Merge pull request PecanProject#2971 from nanu1605/db_global_variable

Fixed some global variables in PEcAn.DB package
DiviyamPathak · Aug 1, 2022 · 1cc3d7f · 1cc3d7f
2 parents 8b55da9 + 1d3ae6c
commit 1cc3d7f
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Showing 4 changed files with 9 additions and 13 deletions.
diff --git a/base/db/R/get.trait.data.pft.R b/base/db/R/get.trait.data.pft.R
@@ -68,7 +68,10 @@ 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)
   prior.distns <- prior.distns[which(!rownames(prior.distns) %in% names(pft$constants)),]
   traits <- rownames(prior.distns)
 

diff --git a/base/db/R/query.dplyr.R b/base/db/R/query.dplyr.R
@@ -268,7 +268,7 @@ load_data_single_run <- function(bety, workflow_id, run_id) {
   ncfile <- list.files(path = outputfolder, pattern = "\\.nc$", full.names = TRUE)[1]
   nc <- ncdf4::nc_open(ncfile)
 
-  globalDF <- tidyr::gather(out, key = var_name, value = vals, names(out)[names(out) != "posix"]) %>%
+  globalDF <- tidyr::gather(out, key = "var_name", value = "vals", names(out)[names(out) != "posix"]) %>%
     dplyr::rename(dates = .data$posix)
   globalDF$workflow_id <- workflow_id
   globalDF$run_id <- run_id

diff --git a/base/db/R/query.prior.R b/base/db/R/query.prior.R
@@ -41,16 +41,9 @@ 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)

diff --git a/base/db/R/utils_db.R b/base/db/R/utils_db.R
@@ -322,7 +322,7 @@ db.exists <- function(params, write = TRUE, table = NA) {
   }
 
   #check table's privilege about read and write permission
-  user.permission <<- tryCatch({
+  user.permission <- tryCatch({
     invisible(db.query(
       paste0("SELECT privilege_type FROM information_schema.role_table_grants ",
              "WHERE grantee='", params$user,