From 8e14ea7d869f964dc018cb2ea01552be73eed335 Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Fri, 2 Jun 2006 14:27:05 +0000
Subject: [PATCH] Rationalised all primary and foreign keys to be INT(10)
UNSIGNED.
Added info_type and info_text to UNIQUE index on xref.
Changed version column in xref to default to NULL.
---
sql/table.sql | 242 +++++++++++++++++++++++++-------------------------
1 file changed, 122 insertions(+), 120 deletions(-)
diff --git a/sql/table.sql b/sql/table.sql
index 60dd72105e..e258c52ead 100755
--- a/sql/table.sql
+++ b/sql/table.sql
@@ -20,13 +20,13 @@
CREATE TABLE oligo_feature (
- oligo_feature_id INT NOT NULL AUTO_INCREMENT,
- seq_region_id INT UNSIGNED NOT NULL,
- seq_region_start INT NOT NULL,
- seq_region_end INT NOT NULL,
+ oligo_feature_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
+ seq_region_id INT(10) UNSIGNED NOT NULL,
+ seq_region_start INT(10) UNSIGNED NOT NULL,
+ seq_region_end INT(10) UNSIGNED NOT NULL,
seq_region_strand TINYINT NOT NULL,
mismatches TINYINT,
- oligo_probe_id INT NOT NULL,
+ oligo_probe_id INT(10) UNSIGNED NOT NULL,
analysis_id INT(10) UNSIGNED NOT NULL,
PRIMARY KEY (oligo_feature_id),
@@ -43,8 +43,8 @@ CREATE TABLE oligo_feature (
CREATE TABLE oligo_probe (
- oligo_probe_id INT NOT NULL AUTO_INCREMENT,
- oligo_array_id INT NOT NULL,
+ oligo_probe_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
+ oligo_array_id INT(10) UNSIGNED NOT NULL,
probeset VARCHAR(40),
name VARCHAR(20),
description TEXT,
@@ -64,8 +64,8 @@ CREATE TABLE oligo_probe (
CREATE TABLE oligo_array (
- oligo_array_id INT NOT NULL auto_increment,
- parent_array_id INT,
+ oligo_array_id INT(10) UNSIGNED NOT NULL auto_increment,
+ parent_array_id INT(10) UNSIGNED,
probe_setsize TINYINT NOT NULL,
name VARCHAR(40) NOT NULL,
type ENUM( 'AFFY', 'OLIGO' ),
@@ -81,8 +81,8 @@ CREATE TABLE oligo_array (
#
CREATE TABLE alt_allele (
- alt_allele_id INT NOT NULL AUTO_INCREMENT,
- gene_id INT NOT NULL,
+ alt_allele_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
+ gene_id INT(10) UNSIGNED NOT NULL,
UNIQUE gene_idx (gene_id),
UNIQUE allele_idx (alt_allele_id, gene_id)
@@ -162,7 +162,7 @@ CREATE TABLE analysis_description (
CREATE TABLE dna (
- seq_region_id INT UNSIGNED NOT NULL,
+ seq_region_id INT(10) UNSIGNED NOT NULL,
sequence MEDIUMTEXT NOT NULL,
PRIMARY KEY (seq_region_id)
@@ -185,7 +185,7 @@ CREATE TABLE dna (
CREATE TABLE dnac (
- seq_region_id INT UNSIGNED NOT NULL,
+ seq_region_id INT(10) UNSIGNED NOT NULL,
sequence MEDIUMBLOB NOT NULL,
n_line TEXT,
@@ -204,7 +204,7 @@ CREATE TABLE dnac (
CREATE TABLE exon (
- exon_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
+ exon_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
seq_region_id INT(10) UNSIGNED NOT NULL,
seq_region_start INT(10) UNSIGNED NOT NULL,
seq_region_end INT(10) UNSIGNED NOT NULL,
@@ -228,7 +228,7 @@ CREATE TABLE exon (
CREATE TABLE exon_stable_id (
- exon_id INT UNSIGNED NOT NULL,
+ exon_id INT(10) UNSIGNED NOT NULL,
stable_id VARCHAR(128) NOT NULL,
version INT(10),
created_date DATETIME NOT NULL,
@@ -250,8 +250,8 @@ CREATE TABLE exon_stable_id (
CREATE TABLE exon_transcript (
- exon_id INT UNSIGNED NOT NULL,
- transcript_id INT UNSIGNED NOT NULL,
+ exon_id INT(10) UNSIGNED NOT NULL,
+ transcript_id INT(10) UNSIGNED NOT NULL,
rank INT(10) NOT NULL,
PRIMARY KEY (exon_id,transcript_id,rank),
