From 1fba37b23702d7b912b281b0b50358ab48f1d8eb Mon Sep 17 00:00:00 2001
From: David JM <biodavidjm@gmail.com>
Date: Fri, 2 Feb 2024 09:36:44 -0800
Subject: [PATCH 1/3] fix package conflicts

This was creating a problem when debugging on Rstudio
---
 NAMESPACE | 5 ++++-
 R/misc.R  | 2 +-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 153a6d58..cf3c48c6 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -63,7 +63,6 @@ import(progress)
 import(purrr)
 import(stringr)
 import(tidyr)
-import(utils)
 import(viridis)
 importFrom(data.table,as.data.table)
 importFrom(data.table,fread)
@@ -81,3 +80,7 @@ importFrom(readr,read_lines)
 importFrom(scales,percent)
 importFrom(stats,median)
 importFrom(stats,reorder)
+importFrom(utils,URLencode)
+importFrom(utils,read.csv)
+importFrom(utils,read.delim)
+importFrom(utils,write.table)
diff --git a/R/misc.R b/R/misc.R
index fbd00f9f..25bdef18 100644
--- a/R/misc.R
+++ b/R/misc.R
@@ -19,7 +19,7 @@
 #' @importFrom stats median reorder
 #' @import stringr
 #' @import tidyr
-#' @import utils
+#' @importFrom utils URLencode read.csv read.delim write.table
 #' @import viridis
 #____________________________________________________________________________
 

From f2ce6ee0b6c61601bad64eb59f8eae237b02ecbc Mon Sep 17 00:00:00 2001
From: David JM <biodavidjm@gmail.com>
Date: Fri, 2 Feb 2024 09:37:04 -0800
Subject: [PATCH 2/3] write release olinks adjustment

---
 R/olink_qc.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/olink_qc.R b/R/olink_qc.R
index 4b054d32..fd8da5fe 100644
--- a/R/olink_qc.R
+++ b/R/olink_qc.R
@@ -1010,7 +1010,7 @@ write_olink_releases <- function(input_results_folder,
     phase_folder_release <- phase_details
   }
   
-  output_folder <- file.path(folder_root, folder_name, phase_folder_release, "prot-ol", folder_tissue, folder_assay)
+  output_folder <- file.path(folder_root, folder_name, phase_folder_release, "proteomics-targeted", folder_tissue, folder_assay)
   
   if(!dir.exists(file.path(output_folder))){
     dir.create(file.path(output_folder), recursive = TRUE)

From 5d268be855277056c3b5ff1a3ee4b282791cb7d0 Mon Sep 17 00:00:00 2001
From: David JM <biodavidjm@gmail.com>
Date: Fri, 2 Feb 2024 09:45:30 -0800
Subject: [PATCH 3/3] New proteomics assay: `PROT_OX`

---
 R/validations.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/validations.R b/R/validations.R
index 423013d2..a0524ff0 100644
--- a/R/validations.R
+++ b/R/validations.R
@@ -254,7 +254,7 @@ check_viallabel_dmaqc <- function(vl_submitted,
 validate_assay <- function(input_results_folder){
   
   assay <- stringr::str_extract(string = input_results_folder,
-                                pattern = "(?<=T\\d{2}/)(IONPNEG|RPNEG|RPPOS|HILICPOS|LRPPOS|LRPNEG|3HIB|AA|AC_DUKE|ACOA|BAIBA|CER_DUKE|CONV|KA|NUC|OA|SPHM|OXYLIPNEG|ETAMIDPOS|AC_MAYO|AMINES|CER_MAYO|TCA|IMM_CRT|IMM_GLC|IMM_INS|PROT_PH|PROT_PR|PROT_AC|PROT_UB|PROT_OL)")
+                                pattern = "(?<=T\\d{2}/)(IONPNEG|RPNEG|RPPOS|HILICPOS|LRPPOS|LRPNEG|3HIB|AA|AC_DUKE|ACOA|BAIBA|CER_DUKE|CONV|KA|NUC|OA|SPHM|OXYLIPNEG|ETAMIDPOS|AC_MAYO|AMINES|CER_MAYO|TCA|IMM_CRT|IMM_GLC|IMM_INS|PROT_PH|PROT_PR|PROT_AC|PROT_UB|PROT_OL|PROT_OX)")
   if(is.na(assay)){
     stop("ASSAY not found in the folder structure")
   }else{