Set up
library(nfportalutils)
synapser::synLogin(authToken = Sys.getenv("SYNAPSE_AUTH_TOKEN"))Give selected access to an individual or team
Sometimes a selected set of private (embargoed) data needs to made available to a collaborator or other researcher outside the project. One way to go about this is to identify the file ids, add the individual/team to the (this creates local sharing settings), and then collect those files into a dataset so a single dataset link can be shared (this makes it easier especially if files are spread across multiple folders).
The main convenience util to do this is
grant_specific_file_access. To test it out, we create a
data folder, and then create and upload mock files.
project_id <- "syn26462036" # this the NF-dev-playground project, replace with your own dev project if needed
folder <- synapser::Folder(name = paste("Demo Dataset -", Sys.Date()), parent = project_id)
folder <- synapser::synStore(folder)
folder_id <- folder$properties$id
# create some temp files with same mock data
file_paths <- mock_files(3)
syn_files <- list()
for(path in file_paths) {
file <- synapser::File(path = path, parent = folder_id)
sf <- synapser::synStore(file)
syn_files <- c(syn_files, sf)
}
file_ids <- sapply(syn_files, function(x) x$properties$id)Now let’s use the function to share with NF-OSI Team as the collaborator (replace example with appropriate project id that you own).
outside_collaborator <- "3342573" # use another appropriate example id if needed
grant_specific_file_access(principal_id = outside_collaborator,
entity_ids = file_ids,
create_dataset = T,
project_id = project_id,
dataset_name = NULL) # optional Clean up by removing the mock folder and files. You can delete the dataset through the UI.
synapser::synDelete(folder_id)Survey files downloadable for Synapse registered users
There’s often reference to “public” files, which usually means files
that are viewable + downloadable to Synapse users. If we just have a
fileview with ids of the files, how do we know which ones are “public”?
The group of Synapse users has id 273948, and we can use a
util called summarize_file_access, passing in this group
id, the permissions we’re checking, and the fileview id.
public_access <- summarize_file_access(principal_id = 273948, "DOWNLOAD", "syn16858331")
public_accessThe results should show that summarize_file_access’s
first step is identifying all the unique benefactors (the parent
container that sets the permissions on the child files) and the current
permissions, then compiles a summary number of files under that
benefactor.
For an even more summarized breakdown as proportions: