diff --git a/misc-scripts/ontology/sql/patch_92_93_a.sql b/misc-scripts/ontology/sql/patch_92_93_a.sql
new file mode 100644
index 0000000000000000000000000000000000000000..22948a2099ae33fa663913594f9312506e87821e
--- /dev/null
+++ b/misc-scripts/ontology/sql/patch_92_93_a.sql
@@ -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_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');
diff --git a/misc-scripts/ontology/sql/tables.sql b/misc-scripts/ontology/sql/tables.sql
index cc08adba5670f0734232b8c18101faa2ce582317..e3eba7119da07f0b348fd5a9e0a8bb72a72b7f57 100644
--- a/misc-scripts/ontology/sql/tables.sql
+++ b/misc-scripts/ontology/sql/tables.sql
@@ -1,12 +1,12 @@
-- 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 (
diff --git a/modules/Bio/EnsEMBL/ApiVersion.pm b/modules/Bio/EnsEMBL/ApiVersion.pm
index 01580013b79756738f6d51359195ddbb4923dd64..1e2ee027cae41447b6d1ebb3452e506ecf0178ad 100644
--- a/modules/Bio/EnsEMBL/ApiVersion.pm
+++ b/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 }
diff --git a/modules/t/test-genome-DBs/circ/core/meta.txt b/modules/t/test-genome-DBs/circ/core/meta.txt
index cb45e16a41b19de29248b5ba6ec7c845257a6f9b..28cac25569ab9802c89e8ebac825d9e0d7618a80 100644
--- a/modules/t/test-genome-DBs/circ/core/meta.txt
+++ b/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
diff --git a/modules/t/test-genome-DBs/circ/core/table.sql b/modules/t/test-genome-DBs/circ/core/table.sql
index 8b852c2b500ed9332c83ce4bec0a8b1e2f806394..471b8dd62e30de9d4fdbfaad2848de8430a63c7b 100644
--- a/modules/t/test-genome-DBs/circ/core/table.sql
+++ b/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 '',
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt b/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
index 7c9ec8780fb658b340aae7c1e4d075724c725f0b..0955043ba26b88e88208acf8735d9c3852d3134c 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
@@ -1,4 +1,4 @@
-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
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/table.sql b/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
index c90aee9a802ed3aef15a01e1228c240966cf665d..17285d829505143bba54e17b39920c05e3a93624 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
+++ b/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 '',
diff --git a/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt b/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
index 7f46683c4a87fa56349c4f2b57263c12954d6b31..83f1c3852f28ebfbfe975b0d2d9f1756be9970e8 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
@@ -1,4 +1,4 @@
-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
diff --git a/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql b/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
index 0265a7bf41dd99645b7a92816f7d8e03b4bb7ecb..4cf4d739071929b41c70253ee02b2c7cbecfe6d1 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
+++ b/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 '',
diff --git a/modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt b/modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
index ee56b6e1e3d9f98b867313b2d651caea778978c1..2469440ef6f48e949ea97c6ea396f679f5691913 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
@@ -1,4 +1,4 @@
-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
diff --git a/modules/t/test-genome-DBs/homo_sapiens/patch/table.sql b/modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
index dd82eee05c0d0a4b247bf61c5c31462ed7f61f67..1e5f50227fca4970fb8bba8eed0cb4be52bd93ba 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
+++ b/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 '',
diff --git a/modules/t/test-genome-DBs/mapping/core/meta.txt b/modules/t/test-genome-DBs/mapping/core/meta.txt
