diff --git a/.docker/.env b/.docker/.env
new file mode 100644
index 0000000000000000000000000000000000000000..6e598a8d0adf7f76559845e3d88b1bc80f314aff
--- /dev/null
+++ b/.docker/.env
@@ -0,0 +1,12 @@
+# UNCOMMENT THE LINES BELOW TO OVERRIDE
+#BASE_URL=http://example.com
+#ADMIN_EMAIL=noreply@example.com
+#LOG_LEVEL=debug
+#IDENTITY_SERVICE_ADMIN_PASSWORD=admin
+#AUTH_SERVICE_ADMIN_PASSWORD=admin
+#METADATA_DB_PASSWORD=dbrepo
+#DATA_DB_PASSWORD=dbrepo
+#AUTH_DB_PASSWORD=dbrepo
+#S3_ACCESS_KEY_ID=seaweedfsadmin
+#S3_SECRET_ACCESS_KEY=seaweedfsadmin
+#SYSTEM_PASSWORD=admin
diff --git a/.docker/config/1_setup-schema.sql b/.docker/config/1_setup-schema.sql
new file mode 100644
index 0000000000000000000000000000000000000000..47ee3a95e2b88a62d4a2405f9c0f4d088167d748
--- /dev/null
+++ b/.docker/config/1_setup-schema.sql
@@ -0,0 +1,564 @@
+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 character varying(255) NOT NULL default ('light'),
+ language character varying(3) NOT NULL default ('en'),
+ PRIMARY KEY (id),
+ UNIQUE (username),
+ UNIQUE (email)
+) WITH SYSTEM VERSIONING;
+
+CREATE TABLE IF NOT EXISTS `mdb_images`
+(
+ id bigint NOT NULL AUTO_INCREMENT,
+ registry character varying(255) NOT NULL DEFAULT 'docker.io',
+ 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,
+ is_default BOOLEAN NOT NULL DEFAULT FALSE,
+ created timestamp NOT NULL DEFAULT NOW(),
+ last_modified timestamp,
+ PRIMARY KEY (id),
+ UNIQUE (name, version),
+ UNIQUE (is_default)
+) 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 default 3306,
+ ui_host character varying(255) NOT NULL default host,
+ ui_port integer NOT NULL default port,
+ ui_additional_flags text,
+ sidecar_host character varying(255),
+ sidecar_port integer,
+ 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,
+ quota integer NOT NULL DEFAULT 50,
+ 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,
+ description 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,
+ image longblob,
+ 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,
+ tName VARCHAR(64) NOT NULL,
+ internal_name VARCHAR(64) NOT NULL,
+ queue_name VARCHAR(255) NOT NULL,
+ routing_key VARCHAR(255),
+ tDescription VARCHAR(2048),
+ num_rows BIGINT,
+ data_length BIGINT,
+ max_data_length BIGINT,
+ avg_row_length BIGINT,
+ `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),
+ UNIQUE (tDBID, internal_name),
+ 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(64),
+ internal_name VARCHAR(64) NOT NULL,
+ 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 BIGINT NULL,
+ ordinal_position INTEGER NOT NULL,
+ index_length BIGINT NULL,
+ description VARCHAR(2048),
+ size BIGINT,
+ d BIGINT,
+ auto_generated BOOLEAN DEFAULT false,
+ is_null_allowed BOOLEAN NOT NULL DEFAULT true,
+ val_min NUMERIC NULL,
+ val_max NUMERIC NULL,
+ mean NUMERIC NULL,
+ median NUMERIC NULL,
+ std_dev Numeric NULL,
+ created timestamp NOT NULL DEFAULT NOW(),
+ last_modified timestamp,
+ FOREIGN KEY (tID) REFERENCES mdb_tables (ID) ON DELETE CASCADE,
+ 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) ON DELETE CASCADE,
+ 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) ON DELETE CASCADE,
+ 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_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,
+ name VARCHAR(255) 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) ON DELETE CASCADE,
+ FOREIGN KEY (rtid) REFERENCES mdb_tables (id)
+) WITH SYSTEM VERSIONING;
+
+CREATE TABLE IF NOT EXISTS `mdb_constraints_primary_key`
+(
+ pkid BIGINT NOT NULL AUTO_INCREMENT,
+ tID BIGINT NOT NULL,
+ cid BIGINT NOT NULL,
+ PRIMARY KEY (pkid),
+ FOREIGN KEY (tID) REFERENCES mdb_tables (id) ON DELETE CASCADE,
+ FOREIGN KEY (cid) REFERENCES mdb_columns (id) ON DELETE CASCADE
