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Strange behavior when trying to create and write to a text file on macOS [duplicate]

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Convert UTF-8 with BOM to UTF-8 with no BOM in Python
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I'm opening a plain text file, parsing it, and adding different lines to existing, empty string variables. I add these variables into a new variable that is a multi-line fstring. Trying to write the data to a new text file is not behaving as expected.
Reading the original file works fine. Text is properly parsed, variables populated.
The multi-line fstring variable seems fine. Prints normally. Even tried formatting it different ways which I show below.
When writing to a new file, that's where the strangeness starts. I've tried 2 ways:
Straight coding the open function with w or w+
Adding the above to a function and using that inside main()
The file is saved to disk with the correct name. Trying to double-click open in Finder produces nothing. Right-click to open produces nothing. Trying to move to trash with command+delete gives an error:
It sounds like the file goes to trash, but as the file disappears from the folder a new one is created with the same name in its place.
If I try to open in TextMate via File > Open, it opens as a blank file with no errors.
Since I can't get rid of the file, I have to delete the directory and create the directory again with the same name, or force delete in Terminal using rm. Restarting the system does not help. Relaunching Finder does nothing. Saving text files from other apps works fine. Directory is chmod 755.
If I copy an existing text file into the output directory, rename it to what the file is expected to be named, and let python overwrite the contents, it doesn't work either. The file modification date changes (and I see the file "blink" in Finder) but the contents remain the same. However, the file is not corrupted and opens normally.
If I do the same but delete the text inside of the copied file first, then run the script, python writes no data to the file, I can't open it by double-clicking on it, and I get error -43 again with the odd non-trashing behavior.
The strangest thing is this: if I add another with open() at the end of the script, and open the file that was just created and supposedly written to, and print its contents, the contents print. It's like when the script ends the file contents are being removed or its being corrupted somehow. Tried to close the file inside the script even though it's not needed, but same behavior persists.
Code:
Here's the code for writing:
FORMAT='utf-8'
OUTPUT_DIR = '/Path/To/SaveFolder'
# as a function
def write_to_file(content, fpath, name):
the_file = os.path.join(fpath, name)
with open(the_file, 'w+', encoding=FORMAT) as t:
t.write(content)
def main():
print(f" Writing File...\n")
filename = f"{pcode}_{author}_{title}_text.txt"
write_to_file(multiline_var, OUTPUT_DIR, filename)
# or hard coded in main()
def main():
print(f" Writing File...\n")
filename = f"{pcode}_{author}_{title}_text.txt"
the_file = os.path.join(OUTPUT_DIR, filename)
with open(the_file, 'w+', encoding=FORMAT) as t:
t.write(multiline_var)
I have tried using w w+ wt and wt+ and with and without encoding='utf-8'
Here is an example of multi-line fstring variable:
# using triple quotes
multiline_var = f"""
[PROJ-{pcode}] {full_title} by {author}
{description}
{URL}
{DIVIDER_1}
{TEXT_BLURB}
Some text here and then {SOME_MORE_TEXT}"
{DIVIDER_1}
{SOME_LINK}
"""
# or inside parens
multiline_var = (
f"[PROJ-{pcode}] {full_title} by {author}\n"
f"{description}\n\n"
f"{URL}\n"
f"{DIVIDER_1}\n"
f"{TEXT_BLURB}\n\n"
f"Some text here and then {SOME_MORE_TEXT}\n"
f"{DIVIDER_1}\n\n"
f"{SOME_LINK}"
)
Using exiftool on the text file shows the following, so it looks the data is there but must be corrupted:
File Size : 1797 bytes
File Modification Date/Time : 2021:12:31 15:55:39-05:00
File Access Date/Time : 2021:12:31 15:58:13-05:00
File Inode Change Date/Time : 2021:12:31 15:55:39-05:00
File Permissions : -rw-r--r--
File Type : TXT
File Type Extension : txt
MIME Type : text/plain
MIME Encoding : utf-8
Byte Order Mark : No
Newlines : Unix LF
Line Count : 55
Word Count : 181
Not sure what I'm doing wrong. VScode shows no syntax errors in the script. There are no errors in Terminal when running the script. Have I made some simple mistake in the above code? Maybe the fstring variable is causing a problem?

