Commit fc4990b5 authored by Tiago Grego's avatar Tiago Grego
Browse files

patched test dbs with patch_96_97_b and updated fixtures

parent 5415237e
-- --
-- Created by SQL::Translator::Producer::SQLite -- Created by SQL::Translator::Producer::SQLite
-- Created on Tue Feb 12 11:45:04 2019 -- Created on Tue Feb 12 15:00:15 2019
-- --
BEGIN TRANSACTION; BEGIN TRANSACTION;
...@@ -142,7 +142,8 @@ CREATE TABLE "biotype" ( ...@@ -142,7 +142,8 @@ CREATE TABLE "biotype" (
"attrib_type_id" integer, "attrib_type_id" integer,
"description" text, "description" text,
"biotype_group" enum, "biotype_group" enum,
"so_acc" varchar(64) "so_acc" varchar(64),
"so_term" varchar(1023)
); );
CREATE UNIQUE INDEX "name_type_idx" ON "biotype" ("name", "object_type"); CREATE UNIQUE INDEX "name_type_idx" ON "biotype" ("name", "object_type");
......
...@@ -127,3 +127,4 @@ ...@@ -127,3 +127,4 @@
127 \N patch patch_94_95_c.sql|ox_key_update 127 \N patch patch_94_95_c.sql|ox_key_update
128 \N patch patch_95_96_a.sql|schema_version 128 \N patch patch_95_96_a.sql|schema_version
129 \N patch patch_96_97_a.sql|schema_version 129 \N patch patch_96_97_a.sql|schema_version
130 \N patch patch_96_97_b.sql|biotype_so_term
...@@ -114,6 +114,7 @@ CREATE TABLE `biotype` ( ...@@ -114,6 +114,7 @@ CREATE TABLE `biotype` (
`description` text, `description` text,
`biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group') DEFAULT NULL, `biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group') DEFAULT NULL,
`so_acc` varchar(64) DEFAULT NULL, `so_acc` varchar(64) DEFAULT NULL,
`so_term` varchar(1023) DEFAULT NULL,
PRIMARY KEY (`biotype_id`), PRIMARY KEY (`biotype_id`),
UNIQUE KEY `name_type_idx` (`name`,`object_type`) UNIQUE KEY `name_type_idx` (`name`,`object_type`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1; ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
...@@ -489,7 +490,7 @@ CREATE TABLE `meta` ( ...@@ -489,7 +490,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`), PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`), UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`) KEY `species_value_idx` (`species_id`,`meta_value`)
) ENGINE=MyISAM AUTO_INCREMENT=130 DEFAULT CHARSET=latin1; ) ENGINE=MyISAM AUTO_INCREMENT=131 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` ( CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '', `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
......
-- --
-- Created by SQL::Translator::Producer::SQLite -- Created by SQL::Translator::Producer::SQLite
-- Created on Tue Feb 12 11:45:08 2019 -- Created on Tue Feb 12 15:00:19 2019
-- --
BEGIN TRANSACTION; BEGIN TRANSACTION;
...@@ -142,7 +142,8 @@ CREATE TABLE "biotype" ( ...@@ -142,7 +142,8 @@ CREATE TABLE "biotype" (
"attrib_type_id" integer, "attrib_type_id" integer,
"description" text, "description" text,
"biotype_group" enum, "biotype_group" enum,
"so_acc" varchar(64) "so_acc" varchar(64),
"so_term" varchar(1023)
); );
CREATE UNIQUE INDEX "name_type_idx" ON "biotype" ("name", "object_type"); CREATE UNIQUE INDEX "name_type_idx" ON "biotype" ("name", "object_type");
......
