patches/applyPatches.sh

@@ -47,4 +47,5 @@ do
 done
 
 cd ../
+
 $UTILSPATH/update_sql_procedures.sh

patches/patch20170316-2.0.27/patch.sh

@@ -35,7 +35,12 @@ fi
 
 check_version $OLD_VERSION
 
-mysql_execute 'DELETE FROM `entities` WHERE id=6; ALTER TABLE `entities` MODIFY COLUMN `role` ENUM("RECORDTYPE","RECORD","FILE","DOMAIN","PROPERTY","DATATYPE","ROLE","QUERYTEMPLATE") NOT NULL; INSERT INTO entities (id, name, description, role, acl) VALUES (8,"QUERYTEMPLATE","The QueryTemplate role.","ROLE",0); UPDATE `entities` SET role="ROLE" WHERE id<100 and name=role; CREATE TABLE `query_template_def` (id INT UNSIGNED PRIMARY KEY, definition MEDIUMTEXT NOT NULL, CONSTRAINT `query_template_def_ibfk_1` FOREIGN KEY (`id`) REFERENCES `entities` (`id`));'
+mysql_execute '
+DELETE FROM `entities` WHERE id=6;
+ALTER TABLE `entities` MODIFY COLUMN `role` ENUM("RECORDTYPE","RECORD","FILE","DOMAIN","PROPERTY","DATATYPE","ROLE","QUERYTEMPLATE") NOT NULL;
+INSERT INTO entities (id, name, description, role, acl) VALUES (8,"QUERYTEMPLATE","The QueryTemplate role.","ROLE",0);
+UPDATE `entities` SET role="ROLE" WHERE id<100 and name=role;
+CREATE TABLE `query_template_def` (id INT UNSIGNED PRIMARY KEY, definition MEDIUMTEXT NOT NULL, CONSTRAINT `query_template_def_ibfk_1` FOREIGN KEY (`id`) REFERENCES `entities` (`id`));'
 
 update_version $NEW_VERSION
 

patches/patch20221122-6.0-SNAPSHOT/create_entity_ids_table.sql

+/*
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2022-2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2022-2023 Timm Fitschen <t.fitschen@indiscale.com>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program. If not, see <https://www.gnu.org/licenses/>.
+ */
+
+-- a little bit of house keeping
+DROP PROCEDURE IF EXISTS retrieveSubEntity;
+DROP PROCEDURE IF EXISTS retrieveDatatype;
+DROP PROCEDURE IF EXISTS retrieveGroup;
+DROP PROCEDURE IF EXISTS getInfo;
+DROP PROCEDURE IF EXISTS getRole;
+DROP PROCEDURE IF EXISTS setPassword;
+DROP PROCEDURE IF EXISTS initAutoIncrement;
+DELETE FROM name_data WHERE entity_id=50;
+DELETE FROM entities WHERE id=50;
+DELETE FROM entities WHERE id=99;
+
+-- this simply is the more appropriate name
+ALTER TABLE entities MODIFY COLUMN
+  `role` enum('RECORDTYPE','RECORD','FILE','DOMAIN','PROPERTY','DATATYPE','ROLE','QUERYTEMPLATE', '_REPLACEMENT') COLLATE utf8_unicode_ci NOT NULL;
+ALTER TABLE archive_entities MODIFY COLUMN
+  `role` enum('RECORDTYPE','RECORD','FILE','DOMAIN','PROPERTY','DATATYPE','ROLE','QUERYTEMPLATE', '_REPLACEMENT') COLLATE utf8_unicode_ci NOT NULL;
+UPDATE entities SET role = "_REPLACEMENT" WHERE role="DOMAIN";
+UPDATE archive_entities SET role = "_REPLACEMENT" WHERE role="DOMAIN";
+ALTER TABLE entities MODIFY COLUMN
+  `role` enum('RECORDTYPE','RECORD','FILE','_REPLACEMENT','PROPERTY','DATATYPE','ROLE','QUERYTEMPLATE') COLLATE utf8_unicode_ci NOT NULL;
+ALTER TABLE archive_entities MODIFY COLUMN
+  `role` enum('RECORDTYPE','RECORD','FILE','_REPLACEMENT','PROPERTY','DATATYPE','ROLE','QUERYTEMPLATE') COLLATE utf8_unicode_ci NOT NULL;
+
+
+
+-- new entity_ids table
+DROP TABLE IF EXISTS `entity_ids`;
+CREATE TABLE `entity_ids` (
+    `id` VARCHAR(255) NOT NULL,
+    `internal_id` int(10) unsigned NOT NULL COMMENT 'Internal ID of an entity. This id is used internally in the *_data tables and elsewhere. This ID is never exposed via the CaosDB API.',
+    PRIMARY KEY `entity_ids_pk` (`id`),
+    CONSTRAINT `entity_ids_internal_id` FOREIGN KEY (`internal_id`) REFERENCES `entities` (`id`)
+) ENGINE=InnoDB COLLATE utf8mb4_bin;
+
+-- fill all existing entities into the new entity_ids table.
+INSERT INTO entity_ids (id, internal_id) SELECT id, id FROM entities WHERE id>0 AND role!="_REPLACEMENT";
+
+ALTER TABLE transaction_log MODIFY COLUMN `entity_id` VARCHAR(255) COLLATE utf8mb4_bin NOT NULL;
+
+ALTER TABLE user_info DROP FOREIGN KEY `subjects_ibfk_1`;
+ALTER TABle user_info MODIFY COLUMN `entity` VARCHAR(255) COLLATE utf8mb4_bin DEFAULT NULL;
+ALTER TABLE user_info ADD CONSTRAINT `subjects_ibfk_2` FOREIGN KEY (`entity`) REFERENCES `entity_ids` (`id`);

patches/patch20221122-6.0-SNAPSHOT/patch.sh

+#!/bin/bash
+#
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2023 Timm Fitschen <t.fitschen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+
+# Update mysql schema to version v5.0.0
+# Drop the 'rules' table.
+
+NEW_VERSION="v6.0.0-SNAPSHOT-EXTIDS"
+OLD_VERSION="v5.0.0"
+
+DROP_TABLE_PASSWORDS='DROP TABLE IF EXISTS passwords;'
+
+if [ -z "$UTILSPATH" ]; then
+ UTILSPATH="../utils"
+fi
+
+. $UTILSPATH/patch_header.sh $*
+
+check_version $OLD_VERSION
+
+mysql_execute "$DROP_TABLE_PASSWORDS"
+mysql_execute_file $PATCH_DIR/create_entity_ids_table.sql
+
+update_version $NEW_VERSION
+
+
+success
+

patches/patch20231018-6.1.0/patch.sh

+#!/bin/bash
+#
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2023 Timm Fitschen <t.fitschen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+
+# Update mysql schema to version v6.1.0
+# No migration of the schema, updating procedures only
+
+NEW_VERSION="v6.1.0"
+OLD_VERSION="v6.0.0-SNAPSHOT-EXTIDS"
+
+if [ -z "$UTILSPATH" ]; then
+ UTILSPATH="../utils"
+fi
+
+. $UTILSPATH/patch_header.sh $*
+
+check_version $OLD_VERSION
+
+# Drop insertUser procedure
+mysql_execute "DROP PROCEDURE IF EXISTS insertUser;"
+
+update_version $NEW_VERSION
+
+success
+

patches/patch20231025-7.0.0/patch.sh

+#!/bin/bash
+#
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2023 Timm Fitschen <t.fitschen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+
+# Update mysql schema to version v7.0.0
+# No migration of the schema, updating procedures only
+
+NEW_VERSION="v7.0.0"
+OLD_VERSION="v6.1.0"
+
+if [ -z "$UTILSPATH" ]; then
+ UTILSPATH="../utils"
+fi
+
+. $UTILSPATH/patch_header.sh $*
+
+check_version $OLD_VERSION
+
+update_version $NEW_VERSION
+
+success
+

