I know that it is quite easy to figure out a terminal's size parameters via the stty -a command. When using local CLI PHP scripts, there is no problem at all on grabbing that output via system() or so.
But I am trying the same thing via a php script started from an ssh command. Sadly, all that stty ever returns is:
stty: standard input: Invalid argument.
The calling code is:
exec('stty -a | head -n 1', $query);
echo $query[0];
So the question is: If I can output to the terminal and read input from it (e.g. can fread() from STDIN and fwrite() to STDOUT in PHP, shouldn't stty also have valid STDIN and STDOUT?
Use ssh -t:
% php ~/src/termtest.php
speed 9600 baud; 39 rows; 127 columns;
% ssh localhost php ~/src/termtest.php
stty: stdin isn't a terminal
% ssh -t localhost php ~/src/termtest.php
speed 9600 baud; 39 rows; 127 columns;Connection to localhost closed.
SSH does not pass in a fully functional terminal by default. Shells and ncurses seem to be able to get them somehow, but to launch something that needs one directly from SSH you need to set -t.
For the same reason you can e.g. launch tmux (or screen) by ssh'ing to a server and then typing tmux at the prompt or through ssh -t _server_ tmux but not through sh _server_ tmux.
Related
I have an Ubuntu VM running in VirtualBox that hosts a server using Apache. The concept of the server is to accept HTTP POST requests, store them in a MySQL database and then execute a Python script with the relevant POST data to be displayed in a Discord channel.
The process itself is working but each time the PHP script calls the Python script, a new process is created that never actually ends. After a few hours of receiving live data the server runs out of available memory due to the amount of lingering processes. The PHP script has the following exec call as the last line of code;
exec("python3 main.py $DATA");
I would like to come up with a way to actually kill the processes created from this exec command (using user www-data), either in the Python file after the script is executed or automatically with an Apache setting that I probably just do not know about.
When running the following command in a terminal I can see the different processes;
ps -o pid,user,%mem,command ax | sort -b -k3 -r
There are 3 separate processes that show up, 1 referencing the actual python3 exec command as marked up in PHP;
9903 www-data 0.4 python3 main.py DATADATADATADATADATADATA
Then another process showing the more common -k start commands;
9907 www-data 0.1 /usr/sbin/apache2 -k start
And lastly another process very similar to the PHP exec command;
9902 www-data 0.0 sh -c python3 main.py DATADATADATADATADATADATA
How can I ensure Apache cleans these processes up - OR what do I need to add into my Python or PHP code to appropriately exec a Python script without leaving behind processes?
Didn't realize the exec command in php would wait for a return output indefinitely. Added this to the end of the string I was using in my exec call; > /dev/null &
i.e.: exec("python3 main.py $DATA > /dev/null &");
Prokka is a tool used to annotate bacterial genomes and can be installed and access using the command line in the local system or server.
So, I have downloaded Prokka using Git clone (git clone https://github.com/tseemann/prokka.git) and complied it on the CentOS (7) server along with all the dependencies with the latest version (NCBI-BLAST 2.10.1, hmmer 3.3, gnu Parallel).
In order to make a prediction server, I have created a webpage using PHP, and in that PHP file, I'm taking input from the user and passing that input to a shell file, and trying to execute that shell file using the shell_exec() function.
Here $fileName and $fn are the input from taken from the webpage.
$output = shell_exec("./path/to/shell/file/invoke.sh $script_path/$fileName $fn");
echo "<pre>$output</pre>";
invoke.sh file:
input_genome="$1";
prefix_genome="$2";
/path/to/prokka/bin/prokka $input_genome --outdir ./results/"$prefix_genome" --prefix $prefix_genome --locustag $prefix_genome --cpus 8 --kingdom Bacteria
Now, if I'm invoking Prokka (/path/to/prokka/bin/prokka) directly from the command line it's working fine and create all the files which ideally it should create. Moreover, if I'm running the shell script (invoke.sh) to invoke the Prokka (/path/to/prokka/bin/prokka) it's again working fine and generate all the files.
Expected and actual output files:
seq.faa
seq.err
seq.fna
seq.txt
seq.ffn
seq.gff
seq.tsv
seq.fsa
seq.gbk
seq.tbl
seq.log
seq.sqn
But the problem is while I'm running the PHP file from the web-browser as mentioned above to run the shell file (invoke.sh) it is running, but the Prokka command is not running properly inside the shell file and therefore not generating all of the output files.
