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create_schema.sql
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create_schema.sql
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# https://docs.python.org/3.4/library/http.cookies.html
CREATE TABLE guser (
id INT PRIMARY KEY AUTO_INCREMENT,
user_name VARCHAR(255),
email VARCHAR(255),
institution VARCHAR(255),
pass VARCHAR(50),
colorblind_mode TINYINT(1) DEFAULT 0,
updates_wanted TINYINT(1),
is_admin TINYINT(1) DEFAULT 0,
help_id VARCHAR(50),
date_created DATETIME DEFAULT CURRENT_TIMESTAMP,
is_gear_curator TINYINT(1) DEFAULT 0
) ENGINE=INNODB DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
# password is a hashlib md5 hexdigest
INSERT INTO guser (id, user_name, email, institution, pass, updates_wanted, is_admin)
VALUES (0, 'gEAR admin', 'admin@localhost', 'UMaryland', 'fcdf1dc2c1ef7dec3dbb1a6e2c5e3c8a', 0, 1);
INSERT INTO guser (email, user_name, institution, pass, updates_wanted, is_admin)
VALUES('jorvis@gmail.com', 'Joshua Orvis', 'IGS', 'e81e78d854d86edc38ba45c443662aee', 0, 1);
# Group is a reserved word, so we get gEAR Group (ggroup)
CREATE TABLE ggroup (
id INT PRIMARY KEY AUTO_INCREMENT,
creator_id INT NOT NULL,
label VARCHAR(255) NOT NULL,
FOREIGN KEY (creator_id) REFERENCES guser(id) ON DELETE CASCADE
) ENGINE=INNODB DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
CREATE TABLE user_group_membership (
id INT PRIMARY KEY AUTO_INCREMENT,
user_id INT NOT NULL,
group_id INT NOT NULL,
FOREIGN KEY (user_id) REFERENCES guser(id) ON DELETE CASCADE,
FOREIGN KEY (group_id) REFERENCES ggroup(id) ON DELETE CASCADE
) ENGINE=INNODB DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
CREATE TABLE user_session (
id INT PRIMARY KEY AUTO_INCREMENT,
user_id INT,
session_id VARCHAR(255),
FOREIGN KEY (user_id)
REFERENCES guser(id)
ON DELETE CASCADE
) ENGINE=INNODB DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
CREATE TABLE organism (
id INT PRIMARY KEY AUTO_INCREMENT,
label VARCHAR(255) NOT NULL,
genus VARCHAR(255),
species VARCHAR(255),
strain VARCHAR(255),
taxon_id INT
) ENGINE=INNODB DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
## DO NOT change these values without making corresponding changes in the annotation loading scripts
INSERT INTO organism (id, label, genus, species, strain, taxon_id)
VALUES (1, 'Mouse', 'Mus', 'musculus', NULL, 10090);
INSERT INTO organism (id, label, genus, species, strain, taxon_id)
VALUES (2, 'Human', 'Homo', 'sapiens', 'sapiens', 9606);
INSERT INTO organism (id, label, genus, species, strain, taxon_id)
VALUES (3, 'Zebrafish', 'Danio', 'rerio', NULL, 7955);
INSERT INTO organism (id, label, genus, species, strain, taxon_id)
VALUES (5, 'Chicken', 'Gallus', 'gallus', NULL, 9031);
INSERT INTO organism (id, label, genus, species, strain, taxon_id)
VALUES (6, 'Rat', 'Rattus', 'norvegicus', NULL, 10116);
INSERT INTO organism (id, label, genus, species, strain, taxon_id)
VALUES (7, 'Marmoset', 'Callithrix', 'jacchus', 'jacchus', 9483);
CREATE TABLE gene (
id INT PRIMARY KEY AUTO_INCREMENT,
ensembl_id VARCHAR(40),
ensembl_version VARCHAR(40),
ensembl_release INT NOT NULL,
genbank_acc VARCHAR(20),
organism_id INT NOT NULL,
molecule varchar(100),
start int(11),
stop int(11),
gene_symbol VARCHAR(20),
product VARCHAR(255),
