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Executing python script with pdflatex using PHP on Ubuntu webserver?

I am trying to execute a python script which uses pdflatex using php. Running the python script via command line works well.
But if I try to call it with php, it throws this error:
I can't write on file mylatex.log'. (Press Enter to retry, or
Control-D to exit; default file extension is `.log') Please type
another transcript file name: ! Emergency stop ! ==> Fatal error
occurred, no output PDF file produced!
So there seems to be a permission error.
This is the way I am trying to call the php file:
$command = escapeshellcmd('python3 /home/ubuntu/test.py');
$output = shell_exec($command);
echo $output;
The mylatex.log file has 777 permission as a test.
Is there a way to execute a python script which uses a library like pdflatex?

I solved the error by adding the php file to the same directory as the python file. Then it works. There seems to be a problem to call pdflatex in a different directory. Thanks for the help.

Windows "No such file or directory"

I am trying to run a bash script from my Python code. I am calling the script in a subprocess like so:
preprocessed = subprocess.check_output([
'bash',
'../Paraphrase_Demo/models/processing_utils/preprocess_data_givenBPE.sh',
phrase, src_lang, tgt_lang, this_dir
])
Here is the script preprocess_data_givenBPE.sh:
#!/usr/bin/env bash
REMOTE_PATH=$4/processing_utils
SCRIPTS=$REMOTE_PATH/tiny-moses
TOKENIZER=$SCRIPTS/tokenizer.perl
DETOKENIZER=$SCRIPTS/detokenizer_v2.perl
CLEAN=$SCRIPTS/clean-corpus-n.perl
NORM_PUNC=$SCRIPTS/normalize-punctuation.perl
REM_NON_PRINT_CHAR=$SCRIPTS/remove-non-printing-char.perl
BPEROOT=$4/zhen/tools/subword-nmt/subword_nmt
text=$1
flan=$2
BPE=$4/$2$3/data/bpecodes
echo $text | perl $NORM_PUNC -l $flan | perl $REM_NON_PRINT_CHAR |
perl $TOKENIZER -a -l $flan -q | python3 $BPEROOT/apply_bpe.py -c $BPE | cat
When I run my Python program I get the following output:
Can't open perl script "C:/Users/Administrator/source/repos/Paraphrasing/Paraphrase_Demo/models/processing_utils/tiny-moses/normalize-punctuation.perl": No such file or directory
Can't open perl script "C:/Users/Administrator/source/repos/Paraphrasing/Paraphrase_Demo/models/processing_utils/tiny-moses/remove-non-printing-char.perl": No such file or directory
Can't open perl script "C:/Users/Administrator/source/repos/Paraphrasing/Paraphrase_Demo/models/processing_utils/tiny-moses/tokenizer.perl": No such file or directory
python3: can't open file 'C:/Users/Administrator/source/repos/Paraphrasing/Paraphrase_Demo/models/zhen/tools/subword-nmt/subword_nmt/apply_bpe.py': [Errno 2] No such file or directory
I have copy and pasted each of those paths into powershell and ls'd to verify that they are correct, but it still says it can't find them. What is going on here? This also happens if I run the bash script directly.
Edit: I've tried using backslashes in the path and received the same error. I also found this post: Bash: cannot execute a perl script using an absolute path?, so I tried using a relative path from the directory of my Bash script but it still says "No such file or directory."

After lots of debugging, I found the issue. While the paths I listed exist if I ls them in powershell, typing bash in powershell doesn't just open a bash shell, it actually changes the directory structure. I think this may be related to the Windows Subsystem for Linux, but the result is that C: changes to /mnt/c once inside the bash shell. Replacing this in all my paths, I was able to run my scripts.

Run a script using full path

I have a folder called TEST with inside :
script.py
script.sh
The bash file is :
#!/bin/bash
# Run the python script
python script.py
If I run the bash file like this :
./TEST/script.sh
I have the following error :
python: can't open file 'script.py': [Errno 2] No such file or directory
How could I do, to tell my script.sh to look in the directory (which may change) and to allow me to run it for inside the TEST directory ?
Tricky, my python file run a sqlite database and I have the same problem when calling the script from outside the folder, it didn't look inside the folder to find the database!

Alternative
You are able to run the script directly by adding this line to the top of your python file:
#!/usr/bin/env python
and then making the file executable:
$ chmod +x script.py
With this, you can run the script directly with ./TEST/script.py
What you asked for specifically
This works to get the path of the script, and then pass that to python.
#!/bin/sh
SCRIPTPATH="$( cd "$(dirname "$0")" ; pwd -P )"
python "$SCRIPTPATH/script.py"
Also potentially useful:
You mentioned having this problem with accessing a sqlite DB in the same folder, if you are running this from a script to solve this problem, it will not work. I imagine this question may be of use to you for that problem: How do I get the path of a the Python script I am running in?

You could use $0 which is the name of the currently executing program, as invoked, combined with dirname which provides the directory component of a file path, to determine the path (absolute or relative) that the shell script was invoked under. Then, you can apply it to the python invocation.
This example worked for me:
$ t/t.sh
Hello, world!
$ cat t/t.sh
#!/bin/bash
python "$(dirname $0)/t.py"
Take it a step farther and change your current working directory which will also be inherited by python, thus helping it to find its database:
$ t/t.sh; cat t/t.sh ; cat t/t.py ; cat t/message.txt
hello, world!
#!/bin/bash
cd "$(dirname $0)"
python t.py
with(open('message.txt')) as msgf:
print(msgf.read())
hello, world!

