I have the following code:
import subprocess
convertargs = ['convert', 'image1.tif', 'img2.tif', 'pdf:-']
print "Content-type: application/pdf\r\n\r\n"
pdf = subprocess.Popen(convertargs, stdout=subprocess.PIPE)
pdf, error = pdf.communicate()
print pdf
It's supposed to take convertargs, use imagemagick's convert to convert the images into a pdf.
I know this works because when I run the following at the shell:
./pdf.py > test.pdf
it creates for me a neat little PDF with the correct images. It does not, however, work when I go to www.myhost.com/pdf.py. And I cannot figure out why.
Here's what my apache error log says:
Traceback (most recent call last):: /Library/WebServer/Documents/pdf.py
File "/Library/WebServer/Documents/pdf.py", line 59, in <module>: /Library/WebServer/Documents/pdf.py
pdf = subprocess.Popen(convertargs, stdout=subprocess.PIPE): /Library/WebServer/Documents/pdf.py
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 710, in __init__: /Library/WebServer/Documents/pdf.py
errread, errwrite): /Library/WebServer/Documents/pdf.py
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1335, in _execute_child: /Library/WebServer/Documents/pdf.py
raise child_exception: /Library/WebServer/Documents/pdf.py
OSError: [Errno 2] No such file or directory: /Library/WebServer/Documents/pdf.py
subprocess.Popen can't find convert, probably because the webserver uses a different $PATH. Try feeding it the full path to convert instead of just convert.
Related
Traceback (most recent call last):
File "C:\Users\Balmeet\PycharmProjects\text&checkBox\venv\lib\site-packages\pdf2image\pdf2image.py", line 441, in pdfinfo_from_path
proc = Popen(command, env=env, stdout=PIPE, stderr=PIPE)
File "C:\Users\Balmeet\AppData\Local\Programs\Python\Python37\lib\subprocess.py", line 756, in __init__
restore_signals, start_new_session)
File "C:\Users\Balmeet\AppData\Local\Programs\Python\Python37\lib\subprocess.py", line 1155, in _execute_child
startupinfo)
FileNotFoundError: [WinError 2] The system cannot find the file specified
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:/Users/Balmeet/PycharmProjects/tables/final.py", line 470, in <module>
pdf2img2.convert_to_image(pdf_file)
File "C:\Users\Balmeet\PycharmProjects\tables\pdf2img2.py", line 42, in convert_to_image
pages = convert_from_path(pdf_file, 600)
File "C:\Users\Balmeet\PycharmProjects\text&checkBox\venv\lib\site-packages\pdf2image\pdf2image.py", line 97, in convert_from_path
page_count = pdfinfo_from_path(pdf_path, userpw, poppler_path=poppler_path)["Pages"]
File "C:\Users\Balmeet\PycharmProjects\text&checkBox\venv\lib\site-packages\pdf2image\pdf2image.py", line 468, in pdfinfo_from_path
"Unable to get page count. Is poppler installed and in PATH?"
pdf2image.exceptions.PDFInfoNotInstalledError: Unable to get page count. Is poppler installed and in PATH?
I have followed steps mentioned in the similar post and set path for poppler but still getting this error
thanks in advance:)
Download Poppler and save it in your folder where u have scripts and try executing with below.
from pdf2image import convert_from_path
pages = convert_from_path(f'dummy.pdf', poppler_path='poppler-20.12.1\\bin')
for page in pages:
n = 1
page.save(f'page{n}.png', 'PNG')
n += 1
I have tested this and I got the pdf file converted to image.
adding this to code working for me, please download poppler from here and extract https://blog.alivate.com.au/poppler-windows/
pages = convert_from_path('document1.pdf', poppler_path='C:/Users/poppler-0.68.0/bin')
I'm running the next piece of code to check the type of my file:
import subprocess as sub
output = sub.check_output(["file", "test.py"]).decode('ascii')
#output=sub.check_output(["file","C:/Users/Roger.That/PycharmProjects/test/test.py"]).decode('ascii')
and I keep getting the following error:
Traceback (most recent call last):
File "C:/Users/Roger That/PycharmProjects/test/test.py", line 2, in <module>
output = sub.check_output(["file", "test.py"]).decode('ascii')
File "C:\Users\Roger That\AppData\Local\Programs\Python\Python37-32\lib\subprocess.py", line 395, in check_output
**kwargs).stdout
File "C:\Users\Roger That\AppData\Local\Programs\Python\Python37-32\lib\subprocess.py", line 472, in run
with Popen(*popenargs, **kwargs) as process:
File "C:\Users\Roger That\AppData\Local\Programs\Python\Python37-32\lib\subprocess.py", line 775, in __init__
restore_signals, start_new_session)
File "C:\Users\Roger That\AppData\Local\Programs\Python\Python37-32\lib\subprocess.py", line 1178, in _execute_child
startupinfo)
FileNotFoundError: [WinError 2] The system cannot find the file specified
The full path of my test.py : "C:/Users/Roger.That/PycharmProjects/test/test.py"
output from gitbash :
$ file /c/Users/Roger\ That/PycharmProjects/test/test.py
/c/Users/Roger That/PycharmProjects/test/test.py: ASCII text, with CRLF line terminators
Any chance that it is related to the fact that I have a dot between "Roger" and "That"? Although it doesn't work also when I use the relative path (only the file name)
Update
I changed my user's dir name from Roger that to Roger.that, but it still didn't help:
python /c/Users/Roger.That/PycharmProjects/test/test.py
same error..
checked also :
import subprocess as sub
output = sub.check_output(["ls" "-l"])
got same error
I created from scratch the virtual environment and it solved my problem.
