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read_data(_, file) closes file prematurely #164

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jackriccomini opened this issue Jan 17, 2025 · 0 comments · May be fixed by #165
Open

read_data(_, file) closes file prematurely #164

jackriccomini opened this issue Jan 17, 2025 · 0 comments · May be fixed by #165

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@jackriccomini
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jackriccomini commented Jan 17, 2025 •
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I'm receiving NRRD files over a network. I want to use pynrrd to parse and validate those files while they're in memory before they've been saved to disk.

I am passing in a file object to nrrd.read_data(). I want to keep using that file object afterwards but nrrd.read_data(_, file) closes the file. I can't reopen the file after passing it to nrrd.read_data() because I haven't yet persisted it to disk. Once the file has been closed, it's gone.

Minimal reproduction using Flask:

from flask import Flask, request
import nrrd

app = Flask(__name__)

@app.route("/process", methods=["POST"])
def process_file():
    file = request.files["file"].stream

    is_file_ok = check_nrrd(file)

    if not is_file_ok:
        return "some error", 400

    file.seek(0)
    do_something_with_file(file)

    return "uploaded"

def check_nrrd(file):
    """Check that the NRRD conforms to our expectations"""
    header = nrrd.read_header(file)
    data = nrrd.read_data(header, file)

    # perform some checks
    file_is_good = ...
    
    return file_is_good

def do_something_with_file(file):
    print(file.read())

Tested with:

$ curl -F 'file=@test.nrrd' http://localhost:5000/process

Log:

127.0.0.1 - - [17/Jan/2025 17:23:11] "POST /process HTTP/1.1" 500 -
[2025-01-17 17:28:39,601] ERROR in app: Exception on /process [POST]
Traceback (most recent call last):
  File "/Users/JackRiccomini/.pyenv/versions/3.12.7/lib/python3.12/site-packages/flask/app.py", line 1511, in wsgi_app
    response = self.full_dispatch_request()
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/JackRiccomini/.pyenv/versions/3.12.7/lib/python3.12/site-packages/flask/app.py", line 919, in full_dispatch_request
    rv = self.handle_user_exception(e)
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/JackRiccomini/.pyenv/versions/3.12.7/lib/python3.12/site-packages/flask/app.py", line 917, in full_dispatch_request
    rv = self.dispatch_request()
         ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/JackRiccomini/.pyenv/versions/3.12.7/lib/python3.12/site-packages/flask/app.py", line 902, in dispatch_request
    return self.ensure_sync(self.view_functions[rule.endpoint])(**view_args)  # type: ignore[no-any-return]
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/tmp/min.py", line 15, in process_file
    file.seek(0)
  File "/Users/JackRiccomini/.pyenv/versions/3.12.7/lib/python3.12/tempfile.py", line 828, in seek
    return self._file.seek(*args)
           ^^^^^^^^^^^^^^^^^^^^^^
ValueError: I/O operation on closed file.
jackriccomini pushed a commit to jackriccomini/pynrrd that referenced this issue Jan 17, 2025
Stop closing files opened by the caller
bfd85c3 
Fixes mhe#164
@jackriccomini jackriccomini linked a pull request Jan 17, 2025 that will close this issue
Open
@jackriccomini jackriccomini changed the title read_data(file) closes file prematurely read_data(_, file) closes file prematurely Jan 17, 2025
jackriccomini pushed a commit to jackriccomini/pynrrd that referenced this issue Jan 20, 2025
Stop closing files opened by the caller
4815e08 
Fixes mhe#164
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Stop closing files opened by the caller jackriccomini/pynrrd
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@jackriccomini