def test_validate_meta_info_invalid_characters1(self):
""" """
# Define meta information - invalid characters in multiple keys
meta_info = {
'info': {
'BIDS': {
'template': 'anat_file',
'Modality': 'invalid._#$*%',
'Ce': 'invalid2.',
'Mod': '_invalid2',
'Filename': ''
}
}
}
# Call function
curate_bids.validate_meta_info(meta_info, BIDS_TEMPLATE)
# Assert 'BIDS.valid' == False
self.assertFalse(meta_info['info']['BIDS']['valid'])
# Assert error message is correct
self.assertEqual(meta_info['info']['BIDS']['error_message'],
"Filename '' is too short\n"+\
"Mod '_invalid2' does not match '^[a-zA-Z0-9]*$'\n"+\
"Modality 'invalid._#$*%' is not one of ['T1w', 'T2w', 'T1rho', 'T1map', 'T2map', 'FLAIR', 'FLASH', 'PD'"+\
", 'PDmap', 'PDT2', 'inplaneT1', 'inplaneT2', 'angio', 'defacemask', 'SWImagandphase']\n"+\
"Ce 'invalid2.' does not match '^[a-zA-Z0-9]*$'")
def test_validate_meta_info_invalid5(self):
""" """
# Define meta information - Task is empty,
meta_info = {
'info': {
'BIDS': {
'template': 'func_file',
'Filename': 'example.nii.gz',
'Modality': 'sbref',
'Task': '',
'Rec': '',
'Run': '01',
'Echo': 'AA'
}
}
}
# Call function
curate_bids.validate_meta_info(meta_info, BIDS_TEMPLATE)
# Assert 'BIDS.valid' == False
self.assertFalse(meta_info['info']['BIDS']['valid'])
# Assert error message is correct
self.assertEqual(
meta_info['info']['BIDS']['error_message'],
"Task '' does not match '^[a-zA-Z0-9]+$'\nEcho 'AA' does not match '^[0-9]*$'"
)
def test_validate_meta_info_BIDS_NA(self):
""" """
# Define meta information w/ BIDS NA
meta_info = {'info': {'BIDS': 'NA'}}
# Call function
curate_bids.validate_meta_info(meta_info, BIDS_TEMPLATE)
# Assert 'BIDS': 'NA' is in meta_info
self.assertEqual(meta_info['info']['BIDS'], 'NA')
def test_validate_meta_info_no_info(self):
""" """
# Define meta information w/o BIDS info
meta_info = {'other_info': 'test'}
# Call function
curate_bids.validate_meta_info(meta_info, BIDS_TEMPLATE)
# Assert 'BIDS': 'NA' is in meta_info
self.assertEqual(meta_info['info']['BIDS'], 'NA')
def test_validate_meta_info_no_BIDS(self):
""" """
# Define meta information w/o BIDS info
meta_info = {'info': {'test1': 'abc', 'test2': 'def'}}
# Call function
curate_bids.validate_meta_info(meta_info, BIDS_TEMPLATE)
# Assert 'BIDS': 'NA' is in meta_info
self.assertEqual(meta_info['info']['BIDS'], 'NA')
def test_validate_meta_info_valid3(self):
""" """
# Define meta information - Folder is empty string - this is ok!!
meta_info = {'info': {'BIDS': {'Folder': '', 'extra': 'test'}}}
# Call function
curate_bids.validate_meta_info(meta_info, BIDS_TEMPLATE)
# Assert 'BIDS.valid' == True
self.assertTrue(meta_info['info']['BIDS']['valid'])
# Assert error message is empty string
self.assertEqual(meta_info['info']['BIDS']['error_message'], '')
def test_validate_meta_info_valid1(self):
""" """
# Define meta information
meta_info = {'info': {'BIDS': {}}}
# Call function
curate_bids.validate_meta_info(meta_info, BIDS_TEMPLATE)
# Assert 'BIDS.valid' == True
self.assertTrue(meta_info['info']['BIDS']['valid'])
# Assert error message is empty string
self.assertEqual(meta_info['info']['BIDS']['error_message'], '')
def test_validate_meta_info_valid5(self):
""" """
