Improved validation of 'annotation' parameter in file_upload function

R/IRICData-class.R

@@ -178,6 +178,16 @@ setMethod(
     f='file_upload',
     signature='IRICData',
     definition=function(object, session, file_path, annotation='', lab='', dataset=''){
+        #Check if annotation can be parsed as JSON
+        if (typeof(annotation) == 'list'){annotation <- toJSON(annotation)}
+        else if (typeof(annotation) == 'character'){
+            validation = jsonlite::validate(annotation)
+            if(!(validation[[1]])){
+                print(paste('Error occured while uploading', file_path,
+                ': the annotation parameter could not be parsed as JSON'))
+                return(NULL)
+            }
+        }
 
         file_form = list(file=httr::upload_file(file_path),
                         lab=lab, annotations=annotation, dataset=dataset)
@@ -273,12 +283,12 @@ setMethod(
             if (is.null(metas[ix][[1]])){
                 next
             }else{
-                ds_details <- rbind(ds_details, data.table(file_name = metas[[ix]]$filename,
-                                                            file_id = files_id[[ix]],
-                                                            hash = metas[[ix]]$hash))
+                ds_details <- rbind(ds_details,
+                                    data.table(file_name = metas[[ix]]$filename,
+                                                file_id = files_id[[ix]],
+                                                hash = metas[[ix]]$hash))
             }
         }
         return(ds_details)
     }
 )
-

README.md

@@ -36,7 +36,7 @@ DL_file(IData, IData_session, file_id, "directory/output/path")
 # To download a file annotations using file db_id or slug_id
 DL_file_annotation(IData, IData_session, file_id, "directory/output/path")
 
-# To upload a file
+# To upload a file, annotation as a named list or JSON formated character.
 file_upload(IData, IData_session, '/path/to/my/file.txt', annotation, lab, dataset)
 
 # To get file metadata using file db_id or slud_id