Merge branch 'f-clean-scripts' into 's-clean-up-stage'

Disentagle mysql scripts

See merge request caosdb/caosdb-mysqlbackend!6

.gitlab-ci.yml

@@ -51,8 +51,8 @@ unittests:
     - echo 'DATABASE_USER_HOST_LIST="%,"' >> .config
     - echo "MYSQL_USER_PASSWORD=$MYSQL_ROOT_PASSWORD" >> .config
     - echo "MYSQL_HOST=mariadb" >> .config
-    - ./make_db test-connection
-    - ./make_db test --fresh
+    - ./utils/make_db test-connection
+    - ./utils/make_db test --fresh
 
 # Build a docker image in which tests for this repository can run
 build-testenv:

config.defaults

@@ -23,13 +23,13 @@
 
 # # Commands
 # The MySQL client program.
-MYSQL_CMD=$(command -v mysql)
+MYSQL_CMD=$(command -v mysql || echo "mysql not found!" >&2)
 # The mysqladmin program which comes with the MySQL client.
-MYSQLADMIN_CMD=$(command -v mysqladmin)
+MYSQLADMIN_CMD=$(command -v mysqladmin || echo "mysqladmin not found!" >&2)
 # The mysqldump program which comes with the MySQL client.
-MYSQLDUMP_CMD=$(command -v mysqldump)
+MYSQLDUMP_CMD=$(command -v mysqldump || echo "mysqldump not found!" >&2)
 # The mysql_config_editor program which is used to store the credentials.
-MYSQL_CONFIG_EDITOR_CMD=$(command -v mysql_config_editor)
+MYSQL_CONFIG_EDITOR_CMD=$(command -v mysql_config_editor || true)
 
 # # MySQL Connection
 # The host of the MySQL server.
@@ -55,5 +55,3 @@ DATABASE_USER_PW=random1234
 # wildcard for all hosts, so `192.168.0.%` permits logins from the local
 # network.
 DATABASE_USER_HOST_LIST=localhost,
-
-

makefile

@@ -22,19 +22,11 @@
 #
 SHELL=/bin/bash
 
-include .config
-
 INSTALL_SQL_FILE=db_2_0.sql
-ifdef LOGIN_PATH
-	M_MYSQL_CONNECTION=--login-path=$(M_LOGIN_PATH)
-else
-	MYSQL_CONNECTION=--host="$(MYSQL_HOST)" --port="$(MYSQL_PORT)"	\
-		--user="$(MYSQL_USER)" --password="$(MYSQL_USER_PASSWORD)"
-endif
 
 .PHONY: test-connection
 test-connection:
-	./make_db test-connection
+	./utils/make_db test-connection
 
 .PHONY: upgrade
 upgrade:
@@ -45,17 +37,17 @@ install: _install _grant upgrade
 
 .PHONY: _install
 _install:
-	./make_db install_db
+	./utils/make_db install_db
 
 .PHONY: _grant
 _grant:
-	./make_db grant
+	./utils/make_db grant
 
 # Drop the user and a given database
 .PHONY: drop-%
 drop-%:
-	./make_db drop $(patsubst drop-%,%,$@)
+	./utils/make_db drop $(patsubst drop-%,%,$@)
 
 .PHONY: test
 test:
-	./make_db test --fresh
+	./utils/make_db test --fresh

patches/applyPatches.sh

@@ -6,6 +6,7 @@
 # Copyright (C) 2018 Research Group Biomedical Physics,
 # Max-Planck-Institute for Dynamics and Self-Organization Göttingen
 # Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
+# Copyright (C) 2020 Daniel Hornung <d.hornung@indiscale.com>
 # Copyright (C) 2020 IndiScale <info@indiscale.com>
 #
 # This program is free software: you can redistribute it and/or modify
@@ -24,16 +25,26 @@
 # ** end header
 #
 
