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Python script called from PHP can't write a file

I have a problem with converting docx to pdf files in my script.
At first I tried to use a pure php-based solution, described here:
https://stackoverflow.com/a/20035739/12812601
Unfortunatelly this does not work (it creates an empty com object, then throws a fatal error).
So I've tried to use a python script to do this.
I use a great script from here:
https://stackoverflow.com/a/20035739/12812601
So here is a problem.
The Python script standalone (run via a command line) works just fine, and saves the converted pdf. Unfortunatelly when I try to call it via PHP it can't save a converted file.
PHP scripts can create and write files oin the same directory without any problem
This supposed to be a local configuration, so I do not care about any portability
Scripts:
*******PHP*******
<?php
//Script only for testing Python calls, tried different methods
error_reporting(E_ALL);
echo '<h1>Begin</h1>';
echo '<h2>Before call</h2>';
exec ('python dp.py');
echo '<h2>After exec call</h2>';
system('python dp.py');
echo '<h2>After Sys Call</h2>';
passthru('python dp.py');
echo '<h2>After Pass Call</h2>';
$w = get_current_user();
var_dump($w);
?>
*****Python*****
import sys
import os
import comtypes.client
import win32com.client
wdFormatPDF = 17
#static file names for testing
in_file = 'C:\\Users\\fake_user\\OneDrive\\Stuff\\f1.docx'
out_file = 'C:\\Users\\fake_user\\OneDrive\\Stuff\\f3.pdf'
print('BEGIN<br>\n')
word = win32com.client.Dispatch('Word.Application')
word.Visible = False
doc = word.Documents.Open(in_file)
print('\nOpened Docx\n<br>')
print(in_file);
doc.SaveAs(out_file, FileFormat=wdFormatPDF)
print('\nSaved\n<br>')
doc.Close()
word.Quit()
print('DONE\n')
*****Output from the browser*****
Begin
Before call
After exec call
BEGIN
Opened Docx
C:\Users\fake_user\OneDrive\Stuff\f1.docx
After Sys Call
BEGIN
Opened Docx
C:\Users\fake_user\OneDrive\Stuff\f1.docx
After Pass Call
string(5) "fake_user"
System configuration
Windows 7 Professional Edition Service Pack 1
Apache/2.4.26 (Win32)
OpenSSL/1.0.2l
PHP/7.1.7
Python 3.8.1
I tried to run Apache both as a system service and as a user who owns the OneDrive (name changed to "fake_user" here), so it shouldn't be a permissions issue (I think)
Any help appreciated

How to check If Path Exists Using Fabric2.x

I am using Fabric2 version and I don't see It has exist method in it to check if folder path has existed in the remote server. Please let me know how can I achieve this in Fabric 2 http://docs.fabfile.org/en/stable/.
I have seen a similar question Check If Path Exists Using Fabric, But this is for fabric 1.x version

You can execute the test command remotely with the -d option to test if the file exist and is a directory while passing the warn parameter to the run method so the execution doesn't stop in case of a non-zero exit status code. Then the value failed on the result will be True in case that the folder doesn't exist and False otherwise.
folder = '/path/to/folder'
if c.run('test -d {}'.format(folder), warn=True).failed:
# Folder doesn't exist
c.run('mkdir {}'.format(folder))

exists method from fabric.contrib.files was moved to patchwork.files with a small signature change, so you can use it like this:
from fabric2 import Connection
from patchwork.files import exists
conn = Connection('host')
if exists(conn, SOME_REMOTE_DIR):
do_something()

The below code is to check the existence of the file (-f), just change to '-d' to check the existence of a directory.
from fabric import Connection
c = Connection(host="host")
if c.run('test -f /opt/mydata/myfile', warn=True).failed:
do.thing()
You can find it in the Fabric 2 documentation below:
https://docs.fabfile.org/en/2.5/getting-started.html?highlight=failed#bringing-it-all-together

Hi That's not so difficult, you have to use traditional python code to check if a path already exists.
from pathlib import Path
from fabric import Connection as connection, task
import os
#task
def deploy(ctx):
parent_deploy_dir = '/var/www'
deploy_dir ='/var/www/my_folder'
host = 'REMOTE_HOST'
user = 'USER'
with connection(host=host, user=user) as c:
with c.cd(parent_deploy_dir):
if not os.path.isdir(Path(deploy_dir)):
c.run('mkdir -p ' + deploy_dir)

Jinja not imported when executing script from another one

I have a web server with CGI script calling python scripts.
When i try to execute in a main file (test1.py) another script called via
os.system('/var/www/cgi-bin/readIRtemp.py '+arg1+' '+arg2+' '+arg3)
I get his error message in /var/log/apache2/error.log :
import: not found
from: can't read /var/mail/jinja2
this is understandable for me since when called directly from the python console my script works !
its content is:
import sys, os
from jinja2 import Environment, FileSystemLoader, select_autoescape
last20values=sys.argv[1]
currTempInDegreesCelcius=sys.argv[2]
print('test '+last20values+' '+currTempInDegreesCelcius)
env = Environment(
loader=FileSystemLoader('/var/www/html/templates'),
autoescape=select_autoescape(['html', 'xml'])
)
template = env.get_template('IR.html')
updatedTemplate=template.render( arrayOfTemp = last20values, currTemp=currTempInDegreesCelcius)
Html_file=open("/var/www/html/IR.html","w")
Html_file.write(updatedTemplate)
Html_file.close()
I read somewhere something like maybe when calling os.system() the script is running with a different user account or some crazy things like that ... please help!
of course i chmod 777 * everything but that doesnt help ...

