Fixed some global variables in PEcAn.DB package

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

@@ -27,11 +27,12 @@
 ##' @param trait.names Character vector of trait names to search. If
 ##'   `NULL` (default), use all traits that have a prior for at least
 ##'   one of the `pfts`.
+##' @param update logical: Rerun the db if result files already exist?
 ##' @return list of PFTs with update posteriorids
 ##' @author David LeBauer, Shawn Serbin, Alexey Shiklomanov
 ##' @export
 get.trait.data <- function(pfts, modeltype, dbfiles, database, forceupdate,
-                           trait.names = NULL) {
+                           trait.names = NULL, update = FALSE) {
   if (!is.list(pfts)) {
     PEcAn.logger::logger.severe('pfts must be a list')
   }
@@ -56,7 +57,7 @@ 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 = update)
     trait.names <- unique(unlist(lapply(all_priors_list, rownames)))
     # Eventually, can replace with this:
     # all_priors <- query_priors(pfts, params = database)
@@ -69,7 +70,8 @@ get.trait.data <- function(pfts, modeltype, dbfiles, database, forceupdate,
                    dbfiles = dbfiles,
                    dbcon = dbcon,
                    forceupdate = forceupdate,
-                   trait.names = trait.names)
+                   trait.names = trait.names,
+                   update = update)
 
   invisible(result)
 }

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

@@ -17,11 +17,12 @@
 ##' @param dbcon database connection
 ##' @param forceupdate set this to true to force an update, auto will check to see if an update is needed.
 ##' @param trait.names list of trait names to retrieve
+##' @param update logical: Rerun the db if result files already exist?
 ##' @return updated pft with posteriorid
 ##' @author David LeBauer, Shawn Serbin, Rob Kooper
 ##' @export
 get.trait.data.pft <- function(pft, modeltype, dbfiles, dbcon, trait.names,
-                               forceupdate = FALSE) {
+                               forceupdate = FALSE, update = FALSE) {
 
   # Create directory if necessary
   if (!file.exists(pft$outdir) && !dir.create(pft$outdir, recursive = TRUE)) {
@@ -68,7 +69,11 @@ 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 = 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 logical: Rerun the db if result files already exist?
 ##'
 ##' @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 = FALSE, ...){
 
   if (inherits(pft, "integer64")) {
     # Convert to character with correct representation
@@ -41,16 +42,9 @@ query.priors <- function(pft, trstr = NULL, con = NULL, ...){
   if (is.null(con)) {
     params <- list(...)
     if (!length(params)) {
-      PEcAn.logger::logger.warn(paste0(
-        "No connection (`con`) or params (`...`) specified. ",
-        'Trying to connect from `settings[[c("database", "bety")]]`.'
-      ))
-      if (!exists("settings")) {
-        PEcAn.logger::logger.severe(
-          "`settings` object not found. Unable to connect to database."
-        )
-      }
-      params <- settings[[c("database", "bety")]]
+      PEcAn.logger::logger.severe(
+        "No connection (`con`) specified and no connection parameters given in `...`.",
+        "Unable to connect to database.")
     }
     con <- db.open(params)
     on.exit(db.close(con), add = TRUE)