diff --git a/modules/t/test-genome-DBs/circ/core/SQLite/table.sql b/modules/t/test-genome-DBs/circ/core/SQLite/table.sql
index 7431c89a7ec87e0e24d7a7115d3eaf1e23c314f7..d2294cc8f0ecbacbb887a7830e2f8ebd48700e79 100644
--- a/modules/t/test-genome-DBs/circ/core/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/circ/core/SQLite/table.sql
@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
--- Created on Mon Dec 16 12:44:49 2019
+-- Created on Wed Nov 6 10:35:32 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(80),
- "new_assembly" varchar(80),
+ "old_assembly" varchar(20) NOT NULL DEFAULT '',
+ "new_assembly" varchar(20) NOT NULL DEFAULT '',
"created" datetime
);
diff --git a/modules/t/test-genome-DBs/circ/core/meta.txt b/modules/t/test-genome-DBs/circ/core/meta.txt
index 975a3cc873888922d305f8cf67231f0b1c57e82e..34314266193b5e5b3be9998762cec2ddc516c8c4 100644
--- a/modules/t/test-genome-DBs/circ/core/meta.txt
+++ b/modules/t/test-genome-DBs/circ/core/meta.txt
@@ -135,4 +135,3 @@
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
diff --git a/modules/t/test-genome-DBs/circ/core/table.sql b/modules/t/test-genome-DBs/circ/core/table.sql
index ec4dc2db10364b4bcdb8552e0fc43f406ad657d7..8866da31b74bf161e881417902a3fe4ea3205ee4 100644
--- a/modules/t/test-genome-DBs/circ/core/table.sql
+++ b/modules/t/test-genome-DBs/circ/core/table.sql
@@ -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(80) COLLATE latin1_bin DEFAULT NULL,
- `new_assembly` varchar(80) COLLATE latin1_bin DEFAULT NULL,
+ `old_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `new_assembly` varchar(20) 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=139 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=138 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/SQLite/table.sql b/modules/t/test-genome-DBs/homo_sapiens/core/SQLite/table.sql
index 1ee6dcd172e0b828f1c920469eeb9a5292c2e879..310b523dd00b4cee7e0a786037f72a6732c7033c 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/SQLite/table.sql
@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
--- Created on Mon Dec 16 12:44:56 2019
+-- Created on Wed Nov 6 10:35:37 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(80),
- "new_assembly" varchar(80),
+ "old_assembly" varchar(20) NOT NULL DEFAULT '',
+ "new_assembly" varchar(20) NOT NULL DEFAULT '',
"created" datetime
);
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 9450cc157087b4acc2bd81b750b2e8252f099978..b538bbe41f8e77402329fcd15c313ef08dfaaffa 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
@@ -114,4 +114,3 @@
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
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 5718d0d93a47552ad4dbb318c58c1ecf00efbb36..60863488cb37a5d686d506684c5bb29f7f5ad6ff 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
@@ -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(80) COLLATE latin1_bin DEFAULT NULL,
- `new_assembly` varchar(80) COLLATE latin1_bin DEFAULT NULL,
+ `old_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `new_assembly` varchar(20) 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=192 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=191 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
diff --git a/modules/t/test-genome-DBs/homo_sapiens/empty/SQLite/table.sql b/modules/t/test-genome-DBs/homo_sapiens/empty/SQLite/table.sql
index 513f3c734a7f276ef305e5760c7cae6b5dd45e1c..16497890a208487ee5472a7c25dd13321660e96e 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/empty/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/empty/SQLite/table.sql
@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
--- Created on Mon Dec 16 12:45:03 2019
+-- Created on Wed Nov 6 10:35:42 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(80),
- "new_assembly" varchar(80),
+ "old_assembly" varchar(20) NOT NULL DEFAULT '',
+ "new_assembly" varchar(20) NOT NULL DEFAULT '',
"created" datetime
);
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 131cafea9f0251a8c0a04a571f0d584221e56dbb..bae2072de4f0626e292d46c4537f7dde2c4e28c2 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
@@ -114,4 +114,3 @@
163 \N patch patch_98_99_a.sql|schema_version
164 \N patch patch_99_100_a.sql|schema_version
165 \N patch patch_99_100_b.sql|alter_externaldb_type_notnull
-166 \N patch patch_99_100_c.sql|alter_mapping_session_assembly_length
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 ba588f7e3df9637e492b7dfe1e851ddc1a66e01c..06e83c39a10d9d3000c9b3e7662fa074d8d2b359 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
@@ -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(80) COLLATE latin1_bin DEFAULT NULL,
- `new_assembly` varchar(80) COLLATE latin1_bin DEFAULT NULL,
+ `old_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `new_assembly` varchar(20) 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=167 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=166 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
diff --git a/modules/t/test-genome-DBs/homo_sapiens/patch/SQLite/table.sql b/modules/t/test-genome-DBs/homo_sapiens/patch/SQLite/table.sql
index 1cd34ad01421c2e05c4fd43cb9a7f2486e3ab84d..46593d23ec7eb581aad694d2a6c77725fa602eeb 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/patch/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/patch/SQLite/table.sql
