Merge pull request #40 from jread-usgs/master

update to file replace/remove

.travis.yml

@@ -12,7 +12,6 @@ before_install:
   - ./travis-tool.sh bootstrap
 install:
   - ./travis-tool.sh install_deps
-script: ./travis-tool.sh run_tests
 
 after_failure:
   - ./travis-tool.sh dump_logs

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: sbtools
 Title: USGS SB tools
 Maintainer: Luke Winslow <lwinslow@usgs.gov>
-Version: 0.7.1
+Version: 0.8.1
 Author: Luke Winslow
 Description: Tools for interacting with SB interfaces. 
 Imports: 

NAMESPACE

@@ -2,15 +2,17 @@
 
 export(authenticate_sb)
 export(folder_create)
-export(item_append_file)
+export(item_append_files)
 export(item_create)
 export(item_exists)
 export(item_file_download)
 export(item_get)
 export(item_get_parent)
 export(item_list_children)
 export(item_list_files)
+export(item_replace_files)
 export(item_rm)
+export(item_rm_files)
 export(item_update)
 export(item_update_identifier)
 export(item_upload_create)

R/file_helpers.R

@@ -0,0 +1,12 @@
+multi_file_body <- function(files){
+	body = list()
+	for(i in 1:length(files)){
+		if(!file.exists(files[i])){
+			stop('This file does not exist or cannot be accessed: ', files[i])
+		}
+
+		body[[paste0('file', i)]] = upload_file(files[i])
+	}
+	names(body) = rep('file', length(body))
+	return(body)
+}

R/item_append_file.R → R/item_append_files.R

@@ -2,7 +2,7 @@
 #'@description Adds a file to an item
 #'
 #'@param id A ScienceBase item ID to upload to.
-#'@param filename A file path to upload.
+#'@param files A file path to upload.
 #'@param sb_session A ScienceBase session object from authenticate_sb.
 #'
 #'@return ScienceBase Item.
@@ -11,20 +11,21 @@
 #'
 #'@examples \dontrun{
 #'  sb_session<-authenticate_sb(sbusername)
-#'  item_append_file("54e265a4e4b08de9379b4dfb", '/foo/bar/baz.zip', sb)
+#'  item_append_files("54e265a4e4b08de9379b4dfb", '/foo/bar/baz.zip', sb)
 #' }
 #'@export
-item_append_file = function(id, filename, session){	
+item_append_files = function(id, files, session){	
 
 	if(!session_validate(session)){
 		stop('Session state is invalid, please re-authenticate')
 	}
 
+	body <- multi_file_body(files)
   url<-paste0(pkg.env$url_upload,'?id=', id)
 
-	POST(url, accept_json(), 
-			 body=list(file=upload_file(filename)), handle=session)
+	r = POST(url, accept_json(), 
+			 body=body, handle=session)
 
-  return(item_get(id,session))
+  return(content(r))
 
 }

R/item_remove_files.R

@@ -0,0 +1,8 @@
+#'@title Remove all files associated with an item
+#'@param item_id a sciencebase item identifier
+#'@param session Authenticated session object (from \link{authenticate_sb})
+#'@description Removes existing files associated with an item. 
+#'@export
+item_rm_files <- function(item_id, session){
+	item_update(item_id,list('files'=vector()), session = session)
+}

R/item_replace_files.R

@@ -0,0 +1,13 @@
+#'@title Replace files associated with an item
+#'@param item_id a sciencebase item identifier
+#'@param files a character vector of file paths
+#'@param session Authenticated session object (from \link{authenticate_sb})
+#'@description replaces existing files associated with an item with a new one. 
+#'(Currently does not support multi-file uploads.) 
+#'This function will not append an existing collection of files. If that 
+#'is desired, use \code{\link{item_append_file}}
+#'@export
+item_replace_files <- function(item_id, files, session){	
+	item_rm_files(item_id, session)
+	item_append_files(id = item_id, filename = files, session)
+}