patches/patch20231101-7.0.1/patch.sh

+#!/bin/bash
+#
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2023 Timm Fitschen <t.fitschen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+
+# Update mysql schema to version v7.0.1
+# Removing remnant tables. This patch version also adds new sanity checks
+# during installation/upgrade
+
+NEW_VERSION="v7.0.1"
+OLD_VERSION="v7.0.0"
+
+if [ -z "$UTILSPATH" ]; then
+ UTILSPATH="../utils"
+fi
+
+. $UTILSPATH/patch_header.sh $*
+
+check_version $OLD_VERSION
+
+mysql_execute "DROP TABLE IF EXISTS groups";
+mysql_execute "DROP TABLE IF EXISTS passwords";
+mysql_execute "DROP TABLE IF EXISTS logging";
+mysql_execute "DROP TABLE IF EXISTS isa";
+
+update_version $NEW_VERSION
+
+success

patches/patch20231211-7.0.2/patch.sh

+#!/bin/bash
+#
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2023 Timm Fitschen <t.fitschen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+
+# Update mysql schema to version v7.0.2
+# Patch the broken data_type table (fix id for file references as per
+# https://gitlab.com/linkahead/linkahead-server/-/issues/246)
+
+NEW_VERSION="v7.0.2"
+OLD_VERSION="v7.0.1"
+
+if [ -z "$UTILSPATH" ]; then
+ UTILSPATH="../utils"
+fi
+
+. $UTILSPATH/patch_header.sh $*
+
+check_version $OLD_VERSION
+
+mysql_execute "UPDATE data_type SET datatype=17 WHERE datatype=3"
+
+update_version $NEW_VERSION
+
+success

patches/patch20241024-8.0.0/patch.sh

+#!/bin/bash
+#
+# This file is a part of the LinkAhead Project.
+#
+# Copyright (C) 2024 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2024 Timm Fitschen <t.fitschen@indiscale.com>
+# Copyright (C) 2024 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+
+# Update mysql schema to version v8.0.0
+#
+# The patch is empty because the change has to be applied manually
+# from ../../dump_updates/2024-10-02.dump_fix_mariadb_10_6.sh if necessary.
+
+NEW_VERSION="v8.0.0"
+OLD_VERSION="v7.0.2"
+
+if [ -z "$UTILSPATH" ]; then
+ UTILSPATH="../utils"
+fi
+
+. $UTILSPATH/patch_header.sh $*
+
+check_version $OLD_VERSION
+
+update_version $NEW_VERSION
+
+success

patches/patch20250130-8.1.0/patch.sh

+#!/bin/bash
+#
+# This file is a part of the Linkahead Project.
+#
+# Copyright (C) 2025 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Daniel Hornung <d.hornung@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+
+# Update mysql schema to version v8.1.0
+#
+# Set the collation so that accents on characters become relevant.
+
+OLD_VERSION="v8.0.0"
+NEW_VERSION="v8.1.0"
+
+if [ -z "$UTILSPATH" ]; then
+  UTILSPATH="../utils"
+fi
+
+. $UTILSPATH/patch_header.sh $*
+
+check_version $OLD_VERSION
+
+# Update charsets and collations.
+
+# Change database default.
+mysql_execute "ALTER DATABASE \`$DATABASE_NAME\` COLLATE = 'uca1400_as_ci';"
+
+# Some columns should be changed manually to prevent text length changes.
+mysql_execute "ALTER TABLE desc_overrides MODIFY description TEXT CHARACTER SET utf8mb4;"
+mysql_execute "ALTER TABLE entities MODIFY description TEXT CHARACTER SET utf8mb4;"
+mysql_execute "ALTER TABLE permissions MODIFY permissions MEDIUMTEXT CHARACTER SET utf8mb4 NOT NULL;"
+mysql_execute "ALTER TABLE query_template_def MODIFY definition MEDIUMTEXT CHARACTER SET utf8mb4 NOT NULL;"
+mysql_execute "ALTER TABLE roles MODIFY description MEDIUMTEXT CHARACTER SET utf8mb4;"
+mysql_execute "ALTER TABLE text_data MODIFY value TEXT CHARACTER SET utf8mb4 NOT NULL;"
+
+# Remove some constraints first.
+mysql_execute 'ALTER TABLE user_info DROP FOREIGN KEY `subjects_ibfk_2`;'
+
+# Get all tables, drop first line, take first column
+tables=$(mysql_execute "SHOW TABLE status where Collation='utf8mb3_unicode_ci';" -B | tail +2 | awk '{print $1}')
+for table in $tables; do
+    mysql_execute "ALTER TABLE $table CONVERT TO CHARACTER SET utf8mb4 COLLATE uca1400_as_ci;"
+done
+
+# Add constraints again.
+mysql_execute 'ALTER TABLE user_info MODIFY COLUMN `entity` VARCHAR(255) COLLATE utf8mb4_bin DEFAULT NULL;'
+mysql_execute 'ALTER TABLE user_info ADD CONSTRAINT `subjects_ibfk_2` FOREIGN KEY (`entity`) REFERENCES `entity_ids` (`id`);'
+
+# Set custom collations for columns
+mysql_execute "ALTER TABLE transaction_log MODIFY entity_id VARCHAR(255) CHARACTER SET utf8mb4 COLLATE utf8mb4_bin NOT NULL;"
+
+
+### Finished ###
+
+update_version $NEW_VERSION
+
+success
+
+
+##### Useful commands #####
+
+# cd git/caosdb-mysqlbackend/
+# UTILSPATH=utils
+# . utils/patch_header.sh
+
+
+# show table status where Collation='utf8mb3_unicode_ci';
+
+# name_data
+# text_data
+
+# show table status like 'name_data';
+# select * from name_data where value like 'Yield%';
+# update name_data SET value='Yield-stréss' where entity_id=354;
+# update name_data SET value='Yield-strés😋s' where entity_id=354;
+# select * from name_data where value='Yield-stress';
+
+# # Unicode 14.0.0
+# ALTER TABLE name_data CONVERT TO CHARACTER SET utf8mb4 COLLATE uca1400_as_ci;
+
+# FULL_COLLATION_NAME: utf8mb4_uca1400_as_ci;
+# COLLATION_NAME: uca1400_as_ci;
+
+# mariadb -h sqldb -u caosdb -prandom1234 --default-character-set=utf8mb4 caosdb
+

procedures/deleteEntity.sql

 /*
- * ** header v3.0
  * This file is a part of the CaosDB Project.
  *
  * Copyright (C) 2018 Research Group Biomedical Physics,
  * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- * Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020-2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 Timm Fitschen <t.fitschen@indiscale.com>
  *
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU Affero General Public License as
@@ -18,8 +18,6 @@
  *
  * You should have received a copy of the GNU Affero General Public License
  * along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
  */
 
 /* Delete a (sparse) Entity from the database.
@@ -31,37 +29,43 @@ have been deleted before.  This can be done for example with the
 Parameters
 ==========
 
-EntityID : UNSIGNED
+EntityID : VARCHAR(255)
     The ID of the Entity.
 */
 
 DROP PROCEDURE IF EXISTS db_5_0.deleteEntity;
 delimiter //
 
-CREATE PROCEDURE db_5_0.deleteEntity(in EntityID INT UNSIGNED)
+CREATE PROCEDURE db_5_0.deleteEntity(in EntityID VARCHAR(255))
 BEGIN
+    DECLARE InternalEntityID INT UNSIGNED DEFAULT NULL;
+
+    SELECT internal_id INTO InternalEntityID from entity_ids WHERE id = EntityID;
 
     -- detele file properties
-    DELETE FROM files where file_id=EntityID;
+    DELETE FROM files where file_id=InternalEntityID;
 
     -- delete datatype stuff
     DELETE FROM data_type
         WHERE ( domain_id = 0
             AND entity_id = 0
-            AND property_id = EntityID )
-        OR datatype = EntityID;
+            AND property_id = InternalEntityID )
+        OR datatype = InternalEntityID;
     DELETE FROM collection_type
         WHERE domain_id = 0
         AND entity_id = 0
-        AND property_id = EntityID;
+        AND property_id = InternalEntityID;
 
     -- delete primary name (in case this is called without a prior call to deleteEntityProperties)
     DELETE FROM name_data
         WHERE domain_id = 0
-        AND entity_id = EntityID
+        AND entity_id = InternalEntityID
         AND property_id = 20;
 
