From ad4f4e10392a210a1f282c07d38c7414e563c6d4 Mon Sep 17 00:00:00 2001 From: pdiakumis Date: Thu, 14 Nov 2024 17:41:03 +1100 Subject: [PATCH] add cttsov2 pld --- NAMESPACE | 1 + R/meta_tso_ctdna_tumor_only.R | 44 +++++++++++++++++++++++++++++++++++ R/meta_umccrise.R | 2 +- R/meta_wts_tumor_only.R | 4 ++-- R/orcabus.R | 2 ++ man/orca_libid2workflows.Rd | 1 + man/orca_wfrid2payload.Rd | 1 + man/pld_cttsov2.Rd | 17 ++++++++++++++ man/pld_umccrise.Rd | 4 ++-- man/pld_wts.Rd | 6 ++--- 10 files changed, 74 insertions(+), 8 deletions(-) create mode 100644 man/pld_cttsov2.Rd diff --git a/NAMESPACE b/NAMESPACE index 595dfea..432e453 100644 --- a/NAMESPACE +++ b/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) diff --git a/R/meta_tso_ctdna_tumor_only.R b/R/meta_tso_ctdna_tumor_only.R index b0f7b62..bafb460 100644 --- a/R/meta_tso_ctdna_tumor_only.R +++ b/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) +} diff --git a/R/meta_umccrise.R b/R/meta_umccrise.R index 805e9e0..03a52c2 100644 --- a/R/meta_umccrise.R +++ b/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. #' diff --git a/R/meta_wts_tumor_only.R b/R/meta_wts_tumor_only.R index cf6ddb6..daa15f2 100644 --- a/R/meta_wts_tumor_only.R +++ b/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 diff --git a/R/orcabus.R b/R/orcabus.R index 23dbacb..715415e 100644 --- a/R/orcabus.R +++ b/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) #' } diff --git a/man/orca_libid2workflows.Rd b/man/orca_libid2workflows.Rd index 68b8f06..1c362ba 100644 --- a/man/orca_libid2workflows.Rd +++ b/man/orca_libid2workflows.Rd @@ -35,6 +35,7 @@ token <- orca_jwt() |> jwt_validate() 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) } diff --git a/man/orca_wfrid2payload.Rd b/man/orca_wfrid2payload.Rd index 488464d..94923a6 100644 --- a/man/orca_wfrid2payload.Rd +++ b/man/orca_wfrid2payload.Rd @@ -24,6 +24,7 @@ Given a workflow run ID, provides the payload. token <- orca_jwt() |> jwt_validate() wfrid <- "wfr.01JCARAVTXKG5581SRA1HKBTD3" wfrid <- "wfr.01JCA5DZFD0T4MFQX0HHEEFBCH" # wts +wfrid <- "wfr.01JBX361HKV0V9WS96RAFG135T" # cttsov2 p <- orca_wfrid2payload(wfrid = wfrid, token = token) } diff --git a/man/pld_cttsov2.Rd b/man/pld_cttsov2.Rd new file mode 100644 index 0000000..a331c07 --- /dev/null +++ b/man/pld_cttsov2.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/meta_tso_ctdna_tumor_only.R +\name{pld_cttsov2} +\alias{pld_cttsov2} +\title{Payload Tidy tso} +\usage{ +pld_cttsov2(pld) +} +\arguments{ +\item{pld}{List with tso workflow parameters.} +} +\value{ +A tidy tibble. +} +\description{ +Payload Tidy tso +} diff --git a/man/pld_umccrise.Rd b/man/pld_umccrise.Rd index 2e517bc..d7c35ba 100644 --- a/man/pld_umccrise.Rd +++ b/man/pld_umccrise.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/meta_umccrise.R \name{pld_umccrise} \alias{pld_umccrise} -\title{Payload for umccrise workflow} +\title{Payload Tidy umccrise} \usage{ pld_umccrise(pld) } @@ -13,5 +13,5 @@ pld_umccrise(pld) A tidy tibble. } \description{ -Payload for umccrise workflow +Payload Tidy umccrise } diff --git a/man/pld_wts.Rd b/man/pld_wts.Rd index f4a4086..9fd7e1e 100644 --- a/man/pld_wts.Rd +++ b/man/pld_wts.Rd @@ -2,16 +2,16 @@ % Please edit documentation in R/meta_wts_tumor_only.R \name{pld_wts} \alias{pld_wts} -\title{Payload for WTS workflow} +\title{Payload Tidy wts} \usage{ pld_wts(pld) } \arguments{ -\item{pld}{List with WTS workflow parameters.} +\item{pld}{List with wts workflow parameters.} } \value{ A tidy tibble. } \description{ -Payload for WTS workflow +Payload Tidy wts }