diff --git a/.gitignore b/.gitignore
index 3b96878..df8fb74 100644
--- a/.gitignore
+++ b/.gitignore
@@ -28,11 +28,13 @@ vignettes/*.pdf
 .Renviron
 *.Rproj
 # Misc files and dirs
-temp_aws_parquet
 *manifest*
 aws
 awscliv2.zip
-parquet_filtered/
-parquet_final/
 session-manager-plugin.deb
 dictionaries
+*.parquet
+*.json
+dev*
+misc*
+*temp*
diff --git a/params.R b/params.R
index 6457a75..445b40f 100644
--- a/params.R
+++ b/params.R
@@ -15,6 +15,7 @@ PARQUET_FOLDER_INTERNAL <- 'syn51406699'
 
 # Local location where parquet bucket files are synced to
 AWS_PARQUET_DOWNLOAD_LOCATION <- './temp_aws_parquet'
+AWS_ARCHIVE_DOWNLOAD_LOCATION <- './temp_aws_archive'
 
 PARQUET_FILTERED_LOCATION <- './parquet_filtered'
 
@@ -26,12 +27,12 @@ datasets_to_filter <- c("dataset_enrolledparticipants",
                         "dataset_healthkitv2workouts", 
                         "dataset_symptomlog")
 
-cols_to_drop <- list(c("EmailAddress", "DateOfBirth", "CustomFields_DeviceOrderInfo", "FirstName", "LastName", "PostalCode", "MiddleName"),
+cols_to_drop <- list(c("EmailAddress", "DateOfBirth", "CustomFields_DeviceOrderInfo", "FirstName", "LastName", "PostalCode", "MiddleName", "MobilePhone"),
                      # c("name"),
                      # c("name"),
                      c("Source_Name"),
                      c("Source_Name", "Device_Name"),
-                     c("Source_Name", "Metadata_HKWorkoutBrandName", "Metadata_Coach", "Metadata_trackerMetadata", "Metadata_SWMetadataKeyCustomWorkoutTitle", "Metadata_location"),
+                     c("Source_Name", "Metadata_HKWorkoutBrandName", "Metadata_Coach", "Metadata_trackerMetadata", "Metadata_SWMetadataKeyCustomWorkoutTitle", "Metadata_location", "metadata_workout_name", "Metadata_name"),
                      c("Value_notes", "Properties"))
 
 PARQUET_FINAL_LOCATION <- './parquet_final'
diff --git a/sts_synindex_external.R b/sts_synindex_external.R
index 1acbec8..b8f1e80 100644
--- a/sts_synindex_external.R
+++ b/sts_synindex_external.R
@@ -4,16 +4,102 @@ library(dplyr)
 library(synapserutils)
 library(rjson)
 
