I think that the issue is not that you not get the output of the executed command, but which fails to find mysql. Using exec you can get the return status of your command, where 0 means successful, and other values indicate an error.

$output = exec(output, $retval);
var_dump($output);
var_dump($retval);

If the $retval is 1 that would mean which doesn't find the mysql binary, and returns an empty line.

I don't know how pdfgrep works but maybe it mixes stdout and stderr? Either way, you could use a construction like this, where you capture the output stream into an output buffer, optionally also mixing stderr into stdout:

$mixStdErrIntoStdOut = false;

ob_start();
$exitCode = 0;
if ($mixStdErrIntoStdOut) 
{
    system("pdfgrep -i $keyword $file 2>&1", &$exitCode);
} else {
    system("pdfgrep -i $keyword $file", &$exitCode);
}
$output = ob_get_clean();

var_dump($output);

On the php manual for shell_exec, it shows that the function returns the output as a string. If you expect output from the program you launch, you need to capture this like so:

$execQuery = "echo -n test_command";
$output = shell_exec($execQuery);
echo $output;

Your question doesn't show trying to capture any data. If you also make sure to connect stdout and stderr when you run your command, you should get a better idea is what is going on. To use your example:

$output = shell_exec("/usr/bin/oneuser create test10 test10 2>&1");
var_dump($output);

That should help you see what is going on. As Shadur suggests, it seems likely that these programs expect an interactive terminal that can enter passwords in order to run. Even if don't need input, they might expect interactive shells. And he's right that su doesn't play nice in this context. There is, however, a correct tool for the job.

You can setup sudo to such that your http user can execute your program as username without a password but NOT be able to do anything else by running visudo or whatever you use to edit your sudoers file and adding this line:

http    ALL=(username) /usr/bin/oneadmin

Then in php your command would look something like this:

$execQuery = "sudo -u username /usr/bin/oneadmin postgres -c '/usr/bin/oneuser create test10 test10'";
$out = shell_exec ("$execQuery 2>&1");
echo $out

You have to use 2>&1 after the restart command

Your command :

$command = "echo 1; /etc/init.d/apache3 restart; echo 2; 2>&1";

yours has "2>&1" at the end which has no use.

Also you will add to 2>&1 after each command in case others uses STDERR

$command = "echo 1; /etc/init.d/apache3 restart 2>&1; echo 2 ";

Add 2>&1 to the end of your shell command to have STDERR returned as well as STDOUT.

$output = shell_exec("ls /root/files/saves 2>&1");

Also, if the user running PHP doesn't have sufficient permissions to view the output in /root/, the above code will return a Permission denied error message.

Source: http://php.net/manual/en/function.shell-exec.php#28994

Because systemctl is not on your path (or not on you system) which systemctl returns the error message

/usr/bin/which: no systemctl in (/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin)

When you run it in PHP using shell_exec('which systemctl'); the standard error is not collected, and the standard out is empty. Hence PHP sees an empty string.

You can get standard error using this command:

shell_exec('which systemctl 2>&1');

You should redirect stderr to stdout.

To do that, change your exec() call like this:

exec("ping -c 1 $domain_bad 2>&1", $output, $return_var);

More info about 2>&1 meaning here.

I changed the sudoers to ALL ALL = (ALL) :NOPASSWD ALL (very un-secure, but just to find something sure to work),

then I did a

sudo -u myusername /path/to/script.sh

where script.sh has export VAR=value export VAR=value

for all the environmental variables that are necessary (you can do a printenv from a user who can properly pacmd to see what you need. probably a good HOME and maybe an XAUTHORITY).

hope that helps

Have you tried to use the full path with your "leaf" reference?

$output = shell_exec("/var/local/leaf $file");

There is a note in php manual page of shell_execute:

Note: This function can return NULL both when an error occurs or the program produces no output. It is not possible to detect execution failures using this function. exec() should be used when access to the program exit code is required.

Source: http://php.net/manual/en/function.shell-exec.php

So your code running with error. Try with exec. If you want, insert your code (or blocks) to be checked.