Formatting changes

Author: maggiecam

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: nidapFunctions
 Type: Package
 Title: Tools for NIDAP Code Workbook Templates
-Version: 0.7.4
+Version: 0.7.6
 Date: 2023-05-23
 Authors@R: person("Cam", "Maggie", email = "maggie.cam@nih.gov", role = c("cre","aut"))
 Maintainer: Cam Maggie <maggie.cam@nih.gov>
@@ -14,6 +14,6 @@ Suggests:
 License: MIT
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.2.1
 VignetteBuilder: knitr
 Language: en-US

NAMESPACE

@@ -1,8 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(loopUnzip)
-export(nidapFilePath)
+export(nidapGetFiles)
 export(nidapGetPath)
 export(nidapLoadPackages)
-export(writeRDS)
 importFrom(utils,unzip)

R/Get_File_Paths.R

@@ -0,0 +1,61 @@
+# This function provides a file path when a transform input file is brought into 
+#    Palantir Foundry's Code Workbook in NIDAP.
+
+#' @title Get Path
+#' @description This function returns the file path from a transform input 
+#'        dataset in NIDAP Code Workbook
+#' @details This function will return a file path from a transform input dataset 
+#'        into a code template or code transform in the NIDAP instance of
+#'        Foundry Code Workbook.
+#' @param input transform input dataset to import
+#' @param name name of input file, usually transform input format
+#' @param type data type, by default, 'r'.
+#' 
+#' @export 
+#' 
+#' @return file path from which to read in data. Note that the original file 
+#'    name will not be retained 
+
+nidapGetPath <- function(input,
+                     name,
+                     type = 'r'){
+  
+  fs <- input$fileSystem()
+  path <- fs$get_path(name, type)
+  return(path)
+}
+
+# This function returns the file path or paths used for loading files brought 
+#  into NIDAP code workbook.
+
+#' @title Get Files
+#' @description This function returns specific file paths for an input dataset  
+#'       in transform input format containing either a single or multiple files. 
+#' @details This method will copy files to the compute node and returns
+#'        the original file names for reading into code workbook. 
+#'
+#' @param dataset Dataset to import, usually in transform input format 
+#' @param ext File extension. For instance, "xlsx", "csv", "'txt, "rds"
+#' @param type Data type, by default, 'r'
+#' 
+#' @export 
+#' 
+#' @return File name(s) to read into code template or code transform 
+#' 
+
+nidapGetFiles <- function(data,
+                          ext,
+                          type = 'r'){
+  fs <- data$fileSystem()
+  file.path <- fs$ls(glob = paste0("*.",ext))
+  files <- lapply(file.path, function(file) { 
+        return(c(file$path, fs$get_path(file$path, type))) })
+  output.names<-list()
+  for (item in files){
+    file.copy(from=item[2], to=item[1], 
+              overwrite = TRUE, recursive = FALSE, 
+              copy.mode = TRUE)
+    output.names <- append(output.names,item[1])
+  }
+  return(unlist(output.names))
+}

R/Get_Path.R

@@ -4,11 +4,11 @@
 #' @description This function will load packages and reorder package priorities
 #'        while suppressing startup messages by default.
 #' @details This method provides a way to automatically (optionally) suppress 
-#'        package startup messages in NIDAP and removes all other unnecessary 
+#'        package start up messages in NIDAP and removes all other unnecessary 
 #'        packages
 #'
-#' @param current.package vector of packages that are being used in the template
-#' @param suppress boolean to suppress messages.  By default set to TRUE
+#' @param current.package Vector of packages that are being used in the template
+#' @param suppress Boolean to suppress messages.  By default set to TRUE
 #' 
 #' @export 
 #' 
@@ -33,11 +33,13 @@ nidapLoadPackages <- function(current.packages,
                         "package:futile.logger",
                         "package:uuid")
 
-    package.list <- search()[ifelse(unlist(gregexpr("package:",search()))==1,TRUE,FALSE)]
+    package.list <- search()[ifelse(unlist(gregexpr("package:",search()))==1,
+                                    TRUE,FALSE)]
     package.list <- setdiff(package.list,basic.packages)
 
     #If there are existing non-basic packages, detach them.
-    if (length(package.list)>0)  for (package in package.list) detach(package, character.only=TRUE)
+    if (length(package.list)>0)  for (package in package.list) 
+              detach(package, character.only=TRUE)
 
     #load current packages with option to suppress startup messages
     for(package in current.packages){

R/Loop_Unzip.R

@@ -0,0 +1,24 @@
+# This function unzips the files brought into NIDAP code workbook.
+
+#' @title Unzip Files in a Loop
+#' @description This function unzips specific file(s) in a file path 
+#' @details This method will return unzipped file(s) for reading into a code 
+#'      workbook template/transform.
+#'
+#' @param dir File path for zipped data file(s)
+#' 
+#' @importFrom utils unzip
+#' 
+#' @export 
+#' 
+#' @return Local file path for unzipped data file(s)
+#' 
+
+
+loopUnzip <- function(dir){
+  while(length(grep(".zip",dir))!=0){
+    dir <- unzip(dir)        
+  }
+  output <- basename(dir)
+  return(output)
+}