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Commit ce31a6c9 authored by Tiago Grego's avatar Tiago Grego
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patch core test dbs with patch_99_100_c.sql

parent 325eab11
Branches patch_99_100_c_master
Tags
1 merge request!460Core db schema patch to support longer assembly names in the mapping_session table.
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with 42 additions and 37 deletions
modules/t/test-genome-DBs/circ/core/SQLite/table.sql
+ 3
− 3
View file @ ce31a6c9
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Wed Nov 6 10:35:32 2019
-- Created on Tue Dec 17 13:11:32 2019
--
BEGIN TRANSACTION;
......@@ -476,8 +476,8 @@ CREATE TABLE "mapping_session" (
"new_db_name" varchar(80) NOT NULL DEFAULT '',
"old_release" varchar(5) NOT NULL DEFAULT '',
"new_release" varchar(5) NOT NULL DEFAULT '',
"old_assembly" varchar(20) NOT NULL DEFAULT '',
"new_assembly" varchar(20) NOT NULL DEFAULT '',
"old_assembly" varchar(80) NOT NULL DEFAULT '',
"new_assembly" varchar(80) NOT NULL DEFAULT '',
"created" datetime
);
......
modules/t/test-genome-DBs/circ/core/meta.txt
+ 1
− 0
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......@@ -135,3 +135,4 @@
135 \N patch patch_98_99_a.sql|schema_version
136 \N patch patch_99_100_a.sql|schema_version
137 \N patch patch_99_100_b.sql|alter_externaldb_type_notnull
138 \N patch patch_99_100_c.sql|alter_mapping_session_assembly_length
modules/t/test-genome-DBs/circ/core/table.sql
+ 3
− 3
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......@@ -420,8 +420,8 @@ CREATE TABLE `mapping_session` (
`new_db_name` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
`old_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
`new_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
`old_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
`new_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
`old_assembly` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
`new_assembly` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
`created` datetime DEFAULT NULL,
PRIMARY KEY (`mapping_session_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
......@@ -490,7 +490,7 @@ 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=138 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=139 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
......
modules/t/test-genome-DBs/homo_sapiens/core/SQLite/table.sql
+ 3
− 3
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--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Wed Nov 6 10:35:37 2019
-- Created on Tue Dec 17 13:11:36 2019
--
BEGIN TRANSACTION;
......@@ -476,8 +476,8 @@ CREATE TABLE "mapping_session" (
"new_db_name" varchar(80) NOT NULL DEFAULT '',
"old_release" varchar(5) NOT NULL DEFAULT '',
"new_release" varchar(5) NOT NULL DEFAULT '',
"old_assembly" varchar(20) NOT NULL DEFAULT '',
"new_assembly" varchar(20) NOT NULL DEFAULT '',
"old_assembly" varchar(80) NOT NULL DEFAULT '',
"new_assembly" varchar(80) NOT NULL DEFAULT '',
"created" datetime
);
......
modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
+ 1
− 0
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......@@ -114,3 +114,4 @@
188 \N patch patch_98_99_a.sql|schema_version
189 \N patch patch_99_100_a.sql|schema_version
190 \N patch patch_99_100_b.sql|alter_externaldb_type_notnull
191 \N patch patch_99_100_c.sql|alter_mapping_session_assembly_length
modules/t/test-genome-DBs/homo_sapiens/core/table.sql
+ 3
− 3
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......@@ -420,8 +420,8 @@ CREATE TABLE `mapping_session` (
`new_db_name` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
`old_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
`new_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
`old_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
`new_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
`old_assembly` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
`new_assembly` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
`created` datetime DEFAULT NULL,
PRIMARY KEY (`mapping_session_id`)
) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
......@@ -490,7 +490,7 @@ 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=191 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=192 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
......
modules/t/test-genome-DBs/homo_sapiens/empty/SQLite/table.sql
+ 1
− 1
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--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Wed Nov 6 10:35:42 2019
-- Created on Tue Dec 17 13:11:39 2019
--
BEGIN TRANSACTION;
......
modules/t/test-genome-DBs/homo_sapiens/patch/SQLite/table.sql
+ 1
− 1
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--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Wed Nov 6 10:35:48 2019
-- Created on Tue Dec 17 13:11:42 2019
--
BEGIN TRANSACTION;
......
modules/t/test-genome-DBs/homo_sapiens/xref/SQLite/table.sql
+ 1
− 1
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--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Wed Nov 6 10:35:49 2019
-- Created on Tue Dec 17 13:11:43 2019
--
BEGIN TRANSACTION;
......
modules/t/test-genome-DBs/mapping/core/SQLite/table.sql
+ 3
− 3
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--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Wed Nov 6 10:35:54 2019
-- Created on Tue Dec 17 13:11:46 2019
--
BEGIN TRANSACTION;
......@@ -476,8 +476,8 @@ CREATE TABLE "mapping_session" (
"new_db_name" varchar(80) NOT NULL DEFAULT '',
"old_release" varchar(5) NOT NULL DEFAULT '',
"new_release" varchar(5) NOT NULL DEFAULT '',
"old_assembly" varchar(20) NOT NULL DEFAULT '',
"new_assembly" varchar(20) NOT NULL DEFAULT '',
"old_assembly" varchar(80) NOT NULL DEFAULT '',
"new_assembly" varchar(80) NOT NULL DEFAULT '',
"created" datetime
);
......
