Merge pull request #3308 from Sweetdevil144/develop

Remove `db.site.lat.lon` function and replace all usages with `query.site`
PecanProject · Jun 21, 2024 · c027ba2 · c027ba2
2 parents 50d0499 + 9b1b976
commit c027ba2
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Showing 5 changed files with 7 additions and 46 deletions.
diff --git a/modules/data.atmosphere/NAMESPACE b/modules/data.atmosphere/NAMESPACE
@@ -14,7 +14,6 @@ export(cfmet.downscale.time)
 export(check_met_input_file)
 export(closest_xy)
 export(cos_solar_zenith_angle)
-export(db.site.lat.lon)
 export(debias.met)
 export(debias.met.regression)
 export(download.Ameriflux)

diff --git a/modules/data.atmosphere/NEWS.md b/modules/data.atmosphere/NEWS.md
@@ -24,6 +24,7 @@
 ## Removed
 
 *  Helper function `robustly` has moved to package PEcAn.utils [@meetagrawal, #3096]
+*  Helper function `db.site.lat.lon` has been removed. Users should use `PEcAn.DB::query.site(id, con)[c("lat", "lon")]` instead [@Sweetdevil144, #3308]
 
 
 # PEcAn.data.atmosphere 1.7.1

diff --git a/modules/data.atmosphere/R/met.process.R b/modules/data.atmosphere/R/met.process.R
@@ -159,9 +159,10 @@ met.process <- function(site, input_met, start_date, end_date, model,
   }
 
   # setup site database number, lat, lon and name and copy for format.vars if new input
+  latlon <- PEcAn.DB::query.site(site$id, con = con)[c("lat", "lon")] 
   new.site <- data.frame(id = as.numeric(site$id), 
-                         lat = db.site.lat.lon(site$id, con = con)$lat, 
-                         lon = db.site.lat.lon(site$id, con = con)$lon)
+                         lat = latlon$lat, 
+                         lon = latlon$lon)
   str_ns <- paste0(new.site$id %/% 1e+09, "-", new.site$id %% 1e+09)
 
   if (is.null(format.vars$lat)) {
@@ -401,27 +402,6 @@ met.process <- function(site, input_met, start_date, end_date, model,
   return(input_met) # Returns an updated $met entry for the settings object.
 } # met.process
 
-################################################################################################################################# 
-
-##' Look up lat/lon from siteid
-##'
-##' @export
-##' @param site.id BeTY ID of site to look up
-##' @param con database connection
-##' @author Betsy Cowdery
-db.site.lat.lon <- function(site.id, con) {
-  site <- PEcAn.DB::db.query(paste("SELECT id, ST_X(ST_CENTROID(geometry)) AS lon, ST_Y(ST_CENTROID(geometry)) AS lat FROM sites WHERE id =", 
-                         site.id), con)
-  if (nrow(site) == 0) {
-   PEcAn.logger::logger.error("Site not found")
-    return(NULL)
-  }
-  if (!(is.na(site$lat)) && !(is.na(site$lat))) {
-    return(list(lat = site$lat, lon = site$lon))
-  } else {
-   PEcAn.logger::logger.severe("We should not be here!")
-  }
-} # db.site.lat.lon
 
 ################################################################################################################################# 
 

diff --git a/modules/data.atmosphere/man/db.site.lat.lon.Rd b/modules/data.atmosphere/man/db.site.lat.lon.Rd
diff --git a/modules/data.land/inst/LoadPalEONsites.R b/modules/data.land/inst/LoadPalEONsites.R
@@ -164,10 +164,10 @@ for(i in seq_along(paleon.sitegroups)){
     sitename <- db.query(paste0("SELECT sitename from sites where id =",site_id),con)
     str_ns <- paste0(site_id %/% 1e+09, "-", site_id %% 1e+09)
     outfile <- paste0("PalEONregional_CF_site_", str_ns)
-
+    latlon <- PEcAn.DB::query.site(site$id, con = con)[c("lat", "lon")] 
     site.info <- rbind(site.info,data.frame(id = site_id, 
-                           lat = db.site.lat.lon(site_id, con = con)$lat, 
-                           lon = db.site.lat.lon(site_id, con = con)$lon,
+                           lat = latlon$lat, 
+                           lon = latlon$lon,
                            str_ns = str_ns,
                            outfile = outfile))
   }