WIP: patch_header.sh now uses env variables + config file.

Also adapted the makefile.

makefile

@@ -38,7 +38,7 @@ test-connection:
 
 .PHONY: upgrade
 upgrade:
-	@cd patches; ./applyPatches.sh $(MYSQL_CONNECTION) --database=$(DATABASE_NAME)
+	@cd patches; ./applyPatches.sh --env=../.config
 
 .PHONY: install
 install: _install _grant upgrade

patches/applyPatches.sh

@@ -30,8 +30,8 @@ export UTILSPATH="./utils"
 
 for p in $PATCHES
 do
-    $p $MYSQL_CONNECTION --database=$DATABASE_NAME --patch=$p
+    $p "$@" --patch=$p
 done
 
 cd ../
-./update_sql_procedures.sh $MYSQL_CONNECTION --database=$DATABASE_NAME
+./update_sql_procedures.sh

patches/utils/patch_header.sh

@@ -4,6 +4,7 @@
 #
 # 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
@@ -23,122 +24,107 @@
 #header for patch scripts
 CMD_MYSQL=mysql
 CMD_MYSQL_DUMP=mysqldump
-USAGE="$1 --database=DATABASE_NAME [ --login-path=LOGIN_PATH | --user=USER [ --password=PASSWORD ] ]\n\n"
-CMD_OPTIONS="options:\n\n-h, --help\n\tShow brief help.\n-l LOGIN_PATH, --login-path=LOGIN_PATH\n\tA login-path for the mysql connection (see 'man mysql' and 'man mysql-config-editor').\n-u USER, --user=USER\n\tA mysql user.\n-p PASSWORD, --password=PASSWORD\n\tThe password for the mysql user.\n"
+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
+    *TODO* Please document this option.
+
+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() {
-  printf -- "$USAGE"
-  printf -- "$CMD_OPTIONS"
+  echo -e "$USAGE"
+  echo -e "$CMD_OPTIONS"
   if [ -n "$PRINT_HELP" ]; then
-    printf -- "$PRINT_HELP"
+    echo -e "$PRINT_HELP"
   fi
   if [ -n "$1" ]; then
-    printf -- "$1"
+    echo -e "$1"
   fi
 }
+
 while test $# -gt 0; do
  case "$1" in
  -h|--help)
   _print_help
   exit 0
   ;;
- -p)
-  shift
-  if test $# -gt 0; then
-   MYSQL_USER_PASSWORD=$1
-  else
-   echo "no database specified"
-   exit 1
-  fi
-  shift
-  ;;
- --password*)
-  MYSQL_USER_PASSWORD=`echo $1 | sed -e 's/^[^=]*=//g'`
-  shift
-  ;;
- -u)
-  shift
-  if test $# -gt 0; then
-   MYSQL_USER=$1
-  else
-   echo "no database specified"
-   exit 1
-  fi
-  shift
-  ;;
- --user*)
-  MYSQL_USER=`echo $1 | sed -e 's/^[^=]*=//g'`
-  shift
-  ;;
- -l)
-  shift
-  if test $# -gt 0; then
-   LOGIN_PATH=$1
-  else
-   echo "no database specified"
-   exit 1
-  fi
-  shift
-  ;;
- --login-path*)
-  LOGIN_PATH=`echo $1 | sed -e 's/^[^=]*=//g'`
-  shift
-  ;;
- -d)
-  shift
-  if test $# -gt 0; then
-   DATABASE_NAME=$1
-  else
-   echo "no database specified"
-   exit 1
-  fi
-  shift
-  ;;
- --database*)
-  DATABASE_NAME=`echo $1 | sed -e 's/^[^=]*=//g'`
+ --env*)
+  ENV_FILE="${1#--*=}"
   shift
   ;;
  --patch*)
-  PATCH=`echo $1 | sed -e 's/^[^=]*=//g'`
+  PATCH="${1#--*=}"
   shift
   ;;
  --backupdir*)
-  BACKUPDIR=`echo $1 | sed -e 's/^[^=]*=//g'`
+  BACKUPDIR="${1#--*=}"
   shift
   ;;
  *)
+  echo "Unknown option $1"
+  exit 1
   shift
   ;;
  esac
 done
 