-    DELETE FROM entities where id=EntityID;
+    DELETE FROM entity_ids
+        WHERE internal_id = InternalEntityID;
+
+    DELETE FROM entities where id=InternalEntityID;
 
     -- clean up unused acl
     DELETE FROM entity_acl

procedures/deleteEntityProperties.sql

 /*
- * ** header v3.0
  * This file is a part of the CaosDB Project.
  *
  * Copyright (C) 2018 Research Group Biomedical Physics,
  * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- * Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
- * Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
+ * Copyright (C) 2020,2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020,2023 Timm Fitschen <t.fitschen@indiscale.com>
  *
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU Affero General Public License as
@@ -19,23 +18,34 @@
  *
  * You should have received a copy of the GNU Affero General Public License
  * along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
  */
 
 DROP PROCEDURE IF EXISTS db_5_0.deleteEntityProperties;
 delimiter //
 
-CREATE PROCEDURE db_5_0.deleteEntityProperties(in EntityID INT UNSIGNED)
+/*
+ * Delete all properties of an entity (i.e. remove them from the *_data tables
+ * and the isa_cache table).
+ *
+ * Parameters
+ * ==========
+ *
+ * EntityID : VARCHAR(255)
+ *    The entity's id.
+ */
+CREATE PROCEDURE db_5_0.deleteEntityProperties(in EntityID VARCHAR(255))
 BEGIN
     DECLARE IVersion INT UNSIGNED DEFAULT NULL;
+    DECLARE InternalEntityID INT UNSIGNED DEFAULT NULL;
+
+    SELECT internal_id INTO InternalEntityID from entity_ids WHERE id = EntityID;
 
-    CALL deleteIsa(EntityID);
+    CALL deleteIsa(InternalEntityID);
 
     IF is_feature_config("ENTITY_VERSIONING", "ENABLED") THEN
         SELECT max(e._iversion) INTO IVersion -- What's the latest version?
             FROM entity_version AS e
-            WHERE e.entity_id = EntityID;
+            WHERE e.entity_id = InternalEntityID;
 
         -- Copy the rows from *_data to archive_*_data ---------------------
         INSERT INTO archive_reference_data (domain_id, entity_id,
@@ -43,142 +53,142 @@ BEGIN
             SELECT domain_id, entity_id, property_id, value, value_iversion,
                 status, pidx, IVersion AS _iversion
             FROM reference_data
-            WHERE (domain_id = 0 AND entity_id = EntityID)
-            OR domain_id = EntityID;
+            WHERE (domain_id = 0 AND entity_id = InternalEntityID)
+            OR domain_id = InternalEntityID;
 
         INSERT INTO archive_null_data (domain_id, entity_id,
                 property_id, status, pidx, _iversion)
             SELECT domain_id, entity_id, property_id, status,
                 pidx, IVersion AS _iversion
             FROM null_data
-            WHERE (domain_id = 0 AND entity_id = EntityID)
-            OR domain_id = EntityID;
+            WHERE (domain_id = 0 AND entity_id = InternalEntityID)
+            OR domain_id = InternalEntityID;
 
         INSERT INTO archive_text_data (domain_id, entity_id,
                 property_id, value, status, pidx, _iversion)
             SELECT domain_id, entity_id, property_id, value, status,
                 pidx, IVersion AS _iversion
             FROM text_data
-            WHERE (domain_id = 0 AND entity_id = EntityID)
-            OR domain_id = EntityID;
+            WHERE (domain_id = 0 AND entity_id = InternalEntityID)
+            OR domain_id = InternalEntityID;
 
         INSERT INTO archive_name_data (domain_id, entity_id,
                 property_id, value, status, pidx, _iversion)
             SELECT domain_id, entity_id, property_id, value, status,
                 pidx, IVersion AS _iversion
             FROM name_data
-            WHERE (domain_id = 0 AND entity_id = EntityID)
-            OR domain_id = EntityID;
+            WHERE (domain_id = 0 AND entity_id = InternalEntityID)
+            OR domain_id = InternalEntityID;
 
         INSERT INTO archive_enum_data (domain_id, entity_id,
                 property_id, value, status, pidx, _iversion)
             SELECT domain_id, entity_id, property_id, value, status,
                 pidx, IVersion AS _iversion
             FROM enum_data
-            WHERE (domain_id = 0 AND entity_id = EntityID)
-            OR domain_id = EntityID;
+            WHERE (domain_id = 0 AND entity_id = InternalEntityID)
+            OR domain_id = InternalEntityID;
 
         INSERT INTO archive_integer_data (domain_id, entity_id,
                 property_id, value, status, pidx, _iversion, unit_sig)
             SELECT domain_id, entity_id, property_id, value, status,
                 pidx, IVersion AS _iversion, unit_sig
             FROM integer_data
-            WHERE (domain_id = 0 AND entity_id = EntityID)
-            OR domain_id = EntityID;
+            WHERE (domain_id = 0 AND entity_id = InternalEntityID)
+            OR domain_id = InternalEntityID;
 
         INSERT INTO archive_double_data (domain_id, entity_id,
                 property_id, value, status, pidx, _iversion, unit_sig)
             SELECT domain_id, entity_id, property_id, value, status,
                 pidx, IVersion AS _iversion, unit_sig
             FROM double_data
-            WHERE (domain_id = 0 AND entity_id = EntityID)
-            OR domain_id = EntityID;
+            WHERE (domain_id = 0 AND entity_id = InternalEntityID)
+            OR domain_id = InternalEntityID;
 
         INSERT INTO archive_datetime_data (domain_id, entity_id,
                 property_id, value, value_ns, status, pidx, _iversion)
             SELECT domain_id, entity_id, property_id, value, value_ns,
                 status, pidx, IVersion AS _iversion
             FROM datetime_data
-            WHERE (domain_id = 0 AND entity_id = EntityID)
-            OR domain_id = EntityID;
+            WHERE (domain_id = 0 AND entity_id = InternalEntityID)
+            OR domain_id = InternalEntityID;
 
         INSERT INTO archive_date_data (domain_id, entity_id,
                 property_id, value, status, pidx, _iversion)
             SELECT domain_id, entity_id, property_id, value, status,
                 pidx, IVersion AS _iversion
             FROM date_data
-            WHERE (domain_id = 0 AND entity_id = EntityID)
-            OR domain_id = EntityID;
+            WHERE (domain_id = 0 AND entity_id = InternalEntityID)
+            OR domain_id = InternalEntityID;
 
         INSERT INTO archive_name_overrides (domain_id, entity_id,
                 property_id, name, _iversion)
             SELECT domain_id, entity_id, property_id, name,
                 IVersion AS _iversion
             FROM name_overrides
-            WHERE (domain_id = 0 AND entity_id = EntityID)
-            OR domain_id = EntityID;
+            WHERE (domain_id = 0 AND entity_id = InternalEntityID)
+            OR domain_id = InternalEntityID;
 
         INSERT INTO archive_desc_overrides (domain_id, entity_id,
                 property_id, description, _iversion)
             SELECT domain_id, entity_id, property_id, description,
                 IVersion AS _iversion
             FROM desc_overrides
-            WHERE (domain_id = 0 AND entity_id = EntityID)
-            OR domain_id = EntityID;
+            WHERE (domain_id = 0 AND entity_id = InternalEntityID)
+            OR domain_id = InternalEntityID;
 
         INSERT INTO archive_data_type (domain_id, entity_id,
                 property_id, datatype, _iversion)
             SELECT domain_id, entity_id, property_id, datatype,
                 IVersion AS _iversion
             FROM data_type
-            WHERE (domain_id = 0 AND entity_id = EntityID)
-            OR domain_id = EntityID;
+            WHERE (domain_id = 0 AND entity_id = InternalEntityID)
+            OR domain_id = InternalEntityID;
 
         INSERT INTO archive_collection_type (domain_id, entity_id,
                 property_id, collection, _iversion)
             SELECT domain_id, entity_id, property_id, collection,
                 IVersion AS _iversion
             FROM collection_type
-            WHERE (domain_id = 0 AND entity_id = EntityID)
-            OR domain_id = EntityID;
+            WHERE (domain_id = 0 AND entity_id = InternalEntityID)
+            OR domain_id = InternalEntityID;
 
