diff --git a/patches/applyPatches.sh b/patches/applyPatches.sh
index a0c8e045e8cb31bff64cb458a091e89a59be80cc..46369e497d3e1e0b93966bfa0aed6d36b2b94d58 100755
--- a/patches/applyPatches.sh
+++ b/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
@@ -33,8 +34,6 @@ set -e
if [ -z "$UTILSPATH" ]; then
UTILSPATH=$(realpath "$(dirname $0)/../utils")
export UTILSPATH
- MAINPATH="$(dirname $UTILSPATH)"
- export MAINPATH
fi
source $UTILSPATH/load_settings.sh
diff --git a/utils/backup.sh b/utils/backup.sh
index aab15415b1490c53cef7809cdb7366fa871b62b3..29422d8f1ba5094c26ae9953e5b1e27b72fd65d5 100755
--- a/utils/backup.sh
+++ b/utils/backup.sh
@@ -5,6 +5,8 @@
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+# Copyright (C) 2020 Daniel Hornung <d.hornung@indiscale.com>
+# Copyright (C) 2020 IndiScale <info@indiscale.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
@@ -27,8 +29,6 @@
if [ -z "$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
@@ -45,14 +45,30 @@ function backup() {
database="$1"
backupdir="$2"
+<<<<<<< HEAD
# Assert backup dir
mkdir -p "$backupdir"
datastring=$(date -u --rfc-3339=ns | sed 's/ /T/g')
backupfile=${BACKUPDIR}/${DATABASE_NAME}.${datastring}.dump.sql
+=======
+ shift 2
+ # parameters: connection, database, outfile
+ if [ -e "$NARG_FILE" ]; then
+ failure "dumpfile already exists."
+ fi
+ echo "Dumping database $NARG_NAME to $NARG_FILE ... "
+ $MYSQLDUMP_CMD $(get_mysql_args_nodb) $* --opt --default-character-set=utf8 --routines \
+ "$NARG_NAME" > "$NARG_FILE"
+>>>>>>> s-clean-up-stage
if [ -e "$backupfile" ]; then
failure "dumpfile already exists."
fi
+<<<<<<< HEAD
+=======
+ success
+}
+>>>>>>> s-clean-up-stage
echo "Dumping database $database to $backupfile ... "
$MYSQLDUMP_CMD $(get_mysql_args_nodb) --opt --default-character-set=utf8\
diff --git a/utils/helpers.sh b/utils/helpers.sh
index 4ecf8789b650d9463639b119dcda1bfe2bce2bcd..cec709d4f8705357110ab308c3c9658293f0c494 100644
--- a/utils/helpers.sh
+++ b/utils/helpers.sh
@@ -2,8 +2,9 @@
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
-# Copyright 2019, 2020 Daniel Hornung
-# Copyright 2020 Henrik tom Wörden, IndiScale GmbH
+# 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
@@ -32,14 +33,12 @@
function mysql_execute {
#TODO is it meaningful that here always the database user is used???
- set +e
- # env | sort
+ set -e
$MYSQL_CMD $(get_db_args) -e "$1"
ret=${PIPESTATUS[0]}
if [ "$ret" -ne 0 ]; then
failure "MYSQL ERROR"
fi
- set -e
}
function get_mysql_args {
diff --git a/utils/load_settings.sh b/utils/load_settings.sh
index a46db58d2c4c3d1e4a87d1f2b831f77bc6163b1b..73d63364dd582dbc514ac3c2d95a37346b5b0eed 100644
--- a/utils/load_settings.sh
+++ b/utils/load_settings.sh
@@ -1,9 +1,10 @@
# This file is a part of the CaosDB Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
-# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
-# Copyright 2019 Daniel Hornung
-# Copyright 2020 Henrik tom Wörden, IndiScale GmbH
+# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+# Copyright (C) 2019, 2020 Daniel Hornung (d.hornung@indiscale.com)
+# Copyright (C) 2020 Henrik tom Wörden
+# Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
@@ -23,29 +24,34 @@
# - .config (in the current directory)
# - The file given in ENV_FILE.
-if [ "$MAINPATH" ]; then
- pushd "$MAINPATH" > /dev/null
- pushed=1
+if [ -z "$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 $UTILSPATH)"
+ export MAINPATH
fi
-if [[ -r "config.defaults" ]] ; then
- source "config.defaults"
-fi
-if [[ -r ".config" ]] ; then
- source ".config"
+# Make a backup of the important environment variables.
+my_env=$(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 not defined!"
+ echo "'mysql' executable not defined!"
exit 1
fi
-if [ $pushed ]; then
- popd > /dev/null
-fi
+# Restore backup.
