Got error during download slides

[Orchardseed]

Describe the bug Hi, I try to used slidescore-api to download slides, but got error.

To Reproduce (slidescoreapi) D:\Python\Yuan\image>slidescore -t D:\Python\Yuan\image\oldkey -s 1361 download-wsis D:\Python\Yuan\image\originalimages 0%| | 0/20 [00:00<?, ?it/s] 0%| | 0/20 [00:00<?, ?it/s] Traceback (most recent call last): File "D:\Python\Anaconda3\envs\slidescoreapi\Scripts\slidescore-script.py", line 33, in sys.exit(load_entry_point('slidescore-api', 'console_scripts', 'slidescore')()) File "d:\python\yuan\slidescore-api-main\slidescore_api\cli.py", line 502, in cli args.subcommand(args) File "d:\python\yuan\slidescore-api-main\slidescore_api\cli.py", line 351, in _download_wsi download_wsis( File "d:\python\yuan\slidescore-api-main\slidescore_api\cli.py", line 332, in download_wsis filename = client.download_slide(study_id, image, save_dir=save_dir) File "d:\python\yuan\slidescore-api-main\slidescore_api\api.py", line 258, in download_slide with tqdm.wrapattr( File "D:\Python\Anaconda3\envs\slidescoreapi\lib\contextlib.py", line 119, in enter return next(self.gen) File "D:\Python\Anaconda3\envs\slidescoreapi\lib\site-packages\tqdm\std.py", line 1528, in wrapattr with cls(total=total, tqdm_kwargs) as t: File "D:\Python\Anaconda3\envs\slidescoreapi\lib\site-packages\tqdm\std.py", line 1109, in init self.refresh(lock_args=self.lock_args) File "D:\Python\Anaconda3\envs\slidescoreapi\lib\site-packages\tqdm\std.py", line 1361, in refresh self.display() File "D:\Python\Anaconda3\envs\slidescoreapi\lib\site-packages\tqdm\std.py", line 1509, in display self.sp(self.str() if msg is None else msg) File "D:\Python\Anaconda3\envs\slidescoreapi\lib\site-packages\tqdm\std.py", line 1165, in str return self.format_meter(self.format_dict) File "D:\Python\Anaconda3\envs\slidescoreapi\lib\site-packages\tqdm\std.py", line 475, in format_meter bool_prefix_colon_already = (prefix[-2:] == ": ") TypeError: 'WindowsPath' object is not subscriptable Exception ignored in: <function tqdm.del at 0x000001C26D7B1DC0> Traceback (most recent call last): File "D:\Python\Anaconda3\envs\slidescoreapi\lib\site-packages\tqdm\std.py", line 1162, in del self.close() File "D:\Python\Anaconda3\envs\slidescoreapi\lib\site-packages\tqdm\std.py", line 1291, in close if self.last_print_t < self.start_t + self.delay: AttributeError: 'tqdm' object has no attribute 'last_print_t'

Expected behavior Command Line should download the slides from slidescore

Environment SlideScore Python API version: How installed: 1. clone from github open in Pycharm / 2. download zip and conda create environment and pip install -e . Python version: 3.9 / 3.9.12 Operating System: Window

Additional context bug.txt

[Orchardseed]

Hi, I tried it in unbuntu but also get this error Environment SlideScore Python API version: How installed: download zip and conda create environment and pip install -e . Python version: 3.9 / 3.9.12 Operating System: unbuntu bug2.txt

[jonasteuwen]

Hi, this seems to be an error in newer versions of tqdm/python. Downgrade to a lower version. @lromor also encountered it, perhaps he can shed some light.

[lromor]

Hi @Orchardseed , try to downgrade tqdm to version 4.50.0!

[lromor]

@jonasteuwen if this fixes it, maybe consider tying tqdm to a specific version in the deps.

[AjeyPaiK]

Hi @Orchardseed, is this problem fixed?

[Orchardseed]

Yes, thanks for help! @AjeyPaiK

[YoniSchirris]

This still leaves me with the top part of the error, for several python versions, on MacOS (M1) and Linux.

