#!/usr/bin/Rscript   
getwd()
setwd("~/git/mosaic_2020/")
getwd()
########################################################################
# TASK: read data 
########################################################################
# load libraries, packages and local imports
source("Header_TT.R")
source("colnames_clinical_meds.R")

########################################################################
maindir = "~/git/mosaic_2020/"
outdir = paste0(maindir, "output/")
ifelse(!dir.exists(outdir), dir.create(outdir), FALSE)

outdir_stats = paste0(maindir, "output/stats/")
ifelse(!dir.exists(outdir_stats), dir.create(outdir_stats), FALSE)

outdir_stats_na = paste0(maindir, "output/stats/non_asthmatics/")
ifelse(!dir.exists(outdir_stats_na), dir.create(outdir_stats_na), FALSE)

outdir_stats_ns = paste0(maindir, "output/stats/non_severe/")
ifelse(!dir.exists(outdir_stats_ns), dir.create(outdir_stats_ns), FALSE)

outdir_stats_s = paste0(maindir, "output/stats/severe/")
ifelse(!dir.exists(outdir_stats_s), dir.create(outdir_stats_s), FALSE)

outdir_stats_a = paste0(maindir, "output/stats/asthma/")
ifelse(!dir.exists(outdir_stats_a), dir.create(outdir_stats_a), FALSE)

outdir_plots = paste0(maindir, "output/plots/")
ifelse(!dir.exists(outdir_plots), dir.create(outdir_plots), FALSE)
########################################################################
# static file read: csv
#==============
# all patients
#==============
all_df <- read.csv("/home/backup/MOSAIC/MEDIATOR_Data/master_file/Mosaic_master_file_from_stata.csv"
                   , fileEncoding = 'latin1') 

# meta data columns                   
#meta_data_cols = c("mosaic", "gender", "age"
#                   , "adult"
#                   , "flustat", "type"
#                   , "obesity"
                   #, "obese2"
                   #, "height", "height_unit"
                   #, "weight", "weight_unit"
                   #, "ia_height_ftin", "ia_height_m", "ia_weight"
                   #, "visual_est_bmi", "bmi_rating"
#                   )

# check if these columns to select are present in the data
meta_clinical_cols%in%colnames(all_df)
if ( all(meta_clinical_cols%in%colnames(all_df)) ){
  metadata_all = all_df[, meta_clinical_cols]
}

#==============
# adult patients
#==============

adult_df = all_df[all_df$age>=18,]

if (table(adult_df$adult == 1)[[1]] == nrow(adult_df) ){
  cat ("\nPASS: adult df extracted successfully")
} else{
  cat ("\nFAIL: adult df number mismatch!")
}

#=================================
# FLU positive: adult patients
#=================================
# extract the flu positive population
fp_adults = adult_df[adult_df$flustat == 1,]

if (table(fp_adults$flustat == 1)[[1]] == nrow(fp_adults) ){
  cat ("\nPASS: adult df extracted successfully")
} else{
  cat ("\nFAIL: adult df number mismatch!")
}
#-----------------------------------
# asthma and copd status correction
# for conflicting field!
#------------------------------------
# Reassign the copd and asthma status and do some checks 
table(fp_adults$ia_exac_copd); sum(is.na(fp_adults$ia_exac_copd))

fp_adults$ia_exac_copd[fp_adults$ia_exac_copd< 1]<- 0
fp_adults$ia_exac_copd[is.na(fp_adults$ia_exac_copd)] <- 0

table(fp_adults$ia_exac_copd); sum(is.na(fp_adults$ia_exac_copd))

# check copd and asthma status
table(fp_adults$ia_exac_copd, fp_adults$asthma)
check_copd_and_asthma_1<- subset(fp_adults, ia_exac_copd ==1 & asthma == 1) # check this is 3 

# reassign these 3 so these are treated as non-asthmatics as copd with asthma is NOT TRUE asthma
fp_adults$asthma[fp_adults$ia_exac_copd == 1 & fp_adults$asthma == 1]= 0 
table(fp_adults$ia_exac_copd, fp_adults$asthma)

foo<- subset(fp_adults, asthma==1 & ia_exac_copd ==1) # check that its 0

rm(check_copd_and_asthma_1, foo)

if ( table(fp_adults$ia_exac_copd, fp_adults$asthma) [[2,2]] == 0 ){
  cat("\nPASS: asthma and copd do not conflict")
} else{
  cat ("\nFAIL: asthma and copd conflict not resolved!")
  quit()
}

#=============================================
# FLU positive adult patients: without asthma
#=============================================
#cat("\nExtracting flu positive without asthma")
#table(fp_adults$asthma)
#cat("\nNo. of asthmatics:", table(fp_adults$asthma)[[2]]
#    , "\nNo. of non-asthmatics:", table(fp_adults$asthma)[[1]])
#str(fp_adults$asthma)

#table(fp_adults$obesity)
#table(fp_adults$obesity, fp_adults$asthma)

#fp_adults_na = fp_adults[fp_adults$asthma == 0,]
#table(fp_adults_na$obesity)
#table(fp_adults_na$obesity, fp_adults_na$asthma)

#============
# hc
#============
#hc_data<- read.csv("/home/backup/MOSAIC/MEDIATOR_Data/master_file/Mediators_for_HC.csv")
#str(hc_data)
#table(hc_data$Timepoint, hc_data$Sample)
########################################################################

# quick sanity checks
table(adult_df$ia_exac_copd==1 & adult_df$asthma == 1) # check this is 4 

table(fp_adults$ia_exac_copd==1 & fp_adults$asthma == 1) # check this is 3

# clear unnecessary variables
#rm(metadata_all)
rm(all_df, adult_df)