64 protein_coding gene core,otherfeatures,rnaseq,vega,presite \N \N coding SO:0001217 64 protein_coding gene core,otherfeatures,rnaseq,vega,presite \N \N coding SO:0001217 protein_coding_gene
65 protein_coding transcript core,otherfeatures,rnaseq,vega,presite \N \N coding SO:0000234 65 protein_coding transcript core,otherfeatures,rnaseq,vega,presite \N \N coding SO:0000234 mRNA
87 tRNA gene core,otherfeatures,presite 76 \N snoncoding SO:0001263 87 tRNA gene core,otherfeatures,presite 76 \N snoncoding SO:0001263 ncRNA_gene
...@@ -106,3 +106,4 @@ ...@@ -106,3 +106,4 @@
173 \N patch patch_94_95_c.sql|ox_key_update 173 \N patch patch_94_95_c.sql|ox_key_update
174 \N patch patch_95_96_a.sql|schema_version 174 \N patch patch_95_96_a.sql|schema_version
175 \N patch patch_96_97_a.sql|schema_version 175 \N patch patch_96_97_a.sql|schema_version
176 \N patch patch_96_97_b.sql|biotype_so_term
...@@ -114,6 +114,7 @@ CREATE TABLE `biotype` ( ...@@ -114,6 +114,7 @@ CREATE TABLE `biotype` (
`description` text, `description` text,
`biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group') DEFAULT NULL, `biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group') DEFAULT NULL,
`so_acc` varchar(64) DEFAULT NULL, `so_acc` varchar(64) DEFAULT NULL,
`so_term` varchar(1023) DEFAULT NULL,
PRIMARY KEY (`biotype_id`), PRIMARY KEY (`biotype_id`),
UNIQUE KEY `name_type_idx` (`name`,`object_type`) UNIQUE KEY `name_type_idx` (`name`,`object_type`)
) ENGINE=MyISAM AUTO_INCREMENT=88 DEFAULT CHARSET=latin1; ) ENGINE=MyISAM AUTO_INCREMENT=88 DEFAULT CHARSET=latin1;
...@@ -489,7 +490,7 @@ CREATE TABLE `meta` ( ...@@ -489,7 +490,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`), PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`), UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`) KEY `species_value_idx` (`species_id`,`meta_value`)
) ENGINE=MyISAM AUTO_INCREMENT=176 DEFAULT CHARSET=latin1; ) ENGINE=MyISAM AUTO_INCREMENT=177 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` ( CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '', `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
......
-- --
-- Created by SQL::Translator::Producer::SQLite -- Created by SQL::Translator::Producer::SQLite
-- Created on Tue Feb 12 11:45:11 2019 -- Created on Tue Feb 12 15:00:22 2019
-- --
BEGIN TRANSACTION; BEGIN TRANSACTION;
...@@ -142,7 +142,8 @@ CREATE TABLE "biotype" ( ...@@ -142,7 +142,8 @@ CREATE TABLE "biotype" (
"attrib_type_id" integer, "attrib_type_id" integer,
"description" text, "description" text,
"biotype_group" enum, "biotype_group" enum,
"so_acc" varchar(64) "so_acc" varchar(64),
"so_term" varchar(1023)
); );
CREATE UNIQUE INDEX "name_type_idx" ON "biotype" ("name", "object_type"); CREATE UNIQUE INDEX "name_type_idx" ON "biotype" ("name", "object_type");
......
...@@ -106,3 +106,4 @@ ...@@ -106,3 +106,4 @@
155 \N patch patch_94_95_c.sql|ox_key_update 155 \N patch patch_94_95_c.sql|ox_key_update
156 \N patch patch_95_96_a.sql|schema_version 156 \N patch patch_95_96_a.sql|schema_version
157 \N patch patch_96_97_a.sql|schema_version 157 \N patch patch_96_97_a.sql|schema_version
158 \N patch patch_96_97_b.sql|biotype_so_term
...@@ -114,6 +114,7 @@ CREATE TABLE `biotype` ( ...@@ -114,6 +114,7 @@ CREATE TABLE `biotype` (
`description` text, `description` text,
`biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group') DEFAULT NULL, `biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group') DEFAULT NULL,
`so_acc` varchar(64) DEFAULT NULL, `so_acc` varchar(64) DEFAULT NULL,
`so_term` varchar(1023) DEFAULT NULL,
PRIMARY KEY (`biotype_id`), PRIMARY KEY (`biotype_id`),
UNIQUE KEY `name_type_idx` (`name`,`object_type`) UNIQUE KEY `name_type_idx` (`name`,`object_type`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1; ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
...@@ -489,7 +490,7 @@ CREATE TABLE `meta` ( ...@@ -489,7 +490,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`), PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`), UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`) KEY `species_value_idx` (`species_id`,`meta_value`)
) ENGINE=MyISAM AUTO_INCREMENT=158 DEFAULT CHARSET=latin1; ) ENGINE=MyISAM AUTO_INCREMENT=159 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` ( CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '', `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
......