biotype VARCHAR(100),
INDEX org_idx (organism_id),
INDEX org_sym (organism_id, gene_symbol),
FOREIGN KEY (organism_id) REFERENCES organism(id)
ON DELETE CASCADE
) ENGINE=INNODB DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
CREATE TABLE gene_cart (
id INT PRIMARY KEY AUTO_INCREMENT,
user_id INT NOT NULL,
organism_id INT NOT NULL,
gctype VARCHAR(50) NOT NULL DEFAULT 'unweighted-list',
label VARCHAR(255) NOT NULL,
ldesc TEXT,
share_id VARCHAR(50),
is_public TINYINT DEFAULT 0,
is_domain TINYINT DEFAULT 0,
date_added DATETIME DEFAULT CURRENT_TIMESTAMP,
FULLTEXT text_idx (label, ldesc),
FOREIGN KEY (user_id) REFERENCES guser(id) ON DELETE CASCADE,
FOREIGN KEY (organism_id) REFERENCES organism(id) ON DELETE CASCADE
) ENGINE=INNODB DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
CREATE TABLE gene_cart_member (
id INT PRIMARY KEY AUTO_INCREMENT,
gene_cart_id INT NOT NULL,
gene_symbol VARCHAR(20) NOT NULL,
FOREIGN KEY (gene_cart_id)
REFERENCES gene_cart(id)
ON DELETE CASCADE
) ENGINE=INNODB DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
CREATE TABLE gene_cart_group_membership (
id INT PRIMARY KEY AUTO_INCREMENT,
gene_cart_id INT NOT NULL,
group_id INT NOT NULL,
FOREIGN KEY (gene_cart_id) REFERENCES gene_cart(id) ON DELETE CASCADE,
FOREIGN KEY (group_id) REFERENCES ggroup(id) ON DELETE CASCADE
) ENGINE=INNODB DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
CREATE TABLE gene_symbol (
id INT PRIMARY KEY AUTO_INCREMENT,
gene_id INT NOT NULL,
label VARCHAR(30),
is_primary TINYINT(1) DEFAULT 0,
INDEX gene_symbol_label_idx (label),
FOREIGN KEY (gene_id) REFERENCES gene(id)
) ENGINE=INNODB DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
CREATE INDEX idx_gene_symbol__gene_id ON gene_symbol (gene_id);
CREATE INDEX idx_gene_symbol__label ON gene_symbol (label);
CREATE TABLE go (
go_id VARCHAR(20) PRIMARY KEY,
name VARCHAR(255) NOT NULL,
namespace VARCHAR(30) NOT NULL,
def TEXT
) ENGINE=INNODB DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
CREATE TABLE gene_go_link (
id INT UNIQUE KEY AUTO_INCREMENT,
gene_id INT NOT NULL,
go_id VARCHAR(20) NOT NULL,
PRIMARY KEY (gene_id, go_id),
FOREIGN KEY (gene_id) REFERENCES gene(id)
) ENGINE=INNODB DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
CREATE TABLE gene_dbxref (
id INT UNIQUE KEY AUTO_INCREMENT,
gene_id INT NOT NULL,
dbxref VARCHAR(100) NOT NULL,
PRIMARY KEY (gene_id, dbxref),
FOREIGN KEY (gene_id) REFERENCES gene(id)
) ENGINE=INNODB DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
CREATE TABLE mirna_family (
id INT PRIMARY KEY AUTO_INCREMENT,
stem_loop_id INT NOT NULL,
mature_id INT NOT NULL,
family_id VARCHAR(20),
family_label VARCHAR(20),
FOREIGN KEY (stem_loop_id) REFERENCES gene(id),
FOREIGN KEY (mature_id) REFERENCES gene(id)
) ENGINE=INNODB DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
CREATE TABLE anatomy (
id INT PRIMARY KEY AUTO_INCREMENT,
organism_id INT NOT NULL,
label VARCHAR(100),
parent_id INT,
FOREIGN KEY (parent_id)
REFERENCES anatomy(id)
ON DELETE CASCADE,
FOREIGN KEY (organism_id)
REFERENCES organism(id)
ON DELETE CASCADE
) ENGINE=INNODB DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
CREATE TABLE dataset (
id VARCHAR(50) PRIMARY KEY,
owner_id INT NOT NULL,
title VARCHAR(255) NOT NULL,
organism_id INT NOT NULL,
