Use 'SHA-256' checksum for sysmeta/object uploads (#257)

R/D1Node.R

@@ -159,8 +159,8 @@ setMethod("D1Node", signature("XMLInternalElementNode"), function(xml) {
 #' newid <- paste("urn:uuid:", UUIDgenerate(), sep="") 
 #' format <- "text/csv"
 #' size <- file.info(csvfile)$size
-#' sha1 <- digest(csvfile, algo="sha1", serialize=FALSE, file=TRUE)
-#' sysmeta <- new("SystemMetadata", identifier=newid, formatId=format, size=size, checksum=sha1)
+#' sha256 <- digest(csvfile, algo="sha256", serialize=FALSE, file=TRUE)
+#' sysmeta <- new("SystemMetadata", identifier=newid, formatId=format, size=size, checksum=sha256)
 #' sysmeta <- addAccessRule(sysmeta, "public", "read")
 #' # Create (upload) the object to DataONE (requires authentication)
 #' \dontrun{

R/MNode.R

@@ -71,9 +71,9 @@
 #' write.csv(testdf, csvfile, row.names=FALSE)
 #' f <- "text/csv"
 #' size <- file.info(csvfile)$size
-#' sha1 <- digest(csvfile, algo="sha1", serialize=FALSE, file=TRUE)
+#' sha256 <- digest(csvfile, algo="sha256", serialize=FALSE, file=TRUE)
 #' sysmeta <- new("SystemMetadata", identifier=newid, formatId=f, size=size,
-#'     checksum=sha1, originMemberNode=mnid, authoritativeMemberNode=mnid)
+#'     checksum=sha256, originMemberNode=mnid, authoritativeMemberNode=mnid)
 #' # Upload data to DataONE (requires authentication)
 #' \dontrun{
 #' response <- createObject(mn, newid, csvfile, sysmeta)
@@ -280,9 +280,9 @@ setMethod("getSystemMetadata", signature("MNode"), function(x, pid) {
 })
 
 #' @rdname getChecksum
-#' @param checksumAlgorithm The algorithm used to calculate the checksum. Default="SHA-1"
+#' @param checksumAlgorithm The algorithm used to calculate the checksum. Default="SHA-256"
 #' @export
-setMethod("getChecksum", signature("MNode"), function(x, pid, checksumAlgorithm="SHA-1") {
+setMethod("getChecksum", signature("MNode"), function(x, pid, checksumAlgorithm="SHA-256") {
   stopifnot(is.character(pid))
   url <- paste(x@endpoint, "checksum", URLencode(pid, reserved=T), sep="/")
   response<-GET(url, query=list(checksumAlgorithm=checksumAlgorithm), user_agent(get_user_agent()))
@@ -346,8 +346,8 @@ setMethod("getChecksum", signature("MNode"), function(x, pid, checksumAlgorithm=
 #' write.csv(testdf, csvfile, row.names=FALSE)
 #' format <- "text/csv"
 #' size <- file.info(csvfile)$size
-#' sha1 <- digest(csvfile, algo="sha1", serialize=FALSE, file=TRUE)
-#' sysmeta <- new("SystemMetadata", identifier=newid, formatId=format, size=size, checksum=sha1)
+#' sha256 <- digest(csvfile, algo="sha256", serialize=FALSE, file=TRUE)
+#' sysmeta <- new("SystemMetadata", identifier=newid, formatId=format, size=size, checksum=sha256)
 #' sysmeta <- addAccessRule(sysmeta, "public", "read")
 #' # Upload the data to DataONE (requires authentication)
 #' \dontrun{

tests/testthat/test.D1Client.R

@@ -95,8 +95,8 @@ test_that("D1Client getDataObject", {
     expect_match(getIdentifier(obj), pid)
     expect_match(getFormatId(obj), "text/csv")
     data <- getData(obj)
-    sha1 <- digest(data, algo="md5", serialize=FALSE, file=FALSE)
-    expect_match(sha1, obj@sysmeta@checksum)
+    sha256 <- digest(data, algo="md5", serialize=FALSE, file=FALSE)
+    expect_match(sha256, obj@sysmeta@checksum)
 })
 
