diff --git a/.docker/docker-compose.yml b/.docker/docker-compose.yml
new file mode 100644
index 0000000000000000000000000000000000000000..1a63292b080f182821935cb5b20b7500bfcf8f63
--- /dev/null
+++ b/.docker/docker-compose.yml
@@ -0,0 +1,23 @@
+version: '3.6'
+services:
+ sqldb:
+ image: mariadb:10.5
+ volumes:
+ - type: volume
+ source: "caosdb-sqldata"
+ target: /var/lib/mysql
+ environment:
+ MYSQL_ROOT_PASSWORD: caosdb1234
+ networks:
+ # available on port 3306, host name 'sqldb'
+ - caosnet
+ ports:
+ - 3306:3306
+
+
+# A well-defined network for caosdb
+volumes:
+ caosdb-sqldata:
+networks:
+ caosnet:
+ driver: bridge
diff --git a/CHANGELOG.md b/CHANGELOG.md
index d49bdeebd6460b7a29bdffcca8876dca5b24c7d7..0b45fe17477c70c91037c453c456be958335952a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -17,6 +17,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Fixed ###
+* make install: Could not connect to MariaDB in local docker
+ container
+ [linkahead-mariadbbackend](https://gitlab.com/linkahead/linkahead-mariadbbackend/-/issues/33)
+* Wrong ids in data_type table due to a bug in the `linkahead-server < v0.11.0`
+ which has been fixed but left broken data. This resulted in server errors
+ [linkahead-mariadbbackend#34](https://gitlab.com/linkahead/linkahead-mariadbbackend/-/issues/34)
+
### Security ###
## [7.0.1] - 2023-11-01
diff --git a/README_SETUP.md b/README_SETUP.md
index 95f975d031ded904b2656230f5ec72d98447a7b6..46d9aeb455384d60116465b9eca489c01a0d38f3 100644
--- a/README_SETUP.md
+++ b/README_SETUP.md
@@ -87,6 +87,19 @@ with the then current version of the stored entities.
* Alternatively, to run the tests in a containerized MariaDB instance, run `make test-docker`,
followed by `make test-docker-stop`.
+
+### Running in a Docker Container
+
+You can use `.docker/docker-compose.yml` to start a docker container
+(`docker-compose -f .docker/docker-compose.yml up -d`) that runs
+mariadb. You need appropriate settings in `.config`:
+`MYSQL_OPTS="--protocol=TCP"` and
+`DATABASE_USER_HOST_LIST=%,`
+After the first start, you need to install the database: `make install`.
+Then, you can connect to it with
+`mariadb --protocol=TCP -u caosdb -prandom1234 caosdb`.
+
+
### Troubleshooting
#### MySQL has failing tests
diff --git a/config.defaults b/config.defaults
index f12278dcf0f5ce772c4cb77e54b149d3f6880921..1860377976c3bf0d9f389570dc0e981f47aa1609 100644
--- a/config.defaults
+++ b/config.defaults
@@ -40,6 +40,12 @@ MYSQL_PORT=3306
# which will then be used by the CaosDB Server.
MYSQL_USER=root
MYSQL_USER_PASSWORD=caosdb1234
+# Additional options for the connection
+# e.g. if you want to connect a dockerized MariaDB at localhost you need to put
+# "--protocol=TCP" here because when host=localhost the connection defaults to
+# SOCKET.
+# MYSQL_OPTS='--protocol=TCP'
+MYSQL_OPTS=
# # DATABASE
# The name of the SQL database.
diff --git a/patches/patch20231211-7.0.2/patch.sh b/patches/patch20231211-7.0.2/patch.sh
new file mode 100755
index 0000000000000000000000000000000000000000..422fc00b9083808446d74776b446c072bdfd73bc
--- /dev/null
+++ b/patches/patch20231211-7.0.2/patch.sh
@@ -0,0 +1,41 @@
+#!/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
diff --git a/utils/backup.sh b/utils/backup.sh
index bdc345cfe1e956024fbd8492c6a1a2d65acc2cdd..4d53da3edafd52be32d9f33507664d6971581360 100755
--- a/utils/backup.sh
+++ b/utils/backup.sh
@@ -56,7 +56,7 @@ function backup() {
fi
echo "Dumping database $database to $backupfile ..."
