From 2dbb099f8ada99543bd6def16c32e1e16e0ad73d Mon Sep 17 00:00:00 2001
From: Vlad Petyuk <petyuk@gmail.com>
Date: Sat, 23 Nov 2024 22:52:13 -0800
Subject: [PATCH] generic reader

---
 R/read_genetic_tool_results_from_DMS.R | 35 ++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)
 create mode 100644 R/read_genetic_tool_results_from_DMS.R

diff --git a/R/read_genetic_tool_results_from_DMS.R b/R/read_genetic_tool_results_from_DMS.R
new file mode 100644
index 0000000..82791d6
--- /dev/null
+++ b/R/read_genetic_tool_results_from_DMS.R
@@ -0,0 +1,35 @@
+#' Reading generic tool output from PNNL's DMS
+#'
+#' @param data_package_num numeric or character; the Data Package ID in the DMS.
+#' @param tool character; MS-GF+ parameter file. No need to specify this
+#'   if there is only one parameter file associated with the jobs.
+#'
+#' @return (data.table) results in the form of one data.table
+#'
+#' @md
+#'
+#' @importFrom data.table data.table rbindlist
+#'
+#' @examples
+#' if (is_PNNL_DMS_connection_successful()) {
+#'   x <- read_generic_job_from_DMS(6148, "Decon2LS_V2")
+#'   (x)
+#' }
+#'
+#' @export
+
+read_generic_job_from_DMS <- function(data_package_num, tool) 
+{
+  if (length(data_package_num) > 1) {
+    job_rec_ls <- lapply(data_package_num, get_job_records_by_dataset_package)
+    jobRecords <- rbindlist(job_rec_ls)
+  }
+  else {
+    jobRecords <- get_job_records_by_dataset_package(data_package_num)
+  }
+  
+  jobRecords <- jobRecords[tool == jobRecords$tool,]
+  results <- get_results_for_multiple_jobs.dt(jobRecords)
+  results <- rbindlist(results)
+  return(results)
+}