+
+# Functions ---------------------------------------------------------------
+
+#' Duplicate a folder
+#'
+#' This function duplicates a folder from the source to the destination. It checks
+#' if the source folder exists, and if the destination folder already exists, it
+#' gives a warning about possible file overwriting.
+#'
+#' @param source_folder The path to the source folder.
+#' @param destination_folder The path to the destination folder.
+#'
+#' @return The path to the destination folder.
+#'
+#' @examples
+#' source_folder <- "path/to/source_folder"
+#' destination_folder <- "path/to/destination_folder"
+#' duplicate_folder(source_folder, destination_folder)
+#' 
+duplicate_folder <- function(source_folder, destination_folder) {
+  if (!dir.exists(source_folder)) {
+    stop("Source folder does not exist.")
+  }
+  
+  if (dir.exists(destination_folder)) {
+    warning("Destination folder already exists. Files might be overwritten.")
+  } else {
+    dir.create(destination_folder)
+  }
+  
+  system(glue::glue('cp -r {source_folder}/* {destination_folder}'))
+  
+  return(destination_folder)
+}
+
+#' Copy folders and reparent
+#'
+#' This function copies folders from the source folder to the destination folder
+#' while re-parenting them. It skips folders that already exist in the destination folder.
+#'
+#' @param source_folder The path to the source folder.
+#' @param destination_folder The path to the destination folder.
+#'
+#' @examples
+#' source_folder <- "path/to/source_folder"
+#' destination_folder <- "path/to/destination_folder"
+#' copy_folders_reparent(source_folder, destination_folder)
+#' 
+copy_folders_reparent <- function(source_folder, destination_folder) {
+  folders_to_copy <- 
+    setdiff(
+      list.dirs(source_folder, recursive = F, full.names = F), 
+      list.dirs(destination_folder, recursive = F, full.names = F))
+  
+  for (folder in folders_to_copy) {
+    source_path <- paste0(source_folder, '/', folder)
+    dest_path <- paste0(destination_folder, '/', folder)
+    
+    if (!dir.exists(dest_path)) {
+      system(glue::glue('cp -r {source_path} {destination_folder}'))
+      cat("Copied:", folder, '\n')
+    } else {
+      cat("Skipped:", folder, "- Folder already exists in", destination_folder, '\n')
+    }
+  }
+}
+
+#' Replace equal sign with underscore
+#'
+#' This function renames a directory path by replacing equal signs with underscores.
+#' If a replacement is performed, it logs the change.
+#'
+#' @param directory_path The path of the directory to rename.
+#'
+#' @examples
+#' replace_equal_with_underscore("path_with=equals")
+#' 
+replace_equal_with_underscore <- function(directory_path) {
+  new_directory_path <- gsub("=", "_", directory_path)
+  if (directory_path != new_directory_path) {
+    file.rename(directory_path, new_directory_path)
+    return(cat("Renamed:", directory_path, "to", new_directory_path, "\n"))
+  }
+}
+
+# Setup -------------------------------------------------------------------
 synapser::synLogin(authToken = Sys.getenv('SYNAPSE_AUTH_TOKEN'))
 source('~/recover-parquet-external/params.R')
 
-#### Get STS token for bucket in order to sync to local dir ####
 
-# Get STS credentials
-token <- synapser::synGetStsStorageToken(
-  entity = PARQUET_FOLDER_INTERNAL,
-  permission = "read_only",
-  output_format = "json")
+# Get STS credentials for input data bucket -------------------------------
+token <- 
+  synapser::synGetStsStorageToken(
+    entity = PARQUET_FOLDER_INTERNAL,
+    permission = "read_only",
+    output_format = "json")
 
 if (PARQUET_BUCKET==token$bucket && PARQUET_BUCKET_BASE_KEY==token$baseKey) {
   base_s3_uri <- paste0('s3://', token$bucket, '/', token$baseKey)
@@ -21,15 +107,16 @@ if (PARQUET_BUCKET==token$bucket && PARQUET_BUCKET_BASE_KEY==token$baseKey) {
   base_s3_uri <- paste0('s3://', PARQUET_BUCKET, '/', PARQUET_BUCKET_BASE_KEY)
 }
 
-base_s3_uri_external <- paste0('s3://', PARQUET_BUCKET_EXTERNAL, '/', PARQUET_BUCKET_BASE_KEY_EXTERNAL)
 base_s3_uri_archive <- paste0('s3://', PARQUET_BUCKET_EXTERNAL, '/', PARQUET_BUCKET_BASE_KEY_ARCHIVE)
 
-# configure the environment with AWS token
+
+# Configure the environment with AWS token --------------------------------
 Sys.setenv('AWS_ACCESS_KEY_ID'=token$accessKeyId,
            'AWS_SECRET_ACCESS_KEY'=token$secretAccessKey,
            'AWS_SESSION_TOKEN'=token$sessionToken)
 
-#### Sync bucket to local dir####
+
+# Sync bucket to local dir ------------------------------------------------
 unlink(AWS_PARQUET_DOWNLOAD_LOCATION, recursive = T, force = T)
 sync_cmd <- glue::glue('aws s3 sync {base_s3_uri} {AWS_PARQUET_DOWNLOAD_LOCATION} --exclude "*owner.txt*" --exclude "*archive*"')
 system(sync_cmd)
@@ -39,44 +126,10 @@ system(sync_cmd)
 source('~/recover-parquet-external/filtering.R')
 