-#apply all available patches.
+###############################################################################
+#                         Apply all available patches                         #
+###############################################################################
+
 set -e
+
+if [ -z "$UTILSPATH" ]; then
+    UTILSPATH=$(realpath "$(dirname $0)/../utils")
+    export UTILSPATH
+fi
+
+source $UTILSPATH/load_settings.sh
+source $UTILSPATH/helpers.sh
+
 PATCHES="./patch*/patch.sh"
-export UTILSPATH="./utils"
 
 for p in $PATCHES
 do
     $p "$@" --patch=$p
 done
 
-source ./utils/patch_header.sh
 cd ../
-./update_sql_procedures.sh
+$UTILSPATH/update_sql_procedures.sh

patches/patch20151022-0/patch.sh

@@ -35,7 +35,7 @@ fi
 check_version $OLD_VERSION
 
 function addIdx {
-    $CMD_MYSQL $MYSQL_CONNECTION -D $DATABASE -e "ALTER TABLE $1 ADD COLUMN pidx TINYINT UNSIGNED NOT NULL DEFAULT 0;"
+    $MYSQL_CMD $(get_db_args) -e "ALTER TABLE $1 ADD COLUMN pidx TINYINT UNSIGNED NOT NULL DEFAULT 0;"
 }
 
 addIdx "reference_data"

utils/backup.sh

@@ -5,6 +5,8 @@
 #
 # 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 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
@@ -24,6 +26,10 @@
 
 # Dump a database with all procedures, permissions, structure and data
 
+if [ -z "$UTILSPATH" ]; then
+    UTILSPATH="$(realpath $(dirname $0))"
+    export UTILSPATH
+fi
 # The directory which the dump is to be stored to. Do not change it here. Use
 # the --backupdir=./my/dir/ option or an environment variable instead.
 BACKUPDIR="${BACKUPDIR:-../backup}"
@@ -58,12 +64,11 @@ backup:
 EOF
         )
 
-# Config and command line parameter loading ###################################
-
-. ../.config
+# Load settings from .config and defaults #####################################
+. $UTILSPATH/load_settings.sh
 
-# load useful stuff - parses the commandline parameters and so on...
-. ../patches/utils/patch_header.sh
+# load useful functions #######################################################
+. $UTILSPATH/helpers.sh
 
 function backup() {
     NARG_NAME="$1"
@@ -75,7 +80,7 @@ function backup() {
         failure "dumpfile already exists."
     fi
     echo "Dumping database $NARG_NAME to $NARG_FILE ... "
-	  $CMD_MYSQL_DUMP $MYSQL_CONNECTION_NO_DB $* --opt --default-character-set=utf8 --routines \
+  $MYSQLDUMP_CMD $(get_mysql_args_nodb) $* --opt --default-character-set=utf8 --routines \
                     "$NARG_NAME" > "$NARG_FILE"
 
     if [[ "$YAML" == "true" ]] ; then

utils/helpers.sh

+# 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) 2019, 2020 Daniel Hornung (d.hornung@indiscale.com)
+# Copyright (C) 2020 Henrik tom Wörden
+# Copyright (C) 2020 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
+# 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/>.
+
+
+
+###############################################################################
+#                         Helper function definitions                         #
+###############################################################################
+
+# When sourcing this file, the following variables must be set:
+#
+# MYSQL_CMD : source $UTILSPATH/load_settings.sh
+
+
+
+function mysql_execute {
+	  #TODO is it meaningful that here always the database user is used???
+	  set -e
+	  $MYSQL_CMD $(get_db_args) -e "$1"
+	  ret=${PIPESTATUS[0]}
+	  if [ "$ret" -ne 0 ]; then
+		    failure "MYSQL ERROR"
+	  fi
+}
+
+function get_mysql_args {
+	echo "$(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
+		mysql_con_arguments="--user=$DATABASE_USER"
+	fi
+	if [ "$DATABASE_USER_PW" ]; then
+		mysql_con_arguments="$mysql_con_arguments --password=$DATABASE_USER_PW"
+	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
+	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
+	fi
+	echo $mysql_con_arguments
+}
+
+function success {
+    echo "[OK]"
+    exit 0
+}
+
+function failure {
+    echo "[FAILED] $*"
+    exit 1
+}
+
+function uptodate {
+    echo "[UPTODATE]"
+    exit 0
+}