index 507a5ae7a973299bdc040b15addeceb231de53fd..1d0729ea246dea8469e631201d9b3e67f00192e3 100644
--- a/modules/t/test-genome-DBs/mapping/core/meta.txt
+++ b/modules/t/test-genome-DBs/mapping/core/meta.txt
@@ -1,4 +1,4 @@
-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
diff --git a/modules/t/test-genome-DBs/mapping/core/table.sql b/modules/t/test-genome-DBs/mapping/core/table.sql
index b47809cfc10452d3aa1dde829449314e092d0bca..908015077cdb646b5ba66b411ed26ff78d15f42f 100644
--- a/modules/t/test-genome-DBs/mapping/core/table.sql
+++ b/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 '',
diff --git a/modules/t/test-genome-DBs/mus_musculus/core/meta.txt b/modules/t/test-genome-DBs/mus_musculus/core/meta.txt
index 16f762f608f8d77a276f78bccfe0249f84681f6f..d816a2a67fb8dbdd5983508cec77ca674099f1cc 100644
--- a/modules/t/test-genome-DBs/mus_musculus/core/meta.txt
+++ b/modules/t/test-genome-DBs/mus_musculus/core/meta.txt
@@ -1,5 +1,5 @@
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
diff --git a/modules/t/test-genome-DBs/mus_musculus/core/table.sql b/modules/t/test-genome-DBs/mus_musculus/core/table.sql
index 171d723fe24c051a1384762c17a69a215afdfa5d..2236b585330ebea7636cf605477960cf6541949f 100644
--- a/modules/t/test-genome-DBs/mus_musculus/core/table.sql
+++ b/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 '',
diff --git a/modules/t/test-genome-DBs/nameless/core/meta.txt b/modules/t/test-genome-DBs/nameless/core/meta.txt
index a97d1fc7d414a6794dc37762d7192fb5599223ca..9d6ec55e30b071db49964c2f0c69150b77c93832 100644
--- a/modules/t/test-genome-DBs/nameless/core/meta.txt
+++ b/modules/t/test-genome-DBs/nameless/core/meta.txt
@@ -1,4 +1,4 @@
-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
diff --git a/modules/t/test-genome-DBs/nameless/core/table.sql b/modules/t/test-genome-DBs/nameless/core/table.sql
index f25960a4f656a24e84ac6027b215c02433b0e14a..caa481fe87238dbd267da2872e300a83e49f6176 100644
--- a/modules/t/test-genome-DBs/nameless/core/table.sql
+++ b/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 '',
diff --git a/modules/t/test-genome-DBs/ontology/ontology/meta.txt b/modules/t/test-genome-DBs/ontology/ontology/meta.txt
index 20dd850c3cb99c7be79614bac331af8ee9022597..ecf7385b71062b8b9d637f373ce1fcc83088744d 100644
--- a/modules/t/test-genome-DBs/ontology/ontology/meta.txt
+++ b/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
diff --git a/modules/t/test-genome-DBs/ontology/ontology/table.sql b/modules/t/test-genome-DBs/ontology/ontology/table.sql
index 0a775a9dda9ec6a9a6239ff21e6271a8e253b27c..b7d5944a5c6b2ea1da7405408fae6d2542c75ec3 100644
--- a/modules/t/test-genome-DBs/ontology/ontology/table.sql
+++ b/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,
diff --git a/modules/t/test-genome-DBs/polyploidy/core/meta.txt b/modules/t/test-genome-DBs/polyploidy/core/meta.txt
index 69a42faa80a9c9949f0a8da6e54243861bf4f575..4bfae9f1880fd70bb529a702734d9fcfeaff3f83 100644
--- a/modules/t/test-genome-DBs/polyploidy/core/meta.txt
+++ b/modules/t/test-genome-DBs/polyploidy/core/meta.txt
@@ -1,5 +1,5 @@
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
diff --git a/modules/t/test-genome-DBs/polyploidy/core/table.sql b/modules/t/test-genome-DBs/polyploidy/core/table.sql
index feb70d4fc906ac19c7f4bf1cffa5660ad6fdb39c..60080e68ef3d34f0aac878f1b164d4b5423791f6 100644
--- a/modules/t/test-genome-DBs/polyploidy/core/table.sql
+++ b/modules/t/test-genome-DBs/polyploidy/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=232 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=233 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
diff --git a/modules/t/test-genome-DBs/test_collection/core/meta.txt b/modules/t/test-genome-DBs/test_collection/core/meta.txt
index 6c8bf4c4f96bf5afe706aa5e2f21363bbf517cd9..08490b7da9f8f8206bce3ff575468ebfebf85103 100644
