From 814d31755ed475550d31c12bb38a4285512cd808 Mon Sep 17 00:00:00 2001
From: Kieron Taylor <ktaylor@ebi.ac.uk>
Date: Tue, 7 Oct 2014 10:54:17 +0100
Subject: [PATCH] [ENSCORESW-1047] Altering column sizes for source in gene and
transcript tables. Also patch test databases.
---
modules/t/test-genome-DBs/circ/core/meta.txt | 4 ++-
modules/t/test-genome-DBs/circ/core/table.sql | 6 ++---
.../homo_sapiens/core/meta.txt | 4 ++-
.../homo_sapiens/core/table.sql | 6 ++---
.../homo_sapiens/empty/meta.txt | 4 ++-
.../homo_sapiens/empty/table.sql | 6 ++---
.../homo_sapiens/patch/meta.txt | 4 ++-
.../homo_sapiens/patch/table.sql | 6 ++---
.../t/test-genome-DBs/nameless/core/meta.txt | 4 ++-
.../t/test-genome-DBs/nameless/core/table.sql | 6 ++---
.../ontology/ontology/meta.txt | 3 ++-
.../ontology/ontology/table.sql | 2 +-
.../test_collection/core/meta.txt | 4 ++-
.../test_collection/core/table.sql | 6 ++---
sql/patch_77_78_b.sql | 27 +++++++++++++++++++
15 files changed, 66 insertions(+), 26 deletions(-)
create mode 100644 sql/patch_77_78_b.sql
diff --git a/modules/t/test-genome-DBs/circ/core/meta.txt b/modules/t/test-genome-DBs/circ/core/meta.txt
index 5b7ce87a02..84328847b2 100644
--- a/modules/t/test-genome-DBs/circ/core/meta.txt
+++ b/modules/t/test-genome-DBs/circ/core/meta.txt
@@ -20,8 +20,10 @@
76 \N patch patch_75_76_b.sql|allow_null_karyotype
77 \N patch patch_75_76_c.sql|remove_alternative_splicing
78 \N patch patch_76_77_a.sql|schema_version
+79 \N patch patch_77_78_a.sql|schema_version
+80 \N patch patch_77_78_b.sql|source_column_increase
1 \N schema_type core
-2 \N schema_version 77
+2 \N schema_version 78
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 035f7ea8c1..5fc7c58741 100644
--- a/modules/t/test-genome-DBs/circ/core/table.sql
+++ b/modules/t/test-genome-DBs/circ/core/table.sql
@@ -284,7 +284,7 @@ CREATE TABLE `gene` (
`seq_region_end` int(10) unsigned NOT NULL,
`seq_region_strand` tinyint(2) NOT NULL,
`display_xref_id` int(10) unsigned DEFAULT NULL,
- `source` varchar(20) NOT NULL,
+ `source` varchar(40) NOT NULL,
`status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN','ANNOTATED') DEFAULT NULL,
`description` text,
`is_current` tinyint(1) NOT NULL DEFAULT '1',
@@ -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=78 DEFAULT CHARSET=latin1;
+) ENGINE=InnoDB AUTO_INCREMENT=81 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL,
@@ -773,7 +773,7 @@ CREATE TABLE `transcript` (
`seq_region_end` int(10) unsigned NOT NULL,
`seq_region_strand` tinyint(2) NOT NULL,
`display_xref_id` int(10) unsigned DEFAULT NULL,
- `source` varchar(20) NOT NULL DEFAULT 'ensembl',
+ `source` varchar(40) NOT NULL DEFAULT 'ensembl',
`biotype` varchar(40) NOT NULL,
`status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN','ANNOTATED') DEFAULT NULL,
`description` text,
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 a348648820..392ef72933 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 77
+1 \N schema_version 78
2 1 assembly.default NCBI34
3 1 species.taxonomy_id 9606
26 1 species.classification Homo sapiens
@@ -55,3 +55,5 @@
115 \N patch patch_75_76_b.sql|allow_null_karyotype
116 \N patch patch_75_76_c.sql|remove_alternative_splicing
117 \N patch patch_76_77_a.sql|schema_version
+118 \N patch patch_77_78_a.sql|schema_version
+119 \N patch patch_77_78_b.sql|source_column_increase
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 c76eac48a8..2e58dc2c5b 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
@@ -284,7 +284,7 @@ CREATE TABLE `gene` (
`seq_region_end` int(10) unsigned NOT NULL,
`seq_region_strand` tinyint(2) NOT NULL,
`display_xref_id` int(10) unsigned DEFAULT NULL,
- `source` varchar(20) NOT NULL,
+ `source` varchar(40) NOT NULL,
`status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN','ANNOTATED') DEFAULT NULL,
`description` text,
`is_current` tinyint(1) NOT NULL DEFAULT '1',
@@ -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=117 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=120 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL,
@@ -772,7 +772,7 @@ CREATE TABLE `transcript` (
`seq_region_end` int(10) unsigned NOT NULL,
`seq_region_strand` tinyint(2) NOT NULL,
`display_xref_id` int(10) unsigned DEFAULT NULL,
- `source` varchar(20) NOT NULL DEFAULT 'ensembl',
+ `source` varchar(40) NOT NULL DEFAULT 'ensembl',