pubmed_id VARCHAR(20),
geo_id VARCHAR(50),
is_public TINYINT DEFAULT 0,
ldesc TEXT,
date_added DATETIME,
dtype VARCHAR(50) NOT NULL DEFAULT 'svg-expression',
# paths are relative to the root, so probably like datasets_uploaded/{dataset_id}.jpg
schematic_image VARCHAR(255),
share_id VARCHAR(50),
math_default VARCHAR(50) NOT NULL DEFAULT 'raw', #options: 'raw', 'log2', 'log10'
marked_for_removal TINYINT DEFAULT 0,
load_status VARCHAR(20), #options: 'pending', 'loading', 'completed', 'failed',
has_h5ad TINYINT DEFAULT 0,
platform_id VARCHAR(255),
instrument_model VARCHAR(255),
library_selection VARCHAR(255),
library_source VARCHAR(255),
library_strategy TEXT,
contact_email VARCHAR(100),
contact_institute VARCHAR(255),
contact_name VARCHAR(100),
annotation_source VARCHAR(20),
plot_default VARCHAR(50), #options: 'bar', 'line', 'violin'
annotation_release INT,
FULLTEXT text_idx (title, ldesc),
FULLTEXT text_with_geo_idx (title, ldesc, geo_id),
FULLTEXT text_with_geo_pubmed_idx (title, ldesc, geo_id, pubmed_id),
FOREIGN KEY (owner_id)
REFERENCES guser(id)
ON DELETE CASCADE,
FOREIGN KEY (organism_id)
REFERENCES organism(id)
ON DELETE CASCADE
) ENGINE=INNODB DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
CREATE TABLE dataset_display (
id INT PRIMARY KEY AUTO_INCREMENT,
dataset_id VARCHAR(50) NOT NULL,
user_id INT NOT NULL,
label VARCHAR(255),
plot_type VARCHAR(20),
plotly_config TEXT,
FOREIGN KEY (dataset_id)
REFERENCES dataset(id)
ON DELETE CASCADE,
FOREIGN KEY (user_id)
REFERENCES guser(id)
ON DELETE CASCADE
) ENGINE=INNODB DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
CREATE TABLE dataset_preference (
user_id INT NOT NULL,
dataset_id VARCHAR(50) NOT NULL,
display_id INT NOT NULL,
is_multigene TINYINT(1) DEFAULT 0,
primary key (user_id, dataset_id, is_multigene),
FOREIGN KEY (dataset_id)
REFERENCES dataset(id)
ON DELETE CASCADE,
FOREIGN KEY (user_id)
REFERENCES guser(id)
ON DELETE CASCADE,
FOREIGN KEY (display_id)
REFERENCES dataset_display(id)
ON DELETE CASCADE
) ENGINE=INNODB DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
# Stores custom external URLs to be displayed with each dataset
CREATE TABLE dataset_link (
id INT PRIMARY KEY AUTO_INCREMENT,
dataset_id VARCHAR(50) NOT NULL,
resource VARCHAR(100) NOT NULL,
label VARCHAR(100) NOT NULL,
url VARCHAR(255) NOT NULL
);
CREATE TABLE dataset_shares (
id INT PRIMARY KEY AUTO_INCREMENT,
dataset_id VARCHAR(50) NOT NULL,
user_id INT NOT NULL,
is_allowed TINYINT(1) DEFAULT 0,
FOREIGN KEY (dataset_id)
REFERENCES dataset(id)
ON DELETE CASCADE,
FOREIGN KEY (user_id)
REFERENCES guser(id)
ON DELETE CASCADE
) ENGINE=INNODB DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
# Recursive organizational table allowing item types (like gene carts
# or profiles) to be grouped into 'folders'
CREATE TABLE folder (
id INT PRIMARY KEY AUTO_INCREMENT,
parent_id INT,
label VARCHAR(100) NOT NULL,
FOREIGN KEY (parent_id) REFERENCES folder(id) ON DELETE CASCADE
) ENGINE=INNODB DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
CREATE TABLE folder_member (
id INT PRIMARY KEY AUTO_INCREMENT,
folder_id INT NOT NULL,
item_id INT NOT NULL,
item_type VARCHAR(20) NOT NULL, #options: 'layout', 'genecart'
FOREIGN KEY (folder_id) REFERENCES folder(id) ON DELETE CASCADE,
