From e90eb6e35feedacf1ae36e64603d13c740a6bb93 Mon Sep 17 00:00:00 2001
From: pdiakumis <peterdiakumis@gmail.com>
Date: Mon, 18 Sep 2023 18:10:48 +1000
Subject: [PATCH] meta: add account argument

---
 R/portal_meta.R                          |  4 ++--
 inst/rmd/umccr_portal/portal_summary.Rmd | 12 ++++++------
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/R/portal_meta.R b/R/portal_meta.R
index 3bb0dbe..634dbcd 100644
--- a/R/portal_meta.R
+++ b/R/portal_meta.R
@@ -470,7 +470,7 @@ meta_main_cols <- function() {
 #' \dontrun{
 #' portal_meta_read(params = "&type_name=rnasum", rows = 4)
 #' }
-portal_meta_read <- function(pmeta = NULL, rows = 100, params = "") {
+portal_meta_read <- function(pmeta = NULL, rows = 100, params = "", account = "prod") {
   au_tz <- "Australia/Melbourne"
   utc_tz <- "UTC"
   if (!is.null(pmeta)) {
@@ -505,7 +505,7 @@ portal_meta_read <- function(pmeta = NULL, rows = 100, params = "") {
     }
   } # else pmeta is NULL, so read via portal API
 
-  base_url <- "https://api.portal.prod.umccr.org/iam"
+  base_url <- glue("https://api.portal.{account}.umccr.org/iam")
   url1 <- utils::URLencode(glue("{base_url}/workflows?rowsPerPage={rows}{params}"))
   awscurl_cmd <- glue(
     "awscurl '{url1}' ",
diff --git a/inst/rmd/umccr_portal/portal_summary.Rmd b/inst/rmd/umccr_portal/portal_summary.Rmd
index 42cbb96..750ff44 100644
--- a/inst/rmd/umccr_portal/portal_summary.Rmd
+++ b/inst/rmd/umccr_portal/portal_summary.Rmd
@@ -100,8 +100,8 @@ get_colours <- function(nc) {
   clrs[seq_len(nc)]
 }
 
-get_sbj_url <- function(x, colour = NULL) {
-  sbj_url <- glue("https://portal.umccr.org/subjects/{x}/overview")
+get_sbj_url <- function(x, colour = NULL, account = "") {
+  sbj_url <- glue("https://portal.{account}umccr.org/subjects/{x}/overview")
   if (!is.null(colour)) {
     return(glue("<a href={sbj_url} style='background-color:{colour}'>{x}</a>"))
   }
@@ -113,8 +113,8 @@ get_sbj_url <- function(x, colour = NULL) {
 ```{r vars}
 # options(width = 150)
 fmt1 <- "%Y-%m-%dT%H:%M:%S"
-date_start <- as.POSIXct("2023-09-02T00:00:01", format = fmt1)
-date_end <- as.POSIXct("2023-09-03T23:59:59", format = fmt1)
+date_start <- as.POSIXct("2023-09-15T00:00:01", format = fmt1)
+date_end <- as.POSIXct("2023-09-18T23:59:59", format = fmt1)
 wf_order <- c(
   "bcl_convert",
   "tso_ctdna_tumor_only",
@@ -130,7 +130,7 @@ lims_rds <- here(glue("nogit/data_portal/lims/{as.Date(date_end)}.rds"))
 # saveRDS(lims_raw, file = lims_rds)
 lims_raw <- readr::read_rds(lims_rds)
 pmeta_rds <- here(glue("nogit/data_portal/workflows/{as.Date(date_end)}.rds"))
-# pmeta_raw <- dracarys::portal_meta_read(rows = 65)
+# pmeta_raw <- dracarys::portal_meta_read(rows = 80, account = "stg")
 # saveRDS(pmeta_raw, file = pmeta_rds)
 pmeta_raw <- readr::read_rds(pmeta_rds)
 pmeta <- pmeta_raw |>
@@ -161,7 +161,7 @@ unique_sbj <- sort(unique(pmeta_sumy$sbjid))
 clrs1 <- get_colours(length(unique_sbj)) |>
   purrr::set_names(unique_sbj) |>
   tibble::enframe(name = "sbjid", value = "color") |>
-  dplyr::mutate(sbj_url = get_sbj_url(.data$sbjid, colour = .data$color))
+  dplyr::mutate(sbj_url = get_sbj_url(.data$sbjid, colour = .data$color, account = "stg."))
 pmeta_sumy_count <- pmeta_sumy |>
   dplyr::count(type_name, .drop = FALSE) |>
   tibble::deframe()