I checked the error_log it showed me this:
[23:43:57] Will use blast to search against /home/group01/html/csspred/prokka/db/kingdom/Bacteria/sprot with 8 CPUs
[23:43:57] Running: cat \/home\/group01\/html\/csspred\/results\/01\-Nov\-23_43_779958414\/seq\/seq\.sprot\.tmp\.18401\.faa | parallel --gnu --plain -j 8 --block 3279 --recstart '>' --pipe blastp -query - -db /home/group01/html/csspred/prokka/db/kingdom/Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > \/home\/group01\/html\/csspred\/results\/01\-Nov\-23_43_779958414\/seq\/seq\.sprot\.tmp\.18401\.blast 2> /dev/null
[23:44:00] Could not run command: cat \/home\/group01\/html\/csspred\/results\/01\-Nov\-23_43_779958414\/seq\/seq\.sprot\.tmp\.18401\.faa | parallel --gnu --plain -j 8 --block 3279 --recstart '>' --pipe blastp -query - -db /home/group01/html/csspred/prokka/db/kingdom/Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > \/home\/group01\/html\/csspred\/results\/01\-Nov\-23_43_779958414\/seq\/seq\.sprot\.tmp\.18401\.blast 2> /dev/null
and generated only four files :
seq.HAMAP.hmm.tmp.12617.faa
seq.HAMAP.hmm.tmp.12617.hmmer3
seq.fna
seq.log
I even used a C file to invoke the execute a shell file which ultimately invokes the Prokka command but again the problem remained the same.
PHP: $output = shell_exec("./invoke.out $script_path/$fileName $fn");
C:
`int main(int argc, char *argv[])
{
char command[1000];
sprintf(command, "%s %s %s", "sh /home/group01/html/csspred/scripts/CSS_pred_new_additions/prokka_test.sh", argv[1], argv[2]);
system(command);
}`
What is the problem and how to solve this? I just wanted to execute my invoke.sh or invoke.out so that at the backend my Prokka command will be able to run correctly and gives me all expected output files.
I am using PHP built in server for testing and I was wondering is there a way you can hide cmd window when launching built in server using command php -S 127.0.0.1:809 -t Folder
I am currently working on Windows 10 so I need a Win solution.
not hundred percent sure on this, but you might try this one from:
What is cmd's equivalent to Bash's & (ampersand) for running a command without waiting for it to terminate?
so yours could be something like:
start /B php -S 127.0.0.1:809 -t Folder
You can create vbs script (run.vbs) and you can put this code in it
Dim oShell
Set oShell = WScript.CreateObject ("WSCript.shell")
oShell.run "cmd /C CD resource\php && php -S 127.0.0.1:809 -t HTML", 0
Set oShell = Nothing
0 in line signal for not displaying command line window.
I'm trying to set up a centralized server which is in charge of monitoring my other servers. This centralized server needs to be able to collect particular information/metrics about a specific server (such as df -h and service httpd status); but it also needs to be able to restart Apache if needed.
If it wasn't for the Apache restart, I could write a listening script to provide a means of giving the centralized server the data it needs without having to SSH in. But because I also want it to be able to restart Apache, it needs to be able to log in and initiate scripts through a combination of PHP and Bash.
At the moment, I'm using PHP's shell_exec to execute this (very simple) Bash script:
#!/bin/sh
ssh -i /path/to/keyFile.pem ec2-user#x.x.x.x;
I'm accessing the external server (which is an EC2 instance) through a private IP. If I launch this script, I can log in without any problem - the problem comes, however, when I then want to send back the output for commands like the ones I've listed above.
In a Bash script, how would I output a command like df -h after SSHing into another server? Is this possible?
There is a PECL extension for SSH.
Other than that you'll probably want to either use the &$output parameter of exec() to grab the output:
$output = array();
exec('bash myscript.sh', $output);
print_r($output);
Or use output redirection
$output = '/path/to/output.txt';
exec("bash myscript.sh > $output");
if( file_exists($output) && is_readable($output) ) {
$mydata = file_get_contents($output);
}
and, of coure, this all assumes your script looks like what jeroen has in his answer.
You could use:
ssh -i /path/to/keyFile.pem ec2-user#x.x.x.x 'df -h'
or for multiple commands:
ssh -i /path/to/keyFile.pem ec2-user#x.x.x.x 'ls -al ; df -h'
That works from the command line but I have not tried it via php's exec (nor on Amazon to be honest...).
If you're doing ssh I'd suggest phpseclib, a pure PHP SSH implementation. It's a ton more portable than the PECL SSH extension and more reliable too.
