From 5de1bf2cdbfcd905824fc09959fb3357b846d48b Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Mon, 29 Oct 2012 12:58:29 +0000
Subject: [PATCH] Adding column edits for columns which have now diverged in
their definitions. Also making sure data_file's collate is set correctly
---
sql/patch_69_70_c.sql | 24 ++++++++++++++++++++++++
sql/table.sql | 30 +++++++++++++++++-------------
2 files changed, 41 insertions(+), 13 deletions(-)
create mode 100644 sql/patch_69_70_c.sql
diff --git a/sql/patch_69_70_c.sql b/sql/patch_69_70_c.sql
new file mode 100644
index 0000000000..2d8b590e4e
--- /dev/null
+++ b/sql/patch_69_70_c.sql
@@ -0,0 +1,24 @@
+# patch_69_70_c.sql
+#
+# Title: Ensure column definitions are consistent in the schema
+#
+# Description: A number of column defintions over time have diverged from their
+# original specification. We are converting those we know are wrong
+
+ALTER TABLE dependent_xref MODIFY COLUMN object_xref_id INT(10) UNSIGNED NOT NULL;
+ALTER TABLE dependent_xref MODIFY COLUMN master_xref_id INT(10) UNSIGNED NOT NULL;
+ALTER TABLE dependent_xref MODIFY COLUMN dependent_xref_id INT(10) UNSIGNED NOT NULL;
+
+ALTER TABLE object_xref MODIFY COLUMN xref_id INT(10) UNSIGNED NOT NULL;
+
+ALTER TABLE data_file MODIFY COLUMN data_file_id INT(10) UNSIGNED NOT NULL;
+ALTER TABLE data_file MODIFY COLUMN coord_system_id INT(10) UNSIGNED NOT NULL;
+ALTER TABLE data_file MODIFY COLUMN analysis_id SMALLINT UNSIGNED NOT NULL;
+
+ALTER TABLE data_file COLLATE=latin1_swedish_ci;
+
+# Patch identifier
+INSERT INTO meta (species_id, meta_key, meta_value)
+ VALUES (NULL, 'patch', 'patch_69_70_c.sql|column_datatype_consistency');
+
+
diff --git a/sql/table.sql b/sql/table.sql
index cef21b19cc..ec582373a9 100755
--- a/sql/table.sql
+++ b/sql/table.sql
@@ -514,6 +514,9 @@ INSERT INTO meta (species_id, meta_key, meta_value) VALUES
INSERT INTO meta (species_id, meta_key, meta_value) VALUES
(NULL, 'patch', 'patch_69_70_b.sql|add_mapping_set_history')
;
+INSERT INTO meta (species_id, meta_key, meta_value) VALUES
+ (NULL, 'patch', 'patch_69_70_c.sql|column_datatype_consistency')
+ ;
/**
@table meta_coord
@@ -2191,9 +2194,9 @@ They are linked to primary external references instead.
CREATE TABLE dependent_xref(
- object_xref_id INT NOT NULL,
- master_xref_id INT NOT NULL,
- dependent_xref_id INT NOT NULL,
+ object_xref_id INT(10) UNSIGNED NOT NULL,
+ master_xref_id INT(10) UNSIGNED NOT NULL,
+ dependent_xref_id INT(10) UNSIGNED NOT NULL,
PRIMARY KEY( object_xref_id ),
KEY dependent ( dependent_xref_id ),
@@ -2342,7 +2345,7 @@ CREATE TABLE object_xref (
ensembl_object_type ENUM('RawContig', 'Transcript', 'Gene',
'Translation', 'Operon', 'OperonTranscript')
NOT NULL,
- xref_id INT UNSIGNED NOT NULL,
+ xref_id INT(10) UNSIGNED NOT NULL,
linkage_annotation VARCHAR(255) DEFAULT NULL,
analysis_id SMALLINT UNSIGNED DEFAULT 0 NOT NULL,
@@ -2575,17 +2578,18 @@ CREATE TABLE interpro (
*/
CREATE TABLE data_file (
- data_file_id int(11) unsigned NOT NULL AUTO_INCREMENT,
- coord_system_id int(11) NOT NULL,
- analysis_id int(11) NOT NULL,
- name varchar(100) NOT NULL,
- version_lock tinyint(1) DEFAULT 0 NOT NULL,
- absolute tinyint(1) DEFAULT 0 NOT NULL,
- url text,
- file_type enum('BAM','BIGBED','BIGWIG','VCF'),
+ data_file_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
+ coord_system_id INT(10) UNSIGNED NOT NULL,
+ analysis_id SMALLINT UNSIGNED NOT NULL,
+ name VARCHAR(100) NOT NULL,
+ version_lock TINYINT(1) DEFAULT 0 NOT NULL,
+ absolute TINYINT(1) DEFAULT 0 NOT NULL,
+ url TEXT,
+ file_type ENUM('BAM','BIGBED','BIGWIG','VCF'),
+
PRIMARY KEY (data_file_id),
UNIQUE KEY df_unq_idx(coord_system_id, analysis_id, name, file_type),
INDEX df_name_idx(name),
INDEX df_analysis_idx(analysis_id)
-) ENGINE=MyISAM;
+) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
--
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