Commit 814d3175 authored by Kieron Taylor's avatar Kieron Taylor 😠
Browse files

[ENSCORESW-1047] Altering column sizes for source in gene and transcript...

[ENSCORESW-1047] Altering column sizes for source in gene and transcript tables. Also patch test databases.
parent 51638038
......@@ -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
......
......@@ -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,
......
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
......@@ -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,
......
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
......@@ -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,
......
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
......@@ -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,
......
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
......@@ -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,
......
......@@ -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
......@@ -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,
......
......@@ -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
......
......@@ -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,
......
-- 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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