R/item_rm.R

@@ -22,6 +22,6 @@ item_rm = function(id, session){
 
 	r = DELETE(paste0(pkg.env$url_item, id), handle=session, accept_json())
 
-	return(url_ok(r))
+	return(r)
 
 }

R/item_upload_create.R

@@ -15,15 +15,7 @@ item_upload_create = function(parent_id, files, session){
 		stop('Session state is invalid, please re-authenticate')
 	}
 
-	body = list()
-	for(i in 1:length(files)){
-		if(!file.exists(files[i])){
-			stop('This file does not exist or cannot be accessed: ', files[i])
-		}
-
-		body[[paste0('file', i)]] = upload_file(files[i])
-	}
-	names(body) = rep('file', length(body))
+	body <- multi_file_body(files)
 
 	url = paste0(pkg.env$url_upload_create, parent_id)
 	r = POST(url, body=body, accept_json(), handle=session, query=list(title='title'))

R/set_endpoint.R

@@ -42,6 +42,7 @@ set_endpoint = function(endpoint="production"){
 	pkg.env$url_item = paste0(pkg.env$url_base, "item/")
 	pkg.env$url_upload = paste0(pkg.env$url_base, 'file/uploadAndUpsertItem/')
 	pkg.env$url_upload_create = paste0(pkg.env$url_base, 'file/uploadAndCreateItem/')
+	pkg.env$url_upload_update = paste0(pkg.env$url_base, 'file/uploadAndUpdateItem/')
 	pkg.env$url_download = paste0(pkg.env$url_base, 'file/get/')
 	pkg.env$url_login = 'https://my.usgs.gov/josso/signon/usernamePasswordLogin.do'
 }

man/item_append_file.Rd → man/item_append_files.Rd

@@ -1,15 +1,15 @@
 % Generated by roxygen2 (4.1.0): do not edit by hand
-% Please edit documentation in R/item_append_file.R
-\name{item_append_file}
-\alias{item_append_file}
+% Please edit documentation in R/item_append_files.R
+\name{item_append_files}
+\alias{item_append_files}
 \title{Upload File to Item}
 \usage{
-item_append_file(id, filename, session)
+item_append_files(id, files, session)
 }
 \arguments{
 \item{id}{A ScienceBase item ID to upload to.}
 
-\item{filename}{A file path to upload.}
+\item{files}{A file path to upload.}
 
 \item{sb_session}{A ScienceBase session object from authenticate_sb.}
 }
@@ -22,7 +22,7 @@ Adds a file to an item
 \examples{
 \dontrun{
  sb_session<-authenticate_sb(sbusername)
- item_append_file("54e265a4e4b08de9379b4dfb", '/foo/bar/baz.zip', sb)
+ item_append_files("54e265a4e4b08de9379b4dfb", '/foo/bar/baz.zip', sb)
 }
 }
 

man/item_replace_files.Rd

@@ -0,0 +1,22 @@
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/item_replace_files.R
+\name{item_replace_files}
+\alias{item_replace_files}
+\title{Replace files associated with an item}
+\usage{
+item_replace_files(item_id, files, session)
+}
+\arguments{
+\item{item_id}{a sciencebase item identifier}
+
+\item{files}{a character vector of file paths}
+
+\item{session}{Authenticated session object (from \link{authenticate_sb})}
+}
+\description{
+replaces existing files associated with an item with a new one.
+(Currently does not support multi-file uploads.)
+This function will not append an existing collection of files. If that
+is desired, use \code{\link{item_append_file}}
+}
+

man/item_rm_files.Rd

@@ -0,0 +1,17 @@
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/item_remove_files.R
+\name{item_rm_files}
+\alias{item_rm_files}
+\title{Remove all files associated with an item}
+\usage{
+item_rm_files(item_id, session)
+}
+\arguments{
+\item{item_id}{a sciencebase item identifier}
+
+\item{session}{Authenticated session object (from \link{authenticate_sb})}
+}
+\description{
+Removes existing files associated with an item.
+}
+