Thanks to #bnaecker for leading me to the solution to this problem.
It appeared that when creating/writing to a text file with a long name, Python can corrupt it. Not sure why, as I save long names for images with Python image libraries all the time. Using a short name like "MyFile.txt" it worked just fine, but that was a red herring.
I have updated this post with my journey to the final solution for using the long names that are needed for my project, though I'm not sure why the problem exists.
First Attempts:
So far creating using a short name and then renaming to a long one.... attempts have failed. I did notice that python is locking the file it creates and never unlocks it. Not sure if this is the problem. Setting chflags with os.system('chflags nouchg') command does not work, not even with sudo, and not even in the Terminal doing it manually.
Using os.rename() in Python corrupts the file
Using os.system('mv oldFile.txt newFile.txt') corrupts the file
Manually using mv command in Terminal corrupts the file
Manually changing the filename in the Finder does not (wtf?)
I kept looking for workarounds but nothing did the job.
Round 2:
Progress!
After much tinkering, I discovered a hidden character inside the file. I ran cat /path/longfilename.txt in Terminal, selected and copied the output and pasted into VScode. Here is what I saw:
Somehow a hidden character is getting into the project code number.
Pasting it into a Unicode search engine it came up as a ZERO WIDTH NO-BREAK SPACE also known in Unicode as EF BB BF. However, when pasting this symbol into TextMate it shows up as <U+FEFF> which is?...
The Byte Order Mark!
Opening a normal utf-8 text file in a hex editor also shows the files starting with EFBBBF for the BOM.
Now, the text file being read and parsed at first has no blank lines to start the file, so I added a line break, and also tried adding some spaces. This time when writing the file I could open it, however, after sending it to the trash, the same behavior occurred and the file was broken again. It seems that because other corrupted versions were in the trash, it added the symbol back to the file name for some reason.
So what appears to be happening, for whatever reason, when Python opens the text file I'm parsing that has no line break at the top, it seems to be grabbing the BOM from the file and adding that to the first variable which is grabbing the first line of the text file. Since that text is a number code that starts the file name, the BOM symbol is being added to the file name as well as the code inside the text file.
Just... wow
The Current Solution:
I have to leave a blank line at the start of the text file that I'm opening and parsing and a simple line break won't do it. I have no idea why this is. I added some spaces for good measure because randomly the BOM would be added to the variable and filename again. So far (knock on wood) as long as the first line of that initial file has some spaces and then a line break, and previous corrupted files have been deleted from the trash, a long file name can be used for all the files I'm creating and writing to without any problems.
This corruption even persists if I remove the encoding flag from both of the open functions I'm using (one to read and parse, the other to create and write).
If anyone knows why this is happening, please share. I've never seen it mentioned before. I'm not sure if it's a python 3.8 bug, a mac OS bug, the way TextMate wrote the original file, or a combination of these.
Correct Solution:
Thanks to #tripleee for the proper way to handle this, as I don't remember seeing this before, though I haven't been using python for very long.
In order to ignore the BOM, reading in the text file to be parsed with an encoding='utf-8-sig' does the job. Seems to be why it exists. :)
Problem solved.

How to detect a file has been truncated while reading

I'm reading lines from a group of files (log files) following them as they are written using pyinotify.
I'm opening and reading the files with python native methods:
file = open(self.file_path, 'r')
# ... later
line = file.readline()
This is generally stable and can handle the file being deleted and re-created. pyinotify will notify the unlink and subsequent link.
However some log files are not being deleted. Instead they are being truncated and new content written to the beginning of the same file.
I'm having trouble reliably detecting when this has occurred since pyinotify will simply report only a write. The only evidence I currently get is that pyinotify reports a write and readline() returns an empty string. BUT, it is possible that two subsiquent writes could trigger the same behavior.
I have thought of comparing a file's size to file.tell() but according to the documentation tell produces an opaque number and it appears this can't be trusted to be a number of bytes.
Is there a simple way to detect a file has been truncated while reading from it?
Edit:
Truncating a file can be simulated with simple shell commands:
echo hello > test.log
echo hello >> test.log
# Truncate test.log
echo goodbye > test.log
To compliment this, a simple python script can be used to confirm that file.tell() does not reduce when the file is truncated:
foo = open('./test.log', 'r')
line = foo.readline()
while line != '':
print(foo.tell())
print(line)
line = foo.readline()
# Put a breakpoint on the following line and
# truncate the file before it executes
print(foo.tell())

Use os.lseek(file.fileno(),0,os.SEEK_CUR) to obtain a byte offset without moving the file pointer. You can’t really use the regular file interface to find out, not least because it may have buffered text (that no longer exists) that it hasn’t made visible to Python yet. If the file is not a byte stream (e.g., the default open in Python 3), it could even be in the middle of a multibyte character and be unable to proceed even if the file immediately grew back past your file offset.

