Commit 67e161b1 authored by Magali Ruffier's avatar Magali Ruffier
Browse files

patch mouse test data

parent a92c4755
This diff is collapsed.
1 \N schema_type core
2 \N schema_version 82
2 \N schema_version 83
3 \N patch patch_65_66_a.sql|schema_version
4 \N patch patch_65_66_b.sql|fix_external_db_id
5 \N patch patch_65_66_c.sql|reorder_unmapped_obj_index
......@@ -146,3 +146,4 @@
1653 1 species.classification Opisthokonta
1654 1 species.classification Eukaryota
1660 1 species.division Ensembl
1661 \N patch patch_82_83_a.sql|schema_version
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Thu Nov 12 12:46:48 2015
--
BEGIN TRANSACTION;
--
-- Table: allele
--
CREATE TABLE allele (
allele_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
variation_id integer NOT NULL,
subsnp_id integer,
allele_code_id integer NOT NULL,
population_id integer,
frequency float,
count integer,
frequency_submitter_handle integer
);
--
-- Table: allele_code
--
CREATE TABLE allele_code (
allele_code_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
allele varchar(100)
);
CREATE UNIQUE INDEX allele_idx ON allele_code (allele);
--
-- Table: associate_study
--
CREATE TABLE associate_study (
study1_id integer NOT NULL,
study2_id integer NOT NULL,
PRIMARY KEY (study1_id, study2_id)
);
--
-- Table: attrib
--
CREATE TABLE attrib (
attrib_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL DEFAULT 0,
attrib_type_id smallint NOT NULL DEFAULT 0,
value text NOT NULL
);
CREATE UNIQUE INDEX type_val_idx ON attrib (attrib_type_id, value);
--
-- Table: attrib_set
--
CREATE TABLE attrib_set (
attrib_set_id integer NOT NULL DEFAULT 0,
attrib_id integer NOT NULL DEFAULT 0
);
CREATE UNIQUE INDEX set_idx ON attrib_set (attrib_set_id, attrib_id);
--
-- Table: attrib_type
--
CREATE TABLE attrib_type (
attrib_type_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL DEFAULT 0,
code varchar(20) NOT NULL DEFAULT '',
name varchar(255) NOT NULL DEFAULT '',
description text
);
CREATE UNIQUE INDEX code_idx ON attrib_type (code);
--
-- Table: compressed_genotype_region
--
CREATE TABLE compressed_genotype_region (
sample_id integer NOT NULL,
seq_region_id integer NOT NULL,
seq_region_start integer NOT NULL,
seq_region_end integer NOT NULL,
seq_region_strand tinyint NOT NULL,
genotypes blob
);
--
-- Table: compressed_genotype_var
--
CREATE TABLE compressed_genotype_var (
variation_id integer NOT NULL,
subsnp_id integer,
genotypes blob
);
--
-- Table: coord_system
--
CREATE TABLE coord_system (
coord_system_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
species_id integer NOT NULL DEFAULT 1,
name varchar(40) NOT NULL,
version varchar(255),
rank integer NOT NULL,
attrib varchar
);
CREATE UNIQUE INDEX name_idx ON coord_system (name, version, species_id);
CREATE UNIQUE INDEX rank_idx ON coord_system (rank, species_id);
--
-- Table: display_group
--
CREATE TABLE display_group (
display_group_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
display_priority integer NOT NULL,
display_name varchar(255) NOT NULL
);
CREATE UNIQUE INDEX display_name ON display_group (display_name);
CREATE UNIQUE INDEX display_priority ON display_group (display_priority);
--
-- Table: failed_allele
--
CREATE TABLE failed_allele (
failed_allele_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
allele_id integer NOT NULL,
failed_description_id integer NOT NULL
);
CREATE UNIQUE INDEX allele_idx02 ON failed_allele (allele_id, failed_description_id);
--
-- Table: failed_description
--
CREATE TABLE failed_description (
failed_description_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
description text NOT NULL
);
--
-- Table: failed_structural_variation
--
CREATE TABLE failed_structural_variation (
failed_structural_variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
structural_variation_id integer NOT NULL,
failed_description_id integer NOT NULL
);
CREATE UNIQUE INDEX structural_variation_idx ON failed_structural_variation (structural_variation_id, failed_description_id);
--
-- Table: failed_variation
--
CREATE TABLE failed_variation (
failed_variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
variation_id integer NOT NULL,
failed_description_id integer NOT NULL
);
CREATE UNIQUE INDEX variation_idx ON failed_variation (variation_id, failed_description_id);
--
-- Table: genotype_code
--
CREATE TABLE genotype_code (
genotype_code_id integer NOT NULL,
allele_code_id integer NOT NULL,
haplotype_id tinyint NOT NULL,
phased tinyint
);
--
-- Table: individual
--
CREATE TABLE individual (
