change_sharing_scope.R

library(synapser)
library(tidyverse)

PROJECT_ID <- "syn12030321"
UDALL_USERS <- "syn18691020"
AT_HOME_PD_USERS <- "syn16786935"


get_users <- function(user_table_id) {
  user_table <- as_tibble(synTableQuery(paste(
    "SELECT guid FROM", user_table_id, "WHERE status LIKE 'Success%'"))$asDataFrame())
  return(user_table)
}

update_tables <- function(project) {
  tables <- synGetChildren(project, includeTypes = list("table"))$asList()
  udall_users <- get_users(UDALL_USERS)
  at_home_pd_users <- get_users(AT_HOME_PD_USERS)
  substudy_users <- bind_rows(udall_users, at_home_pd_users)
  purrr::map(tables, function(t) {
    table_id <- t$id
    table <- synTableQuery(paste("select * from", table_id))$asDataFrame()
    if (has_name(table, "externalId")) {
      affected_rows <- table %>%
        semi_join(substudy_users, by = c("externalId" = "guid"))
      if (has_name(affected_rows, "userSharingScope")) {
        snapshot <- synRestPOST(paste0("/entity/", table_id, "/table/snapshot"), body = "{}")
        affected_rows <- affected_rows %>%
          mutate(userSharingScope = "ALL_QUALIFIED_RESEARCHERS")
        synStore(Table(table_id, affected_rows))
      }
    }
  })
}

main <- function() {
  synLogin()
  update_tables(PROJECT_ID)
}

main()