structured dwnl file & annotations like pyriricdata

R/IRICData-class.R

@@ -77,67 +77,67 @@ setMethod(
 
 #Download file from db_id or slug_id
 setGeneric(
-    name="DL_file",
-    def=function(object, session, file_id, path_out){
-        standardGeneric("DL_file")
+    name="dwnl_file_content",
+    def=function(object, session, folder_out, filename){
+        standardGeneric("dwnl_file_content")
     }
 )
 setMethod(
-    f="DL_file",
+    f="dwnl_file_content",
     signature="IRICData",
-    definition=function(object, session, file_id, path_out) {
+    definition=function(object, session, folder_out='', filename='') {
         # create directory output
-        dir.create(path_out, showWarnings = FALSE)
-        resp = rvest::jump_to(session, paste(object@url, 'secure/datafiles/download', file_id, sep='/'))
-        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'))
+        dir.create(folder_out, showWarnings = FALSE)
+        resp = rvest::jump_to(session, paste(object@url, 'secure/datafiles/download', filename, sep='/'))
+        datafile_name = unlist(resp$response$headers[grep("content-disposition", names((resp$response$headers)))])
+        datafile_name = unlist(strsplit(datafile_name, "UTF-8''"))[2]
+        file_out = file.path(folder_out, datafile_name)
+        cat(paste('Downloading', datafile_name,'\n'))
         writeBin(resp$response$content, file_out)
     }
 )
 
 #Download file annotation as JSON from db_id or slug_id
 setGeneric(
-    name="DL_file_annotation",
-    def=function(object, session, file_id, path_out){
-        standardGeneric("DL_file_annotation")
+    name="dwnl_file_annotation",
+    def=function(object, session, folder_out, filename){
+        standardGeneric("dwnl_file_annotation")
     }
 )
 setMethod(
-    f="DL_file_annotation",
+    f="dwnl_file_annotation",
     signature="IRICData",
-    definition=function(object, session, file_id, path_out) {
-        # create directory output
-        dir.create(path_out, showWarnings = FALSE)
-        annotations = get_file_annotation(object, session, file_id)
-        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'))
+    definition=function(object, session, folder_out='', filename='') {
+        dir.create(folder_out, showWarnings = FALSE)
+        annotations = get_file_annotation(object, session, filename)
+        datafile_name = unlist(resp$response$headers[grep("content-disposition", names((resp$response$headers)))])
+        datafile_name = unlist(strsplit(datafile_name, "UTF-8''"))[2]
+        file_out = file.path(folder_out, datafile_name)
+        cat(paste('Downloading', datafile_name, '\n'))
         writeBin(annotations, file_out)
     }
 )
 
 #Download an entire dataset
 setGeneric(
-    name="DL_dataset",
-    def=function(object, session, id_dataset, path_out){
-        standardGeneric("DL_dataset")
+    name="dwnl_dataset",
+    def=function(object, session, folder_out, datasetname){
+        standardGeneric("dwnl_dataset")
     }
 )
 setMethod(
-    f="DL_dataset",
+    f="dwnl_dataset",
     signature="IRICData",
-    definition=function(object, session, id_dataset, path_out) {
-        # create directory output
-        #Get all files of a dataset
-        resp = rvest::jump_to(session, paste(object@url,"/secure/dataset/", id_dataset, "/file-list", sep=""))
+    definition=function(object, session, folder_out='', datasetname='') {
+        dir.create(folder_out, showWarnings = FALSE)
+        resp = rvest::jump_to(session, paste(object@url,"/secure/dataset/", datasetname, "/file-list", sep=""))
         files_to_DL = unlist(strsplit(rawToChar(resp$response$content), "\n"))
         files_id = unique(unlist(lapply(files_to_DL, function(x) tail(unlist(strsplit(x,'/')), 1))))
-        #DL all file in path_out
+        if(folder_out !=""){ folder_out=file.path(folder_out, datasetname) }
+        else{ folder_out=datasetname }
         for (id_ in files_id) {
-        DL_file(object, session, id_, path_out)
+            dwnl_file_content(object, session, folder_out, id_)
+            dwnl_file_annotation(object, session, folder_out, id_)
         }
     }
 )
@@ -283,13 +283,13 @@ setMethod(
 
 #Return a data.table of file_name, file_id and hash for every files in dataset
 setGeneric(
-    name='get_dataset_hash',
+    name='get_dataset_filelist',
     def=function(object, session, dataset_id){
-        standardGeneric('get_dataset_hash')
+        standardGeneric('get_dataset_filelist')
     }
 )
 setMethod(
-    f='get_dataset_hash',
+    f='get_dataset_filelist',
     signature='IRICData',
     definition=function(object, session, dataset_id){
         ds_details <- data.table()
@@ -307,7 +307,8 @@ setMethod(
                 ds_details <- rbind(ds_details,
                                     data.table(file_name = metas[[ix]]$filename,
                                                 file_id = files_id[[ix]],
-                                                hash = metas[[ix]]$hash))
+                                                file_hash = metas[[ix]]$hash,
+                                                file_slug = metas[[ix]]$iric_data_id))
             }
         }
         return(ds_details)