token=keyring::key_get("TALOS_REDCAP_API")

## Primary data set of recorded data

inst <- REDCapR::redcap_instruments(redcap_uri = "https://redcap.au.dk/api/",token = token)$data

tools <- tolower(c(
  "PASE",
  "MFI",
  "mdi",
  "mmse",
  "mrs",
  "SDMT",
  "who",
  "ham",
  "bi",
  "grad", 
  "nihss"
))

vec_starts_with <- function(d,v){
  filt <- paste0("^(", paste(v, collapse="|"), ")")
  
  d[grep(filt,d)]
}

vec_ends_with <- function(d,v){
  filt <- paste0("(", paste(v, collapse="|"), ")$")
  # sub(paste0(".*?_(",paste(v,collapse = "|"),")$"),"\\1",colnames(d))
  d[grep(filt,d)]
}

# vec_starts_with(inst$instrument_name,tools)

data <- REDCapR::redcap_read(redcap_uri = "https://redcap.au.dk/api/",token = token,
                     forms = vec_starts_with(inst$instrument_name,tools),
                     fields = "record_id")$data

ds <- data |> select(!ends_with("complete"))

talos2long <- function(ds,exclude=c("talos","record"),instance_vals=c("0","1","2","4"),exclude_col_ends=c("user","lock")){
  nms <- unique(do.call(c,lapply(strsplit(colnames(ds),"_"),"[[",1)))
  nms <- nms[!nms %in% exclude]
  
  ls <- lapply(seq_along(nms),function(i){
    cols <- c("record_id",vec_starts_with(colnames(ds),c(paste0("talos_",nms[i]),nms[i])))
    
    d <- select(ds,all_of(cols))
    
    ends <- unique(do.call(c,lapply(strsplit(colnames(d),"_"),function(i){
      i[length(i)]
      })))
    
    ins <- colnames(d) %in% vec_ends_with(colnames(d),paste0("_",instance_vals))
    
    ls_ins <- split.default(d[-1],factor(stRoke::str_extract(colnames(d[ins]),paste0("[",paste(instance_vals,collapse=""),"]$"))))
    
    dat <- lapply(seq_along(ls_ins),function(i){
      dr <- cbind(d[1],instance=names(ls_ins)[i],ls_ins[[i]])
      colnames(dr) <- unique(gsub(pattern = paste0("_[",paste(instance_vals,collapse=""),"]$"),"",colnames(dr)))
      dr |> select(record_id,contains("_sys_"),instance,everything())
      }) |> bind_rows() |> rename(rnumb=record_id) |> mutate(rnumb=as.character(rnumb))
    
    ## Col name ending on 00 is date col of measure in all tools
    dat[,vec_ends_with(colnames(dat),"00")] <- as.Date(dat[,vec_ends_with(colnames(dat),"00")])
    
    dat |> select(!ends_with(exclude_col_ends))
  })
  
  names(ls) <- nms
  ls
  
}

ls_sel <- data |> select(!ends_with("complete"))|> talos2long() 

## Data set of baseline and DAP data

subjects_raw <-
  REDCapR::redcap_read(
    redcap_uri = "https://redcap.au.dk/api/",
    token = token,
    forms = vec_starts_with(inst$instrument_name, c("end", "inkl", "reg", "basis")),
    fields = "record_id"
  )$data 

subjects <- subjects_raw |>
  select(
    record_id,
    talos_end00,
    talos_end01,
    rdate,
    rtreat,
    cpr,
    basis_kon,
    starts_with("reg_")
  ) |> select(!ends_with("complete")) |> 
  rename(rnumb = record_id,
         enddate = talos_end00,
         eos_early = talos_end01,
         sex=basis_kon) |>
  mutate(
    enddate = as.Date(enddate),
    rdate = as.Date(rdate),
    inc_time = as.numeric(difftime(enddate, rdate, units = "days")),
    age = stRoke::age_calc(as.Date(stRoke::cpr_dob(cpr,"%Y-%m-%d")),enddate=rdate)
  )

# colnames(subjects)  <- gsub("^reg_","",colnames(subjects))