From 700462af1d70c632be31266dfcd8dbdcc174589f Mon Sep 17 00:00:00 2001
From: LDSamson <l.d.samson@gmail.com>
Date: Fri, 19 Jan 2024 18:15:49 +0100
Subject: [PATCH 01/22] Add functionality to show local reverse dependencies of
 a selected package

---
 DESCRIPTION                               |  3 +-
 R/mod_packageDependencies.R               | 18 ++++++-
 tests/testthat/test-packageDependencies.R | 57 ++++++++++++++++++++++-
 3 files changed, 74 insertions(+), 4 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f7e361533..639ca7c0e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -78,7 +78,8 @@ Suggests:
     shinytest2,
     spelling,
     testthat (>= 3.0.0),
-    tinytex
+    tinytex,
+    withr
 Config/testthat/edition: 3
 Language: en-US
 Depends: 
diff --git a/R/mod_packageDependencies.R b/R/mod_packageDependencies.R
index dd1b0fc4c..2ab3cde2d 100644
--- a/R/mod_packageDependencies.R
+++ b/R/mod_packageDependencies.R
@@ -40,6 +40,7 @@ packageDependenciesServer <- function(id, selected_pkg, user, parent) {
     depends  <- reactiveVal(value = NULL)
     suggests <- reactiveVal(value = NULL)
     revdeps  <- reactiveVal(value = NULL)
+    revdeps_local <- reactiveVal(value = NULL)
     rev_pkg  <- reactiveVal(value = 0L)
     toggled  <- reactiveVal(value = 0L)
     pkg_updates <- reactiveValues()
@@ -93,6 +94,8 @@ packageDependenciesServer <- function(id, selected_pkg, user, parent) {
       if (rlang::is_empty(pkgref()$dependencies[[1]])) depends(dplyr::tibble(package = character(0), type = character(0)))
         
       revdeps(pkgref()$reverse_dependencies[[1]] %>% as.vector())
+      revdeps_local(with(loaded2_db(), name[name %in% revdeps()]))
+      
       # send either depends() or both to build_dep_cards(), depending on toggled()
       if (toggled() == 0L) {
         cards(build_dep_cards(data = depends(), loaded = loaded2_db()$name, toggled = 0L))
@@ -263,8 +266,19 @@ packageDependenciesServer <- function(id, selected_pkg, user, parent) {
                     })
                 ) # column
               ), # fluidRow
-              br(),
-              h4(glue::glue("Reverse Dependencies: {length(revdeps())}"), style = "text-align: left;"),
+              br(), 
+              h4(glue::glue("Reverse Dependencies available in database: {length(revdeps_local())}"), style = "text-align: left;"),
+              br(), br(),
+              fluidRow(
+                column(
+                  width = 8,
+                  wellPanel(
+                    renderText(revdeps_local() %>% sort()),
+                    style = "max-height: 500px; overflow: auto"
+                  )
+                )
+              ),
+              h4(glue::glue("All reverse Dependencies: {length(revdeps())}"), style = "text-align: left;"),
               br(), br(),
               fluidRow(
                 column(
diff --git a/tests/testthat/test-packageDependencies.R b/tests/testthat/test-packageDependencies.R
index 483340eb3..83d3001a1 100644
--- a/tests/testthat/test-packageDependencies.R
+++ b/tests/testthat/test-packageDependencies.R
@@ -41,4 +41,59 @@ test_that("module can produce a table of package dependencies", {
   unlink("app_db_loc")
   rm(out_htm, id_strng, json, actual, expected, app_db_loc)
 
-})
\ No newline at end of file
+})
+
+test_that(
+  "Feature 1. module packageDependencies selects all reverse dependencies 
+  in the database.
+    Scenario 1. Given the selected package is 'dplyr',  
+    and the packages names in the package database are 'dplyr' and 'dbplyr', 
+    I expect that the package names 'plotly', 'admiral', 'dbplyr' and 'glue' are found in [revdeps],
+    and that [revdeps_local] is equal to 'dbplyr'.",
+  {
+    testargs <- list(
+      selected_pkg =  list(
+        name = reactiveVal("dplyr")
+      ),
+      user = "test_user",
+      parent = reactiveValues(
+        input = reactiveValues(
+          tabs = "Package Metrics",
+          metric_type = "dep"
+        )
+      )
+    )
+    
+    test_db_loc <- system.file("testdata", "upload_format.database", 
+                               package = "riskassessment")
+    temp_db_loc <- withr::local_tempfile(fileext = ".database")
+    file.copy(test_db_loc, temp_db_loc)
+    con <- withr::local_db_connection(
+      DBI::dbConnect(RSQLite::SQLite(), temp_db_loc)
+    )
+    # because only the dplyr package is in the test dataset, we add one of its 
+    # known reverse dependencies:
+    DBI::dbAppendTable(
+      con, 
+      "package", 
+      data.frame(
+        name = "dbplyr",
+        version = "1.0.0",
+        score = "0.32"
+      )
+    )
+    # add test db location to the app session:
+    app_session <- MockShinySession$new()
+    app_session$options$golem_options <- list(
+      assessment_db_name = temp_db_loc
+    )
+    
+    testServer(packageDependenciesServer, args = testargs,  {
+      session$flushReact()
+      expect_true(all(c("plotly", "admiral", "dbplyr", "glue") %in% revdeps()))
+      expect_equal(revdeps_local(), "dbplyr")
+    },
+    session = app_session)
+  }
+)
+

From 4b5da3b92a4447c64cb5c98f2086e47ede34271c Mon Sep 17 00:00:00 2001
From: LDSamson <l.d.samson@gmail.com>
Date: Mon, 22 Jan 2024 11:34:10 +0100
Subject: [PATCH 02/22] slight update for consistent line breaks