@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
--- Created on Mon Dec 16 12:45:11 2019
+-- Created on Wed Nov 6 10:35:48 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(80),
- "new_assembly" varchar(80),
+ "old_assembly" varchar(20) NOT NULL DEFAULT '',
+ "new_assembly" varchar(20) NOT NULL DEFAULT '',
"created" datetime
);
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 c2b57d5728324add486213430146e8fc84364177..185b545bc758dbc432bd96b1e6a95ba18ce125cc 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
@@ -119,4 +119,3 @@
2126 \N patch patch_98_99_a.sql|schema_version
2127 \N patch patch_99_100_a.sql|schema_version
2128 \N patch patch_99_100_b.sql|alter_externaldb_type_notnull
-2129 \N patch patch_99_100_c.sql|alter_mapping_session_assembly_length
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 cd11c25c9eacedfba98b1af3fd6b84a8caa8331d..5ae6e282c7f73c2fb05c700f0737337da380ff8d 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
@@ -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(80) COLLATE latin1_bin DEFAULT NULL,
- `new_assembly` varchar(80) COLLATE latin1_bin DEFAULT NULL,
+ `old_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `new_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
`created` datetime DEFAULT NULL,
PRIMARY KEY (`mapping_session_id`)
) ENGINE=MyISAM AUTO_INCREMENT=394 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=2130 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=2129 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt
index 70f7130609f05af5a16466062119685bac28b119..3e03d2bcfde182c75fdb1cc13e43960956348ecc 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt
@@ -49,5 +49,3 @@
49 \N patch patch_98_99_d.sql|add key data_source_attrib
50 \N patch patch_98_99_e.sql|Fix attrib ids in table variation_citation
51 \N patch patch_99_100_a.sql|schema version
-52 \N patch patch_99_100_b.sql|add frequency to structural variation
-53 \N patch patch_99_100_c.sql|add class_attrib_id column to phenotype
diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/phenotype.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/phenotype.txt
index 9590f4a85866ac34aef2ec3726679d05c7cd2cdd..5d21f089e758f71ee359362beb8b7b40f4b50496 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/variation/phenotype.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/variation/phenotype.txt
@@ -1,2 +1,2 @@
-1 \N phenotype \N \N
-2 \N phenotype2 \N \N
+1 \N phenotype \N
+2 \N phenotype2 \N
diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/structural_variation_feature.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/structural_variation_feature.txt
index f345a606bd4937a1c90d14bea5973812caa98839..02ddd82bd3490ba167acd737c520d4093abaf643 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/variation/structural_variation_feature.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/variation/structural_variation_feature.txt
@@ -1,3 +1,3 @@
-1 469283 \N 30253000 \N \N 30254000 \N 1 1 nsv12345 1 1 208 \N 0 0 \N \N 1 \N \N
-2 469283 \N 30255000 \N \N 30256000 \N 1 2 nsv67890 1 1 208 \N 0 1 \N \N 1 \N \N
-3 469283 \N 30257000 \N \N 30258000 \N 1 3 nsv09876 1 1 114 \N 0 0 \N \N \N \N
+1 469283 \N 30253000 \N \N 30254000 \N 1 1 nsv12345 1 1 208 \N 0 0 \N \N 1
+2 469283 \N 30255000 \N \N 30256000 \N 1 2 nsv67890 1 1 208 \N 0 1 \N \N 1
+3 469283 \N 30257000 \N \N 30258000 \N 1 3 nsv09876 1 1 114 \N 0 0 \N \N
diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/table.sql b/modules/t/test-genome-DBs/homo_sapiens/variation/table.sql
index 68d6a37739db569da19a5b79e5d953c818449cad..84e276006bc42b5875f6201d06b4c4fc105878fa 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/variation/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/variation/table.sql
@@ -186,7 +186,7 @@ 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=54 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=52 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL,
@@ -220,7 +220,6 @@ CREATE TABLE `phenotype` (
`stable_id` varchar(255) DEFAULT NULL,
`name` varchar(50) DEFAULT NULL,
`description` varchar(255) DEFAULT NULL,
- `class_attrib_id` int(11) DEFAULT NULL,
PRIMARY KEY (`phenotype_id`),
UNIQUE KEY `desc_idx` (`description`),
KEY `name_idx` (`name`),
@@ -474,8 +473,6 @@ CREATE TABLE `structural_variation_feature` (
`breakpoint_order` tinyint(4) DEFAULT NULL,
`length` int(10) DEFAULT NULL,
`variation_set_id` set('1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','23','24','25','26','27','28','29','30','31','32','33','34','35','36','37','38','39','40','41','42','43','44','45','46','47','48','49','50','51','52','53','54','55','56','57','58','59','60','61','62','63','64') NOT NULL DEFAULT '',
- `allele_freq` float DEFAULT NULL,
- `allele_count` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`structural_variation_feature_id`),
KEY `pos_idx` (`seq_region_id`,`seq_region_start`,`seq_region_end`),
KEY `structural_variation_idx` (`structural_variation_id`),
diff --git a/modules/t/test-genome-DBs/homo_sapiens/xref/SQLite/table.sql b/modules/t/test-genome-DBs/homo_sapiens/xref/SQLite/table.sql
index 5f936abeb5b9843380a3d1c2357a4001cf4532a2..6fd0b874a0dd76b4bb3ba13314f3a5e01f66d254 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/xref/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/xref/SQLite/table.sql
@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
