Select Git revision
setup-schema.sql
Martin Weise authored
setup-schema.sql 20.77 KiB
BEGIN;
CREATE TABLE IF NOT EXISTS `mdb_users`
(
id character varying(36) NOT NULL,
username character varying(255) NOT NULL,
firstname character varying(255),
lastname character varying(255),
email character varying(255) NOT NULL,
orcid character varying(255),
affiliation character varying(255),
mariadb_password character varying(255) NOT NULL,
theme_dark boolean,
PRIMARY KEY (id),
UNIQUE (username),
UNIQUE (email)
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_images`
(
id bigint NOT NULL AUTO_INCREMENT,
name character varying(255) NOT NULL,
version character varying(255) NOT NULL,
default_port integer NOT NULL,
dialect character varying(255) NOT NULL,
driver_class character varying(255) NOT NULL,
jdbc_method character varying(255) NOT NULL,
created timestamp NOT NULL DEFAULT NOW(),
last_modified timestamp,
PRIMARY KEY (id),
UNIQUE (name, version)
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_images_date`
(
id bigint NOT NULL AUTO_INCREMENT,
iid bigint NOT NULL,
database_format character varying(255) NOT NULL,
unix_format character varying(255) NOT NULL,
example character varying(255) NOT NULL,
has_time boolean NOT NULL,
created_at timestamp NOT NULL DEFAULT NOW(),
PRIMARY KEY (id),
FOREIGN KEY (iid) REFERENCES mdb_images (id),
UNIQUE (database_format, unix_format, example)
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_containers`
(
id bigint NOT NULL AUTO_INCREMENT,
internal_name character varying(255) NOT NULL,
name character varying(255) NOT NULL,
host character varying(255) NOT NULL,
port integer NOT NULL,
sidecar_host character varying(255) NOT NULL,
sidecar_port integer NOT NULL,
image_id bigint NOT NULL,
created timestamp NOT NULL DEFAULT NOW(),
last_modified timestamp,
privileged_username character varying(255) NOT NULL,
privileged_password character varying(255) NOT NULL,
PRIMARY KEY (id),
FOREIGN KEY (image_id) REFERENCES mdb_images (id)
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_data`
(
ID bigint NOT NULL AUTO_INCREMENT,
PROVENANCE text,
FileEncoding text, FileType character varying(100),
Version text,
Seperator text,
PRIMARY KEY (ID)
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_licenses`
(
identifier character varying(255) NOT NULL,
uri text NOT NULL,
PRIMARY KEY (identifier),
UNIQUE (uri(200))
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_databases`
(
id bigint NOT NULL AUTO_INCREMENT,
cid bigint NOT NULL,
name character varying(255) NOT NULL,
internal_name character varying(255) NOT NULL,
exchange_name character varying(255) NOT NULL,
description text,
engine character varying(20),
is_public boolean NOT NULL DEFAULT TRUE,
created_by character varying(36),
owned_by character varying(36),
contact_person character varying(36),
created timestamp NOT NULL DEFAULT NOW(),
last_modified timestamp,
PRIMARY KEY (id),
FOREIGN KEY (cid) REFERENCES mdb_containers (id) /* currently we only support one-to-one */,
FOREIGN KEY (created_by) REFERENCES mdb_users (id),
FOREIGN KEY (owned_by) REFERENCES mdb_users (id),
FOREIGN KEY (contact_person) REFERENCES mdb_users (id)
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_databases_subjects`
(
dbid BIGINT NOT NULL,
subjects character varying(255) NOT NULL,
PRIMARY KEY (dbid, subjects)
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_tables`
