addFile: Manipulate Entity Files

In Sage-Bionetworks/rSynapseClientRewrite: Synapse R Client from Sage Bionetworks

Description

Functions for manipulating the files belonging to an entity.

Usage

  addFile(entity, file, path)
  deleteFile(entity, file)
  moveFile(entity, src, dest)

Arguments

entity	The entity whose files will be modified.
file	A path to the file on the local file system, when adding, or the relative path to the file when deleting (see Details).
path	relative path in the entity's cache directory where the file should be placed.
src	full path to the source file relative to the entity's cache directory.
dest	destination path relative to the root of the entity's cache directory.

Details

Synapse has the ability to store only a single file for entities that are "locationable", which are represented as the LocationOwner class in the Synapse R client. To get around the single file limitation, the Synapse R client provides methods for maintaining a "cache" of files that can be zipped into a single archive and uploaded to Synapse by calling the storeEntity method.

When adding a file to an entity, the file argument is the path to the file being added and the path argument is the relative path in the entity's cached directory where the file should be placed. When moving or deleting a file, the file and src arguments should be the path to the file that should be moved/deleted relative to the root of the cache directory.

The behavior of the dest argument is slightly more complex. If this arguments contains a trailing slash (i.e. "/"), they will be interpreted as a path to the directory in which the file specified by the src argument should be placed. Absent the trailing slash, dest will be interpreted as a path followed by a filename to which the source file src will be renamed.

Value

The modified entity.

Note

If the return value is not captured, the entity will not be modified.

Author(s)

Matthew D. Furia <[e-mail]>

See Also

addObject moveObject deleteObject storeEntity downloadEntity

Examples

  ## create a Data entity (LocationOwner sub-class).
  entity <- Data()
  
  ## create a plot that will be added to the Media entity
  datFile <- tempfile(fileext=".txt")
  write.table(data.frame(diag(10)), file=datFile, row.names=F, col.names=F)

  ## add the file to the root of the entity's cache
  ## BE SURE TO CAPTURE THE RETURN VALUE
  entity <- addFile(entity, datFile)
  
  ## move the file to a subdirectory named foo
  entity <- moveFile(entity, entity$files[1], "/foo/")
  
  ## change the files name
  entity <- moveFile(entity, entity$files[1], "/foo/plot.jpg")
  
  ## delete the file
  entity <- deleteFile(entity, entity$files[1])

Sage-Bionetworks/rSynapseClientRewrite documentation built on May 9, 2019, 7:06 p.m.