@@ -268,7 +268,7 @@ CREATE TABLE exon_transcript (
CREATE TABLE simple_feature (
- simple_feature_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
+ simple_feature_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
seq_region_id INT(10) UNSIGNED NOT NULL,
seq_region_start INT(10) UNSIGNED NOT NULL,
seq_region_end INT(10) UNSIGNED NOT NULL,
@@ -292,7 +292,7 @@ CREATE TABLE simple_feature (
CREATE TABLE protein_align_feature (
- protein_align_feature_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
+ protein_align_feature_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
seq_region_id INT(10) UNSIGNED NOT NULL,
seq_region_start INT(10) UNSIGNED NOT NULL,
seq_region_end INT(10) UNSIGNED NOT NULL,
@@ -322,7 +322,7 @@ CREATE TABLE protein_align_feature (
CREATE TABLE dna_align_feature (
- dna_align_feature_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
+ dna_align_feature_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
seq_region_id INT(10) UNSIGNED NOT NULL,
seq_region_start INT(10) UNSIGNED NOT NULL,
seq_region_end INT(10) UNSIGNED NOT NULL,
@@ -355,7 +355,7 @@ CREATE TABLE dna_align_feature (
CREATE TABLE repeat_consensus (
- repeat_consensus_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
+ repeat_consensus_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
repeat_name VARCHAR(255) NOT NULL,
repeat_class VARCHAR(100) NOT NULL,
repeat_type VARCHAR(40) NOT NULL,
@@ -376,7 +376,7 @@ CREATE TABLE repeat_consensus (
CREATE TABLE repeat_feature (
- repeat_feature_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
+ repeat_feature_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
seq_region_id INT(10) UNSIGNED NOT NULL,
seq_region_start INT(10) UNSIGNED NOT NULL,
seq_region_end INT(10) UNSIGNED NOT NULL,
@@ -402,14 +402,14 @@ CREATE TABLE repeat_feature (
CREATE TABLE gene (
- gene_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
+ gene_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
biotype VARCHAR(40) NOT NULL,
analysis_id INT(10) UNSIGNED NOT NULL,
seq_region_id INT(10) UNSIGNED NOT NULL,
seq_region_start INT(10) UNSIGNED NOT NULL,
seq_region_end INT(10) UNSIGNED NOT NULL,
seq_region_strand TINYINT(2) NOT NULL,
- display_xref_id INT UNSIGNED,
+ display_xref_id INT(10) UNSIGNED,
source VARCHAR(20) NOT NULL,
status ENUM('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN'),
description TEXT,
@@ -449,9 +449,9 @@ CREATE TABLE gene_stable_id (
CREATE TABLE supporting_feature (
- exon_id INT(11) DEFAULT '0' NOT NULL,
+ exon_id INT(10) UNSIGNED DEFAULT '0' NOT NULL,
feature_type ENUM('dna_align_feature','protein_align_feature'),
- feature_id INT(11) DEFAULT '0' NOT NULL,
+ feature_id INT(10) UNSIGNED DEFAULT '0' NOT NULL,
UNIQUE all_idx (exon_id,feature_type,feature_id),
KEY feature_idx (feature_type,feature_id)
@@ -466,9 +466,9 @@ CREATE TABLE supporting_feature (
CREATE TABLE transcript_supporting_feature (
- transcript_id INT(11) DEFAULT '0' NOT NULL,
+ transcript_id INT(10) UNSIGNED DEFAULT '0' NOT NULL,
feature_type ENUM('dna_align_feature','protein_align_feature'),
- feature_id INT(11) DEFAULT '0' NOT NULL,
+ feature_id INT(10) UNSIGNED DEFAULT '0' NOT NULL,
UNIQUE all_idx (transcript_id,feature_type,feature_id),
KEY feature_idx (feature_type,feature_id)
@@ -483,14 +483,14 @@ CREATE TABLE transcript_supporting_feature (
CREATE TABLE transcript (
- transcript_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
