From cfe26ad219e6a815d15596c18c75833a1e96061a Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Fri, 5 Dec 2014 13:15:39 +0000
Subject: [PATCH] update master schema to release 79
---
modules/Bio/EnsEMBL/ApiVersion.pm | 2 +-
.../circ/core/SQLite/table.sql | 2 +-
modules/t/test-genome-DBs/circ/core/meta.txt | 3 ++-
modules/t/test-genome-DBs/circ/core/table.sql | 2 +-
.../homo_sapiens/core/SQLite/table.sql | 2 +-
.../homo_sapiens/core/meta.txt | 3 ++-
.../homo_sapiens/core/table.sql | 2 +-
.../homo_sapiens/empty/SQLite/table.sql | 2 +-
.../homo_sapiens/empty/meta.txt | 3 ++-
.../homo_sapiens/empty/table.sql | 2 +-
.../homo_sapiens/patch/SQLite/table.sql | 2 +-
.../homo_sapiens/patch/meta.txt | 3 ++-
.../homo_sapiens/patch/table.sql | 2 +-
.../mapping/core/SQLite/table.sql | 2 +-
.../nameless/core/SQLite/table.sql | 2 +-
.../t/test-genome-DBs/nameless/core/meta.txt | 3 ++-
.../t/test-genome-DBs/nameless/core/table.sql | 2 +-
.../ontology/ontology/SQLite/table.sql | 5 ++--
.../test_collection/core/SQLite/table.sql | 2 +-
.../test_collection/core/meta.txt | 3 ++-
.../test_collection/core/table.sql | 2 +-
sql/patch_78_79_a.sql | 26 +++++++++++++++++++
sql/table.sql | 8 ++----
23 files changed, 57 insertions(+), 28 deletions(-)
create mode 100644 sql/patch_78_79_a.sql
diff --git a/modules/Bio/EnsEMBL/ApiVersion.pm b/modules/Bio/EnsEMBL/ApiVersion.pm
index 2427a8664b..720f40f8a3 100644
--- a/modules/Bio/EnsEMBL/ApiVersion.pm
+++ b/modules/Bio/EnsEMBL/ApiVersion.pm
@@ -55,7 +55,7 @@ use base qw( Exporter );
our @EXPORT = qw( software_version );
-my $API_VERSION = 78;
+my $API_VERSION = 79;
sub software_version { return $API_VERSION }
diff --git a/modules/t/test-genome-DBs/circ/core/SQLite/table.sql b/modules/t/test-genome-DBs/circ/core/SQLite/table.sql
index 9b0388595f..ce53157a17 100644
--- a/modules/t/test-genome-DBs/circ/core/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/circ/core/SQLite/table.sql
@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Oct 28 16:45:25 2014
+-- Created on Fri Dec 5 13:10:29 2014
--
BEGIN TRANSACTION;
diff --git a/modules/t/test-genome-DBs/circ/core/meta.txt b/modules/t/test-genome-DBs/circ/core/meta.txt
index 04b00914d7..2d1b6eecaa 100644
--- a/modules/t/test-genome-DBs/circ/core/meta.txt
+++ b/modules/t/test-genome-DBs/circ/core/meta.txt
@@ -23,8 +23,9 @@
79 \N patch patch_77_78_a.sql|schema_version
80 \N patch patch_77_78_b.sql|source_column_increase
81 \N patch patch_77_78_c.sql|Change unmapped_reason_id from smallint to int
+82 \N patch patch_78_79_a.sql|schema_version
1 \N schema_type core
-2 \N schema_version 78
+2 \N schema_version 79
8 1 assembly.accession GCA_000292705.1
10 1 assembly.date 2012-08
7 1 assembly.default GCA_000292705.1
diff --git a/modules/t/test-genome-DBs/circ/core/table.sql b/modules/t/test-genome-DBs/circ/core/table.sql
index 544ad6534e..1b6e077e1a 100644
--- a/modules/t/test-genome-DBs/circ/core/table.sql
+++ b/modules/t/test-genome-DBs/circ/core/table.sql
@@ -469,7 +469,7 @@ 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=InnoDB AUTO_INCREMENT=82 DEFAULT CHARSET=latin1;
+) ENGINE=InnoDB AUTO_INCREMENT=83 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL,
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/SQLite/table.sql b/modules/t/test-genome-DBs/homo_sapiens/core/SQLite/table.sql
index 1f1ff0af47..e1dd01eb70 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/SQLite/table.sql
@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Oct 28 16:45:34 2014
+-- Created on Fri Dec 5 13:10:39 2014
--
BEGIN TRANSACTION;
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 7463f27855..f1a726db62 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 78
+1 \N schema_version 79
2 1 assembly.default NCBI34
3 1 species.taxonomy_id 9606
26 1 species.classification Homo sapiens
@@ -58,3 +58,4 @@
118 \N patch patch_77_78_a.sql|schema_version
119 \N patch patch_77_78_b.sql|source_column_increase
120 \N patch patch_77_78_c.sql|Change unmapped_reason_id from smallint to int