 test_that("D1Client uploadDataObject with raw data works", {

tests/testthat/test.MNode.R

@@ -130,9 +130,9 @@ test_that("MNode describeObject() with authentication", {
         # Create SystemMetadata for the object
         format <- "text/csv"
         size <- file.info(csvfile)$size
-        sha1 <- digest(csvfile, algo="sha1", serialize=FALSE, file=TRUE)
+        sha256 <- digest(csvfile, algo="sha256", serialize=FALSE, file=TRUE)
         # specify series id for this sysmeta. This will only be used if uploading to a DataONE v2 node
-        sysmeta <- new("SystemMetadata", identifier=newid, formatId=format, size=size, checksum=sha1,
+        sysmeta <- new("SystemMetadata", identifier=newid, formatId=format, size=size, checksum=sha256,
                        originMemberNode=mnTest@identifier, authoritativeMemberNode=mnTest@identifier)
         # sysmeta <- addAccessRule(sysmeta, "public", "read")
         # Upload the data to the MN using createObject(), checking for success and a returned identifier
@@ -186,13 +186,13 @@ test_that("MNode createObject(), updateObject(), archive()", {
         # Create SystemMetadata for the object
         format <- "text/csv"
         size <- file.info(csvfile)$size
-        sha1 <- digest(csvfile, algo="sha1", serialize=FALSE, file=TRUE)
+        sha256 <- digest(csvfile, algo="sha256", serialize=FALSE, file=TRUE)
         # specify series id for this sysmeta. This will only be used if uploading to a DataONE v2 node
         seriesId <- UUIDgenerate()
-        sysmeta <- new("SystemMetadata", identifier=newid, formatId=format, size=size, checksum=sha1,
+        sysmeta <- new("SystemMetadata", identifier=newid, formatId=format, size=size, checksum=sha256,
                        originMemberNode=mnTest@identifier, authoritativeMemberNode=mnTest@identifier, seriesId=seriesId)
         sysmeta <- addAccessRule(sysmeta, "public", "read")
-        expect_that(sysmeta@checksum, equals(sha1))
+        expect_that(sysmeta@checksum, equals(sha256))
         expect_that(sysmeta@originMemberNode, equals(mnTest@identifier))
         expect_that(sysmeta@authoritativeMemberNode, equals(mnTest@identifier))
 
@@ -207,10 +207,10 @@ test_that("MNode createObject(), updateObject(), archive()", {
         csvfile <- paste(tempfile(), ".csv", sep="")
         write.csv(testdf, csvfile, row.names=FALSE)
         size <- file.info(csvfile)$size
-        sha1 <- digest(csvfile, algo="sha1", serialize=FALSE, file=TRUE)
+        sha256 <- digest(csvfile, algo="sha256", serialize=FALSE, file=TRUE)
         sysmeta@identifier <- updateid
         sysmeta@size <- size
-        sysmeta@checksum <- sha1
+        sysmeta@checksum <- sha256
         sysmeta@obsoletes <- newid
         newId <- updateObject(mnTest, newid, csvfile, updateid, sysmeta)
         expect_false(is.null(newId))
@@ -270,12 +270,12 @@ test_that("MNode createObject() with in-memory object", {
         # Create SystemMetadata for the object
         format <- "text/csv"
         size <- length(csvdata)
-        sha1 <- digest(csvdata, algo="sha1", serialize=FALSE, file=FALSE)
+        sha256 <- digest(csvdata, algo="sha256", serialize=FALSE, file=FALSE)
         # specify series id for this sysmeta. This will only be used if uploading to a DataONE v2 node
 
-        sysmeta <- new("SystemMetadata", identifier=newid, formatId=format, size=size, checksum=sha1)
+        sysmeta <- new("SystemMetadata", identifier=newid, formatId=format, size=size, checksum=sha256)
         sysmeta <- addAccessRule(sysmeta, "public", "read")
-        expect_that(sysmeta@checksum, equals(sha1))
+        expect_that(sysmeta@checksum, equals(sha256))
 
         # Upload the data to the MN using createObject(), checking for success and a returned identifier
         createdId <- createObject(mnTest, newid, sysmeta = sysmeta, dataobj=csvdata)
@@ -322,10 +322,10 @@ test_that("MNode createObject() works for large files", {
       # Create SystemMetadata for the object
       format <- "text/csv"
       size <- file.info(csvfile)$size
-      sha1 <- digest(csvfile, algo="sha1", serialize=FALSE, file=TRUE)
-      sysmeta <- new("SystemMetadata", identifier=newid, formatId=format, size=size, checksum=sha1, originMemberNode=mnTest@identifier, authoritativeMemberNode=mnTest@identifier)
+      sha256 <- digest(csvfile, algo="sha256", serialize=FALSE, file=TRUE)
+      sysmeta <- new("SystemMetadata", identifier=newid, formatId=format, size=size, checksum=sha256, originMemberNode=mnTest@identifier, authoritativeMemberNode=mnTest@identifier)
       sysmeta <- addAccessRule(sysmeta, "public", "read")
-      expect_that(sysmeta@checksum, equals(sha1))
+      expect_that(sysmeta@checksum, equals(sha256))
       expect_that(sysmeta@originMemberNode, equals(mnTest@identifier))
       expect_that(sysmeta@authoritativeMemberNode, equals(mnTest@identifier))