FIX: fix the mess of paths

config.defaults

@@ -56,4 +56,5 @@ DATABASE_USER_PW=random1234
 # network.
 DATABASE_USER_HOST_LIST=localhost,
 
-
+# path to utility scripts
+UTILSPATH=`realpath "utils"`

patches/applyPatches.sh

@@ -27,10 +27,8 @@
 #apply all available patches.
 set -e
 PATCHES="./patch*/patch.sh"
-export UTILSPATH="../utils"
 
-. ../utils/load_settings.sh
-. ../utils/helpers.sh
+. $UTILSPATH/helpers.sh
 for p in $PATCHES
 do
     $p "$@" --patch=$p

patches/utils/patch_header.sh

-#
-# ** header v3.0
-# This file is a part of the CaosDB Project.
-#
-# Copyright (C) 2018 Research Group Biomedical Physics,
-# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
-# Copyright 2019 Daniel Hornung
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU Affero General Public License as
-# published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU Affero General Public License for more details.
-#
-# You should have received a copy of the GNU Affero General Public License
-# along with this program. If not, see <https://www.gnu.org/licenses/>.
-#
-# ** end header
-#
-#header for patch scripts
-
-. load_settings.sh
-. helpers.sh
-
-USAGE="$1 [ --env=ENV_FILE ] [ --patch=PATCH ] [ --backupdir=BACKUPDIR ]\n\n"
-CMD_OPTIONS=$(cat <<EOF
-options:
-
--h, --help
-    Show brief help.
---env=ENV_FILE
-    A file where variables are stored in the format of shell environment
-    variables.  Content of this file overrides environment variables already
-    present.
---patch=PATCH
-    *TODO* Please document this option.
---backupdir=BACKUPDIR
-    The directory where backup files are stored to.
---yaml[=True|False]
-    If given (and the optional value is not False), additional machine-readable
-    YAML output is emitted.  Only implemented for some commands yet.
-
-This script basically uses the same environment variables as the server
-configuration make file.  Notable examples are:
-
-- LOGIN_PATH
-- MYSQL_HOST
-- MYSQL_PORT
-- DATABASE_NAME
-- DATABASE_USER
-- DATABASE_USER_PW
-
-EOF
-              )
-set -e
-
-function _print_help() {
-  echo -e "$USAGE"
-  echo -e "$CMD_OPTIONS"
-  if [ -n "$PRINT_HELP" ]; then
-    echo -e "$PRINT_HELP"
-  fi
-  if [ -n "$1" ]; then
-    echo -e "$1"
-  fi
-}
-
-while test $# -gt 0; do
- case "$1" in
- -h|--help)
-  _print_help
-  exit 0
-  ;;
- --env*)
-  ENV_FILE="${1#--*=}"
-  shift
-  ;;
- --patch*)
-  PATCH="${1#--*=}"
-  shift
-  ;;
- --backupdir*)
-  BACKUPDIR="${1#--*=}"
-  shift
-  ;;
- --yaml*)
-     if [[ "$1" == "--yaml" ]] ; then
-         YAML="True"
-     else
-         YAML="${1#--*=}"
-     fi
-  shift
-  ;;
- *)
-  echo "Unknown option $1"
-  exit 1
-  shift
-  ;;
- esac
-done
-
-
-if [ -n "$PATCH" ]; then
-    echo -ne "applying patch $PATCH to $DATABASE_NAME ... "
-fi
-# @param $1: db version string, e.g. v2.0.0
-# @return: 0 on success, 1 on failure
-function check_version {
-    local version=$($MYSQL_CMD $MYSQL_CONNECTION -B -e "Select CaosDBVersion();")
-	  if [[ "$(echo $version | sed 's/^CaosDBVersion()\s//')" = "$1" ]]; then
-        return 0
-	  fi
-    uptodate
-}
-
-# @param $1: new version string
-function update_version {
-    mysql_execute "DROP FUNCTION IF EXISTS CaosDBVersion; CREATE FUNCTION CaosDBVersion() RETURNS VARCHAR(255) DETERMINISTIC RETURN '$1';"
-}

utils/load_settings.sh

@@ -18,16 +18,14 @@
 # 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/>.
 
-UTILS_PATH=`dirname "$(realpath $0)"`
-MAIN_PATH=`dirname "${UTILS_PATH}"`
-
-[[ -n "${MAIN_PATH}/config.defaults" ]] && source "${MAIN_PATH}/config.defaults"
-[[ -n "${MAIN_PATH}/.config" ]] && source "${MAIN_PATH}/.config"
+[[ -n "config.defaults" ]] && source "config.defaults"
+[[ -n ".config" ]] && source ".config"
 [[ -n "$ENV_FILE" ]] && source "$ENV_FILE"
 
 if [[ -z "$DATABASE_NAME" && -z "$MYSQL_CONNECTION" ]]
 then
- _print_help "Please specify the database."
+ echo "A database or a mysql connection need to be set via the corresponding" \
+ "environment variables."
  exit 1
 fi
 
@@ -57,7 +55,7 @@ elif [[ -z "$MYSQL_CONNECTION" ]]; then
   MYSQL_CONNECTION="$MYSQL_CONNECTION --database=$DATABASE_NAME"
 fi
 
-# TODO is this a good idea?
 export MYSQL_CONNECTION
 export MYSQL_CONNECTION_NO_DB
 export DATABASE_NAME
+export UTILSPATH

utils/patch_header.sh

@@ -24,8 +24,7 @@
 #header for patch scripts
 
 # load useful functions #######################################################
-UTILS_PATH=`dirname "$(realpath $0)"`
-. $UTILS_PATH/helpers.sh
+. $UTILSPATH/helpers.sh
 
 USAGE="$1 [ --env=ENV_FILE ] [ --patch=PATCH ] [ --backupdir=BACKUPDIR ]\n\n"
 CMD_OPTIONS=$(cat <<EOF