individual_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
name varchar(255),
description text,
gender enum NOT NULL DEFAULT 'Unknown',
father_individual_id integer,
mother_individual_id integer,
individual_type_id integer NOT NULL DEFAULT 0
);
--
-- Table: individual_synonym
--
CREATE TABLE individual_synonym (
synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
individual_id integer NOT NULL,
source_id integer NOT NULL,
name varchar(255)
);
--
-- Table: individual_type
--
CREATE TABLE individual_type (
individual_type_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
name varchar(255) NOT NULL,
description text
);
--
-- Table: meta
--
CREATE TABLE meta (
meta_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
species_id integer DEFAULT 1,
meta_key varchar(40) NOT NULL,
meta_value varchar(255) NOT NULL
);
CREATE UNIQUE INDEX species_key_value_idx ON meta (species_id, meta_key, meta_value);
--
-- Table: meta_coord
--
CREATE TABLE meta_coord (
table_name varchar(40) NOT NULL,
coord_system_id integer NOT NULL,
max_length integer
);
CREATE UNIQUE INDEX table_name ON meta_coord (table_name, coord_system_id);
--
-- Table: motif_feature_variation
--
CREATE TABLE motif_feature_variation (
motif_feature_variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
variation_feature_id integer NOT NULL,
feature_stable_id varchar(128),
motif_feature_id integer NOT NULL,
allele_string text,
somatic tinyint NOT NULL DEFAULT 0,
consequence_types varchar,
motif_name varchar(60),
motif_start integer,
motif_end integer,
motif_score_delta float,
in_informative_position tinyint NOT NULL DEFAULT 0
);
--
-- Table: phenotype
--
CREATE TABLE phenotype (
phenotype_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
stable_id varchar(255),
name varchar(50),
description varchar(255)
);
CREATE UNIQUE INDEX desc_idx ON phenotype (description);
--
-- Table: phenotype_feature
--
CREATE TABLE phenotype_feature (
phenotype_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
phenotype_id integer,
source_id integer,
study_id integer,
type enum,
object_id varchar(255),
is_significant tinyint DEFAULT 1,
seq_region_id integer,
seq_region_start integer,
seq_region_end integer,
seq_region_strand tinyint
);
--
-- Table: phenotype_feature_attrib
--
CREATE TABLE phenotype_feature_attrib (
phenotype_feature_id integer NOT NULL,
attrib_type_id integer,
value varchar(255)
);
--
-- Table: population
--
CREATE TABLE population (
population_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
name varchar(255),
size integer,
description text,
collection tinyint DEFAULT 0,
freqs_from_gts tinyint,
display enum DEFAULT 'UNDISPLAYABLE',
display_group_id tinyint
);
--
-- Table: population_genotype
--
CREATE TABLE population_genotype (
population_genotype_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
variation_id integer NOT NULL,
subsnp_id integer,
genotype_code_id integer,
frequency float,
population_id integer,
count integer
);
--
-- Table: population_structure
--
CREATE TABLE population_structure (
super_population_id integer NOT NULL,
sub_population_id integer NOT NULL
);
CREATE UNIQUE INDEX super_population_idx ON population_structure (super_population_id, sub_population_id);
--
-- Table: population_synonym
--
CREATE TABLE population_synonym (
synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
population_id integer NOT NULL,
source_id integer NOT NULL,
name varchar(255)
);
--
-- Table: protein_function_predictions
--
CREATE TABLE protein_function_predictions (
translation_md5_id integer NOT NULL,
analysis_attrib_id integer NOT NULL,
prediction_matrix mediumblob,
PRIMARY KEY (translation_md5_id, analysis_attrib_id)
);
--
-- Table: protein_function_predictions_attrib
--
CREATE TABLE protein_function_predictions_attrib (
translation_md5_id integer NOT NULL,
analysis_attrib_id integer NOT NULL,
attrib_type_id integer NOT NULL,
position_values blob,
PRIMARY KEY (translation_md5_id, analysis_attrib_id, attrib_type_id)
);
--
-- Table: publication
--
CREATE TABLE publication (
publication_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
title varchar(255),
authors varchar(255),
pmid integer,
pmcid varchar(255),
year integer,
doi varchar(50),
ucsc_id varchar(50)
);
--
-- Table: read_coverage
--
CREATE TABLE read_coverage (
seq_region_id integer NOT NULL,
seq_region_start integer NOT NULL,
seq_region_end integer NOT NULL,
level tinyint NOT NULL,
sample_id integer NOT NULL
);
--
-- Table: regulatory_feature_variation
--
CREATE TABLE regulatory_feature_variation (
