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library(jsonlite)
library(readr)
library(stringr)
library(dplyr)

## Warning: package 'dplyr' was built under R version 4.3.3

## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

# File paths
apsimx_file <- "D:/Mes Donnees/R/Biomass_Crops/Modeling/APSIM/apsimx_runs/BioCrops_Base200.apsimx"
apsimx_out  <- "D:/Mes Donnees/R/Biomass_Crops/Modeling/APSIM/apsimx_runs/BioCrops_Final200.apsimx"
par_dir     <- "D:/Mes Donnees/R/Biomass_Crops/Modeling/APSIM/soils_par"
weather_dir <- "D:/Mes Donnees/R/Biomass_Crops/Modeling/APSIM/weather"

# Helper: constrain values
clip_soil_layer <- function(x, lower = -Inf, upper = Inf) {
  x <- pmax(x, lower)
  x <- pmin(x, upper)
  return(x)
}

# Update soil node
update_soil_from_par <- function(existing_soil, par_path) {
  lines <- read_lines(par_path)
  data <- lines[!str_starts(lines, "\\*") & str_detect(lines, "=")]
  data <- str_split_fixed(data, "=", 2)
  df <- as.data.frame(data, stringsAsFactors = FALSE)
  colnames(df) <- c("key", "value")
  df <- df %>% mutate(key = tolower(trimws(key)), value = trimws(value))
  
  get_val <- function(k) df$value[df$key == tolower(k)]
  parse_num_vec <- function(k) {
    if (tolower(k) %in% df$key) {
      as.numeric(unlist(str_split(get_val(k), ",")))
    } else {
      NULL
    }
  }

  idx_physical <- which(sapply(existing_soil$Children, \(x) x$Name == "Physical"))
  if (length(idx_physical) == 1) {
    physical <- existing_soil$Children[[idx_physical]]
    if (!is.null(v <- parse_num_vec("dlayer")))  physical$Thickness <- v
    if (!is.null(v <- parse_num_vec("bd")))      physical$BD <- v
    if (!is.null(v <- parse_num_vec("airdry")))  physical$AirDry <- v
    if (!is.null(v <- parse_num_vec("ll15")))    physical$LL15 <- clip_soil_layer(v, lower = physical$AirDry)
    if (!is.null(v <- parse_num_vec("dul")))     physical$DUL  <- clip_soil_layer(v, lower = physical$LL15)
    if (!is.null(v <- parse_num_vec("sat")))     physical$SAT  <- clip_soil_layer(v, lower = physical$DUL)
    if (!is.null(v <- parse_num_vec("ks")))      physical$KS   <- v
    
    # Add sand and clay
    sand <- parse_num_vec("sand")
    clay <- parse_num_vec("clay")
    if (!is.null(sand)) physical$ParticleSizeSand <- sand
    if (!is.null(clay)) physical$ParticleSizeClay <- clay

    # Compute silt if sand and clay are present
    if (!is.null(sand) && !is.null(clay)) {
      silt <- 100 - sand - clay
      physical$ParticleSizeSilt <- clip_soil_layer(silt, lower = 0)
    }

    existing_soil$Children[[idx_physical]] <- physical
  }

  idx_organic <- which(sapply(existing_soil$Children, \(x) x$Name == "Organic"))
  if (length(idx_organic) == 1) {
    organic <- existing_soil$Children[[idx_organic]]
    if (!is.null(v <- parse_num_vec("carbon"))) {
      organic$Carbon <- v
      organic$Thickness <- parse_num_vec("dlayer")
      existing_soil$Children[[idx_organic]] <- organic
    }
  }

  idx_chemical <- which(sapply(existing_soil$Children, \(x) x$Name == "Chemical"))
  if (length(idx_chemical) == 1) {
    chemical <- existing_soil$Children[[idx_chemical]]
    if (!is.null(v <- parse_num_vec("ph")))  chemical$PH <- v
    if (!is.null(v <- parse_num_vec("cec"))) chemical$CEC <- v
    if (!is.null(v <- parse_num_vec("ec")))  chemical$EC <- v
    if (!is.null(v <- parse_num_vec("dlayer"))) chemical$Thickness <- v
    existing_soil$Children[[idx_chemical]] <- chemical
  }

  idx_water <- which(sapply(existing_soil$Children, \(x) x$Name == "Water"))
  if (length(idx_water) == 1 && exists("physical")) {
    iw <- existing_soil$Children[[idx_water]]
    if (
      !is.null(iw$InitialValues) &&
      is.numeric(iw$InitialValues) &&
      !is.null(physical$SAT) &&
      is.numeric(physical$SAT)
    ) {
      n <- min(length(iw$InitialValues), length(physical$SAT), length(physical$Thickness))
      if (n > 0) {
        iw$InitialValues <- iw$InitialValues[1:n]
        iw$InitialValues <- clip_soil_layer(iw$InitialValues, upper = physical$SAT[1:n])
        iw$Thickness <- physical$Thickness[1:n]
        existing_soil$Children[[idx_water]] <- iw
      }
    }
  }

  # Meta fields
  if (!is.null(v <- get_val("latitude")))  existing_soil$Latitude <- as.numeric(v)
  if (!is.null(v <- get_val("longitude"))) existing_soil$Longitude <- as.numeric(v)
  if (!is.null(v <- get_val("site")))      existing_soil$Site     <- v
  if (!is.null(v <- get_val("country")))   existing_soil$Country  <- v

  return(existing_soil)
}

# Load APSIMX file
apsim_json <- fromJSON(apsimx_file, simplifyVector = FALSE)

# Loop through all simulations
for (i in seq_along(apsim_json$Children)) {
  sim <- apsim_json$Children[[i]]
  if (sim$`$type` == "Models.Core.Simulation, Models") {
    sim_name <- sim$Name
    point_id <- str_extract(sim_name, "point\\d+")
    if (is.na(point_id)) next
    par_file <- file.path(par_dir, paste0(point_id, ".par"))
    weather_file <- file.path(weather_dir, paste0(point_id, ".met"))

    for (j in seq_along(sim$Children)) {
      if (sim$Children[[j]]$`$type` == "Models.Climate.Weather, Models") {
        sim$Children[[j]]$FileName <- weather_file
      }
    }

    existing_soil <- sim$Children[[6]]$Children[[3]]
    updated_soil <- update_soil_from_par(existing_soil, par_file)
    sim$Children[[6]]$Children[[3]] <- updated_soil
    apsim_json$Children[[i]] <- sim

    message(paste0("✅ Updated simulation: ", sim_name))
  }
}

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# Write the modified APSIMX
json_text <- toJSON(apsim_json, pretty = TRUE, auto_unbox = TRUE, null = "null")
writeLines(json_text, apsimx_out)

cat("\n🎉 All simulations updated successfully!\n")

## 
## 🎉 All simulations updated successfully!

cat("📁 Updated APSIMX saved to:\n", apsimx_out, "\n")

## 📁 Updated APSIMX saved to:
##  D:/Mes Donnees/R/Biomass_Crops/Modeling/APSIM/apsimx_runs/BioCrops_Final200.apsimx