From f93a3735fe49f331b383a7659b52b5168ac2c972 Mon Sep 17 00:00:00 2001
From: Daniel <daniel@harvey>
Date: Fri, 27 Mar 2020 13:13:14 +0100
Subject: [PATCH] FIX: Runs in Docker again.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Also:
- More strict `set -e`
- Global path variables.
- A few more comments
- Copyright notices
== Technically, this is a big squash merge: ===
Squashed commit of the following:
commit 5c26e223e78192ba3d788ab2c640e8c3a1c73866
Author: Daniel <daniel@harvey>
Date: Fri Mar 27 13:11:43 2020 +0100
MAINT: No warning if mysql_config_editor can not be found.
commit 06c3f1d25e3bd1a37942f7f0630daac82c8a7738
Author: Daniel <daniel@harvey>
Date: Fri Mar 27 12:57:15 2020 +0100
MAINT: Moved `set -e` more to the front.
commit 68ad8469e0dd8c5dc3c4d93f41b4902e622f579f
Author: Daniel <daniel@harvey>
Date: Fri Mar 27 12:56:37 2020 +0100
MAINT: Removed debugging output, added copyright lines.
commit 7ed57cdaf1d1299b5cb8d412988409410eee9b45
Author: Daniel <daniel@harvey>
Date: Fri Mar 27 11:59:37 2020 +0100
MAINT: moved MAINPATH definition into load_settings.sh
commit b34f82812a59e8913d40d71c3ae34f3f0106fdf2
Author: Daniel <daniel@harvey>
Date: Fri Mar 27 10:59:57 2020 +0100
MAINT: A bit of cleanup.
commit 4a88516991f39091edf628bcad066b6873b347c0
Author: Daniel <daniel@harvey>
Date: Fri Mar 27 09:35:16 2020 +0100
STY: Whitespace fixup.
commit 4724ee7014c65d26fe19cf1d530d45318056b5e3
Author: Henrik tom Wörden <henrik@trineo.org>
Date: Fri Mar 27 08:22:53 2020 +0100
FIX: added missing env setting in applypatches
commit 1d79730089c040cdd0751b59d347c290c01207f1
Author: Henrik tom Wörden <henrik@trineo.org>
Date: Fri Mar 27 08:18:47 2020 +0100
MAINT: make calling skripts more cwd independent
commit c908d69b6a945cb45e53bf9602dd6c684834ea84
Author: Daniel <daniel@harvey>
Date: Thu Mar 26 19:48:58 2020 +0100
MAINT: Failing fast if no SQL is found.
commit 2fa7d1bbfa127e23c16c1e06d3f5667e47e58058
Author: Daniel <daniel@harvey>
Date: Thu Mar 26 19:26:57 2020 +0100
Debug
commit a520f4a2f5d95341e762bb7491a3df69be983622
Author: Daniel <daniel@harvey>
Date: Thu Mar 26 19:22:48 2020 +0100
Debug
commit fb60953d3d1f3a3cd64a218cc3ae8c5a96843bb0
Author: Daniel <daniel@harvey>
Date: Thu Mar 26 19:10:56 2020 +0100
FIX: Loading load_settings.sh
commit d176828716313484df56f89887a20ff97767a55f
Author: Daniel <daniel@harvey>
Date: Thu Mar 26 19:01:40 2020 +0100
DBG .
commit b1c5d47ca98735d6f1780572dab4c338254aadb3
Author: Daniel <daniel@harvey>
Date: Thu Mar 26 18:55:21 2020 +0100
FIX: Load definitions first.
commit ed5c4d9c722690b5fe9492aa16bcc7528971a793
Author: Daniel <daniel@harvey>
Date: Thu Mar 26 18:44:03 2020 +0100
DBG
commit 0763ef3af2eebbbaf3f0c3caa6e8192a7bfe6a2f
Author: Daniel <daniel@harvey>
Date: Thu Mar 26 18:19:40 2020 +0100
FIX: Set UTILSPATH in applyPatches.sh
commit f351acebea56076f1a30bbbb46930ca19f7b5c9e
Author: Daniel <daniel@harvey>
Date: Thu Mar 26 18:08:03 2020 +0100
FIX: More strinct error handling, message if commands are not found.
commit 0338357e48702e1b0b7b228adbec1b3b77473045
Author: Daniel <daniel@harvey>
Date: Thu Mar 26 17:26:04 2020 +0100
DBG .
commit 8f0545c26ec06f4ad271875335aaa243adbaaf85
Author: Daniel <daniel@harvey>
Date: Thu Mar 26 16:46:15 2020 +0100
MAINT: Earlier set -e, also documentation.
---
config.defaults | 8 ++--
patches/applyPatches.sh | 15 ++++++-
utils/backup.sh | 19 ++++-----
utils/helpers.sh | 33 ++++++++++-----
utils/load_settings.sh | 37 ++++++++++++++---
utils/make_db | 74 +++++++++++++++++-----------------
utils/patch_header.sh | 15 +++++--
utils/update_sql_procedures.sh | 18 ++++++---
8 files changed, 141 insertions(+), 78 deletions(-)
diff --git a/config.defaults b/config.defaults
index bd669cb..bf6c941 100644
--- a/config.defaults
+++ b/config.defaults
@@ -23,13 +23,13 @@
# # 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 || true)
# # MySQL Connection
# The host of the MySQL server.
diff --git a/patches/applyPatches.sh b/patches/applyPatches.sh
index 56cbac7..735dd3e 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
@@ -24,8 +25,20 @@
# ** end header
#
-#apply all available patches.
+###############################################################################
+# Apply all available patches #
+###############################################################################
+
set -e
+
+if [ -z "$UTILSPATH" ]; then
+ UTILSPATH=$(realpath "$(dirname $0)/../utils")
+ export UTILSPATH
+fi
+
+source $UTILSPATH/load_settings.sh
+source $UTILSPATH/helpers.sh
+
PATCHES="./patch*/patch.sh"
for p in $PATCHES
diff --git a/utils/backup.sh b/utils/backup.sh
index 752c4e4..56ca609 100755
--- a/utils/backup.sh
+++ b/utils/backup.sh
@@ -5,6 +5,8 @@
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+# Copyright (C) 2020 Daniel Hornung <d.hornung@indiscale.com>
+# Copyright (C) 2020 IndiScale <info@indiscale.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
@@ -24,10 +26,9 @@
# Dump a database with all procedures, permissions, structure and data
-
if [ -z "$UTILSPATH" ]; then
- UTILSPATH="$(realpath $(dirname $0))"
- export UTILSPATH
+ UTILSPATH="$(realpath $(dirname $0))"
+ export UTILSPATH
fi
# The directory which the dump is to be stored to. Do not change it here. Use
# the --backupdir=./my/dir/ option or an environment variable instead.
@@ -74,18 +75,18 @@ function backup() {
NARG_FILE="$2"
shift 2
- # parameters: connection, database, outfile
- if [ -e "$NARG_FILE" ]; then
- failure "dumpfile already exists."
- fi
+ # 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 \
+ $MYSQLDUMP_CMD $(get_mysql_args_nodb) $* --opt --default-character-set=utf8 --routines \
"$NARG_NAME" > "$NARG_FILE"
if [[ "$YAML" == "true" ]] ; then
yaml_success "$NARG_FILE" "$DATE"
fi
- success
+ success
}
# Print a YAML failure message, if YAML is true.
diff --git a/utils/helpers.sh b/utils/helpers.sh
index b1f6d19..3791440 100644
--- a/utils/helpers.sh
+++ b/utils/helpers.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
@@ -19,15 +20,25 @@
# 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
+ $MYSQL_CMD $(get_db_args) -e "$1"
+ ret=${PIPESTATUS[0]}
+ if [ "$ret" -ne 0 ]; then
+ failure "MYSQL ERROR"
+ fi
}
function get_mysql_args {
diff --git a/utils/load_settings.sh b/utils/load_settings.sh
index a001b98..5cacc0d 100644
--- a/utils/load_settings.sh
+++ b/utils/load_settings.sh
@@ -1,9 +1,10 @@
# This file is a part of the CaosDB Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
-# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
-# Copyright 2019 Daniel Hornung
-# Copyright 2020 Henrik tom Wörden, IndiScale GmbH
+# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+# Copyright (C) 2019, 2020 Daniel Hornung (d.hornung@indiscale.com)
+# Copyright (C) 2020 Henrik tom Wörden
+# Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
@@ -18,9 +19,33 @@
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
-[[ -n "config.defaults" ]] && source "config.defaults"
-[[ -n ".config" ]] && source ".config"
-[[ -n "$ENV_FILE" ]] && source "$ENV_FILE"
+# Load setting from different files, in this order:
+# - config.defaults (in the current directory)
+# - .config (in the current directory)
+# - The file given in ENV_FILE.