         INSERT INTO archive_query_template_def (id, definition, _iversion)
             SELECT id, definition, IVersion AS _iversion
             FROM query_template_def
-            WHERE id = EntityID;
+            WHERE id = InternalEntityID;
 
     END IF;
 
     DELETE FROM reference_data
-    where (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
+    where (domain_id=0 AND entity_id=InternalEntityID) OR domain_id=InternalEntityID;
     DELETE FROM null_data
-    where (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
+    where (domain_id=0 AND entity_id=InternalEntityID) OR domain_id=InternalEntityID;
     DELETE FROM text_data
-    where (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
+    where (domain_id=0 AND entity_id=InternalEntityID) OR domain_id=InternalEntityID;
     DELETE FROM name_data
-    where (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
+    where (domain_id=0 AND entity_id=InternalEntityID) OR domain_id=InternalEntityID;
     DELETE FROM enum_data
-    where (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
+    where (domain_id=0 AND entity_id=InternalEntityID) OR domain_id=InternalEntityID;
     DELETE FROM integer_data
-    where (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
+    where (domain_id=0 AND entity_id=InternalEntityID) OR domain_id=InternalEntityID;
     DELETE FROM double_data
-    where (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
+    where (domain_id=0 AND entity_id=InternalEntityID) OR domain_id=InternalEntityID;
     DELETE FROM datetime_data
-    where (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
+    where (domain_id=0 AND entity_id=InternalEntityID) OR domain_id=InternalEntityID;
     DELETE FROM date_data
-    where (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
+    where (domain_id=0 AND entity_id=InternalEntityID) OR domain_id=InternalEntityID;
 
     DELETE FROM name_overrides
-    WHERE (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
+    WHERE (domain_id=0 AND entity_id=InternalEntityID) OR domain_id=InternalEntityID;
     DELETE FROM desc_overrides
-    WHERE (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
+    WHERE (domain_id=0 AND entity_id=InternalEntityID) OR domain_id=InternalEntityID;
 
     DELETE FROM data_type
-    WHERE (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
+    WHERE (domain_id=0 AND entity_id=InternalEntityID) OR domain_id=InternalEntityID;
     DELETE FROM collection_type
-    WHERE (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
+    WHERE (domain_id=0 AND entity_id=InternalEntityID) OR domain_id=InternalEntityID;
 
-    DELETE FROM query_template_def WHERE id=EntityID;
+    DELETE FROM query_template_def WHERE id=InternalEntityID;
 
 END;
 //

procedures/deleteIsaCache.sql

 /*
- * ** header v3.0
  * This file is a part of the CaosDB Project.
  *
  * Copyright (C) 2018 Research Group Biomedical Physics,
  * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- * Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
- * Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
+ * Copyright (C) 2020,2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020,2023 Timm Fitschen <t.fitschen@indiscale.com>
  *
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU Affero General Public License as
@@ -19,8 +18,6 @@
  *
  * You should have received a copy of the GNU Affero General Public License
  * along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
  */
 SET GLOBAL log_bin_trust_function_creators = 1;
 
@@ -38,30 +35,30 @@ parameter entity is a child or inside the rpath.
 Parameters
 ==========
 
-EntityID : UNSIGNED
+InternalEntityID : UNSIGNED
     Child entity for which all parental relations should be deleted.
 */
-CREATE PROCEDURE db_5_0.deleteIsa(IN EntityID INT UNSIGNED)
+CREATE PROCEDURE db_5_0.deleteIsa(IN InternalEntityID INT UNSIGNED)
 BEGIN
     DECLARE IVersion INT UNSIGNED DEFAULT NULL;
 
     IF is_feature_config("ENTITY_VERSIONING", "ENABLED") THEN
         SELECT max(_iversion) INTO IVersion
             FROM entity_version
-            WHERE entity_id = EntityID;
+            WHERE entity_id = InternalEntityID;
 
         -- move to archive_isa before deleting
         INSERT IGNORE INTO archive_isa (child, child_iversion, parent, direct)
-            SELECT e.child, IVersion AS child_iversion, e.parent, rpath = EntityID
+            SELECT e.child, IVersion AS child_iversion, e.parent, rpath = InternalEntityID
             FROM isa_cache AS e
-            WHERE e.child = EntityID;
+            WHERE e.child = InternalEntityID;
     END IF;
 
     DELETE FROM isa_cache
-        WHERE child = EntityID
-        OR rpath = EntityID
-        OR rpath LIKE concat('%>', EntityID)
-        OR rpath LIKE concat('%>', EntityID, '>%');
+        WHERE child = InternalEntityID
+        OR rpath = InternalEntityID
+        OR rpath LIKE concat('%>', InternalEntityID)
+        OR rpath LIKE concat('%>', InternalEntityID, '>%');
 
 END;
 //

procedures/entityVersioning.sql

 /*
- * This file is a part of the CaosDB Project.
- *
- * Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
- * Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
+ * This file is a part of the LinkAhead Project.
  *
+ * Copyright (C) 2020-2024 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020,2023 Timm Fitschen <t.fitschen@indiscale.com>
+ * Copyright (C) 2024 Daniel Hornung <d.hornung@indiscale.com>
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU Affero General Public License as
  * published by the Free Software Foundation, either version 3 of the
@@ -27,23 +27,23 @@ DROP PROCEDURE IF EXISTS db_5_0.insert_single_child_version //
  *
  * Parameters
  * ----------
- * EntityID
- *   The ID of the versioned entity.
- * Hash
+ * InternalEntityID : INT UNSIGNED
+ *   The internal ID of the versioned entity.
+ * Hash : VARBINARY(255)
  *   A hash of the entity. This is currently not implemented properly and only
  *   there for future use.
- * Version
+ * Version : VARBINARY(255)
  *   The new version ID of the entity, must be produced by the caller.  Must be unique for each
  *   EntityID.
- * Parent
+ * Parent : VARBINARY(255)
  *   The version ID of the primary parent (i.e. predecessor).  May be NULL; but if given, it must
  *   exist.
- * Transaction
+ * Transaction : VARBINARY(255)
  *   The transaction ID which created this entity version (by inserting
  *   or updating an entity).
  */
 CREATE PROCEDURE db_5_0.insert_single_child_version(
-    in EntityID INT UNSIGNED,
+    in InternalEntityID INT UNSIGNED,
     in Hash VARBINARY(255),
     in Version VARBINARY(255),
     in Parent VARBINARY(255),
@@ -57,12 +57,12 @@ BEGIN
     IF Parent IS NOT NULL THEN
         SELECT e._iversion INTO newipparent
             FROM entity_version AS e
-            WHERE e.entity_id = EntityID
+            WHERE e.entity_id = InternalEntityID
             AND e.version = Parent;
         IF newipparent IS NULL THEN
             -- throw error;
             SELECT concat("This parent does not exists: ", Parent)
-            FROM nonexisting;
+            FROM parent_version_does_not_exist;
         END IF;
     END IF;
 
@@ -70,7 +70,7 @@ BEGIN
     -- generate _iversion
     SELECT max(e._iversion)+1 INTO newiversion
         FROM entity_version AS e
-        WHERE e.entity_id=EntityID;
+        WHERE e.entity_id=InternalEntityID;
     IF newiversion IS NULL THEN
         SET newiversion = 1;
     END IF;
@@ -78,7 +78,7 @@ BEGIN
     INSERT INTO entity_version
         (entity_id, hash, version, _iversion, _ipparent, srid)
         VALUES
-        (EntityID, Hash, Version, newiversion, newipparent, Transaction);
+        (InternalEntityID, Hash, Version, newiversion, newipparent, Transaction);
 
 
 
@@ -87,22 +87,28 @@ END;
 
 DROP PROCEDURE IF EXISTS db_5_0.delete_all_entity_versions //
 
+/* THIS PROCEDURE HAS NEVER BEEN USED (outside of the tests). Reactivate when
+ * versioning's FORGET is being implemented. */
 /**
  * Remove all records in the entity_version table for the given entity.
  *
  * Parameters
  * ----------
- * EntityID
+ * EntityID : VARCHAR(255)
  *   The id of the versioned entity.
  */
-CREATE PROCEDURE db_5_0.delete_all_entity_versions(
-    in EntityID INT UNSIGNED)
+/* CREATE PROCEDURE db_5_0.delete_all_entity_versions(
+    in EntityID VARCHAR(255))
 BEGIN
+    DECLARE InternalEntityID INT UNSIGNED DEFAULT NULL;
+
+    SELECT internal_id INTO InternalEntityID FROM entity_ids WHERE id = EntityID;
 