-- --
-- Created by SQL::Translator::Producer::SQLite -- Created by SQL::Translator::Producer::SQLite
-- Created on Tue Feb 12 11:45:14 2019 -- Created on Tue Feb 12 15:00:25 2019
-- --
BEGIN TRANSACTION; BEGIN TRANSACTION;
...@@ -142,7 +142,8 @@ CREATE TABLE "biotype" ( ...@@ -142,7 +142,8 @@ CREATE TABLE "biotype" (
"attrib_type_id" integer, "attrib_type_id" integer,
"description" text, "description" text,
"biotype_group" enum, "biotype_group" enum,
"so_acc" varchar(64) "so_acc" varchar(64),
"so_term" varchar(1023)
); );
CREATE UNIQUE INDEX "name_type_idx" ON "biotype" ("name", "object_type"); CREATE UNIQUE INDEX "name_type_idx" ON "biotype" ("name", "object_type");
......
...@@ -111,3 +111,4 @@ ...@@ -111,3 +111,4 @@
2118 \N patch patch_94_95_c.sql|ox_key_update 2118 \N patch patch_94_95_c.sql|ox_key_update
2119 \N patch patch_95_96_a.sql|schema_version 2119 \N patch patch_95_96_a.sql|schema_version
2120 \N patch patch_96_97_a.sql|schema_version 2120 \N patch patch_96_97_a.sql|schema_version
2121 \N patch patch_96_97_b.sql|biotype_so_term
...@@ -114,6 +114,7 @@ CREATE TABLE `biotype` ( ...@@ -114,6 +114,7 @@ CREATE TABLE `biotype` (
`description` text, `description` text,
`biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group') DEFAULT NULL, `biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group') DEFAULT NULL,
`so_acc` varchar(64) DEFAULT NULL, `so_acc` varchar(64) DEFAULT NULL,
`so_term` varchar(1023) DEFAULT NULL,
PRIMARY KEY (`biotype_id`), PRIMARY KEY (`biotype_id`),
UNIQUE KEY `name_type_idx` (`name`,`object_type`) UNIQUE KEY `name_type_idx` (`name`,`object_type`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1; ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
...@@ -489,7 +490,7 @@ CREATE TABLE `meta` ( ...@@ -489,7 +490,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`), PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`), UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`) KEY `species_value_idx` (`species_id`,`meta_value`)
) ENGINE=MyISAM AUTO_INCREMENT=2121 DEFAULT CHARSET=latin1; ) ENGINE=MyISAM AUTO_INCREMENT=2122 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` ( CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '', `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
......
-- --
-- Created by SQL::Translator::Producer::SQLite -- Created by SQL::Translator::Producer::SQLite
-- Created on Tue Feb 12 11:45:15 2019 -- Created on Tue Feb 12 15:00:26 2019
-- --
BEGIN TRANSACTION; BEGIN TRANSACTION;
......
