Conditionally run withdrawal code

config.yml

@@ -22,6 +22,7 @@ prod:
   PII_COLS_TO_DROP: syn52523394
   DEID_VALS_TO_REVIEW: syn52409518
   STAGING_TO_ARCHIVE_DOWNLOAD_LOCATION: ./temp_staging_to_archive/
+  POST_WITHDRAW_LOCATION: ./temp_post_withdraw
 
 staging:
   inherits: prod

remove_withdrawn_participants.R

@@ -44,53 +44,60 @@ participants_to_withdraw <-
   dplyr::pull(ParticipantIdentifier) %>% 
   unique()
 
-# Store list of datasets that do not contain ParticipantIdentifier column
-contains_pid_false <- 
-  sapply(list.dirs(AWS_PARQUET_DOWNLOAD_LOCATION, recursive = F), function(x) {
-    grepl("ParticipantIdentifier", open_dataset(x)$metadata$org.apache.spark.sql.parquet.row.metadata)
-  }) %>% 
-  tibble::enframe() %>% 
-  dplyr::filter(value==FALSE) %>% 
-  dplyr::select(name)
-
-# Store mapping ID var name for corresponding datasets
-contains_pid_false$mappingID <- 
-  dplyr::case_when(
-    grepl("fitbitsleeplogs", contains_pid_false$name) == TRUE ~ "LogId",
-    grepl("healthkitv2electrocardiogram", contains_pid_false$name) == TRUE ~ "HealthKitECGSampleKey",
-    grepl("healthkitv2heartbeat", contains_pid_false$name) == TRUE ~ "HealthKitHeartbeatSampleKey",
-    grepl("healthkitv2workout", contains_pid_false$name) == TRUE ~ "HealthKitWorkoutKey",
-    grepl("symptomlog_value", contains_pid_false$name) == TRUE ~ "DataPointKey"
-  )
-
-# Get values of mapping ID vars for participants to withdraw
-contains_pid_false$participants_to_withdraw <- 
-  dplyr::case_when(
-    grepl("fitbitsleeplogs", contains_pid_false$name) == TRUE ~ list(get_mappingID_vals_to_withdraw("dataset_fitbitsleeplogs", "LogId")),
-    grepl("healthkitv2electrocardiogram", contains_pid_false$name) == TRUE ~ list(get_mappingID_vals_to_withdraw("dataset_healthkitv2electrocardiogram", "HealthKitECGSampleKey")),
-    grepl("healthkitv2heartbeat", contains_pid_false$name) == TRUE ~ list(get_mappingID_vals_to_withdraw("dataset_healthkitv2heartbeat", "HealthKitHeartbeatSampleKey")),
-    grepl("healthkitv2workout", contains_pid_false$name) == TRUE ~ list(get_mappingID_vals_to_withdraw("dataset_healthkitv2workouts", "HealthKitWorkoutKey")),
-    grepl("symptomlog_value", contains_pid_false$name) == TRUE ~ list(get_mappingID_vals_to_withdraw("dataset_symptomlog", "DataPointKey"))
-  )
-
-# Remove data for withdrawn participants from parquet datasets based on mapping ID variables
-lapply(list.dirs(AWS_PARQUET_DOWNLOAD_LOCATION, recursive = F), function(x) {
-  if (x %in% contains_pid_false$name) {
-    tmpret <- unlist(contains_pid_false$participants_to_withdraw[x == contains_pid_false$name])
-    d <- 
-      arrow::open_dataset(x) %>%
-      filter(!(!!(as.symbol(contains_pid_false$mappingID[x == contains_pid_false$name]))) %in% tmpret)
-  } else {
-    d <-
-      arrow::open_dataset(x) %>%
-      filter(!ParticipantIdentifier %in% participants_to_withdraw)
-  }
-  d %>% 
-    arrow::write_dataset(
-      path = x,
-      max_rows_per_file = 100000,
-      partitioning = "cohort",
-      existing_data_behavior = 'delete_matching',
-      basename_template = paste0("part-0000{i}.", as.character("parquet"))