-if [ -z "$DATABASE_NAME" ]
+[[ -n "$ENV_FILE" ]] && source "$ENV_FILE"
+
+if [[ -z "$DATABASE_NAME" && -z "$MYSQL_CONNECTION" ]]
 then
  _print_help "Please specify the database."
  exit 1
 fi
 
-if [ "$LOGIN_PATH" ]
-then
+if [ "$LOGIN_PATH" ]; then
   MYSQL_CONNECTION="--login-path=$LOGIN_PATH"
-else
+  MYSQL_CONNECTION_NO_DB="$MYSQL_CONNECTION"
+  MYSQL_CONNECTION="$MYSQL_CONNECTION --database=$DATABASE_NAME"
+
+elif [[ -z "$MYSQL_CONNECTION" ]]; then
   MYSQL_CONNECTION=""
-  if [ "$MYSQL_USER" ]
+  if [ "$DATABASE_USER" ]
   then
-    MYSQL_CONNECTION="--user=$MYSQL_USER"
+    MYSQL_CONNECTION="--user=$DATABASE_USER"
   fi
-  if [ "$MYSQL_USER_PASSWORD" ]
+  if [ "$DATABASE_USER_PW" ]
   then
-    MYSQL_CONNECTION="$MYSQL_CONNECTION --password=$MYSQL_USER_PASSWORD"
+    MYSQL_CONNECTION="$MYSQL_CONNECTION --password=$DATABASE_USER_PW"
   fi
-  if [ "$MYSQL_HOST" != "localhost" ]; then
-      MYSQL_CONNECTION="$MYSQL_CONNECTION --host $MYSQL_HOST"
+  if [[ "$MYSQL_HOST" && ( "$MYSQL_HOST" != "localhost" ) ]]; then
+      MYSQL_CONNECTION="$MYSQL_CONNECTION --host=$MYSQL_HOST"
       if [ "$MYSQL_PORT" ]; then
-          MYSQL_CONNECTION="$MYSQL_CONNECTION --port $MYSQL_PORT"
+          MYSQL_CONNECTION="$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 ... "
@@ -161,7 +147,7 @@ function uptodate {
 # @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 -D $DATABASE_NAME -B -e "Select CaosDBVersion();")
+    local version=$($CMD_MYSQL $MYSQL_CONNECTION -B -e "Select CaosDBVersion();")
 	if [[ "$(echo $version | sed 's/^CaosDBVersion()\s//')" = "$1" ]]; then
         return 0
 	fi
@@ -174,13 +160,13 @@ function update_version {
 }
 
 function dump_table {
-    $CMD_MYSQL_DUMP $MYSQL_CONNECTION $DATABASE_NAME $1 > ${DATABASE_NAME}.${1}.${OLD_VERSION}.dump.sql
+    $CMD_MYSQL_DUMP $MYSQL_CONNECTION_NO_DB $DATABASE_NAME $1 > ${DATABASE_NAME}.${1}.${OLD_VERSION}.dump.sql
 }
 
 
 function mysql_execute {
 	set +e
-	$CMD_MYSQL $MYSQL_CONNECTION -D $DATABASE_NAME -e "$1"
+	$CMD_MYSQL $MYSQL_CONNECTION -e "$1"
 	ret=${PIPESTATUS[0]}
 	if [ "$ret" -ne 0 ]; then
 		failure "MYSQL ERROR"
@@ -189,5 +175,5 @@ function mysql_execute {
 }
 
 function redo_table {
-	$CMD_MYSQL $MYSQL_CONNECTION -D $DATABASE_NAME < ${DATABASE_NAME}.${1}.${OLD_VERSION}.dump.sql
+	$CMD_MYSQL $MYSQL_CONNECTION < ${DATABASE_NAME}.${1}.${OLD_VERSION}.dump.sql
 }