- gene_id INT UNSIGNED NOT NULL,
+ transcript_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
+ gene_id INT(10) UNSIGNED NOT NULL,
analysis_id INT(10) UNSIGNED NOT NULL,
seq_region_id INT(10) UNSIGNED NOT NULL,
seq_region_start INT(10) UNSIGNED NOT NULL,
seq_region_end INT(10) UNSIGNED NOT NULL,
seq_region_strand TINYINT(2) NOT NULL,
- display_xref_id INT UNSIGNED,
+ display_xref_id INT(10) UNSIGNED,
biotype VARCHAR(40) NOT NULL,
status ENUM('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN'),
description TEXT,
@@ -512,7 +512,7 @@ CREATE TABLE transcript (
CREATE TABLE transcript_stable_id (
- transcript_id INT UNSIGNED NOT NULL,
+ transcript_id INT(10) UNSIGNED NOT NULL,
stable_id VARCHAR(128) NOT NULL,
version INT(10),
created_date DATETIME NOT NULL,
@@ -534,12 +534,12 @@ CREATE TABLE transcript_stable_id (
CREATE TABLE translation (
- translation_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
- transcript_id INT UNSIGNED NOT NULL,
+ translation_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
+ transcript_id INT(10) UNSIGNED NOT NULL,
seq_start INT(10) NOT NULL, # relative to exon start
- start_exon_id INT UNSIGNED NOT NULL,
+ start_exon_id INT(10) UNSIGNED NOT NULL,
seq_end INT(10) NOT NULL, # relative to exon start
- end_exon_id INT UNSIGNED NOT NULL,
+ end_exon_id INT(10) UNSIGNED NOT NULL,
PRIMARY KEY (translation_id),
KEY (transcript_id)
@@ -553,7 +553,7 @@ CREATE TABLE translation (
#
CREATE TABLE translation_stable_id (
- translation_id INT UNSIGNED NOT NULL,
+ translation_id INT(10) UNSIGNED NOT NULL,
stable_id VARCHAR(128) NOT NULL,
version INT(10),
created_date DATETIME NOT NULL,
@@ -585,7 +585,7 @@ CREATE TABLE translation_stable_id (
CREATE TABLE assembly (
- asm_seq_region_id INT UNSIGNED NOT NULL,
+ asm_seq_region_id INT(10) UNSIGNED NOT NULL,
cmp_seq_region_id INT(10) UNSIGNED NOT NULL,
asm_start INT(10) NOT NULL,
asm_end INT(10) NOT NULL,
@@ -608,7 +608,7 @@ CREATE TABLE assembly (
CREATE TABLE protein_feature (
protein_feature_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
- translation_id INT NOT NULL,
+ translation_id INT(10) UNSIGNED NOT NULL,
seq_start INT(10) NOT NULL,
seq_end INT(10) NOT NULL,
hit_start INT(10) NOT NULL,
@@ -649,8 +649,8 @@ CREATE TABLE interpro (
#
CREATE TABLE karyotype (
- karyotype_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
- seq_region_id INT UNSIGNED NOT NULL,
+ karyotype_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
+ seq_region_id INT(10) UNSIGNED NOT NULL,
seq_region_start INT(10) NOT NULL,
seq_region_end INT(10) NOT NULL,
band VARCHAR(40) NOT NULL,
@@ -669,8 +669,8 @@ CREATE TABLE karyotype (
CREATE TABLE object_xref (
- object_xref_id INT NOT NULL AUTO_INCREMENT,
- ensembl_id INT UNSIGNED NOT NULL,
+ object_xref_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
+ ensembl_id INT(10) UNSIGNED NOT NULL,
ensembl_object_type ENUM('RawContig', 'Transcript', 'Gene',
'Translation', 'regulatory_factor',
'regulatory_feature')
@@ -689,9 +689,9 @@ CREATE TABLE object_xref (
# Table structure for table 'identity_xref'
#
-CREATE TABLE identity_xref(
+CREATE TABLE identity_xref (
- object_xref_id INT UNSIGNED NOT NULL ,
+ object_xref_id INT(10) UNSIGNED NOT NULL,
query_identity INT(5),
target_identity INT(5),
@@ -735,17 +735,17 @@ CREATE TABLE go_xref (
CREATE TABLE xref (
- xref_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