regulatory_feature_variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
variation_feature_id integer NOT NULL,
feature_stable_id varchar(128),
feature_type text,
allele_string text,
somatic tinyint NOT NULL DEFAULT 0,
consequence_types varchar
);
--
-- Table: sample
--
CREATE TABLE sample (
sample_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
individual_id integer NOT NULL,
name varchar(255),
description text,
study_id integer,
display enum DEFAULT 'UNDISPLAYABLE',
has_coverage tinyint NOT NULL DEFAULT 0,
variation_set_id varchar
);
--
-- Table: sample_genotype_multiple_bp
--
CREATE TABLE sample_genotype_multiple_bp (
variation_id integer NOT NULL,
subsnp_id integer,
allele_1 varchar(100),
allele_2 varchar(100),
sample_id integer
);
--
-- Table: sample_population
--
CREATE TABLE sample_population (
sample_id integer NOT NULL,
population_id integer NOT NULL
);
--
-- Table: seq_region
--
CREATE TABLE seq_region (
seq_region_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
name varchar(40) NOT NULL,
coord_system_id integer NOT NULL
);
CREATE UNIQUE INDEX name_cs_idx ON seq_region (name, coord_system_id);
--
-- Table: source
--
CREATE TABLE source (
source_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
name varchar(24) NOT NULL,
version integer,
description varchar(255),
url varchar(255),
type enum,
somatic_status enum DEFAULT 'germline',
data_types varchar
);
--
-- Table: structural_variation
--
CREATE TABLE structural_variation (
structural_variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
variation_name varchar(255),
alias varchar(255),
source_id integer NOT NULL,
study_id integer,
class_attrib_id integer NOT NULL DEFAULT 0,
clinical_significance varchar,
validation_status enum,
is_evidence tinyint DEFAULT 0,
somatic tinyint NOT NULL DEFAULT 0,
copy_number tinyint
);
CREATE UNIQUE INDEX variation_name ON structural_variation (variation_name);
--
-- Table: structural_variation_association
--
CREATE TABLE structural_variation_association (
structural_variation_id integer NOT NULL,
supporting_structural_variation_id integer NOT NULL,
PRIMARY KEY (structural_variation_id, supporting_structural_variation_id)
);
--
-- Table: structural_variation_feature
--
CREATE TABLE structural_variation_feature (
structural_variation_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
seq_region_id integer NOT NULL,
outer_start integer,
seq_region_start integer NOT NULL,
inner_start integer,
inner_end integer,
seq_region_end integer NOT NULL,
outer_end integer,
seq_region_strand tinyint NOT NULL,
structural_variation_id integer NOT NULL,
variation_name varchar(255),
source_id integer NOT NULL,
study_id integer,
class_attrib_id integer NOT NULL DEFAULT 0,
allele_string longtext,
is_evidence tinyint NOT NULL DEFAULT 0,
variation_set_id varchar NOT NULL DEFAULT '',
somatic tinyint NOT NULL DEFAULT 0,
breakpoint_order tinyint,
length integer
);
--
-- Table: structural_variation_sample
--
CREATE TABLE structural_variation_sample (
structural_variation_sample_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
structural_variation_id integer NOT NULL,
sample_id integer
);
--
-- Table: study
--
CREATE TABLE study (
study_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
source_id integer NOT NULL,
name varchar(255),
description text,
url varchar(255),
external_reference varchar(255),
study_type varchar(255)
);
--
-- Table: submitter_handle
--
CREATE TABLE submitter_handle (
handle_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
handle varchar(25)
);
CREATE UNIQUE INDEX handle ON submitter_handle (handle);
--
-- Table: subsnp_handle
--
CREATE TABLE subsnp_handle (
subsnp_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
handle varchar(20)
);
--
-- Table: subsnp_map
--
CREATE TABLE subsnp_map (
variation_id integer NOT NULL,
subsnp_id integer
);
--
-- Table: tagged_variation_feature
--
CREATE TABLE tagged_variation_feature (
variation_feature_id integer NOT NULL,
tagged_variation_feature_id integer,
population_id integer NOT NULL
);
--
-- Table: tmp_sample_genotype_single_bp
--
CREATE TABLE tmp_sample_genotype_single_bp (
variation_id integer NOT NULL,
subsnp_id integer,
allele_1 char(1),
allele_2 char(1),
sample_id integer NOT NULL
);
--
-- Table: transcript_variation
--
CREATE TABLE transcript_variation (
transcript_variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
variation_feature_id integer NOT NULL,
feature_stable_id varchar(128),
allele_string text,
somatic tinyint NOT NULL DEFAULT 0,