utils/load_settings.sh

+# 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) 2019, 2020 Daniel Hornung (d.hornung@indiscale.com)
+# Copyright (C) 2020 Henrik tom Wörden
+# Copyright (C) 2020 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
+# 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/>.
+
+# Load setting from different files, in this order:
+# - config.defaults (in the current directory)
+# - .config (in the current directory)
+# - The file given in ENV_FILE.
+
+if [ -z "$MAINPATH" ]; then
+    if [ -z "$UTILSPATH" ] ; then
+        echo "At least one of MAINPATH and UTILSPATH must be defined in load_settings.sh" >&2
+        exit 1
+    fi
+    MAINPATH="$(dirname $UTILSPATH)"
+    export MAINPATH
+fi
+
+# Make a backup of the important environment variables.
+my_env=$(export -p | grep -E '(MYSQL|DATABASE)')
+
+source "$MAINPATH/config.defaults"
+
+if [[ -r "$MAINPATH/.config" ]] ; then
+    source "$MAINPATH/.config"
+fi
+if [[ -n "$ENV_FILE" ]] ; then
+    source "$ENV_FILE"
+fi
+
+if [[ -z "$MYSQL_CMD" ]] ; then
+    echo "'mysql' executable not defined!"
+    exit 1
+fi
+
+# Restore backup.
+eval "$my_env"
+
+export MYSQL_CMD
+export MYSQLDUMP_CMD
+export MYSQLADMIN_CMD
+export MYSQL_CONFIG_EDITOR_CMD
+export MYSQL_HOST
+export MYSQL_PORT
+export MYSQL_USER
+export DATABASE_NAME
+export DATABASE_USER
+export DATABASE_USER_PW
+export DATABASE_USER_HOST_LIST

make_db → utils/make_db

@@ -3,8 +3,9 @@
 # ** header v3.0
 # This file is a part of the CaosDB Project.
 #
-# Copyright (C) 2019 Daniel Hornung, Göttingen
+# Copyright (C) 2019, 2020 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>
 #
 # This program is free software: you can redistribute it and/or modify
@@ -22,13 +23,17 @@
 #
 # ** end header
 
-# To fail fast, but beware https://mywiki.wooledge.org/BashFAQ/105
 set -e
 
-function fail() {
-  echo "Some error occured, exiting."
-  exit 1
-}
+INSTALL_SQL_FILE="db_2_0.sql"
+
+if [ -z "$UTILSPATH" ]; then
+    UTILSPATH="$(realpath $(dirname $0))"
+    export UTILSPATH
+fi
+
+source $UTILSPATH/load_settings.sh
+source $UTILSPATH/helpers.sh
 
 UNITTEST_DATABASE=${UNITTEST_DATABASE-_caosdb_schema_unit_tests}
 
@@ -39,7 +44,7 @@ function runtests() {
 
     _install_unit_test_database $@
 
-    _execute_tests || ( echo "[FAILURE]" && exit 1 )
+    _execute_tests || ( failure )
     echo "[PASS]"
 }
 
@@ -51,7 +56,7 @@ function _execute_tests () {
     for tfile in $TESTS ; do
         echo "Running $tfile"
         echo "----- $tfile -----" >> .TEST_RESULTS
-        cat $tfile | $SQL --disable-pager --batch --raw --skip-column-names --unbuffered >> .TEST_RESULTS
+        cat $tfile | $MYSQL_CMD $(get_db_args_nodb) --disable-pager --batch --raw --skip-column-names --unbuffered >> .TEST_RESULTS
     done;
 
     popd
@@ -72,9 +77,9 @@ function _install_unit_test_database () {
         fi
     fi
 
-    sed "s/db_2_0/$DATABASE_NAME/g" "$INSTALL_SQL_FILE" | $SQL
+    sed "s/db_2_0/$DATABASE_NAME/g" "$INSTALL_SQL_FILE" | $MYSQL_CMD $(get_mysql_args_nodb)
 
-    # crate test user
+    # create test user
     grant
 
     # update to latest
@@ -92,15 +97,15 @@ function _setup_mytap() {
         echo MyTAB framework is already installed [OK]
         return 0
     fi
-    echo -n "Installing MyTAB framework ... "
+    echo -n "Installing MyTAP framework ... "
     pushd libs > /dev/null
     unzip -u mytap*.zip > /dev/null
     pushd mytap*/ > /dev/null
-    $SQL < mytap.sql > /dev/null || exit 1
+    $MYSQL_CMD $(get_mysql_args_nodb) < mytap.sql > /dev/null || exit 1
     popd > /dev/null
     rm -r mytap*/
     popd > /dev/null
-    echo [DONE]
+    echo "[DONE]"
 }
 
 function install_db() {
@@ -112,17 +117,17 @@ Call 'make drop-$DATABASE_NAME' to delete that database or reconfigure with
         exit 0
     fi
 
-	  sed "s/db_2_0/$DATABASE_NAME/g" "$INSTALL_SQL_FILE" | $SQL
+    sed "s/db_2_0/$DATABASE_NAME/g" "$INSTALL_SQL_FILE" | $MYSQL_CMD $(get_mysql_args_nodb)
 }
 
