...
 
Commits (2)
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Wed Apr 15 05:23:14 2020
-- Created on Tue Jun 23 22:56:54 2020
--
BEGIN TRANSACTION;
......
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Wed Apr 15 05:23:19 2020
-- Created on Tue Jun 23 22:57:02 2020
--
BEGIN TRANSACTION;
......
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Wed Apr 15 05:23:24 2020
-- Created on Tue Jun 23 22:57:09 2020
--
BEGIN TRANSACTION;
......
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Wed Apr 15 05:23:29 2020
-- Created on Tue Jun 23 22:57:16 2020
--
BEGIN TRANSACTION;
......
1 \N schema_type variation
2 \N schema_version 101
2 \N schema_version 102
3 \N patch patch_84_85_a.sql|schema version
4 \N patch patch_84_85_b.sql|create sample_synonym
5 \N patch patch_84_85_c.sql|drop column moltype from variation_synonym
......@@ -53,3 +53,5 @@
53 \N patch patch_99_100_c.sql|add class_attrib_id column to phenotype
54 \N patch patch_100_101_a.sql|schema version
55 \N patch patch_100_101_b.sql|Add new data_source_attrib to variation_citation
56 \N patch patch_101_102_a.sql|schema version
57 \N patch patch_101_102_b.sql|Add new clinical_significance to variation, variation_feature and structural_variation
......@@ -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=56 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=58 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL,
......@@ -433,7 +433,7 @@ CREATE TABLE `structural_variation` (
`source_id` int(10) unsigned NOT NULL,
`study_id` int(10) unsigned DEFAULT NULL,
`class_attrib_id` int(10) unsigned NOT NULL DEFAULT '0',
`clinical_significance` set('uncertain significance','not provided','benign','likely benign','likely pathogenic','pathogenic','drug response','histocompatibility','other','confers sensitivity','risk factor','association','protective') DEFAULT NULL,
`clinical_significance` set('uncertain significance','not provided','benign','likely benign','likely pathogenic','pathogenic','drug response','histocompatibility','other','confers sensitivity','risk factor','association','protective','affects') DEFAULT NULL,
`validation_status` enum('validated','not validated','high quality') DEFAULT NULL,
`is_evidence` tinyint(4) DEFAULT '0',
`somatic` tinyint(1) NOT NULL DEFAULT '0',
......@@ -585,7 +585,7 @@ CREATE TABLE `variation` (
`minor_allele` varchar(50) DEFAULT NULL,
`minor_allele_freq` float DEFAULT NULL,
`minor_allele_count` int(10) unsigned DEFAULT NULL,
`clinical_significance` set('uncertain significance','not provided','benign','likely benign','likely pathogenic','pathogenic','drug response','histocompatibility','other','confers sensitivity','risk factor','association','protective') DEFAULT NULL,
`clinical_significance` set('uncertain significance','not provided','benign','likely benign','likely pathogenic','pathogenic','drug response','histocompatibility','other','confers sensitivity','risk factor','association','protective','affects') DEFAULT NULL,
`evidence_attribs` set('367','368','369','370','371','372','418','421','573','585') DEFAULT NULL,
`display` int(1) DEFAULT '1',
PRIMARY KEY (`variation_id`),
......@@ -631,7 +631,7 @@ CREATE TABLE `variation_feature` (
`minor_allele_count` int(10) unsigned DEFAULT NULL,
`alignment_quality` double DEFAULT NULL,
`evidence_attribs` set('367','368','369','370','371','372','418','421','573','585') DEFAULT NULL,
`clinical_significance` set('uncertain significance','not provided','benign','likely benign','likely pathogenic','pathogenic','drug response','histocompatibility','other','confers sensitivity','risk factor','association','protective') DEFAULT NULL,
`clinical_significance` set('uncertain significance','not provided','benign','likely benign','likely pathogenic','pathogenic','drug response','histocompatibility','other','confers sensitivity','risk factor','association','protective','affects') DEFAULT NULL,
`display` int(1) DEFAULT '1',
PRIMARY KEY (`variation_feature_id`),
KEY `pos_idx` (`seq_region_id`,`seq_region_start`,`seq_region_end`),
......
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Wed Apr 15 05:23:30 2020
-- Created on Tue Jun 23 22:57:18 2020
--
BEGIN TRANSACTION;
......
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Wed Apr 15 05:23:35 2020
-- Created on Tue Jun 23 22:57:24 2020
--
BEGIN TRANSACTION;
......