--- Created on Mon Dec 16 12:45:12 2019
+-- Created on Wed Nov 6 10:35:49 2019
--
BEGIN TRANSACTION;
diff --git a/modules/t/test-genome-DBs/mapping/core/SQLite/table.sql b/modules/t/test-genome-DBs/mapping/core/SQLite/table.sql
index f478245225ca7b07ca0203c680cdd9f61a3372b7..beaf999fd3ba7866463ea3f5556f4929b434c459 100644
--- a/modules/t/test-genome-DBs/mapping/core/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/mapping/core/SQLite/table.sql
@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
--- Created on Mon Dec 16 12:45:19 2019
+-- Created on Wed Nov 6 10:35:54 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(80),
- "new_assembly" varchar(80),
+ "old_assembly" varchar(20) NOT NULL DEFAULT '',
+ "new_assembly" varchar(20) NOT NULL DEFAULT '',
"created" datetime
);
diff --git a/modules/t/test-genome-DBs/mapping/core/meta.txt b/modules/t/test-genome-DBs/mapping/core/meta.txt
index 6cc475bc7df35a3381c67271a3823759fb7ca61d..ee84ac3b6b8fafb2801e0a305f22fd3f3445533d 100644
--- a/modules/t/test-genome-DBs/mapping/core/meta.txt
+++ b/modules/t/test-genome-DBs/mapping/core/meta.txt
@@ -75,4 +75,3 @@
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
diff --git a/modules/t/test-genome-DBs/mapping/core/table.sql b/modules/t/test-genome-DBs/mapping/core/table.sql
index fe91bc2ebbd293dea06b3e9341c7b05abe5afb29..ccf60eb44a3d48f2b6aff5b91d5362e07ea3a149 100644
--- a/modules/t/test-genome-DBs/mapping/core/table.sql
+++ b/modules/t/test-genome-DBs/mapping/core/table.sql
@@ -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(80) COLLATE latin1_bin DEFAULT NULL,
- `new_assembly` varchar(80) COLLATE latin1_bin DEFAULT NULL,
+ `old_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `new_assembly` varchar(20) 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=172 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 '',
diff --git a/modules/t/test-genome-DBs/multi/compara/SQLite/table.sql b/modules/t/test-genome-DBs/multi/compara/SQLite/table.sql
index a94b170679144a6caaf3a9dc4e945dad8f1ce565..b9ab265bdfe0b90b65837da1dad84920fea1379d 100644
--- a/modules/t/test-genome-DBs/multi/compara/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/multi/compara/SQLite/table.sql
@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
--- Created on Mon Dec 16 12:45:24 2019
+-- Created on Wed Nov 6 10:35:58 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")
);
@@ -426,7 +426,7 @@ CREATE TABLE "homology" (
-- Table: "homology_member"
--
CREATE TABLE "homology_member" (
- "homology_id" bigint NOT NULL,
+ "homology_id" integer NOT NULL,
"gene_member_id" integer NOT NULL,
"seq_member_id" integer,
"cigar_line" mediumtext,
@@ -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
diff --git a/modules/t/test-genome-DBs/multi/compara/meta.txt b/modules/t/test-genome-DBs/multi/compara/meta.txt
index 2cf2d385be8033ff3be88683aa0d8ef0d02e1b64..711f2ba8a661cf96ea3608ba4d0e030c8bdf239d 100644
--- a/modules/t/test-genome-DBs/multi/compara/meta.txt
+++ b/modules/t/test-genome-DBs/multi/compara/meta.txt
@@ -1,4 +1,4 @@
-72 \N schema_version 101
+69 \N schema_version 100
2 \N schema_type compara
3 \N patch patch_84_85_a.sql|schema_version
4 \N patch patch_84_85_b.sql|gene_tree_root_attr
@@ -55,5 +55,3 @@
67 \N patch patch_97_98_b.sql|division_name
68 \N patch patch_98_99_a.sql|schema_version
70 \N patch patch_99_100_a.sql|schema_version
-71 \N patch patch_99_100_b.sql|homology_id_64-bits
-73 \N patch patch_100_101_a.sql|schema_version
diff --git a/modules/t/test-genome-DBs/multi/compara/table.sql b/modules/t/test-genome-DBs/multi/compara/table.sql
index 3c454b69357c62e76f6f8bfc24db573f1bb5a4a0..7a15ccb8b2824b48a91cb987c346b45cdc52039c 100644
--- a/modules/t/test-genome-DBs/multi/compara/table.sql
+++ b/modules/t/test-genome-DBs/multi/compara/table.sql
@@ -24,8 +24,8 @@ CREATE TABLE `conservation_score` (
`genomic_align_block_id` bigint(20) unsigned NOT NULL,
`window_size` smallint(5) unsigned NOT NULL,
`position` int(10) unsigned NOT NULL,
- `expected_score` blob,
- `diff_score` blob,
+ `expected_score` blob DEFAULT NULL,
+ `diff_score` blob DEFAULT NULL,
KEY `genomic_align_block_id` (`genomic_align_block_id`,`window_size`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=15000000 AVG_ROW_LENGTH=841;
@@ -36,8 +36,8 @@ CREATE TABLE `constrained_element` (
`dnafrag_end` int(12) unsigned NOT NULL,
`dnafrag_strand` int(2) NOT NULL,
`method_link_species_set_id` int(10) unsigned NOT NULL,
- `p_value` double NOT NULL DEFAULT '0',
- `score` double NOT NULL DEFAULT '0',
+ `p_value` double NOT NULL DEFAULT 0,
+ `score` double NOT NULL DEFAULT 0,
KEY `dnafrag_id` (`dnafrag_id`),
KEY `constrained_element_id_idx` (`constrained_element_id`),
KEY `mlssid_dfId_dfStart_dfEnd_idx` (`method_link_species_set_id`,`dnafrag_id`,`dnafrag_start`,`dnafrag_end`)
@@ -45,23 +45,23 @@ CREATE TABLE `constrained_element` (
CREATE TABLE `dnafrag` (
`dnafrag_id` bigint(20) unsigned NOT NULL AUTO_INCREMENT,
- `length` int(11) NOT NULL DEFAULT '0',
+ `length` int(11) NOT NULL DEFAULT 0,
`name` varchar(255) NOT NULL DEFAULT '',
`genome_db_id` int(10) unsigned NOT NULL,
`coord_system_name` varchar(40) NOT NULL DEFAULT '',
`cellular_component` enum('NUC','MT','PT') NOT NULL DEFAULT 'NUC',
- `is_reference` tinyint(1) NOT NULL DEFAULT '1',
- `codon_table_id` tinyint(2) unsigned NOT NULL DEFAULT '1',
