Merge pull request #35 from florisvdh/download

Some work on zen4R::download_zenodo()

DESCRIPTION

@@ -8,7 +8,7 @@ Authors@R: c(
   person("Stephen", "Eglen", role = c("ctb"), comment = c(ORCID = "0000-0001-8607-8025")))
 Maintainer: Emmanuel Blondel <[email protected]>
 Depends: R (>= 3.3.0), methods
-Imports: R6, httr, jsonlite, xml2, keyring, tools
+Imports: R6, httr, jsonlite, xml2, keyring, tools, parallel
 Suggests: testthat
 Description: Provides an Interface to 'Zenodo' (<https://zenodo.org>) REST API, 
   including management of depositions, attribution of DOIs by 'Zenodo' and 
@@ -17,5 +17,6 @@ License: MIT + file LICENSE
 URL: https://github.com/eblondel/zen4R
 BugReports: https://github.com/eblondel/zen4R/issues
 LazyLoad: yes
-RoxygenNote: 7.1.0
-Roxygen: list(r6 = FALSE)
+RoxygenNote: 7.1.1
+Roxygen: list(r6 = FALSE)
+Encoding: UTF-8

NAMESPACE

@@ -12,5 +12,6 @@ import(keyring)
 import(methods)
 import(xml2)
 importFrom(R6,R6Class)
+importFrom(parallel,mclapply)
 importFrom(tools,file_path_as_absolute)
 importFrom(tools,md5sum)

R/ZenodoRecord.R

@@ -340,6 +340,9 @@
 #'    \code{makeCluster} and passed as \code{cl} argument. After downloading all files, the cluster
 #'    will be stopped automatically.
 #'    
+#'    The logical argument \code{quiet} (default is \code{FALSE}) can be set to 
+#'    suppress informative messages (not warnings).
+#'    
 #'    Additional arguments inherited from \code{parallel::mclapply} or the custom \code{parallel_handler}
 #'    can be added (eg. \code{mc.cores} for \code{mclapply})
 #'    
@@ -1148,58 +1151,66 @@ ZenodoRecord <-  R6Class("ZenodoRecord",
     },
 
     #downloadFiles
-    downloadFiles = function(path = ".", parallel = FALSE, parallel_handler = NULL, cl = NULL, ...){
+    downloadFiles = function(path = ".", parallel = FALSE, parallel_handler = NULL, cl = NULL, quiet = FALSE, ...){
       if(length(self$files)==0){
         self$WARN(sprintf("No files to download for record '%s' (doi: '%s')",
                           self$id, self$doi))
       }else{
-        files_summary <- sprintf("Download %s file%s from record '%s' (doi: '%s') - total size: %s",
+        files_summary <- sprintf("Will download %s file%s from record '%s' (doi: '%s') - total size: %s",
                                 length(self$files), ifelse(length(self$files)>1,"s",""), self$id, 
                                 self$doi, sum(sapply(self$files, function(x){x$filesize})))
 
         #download_file util
         download_file <- function(file){
-          cat(sprintf("[zen4R][INFO] Downloading file '%s' from record '%s' (doi: '%s') - size: %s\n", 
-                            file$filename, self$id, self$doi, file$filesize))
+          if (!quiet) cat(sprintf("[zen4R][INFO] Downloading file '%s' - size: %s\n", 
+                            file$filename, file$filesize))
+          target_file <-file.path(path, file$filename)
+          download.file(url = file$links$download, destfile = target_file, 
+                        quiet = quiet)
+        }          
+        #check_integrity util
+        check_integrity <- function(file){
           target_file <-file.path(path, file$filename)
-          download.file(url = file$links$download, destfile = target_file)
-
-          #check md5sum
           target_file_md5sum <- tools::md5sum(target_file)
           if(target_file_md5sum==file$checksum){
-            cat(sprintf("[zen4R][INFO] File '%s' successfully downloaded at '%s' and its integrity verified (md5sum: %s)\n",
-                        file$filename, tools::file_path_as_absolute(target_file), file$checksum))
+            if (!quiet) cat(sprintf("[zen4R][INFO] File '%s': integrity verified (md5sum: %s)\n",
+                        file$filename, file$checksum))
           }else{
-            warnMsg <- sprintf("[zen4R][WARN] Download issue: md5sum (%s) of file '%s' does not match Zenodo archive md4sum (%s)\n", 
+            warnMsg <- sprintf("[zen4R][WARN] Download issue: md5sum (%s) of file '%s' does not match Zenodo archive md5sum (%s)\n", 
                                target_file_md5sum, tools::file_path_as_absolute(target_file), file$checksum)
             cat(warnMsg)
             warning(warnMsg)
           }
         }
+
 