---
 R/mod_packageDependencies.R | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/R/mod_packageDependencies.R b/R/mod_packageDependencies.R
index 2ab3cde2d..bb889e949 100644
--- a/R/mod_packageDependencies.R
+++ b/R/mod_packageDependencies.R
@@ -266,9 +266,9 @@ packageDependenciesServer <- function(id, selected_pkg, user, parent) {
                     })
                 ) # column
               ), # fluidRow
-              br(), 
+              br(), br(),  
               h4(glue::glue("Reverse Dependencies available in database: {length(revdeps_local())}"), style = "text-align: left;"),
-              br(), br(),
+              br(), 
               fluidRow(
                 column(
                   width = 8,
@@ -278,8 +278,9 @@ packageDependenciesServer <- function(id, selected_pkg, user, parent) {
                   )
                 )
               ),
-              h4(glue::glue("All reverse Dependencies: {length(revdeps())}"), style = "text-align: left;"),
               br(), br(),
+              h4(glue::glue("All reverse Dependencies: {length(revdeps())}"), style = "text-align: left;"),
+              br(),
               fluidRow(
                 column(
                   width = 8,

From 5c5b6ad630a0a01df91bfbff14da81d59835af33 Mon Sep 17 00:00:00 2001
From: LDSamson <l.d.samson@gmail.com>
Date: Tue, 23 Jan 2024 11:41:06 +0100
Subject: [PATCH 03/22] improve temp db connection in test

---
 tests/testthat/test-packageDependencies.R | 25 +++++++++++++----------
 1 file changed, 14 insertions(+), 11 deletions(-)

diff --git a/tests/testthat/test-packageDependencies.R b/tests/testthat/test-packageDependencies.R
index 83d3001a1..f7e0ad990 100644
--- a/tests/testthat/test-packageDependencies.R
+++ b/tests/testthat/test-packageDependencies.R
@@ -68,19 +68,22 @@ test_that(
                                package = "riskassessment")
     temp_db_loc <- withr::local_tempfile(fileext = ".database")
     file.copy(test_db_loc, temp_db_loc)
-    con <- withr::local_db_connection(
-      DBI::dbConnect(RSQLite::SQLite(), temp_db_loc)
-    )
+    
     # because only the dplyr package is in the test dataset, we add one of its 
     # known reverse dependencies:
-    DBI::dbAppendTable(
-      con, 
-      "package", 
-      data.frame(
-        name = "dbplyr",
-        version = "1.0.0",
-        score = "0.32"
-      )
+    withr::with_db_connection(
+      list(con = DBI::dbConnect(RSQLite::SQLite(), temp_db_loc)),
+      {
+        DBI::dbAppendTable(
+          con, 
+          "package", 
+          data.frame(
+            name = "dbplyr",
+            version = "1.0.0",
+            score = "0.32"
+          )
+        )
+      }
     )
     # add test db location to the app session:
     app_session <- MockShinySession$new()

From 1da48a7e402d089260866f983cb394aa21eaa8e7 Mon Sep 17 00:00:00 2001
From: Jeff Thompson <jeff.thompson51317@gmail.com>
Date: Wed, 31 Jan 2024 14:33:53 -0500
Subject: [PATCH 04/22] Repair test

---
 R/mod_packageDependencies.R               | 2 +-
 tests/testthat/test-packageDependencies.R | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/mod_packageDependencies.R b/R/mod_packageDependencies.R
index b80b7487e..181ff70c7 100644
--- a/R/mod_packageDependencies.R
+++ b/R/mod_packageDependencies.R
@@ -93,7 +93,7 @@ packageDependenciesServer <- function(id, selected_pkg, user, parent) {
       if (rlang::is_empty(pkgref()$dependencies[[1]])) depends(dplyr::tibble(package = character(0), type = character(0), name = character(0)))
         
       revdeps(pkgref()$reverse_dependencies[[1]] %>% as.vector())
-      revdeps_local(with(loaded2_db(), name[name %in% revdeps()]))
+      revdeps_local(with(session$userData$loaded2_db(), name[name %in% revdeps()]))
       
       # send either depends() or both to build_dep_cards(), depending on toggled()
       if (toggled() == 0L) {
diff --git a/tests/testthat/test-packageDependencies.R b/tests/testthat/test-packageDependencies.R
index f7e0ad990..5c20d2f51 100644
--- a/tests/testthat/test-packageDependencies.R
+++ b/tests/testthat/test-packageDependencies.R
@@ -90,6 +90,7 @@ test_that(
     app_session$options$golem_options <- list(
       assessment_db_name = temp_db_loc
     )
+    app_session$userData$loaded2_db <- reactiveVal(dbSelect("SELECT name, version, score FROM package", temp_db_loc))
     
     testServer(packageDependenciesServer, args = testargs,  {
       session$flushReact()

From 25f0c4c705537082f14c059d91a4e1a17623e705 Mon Sep 17 00:00:00 2001
From: LDSamson <l.d.samson@gmail.com>
Date: Sun, 4 Feb 2024 10:16:03 +0100
Subject: [PATCH 05/22] Implement local revdeps table

---
 NAMESPACE                   |   1 +
 R/mod_packageDependencies.R | 131 ++++++++++++------------------------
 R/utils.R                   | 118 +++++++++++++++++++++++++++++++-
 man/add_buttons_to_table.Rd |  33 +++++++++
 man/datatable_custom.Rd     |  34 ++++++++++
 5 files changed, 227 insertions(+), 90 deletions(-)
 create mode 100644 man/add_buttons_to_table.Rd
 create mode 100644 man/datatable_custom.Rd

diff --git a/NAMESPACE b/NAMESPACE
index a73fff296..3d978267f 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(add_buttons_to_table)
 export(app_theme)
 export(build_comm_plotly)
 export(generate_comm_data)
diff --git a/R/mod_packageDependencies.R b/R/mod_packageDependencies.R
index 181ff70c7..b4734a422 100644
--- a/R/mod_packageDependencies.R
+++ b/R/mod_packageDependencies.R
@@ -35,7 +35,6 @@ packageDependenciesServer <- function(id, selected_pkg, user, parent) {
     depends  <- reactiveVal(value = NULL)
     suggests <- reactiveVal(value = NULL)
     revdeps  <- reactiveVal(value = NULL)
-    revdeps_local <- reactiveVal(value = NULL)
     rev_pkg  <- reactiveVal(value = 0L)
     toggled  <- reactiveVal(value = 0L)
     pkg_updates <- reactiveValues()
@@ -93,7 +92,6 @@ packageDependenciesServer <- function(id, selected_pkg, user, parent) {
       if (rlang::is_empty(pkgref()$dependencies[[1]])) depends(dplyr::tibble(package = character(0), type = character(0), name = character(0)))
         
       revdeps(pkgref()$reverse_dependencies[[1]] %>% as.vector())
-      revdeps_local(with(session$userData$loaded2_db(), name[name %in% revdeps()]))
       
       # send either depends() or both to build_dep_cards(), depending on toggled()
       if (toggled() == 0L) {
@@ -150,24 +148,20 @@ packageDependenciesServer <- function(id, selected_pkg, user, parent) {
     }, ignoreInit = TRUE)
     
     data_table <- eventReactive(pkg_df(), {
-      cbind(
-        pkg_df(),
-        data.frame(
-          Actions = shinyInput(
-            actionButton, nrow(pkg_df()),
-            "button_",
-            size = "xs",
-            style = "height:24px; padding-top:1px;",
-            label = icon("arrow-right", class = "fa-regular", lib = "font-awesome"),
-            onclick = paste0('Shiny.setInputValue(\"', ns("select_button"), '\", this.id, {priority: "event"})')
-          )
-        )
-      ) %>% # remove action button if there is nothing to review
+      add_buttons_to_table(pkg_df(), ns("select_button")) %>% 
+        # remove action button if there is nothing to review
         mutate(Actions = if_else(identical(package, character(0)) | name %in% c(rownames(installed.packages(priority = "base"))), "", Actions)) %>% 
         # if package name not yet loaded, switch the actionbutton to fa-upload
         mutate(Actions = if_else(!name %in% session$userData$loaded2_db()$name, gsub("fas fa-arrow-right fa-regular", "fas fa-upload fa-solid", Actions), Actions))
     })
     
+    table_revdeps_local <- reactive({
+      df <- session$userData$loaded2_db()
+      req(df, df$name)
+      with(df, df[name %in% revdeps(),]) |> 
+      add_buttons_to_table(ns("go_to_revdep"))
+    })
+    
     # Create metric grid card.
     metricGridServer(id = 'metricGrid', metrics = cards) 
     
@@ -221,70 +215,20 @@ packageDependenciesServer <- function(id, selected_pkg, user, parent) {
                 column(
                   width = 8,
                     DT::renderDataTable(server = FALSE, {
-                      # Hiding name from DT table. target contains index for "name"
-                      # The - 1 is because js uses 0 index instead of 1 like R
-                      target <- which(names(data_table()) %in% c("name")) - 1
-                      
-                      formattable::as.datatable(
-                        formattable::formattable(
-                          data_table(),
-                          list(
-                            score = formattable::formatter(
-                              "span",
-                              style = x ~ formattable::style(
-                                display = "block",
-                                "border-radius" = "4px",
-                                "padding-right" = "4px",
-                                "color" = "#000000",
-                                "order" = x,
-                                "background-color" = formattable::csscolor(
-                                  setColorPalette(100)[round(as.numeric(x)*100)]
-                                )
-                              )
-                            ),
-                            decision = formattable::formatter(
-                              "span",
-                              style = x ~ formattable::style(
-                                display = "block",
-                                "border-radius" = "4px",
-                                "padding-right" = "4px",
-                                "font-weight" = "bold",
-                                "color" = ifelse(x %in% decision_lst, "white", "inherit"),
-                                "background-color" =
-                                  ifelse(x %in% decision_lst,
-                                         color_lst[x],
-                                         "transparent"
-                                  )
-                              )
-                            )
-                          )
-                        ),
-                        selection = "none",
-                        colnames = c("Package", "Type", "Name", "Version", "Score", "Review Package"),
-                        rownames = FALSE,
-                        options = list(
-                          lengthMenu = list(c(15, -1), c("15", "All")),
-                          columnDefs = list(list(visible = FALSE, targets = target)),
-                          searchable = FALSE
-                        ),
-                        style = "default"
-                      ) %>%
-                        DT::formatStyle(names(data_table()), textAlign = "center")
-                    })
-                ) # column
-              ), # fluidRow
-              br(), br(),  
-              h4(glue::glue("Reverse Dependencies available in database: {length(revdeps_local())}"), style = "text-align: left;"),
-              br(), 
-              fluidRow(
-                column(
-                  width = 8,
-                  wellPanel(
-                    renderText(revdeps_local() %>% sort()),
-                    style = "max-height: 500px; overflow: auto"
-                  )
+                    datatable_custom(data_table())                      
+                    }),
+                  br(), br(),  
+                  h4(glue::glue("Reverse Dependencies available in database: {nrow(table_revdeps_local()) %||% 0}"), style = "text-align: left;"),
+                  br(), 
+                  DT::renderDataTable({
+                    datatable_custom(
+                      table_revdeps_local(), 
+                      colnames = c("Package", "Version", "Score", "Review Package"),
+                      hide_names = NULL
+                    )
+                  })
                 )
-              ),
+              ), 
               br(), br(),
               h4(glue::glue("All reverse Dependencies: {length(revdeps())}"), style = "text-align: left;"),
               br(),
@@ -302,21 +246,30 @@ packageDependenciesServer <- function(id, selected_pkg, user, parent) {
       }
     }) # renderUI
     
