R/l2_lab_gen.R

In raphidoc/lighthouse: Database management and processing workflow for ocean optics science

#' @export
#' @import dplyr
#' @import lubridate
#' @import stringr
#'

# Function to generate Lab L2 from L1 and Log table

#library(data.table)
#library(dplyr)
#library(stringr)
#library(lubridate)

# Think about how to define absolute project path in a user point of view ?
# some generic settings to define
# User should be responsible to set project directory as working directory (setwd()) before calling function
# Or manually enter desired project directory

#project <- "/home/raphael/TEST"
#setwd(project)

l2_water_sample_gen <- function(project, Var = c("Ag","Ap")) {

	# Set L1 and L2 absolute path
	L1 = file.path(project,"L1","Lab")
	L2 = file.path(project,"L2")

	# Check project before doing any manipulation
	CheckList <- check_project(project, L1, L2, set="Lab")

	if (CheckList["Proot"][[1]] == F) {stop("project path is not set at a project root folder")}
	if (CheckList["L2exists"][[1]] == T) {
		stop("L2 structure for Lab is alredy present. You better be sure of what your doing ...\n
			take care of this by yourself !")}

	# Read Lab sampling log
	LabLog <- list.files(path = L1, pattern = "Lab_Log", full.names = T)
	LabLog <- data.table::fread(file = LabLog,
				colClasses = c(ID = "character"),
				data.table = F)

	if (any(str_detect(Var, "Ag"))){

		# Match sample ID, station name along with L1path
		AgFiles <- list.files(path = file.path(L1,"Ag","RData"), "[[:digit:]]{3}([[:alpha:]])?.RData",
						  full.names = T)

		AgLog <- data.frame(L1path = AgFiles)
		AgLog <- AgLog %>%
			mutate(ID= str_extract(AgFiles, "(?<=/)[[:digit:]]{3}([[:alpha:]])?(?=.RData)"))

		AgLog <- AgLog %>% left_join(LabLog, by="ID")

		# Create corresponding L2 path

		if (any(names(AgLog) == "Boat")) {
			AgLog <- AgLog %>%
				mutate(L2path = file.path(L2,
									 paste0(gsub("-", "", as.character(lubridate::date(Date))),
									 	  "_Station",Station),
									 paste0("Lab_",Boat),paste0("Ag_",ID,"_",Depth,"Z",".RData")))
		} else {
			AgLog <- AgLog %>%
				mutate(L2path =file.path(L2,
									paste0(gsub("-", "", as.character(lubridate::date(Date))),
										  "_Station",Station),
									"Lab",paste0("Ag_",ID,"_",Depth,"Z",".RData")))
		}

		L2Ag <- unique(str_extract(AgLog$L2path, ".*(?=/[:alpha:]{2,5}_[:digit:]{3}.*.RData)"))

		for (i in L2Ag){
			dir.create(i, recursive = T)
		}

		file.copy(as.character(AgLog$L1path), as.character(AgLog$L2path), recursive = F)
	}
	if (any(str_detect(Var, "Ap"))) {
		# Match sample ID, station name along with L1path
		ApFiles <- list.files(path = file.path(L1,"Ap_nap","RData"), "[[:digit:]]{3}([[:alpha:]])?.RData",
						  full.names = T)
		ApLog <- data.frame(L1path = ApFiles)
		ApLog <- ApLog %>%
			mutate(ID= str_extract(ApFiles, "(?<=/)[[:digit:]]{3}([[:alpha:]])?(?=.RData)"))

		ApLog <- ApLog %>% left_join(LabLog, by="ID")

		# Create corresponding L2 path

		if (any(names(ApLog) == "Boat")) {
			ApLog <- ApLog %>%
				mutate(L2path = file.path(L2,
									 paste0(gsub("-", "", as.character(lubridate::date(Date))),
									 	  "_Station",Station),
									 paste0("Lab_",Boat),paste0("Ap_",ID,"_",Depth,"Z",".RData")))
		} else {
			ApLog <- ApLog %>%
				mutate(L2path = file.path(L2,
									 paste0(gsub("-", "", as.character(lubridate::date(Date))),
									 	  "_Station",Station),
									 "Lab",paste0("Ap_",ID,"_",Depth,"Z",".RData")))
		}

		L2Ap <- unique(str_extract(ApLog$L2path, ".*(?=/[:alpha:]{2,5}_[:digit:]{3}.*.RData)"))

		for (i in L2Ap){
			dir.create(i, recursive = T)
		}

		file.copy(as.character(ApLog$L1path), as.character(ApLog$L2path), recursive = F)
	}
}