-    DELETE FROM entity_version WHERE entity_id = EntityID;
+    DELETE FROM entity_version WHERE entity_id = InternalEntityID;
 
 END;
 //
+*/
 
 DROP FUNCTION IF EXISTS db_5_0.get_iversion //
 
@@ -111,9 +117,9 @@ DROP FUNCTION IF EXISTS db_5_0.get_iversion //
  *
  * Parameters
  * ----------
- * EntityID
- *   The entity's id.
- * Version
+ * InternalEntityID : INT UNSIGNED
+ *   The entity's internal id.
+ * Version : VARBINARY(255)
  *   The (official, externally used) version id.
  *
  * Returns
@@ -121,7 +127,7 @@ DROP FUNCTION IF EXISTS db_5_0.get_iversion //
  * The internal version id.
  */
 CREATE FUNCTION db_5_0.get_iversion(
-    EntityID INT UNSIGNED,
+    InternalEntityID INT UNSIGNED,
     Version VARBINARY(255))
 RETURNS INT UNSIGNED
 READS SQL DATA
@@ -129,7 +135,7 @@ BEGIN
     RETURN (
         SELECT e._iversion
             FROM entity_version AS e
-            WHERE e.entity_id = EntityID
+            WHERE e.entity_id = InternalEntityID
                 AND e.version = Version
         );
 END;
@@ -143,9 +149,9 @@ DROP FUNCTION IF EXISTS db_5_0.get_primary_parent_version //
  *
  * Parameters
  * ----------
- * EntityID
+ * EntityID : VARCHAR(255)
  *   The entity id.
- * Version
+ * Version : VARBINARY(255)
  *   The version id.
  *
  * Returns
@@ -153,17 +159,21 @@ DROP FUNCTION IF EXISTS db_5_0.get_primary_parent_version //
  * The id of the given version's primary parent version.
  */
 CREATE FUNCTION db_5_0.get_primary_parent_version(
-    EntityID INT UNSIGNED,
+    EntityID VARCHAR(255),
     Version VARBINARY(255))
 RETURNS VARBINARY(255)
 READS SQL DATA
 BEGIN
+    DECLARE InternalEntityID INT UNSIGNED DEFAULT NULL;
+
+    SELECT internal_id INTO InternalEntityID FROM entity_ids WHERE id = EntityID;
+
     RETURN (
         SELECT p.version
             FROM entity_version AS e INNER JOIN entity_version AS p
                 ON (e._ipparent = p._iversion
                     AND e.entity_id = p.entity_id)
-            WHERE e.entity_id = EntityID
+            WHERE e.entity_id = InternalEntityID
                 AND e.version = Version
         );
 END;
@@ -177,9 +187,9 @@ DROP FUNCTION IF EXISTS db_5_0.get_version_timestamp //
  *
  * Parameters
  * ----------
- * EntityID
+ * EntityID : VARCHAR(255)
  *   The entity id.
- * Version
+ * Version : VARBINARY(255)
  *   The version id.
  *
  * Returns
@@ -188,16 +198,20 @@ DROP FUNCTION IF EXISTS db_5_0.get_version_timestamp //
  * Note that the dot `.` here is not necessarily a decimal separator.
  */
 CREATE FUNCTION db_5_0.get_version_timestamp(
-    EntityID INT UNSIGNED,
+    EntityID VARCHAR(255),
     Version VARBINARY(255))
 RETURNS VARCHAR(255)
 READS SQL DATA
 BEGIN
+    DECLARE InternalEntityID INT UNSIGNED DEFAULT NULL;
+
+    SELECT internal_id INTO InternalEntityID FROM entity_ids WHERE id = EntityID;
+
     RETURN (
         SELECT concat(t.seconds, '.', t.nanos)
             FROM entity_version AS e INNER JOIN transactions AS t
                 ON ( e.srid = t.srid )
-            WHERE e.entity_id = EntityID
+            WHERE e.entity_id = InternalEntityID
             AND e.version = Version
     );
 END;
@@ -210,7 +224,7 @@ DROP FUNCTION IF EXISTS db_5_0.get_head_version //
  *
  * Parameters
  * ----------
- * EntityID
+ * EntityID : VARCHAR(255)
  *   The entity id.
  *
  * Returns
@@ -218,7 +232,7 @@ DROP FUNCTION IF EXISTS db_5_0.get_head_version //
  * The version id of the HEAD.
  */
 CREATE FUNCTION db_5_0.get_head_version(
-    EntityID INT UNSIGNED)
+    EntityID VARCHAR(255))
 RETURNS VARBINARY(255)
 READS SQL DATA
 BEGIN
@@ -233,15 +247,15 @@ DROP FUNCTION IF EXISTS db_5_0._get_head_iversion //
  *
  * Parameters
  * ----------
- * EntityID
- *   The entity id.
+ * InternalEntityID : INT UNSIGNED
+ *   The entity's internal id.
  *
  * Returns
  * -------
  * The _iversion of the HEAD.
  */
 CREATE FUNCTION db_5_0._get_head_iversion(
-    EntityID INT UNSIGNED)
+    InternalEntityID INT UNSIGNED)
 RETURNS INT UNSIGNED
 READS SQL DATA
 BEGIN
@@ -252,7 +266,7 @@ BEGIN
     RETURN (
         SELECT e._iversion
             FROM entity_version AS e
-            WHERE e.entity_id = EntityID
+            WHERE e.entity_id = InternalEntityID
             ORDER BY e._iversion DESC
             LIMIT 1
         );
@@ -267,9 +281,9 @@ DROP FUNCTION IF EXISTS db_5_0.get_head_relative //
  *
  * Parameters
  * ----------
- * EntityID
+ * EntityID : VARCHAR(255)
  *   The entity id.
- * Offset
+ * HeadOffset : INT UNSIGNED
  *   Distance in the sequence of primary parents of the entity. E.g. `0` is the
  *   HEAD itself. `1` is the primary parent of the HEAD. `2` is the primary
  *   parent of the primary parent of the HEAD, and so on.
@@ -279,11 +293,15 @@ DROP FUNCTION IF EXISTS db_5_0.get_head_relative //
  * The version id of the HEAD.
  */
 CREATE FUNCTION db_5_0.get_head_relative(
-    EntityID INT UNSIGNED,
-    Offset INT UNSIGNED)
+    EntityID VARCHAR(255),
+    HeadOffset INT UNSIGNED)
 RETURNS VARBINARY(255)
 READS SQL DATA
 BEGIN
+    DECLARE InternalEntityID INT UNSIGNED DEFAULT NULL;
+
+    SELECT internal_id INTO InternalEntityID FROM entity_ids WHERE id = EntityID;
+
     -- This implementation assumes that the distance from the head equals the
     -- difference between the _iversion numbers. This will not be correct anymore
     -- as soon as branches may split and merge. Then, a walk over the primary
@@ -291,9 +309,9 @@ BEGIN
     RETURN (
         SELECT e.version
             FROM entity_version AS e
-            WHERE e.entity_id = EntityID
+            WHERE e.entity_id = InternalEntityID
             ORDER BY e._iversion DESC
-            LIMIT 1 OFFSET Offset
+            LIMIT 1 OFFSET HeadOffset
         );
 END;
 //
@@ -304,24 +322,24 @@ DROP FUNCTION IF EXISTS db_5_0._get_version //
  *
  * Parameters
  * ----------
- * EntityID
- *   The entity id.
+ * InternalEntityID : INT UNSIGNED
+ *   The entity's internal id.
  * IVersion
  *   Internal version id (integer).
  *
  * Returns
  * -------
- * The version id.
+ * The (external) version id.
  */
 CREATE FUNCTION db_5_0._get_version(
-    EntityID INT UNSIGNED,
+    InternalEntityID INT UNSIGNED,
     IVersion INT UNSIGNED)
 RETURNS VARBINARY(255)
 READS SQL DATA
 BEGIN
     RETURN (
         SELECT version FROM entity_version
-            WHERE entity_id = EntityID
+            WHERE entity_id = InternalEntityID
             AND _iversion = IVersion
         );
 END;
@@ -335,7 +353,7 @@ DROP PROCEDURE IF EXISTS db_5_0.get_version_history //
  *
  * Parameters
  * ----------
- * EntityID
+ * EntityID : VARCHAR(255)
  *   The entity id.
  *
  * Selects
@@ -344,8 +362,12 @@ DROP PROCEDURE IF EXISTS db_5_0.get_version_history //
  *   child_realm). `child` and `parent` are version IDs.
  */
 CREATE PROCEDURE db_5_0.get_version_history(
-    in EntityID INT UNSIGNED)
+    in EntityID VARCHAR(255))
 BEGIN
+    DECLARE InternalEntityID INT UNSIGNED DEFAULT NULL;
+
+    SELECT internal_id INTO InternalEntityID FROM entity_ids WHERE id = EntityID;
+
     -- retrieve root(s) (initial versions)
     SELECT c.version AS child,
             NULL as parent,
@@ -355,7 +377,7 @@ BEGIN
             t.realm AS child_realm
         FROM entity_version AS c INNER JOIN transactions as t
         ON ( c.srid = t.srid )
-        WHERE c.entity_id = EntityID
+        WHERE c.entity_id = InternalEntityID
         AND c._ipparent is Null
 
