sapiens/patch/SQLite/table.sql
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--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Fri Apr 6 15:16:07 2018
-- Created on Tue Apr 24 11:42:12 2018
--

BEGIN TRANSACTION;
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3 changes: 2 additions & 1 deletion modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
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@@ -1,4 +1,4 @@
1 \N schema_version 93
1 \N schema_version 94
2014 1 species.classification Haplorrhini
40 1 assembly.default GRCh37
41 1 assembly.date 2009-02
Expand Down Expand Up @@ -103,3 +103,4 @@
2110 \N patch patch_92_93_a.sql|schema_version
2111 \N patch patch_92_93_b.sql|biotype_table
2112 \N patch patch_92_93_c.sql|collate_index_interpro
2113 \N patch patch_93_94_a.sql|schema_version
2 changes: 1 addition & 1 deletion modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
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Expand Up @@ -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=2113 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=2114 DEFAULT CHARSET=latin1;

CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
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2 changes: 1 addition & 1 deletion modules/t/test-genome-DBs/mapping/core/SQLite/table.sql
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--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Fri Apr 6 15:16:11 2018
-- Created on Tue Apr 24 11:42:24 2018
--

BEGIN TRANSACTION;
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3 changes: 2 additions & 1 deletion modules/t/test-genome-DBs/mapping/core/meta.txt
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@@ -1,4 +1,4 @@
1 \N schema_version 93
1 \N schema_version 94
2 1 assembly.default MULTIMAP
3 1 species.taxonomy_id 1
4 1 assembly.mapping chromosome:MULTIMAP#contig
Expand Down Expand Up @@ -59,3 +59,4 @@
152 \N patch patch_92_93_a.sql|schema_version
153 \N patch patch_92_93_b.sql|biotype_table
154 \N patch patch_92_93_c.sql|collate_index_interpro
155 \N patch patch_93_94_a.sql|schema_version
2 changes: 1 addition & 1 deletion modules/t/test-genome-DBs/mapping/core/table.sql
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Expand Up @@ -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=156 DEFAULT CHARSET=latin1;

CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
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2 changes: 1 addition & 1 deletion modules/t/test-genome-DBs/multi/compara/SQLite/table.sql
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@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Fri Apr 6 15:16:13 2018
-- Created on Tue Apr 24 11:42:33 2018
--

BEGIN TRANSACTION;
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2 changes: 1 addition & 1 deletion modules/t/test-genome-DBs/mus_musculus/core/SQLite/table.sql
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@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Fri Apr 6 15:16:17 2018
-- Created on Tue Apr 24 11:42:43 2018
--

BEGIN TRANSACTION;
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3 changes: 2 additions & 1 deletion modules/t/test-genome-DBs/mus_musculus/core/meta.txt
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@@ -1,5 +1,5 @@
1 \N schema_type core
2 \N schema_version 93
2 \N schema_version 94
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
Expand Down Expand Up @@ -176,3 +176,4 @@
1688 \N patch patch_92_93_a.sql|schema_version
1689 \N patch patch_92_93_b.sql|biotype_table
1690 \N patch patch_92_93_c.sql|collate_index_interpro
1691 \N patch patch_93_94_a.sql|schema_version
2 changes: 1 addition & 1 deletion modules/t/test-genome-DBs/mus_musculus/core/table.sql
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Expand Up @@ -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=1691 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=1692 DEFAULT CHARSET=latin1;

CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
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2 changes: 1 addition & 1 deletion modules/t/test-genome-DBs/nameless/core/SQLite/table.sql
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@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Fri Apr 6 15:16:20 2018
-- Created on Tue Apr 24 11:42:53 2018
--

BEGIN TRANSACTION;
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3 changes: 2 additions & 1 deletion modules/t/test-genome-DBs/nameless/core/meta.txt
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@@ -1,4 +1,4 @@
1 \N schema_version 93
1 \N schema_version 94
2 1 assembly.default NCBI34
3 1 species.taxonomy_id 9606
26 1 species.classification Homo sapiens
Expand Down Expand Up @@ -97,3 +97,4 @@
151 \N patch patch_92_93_a.sql|schema_version
152 \N patch patch_92_93_b.sql|biotype_table
153 \N patch patch_92_93_c.sql|collate_index_interpro
154 \N patch patch_93_94_a.sql|schema_version
2 changes: 1 addition & 1 deletion modules/t/test-genome-DBs/nameless/core/table.sql
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Expand Up @@ -479,7 +479,7 @@ 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=154 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=155 DEFAULT CHARSET=latin1;

CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
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2 changes: 1 addition & 1 deletion modules/t/test-genome-DBs/ontology/ontology/SQLite/table.sql
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@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Fri Apr 6 15:16:22 2018
-- Created on Tue Apr 24 11:42:58 2018
--

BEGIN TRANSACTION;
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3 changes: 2 additions & 1 deletion modules/t/test-genome-DBs/ontology/ontology/meta.txt
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Expand Up @@ -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 93 \N
15 schema_version 94 \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
Expand All @@ -35,3 +35,4 @@
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
41 patch patch_93_94_a.sql|schema_version \N
2 changes: 1 addition & 1 deletion modules/t/test-genome-DBs/ontology/ontology/table.sql
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Expand Up @@ -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=41 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=42 DEFAULT CHARSET=latin1;

CREATE TABLE `ontology` (
`ontology_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
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2 changes: 1 addition & 1 deletion modules/t/test-genome-DBs/polyploidy/core/SQLite/table.sql
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@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Fri Apr 6 15:16:25 2018
-- Created on Tue Apr 24 11:43:09 2018
--

BEGIN TRANSACTION;
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3 changes: 2 additions & 1 deletion modules/t/test-genome-DBs/polyploidy/core/meta.txt
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@@ -1,5 +1,5 @@
1 \N schema_type core
2 \N schema_version 93
2 \N schema_version 94
3 \N patch patch_68_69_a.sql|schema_version
4 1 species.taxonomy_id 4565
6 1 species.alias bread wheat
Expand Down Expand Up @@ -152,3 +152,4 @@
232 \N patch patch_92_93_a.sql|schema_version
233 \N patch patch_92_93_b.sql|biotype_table
234 \N patch patch_92_93_c.sql|collate_index_interpro
235 \N patch patch_93_94_a.sql|schema_version
2 changes: 1 addition & 1 deletion modules/t/test-genome-DBs/polyploidy/core/table.sql
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Expand Up @@ -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=235 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=236 DEFAULT CHARSET=latin1;

CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
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2 changes: 1 addition & 1 deletion modules/t/test-genome-DBs/test_collection/core/SQLite/table.sql
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@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Fri Apr 6 15:16:28 2018
-- Created on Tue Apr 24 11:43:20 2018
--

BEGIN TRANSACTION;
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3 changes: 2 additions & 1 deletion modules/t/test-genome-DBs/test_collection/core/meta.txt
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Expand Up @@ -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 93
2 \N schema_version 94
8 1 assembly.accession GCA_000292705.1
10 1 assembly.date 2012-08
7 1 assembly.default GCA_000292705.1
Expand Down Expand Up @@ -172,3 +172,4 @@
214 \N patch patch_92_93_a.sql|schema_version
215 \N patch patch_92_93_b.sql|biotype_table
216 \N patch patch_92_93_c.sql|collate_index_interpro
217 \N patch patch_93_94_a.sql|schema_version
2 changes: 1 addition & 1 deletion modules/t/test-genome-DBs/test_collection/core/table.sql
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Expand Up @@ -479,7 +479,7 @@ 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=217 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=218 DEFAULT CHARSET=latin1;

CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
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27 changes: 27 additions & 0 deletions sql/patch_93_94_a.sql
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@@ -0,0 +1,27 @@
-- 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_93_94_a.sql
#
# Title: Update schema version.
#
# Description:
# Update schema_version in meta table to 94.

UPDATE meta SET meta_value='94' WHERE meta_key='schema_version';

# Patch identifier
INSERT INTO meta (species_id, meta_key, meta_value)
VALUES (NULL, 'patch', 'patch_93_94_a.sql|schema_version');
9 changes: 2 additions & 7 deletions sql/table.sql
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Expand Up @@ -308,19 +308,14 @@ CREATE TABLE IF NOT EXISTS meta (
# Add schema type and schema version to the meta table.
INSERT INTO meta (species_id, meta_key, meta_value) VALUES
(NULL, 'schema_type', 'core'),
(NULL, 'schema_version', '93');
(NULL, 'schema_version', '94');

# Patches included in this schema file:
# NOTE: At start of release cycle, remove patch entries from last release.
# NOTE: Avoid line-breaks in values.
INSERT INTO meta (species_id, meta_key, meta_value)
VALUES (NULL, 'patch', 'patch_92_93_a.sql|schema_version');
VALUES (NULL, 'patch', 'patch_93_94_a.sql|schema_version');

INSERT INTO meta (species_id, meta_key, meta_value)
VALUES (NULL, 'patch', 'patch_92_93_b.sql|biotype_table');

INSERT INTO meta (species_id, meta_key, meta_value)
VALUES (NULL, 'patch', 'patch_92_93_c.sql|collate_index_interpro');

/**
@table meta_coord
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