(
ID bigint NOT NULL AUTO_INCREMENT,
tDBID bigint NOT NULL,
internal_name character varying(255) NOT NULL,
queue_name character varying(255) NOT NULL,
routing_key character varying(255) NOT NULL,
tName VARCHAR(50),
tDescription TEXT,
NumCols INTEGER,
NumRows INTEGER,
`separator` CHAR(1),
quote CHAR(1),
element_null VARCHAR(50),
skip_lines BIGINT,
element_true VARCHAR(50),
element_false VARCHAR(50),
Version TEXT,
created timestamp NOT NULL DEFAULT NOW(),
versioned boolean not null default true,
created_by character varying(36) NOT NULL,
owned_by character varying(36) NOT NULL,
last_modified timestamp,
PRIMARY KEY (ID),
FOREIGN KEY (tDBID) REFERENCES mdb_databases (id),
FOREIGN KEY (created_by) REFERENCES mdb_users (id),
FOREIGN KEY (owned_by) REFERENCES mdb_users (id)) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_columns`
(
ID bigint NOT NULL AUTO_INCREMENT,
tID bigint NOT NULL,
dfID bigint,
cName VARCHAR(100),
internal_name VARCHAR(100) NOT NULL,
alias VARCHAR(100),
Datatype ENUM ('CHAR','VARCHAR','BINARY','VARBINARY','TINYBLOB','TINYTEXT','TEXT','BLOB','MEDIUMTEXT','MEDIUMBLOB','LONGTEXT','LONGBLOB','ENUM','SET','BIT','TINYINT','BOOL','SMALLINT','MEDIUMINT','INT','BIGINT','FLOAT','DOUBLE','DECIMAL','DATE','DATETIME','TIMESTAMP','TIME','YEAR'),
length INT NULL,
ordinal_position INTEGER NOT NULL,
is_primary_key BOOLEAN NOT NULL,
index_length INT NULL,
size INT,
d INT,
auto_generated BOOLEAN DEFAULT false,
is_null_allowed BOOLEAN NOT NULL DEFAULT true,
created timestamp NOT NULL DEFAULT NOW(),
last_modified timestamp,
FOREIGN KEY (tID) REFERENCES mdb_tables (ID),
PRIMARY KEY (ID)
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_columns_enums`
(
id bigint NOT NULL AUTO_INCREMENT,
column_id bigint NOT NULL,
value CHARACTER VARYING(255) NOT NULL,
FOREIGN KEY (column_id) REFERENCES mdb_columns (ID),
PRIMARY KEY (id)
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_columns_sets`
(
id bigint NOT NULL AUTO_INCREMENT,
column_id bigint NOT NULL,
value CHARACTER VARYING(255) NOT NULL,
FOREIGN KEY (column_id) REFERENCES mdb_columns (ID),
PRIMARY KEY (id)
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_columns_nom`
(
tID bigint,
cID bigint,
maxlength INTEGER,
last_modified timestamp,
created timestamp NOT NULL DEFAULT NOW(),
FOREIGN KEY (tID, cID) REFERENCES mdb_columns (tID, ID),
PRIMARY KEY (tID, cID)
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_columns_num`
(
tID bigint,
cID bigint,
SIunit TEXT,
MaxVal NUMERIC,
MinVal NUMERIC,
Mean NUMERIC,
Median NUMERIC,
Sd Numeric,
-- Histogram INTEGER[],
last_modified timestamp,
created timestamp NOT NULL DEFAULT NOW(),
FOREIGN KEY (tID, cID) REFERENCES mdb_columns (tID, ID),
PRIMARY KEY (tID, cID)
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_columns_cat`
(
tID bigint,
cID bigint,
num_cat INTEGER,
-- cat_array TEXT[],
last_modified timestamp,
created timestamp NOT NULL DEFAULT NOW(),
FOREIGN KEY (tID, cID) REFERENCES mdb_columns (tID, ID),
PRIMARY KEY (tID, cID)
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_constraints_foreign_key`
(
fkid BIGINT NOT NULL AUTO_INCREMENT,
tid BIGINT NOT NULL,
rtid BIGINT NOT NULL,
on_update VARCHAR(50) NULL,
on_delete VARCHAR(50) NULL,
position INT NULL,
PRIMARY KEY (fkid),
FOREIGN KEY (tid) REFERENCES mdb_tables (id),
FOREIGN KEY (rtid) REFERENCES mdb_tables (id)
