I have a Python program where the initiation script looks like this:
if __name__ == "__main__":
main(sys.argv[1:])
To run this, I have to use Shell or Terminal like this:
myscript somefile.xml
The script accepts a file and then does all the rest of the work.
Now, I am trying to run this program on a web server.
SO I use a HTML Form to submit the file to this script.
In my Python script, I am doing like this:
....
elif req.form.has_key("filename"):
item=req.form["filename"]
if item.file:
req.write("I GO HERE")
myscript.main(item)
....
As you can see here, I am trying to send the file directly to the "main" function.
Is this the right way to do?
I dont get any script error, but the Python script is not producing the expected results.
Any help?
Thanks
Write the uploaded file contents to a temporary file (using tempfile.mkstemp()) and pass the filename of the temporary file into main() wrapped in a list.
For example (untested):
import os
import tempfile
fd, temp_filename = tempfile.mkstemp()
try:
with os.fdopen(fd, "wb") as f:
# Copy file data to temp file
while True:
chunk = item.file.read(100000)
if not chunk: break
f.write(chunk)
# Call script's main() function
myscript.main([temp_filename])
finally:
os.remove(temp_filename)
Related
def main():
print('writing multiple lines in a file through user input')
infile=open("xyz.txt", "w")
for line in iter(input, ''):
infile.write(line + '\n');
infile.close()
infile=open("xyz.txt", "r")
for line in infile:
print(line)
infile.close()'
if __name__ == "__main__":
main()
This is the main program and i have attached the output file as well which i want the output to be executed.output
You can execute a python file by invoking a python subprocess:
import subprocess
subprocess.call(['python3', 'xyz.txt'])
This will run python3 and execute the script in the "xyz.txt" file. This code has only been tested on Linux/Mac, so if you are on windows you may have to put the full path to python3 where it is installed - haven't tested, sorry.
Use the inbuilt os library
import os
os.system("python other_file.py")
This way you can use any commands from the os environment, so the possibilities are not limited to python.
But if you would like to read the output of the given script you subprocess instead
import subprocess
output = subprocess.check_output("python 2.py", shell=True)
print(output)
I have a big list of links to PDF files that I need to download (500+) and I was trying to make a program to download them all because I don't want to manually do them.
This is what I have and when I try to run it, the console just opens up and closes.
import wget
def main():
f = open("list.txt", "r")
f1 = f.readlines()
for x in f1:
wget.download(x, 'C:/Users/ALEXJ/OneDrive/Desktop/Books')
print("Downloaded" + x)
The problem is that you are defining the function main() but you are not calling it anywhere else.
Here is a complete example to achieve what you want:
import wget
def main():
books_folder = 'C:/Users/ALEXJ/OneDrive/Desktop/Books'
books_list = 'list.txt'
with open(books_list) as books:
for book in books:
wget.download(book.strip(), books_folder)
print('Downloaded', book)
if __name__ == '__main__':
main()
Make sure you add the function call at the end of your script, is good practice to use the if __name__ == '__main__': before the code of code you want to execute (although is not mandatory it will help so if you import this file into another your code will not get executed without your knowledge)
if __name__ == '__main__':
main()
I am trying to tail a log file on a remote server using a Python script. The log file rolls over very fast, I am using the python-sshtail module to tail the log file and capture the output of the tail in a file on my local machine. I was able to capture the log file and save it to a file on my local machine but the my script seems to be writing it twice and data is formatted.
The script is working but not the way I want it to, I should be able to run the script, perform some actions on the servers, tail the logs, save the output to a file on my local machine and kill the script using CTRL-C.
I did write some code and it does work but not the way it should. For now I am using time.sleep to wait for the output to be written to the output file on my local machine.
