I need to run a python script from php

Question

I have to design a interface using PHP for a software written in python. Currently this software is used from command line by passing input, mostly the input is a text file. There are series of steps and for every step a python script is called. Every step takes a text file as input and an generates an output text file in the folder decided by the user. I am using system() of php but I can't see the output but when I use the same command from command line it generates the output. Example of command :
python /software/qiime-1.4.0-release/bin/check_id_map.py -m /home/qiime/sample/Fasting_Map.txt -o /home/qiime/sample/mapping_output -v

Answer 1

try this

$script = 'software/qiime-1.4.0-release/bin/check_id_map.py -m /home/qiime/sample/Fasting_Map.txt -o /home/qiime/sample/mapping_output -v';
$a = exec($script);

Answer 2

instead of system() try surrounding the code in `ticks`...

It has a similar functionality but behaves a little differently in the way it returns the output..

Answer 3

If you are not on windows, have you tried adding 2>&1 (redirect stderr to stdout) to the end of the command?

$output = system("python /software/qiime-1.4.0-release/bin/check_id_map.py -m /home/qiime/sample/Fasting_Map.txt -o /home/qiime/sample/mapping_output -v 2>&1", $exitcode);

Found from http://www.php.net/manual/en/function.system.php#108713

Also the doc says that it

Returns the last line of the command output on success, and FALSE on failure.

So if you are trying to get multiple lines, you may need to redirect it to a file and read that in.