         if(parallel){
-          self$INFO("Download in parallel mode")
+          if (!quiet) self$INFO("Download in parallel mode")
           if(is.null(parallel_handler)){
-            self$INFO("Using default parallel 'mclapply' handler")
-            self$INFO(files_summary)
+            if (!quiet) self$INFO("Using default parallel 'mclapply' handler")
+            if (!quiet) self$INFO(files_summary)
             invisible(mclapply(self$files, download_file, ...))
           }else{
-            self$INFO("Using cluster-based parallel handler")
+            if (!quiet) self$INFO("Using cluster-based parallel handler")
             if(is.null(cl)){
               errMsg <- "No cluster object defined as 'cl' argument. Aborting file download..."
               self$ERROR(errMsg)
               stop(errMsg)
             }
-            self$INFO(files_summary)
+            if (!quiet) self$INFO(files_summary)
             invisible(parallel_handler(cl, self$files, download_file, ...))
             try(stopCluster(cl))
           }
         }else{
-          self$INFO("Download in sequential mode")
-          self$INFO(files_summary) 
+          if (!quiet) self$INFO("Download in sequential mode")
+          if (!quiet) self$INFO(files_summary) 
           invisible(lapply(self$files, download_file))
         }
-        self$INFO("End of download")
+        if (!quiet) cat(sprintf("[zen4R][INFO] File%s downloaded at '%s'.\n",
+                                ifelse(length(self$files)>1,"s",""), tools::file_path_as_absolute(path)))
+        if (!quiet) self$INFO("Verifying file integrity...")
+        invisible(lapply(self$files, check_integrity))
+        if (!quiet) self$INFO("End of download")
       }
     }
 

R/zen4R.R

@@ -11,6 +11,7 @@
 #' @import keyring
 #' @importFrom tools file_path_as_absolute
 #' @importFrom tools md5sum
+#' @importFrom parallel mclapply
 #' 
 #' @title Interface to 'Zenodo' REST API
 #' @description Provides an Interface to 'Zenodo' (<https://zenodo.org>) REST API, 

R/zen4R_downloader.R

@@ -4,18 +4,23 @@
 #' @description \code{download_zenodo} allows to download archives attached to a Zenodo
 #' record, identified by its DOI or concept DOI.
 #'
-#' @usage download_zenodo("10.5281/zenodo.2547036")
+#' @examples 
+#' \dontrun{
+#' download_zenodo("10.5281/zenodo.2547036")
+#' }
 #'                 
 #' @param doi a Zenodo DOI or concept DOI
 #' @param path the target directory where to download files
 #' @param logger a logger to print messages. The logger can be either NULL, 
 #' "INFO" (with minimum logs), or "DEBUG" (for complete curl http calls logs)
+#' @param quiet Logical (\code{FALSE} by default).
+#' Do you want to suppress informative messages (not warnings)?
 #' @param ... any other arguments for parallel downloading (more information at
-#'\link{ZenodoManager}, \code{downloadFiles()} documentation)
+#'\link{ZenodoRecord}, \code{downloadFiles()} documentation)
 #' 
 #' @export
 #' 
-download_zenodo = function(doi, path = ".", logger = NULL, ...){
+download_zenodo = function(doi, path = ".", logger = NULL, quiet = FALSE, ...){
 
   zenodo <- ZenodoManager$new(logger = logger)
   rec <- zenodo$getRecordByDOI(doi)
@@ -27,5 +32,5 @@ download_zenodo = function(doi, path = ".", logger = NULL, ...){
     }
   }
   #download
-  rec$downloadFiles(path = path, ...)
+  rec$downloadFiles(path = path, quiet = quiet, ...)
 }

R/zen4R_versioning.R

@@ -3,7 +3,10 @@
 #' @title get_versions
 #' @description \code{get_versions} allows to execute a workflow
 #'
-#' @usage get_versions("10.5281/zenodo.2547036")
+#' @examples 
+#' \dontrun{
+#' get_versions("10.5281/zenodo.2547036")
+#' }
 #'                 
 #' @param doi a Zenodo DOI or concept DOI
 #' @param logger a logger to print messages. The logger can be either NULL,