- $MYSQLDUMP_CMD $(get_mysql_args_nodb) --opt --default-character-set=utf8 \
+ $MYSQLDUMP_CMD $(get_db_args_nodb) --opt --default-character-set=utf8 \
--routines "$database" > "$backupfile"
success
diff --git a/utils/helpers.sh b/utils/helpers.sh
index 6adb318503e26061369a1144568dea4f60ef3d46..e3132335b4431a9ede66c8180bc4bbde6db23a9e 100644
--- a/utils/helpers.sh
+++ b/utils/helpers.sh
@@ -52,47 +52,25 @@ function mysql_execute_file {
fi
}
-
-function get_mysql_args {
- echo "$(get_mysql_args_nodb) --database=$DATABASE_NAME"
-}
-
function get_db_args {
echo "$(get_db_args_nodb) --database=$DATABASE_NAME"
}
function get_db_args_nodb {
- if [ "$DATABASE_USER" ]; then
+ if [ -n "$DATABASE_USER" ]; then
mysql_con_arguments="--user=$DATABASE_USER"
fi
- if [ "$DATABASE_USER_PW" ]; then
+ if [ -n "$DATABASE_USER_PW" ]; then
mysql_con_arguments="$mysql_con_arguments --password=$DATABASE_USER_PW"
fi
- if [[ "$MYSQL_HOST" && ( "$MYSQL_HOST" != "localhost" ) ]]; then
+ if [ -n "$MYSQL_HOST" ] && [ "$MYSQL_HOST" != "localhost" ]; then
mysql_con_arguments="$mysql_con_arguments --host=$MYSQL_HOST"
- if [ "$MYSQL_PORT" ]; then
- mysql_con_arguments="$mysql_con_arguments --port=$MYSQL_PORT"
- fi
fi
- echo $mysql_con_arguments
-}
-
-function get_mysql_args_nodb {
- if [ "$LOGIN_PATH" ]; then
- mysql_con_arguments="--login-path=$LOGIN_PATH"
- else
- if [ "$MYSQL_USER" ]; then
- mysql_con_arguments="--user=$MYSQL_USER"
- fi
- if [ "$MYSQL_USER_PASSWORD" ]; then
- mysql_con_arguments="$mysql_con_arguments --password=$MYSQL_USER_PASSWORD"
- fi
- if [[ "$MYSQL_HOST" && ( "$MYSQL_HOST" != "localhost" ) ]]; then
- mysql_con_arguments="$mysql_con_arguments --host=$MYSQL_HOST"
- if [ "$MYSQL_PORT" ]; then
- mysql_con_arguments="$mysql_con_arguments --port=$MYSQL_PORT"
- fi
- fi
+ if [ -n "$MYSQL_PORT" ] && [ "$MYSQL_PORT" != "3306" ]; then
+ mysql_con_arguments="$mysql_con_arguments --port=$MYSQL_PORT"
+ fi
+ if [ -n "$MYSQL_OPTS" ] ; then
+ mysql_con_arguments="$mysql_con_arguments $MYSQL_OPTS"
fi
echo $mysql_con_arguments
}
diff --git a/utils/load_settings.sh b/utils/load_settings.sh
index c24a0f4baf6e9e15e56e7ffeacb265b0b5f01673..d25dce5b1bf3b7a16ee62c67143ad0cd4e080cf1 100644
--- a/utils/load_settings.sh
+++ b/utils/load_settings.sh
@@ -65,6 +65,7 @@ export MYSQL_CONFIG_EDITOR_CMD
export MYSQL_HOST
export MYSQL_PORT
export MYSQL_USER
+export MYSQL_OPTS
export DATABASE_NAME
export DATABASE_USER
export DATABASE_USER_PW
diff --git a/utils/make_db b/utils/make_db
index 4a90931708c667d44fc1c021eb3467850b094737..35ed2d933ab3479f88556e08052b977bd2b0507c 100755
--- a/utils/make_db
+++ b/utils/make_db
@@ -87,7 +87,7 @@ function _install_unit_test_database () {
if _db_exists "$DATABASE_NAME"; then
echo "using $DATABASE_NAME"
else
- sed "s/db_5_0/$DATABASE_NAME/g" "$INSTALL_SQL_FILE" | $MYSQL_CMD $(get_mysql_args_nodb)
+ sed "s/db_5_0/$DATABASE_NAME/g" "$INSTALL_SQL_FILE" | $MYSQL_CMD $(get_db_args_nodb)
# create test user
grant
@@ -113,7 +113,7 @@ function _setup_mytap() {
pushd libs > /dev/null
unzip -u mytap*.zip > /dev/null
pushd mytap*/ > /dev/null
- $MYSQL_CMD $(get_mysql_args_nodb) < mytap.sql > /dev/null || exit 1
+ $MYSQL_CMD $(get_db_args_nodb) < mytap.sql > /dev/null || exit 1
popd > /dev/null
rm -r mytap*/
popd > /dev/null
@@ -129,14 +129,14 @@ name in your .config file "
exit 0
fi
- sed "s/db_5_0/$DATABASE_NAME/g" "$INSTALL_SQL_FILE" | $MYSQL_CMD $(get_mysql_args_nodb)
+ sed "s/db_5_0/$DATABASE_NAME/g" "$INSTALL_SQL_FILE" | $MYSQL_CMD $(get_db_args_nodb)
}
function sanity_check() {
trap "$(shopt -po errexit)" RETURN
set +e
echo -n "running sanity checks ..."