I'm trying to establish an interactive SSH connection to a remote server using PHP via the command line on Mac OS X 10.6. I'm currently using PHP's proc_open function to execute the following command:
ssh -t -t -p 22 user#server.com
This almost works. The -t -t options are supposed to force a pseudo terminal which they almost do. I am able to enter the SSH password and press enter. However, after pressing enter the terminal appears to simply hang. No output, no nothing - it's as if the SSH session has failed. I can't run commands or anything and have to kill the whole thing using Ctrl+C. I know the login is successful because I can execute a command like ssh -t -t -p 22 user#server.com "ls -la" and get the correct output.
I thought the problem must be related to the fact that I was using standard pipes in my proc_open call, so I replaced them with pty. I get the following error: "pty pseudo terminal not supported on this system..."
Does Mac OS X simply not support pty or pseudo terminals? (I'm pretty new at using all this shell terminology).
Here's the PHP code:
$descriptorspec = array(0 => array("pty"), 1 => array("pty"), 2 => array("pty"));
$cwd = getcwd();
$process = proc_open('ssh -t -t -p 22 user#server.com', $descriptorspec, $pipes, $cwd);
if (is_resource($process))
{
while (true)
{
echo(stream_get_contents($pipes[1]));
$status = proc_get_status($process);
if (! $status["running"])
break;
}
}
(Sorry - cannot for the life of me figure out SO's formatting instructions...)
What am I doing wrong? Why can't I use pty? Is this just impossible on Mac OS X? Thanks for your help!
You should use public key authentication rather than trying to programmatically bypass interactive password authentication.
The password prompt is supposed to be used from a tty and I believe it was made intentionally difficult to use otherwise. Also the -t -t argument only takes effect once you are connected to the remote host. And I don't believe the PHP function proc_open() can run a command inside a virtual terminal.
To setup public key authentication:
# Generate keypair
ssh-keygen -t rsa
# Copy public key to server
scp ~/.ssh/id_rsa.pub example.com:.ssh/authorized_keys
# Now you shouldn't be prompted for a password when connecting to example.com
# from this host and user account.
ssh example.com
# Since the web server (and thus PHP) probably has its own user account...
# Copy the ~/.ssh/id_rsa file somewhere else
cp ~/.ssh/id_rsa /some_path/id_rsa
# Change ownership of the file to the web server account
chown www-data:www-data /some_path/id_rsa
# Fix the file permissions (ssh ignore the keyfile if it is world readable)
chown 600 /some_path/id_rsa
# Try connecting to the server through the web server account
su -c "ssh -i /some_path/id_rsa -o UserKnownHostsFile=/some_path/known_hosts example.com" www-data
# Add the host to the known hosts file when prompted
Alternately, you could use plink (part of PuTTY for Linux) instead of OpenSSH as it can take the password on the command line plink -pw password example.com. But doing so presents a security risk as anyone who runs ps aux on the server can see the password in the process list.
There is also a program called sshpass that takes the password from an environment variable or command argument and passes it to ssh.
It looks like the problem is best solved using PHP's passthru() function. After alot more (rather painful) research I was able to issue a command through this function and could interact with the remote server through the terminal as if I had run ssh and svn export by hand (they both require passwords, therefore were good tests). What I'm going to have to do is construct a (potentially very long) string of commands separated by && and attach them to the end of the ssh command: ssh -t -t -p 22 hostname command1 && command2 ... The output will be sent to my terminal in Mac OS X even though the commands are being executed on the remote server. Looks like this is the solution I was looking for the whole time - pretty simple really! Thanks to everyone who helped me with this. I gave Alexandre the "green checkmark" because he was the only one who kept responding and was quite helpful in deducing the final answer to the problem. Thanks Alexandre!
This is old, but for any googlers out there, here is an actual solution using proc_open:
Pty descriptors are available in PHP, but have to be configured during compilation (see this 10yr old bug report https://bugs.php.net/bug.php?id=33147)
But in python however, we don't have that problem. So instead of running the ssh command directly, run this python script:
import sys
import pty
args = " ".join(sys.argv[1:])
pty.spawn(['/usr/bin/ssh', args])
About pty.spawn from python docs:
Spawn a process, and connect its controlling terminal with the current
process’s standard io. This is often used to baffle programs which
insist on reading from the controlling terminal.
Have you tried the PHP SSH2 extension?
Have you tried phpseclib, a pure PHP SSH implementation?:
<?php
include('Net/SSH2.php');
$ssh = new Net_SSH2('www.domain.tld');
if (!$ssh->login('username', 'password')) {
exit('Login Failed');
}
echo $ssh->read('username#username:~$');
$ssh->write("ls -la\n");
echo $ssh->read('username#username:~$');
?>
I wrote a ssh client on php with ssh2 extension, you can take a look to the source code on the github page https://github.com/roke22/PHP-SSH2-Web-Client
Please send some feedback.