     -- TODO This first SELECT statement is necessary because the second one
@@ -375,7 +397,7 @@ BEGIN
             ON (c._ipparent = p._iversion
                 AND c.entity_id = p.entity_id
                 AND t.srid = c.srid)
-        WHERE p.entity_id = EntityID;
+        WHERE p.entity_id = InternalEntityID;
 END;
 //
 
@@ -412,56 +434,6 @@ BEGIN
 END //
 
 
-
-DROP PROCEDURE IF EXISTS setFileProperties //
-/**
- * Insert/Update file properties.
- *
- * If ENTITY_VERSIONING is enabled the old file properties are moved to
- * `archive_files`.
- *
- * Parameters
- * ----------
- * EntityID
- *   The file's id.
- * FilePath
- *   Path of the file in the internal file system.  If NULL, an existing file
- *   entity is simply deleted.
- * FileSize
- *   Size of the file in bytes.
- * FileHash
- *   A Sha512 Hash of the file.
- */
-CREATE PROCEDURE setFileProperties (
-    in EntityID INT UNSIGNED,
-    in FilePath TEXT,
-    in FileSize BIGINT UNSIGNED,
-    in FileHash VARCHAR(255)
-)
-BEGIN
-    DECLARE IVersion INT UNSIGNED DEFAULT NULL;
-    IF is_feature_config("ENTITY_VERSIONING", "ENABLED") THEN
-        SELECT max(e._iversion) INTO IVersion
-            FROM entity_version AS e
-            WHERE e.entity_id = EntityID;
-
-        INSERT INTO archive_files (file_id, path, size, hash,
-                _iversion)
-            SELECT file_id, path, size, hash, IVersion AS _iversion
-            FROM files
-            WHERE file_id = EntityID;
-    END IF;
-
-    DELETE FROM files WHERE file_id = EntityID;
-
-    IF FilePath IS NOT NULL THEN
-        INSERT INTO files (file_id, path, size, hash)
-            VALUES (EntityID, FilePath, FileSize, unhex(FileHash));
-    END IF;
-
-END //
-
-
 DROP PROCEDURE IF EXISTS retrieveQueryTemplateDef //
 
 /**
@@ -469,9 +441,9 @@ DROP PROCEDURE IF EXISTS retrieveQueryTemplateDef //
  *
  * Parameters
  * ----------
- * EntityID
+ * EntityID : VARCHAR(255)
  *   The QueryTemplate's id.
- * Version
+ * Version : VARBINARY(255)
  *   The QueryTemplate's version's id.
  *
  * Returns
@@ -480,12 +452,16 @@ DROP PROCEDURE IF EXISTS retrieveQueryTemplateDef //
  * QueryTemplate.
  */
 CREATE PROCEDURE retrieveQueryTemplateDef (
-    in EntityID INT UNSIGNED,
+    in EntityID VARCHAR(255),
     in Version VARBINARY(255))
 retrieveQueryTemplateDefBody: BEGIN
 
     DECLARE IVersion INT UNSIGNED DEFAULT NULL;
     DECLARE IsHead BOOLEAN DEFAULT TRUE;
+    DECLARE InternalEntityID INT UNSIGNED DEFAULT NULL;
+
+    SELECT internal_id INTO InternalEntityID FROM entity_ids WHERE id = EntityID;
+
 
     IF is_feature_config("ENTITY_VERSIONING", "ENABLED") THEN
         -- Are we at the head?
@@ -494,11 +470,7 @@ retrieveQueryTemplateDefBody: BEGIN
         END IF;
 
         IF IsHead IS FALSE THEN
-            -- TODO Use get_iversion(EntityID, Version) instead?  Or will that be much slower?
-            SELECT e._iversion INTO IVersion
-                FROM entity_version as e
-                WHERE e.entity_id = EntityID
-                AND e.version = Version;
+            SET IVersion = get_iversion(InternalEntityID, Version);
 
             IF IVersion IS NULL THEN
                 -- RETURN EARLY - Version does not exist.
@@ -507,7 +479,7 @@ retrieveQueryTemplateDefBody: BEGIN
 
             SELECT definition
             FROM archive_query_template_def
-            WHERE id = EntityID
+            WHERE id = InternalEntityID
             AND _iversion = IVersion;
 
             LEAVE retrieveQueryTemplateDefBody;
@@ -516,7 +488,7 @@ retrieveQueryTemplateDefBody: BEGIN
 
     SELECT definition
     FROM query_template_def
-    WHERE id = EntityID;
+    WHERE id = InternalEntityID;
 
 END //
 

procedures/getDependentEntities.sql

 /*
- * ** header v3.0
  * This file is a part of the CaosDB Project.
  *
  * Copyright (C) 2018 Research Group Biomedical Physics,
  * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+ * Copyright (C) 2023 IndiScale GmbH <www.indiscale.com>
+ * Copyright (C) 2023 Timm Fitschen <t.fitschen@indiscale.com>
  *
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU Affero General Public License as
@@ -18,56 +19,76 @@
  * You should have received a copy of the GNU Affero General Public License
  * along with this program. If not, see <https://www.gnu.org/licenses/>.
  *
- * ** end header
  */
 
 
-
 DROP PROCEDURE IF EXISTS db_5_0.getDependentEntities;
 delimiter //
 
-CREATE PROCEDURE db_5_0.getDependentEntities(in EntityID INT UNSIGNED)
+/*
+ * Return all entities which either reference the given entity, use the given
+ * reference as data type, or are direct children of the given entity.
+ *
+ * This function used to make sure that no entity can be deleted which
+ * is still needed by others.
+ *
+ * Parameters
+ * ----------
+ * EntityID : VARCHAR(255)
+ *    The entity id.
+ *
+ * ResultSet
+ * ---------
+ * EntityID : VARCHAR(255)
+ *
+ */
+CREATE PROCEDURE db_5_0.getDependentEntities(in EntityID VARCHAR(255))
 BEGIN
 
-DROP TEMPORARY TABLE IF EXISTS refering;		
-CREATE TEMPORARY TABLE refering (
+    DECLARE InternalEntityID INT UNSIGNED DEFAULT NULL;
+
+    DROP TEMPORARY TABLE IF EXISTS referring;
+    CREATE TEMPORARY TABLE referring (
         id INT UNSIGNED UNIQUE
     );
 
