Simpler str_ns handling

modules/data.atmosphere/R/met.process.R

@@ -139,15 +139,34 @@ met.process <- function(site, input_met, start_date, end_date, model,
   if(is.null(model)){
     stage$model <- FALSE
   }
-  
-  
+
+
   # setup site database number, lat, lon and name and copy for format.vars if new input
-  latlon <- PEcAn.DB::query.site(site$id, con = con)[c("lat", "lon")] 
-  new.site <- data.frame(id = as.numeric(site$id), 
-                         lat = latlon$lat, 
-                         lon = latlon$lon)
-  str_ns <- paste0(new.site$id %/% 1e+09, "-", new.site$id %% 1e+09)
-
+  # TODO why are this and the original site object passed around together?
+  # Could we mutate `site` instead of assigning `new.site`?
+  new.site <- list(
+    id = site$id,
+    lat = site$lat,
+    lon = site$lon
+  )
+  if (is.null(new.site$id)) {
+    PEcAn.logger::logger.info(
+      "no site ID provided. Generating one from lat and lon"
+    )
+    new.site$id <- paste0("lat", new.site$lat, "_lon", new.site$lon)
+  }
+  if (is.null(site$lat) || is.null(new.site$lon)) {
+    latlon <- PEcAn.DB::query.site(site$id, con = con)[c("lat", "lon")]
+    new.site$lat <- latlon$lat
+    new.site$lon <- latlon$lon
+  }
+  if (is.numeric(new.site$id) && new.site$id > 1e9) {
+    # Assume this is a BETY id, format as [server id]-[record number]
+    str_ns <- paste0(new.site$id %/% 1e+09, "-", new.site$id %% 1e+09)
+  } else {
+    str_ns <- as.character(new.site$id)
+  }
+
   if (is.null(format.vars$lat)) {
     format.vars$lat <- new.site$lat
   }

modules/data.land/R/ic_process.R

@@ -13,15 +13,16 @@ ic_process <- function(settings, input, dir, overwrite = FALSE){
 
   #--------------------------------------------------------------------------------------------------#
   # Extract info from settings and setup
-  site       <- settings$run$site
-  model <- list()
-    model$type <- settings$model$type
-    model$id <- settings$model$id
-  host       <- settings$host
-  dbparms    <- settings$database
+  site <- settings$run$site
+  model <- list(
+    type = settings$model$type,
+    id = settings$model$id
+  )
+  host <- settings$host
+  dbparms <- settings$database
 
   # Handle IC Workflow locally
-  if(host$name != "localhost"){
+  if (host$name != "localhost") {
     host$name <- "localhost"
     dir       <- settings$database$dbfiles
   }
@@ -48,26 +49,27 @@ ic_process <- function(settings, input, dir, overwrite = FALSE){
   # set up bety connection
   con <- PEcAn.DB::db.open(dbparms$bety)
   on.exit(PEcAn.DB::db.close(con), add = TRUE)
-  
+
   #grab site lat and lon info
 
   # check if site metadata is available in the settings$run$site
-  if (isTRUE(nzchar(settings$run$site$lat)) && isTRUE(nzchar(settings$run$site$lon))) {
+  if (isTRUE(nzchar(site$lat)) && isTRUE(nzchar(site$lon))) {
     # if lat and lon are available, use them directly
-    latlon <- data.frame(lat = settings$run$site$lat, lon = settings$run$site$lon)
+    latlon <- data.frame(lat = site$lat, lon = site$lon)
   } else {
     # otherwise, query the site information from the database
     latlon <- PEcAn.DB::query.site(site$id, con = con)[c("lat", "lon")]
   }
 
   # setup site database number, lat, lon and name and copy for format.vars if new input
-  new.site <- data.frame(id = as.numeric(site$id),
-                         lat = latlon$lat,
-                         lon = latlon$lon)
-
-  new.site$name <- settings$run$site$name
-
-  if (isTRUE(new.site$id > 1e9)) {
+  new.site <- list(
+    id = site$id,
+    lat = latlon$lat,
+    lon = latlon$lon,
+    name = site$name
+  )
+
+  if (is.numeric(new.site$id) && isTRUE(new.site$id > 1e9)) {
     # Assume this is a BETYdb id, condense for readability
     str_ns <- paste0(new.site$id %/% 1e+09, "-", new.site$id %% 1e+09)
   } else {

modules/data.land/R/soil_params_ensemble.R

@@ -159,9 +159,13 @@ soil_params_ensemble_soilgrids <- function(settings,sand,clay,silt,outdir,write_
   PATH <- foreach::foreach(i = seq_along(dat), .packages = c("Kendall", "purrr", "PEcAn.data.land"), .options.snow=opts) %dopar% {
     samples_ens <- list()
     paths <- c()
-    siteid <- as.numeric(unique(dat[[i]]$siteid))
+    siteid <- unique(dat[[i]]$siteid)
     soil_depth <- unique(dat[[i]]$soil_depth)
-    str_ns <- paste0(siteid %/% 1e+09, "-", siteid %% 1e+09)
+    if (is.numeric(siteid) && siteid > 1e9) {
+      str_ns <- paste0(siteid %/% 1e+09, "-", siteid %% 1e+09)
+    } else {
+      str_ns <- as.character(siteid)
+    }
     temp_outdir <- file.path(outdir, siteid)
     dir.create(temp_outdir)
     # Estimate Dirichlet parameters for each depth at each site

modules/data.land/R/soil_process.R

@@ -31,12 +31,14 @@ soil_process <- function(settings, input, dbfiles, overwrite = FALSE,run.local=T
   con <- PEcAn.DB::db.open(dbparms$bety)
   on.exit(PEcAn.DB::db.close(con), add = TRUE)
   # get site info
-  latlon <- PEcAn.DB::query.site(site$id, con = con)[c("lat", "lon")]
-  new.site <- data.frame(id = as.numeric(site$id),
-                         lat = latlon$lat,
-                         lon = latlon$lon)
+  if (isTRUE(nzchar(site$lat)) && isTRUE(nzchar(site$lon))) {
+    latlon <- data.frame(lat = site$lat, lon = site$lon)
+  } else {
+    latlon <- PEcAn.DB::query.site(site$id, con = con)[c("lat", "lon")]
+  }
+  new.site <- list(id = site$id, lat = latlon$lat, lon = latlon$lon)
 
-  if (isTRUE(new.site$id > 1e9)) {
+  if (is.numeric(new.site$id) && isTRUE(new.site$id > 1e9)) {
     # Assume this is a BETYdb id, condense for readability
     str_ns <- paste0(new.site$id %/% 1e+09, "-", new.site$id %% 1e+09)
   } else {
@@ -45,7 +47,7 @@ soil_process <- function(settings, input, dbfiles, overwrite = FALSE,run.local=T
 
   outfolder <- file.path(dbfiles, paste0(input$source, "_site_", str_ns))
 
-  if(!dir.exists(outfolder)) dir.create(outfolder)
+  if (!dir.exists(outfolder)) dir.create(outfolder)
   #--------------------------------------------------------------------------------------------------#
   # if we are reading from gSSURGO
   if (input$source=="gSSURGO"){