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Add flat-file bypass for get.trait.data() #3601

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Add flat-file bypass for get.trait.data() #3601

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67b6e52
added changed to read values from csv file
Aug 21, 2025
35b8fb6
updated get.trait.data to accept input_file for file_path
Aug 28, 2025
3d0956d
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infotroph Sep 22, 2025
95fdc7a
Merge branch 'develop' into render_get.trait.data
infotroph Sep 29, 2025
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42 changes: 41 additions & 1 deletion base/db/R/get.trait.data.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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')
Expand All @@ -42,6 +43,45 @@ 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
if(is.null(file_path)){
file.path <- pfts$file_path
}
use_flatfile <- !is.null(file_path) && file.exists(file_path)
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I suggest throwing an error if file_path is specified but the file doesn't exist, rather than revert to DB mode (which would be surprising to the user).


if (use_flatfile) {
Comment on lines +46 to +53
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Possible implementation of the error-if-not-exist pattern (If you like this, need to also add @importFrom rlang %||% in the Roxygen block above):

Suggested change
#check for flatfile path if present use it
file_path <- input_file
if(is.null(file_path)){
file.path <- pfts$file_path
}
use_flatfile <- !is.null(file_path) && file.exists(file_path)
if (use_flatfile) {
#check for flatfile path, if present use it
file_path <- input_file %||% pfts$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(pfts$file_path, stringsAsFactors = FALSE)
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Suggested change
trait_data_flat <- read.csv(pfts$file_path, stringsAsFactors = FALSE)
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)

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