- msg="$($MYSQL_CMD $(get_mysql_args) < "utils/sanity_check.sql" 2>/dev/null)"
+ msg="$($MYSQL_CMD $(get_db_args) < "utils/sanity_check.sql" 2>/dev/null)"
code="$?"
if [ "$code" -eq "0" ] ; then
echo " [OK]"
@@ -150,7 +150,7 @@ function sanity_check() {
# Inserts the dump (arg 1) into the database
function restore_db() {
SQL_FILE="$1"
- $MYSQL_CMD $(get_mysql_args) < "$SQL_FILE"
+ $MYSQL_CMD $(get_db_args) < "$SQL_FILE"
cat <<EOF
If this is not the same SQL server where the SQL dump was originally created
from, make sure that a user with sufficient permissions exists. Note that you
@@ -159,7 +159,7 @@ EOF
}
function test-connection() {
- $MYSQL_CMD $(get_mysql_args_nodb) -e "select 0;"
+ $MYSQL_CMD $(get_db_args_nodb) -e "select 0;"
}
# Creates a user and grants it sufficient rights.
@@ -183,7 +183,7 @@ function grant() {
if [[ $1 = "--strict" ]] ; then
for host in ${DATABASE_USER_HOST_LIST//,/ } ; do
CMD="SELECT COUNT(*) FROM mysql.user WHERE user='${DATABASE_USER}' AND host='${host}';"
- [[ $($MYSQL_CMD $(get_mysql_args_nodb) -s -N -e "$CMD") = 0 ]] || {
+ [[ $($MYSQL_CMD $(get_db_args_nodb) -s -N -e "$CMD") = 0 ]] || {
echo "The user '${DATABASE_USER}@${host}' is already in the database."
echo "Please use another user or delete it, e.g. with"
echo "'mysql -u ${MYSQL_USER} -p -e \"DROP USER ${DATABASE_USER}@${host};\"'"
@@ -197,7 +197,7 @@ function grant() {
# FIXME Are all these permissions necessary? See
# https://gitlab.indiscale.com/caosdb/src/caosdb-mysqlbackend/-/issues/28 "Default
# installation target does not work for existing databases"
- $MYSQL_CMD $(get_mysql_args_nodb) <<EOF
+ $MYSQL_CMD $(get_db_args_nodb) <<EOF
CREATE USER IF NOT EXISTS
'$DATABASE_USER'@'$host' identified by '$DATABASE_USER_PW';
GRANT USAGE ON *.* TO '$DATABASE_USER'@'$host';
@@ -212,16 +212,16 @@ EOF
function drop() {
DROPDB="$1"
for host in ${DATABASE_USER_HOST_LIST//,/ } ; do
- $MYSQL_CMD $(get_mysql_args_nodb) -e "DROP USER '${DATABASE_USER}'@'${host}';" || true
+ $MYSQL_CMD $(get_db_args_nodb) -e "DROP USER '${DATABASE_USER}'@'${host}';" || true
done
- "$MYSQLADMIN_CMD" $(get_mysql_args_nodb) -f drop "$DROPDB"
+ "$MYSQLADMIN_CMD" $(get_db_args_nodb) -f drop "$DROPDB"
}
# Returns 0 or non-zero, depending on whether the database exists already.
# Optional parameter: [DATABASE_NAME], else $DATABASE_NAME is used.
function _db_exists() {
- $MYSQL_CMD $(get_mysql_args_nodb) -D "${1-${DATABASE_NAME}}" -e "show tables;" > /dev/null 2>&1 \
+ $MYSQL_CMD $(get_db_args_nodb) -D "${1-${DATABASE_NAME}}" -e "show tables;" > /dev/null 2>&1 \
&& return 0 || return 1
}
@@ -250,7 +250,7 @@ function grant-permission() {
fi
cmd="SELECT COUNT(1) from roles where name='${role}';"
- count=$($MYSQL_CMD $(get_mysql_args) -AN -e "$cmd")
+ count=$($MYSQL_CMD $(get_db_args) -AN -e "$cmd")
if [[ $count == "0" ]]; then
echo "Role not found!"
exit 1
@@ -259,7 +259,7 @@ function grant-permission() {
cmd="INSERT INTO permissions (role, permissions) VALUE ('${role}', '${permissions}')"
cmd+="ON DUPLICATE KEY UPDATE role='${role}', permissions='${permissions}'"
cmd+=";"
- $MYSQL_CMD $(get_mysql_args) -e "$cmd"
+ $MYSQL_CMD $(get_db_args) -e "$cmd"
}