Merge pull request #95 from umccr/hrd_sig_report

umccrise: support S3 outputs

.gitignore

@@ -3,6 +3,7 @@
 __pycache__/
 *.py[cod]
 .Rproj.user
+.Rhistory
 
 /nogit
 /docs

NAMESPACE

@@ -62,6 +62,8 @@ export(multiqc_tidy_json)
 export(portal_meta_read)
 export(rdf2tab)
 export(read)
+export(s3_files_list_filter_relevant)
+export(s3_search)
 export(session_info_kable)
 export(time_metrics_process)
 export(tso_rmd)

R/s3.R

@@ -0,0 +1,101 @@
+#' List Relevant Files In AWS S3 Directory
+#'
+#' Lists relevant files in an AWS S3 directory.
+#'
+#' @param s3dir GDS directory.
+#' @param pattern Pattern to further filter the returned file type tibble.
+#' @param page_size The size of each page to get in the AWS service call (def: 1000).
+#' @param max_items The total number of items to return in the command’s output (def: 1000).
+#' @param presign Include presigned URLs (def: FALSE).
+#' @param expiry_sec Number of seconds the presigned URL will be valid for (if generated) (def: 43200 (12hrs)).
+#'
+#' @return A tibble with path, date, file size, file type, and presigned URL if requested.
+#' @examples
+#' \dontrun{
+#' s3dir <- "s3://umccr-primary-data-prod/Accreditation/ALLOCATE-134131/WGS/2021-07-26/umccrised/ALLOCATE-134131__ALLOCATE-134131_MDx150892_Missing/cancer_report_tables"
+#' s3_files_list_filter_relevant(s3dir = s3dir, presign = TRUE)
+#' }
+#' @export
+s3_files_list_filter_relevant <- function(s3dir, pattern = NULL, page_size = 1000, max_items = 1000, presign = FALSE, expiry_sec = 43200) {
+  assertthat::assert_that(grepl("^s3://", s3dir), rlang::is_logical(presign))
+  pattern <- pattern %||% ".*" # keep all recognisable files by default
+  b <- sub("s3://(.*?)/.*", "\\1", s3dir)
+  p <- sub("s3://(.*?)/(.*)", "\\2", s3dir)
+  cmd <- glue(
+    "aws --output json s3api list-objects-v2 --bucket {b} --prefix {p} ",
+    "--max-items {max_items} --page-size {page_size}"
+  )
+  l <- system(cmd, intern = TRUE)
+  j <- jsonlite::fromJSON(l)
+  assertthat::assert_that("Contents" %in% names(j))
+  d <- j[["Contents"]] |>
+    tibble::as_tibble() |>
+    dplyr::mutate(
+      path = glue("s3://{b}/{.data$Key}"),
+      date_utc = .data$LastModified,
+      size = fs::as_fs_bytes(.data$Size)
+    ) |>
+    dplyr::rowwise() |>
+    dplyr::mutate(
+      bname = basename(.data$path),
+      type = purrr::map_chr(.data$bname, match_regex)
+    ) |>
+    dplyr::ungroup() |>
+    dplyr::filter(!is.na(.data$type), grepl(pattern, .data$type)) |>
+    dplyr::select("path", "date_utc", "size", "type")
+
+  if (presign) {
+    d <- d |>
+      dplyr::rowwise() |>
+      dplyr::mutate(presigned_url = s3_file_presignedurl(.data$path, expiry_seconds = expiry_sec)) |>
+      dplyr::ungroup()
+  }
+  d
+}
+
+s3_file_presignedurl <- function(s3path, expiry_seconds = 3600) {
+  p <- system(glue("aws s3 presign {s3path} --expires-in {expiry_seconds}"), intern = TRUE)
+  p
+}
+
+#' Search AWS S3 Objects
+#'
+#' Searches for the given pattern in the UMCCR `umccr-primary-data-prod` AWS S3
+#' bucket.
+#'
+#' @param pat Pattern to search for (e.g. 'multiqc_data.json').
+#' @param rows Max number of rows to return.
+#'
+#' @return Tibble with S3 path, object size, date modified, id, unique hash.
+#'
+#' @examples
+#' \dontrun{
+#' pat <- "qc_summary.tsv.gz"
+#' s3_search(pat, 10)
+#' }
+#' @export
+s3_search <- function(pat, rows) {
+  au_tz <- "Australia/Melbourne"
+  utc_tz <- "UTC"
+  base_url <- "https://api.portal.prod.umccr.org/iam/s3"
+  url1 <- utils::URLencode(glue("{base_url}?rowsPerPage={rows}&search={pat}"))
+  awscurl_cmd <- glue(
+    "awscurl '{url1}' ",
+    "--header 'Accept: application/json'"
+  )
+  message(glue("Running {awscurl_cmd}"))
+  j <- system(awscurl_cmd, intern = TRUE)
+  date_fmt <- "%Y-%m-%dT%H:%M:%S"
+  d <- j |>
+    jsonlite::fromJSON() |>
+    purrr::pluck("results") |>
+    tibble::as_tibble()
+  d |>
+    dplyr::mutate(
+      date1 = as.POSIXct(.data$last_modified_date, tz = utc_tz, format = date_fmt),
+      date_aest = lubridate::with_tz(.data$date1, tz = au_tz),
+      path = glue("s3://{bucket}/{key}"),
+      size = fs::as_fs_bytes(.data$size)
+    ) |>
+    dplyr::select("path", "size", "date_aest", "id", "unique_hash")
+}