+ `is_reference` tinyint(1) NOT NULL DEFAULT 1,
+ `codon_table_id` tinyint(2) unsigned NOT NULL DEFAULT 1,
PRIMARY KEY (`dnafrag_id`),
UNIQUE KEY `name` (`genome_db_id`,`name`)
) ENGINE=MyISAM AUTO_INCREMENT=14026981 DEFAULT CHARSET=latin1;
CREATE TABLE `dnafrag_region` (
- `synteny_region_id` int(10) unsigned NOT NULL DEFAULT '0',
- `dnafrag_id` bigint(20) unsigned NOT NULL DEFAULT '0',
- `dnafrag_start` int(10) unsigned NOT NULL DEFAULT '0',
- `dnafrag_end` int(10) unsigned NOT NULL DEFAULT '0',
- `dnafrag_strand` tinyint(4) NOT NULL DEFAULT '0',
+ `synteny_region_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `dnafrag_id` bigint(20) unsigned NOT NULL DEFAULT 0,
+ `dnafrag_start` int(10) unsigned NOT NULL DEFAULT 0,
+ `dnafrag_end` int(10) unsigned NOT NULL DEFAULT 0,
+ `dnafrag_strand` tinyint(4) NOT NULL DEFAULT 0,
KEY `synteny` (`synteny_region_id`,`dnafrag_id`),
KEY `synteny_reversed` (`dnafrag_id`,`synteny_region_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
@@ -72,7 +72,7 @@ CREATE TABLE `exon_boundaries` (
`dnafrag_start` int(11) NOT NULL,
`dnafrag_end` int(11) NOT NULL,
`sequence_length` int(10) unsigned NOT NULL,
- `left_over` tinyint(1) NOT NULL DEFAULT '0',
+ `left_over` tinyint(1) NOT NULL DEFAULT 0,
KEY `seq_member_id` (`seq_member_id`),
KEY `gene_member_id` (`gene_member_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
@@ -87,7 +87,7 @@ CREATE TABLE `external_db` (
`type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') DEFAULT NULL,
`secondary_db_name` varchar(255) DEFAULT NULL,
`secondary_db_table` varchar(255) DEFAULT NULL,
- `description` text,
+ `description` text DEFAULT NULL,
PRIMARY KEY (`external_db_id`),
UNIQUE KEY `db_name_db_release_idx` (`db_name`,`db_release`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
@@ -97,7 +97,7 @@ CREATE TABLE `family` (
`stable_id` varchar(40) NOT NULL,
`version` int(10) unsigned NOT NULL,
`method_link_species_set_id` int(10) unsigned NOT NULL,
- `description` text,
+ `description` text DEFAULT NULL,
`description_score` double DEFAULT NULL,
PRIMARY KEY (`family_id`),
UNIQUE KEY `stable_id` (`stable_id`),
@@ -108,7 +108,7 @@ CREATE TABLE `family` (
CREATE TABLE `family_member` (
`family_id` int(10) unsigned NOT NULL,
`seq_member_id` int(10) unsigned NOT NULL,
- `cigar_line` mediumtext,
+ `cigar_line` mediumtext DEFAULT NULL,
PRIMARY KEY (`family_id`,`seq_member_id`),
KEY `seq_member_id` (`seq_member_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
@@ -117,14 +117,14 @@ CREATE TABLE `gene_align` (
`gene_align_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`seq_type` varchar(40) DEFAULT NULL,
`aln_method` varchar(40) NOT NULL DEFAULT '',
- `aln_length` int(10) NOT NULL DEFAULT '0',
+ `aln_length` int(10) NOT NULL DEFAULT 0,
PRIMARY KEY (`gene_align_id`)
) ENGINE=MyISAM AUTO_INCREMENT=100000189 DEFAULT CHARSET=latin1;
CREATE TABLE `gene_align_member` (
`gene_align_id` int(10) unsigned NOT NULL,
`seq_member_id` int(10) unsigned NOT NULL,
- `cigar_line` mediumtext,
+ `cigar_line` mediumtext DEFAULT NULL,
PRIMARY KEY (`gene_align_id`,`seq_member_id`),
KEY `seq_member_id` (`seq_member_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
@@ -132,13 +132,13 @@ CREATE TABLE `gene_align_member` (
CREATE TABLE `gene_member` (
`gene_member_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`stable_id` varchar(128) NOT NULL,
- `version` int(10) DEFAULT '0',
+ `version` int(10) DEFAULT 0,
`source_name` enum('ENSEMBLGENE','EXTERNALGENE') NOT NULL,
`taxon_id` int(10) unsigned NOT NULL,
`genome_db_id` int(10) unsigned DEFAULT NULL,
`biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group','current_notdumped','notcurrent') NOT NULL DEFAULT 'coding',
`canonical_member_id` int(10) unsigned DEFAULT NULL,
- `description` text,
+ `description` text DEFAULT NULL,
`dnafrag_id` bigint(20) unsigned DEFAULT NULL,
`dnafrag_start` int(10) DEFAULT NULL,
`dnafrag_end` int(10) DEFAULT NULL,
@@ -159,12 +159,12 @@ CREATE TABLE `gene_member` (
CREATE TABLE `gene_member_hom_stats` (
`gene_member_id` int(10) unsigned NOT NULL,
`collection` varchar(40) NOT NULL,
- `families` int(10) unsigned NOT NULL DEFAULT '0',
- `gene_trees` tinyint(1) unsigned NOT NULL DEFAULT '0',
- `gene_gain_loss_trees` tinyint(1) unsigned NOT NULL DEFAULT '0',
- `orthologues` int(10) unsigned NOT NULL DEFAULT '0',
- `paralogues` int(10) unsigned NOT NULL DEFAULT '0',
- `homoeologues` int(10) unsigned NOT NULL DEFAULT '0',
+ `families` int(10) unsigned NOT NULL DEFAULT 0,
+ `gene_trees` tinyint(1) unsigned NOT NULL DEFAULT 0,
+ `gene_gain_loss_trees` tinyint(1) unsigned NOT NULL DEFAULT 0,
+ `orthologues` int(10) unsigned NOT NULL DEFAULT 0,
+ `paralogues` int(10) unsigned NOT NULL DEFAULT 0,
+ `homoeologues` int(10) unsigned NOT NULL DEFAULT 0,
PRIMARY KEY (`gene_member_id`,`collection`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
@@ -184,9 +184,9 @@ CREATE TABLE `gene_tree_node` (
`node_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`parent_id` int(10) unsigned DEFAULT NULL,
`root_id` int(10) unsigned DEFAULT NULL,
- `left_index` int(10) NOT NULL DEFAULT '0',
- `right_index` int(10) NOT NULL DEFAULT '0',
- `distance_to_parent` double NOT NULL DEFAULT '1',
+ `left_index` int(10) NOT NULL DEFAULT 0,
+ `right_index` int(10) NOT NULL DEFAULT 0,
+ `distance_to_parent` double NOT NULL DEFAULT 1,
`seq_member_id` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`node_id`),
