Add flat-file bypass for get.trait.data()

base/db/R/get.trait.data.R

@@ -31,7 +31,8 @@ get.trait.data <-
            database,
            forceupdate,
            write = FALSE,
-           trait.names = NULL) {
+           trait.names = NULL,
+           input_file = NULL) {
 
   if (!is.list(pfts)) {
     PEcAn.logger::logger.severe('pfts must be a list')
@@ -42,6 +43,43 @@ get.trait.data <-
     PEcAn.logger::logger.severe('At least one pft in settings is missing its "outdir"')
   }
 
+  #check for flatfile path, if present use it 
+  file_path <- input_file %||% pfts$file_path
+  if (!is.null(file_path)) {
+    if (!file.exists(file_path) {
+      PEcAn.logger::logger.error("trait data file not found at specified path", sQuote(file_path))
+    }
+    PEcAn.logger::logger.info("Using flat file for trait data instead of database")
+
+    # Load flat file as data.frame
+    trait_data_flat <- read.csv(file_path, stringsAsFactors = FALSE)
+
+    # Build trait.names from flat file if not already provided
+    if (is.null(trait.names)) {
+      pft_names <- vapply(pfts, "[[", character(1), "name")
+      pft_ids <- unique(trait_data_flat$pft_id[
+        trait_data_flat$pft_name %in% pft_names &
+          trait_data_flat$pft_type == modeltype
+      ])
+      trait.names <- unique(trait_data_flat$trait_name[
+        trait_data_flat$pft_id %in% pft_ids
+      ])
+    }
+
+    # Call get.trait.data.pft with trait_data instead of dbcon
+    result <- lapply(pfts, get.trait.data.pft,
+                     modeltype   = modeltype,
+                     dbfiles     = dbfiles,
+                     dbcon       = NULL,             
+                     trait_data  = trait_data_flat,  
+                     write       = write,
+                     forceupdate = forceupdate,
+                     trait.names = trait.names)
+
+    return(invisible(result))  
+  }
+
+
   dbcon <- db.open(database)
   on.exit(db.close(dbcon), add = TRUE)