Activate Virtual Environment and Install Packages via Script

I often find myself recreating file structures for Flask apps so I have decided to make a script to do all that for me. I would like the script to create all the folders I need as well as the files with some basic boilerplate, which it does, that part is working fine. However I would also like to create a virtual environment and install Flask to that environment. That is where I am encountering the problem. The script runs but it installs Flask to my system installation of Python.
I followed the advice in this question here but it's not working. I am running Ubuntu 12.04.4 LTS via crouton on a Chromebook.
#!/usr/bin/python
from os import mkdir, chdir, getcwd, system
import sys
APP_NAME = sys.argv[1]
ROOT = getcwd()
PROJECT_ROOT = ROOT + '/' + APP_NAME
# dictionary represents folder structure. Key is the folder name and the value is it's contents
folders = {APP_NAME : {'app' : {'static': {'css' : '', 'img' : '', 'js' : ''}, 'templates' : ''} } }
def create_folders(dic):
for key in dic:
if isinstance(dic[key], dict):
mkdir(key)
prev = getcwd() + '/' + key
chdir(prev)
create_folders(dic[key])
else:
mkdir(key)
create_folders(folders)
chdir(PROJECT_ROOT)
open('config.py', 'a').close()
with open('run.py', 'a') as run:
run.write("""stuff""")
with open('app/__init__.py', 'a') as init:
init.write("""stuff""")
with open('app/views.py', 'a') as views:
views.write("""stuff""")
open('app/models.py', 'a').close()
open('app/forms.py', 'a').close()
with open('app/templates/layout.html', 'a') as layout:
layout.write("""stuff""")
system('chmod a+x run.py')
system('virtualenv venv')
system('. venv/bin/activate;sudo pip install flask') # this does not seem to be working the way I am expecting it to

I suppose your calls are not within the same console session and therefore the console environment is not as expected. I suggest to concatenate the related commands in one system call using subprocess.Popen like this (including suggestions by limasxgoesto0):
subprocess.Popen('virtualenv venv;source venv/bin/activate;pip install flask')
You should probably be using subprocess; os.system is deprecated.

How do you define the host for Fabric to push to GitHub?

Original Question
I've got some python scripts which have been using Amazon S3 to upload screenshots taken following Selenium tests within the script.
Now we're moving from S3 to use GitHub so I've found GitPython but can't see how you use it to actually commit to the local repo and push to the server.
My script builds a directory structure similar to \images\228M\View_Use_Case\1.png in the workspace and when uploading to S3 it was a simple process;
for root, dirs, files in os.walk(imagesPath):
for name in files:
filename = os.path.join(root, name)
k = bucket.new_key('{0}/{1}/{2}'.format(revisionNumber, images_process, name)) # returns a new key object
k.set_contents_from_filename(filename, policy='public-read') # opens local file buffers to key on S3
k.set_metadata('Content-Type', 'image/png')
Is there something similar for this or is there something as simple as a bash type git add images command in GitPython that I've completely missed?
Updated with Fabric
So I've installed Fabric on kracekumar's recommendation but I can't find docs on how to define the (GitHub) hosts.
My script is pretty simple to just try and get the upload to work;
from __future__ import with_statement
from fabric.api import *
from fabric.contrib.console import confirm
import os
def git_server():
env.hosts = ['github.com']
env.user = 'git'
env.passowrd = 'password'
def test():
process = 'View Employee'
os.chdir('\Work\BPTRTI\main\employer_toolkit')
with cd('\Work\BPTRTI\main\employer_toolkit'):
result = local('ant viewEmployee_git')
if result.failed and not confirm("Tests failed. Continue anyway?"):
abort("Aborting at user request.")
def deploy():
process = "View Employee"
os.chdir('\Documents and Settings\markw\GitTest')
with cd('\Documents and Settings\markw\GitTest'):
local('git add images')
local('git commit -m "Latest Selenium screenshots for %s"' % (process))
local('git push -u origin master')
def viewEmployee():
#test()
deploy()
It Works \o/ Hurrah.

You should look into Fabric. http://docs.fabfile.org/en/1.4.1/index.html. Automated server deployment tool. I have been using this quite some time, it works pretty fine.
Here is my one of the application which uses it, https://github.com/kracekumar/sachintweets/blob/master/fabfile.py

It looks like you can do this:
index = repo.index
index.add(['images'])
new_commit = index.commit("my commit message")
and then, assuming you have origin as the default remote:
origin = repo.remotes.origin
origin.push()