+    # the package selected in the table to either browser to or to upload:
+    selected_package <- reactiveVal() 
     pkgname <- reactiveVal()
+    observeEvent(input$select_button, {
+      req(pkg_df())
+      selectedRow <- as.numeric(strsplit(input$select_button, "_")[[1]][2])
+      selected_package(with(pkg_df(), name[selectedRow]))
+      pkgname("-")
+    })
+    observeEvent(input$go_to_revdep, {
+      req(table_revdeps_local())
+      selectedRow <- as.numeric(strsplit(input$go_to_revdep, "_")[[1]][2])
+      selected_package(with(table_revdeps_local(), name[selectedRow]))
+    })
     
-    observeEvent(input$select_button,
+    observeEvent(selected_package(),
      {
-       req(pkg_df())
        rev_pkg(0L)
-       
-       selectedRow <- as.numeric(strsplit(input$select_button, "_")[[1]][2])
-       
-       # grab the package name
-       pkg_name <- pkg_df()[selectedRow, 3] %>% pull()
        pkgname("-")
-       
-       if (!pkg_name %in% session$userData$loaded2_db()$name) {
-         pkgname(pkg_name)
+       # to ensure that if the same package is clicked on, this observeEvent will 
+       # run again:
+       on.exit(selected_package(NULL)) 
+       if (!selected_package() %in% session$userData$loaded2_db()$name) {
+         pkgname(selected_package())
          shiny::showModal(modalDialog(
            size = "l",
            easyClose = TRUE,
@@ -341,7 +294,7 @@ packageDependenciesServer <- function(id, selected_pkg, user, parent) {
            session = parent,
            inputId = "sidebar-select_pkg",
            choices = c("-", session$userData$loaded2_db()$name),
-           selected = pkg_name
+           selected = selected_package()
          )
        }
      },
diff --git a/R/utils.R b/R/utils.R
index b9f22454e..38f2769e1 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -540,4 +540,120 @@ shinyInput <- function(FUN, len, id, ...) {
     inputs[i] <- as.character(FUN(paste0(id, i), ...))
   }
   inputs
-}
\ No newline at end of file
+}
+
+#' Custom datatable
+#'
+#' Small helper function to create a `DT::datatable()` object in a consistent
+#' style.
+#'
+#' @param data A data frame as input.
+#' @param colnames 
+#' @param hide_names Character vector. Whether to hide columns in the data
+#'   frame.
+#' @param ... Other options. Currently not in use.
+#'
+#' @return a DT::datatable object. 
+#'
+#' @examples datatable_custom(mtcars, colnames = paste0("custom_", names(mtcars)))
+#' 
+datatable_custom <- function(
+    data, 
+    colnames = c("Package", "Type", "Name", "Version", "Score", "Review Package"), 
+    hide_names = "name",
+    ...
+){
+  colnames <- colnames %||% character(0)
+  hide_names <- hide_names %||% character(0)
+  data <- data %||% as.data.frame(matrix(nrow = 0, ncol = pmax(length(colnames), 1) )) 
+  stopifnot(is.data.frame(data))
+  stopifnot(is.character(hide_names))
+  stopifnot(is.character(colnames))
+  # Hiding name from DT table. 
+  # The - 1 is because js uses 0 index instead of 1 like R
+  target <- which(names(data) %in% hide_names) - 1
+  
+  formattable::as.datatable(
+    formattable::formattable(
+      data,
+      list(
+        score = formattable::formatter(
+          "span",
+          style = x ~ formattable::style(
+            display = "block",
+            "border-radius" = "4px",
+            "padding-right" = "4px",
+            "color" = "#000000",
+            "order" = x,
+            "background-color" = formattable::csscolor(
+              setColorPalette(100)[round(as.numeric(x)*100)]
+            )
+          )
+        ),
+        decision = formattable::formatter(
+          "span",
+          style = x ~ formattable::style(
+            display = "block",
+            "border-radius" = "4px",
+            "padding-right" = "4px",
+            "font-weight" = "bold",
+            "color" = ifelse(x %in% decision_lst, "white", "inherit"),
+            "background-color" =
+              ifelse(x %in% decision_lst,
+                     color_lst[x],
+                     "transparent"
+              )
+          )
+        )
+      )
+    ),
+    selection = "none",
+    colnames = if(length(colnames) == 0) names(data) else colnames,
+    rownames = FALSE,
+    options = list(
+      lengthMenu = list(c(15, -1), c("15", "All")),
+      columnDefs = list(list(visible = FALSE, targets = target)),
+      searchable = FALSE
+    ),
+    style = "default"
+  ) %>%
+    DT::formatStyle(names(data), textAlign = "center")
+}
+
+#' Add buttons to data frame
+#' 
+#' Small helper function to add Shiny action buttons to a data frame.
+#'
+#' @param data A data frame. 
+#' @param id Character vector. the main id of the buttons.
+#' @param label Label to use for the button. 
+#' @param ... For future expansions. Currently not in use. 
+#'
+#' @return A data frame with a button in each table row. 
+#' @export
+#'
+#' @examples 
+#' add_buttons_to_table(mtcars[, 1:5], "button_id", "click me") |> 
+#'   datatable_custom()
+#'   
+add_buttons_to_table <- function(
+    data, 
+    id,
+    label = icon("arrow-right", class = "fa-regular", lib = "font-awesome"),
+    ...
+){
+  stopifnot(is.data.frame(data))
+  cbind(
+    data,
+    data.frame(
+      Actions = shinyInput(
+        actionButton, nrow(data),
+        "button_",
+        size = "xs",
+        style = "height:24px; padding-top:1px;",
+        label = label,
+        onclick = paste0('Shiny.setInputValue(\"', id, '\", this.id, {priority: "event"})')
+      )
+    )
+  )
+}
diff --git a/man/add_buttons_to_table.Rd b/man/add_buttons_to_table.Rd
new file mode 100644
index 000000000..ec5a97858
--- /dev/null
+++ b/man/add_buttons_to_table.Rd
@@ -0,0 +1,33 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{add_buttons_to_table}
+\alias{add_buttons_to_table}
+\title{Add buttons to data frame}
+\usage{
+add_buttons_to_table(
+  data,
+  id,
+  label = icon("arrow-right", class = "fa-regular", lib = "font-awesome"),
+  ...
+)
+}
+\arguments{
+\item{data}{A data frame.}
+
+\item{id}{Character vector. the main id of the buttons.}
+
+\item{label}{Label to use for the button.}
+
+\item{...}{For future expansions. Currently not in use.}
+}
+\value{
+A data frame with a button in each table row.
+}
+\description{
+Small helper function to add Shiny action buttons to a data frame.
+}
+\examples{
+add_buttons_to_table(mtcars[, 1:5], "button_id", "click me") |> 
+  datatable_custom()
+  
+}
diff --git a/man/datatable_custom.Rd b/man/datatable_custom.Rd
new file mode 100644
index 000000000..646607de2
--- /dev/null
+++ b/man/datatable_custom.Rd
@@ -0,0 +1,34 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{datatable_custom}
+\alias{datatable_custom}
+\title{Custom datatable}
+\usage{
+datatable_custom(
+  data,
+  colnames = c("Package", "Type", "Name", "Version", "Score", "Review Package"),
+  hide_names = "name",
+  ...
+)
+}
+\arguments{
+\item{data}{A data frame as input.}
+
+\item{colnames}{}
+
+\item{hide_names}{Character vector. Whether to hide columns in the data
+frame.}
+
+\item{...}{Other options. Currently not in use.}
+}
+\value{
+a DT::datatable object.
+}
+\description{
+Small helper function to create a \code{DT::datatable()} object in a consistent
+style.
+}
+\examples{
+datatable_custom(mtcars, colnames = paste0("custom_", names(mtcars)))
+
+}