- external_db_id INT NOT NULL,
+ xref_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
+ external_db_id INT(10) UNSIGNED NOT NULL,
dbprimary_acc VARCHAR(40) NOT NULL,
display_label VARCHAR(128) NOT NULL,
- version VARCHAR(10) DEFAULT '' NOT NULL,
+ version VARCHAR(10) DEFAULT '0' NOT NULL,
description VARCHAR(255),
info_type ENUM('PROJECTION', 'MISC'),
info_text VARCHAR(255),
PRIMARY KEY (xref_id),
- UNIQUE KEY id_index (dbprimary_acc, external_db_id),
+ UNIQUE KEY id_index (dbprimary_acc, external_db_id, info_type, info_text),
KEY display_index (display_label),
KEY info_type_idx (info_type)
@@ -759,7 +759,7 @@ CREATE TABLE xref (
CREATE TABLE external_synonym (
- xref_id INT UNSIGNED NOT NULL,
+ xref_id INT(10) UNSIGNED NOT NULL,
synonym VARCHAR(40) NOT NULL,
PRIMARY KEY (xref_id, synonym),
@@ -775,7 +775,7 @@ CREATE TABLE external_synonym (
CREATE TABLE external_db (
- external_db_id INT NOT NULL,
+ external_db_id INT(10) UNSIGNED NOT NULL,
db_name VARCHAR(27) NOT NULL,
db_release VARCHAR(40) NOT NULL,
status ENUM('KNOWNXREF','KNOWN','XREF','PRED','ORTH',
@@ -798,12 +798,12 @@ CREATE TABLE external_db (
CREATE TABLE prediction_exon (
- prediction_exon_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
- prediction_transcript_id INT UNSIGNED NOT NULL,
+ prediction_exon_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
+ prediction_transcript_id INT(10) UNSIGNED NOT NULL,
exon_rank SMALLINT UNSIGNED NOT NULL,
- seq_region_id INT UNSIGNED NOT NULL,
- seq_region_start INT UNSIGNED NOT NULL,
- seq_region_end INT UNSIGNED NOT NULL,
+ seq_region_id INT(10) UNSIGNED NOT NULL,
+ seq_region_start INT(10) UNSIGNED NOT NULL,
+ seq_region_end INT(10) UNSIGNED NOT NULL,
seq_region_strand TINYINT NOT NULL,
start_phase TINYINT NOT NULL,
score DOUBLE,
@@ -823,10 +823,10 @@ CREATE TABLE prediction_exon (
CREATE TABLE prediction_transcript (
- prediction_transcript_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
- seq_region_id INT UNSIGNED NOT NULL,
- seq_region_start INT UNSIGNED NOT NULL,
- seq_region_end INT UNSIGNED NOT NULL,
+ prediction_transcript_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
+ seq_region_id INT(10) UNSIGNED NOT NULL,
+ seq_region_start INT(10) UNSIGNED NOT NULL,
+ seq_region_end INT(10) UNSIGNED NOT NULL,
seq_region_strand TINYINT NOT NULL,
analysis_id INT(10) UNSIGNED NOT NULL,
display_label VARCHAR(255),
@@ -857,7 +857,7 @@ CREATE TABLE meta (
# Auto add schema version to database
-INSERT INTO meta (meta_key, meta_value) VALUES ("schema_version", "39");
+INSERT INTO meta (meta_key, meta_value) VALUES ("schema_version", "40");
# patches included in this schema file
INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_38_39_a.sql|status_enum');
@@ -865,7 +865,9 @@ INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_38_39_b.sql|uniq
INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_38_39_c.sql|multiversion_objects');
INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_38_39_d.sql|schema_version');
INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_38_39_e.sql|unknown_status_enum');
-
+INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_39_40_a.sql|rationalise_key_columns');
+INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_39_40_a.sql|xref_unique_constraint');
+INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_39_40_c.sql|xref_version');