 # Copy unfiltered parquet datasets to new location with filtered parquet datasets
-duplicate_folder <- function(source_folder, destination_folder) {
-  if (dir.exists(source_folder)) {
-    if (!dir.exists(destination_folder)) {
-      dir.create(destination_folder)
-    } else {
-      warning("Destination folder already exists. Files might be overwritten.")
-    }
-    
-    system(glue::glue('cp -r {source_folder}/* {destination_folder}'))
-    
-    return(destination_folder)
-  } else {
-    stop("Source folder does not exist.")
-  }
-}
-
 unlink(PARQUET_FINAL_LOCATION, recursive = T, force = T)
 duplicate_folder(source_folder = PARQUET_FILTERED_LOCATION, 
                  destination_folder = PARQUET_FINAL_LOCATION)
 
-copy_folders_reparent <- function(source_folder, destination_folder) {
-  folders_to_copy <- setdiff(list.dirs(source_folder, recursive = F, full.names = F), 
-                             list.dirs(destination_folder, recursive = F, full.names = F))
-  
-  for (folder in folders_to_copy) {
-    source_path <- paste0(AWS_PARQUET_DOWNLOAD_LOCATION, '/', folder)
-    dest_path <- paste0(PARQUET_FINAL_LOCATION, '/', folder)
-
-    if (!dir.exists(dest_path)) {
-      system(glue::glue('cp -r {source_path} {destination_folder}'))
-
-      cat("Copied:", folder, '\n')
-    } else {
-      cat("Skipped:", folder, "- Folder already exists in", destination_folder, '\n')
-    }
-  }
-}
-
 copy_folders_reparent(AWS_PARQUET_DOWNLOAD_LOCATION, PARQUET_FINAL_LOCATION)
 
 # Remove intermediate folders
@@ -86,109 +139,96 @@ unlink(PARQUET_FILTERED_LOCATION, recursive = T, force = T)
 # De-identify parquet datasets --------------------------------------------
 source('~/recover-parquet-external/deidentification.R')
 
-# Sync final parquets to bucket -------------------------------------------
 
+# Sync final parquets to bucket -------------------------------------------
 date <- lubridate::today()
 sync_cmd <- glue::glue('aws s3 --profile service-catalog sync {PARQUET_FINAL_LOCATION} {base_s3_uri_archive}{date}/ --exclude "*owner.txt*" --exclude "*archive*"')
 system(sync_cmd)
 
 
-# Upload parquet datasets directory tree to Synapse ------------------------
-
-existing_dirs <- synGetChildren(PARQUET_FOLDER_ARCHIVE) %>% as.list()
+# Recreate directory tree of parquet datasets bucket location in S --------
+# existing_dirs <- synGetChildren(PARQUET_FOLDER_ARCHIVE) %>% as.list()
+# 
+# if(length(existing_dirs)>0) {
+#   for (i in seq_along(existing_dirs)) {
+#     synDelete(existing_dirs[[i]]$id)
+#   }
+# }
 
-if(length(existing_dirs)>0) {
-  for (i in seq_along(existing_dirs)) {
-    synDelete(existing_dirs[[i]]$id)
-  }
-}
+# Generate manifest of existing files
+unlink(AWS_ARCHIVE_DOWNLOAD_LOCATION, recursive = T, force = T)
+sync_cmd <- glue::glue('aws s3 --profile service-catalog sync {base_s3_uri_archive} {AWS_ARCHIVE_DOWNLOAD_LOCATION} --exclude "*owner.txt*" --exclude "*archive*"')
+system(sync_cmd)
 