`biotype` varchar(40) NOT NULL,
`status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN','ANNOTATED') DEFAULT NULL,
`description` text,
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 84d7f1f493..910038c643 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 77
+1 \N schema_version 78
2 1 assembly.default NCBI34
33 1 species.classification Chordata
32 1 species.classification Vertebrata
@@ -55,3 +55,5 @@
104 \N patch patch_75_76_b.sql|allow_null_karyotype
105 \N patch patch_75_76_c.sql|remove_alternative_splicing
106 \N patch patch_76_77_a.sql|schema_version
+107 \N patch patch_77_78_a.sql|schema_version
+108 \N patch patch_77_78_b.sql|source_column_increase
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 ca03938564..9223b130d8 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
@@ -283,7 +283,7 @@ CREATE TABLE `gene` (
`seq_region_end` int(10) unsigned NOT NULL,
`seq_region_strand` tinyint(2) NOT NULL,
`display_xref_id` int(10) unsigned DEFAULT NULL,
- `source` varchar(20) NOT NULL,
+ `source` varchar(40) NOT NULL,
`status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
`description` text,
`is_current` tinyint(1) NOT NULL DEFAULT '1',
@@ -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=105 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=109 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL DEFAULT '',
@@ -765,7 +765,7 @@ CREATE TABLE `transcript` (
`seq_region_end` int(10) unsigned NOT NULL,
`seq_region_strand` tinyint(2) NOT NULL,
`display_xref_id` int(10) unsigned DEFAULT NULL,
- `source` varchar(20) NOT NULL DEFAULT 'ensembl',
+ `source` varchar(40) NOT NULL DEFAULT 'ensembl',
`biotype` varchar(40) NOT NULL,
`status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
`description` text,
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 ac8135a1d7..a9970bba4d 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 77
+1 \N schema_version 78
2014 1 species.classification Haplorrhini
40 1 assembly.default GRCh37
41 1 assembly.date 2009-02
@@ -59,3 +59,5 @@
2066 \N patch patch_75_76_b.sql|allow_null_karyotype
2067 \N patch patch_75_76_c.sql|remove_alternative_splicing
2068 \N patch patch_76_77_a.sql|schema_version
+2069 \N patch patch_77_78_a.sql|schema_version
+2070 \N patch patch_77_78_b.sql|source_column_increase
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 306a0ade7d..219a845172 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
@@ -282,7 +282,7 @@ CREATE TABLE `gene` (
`seq_region_end` int(10) unsigned NOT NULL,
`seq_region_strand` tinyint(2) NOT NULL,
`display_xref_id` int(10) unsigned DEFAULT NULL,
- `source` varchar(20) NOT NULL,
+ `source` varchar(40) NOT NULL,
`status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
`description` text,
`is_current` tinyint(1) NOT NULL DEFAULT '1',
@@ -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=2067 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=2071 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
@@ -762,7 +762,7 @@ CREATE TABLE `transcript` (
`seq_region_end` int(10) unsigned NOT NULL,
`seq_region_strand` tinyint(2) NOT NULL,
`display_xref_id` int(10) unsigned DEFAULT NULL,
- `source` varchar(20) NOT NULL DEFAULT 'ensembl',
+ `source` varchar(40) NOT NULL DEFAULT 'ensembl',
`biotype` varchar(40) NOT NULL,
`status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
`description` text,
diff --git a/modules/t/test-genome-DBs/nameless/core/meta.txt b/modules/t/test-genome-DBs/nameless/core/meta.txt
index 6507d92bbd..e34798c78f 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 77
+1 \N schema_version 78
2 1 assembly.default NCBI34
3 1 species.taxonomy_id 9606
26 1 species.classification Homo sapiens
@@ -54,3 +54,5 @@
108 \N patch patch_75_76_b.sql|allow_null_karyotype
109 \N patch patch_75_76_c.sql|remove_alternative_splicing
110 \N patch patch_76_77_a.sql|schema_version
+111 \N patch patch_77_78_a.sql|schema_version
+112 \N patch patch_77_78_b.sql|source_column_increase
diff --git a/modules/t/test-genome-DBs/nameless/core/table.sql b/modules/t/test-genome-DBs/nameless/core/table.sql
index 93963122e6..14e213cb92 100644
--- a/modules/t/test-genome-DBs/nameless/core/table.sql
+++ b/modules/t/test-genome-DBs/nameless/core/table.sql
@@ -284,7 +284,7 @@ CREATE TABLE `gene` (
`seq_region_end` int(10) unsigned NOT NULL,