+eval "$my_env"
export MYSQL_CMD
export MYSQLDUMP_CMD
diff --git a/utils/make_db b/utils/make_db
index 92a8541c73d55b9a2c5d779926afb27b2ed2415d..323a116f230a142b0ba0db21b41ef3fe3b96a42c 100755
--- a/utils/make_db
+++ b/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
@@ -27,20 +28,13 @@ set -e
INSTALL_SQL_FILE="db_2_0.sql"
if [ -z "$UTILSPATH" ]; then
- UTILSPATH="$(realpath $(dirname $0))"
- export UTILSPATH
- MAINPATH="$(dirname $UTILSPATH)"
- export MAINPATH
+ UTILSPATH="$(realpath $(dirname $0))"
+ export UTILSPATH
fi
source $UTILSPATH/load_settings.sh
source $UTILSPATH/helpers.sh
-function fail() {
- echo "Some error occured, exiting."
- exit 1
-}
-
UNITTEST_DATABASE=${UNITTEST_DATABASE-_caosdb_schema_unit_tests}
# optional parameter: [--fresh] for installing a fresh data base. Otherwise an existing one would be reused.
@@ -50,7 +44,7 @@ function runtests() {
_install_unit_test_database $@
- _execute_tests || ( echo "[FAILURE]" && exit 1 )
+ _execute_tests || ( failure )
echo "[PASS]"
}
@@ -103,7 +97,7 @@ function _setup_mytap() {
echo MyTAB framework is already installed [OK]
return 0
fi
- echo -n "Installing MyTAB framework ... "
+ echo -n "Installing MyTAP framework ... "
pushd libs > /dev/null
unzip -u mytap*.zip > /dev/null
pushd mytap*/ > /dev/null
@@ -111,7 +105,7 @@ function _setup_mytap() {
popd > /dev/null
rm -r mytap*/
popd > /dev/null
- echo [DONE]
+ echo "[DONE]"
}
function install_db() {
@@ -123,7 +117,7 @@ Call 'make drop-$DATABASE_NAME' to delete that database or reconfigure with
exit 0
fi
- sed "s/db_2_0/$DATABASE_NAME/g" "$INSTALL_SQL_FILE" | $MYSQL_CMD $(get_mysql_args_nodb)
+ sed "s/db_2_0/$DATABASE_NAME/g" "$INSTALL_SQL_FILE" | $MYSQL_CMD $(get_mysql_args_nodb)
}
# Inserts the dump (arg 1) into the database
@@ -144,7 +138,7 @@ function grant() {
while true; do
read -p "Please enter the password for ${DATABASE_USER}: " \
-s password
- echo
+ echo
read -p "Please repeat the password: " -s password2
echo
[[ "$password" == "$password2" ]] && {
@@ -158,7 +152,7 @@ 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}';"
- [[ $($MYSQL_CMD $(get_mysql_args_nodb) -s -N -e "$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};\"'"
@@ -199,12 +193,12 @@ function _db_exists() {
case $1 in
- "drop") drop $2 ;;
- "grant") grant $2 ;;
- "test") shift ; runtests $@ ;;
- "test-connection") test-connection ;;
- "install_db") install_db ;;
- "restore_db") restore_db $2 ;;
- # "prep_sql") prepare_sql ;;
- *) echo "Unknown action: $1"
+ "drop") drop $2 ;;
+ "grant") grant $2 ;;
+ "test") shift ; runtests $@ ;;
+ "test-connection") test-connection ;;
+ "install_db") install_db ;;
+ "restore_db") restore_db $2 ;;
+ # "prep_sql") prepare_sql ;;
+ *) echo "Unknown action: $1"
esac
diff --git a/utils/patch_header.sh b/utils/patch_header.sh
index f53266aabd96b316ecf2c17948384c505e5a9d87..488b7a0f4df0c20bde1909872d923ea4c352cacc 100644
--- a/utils/patch_header.sh
+++ b/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
@@ -21,7 +23,12 @@
#
# ** end header
#
-#header for patch scripts
+
+###############################################################################
+# header for patch scripts #
+###############################################################################
+
+set -e
# load useful functions #######################################################
source $UTILSPATH/load_settings.sh
@@ -57,7 +64,6 @@ configuration make file. Notable examples are:
EOF
)
-set -e
function _print_help() {
echo -e "$USAGE"
diff --git a/utils/update_sql_procedures.sh b/utils/update_sql_procedures.sh
index 2b78ab8cca5b1d337fa03d9ab3bb2e2e120a3be0..8850d5c3311c4ee1a6c7cd635bb1b1bb98fe218c 100755
--- a/utils/update_sql_procedures.sh
+++ b/utils/update_sql_procedures.sh
@@ -4,7 +4,10 @@
# 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
+# 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
@@ -24,24 +27,21 @@
# Updates all SQL procedures
+set -e
+
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
+source $UTILSPATH/helpers.sh
echo -n "updating rules ... "
-set -e
mysql_execute "$(sed s/db_2_0/$DATABASE_NAME/g rules.sql)"
echo "OK"
echo -n "updating procedures ... "
-mysql_execute "$(sed s/db_2_0/$DATABASE_NAME/g procedures/*.sql procedures/query/*.sql)"
+mysql_execute "$(sed s/db_2_0/$DATABASE_NAME/g procedures/*.sql procedures/query/*.sql)"
echo "OK"
-
-