#!/usr/bin/python3
import time
import sshtail.tailers as t
import sys
import datetime
username = "username"
logfile = "/var/log/file.log"
k = t.paramiko.RSAKey.from_private_key_file('keyfile')
conn = t.SSHTailer(username,logfile, k, verbose=True)
try:
conn.connect()
print(f"Connected to {conn.host}")
print("Tailing the file..")
except:
print("Connection unsuccesful...")
conn.tail()
for line in conn.tail():
print(line)
for line in conn.get_new_lines():
print(line)
x = conn.remote_file_size
print(f"The file size is: {x}")
time.sleep(10)
output_file = str(conn.host)+"_"+str(datetime.datetime.now().strftime("%Y-%m-%d_%H:%M:%S"))+".txt"
with open(output_file, "a") as f:
for line in conn.get_new_lines():
print(line)
f.write(line)
conn.disconnect()
I recommend replacing time.sleep with asyncio.sleep
In my code, user uploads file which is saved on server and read using the server path. I'm trying to delete the file from that path after I'm done reading it. But it gives me following error instead:
An error occurred while reading file. [WinError 32] The process cannot access the file because it is being used by another process
I'm reading file using with, and I've tried f.close() and also f.closed but its the same error every time.
This is my code:
f = open(filePath)
with f:
line = f.readline().strip()
tempLst = line.split(fileSeparator)
if(len(lstHeader) != len(tempLst)):
headerErrorMsg = "invalid headers"
hjsonObj["Line No."] = 1
hjsonObj["Error Detail"] = headerErrorMsg
data['lstErrorData'].append(hjsonObj)
data["status"] = True
f.closed
return data
f.closed
after this code I call the remove function:
os.remove(filePath)
Edit: using with open(filePath) as f: and then trying to remove the file gives the same error.
Instead of:
f.closed
You need to say:
f.close()
closed is just a boolean property on the file object to indicate if the file is actually closed.
close() is method on the file object that actually closes the file.
Side note: attempting a file delete after closing a file handle is not 100% reliable. The file might still be getting scanned by the virus scanner or indexer. Or some other system hook is holding on to the file reference, etc... If the delete fails, wait a second and try again.
Use below code:
import os
os.startfile('your_file.py')
To delete after completion:
os.remove('your_file.py')
This
import os
path = 'path/to/file'
with open(path) as f:
for l in f:
print l,
os.remove(path)
should work, with statement will automatically close the file after the nested block of code
if it fails, File could be in use by some external factor. you can use Redo pattern.
while True:
try:
os.remove(path)
break
except:
time.sleep(1)
There is probably an application that is opening the file; check and close the application before executing your code:
os.remove(file_path)
Delete files that are not used by another application.
I am working on python and biopython right now. I have a file upload form and whatever file is uploaded suppose(abc.fasta) then i want to pass same name in execute (abc.fasta) function parameter and display function parameter (abc.aln). Right now i am changing file name manually, but i want to have it automatically.
Workflow goes like this.
----If submit is not true then display only header and form part
--- if submit is true then call execute() and get file name from form input
--- Then displaying result file name is same as executed file name but only change in extension
My raw code is here -- http://pastebin.com/FPUgZSSe
Any suggestions, changes and algorithm is appreciated
Thanks
You need to read the uploaded file out of the cgi.FieldStorage() and save it onto the server. Ususally a temp directory (/tmp on Linux) is used for this. You should remove these files after processing or on some schedule to clean up the drive.
def main():
import cgi
import cgitb; cgitb.enable()
f1 = cgi.FieldStorage()
if "dfile" in f1:
fileitem = f1["dfile"]
pathtoTmpFile = os.path.join("path/to/temp/directory", fileitem.filename)
fout = file(pathtoTmpFile, 'wb')
while 1:
chunk = fileitem.file.read(100000)
if not chunk: break
fout.write (chunk)
fout.close()
execute(pathtoTmpFile)
os.remove(pathtoTmpFile)
else:
header()
form()
This modified the execute to take the path to the newly saved file.
cline = ClustalwCommandline("clustalw", infile=pathToFile)
For the result file, you could also stream it back so the user gets a "Save as..." dialog. That might be a little more usable than displaying it in HTML.