Commit a4acb299 authored by Magali Ruffier's avatar Magali Ruffier
Browse files

update to latest schema

parent 9a09f02e
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Wed Apr 25 09:28:53 2018
-- Created on Tue Jul 3 16:05:34 2018
--
BEGIN TRANSACTION;
......@@ -301,7 +301,7 @@ CREATE TABLE gene_tree_root_attr (
--
CREATE TABLE gene_tree_root_tag (
root_id integer NOT NULL,
tag varchar(50) NOT NULL,
tag varchar(255),
value mediumtext NOT NULL
);
......@@ -408,7 +408,7 @@ CREATE TABLE hmm_profile (
CREATE TABLE homology (
homology_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
method_link_species_set_id integer NOT NULL,
description enum,
description enum NOT NULL,
is_tree_compliant tinyint NOT NULL DEFAULT 0,
dn float(10,5),
ds float(10,5),
......@@ -479,7 +479,8 @@ CREATE UNIQUE INDEX species_key_value_idx ON meta (species_id, meta_key, meta_va
CREATE TABLE method_link (
method_link_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
type varchar(50) NOT NULL DEFAULT '',
class varchar(50) NOT NULL DEFAULT ''
class varchar(50) NOT NULL DEFAULT '',
display_name varchar(255) NOT NULL DEFAULT ''
);
CREATE UNIQUE INDEX type02 ON method_link (type);
......
......@@ -43,3 +43,5 @@
50 \N patch patch_91_92_c.sql|gene_tree_root_tag_255
52 \N patch patch_92_93_a.sql|schema_version
54 \N patch patch_93_94_a.sql|schema_version
55 \N patch patch_93_94_b.sql|homology_description_not_null
56 \N patch patch_93_94_c.sql|method_link_display_name
401 PROTEIN_TREES ProteinTree.protein_tree_node
201 ENSEMBL_ORTHOLOGUES Homology.homology
202 ENSEMBL_PARALOGUES Homology.homology
402 NC_TREES NCTree.nc_tree_node
101 SYNTENY SyntenyRegion.synteny
16 LASTZ_NET GenomicAlignBlock.pairwise_alignment
401 PROTEIN_TREES ProteinTree.protein_tree_node Protein-trees
201 ENSEMBL_ORTHOLOGUES Homology.homology Orthologues
202 ENSEMBL_PARALOGUES Homology.homology Paralogues
402 NC_TREES NCTree.nc_tree_node ncRNA-trees
101 SYNTENY SyntenyRegion.synteny Synteny
16 LASTZ_NET GenomicAlignBlock.pairwise_alignment LastZ
......@@ -375,7 +375,7 @@ CREATE TABLE `hmm_profile` (
CREATE TABLE `homology` (
`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') DEFAULT 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',
`dn` float(10,5) DEFAULT NULL,
`ds` float(10,5) DEFAULT NULL,
......@@ -436,12 +436,13 @@ CREATE TABLE `meta` (
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=55 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=57 DEFAULT CHARSET=latin1;
CREATE TABLE `method_link` (
`method_link_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`type` varchar(50) NOT NULL DEFAULT '',
`class` varchar(50) NOT NULL DEFAULT '',
`display_name` varchar(255) NOT NULL DEFAULT '',
PRIMARY KEY (`method_link_id`),
UNIQUE KEY `type` (`type`)
) ENGINE=MyISAM AUTO_INCREMENT=403 DEFAULT CHARSET=latin1;
......
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