-- --
-- Created by SQL::Translator::Producer::SQLite -- Created by SQL::Translator::Producer::SQLite
-- Created on Tue Feb 12 11:45:18 2019 -- Created on Tue Feb 12 15:00:29 2019
-- --
BEGIN TRANSACTION; BEGIN TRANSACTION;
...@@ -142,7 +142,8 @@ CREATE TABLE "biotype" ( ...@@ -142,7 +142,8 @@ CREATE TABLE "biotype" (
"attrib_type_id" integer, "attrib_type_id" integer,
"description" text, "description" text,
"biotype_group" enum, "biotype_group" enum,
"so_acc" varchar(64) "so_acc" varchar(64),
"so_term" varchar(1023)
); );
CREATE UNIQUE INDEX "name_type_idx" ON "biotype" ("name", "object_type"); CREATE UNIQUE INDEX "name_type_idx" ON "biotype" ("name", "object_type");
......
...@@ -67,3 +67,4 @@ ...@@ -67,3 +67,4 @@
160 \N patch patch_94_95_c.sql|ox_key_update 160 \N patch patch_94_95_c.sql|ox_key_update
161 \N patch patch_95_96_a.sql|schema_version 161 \N patch patch_95_96_a.sql|schema_version
162 \N patch patch_96_97_a.sql|schema_version 162 \N patch patch_96_97_a.sql|schema_version
163 \N patch patch_96_97_b.sql|biotype_so_term
...@@ -114,6 +114,7 @@ CREATE TABLE `biotype` ( ...@@ -114,6 +114,7 @@ CREATE TABLE `biotype` (
`description` text, `description` text,
`biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group') DEFAULT NULL, `biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group') DEFAULT NULL,
`so_acc` varchar(64) DEFAULT NULL, `so_acc` varchar(64) DEFAULT NULL,
`so_term` varchar(1023) DEFAULT NULL,
PRIMARY KEY (`biotype_id`), PRIMARY KEY (`biotype_id`),
UNIQUE KEY `name_type_idx` (`name`,`object_type`) UNIQUE KEY `name_type_idx` (`name`,`object_type`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1; ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
...@@ -489,7 +490,7 @@ CREATE TABLE `meta` ( ...@@ -489,7 +490,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`), PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`), UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`) KEY `species_value_idx` (`species_id`,`meta_value`)
) ENGINE=MyISAM AUTO_INCREMENT=163 DEFAULT CHARSET=latin1; ) ENGINE=MyISAM AUTO_INCREMENT=164 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` ( CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '', `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
......
-- --
-- Created by SQL::Translator::Producer::SQLite -- Created by SQL::Translator::Producer::SQLite
-- Created on Tue Feb 12 11:45:21 2019 -- Created on Tue Feb 12 15:00:32 2019
-- --
BEGIN TRANSACTION; BEGIN TRANSACTION;
......
-- --
-- Created by SQL::Translator::Producer::SQLite -- Created by SQL::Translator::Producer::SQLite
-- Created on Tue Feb 12 11:45:24 2019 -- Created on Tue Feb 12 15:00:36 2019
-- --
BEGIN TRANSACTION; BEGIN TRANSACTION;
...@@ -142,7 +142,8 @@ CREATE TABLE "biotype" ( ...@@ -142,7 +142,8 @@ CREATE TABLE "biotype" (
"attrib_type_id" integer, "attrib_type_id" integer,
"description" text, "description" text,
"biotype_group" enum, "biotype_group" enum,
"so_acc" varchar(64) "so_acc" varchar(64),
"so_term" varchar(1023)
); );
CREATE UNIQUE INDEX "name_type_idx" ON "biotype" ("name", "object_type"); CREATE UNIQUE INDEX "name_type_idx" ON "biotype" ("name", "object_type");
......
...@@ -184,3 +184,4 @@ ...@@ -184,3 +184,4 @@
1696 \N patch patch_94_95_c.sql|ox_key_update 1696 \N patch patch_94_95_c.sql|ox_key_update
1697 \N patch patch_95_96_a.sql|schema_version 1697 \N patch patch_95_96_a.sql|schema_version
1698 \N patch patch_96_97_a.sql|schema_version 1698 \N patch patch_96_97_a.sql|schema_version
1699 \N patch patch_96_97_b.sql|biotype_so_term
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