From 2abf267bfadabd4cde0c3d9a67d79c9458cbc1c7 Mon Sep 17 00:00:00 2001
From: LDSamson <l.d.samson@gmail.com>
Date: Sun, 4 Feb 2024 11:26:16 +0100
Subject: [PATCH 06/22] Fix selected package name not showing in 'confirm to
 upload package' modal

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

diff --git a/R/mod_packageDependencies.R b/R/mod_packageDependencies.R
index b4734a422..4f2991343 100644
--- a/R/mod_packageDependencies.R
+++ b/R/mod_packageDependencies.R
@@ -279,7 +279,7 @@ packageDependenciesServer <- function(id, selected_pkg, user, parent) {
            fluidRow(
              column(
                width = 12,
-               "Please confirm to load this package: ", span(class = "text-info", input$decision),
+               "Please confirm to load this package: ", span(class = "text-info", selected_package()),
              )
            ),
            br(),

From 177e900a91c0b2bfafc7c4644b34afb6743feb7a Mon Sep 17 00:00:00 2001
From: LDSamson <l.d.samson@gmail.com>
Date: Sun, 4 Feb 2024 11:41:27 +0100
Subject: [PATCH 07/22] Add utils tests and fix module test

---
 tests/testthat/test-packageDependencies.R |  7 ++--
 tests/testthat/test-utils.R               | 42 +++++++++++++++++++++++
 2 files changed, 47 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-packageDependencies.R b/tests/testthat/test-packageDependencies.R
index 5c20d2f51..df99f56c1 100644
--- a/tests/testthat/test-packageDependencies.R
+++ b/tests/testthat/test-packageDependencies.R
@@ -49,7 +49,8 @@ test_that(
     Scenario 1. Given the selected package is 'dplyr',  
     and the packages names in the package database are 'dplyr' and 'dbplyr', 
     I expect that the package names 'plotly', 'admiral', 'dbplyr' and 'glue' are found in [revdeps],
-    and that [revdeps_local] is equal to 'dbplyr'.",
+    and that [table_revdeps_local] contains the package name 'dbplyr',
+    and that [table_revdeps_local] contains an action button",
   {
     testargs <- list(
       selected_pkg =  list(
@@ -95,7 +96,9 @@ test_that(
     testServer(packageDependenciesServer, args = testargs,  {
       session$flushReact()
       expect_true(all(c("plotly", "admiral", "dbplyr", "glue") %in% revdeps()))
-      expect_equal(revdeps_local(), "dbplyr")
+      expect_equal(table_revdeps_local()$name, "dbplyr")
+      # the table contains an action button:
+      expect_true(grepl('button id=\"button_1\"',table_revdeps_local()$Actions))
     },
     session = app_session)
   }
diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
index a755a0cc0..354d7641e 100644
--- a/tests/testthat/test-utils.R
+++ b/tests/testthat/test-utils.R
@@ -165,3 +165,45 @@ test_that("Test that get_time() works", {
 test_that("Test that build_dep_cards() works", {
   skip("Placeholder for build_dep_cards()")
 })
+
+test_that("add_buttons_to_table works", {
+  expect_no_error(add_buttons_to_table(mtcars, "testid", "click me"))
+})
+test_that("add_buttons_to_table adds unique buttons to each table row", {
+  output <- add_buttons_to_table(mtcars, "testid", "click me")
+  # individual buttons are added to each row:
+  expected_button_ids <- paste0('<button id=\"button_', 1:nrow(mtcars))
+  sapply(
+    seq_along(output$Actions), 
+    \(x){expect_true(grepl(expected_button_ids[x], output$Actions[x]))}
+  )
+})
+test_that(
+  "add_buttons_to_table can handle zero-row data frames and 
+    errors if not a data frame is provided", 
+  {
+    #it does not error with a zero-row data frame: 
+    expect_no_error(add_buttons_to_table(data.frame(), "testid", "click me"))
+    
+    # it errors if not a data frame is provided
+    expect_error(add_buttons_to_table(matrix(), "testid", "click me"))
+  }
+) 
+
+test_that("datatable_custom works", {
+  output <- datatable_custom(mtcars, colnames = paste0("custom_", names(mtcars)))
+  expect_true(inherits(output, "datatables"))
+  # it errors off not a data frame is provided:
+  datatable_custom(mtcars[, 1:2], colnames = c("a", "b", "c"))
+  
+  #it returns an empty datatable if the data frame provided is NULL
+  output_no_df <- datatable_custom(NULL, colnames = paste0("custom_", names(mtcars)))
+  expect_true(inherits(output_no_df, "datatables"))
+  expect_equal(nrow(output_no_df$x$data), 0)
+  # and if the colnames parameter is also NULL:
+  output_no_df_no_colnames <- datatable_custom(NULL, colnames = NULL)
+  expect_true(inherits(output_no_df_no_colnames, "datatables"))
+  expect_equal(nrow(output_no_df_no_colnames$x$data), 0)
+  
+})
+