 # Modify cohort identifier in dir name
-replace_equal_with_underscore <- function(directory_path) {
-  new_directory_path <- gsub("=", "_", directory_path)
-  if (directory_path != new_directory_path) {
-    file.rename(directory_path, new_directory_path)
-    cat("Renamed:", directory_path, "to", new_directory_path, "\n")
-  }
+junk <- sapply(list.dirs(AWS_ARCHIVE_DOWNLOAD_LOCATION), replace_equal_with_underscore)
+
+SYNAPSE_AUTH_TOKEN <- Sys.getenv('SYNAPSE_AUTH_TOKEN')
+manifest_cmd <- glue::glue('SYNAPSE_AUTH_TOKEN="{SYNAPSE_AUTH_TOKEN}" synapse manifest --parent-id {PARQUET_FOLDER_ARCHIVE} --manifest ./current_manifest.tsv {AWS_ARCHIVE_DOWNLOAD_LOCATION}')
+system(manifest_cmd)
+
+
+# Index files in Synapse --------------------------------------------------
+# Get a list of all files to upload and their synapse locations (parentId)
+STR_LEN_PARQUET_FINAL_LOCATION <- stringr::str_length(PARQUET_FINAL_LOCATION)
+
+## List all local files present (from manifest)
+synapse_manifest <- 
+  read.csv('./current_manifest.tsv', sep = '\t', stringsAsFactors = F) %>%
+  dplyr::filter(!grepl('owner.txt', path)) %>%
+  dplyr::rowwise() %>%
+  dplyr::mutate(file_key = stringr::str_sub(string = path, start = STR_LEN_PARQUET_FINAL_LOCATION)) %>%
+  dplyr::mutate(s3_file_key = paste0(PARQUET_BUCKET_BASE_KEY_ARCHIVE, file_key)) %>%
+  dplyr::mutate(md5_hash = as.character(tools::md5sum(path))) %>%
+  dplyr::ungroup()
+
+# List all files currently indexed in Synapse
+synapse_fileview <- 
+  synapser::synTableQuery(paste0('SELECT * FROM ', SYNAPSE_FILEVIEW_ID))$filepath %>%
+  read.csv()
+synapse_fileview <- 
+  synapser::synTableQuery(paste0('SELECT * FROM ', SYNAPSE_FILEVIEW_ID))$filepath %>% 
+  read.csv()
+
+# Find the files in the manifest that are not yet indexed in Synapse
+if (nrow(synapse_fileview)>0) {
+  synapse_manifest_to_upload <-
+    synapse_manifest %>%
+    dplyr::anti_join(
+      synapse_fileview %>%
+        dplyr::select(parent = parentId,
+                      s3_file_key = dataFileKey,
+                      md5_hash = dataFileMD5Hex))
+} else {
+  synapse_manifest_to_upload <- synapse_manifest
 }
 
-invisible(lapply(list.dirs(PARQUET_FINAL_LOCATION), replace_equal_with_underscore))
+synapse_manifest_to_upload <-
+  synapse_manifest_to_upload %>%
+  mutate(file_key = gsub("cohort_", "cohort=", file_key),
+         s3_file_key = gsub("cohort_", "cohort=", s3_file_key))
 
-# Generate manifest of existing files
-sync_cmd <- glue::glue('aws s3 --profile service-catalog sync {base_s3_uri_archive} ./archive --exclude "*owner.txt*" --exclude "*archive*"')
-system(sync_cmd)
+# Index each file in Synapse
+if(nrow(synapse_manifest_to_upload) > 0){
+  for(file_number in seq_len(nrow(synapse_manifest_to_upload))){
+    tmp <- synapse_manifest_to_upload[file_number, c("path", "parent", "s3_file_key")]
+    
+    absolute_file_path <- tools::file_path_as_absolute(tmp$path)
 
-SYNAPSE_AUTH_TOKEN <- Sys.getenv('SYNAPSE_AUTH_TOKEN')
-manifest_cmd <- glue::glue('SYNAPSE_AUTH_TOKEN="{SYNAPSE_AUTH_TOKEN}" synapse manifest --parent-id {PARQUET_FOLDER_ARCHIVE} --manifest ./current_manifest.tsv ./archive')
-system(manifest_cmd)
+    temp_syn_obj <- 
+      synapser::synCreateExternalS3FileHandle(
+        bucket_name = PARQUET_BUCKET_EXTERNAL,
+        s3_file_key = tmp$s3_file_key,
+        file_path = absolute_file_path,
+        parent = tmp$parent)
 
+    new_fileName <- stringr::str_replace_all(temp_syn_obj$fileName, ':', '_colon_')
 
-# # Index files in Synapse folder -------------------------------------------
-# 
-# ## Get a list of all files to upload and their synapse locations(parentId) 
-# STR_LEN_PARQUET_FINAL_LOCATION <- stringr::str_length(PARQUET_FINAL_LOCATION)
-# 
-# ## All files present locally from manifest
-# synapse_manifest <- read.csv('./current_manifest.tsv', sep = '\t', stringsAsFactors = F) %>% 
-#   dplyr::filter(path != paste0(PARQUET_FINAL_LOCATION,'/owner.txt')) %>%  # need not create a dataFileHandleId for owner.txt
-#   dplyr::rowwise() %>% 
-#   dplyr::mutate(file_key = stringr::str_sub(string = path, start = STR_LEN_PARQUET_FINAL_LOCATION+2)) %>% # location of file from home folder of S3 bucket
-#   dplyr::mutate(s3_file_key = paste0('main/parquet/', file_key)) %>% # the namespace for files in the S3 bucket is S3::bucket/main/
-#   dplyr::mutate(md5_hash = as.character(tools::md5sum(path))) %>% 
-#   dplyr::ungroup()
-# 
-# ## All currently indexed files in Synapse
-# synapse_fileview <- synapser::synTableQuery(paste0('SELECT * FROM ', SYNAPSE_FILEVIEW_ID))$filepath %>% read.csv()
-# synapse_fileview <- synapser::synTableQuery(paste0('SELECT * FROM ', SYNAPSE_FILEVIEW_ID))$filepath %>% read.csv()
-# 
-# ## find those files that are not in the fileview - files that need to be indexed
-# if (nrow(synapse_fileview)>0) {
-#   synapse_manifest_to_upload <- 
-#     synapse_manifest %>% 
-#     dplyr::anti_join(
-#       synapse_fileview %>% 
-#         dplyr::select(parent = parentId,
-#                       s3_file_key = dataFileKey,
-#                       md5_hash = dataFileMD5Hex))
-#   synapse_manifest_to_upload <- 
-#     synapse_manifest_to_upload %>% 
-#     mutate(file_key = gsub("cohort_", "cohort=", file_key),
-#            s3_file_key = gsub("cohort_", "cohort=", s3_file_key))
-# } else {
-#   synapse_manifest_to_upload <- 
-#     synapse_manifest %>% 
-#     mutate(file_key = gsub("cohort_", "cohort=", file_key),
-#            s3_file_key = gsub("cohort_", "cohort=", s3_file_key))
-# }
-# 
-# ## For each file index it in Synapse given a parent synapse folder
-# if(nrow(synapse_manifest_to_upload) > 0){ # there are some files to upload
-#   for(file_number in seq(nrow(synapse_manifest_to_upload))){
-#     
-#     # file and related synapse parent id 
-#     file_= synapse_manifest_to_upload$path[file_number]
-#     parent_id = synapse_manifest_to_upload$parent[file_number]
-#     s3_file_key = synapse_manifest_to_upload$s3_file_key[file_number]
-#     # this would be the location of the file in the S3 bucket, in the local it is at {AWS_PARQUET_DOWNLOAD_LOCATION}/
-#     
-#     absolute_file_path <- tools::file_path_as_absolute(file_) # local absolute path
-#     
-#     temp_syn_obj <- synapser::synCreateExternalS3FileHandle(
-#       bucket_name = PARQUET_BUCKET_EXTERNAL,
-#       s3_file_key = s3_file_key, #
-#       file_path = absolute_file_path,
-#       parent = parent_id
-#     )
-#     
-#     # synapse does not accept ':' (colon) in filenames, so replacing it with '_colon_'
-#     new_fileName <- stringr::str_replace_all(temp_syn_obj$fileName, ':', '_colon_')
-#     
-#     f <- File(dataFileHandleId=temp_syn_obj$id,
-#               parentId=parent_id,
-#               name = new_fileName) ## set the new file name
-#     
-#     f <- synStore(f)
-#     
-#   }
-# }
+    f <- 
+      synStore(
+        File(dataFileHandleId = temp_syn_obj$id,
+             parentId = tmp$parent,
+             name = new_fileName))
 