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_constraints_foreign_key_reference`
(
id BIGINT NOT NULL AUTO_INCREMENT,
fkid BIGINT NOT NULL,
cid BIGINT NOT NULL,
rcid BIGINT NOT NULL,
PRIMARY KEY (id),
FOREIGN KEY (fkid) REFERENCES mdb_constraints_foreign_key (fkid) ON UPDATE CASCADE,
FOREIGN KEY (cid) REFERENCES mdb_columns (id),
FOREIGN KEY (rcid) REFERENCES mdb_columns (id)
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_constraints_unique`
(
uid BIGINT NOT NULL AUTO_INCREMENT,
tid BIGINT NOT NULL,
position INT NULL,
PRIMARY KEY (uid),
FOREIGN KEY (tid) REFERENCES mdb_tables (id)
);
CREATE TABLE IF NOT EXISTS `mdb_constraints_unique_columns`
(
id BIGINT NOT NULL AUTO_INCREMENT,
uid BIGINT NOT NULL,
cid BIGINT NOT NULL,
PRIMARY KEY (id),
FOREIGN KEY (uid) REFERENCES mdb_constraints_unique (uid),
FOREIGN KEY (cid) REFERENCES mdb_columns (id)
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_constraints_checks`
(
id BIGINT NOT NULL AUTO_INCREMENT,
tid BIGINT NOT NULL,
checks VARCHAR(255) NOT NULL,
PRIMARY KEY (id),
FOREIGN KEY (tid) REFERENCES mdb_tables (id)
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_concepts`
(
id bigint NOT NULL AUTO_INCREMENT,
uri text not null, name VARCHAR(255) null,
description TEXT null,
created timestamp NOT NULL DEFAULT NOW(),
PRIMARY KEY (id),
UNIQUE (uri(200))
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_units`
(
id bigint NOT NULL AUTO_INCREMENT,
uri text not null,
name VARCHAR(255) null,
description TEXT null,
created timestamp NOT NULL DEFAULT NOW(),
PRIMARY KEY (id),
UNIQUE (uri(200))
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_columns_concepts`
(
id bigint NOT NULL,
cID bigint NOT NULL,
created timestamp NOT NULL DEFAULT NOW(),
PRIMARY KEY (id),
FOREIGN KEY (cID) REFERENCES mdb_columns (ID)
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_columns_units`
(
id bigint NOT NULL,
cID bigint NOT NULL,
created timestamp NOT NULL DEFAULT NOW(),
PRIMARY KEY (id),
FOREIGN KEY (cID) REFERENCES mdb_columns (ID)
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_view`
(
id bigint NOT NULL AUTO_INCREMENT,
vdbid bigint NOT NULL,
vName VARCHAR(255) NOT NULL,
internal_name VARCHAR(255) NOT NULL,
Query TEXT NOT NULL,
query_hash VARCHAR(255) NOT NULL,
Public BOOLEAN NOT NULL,
NumCols INTEGER,
NumRows INTEGER,
InitialView BOOLEAN NOT NULL,
created timestamp NOT NULL DEFAULT NOW(),
last_modified timestamp,
created_by character varying(36) NOT NULL,
PRIMARY KEY (id),
FOREIGN KEY (vdbid) REFERENCES mdb_databases (id),
FOREIGN KEY (created_by) REFERENCES mdb_users (id)
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_banner_messages`
(
id bigint NOT NULL AUTO_INCREMENT,
type ENUM ('ERROR', 'WARNING', 'INFO') NOT NULL default 'INFO',
message TEXT NOT NULL,
link TEXT NULL,
link_text VARCHAR(255) NULL,
display_start timestamp NULL,
display_end timestamp NULL,
PRIMARY KEY (id)
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_ontologies`
( id bigint NOT NULL AUTO_INCREMENT,
prefix VARCHAR(8) NOT NULL,
uri TEXT NOT NULL,
uri_pattern TEXT,
sparql_endpoint TEXT NULL,
last_modified timestamp,
created timestamp NOT NULL DEFAULT NOW(),
UNIQUE (prefix),
UNIQUE (uri(200)),
PRIMARY KEY (id)
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_view_columns`
(
id BIGINT NOT NULL AUTO_INCREMENT,
cid BIGINT NOT NULL,
vid BIGINT NOT NULL,
