Merge pull request #77 from ErikKusch/Development

Development

.Rbuildignore

@@ -3,3 +3,5 @@
 ^packrat/
 ^\.Rprofile$
 ^LICENSE\.md$
+^data-raw$
+^metadata$

.gitignore

@@ -4,5 +4,14 @@
 .Ruserdata
 
 packrat/
-**/Test/*
 
+
+# OS generated files #
+######################
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db

DESCRIPTION

@@ -1,36 +1,33 @@
 Package: KrigR
 Type: Package
-Title: Downloading, Aggregating, and Kriging of ERA5(Land)-Data
-Version: 0.1.3
+Title: Downloading, Aggregating, and Kriging of ECMWF CDS-Data
+Version: 0.3.0
 Authors@R: as.person(c(
     "Erik Kusch <[email protected]> [aut, cre]", 
     "Richard Davy <[email protected]> [aut]"
   ))
-Description: An R Package for downloading, preprocessing, and statistical downscaling of the European Centre for Medium-range Weather Forecasts ReAnalysis 5 (ERA5) family provided by the European Centre for Medium‐Range Weather Forecasts (ECMWF).
+Description: An R Package for downloading, preprocessing, and statistical downscaling of data provided by the European Centre for Medium‐Range Weather Forecasts (ECMWF).
     KrigR contains functions for:
-    - Downloading Era5(Land) data directly from within R
-    - Downloading USGS GMTED 2010 elevation data
+    - Downloading ECMWF data directly from within R
+    - Downloading USGS GMTED 2010 elevation data - Working towards also implementing support for HWSD data
+    - Preparing covariate data for Kriging
     - Kriging spatial input to desired output using user-specified covariates
-    - Downloading and Kriging Era5(Land) data using USGS GMTED 2010 elevation as coviariate data in one function call
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.3
-Depends: 
-    ncdf4, 
+RoxygenNote: 7.3.1
+Imports:
     ecmwfr,
-    keyring,
-    stringr, 
-    raster,
-    rgdal,
-    doParallel,
-    foreach,
-    doSNOW, 
-    automap,
+    httr,
+    stringr,
     lubridate,
-    sp,
     sf,
-    fasterize,
-    stars,
-    httr,
-    terra
+    terra,
+    ncdf4,
+    automap,
+    foreach,
+    tools,
+    progress,
+    doSNOW,
+    pbapply
+Depends: R (>= 4.0.0) 

NAMESPACE

@@ -1,10 +1,75 @@
 # Generated by roxygen2: do not edit by hand
 
 export(BioClim)
+export(Buffer.pts)
+export(CDownloadS)
+export(Check.File)
+export(CovariateSetup)
+export(Ext.Check)
+export(Handle.Spatial)
+export(Kriging)
+export(Make.SpatialPoints)
+export(Make.UTC)
+export(Meta.DOI)
+export(Meta.List)
+export(Meta.QuickFacts)
+export(Meta.Read)
+export(Meta.Variables)
 export(SummarizeRaster)
 export(buffer_Points)
-export(check_Krig)
 export(download_DEM)
 export(download_ERA)
 export(krigR)
 export(mask_Shape)
+importFrom(automap,autoKrige)
+importFrom(doSNOW,registerDoSNOW)
+importFrom(ecmwfr,wf_get_key)
+importFrom(ecmwfr,wf_request)
+importFrom(ecmwfr,wf_set_key)
+importFrom(ecmwfr,wf_transfer)
+importFrom(foreach,"%dopar%")
+importFrom(foreach,foreach)
+importFrom(httr,DELETE)
+importFrom(httr,GET)
+importFrom(httr,add_headers)
+importFrom(httr,authenticate)
+importFrom(httr,progress)
+importFrom(httr,write_disk)
+importFrom(lubridate,days_in_month)
+importFrom(methods,getClass)
+importFrom(ncdf4,nc_close)
+importFrom(ncdf4,nc_open)
+importFrom(ncdf4,ncatt_get)
+importFrom(ncdf4,ncatt_put)
+importFrom(parallel,makeCluster)
+importFrom(parallel,stopCluster)
+importFrom(pbapply,pblapply)
+importFrom(progress,progress_bar)
+importFrom(sf,st_as_sf)
+importFrom(sf,st_bbox)
+importFrom(sf,st_buffer)
+importFrom(sf,st_coordinates)
+importFrom(sf,st_drop_geometry)
+importFrom(sf,st_union)
+importFrom(stringr,str_c)
+importFrom(stringr,str_pad)
+importFrom(terra,aggregate)
+importFrom(terra,app)
+importFrom(terra,crop)
+importFrom(terra,crs)
+importFrom(terra,ext)
+importFrom(terra,mask)
+importFrom(terra,metags)
+importFrom(terra,nlyr)
+importFrom(terra,rast)
+importFrom(terra,res)
+importFrom(terra,resample)
+importFrom(terra,subset)
+importFrom(terra,tapp)
+importFrom(terra,time)
+importFrom(terra,units)
+importFrom(terra,values)
+importFrom(terra,varnames)
+importFrom(terra,writeCDF)
+importFrom(terra,writeRaster)
+importFrom(tools,file_path_sans_ext)

