Showing results python command to the web cgi

Question

I have a python script and it runs well if executed in a terminal or command line , but after I try even internal server error occurred . how to enhance the script to be run on the web.

HTML

<html><body>
<form enctype="multipart/form-data" action="http://localhost/cgi-bin/coba5.py" method="post">
<p>File: <input type="file" name="file"></p>
<p><input type="submit" value="Upload"></p>
</form>
</body></html>

PYTHON

#!/usr/bin/python
import cgi, os
import cgitb; cgitb.enable()
import simplejson as json
import optparse
import sys

try: # Windows needs stdio set for binary mode.
    import msvcrt
    msvcrt.setmode (0, os.O_BINARY) # stdin  = 0
    msvcrt.setmode (1, os.O_BINARY) # stdout = 1
except ImportError:
    pass

form = cgi.FieldStorage()

# A nested FieldStorage instance holds the file
fileitem = form['file']
fn = os.path.basename(fileitem.filename)
data = open('/tmp/upload-cgi/' + fn, 'wb').write(fileitem.file.read())
data=fileitem.file.read()
location_database = open('/home/bioinformatics2/DW/taxo.json', 'r')
database = json.load(location_database)

for line in data: 
 for taxonomy in database:  
  if taxonomy["genus"] == line.replace('\n','') :
   print "Kingdom: %s," % taxonomy['kingdom'],
   print "phylum: %s," % taxonomy['phylum'],
   print "class: %s," % taxonomy['class'],
   print "order: %s," % taxonomy['order'],
   print "family: %s," % taxonomy['family'],
   print "genus: %s" % taxonomy['genus']
   break
 else:
  print ("No found genus on taxanomy")

J Earls · Accepted Answer · 2016-09-09 04:02:22Z

1

You're not outputting the HTTP header. At a minimum, you need to output:

print "Content-Type: text/plain"
print ""

You are also reading the file twice:

data = open('/tmp/upload-cgi/' + fn, 'wb').write(fileitem.file.read())
data=fileitem.file.read()

The second fileitem.file.read() will probably not read any content, since the file should already be at the end-of-file, and so data will be empty.

edited Sep 9, 2016 at 4:02

answered Sep 9, 2016 at 3:17

J Earls

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7 Comments

irwan dwiyanto Over a year ago

I tried to add print "Content-Type: text/plain" it above print "Kingdom: %s," % taxonomy['kingdom'], but still the same error

J Earls Over a year ago

You need both lines - the Content-Type line and the blank line.

J Earls Over a year ago

Please edit the question to include the output from running the script on the command line and, if you have access to it, the error output from the web server's error log

J Earls Over a year ago

output from running the script on the command line is blank white?

irwan dwiyanto Over a year ago

blank white results from the web , if from the command line work and generate an output value

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