position INTEGER NULL,
PRIMARY KEY (id),
FOREIGN KEY (vid) REFERENCES mdb_view (id),
FOREIGN KEY (cid) REFERENCES mdb_columns (ID)
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_identifiers`
(
id bigint NOT NULL AUTO_INCREMENT,
dbid bigint,
qid bigint,
vid bigint,
publisher VARCHAR(255) NOT NULL,
language VARCHAR(2),
visibility ENUM ('SELF', 'EVERYONE') NOT NULL default 'EVERYONE',
publication_year INTEGER NOT NULL,
publication_month INTEGER,
publication_day INTEGER,
identifier_type ENUM ('DATABASE', 'SUBSET', 'VIEW') NOT NULL,
query TEXT,
query_normalized TEXT,
query_hash VARCHAR(255),
execution timestamp,
result_hash VARCHAR(255),
result_number bigint,
doi VARCHAR(255),
created timestamp NOT NULL DEFAULT NOW(),
created_by character varying(36) NOT NULL,
last_modified timestamp,
PRIMARY KEY (id), /* must be a single id from persistent identifier concept */
FOREIGN KEY (dbid) REFERENCES mdb_databases (id),
UNIQUE (dbid, qid),
FOREIGN KEY (created_by) REFERENCES mdb_users (id)
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_identifier_licenses`
(
pid bigint NOT NULL,
license_id VARCHAR(255) NOT NULL,
PRIMARY KEY (pid, license_id),
FOREIGN KEY (pid) REFERENCES mdb_identifiers (id),
FOREIGN KEY (license_id) REFERENCES mdb_licenses (identifier)
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_identifier_titles`
(
id bigint NOT NULL AUTO_INCREMENT,
pid bigint NOT NULL,
title text NOT NULL,
title_type ENUM ('ALTERNATIVE_TITLE', 'SUBTITLE', 'TRANSLATED_TITLE', 'OTHER'),
language VARCHAR(2),
PRIMARY KEY (id),
FOREIGN KEY (pid) REFERENCES mdb_identifiers (id)) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_identifier_funders`
(
id bigint NOT NULL AUTO_INCREMENT,
pid bigint NOT NULL,
funder_name VARCHAR(255) NOT NULL,
funder_identifier TEXT,
funder_identifier_type ENUM ('CROSSREF_FUNDER_ID', 'GRID', 'ISNI', 'ROR', 'OTHER'),
scheme_uri text,
award_number VARCHAR(255),
award_title text,
language VARCHAR(255),
PRIMARY KEY (id),
FOREIGN KEY (pid) REFERENCES mdb_identifiers (id)
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_identifier_descriptions`
(
id bigint NOT NULL AUTO_INCREMENT,
pid bigint NOT NULL,
description text NOT NULL,
description_type ENUM ('ABSTRACT', 'METHODS', 'SERIES_INFORMATION', 'TABLE_OF_CONTENTS', 'TECHNICAL_INFO', 'OTHER'),
language VARCHAR(2),
PRIMARY KEY (id),
FOREIGN KEY (pid) REFERENCES mdb_identifiers (id)
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_related_identifiers`
(
id bigint NOT NULL AUTO_INCREMENT,
pid bigint NOT NULL,
value varchar(255) NOT NULL,
type varchar(255),
relation varchar(255),
PRIMARY KEY (id), /* must be a single id from persistent identifier concept */
FOREIGN KEY (pid) REFERENCES mdb_identifiers (id),
UNIQUE (pid, value)
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_identifier_creators`
(
id bigint NOT NULL AUTO_INCREMENT,
pid bigint NOT NULL,
given_names text,
family_name text,
creator_name VARCHAR(255) NOT NULL,
name_type ENUM ('PERSONAL', 'ORGANIZATIONAL') default 'PERSONAL',
name_identifier text,
name_identifier_scheme ENUM ('ROR', 'GRID', 'ISNI', 'ORCID'),
name_identifier_scheme_uri text,
affiliation VARCHAR(255),
affiliation_identifier text,
affiliation_identifier_scheme ENUM ('ROR', 'GRID', 'ISNI'),
affiliation_identifier_scheme_uri text,
PRIMARY KEY (id),
FOREIGN KEY (pid) REFERENCES mdb_identifiers (id)