UNIQUE KEY uk_folder_item (folder_id, item_id, item_type)
) ENGINE=INNODB DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
CREATE TABLE layout (
id INT PRIMARY KEY AUTO_INCREMENT,
user_id INT NOT NULL,
label VARCHAR(255),
is_current TINYINT(1) DEFAULT 0,
is_domain TINYINT(1) DEFAULT 0,
share_id VARCHAR(24),
FOREIGN KEY (user_id)
REFERENCES guser(id)
ON DELETE CASCADE
) ENGINE=INNODB DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
INSERT INTO layout VALUES (0, 0, NULL, "Hearing (default)", 1);
INSERT INTO layout VALUES (10000, 0, NULL, "Brain development (default)", 0);
INSERT INTO layout VALUES (10001, 0, NULL, "Huntingtons disease (default)", 0);
CREATE TABLE layout_members (
id INT PRIMARY KEY AUTO_INCREMENT,
layout_id INT NOT NULL,
dataset_id VARCHAR(50) NOT NULL,
grid_position INT NOT NULL,
grid_width INT NOT NULL,
mg_grid_width INT NOT NULL,
math_preference VARCHAR(50), #options: 'raw', 'log2', 'log10'
plot_preference VARCHAR(50), #options: 'bar', 'line', 'violin'
FOREIGN KEY (layout_id)
REFERENCES layout(id)
ON DELETE CASCADE,
FOREIGN KEY (dataset_id)
REFERENCES dataset(id)
ON DELETE CASCADE
) ENGINE=INNODB DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
CREATE TABLE layout_group_membership (
id INT PRIMARY KEY AUTO_INCREMENT,
layout_id INT NOT NULL,
group_id INT NOT NULL,
FOREIGN KEY (layout_id) REFERENCES layout(id) ON DELETE CASCADE,
FOREIGN KEY (group_id) REFERENCES ggroup(id) ON DELETE CASCADE
) ENGINE=INNODB DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
CREATE TABLE supplemental_images (
id INT PRIMARY KEY AUTO_INCREMENT,
# label is a meant to identify the class of image
label VARCHAR(50),
ensembl_id VARCHAR(20),
gene_symbol VARCHAR(20),
image_url VARCHAR(200),
index gene_sym_idx(gene_symbol)
) ENGINE=INNODB DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
CREATE TABLE tag (
id INT PRIMARY KEY AUTO_INCREMENT,
label VARCHAR(55)
) ENGINE=INNODB DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
# multiple tags to multiple comments
CREATE TABLE comment_tag (
id INT PRIMARY KEY AUTO_INCREMENT,
tag_id INT,
comment_id INT,
FOREIGN KEY (tag_id) REFERENCES tag(id),
FOREIGN KEY (comment_id)
REFERENCES comment(id)
ON DELETE CASCADE
) ENGINE=INNODB DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
CREATE TABLE dataset_tag (
id INT PRIMARY KEY AUTO_INCREMENT,
tag_id INT,
dataset_id VARCHAR(50) NOT NULL,
FOREIGN KEY (tag_id)
REFERENCES tag(id),
FOREIGN KEY (dataset_id)
REFERENCES dataset(id)
ON DELETE CASCADE
) ENGINE=INNODB DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
CREATE TABLE note (
id INT PRIMARY KEY AUTO_INCREMENT,
title VARCHAR(100),
ldesc TEXT,
user_id INT,
dataset_id VARCHAR(50),
is_public TINYINT DEFAULT 0,
date_added DATETIME,
date_last_change DATETIME,
FOREIGN KEY (user_id)
REFERENCES guser(id),
FOREIGN KEY (dataset_id)
REFERENCES dataset(id)
) ENGINE=INNODB DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;
CREATE TABLE `dataset_epiviz` (
`id` varchar(50) NOT NULL,
`owner_id` int(11) NOT NULL,
`annotation` text,
`type` varchar(10) NOT NULL,
`url` text NOT NULL,
`title` text,
`is_public` tinyint(4) DEFAULT '0',
`description` text,
`share_id` varchar(50) NOT NULL,
`organism` varchar(100) DEFAULT NULL
) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci;