diff --git a/.docker/Dockerfile b/.docker/Dockerfile
index 5c49eb7e9c88346b8423a611dc14aca2e85cf346..f9a4145fdf1a70e7be1ede3649261757a12d2c65 100644
--- a/.docker/Dockerfile
+++ b/.docker/Dockerfile
@@ -1,4 +1,4 @@
-FROM debian:buster
+FROM debian:bookworm
RUN apt-get update \
&& \
apt-get install -y \
@@ -11,4 +11,8 @@ RUN apt-get update \
python3-sqlparse \
python3-sphinx \
doxygen
-RUN pip3 install breathe sphinx-rtd-theme recommonmark
+RUN pip3 install --break-system-packages \
+ breathe \
+ sphinx-rtd-theme \
+ pytest \
+ recommonmark
diff --git a/.gitignore b/.gitignore
index 26060c8b9c3986ed5a0803bcf1e1e2a88acee1a3..6f952db9ec3600b624a0151d97db6d299cbd53ca 100644
--- a/.gitignore
+++ b/.gitignore
@@ -13,4 +13,5 @@ libs/*
# Generated files
_doxygen/
_generated/
-/build/
\ No newline at end of file
+/build/
+*~
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 3878ddb5d95b9319fc6c44481efe9a63d284da41..310aad61e9ec2a7f69d9fafbf816e91ce81c02da 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,9 +1,11 @@
#
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+# Copyright (C) 2024 Indiscale GmbH <info@indiscale.com>
# Copyright (C) 2019 Henrik tom Wörden
+# 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
@@ -57,11 +59,17 @@ unittests-mariadb:
tags: [ docker ]
stage: test
services:
- - mariadb:10.4
-
+ - mariadb:10.11
script:
- make pipeline-test SQL_HOST=mariadb
+# Run the dump update tests
+test-dump-update:
+ tags: [ docker ]
+ stage: test
+ script:
+ - make test-dump-update
+
# Run the unit tests with MySQL 5
unittests-mysql-5:
tags: [ docker ]
@@ -78,6 +86,7 @@ unittests-mysql-5:
- sed -i "/col_default_is.*NULL/d" tests/test_autotap.sql
- sed -i "/col_default_is.*INACTIVE/d" tests/test_autotap.sql
- sed -i "/col_default_is.*SHA/d" tests/test_autotap.sql
+ - sed -i "s/utf8mb3/utf8/" tests/test_autotap.sql
- make pipeline-test SQL_HOST=mysql
######## Deploy ########
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8e60d21354ab01b1c47ac9fcdff90af44686c30e..9b8478fd5e4a9f5b991c4e9a01a3ec2bf5abadc6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,21 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+## [8.0.0] - 2024-10-24 ##
+
+### Added ###
+
+- Script to update outdated database dumps.
+
+### Changed ###
+
+- `OFFSET` is a reserved keyword in MariaDB 10.6, so the former
+ `OFFSET` parameter name in the `get_head_relative` function was
+ changed to HeadOffset. See
+ [`update_dumps/README.md`](update_dumps/README.md) for information
+ on how to update old SQL dumps to be compatible with this renaming
+ and MariaDB >= 10.6.
+
## [7.0.2] - 2023-12-12 ##
(Timm Fitschen)
diff --git a/CITATION.cff b/CITATION.cff
new file mode 100644
index 0000000000000000000000000000000000000000..3d997f969ded2b5b3b8f9975835e51be7e86b30a
--- /dev/null
+++ b/CITATION.cff
@@ -0,0 +1,28 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+ - family-names: Fitschen
+ given-names: Timm
+ orcid: https://orcid.org/0000-0002-4022-432X
+ - family-names: Schlemmer
+ given-names: Alexander
+ orcid: https://orcid.org/0000-0003-4124-9649
+ - family-names: Hornung
+ given-names: Daniel
+ orcid: https://orcid.org/0000-0002-7846-6375
+ - family-names: tom Wörden
+ given-names: Henrik
+ orcid: https://orcid.org/0000-0002-5549-578X
+ - family-names: Spreckelsen
+ given-names: Florian
+ orcid: https://orcid.org/0000-0002-6856-2910
+ - family-names: Parlitz
+ given-names: Ulrich
+ orcid: https://orcid.org/0000-0003-3058-1435
+ - family-names: Luther
+ given-names: Stefan
+ orcid: https://orcid.org/0000-0001-7214-8125
+title: "LinkAhead - MariaDB Backend"
+version: 8.0.0
+doi: 10.3390/data4020083
+date-released: 2024-10-10
diff --git a/Makefile b/Makefile
index 7c1ec3effb5cea166649aedcba188d6974d2cb6f..0204e012088c322ade92e529ebabe1b27fe3a469 100644
--- a/Makefile
+++ b/Makefile
@@ -1,7 +1,7 @@
+# This file is a part of the Linkahead Project.
#
-# ** header v3.0
-# This file is a part of the CaosDB Project.
-#
+# Copyright (C) 2024 Daniel Hornung <d.hornung@indiscale.com>
+# Copyright (C) 2024 IndiScale GmbH <info@indiscale.com>
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
#
@@ -18,8 +18,7 @@
# 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
-#
+
SHELL=/bin/bash
INSTALL_SQL_FILE=db_5_0.sql
@@ -56,23 +55,26 @@ drop-%:
test:
./utils/make_db test --fresh
-# Run tests with a database which is started in a Docker container
+.PHONY: test-dump-update
+test-dump-update:
+ pytest dump_updates
+
+# Run tests with a database which is started in a MariaDB Docker container
.PHONY: test-docker
test-docker:
@docker kill caosdb-mysqlserver-test || true
- @docker container rm caosdb-mysqlserver-test || true
+ @docker container rm -v caosdb-mysqlserver-test || true
@docker run --name caosdb-mysqlserver-test -p "3306:3306" \
- -e MYSQL_ROOT_PASSWORD="pass-for-test" -d mariadb
+ -e MYSQL_ROOT_PASSWORD="pass-for-test" -d mariadb:10.11
@sleep 10
MAINPATH=$(realpath tests/docker_env) utils/make_db test --fresh
- @docker kill caosdb-mysqlserver-test
- @docker container rm caosdb-mysqlserver-test
+ make test-docker-stop
# if automatic stopping failed
.PHONY: test-docker-stop
test-docker-stop:
docker kill caosdb-mysqlserver-test
- docker container rm caosdb-mysqlserver-test
+ docker container rm -v caosdb-mysqlserver-test
# Compile the standalone documentation
.PHONY: doc
diff --git a/README_SETUP.md b/README_SETUP.md
index 581cc31411a6b6e510f10414c21ce6304697cb85..4e599ac3f3d019908143038e9415bef9fbcab1c5 100644
--- a/README_SETUP.md
+++ b/README_SETUP.md
@@ -114,6 +114,13 @@ obviously what was expected.
Please look carefully through the tests. If something more serious than that
comes up, please report a bug.
+#### Failure to restore a database dump created with an older MariaDB version ####
+
+Have a look into the `dump_updates/README.md`. In cases of version
+incompatibilities, the necessary steps to migrate the dump are
+probably described there and scripts for the migrations are provided
+in the same directory.
+
## Documentation #
Build documentation in `build/` with `make doc`.
diff --git a/RELEASE_GUIDELINES.md b/RELEASE_GUIDELINES.md
index 3497909d850c646a220c36188b3760df5d659f3b..c1d73359114379b74baf19e2bdf35e74be11077f 100644
--- a/RELEASE_GUIDELINES.md
+++ b/RELEASE_GUIDELINES.md
@@ -6,7 +6,8 @@ guidelines of the CaosDB Project
## General Prerequisites
-* All tests are passing.
+* All tests are passing. (Note that pipelines may fail if the major
+ version increased. Rely on manual tests in that case.)
* (FEATURES.md is up-to-date and a public API is being declared in that document.)
* CHANGELOG.md is up-to-date.
* (DEPENDENCIES.md is up-to-date.)
@@ -22,7 +23,7 @@ guidelines of the CaosDB Project
3. Assure that the latest patch actually updates the CaosDBVersion() procedure
and that the version matches the version you are about to release.
-4. Update version in `doc/conf.py`.
+4. Update version in `doc/conf.py` and in `CITATION.cff`.
5. Merge the release branch into the main branch.
@@ -36,3 +37,6 @@ guidelines of the CaosDB Project
section to the CHANGELOG.
10. Create a release at the [gitlab repo](https://gitlab.com/linkahead/linkahead-mariadbbackend/-/releases)
+
+11. If necessary, i.e., if the patch or major versions were increased
+ with the release, do a LinkAhead server release.
diff --git a/config.defaults b/config.defaults
index 1860377976c3bf0d9f389570dc0e981f47aa1609..d44a9f43fbedb1e7f3274825fb4cde99183cfff6 100644
--- a/config.defaults
+++ b/config.defaults
@@ -1,7 +1,7 @@
+# This file is a part of the LinkAhead Project.
#
-# ** header v2.0
-# This file is a part of the CaosDB Project.
-#
+# Copyright (C) 2024 Daniel Hornung <d.hornung@indiscale.com>
+# Copyright (C) 2024 IndiScale GmbH <info@indiscale.com>
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
#
@@ -15,11 +15,9 @@
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
-# You should have received a copy of the GNU General Public License
+# 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
-#
# # Commands
# The MySQL client program.
diff --git a/doc/conf.py b/doc/conf.py
index 5fdc05d730471fc610d2b3c5971ced9cfc14f192..d7968a2638e7131c9eba66fa69931e345f05b70e 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -22,13 +22,13 @@ import sphinx_rtd_theme
# -- Project information -----------------------------------------------------
project = 'caosdb-mysqlbackend'
-copyright = '2021, IndiScale GmbH'
+copyright = '2021 - 2024, IndiScale GmbH'
author = 'Daniel Hornung'
# The short X.Y version
-version = '7.0.2'
+version = '8.0.0'
# The full version, including alpha/beta/rc tags
-release = '7.0.2'
+release = '8.0.0'
# -- General configuration ---------------------------------------------------
diff --git a/doc/index.rst b/doc/index.rst
index 3924201bb5ab51ac7e1517f4eb1de95968dcb7b8..eac53ba65a937e1d57664af6a22780b262e35492 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -10,7 +10,9 @@ Welcome to documentation of CaosDB's MySQL Backend!
Getting started <README_SETUP>
Concepts <concepts>
Maintenance
- API documentation<functions>
+ API documentation <functions>
+ Related Projects <related_projects/index>
+ Back to Overview <https://docs.indiscale.com/>
This documentation helps you to :doc:`get started<README_SETUP>`, explains the most important
:doc:`concepts<concepts>` .
diff --git a/doc/related_projects/index.rst b/doc/related_projects/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..78abfd939a097245042a8487eee8ae0d6b4d9e44
--- /dev/null
+++ b/doc/related_projects/index.rst
@@ -0,0 +1,25 @@
+Related Projects
+++++++++++++++++
+
+.. toctree::
+ :maxdepth: 2
+ :caption: Contents:
+ :hidden:
+
+.. container:: projects
+
+ For in-depth documentation for users, administrators and developers, you may want to visit the subproject-specific documentation pages for:
+
+ :`Server <https://docs.indiscale.com/caosdb-server>`_: The Java part of the LinkAhead server.
+
+ :`WebUI <https://docs.indiscale.com/caosdb-webui>`_: The default web frontend for the LinkAhead server.
+
+ :`PyLinkAhead <https://docs.indiscale.com/caosdb-pylib>`_: The LinkAhead Python library.
+
+ :`Advanced user tools <https://docs.indiscale.com/caosdb-advanced-user-tools>`_: The advanced Python tools for LinkAhead.
+
+ :`LinkAhead Crawler <https://docs.indiscale.com/caosdb-crawler/>`_: The crawler is the main tool for automatic data integration in LinkAhead.
+
+ :`LinkAhead <https://docs.indiscale.com/caosdb-deploy>`_: Your all inclusive LinkAhead software package.
+
+ :`Back to Overview <https://docs.indiscale.com/>`_: LinkAhead Documentation.
diff --git a/dump_updates/2024-10-02.dump_fix_mariadb_10_6.sh b/dump_updates/2024-10-02.dump_fix_mariadb_10_6.sh
new file mode 100755
index 0000000000000000000000000000000000000000..4450b831f47d1ba8787b87708b6b8e2ec3be6e8d
--- /dev/null
+++ b/dump_updates/2024-10-02.dump_fix_mariadb_10_6.sh
@@ -0,0 +1,44 @@
+#!/usr/bin/env bash
+
+# This file is a part of the LinkAhead Project.
+#
+# Copyright (C) 2024 IndiScale GmbH <info@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
+# 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/>.
+
+# About this script
+# =================
+#
+# Fix the use of "offset" as a procedure parameter name. "OFFSET" became a reserved keyword in
+# MariaDB 10.6.
+#
+# This script takes an SQL dump from stdin and prints the fixed SQL to stdout.
+#
+# Usage
+# -----
+#
+# 2024-10-02.dump_fix_mariadb_10_6.sh < yourdump.sql > yourdump.fixed.sql
+
+set -euo pipefail
+IFS=$'\n\t'
+
+script='
+s/Offset INT UNSIGNED) RETURNS varbinary(255)/HeadOffset INT UNSIGNED) RETURNS varbinary(255)/
+s/LIMIT 1 OFFSET Offset/LIMIT 1 OFFSET HeadOffset/
+'
+
+sed -e "$script"
+
+unset script
diff --git a/dump_updates/README.md b/dump_updates/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..704ea80321a9a873185d0c6959e2000ad26fa10d
--- /dev/null
+++ b/dump_updates/README.md
@@ -0,0 +1,21 @@
+# SQL dump updates #
+
+## Dump ##
+
+This directory contains scripts to update database dumps to newer versions of the MariaDB server.
+
+## Background ##
+
+In some cases, restoring the database content from existing SQL dumps may not be possible in a
+straightforward manner. For those cases, this directory contains scripts to help with known issues.
+
+Examples for problems include:
+
+- New reserved keywords in MariaDB, that were previously used as identifiers in code.
+
+# Known issues and their fix #
+
+- SQL syntax error near `Offset INT UNSIGNED`: If a dump was made before MariaDB 10.6 (LinkAhead <
+ 0.15) and with the SQL backend before 7.0.3, there was a pramater named `Offset`. With MariaDB
+ 10.6 however, `OFFSET` became a reserved keyword. This can be fixed by running
+ `2024-10-02.dump_fix_mariadb_10_6.sh < yourdump.sql > yourdump.fixed.sql`
diff --git a/dump_updates/test/test_all.py b/dump_updates/test/test_all.py
new file mode 100644
index 0000000000000000000000000000000000000000..8e97d2a1cea461dc0f5613a5ea94eeac663d5b3c
--- /dev/null
+++ b/dump_updates/test/test_all.py
@@ -0,0 +1,70 @@
+#!/usr/bin/env python3
+
+# This file is a part of the LinkAhead Project.
+#
+# Copyright (C) 2024 IndiScale GmbH <www.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
+# 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/>.
+
+"""Testing the dump update scripts
+"""
+
+import filecmp
+from pathlib import Path
+from subprocess import run
+from tempfile import NamedTemporaryFile
+
+
+def get_basedir() -> str:
+ """Return the assumped base dir for the dump updates.
+ """
+ path = Path(__file__).parents[1]
+ return str(path)
+
+
+def get_test_data(basename: str) -> list[tuple[str, str]]:
+ """Return a list of [input, expectedoutput] tuples.
+
+ The output may be an empty string if no corresponding file can be found.
+ """
+ basedir = get_basedir()
+ datadir = Path(basedir) / "test" / "test_data"
+ results = []
+ for input_path in datadir.glob(f"{basename}.example*[0-9].sql"):
+ expected_path = datadir / f"{input_path.name[:-4]}.expected.sql"
+ if expected_path.exists():
+ expected = str(expected_path)
+ else:
+ expected = ""
+ results.append((str(input_path), expected))
+ return results
+
+
+def test_2024_10_02(tmpdir):
+ """``Offset`` became a reserved keyword in MariaDB 10.6.
+ """
+ script = "2024-10-02.dump_fix_mariadb_10_6.sh"
+ script_fullname = str(Path(get_basedir()) / script)
+ test_data = get_test_data(script[:-3])
+ for infile, expectedfile in test_data:
+ with (NamedTemporaryFile(dir=tmpdir, suffix=".sql", delete=True) as output,
+ open(infile, mode="rb") as infile_stream
+ ):
+ run([script_fullname],
+ stdin=infile_stream,
+ stdout=output,
+ check=True
+ )
+ assert filecmp.cmp(output.name, expectedfile), "Output does not match expected output."
diff --git a/dump_updates/test/test_data/2024-10-02.dump_fix_mariadb_10_6.example1.expected.sql b/dump_updates/test/test_data/2024-10-02.dump_fix_mariadb_10_6.example1.expected.sql
new file mode 100644
index 0000000000000000000000000000000000000000..1a58223ba65827231ce658f1a655a68706bf8088
--- /dev/null
+++ b/dump_updates/test/test_data/2024-10-02.dump_fix_mariadb_10_6.example1.expected.sql
@@ -0,0 +1,36 @@
+/* Just a short snippt with the problem */
+
+
+/*!50003 SET @saved_col_connection = @@collation_connection */ ;
+/*!50003 SET character_set_client = utf8 */ ;
+/*!50003 SET character_set_results = utf8 */ ;
+/*!50003 SET collation_connection = utf8_general_ci */ ;
+DELIMITER ;;
+CREATE DEFINER=`root`@`%` FUNCTION `get_head_relative`(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;
+
+
+
+
+
+ RETURN (
+ SELECT e.version
+ FROM entity_version AS e
+ WHERE e.entity_id = InternalEntityID
+ ORDER BY e._iversion DESC
+ LIMIT 1 OFFSET HeadOffset
+ );
+END ;;
+DELIMITER ;
+/*!50003 SET sql_mode = @saved_sql_mode */ ;
+/*!50003 SET character_set_client = @saved_cs_client */ ;
+/*!50003 SET character_set_results = @saved_cs_results */ ;
+/*!50003 SET collation_connection = @saved_col_connection */ ;
+/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
+/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
+/*!50003 D */
diff --git a/dump_updates/test/test_data/2024-10-02.dump_fix_mariadb_10_6.example1.sql b/dump_updates/test/test_data/2024-10-02.dump_fix_mariadb_10_6.example1.sql
new file mode 100644
index 0000000000000000000000000000000000000000..a5476af3268360476f2c1ef741cb25007e29ce5d
--- /dev/null
+++ b/dump_updates/test/test_data/2024-10-02.dump_fix_mariadb_10_6.example1.sql
@@ -0,0 +1,36 @@
+/* Just a short snippt with the problem */
+
+
+/*!50003 SET @saved_col_connection = @@collation_connection */ ;
+/*!50003 SET character_set_client = utf8 */ ;
+/*!50003 SET character_set_results = utf8 */ ;
+/*!50003 SET collation_connection = utf8_general_ci */ ;
+DELIMITER ;;
+CREATE DEFINER=`root`@`%` FUNCTION `get_head_relative`(EntityID VARCHAR(255),
+ Offset 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;
+
+
+
+
+
+ RETURN (
+ SELECT e.version
+ FROM entity_version AS e
+ WHERE e.entity_id = InternalEntityID
+ ORDER BY e._iversion DESC
+ LIMIT 1 OFFSET Offset
+ );
+END ;;
+DELIMITER ;
+/*!50003 SET sql_mode = @saved_sql_mode */ ;
+/*!50003 SET character_set_client = @saved_cs_client */ ;
+/*!50003 SET character_set_results = @saved_cs_results */ ;
+/*!50003 SET collation_connection = @saved_col_connection */ ;
+/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
+/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
+/*!50003 D */
diff --git a/patches/applyPatches.sh b/patches/applyPatches.sh
index 735dd3ea48a43d033b46dad1c7eb1700bda5c9b1..85bdad86d2fa80d0e304c2a1105ce6ded05257a4 100755
--- a/patches/applyPatches.sh
+++ b/patches/applyPatches.sh
@@ -47,4 +47,5 @@ do
done
cd ../
+
$UTILSPATH/update_sql_procedures.sh
diff --git a/patches/patch20241024-8.0.0/patch.sh b/patches/patch20241024-8.0.0/patch.sh
new file mode 100755
index 0000000000000000000000000000000000000000..2573c95864518363088af121a705d87f786b07ca
--- /dev/null
+++ b/patches/patch20241024-8.0.0/patch.sh
@@ -0,0 +1,41 @@
+#!/bin/bash
+#
+# This file is a part of the LinkAhead Project.
+#
+# Copyright (C) 2024 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2024 Timm Fitschen <t.fitschen@indiscale.com>
+# Copyright (C) 2024 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+
+# Update mysql schema to version v8.0.0
+#
+# The patch is empty because the change has to be applied manually
+# from ../../dump_updates/2024-10-02.dump_fix_mariadb_10_6.sh if necessary.
+
+NEW_VERSION="v8.0.0"
+OLD_VERSION="v7.0.2"
+
+if [ -z "$UTILSPATH" ]; then
+ UTILSPATH="../utils"
+fi
+
+. $UTILSPATH/patch_header.sh $*
+
+check_version $OLD_VERSION
+
+update_version $NEW_VERSION
+
+success
diff --git a/procedures/entityVersioning.sql b/procedures/entityVersioning.sql
index b474d0121130a1695d69616e1de4cc54468b5e64..a71c0c729f9fae5e710b8cfd8e37618e7615ff20 100644
--- a/procedures/entityVersioning.sql
+++ b/procedures/entityVersioning.sql
@@ -1,9 +1,9 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
- * Copyright (C) 2020,2023 IndiScale GmbH <info@indiscale.com>
+ * 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
@@ -283,7 +283,7 @@ DROP FUNCTION IF EXISTS db_5_0.get_head_relative //
* ----------
* EntityID : VARCHAR(255)
* The entity id.
- * Offset : INT UNSIGNED
+ * 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.
@@ -294,7 +294,7 @@ DROP FUNCTION IF EXISTS db_5_0.get_head_relative //
*/
CREATE FUNCTION db_5_0.get_head_relative(
EntityID VARCHAR(255),
- Offset INT UNSIGNED)
+ HeadOffset INT UNSIGNED)
RETURNS VARBINARY(255)
READS SQL DATA
BEGIN
@@ -311,7 +311,7 @@ BEGIN
FROM entity_version AS e
WHERE e.entity_id = InternalEntityID
ORDER BY e._iversion DESC
- LIMIT 1 OFFSET Offset
+ LIMIT 1 OFFSET HeadOffset
);
END;
//
diff --git a/procedures/query/initEntity.sql b/procedures/query/initEntity.sql
index d63c7773867cb9e5c29bdc4f95cbe866c3b426c4..5d1f978baabae19691bb84eb172bb06898ed61b9 100644
--- a/procedures/query/initEntity.sql
+++ b/procedures/query/initEntity.sql
@@ -80,9 +80,10 @@ initEntityLabel: BEGIN
IF(versioned,
'` (id, _iversion) SELECT eids.internal_id, _get_head_iversion(eids.internal_id) ',
'` (id) SELECT eids.internal_id '),
- 'FROM entity_ids AS eids WHERE eids.id=',eid,';');
+ 'FROM entity_ids AS eids WHERE eids.id=?;');
+ SET @query_param = eid;
PREPARE initEntityStmt FROM @initEntityStmtStr;
- EXECUTE initEntityStmt;
+ EXECUTE initEntityStmt USING @query_param;
DEALLOCATE PREPARE initEntityStmt;
END IF;
diff --git a/tests/test_autotap.sql b/tests/test_autotap.sql
index 6109dbe7d39dd62f21232e823fc639d71c5c8a6f..168758c1482d21345e025f3d3ca2e33a9e0c607c 100644
--- a/tests/test_autotap.sql
+++ b/tests/test_autotap.sql
@@ -38,7 +38,7 @@ SELECT tap.has_schema('_caosdb_schema_unit_tests','');
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','archive_isa','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','archive_isa','utf8_unicode_ci','');
+SELECT tap.table_collation_is('_caosdb_schema_unit_tests','archive_isa','utf8mb3_unicode_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','archive_isa','InnoDB','');
-- COLUMNS
@@ -116,7 +116,7 @@ SELECT tap.fk_on_update('_caosdb_schema_unit_tests','archive_isa','archive_isa_i
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','collection_type','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','collection_type','utf8_unicode_ci','');
+SELECT tap.table_collation_is('_caosdb_schema_unit_tests','collection_type','utf8mb3_unicode_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','collection_type','InnoDB','');
-- COLUMNS
@@ -155,8 +155,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','collection_type','collection'
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','collection_type','collection','varchar(255)','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','collection_type','collection','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','collection_type','collection',NULL,'');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','collection_type','collection','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','collection_type','collection','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','collection_type','collection','utf8mb3','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','collection_type','collection','utf8mb3_unicode_ci','');
-- INDEXES
SELECT tap.indexes_are('_caosdb_schema_unit_tests','collection_type','`domain_id`,`entity_id`,`property_id`','');
@@ -208,7 +208,7 @@ SELECT tap.fk_on_update('_caosdb_schema_unit_tests','collection_type','collectio
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','data_type','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','data_type','utf8_unicode_ci','');
+SELECT tap.table_collation_is('_caosdb_schema_unit_tests','data_type','utf8mb3_unicode_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','data_type','InnoDB','');
-- COLUMNS
@@ -300,7 +300,7 @@ SELECT tap.constraint_type_is('_caosdb_schema_unit_tests','data_type','datatype_
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','date_data','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','date_data','utf8_unicode_ci','');
+SELECT tap.table_collation_is('_caosdb_schema_unit_tests','date_data','utf8mb3_unicode_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','date_data','InnoDB','');
-- COLUMNS
@@ -348,8 +348,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','date_data','status','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','date_data','status','enum(\'OBLIGATORY\',\'RECOMMENDED\',\'SUGGESTED\',\'FIX\')','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','date_data','status','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','date_data','status','NULL','');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','date_data','status','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','date_data','status','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','date_data','status','utf8mb3','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','date_data','status','utf8mb3_unicode_ci','');
-- COLUMN date_data.pidx
@@ -398,7 +398,7 @@ SELECT tap.fk_on_update('_caosdb_schema_unit_tests','date_data','date_ov_forkey_
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','datetime_data','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','datetime_data','utf8_unicode_ci','');
+SELECT tap.table_collation_is('_caosdb_schema_unit_tests','datetime_data','utf8mb3_unicode_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','datetime_data','InnoDB','');
-- COLUMNS
@@ -437,8 +437,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','datetime_data','status','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','datetime_data','status','enum(\'OBLIGATORY\',\'RECOMMENDED\',\'SUGGESTED\',\'FIX\',\'REPLACEMENT\')','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','datetime_data','status','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','datetime_data','status',NULL,'');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','datetime_data','status','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','datetime_data','status','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','datetime_data','status','utf8mb3','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','datetime_data','status','utf8mb3_unicode_ci','');
-- COLUMN datetime_data.pidx
@@ -505,7 +505,7 @@ SELECT tap.fk_on_update('_caosdb_schema_unit_tests','datetime_data','dat_propert
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','desc_overrides','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','desc_overrides','utf8_unicode_ci','');
+SELECT tap.table_collation_is('_caosdb_schema_unit_tests','desc_overrides','utf8mb3_unicode_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','desc_overrides','InnoDB','');
-- COLUMNS
@@ -544,8 +544,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','desc_overrides','description'
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','desc_overrides','description','text','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','desc_overrides','description','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','desc_overrides','description','NULL','');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','desc_overrides','description','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','desc_overrides','description','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','desc_overrides','description','utf8mb3','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','desc_overrides','description','utf8mb3_unicode_ci','');
-- INDEXES
SELECT tap.indexes_are('_caosdb_schema_unit_tests','desc_overrides','`desc_ov_dom_ent_idx`','');
@@ -590,7 +590,7 @@ SELECT tap.constraint_type_is('_caosdb_schema_unit_tests','desc_overrides','desc
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','double_data','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','double_data','utf8_unicode_ci','');
+SELECT tap.table_collation_is('_caosdb_schema_unit_tests','double_data','utf8mb3_unicode_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','double_data','InnoDB','');
-- COLUMNS
@@ -638,8 +638,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','double_data','status','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','double_data','status','enum(\'OBLIGATORY\',\'RECOMMENDED\',\'SUGGESTED\',\'FIX\',\'REPLACEMENT\')','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','double_data','status','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','double_data','status',NULL,'');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','double_data','status','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','double_data','status','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','double_data','status','utf8mb3','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','double_data','status','utf8mb3_unicode_ci','');
-- COLUMN double_data.pidx
@@ -697,7 +697,7 @@ SELECT tap.fk_on_update('_caosdb_schema_unit_tests','double_data','dou_property_
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','entities','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','entities','utf8_unicode_ci','');
+SELECT tap.table_collation_is('_caosdb_schema_unit_tests','entities','utf8mb3_unicode_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','entities','InnoDB','');
-- COLUMNS
@@ -718,8 +718,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','entities','description','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','entities','description','text','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','entities','description','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','entities','description','NULL','');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','entities','description','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','entities','description','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','entities','description','utf8mb3','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','entities','description','utf8mb3_unicode_ci','');
-- COLUMN entities.role
@@ -727,8 +727,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','entities','role','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','entities','role','enum(\'RECORDTYPE\',\'RECORD\',\'FILE\',\'_REPLACEMENT\',\'PROPERTY\',\'DATATYPE\',\'ROLE\',\'QUERYTEMPLATE\')','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','entities','role','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','entities','role',NULL,'');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','entities','role','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','entities','role','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','entities','role','utf8mb3','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','entities','role','utf8mb3_unicode_ci','');
-- COLUMN entities.acl
@@ -760,7 +760,7 @@ SELECT tap.col_is_pk('_caosdb_schema_unit_tests','entities','`id`','');
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','entity_acl','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','entity_acl','utf8_unicode_ci','');
+SELECT tap.table_collation_is('_caosdb_schema_unit_tests','entity_acl','utf8mb3_unicode_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','entity_acl','InnoDB','');
-- COLUMNS
@@ -807,7 +807,7 @@ SELECT tap.col_is_pk('_caosdb_schema_unit_tests','entity_acl','`id`','');
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','enum_data','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','enum_data','utf8_unicode_ci','');
+SELECT tap.table_collation_is('_caosdb_schema_unit_tests','enum_data','utf8mb3_unicode_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','enum_data','InnoDB','');
-- COLUMNS
@@ -855,8 +855,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','enum_data','status','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','enum_data','status','enum(\'OBLIGATORY\',\'RECOMMENDED\',\'SUGGESTED\',\'FIX\')','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','enum_data','status','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','enum_data','status','NULL','');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','enum_data','status','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','enum_data','status','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','enum_data','status','utf8mb3','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','enum_data','status','utf8mb3_unicode_ci','');
-- COLUMN enum_data.pidx
@@ -905,7 +905,7 @@ SELECT tap.fk_on_update('_caosdb_schema_unit_tests','enum_data','enum_ov_forkey_
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','files','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','files','utf8_unicode_ci','');
+SELECT tap.table_collation_is('_caosdb_schema_unit_tests','files','utf8mb3_unicode_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','files','InnoDB','');
-- COLUMNS
@@ -926,8 +926,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','files','path','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','files','path','varchar(255)','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','files','path','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','files','path',NULL,'');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','files','path','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','files','path','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','files','path','utf8mb3','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','files','path','utf8mb3_unicode_ci','');
-- COLUMN files.size
@@ -977,7 +977,7 @@ SELECT tap.col_is_pk('_caosdb_schema_unit_tests','files','`file_id`','');
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','integer_data','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','integer_data','utf8_unicode_ci','');
+SELECT tap.table_collation_is('_caosdb_schema_unit_tests','integer_data','utf8mb3_unicode_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','integer_data','InnoDB','');
-- COLUMNS
@@ -1025,8 +1025,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','integer_data','status','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','integer_data','status','enum(\'OBLIGATORY\',\'RECOMMENDED\',\'SUGGESTED\',\'FIX\',\'REPLACEMENT\')','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','integer_data','status','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','integer_data','status',NULL,'');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','integer_data','status','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','integer_data','status','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','integer_data','status','utf8mb3','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','integer_data','status','utf8mb3_unicode_ci','');
-- COLUMN integer_data.pidx
