[merge] remote-tracking branch 'origin/dave_batch_experiments2' into …

…dave_and_ben_changes

R/get_batch_experiments.R

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+#' Get experiment details for all LC-MS runs in a batch
+#'
+#' @description This function retrieves detailed experiment information for all LC-MS runs
+#' in a specified batch from the DMS database. It can return either a simplified view with
+#' key columns or all available experiment details.
+#'
+#' @param batch_id The batch number to query (numeric)
+#' @param simplified Logical; if TRUE returns simplified view with key columns, 
+#'        if FALSE returns all experiment columns. Default is TRUE.
+#' @return A data frame containing experiment details for all runs in the batch.
+#'   The returned columns depend on the simplified parameter.
+#'
+#' @examples
+#' \dontrun{
+#'   if (is_PNNL_DMS_connection_successful()) {
+#'     # Get simplified view
+#'     batch_details <- get_batch_experiments(11495)
+#'     
+#'     # Get all experiment columns
+#'     batch_details_full <- get_batch_experiments(11495, simplified = FALSE)
+#'   }
+#' }
+#'
+#' @importFrom DBI dbConnect dbSendQuery dbFetch dbClearResult dbDisconnect
+#' @importFrom dplyr %>% select arrange distinct
+#' @export
+get_batch_experiments <- function(batch_id, simplified = TRUE) {
+   # Input validation
+   if (!is.numeric(batch_id)) {
+      stop("batch_id must be numeric")
+   }
+
+   # Get database connection
+   con <- get_db_connection()
+   on.exit(dbDisconnect(con))
+
+   if (simplified) {
+      # Original simplified query with key columns
+      strSQL <- sprintf("
+      SELECT DISTINCT
+        bt.batch,
+        bt.name as batch_name,
+        bt.status,
+        bt.dataset_id,
+        bt.dataset,
+        bt.instrument,
+        bt.lc_column,
+        bt.start as acquisition_start,
+        bt.block,
+        bt.run_order,
+        d.exp_id,
+        exp.experiment as experiment,
+        exp.campaign_id,
+        c.campaign,
+        exp.reason,
+        exp.comment,
+        exp.sample_concentration,
+        exp.created as experiment_created
+      FROM v_batch_tracking_list_report bt
+      LEFT JOIN t_dataset d ON bt.dataset_id = d.dataset_id
+      LEFT JOIN t_experiments exp ON d.exp_id = exp.exp_id
+      LEFT JOIN t_campaign c ON exp.campaign_id = c.campaign_id
+      WHERE bt.batch = %d
+      ORDER BY bt.start;", 
+                        batch_id)
+   } else {
+      # Expanded query with all experiment columns
+      strSQL <- sprintf("
+      SELECT DISTINCT
+        bt.batch,
+        bt.name as batch_name,
+        bt.status,
+        bt.dataset_id,
+        bt.dataset,
+        bt.instrument,
+        bt.lc_column,
+        bt.start as acquisition_start,
+        bt.block,
+        bt.run_order,
+        exp.*,  -- Include all experiment columns
+        c.campaign
+      FROM v_batch_tracking_list_report bt
+      LEFT JOIN t_dataset d ON bt.dataset_id = d.dataset_id
+      LEFT JOIN t_experiments exp ON d.exp_id = exp.exp_id
+      LEFT JOIN t_campaign c ON exp.campaign_id = c.campaign_id
+      WHERE bt.batch = %d
+      ORDER BY bt.start;", 
+                        batch_id)
+   }
+
+   qry <- dbSendQuery(con, strSQL)
+   results <- dbFetch(qry)
+   dbClearResult(qry)
+
+   if (nrow(results) == 0) {
+      warning(sprintf("No experiments found for batch %d", batch_id))
+      return(NULL)
+   }
+
+   return(results)
+}