From the shell script, you can always find your current directory: Getting the source directory of a Bash script from within. While the accepted answer to this question provide a very comprehensive and robust solution, your relatively simple case only really needs something like
#!/bin/bash
dir="$(dirname "${BASH_SOURCE[0]}")"
# Run the python script
python "$(dir)"/script.py
Another way to do it would be to change the directory from which you run the script:
#!/bin/bash
dir="$(dirname "${BASH_SOURCE[0]}")"
# Run the python script
(cd "$dir"; python script.py)
The parentheses ((...)) around cd and python create a subprocess, so that the directory does not change for the rest of your bash script. This may not be necessary if you don't do anything else in the bash portion, but is still useful to have if you ever decide to say source your script instead of running it as a subprocess.
If you do not change the directory in bash, you can do it in Python using a combination of sys.argv\[0\], os.path.dirname and os.chdir:
import sys
import os
...
os.chdir(os.path.dirname(sys.argv[0]))

Run python from bash script that is run by another bash script

I currently have a folder structure that will contain a few python scripts which need to be fired from a certain folder but I would like to write a global script that runs each python script via a seperate script in each folder.
-Obtainer
--Persona
---Arthur
----start.sh
--Initialise.sh
-Persona
--Arthur
---lib
----pybot
-----pybot.py
When I run initialise I am aiming to make initialise run "start.sh" Arthur is the bot and there will be more folders with different names and initialise with find and fire each start.sh.
In initialise.sh I have:
#!/bin/bash
. ./Persona/Arthur/start.sh
In start.sh I have:
#!/bin/bash
python ../../../Persona/Arthur/lib/pybot/pybot.py
I get this error:
python: can't open file '../../../Persona/Arthur/lib/pybot/pybot.py': [Errno 2] No such file or directory
However if I run the start.sh itself from its directory it runs fine. This is because I assume it's running it from the proper shell and consequently directory. Is there a way to make the main script run the start.sh in it's own shell like it is being run by itself? The reason why is because the pybot.py saves a bunch of files to where the start script is and because there will be more than one bot I need them to save in each seperate folder.

In the first place, do not source when you mean calling it,
#!/bin/bash
. ./Persona/Arthur/start.sh
Don't do this.
Your script has a number of issue. It won't work because of your current working directory is uncertain. You'd better have your script derive the path to relieve yourself from the hustle of abs paths or relative paths.
The general code could be
script_dir=`dirname "${BASH_SOURCE[0]}"`
then you can use this to derive the path of your target file,
#!/bin/bash
script_dir=`dirname "${BASH_SOURCE[0]}"`
"$script_dir/Persona/Arthur/start.sh"
Your python invocation becomes:
#!/bin/bash
script_dir=`dirname "${BASH_SOURCE[0]}"`
python "$script_dir/../../../Persona/Arthur/lib/pybot/pybot.py"
This should work out properly.
Regarding BASH_SOURCE, check out https://www.gnu.org/software/bash/manual/html_node/Bash-Variables.html
If you want the directory of start.sh to be cwd, you should call cd:
#!/bin/bash
script_dir=`dirname "${BASH_SOURCE[0]}"`
cd "$script_dir"
python "$script_dir/../../../Persona/Arthur/lib/pybot/pybot.py"

executing a .sh file from python indicating an absolute path

im kinda new to the python world and im having some issues running a bash file that will be automatically from my python script (using linux) .
i set my python script to create both a text file .geo and a Bash file .sh in a directory somewhere in my Desktop like this :
basedirectory="/home/pst2/Desktop/";
*//Writing the .geo file*
file = open(basedirectory+nomdossier+"/"+nomfichier+".geo", 'w');
file.write
..blabla
..blabla
file.close();
//Writing the .sh file
file = open(basedirectory+nomdossier+"/"+nomfichier+".sh", 'w');
file.write
..blabla
..blabla
file.close();
Now at this point my script works perfectly with all the variables set up and working fine and both those files that i created find themselves in this directory (for exemple after running the python script and entering the variables)
/home/pst2/Desktop/test/
(and in here you will find the new test.geo and test.sh that were created via the python script)
basically the test.sh when executed "manually" with Bash test.sh ( whenever i am in its directory on ubuntu) will create another file called test.msh in the same directory
and i cant seem to find the right coding , using the subprocess modules to execute the newly created test.sh file automatically from the script .
is there a way to do so , like with indicating the absolute path to the .sh file
(in our case basedirectory+nomdossier+"/"+nomfichier+".sh ) ?

take a look at the os module.
I believe
os.system("command_line_with_args")
could be what your looking for

Not sure what you are writing into the .sh file.
But to start with:
Have you started your .sh-file with the hashbang? #!/bin/sh
Have you modded your file as executable? chmod +x
After you have done this, you should be able to use subprocess module and do something like the example from the manual for subprocess:
subprocess.call([path_to_script+'/script.sh'])
I might have to update this answer if & when new information comes to my attention

Roughly equivalent to "manually" executing bash test.sh with the current directory being the one where test.sh has been written by your posted code is:
from subprocess import call
call(['bash', 'test.sh'], cwd=basedirectory+nomdossier)