KEY `parent_id` (`parent_id`),
@@ -281,8 +281,8 @@ CREATE TABLE `genome_db` (
`name` varchar(128) NOT NULL DEFAULT '',
`assembly` varchar(100) NOT NULL DEFAULT '',
`genebuild` varchar(100) NOT NULL DEFAULT '',
- `has_karyotype` tinyint(1) NOT NULL DEFAULT '0',
- `is_good_for_alignment` tinyint(1) NOT NULL DEFAULT '0',
+ `has_karyotype` tinyint(1) NOT NULL DEFAULT 0,
+ `is_good_for_alignment` tinyint(1) NOT NULL DEFAULT 0,
`genome_component` varchar(5) DEFAULT NULL,
`strain_name` varchar(40) DEFAULT NULL,
`display_name` varchar(255) DEFAULT NULL,
@@ -297,13 +297,13 @@ CREATE TABLE `genome_db` (
CREATE TABLE `genomic_align` (
`genomic_align_id` bigint(20) unsigned NOT NULL AUTO_INCREMENT,
`genomic_align_block_id` bigint(20) unsigned NOT NULL,
- `method_link_species_set_id` int(10) unsigned NOT NULL DEFAULT '0',
- `dnafrag_id` bigint(20) unsigned NOT NULL DEFAULT '0',
- `dnafrag_start` int(10) NOT NULL DEFAULT '0',
- `dnafrag_end` int(10) NOT NULL DEFAULT '0',
- `dnafrag_strand` tinyint(4) NOT NULL DEFAULT '0',
+ `method_link_species_set_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `dnafrag_id` bigint(20) unsigned NOT NULL DEFAULT 0,
+ `dnafrag_start` int(10) NOT NULL DEFAULT 0,
+ `dnafrag_end` int(10) NOT NULL DEFAULT 0,
+ `dnafrag_strand` tinyint(4) NOT NULL DEFAULT 0,
`cigar_line` mediumtext NOT NULL,
- `visible` tinyint(2) unsigned NOT NULL DEFAULT '1',
+ `visible` tinyint(2) unsigned NOT NULL DEFAULT 1,
`node_id` bigint(20) unsigned DEFAULT NULL,
PRIMARY KEY (`genomic_align_id`),
KEY `genomic_align_block_id` (`genomic_align_block_id`),
@@ -314,12 +314,12 @@ CREATE TABLE `genomic_align` (
CREATE TABLE `genomic_align_block` (
`genomic_align_block_id` bigint(20) unsigned NOT NULL AUTO_INCREMENT,
- `method_link_species_set_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `method_link_species_set_id` int(10) unsigned NOT NULL DEFAULT 0,
`score` double DEFAULT NULL,
`perc_id` tinyint(3) unsigned DEFAULT NULL,
`length` int(10) NOT NULL,
`group_id` bigint(20) unsigned DEFAULT NULL,
- `level_id` tinyint(2) unsigned NOT NULL DEFAULT '0',
+ `level_id` tinyint(2) unsigned NOT NULL DEFAULT 0,
PRIMARY KEY (`genomic_align_block_id`),
KEY `method_link_species_set_id` (`method_link_species_set_id`)
) ENGINE=MyISAM AUTO_INCREMENT=6770001148336 DEFAULT CHARSET=latin1;
@@ -327,12 +327,12 @@ CREATE TABLE `genomic_align_block` (
CREATE TABLE `genomic_align_tree` (
`node_id` bigint(20) unsigned NOT NULL AUTO_INCREMENT,
`parent_id` bigint(20) unsigned DEFAULT NULL,
- `root_id` bigint(20) unsigned NOT NULL DEFAULT '0',
- `left_index` int(10) NOT NULL DEFAULT '0',
- `right_index` int(10) NOT NULL DEFAULT '0',
+ `root_id` bigint(20) unsigned NOT NULL DEFAULT 0,
+ `left_index` int(10) NOT NULL DEFAULT 0,
+ `right_index` int(10) NOT NULL DEFAULT 0,
`left_node_id` bigint(10) DEFAULT NULL,
`right_node_id` bigint(10) DEFAULT NULL,
- `distance_to_parent` double NOT NULL DEFAULT '1',
+ `distance_to_parent` double NOT NULL DEFAULT 1,
PRIMARY KEY (`node_id`),
KEY `parent_id` (`parent_id`),
KEY `left_index` (`root_id`,`left_index`)
@@ -350,8 +350,8 @@ CREATE TABLE `hmm_curated_annot` (
`seq_member_stable_id` varchar(40) NOT NULL,
`model_id` varchar(40) DEFAULT NULL,
`library_version` varchar(40) NOT NULL,
- `annot_date` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP,
- `reason` mediumtext,
+ `annot_date` timestamp NOT NULL DEFAULT current_timestamp(),
+ `reason` mediumtext DEFAULT NULL,
PRIMARY KEY (`seq_member_stable_id`),
KEY `model_id` (`model_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
@@ -360,16 +360,16 @@ CREATE TABLE `hmm_profile` (
`model_id` varchar(40) NOT NULL,
`name` varchar(40) DEFAULT NULL,
`type` varchar(40) NOT NULL,
- `compressed_profile` mediumblob,
- `consensus` mediumtext,
+ `compressed_profile` mediumblob DEFAULT NULL,
+ `consensus` mediumtext DEFAULT NULL,
PRIMARY KEY (`model_id`,`type`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `homology` (
- `homology_id` bigint(20) unsigned NOT NULL AUTO_INCREMENT,
+ `homology_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`method_link_species_set_id` int(10) unsigned NOT NULL,
`description` enum('ortholog_one2one','ortholog_one2many','ortholog_many2many','within_species_paralog','other_paralog','gene_split','between_species_paralog','alt_allele','homoeolog_one2one','homoeolog_one2many','homoeolog_many2many') NOT NULL,
- `is_tree_compliant` tinyint(1) NOT NULL DEFAULT '0',
+ `is_tree_compliant` tinyint(1) NOT NULL DEFAULT 0,
`dn` float(10,5) DEFAULT NULL,
`ds` float(10,5) DEFAULT NULL,
`n` float(10,1) DEFAULT NULL,
@@ -389,13 +389,13 @@ CREATE TABLE `homology` (
) ENGINE=MyISAM AUTO_INCREMENT=100990070 DEFAULT CHARSET=latin1;
CREATE TABLE `homology_member` (
- `homology_id` bigint(20) unsigned NOT NULL,
+ `homology_id` int(10) unsigned NOT NULL,
`gene_member_id` int(10) unsigned NOT NULL,
`seq_member_id` int(10) unsigned DEFAULT NULL,
- `cigar_line` mediumtext,
- `perc_cov` float unsigned DEFAULT '0',
- `perc_id` float unsigned DEFAULT '0',
- `perc_pos` float unsigned DEFAULT '0',
+ `cigar_line` mediumtext DEFAULT NULL,
+ `perc_cov` float unsigned DEFAULT 0,
+ `perc_id` float unsigned DEFAULT 0,
+ `perc_pos` float unsigned DEFAULT 0,
PRIMARY KEY (`homology_id`,`gene_member_id`),
KEY `gene_member_id` (`gene_member_id`),
KEY `seq_member_id` (`seq_member_id`)
