user last activity check

2021-09-29_katya_pfizer_user_frq.R

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+# Description: Determine if I can access Synapse user login information.  
+# Author: Haley Hunter-Zinck
+# Date: 2021-09-29
+
+# setup ----------------------------
+
+tic = as.double(Sys.time())
+
+library(glue)
+library(dplyr)
+library(synapser)
+synLogin()
+
+# files
+file_users <- "user_names.txt"
+project_names <- c("GENIE BioPharma Collaborative")
+file_output <- "2021-09-29_pfizer_user_synapse_bpc_last_activity.csv"
+
+# synapse
+synid_folder_output <- "syn26263015"
+synid_file_user_names <- "syn26263016"
+
+# functions ----------------------------
+
+#' Get the user Synapse ID from the user's Synapse user name.
+#' 
+#' @param user_name Synapse user name
+#' @return Synapse user ID number
+#' @example get_user_id("hhz")
+get_user_id <- function(user_name) {
+  return(synGetUserProfile(user_name)$ownerId)
+}
+
+get_project_last_activity <- function(user_name, project_name) {
+
+  user_id <- get_user_id(user_name)
+
+  if (is.na(user_id)) {
+    return(NA)
+  }
+
+  access <- synRestGET(glue("/projects/user/{user_id}"))
+
+  project_names <- unlist(lapply(access$results, function(x) {return(x$name)}))
+
+  if (is.element(project_name, project_names)) {
+    la <- access$results[[which(project_names == project_name)]]$lastActivity
+    return(as.character(as.POSIXct(la, format = "%Y-%m-%dT%H:%M:%OS", tz = "UTC")))
+  }
+
+  return(NA)
+}
+
+save_to_synapse <- function(path, 
+                            parent_id, 
+                            file_name = NA, 
+                            prov_name = NA, 
+                            prov_desc = NA, 
+                            prov_used = NA, 
+                            prov_exec = NA) {
+
+  if (is.na(file_name)) {
+    file_name = path
+  } 
+  file <- File(path = path, parentId = parent_id, name = file_name)
+
+  if (!is.na(prov_name) || !is.na(prov_desc) || !is.na(prov_used) || !is.na(prov_exec)) {
+    act <- Activity(name = prov_name,
+                    description = prov_desc,
+                    used = prov_used,
+                    executed = prov_exec)
+    file <- synStore(file, activity = act)
+  } else {
+    file <- synStore(file)
+  }
+
+  return(T)
+}
+
+get_synapse_entity_data_in_csv <- function(synapse_id, 
+                                           sep = ",", 
+                                           na.strings = c("NA"),
+                                           header = F) {
+
+  data <- read.csv(synGet(synapse_id)$path, stringsAsFactors = F, 
+                   na.strings = na.strings, sep = sep, header = header)
+  return(data)
+}
+
+
+# read ----------------------------
+
+user_names <- get_synapse_entity_data_in_csv (synid_file_user_names)
+user_names <- as.character(unlist(user_names))
+
+# main ----------------------------
+
+last_activity <- matrix(NA, nrow = length(user_names), 
+                        ncol = length(project_names),
+                        dimnames = list(user_names, project_names))
+
+# access date
+for (user_name in user_names) {
+  for (project_name in project_names) {
+    last_activity[user_name, project_name] <- get_project_last_activity(user_name = user_name,
+                                               project_name = project_name)
+  }
+}
+
+# write to file ------------------------
+
+write.csv(last_activity, row.names = T, 
+          file = file_output)
+save_to_synapse(path = file_output, 
+                parent_id = synid_folder_output, 
+                prov_name = "last activity", 
+                prov_desc = "last activity for BPC project for list of user names", 
+                prov_used = synid_file_user_names, 
+                prov_exec = "https://github.com/hhunterzinck/genie_requests/blob/main/2021-09-29_katya_pfizer_user_frq.R")
+file.remove(file_output)
+
+# close out ----------------------------
+
+toc = as.double(Sys.time())
+print(glue("Runtime: {round(toc - tic)} s"))