allow user to remove unzipped monthly folders by request

neonDataStackR/R/cleanUp.R

@@ -0,0 +1,25 @@
+##############################################################################################
+#' @title Clean up folder after stacking
+
+#' @author
+#' Christine Laney \email{claney@battelleecology.org}
+
+#' @description
+#' Remove unzipped monthly data folders
+#'
+#' @keywords internal
+#' @param folder The file path to the folder that needs to be cleaned up (the root directory of the data package)
+#' @return Any existing directory except for stackedFiles will be removed. Nothing is returned.
+
+#' @references
+#' License: GNU AFFERO GENERAL PUBLIC LICENSE Version 3, 19 November 2007
+
+# Changelog and author contributions / copyrights
+#   Christine Laney (2018-01-10)
+##############################################################################################
+cleanUp <- function(folder) {
+  dirs <- list.dirs(folder, recursive = FALSE)
+  dirsNotStacked <- dirs[-grep(pattern = "stackedFiles", x = dirs)]
+  if(length(dirsNotStacked) > 0) {unlink(dirsNotStacked, recursive = TRUE)}
+  writeLines("All unzipped monthly data folders have been removed.")
+}

neonDataStackR/R/getProductInfo.R

@@ -9,7 +9,7 @@
 
 #' @importFrom jsonlite fromJSON
 #' @importFrom httr GET
-#' @param dpid The data product id (optional), formated as DP0.00000.000
+#' @param dpID The data product id (optional), formated as DP0.00000.000
 #' @return A data table with product information
 
 #' @references

neonDataStackR/R/stackByTable.R

@@ -11,6 +11,7 @@
 
 #' @param filepath The location of the zip file
 #' @param folder T or F: does the filepath point to a parent, unzipped folder, or a zip file? If F, assumes the filepath points to a zip file. Defaults to F.
+#' @param saveUnzippedFiles T or F: should the unzipped monthly data folders be retained?
 #' @return All files are unzipped and one file for each table type is created and written.
 
 #' @export
@@ -23,14 +24,16 @@
 #   Claire Lunch (2017-09-28)
 ##############################################################################################
 
-stackByTable <- function(filepath, folder=FALSE){
+stackByTable <- function(filepath, folder=FALSE, saveUnzippedFiles = TRUE){
   if(folder==FALSE) {
     location.data <- substr(filepath, 1, nchar(filepath)-4)
     unzipZipfile(zippath = filepath, outpath = location.data, level = "all")
     stackDataFiles(location.data)
+    if(saveUnzippedFiles == FALSE){cleanUp(location.data)}
   } else {
     unzipZipfile(zippath = filepath, outpath = filepath, level = "in")
     stackDataFiles(filepath)
+    if(saveUnzippedFiles == FALSE){cleanUp(filepath)}
   }
 }
 

neonDataStackR/R/update_table_types.R

@@ -18,10 +18,9 @@
 ##############################################################################################
 
 update_table_types <- function(){
-  library(RMySQL)
-  dps_con <-  dbConnect(drv=RMySQL::MySQL(), dbname="dps_database", username="root",password="p@ssw0rd", host="10.206.27.43", root = 3306)
-  table_types <- dbGetQuery(dps_con, "SELECT * from dpTable WHERE dpTable.tableType NOT IN ('ingest', 'L0prime')")
+  dps_con <-  RMySQL::dbConnect(drv=RMySQL::MySQL(), dbname="dps_database", username="root",password="p@ssw0rd", host="10.206.27.43", root = 3306)
+  table_types <- RMySQL::dbGetQuery(dps_con, "SELECT * from dpTable WHERE dpTable.tableType NOT IN ('ingest', 'L0prime')")
   table_types$tableName <- gsub(pattern = "_pub", replacement = "", x = table_types$tableName)
   save(table_types, file = "data/table_types.rda")
-  dbDisconnect(dps_con)
+  RMySQL::dbDisconnect(dps_con)
 }