+) 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),
+ UNIQUE (fkid, cid, rcid),
+ 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,
+ name VARCHAR(255) NOT NULL,
+ tid BIGINT NOT NULL,
+ position INT NULL,
+ PRIMARY KEY (uid),
+ FOREIGN KEY (tid) REFERENCES mdb_tables (id) ON DELETE CASCADE
+);
+
+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) ON DELETE CASCADE
+) 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) ON DELETE CASCADE
+) 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, cid),
+ 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, cID),
+ 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(64) NOT NULL,
+ internal_name VARCHAR(64) NOT NULL,
+ Query TEXT NOT NULL,
+ query_hash VARCHAR(255) NOT NULL,
+ Public BOOLEAN NOT NULL,
+ 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,
+ rdf_path 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,
+ view_id BIGINT NOT NULL,
+ dfID BIGINT,
+ name VARCHAR(64),
+ internal_name VARCHAR(64) NOT NULL,
+ column_type 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'),
+ ordinal_position INTEGER NOT NULL,
+ size BIGINT,
+ d BIGINT,
+ auto_generated BOOLEAN DEFAULT false,
+ is_null_allowed BOOLEAN NOT NULL DEFAULT true,
+ PRIMARY KEY (id),
+ FOREIGN KEY (view_id) REFERENCES mdb_view (id)
+) WITH SYSTEM VERSIONING;
+
+CREATE TABLE IF NOT EXISTS `mdb_identifiers`
+(
+ id BIGINT NOT NULL AUTO_INCREMENT,
+ dbid BIGINT NOT NULL,
+ qid BIGINT,
+ vid BIGINT,
+ tid BIGINT,
+ publisher VARCHAR(255) NOT NULL,
+ language VARCHAR(2),
+ publication_year INTEGER NOT NULL,
+ publication_month INTEGER,
+ publication_day INTEGER,
+ identifier_type ENUM ('DATABASE', 'SUBSET', 'VIEW', 'TABLE') NOT NULL,
+ status ENUM ('DRAFT', 'PUBLISHED') NOT NULL DEFAULT ('PUBLISHED'),
+ 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 VARCHAR(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),
+ 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) NOT NULL,
+ relation varchar(255) NOT NULL,
+ 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_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, description)
+VALUES ('CC0-1.0', 'https://creativecommons.org/publicdomain/zero/1.0/legalcode',
+ 'CC0 waives copyright interest in a work you''ve created and dedicates it to the world-wide public domain. Use CC0 to opt out of copyright entirely and ensure your work has the widest reach.'),
+ ('CC-BY-4.0', 'https://creativecommons.org/licenses/by/4.0/legalcode',
+ 'The Creative Commons Attribution license allows re-distribution and re-use of a licensed work on the condition that the creator is appropriately credited.');
+
+INSERT INTO `mdb_images` (name, registry, version, default_port, dialect, driver_class, jdbc_method)
+VALUES ('mariadb', 'docker.io', '11.1.3', 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),
+ (1, '%d.%c.%Y', 'dd.MM.yyyy', '30.01.2022', false);
+
+INSERT INTO `mdb_ontologies` (prefix, uri, uri_pattern, sparql_endpoint, rdf_path)
+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, 'rdf/om-2.0.rdf'),
+ ('wd', 'http://www.wikidata.org/', 'http://www.wikidata.org/entity/.*', 'https://query.wikidata.org/sparql',
+ null),
+ ('mo', 'http://purl.org/ontology/mo/', 'http://purl.org/ontology/mo/.*', null, null),
+ ('dc', 'http://purl.org/dc/elements/1.1/', null, null, null),
+ ('xsd', 'http://www.w3.org/2001/XMLSchema#', null, null, null),
+ ('tl', 'http://purl.org/NET/c4dm/timeline.owl#', null, null, null),
+ ('foaf', 'http://xmlns.com/foaf/0.1/', null, null, null),
+ ('schema', 'http://schema.org/', null, null, null),
+ ('rdf', 'http://www.w3.org/1999/02/22-rdf-syntax-ns#', null, null, null),
+ ('rdfs', 'http://www.w3.org/2000/01/rdf-schema#', null, null, null),
+ ('owl', 'http://www.w3.org/2002/07/owl#', null, null, null),
