Merge branch 'f-clean-scripts-daniel' into f-new-tools

config.defaults

@@ -23,13 +23,14 @@
 
 # # 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 \
+                              || echo "mysql_config_editor not found!" >&2)
 
 # # MySQL Connection
 # The host of the MySQL server.

patches/applyPatches.sh

@@ -24,12 +24,29 @@
 # ** end header
 #
 
-#apply all available patches.
+###############################################################################
+#                         Apply all available patches                         #
+###############################################################################
+
 set -e
+
+if [ -z "$UTILSPATH" ]; then
+    UTILSPATH=$(realpath "$(dirname $0)/../utils")
+    export UTILSPATH
+	MAINPATH="$(dirname $UTILSPATH)"
+	export MAINPATH
+fi
+
+source $UTILSPATH/load_settings.sh
+source $UTILSPATH/helpers.sh
+
 PATCHES="./patch*/patch.sh"
 
 for p in $PATCHES
 do
+    echo "$p"
+    env | grep MYSQL | sort
+    export | grep MYSQL | sort
     $p "$@" --patch=$p
 done
 

utils/backup.sh

@@ -24,10 +24,11 @@
 
 # Dump a database with all procedures, permissions, structure and data
 
-
 if [ -z "$UTILSPATH" ]; then
 	UTILSPATH="$(realpath $(dirname $0))"
 	export UTILSPATH
+	MAINPATH="$(dirname $UTILSPATH)"
+	export MAINPATH
 fi
 
 # The directory which the dump is to be stored to. Do not change it here. Use

utils/helpers.sh

@@ -2,7 +2,7 @@
 #
 # Copyright (C) 2018 Research Group Biomedical Physics,
 # Max-Planck-Institute for Dynamics and Self-Organization Göttingen
-# Copyright 2019 Daniel Hornung
+# Copyright 2019, 2020 Daniel Hornung
 # Copyright 2020 Henrik tom Wörden, IndiScale GmbH
 #
 # This program is free software: you can redistribute it and/or modify
@@ -19,15 +19,27 @@
 # 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
-	set -e
+	  #TODO is it meaningful that here always the database user is used???
+	  set +e
+    # env | sort
+	  $MYSQL_CMD $(get_db_args) -e "$1"
+	  ret=${PIPESTATUS[0]}
+	  if [ "$ret" -ne 0 ]; then
+		    failure "MYSQL ERROR"
+	  fi
+	  set -e
 }
 
 function get_mysql_args {

utils/load_settings.sh

@@ -18,9 +18,34 @@
 # You should have received a copy of the GNU Affero General Public License
 # along with this program. If not, see <https://www.gnu.org/licenses/>.
 
-[[ -n "config.defaults" ]] && source "config.defaults"
-[[ -n ".config" ]] && source ".config"
-[[ -n "$ENV_FILE" ]] && source "$ENV_FILE"
+# 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 [ "$MAINPATH" ]; then
+    pushd "$MAINPATH" > /dev/null
+    pushed=1
+fi
+
+if [[ -r "config.defaults" ]] ; then
+    source "config.defaults"
+fi
+if [[ -r ".config" ]] ; then
+    source ".config"
+fi
+if [[ -n "$ENV_FILE" ]] ; then
+    source "$ENV_FILE"
+fi
+
+if [[ -z "$MYSQL_CMD" ]] ; then
+    echo "mysql not defined!"
+    exit 1
+fi
+
+if [ $pushed ]; then
+    popd > /dev/null
+fi
 
 export MYSQL_CMD
 export MYSQLDUMP_CMD

utils/make_db

@@ -22,18 +22,20 @@
 #
 # ** end header
 
+set -e
+
 INSTALL_SQL_FILE="db_2_0.sql"
 
 if [ -z "$UTILSPATH" ]; then
 	UTILSPATH="$(realpath $(dirname $0))"
 	export UTILSPATH
+	MAINPATH="$(dirname $UTILSPATH)"
+	export MAINPATH
 fi
 
 source $UTILSPATH/load_settings.sh
 source $UTILSPATH/helpers.sh
 
-set -e
-
 function fail() {
   echo "Some error occured, exiting."
   exit 1
@@ -131,6 +133,7 @@ function restore_db() {
 }
 
 function test-connection() {
+    echo $MYSQL_CMD $(get_mysql_args_nodb) -e "select 0;"
     $MYSQL_CMD $(get_mysql_args_nodb) -e "select 0;"
 }
 

utils/patch_header.sh

@@ -24,7 +24,8 @@
 #header for patch scripts
 
 # load useful functions #######################################################
-. $UTILSPATH/helpers.sh
+source $UTILSPATH/load_settings.sh
+source $UTILSPATH/helpers.sh
 
 USAGE="$1 [ --env=ENV_FILE ] [ --patch=PATCH ] [ --backupdir=BACKUPDIR ]\n\n"
 CMD_OPTIONS=$(cat <<EOF

utils/update_sql_procedures.sh

@@ -24,7 +24,15 @@
 
 # Updates all SQL procedures
 
+if [ -z "$UTILSPATH" ]; then
+    UTILSPATH=$(realpath "$(dirname $0)")
+    export UTILSPATH
+	MAINPATH="$(dirname $UTILSPATH)"
+	export MAINPATH
+fi
+
 source $UTILSPATH/helpers.sh
+source $UTILSPATH/load_settings.sh
 
 echo -n "updating rules ... "
 set -e