@@ -404,7 +404,7 @@ CREATE TABLE `homology_member` (
CREATE TABLE `mapping_session` (
`mapping_session_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`type` enum('family','tree','hmm') DEFAULT NULL,
- `when_mapped` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP,
+ `when_mapped` timestamp NOT NULL DEFAULT current_timestamp(),
`rel_from` int(10) unsigned DEFAULT NULL,
`rel_to` int(10) unsigned DEFAULT NULL,
`prefix` char(4) NOT NULL,
@@ -422,13 +422,13 @@ CREATE TABLE `member_xref` (
CREATE TABLE `meta` (
`meta_id` int(11) NOT NULL AUTO_INCREMENT,
- `species_id` int(10) unsigned DEFAULT '1',
+ `species_id` int(10) unsigned DEFAULT 1,
`meta_key` varchar(40) NOT NULL,
`meta_value` text NOT NULL,
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`(255)),
KEY `species_value_idx` (`species_id`,`meta_value`(255))
-) ENGINE=MyISAM AUTO_INCREMENT=74 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=71 DEFAULT CHARSET=latin1;
CREATE TABLE `method_link` (
`method_link_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -490,10 +490,10 @@ CREATE TABLE `ncbi_taxa_node` (
`taxon_id` int(10) unsigned NOT NULL,
`parent_id` int(10) unsigned NOT NULL,
`rank` char(32) NOT NULL DEFAULT '',
- `genbank_hidden_flag` tinyint(1) NOT NULL DEFAULT '0',
- `left_index` int(10) NOT NULL DEFAULT '0',
- `right_index` int(10) NOT NULL DEFAULT '0',
- `root_id` int(10) NOT NULL DEFAULT '1',
+ `genbank_hidden_flag` tinyint(1) NOT NULL DEFAULT 0,
+ `left_index` int(10) NOT NULL DEFAULT 0,
+ `right_index` int(10) NOT NULL DEFAULT 0,
+ `root_id` int(10) NOT NULL DEFAULT 1,
PRIMARY KEY (`taxon_id`),
KEY `parent_id` (`parent_id`),
KEY `rank` (`rank`),
@@ -515,11 +515,11 @@ CREATE TABLE `peptide_align_feature` (
`hmember_id` int(10) unsigned NOT NULL,
`qgenome_db_id` int(10) unsigned DEFAULT NULL,
`hgenome_db_id` int(10) unsigned DEFAULT NULL,
- `qstart` int(10) NOT NULL DEFAULT '0',
- `qend` int(10) NOT NULL DEFAULT '0',
- `hstart` int(11) NOT NULL DEFAULT '0',
- `hend` int(11) NOT NULL DEFAULT '0',
- `score` double(16,4) NOT NULL DEFAULT '0.0000',
+ `qstart` int(10) NOT NULL DEFAULT 0,
+ `qend` int(10) NOT NULL DEFAULT 0,
+ `hstart` int(11) NOT NULL DEFAULT 0,
+ `hend` int(11) NOT NULL DEFAULT 0,
+ `score` double(16,4) NOT NULL DEFAULT 0.0000,
`evalue` double NOT NULL,
`align_length` int(10) NOT NULL,
`identical_matches` int(10) NOT NULL,
@@ -527,22 +527,22 @@ CREATE TABLE `peptide_align_feature` (
`positive_matches` int(10) NOT NULL,
`perc_pos` int(10) NOT NULL,
`hit_rank` int(10) NOT NULL,
- `cigar_line` mediumtext,
+ `cigar_line` mediumtext DEFAULT NULL,
PRIMARY KEY (`peptide_align_feature_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=133;
CREATE TABLE `seq_member` (
`seq_member_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`stable_id` varchar(128) NOT NULL,
- `version` int(10) DEFAULT '0',
+ `version` int(10) DEFAULT 0,
`source_name` enum('ENSEMBLPEP','ENSEMBLTRANS','Uniprot/SPTREMBL','Uniprot/SWISSPROT','EXTERNALPEP','EXTERNALTRANS','EXTERNALCDS') NOT NULL,
`taxon_id` int(10) unsigned NOT NULL,
`genome_db_id` int(10) unsigned DEFAULT NULL,
`sequence_id` int(10) unsigned DEFAULT NULL,
`gene_member_id` int(10) unsigned DEFAULT NULL,
- `has_transcript_edits` tinyint(1) NOT NULL DEFAULT '0',
- `has_translation_edits` tinyint(1) NOT NULL DEFAULT '0',
- `description` text,
+ `has_transcript_edits` tinyint(1) NOT NULL DEFAULT 0,
+ `has_translation_edits` tinyint(1) NOT NULL DEFAULT 0,
+ `description` text DEFAULT NULL,
`dnafrag_id` bigint(20) unsigned DEFAULT NULL,
`dnafrag_start` int(10) DEFAULT NULL,
`dnafrag_end` int(10) DEFAULT NULL,
@@ -612,9 +612,9 @@ CREATE TABLE `species_tree_node` (
`node_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`parent_id` int(10) unsigned DEFAULT NULL,
`root_id` int(10) unsigned DEFAULT NULL,
- `left_index` int(10) NOT NULL DEFAULT '0',
- `right_index` int(10) NOT NULL DEFAULT '0',
- `distance_to_parent` double DEFAULT '1',
+ `left_index` int(10) NOT NULL DEFAULT 0,
+ `right_index` int(10) NOT NULL DEFAULT 0,
+ `distance_to_parent` double DEFAULT 1,
`taxon_id` int(10) unsigned DEFAULT NULL,
`genome_db_id` int(10) unsigned DEFAULT NULL,
`node_name` varchar(255) DEFAULT NULL,
diff --git a/modules/t/test-genome-DBs/mus_musculus/core/SQLite/table.sql b/modules/t/test-genome-DBs/mus_musculus/core/SQLite/table.sql
index 8b21331963b8858212bbf1e26f9b78653868b55e..618c484df9c4e70eb1ea6c5cea7a89ad5de2e290 100644
--- a/modules/t/test-genome-DBs/mus_musculus/core/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/mus_musculus/core/SQLite/table.sql
@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
--- Created on Mon Dec 16 12:45:31 2019
+-- Created on Wed Nov 6 10:36:03 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(80),
- "new_assembly" varchar(80),
+ "old_assembly" varchar(20) NOT NULL DEFAULT '',
+ "new_assembly" varchar(20) NOT NULL DEFAULT '',
"created" datetime
);
diff --git a/modules/t/test-genome-DBs/mus_musculus/core/meta.txt b/modules/t/test-genome-DBs/mus_musculus/core/meta.txt
index 95575b6a50e67c64b1ca12ded0bca9c3766775ec..64df46e580a146dfcd0fcc49f1607deed5de81a1 100644
--- a/modules/t/test-genome-DBs/mus_musculus/core/meta.txt
+++ b/modules/t/test-genome-DBs/mus_musculus/core/meta.txt
@@ -192,4 +192,3 @@
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
diff --git a/modules/t/test-genome-DBs/mus_musculus/core/table.sql b/modules/t/test-genome-DBs/mus_musculus/core/table.sql
