fixing fetchNASIS(from = "pedon_report")

uncode was set to use local db, now using the cached metadata file

R/fetchNASIS_pedons.R

@@ -3,9 +3,9 @@
 # get NASIS site/pedon/horizon/diagnostic feature data
 .fetchNASIS_pedons <- function(SS=TRUE, rmHzErrors=TRUE, nullFragsAreZero=TRUE, soilColorState='moist', lab=FALSE, stringsAsFactors = default.stringsAsFactors()) {
 
-  # test connection, should not be required, can be used if from = "pedon_report"
+  # test connection
   if(! 'nasis_local' %in% names(RODBC::odbcDataSources()))
-    warning('Local NASIS ODBC connection has not been setup. Please see `http://ncss-tech.github.io/AQP/soilDB/setup_local_nasis.html`.')
+    stop('Local NASIS ODBC connection has not been setup. Please see `http://ncss-tech.github.io/AQP/soilDB/setup_local_nasis.html`.')
 
   # sanity check
   if(! soilColorState %in% c('dry', 'moist'))

R/fetchNASIS_report.R

@@ -41,7 +41,7 @@
       # remove
       x2 <- x2[!is.na(x2$peiid), - ncol(x2)]
       idx <- names(x2) %in% c("pmkind", "pmorigin")
-      x2[!idx] <- uncode(x2[!idx])
+      x2[!idx] <- uncode(x2[!idx], db = "LIMS")
       idx <- sapply(x2, is.character)
       x2[idx] <- lapply(x2[idx], function(x) ifelse(x == "", NA, x))
       return(x2)
@@ -154,7 +154,7 @@
   # remove
   temp = temp[!is.na(temp$peiid), - ncol(temp)]
   idx  = names(temp) %in% c("pmkind", "pmorigin")
-  temp[!idx] = uncode(temp[!idx])
+  temp[!idx] = uncode(temp[!idx], db = "LIMS")
   idx  = sapply(temp, is.character)
   temp[idx] = lapply(temp[idx], function(x) ifelse(x == "", NA, x))
   # temp = within(temp, {
@@ -193,7 +193,7 @@
   # NASIS text reports return empty columns
   # remove
   temp = temp[!is.na(temp$peiid), - ncol(temp)]
-  temp = uncode(temp)
+  temp = uncode(temp, db = "LIMS")
   # temp = within(temp, {
   #   obsdate   = as.Date(as.character(obsdate))
   #   classdate = as.Date(as.character(classdate))