 # Inserts the dump (arg 1) into the database
 function restore_db() {
     SQL_FILE="$1"
-    $SQL -D "$DATABASE_NAME" < "$SQL_FILE"
+    $MYSQL_CMD $(get_mysql_args) < "$SQL_FILE"
 }
 
 function test-connection() {
-    $SQL -e "select 0;"
+    $MYSQL_CMD $(get_mysql_args_nodb) -e "select 0;"
 }
 
 # Creates a user and grants it sufficient rights.
@@ -146,7 +151,7 @@ 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}';"
-		        [[ $($SQL -s -N -e "$CMD") == 0 ]] || {
+            [[ $($MYSQL_CMD $(get_mysql_args_nodb) -s -N -e "$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};\"'"
@@ -157,7 +162,7 @@ function grant() {
 
     for host in ${DATABASE_USER_HOST_LIST//,/ } ; do
         echo "Granting admin privileges to '$DATABASE_USER'@'$host'"
-        $SQL <<EOF
+        $MYSQL_CMD $(get_mysql_args_nodb) <<EOF
 CREATE USER IF NOT EXISTS
     '$DATABASE_USER'@'$host' identified by '$DATABASE_USER_PW';
 GRANT USAGE ON *.* TO '$DATABASE_USER'@'$host';
@@ -172,31 +177,19 @@ EOF
 function drop() {
     DROPDB="$1"
     for host in ${DATABASE_USER_HOST_LIST//,/ } ; do
-        $SQL -e "DROP USER '${DATABASE_USER}'@'${host}';" || true
+        $MYSQL_CMD $(get_mysql_args_nodb) -e "DROP USER '${DATABASE_USER}'@'${host}';" || true
     done
-    "$MYSQLADMIN_CMD" $MYSQL_CONNECTION -f drop "$DROPDB"
+    "$MYSQLADMIN_CMD" $(get_mysql_args_nodb) -f drop "$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() {
-    $SQL -D "${1-${DATABASE_NAME}}" -e "show tables;" > /dev/null 2>&1 \
+    $MYSQL_CMD $(get_mysql_args_nodb) -D "${1-${DATABASE_NAME}}" -e "show tables;" > /dev/null 2>&1 \
         && return 0 || return 1
 }
 
-source .config || true
-
-INSTALL_SQL_FILE="db_2_0.sql"
-if [ -z $LOGIN_PATH ] ; then
-    MYSQL_CONNECTION="--host=${MYSQL_HOST} --port=${MYSQL_PORT}
- --user=${MYSQL_USER}
- --password=${MYSQL_USER_PASSWORD}"
-else
-    MYSQL_CONNECTION="--login-path=$LOGIN_PATH"
-fi
-
-SQL="$MYSQL_CMD $MYSQL_CONNECTION"
 
 case $1 in
     "drop") drop $2 ;;

patches/utils/patch_header.sh → utils/patch_header.sh

@@ -4,7 +4,9 @@
 #
 # Copyright (C) 2018 Research Group Biomedical Physics,
 # Max-Planck-Institute for Dynamics and Self-Organization Göttingen
-# Copyright 2019 Daniel Hornung
+# Copyright (C) 2019, 2020 Daniel Hornung <d.hornung@indiscale.com>
+# Copyright (C) 2020 Henrik tom Wörden <h.tomwoerden@indiscale.com>
+# Copyright (C) 2020 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
@@ -21,9 +23,17 @@
 #
 # ** end header
 #
-#header for patch scripts
-CMD_MYSQL=mysql
-CMD_MYSQL_DUMP=mysqldump
+
+###############################################################################
+#                          header for patch scripts                           #
+###############################################################################
+
+set -e
+
+# load useful functions #######################################################
+source $UTILSPATH/load_settings.sh
+source $UTILSPATH/helpers.sh
+
 USAGE="$1 [ --env=ENV_FILE ] [ --patch=PATCH ] [ --backupdir=BACKUPDIR ]\n\n"
 CMD_OPTIONS=$(cat <<EOF
 options:
@@ -54,7 +64,6 @@ configuration make file.  Notable examples are:
 
 EOF
               )
-set -e
 
 function _print_help() {
   echo -e "$USAGE"
@@ -101,65 +110,14 @@ while test $# -gt 0; do
  esac
 done
 