From d8bbd186536b9ab18af88cb40c4cf3503b38ead8 Mon Sep 17 00:00:00 2001
From: LDSamson <l.d.samson@gmail.com>
Date: Mon, 5 Feb 2024 08:45:27 +0100
Subject: [PATCH 08/22] Fix missing test condition

---
 R/utils.R                   |  8 +++++++-
 tests/testthat/test-utils.R | 11 ++++++++---
 2 files changed, 15 insertions(+), 4 deletions(-)

diff --git a/R/utils.R b/R/utils.R
index 38f2769e1..daa997417 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -569,6 +569,12 @@ datatable_custom <- function(
   stopifnot(is.data.frame(data))
   stopifnot(is.character(hide_names))
   stopifnot(is.character(colnames))
+  colnames <- if(length(colnames) == 0) names(data) else colnames
+  if(length(colnames) != ncol(data)) {
+    warning("number of provided colnames unequal to number of columns in data. 
+            Defaulting to original data frame names.")
+    colnames <- names(data)
+  } 
   # Hiding name from DT table. 
   # The - 1 is because js uses 0 index instead of 1 like R
   target <- which(names(data) %in% hide_names) - 1
@@ -608,7 +614,7 @@ datatable_custom <- function(
       )
     ),
     selection = "none",
-    colnames = if(length(colnames) == 0) names(data) else colnames,
+    colnames = colnames,
     rownames = FALSE,
     options = list(
       lengthMenu = list(c(15, -1), c("15", "All")),
diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
index 354d7641e..5095b5406 100644
--- a/tests/testthat/test-utils.R
+++ b/tests/testthat/test-utils.R
@@ -193,9 +193,14 @@ test_that(
 test_that("datatable_custom works", {
   output <- datatable_custom(mtcars, colnames = paste0("custom_", names(mtcars)))
   expect_true(inherits(output, "datatables"))
-  # it errors off not a data frame is provided:
-  datatable_custom(mtcars[, 1:2], colnames = c("a", "b", "c"))
-  
+  # it errors if not a data frame is provided:
+  expect_error(datatable_custom(matrix()))
+  # it defaults to data frame names with a warning if colnames is not of equal 
+  # length as names(data)
+  expect_warning(
+    datatable_custom(mtcars[, 1:2], colnames = c("a", "b", "c")),
+    "Defaulting to original data frame names"
+  )
   #it returns an empty datatable if the data frame provided is NULL
   output_no_df <- datatable_custom(NULL, colnames = paste0("custom_", names(mtcars)))
   expect_true(inherits(output_no_df, "datatables"))

From 882ed35fe949fec862f59f24df76d3008d566de8 Mon Sep 17 00:00:00 2001
From: Jeff Thompson <85879620+Jeff-Thompson12@users.noreply.github.com>
Date: Tue, 27 Feb 2024 09:31:25 -0500
Subject: [PATCH 09/22] Remove Rd's for new functions

---
 R/utils.R                   |  4 ++++
 man/add_buttons_to_table.Rd | 33 ---------------------------------
 man/datatable_custom.Rd     | 34 ----------------------------------
 3 files changed, 4 insertions(+), 67 deletions(-)
 delete mode 100644 man/add_buttons_to_table.Rd
 delete mode 100644 man/datatable_custom.Rd

diff --git a/R/utils.R b/R/utils.R
index daa997417..d923168ef 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -557,6 +557,8 @@ shinyInput <- function(FUN, len, id, ...) {
 #'
 #' @examples datatable_custom(mtcars, colnames = paste0("custom_", names(mtcars)))
 #' 
+#' @noRd
+#' 
 datatable_custom <- function(
     data, 
     colnames = c("Package", "Type", "Name", "Version", "Score", "Review Package"), 
@@ -642,6 +644,8 @@ datatable_custom <- function(
 #' add_buttons_to_table(mtcars[, 1:5], "button_id", "click me") |> 
 #'   datatable_custom()
 #'   
+#' @noRd
+#'   
 add_buttons_to_table <- function(
     data, 
     id,
diff --git a/man/add_buttons_to_table.Rd b/man/add_buttons_to_table.Rd
deleted file mode 100644
index ec5a97858..000000000
--- a/man/add_buttons_to_table.Rd
+++ /dev/null
@@ -1,33 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{add_buttons_to_table}
-\alias{add_buttons_to_table}
-\title{Add buttons to data frame}
-\usage{
-add_buttons_to_table(
-  data,
-  id,
-  label = icon("arrow-right", class = "fa-regular", lib = "font-awesome"),
-  ...
-)
-}
-\arguments{
-\item{data}{A data frame.}
-
-\item{id}{Character vector. the main id of the buttons.}
-
-\item{label}{Label to use for the button.}
-
-\item{...}{For future expansions. Currently not in use.}
-}
-\value{
-A data frame with a button in each table row.
-}
-\description{
-Small helper function to add Shiny action buttons to a data frame.
-}
-\examples{
-add_buttons_to_table(mtcars[, 1:5], "button_id", "click me") |> 
-  datatable_custom()
-  
-}
diff --git a/man/datatable_custom.Rd b/man/datatable_custom.Rd
deleted file mode 100644
index 646607de2..000000000
--- a/man/datatable_custom.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{datatable_custom}
-\alias{datatable_custom}
-\title{Custom datatable}
-\usage{
-datatable_custom(
-  data,
-  colnames = c("Package", "Type", "Name", "Version", "Score", "Review Package"),
-  hide_names = "name",
-  ...
-)
-}
-\arguments{
-\item{data}{A data frame as input.}
-
-\item{colnames}{}
-
-\item{hide_names}{Character vector. Whether to hide columns in the data
-frame.}
-
-\item{...}{Other options. Currently not in use.}
-}
-\value{
-a DT::datatable object.
-}
-\description{
-Small helper function to create a \code{DT::datatable()} object in a consistent
-style.
-}
-\examples{
-datatable_custom(mtcars, colnames = paste0("custom_", names(mtcars)))
-
-}

From b47c706957be3f30945e463b82a6af37a7139e95 Mon Sep 17 00:00:00 2001
From: Jeff Thompson <85879620+Jeff-Thompson12@users.noreply.github.com>
Date: Tue, 27 Feb 2024 09:40:53 -0500
Subject: [PATCH 10/22] Fix partial match of `use.name` to `use.names` in
 `unlist()`

---
 R/mod_addComment.R          |  2 +-
 R/mod_code_explorer.R       |  2 +-
 R/mod_communityMetrics.R    |  2 +-
 R/mod_decision_automation.R | 18 +++++++++---------
 R/mod_introJS.R             |  2 +-
 R/mod_maintenanceMetrics.R  |  2 +-
 R/mod_pkg_explorer.R        |  2 +-
 R/mod_reportPreview.R       |  2 +-
 R/mod_reweightView.R        | 10 +++++-----
 R/mod_sidebar.R             | 20 ++++++++++----------
 R/mod_uploadPackage.R       | 14 +++++++-------
 R/mod_user_roles.R          |  2 +-
 12 files changed, 39 insertions(+), 39 deletions(-)

diff --git a/R/mod_addComment.R b/R/mod_addComment.R
index 59b594595..5a632c2af 100644
--- a/R/mod_addComment.R
+++ b/R/mod_addComment.R
@@ -57,7 +57,7 @@ addCommentServer <- function(id, metric_abrv, user, credentials, pkg_name) {
     
     observeEvent(input$submit_comment, {
       req(input$add_comment)
-      req("general_comment" %in% unlist(credentials$privileges[user$role], use.name = FALSE))
+      req("general_comment" %in% unlist(credentials$privileges[user$role], use.names = FALSE))
       
       comment <- trimws(input$add_comment)
       
diff --git a/R/mod_code_explorer.R b/R/mod_code_explorer.R
index 571cd005b..5a2cf155d 100644
--- a/R/mod_code_explorer.R
+++ b/R/mod_code_explorer.R
@@ -73,7 +73,7 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgdir = reactiveVal(), c
           ),
           br(), br(),
           div(id = ns("comments_for_fe"), fluidRow(
-            if ("general_comment" %in% unlist(credentials$privileges[user$role], use.name = FALSE)) addCommentUI(id = ns("add_comment")),
+            if ("general_comment" %in% unlist(credentials$privileges[user$role], use.names = FALSE)) addCommentUI(id = ns("add_comment")),
             viewCommentsUI(id = ns("view_comments"))))
         )
       }
diff --git a/R/mod_communityMetrics.R b/R/mod_communityMetrics.R
index fb1973303..c9b812e28 100644
--- a/R/mod_communityMetrics.R
+++ b/R/mod_communityMetrics.R
@@ -51,7 +51,7 @@ communityMetricsServer <- function(id, selected_pkg, community_metrics, user, cr
                      plotly::plotlyOutput(NS(id, "downloads_plot"), height = "500px")))),
             br(), br(),
             div(id = "comments_for_cum", fluidRow( 
-              if ("general_comment" %in% unlist(credentials$privileges[user$role], use.name = FALSE)) addCommentUI(id = session$ns("add_comment")),
+              if ("general_comment" %in% unlist(credentials$privileges[user$role], use.names = FALSE)) addCommentUI(id = session$ns("add_comment")),
               viewCommentsUI(id = session$ns("view_comments"))))
           )
       }
diff --git a/R/mod_decision_automation.R b/R/mod_decision_automation.R
index a676e62d9..b44e1d84e 100644
--- a/R/mod_decision_automation.R
+++ b/R/mod_decision_automation.R
@@ -428,7 +428,7 @@ mod_decision_automation_server <- function(id, user, credentials){
     #### Outputs ####
     purrr::walk(c("auto_dropdown", "auto_dropdown2"), ~
                   observeEvent(input[[.x]], {
-                    req("auto_decision_adjust" %in% unlist(credentials$privileges[user$role], use.name = FALSE))
+                    req("auto_decision_adjust" %in% unlist(credentials$privileges[user$role], use.names = FALSE))
                     