-INSERT IGNORE INTO refering (id) SELECT entity_id FROM reference_data WHERE (value=EntityID OR property_id=EntityID) AND domain_id=0 AND entity_id!=EntityID;
-INSERT IGNORE INTO refering (id) SELECT domain_id FROM reference_data WHERE (value=EntityID OR property_id=EntityID) AND domain_id!=EntityID AND entity_id!=EntityID AND domain_id!=0; 
+    SELECT internal_id INTO InternalEntityID from entity_ids WHERE id = EntityID;
+
+    INSERT IGNORE INTO referring (id) SELECT entity_id FROM reference_data WHERE (value=InternalEntityID OR property_id=InternalEntityID) AND domain_id=0 AND entity_id!=InternalEntityID;
+    INSERT IGNORE INTO referring (id) SELECT domain_id FROM reference_data WHERE (value=InternalEntityID OR property_id=InternalEntityID) AND domain_id!=InternalEntityID AND entity_id!=InternalEntityID AND domain_id!=0;
 
-INSERT IGNORE INTO refering (id) SELECT entity_id FROM text_data WHERE property_id=EntityID AND domain_id=0 AND entity_id!=EntityID;
-INSERT IGNORE INTO refering (id) SELECT domain_id FROM text_data WHERE property_id=EntityID AND domain_id!=EntityID AND entity_id!=EntityID AND domain_id!=0; 
+    INSERT IGNORE INTO referring (id) SELECT entity_id FROM text_data WHERE property_id=InternalEntityID AND domain_id=0 AND entity_id!=InternalEntityID;
+    INSERT IGNORE INTO referring (id) SELECT domain_id FROM text_data WHERE property_id=InternalEntityID AND domain_id!=InternalEntityID AND entity_id!=InternalEntityID AND domain_id!=0;
 
-INSERT IGNORE INTO refering (id) SELECT entity_id FROM enum_data WHERE property_id=EntityID AND domain_id=0 AND entity_id!=EntityID;
-INSERT IGNORE INTO refering (id) SELECT domain_id FROM enum_data WHERE property_id=EntityID AND domain_id!=EntityID AND entity_id!=EntityID AND domain_id!=0; 
+    INSERT IGNORE INTO referring (id) SELECT entity_id FROM enum_data WHERE property_id=InternalEntityID AND domain_id=0 AND entity_id!=InternalEntityID;
+    INSERT IGNORE INTO referring (id) SELECT domain_id FROM enum_data WHERE property_id=InternalEntityID AND domain_id!=InternalEntityID AND entity_id!=InternalEntityID AND domain_id!=0;
 
-INSERT IGNORE INTO refering (id) SELECT entity_id FROM name_data WHERE property_id=EntityID AND domain_id=0 AND entity_id!=EntityID;
-INSERT IGNORE INTO refering (id) SELECT domain_id FROM name_data WHERE property_id=EntityID AND domain_id!=EntityID AND entity_id!=EntityID AND domain_id!=0; 
+    INSERT IGNORE INTO referring (id) SELECT entity_id FROM name_data WHERE property_id=InternalEntityID AND domain_id=0 AND entity_id!=InternalEntityID;
+    INSERT IGNORE INTO referring (id) SELECT domain_id FROM name_data WHERE property_id=InternalEntityID AND domain_id!=InternalEntityID AND entity_id!=InternalEntityID AND domain_id!=0;
 
-INSERT IGNORE INTO refering (id) SELECT entity_id FROM integer_data WHERE property_id=EntityID AND domain_id=0 AND entity_id!=EntityID;
-INSERT IGNORE INTO refering (id) SELECT domain_id FROM integer_data WHERE property_id=EntityID AND domain_id!=EntityID AND entity_id!=EntityID AND domain_id!=0; 
+    INSERT IGNORE INTO referring (id) SELECT entity_id FROM integer_data WHERE property_id=InternalEntityID AND domain_id=0 AND entity_id!=InternalEntityID;
+    INSERT IGNORE INTO referring (id) SELECT domain_id FROM integer_data WHERE property_id=InternalEntityID AND domain_id!=InternalEntityID AND entity_id!=InternalEntityID AND domain_id!=0;
 
-INSERT IGNORE INTO refering (id) SELECT entity_id FROM double_data WHERE property_id=EntityID AND domain_id=0 AND entity_id!=EntityID;
-INSERT IGNORE INTO refering (id) SELECT domain_id FROM double_data WHERE property_id=EntityID AND domain_id!=EntityID AND entity_id!=EntityID AND domain_id!=0; 
+    INSERT IGNORE INTO referring (id) SELECT entity_id FROM double_data WHERE property_id=InternalEntityID AND domain_id=0 AND entity_id!=InternalEntityID;
+    INSERT IGNORE INTO referring (id) SELECT domain_id FROM double_data WHERE property_id=InternalEntityID AND domain_id!=InternalEntityID AND entity_id!=InternalEntityID AND domain_id!=0;
 
-INSERT IGNORE INTO refering (id) SELECT entity_id FROM datetime_data WHERE property_id=EntityID AND domain_id=0 AND entity_id!=EntityID;
-INSERT IGNORE INTO refering (id) SELECT domain_id FROM datetime_data WHERE property_id=EntityID AND domain_id!=EntityID AND entity_id!=EntityID AND domain_id!=0; 
+    INSERT IGNORE INTO referring (id) SELECT entity_id FROM datetime_data WHERE property_id=InternalEntityID AND domain_id=0 AND entity_id!=InternalEntityID;
+    INSERT IGNORE INTO referring (id) SELECT domain_id FROM datetime_data WHERE property_id=InternalEntityID AND domain_id!=InternalEntityID AND entity_id!=InternalEntityID AND domain_id!=0;
 
-INSERT IGNORE INTO refering (id) SELECT entity_id FROM date_data WHERE property_id=EntityID AND domain_id=0 AND entity_id!=EntityID;
-INSERT IGNORE INTO refering (id) SELECT domain_id FROM date_data WHERE property_id=EntityID AND domain_id!=EntityID AND entity_id!=EntityID AND domain_id!=0; 
+    INSERT IGNORE INTO referring (id) SELECT entity_id FROM date_data WHERE property_id=InternalEntityID AND domain_id=0 AND entity_id!=InternalEntityID;
+    INSERT IGNORE INTO referring (id) SELECT domain_id FROM date_data WHERE property_id=InternalEntityID AND domain_id!=InternalEntityID AND entity_id!=InternalEntityID AND domain_id!=0;
 
-INSERT IGNORE INTO refering (id) SELECT entity_id FROM null_data WHERE property_id=EntityID AND domain_id=0 AND entity_id!=EntityID;
-INSERT IGNORE INTO refering (id) SELECT domain_id FROM null_data WHERE property_id=EntityID AND domain_id!=EntityID AND entity_id!=EntityID AND domain_id!=0; 
+    INSERT IGNORE INTO referring (id) SELECT entity_id FROM null_data WHERE property_id=InternalEntityID AND domain_id=0 AND entity_id!=InternalEntityID;
+    INSERT IGNORE INTO referring (id) SELECT domain_id FROM null_data WHERE property_id=InternalEntityID AND domain_id!=InternalEntityID AND entity_id!=InternalEntityID AND domain_id!=0;
 
-INSERT IGNORE INTO refering (id) SELECT entity_id from data_type WHERE datatype=EntityID AND domain_id=0 AND entity_id!=EntityID;
-INSERT IGNORE INTO refering (id) SELECT domain_id from data_type WHERE datatype=EntityID;
+    INSERT IGNORE INTO referring (id) SELECT entity_id from data_type WHERE datatype=InternalEntityID AND domain_id=0 AND entity_id!=InternalEntityID;
+    INSERT IGNORE INTO referring (id) SELECT domain_id from data_type WHERE datatype=InternalEntityID;
 
+    INSERT IGNORE INTO referring (id) SELECT child FROM isa_cache WHERE parent = InternalEntityID AND rpath = child;
 
-Select id from refering WHERE id!=0 and id!=EntityID;
+    SELECT e.id FROM referring AS r LEFT JOIN entity_ids AS e ON r.id = e.internal_id WHERE r.id!=0 AND e.internal_id!=InternalEntityID;
 
-DROP TEMPORARY TABLE refering;
+    DROP TEMPORARY TABLE referring;
 
 END;
 //

procedures/getFileIdByPath.sql

 /*
- * ** header v3.0
  * This file is a part of the CaosDB Project.
  *
  * Copyright (C) 2018 Research Group Biomedical Physics,
  * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+ * Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 Timm Fitschen <t.fitschen@indiscale.com>
  *
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU Affero General Public License as
@@ -17,16 +18,27 @@
  *
  * You should have received a copy of the GNU Affero General Public License
  * along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
  */
 