R/BioClim.R

@@ -60,6 +60,8 @@ BioClim <- function(Water_Var = "volumetric_soil_water_layer_1", # could also be
                     TimeOut = 36000,
                     SingularDL = FALSE){
 
+  stop("Function currently deprecated as KrigR undergoes major re-development. Please use the stable release to gain access to this functionality.")
+
   Vars <- c("2m_temperature", Water_Var)
 
   if(Y_end == year(Sys.Date())){

R/CDSAPI.R

@@ -0,0 +1,205 @@
+### CDS API Credentials ========================================================
+#' Register CDS API Credentials
+#'
+#' Just checks if provided API user and Key have already been added to keychain and adds them if necessary.
+#'
+#' @param API_User Character. CDS API User
+#' @param API_Key Character. CDS API Key
+#'
+#' @importFrom ecmwfr wf_get_key
+#' @importFrom ecmwfr wf_set_key
+#'
+#' @return No R object. An addition to the keychain if necessary.
+#'
+#' @seealso \code{\link{Make.Request}}, \code{\link{Execute.Requests}}.
+#'
+Register.Credentials <- function(API_User, API_Key){
+  API_Service = "cds"
+  KeyRegisterCheck <- tryCatch(ecmwfr::wf_get_key(user = API_User, service = API_Service),
+                               error = function(e){e})
+  if(any(class(KeyRegisterCheck) == "simpleError")){
+    ecmwfr::wf_set_key(user = API_User,
+                       key = as.character(API_Key),
+                       service = API_Service)
+  }
+}
+### FORMING CDS Requests =======================================================
+#' Form CDS Requests
+#'
+#' Loops over time windows of defined size and creates a list of CDS requests.
+#'
+#' @param QueryTimeWindows List. List of date ranges created by \code{\link{Make.RequestWindows}}.
+#' @param QueryDataSet Character. Dataset specified by user.
+#' @param QueryType Character. Dataset type specified by user.
+#' @param QueryVariable Character. CDS internal variable name.
+#' @param QueryTimes Character. Layers of data in the raw data set
+#' @param QueryExtent Character. Extent object created by Check.Ext(Extent)[c(4,1,3,2)]
+#' @param QueryFormat Character. File format queried by user
+#' @param Dir Directory pointer. Where to store CDS request outcomes.
+#' @param verbose Logical. Whether to print/message function progress in console or not.
+#' @param API_User Character. CDS API User
+#' @param API_Key Character. CDS API Key
+#'
+#' @importFrom ecmwfr wf_request
+#'
+#' @return List. Each element holding either (1) a list object representing a CDS request or (2) the value NA indicating that a file of this name is already present.
+#'
+#' @seealso \code{\link{Make.RequestWindows}}, \code{\link{Register.Credentials}}, \code{\link{Execute.Requests}}.
+#'
+Make.Request <- function(QueryTimeWindows, QueryDataSet, QueryType, QueryVariable,
+                         QueryTimes, QueryExtent, QueryFormat, Dir = getwd(), verbose = TRUE,
+                         API_User, API_Key){
+  #' Make list of CDS Requests
+  Requests_ls <- lapply(1:length(QueryTimeWindows), FUN = function(requestID){
+    FName <- paste("TEMP", QueryVariable, stringr::str_pad(requestID, 5, "left", "0"), sep = "_")
+    if(grepl("month", QueryType)){ # monthly data needs to be specified with year, month fields
+      list('dataset_short_name' = QueryDataSet,
+           'product_type'   = QueryType,
+           'variable'       = QueryVariable,
+           'year'           = unique(as.numeric(format(as.POSIXct(QueryTimeWindows[[requestID]]), "%Y"))),
+           'month'          = unique(as.numeric(format(QueryTimeWindows[[requestID]], "%m"))),
+           'time'           = QueryTimes,
+           'area'           = QueryExtent,
+           'format'         = QueryFormat,
+           'target'         = FName
+           # ,
+           # 'grid'           = QueryGrid
+      )
+    }else{
+      list('dataset_short_name' = QueryDataSet,
+           'product_type'   = QueryType,
+           'variable'       = QueryVariable,
+           'date'           = paste0(
+             head(QueryTimeWindows[[requestID]], n = 1),
+             "/",
+             tail(QueryTimeWindows[[requestID]], n = 1)),
+           'time'           = QueryTimes,
+           'area'           = QueryExtent,
+           'format'         = QueryFormat,
+           'target'         = FName
+           # ,
+           # 'grid'           = QueryGrid
+      )
+    }
+
+  })
+  ## making list names useful for request execution updates to console
+  Iterators <- paste0("[", 1:length(Requests_ls), "/", length(Requests_ls), "] ")
+  FNames <- unlist(lapply(Requests_ls, "[[", "target"))
+  Dates <- unlist(lapply(lapply(Requests_ls, "[[", "date"), gsub, pattern = "/", replacement = " - "))