+ ('prov', 'http://www.w3.org/ns/prov#', null, null, null),
+ ('db', 'http://dbpedia.org', 'http://dbpedia.org/ontology/.*', 'http://dbpedia.org/sparql', null);
+COMMIT;
diff --git a/.docker/config/2_setup-data.sql b/.docker/config/2_setup-data.sql
new file mode 100644
index 0000000000000000000000000000000000000000..e806e1e181dbdcc3f0e4e29f837bffac7123317c
--- /dev/null
+++ b/.docker/config/2_setup-data.sql
@@ -0,0 +1,8 @@
+BEGIN;
+
+INSERT INTO `mdb_containers` (name, internal_name, image_id, host, port, ui_host, ui_port, sidecar_host, sidecar_port,
+ privileged_username, privileged_password)
+VALUES ('mariadb:11.1.3-debian-11-r6', 'mariadb_11_1_3', 1, 'data-db', 3306, 'localhost', 3306, 'data-db-sidecar', 8080,
+ 'root', 'dbrepo');
+
+COMMIT;
diff --git a/.docker/config/advanced.config b/.docker/config/advanced.config
new file mode 100644
index 0000000000000000000000000000000000000000..4445ea601954e5c93c32edeba1638135c5af5e59
--- /dev/null
+++ b/.docker/config/advanced.config
@@ -0,0 +1,17 @@
+[
+ {
+ rabbitmq_auth_backend_ldap,
+ [
+ {
+ tag_queries, [
+ {
+ administrator, {in_group_nested, "cn=system,ou=users,dc=dbrepo,dc=at", "member"}
+ },
+ {
+ management, {constant, true}
+ }
+ ]
+ }
+ ]
+ }
+].
\ No newline at end of file
diff --git a/.docker/config/dbrepo.conf b/.docker/config/dbrepo.conf
new file mode 100644
index 0000000000000000000000000000000000000000..8ac239d464398ec381b98d71c91192ea6ba061ab
--- /dev/null
+++ b/.docker/config/dbrepo.conf
@@ -0,0 +1,167 @@
+client_max_body_size 20G;
+
+resolver 127.0.0.11 valid=30s; # docker dns
+
+upstream auth {
+ server auth-service:8080;
+}
+
+upstream broker {
+ server broker-service:15672;
+}
+
+upstream analyse {
+ server analyse-service:8080;
+}
+
+upstream data {
+ server data-service:8080;
+}
+
+upstream metadata {
+ server metadata-service:8080;
+}
+
+upstream search {
+ server search-service:8080;
+}
+
+upstream ui {
+ server ui:3000;
+}
+
+upstream upload {
+ server upload-service:8080;
+}
+
+server {
+ listen 80 default_server;
+ server_name _;
+
+ location /admin/broker {
+ proxy_set_header Host $host;
+ proxy_set_header X-Real-IP $remote_addr;
+ proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+ proxy_set_header X-Forwarded-Proto $scheme;
+ proxy_pass http://broker;
+ proxy_read_timeout 90;
+ }
+
+ location /api/search {
+ proxy_set_header Host $host;
+ proxy_set_header X-Real-IP $remote_addr;
+ proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+ proxy_set_header X-Forwarded-Proto $scheme;
+ proxy_pass http://search;
+ proxy_read_timeout 90;
+ }
+
+ location /api/broker {
+ rewrite /api/broker/(.*) /admin/broker/api/$1 break;
+ proxy_set_header Host $host;
+ proxy_set_header X-Real-IP $remote_addr;
+ proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+ proxy_set_header X-Forwarded-Proto $scheme;
+ proxy_pass http://broker;
+ proxy_read_timeout 90;
+ }
+
+ location /api/upload {
+# allow 128.130.0.0/16;
+# deny all;
+ proxy_set_header Host $host;
+ proxy_set_header X-Real-IP $remote_addr;
+ proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+ proxy_set_header X-Forwarded-Proto $scheme;
+ proxy_set_header X-Forwarded-Host $host;
+ proxy_pass http://upload;
+ proxy_read_timeout 90;
+ # Disable request and response buffering
+ proxy_request_buffering off;
+ proxy_buffering off;
+ proxy_http_version 1.1;
+ }
+
+ location /api/analyse {
+ proxy_set_header Host $host;
+ proxy_set_header X-Real-IP $remote_addr;
+ proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+ proxy_set_header X-Forwarded-Proto $scheme;
+ proxy_pass http://analyse;
+ proxy_read_timeout 90;
+ }
+
+ location /api/auth {
+ rewrite /api/auth/(.*) /$1 break;
+ proxy_set_header Host $host;
