Merge pull request #28 from umccr/cttso_payload

Add cttsov2 tidy payload

NAMESPACE

@@ -28,6 +28,7 @@ export(orca_query_url)
 export(orca_wfrid2payload)
 export(orca_wfrid2state)
 export(orca_workflow_list)
+export(pld_cttsov2)
 export(pld_umccrise)
 export(pld_wts)
 export(portaldb_query)

R/meta_tso_ctdna_tumor_only.R

@@ -51,3 +51,47 @@ meta_tso_ctdna_tumor_only <- function(pmeta, status = c("Succeeded")) {
       cttso_rerun = "rerun"
     )
 }
+
+#' Payload Tidy tso
+#'
+#' @param pld List with tso workflow parameters.
+#'
+#' @return A tidy tibble.
+#' @export
+pld_cttsov2 <- function(pld) {
+  payload_okay(pld)
+  pdata <- pld[["data"]]
+  id <- pld[["orcabusId"]]
+  # collapse FastqListRowIds into single string
+  pdata[["tags"]][["fastqListRowIds"]] <- pdata[["tags"]][["fastqListRowIds"]] |>
+    paste(collapse = ", ")
+  tags <- pdata[["tags"]] |>
+    tibble::as_tibble_row() |>
+    dplyr::mutate(orcabusId = id)
+  # ignore verbose inputs$samplesheet
+  inputs <- pdata[["inputs"]]
+  inputs[["samplesheet"]] <- NULL
+  inputs[["fastqListRows"]] <- inputs[["fastqListRows"]] |>
+    purrr::map(tibble::as_tibble_row) |>
+    dplyr::bind_rows()
+  inputs[["fastqListRows"]] <- list(inputs[["fastqListRows"]])
+  inputs <- inputs |>
+    tibble::as_tibble_row() |>
+    rlang::set_names(\(x) glue("input_{x}")) |>
+    dplyr::mutate(orcabusId = id)
+  outputs <- pdata[["outputs"]] |>
+    purrr::map(\(x) x |> stringr::str_replace("/$", "")) |>
+    tibble::as_tibble_row() |>
+    rlang::set_names(\(x) glue("output_{x}")) |>
+    dplyr::mutate(orcabusId = id)
+  engpar <- pdata[["engineParameters"]] |>
+    purrr::map(\(x) x |> stringr::str_replace("/$", "")) |>
+    tibble::as_tibble_row() |>
+    rlang::set_names(\(x) glue("engparam_{x}")) |>
+    dplyr::mutate(orcabusId = id)
+  d <- tags |>
+    dplyr::left_join(inputs, by = "orcabusId") |>
+    dplyr::left_join(outputs, by = "orcabusId") |>
+    dplyr::left_join(engpar, by = "orcabusId")
+  return(d)
+}

R/meta_umccrise.R

@@ -98,7 +98,7 @@ meta_umccrise <- function(pmeta, status = "Succeeded") {
     )
 }
 
-#' Payload for umccrise workflow
+#' Payload Tidy umccrise
 #'
 #' @param pld List with umccrise workflow parameters.
 #'

R/meta_wts_tumor_only.R

@@ -62,9 +62,9 @@ meta_wts_tumor_only <- function(pmeta, status = "Succeeded") {
     )
 }
 
-#' Payload for WTS workflow
+#' Payload Tidy wts
 #'
-#' @param pld List with WTS workflow parameters.
+#' @param pld List with wts workflow parameters.
 #'
 #' @return A tidy tibble.
 #' @export

R/orcabus.R

@@ -84,6 +84,7 @@ orca_wfrid2state <- function(wfrid, token, stage = "prod") {
 #' token <- orca_jwt() |> jwt_validate()
 #' wfrid <- "wfr.01JCARAVTXKG5581SRA1HKBTD3"
 #' wfrid <- "wfr.01JCA5DZFD0T4MFQX0HHEEFBCH" # wts
+#' wfrid <- "wfr.01JBX361HKV0V9WS96RAFG135T" # cttsov2
 #' p <- orca_wfrid2payload(wfrid = wfrid, token = token)
 #' }
 #'
@@ -139,6 +140,7 @@ orca_prid2wfpayload <- function(prid, token, stage = "prod") {
 #' libid <- "L2401591" # wgs
 #' libid <- "L2401074" # wts # nothing
 #' libid <- "L2401577" # wts
+#' libid <- "L2401558" # cttsov2
 #' wf_name <- NULL
 #' d <- orca_libid2workflows(libid = libid, token = token, wf_name = wf_name, page_size = 20)
 #' }