Downloading data by Synapse ID

This tutorial shows how to download any set of files from Synapse using their Synapse IDs. Rather than syncing an entire project or folder, this approach lets you target exactly the files you need and download them concurrently — even directing each file to a different local directory.

Tutorial Purpose

In this tutorial you will:

Build a mapping of Synapse IDs to local download directories
Download all files to their mapped directories

Prerequisites

Make sure that you have completed the following tutorials:
- Folder
- File
The target directories (~/temp/subdir1, etc.) must exist before running the script. Create them or replace them with directories of your choice.

1. Build a mapping of Synapse IDs to download directories

Create a named vector that maps each Synapse ID to the local path where that file should be saved. Files can be directed to different directories as needed.

library(synapser)
synLogin()

# A mapping of Synapse IDs to the local directory each file should be downloaded to.
# Files can be directed to different directories as needed.
SYN_IDS_AND_PATHS <- c(
  "syn60584250" = "~/temp/subdir1",
  "syn60584256" = "~/temp/subdir1",
  "syn60584248" = "~/temp/subdir1",
  "syn60584252" = "~/temp/subdir1",
  "syn60584258" = "~/temp/subdir1",
  "syn60584260" = "~/temp/subdir1",
  "syn60584257" = "~/temp/subdir1",
  "syn60584251" = "~/temp/subdir1",
  "syn60584253" = "~/temp/subdir1",
  "syn60584390" = "~/temp/subdir1",
  "syn60584405" = "~/temp/subdir2",
  "syn60584400" = "~/temp/subdir3"
)

2. Download all files

Loop over the mapping and use synGet() with FileOptions(download_location = ...) to download each file to its mapped directory.

results <- list()
for (syn_id in names(SYN_IDS_AND_PATHS)) {
  results[[syn_id]] <- synGet(
    syn_id,
    file_options = FileOptions(download_location = SYN_IDS_AND_PATHS[[syn_id]])
  )
}

print(sprintf("Retrieved %d files", length(results)))

After all downloads finish you’ll see output like:

[1] "Retrieved 12 files"

Downloading data by Synapse ID