How to not lose Intermediate Data in File

While Learning Python, we do Print to screen but eventually graduate to printing to output files... However most times all errors are not resolved in the code... In such cases the code aborts after running some 10 20 loops or say 80% of the code and then aborts.. However during this time the data that is printed to the file is lost as the file.close() is not executed.
In Python is there a way in which we can save the WIP file. I want to do this without closing and reopening the file once again multiple times in append modes. This will help in Debugging and also not losing the data that has been accumulated before the error was occurred.
After searching i did not find something like this .... if someone has or can give any ideas how to make a module for this that will be great... What we need is a generic catchall... in case of any error.. execute the catchall code to close the file and then exit from Python.

You can flush the internal file buffer by calling f.flush() on the file object in question.
Even better is to wrap the file access in a with block. If an exception is raised, the file is closed.
with open('tmp.txt', 'r') as f:
do_stuff_with(f)

On the documentation of File objects : https://docs.python.org/2/library/stdtypes.html?highlight=flush#file.flush
Use the flush function. There is also a note on the doc with os.fsync function to be sure the data are written on the disc.

read() from a ExFileObject always cause StreamError exception

I am trying to read only one file from a tar.gz file. All operations over tarfile object works fine, but when I read from concrete member, always StreamError is raised, check this code:
import tarfile
fd = tarfile.open('file.tar.gz', 'r|gz')
for member in fd.getmembers():
if not member.isfile():
continue
cfile = fd.extractfile(member)
print cfile.read()
cfile.close()
fd.close()
cfile.read() always causes "tarfile.StreamError: seeking backwards is not allowed"
I need to read contents to mem, not dumping to file (extractall works fine)
Thank you!

The problem is this line:
fd = tarfile.open('file.tar.gz', 'r|gz')
You don't want 'r|gz', you want 'r:gz'.
If I run your code on a trivial tarball, I can even print out the member and see test/foo, and then I get the same error on read that you get.
If I fix it to use 'r:gz', it works.
From the docs:
mode has to be a string of the form 'filemode[:compression]'
...
For special purposes, there is a second format for mode: 'filemode|[compression]'. tarfile.open() will return a TarFile object that processes its data as a stream of blocks. No random seeking will be done on the file… Use this variant in combination with e.g. sys.stdin, a socket file object or a tape device. However, such a TarFile object is limited in that it does not allow to be accessed randomly, see Examples.
'r|gz' is meant for when you have a non-seekable stream, and it only provides a subset of the operations. Unfortunately, it doesn't seem to document exactly which operations are allowed—and the link to Examples doesn't help, because none of the examples use this feature. So, you have to either read the source, or figure it out through trial and error.
But, since you have a normal, seekable file, you don't have to worry about that; just use 'r:gz'.

In addition to the file mode, I attempted to seek on a network stream.
I had the same error when trying to requests.get the file, so I extracted all to a tmp directory:
# stream == requests.get
inputs = [tarfile.open(fileobj=LZMAFile(stream), mode='r|')]
t = "/tmp"
for tarfileobj in inputs:
tarfileobj.extractall(path=t, members=None)
for fn in os.listdir(t):
with open(os.path.join(t, fn)) as payload:
print(payload.read())

python open('file','r+') giving weird result

After reading some posts, it seems like you can open a file for both reading and writing with the mode of 'r+' or 'w+'. However, trying to use these modes always give me weird results:
If I use 'r+', call file.read(), and then call file.write('str'),
there'll be an error of "IOError: [Errno 0] Error"
If I use 'r+', call file.write('str'), and then call file.read(),
it'll return unexpected and very long content(looks like the inside
of some object)
If I use 'w+', calling file.read() will return empty string
What I'm trying to do is open a file, read the content, modify it, and write back. Currently I'm opening it with 'r', change the content, and open it again with 'w' and write back. Is this a good way of doing it?
There's an example at http://snipt.org/zglJ0
I'm using window 7 and python 2.7.2

You have to flush() when switching between reading and writing a file that's been opened in an update mode. Or I think you can also seek(). This is caused by some weird behavior in the Windows file implementation in Python 2.x; they fixed it in 3.x.