+121 \N patch patch_78_79_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 b09b695f31..99f1312ec7 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
@@ -468,7 +468,7 @@ 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=121 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=122 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL,
diff --git a/modules/t/test-genome-DBs/homo_sapiens/empty/SQLite/table.sql b/modules/t/test-genome-DBs/homo_sapiens/empty/SQLite/table.sql
index 1adafc3b0c..a1cc9f02c8 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/empty/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/empty/SQLite/table.sql
@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Oct 28 16:45:41 2014
+-- Created on Fri Dec 5 13:10:45 2014
--
BEGIN TRANSACTION;
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 ef540964cc..d346abb002 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 78
+1 \N schema_version 79
2 1 assembly.default NCBI34
33 1 species.classification Chordata
32 1 species.classification Vertebrata
@@ -58,3 +58,4 @@
107 \N patch patch_77_78_a.sql|schema_version
108 \N patch patch_77_78_b.sql|source_column_increase
109 \N patch patch_77_78_c.sql|Change unmapped_reason_id from smallint to int
+110 \N patch patch_78_79_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 c15941ea24..565a3f0f7e 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
@@ -463,7 +463,7 @@ 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=110 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=111 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL DEFAULT '',
diff --git a/modules/t/test-genome-DBs/homo_sapiens/patch/SQLite/table.sql b/modules/t/test-genome-DBs/homo_sapiens/patch/SQLite/table.sql
index 92b847058c..efaa6a5899 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/patch/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/patch/SQLite/table.sql
@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Oct 28 16:45:49 2014
+-- Created on Fri Dec 5 13:10:53 2014
--
BEGIN TRANSACTION;
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 ac41012e02..8cf41cddc8 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 78
+1 \N schema_version 79
2014 1 species.classification Haplorrhini
40 1 assembly.default GRCh37
41 1 assembly.date 2009-02
@@ -62,3 +62,4 @@
2069 \N patch patch_77_78_a.sql|schema_version
2070 \N patch patch_77_78_b.sql|source_column_increase
2071 \N patch patch_77_78_c.sql|Change unmapped_reason_id from smallint to int
+2072 \N patch patch_78_79_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 09508b3ea8..97aa7fc008 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
@@ -462,7 +462,7 @@ 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=2072 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=2073 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/SQLite/table.sql b/modules/t/test-genome-DBs/mapping/core/SQLite/table.sql
index 6700884cb7..52eb1eca9e 100644
--- a/modules/t/test-genome-DBs/mapping/core/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/mapping/core/SQLite/table.sql
@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
--- Created on Fri May 30 13:08:11 2014
+-- Created on Fri Dec 5 13:11:00 2014
--
BEGIN TRANSACTION;
diff --git a/modules/t/test-genome-DBs/nameless/core/SQLite/table.sql b/modules/t/test-genome-DBs/nameless/core/SQLite/table.sql
index 17bc444bb1..0604fd3fab 100644
--- a/modules/t/test-genome-DBs/nameless/core/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/nameless/core/SQLite/table.sql
@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Oct 28 16:45:58 2014
+-- Created on Fri Dec 5 13:11:06 2014
--
BEGIN TRANSACTION;
diff --git a/modules/t/test-genome-DBs/nameless/core/meta.txt b/modules/t/test-genome-DBs/nameless/core/meta.txt
index 680d8360d3..02187dbebd 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 78
+1 \N schema_version 79
2 1 assembly.default NCBI34
3 1 species.taxonomy_id 9606
26 1 species.classification Homo sapiens
@@ -57,3 +57,4 @@
111 \N patch patch_77_78_a.sql|schema_version
112 \N patch patch_77_78_b.sql|source_column_increase
