| import yaml | |
| import sys | |
| def check_config_file(task,config_file): | |
| with open(config_file) as f: | |
| config = yaml.safe_load(f) | |
| if task=='Phenotype': | |
| disease_label = config['disease_label'] | |
| else : | |
| disease_label = "" | |
| time = config['timePrediction'] | |
| label = task | |
| timeW = config['timeWindow'] | |
| include=int(timeW.split()[1]) | |
| bucket = config['timebucket'] | |
| radimp = config['radimp'] | |
| predW = config['predW'] | |
| disease_filter = config['disease_filter'] | |
| icu_no_icu = config['icu_no_icu'] | |
| groupingDiag = config['groupingDiag'] | |
| assert( icu_no_icu in ['ICU','Non-ICU' ], "Chossen data should be one of the following: ICU, Non-ICU") | |
| data_icu = icu_no_icu=='ICU' | |
| if data_icu: | |
| chart_flag = config['chart'] | |
| output_flag = config['output'] | |
| select_chart = config['select_chart'] | |
| lab_flag = False | |
| select_lab = False | |
| else: | |
| lab_flag =config['lab'] | |
| select_lab = config['select_lab'] | |
| groupingMed = config['groupingMed'] | |
| groupingProc = config['groupingProc'] | |
| chart_flag = False | |
| output_flag = False | |
| select_chart = False | |
| diag_flag= config['diagnosis'] | |
| proc_flag = config['proc'] | |
| meds_flag = config['meds'] | |
| select_diag= config['select_diag'] | |
| select_med= config['select_med'] | |
| select_proc= config['select_proc'] | |
| select_out = config['select_out'] | |
| outlier_removal=config['outlier_removal'] | |
| thresh=config['outlier'] | |
| left_thresh=config['left_outlier'] | |
| if data_icu: | |
| assert (isinstance(select_diag,bool) and isinstance(select_med,bool) and isinstance(select_proc,bool) and isinstance(select_out,bool) and isinstance(select_chart,bool), " select_diag, select_chart, select_med, select_proc, select_out should be boolean") | |
| assert (isinstance(chart_flag,bool) and isinstance(output_flag,bool) and isinstance(diag_flag,bool) and isinstance(proc_flag,bool) and isinstance(meds_flag,bool), "chart_flag, output_flag, diag_flag, proc_flag, meds_flag should be boolean") | |
| else: | |
| assert (isinstance(select_diag,bool) and isinstance(select_med,bool) and isinstance(select_proc,bool) and isinstance(select_out,bool) and isinstance(select_lab,bool), " select_diag, select_lab, select_med, select_proc, select_out should be boolean") | |
| assert (isinstance(lab_flag,bool) and isinstance(diag_flag,bool) and isinstance(proc_flag,bool) and isinstance(meds_flag,bool), "lab_flag, diag_flag, proc_flag, meds_flag should be boolean") | |
| if task=='Phenotype': | |
| if disease_label=='Heart Failure': | |
| label='Readmission' | |
| time=30 | |
| disease_label='I50' | |
| elif disease_label=='CAD': | |
| label='Readmission' | |
| time=30 | |
| disease_label='I25' | |
| elif disease_label=='CKD': | |
| label='Readmission' | |
| time=30 | |
| disease_label='N18' | |
| elif disease_label=='COPD': | |
| label='Readmission' | |
| time=30 | |
| disease_label='J44' | |
| else : | |
| raise ValueError('Disease label not correct provide one in the list: Heart Failure, CAD, CKD, COPD') | |
| predW=0 | |
| assert (timeW[0]=='Last' and include<=72 and include>=24, "Time window should be between Last 24 and Last 72") | |
| elif task=='Mortality': | |
| time=0 | |
| label= 'Mortality' | |
| assert (predW<=8 and predW>=2, "Prediction window should be between 2 and 8") | |
| assert (timeW[0]=='Fisrt' and include<=72 and include>=24, "Time window should be between First 24 and First 72") | |
| elif task=='Length_of_Stay': | |
| label= 'Length of Stay' | |
| assert (timeW[0]=='Fisrt' and include<=72 and include>=24, "Time window should be between Fisrt 24 and Fisrt 72") | |
| assert (time<=10 and time>=1, "Length of stay should be between 1 and 10") | |
| predW=0 | |
| elif task=='Readmission': | |
| label= 'Readmission' | |
| assert (timeW[0]=='Last' and include<=72 and include>=24, "Time window should be between Last 24 and Last 72") | |
| assert (time<=150 and time>=10 and time%10==0, "Readmission window should be between 10 and 150 with a step of 10") | |
| predW=0 | |
| else: | |
| raise ValueError('Task not correct') | |
| assert( disease_filter in ['Heart Failure','COPD','CKD','CAD',""], "Disease filter should be one of the following: Heart Failure, COPD, CKD, CAD or empty") | |
| assert( groupingDiag in ['Convert ICD-9 to ICD-10 and group ICD-10 codes','Keep both ICD-9 and ICD-10 codes','Convert ICD-9 to ICD-10 codes'], "Grouping ICD should be one of the following: Convert ICD-9 to ICD-10 and group ICD-10 codes, Keep both ICD-9 and ICD-10 codes, Convert ICD-9 to ICD-10 codes") | |
| assert (bucket<=6 and bucket>=1 and isinstance(bucket, int), "Time bucket should be between 1 and 6 and an integer") | |
| assert (radimp in ['No Imputation', 'forward fill and mean','forward fill and median'], "imputation should be one of the following: No Imputation, forward fill and mean, forward fill and median") | |
| if chart_flag: | |
| assert (left_thresh>=0 and left_thresh<=10 and isinstance(left_thresh, int), "Left outlier threshold should be between 0 and 10 and an integer") | |
| assert (thresh>=90 and thresh<=99 and isinstance(thresh, int), "Outlier threshold should be between 90 and 99 and an integer") | |
| assert (outlier_removal in ['No outlier detection','Impute Outlier (default:98)','Remove outliers (default:98)'], "Outlier removal should be one of the following: No outlier detection, Impute Outlier (default:98), Remove outliers (default:98)") | |
| if lab_flag: | |
| assert (left_thresh>=0 and left_thresh<=10 and isinstance(left_thresh, int), "Left outlier threshold should be between 0 and 10 and an integer") | |
| assert (thresh>=90 and thresh<=99 and isinstance(thresh, int), "Outlier threshold should be between 90 and 99 and an integer") | |
| assert (outlier_removal in ['No outlier detection','Impute Outlier (default:98)','Remove outliers (default:98)'], "Outlier removal should be one of the following: No outlier detection, Impute Outlier (default:98), Remove outliers (default:98)") | |
| assert (groupingProc in ['ICD-9 and ICD-10','ICD-10'], "Grouping procedure should be one of the following: ICD-9 and ICD-10, ICD-10") | |
| assert (groupingMed in ['Yes','No'], "Do you want to group Medication codes to use Non propietary names? : Grouping medication should be one of the following: Yes, No") | |
| return label, time, disease_label, predW |