index 1ed63798da3f1ef937b04a1f68fc27b77c822839..d4c3867375d62ba48453d55a13353ce73ed956de 100644
--- a/modules/t/test-genome-DBs/mus_musculus/core/table.sql
+++ b/modules/t/test-genome-DBs/mus_musculus/core/table.sql
@@ -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(80) COLLATE latin1_bin DEFAULT NULL,
- `new_assembly` varchar(80) COLLATE latin1_bin DEFAULT NULL,
+ `old_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `new_assembly` varchar(20) 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=1708 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=1707 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
diff --git a/modules/t/test-genome-DBs/mus_musculus/variation/meta.txt b/modules/t/test-genome-DBs/mus_musculus/variation/meta.txt
index 8c83a75f86ea1c84912fd7f26f3a6e091c4c3f6e..186af1589382f06eb049ce6937c849cbb4d3face 100644
--- a/modules/t/test-genome-DBs/mus_musculus/variation/meta.txt
+++ b/modules/t/test-genome-DBs/mus_musculus/variation/meta.txt
@@ -76,5 +76,3 @@
82 \N patch patch_98_99_d.sql|add key data_source_attrib
83 \N patch patch_98_99_e.sql|Fix attrib ids in table variation_citation
84 \N patch patch_99_100_a.sql|schema version
-85 \N patch patch_99_100_b.sql|add frequency to structural variation
-86 \N patch patch_99_100_c.sql|add class_attrib_id column to phenotype
diff --git a/modules/t/test-genome-DBs/mus_musculus/variation/table.sql b/modules/t/test-genome-DBs/mus_musculus/variation/table.sql
index 694e6e446bf4d0865818f27c65b1b5d29ff90209..cb7051359fbeeb697b18c7a0d55f9221d1ce18f4 100644
--- a/modules/t/test-genome-DBs/mus_musculus/variation/table.sql
+++ b/modules/t/test-genome-DBs/mus_musculus/variation/table.sql
@@ -186,7 +186,7 @@ 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=87 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=85 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL,
@@ -220,7 +220,6 @@ CREATE TABLE `phenotype` (
`stable_id` varchar(255) DEFAULT NULL,
`name` varchar(50) DEFAULT NULL,
`description` varchar(255) DEFAULT NULL,
- `class_attrib_id` int(11) DEFAULT NULL,
PRIMARY KEY (`phenotype_id`),
UNIQUE KEY `desc_idx` (`description`),
KEY `name_idx` (`name`),
@@ -474,8 +473,6 @@ CREATE TABLE `structural_variation_feature` (
`somatic` tinyint(1) NOT NULL DEFAULT '0',
`breakpoint_order` tinyint(4) DEFAULT NULL,
`length` int(10) DEFAULT NULL,
- `allele_freq` float DEFAULT NULL,
- `allele_count` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`structural_variation_feature_id`),
KEY `pos_idx` (`seq_region_id`,`seq_region_start`,`seq_region_end`),
KEY `structural_variation_idx` (`structural_variation_id`),
diff --git a/modules/t/test-genome-DBs/nameless/core/SQLite/table.sql b/modules/t/test-genome-DBs/nameless/core/SQLite/table.sql
index b4f32a222b74c46fd9943eebe1df0167b9147569..671abdbb2ee572d99691daa7f6d4a6d669ccd037 100644
--- a/modules/t/test-genome-DBs/nameless/core/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/nameless/core/SQLite/table.sql
@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
--- Created on Mon Dec 16 12:45:38 2019
+-- Created on Wed Nov 6 10:36:08 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(80),
- "new_assembly" varchar(80),
+ "old_assembly" varchar(20) NOT NULL DEFAULT '',
+ "new_assembly" varchar(20) NOT NULL DEFAULT '',
"created" datetime
);
diff --git a/modules/t/test-genome-DBs/nameless/core/meta.txt b/modules/t/test-genome-DBs/nameless/core/meta.txt
index 10ac39f81c47985879e1ae1e3ca4cd8f4078eab2..39c312be17e285bdae1d9ae15117d148ee68f4df 100644
--- a/modules/t/test-genome-DBs/nameless/core/meta.txt
+++ b/modules/t/test-genome-DBs/nameless/core/meta.txt
@@ -113,4 +113,3 @@
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
diff --git a/modules/t/test-genome-DBs/nameless/core/table.sql b/modules/t/test-genome-DBs/nameless/core/table.sql
index 2b37a35ed71b9d93d501f1c87046a237dc30f943..63c28b3252d2ac9afff804afde2592db1a997fc6 100644
--- a/modules/t/test-genome-DBs/nameless/core/table.sql
+++ b/modules/t/test-genome-DBs/nameless/core/table.sql
@@ -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(80) COLLATE latin1_bin DEFAULT NULL,
- `new_assembly` varchar(80) COLLATE latin1_bin DEFAULT NULL,
+ `old_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `new_assembly` varchar(20) 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=171 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=170 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
diff --git a/modules/t/test-genome-DBs/ontology/ontology/SQLite/table.sql b/modules/t/test-genome-DBs/ontology/ontology/SQLite/table.sql
index 89cba6740865c1fe28bf4354c8f2c1f2629995c0..3f73da74ab2b818b296f0ad8ed9e94ce80f06c6f 100644
--- a/modules/t/test-genome-DBs/ontology/ontology/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/ontology/ontology/SQLite/table.sql
@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
--- Created on Mon Dec 16 12:45:41 2019
+-- Created on Wed Nov 6 10:36:10 2019
--
BEGIN TRANSACTION;
diff --git a/modules/t/test-genome-DBs/polyploidy/core/SQLite/table.sql b/modules/t/test-genome-DBs/polyploidy/core/SQLite/table.sql
index 480c1ccc8e631f3137465621010874b7dff47a27..baa70ca65928d055fe3a26c4a3736e28bd15a679 100644
--- a/modules/t/test-genome-DBs/polyploidy/core/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/polyploidy/core/SQLite/table.sql
