Add function to Optionally get site.info if not present

base/db/NAMESPACE

@@ -30,6 +30,7 @@ export(derive.traits)
 export(dplyr.count)
 export(fancy_scientific)
 export(get.id)
+export(get.new.site)
 export(get.trait.data)
 export(get.trait.data.pft)
 export(get_postgres_envvars)

base/db/R/get.new.site.R

@@ -0,0 +1,53 @@
+#-------------------------------------------------------------------------------
+# Copyright (c) 2012 University of Illinois, NCSA.
+# All rights reserved. This program and the accompanying materials
+# are made available under the terms of the
+# University of Illinois/NCSA Open Source License
+# which accompanies this distribution, and is available at
+# http://opensource.ncsa.illinois.edu/license.html
+#-------------------------------------------------------------------------------
+
+##' Get new site info using provided site information
+##'
+##' @title Get New Site Info
+##' @param site a dataframe with site information including id, lat, lon, and time_zone.
+##' @param con Database connection object.
+##' @param latlon Optional global latlon object which will store updated lat/lon.
+##' @return a dataframe with new site information on lat, lon and time_zone
+##' @export
+##' @author Abhinav Pandey
+##'
+##' @examples
+##' get.new.site(site=data.frame(id=1,lat=40.1,lon=-88.2,time_zone="UTC"),con=con,latlon=NULL)
+
+get.new.site <- function(site, con, latlon = NULL) {
+    # Check if site dataframe has an id column
+    if (is.null(site$id)) {
+        # Trying to stop current running process if no ID present.
+        # Currently, i want to replace this with a helper function which will check for the ID
+        ## If ID is not present, the helper function will generate a new one.
+        PEcAn.logger::logger.error("Site dataframe does not have an id column")
+    }
+
+    # setup site database number, lat, lon and name and copy for format.vars if new input
+    if (is.null(site$lat) | is.null(site$lon)) {
+        latlon <- query.site(site$id, con = con)[c("lat", "lon")]
+        new.site <- data.frame(
+            id = as.numeric(site$id),
+            lat = latlon$lat,
+            lon = latlon$lon
+        )
+        str_ns <- paste0(new.site$lat, "-", new.site$lon)
+    } else {
+        new.site <- data.frame(
+            id = as.numeric(site$id),
+            lat = site$lat,
+            lon = site$lon
+        )
+        str_ns <- paste0(site$lat, "-", site$lon)
+    }
+
+    site.info <- list(new.site = new.site, str_ns = str_ns)
+
+    return(site.info)
+}

base/workflow/R/do_conversions.R

@@ -9,6 +9,10 @@
 ##' @author Ryan Kelly, Rob Kooper, Betsy Cowdery, Istem Fer
 
 do_conversions <- function(settings, overwrite.met = FALSE, overwrite.fia = FALSE, overwrite.ic = FALSE) {
+
+  # extract site info from settings to be utilizes later in processing.
+  site.info <- settings$run$site
+
   if (PEcAn.settings::is.MultiSettings(settings)) {
     return(PEcAn.settings::papply(settings, do_conversions))
   }
@@ -52,7 +56,7 @@ do_conversions <- function(settings, overwrite.met = FALSE, overwrite.fia = FALS
     # IC conversion : for now for ED only, hence the css/pss/site check
     # <useic>TRUE</useic>
     if (ic.flag) {
-      settings <- PEcAn.data.land::ic_process(settings, input, dir = dbfiles, overwrite  = overwrite.ic)
+      settings <- PEcAn.data.land::ic_process(settings, input, dir = dbfiles, overwrite  = overwrite.ic, site = site.info)
       needsave <- TRUE
     }
 
@@ -88,7 +92,7 @@ do_conversions <- function(settings, overwrite.met = FALSE, overwrite.fia = FALS
         PEcAn.logger::logger.info("calling met.process: ",settings$run$inputs[[i]][['path']])
         settings$run$inputs[[i]] <- 
           PEcAn.data.atmosphere::met.process(
-            site       = settings$run$site, 
+            site       = site.info, 
             input_met  = settings$run$inputs$met,
             start_date = settings$run$start.date,
             end_date   = settings$run$end.date,

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

@@ -159,11 +159,12 @@ 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 = latlon$lat, 
-                         lon = latlon$lon)
-  str_ns <- paste0(new.site$id %/% 1e+09, "-", new.site$id %% 1e+09)
+  latlon <- NULL
+  site.info <- PEcAn.DB::get.new.site(site, con, latlon = latlon)
+
+  # extract new.site and str_ns from site.info
+  new.site <- site.info$new.site
+  str_ns <- site.info$str_ns
 
   if (is.null(format.vars$lat)) {
     format.vars$lat <- new.site$lat

modules/data.atmosphere/tests/testthat/test.met.process.R

@@ -8,7 +8,7 @@ test_that("`met.process` able to call .download.raw.met.module based on met proc
   mockery::stub(met.process, 'PEcAn.DB::query.format.vars', list())
   mockery::stub(met.process, 'PEcAn.DB::dbfile.check', list(id = 1))
   mockery::stub(met.process, 'assign', 1)
-  mockery::stub(met.process, 'PEcAn.DB::query.site', list(lat = 0, lon = 0))
+  mockery::stub(met.process, 'get.new.site', list(new.site = data.frame(id = 1, lat = 0, lon = 0), str_ns = "0-0"))
   mockery::stub(met.process, 'met.process.stage', list(download.raw = TRUE, met2cf = FALSE, standardize = FALSE, met2model = FALSE))
 
   mocked_res <- mockery::mock(1)

modules/data.land/R/ic_process.R

@@ -6,14 +6,14 @@
 ##' @param input Taken from settings$run$inputs. This should include id, path, and source
 ##' @param dir settings$database$dbfiles
 ##' @param overwrite Default = FALSE. whether to force ic_process to proceed
+##' @param site Current site information
 ##'
 ##' @author Istem Fer, Hamze Dokoohaki
-ic_process <- function(settings, input, dir, overwrite = FALSE){
+ic_process <- function(settings, input, dir, overwrite = FALSE, site = settings$run$site){
 
 
   #--------------------------------------------------------------------------------------------------#
   # Extract info from settings and setup
-  site       <- settings$run$site
   model <- list()
     model$type <- settings$model$type
     model$id <- settings$model$id
@@ -49,12 +49,13 @@ ic_process <- function(settings, input, dir, overwrite = FALSE){
   con <- PEcAn.DB::db.open(dbparms$bety)
   on.exit(PEcAn.DB::db.close(con), add = TRUE)
 
-  #grab site lat and lon info
-  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)
+  latlon <- NULL
+  site.info <- PEcAn.DB::get.new.site(site, con, latlon = latlon)
+
+  # extract new.site and str_ns from site.info
+  new.site <- site.info$new.site
+  str_ns <- site.info$str_ns
 
   new.site$name <- settings$run$site$name
 

modules/data.land/R/soil_process.R

@@ -28,13 +28,14 @@ soil_process <- function(settings, input, dbfiles, overwrite = FALSE,run.local=T
   # set up bety connection
   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$lon)
-
-  str_ns <- paste0(new.site$id %/% 1e+09, "-", new.site$id %% 1e+09)
+
+  # setup site database number, lat, lon and name and copy for format.vars if new input
+  latlon <- NULL
+  site.info <- PEcAn.DB::get.new.site(site, con, latlon = latlon)
+
+  # extract new.site and str_ns from site.info
+  new.site <- site.info$new.site
+  str_ns <- site.info$str_ns
 
   outfolder <- file.path(dbfiles, paste0(input$source, "_site_", str_ns))