Fixes #973 issue with pinnacle export CLI

[pchlap]

This fixes the issue reported in #973 where the trial couldn't be set using the command line interface.

@SimonBiggs I don't have a test which covers this code, since it's part of the CLI. Would you expect to have a test for the CLI functions?

[SimonBiggs]

Would you expect to have a test for the CLI functions?

Yup, certainly, if that's okay.

Here is an example:

pymedphys/pymedphys/tests/dicom/test_header_tweaks.py

Lines 44 to 54 in ed39ad7

	def compare_dicom_cli(command, original, expected):
	pydicom.write_file(ORIGINAL_DICOM_FILENAME, original)
	try:
	subprocess.check_call(command)
	cli_adjusted_ds = pydicom.read_file(ADJUSTED_DICOM_FILENAME, force=True)
	assert str(cli_adjusted_ds) == str(expected)
	finally:
	remove_file(ORIGINAL_DICOM_FILENAME)
	remove_file(ADJUSTED_DICOM_FILENAME)

Although there I removed the file after, it is much better to use a temp directory like the following:

pymedphys/pymedphys/tests/experimental/pseudonymisation/test_pseudonymisation.py

Lines 92 to 114 in ed39ad7

	with tempfile.TemporaryDirectory() as output_directory:
	pseudonymised_file_path = anonymise_file(
	dicom_filepath=test_file_path,
	output_filepath=output_directory,
	delete_original_file=False,
	anonymise_filename=True,
	replace_values=True,
	# keywords_to_leave_unchanged=None,
	delete_private_tags=True,
	delete_unknown_tags=True,
	replacement_strategy=replacement_strategy,
	identifying_keywords=identifying_keywords_for_pseudo,
	)
	# debug print + Assert to force the print
	# print("Pseudonymised file at: ", pseudonymised_file_path)
	# assert False
	assert exists(pseudonymised_file_path)
	ds_input = pydicom.dcmread(test_file_path, force=True)
	ds_pseudo = pydicom.dcmread(pseudonymised_file_path, force=True)
	# simplistic stand-in to make sure *something* is happening
	assert ds_input["PatientID"].value != ds_pseudo["PatientID"].value
	# make sure that we are not accidentally using the hardcode replacement approach
	assert ds_pseudo["PatientID"].value not in ["", "Anonymous"]

[SimonBiggs]

You can feel free to ignore the following test failure:

Unfortunately it is intermittent... I need to get to the bottom of that :(.

[pchlap]

Would you expect to have a test for the CLI functions?

Yup, certainly, if that's okay.

Cool, thanks for the examples. I'll sort that out, hopefully I can get that done tomorrow morning :)

[pchlap]

Hi @SimonBiggs ,

I've added some tests for the CLI, let me know what you think. If you're happy we can merge this and let it roll out in the next release. Thanks a lot!

[SimonBiggs]

Yup, LGTM. From what I gather, here you're mostly just doing some basic sanity checks on the CLI.