Using exec() to run python script in PHP

Question

I want the user to upload a file and then a php file checks if it is valid or not. My problem is in running the script_template.py , i used the function exec() to run in command line but it does not return something and i don't understand why. Thanks in advance. I am using xampp.

index.html

<form id="upload" method="post" action="upload.php" enctype="multipart/form-data">
 <div id="drop">
 Drop Here
 <a>Browse</a>
 <input type="file" name="upl" multiple />
 </div>
 <input type="submit" value="Upload Image" name="submit">
 </form>

php file

$allowed = array('png', 'jpg', 'gif','txt','xlsx','xls');
if(isset($_FILES['upl']) && $_FILES['upl']['error'] == 0){
 $extension = pathinfo($_FILES['upl']['name'], PATHINFO_EXTENSION);
 if(!in_array(strtolower($extension), $allowed)){
 echo '{"status":"error"}';
 echo ' <p>The uploaded file extension is incorrect, please try again with the correct file </p>'; 
 exit;
 }
 $x=file_validation ( $_FILES['upl']['tmp_name'] ) ;
echo $x;
 if(move_uploaded_file($_FILES['upl']['tmp_name'], 'uploads/'.$_FILES['upl']['name'])){
 echo '{"status":"success"}';
 exit;
 }
}
echo '{"status":"error"}';
echo 'erro';
exit;
function file_validation($fich) {
 $validation= exec('python script_template.py '.$fich) ;
 echo $validation ;
 }

python file

#!C:\Python27\python.exe
print "Content-Type: text/html\n"
import sys
fich_input= sys.argv[1] 
print fich_input
def header(fich):
 """
 Extracts the header and it's values from tab separated file
 Requires: fich is tab separated file
 Ensures: dic and aux are dictionaries, where aux associates each header to it's order
 and dic associates each header value to the order number.
 """
 input_fil=open(fich,'r')
 contador_linha=0
 lines =input_fil.readlines()
 dic={}
 aux={}
 for line in lines:
 contador_linha+=1
 line_words=line.split('\t')
 if contador_linha==1: #header
 aux_counter=1
 header_len=len(line_words)
 for elem in line_words:
 if elem != '\n':
 aux[aux_counter]=elem
 aux_counter+=1
 elif contador_linha==2:#create values for keys in header
 aux_counter=1
 for elem2 in line_words:
 if elem2 != '\n':
 dic[aux_counter]=[elem2]
 aux_counter+=1
 return (aux,dic)
def header_value(dic1,dic2):
 """
 joins header and it's value
 Requires: dic1 is aux from header(fich) and dic2 is dic from header(fich)
 Ensures: final_dic is a dictionary which associates eache header to value
 """
 final_dic={}
 header_len=len(dic1.keys())
 for number in range(1,header_len+1):
 final_dic[dic1[number]]=dic2[number]
 return final_dic
def mol_name(final_dic):
 """
 Finds molecule name for just labelling
 Requires: final_dic is a dictionary returned by header_value
 Ensures: string representing molecule name
 """
 return final_dic['Mol_name'] 
def print_info(final_dic):
 """
 prints in the screen all information contained in the file given by researcher
 Requires: final_dic from header_value
 Ensures: information in the screen
 """
 print str(mol_name(final_dic))
 for key in final_dic:
 print key,':',final_dic[key]
 print '\n'
def general_operation(fich):
 """
 Gathers information required to start database operations and if not give an error
 Requires: fich is a Tab separated file, dic12 is 
 Ensures: Crucial information to database operations
 """
 dics=header(fich)
 header_values= header_value(dics[0],dics[1])
 type_file=''
 if len(header_values) < 21 :
 type_file='no_ref'
 else:
 type_file='ref'
 return (type_file,header_values)
print 'yes'
print general_operation(fich_input) 

The python script is running just fine, php simply ignores it.

• dylrei: All your Python script does is print to console. I wouldn't expect that to return anything to the PHP script calling it. Perhaps you wanted to write to standard output?
• João Pedro: I tried return general_operation(fich_input) in the end and still does not send anything. I wrote print instead of return to see if anything comes up in the scene but it does not.

Answer 1

(I'm assuming you're using Windows.)

I think you need to call Python differently. If you run

python http://localhost/bioinformatica/processa_tsv/AJAX_upload/script_template.py

from the command line on your computer, does it work? I'm guessing not, because the first argument to python should be the name of a Python file on the local drive.

Try running something like python C:\path\to\script.py to test the command line you'll put in exec().

• João Pedro: $validation= exec('python script_template.py '.$fich) (note: script_template.py is in the same directory of php file)
• Bram Geron: Can you try it from the command prompt? You can open the command prompt using Windows+R, type "cmd", press enter. If it works in the command line, it should work in PHP's exec.
• Bram Geron: If you call var_dump on the result of exec, what does it show?
• Bram Geron: That might be the correct answer; recall that exec returns the last line of the program output. You can use system to output all program output, or use exec in a more complicated way to put all output in a string. See php.net/manual/en/function.exec.php.
• Bram Geron: You need to be more specific than "does not work". What do you see? What is the result?

Answer 2

Solved it, just by editing this part of the code to:

function file_validation($fich) {
 $validation=""
 exec('python script_template.py '.$fich,$validation) ;
 return $validation ;
 }