-source "$ENV_FILE" || true
-
-if [[ -z "$DATABASE_NAME" && -z "$MYSQL_CONNECTION" ]]
-then
- _print_help "Please specify the database."
- exit 1
-fi
-
-if [ "$LOGIN_PATH" ]; then
-  MYSQL_CONNECTION="--login-path=$LOGIN_PATH"
-  MYSQL_CONNECTION_NO_DB="$MYSQL_CONNECTION"
-  MYSQL_CONNECTION="$MYSQL_CONNECTION --database=$DATABASE_NAME"
-
-elif [[ -z "$MYSQL_CONNECTION" ]]; then
-  MYSQL_CONNECTION=""
-  if [ "$DATABASE_USER" ]
-  then
-    MYSQL_CONNECTION="--user=$DATABASE_USER"
-  fi
-  if [ "$DATABASE_USER_PW" ]
-  then
-    MYSQL_CONNECTION="$MYSQL_CONNECTION --password=$DATABASE_USER_PW"
-  fi
-  if [[ "$MYSQL_HOST" && ( "$MYSQL_HOST" != "localhost" ) ]]; then
-      MYSQL_CONNECTION="$MYSQL_CONNECTION --host=$MYSQL_HOST"
-      if [ "$MYSQL_PORT" ]; then
-          MYSQL_CONNECTION="$MYSQL_CONNECTION --port=$MYSQL_PORT"
-      fi
-  fi
-  # This option should come last, so we also have one version without the database
-  MYSQL_CONNECTION_NO_DB="$MYSQL_CONNECTION"
-  MYSQL_CONNECTION="$MYSQL_CONNECTION --database=$DATABASE_NAME"
-fi
-export MYSQL_CONNECTION
-export MYSQL_CONNECTION_NO_DB
-export DATABASE_NAME
 
 if [ -n "$PATCH" ]; then
     echo -ne "applying patch $PATCH to $DATABASE_NAME ... "
 fi
-
-function success {
-    echo "[OK]"
-    exit 0
-}
-
-function failure {
-    echo "[FAILED] $*"
-    exit 1
-}
-
-function uptodate {
-    echo "[UPTODATE]"
-    exit 0
-}
 # @param $1: db version string, e.g. v2.0.0
 # @return: 0 on success, 1 on failure
 function check_version {
-    local version=$($CMD_MYSQL $MYSQL_CONNECTION -B -e "Select CaosDBVersion();")
+    local version=$($MYSQL_CMD $(get_db_args) -B -e "Select CaosDBVersion();")
 	  if [[ "$(echo $version | sed 's/^CaosDBVersion()\s//')" = "$1" ]]; then
         return 0
 	  fi
@@ -172,22 +130,12 @@ function update_version {
 }
 
 function dump_table {
-    $CMD_MYSQL_DUMP $MYSQL_CONNECTION_NO_DB $DATABASE_NAME $1 \
+    $MYSQLDUMP_CMD $(get_db_args_nodb) $DATABASE_NAME $1 \
                     > ${DATABASE_NAME}.${1}.${OLD_VERSION}.dump.sql
 }
 
-
-function mysql_execute {
-	set +e
-	$CMD_MYSQL $MYSQL_CONNECTION -e "$1"
-	ret=${PIPESTATUS[0]}
-	if [ "$ret" -ne 0 ]; then
-		failure "MYSQL ERROR"
-	fi
-	set -e
-}
-
 function redo_table {
-	  $CMD_MYSQL $MYSQL_CONNECTION < ${DATABASE_NAME}.${1}.${OLD_VERSION}.dump.sql
+         $MYSQL_CMD $(get_db_args) < ${DATABASE_NAME}.${1}.${OLD_VERSION}.dump.sql
 }
 
+

update_sql_procedures.sh → utils/update_sql_procedures.sh

@@ -5,6 +5,9 @@
 #
 # 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 Henrik tom Wörden <h.tomwoerden@indiscale.com>
+# Copyright (C) 2020 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
@@ -24,16 +27,21 @@
 
 # Updates all SQL procedures
 
-source patches/utils/patch_header.sh
+set -e
+
+if [ -z "$UTILSPATH" ]; then
+    UTILSPATH=$(realpath "$(dirname $0)")
+    export UTILSPATH
+fi
+
+source $UTILSPATH/load_settings.sh
+source $UTILSPATH/helpers.sh
 
 echo -n "updating rules ... "
-set -e
 
 mysql_execute "$(sed s/db_2_0/$DATABASE_NAME/g rules.sql)"
-echo "[OK]"
+echo "OK"
 
 echo -n "updating procedures ... "
 mysql_execute "$(sed s/db_2_0/$DATABASE_NAME/g procedures/*.sql procedures/query/*.sql)"
-success
-
-
+echo "OK"