@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
--- Created on Mon Dec 16 12:45:48 2019
+-- Created on Wed Nov 6 10:36:15 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(80),
- "new_assembly" varchar(80),
+ "old_assembly" varchar(20) NOT NULL DEFAULT '',
+ "new_assembly" varchar(20) NOT NULL DEFAULT '',
"created" datetime
);
diff --git a/modules/t/test-genome-DBs/polyploidy/core/meta.txt b/modules/t/test-genome-DBs/polyploidy/core/meta.txt
index 19548e74ca18a9f4fea7bbcac76f1e4c15b11544..2c867489de5b99efc7bb3287f09e15afaf75d729 100644
--- a/modules/t/test-genome-DBs/polyploidy/core/meta.txt
+++ b/modules/t/test-genome-DBs/polyploidy/core/meta.txt
@@ -168,4 +168,3 @@
248 \N patch patch_98_99_a.sql|schema_version
249 \N patch patch_99_100_a.sql|schema_version
250 \N patch patch_99_100_b.sql|alter_externaldb_type_notnull
-251 \N patch patch_99_100_c.sql|alter_mapping_session_assembly_length
diff --git a/modules/t/test-genome-DBs/polyploidy/core/table.sql b/modules/t/test-genome-DBs/polyploidy/core/table.sql
index 3ca8defa4f7edb99a0c6eca7726dcdbab8c1677d..dd3f8de10ab17fab204f4405dfd2d74c4eb632ae 100644
--- a/modules/t/test-genome-DBs/polyploidy/core/table.sql
+++ b/modules/t/test-genome-DBs/polyploidy/core/table.sql
@@ -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(80) COLLATE latin1_bin DEFAULT NULL,
- `new_assembly` varchar(80) COLLATE latin1_bin DEFAULT NULL,
+ `old_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `new_assembly` varchar(20) 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=252 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=251 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
diff --git a/modules/t/test-genome-DBs/test_collection/core/SQLite/table.sql b/modules/t/test-genome-DBs/test_collection/core/SQLite/table.sql
index 5c335d517eb55ecf5554c4c619a8b2e04bd4fe0c..e434f5580ecae7f52c91b64ed12cf95925b8dc1f 100644
--- a/modules/t/test-genome-DBs/test_collection/core/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/test_collection/core/SQLite/table.sql
@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
--- Created on Mon Dec 16 12:46:22 2019
+-- Created on Wed Nov 6 10:36:20 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(80),
- "new_assembly" varchar(80),
+ "old_assembly" varchar(20) NOT NULL DEFAULT '',
+ "new_assembly" varchar(20) NOT NULL DEFAULT '',
"created" datetime
);
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 48b8e20c702ea69f6ce99d695ad3296cce645c8d..be72c192df2aae7974da9261b8c01661779b82da 100644
--- a/modules/t/test-genome-DBs/test_collection/core/meta.txt
+++ b/modules/t/test-genome-DBs/test_collection/core/meta.txt
@@ -188,4 +188,3 @@
230 \N patch patch_98_99_a.sql|schema_version
231 \N patch patch_99_100_a.sql|schema_version
232 \N patch patch_99_100_b.sql|alter_externaldb_type_notnull
-233 \N patch patch_99_100_c.sql|alter_mapping_session_assembly_length
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 5cc4f1426d3aa4bc7e0bd3dbdf7bfdd64d49d85c..d7ba949c27b8d3217b9601b664e92ca6e49bf572 100644
--- a/modules/t/test-genome-DBs/test_collection/core/table.sql
+++ b/modules/t/test-genome-DBs/test_collection/core/table.sql
@@ -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(80) COLLATE latin1_bin DEFAULT NULL,
- `new_assembly` varchar(80) COLLATE latin1_bin DEFAULT NULL,
+ `old_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `new_assembly` varchar(20) 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=234 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=233 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
diff --git a/sql/patch_99_100_c.sql b/sql/patch_99_100_c.sql
deleted file mode 100644
index 14665b2e706f803f9d470a9f3085d3aca508185a..0000000000000000000000000000000000000000
--- a/sql/patch_99_100_c.sql
+++ /dev/null
@@ -1,28 +0,0 @@
--- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2019] 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_99_100_c.sql
-#
-# Title: Update mapping_session.old_assembly and mapping_session.new_assembly columns to VARCHAR(80).
-#
-# Description:
-# Title: Update mapping_session.old_assembly and mapping_session.new_assembly columns to VARCHAR(80).
-
-ALTER TABLE mapping_session MODIFY COLUMN old_assembly VARCHAR(80);
-ALTER TABLE mapping_session MODIFY COLUMN new_assembly VARCHAR(80);
-
-# Patch identifier
-INSERT INTO meta (species_id, meta_key, meta_value)
- VALUES (NULL, 'patch', 'patch_99_100_c.sql|alter_mapping_session_assembly_length');
diff --git a/sql/table.sql b/sql/table.sql
index 2c7dc25e4937f4e8b3894dc38675c0ec916d0ac6..568a5337cb5a04cd9dd4d59b793872569b6ab7fb 100755
--- a/sql/table.sql
+++ b/sql/table.sql
@@ -319,9 +319,6 @@ INSERT INTO meta (species_id, meta_key, meta_value)
INSERT INTO meta (species_id, meta_key, meta_value)
VALUES (NULL, 'patch', 'patch_99_100_b.sql|alter_externaldb_type_notnull');
-INSERT INTO meta (species_id, meta_key, meta_value)
- VALUES (NULL, 'patch', 'patch_99_100_c.sql|alter_mapping_session_assembly_length');
-
/**
@table meta_coord
@colour #C70C09
@@ -1918,8 +1915,8 @@ 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(80) NOT NULL DEFAULT '',
- new_assembly VARCHAR(80) NOT NULL DEFAULT '',
+ old_assembly VARCHAR(20) NOT NULL DEFAULT '',
+ new_assembly VARCHAR(20) NOT NULL DEFAULT '',
created DATETIME NOT NULL,
PRIMARY KEY (mapping_session_id)