syncFromSynapse: syncFromSynapse

In Sage-Bionetworks/synapserutils: Collection of utilities building on top of synapser

syncFromSynapse

Description

Synchronizes a File entity, or a Folder entity, meaning all the files in a folder (including subfolders) from Synapse, and adds a readme manifest with file metadata.

Usage

syncFromSynapse(entity, path=NULL, ifcollision="overwrite.local", allFiles=NULL, followLink=FALSE, manifest="all",
    downloadFile=TRUE)

Arguments

entity	A Synapse ID, a Synapse Entity object of type file, folder or project.
path	An optional path where the file hierarchy will be reproduced. If not specified the files will by default be placed in the .synapseCache. A path is required in order to create a manifest file. A manifest is TSV file that is automatically created that contains metadata (annotations, storage location and provenance) of all downloaded files. If no files were downloaded, no manifest file will be created. Defaults to NULL.
ifcollision	Determines how to handle file collisions. May be "overwrite.local", "keep.local", or "keep.both". Defaults to "overwrite.local".
allFiles	Deprecated and not to be used. This will be removed in the synapseclient v5.0.0. Defaults to NULL.
followLink	Determines whether the link returns the target Entity. Defaults to FALSE.
manifest	Determines whether creating manifest file automatically. The optional values are "all", "root", or "suppress". Defaults to "all".
downloadFile	Determines whether downloading the files. Defaults to TRUE.

Details

When entity is a Project or Folder, this function will crawl all subfolders of the project/folder specified by 'entity' and download all files that have not already been downloaded. When entity is a File the function will download the latest version of the file unless version is denoted in the synid with .version notiation (e.g. syn123.1) If there are newer files in Synapse (or a local file
has been edited outside of the cache) since the last download then local the file will be replaced by the new file unless "ifcollision" is changed.

If the files are being downloaded to a specific location outside of the Synapse cache a file (SYNAPSE_METADATA_MANIFEST.tsv) will also be added in the path that contains the metadata (annotations, storage location and provenance of all
downloaded files).

See also: syncToSynapse

Value

List of entities (files, tables, links)

Examples

  ## Not run: 
    syncFromSynapse("syn123","path/to/your_folder")
  
## End(Not run)

Sage-Bionetworks/synapserutils documentation built on Aug. 31, 2024, 10:42 a.m.