chore(moduleServer): use more modern module server for network server

DESCRIPTION

@@ -24,7 +24,7 @@ Authors@R: c(
     person("Olga", "Vitek", email = "o.vitek@northeastern.edu", role = "aut"))
 License: Artistic-2.0
 Depends: R (>= 4.2)
-Imports: shiny, shinyBS, shinyjs, shinybusy, dplyr, ggplot2, plotly, data.table, Hmisc, shinyFiles,
+Imports: shiny (>= 1.5.0), shinyBS, shinyjs, shinybusy, dplyr, ggplot2, plotly, data.table, Hmisc, shinyFiles,
   MSstats,MSstatsBig, MSstatsTMT, MSstatsPTM, MSstatsConvert, gplots, marray, DT, readxl,
   ggrepel, uuid, utils, stats, htmltools, methods, tidyr, grDevices, graphics, mockery, MSstatsBioNet,
   shinydashboard, arrow, tools, MSstatsResponse, stringr

NAMESPACE

@@ -112,6 +112,7 @@ importFrom(shiny,img)
 importFrom(shiny,insertUI)
 importFrom(shiny,isolate)
 importFrom(shiny,mainPanel)
+importFrom(shiny,moduleServer)
 importFrom(shiny,navbarMenu)
 importFrom(shiny,navbarPage)
 importFrom(shiny,nearPoints)

R/module-visualize-network-server.R

@@ -307,18 +307,17 @@ extractSubnetwork <- function(annotated_df, pValue, evidence, statementTypes,
 
 #' Server logic for network visualization module
 #'
-#' @param input Shiny input object
-#' @param output Shiny output object
-#' @param session Shiny session object
+#' @param id Module ID string
 #' @param parent_session Parent Shiny session
 #' @param dataComparison Reactive expression containing comparison data
 #'
 #' @return None (side effects only)
 #' 
 #' @importFrom MSstatsBioNet annotateProteinInfoFromIndra getSubnetworkFromIndra
 #' @importFrom DT renderDT datatable
-#' @importFrom shiny updateSelectizeInput showNotification outputOptions
-visualizeNetworkServer <- function(input, output, session, parent_session, dataComparison) {
+#' @importFrom shiny moduleServer updateSelectizeInput showNotification outputOptions
+visualizeNetworkServer <- function(id, parent_session, dataComparison) {
+  moduleServer(id, function(input, output, session) {
 
   # Output to control conditional panels
   output$hasValidDataComparison <- reactive({
@@ -714,4 +713,5 @@ visualizeNetworkServer <- function(input, output, session, parent_session, dataC
     updateLabelChoices(session, current_df)
     updateProteinChoices(session, current_df)
   })
+  }) # end moduleServer
 }

R/server.R

@@ -62,7 +62,7 @@ server = function(input, output, session) {
   })
 
   # visualizeNetworkServer - keep callModule if not yet refactored
-  callModule(visualizeNetworkServer, "network", session, data_comparison)
+  visualizeNetworkServer("network", parent_session = session, dataComparison = data_comparison)
 
   observe({
     if(input$"loadpage-DDA_DIA" %in% c("TMT") && input$"loadpage-BIO" %in% c("PTM")) {