(slidescore-api) y.schirris@eratosthenes:~/til-validation/1_download_wsis_from_slidescore$ slidescore         --slidescore-url https://slidescore.nki.nl/         -s 2540         -v         download-wsis         ./data/
  0%|                                                                         | 0/3826 [00:00<?, ?it/s]
  0%|                                                                         | 0/3826 [00:00<?, ?it/s]
Traceback (most recent call last):
  File "/home/y.schirris/miniconda3/envs/slidescore-api/bin/slidescore", line 8, in <module>
    sys.exit(cli())
  File "/home/y.schirris/slidescore-api/slidescore_api/cli.py", line 607, in cli
    args.subcommand(args)
  File "/home/y.schirris/slidescore-api/slidescore_api/cli.py", line 426, in _download_wsi
    download_wsis(
  File "/home/y.schirris/slidescore-api/slidescore_api/cli.py", line 407, in download_wsis
    filename = client.download_slide(study_id, image, save_dir=save_dir)
  File "/home/y.schirris/slidescore-api/slidescore_api/api.py", line 262, in download_slide
    with tqdm.wrapattr(
  File "/home/y.schirris/miniconda3/envs/slidescore-api/lib/python3.8/contextlib.py", line 113, in __enter__
    return next(self.gen)
  File "/home/y.schirris/miniconda3/envs/slidescore-api/lib/python3.8/site-packages/tqdm/std.py", line 1488, in wrapattr
    with tclass(total=total, **tkwargs) as t:
  File "/home/y.schirris/miniconda3/envs/slidescore-api/lib/python3.8/site-packages/tqdm/std.py", line 1048, in __init__
    self.refresh(lock_args=self.lock_args)
  File "/home/y.schirris/miniconda3/envs/slidescore-api/lib/python3.8/site-packages/tqdm/std.py", line 1336, in refresh
    self.display()
  File "/home/y.schirris/miniconda3/envs/slidescore-api/lib/python3.8/site-packages/tqdm/std.py", line 1469, in display
    self.sp(self.__repr__() if msg is None else msg)
  File "/home/y.schirris/miniconda3/envs/slidescore-api/lib/python3.8/site-packages/tqdm/std.py", line 1087, in __repr__
    return self.format_meter(**self.format_dict)
  File "/home/y.schirris/miniconda3/envs/slidescore-api/lib/python3.8/site-packages/tqdm/std.py", line 423, in format_meter
    bool_prefix_colon_already = (prefix[-2:] == ": ")
TypeError: 'PosixPath' object is not subscriptable
Exception ignored in: <function tqdm.__del__ at 0x7f660b5881f0>
Traceback (most recent call last):
  File "/home/y.schirris/miniconda3/envs/slidescore-api/lib/python3.8/site-packages/tqdm/std.py", line 1084, in __del__
    self.close()
  File "/home/y.schirris/miniconda3/envs/slidescore-api/lib/python3.8/site-packages/tqdm/std.py", line 1291, in close
    self.display(pos=0)
  File "/home/y.schirris/miniconda3/envs/slidescore-api/lib/python3.8/site-packages/tqdm/std.py", line 1469, in display
    self.sp(self.__repr__() if msg is None else msg)
  File "/home/y.schirris/miniconda3/envs/slidescore-api/lib/python3.8/site-packages/tqdm/std.py", line 1087, in __repr__
    return self.format_meter(**self.format_dict)
  File "/home/y.schirris/miniconda3/envs/slidescore-api/lib/python3.8/site-packages/tqdm/std.py", line 423, in format_meter
    bool_prefix_colon_already = (prefix[-2:] == ": ")
TypeError: 'PosixPath' object is not subscriptable
(slidescore-api) y.schirris@eratosthenes:~/til-validation/1_download_wsis_from_slidescore$ python --version
Python 3.8.13
(slidescore-api) y.schirris@eratosthenes:~/til-validation/1_download_wsis_from_slidescore$ python
Python 3.8.13 (default, Oct 21 2022, 23:50:54)
[GCC 11.2.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import tqdm
>>> tqdm.__version__
'4.45.0'
>>>

[YoniSchirris]

It appears that the above still exists because a Path object is passed to TQDM, while TQDM expects a str. The above merge requests fixes both issues discussed in this issue

1. It hardcodes the version to 4.45.0
2. It converst the Path to str before passing it to TQDM, not changing the object itself for the rest of the script

[Orchardseed]

Hi Yoni. Did you try to upgrade tqdm to version 4.50.0? I forget the details, but it worked for me last time. If it still doesn't work, we can ask to fix them again.

[YoniSchirris]

that solves

Exception ignored in: <function tqdm.del at 0x000001C26D7B1DC0>
Traceback (most recent call last):
File "D:\Python\Anaconda3\envs\slidescoreapi\lib\site-packages\tqdm\std.py", line 1162, in del
self.close()
File "D:\Python\Anaconda3\envs\slidescoreapi\lib\site-packages\tqdm\std.py", line 1291, in close
if self.last_print_t < self.start_t + self.delay:
AttributeError: 'tqdm' object has no attribute 'last_print_t'

but that doesn't solve the problem above it, where tqdm expects a string and we give it a pathlib.Path object.

PR #39 should solve both these issues