Added annotation & metadata download, and single file download.

R/IRICData-class.R

@@ -27,7 +27,7 @@ IRICData <- setClass(
   prototype = list(
     user="",
     pwd="",
-    url="https://thepond.bioinfo.iric.ca"
+    url=""
   ),
 
   # Make a function that can test to see if the data is consistent.
@@ -65,6 +65,30 @@ setMethod(
 #' ### Accessors
 #' ###
 
+#Download file from file_url
+setGeneric(
+  name="DL_file",
+  def=function(object, session, file_url, path_out){
+    standardGeneric("DL_file")
+  }
+)
+setMethod(
+  f="DL_file",
+  signature="IRICData",
+  definition=function(object, session, file_url, path_out) {
+    # create directory output
+    dir.create(path_out, showWarnings = FALSE)
+    resp = rvest::jump_to(session,file_url)
+    file_name = unlist(resp$response$headers[grep("content-disposition", names((resp$response$headers)))])
+    file_name = unlist(strsplit(file_name, "UTF-8''"))[2]
+    file_out = file.path(path_out, file_name)
+    cat(paste('Downloading',file_name,'\n'))
+    writeBin(resp$response$content, file_out)
+  }
+)
+
+
+#Download an entire dataset
 setGeneric(
   name="DL_dataset",
   def=function(object, session, id_dataset, path_out){
@@ -76,24 +100,19 @@ setMethod(
   signature="IRICData",
   definition=function(object, session, id_dataset, path_out) {
     # create directory output
-    dir.create(path_out, showWarnings = FALSE)
-
+    #dir.create(path_out, showWarnings = FALSE)
     #Get all files of a dataset
     resp = rvest::jump_to(session, paste(object@url,"/secure/dataset/", id_dataset, "/file-list", sep=""))
     files_to_DL = unlist(strsplit(rawToChar(resp$response$content), "\n"))
 
     #DL all file in path_out
     for (file_url in files_to_DL) {
-      resp = rvest::jump_to(session,file_url)
-      file_name = unlist(resp$response$headers[grep("content-disposition", names((resp$response$headers)))])
-      file_name = unlist(strsplit(file_name, "UTF-8''"))[2]
-      file_out = file.path(path_out, file_name)
-
-      writeBin(resp$response$content, file_out)
+      DL_file(object, session, file_url, path_out)
     }
   }
 )
 
+
 #Fetch file metadata as JSON
 setGeneric(
   name='get_file_metadata',
@@ -111,6 +130,7 @@ setMethod(
   }
 )
 
+
 #Fetch file annotation as JSON
 setGeneric(
   name='get_file_annotation',