import tmtk
from .base import ParamsBase
[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):
params_ = {
"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.'
}
}
if not tmtk.options.transmart_batch_mode:
params_.update({
"ONTOLOGY_MAP_FILE": {
'helptext': 'Points to the ontology mapping for this study.'
},
"MODIFIERS_FILE": {
'helptext': 'Points to the modifiers file for this study.'
},
"TRIAL_VISITS_FILE": {
'helptext': 'Points to the trial visits file for this study.'
}
})
return params_