# Define meta information - not required fields...
meta_info = {'info': {'BIDS': {'Run': 1}}}
# Call function
curate_bids.validate_meta_info(meta_info, BIDS_TEMPLATE)
# Assert 'BIDS.valid' == True
self.assertTrue(meta_info['info']['BIDS']['valid'])
# Assert error message is empty string
self.assertEqual(meta_info['info']['BIDS']['error_message'], '')
# Assert run numebr is still an integer
self.assertEqual(meta_info['info']['BIDS']['Run'], 1)
def test_validate_meta_info_invalid4(self):
""" """
# Define meta information - invalid/unknown/NO_MATCH template
meta_info = {
'info': {
'BIDS': {
'template': 'NO_MATCH',
'Modality': 'bold'
}
}
}
# Call function
curate_bids.validate_meta_info(meta_info, BIDS_TEMPLATE)
# Assert 'BIDS.valid' == False
self.assertFalse(meta_info['info']['BIDS']['valid'])
# Assert error message is correct
self.assertEqual(meta_info['info']['BIDS']['error_message'],
'Unknown template: NO_MATCH. ')
def test_validate_meta_info_already_valid(self):
""" """
# Define meta information - not required fields...
meta_info = {
'info': {
'BIDS': {
'Filename': 'sub-01_ses-02_T1w.nii.gz',
'Modality': 'T1w',
'valid': True,
'error_message': ''
}
}
}
# Call function
curate_bids.validate_meta_info(meta_info, BIDS_TEMPLATE)
# Assert 'BIDS.valid' == True
self.assertTrue(meta_info['info']['BIDS']['valid'])
# Assert error message is empty string
self.assertEqual(meta_info['info']['BIDS']['error_message'], '')
def test_validate_meta_info_invalid1(self):
""" """
# Define meta information - Task value is missing
meta_info = {
'info': {
'BIDS': {
'template': 'task_events_file',
'Filename': 'example.tsv',
'Task': '',
'Modality': 'bold'
}
}
}
# Call function
curate_bids.validate_meta_info(meta_info, BIDS_TEMPLATE)
# Assert 'BIDS.valid' == False
self.assertFalse(meta_info['info']['BIDS']['valid'])
# Assert error message is correct
self.assertEqual(meta_info['info']['BIDS']['error_message'],
u"Task '' does not match '^[a-zA-Z0-9]+$'")
def test_validate_meta_info_valid4(self):
""" """
# Define meta information - not required fields...
meta_info = {
'info': {
'BIDS': {
'Run': '',
'Ce': '',
'Mod': '',
'Acq': '',
'Rec': ''
}
}
}
# Call function
curate_bids.validate_meta_info(meta_info, BIDS_TEMPLATE)
# Assert 'BIDS.valid' == True
self.assertTrue(meta_info['info']['BIDS']['valid'])
# Assert error message is empty string
self.assertEqual(meta_info['info']['BIDS']['error_message'], '')
def test_validate_meta_info_was_invalid(self):
""" """
# Define meta information - not required fields...
meta_info = {
'info': {
'BIDS': {
'Task': 'testtask',
'Modality': 'bold',
'Filename': 'sub-01_ses-02_task-testtask_bold.nii.gz',
'valid': False,
'error_message': 'Missing required property: Task. ',
}
}
}
# Call function
curate_bids.validate_meta_info(meta_info, BIDS_TEMPLATE)
# Assert 'BIDS.valid' == True
self.assertTrue(meta_info['info']['BIDS']['valid'])
# Assert error message is empty string
self.assertEqual(meta_info['info']['BIDS']['error_message'], '')
def test_validate_meta_info_invalid3(self):
""" """
# Define meta information - Modality value is missing
meta_info = {
'info': {
'BIDS': {
'template': 'anat_file',
'Filename': 'example.nii.gz',
'Modality': ''
}
}
}
# Call function
curate_bids.validate_meta_info(meta_info, BIDS_TEMPLATE)
# Assert 'BIDS.valid' == False
self.assertFalse(meta_info['info']['BIDS']['valid'])
# Assert error message is correct
self.assertEqual(meta_info['info']['BIDS']['error_message'],
"Modality '' is not one of ['T1w', 'T2w', 'T1rho', 'T1map', 'T2map', 'FLAIR', 'FLASH', 'PD',"+\
" 'PDmap', 'PDT2', 'inplaneT1', 'inplaneT2', 'angio', 'defacemask', 'SWImagandphase']")
def test_validate_meta_info_invalid2(self):
""" """
# Define meta information - Filename is missing
meta_info = {
'info': {
'BIDS': {
'template': 'anat_file',
'Filename': '',
'extra': 'test'
}
}
}
# Call function
curate_bids.validate_meta_info(meta_info, BIDS_TEMPLATE)
# Assert 'BIDS.valid' == False
self.assertFalse(meta_info['info']['BIDS']['valid'])
# Assert error message is correct
self.assertEqual(
meta_info['info']['BIDS']['error_message'],
u"Filename '' is too short\n'Modality' is a required property")