`seq_region_strand` tinyint(2) NOT NULL,
`display_xref_id` int(10) unsigned DEFAULT NULL,
- `source` varchar(20) NOT NULL,
+ `source` varchar(40) NOT NULL,
`status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN','ANNOTATED') DEFAULT NULL,
`description` text,
`is_current` tinyint(1) NOT NULL DEFAULT '1',
@@ -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=109 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=113 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL,
@@ -772,7 +772,7 @@ CREATE TABLE `transcript` (
`seq_region_end` int(10) unsigned NOT NULL,
`seq_region_strand` tinyint(2) NOT NULL,
`display_xref_id` int(10) unsigned DEFAULT NULL,
- `source` varchar(20) NOT NULL DEFAULT 'ensembl',
+ `source` varchar(40) NOT NULL DEFAULT 'ensembl',
`biotype` varchar(40) NOT NULL,
`status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN','ANNOTATED') DEFAULT NULL,
`description` text,
diff --git a/modules/t/test-genome-DBs/ontology/ontology/meta.txt b/modules/t/test-genome-DBs/ontology/ontology/meta.txt
index e490a99bdc..775e4f2d54 100644
--- a/modules/t/test-genome-DBs/ontology/ontology/meta.txt
+++ b/modules/t/test-genome-DBs/ontology/ontology/meta.txt
@@ -9,6 +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 77 \N
+15 schema_version 78 \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
diff --git a/modules/t/test-genome-DBs/ontology/ontology/table.sql b/modules/t/test-genome-DBs/ontology/ontology/table.sql
index 53d84bd54f..714550abb8 100644
--- a/modules/t/test-genome-DBs/ontology/ontology/table.sql
+++ b/modules/t/test-genome-DBs/ontology/ontology/table.sql
@@ -138,7 +138,7 @@ 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=17 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=19 DEFAULT CHARSET=latin1;
CREATE TABLE `ontology` (
`ontology_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
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 c1ee0b324f..7ff56bcee1 100644
--- a/modules/t/test-genome-DBs/test_collection/core/meta.txt
+++ b/modules/t/test-genome-DBs/test_collection/core/meta.txt
@@ -20,8 +20,10 @@
171 \N patch patch_75_76_b.sql|allow_null_karyotype
172 \N patch patch_75_76_c.sql|remove_alternative_splicing
173 \N patch patch_76_77_a.sql|schema_version
+174 \N patch patch_77_78_a.sql|schema_version
+175 \N patch patch_77_78_b.sql|source_column_increase
1 \N schema_type core
-2 \N schema_version 77
+2 \N schema_version 78
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 8e21851d83..e1ff9e4459 100644
--- a/modules/t/test-genome-DBs/test_collection/core/table.sql
+++ b/modules/t/test-genome-DBs/test_collection/core/table.sql
@@ -284,7 +284,7 @@ CREATE TABLE `gene` (
`seq_region_end` int(10) unsigned NOT NULL,
`seq_region_strand` tinyint(2) NOT NULL,
`display_xref_id` int(10) unsigned DEFAULT NULL,
- `source` varchar(20) NOT NULL,
+ `source` varchar(40) NOT NULL,
`status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN','ANNOTATED') DEFAULT NULL,
`description` text,
`is_current` tinyint(1) NOT NULL DEFAULT '1',
@@ -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=173 DEFAULT CHARSET=latin1;
+) ENGINE=InnoDB AUTO_INCREMENT=176 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL,
@@ -773,7 +773,7 @@ CREATE TABLE `transcript` (
`seq_region_end` int(10) unsigned NOT NULL,
`seq_region_strand` tinyint(2) NOT NULL,
`display_xref_id` int(10) unsigned DEFAULT NULL,
- `source` varchar(20) NOT NULL DEFAULT 'ensembl',
+ `source` varchar(40) NOT NULL DEFAULT 'ensembl',
`biotype` varchar(40) NOT NULL,
`status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN','ANNOTATED') DEFAULT NULL,
`description` text,
diff --git a/sql/patch_77_78_b.sql b/sql/patch_77_78_b.sql
new file mode 100644
index 0000000000..89b9d0b30f
--- /dev/null
+++ b/sql/patch_77_78_b.sql
@@ -0,0 +1,27 @@
+-- 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_77_78_b.sql
+#
+# Title: Increase source column size
+#
+# Description:
+# RefSeq data requires more characters in the gene and transcript source column.
+
+ALTER TABLE gene MODIFY COLUMN source VARCHAR(40) NOT NULL;
+ALTER TABLE transcript MODIFY COLUMN source VARCHAR(40) NOT NULL default 'ensembl';
+
+# Patch identifier
+INSERT INTO meta (species_id, meta_key, meta_value)
+ VALUES (NULL, 'patch', 'patch_77_78_b.sql|source_column_increase');
--
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