################################################################################
#
@@ -873,8 +875,8 @@ INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_38_39_e.sql|unkn
CREATE TABLE marker_synonym (
- marker_synonym_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
- marker_id INT UNSIGNED NOT NULL,
+ marker_synonym_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
+ marker_id INT(10) UNSIGNED NOT NULL,
source VARCHAR(20),
name VARCHAR(30),
@@ -891,8 +893,8 @@ CREATE TABLE marker_synonym (
CREATE TABLE marker (
- marker_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
- display_marker_synonym_id INT UNSIGNED,
+ marker_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
+ display_marker_synonym_id INT(10) UNSIGNED,
left_primer VARCHAR(100) NOT NULL,
right_primer VARCHAR(100) NOT NULL,
min_primer_dist INT(10) UNSIGNED NOT NULL,
@@ -912,8 +914,8 @@ CREATE TABLE marker (
CREATE TABLE marker_feature (
- marker_feature_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
- marker_id INT UNSIGNED NOT NULL,
+ marker_feature_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
+ marker_id INT(10) UNSIGNED NOT NULL,
seq_region_id INT(10) UNSIGNED NOT NULL,
seq_region_start INT(10) UNSIGNED NOT NULL,
seq_region_end INT(10) UNSIGNED NOT NULL,
@@ -933,10 +935,10 @@ CREATE TABLE marker_feature (
CREATE TABLE marker_map_location (
- marker_id INT UNSIGNED NOT NULL,
- map_id INT UNSIGNED NOT NULL,
+ marker_id INT(10) UNSIGNED NOT NULL,
+ map_id INT(10) UNSIGNED NOT NULL,
chromosome_name VARCHAR(15) NOT NULL,
- marker_synonym_id INT UNSIGNED NOT NULL,
+ marker_synonym_id INT(10) UNSIGNED NOT NULL,
position VARCHAR(15) NOT NULL,
lod_score DOUBLE,
@@ -952,7 +954,7 @@ CREATE TABLE marker_map_location (
CREATE TABLE map (
- map_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
+ map_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
map_name VARCHAR(30) NOT NULL,
PRIMARY KEY (map_id)
@@ -1123,12 +1125,12 @@ CREATE TABLE misc_feature_misc_set (
CREATE TABLE qtl (
- qtl_id INT UNSIGNED AUTO_INCREMENT NOT NULL,
+ qtl_id INT(10) UNSIGNED AUTO_INCREMENT NOT NULL,
trait VARCHAR(255) NOT NULL,
lod_score FLOAT,
- flank_marker_id_1 INT,
- flank_marker_id_2 INT,
- peak_marker_id INT,
+ flank_marker_id_1 INT(10) UNSIGNED,
+ flank_marker_id_2 INT(10) UNSIGNED,
+ peak_marker_id INT(10) UNSIGNED,
PRIMARY KEY (qtl_id),
KEY trait_idx (trait)
@@ -1143,8 +1145,8 @@ CREATE TABLE qtl (
CREATE TABLE qtl_synonym (
- qtl_synonym_id INT UNSIGNED AUTO_INCREMENT NOT NULL,
- qtl_id INT UNSIGNED NOT NULL,
+ qtl_synonym_id INT(10) UNSIGNED AUTO_INCREMENT NOT NULL,
+ qtl_id INT(10) UNSIGNED NOT NULL,
source_database ENUM("rat genome database", "ratmap") NOT NULL,
source_primary_id VARCHAR(255) NOT NULL,
@@ -1161,10 +1163,10 @@ CREATE TABLE qtl_synonym (
CREATE TABLE qtl_feature (
- seq_region_id INT NOT NULL,
- seq_region_start INT NOT NULL,
- seq_region_end INT NOT NULL,
- qtl_id INT NOT NULL,
+ seq_region_id INT(10) UNSIGNED NOT NULL,
+ seq_region_start INT(10) UNSIGNED NOT NULL,
+ seq_region_end INT(10) UNSIGNED NOT NULL,
+ qtl_id INT(10) UNSIGNED NOT NULL,
analysis_id INT(10) UNSIGNED NOT NULL,
KEY (qtl_id),
@@ -1181,7 +1183,7 @@ CREATE TABLE qtl_feature (
CREATE TABLE mapping_session (
- mapping_session_id INT(11) NOT NULL AUTO_INCREMENT,
+ mapping_session_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