In My Flask App, i want to upload a file to a remote server.
i tried this code but i get an error
import subprocess
import os
c_dir = os.path.dirname(os.path.abspath(__file__))
myfile = open(c_dir + '\\cape-kid.png')
p = subprocess.Popen(["scp", myfile, destination])
sts = os.waitpid(p.pid, 0)
this was just a test file. there's an image in the same directory as my test python file. the error said:
Traceback (most recent call last): File
"C:\Users\waite-ryan-m\Desktop\remote-saving\test-send.py", line 20,
in
p = subprocess.Popen(["scp", c_dir + '\cape-kid.png', 'destination']) File
"C:\Users\waite-ryan-m\Desktop\WPython\WinPython-64bit-2.7.12.1Zero\python-2.7.12.amd64\lib\subprocess.py",
line 711, in init
errread, errwrite) File "C:\Users\waite-ryan-m\Desktop\WPython\WinPython-64bit-2.7.12.1Zero\python-2.7.12.amd64\lib\subprocess.py",
line 959, in _execute_child
startupinfo) WindowsError: [Error 2] The system cannot find the file specified
With open() you open an file to read or write on it. What you want is to concatinate the string and use this as parameter for scp. Maybe the file you want to copy also doesn't exist - have you tried printing the path you constructed and checking it manually?
And have you defined destination anywhere? This message could also mean, that the system cannot find scp.
I want to use MafftCommandline to align my data, but i get following error:
Traceback (most recent call last):
File "C:\Users\Rimvis\Desktop\asd\bioinformatika2_Working.py", line 35, in <mo
dule>
stdout, stderr = mafftCline() # Note that MAFFT will write the alignment to
stdout, which you may want to save to a file and then parse
File "C:\Python27\lib\site-packages\Bio\Application\__init__.py", line 475, in
__call__
shell=(sys.platform!="win32"))
File "C:\Python27\lib\subprocess.py", line 679, in __init__
errread, errwrite)
File "C:\Python27\lib\subprocess.py", line 896, in _execute_child
startupinfo)
WindowsError: [Error 2] The system cannot find the file specified
my code is as following :
dataToProcess = "dataToProcess.fa"
file = open(dataToProcess, "w")
arrayOfSequences = []
for sequence in blast.alignments:
if sequence.length > blast.alignments[0].length * 80 / 100:
sequenceToAppend = SeqRecord(Seq(sequence.hsps[0].sbjct), id=sequence.title)
arrayOfSequences.append(sequenceToAppend)
SeqIO.write(arrayOfSequences, file, "fasta")
file.close()
maffPath = "..\mafft-win\mafft.bat"
mafftCline = MafftCommandline(maffPath, input=dataToProcess)
stdout, stderr = mafftCline() # Note that MAFFT will write the alignment to stdout, which you may want to save to a file and then parse
alignedData = "aligned.fa"
alignedFile = open(alignedData, "w")
alignedFile.write(stdout)
alignedFile.close()
aligned = AlignIO.read(alignedData, "fasta")
i was using this tutorial as an example
As #willOEM has said, the script is looking for a file in a relative directory.
Your script assumes that its file is located in the same directory as your "dataToProcess" fasta file.
If you have moved your script or are trying to open a file located elsewhere then it will raise this error.
You'll need to change your dataToProcess, maffPath and alignedFile to refer to the absolute path.
The problem was that i needed to escape slashes.
And use maffPath = "..\\mafft-win\\mafft.bat" instead of maffPath = "..\mafft-win\mafft.bat"
I have the following (simplified) code:
with NamedTemporaryFile() as f:
f.write(zip_data)
f.flush()
subprocess.call("/usr/bin/7z x %s" % f.name)
It dies with the following error:
Traceback (most recent call last):
File "decrypt_resource.py", line 70, in <module>
unpack(sys.argv[2])
File "decrypt_resource.py", line 28, in unpack
print(subprocess.check_output(cmd))
File "/usr/lib/python2.7/subprocess.py", line 568, in check_output
process = Popen(stdout=PIPE, *popenargs, **kwargs)
File "/usr/lib/python2.7/subprocess.py", line 711, in __init__
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1308, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
However, if I use NamedTemporaryFile(delete=False) and then print & execute the command, it works. What's wrong here?
My System is an ArchLinux with a 3.9.5-1-ARCH kernel.
You are using subprocess.call() incorrectly.
Pass in a list of arguments:
subprocess.call(["/usr/bin/7z", "x", f.name])
The argument is not handled by a shell and is not parsed out like a shell would do. This is a good thing as it prevents a security problem with untrusted command line arguments.
Your other options include using shlex.split() to do the whitespace splitting for you, or, as a last resort, telling subprocess to use a shell for your command with the shell=True flag. See the big warning on the subprocess documentation about enabling the shell.