MAINT: extract commonly used code from patch_header

backup.sh

@@ -27,15 +27,12 @@
 BACKUPDIR=./backup #The directory which the dump is to be stored to. Do not change it here. Use the --backupdir=./my/dir/ option!
 PRINT_HELP="--backupdir=BACKUPDIR\n\tThe directory which the dump is to be stored to. (Defaults to ./backup)\n"
 
-. .config
-# load useful stuff - scans the parameters and so on...
-. patches/utils/patch_header.sh
+. load_settings.sh
+. utils.sh
 
 #create backup dir if not exists
 [ -d $BACKUPDIR ] || mkdir $BACKUPDIR
 
-
-
 function backup {
     NARG_NAME=$1
     NARG_FILE=$2
@@ -50,18 +47,11 @@ function backup {
 	success
 }
 
-
-
-
-
 ##test dump file exists
 #touch dumpfile.tmp
 #backup 0 1 2 "dumpfile.tmp"
 #rm dumpfile.tmp
 
-
 DATE=$(date -u --rfc-3339=ns | sed 's/ /T/g')
 BACKUPFILE=${BACKUPDIR}/${DATABASE_NAME}.${DATE}.dump.sql
 backup $DATABASE_NAME $BACKUPFILE
-
-

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 2019 Daniel Hornung
+# Copyright 2020 Henrik tom Wörden, IndiScale GmbH
+#
+# 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/>.
+
+[[ -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."
+ 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
+
+# TODO is this a good idea?
+export MYSQL_CONNECTION
+export MYSQL_CONNECTION_NO_DB
+export DATABASE_NAME

patches/utils/patch_header.sh

@@ -22,6 +22,10 @@
 # ** end header
 #
 #header for patch scripts
+
+. ../../load_settings.sh
+. ../../utils.sh
+
 USAGE="$1 [ --env=ENV_FILE ] [ --patch=PATCH ] [ --backupdir=BACKUPDIR ]\n\n"
 CMD_OPTIONS=cat <<EOF
 options:
@@ -88,61 +92,11 @@ while test $# -gt 0; do
  esac
 done
 
-[[ -n "$ENV_FILE" ]] && source "$ENV_FILE"
-
-if [[ -z "$DATABASE_NAME" && -z "$MYSQL_CONNECTION" ]]
-then
- _print_help "Please specify the database."
- exit 1
-fi
-
-if [ "$LOGIN_PATH" ]; then
-  MYSQL_CONNECTION="--login-path=$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 {
@@ -157,24 +111,3 @@ function check_version {
 function update_version {
     mysql_execute "DROP FUNCTION IF EXISTS CaosDBVersion; CREATE FUNCTION CaosDBVersion() RETURNS VARCHAR(255) DETERMINISTIC RETURN '$1';"
 }
-
-function dump_table {
-    $MYSQLDUMP_CMD $MYSQL_CONNECTION_NO_DB $DATABASE_NAME $1 \
-                    > ${DATABASE_NAME}.${1}.${OLD_VERSION}.dump.sql
-}
-
-
-function mysql_execute {
-	set +e
-	$MYSQL_CMD $MYSQL_CONNECTION -e "$1"
-	ret=${PIPESTATUS[0]}
-	if [ "$ret" -ne 0 ]; then
-		failure "MYSQL ERROR"
-	fi
-	set -e
-}
-
-function redo_table {
-	  $MYSQL_CMD $MYSQL_CONNECTION < ${DATABASE_NAME}.${1}.${OLD_VERSION}.dump.sql
-}
-

update_sql_procedures.sh

@@ -24,13 +24,13 @@
 
 # Updates all SQL procedures
 
-source patches/utils/patch_header.sh
+. load_settings
 
 echo -n "updating rules ... "
 set -e
 
 mysql_execute "$(sed s/db_2_0/$DATABASE_NAME/g rules.sql)"
-echo "[OK]"
+success
 
 echo -n "updating procedures ... "
 mysql_execute "$(sed s/db_2_0/$DATABASE_NAME/g procedures/*.sql procedures/query/*.sql)" 

utils.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 2019 Daniel Hornung
+# Copyright 2020 Henrik tom Wörden, IndiScale GmbH
+#
+# 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/>.
+
+function dump_table {
+    $MYSQLDUMP_CMD $MYSQL_CONNECTION_NO_DB $DATABASE_NAME $1 \
+                    > ${DATABASE_NAME}.${1}.${OLD_VERSION}.dump.sql
+}
+
+function mysql_execute {
+	set +e
+	$MYSQL_CMD $MYSQL_CONNECTION -e "$1"
+	ret=${PIPESTATUS[0]}
+	if [ "$ret" -ne 0 ]; then
+		failure "MYSQL ERROR"
+	fi
+	set -e
+}
+
+function redo_table {
+	  $MYSQL_CMD $MYSQL_CONNECTION < ${DATABASE_NAME}.${1}.${OLD_VERSION}.dump.sql
+}
+
+function success {
+    echo "[OK]"
+    exit 0
+}
+
+function failure {
+    echo "[FAILED] $*"
+    exit 1
+}
+
+function uptodate {
+    echo "[UPTODATE]"
+    exit 0
+}