--- a/modules/t/test-genome-DBs/test_collection/core/meta.txt
+++ b/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 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
@@ -169,3 +169,4 @@
211 \N patch patch_90_91_d.sql|remove_external_data
212 \N patch patch_91_92_a.sql|schema_version
213 \N patch patch_91_92_b.sql|add_cigar_line_align_type
+214 \N patch patch_92_93_a.sql|schema_version
diff --git a/modules/t/test-genome-DBs/test_collection/core/table.sql b/modules/t/test-genome-DBs/test_collection/core/table.sql
index 3211e6cc9a097f7be3a1c0ae85689abd4e7d2884..a83c8221fad827c8540d83171fd0f582a0a93d3d 100644
--- a/modules/t/test-genome-DBs/test_collection/core/table.sql
+++ b/modules/t/test-genome-DBs/test_collection/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=214 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=215 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
diff --git a/sql/patch_92_93_a.sql b/sql/patch_92_93_a.sql
new file mode 100644
index 0000000000000000000000000000000000000000..22948a2099ae33fa663913594f9312506e87821e
--- /dev/null
+++ b/sql/patch_92_93_a.sql
@@ -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_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');
diff --git a/sql/table.sql b/sql/table.sql
index b06677cd1d1a064eda8e8bfcd0a0ba254e4fafdb..18e6b1f44d9c37dab3e32bd7ca2d2646bca6ba8e 100755
--- a/sql/table.sql
+++ b/sql/table.sql
@@ -1,12 +1,12 @@
-- 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.
@@ -301,16 +301,14 @@ 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', '92');
+ (NULL, 'schema_type', 'core'),
+ (NULL, 'schema_version', '93');
# 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_91_92_a.sql|schema_version');
-INSERT INTO meta (species_id, meta_key, meta_value)
- VALUES (NULL, 'patch', 'patch_91_92_b.sql|add_cigar_line_align_type');
+ VALUES (NULL, 'patch', 'patch_92_93_a.sql|schema_version');
/**
@table meta_coord
@@ -438,8 +436,8 @@ CREATE TABLE seq_region_attrib (
*/
CREATE TABLE alt_allele (
- alt_allele_id INT UNSIGNED AUTO_INCREMENT,
- alt_allele_group_id INT UNSIGNED NOT NULL,
+ alt_allele_id INT UNSIGNED AUTO_INCREMENT,
+ alt_allele_group_id INT UNSIGNED NOT NULL,
gene_id INT UNSIGNED NOT NULL,
PRIMARY KEY (alt_allele_id),
@@ -1116,7 +1114,7 @@ CREATE TABLE translation (
/**
-@table translation_attrib
+@table translation_attrib
@desc Enables storage of attributes that relate to translations.
@column translation_id Foreign key references to the @link transcript table.
@@ -1184,13 +1182,13 @@ CREATE TABLE density_feature (
@table density_type
@desc Describes type representing a density, or percentage
coverage etc. in a given region.
-
+
@column density_type_id Primary key, internal identifier.
@column analysis_id Foreign key references to the @link analysis table.
@column block_size Block size.
@column region_features The number of features per sequence region inside this density type.
@column value_type Value type, e.g. 'sum', 'ratio'.
-
+
@see density_feature
@@ -1299,7 +1297,7 @@ CREATE TABLE ditag_feature (
@column seq_region_end Sequence end position.
@column seq_region_strand Sequence region strand: 1 - forward; -1 - reverse.
@column hit_name External entity name/identifier.
-@column score Score supporting the intron
+@column score Score supporting the intron
@column score_type The type of score e.g. NONE
@column is_splice_canonical Indicates if the splice junction can be considered canonical i.e. behaves according to accepted rules
@@ -2372,7 +2370,7 @@ CREATE TABLE xref (
info_type ENUM( 'NONE', 'PROJECTION', 'MISC', 'DEPENDENT',
'DIRECT', 'SEQUENCE_MATCH',
'INFERRED_PAIR', 'PROBE',
- 'UNMAPPED', 'COORDINATE_OVERLAP',
+ 'UNMAPPED', 'COORDINATE_OVERLAP',
'CHECKSUM' ) DEFAULT 'NONE' NOT NULL,
info_text VARCHAR(255) DEFAULT '' NOT NULL,