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Restrict the Python file to read and write

I'm trying to restrict write and read access to a Python file. Suppose I have the following code:
with open('test.py', 'w+') as file:
file.write('''
open("document.txt", "w+").write("Hello, World!")
open("document.txt", "r+").read()
''')
By executing this code, a new file is created that in the new file there are two lines of code to write and read a another file.
I want the file created by executing this code (test.py) to hit PermissionError while running and not be able to create a new file or read it; Also, this file is only executable and normal commands work in it, but it can not access other files.

If I read you correctly, this is not a python problem, but an environment problem. I understand the question as something like 'how do I prevent python code from executing arbitrary reads or writes?'. There would be a trivial solution (modifying the generated test.py so it throws an error) but presumably that's not what you want.
The easiest way to make python hit a PermissionError... is to make sure it doesn't have permissions. So run your code as a user with extremely limited permissions---specifically no write permissions anywhere---or perhaps no default permissions at all, and use something like facls to grant permission to read specific files explicitly from a more priveleged sentinel process. (This assumes you are running Linux, but there are likely other ways to do this in different OSs).
Alternatively, look into various sandboxing techniques to give you a python interpreter with the relavent modules replaced with modules which throw errors, or an environment where outside modification is impossible.
It would help if you made it clearer why this is important, and why you are writing a python script with another python script (is this just an example of malicious action?).

You could technically change the permission of the file itself on the filesystem your trying to access.
Check the previous thread about changing permissions
os.chmod(path, <permission value>)
Where 000 is to disable anyone other than root to edit on linux.

Code inside of a python file deleted

The code inside of a python file randomly deleted, is there anyway to restore? It is a file of 3.70 KB but when opened and put into a text document there is nothing.

Open with python to see what it contains
with open('deleted.py', 'rb') as f:
print(repr(f.read()))

Since you are a new user I am assuming you are new to code development etc. Therefore, you should look at some versioning control tools like:
SVN
Github
Gitlab
There are some more, but these are the most common ones. They are used to store your code and to revert you code if you mess up. They are also used to merge codes when different programmers are changing it. For the moment this will not help but will help in the future.
For now you may look at some restore tools but I highly doubt it that you are able to recreate the file. Another possiblity is: when you haven IDE to look at your command history. Maybe you executed the script and you can find the executed script as commands in the command history.

How the OS handles python and subprocesses of a python script...?

My question is somewhat unique. I am currently working on a project for my computer forensics class. This project is aimed at hiding disk data from investigators. The method by which this is supposed to be achieved is by writing the bytes of a "clean" file over the "bad" file. Once overwritten, the "bad" file is deleted.
This concept sounds simple enough, but what my partner and I have observed is interesting. If we open a file in a python script, we can easily overwrite the memory associated with that file on disk (verified using dd). We can also easily delete a file using from inside the script. However, a write then delete results in no write actually taking place, only the file's removal.
This makes sense from an OS optimization standpoint. From that point, we thought it might work if we split the writing and deleting into two separate scripts, and controlled both by a third. However, it seems that even if we run the scripts as a subprocess of another script, the same thing happens. We've tried to use bash scripts for the deletion process instead of pure python, and still, nothing sticks.
This project was supposed to be a whole mess of little anti-forensics tools like this, but this particular one has captured our whole attention because of this issue. Does anyone have an idea as to why this is happening and what we can do to move forward?
We know this can be achieved in C, etc, but we want to solve this using python because of the interesting constraints it's presented.
---EDIT---
This is a snippet from our controller, it calls "ghost.py" with the associated params.
ghost.py prints the edited file names/paths to stdout.
Relevant code follows:
proc = subprocess.Popen(['python', 'ghost.py', '-c', 'good.txt', '-d','/mnt/evil.txt'], stdout=subprocess.PIPE,)
files = proc.communicate()
for i in files:
if i != None and i != "\n":
os.system("./del.sh " + i)

Using a subprocess doesn't change any interesting aspect of your design, so don't use them. You probably need os.fsync(). Try this pattern:
myfile.write('all of my good data')
myfile.flush()
os.fsync(myfile.fileno())
myfile.close()
os.remove(myfile)
Reference: https://docs.python.org/2/library/os.html#os.fsync

How to Make a Python Program Recogize first-time use

Everyone!
I'm trying to make a Python 3.3 program recognize that it is the first time the user has used the program. I'm not sure how to proceed or if it's possible.

you need to
Write something somewhere
a> Create A File somewhere
b> write a registry key
c> register use with some website
or probably any other number of ways to do it

I just created a file in the program directory, and used os.path.exists to make Python recognize the user's first time use.

You could keep a text file containing a list of all the users that have used the program and then compare against it during the execution of the program.

You could create a file in running directory containing a firststartup flag, i used that for a java program, havent used python much.
psuedocode: maybe this will help you find the answer.
check if file exists
if file does exist assume it is not first time, else, if file does not exist create the file and asume that it is indeed first startup.
rest of program.

As bad as sounds, you should probably use a file, like the others are saying. It sounds bad because I am guessing you don't want to write files you don't have to, but in all honesty, it will work out well.
one way you could do it, is have a 'firstuse.txt' in the directory when the user starts it, and when it runs, it deletes that file. That way you can keep things a little cleaner.

Reading a windows file without preventing another process from writing to it

I have a file that I want to read. The file may at any time be overwritten by another process. I do not want to block that writing. I am prepared to manage corruption to the data that I read, but do not want my reading to be in any way change the behaviour of the writing process.
The process that is writing the file is a delphi program running locally on the server. It opens the file using fmCreate. fmCreate tries to open the file exclusively and fails if there are any other handles on the file.
I am reading the file from a python script that accesses the file remotely across our network.
I am interested in whether there is a solution, independent of whether it is supported by python or delphi. I want to know if there is any way of achieving this under windows without modifying the writing program.
Edit: To reiterate, this is not a duplicate. The other question was trying to get read access to a file that is being written to. I want to the writer to have access to a file that I have open for reading. These are different questions (although I fear the answer will be similar, that it can't be done.)

I think the real answer here, all of these years later, is to use opportunistic locks. With this, you can open the file for read access, while telling the OS that you want to be notified if another program wants to access the file. Basically, you can use the file as long as you like, and then back off if someone else needs it. This avoids the sharing/access violation that the other program would normally get, if you had just opened the file "normally".
There is an MSDN article on Opportunistic Locks. Raymond Chen also has a blog article about this, complete with sample code: Using opportunistic locks to get out of the way if somebody wants the file
The key is calling the DeviceIoControl function, with the FSCTL_REQUEST_OPLOCK flag, and passing it the handle to an event that you previously created by calling CreateEvent.
It should be straightforward to use this from Delphi, since it supports calling Windows API functions. I am not so sure about Python. But, given the arrangement in the question, it should not be necessary to modify the Python code. Just make your Delphi code use the opportunistic lock when it opens the file, and let it get out of the way when the Python script needs the file.
Also much easier and lighter weight than a filter driver or the Volume Shadow Copy service.

You can setup a filter driver which can act in two ways: (1) modify the flags when the file is opened, and (2) it can capture the data when it's written to the file and save a copy of the data elsewhere.
This approach is much more lightweight and efficient than volume shadow copy service, mentioned in comments, however it requires having a filter driver. There exist several drivers on the market (i.e. those are products which include a driver and let you write business logic in user mode) yet they are costly and can be an overkill in your case. Still, if you need the thing for private use only, contact me privately for a license for our CallbackFilter.
Update: if you want to let the writer open the file which has been already opened, then a filter which will modify flags when the file is being opened is your only option.