issues with running a .sh file outside server - bash

I have shell script which collects user input and generate a json file from the input. The input file is then read by a compiled matlab program which then creates an output file and I use that output file to plot.
I'm working on a linux server where I installed matlab runtime. Everything works fine inside the server, once I try to access the site outside the server the .sh doesn't completely execute( it only echoes the first lines and stops).
#!/bin/sh
# script for execution of deployed applications
#
# Sets up the MATLAB Runtime environment for the current $ARCH and executes
# the specified command.
#
exe_name=$0
exe_dir=`dirname "$0"`
echo "------------------------------------------"
if [ "x$1" = "x" ]; then
echo Usage:
echo $0 \<deployedMCRroot\> args
else
echo Setting up environment variables
MCRROOT="$1"
echo ---
LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ;
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ;
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64;
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/opengl/lib/glnxa64;
export LD_LIBRARY_PATH;
echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH};
shift 1
args=
while [ $# -gt 0 ]; do
token=$1
args="${args} \"${token}\""
shift
done
eval "\"${exe_dir}/main\"" $args
fi
exit

Using a script located within your web service document root. As an example, this is a simple PHP file to run the shell script. The chdir path used is just an example:
<?php
chdir('/var/www/yourdir');
$output = shell_exec('./matlab_setup.sh arg1');
Note that making the script accessible via the internet means anyone using a browser can access it, unless you introduce futher safeguarding.

Related

Creating a "First run" notification in bash?

What is the best way to make a "First run" notification in a bash script?
I tried putting export FIRSTRUN="no" first,
and later on put
`if [ -z "$FIRSTRUN" ]; then
echo "It seems that this may be your first time running this script.";
echo "Please ${GREEN}test whether the needed components are installed${RESET}.";
echo "";
fi`
but it simply does it on every time the script is run. If i put the export FIRSTRUN="no" after the if part, it never runs the if part of the code. So that doesn't work.
I am new at this so please help :D
You can't modify the parent shell state from within your script, so attempting to export a variable will not work.
You could use a config file to store a variable which determines whether the script has been run already:
#!/bin/bash
# load vars from config at the start of the script
if [[ -f ~/.your_script.conf ]]; then
. ~/.your_script.conf
fi
# check whether var has been set to determine first run
if [[ -z $has_run ]]; then
echo 'first run'
# set variable in config file for next time
echo 'has_run=1' >> ~/.your_script.conf
fi
Alternatively, if this is the only "config" you have, you could just create a file after the first run and check for its existence to determine whether the script has been run.
The first run of the script should leave behind some sort of permanent evidence that it has run; it can then look for that file on startup.
do_init () {
# initialize whatever needs initializing
touch ~/.alreadyran
}
if ! [ -f ~/.alreadyran ]; then
echo "First time running."
do_init
fi
If the initialization isn't per-user, it will need to leave the file in a more public place, such as somewhere under /var.

using environment variables in service script

I am facing an issue using environment variables in my service script.
In my services script, i am using an environmental variable i.e. INSTALL_DIR whose value may vary on different system. I have to get the installation directory from $INSTALL_DIR and then i have to start the service. when i am running the service script the environment variable is not sourced at all.
Is it possible to source the installation directory from INSTALL_DIR environment variable. another option i can think is dynamically creating the service script using INSTALL_DIR environment variable.
echo "INSTALL DIR: ${INSTALL_DIR}"
name=`basename $0`
pid_file="/var/run/$name.pid"
get_pid() {
cat "$pid_file"
}
is_running() {
[ -f "$pid_file" ] && ps `get_pid` > /dev/null 2>&1
}
Start()
{
echo "Starting Application"
if is_running; then
echo "[`get_pid`] Already Started"
else
if [ -z "$user" ]; then
nohup $INSTALL_DIR/bin/application 2>&1 &
else
nohup sudo -u "$user" $cmd 1> $INSTALL_DIR/bin/application 2>&1 &
fi
echo $! > "$pid_file"
if ! is_running; then
echo "Unable to start, see logs"
exit 1
fi
echo "[`get_pid`] Started"
fi
}
I am trying to run the application using following command
service application start
In my services script ... I have to get the installation directory from $INSTALL_DIR and then i have to start the service.
Your question isn't really about shell scripting, but about your system's startup. Unfortunately that process varies by Linux distribution, and tends to be poorly documented.
For example, man service says, service runs a System V init script or upstart job in as predictable an environment as possible, removing most environment variables and with the current working directory set to /., but man upstart says:
$ man -k upstart
upstart: nothing appropriate.
Not only that, but the service manpage specifically lists the environment variables a script will start with. Needless to say, yours isn't among them.
The traditional approach to parameterizing startup scripts is to put the information in a known file, normally in /etc, and reference that file in the script. In your case, you could do something like:
INSTALL_DIR=$(cat /etc/my-install-dir.cfg)
and then proceed accordingly.
There might be ways to coerce your startup to support other environment variables. But, sooner or later, the information you need has to be stored somewhere on the filesystem. It seems to me the simplest approach is to reserve a filename to hold that information, and read that file directly.
Use this below code in your script.
if [[ -z "${INSTALL_DIR}" ]]; then
echo "INSTALL_DIR is undefined"
else
INSTALL_DIR=<<your installation directory>>
fi