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Wed Apr 15 05:23:39 2020
-- Created on Tue Jun 23 22:57:30 2020
--
BEGIN TRANSACTION;
......@@ -10,8 +10,8 @@ BEGIN TRANSACTION;
--
CREATE TABLE "CAFE_gene_family" (
"cafe_gene_family_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
"root_id" integer NOT NULL,
"lca_id" integer NOT NULL,
"root_id" bigint NOT NULL,
"lca_id" bigint NOT NULL,
"gene_tree_root_id" integer NOT NULL,
"pvalue_avg" double precision(5,4),
"lambdas" varchar(100)
......@@ -22,7 +22,7 @@ CREATE TABLE "CAFE_gene_family" (
--
CREATE TABLE "CAFE_species_gene" (
"cafe_gene_family_id" integer NOT NULL,
"node_id" integer NOT NULL,
"node_id" bigint NOT NULL,
"n_members" integer NOT NULL,
"pvalue" double precision(5,4),
PRIMARY KEY ("cafe_gene_family_id", "node_id")
......@@ -223,7 +223,7 @@ CREATE TABLE "gene_tree_node" (
CREATE TABLE "gene_tree_node_attr" (
"node_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
"node_type" enum,
"species_tree_node_id" integer,
"species_tree_node_id" bigint,
"bootstrap" tinyint,
"duplication_confidence_score" double precision(5,4)
);
......@@ -256,7 +256,7 @@ CREATE TABLE "gene_tree_root" (
"tree_type" enum NOT NULL,
"clusterset_id" varchar(20) NOT NULL DEFAULT 'default',
"method_link_species_set_id" integer NOT NULL,
"species_tree_root_id" integer,
"species_tree_root_id" bigint,
"gene_align_id" integer,
"ref_root_id" integer,
"stable_id" varchar(40),
......@@ -289,7 +289,7 @@ CREATE TABLE "gene_tree_root_attr" (
"tree_num_dup_nodes" integer,
"tree_num_leaves" integer,
"tree_num_spec_nodes" integer,
"lca_node_id" integer,
"lca_node_id" bigint,
"taxonomic_coverage" float,
"ratio_species_genes" float,
"model_name" varchar(40)
......@@ -415,7 +415,7 @@ CREATE TABLE "homology" (
"n" float(10,1),
"s" float(10,1),
"lnl" float(10,3),
"species_tree_node_id" integer,
"species_tree_node_id" bigint,
"gene_tree_node_id" integer,
"gene_tree_root_id" integer,
"goc_score" tinyint,
......@@ -671,8 +671,8 @@ CREATE TABLE "species_set_tag" (
--
CREATE TABLE "species_tree_node" (
"node_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
"parent_id" integer,
"root_id" integer,
"parent_id" bigint,
"root_id" bigint,
"left_index" integer NOT NULL DEFAULT 0,
"right_index" integer NOT NULL DEFAULT 0,
"distance_to_parent" double precision DEFAULT 1,
......@@ -717,7 +717,7 @@ CREATE TABLE "species_tree_node_attr" (
-- Table: "species_tree_node_tag"
--
CREATE TABLE "species_tree_node_tag" (
"node_id" integer NOT NULL,
"node_id" bigint NOT NULL,
"tag" varchar(50) NOT NULL,
"value" mediumtext NOT NULL
);
......@@ -726,7 +726,7 @@ CREATE TABLE "species_tree_node_tag" (
-- Table: "species_tree_root"
--
CREATE TABLE "species_tree_root" (
"root_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
"root_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL DEFAULT 0,
"method_link_species_set_id" integer NOT NULL,
"label" varchar(256) NOT NULL DEFAULT 'default'
);
......