@@ -1084,7 +1084,7 @@ SELECT tap.fk_on_update('_caosdb_schema_unit_tests','integer_data','int_property
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','isa_cache','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','isa_cache','utf8_unicode_ci','');
+SELECT tap.table_collation_is('_caosdb_schema_unit_tests','isa_cache','utf8mb3_unicode_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','isa_cache','InnoDB','');
-- COLUMNS
@@ -1114,8 +1114,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','isa_cache','rpath','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','isa_cache','rpath','varchar(255)','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','isa_cache','rpath','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','isa_cache','rpath',NULL,'');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','isa_cache','rpath','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','isa_cache','rpath','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','isa_cache','rpath','utf8mb3','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','isa_cache','rpath','utf8mb3_unicode_ci','');
-- CONSTRAINTS
SELECT tap.constraints_are('_caosdb_schema_unit_tests','isa_cache','`PRIMARY`,`isa_cache_child_entity`,`isa_cache_parent_entity`','');
@@ -1145,7 +1145,7 @@ SELECT tap.col_is_pk('_caosdb_schema_unit_tests','isa_cache','`child`,`parent`,`
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','name_data','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','name_data','utf8_unicode_ci','');
+SELECT tap.table_collation_is('_caosdb_schema_unit_tests','name_data','utf8mb3_unicode_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','name_data','InnoDB','');
-- COLUMNS
@@ -1184,8 +1184,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','name_data','value','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','name_data','value','varchar(255)','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','name_data','value','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','name_data','value',NULL,'');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','name_data','value','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','name_data','value','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','name_data','value','utf8mb3','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','name_data','value','utf8mb3_unicode_ci','');
-- COLUMN name_data.status
@@ -1193,8 +1193,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','name_data','status','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','name_data','status','enum(\'OBLIGATORY\',\'RECOMMENDED\',\'SUGGESTED\',\'FIX\',\'REPLACEMENT\')','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','name_data','status','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','name_data','status',NULL,'');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','name_data','status','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','name_data','status','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','name_data','status','utf8mb3','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','name_data','status','utf8mb3_unicode_ci','');
-- COLUMN name_data.pidx
@@ -1266,7 +1266,7 @@ SELECT tap.fk_on_update('_caosdb_schema_unit_tests','name_data','name_data_prope
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','name_overrides','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','name_overrides','utf8_unicode_ci','');
+SELECT tap.table_collation_is('_caosdb_schema_unit_tests','name_overrides','utf8mb3_unicode_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','name_overrides','InnoDB','');
-- COLUMNS
@@ -1305,8 +1305,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','name_overrides','name','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','name_overrides','name','varchar(255)','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','name_overrides','name','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','name_overrides','name','NULL','');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','name_overrides','name','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','name_overrides','name','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','name_overrides','name','utf8mb3','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','name_overrides','name','utf8mb3_unicode_ci','');
-- INDEXES
SELECT tap.indexes_are('_caosdb_schema_unit_tests','name_overrides','`name_ov_dom_ent_idx`','');
@@ -1351,7 +1351,7 @@ SELECT tap.constraint_type_is('_caosdb_schema_unit_tests','name_overrides','name
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','null_data','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','null_data','utf8_unicode_ci','');
+SELECT tap.table_collation_is('_caosdb_schema_unit_tests','null_data','utf8mb3_unicode_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','null_data','InnoDB','');
-- COLUMNS
@@ -1390,8 +1390,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','null_data','status','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','null_data','status','enum(\'OBLIGATORY\',\'RECOMMENDED\',\'SUGGESTED\',\'FIX\')','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','null_data','status','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','null_data','status','NULL','');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','null_data','status','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','null_data','status','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','null_data','status','utf8mb3','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','null_data','status','utf8mb3_unicode_ci','');
-- COLUMN null_data.pidx
@@ -1440,7 +1440,7 @@ SELECT tap.fk_on_update('_caosdb_schema_unit_tests','null_data','null_forkey_pro
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','passwd','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','passwd','utf8_unicode_ci','');
+SELECT tap.table_collation_is('_caosdb_schema_unit_tests','passwd','utf8mb3_unicode_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','passwd','InnoDB','');
-- COLUMNS
@@ -1470,8 +1470,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','passwd','alg','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','passwd','alg','varchar(255)','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','passwd','alg','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','passwd','alg','\'SHA-512\'','');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','passwd','alg','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','passwd','alg','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','passwd','alg','utf8mb3','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','passwd','alg','utf8mb3_unicode_ci','');
-- COLUMN passwd.it
@@ -1505,7 +1505,7 @@ SELECT tap.col_is_pk('_caosdb_schema_unit_tests','passwd','`principal`','');
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','permissions','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','permissions','utf8_unicode_ci','');
+SELECT tap.table_collation_is('_caosdb_schema_unit_tests','permissions','utf8mb3_unicode_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','permissions','InnoDB','');
-- COLUMNS
@@ -1526,8 +1526,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','permissions','permissions',''
