Extractor failure because file does not exist
I have the following entry in the tasks list of my OpenREM 1.0.0 beta installation (I’ve manually reformatted it here to make it more readable:
UUID: 853512a7-0e66-482c-9804-ac063b1988c7
Task type: import_rdsr
Info: None
Error: Traceback (most recent call last):
File "e:\openrem-src\openrem\remapp\tools\background.py", line 148, in run_as_task func(*args, **kwargs)
File "e:\openrem-src\openrem\remapp\extractors\rdsr.py", line 605, in rdsr dataset = pydicom.dcmread(rdsr_file)
File "E:\venv311\Lib\site-packages\pydicom\filereader.py", line 993, in dcmread fp = open(fp, 'rb')
FileNotFoundError: [Errno 2] No such file or directory: 'E:\\orthanc\\dicom\\39e3416e-d8a8dbee-ead64288-11840341-de16482f.dcm'
Started: 23 May 2023, 10 a.m.
State: Failure
I would like to add a try
accept
around the dataset = pydicom.dcmread(rdsr_file)
line in rdsr.py
so that the FileNotFoundError
is caught and logged, along the lines of:
try:
dataset = pydicom.dcmread(rdsr_file)
except FileNotFoundError:
logger.warning(
"rdsr.py not attempting to extract from {0}, the file does not exist".format(
rdsr_file
)
)
record_task_error_exit(
f"Not attempting to extract from {rdsr_file}, the file does not exist"
)
return 1
I also think we should do this for the other extractors.
Comments (8)
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reporter I can’t think of a way to do that. Have you seen the same error on your test system?
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reporter Added check that file exists in extractors and updated changes file. The ct_toshiba extractor already has try except around file reading. Refs issue
#993→ <<cset 53f3fad004e7>>
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reporter Using f-strings after reading Codacy comments. Refs issue
#993→ <<cset b39d5da27328>>
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reporter Addressing codacy issue. Refs issue
#993→ <<cset 9db4f331fe45>>
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reporter - changed milestone to 1.0.0
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assigned issue to
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reporter Merged in issue993extractorFailureFileDoesNotExist (pull request #590)
Added check that file exists in extractors and updated changes file. The ct_toshiba extractor already has try except around file reading. Refs issue
#993Approved-by: Ed McDonagh
Fixes issue
#993→ <<cset 0371d8370f66>>
-
reporter - changed status to resolved
Merged in issue993extractorFailureFileDoesNotExist (pull request #590)
Added check that file exists in extractors and updated changes file. The ct_toshiba extractor already has try except around file reading. Refs issue
#993Approved-by: Ed McDonagh
Fixes issue
#993→ <<cset 0371d8370f66>>
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I don’t suppose there's a way of working out why the file is not found?