......@@ -63,3 +63,5 @@
77 \N patch patch_100_101_e.sql|positive_int
78 \N patch patch_100_101_f.sql|gab.direction
80 \N patch patch_101_102_a.sql|schema_version
81 \N patch patch_101_102_b.sql|enum_other
82 \N patch patch_101_102_c.sql|stn_node_id_bigint
CREATE TABLE `CAFE_gene_family` (
`cafe_gene_family_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`root_id` int(10) unsigned NOT NULL,
`lca_id` int(10) unsigned NOT NULL,
`root_id` bigint(20) unsigned NOT NULL,
`lca_id` bigint(20) unsigned NOT NULL,
`gene_tree_root_id` int(10) unsigned NOT NULL,
`pvalue_avg` double(5,4) DEFAULT NULL,
`lambdas` varchar(100) DEFAULT NULL,
......@@ -13,7 +13,7 @@ CREATE TABLE `CAFE_gene_family` (
CREATE TABLE `CAFE_species_gene` (
`cafe_gene_family_id` int(10) unsigned NOT NULL,
`node_id` int(10) unsigned NOT NULL,
`node_id` bigint(20) unsigned NOT NULL,
`n_members` int(4) unsigned NOT NULL,
`pvalue` double(5,4) DEFAULT NULL,
PRIMARY KEY (`cafe_gene_family_id`,`node_id`),
......@@ -49,7 +49,7 @@ CREATE TABLE `dnafrag` (
`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',
`cellular_component` enum('NUC','MT','PT','OTHER') NOT NULL DEFAULT 'NUC',
`is_reference` tinyint(1) NOT NULL DEFAULT '1',
`codon_table_id` tinyint(2) unsigned NOT NULL DEFAULT '1',
PRIMARY KEY (`dnafrag_id`),
......@@ -197,7 +197,7 @@ CREATE TABLE `gene_tree_node` (
CREATE TABLE `gene_tree_node_attr` (
`node_id` int(10) unsigned NOT NULL,
`node_type` enum('duplication','dubious','speciation','sub-speciation','gene_split') DEFAULT NULL,
`species_tree_node_id` int(10) unsigned DEFAULT NULL,
`species_tree_node_id` bigint(20) unsigned DEFAULT NULL,
`bootstrap` tinyint(3) unsigned DEFAULT NULL,
`duplication_confidence_score` double(5,4) DEFAULT NULL,
PRIMARY KEY (`node_id`),
......@@ -225,7 +225,7 @@ CREATE TABLE `gene_tree_root` (
`tree_type` enum('clusterset','supertree','tree') NOT NULL,
`clusterset_id` varchar(20) NOT NULL DEFAULT 'default',
`method_link_species_set_id` int(10) unsigned NOT NULL,
`species_tree_root_id` int(10) unsigned DEFAULT NULL,
`species_tree_root_id` bigint(20) unsigned DEFAULT NULL,
`gene_align_id` int(10) unsigned DEFAULT NULL,
`ref_root_id` int(10) unsigned DEFAULT NULL,
`stable_id` varchar(40) DEFAULT NULL,
......@@ -259,7 +259,7 @@ CREATE TABLE `gene_tree_root_attr` (
`tree_num_dup_nodes` int(10) unsigned DEFAULT NULL,
`tree_num_leaves` int(10) unsigned DEFAULT NULL,
`tree_num_spec_nodes` int(10) unsigned DEFAULT NULL,
`lca_node_id` int(10) unsigned DEFAULT NULL,
`lca_node_id` bigint(20) unsigned DEFAULT NULL,
`taxonomic_coverage` float DEFAULT NULL,
`ratio_species_genes` float DEFAULT NULL,
`model_name` varchar(40) DEFAULT NULL,
......@@ -376,7 +376,7 @@ CREATE TABLE `homology` (
`n` float(10,1) DEFAULT NULL,
`s` float(10,1) DEFAULT NULL,
`lnl` float(10,3) DEFAULT NULL,
`species_tree_node_id` int(10) unsigned DEFAULT NULL,
`species_tree_node_id` bigint(20) unsigned DEFAULT NULL,
`gene_tree_node_id` int(10) unsigned DEFAULT NULL,
`gene_tree_root_id` int(10) unsigned DEFAULT NULL,
`goc_score` tinyint(3) unsigned DEFAULT NULL,
......@@ -429,7 +429,7 @@ 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=81 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=83 DEFAULT CHARSET=latin1;
CREATE TABLE `method_link` (
`method_link_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -609,9 +609,9 @@ CREATE TABLE `species_set_tag` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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,
`node_id` bigint(20) unsigned NOT NULL AUTO_INCREMENT,
`parent_id` bigint(20) unsigned DEFAULT NULL,
`root_id` bigint(20) 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',
......@@ -626,7 +626,7 @@ CREATE TABLE `species_tree_node` (
) ENGINE=MyISAM AUTO_INCREMENT=40102221 DEFAULT CHARSET=latin1;
CREATE TABLE `species_tree_node_attr` (
`node_id` int(10) unsigned NOT NULL,
`node_id` bigint(20) unsigned NOT NULL,
`nb_long_genes` int(11) DEFAULT NULL,
`nb_short_genes` int(11) DEFAULT NULL,
`avg_dupscore` float DEFAULT NULL,
......@@ -656,7 +656,7 @@ CREATE TABLE `species_tree_node_attr` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `species_tree_node_tag` (
`node_id` int(10) unsigned NOT NULL,
`node_id` bigint(20) unsigned NOT NULL,
`tag` varchar(50) NOT NULL,
`value` mediumtext NOT NULL,
KEY `node_id_tag` (`node_id`,`tag`),
......@@ -664,7 +664,7 @@ CREATE TABLE `species_tree_node_tag` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `species_tree_root` (
`root_id` int(10) unsigned NOT NULL,
`root_id` bigint(20) unsigned NOT NULL DEFAULT '0',
`method_link_species_set_id` int(10) unsigned NOT NULL,
`label` varchar(256) NOT NULL DEFAULT 'default',
PRIMARY KEY (`root_id`),
......