 Drop Procedure if exists db_5_0.getFileIdByPath;
 Delimiter //
-Create Procedure db_5_0.getFileIdByPath (in FilePath VARCHAR(255))
+
+/*
+ * Return a file's id for a given path or nothing if the path is unknown.
+ *
+ * Parameters
+ * ----------
+ * FilePath : TEXT
+ *    The file's path.
+ *
+ * Returns
+ * -------
+ * EntityID : VARCHAR(255)
+ */
+Create Procedure db_5_0.getFileIdByPath (in FilePath TEXT)
 BEGIN
 
-Select file_id as FileID from files where path=FilePath LIMIT 1;
+    SELECT e.id AS FileID FROM files AS f LEFT JOIN entity_ids ON e.internal_in = f.file_id WHERE f.path=FilePath LIMIT 1;
 
 END;
 //

procedures/retrieveSubentity.sql → procedures/getIdByName.sql

 /*
- * ** header v3.0
  * This file is a part of the CaosDB Project.
  *
- * Copyright (C) 2018 Research Group Biomedical Physics,
- * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+ * Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 Timm Fitschen <t.fitschen@indiscale.com>
  *
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU Affero General Public License as
@@ -17,31 +16,48 @@
  *
  * You should have received a copy of the GNU Affero General Public License
  * along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
  */
+
+DROP PROCEDURE IF EXISTS db_5_0.getIdByName;
 DELIMITER //
-DROP PROCEDURE IF EXISTS db_5_0.retrieveSubEntity //
-/**
-CREATE PROCEDURE db_5_0.retrieveSubEntity(in EntityID INT UNSIGNED, in DomainID INT UNSIGNED)
+
+/*
+ * Return the Entity id(s) for a given name. Optionally, filter by role and set
+ * a limit.
+ *
+ * Parameters
+ * ----------
+ * Name : VARCHAR(255)
+ *    The entity's name.
+ * Role : VARCHAR(255)
+ *    E.g. RecordType, Record, Property,...
+ * Lmt : INT UNSIGNED
+ *    Limit the number of returned entity ids.
+ *
+ * Returns
+ * -------
+ * EntityID : VARCHAR(255)
+ */
+CREATE PROCEDURE db_5_0.getIdByName(in Name VARCHAR(255), in Role VARCHAR(255), in Lmt INT UNSIGNED)
 BEGIN
-	DECLARE FilePath VARCHAR(255) DEFAULT NULL;
-	DECLARE FileSize VARCHAR(255) DEFAULT NULL;
-	DECLARE FileHash VARCHAR(255) DEFAULT NULL;
 
-	Select path, size, hex(hash) into FilePath, FileSize, FileHash from files where file_id = EntityID LIMIT 1;
-		Select DomainID as DomainID,
-			EntityID as EntityID, 
-			e.name as EntityName, 
-			e.description as EntityDesc, 
-			e.role as EntityRole, 
-			FileSize as FileSize, 
-			FilePath as FilePath, 
-			FileHash as FileHash 
-		from entities e where id = EntityID LIMIT 1;
+    SET @stmtStr = "SELECT e.id AS id FROM name_data AS n JOIN entity_ids AS e ON (n.domain_id=0 AND n.property_id=20 AND e.internal_id = n.entity_id) JOIN entities AS i ON (i.id = e.internal_id) WHERE n.value = ?";
+
+    IF Role IS NULL THEN
+        SET @stmtStr = CONCAT(@stmtStr, " AND i.role!='ROLE'");
+    ELSE
+        SET @stmtStr = CONCAT(@stmtStr, " AND i.role='", Role, "'");
+    END IF;
+
+    IF Lmt IS NOT NULL THEN
+        SET @stmtStr = CONCAT(@stmtStr, " LIMIT ", Lmt);
+    END IF;
+
+    SET @vName = Name;
+    PREPARE stmt FROM @stmtStr;
+    EXECUTE stmt USING @vName;
+    DEALLOCATE PREPARE stmt;
 
 END;
 //
-
-**/
 DELIMITER ;

procedures/getInfo.sql

-/*
- * ** header v3.0
- * This file is a part of the CaosDB Project.
- *
- * Copyright (C) 2018 Research Group Biomedical Physics,
- * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Affero General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU Affero General Public License for more details.
- *
- * You should have received a copy of the GNU Affero General Public License
- * along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
- */
-#-- old procedure.
-Drop Procedure if exists db_5_0.getInfo;

procedures/insertEntity.sql

 /*
- * ** header v3.0
  * This file is a part of the CaosDB Project.
  *
  * Copyright (C) 2018 Research Group Biomedical Physics,
  * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- * Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
- * Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale
+ * Copyright (C) 2020,2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020,2023 Timm Fitschen <t.fitschen@indiscale>
  *
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU Affero General Public License as
@@ -19,8 +18,6 @@
  *
  * You should have received a copy of the GNU Affero General Public License
  * along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
  */
 
 
@@ -31,12 +28,14 @@ delimiter //
 Parameters
 ==========
 
+EntityID : VARCHAR(255)
+    The entity id.
 EntityName : VARCHAR(255)
 
 EntityDesc : TEXT
 
 EntityRole : VARCHAR(255)
-Currently one of 'RECORDTYPE', 'RECORD', 'FILE', 'DOMAIN', 'PROPERTY',
+Currently one of 'RECORDTYPE', 'RECORD', 'FILE', 'PROPERTY',
 'DATATYPE', 'ROLE', 'QUERYTEMPLATE'
 
 ACL : VARBINARY(65525)
@@ -44,17 +43,17 @@ ACL : VARBINARY(65525)
 Select
 ======
 
-A tuple (EntityID, Version)
+(Version)
 */
-CREATE PROCEDURE db_5_0.insertEntity(in EntityName VARCHAR(255), in EntityDesc TEXT, in EntityRole VARCHAR(255), in ACL VARBINARY(65525))
+CREATE PROCEDURE db_5_0.insertEntity(in EntityID VARCHAR(255), in EntityName VARCHAR(255), in EntityDesc TEXT, in EntityRole VARCHAR(255), in ACL VARBINARY(65525))
 BEGIN
-    DECLARE NewEntityID INT UNSIGNED DEFAULT NULL;
     DECLARE NewACLID INT UNSIGNED DEFAULT NULL;
     DECLARE Hash VARBINARY(255) DEFAULT NULL;
     DECLARE Version VARBINARY(255) DEFAULT NULL;
     DECLARE Transaction VARBINARY(255) DEFAULT NULL;
+    DECLARE InternalEntityID INT UNSIGNED DEFAULT NULL;
 
-    -- insert the acl. the new acl id is being written (c-style) into the
+    -- insert the acl. The new acl id is written (c-style) into the
     -- variable NewACLID.
     call entityACL(NewACLID, ACL);
 
@@ -63,13 +62,15 @@ BEGIN
         VALUES (EntityDesc, EntityRole, NewACLID);
 
     -- ... and return the generated id
-    SET NewEntityID = LAST_INSERT_ID();
+    SET InternalEntityID = LAST_INSERT_ID();
+
+    INSERT INTO entity_ids (internal_id, id) VALUES (InternalEntityID, EntityID);
 
     IF is_feature_config("ENTITY_VERSIONING", "ENABLED") THEN
         -- TODO this is transaction-scoped variable. Is this a good idea?
         SET Transaction = @SRID;
         SET Version = SHA1(UUID());
-        CALL insert_single_child_version(NewEntityID, Hash, Version, Null, Transaction);
+        CALL insert_single_child_version(InternalEntityID, Hash, Version, Null, Transaction);
     END IF;
 
     -- insert the name of the entity into name_data table
@@ -77,10 +78,10 @@ BEGIN
     IF EntityName IS NOT NULL THEN
         INSERT INTO name_data
             (domain_id, entity_id, property_id, value, status, pidx)
-            VALUES (0, NewEntityID, 20, EntityName, "FIX", 0);
+            VALUES (0, InternalEntityID, 20, EntityName, "FIX", 0);
     END IF;
 
-    SELECT NewEntityID as EntityID, Version as Version;
+    SELECT Version as Version;
 
 END;
 //