old_db_name VARCHAR(80) NOT NULL DEFAULT '',
new_db_name VARCHAR(80) NOT NULL DEFAULT '',
old_release VARCHAR(5) NOT NULL DEFAULT '',
@@ -1206,7 +1208,7 @@ CREATE TABLE stable_id_event (
old_version SMALLINT,
new_stable_id VARCHAR(128),
new_version SMALLINT,
- mapping_session_id INT(11) NOT NULL DEFAULT '0',
+ mapping_session_id INT(10) UNSIGNED NOT NULL DEFAULT '0',
type ENUM('gene', 'transcript', 'translation') NOT NULL,
UNIQUE KEY uni_idx (mapping_session_id, old_stable_id, old_version,
@@ -1231,8 +1233,8 @@ CREATE TABLE gene_archive (
transcript_version SMALLINT NOT NULL,
translation_stable_id VARCHAR(128) NOT NULL,
translation_version SMALLINT NOT NULL,
- peptide_archive_id INT NOT NULL,
- mapping_session_id INT NOT NULL,
+ peptide_archive_id INT(10) UNSIGNED NOT NULL,
+ mapping_session_id INT(10) UNSIGNED NOT NULL,
KEY gene_idx (gene_stable_id, gene_version),
KEY transcript_idx (transcript_stable_id, transcript_version),
@@ -1248,7 +1250,7 @@ CREATE TABLE gene_archive (
CREATE TABLE peptide_archive (
- peptide_archive_id INT NOT NULL AUTO_INCREMENT,
+ peptide_archive_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
md5_checksum char(32),
peptide_seq MEDIUMTEXT NOT NULL,
@@ -1267,7 +1269,7 @@ CREATE TABLE seq_region (
seq_region_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
name VARCHAR(40) NOT NULL,
- coord_system_id INT(10) NOT NULL,
+ coord_system_id INT(10) UNSIGNED NOT NULL,
length INT(10) NOT NULL,
UNIQUE (coord_system_id, name),
@@ -1285,13 +1287,13 @@ CREATE TABLE seq_region (
CREATE TABLE assembly_exception (
assembly_exception_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
- seq_region_id INT NOT NULL,
- seq_region_start INT NOT NULL,
- seq_region_end INT NOT NULL,
+ seq_region_id INT(10) UNSIGNED NOT NULL,
+ seq_region_start INT(10) UNSIGNED NOT NULL,
+ seq_region_end INT(10) UNSIGNED NOT NULL,
exc_type ENUM('HAP', 'PAR') NOT NULL,
- exc_seq_region_id INT NOT NULL,
- exc_seq_region_start INT NOT NULL,
- exc_seq_region_end INT NOT NULL,
+ exc_seq_region_id INT(10) UNSIGNED NOT NULL,
+ exc_seq_region_start INT(10) UNSIGNED NOT NULL,
+ exc_seq_region_end INT(10) UNSIGNED NOT NULL,
ori INT NOT NULL,
PRIMARY KEY (assembly_exception_id),
@@ -1308,7 +1310,7 @@ CREATE TABLE assembly_exception (
CREATE TABLE coord_system (
- coord_system_id INT NOT NULL AUTO_INCREMENT,
+ coord_system_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
name VARCHAR(40) NOT NULL,
version VARCHAR(40),
rank INT NOT NULL,
@@ -1329,7 +1331,7 @@ CREATE TABLE coord_system (
CREATE TABLE meta_coord (
table_name VARCHAR(40) NOT NULL,
- coord_system_id INT NOT NULL,
+ coord_system_id INT(10) UNSIGNED NOT NULL,
max_length INT,
UNIQUE(table_name, coord_system_id)
@@ -1344,11 +1346,11 @@ CREATE TABLE meta_coord (
CREATE TABLE density_feature (
- density_feature_id INT NOT NULL AUTO_INCREMENT,
- density_type_id INT NOT NULL,
- seq_region_id INT NOT NULL,
- seq_region_start INT NOT NULL,
- seq_region_end INT NOT NULL,
+ density_feature_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
+ density_type_id INT(10) UNSIGNED NOT NULL,
+ seq_region_id INT(10) UNSIGNED NOT NULL,
+ seq_region_start INT(10) UNSIGNED NOT NULL,
+ seq_region_end INT(10) UNSIGNED NOT NULL,
density_value FLOAT NOT NULL,
PRIMARY KEY (density_feature_id),
@@ -1365,7 +1367,7 @@ CREATE TABLE density_feature (
CREATE TABLE density_type (
- density_type_id INT NOT NULL AUTO_INCREMENT,