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','permissions','permissions','mediumtext','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','permissions','permissions','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','permissions','permissions',NULL,'');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','permissions','permissions','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','permissions','permissions','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','permissions','permissions','utf8mb3','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','permissions','permissions','utf8mb3_unicode_ci','');
-- CONSTRAINTS
SELECT tap.constraints_are('_caosdb_schema_unit_tests','permissions','`PRIMARY`,`perm_name_roles`','');
@@ -1550,7 +1550,7 @@ SELECT tap.col_is_pk('_caosdb_schema_unit_tests','permissions','`role`','');
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','query_template_def','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','query_template_def','utf8_unicode_ci','');
+SELECT tap.table_collation_is('_caosdb_schema_unit_tests','query_template_def','utf8mb3_unicode_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','query_template_def','InnoDB','');
-- COLUMNS
@@ -1571,8 +1571,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','query_template_def','definiti
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','query_template_def','definition','mediumtext','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','query_template_def','definition','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','query_template_def','definition',NULL,'');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','query_template_def','definition','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','query_template_def','definition','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','query_template_def','definition','utf8mb3','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','query_template_def','definition','utf8mb3_unicode_ci','');
-- CONSTRAINTS
SELECT tap.constraints_are('_caosdb_schema_unit_tests','query_template_def','`PRIMARY`,`query_template_def_ibfk_1`','');
@@ -1595,7 +1595,7 @@ SELECT tap.fk_on_update('_caosdb_schema_unit_tests','query_template_def','query_
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','reference_data','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','reference_data','utf8_unicode_ci','');
+SELECT tap.table_collation_is('_caosdb_schema_unit_tests','reference_data','utf8mb3_unicode_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','reference_data','InnoDB','');
-- COLUMNS
@@ -1643,8 +1643,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','reference_data','status','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','reference_data','status','enum(\'OBLIGATORY\',\'RECOMMENDED\',\'SUGGESTED\',\'FIX\',\'REPLACEMENT\')','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','reference_data','status','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','reference_data','status',NULL,'');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','reference_data','status','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','reference_data','status','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','reference_data','status','utf8mb3','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','reference_data','status','utf8mb3_unicode_ci','');
-- COLUMN reference_data.pidx
@@ -1722,7 +1722,7 @@ SELECT tap.fk_on_update('_caosdb_schema_unit_tests','reference_data','reference_
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','roles','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','roles','utf8_unicode_ci','');
+SELECT tap.table_collation_is('_caosdb_schema_unit_tests','roles','utf8mb3_unicode_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','roles','InnoDB','');
-- COLUMNS
@@ -1743,8 +1743,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','roles','description','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','roles','description','mediumtext','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','roles','description','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','roles','description','NULL','');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','roles','description','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','roles','description','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','roles','description','utf8mb3','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','roles','description','utf8mb3_unicode_ci','');
-- CONSTRAINTS
SELECT tap.constraints_are('_caosdb_schema_unit_tests','roles','`PRIMARY`','');
@@ -1760,7 +1760,7 @@ SELECT tap.col_is_pk('_caosdb_schema_unit_tests','roles','`name`','');
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','stats','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','stats','utf8_unicode_ci','');
+SELECT tap.table_collation_is('_caosdb_schema_unit_tests','stats','utf8mb3_unicode_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','stats','InnoDB','');
-- COLUMNS
@@ -1772,8 +1772,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','stats','name','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','stats','name','varchar(255)','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','stats','name','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','stats','name',NULL,'');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','stats','name','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','stats','name','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','stats','name','utf8mb3','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','stats','name','utf8mb3_unicode_ci','');
-- COLUMN stats.value
@@ -1798,7 +1798,7 @@ SELECT tap.col_is_pk('_caosdb_schema_unit_tests','stats','`name`','');
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','text_data','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','text_data','utf8_unicode_ci','');
+SELECT tap.table_collation_is('_caosdb_schema_unit_tests','text_data','utf8mb3_unicode_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','text_data','InnoDB','');
-- COLUMNS
@@ -1837,8 +1837,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','text_data','value','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','text_data','value','text','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','text_data','value','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','text_data','value',NULL,'');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','text_data','value','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','text_data','value','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','text_data','value','utf8mb3','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','text_data','value','utf8mb3_unicode_ci','');
-- COLUMN text_data.status
@@ -1846,8 +1846,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','text_data','status','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','text_data','status','enum(\'OBLIGATORY\',\'RECOMMENDED\',\'SUGGESTED\',\'FIX\',\'REPLACEMENT\')','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','text_data','status','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','text_data','status',NULL,'');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','text_data','status','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','text_data','status','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','text_data','status','utf8mb3','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','text_data','status','utf8mb3_unicode_ci','');
-- COLUMN text_data.pidx
@@ -1896,7 +1896,7 @@ SELECT tap.fk_on_update('_caosdb_schema_unit_tests','text_data','str_property_id
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','transaction_log','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','transaction_log','utf8_unicode_ci','');