+ proxy_set_header X-Real-IP $remote_addr;
+ proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+ proxy_set_header X-Forwarded-Proto $scheme;
+ proxy_pass http://auth;
+ proxy_read_timeout 90;
+ }
+
+ location ~ /api/database/([0-9]+)/table/([0-9]+)/(data|history|export|statistic) {
+ proxy_set_header Host $host;
+ proxy_set_header X-Real-IP $remote_addr;
+ proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+ proxy_set_header X-Forwarded-Proto $scheme;
+ proxy_pass http://data;
+ proxy_read_timeout 90;
+ }
+
+ location ~ /api/database/([0-9]+)/view/([0-9]+)/data {
+ proxy_set_header Host $host;
+ proxy_set_header X-Real-IP $remote_addr;
+ proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+ proxy_set_header X-Forwarded-Proto $scheme;
+ proxy_pass http://data;
+ proxy_read_timeout 90;
+ }
+
+ location ~ /api/database/([0-9]+)/view {
+ proxy_set_header Host $host;
+ proxy_set_header X-Real-IP $remote_addr;
+ proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+ proxy_set_header X-Forwarded-Proto $scheme;
+ proxy_pass http://metadata;
+ proxy_read_timeout 90;
+ }
+
+ location ~ /api/database/([0-9]+)/subset {
+ proxy_set_header Host $host;
+ proxy_set_header X-Real-IP $remote_addr;
+ proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+ proxy_set_header X-Forwarded-Proto $scheme;
+ proxy_pass http://data;
+ proxy_read_timeout 600;
+ }
+
+ location ~ /api/(database|concept|container|identifier|image|message|license|oai|ontology|unit|user) {
+ proxy_set_header Host $host;
+ proxy_set_header X-Real-IP $remote_addr;
+ proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+ proxy_set_header X-Forwarded-Proto $scheme;
+ proxy_pass http://metadata;
+ proxy_read_timeout 90;
+ }
+
+ location ~ /pid/([0-9]+) {
+ rewrite /pid/(.*) /api/identifier/$1 break;
+ proxy_set_header Host $host;
+ proxy_set_header X-Real-IP $remote_addr;
+ proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+ proxy_set_header X-Forwarded-Proto $scheme;
+ proxy_pass http://metadata;
+ proxy_read_timeout 90;
+ }
+
+ location / {
+ proxy_set_header Host $host;
+ proxy_set_header X-Real-IP $remote_addr;
+ proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+ proxy_set_header X-Forwarded-Proto $scheme;
+ proxy_pass http://ui;
+ proxy_read_timeout 90;
+ }
+}
diff --git a/.docker/config/definitions.json b/.docker/config/definitions.json
new file mode 100644
index 0000000000000000000000000000000000000000..a3b70c989de5cb287e37588860e664afb6b7d6ec
--- /dev/null
+++ b/.docker/config/definitions.json
@@ -0,0 +1,52 @@
+{
+ "bindings": [
+ {
+ "arguments": {},
+ "destination": "dbrepo",
+ "destination_type": "queue",
+ "routing_key": "dbrepo.#",
+ "source": "dbrepo",
+ "vhost": "dbrepo"
+ }
+ ],
+ "exchanges": [
+ {
+ "arguments": {},
+ "auto_delete": false,
+ "durable": true,
+ "name": "dbrepo",
+ "type": "topic",
+ "vhost": "dbrepo"
+ }
+ ],
+ "global_parameters": [],
+ "parameters": [],
+ "permissions": [],
+ "policies": [],
+ "queues": [
+ {
+ "arguments": {
+ "x-queue-type": "quorum"
+ },
+ "auto_delete": false,
+ "durable": true,
+ "name": "dbrepo",
+ "type": "quorum",
+ "vhost": "dbrepo"
+ }
+ ],
+ "rabbit_version": "3.10.25",
+ "rabbitmq_version": "3.10.25",
+ "topic_permissions": [],
+ "users": [],
+ "vhosts": [
+ {
+ "limits": [],
+ "metadata": {
+ "description": "Default virtual host",
+ "tags": []
+ },
+ "name": "dbrepo"
+ }
+ ]
+}
\ No newline at end of file
diff --git a/.docker/config/enabled_plugins b/.docker/config/enabled_plugins
new file mode 100644
index 0000000000000000000000000000000000000000..95f1c0014dd4ee232580adea29176756a25274ed
--- /dev/null
+++ b/.docker/config/enabled_plugins
@@ -0,0 +1 @@
+[rabbitmq_prometheus,rabbitmq_auth_backend_ldap,rabbitmq_auth_mechanism_ssl,rabbitmq_management].