113 \N patch patch_77_78_c.sql|Change unmapped_reason_id from smallint to int
+114 \N patch patch_78_79_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 11f314b7e7..3d169ef7f6 100644
--- a/modules/t/test-genome-DBs/nameless/core/table.sql
+++ b/modules/t/test-genome-DBs/nameless/core/table.sql
@@ -468,7 +468,7 @@ 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=114 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=115 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL,
diff --git a/modules/t/test-genome-DBs/ontology/ontology/SQLite/table.sql b/modules/t/test-genome-DBs/ontology/ontology/SQLite/table.sql
index 4e932af9a7..cb29d96585 100644
--- a/modules/t/test-genome-DBs/ontology/ontology/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/ontology/ontology/SQLite/table.sql
@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Oct 28 16:46:06 2014
+-- Created on Fri Dec 5 13:11:12 2014
--
BEGIN TRANSACTION;
@@ -270,7 +270,8 @@ CREATE UNIQUE INDEX name_idx02 ON subset (name);
CREATE TABLE synonym (
synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
term_id integer NOT NULL,
- name text NOT NULL
+ name text NOT NULL,
+ type enum
);
CREATE UNIQUE INDEX term_synonym_idx ON synonym (term_id, synonym_id);
diff --git a/modules/t/test-genome-DBs/test_collection/core/SQLite/table.sql b/modules/t/test-genome-DBs/test_collection/core/SQLite/table.sql
index 9fe98e7ce2..763da69e47 100644
--- a/modules/t/test-genome-DBs/test_collection/core/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/test_collection/core/SQLite/table.sql
@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Oct 28 16:46:13 2014
+-- Created on Fri Dec 5 13:11:19 2014
--
BEGIN TRANSACTION;
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 335a17b5a7..a6c6161b53 100644
--- a/modules/t/test-genome-DBs/test_collection/core/meta.txt
+++ b/modules/t/test-genome-DBs/test_collection/core/meta.txt
@@ -23,8 +23,9 @@
174 \N patch patch_77_78_a.sql|schema_version
175 \N patch patch_77_78_b.sql|source_column_increase
176 \N patch patch_77_78_c.sql|Change unmapped_reason_id from smallint to int
+177 \N patch patch_78_79_a.sql|schema_version
1 \N schema_type core
-2 \N schema_version 78
+2 \N schema_version 79
8 1 assembly.accession GCA_000292705.1
10 1 assembly.date 2012-08
7 1 assembly.default GCA_000292705.1
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 4099210f61..98d3105655 100644
--- a/modules/t/test-genome-DBs/test_collection/core/table.sql
+++ b/modules/t/test-genome-DBs/test_collection/core/table.sql
@@ -469,7 +469,7 @@ 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=InnoDB AUTO_INCREMENT=177 DEFAULT CHARSET=latin1;
+) ENGINE=InnoDB AUTO_INCREMENT=178 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL,
diff --git a/sql/patch_78_79_a.sql b/sql/patch_78_79_a.sql
new file mode 100644
index 0000000000..fe5371bbb0
--- /dev/null
+++ b/sql/patch_78_79_a.sql
@@ -0,0 +1,26 @@
+-- Copyright [1999-2014] Wellcome Trust Sanger Institute and the 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_78_79_a.sql
+#
+# Title: Update schema version.
+#
+# Description:
+# Update schema_version in meta table to 79.
+
+UPDATE meta SET meta_value='79' WHERE meta_key='schema_version';
+
+# Patch identifier
+INSERT INTO meta (species_id, meta_key, meta_value)
+ VALUES (NULL, 'patch', 'patch_78_79_a.sql|schema_version');
diff --git a/sql/table.sql b/sql/table.sql
index f7b6d1dae4..72191fa018 100755
--- a/sql/table.sql
+++ b/sql/table.sql
@@ -302,17 +302,13 @@ 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', '78');
+ (NULL, 'schema_version', '79');
# 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_77_78_a.sql|schema_version');
-INSERT INTO meta (species_id, meta_key, meta_value)
- VALUES (NULL, 'patch', 'patch_77_78_b.sql|source_column_increase');
-INSERT INTO meta (species_id, meta_key, meta_value)
- VALUES (NULL, 'patch', 'patch_77_78_c.sql|Change unmapped_reason_id from smallint to int');
+ VALUES (NULL, 'patch', 'patch_78_79_a.sql|schema_version');
/**
@table meta_coord
--
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