+ density_type_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
analysis_id INT(10) UNSIGNED NOT NULL,
block_size INT NOT NULL,
region_features INT NOT NULL,
@@ -1385,14 +1387,14 @@ CREATE TABLE density_type (
CREATE TABLE regulatory_feature (
- regulatory_feature_id INT NOT NULL AUTO_INCREMENT,
+ regulatory_feature_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
name VARCHAR(255) NOT NULL,
- seq_region_id INT NOT NULL,
- seq_region_start INT NOT NULL,
- seq_region_end INT NOT NULL,
+ seq_region_id INT(10) UNSIGNED NOT NULL,
+ seq_region_start INT(10) UNSIGNED NOT NULL,
+ seq_region_end INT(10) UNSIGNED NOT NULL,
seq_region_strand TINYINT NOT NULL,
analysis_id INT(10) UNSIGNED NOT NULL,
- regulatory_factor_id INT,
+ regulatory_factor_id INT(10) UNSIGNED,
PRIMARY KEY (regulatory_feature_id),
KEY seq_region_idx (seq_region_id, analysis_id, seq_region_start),
@@ -1408,7 +1410,7 @@ CREATE TABLE regulatory_feature (
CREATE TABLE regulatory_factor (
- regulatory_factor_id INT NOT NULL AUTO_INCREMENT,
+ regulatory_factor_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
name VARCHAR(255) NOT NULL,
type ENUM('miRNA_target', 'transcription_factor',
'transcription_factor_complex'),
@@ -1426,9 +1428,9 @@ CREATE TABLE regulatory_factor (
CREATE TABLE regulatory_feature_object (
- regulatory_feature_id INT NOT NULL,
+ regulatory_feature_id INT(10) UNSIGNED NOT NULL,
ensembl_object_type ENUM('Transcript', 'Translation', 'Gene') NOT NULL,
- ensembl_object_id INT NOT NULL, # FK to transcript,gene etc
+ ensembl_object_id INT(10) UNSIGNED NOT NULL, # FK to transcript,gene etc
influence ENUM('positive', 'negative', 'mixed', 'unknown'),
evidence VARCHAR(255),
@@ -1446,9 +1448,9 @@ CREATE TABLE regulatory_feature_object (
CREATE TABLE regulatory_factor_coding (
- regulatory_factor_id INT NOT NULL,
- transcript_id INT,
- gene_id INT,
+ regulatory_factor_id INT(10) UNSIGNED NOT NULL,
+ transcript_id INT(10) UNSIGNED,
+ gene_id INT(10) UNSIGNED,
KEY transcript_idx (transcript_id),
KEY gene_idx (gene_id),
@@ -1465,15 +1467,15 @@ CREATE TABLE regulatory_factor_coding (
CREATE TABLE regulatory_search_region (
- regulatory_search_region_id INT NOT NULL AUTO_INCREMENT,
+ regulatory_search_region_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
name VARCHAR(255) NOT NULL,
- seq_region_id INT NOT NULL,
- seq_region_start INT NOT NULL,
- seq_region_end INT NOT NULL,
+ seq_region_id INT(10) UNSIGNED NOT NULL,
+ seq_region_start INT(10) UNSIGNED NOT NULL,
+ seq_region_end INT(10) UNSIGNED NOT NULL,
seq_region_strand TINYINT NOT NULL,
ensembl_object_type ENUM('Transcript', 'Translation', 'Gene')
NOT NULL,
- ensembl_object_id INT, # FK to gene/transcript/translation
+ ensembl_object_id INT(10) UNSIGNED, # FK to gene/transcript/translation
analysis_id INT(10) UNSIGNED NOT NULL,
PRIMARY KEY (regulatory_search_region_id),
@@ -1493,10 +1495,10 @@ CREATE TABLE regulatory_search_region (
CREATE TABLE unmapped_object (
- unmapped_object_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
+ unmapped_object_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
type ENUM('xref', 'cDNA', 'Marker') NOT NULL,
analysis_id INT(10) UNSIGNED NOT NULL,
- external_db_id INT NOT NULL,
+ external_db_id INT(10) UNSIGNED NOT NULL,
identifier VARCHAR(255) NOT NULL,
unmapped_reason_id SMALLINT(5) UNSIGNED NOT NULL,
query_score DOUBLE,
--
GitLab