Fixed some global variables in PEcAn.DB package

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

@@ -56,7 +56,7 @@ get.trait.data <- function(pfts, modeltype, dbfiles, database, forceupdate,
     # `query_priors`, but haven't done so yet because that requires
     # prepared statements and therefore requires the Postgres driver. 
     all_priors_list <- lapply(format(pft_ids, scientific = FALSE), query.priors,
-                              con = dbcon, trstr = trait.names)
+                              con = dbcon, trstr = trait.names, update = settings$db$update)
     trait.names <- unique(unlist(lapply(all_priors_list, rownames)))
     # Eventually, can replace with this:
     # all_priors <- query_priors(pfts, params = database)

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

@@ -68,7 +68,7 @@ get.trait.data.pft <- function(pft, modeltype, dbfiles, dbcon, trait.names,
     dplyr::mutate_if(is.character, ~dplyr::na_if(., ""))
 
   # get the priors
-  prior.distns <- PEcAn.DB::query.priors(pft = pftid, trstr = PEcAn.utils::vecpaste(trait.names), con = dbcon)
+  prior.distns <- PEcAn.DB::query.priors(pft = pftid, trstr = PEcAn.utils::vecpaste(trait.names), con = dbcon, update = settings$db$update)
   prior.distns <- prior.distns[which(!rownames(prior.distns) %in% names(pft$constants)),]
   traits <- rownames(prior.distns)
 

base/db/R/query.prior.R

@@ -22,6 +22,7 @@
 ##' @param con Database connection object.
 ##' @param ... Optional arguments for connecting to database (e.g.
 ##'   password, user name, database).
+##' @param update 
 ##'
 ##' @return `data.frame` of priors for each trait and the given PFT.
 ##' @export query.priors
@@ -31,7 +32,7 @@
 ##'   con <- db.open(...)
 ##'   query.priors("ebifarm.pavi", c("SLA", "Vcmax", "leaf_width"), con = con)
 ##' }
-query.priors <- function(pft, trstr = NULL, con = NULL, ...){
+query.priors <- function(pft, trstr = NULL, con = NULL, update, ...){
 
   if (inherits(pft, "integer64")) {
     # Convert to character with correct representation
@@ -50,7 +51,7 @@ query.priors <- function(pft, trstr = NULL, con = NULL, ...){
           "`settings` object not found. Unable to connect to database."
         )
       }
-      params <- settings[[c("database", "bety")]]
+      params <- update[[c("database", "bety")]]
     }
     con <- db.open(params)
     on.exit(db.close(con), add = TRUE)