+
+if [ -z "$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 $UTILSPATH)"
+ export MAINPATH
+fi
+
+source "$MAINPATH/config.defaults"
+
+if [[ -r "$MAINPATH/.config" ]] ; then
+ source "$MAINPATH/.config"
+fi
+if [[ -n "$ENV_FILE" ]] ; then
+ source "$ENV_FILE"
+fi
+
+if [[ -z "$MYSQL_CMD" ]] ; then
+ echo "'mysql' executable not defined!"
+ exit 1
+fi
export MYSQL_CMD
export MYSQLDUMP_CMD
diff --git a/utils/make_db b/utils/make_db
index 72a49da..4dbc80e 100755
--- a/utils/make_db
+++ b/utils/make_db
@@ -3,8 +3,9 @@
# ** header v3.0
# This file is a part of the CaosDB Project.
#
-# Copyright (C) 2019 Daniel Hornung, Göttingen
+# Copyright (C) 2019, 2020 Daniel Hornung <d.hornung@indiscale.com>
# Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
+# Copyright (C) 2020 Henrik tom Wörden <h.tomwoerden@indiscale.com>
# Copyright (C) 2020 IndiScale <info@indiscale.com>
#
# This program is free software: you can redistribute it and/or modify
@@ -22,23 +23,18 @@
#
# ** end header
+set -e
+
INSTALL_SQL_FILE="db_2_0.sql"
if [ -z "$UTILSPATH" ]; then
- UTILSPATH="$(realpath $(dirname $0))"
- export UTILSPATH
+ UTILSPATH="$(realpath $(dirname $0))"
+ export UTILSPATH
fi
source $UTILSPATH/load_settings.sh
source $UTILSPATH/helpers.sh
-set -e
-
-function fail() {
- echo "Some error occured, exiting."
- exit 1
-}
-
UNITTEST_DATABASE=${UNITTEST_DATABASE-_caosdb_schema_unit_tests}
# optional parameter: [--fresh] for installing a fresh data base. Otherwise an existing one would be reused.
@@ -48,7 +44,7 @@ function runtests() {
_install_unit_test_database $@
- _execute_tests || ( echo "[FAILURE]" && exit 1 )
+ _execute_tests || ( failure )
echo "[PASS]"
}
@@ -113,22 +109,24 @@ function _setup_mytap() {
}
function setup_os() {
- # - mariadb-client :: For SQL server configuration.
- PACKAGES="git
- make
- mariadb-client
- maven
- openjdk-8-jdk-headless
- python3-pip
- screen
- unzip
-"
- # - vim :: For debugging
- PACKAGES+="vim
-"
- apt-get update
- apt-get dist-upgrade -y
- apt-get install -y $PACKAGES
+ # - mariadb-client :: For SQL server configuration.
+ PACKAGES="
+ git
+ make
+ mariadb-client
+ maven
+ openjdk-8-jdk-headless
+ python3-pip
+ screen
+ unzip
+ "
+ # - vim :: For debugging
+ PACKAGES+="
+ vim
+ "
+ apt-get update
+ apt-get dist-upgrade -y
+ apt-get install -y $PACKAGES
}
function install_db() {
@@ -140,7 +138,7 @@ Call 'make drop-$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
@@ -160,7 +158,7 @@ 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" ]] && {
@@ -174,7 +172,7 @@ 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};\"'"
@@ -215,12 +213,12 @@ 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 7f85505..488b7a0 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
@@ -21,10 +23,16 @@
#
# ** end header
#
-#header for patch scripts
+
+###############################################################################
+# header for patch scripts #
+###############################################################################
+
+set -e
# 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
@@ -56,7 +64,6 @@ configuration make file. Notable examples are:
EOF
)
-set -e
function _print_help() {
echo -e "$USAGE"
diff --git a/utils/update_sql_procedures.sh b/utils/update_sql_procedures.sh
index 73f6bac..8850d5c 100755
--- a/utils/update_sql_procedures.sh
+++ b/utils/update_sql_procedures.sh
@@ -4,7 +4,10 @@
# This file is a part of the CaosDB Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
-# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+# Copyright (C) 2020 Daniel Hornung <d.hornung@indiscale.com>
+# Copyright (C) 2020 Henrik tom Wörden <h.tomwoerden@indiscale.com>
+# Copyright (C) 2020 IndiScale <info@indiscale.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
@@ -24,16 +27,21 @@
# Updates all SQL procedures
+set -e
+
+if [ -z "$UTILSPATH" ]; then
+ UTILSPATH=$(realpath "$(dirname $0)")
+ export UTILSPATH
+fi
+
+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"
-
-
--
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