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_feed`
(
fDBID bigint,
fID bigint,
fUserId character varying(36) not null,
fDataID bigint REFERENCES mdb_data (ID),
created timestamp NOT NULL DEFAULT NOW(),
PRIMARY KEY (fDBID, fID, fUserId, fDataID),
FOREIGN KEY (fDBID, fID) REFERENCES mdb_tables (tDBID, ID),
FOREIGN KEY (fUserId) REFERENCES mdb_users (id)
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_update`
(
uUserID character varying(255) NOT NULL,
uDBID bigint NOT NULL,
created timestamp NOT NULL DEFAULT NOW(),
PRIMARY KEY (uUserID, uDBID),
FOREIGN KEY (uDBID) REFERENCES mdb_databases (id)
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_access`
(
aUserID character varying(255) NOT NULL,
aDBID bigint REFERENCES mdb_databases (id),
attime TIMESTAMP,
download BOOLEAN,
created timestamp NOT NULL DEFAULT NOW(),
PRIMARY KEY (aUserID, aDBID)
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_have_access`
(
user_id character varying(36) NOT NULL,
database_id bigint REFERENCES mdb_databases (id),
access_type ENUM ('READ', 'WRITE_OWN', 'WRITE_ALL') NOT NULL,
created timestamp NOT NULL DEFAULT NOW(),
PRIMARY KEY (user_id, database_id),
FOREIGN KEY (user_id) REFERENCES mdb_users (id)
) WITH SYSTEM VERSIONING;
COMMIT;
BEGIN;
INSERT INTO `mdb_licenses` (identifier, uri)
VALUES ('MIT', 'https://opensource.org/licenses/MIT'),
('GPL-3.0-only', 'https://www.gnu.org/licenses/gpl-3.0-standalone.html'),
('BSD-3-Clause', 'https://opensource.org/licenses/BSD-3-Clause'),
('BSD-4-Clause', 'http://directory.fsf.org/wiki/License:BSD_4Clause'),
('Apache-2.0', 'https://opensource.org/licenses/Apache-2.0'),
('CC0-1.0', 'https://creativecommons.org/publicdomain/zero/1.0/legalcode'),
('CC-BY-4.0', 'https://creativecommons.org/licenses/by/4.0/legalcode');
INSERT INTO `mdb_images` (name, version, default_port, dialect, driver_class, jdbc_method)
VALUES ('mariadb', '10.5', 3306, 'org.hibernate.dialect.MariaDBDialect', 'org.mariadb.jdbc.Driver', 'mariadb');
INSERT INTO `mdb_images_date` (iid, database_format, unix_format, example, has_time)
VALUES (1, '%Y-%c-%d %H:%i:%S.%f', 'yyyy-MM-dd HH:mm:ss.SSSSSS', '2022-01-30 13:44:25.499', true),
(1, '%Y-%c-%d %H:%i:%S', 'yyyy-MM-dd HH:mm:ss', '2022-01-30 13:44:25', true),
(1, '%Y-%c-%d', 'yyyy-MM-dd', '2022-01-30', false),
(1, '%H:%i:%S', 'HH:mm:ss', '13:44:25', true);
INSERT INTO `mdb_ontologies` (prefix, uri, uri_pattern, sparql_endpoint)
VALUES ('om', 'http://www.ontology-of-units-of-measure.org/resource/om-2/',
'http://www.ontology-of-units-of-measure.org/resource/om-2/.*', null),
('wd', 'http://www.wikidata.org/', 'http://www.wikidata.org/entity/.*', 'https://query.wikidata.org/sparql'),
('mo', 'http://purl.org/ontology/mo/', 'http://purl.org/ontology/mo/.*', null),
('dc', 'http://purl.org/dc/elements/1.1/', null, null),
('xsd', 'http://www.w3.org/2001/XMLSchema#', null, null),
('tl', 'http://purl.org/NET/c4dm/timeline.owl#', null, null),
('foaf', 'http://xmlns.com/foaf/0.1/', null, null),
('schema', 'http://schema.org/', null, null),
('rdf', 'http://www.w3.org/1999/02/22-rdf-syntax-ns#', null, null),
('rdfs', 'http://www.w3.org/2000/01/rdf-schema#', null, null),
('owl', 'http://www.w3.org/2002/07/owl#', null, null),
('prov', 'http://www.w3.org/ns/prov#', null, null),
('db', 'http://dbpedia.org', 'http://dbpedia.org/ontology/.*', 'http://dbpedia.org/sparql');
COMMIT;