From e892f49d98995c20bc7023fc3e1889786e126f11 Mon Sep 17 00:00:00 2001
From: Ivo Leist <ivo.leist@googlemail.com>
Date: Wed, 28 Feb 2024 17:16:22 +0100
Subject: [PATCH] added forgotten commit

---
 phenoRankeR/R/mod_patient_mode.R | 26 ++++++++++++++++++++------
 1 file changed, 20 insertions(+), 6 deletions(-)

diff --git a/phenoRankeR/R/mod_patient_mode.R b/phenoRankeR/R/mod_patient_mode.R
index 478c32f..8bf78a7 100644
--- a/phenoRankeR/R/mod_patient_mode.R
+++ b/phenoRankeR/R/mod_patient_mode.R
@@ -493,16 +493,30 @@ mod_patient_mode_server <- function(
       )
 
       for (i in 1:nrow(input$referenceFiles)) {
-        file <- input$referenceFiles[i, ]
-        # file_ext <- file_ext(file$name)
+      total_individual_counts <- 0
+        uploaded_file <- input$referenceFiles[i, ]
 
-        if (!(get_file_ext(file$name) %in% allowed_types)) {
+        file_con <- file(uploaded_file$datapath, "r")   
+        individual_counts <- as.numeric(jq(file_con, "length"))
+        close(file_con)
+
+        total_individual_counts <- total_individual_counts + individual_counts
+        if (total_individual_counts > 1000) {
+          showNotification(
+            "The maximum number of individuals is 1000",
+            type = "error"
+          )
+          reset("referenceFiles")
+          return()
+        }
+
+        if (!(get_file_ext(uploaded_file$name) %in% allowed_types)) {
           showNotification("Invalid file type!", type = "error")
           reset("referenceFiles")
           return()
         }
 
-        json_data <- fromJSON(readLines(file$datapath))
+        json_data <- fromJSON(readLines(uploaded_file$datapath))
         rv_patient$inputFormat <- "bff"
         if ("subject" %in% names(json_data)) {
           rv_patient$inputFormat <- "pxf"
@@ -520,7 +534,7 @@ mod_patient_mode_server <- function(
 
         str_references <- paste0(
           str_references,
-          file$name,
+          uploaded_file$name,
           ":C",
           i,
           "\n"
@@ -543,7 +557,7 @@ mod_patient_mode_server <- function(
         )
 
         file.copy(
-          file$datapath,
+          uploaded_file$datapath,
           file_path
         )