+if (length(participants_to_withdraw) > 0) {
+  # Store list of datasets that do not contain ParticipantIdentifier column
+  contains_pid_false <- 
+    sapply(list.dirs(AWS_PARQUET_DOWNLOAD_LOCATION, recursive = F), function(x) {
+      grepl("ParticipantIdentifier", open_dataset(x)$metadata$org.apache.spark.sql.parquet.row.metadata)
+    }) %>% 
+    tibble::enframe() %>% 
+    dplyr::filter(value==FALSE) %>% 
+    dplyr::select(name)
+
+  # Store mapping ID var name for corresponding datasets
+  contains_pid_false$mappingID <- 
+    dplyr::case_when(
+      grepl("fitbitsleeplogs", contains_pid_false$name) == TRUE ~ "LogId",
+      grepl("healthkitv2electrocardiogram", contains_pid_false$name) == TRUE ~ "HealthKitECGSampleKey",
+      grepl("healthkitv2heartbeat", contains_pid_false$name) == TRUE ~ "HealthKitHeartbeatSampleKey",
+      grepl("healthkitv2workout", contains_pid_false$name) == TRUE ~ "HealthKitWorkoutKey",
+      grepl("symptomlog_value", contains_pid_false$name) == TRUE ~ "DataPointKey"
     )
-})
+
+  # Get values of mapping ID vars for participants to withdraw
+  contains_pid_false$participants_to_withdraw <- 
+    dplyr::case_when(
+      grepl("fitbitsleeplogs", contains_pid_false$name) == TRUE ~ list(get_mappingID_vals_to_withdraw("dataset_fitbitsleeplogs", "LogId")),
+      grepl("healthkitv2electrocardiogram", contains_pid_false$name) == TRUE ~ list(get_mappingID_vals_to_withdraw("dataset_healthkitv2electrocardiogram", "HealthKitECGSampleKey")),
+      grepl("healthkitv2heartbeat", contains_pid_false$name) == TRUE ~ list(get_mappingID_vals_to_withdraw("dataset_healthkitv2heartbeat", "HealthKitHeartbeatSampleKey")),
+      grepl("healthkitv2workout", contains_pid_false$name) == TRUE ~ list(get_mappingID_vals_to_withdraw("dataset_healthkitv2workouts", "HealthKitWorkoutKey")),
+      grepl("symptomlog_value", contains_pid_false$name) == TRUE ~ list(get_mappingID_vals_to_withdraw("dataset_symptomlog", "DataPointKey"))
+    )
+
+  # Remove data for withdrawn participants from parquet datasets based on mapping ID variables
+  lapply(list.dirs(AWS_PARQUET_DOWNLOAD_LOCATION, recursive = F), function(x) {
+    if (x %in% contains_pid_false$name) {
+      tmpret <- unlist(contains_pid_false$participants_to_withdraw[x == contains_pid_false$name])
+      d <- 
+        arrow::open_dataset(x) %>%
+        filter(!(!!(as.symbol(contains_pid_false$mappingID[x == contains_pid_false$name]))) %in% tmpret)
+    } else {
+      d <-
+        arrow::open_dataset(x) %>%
+        filter(!ParticipantIdentifier %in% participants_to_withdraw)
+    }
+    d %>% 
+      arrow::write_dataset(
+        path = file.path(POST_WITHDRAW_LOCATION, basename(x)),
+        max_rows_per_file = 5000000,
+        partitioning = "cohort",
+        existing_data_behavior = 'delete_matching',
+        basename_template = paste0("part-0000{i}.", as.character("parquet"))
+      )
+  })
+
+  unlink(AWS_PARQUET_DOWNLOAD_LOCATION, recursive = T, force = T)
+  system(glue::glue("cp -r {POST_WITHDRAW_LOCATION} {AWS_PARQUET_DOWNLOAD_LOCATION}"))
+  unlink(POST_WITHDRAW_LOCATION, recursive = T, force = T)
+}
+