multiqc: include more metrics in map

umccr · Sep 25, 2023 · a83bd4c · a83bd4c
1 parent cc82391
commit a83bd4c
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Showing 7 changed files with 207 additions and 6 deletions.
diff --git a/R/ica.R b/R/ica.R
@@ -8,15 +8,16 @@
 #' @param include Use PresignedUrl to include presigned URLs to all files within
 #' @param page_size Page size (def: 100).
 #' the GDS directory.
+#' @param regexes Tibble with regex and function name.
 #'
 #' @return A tibble with type, bname, size, file_id, path, and presigned URL.
 #' @export
-gds_files_list_filter_relevant <- function(gdsdir, token, pattern = NULL, include = NULL, page_size = 100) {
+gds_files_list_filter_relevant <- function(gdsdir, token, pattern = NULL, include = NULL, page_size = 100, regexes = DR_FILE_REGEX) {
   pattern <- pattern %||% ".*" # keep all recognisable files by default
   cols_sel <- c("type", "bname", "size", "file_id", "path", "presigned_url")
   d <- dracarys::gds_files_list(gdsdir, token, include = include, page_size = page_size) |>
     dplyr::rowwise() |>
-    dplyr::mutate(type = purrr::map_chr(.data$bname, match_regex)) |>
+    dplyr::mutate(type = purrr::map_chr(.data$bname, \(x) match_regex(x, regexes))) |>
     dplyr::ungroup() |>
     dplyr::filter(!is.na(.data$type), grepl(pattern, .data$type)) |>
     dplyr::select(dplyr::any_of(cols_sel))

diff --git a/R/multiqc.R b/R/multiqc.R
@@ -128,7 +128,7 @@ multiqc_rename_cols <- function(d) {
     rename_vec <- purrr::set_names(m[["raw"]], m[["clean"]])
     d <- dplyr::rename(d, !!!rename_vec)
   }
-  return(d)
+  return(dplyr::distinct(d))
 }
 
 .multiqc_guess_workflow <- function(p) {

diff --git a/R/portal_meta.R b/R/portal_meta.R
@@ -462,6 +462,7 @@ meta_main_cols <- function() {
 #' @param params String containing additional params to pass to the `/workflows`
 #' endpoint, e.g. `'&type_name=bclconvert'`.
 #' @param pmeta Path to downloaded portal metadata file, or already parsed metadata tibble.
+#' @param account UMCCR portal account (one of "prod", "dev", "stg").
 #'
 #' @return A tibble of the results from the given query.
 #' @export
@@ -471,6 +472,7 @@ meta_main_cols <- function() {
 #' portal_meta_read(params = "&type_name=rnasum", rows = 4)
 #' }
 portal_meta_read <- function(pmeta = NULL, rows = 100, params = "", account = "prod") {
+  assertthat::assert_that(account %in% c("prod", "dev", "stg"))
   au_tz <- "Australia/Melbourne"
   utc_tz <- "UTC"
   if (!is.null(pmeta)) {

diff --git a/inst/extdata/multiqc_column_map.tsv b/inst/extdata/multiqc_column_map.tsv
diff --git a/man/gds_files_list_filter_relevant.Rd b/man/gds_files_list_filter_relevant.Rd
diff --git a/man/portal_meta_read.Rd b/man/portal_meta_read.Rd
diff --git a/tests/testthat/test-roxytest-testexamples-multiqc.R b/tests/testthat/test-roxytest-testexamples-multiqc.R
@@ -2,7 +2,7 @@
 
 # File R/multiqc.R: @testexamples
 
-test_that("Function multiqc_date_fmt() @ L279", {
+test_that("Function multiqc_date_fmt() @ L284", {
 
   cdate <- "2023-04-07, 09:09 UTC"
   (res1 <- multiqc_date_fmt(cdate))