\ No newline at end of file
diff --git a/.docker/config/rabbitmq.conf b/.docker/config/rabbitmq.conf
new file mode 100644
index 0000000000000000000000000000000000000000..ff592bb3ecd4b003d180dbb44d8bd9acc5a70394
--- /dev/null
+++ b/.docker/config/rabbitmq.conf
@@ -0,0 +1,30 @@
+# user
+default_vhost = dbrepo
+default_user_tags.administrator = false
+
+# enable http outside localhost
+listeners.tcp.1 = 0.0.0.0:5672
+
+# management prefix (https://www.rabbitmq.com/management.html#path-prefix)
+management.path_prefix = /admin/broker
+management.load_definitions = /app/definitions.json
+
+# logging
+log.console = true
+log.console.level = warning
+auth_ldap.log = true
+
+# Obviously your authentication server cannot vouch for itself, so you'll need another backend with at least one user in
+# it. You should probably use the internal database
+auth_backends.1.authn = ldap
+auth_backends.1.authz = ldap
+auth_backends.2 = internal
+
+# LDAP
+auth_ldap.servers.1 = identity-service
+auth_ldap.port = 1389
+auth_ldap.user_dn_pattern = ${username}
+auth_ldap.dn_lookup_base = dc=dbrepo,dc=at
+auth_ldap.dn_lookup_attribute = uid
+auth_ldap.dn_lookup_bind.user_dn = cn=admin,dc=dbrepo,dc=at
+auth_ldap.dn_lookup_bind.password = admin
diff --git a/.docker/config/s3_config.json b/.docker/config/s3_config.json
new file mode 100644
index 0000000000000000000000000000000000000000..f270753cdc96278a039e483966ea864a16781cfe
--- /dev/null
+++ b/.docker/config/s3_config.json
@@ -0,0 +1,20 @@
+{
+ "identities": [
+ {
+ "name": "admin",
+ "credentials": [
+ {
+ "accessKey": "seaweedfsadmin",
+ "secretKey": "seaweedfsadmin"
+ }
+ ],
+ "actions": [
+ "Read",
+ "Write",
+ "List",
+ "Tagging",
+ "Admin"
+ ]
+ }
+ ]
+}
\ No newline at end of file
diff --git a/.docker/dist.tar.gz b/.docker/dist.tar.gz
index 411c92f64cd600841b98f1375c32b920895df2e0..f6c45cbd78ee20a3280a4b2bd6ec8b4cc37050e1 100644
Binary files a/.docker/dist.tar.gz and b/.docker/dist.tar.gz differ
diff --git a/.env.unix.example b/.env.unix.example
deleted file mode 100644
index cc42c2445172e19016c48e55a5a599df5961de38..0000000000000000000000000000000000000000
--- a/.env.unix.example
+++ /dev/null
@@ -1 +0,0 @@
-LOG_LEVEL=trace # error, warning, info, debug, trace
\ No newline at end of file
diff --git a/.gitignore b/.gitignore
index e552ece0ec2f4b90e55a0973c942ce3fdc850473..4d7b82f6e6aac7adad8b9865fc2482f7c065e8f2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -13,7 +13,6 @@ build/
tmp.yaml
.docs/.swagger/api-*
.scannerwork/
-.docker/config/*
# docs
.docs/.swagger/dist/