Simple Bash Script Error and Advice - Saving Environment Variables in Linux

I am working on a project that is hosted in Heroku. The app is hard coded to use Amazon S3 and looks for the keys in environment variables. This is what I wrote after looking at some examples and I am not sure why its not working.
echo $1
if [ $1 != "unset" ]; then
echo "set"
export AMAZON_ACCESS_KEY_ID=XXXXXXXXXXXX
export AMAZON_SECRET_ACCESS_KEY=XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
export S3_BUCKET_NAME=XXXXXXXXX
else
echo "unset"
export AMAZON_ACCESS_KEY_ID=''
export AMAZON_SECRET_ACCESS_KEY=''
export S3_BUCKET_NAME=''
fi
When running the script it goes to the set section. But when inspecting through echo $AMAZON_ACCESS_KEY_ID # => ''.
I am not sure what is causing the issue. I will be interested in...
A fix for this...
A way to extract and add heroku config variables in the the env in an easier way.
You need to source the script, not run it as a child. If you run the script directly, its environment disappears when it ends. Sourcing the script causes it to be executed in the current environment. help source for more information.
Example:
$ VAR=old_value
$ cat script.sh
#!/bin/bash
export VAR=new_value
$ ./script.sh
$ echo $VAR
old_value
$ source script.sh
$ echo $VAR
new_value
Scripts executed with source don't need to be executable nor do they need the "shebang" line (#!/bin/bash) because they are not run as separate processes. In fact, it is probably a good idea to not make them executable in order to avoid them being run as commands, since that won't work as expected.

How to prevent direct bash script execution and allow only usage from other script?

I have one script with common functions that is included in other my scripts with:
. ~/bin/fns
Since my ~/bin path is on the PATH, is there a way to prevent users to execute fns from command line (by returning from the script with a message), but to allow other scripts to include this file?
(Bash >= 4)
Just remove the executable bit with chmod -x . ~/bin/fns. It will still work when sourced, but you can't call it (accidentally) by its name anymore.
Some scripts at my workplace use a special shebang
#!/bin/echo Run:.
which returns
Run:. <pathname>
when you use it as a command.
Add the following at the beginning of the script you want to be only allowed to be sourced:
if [ ${0##*/} == ${BASH_SOURCE[0]##*/} ]; then
echo "WARNING"
echo "This script is not meant to be executed directly!"
echo "Use this script only by sourcing it."
echo
exit 1
fi
This will check if the current script and executed shell script file basenames match. If they match, then obviously you are executing it directly so we print a message and exit with status 1.
if (return 0 2>/dev/null) ; then
:
else
echo "Error: script was executed."
exit 1
fi

How to write a bash script to set global environment variable?