+  if(length(Dates) == 0){ # this happens for monthly data queries
+    Dates <- unlist(lapply(lapply(Requests_ls, "[[", "year"), FUN = function(x){
+      paste0(head(x, 1), " - ", tail(x, 1))
+    }))
+  }
+  names(Requests_ls) <- paste0(Iterators, FNames, " (UTC: ", Dates, ")")
+  ## check if files are already present
+  FCheck <- sapply(FNames, Check.File, Dir = Dir, loadFun = "terra::rast", load = FALSE,
+                   verbose = FALSE)
+  if(length(names(unlist(FCheck))) > 0){
+    Requests_ls[match(names(unlist(FCheck)), FNames)] <- NA
+  }
+  Requests_ls
+
+  if(verbose){print("## Staging CDS Requests")}
+  for(requestID in 1:length(Requests_ls)){ ## looping over CDS requests
+    if(verbose){print(names(Requests_ls)[requestID])}
+    if(class(Requests_ls[[requestID]]) == "logical"){
+      # if(verbose){print("File with this name is already present.")}
+      next()
+    }
+    API_request <- suppressMessages({
+      ecmwfr::wf_request(user = API_User,
+                         request = Requests_ls[[requestID]],
+                         transfer = FALSE,
+                         path = Dir,
+                         verbose = verbose,
+                         time_out = TimeOut)
+    })
+    Requests_ls[[requestID]]$API_request <- API_request
+  }
+  Requests_ls
+}
+
+### EXECUTING CDS REQUESTS  ====================================================
+#' Execute CDS Requests
+#'
+#' Loops over list of fully formed ecmwfr requests and executes these on CDS.
+#'
+#' @param Requests_ls List. ecmwfr-ready CDS requests formed with \code{\link{Make.Request}}.
+#' @param Dir Character. Directory where to save raw data.
+#' @param API_User Character. CDS API User
+#' @param API_Key Character. CDS API Key
+#' @param TryDown Numeric. How often to retry a failing request/download
+#' @param verbose Logical. Whether to print/message function progress in console or not.
+#'
+#' @importFrom ecmwfr wf_transfer
+#' @importFrom httr DELETE
+#' @importFrom httr authenticate
+#' @importFrom httr add_headers
+#'
+#' @return No R object. Resulting files of CDS query/queries in signated directory.
+#'
+#' @seealso \code{\link{Register.Credentials}}, \code{\link{Make.Request}}.
+#'
+Execute.Requests <- function(Requests_ls, Dir, API_User, API_Key, TryDown, verbose = TRUE){
+  if(verbose){print("## Listening for CDS Requests")}
+  for(requestID in 1:length(Requests_ls)){ ## looping over CDS requests
+    if(verbose){print(names(Requests_ls)[requestID])}
+    if(class(Requests_ls[[requestID]]) == "logical"){
+      if(verbose){print("File with this name is already present.")}
+      next()
+    }
+    API_request <- Requests_ls[[requestID]]$API_request
+    FileDown <- list(state = "queued")
+    Down_try <- 0
+    while(FileDown$state != "completed" & Down_try <= TryDown){
+      ## console output that shows the status of the request on CDS
+      if(verbose){
+        if(FileDown$state == "queued"){
+          for(rep_iter in 1:10){
+            cat(rep(" ", 100))
+            flush.console()
+            cat('\r', "Waiting for CDS to start processing the query", rep(".", rep_iter))
+            flush.console()
+            Sys.sleep(0.5)
+          }
+        }
+        if(FileDown$state == "running"){
+          for(rep_iter in 1:10){
+            cat(rep(" ", 100))
+            flush.console()
+            cat('\r', "CDS is processing the query", rep(".", rep_iter))
+            flush.console()
+            Sys.sleep(0.5)
+          }
+        }
+      }
+      ## download file for current request when ready
+      FileDown <- tryCatch(ecmwfr::wf_transfer(url = API_request$get_url(),
+                                               user = API_User,
+                                               service = "cds",
+                                               verbose = TRUE,
+                                               path = Dir,
+                                               filename = API_request$get_request()$target),
+                           error = function(e){e}
+      )
+      if(Down_try == TryDown){
+        stop("Download of CDS query result continues to fail after ", Down_try, " trys. The most recent error message is: \n", FileDown,  "Assess issues at https://cds.climate.copernicus.eu/cdsapp#!/yourrequests.")
+      }
+      if(any(class(FileDown) == "simpleError")){
+        FileDown <- list(state = "queued")
+        Down_try <- Down_try+1
+      }
+    }
+    if(FileDown$state == "completed"){
+      delete <- httr::DELETE(
+        API_request$get_url(),
+        httr::authenticate(API_User, API_Key),
+        httr::add_headers(
+          "Accept" = "application/json",
+          "Content-Type" = "application/json")
+      )
+    }
+  }
+}