+SELECT tap.table_collation_is('_caosdb_schema_unit_tests','transaction_log','utf8mb3_unicode_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','transaction_log','InnoDB','');
-- COLUMNS
@@ -1908,8 +1908,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','transaction_log','transaction
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','transaction_log','transaction','varchar(255)','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','transaction_log','transaction','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','transaction_log','transaction',NULL,'');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','transaction_log','transaction','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','transaction_log','transaction','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','transaction_log','transaction','utf8mb3','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','transaction_log','transaction','utf8mb3_unicode_ci','');
-- COLUMN transaction_log.entity_id
@@ -1970,7 +1970,7 @@ SELECT tap.is_indexed('_caosdb_schema_unit_tests','transaction_log','`entity_id`
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','units_lin_con','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','units_lin_con','utf8_unicode_ci','');
+SELECT tap.table_collation_is('_caosdb_schema_unit_tests','units_lin_con','utf8mb3_unicode_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','units_lin_con','InnoDB','');
-- COLUMNS
@@ -2044,7 +2044,7 @@ SELECT tap.col_is_pk('_caosdb_schema_unit_tests','units_lin_con','`signature_fro
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','user_info','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','user_info','utf8_unicode_ci','');
+SELECT tap.table_collation_is('_caosdb_schema_unit_tests','user_info','utf8mb3_unicode_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','user_info','InnoDB','');
-- COLUMNS
@@ -2083,8 +2083,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','user_info','status','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','user_info','status','enum(\'ACTIVE\',\'INACTIVE\')','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','user_info','status','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','user_info','status','\'INACTIVE\'','');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','user_info','status','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','user_info','status','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','user_info','status','utf8mb3','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','user_info','status','utf8mb3_unicode_ci','');
-- COLUMN user_info.entity
@@ -2125,7 +2125,7 @@ SELECT tap.fk_on_update('_caosdb_schema_unit_tests','user_info','subjects_ibfk_2
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','user_roles','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','user_roles','utf8_unicode_ci','');
+SELECT tap.table_collation_is('_caosdb_schema_unit_tests','user_roles','utf8mb3_unicode_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','user_roles','InnoDB','');
-- COLUMNS
@@ -2179,7 +2179,7 @@ SELECT tap.fk_on_update('_caosdb_schema_unit_tests','user_roles','user_roles_ibf
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','entity_version','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','entity_version','utf8_unicode_ci','');
+SELECT tap.table_collation_is('_caosdb_schema_unit_tests','entity_version','utf8mb3_unicode_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','entity_version','InnoDB','');
-- COLUMNS
diff --git a/utils/helpers.sh b/utils/helpers.sh
index 86f7d5981c7497fe478bccb3f391932585934545..f335dfa179e26e0237149572168884b554ee5f91 100644
--- a/utils/helpers.sh
+++ b/utils/helpers.sh
@@ -1,10 +1,10 @@
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
-# Copyright (C) 2019, 2020 Daniel Hornung (d.hornung@indiscale.com)
+# Copyright (C) 2019, 2020, 2024 Daniel Hornung (d.hornung@indiscale.com)
# Copyright (C) 2020 Henrik tom Wörden
-# Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2020, 2024 IndiScale GmbH <info@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
@@ -52,10 +52,16 @@ function mysql_execute_file {
fi
}
+# Return the arguments from `get_db_args_nodb` and additionally the database name as
+# `--database=mydatabasename`.
function get_db_args {
echo "$(get_db_args_nodb) --database=$DATABASE_NAME"
}
+# Return arguments for user, password, host, port and additional options in MYSQL_OPTS.
+#
+# For example, the output may be:
+# --user=myuser --password=mypassword --host=example.com --port=1234 --other --option
function get_db_args_nodb {
if [ -n "$MYSQL_USER" ]; then
mysql_con_arguments="--user=$MYSQL_USER"
diff --git a/utils/load_settings.sh b/utils/load_settings.sh
index d25dce5b1bf3b7a16ee62c67143ad0cd4e080cf1..398fb9e59df9efc56b84ddd03ed6782eb180a6d7 100644
--- a/utils/load_settings.sh
+++ b/utils/load_settings.sh
@@ -1,10 +1,10 @@
-# This file is a part of the CaosDB Project.
+# This file is a part of the Linkahead Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
-# Copyright (C) 2019, 2020 Daniel Hornung (d.hornung@indiscale.com)
+# Copyright (C) 2019, 2020, 2024 Daniel Hornung <d.hornung@indiscale.com>
# Copyright (C) 2020 Henrik tom Wörden
-# Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2020, 2024 IndiScale GmbH <info@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
@@ -62,10 +62,12 @@ export MYSQL_CMD
export MYSQLDUMP_CMD
export MYSQLADMIN_CMD
export MYSQL_CONFIG_EDITOR_CMD
+
export MYSQL_HOST
export MYSQL_PORT
export MYSQL_USER
export MYSQL_OPTS
+
export DATABASE_NAME
export DATABASE_USER
export DATABASE_USER_PW
diff --git a/utils/make_db b/utils/make_db
index 35ed2d933ab3479f88556e08052b977bd2b0507c..c7f94fd2d57944758cb48f0aedb2ac2672ec16d3 100755
--- a/utils/make_db
+++ b/utils/make_db
@@ -1,10 +1,9 @@
#!/bin/bash
-# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
-# Copyright (C) 2021 Indiscale GmbH <info@indiscale.com>
-# Copyright (C) 2019, 2020, 2021 Daniel Hornung <d.hornung@indiscale.com>
+# Copyright (C) 2021, 2024 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2019, 2020, 2021, 2024 Daniel Hornung <d.hornung@indiscale.com>
# Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
# Copyright (C) 2020 Henrik tom Wörden <h.tomwoerden@indiscale.com>
# Copyright (C) 2020 IndiScale <info@indiscale.com>
@@ -22,7 +21,6 @@
# 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
# Although some sanity checks are performed, this script still allows lots of SQL injection
# possibilities.
diff --git a/utils/update_sql_procedures.sh b/utils/update_sql_procedures.sh
index b9a9e7fe21d1f47b4d7d235ce1a7ac040a060cf3..2fe1febfc7d5bbe45a8bc68c630e13d1cef6707f 100755
--- a/utils/update_sql_procedures.sh
+++ b/utils/update_sql_procedures.sh
@@ -1,13 +1,12 @@
#!/bin/bash
#
-# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
-# Copyright (C) 2020 Daniel Hornung <d.hornung@indiscale.com>
+# Copyright (C) 2020, 2024 Daniel Hornung <d.hornung@indiscale.com>
# Copyright (C) 2020 Henrik tom Wörden <h.tomwoerden@indiscale.com>
-# Copyright (C) 2020 IndiScale <info@indiscale.com>
+# Copyright (C) 2020, 2024 IndiScale <info@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
@@ -22,8 +21,6 @@
# 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
-#
# Updates all SQL procedures
@@ -37,7 +34,7 @@ fi
source $UTILSPATH/load_settings.sh
source $UTILSPATH/helpers.sh
-echo -n "updating procedures ... "
+echo "Updating procedures ... "
temp_proc_sql=$(mktemp --suffix=.sql)
sed -e "s/db_5_0/$DATABASE_NAME/g" procedures/*.sql procedures/query/*.sql \
> "$temp_proc_sql"