+  }
+}
diff --git a/tests/testthat.R b/tests/testthat.R
new file mode 100644
index 0000000..e39dfed
--- /dev/null
+++ b/tests/testthat.R
@@ -0,0 +1,12 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
+library(testthat)
+library(recover-parquet-external)
+
+test_check("recover-parquet-external")
diff --git a/tests/testthat/test-sts_synindex_external.R b/tests/testthat/test-sts_synindex_external.R
new file mode 100644
index 0000000..31c3b25
--- /dev/null
+++ b/tests/testthat/test-sts_synindex_external.R
@@ -0,0 +1,58 @@
+library(testthat)
+
+# Test for duplicate_folder
+test_that("duplicate_folder correctly duplicates a folder", {
+  td <- "tmpdir"
+  dir.create(td)
+  source_folder <- file.path(td, "source_folder")
+  destination_folder <- file.path(td, "destination_folder")
+  dir.create(source_folder)
+  file.create(file.path(source_folder, "file1.txt"))
+  
+  # Create a separate temporary directory for the destination
+  expect_true(dir.exists(source_folder))
+  result <- duplicate_folder(source_folder, destination_folder)
+  
+  expect_true(file.exists(file.path(destination_folder, "file1.txt")))
+  expect_equal(result, destination_folder)
+  
+  # Use expect_message to capture the warning
+  # expect_message(result, "Destination folder already exists. Files might be overwritten.")
+  
+  # Clean up the temporary directories
+  unlink(td, recursive = T)
+})
+
+# Test for copy_folders_reparent
+test_that("copy_folders_reparent correctly copies folders", {
+  td <- "tmpdir"
+  dir.create(td)
+  source_folder <- file.path(td, "source_folder")
+  destination_folder <- file.path(td, "destination_folder")
+  dir.create(source_folder)
+  dir.create(destination_folder)
+  dir.create(file.path(source_folder, "folder1"))
+  file.create(file.path(source_folder, "folder1", "folder1.txt"))
+  dir.create(file.path(source_folder, "folder2"))
+  file.create(file.path(source_folder, "folder2", "folder2.txt"))
+  result <- copy_folders_reparent(source_folder, destination_folder)
+  expect_true(dir.exists(file.path(destination_folder, "folder1")))
+  expect_true(dir.exists(file.path(destination_folder, "folder2")))
+  expect_true(file.exists(file.path(destination_folder, "folder1", "folder1.txt")))
+  expect_true(file.exists(file.path(destination_folder, "folder2", "folder2.txt")))
+  # expect_output(result, "Copied.*")
+  unlink(td, recursive = T)
+})
+
+# Test for replace_equal_with_underscore
+test_that("replace_equal_with_underscore correctly replaces equal sign with underscore", {
+  td <- "tmpdir"
+  dir.create(td)
+  original_path <- "path=with=equals"
+  dir.create(file.path(td, original_path))
+  replace_equal_with_underscore(file.path(td, original_path))
+  expect_equal(list.dirs(td, recursive = F, full.names = F), "path_with_equals")
+  expect_true(dir.exists(list.dirs(td, recursive = F, full.names = T)))
+  # expect_output(new_path, "Renamed.*")
+  unlink(td, recursive = T)
+})