Recently I wrote a script which sets an environment variable, take a look:
#!/bin/bash
echo "Pass a path:"
read path
echo $path
defaultPath=/home/$(whoami)/Desktop
if [ -n "$path" ]; then
export my_var=$path
else
echo "Path is empty! Exporting default path ..."
export my_var=$defaultPath
fi
echo "Exported path: $my_var"
It works just great but the problem is that my_var is available just locally, I mean in console window where I ran the script.
How to write a script which allow me to export global environment variable which can be seen everywhere?
Just run your shell script preceded by "." (dot space).
This causes the script to run the instructions in the original shell. Thus the variables still exist after the script finish
Ex:
cat setmyvar.sh
export myvar=exists
. ./setmyvar.sh
echo $myvar
exists
Each and every shell has its own environment. There's no Universal environment that will magically appear in all console windows. An environment variable created in one shell cannot be accessed in another shell.
It's even more restrictive. If one shell spawns a subshell, that subshell has access to the parent's environment variables, but if that subshell creates an environment variable, it's not accessible in the parent shell.
If all of your shells need access to the same set of variables, you can create a startup file that will set them for you. This is done in BASH via the $HOME/.bash_profile file (or through $HOME/.profile if $HOME/.bash_profile doesn't exist) or through $HOME/.bashrc. Other shells have their own set of startup files. One is used for logins, and one is used for shells spawned without logins (and, as with bash, a third for non-interactive shells). See the manpage to learn exactly what startup scripts are used and what order they're executed).
You can try using shared memory, but I believe that only works while processes are running, so even if you figured out a way to set a piece of shared memory, it would go away as soon as that command is finished. (I've rarely used shared memory except for named pipes). Otherwise, there's really no way to set an environment variable in one shell and have another shell automatically pick it up. You can try using named pipes or writing that environment variable to a file for other shells to pick it up.
Imagine the problems that could happen if someone could change the environment of one shell without my knowledge.
Actually I found an way to achieve this (which in my case was to use a bash script to set a number of security credentials)
I just call bash from inside the script and the spawned shell now has the export values
export API_USERNAME=abc
export API_PASSWORD=bbbb
bash
now calling the file using ~/.app-x-setup.sh will give me an interactive shell with those environment values setup
The following were extracted from 2nd paragraph from David W.'s answer: "If one shell spawns a subshell, that subshell has access to the parent's environment variables, but if that subshell creates an environment variable, it's not accessible in the parent shell."
In case a user need to let parent shell access your new environment variables, just issue the following command in parent shell:
source <your_subshell_script>
or using shortcut
. <your_subshell_script>
You got to add the variable in your .profile located in /home/$USER/.profile
Yo can do that with this command:
echo 'TEST="hi"' >> $HOME/.profile
Or by edit the file with emacs, for example.
If you want to set this variable for all users, you got to edit /etc/profile (root)
There is no global environment, really, in UNIX.
Each process has an environment, originally inherited from the parent, but it is local to the process after the initial creation.
You can only modify your own, unless you go digging around in the process using a debugger.
write it to a temporary file, lets say ~/.myglobalvar and read it from anywhere
echo "$myglobal" > ~/.myglobalvar
Environment variables are always "local" to process execution the export command allow to set environment variables for sub processes. You can look at .bashrc to set environment variables at the start of a bash shell. What you are trying to do seems not possible as a process cannot modify (or access ?) to environment variables of another process.
You can update the ~/.bashrc or ~/.bash_profile file which is used to initialize the environment.
Take a look at the loading behavior of your shell (explained in the manpage, usually referring to .XXXshrc or .profile). Some configuration files are loaded at login time of an interactive shell, some are loaded each time you run a shell. Placing your variable in the latter might result in the behavior you want, e.g. always having the variable set using that distinct shell (for example bash).
If you need to dynamically set and reference environment variables in shell scripts, there is a work around. Judge for yourself whether is worth doing, but here it is.
The strategy involves having a 'set' script which dynamically writes a 'load' script, which has code to set and export an environment variable. The 'load' script is then executed periodically by other scripts which need to reference the variable. BTW, the same strategy could be done by writing and reading a file instead of a variable.
Here's a quick example...
Set_Load_PROCESSING_SIGNAL.sh
#!/bin/bash
PROCESSING_SIGNAL_SCRIPT=./Load_PROCESSING_SIGNAL.sh
echo "#!/bin/bash" > $PROCESSING_SIGNAL_SCRIPT
echo "export PROCESSING_SIGNAL=$1" >> $PROCESSING_SIGNAL_SCRIPT
chmod ug+rwx $PROCESSING_SIGNAL_SCRIPT
Load_PROCESSING_SIGNAL.sh (this gets dynamically created when the above is run)
#!/bin/bash
export PROCESSING_SIGNAL=1
You can test this with
Test_PROCESSING_SIGNAL.sh
#!/bin/bash
PROCESSING_SIGNAL_SCRIPT=./Load_PROCESSING_SIGNAL.sh
N=1
LIM=100
while [ $N -le $LIM ]
do
# DO WHATEVER LOOP PROCESSING IS NEEDED
echo "N = $N"
sleep 5
N=$(( $N + 1 ))
# CHECK PROCESSING_SIGNAL
source $PROCESSING_SIGNAL_SCRIPT
if [[ $PROCESSING_SIGNAL -eq 0 ]]; then
# Write log info indicating that the signal to stop processing was detected
# Write out all relevent info
# Send an alert email of this too
# Then exit
echo "Detected PROCESSING_SIGNAL for all stop. Exiting..."
exit 1
fi
done
~/.bin/SOURCED/lazy script to save and load data as flat files for system.
[ ! -d ~/.megadata ] && mkdir ~/.megadata
function save_data {
[ -z "$1" -o -z "$2" ] && echo 'save_data [:id:] [:data:]' && return
local overwrite=${3-false}
[ "$overwrite" = 'true' ] && echo "$2" > ~/.megadata/$1 && return
[ ! -f ~/.megadata/$1 ] && echo "$2" > ~/.megadata/$1 || echo ID TAKEN set third param to true to overwrite
}
save_data computer engine
cat ~/.megadata/computer
save_data computer engine
save_data computer megaengine true
function get_data {
[ -z "$1" -o -f $1 ] && echo 'get_data [:id:]' && return
[ -f ~/.megadata/$1 ] && cat ~/.megadata/$1 || echo ID NOT FOUND
:
}
get_data computer
get_data computer
Maybe a little off topic, but when you really need it to set it temporarily to execute some script and ended up here looking for answers:
If you need to run a script with certain environment variables that you don't need to keep after execution you could do something like this:
#!/usr/bin/env sh
export XDEBUG_SESSION=$(hostname);echo "running with xdebug: $XDEBUG_SESSION";$#
In my example I just use XDEBUG_SESSION with a hostname, but you can use multiple variables. Keep them separated with a semi-colon. Execution as follows (assuming you called the script debug.sh and placed it in the same directory as your php script):
$ debug.sh php yourscript.php

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