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Wed Apr 15 05:23:44 2020
-- Created on Tue Jun 23 22:57:36 2020
--
BEGIN TRANSACTION;
......
1 \N schema_type variation
2 \N schema_version 101
2 \N schema_version 102
6 1 species.production_name mus_musculus
15 1 web_config sv_study#Keane 2011 (DGVa study estd118)#Keane 2011#estd118
14 1 web_config set#All failed variants#All failed variants#variation_set_fail_all#failed
......@@ -80,3 +80,5 @@
86 \N patch patch_99_100_c.sql|add class_attrib_id column to phenotype
87 \N patch patch_100_101_a.sql|schema version
88 \N patch patch_100_101_b.sql|Add new data_source_attrib to variation_citation
89 \N patch patch_101_102_a.sql|schema version
90 \N patch patch_101_102_b.sql|Add new clinical_significance to variation, variation_feature and structural_variation
......@@ -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=89 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=91 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL,
......@@ -433,7 +433,7 @@ CREATE TABLE `structural_variation` (
`source_id` int(10) unsigned NOT NULL,
`study_id` int(10) unsigned DEFAULT NULL,
`class_attrib_id` int(10) unsigned NOT NULL DEFAULT '0',
`clinical_significance` set('uncertain significance','not provided','benign','likely benign','likely pathogenic','pathogenic','drug response','histocompatibility','other','confers sensitivity','risk factor','association','protective') DEFAULT NULL,
`clinical_significance` set('uncertain significance','not provided','benign','likely benign','likely pathogenic','pathogenic','drug response','histocompatibility','other','confers sensitivity','risk factor','association','protective','affects') DEFAULT NULL,
`validation_status` enum('validated','not validated','high quality') DEFAULT NULL,
`is_evidence` tinyint(4) DEFAULT '0',
`somatic` tinyint(1) NOT NULL DEFAULT '0',
......@@ -591,7 +591,7 @@ CREATE TABLE `variation` (
`minor_allele` varchar(50) DEFAULT NULL,
`minor_allele_freq` float DEFAULT NULL,
`minor_allele_count` int(10) unsigned DEFAULT NULL,
`clinical_significance` set('uncertain significance','not provided','benign','likely benign','likely pathogenic','pathogenic','drug response','histocompatibility','other','confers sensitivity','risk factor','association','protective') DEFAULT NULL,
`clinical_significance` set('uncertain significance','not provided','benign','likely benign','likely pathogenic','pathogenic','drug response','histocompatibility','other','confers sensitivity','risk factor','association','protective','affects') DEFAULT NULL,
`evidence_attribs` set('367','368','369','370','371','372','418','421','573','585') DEFAULT NULL,
`display` int(1) DEFAULT '1',
PRIMARY KEY (`variation_id`),
......@@ -637,7 +637,7 @@ CREATE TABLE `variation_feature` (
`minor_allele_count` int(10) unsigned DEFAULT NULL,
`alignment_quality` double DEFAULT NULL,
`evidence_attribs` set('367','368','369','370','371','372','418','421','573','585') DEFAULT NULL,
`clinical_significance` set('uncertain significance','not provided','benign','likely benign','likely pathogenic','pathogenic','drug response','histocompatibility','other','confers sensitivity','risk factor','association','protective') DEFAULT NULL,
`clinical_significance` set('uncertain significance','not provided','benign','likely benign','likely pathogenic','pathogenic','drug response','histocompatibility','other','confers sensitivity','risk factor','association','protective','affects') DEFAULT NULL,
`display` int(1) DEFAULT '1',
PRIMARY KEY (`variation_feature_id`),
KEY `pos_idx` (`seq_region_id`,`seq_region_start`,`seq_region_end`),
......
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Wed Apr 15 05:23:49 2020
-- Created on Tue Jun 23 22:57:41 2020
--
BEGIN TRANSACTION;
......
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Wed Apr 15 05:23:52 2020
-- Created on Tue Jun 23 22:57:45 2020
--
BEGIN TRANSACTION;
......
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Wed Apr 15 05:23:57 2020
-- Created on Tue Jun 23 22:58:08 2020
--
BEGIN TRANSACTION;
......
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Wed Apr 15 05:24:02 2020
-- Created on Tue Jun 23 22:58:14 2020
--
BEGIN TRANSACTION;
......