from .ParamsBase import ParamsBase
import os
[docs]class ClinicalParams(ParamsBase):
docslink = "https://github.com/thehyve/transmart-batch/blob/master/docs/clinical.md"
@property
def mandatory(self):
return {'COLUMN_MAP_FILE': {
'mandatory': True,
'helptext': 'Points to the column file.'
}
}
@property
def optional(self):
return {"WORD_MAP_FILE": {
'helptext': 'Points to the file with dictionary to be used.'
},
"XTRIAL_FILE": {
'helptext': 'Points to the cross study concepts file.'
},
"TAGS_FILE": {
'helptext': 'Points to the concepts tags file.'
}
}
[docs] def is_viable(self):
"""
:return: True if both the column mapping file is located, else returns False.
"""
if self.get('COLUMN_MAP_FILE', None):
file_found = os.path.exists(os.path.join(self.dirname, self.COLUMN_MAP_FILE))
return file_found
else:
return False