modules/t/test-genome-DBs/mapping/core/meta.txt
+ 1
− 0
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......@@ -75,3 +75,4 @@
168 \N patch patch_98_99_a.sql|schema_version
169 \N patch patch_99_100_a.sql|schema_version
170 \N patch patch_99_100_b.sql|alter_externaldb_type_notnull
171 \N patch patch_99_100_c.sql|alter_mapping_session_assembly_length
modules/t/test-genome-DBs/mapping/core/table.sql
+ 3
− 3
View file @ ce31a6c9
......@@ -420,8 +420,8 @@ CREATE TABLE `mapping_session` (
`new_db_name` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
`old_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
`new_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
`old_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
`new_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
`old_assembly` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
`new_assembly` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
`created` datetime DEFAULT NULL,
PRIMARY KEY (`mapping_session_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
......@@ -490,7 +490,7 @@ 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=171 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=172 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
......
modules/t/test-genome-DBs/multi/compara/SQLite/table.sql
+ 3
− 3
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--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Wed Nov 6 10:35:58 2019
-- Created on Tue Dec 17 13:11:48 2019
--
BEGIN TRANSACTION;
......@@ -384,7 +384,7 @@ CREATE TABLE "hmm_curated_annot" (
"seq_member_stable_id" varchar(40) NOT NULL,
"model_id" varchar(40),
"library_version" varchar(40) NOT NULL,
"annot_date" timestamp NOT NULL DEFAULT 'current_timestamp()',
"annot_date" timestamp NOT NULL DEFAULT current_timestamp,
"reason" mediumtext,
PRIMARY KEY ("seq_member_stable_id")
);
......@@ -442,7 +442,7 @@ CREATE TABLE "homology_member" (
CREATE TABLE "mapping_session" (
"mapping_session_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
"type" enum,
"when_mapped" timestamp NOT NULL DEFAULT 'current_timestamp()',
"when_mapped" timestamp NOT NULL DEFAULT current_timestamp,
"rel_from" integer,
"rel_to" integer,
"prefix" char(4) NOT NULL
......
modules/t/test-genome-DBs/mus_musculus/core/SQLite/table.sql
+ 3
− 3
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--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Wed Nov 6 10:36:03 2019
-- Created on Tue Dec 17 13:11:52 2019
--
BEGIN TRANSACTION;
......@@ -476,8 +476,8 @@ CREATE TABLE "mapping_session" (
"new_db_name" varchar(80) NOT NULL DEFAULT '',
"old_release" varchar(5) NOT NULL DEFAULT '',
"new_release" varchar(5) NOT NULL DEFAULT '',
"old_assembly" varchar(20) NOT NULL DEFAULT '',
"new_assembly" varchar(20) NOT NULL DEFAULT '',
"old_assembly" varchar(80) NOT NULL DEFAULT '',
"new_assembly" varchar(80) NOT NULL DEFAULT '',
"created" datetime
);
......
modules/t/test-genome-DBs/mus_musculus/core/meta.txt
+ 1
− 0
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......@@ -192,3 +192,4 @@
1704 \N patch patch_98_99_a.sql|schema_version
1705 \N patch patch_99_100_a.sql|schema_version
1706 \N patch patch_99_100_b.sql|alter_externaldb_type_notnull
1707 \N patch patch_99_100_c.sql|alter_mapping_session_assembly_length
modules/t/test-genome-DBs/mus_musculus/core/table.sql
+ 3
− 3
View file @ ce31a6c9
......@@ -420,8 +420,8 @@ CREATE TABLE `mapping_session` (
`new_db_name` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
`old_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
`new_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
`old_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
`new_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
`old_assembly` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
`new_assembly` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
`created` datetime DEFAULT NULL,
PRIMARY KEY (`mapping_session_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
......@@ -490,7 +490,7 @@ 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=1707 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=1708 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
......
modules/t/test-genome-DBs/nameless/core/SQLite/table.sql
+ 3
− 3
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--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Wed Nov 6 10:36:08 2019
-- Created on Tue Dec 17 13:11:55 2019
--
BEGIN TRANSACTION;
......@@ -465,8 +465,8 @@ CREATE TABLE "mapping_session" (
"new_db_name" varchar(80) NOT NULL DEFAULT '',
"old_release" varchar(5) NOT NULL DEFAULT '',
"new_release" varchar(5) NOT NULL DEFAULT '',
"old_assembly" varchar(20) NOT NULL DEFAULT '',
"new_assembly" varchar(20) NOT NULL DEFAULT '',
"old_assembly" varchar(80) NOT NULL DEFAULT '',
"new_assembly" varchar(80) NOT NULL DEFAULT '',
"created" datetime
);
......
modules/t/test-genome-DBs/nameless/core/meta.txt
+ 1
− 0
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......@@ -113,3 +113,4 @@
167 \N patch patch_98_99_a.sql|schema_version
168 \N patch patch_99_100_a.sql|schema_version
169 \N patch patch_99_100_b.sql|alter_externaldb_type_notnull
170 \N patch patch_99_100_c.sql|alter_mapping_session_assembly_length
modules/t/test-genome-DBs/nameless/core/table.sql
+ 3
− 3
View file @ ce31a6c9
......@@ -410,8 +410,8 @@ CREATE TABLE `mapping_session` (
`new_db_name` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
`old_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
`new_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
`old_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
`new_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
`old_assembly` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
`new_assembly` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
`created` datetime DEFAULT NULL,
PRIMARY KEY (`mapping_session_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
......@@ -480,7 +480,7 @@ 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=170 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=171 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
......
modules/t/test-genome-DBs/ontology/ontology/SQLite/table.sql
+ 1
− 1
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--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Wed Nov 6 10:36:10 2019
-- Created on Tue Dec 17 13:11:56 2019
--
BEGIN TRANSACTION;
......
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