                     showModal(modalDialog(
                       size = "l",
@@ -515,7 +515,7 @@ mod_decision_automation_server <- function(id, user, credentials){
     })
     
     output$auto_classify <- renderUI({
-      if ("auto_decision_adjust" %in% unlist(credentials$privileges[user$role], use.name = FALSE)) {
+      if ("auto_decision_adjust" %in% unlist(credentials$privileges[user$role], use.names = FALSE)) {
         tagList(
           br(),br(),
           hr(),
@@ -540,7 +540,7 @@ mod_decision_automation_server <- function(id, user, credentials){
     })
     
     output$decision_rule_div <- renderUI({
-      req("auto_decision_adjust" %in% unlist(credentials$privileges[user$role], use.name = FALSE))
+      req("auto_decision_adjust" %in% unlist(credentials$privileges[user$role], use.names = FALSE))
       tagList(
         div(
           style = "display: flex",
@@ -625,7 +625,7 @@ mod_decision_automation_server <- function(id, user, credentials){
 
     output$auto_settings <-
       renderUI({
-        req("auto_decision_adjust" %in% unlist(credentials$privileges[user$role], use.name = FALSE))
+        req("auto_decision_adjust" %in% unlist(credentials$privileges[user$role], use.names = FALSE))
         
         div(
           style = "float: right;",
@@ -637,7 +637,7 @@ mod_decision_automation_server <- function(id, user, credentials){
     
     output$auto_settings2 <-
       renderUI({
-        req("auto_decision_adjust" %in% unlist(credentials$privileges[user$role], use.name = FALSE))
+        req("auto_decision_adjust" %in% unlist(credentials$privileges[user$role], use.names = FALSE))
         
         div(
           style = "float: right;",
@@ -721,7 +721,7 @@ mod_decision_automation_server <- function(id, user, credentials){
       })
     
     observeEvent(input$submit_auto, {
-      req("auto_decision_adjust" %in% unlist(credentials$privileges[user$role], use.name = FALSE))
+      req("auto_decision_adjust" %in% unlist(credentials$privileges[user$role], use.names = FALSE))
       
       showModal(modalDialog(
         size = "l",
@@ -752,7 +752,7 @@ mod_decision_automation_server <- function(id, user, credentials){
     })
     
     observeEvent(input$submit_color, {
-      req("auto_decision_adjust" %in% unlist(credentials$privileges[user$role], use.name = FALSE))
+      req("auto_decision_adjust" %in% unlist(credentials$privileges[user$role], use.names = FALSE))
       
       showModal(modalDialog(
         size = "l",
@@ -784,7 +784,7 @@ mod_decision_automation_server <- function(id, user, credentials){
     })
     
     observeEvent(input$confirm_submit_auto, {
-      req("auto_decision_adjust" %in% unlist(credentials$privileges[user$role], use.name = FALSE))
+      req("auto_decision_adjust" %in% unlist(credentials$privileges[user$role], use.names = FALSE))
       req(!disable_auto_submit())
       
       out_lst <- purrr::compact(reactiveValuesToList(auto_decision))
@@ -829,7 +829,7 @@ mod_decision_automation_server <- function(id, user, credentials){
       
     
     observeEvent(input$confirm_submit_col, {
-      req("auto_decision_adjust" %in% unlist(credentials$privileges[user$role], use.name = FALSE))
+      req("auto_decision_adjust" %in% unlist(credentials$privileges[user$role], use.names = FALSE))
       
       selected_colors <- 
         decision_lst %>%
diff --git a/R/mod_introJS.R b/R/mod_introJS.R
index 06637d662..d96d9b716 100644
--- a/R/mod_introJS.R
+++ b/R/mod_introJS.R
@@ -37,7 +37,7 @@ introJSServer <- function(id, text, user, credentials) {
   moduleServer(id, function(input, output, session) {
     
     steps <- reactive({
-      if(user$admin || "weight_adjust" %in% unlist(credentials$privileges[user$role], use.name = FALSE)) {
+      if(user$admin || "weight_adjust" %in% unlist(credentials$privileges[user$role], use.names = FALSE)) {
         apptab_steps <- bind_rows(apptab_admn, apptab_steps)
       }
       
diff --git a/R/mod_maintenanceMetrics.R b/R/mod_maintenanceMetrics.R
index 79cbd8900..fafc99390 100644
--- a/R/mod_maintenanceMetrics.R
+++ b/R/mod_maintenanceMetrics.R
@@ -39,7 +39,7 @@ maintenanceMetricsServer <- function(id, selected_pkg, maint_metrics, user, cred
             metricGridUI(NS(id, 'metricGrid')),
             br(), br(),
             fluidRow(div(id = "comments_for_mm",
-                         if ("general_comment" %in% unlist(credentials$privileges[user$role], use.name = FALSE)) addCommentUI(NS(id, 'add_comment')),
+                         if ("general_comment" %in% unlist(credentials$privileges[user$role], use.names = FALSE)) addCommentUI(NS(id, 'add_comment')),
                          viewCommentsUI(NS(id, 'view_comments')))
             )
           )
diff --git a/R/mod_pkg_explorer.R b/R/mod_pkg_explorer.R
index 050f7f73e..5090d9ca8 100644
--- a/R/mod_pkg_explorer.R
+++ b/R/mod_pkg_explorer.R
@@ -68,7 +68,7 @@ mod_pkg_explorer_server <- function(id, selected_pkg,
             ),
             br(), br(),
             div(id = ns("comments_for_se"), fluidRow(
-              if ("general_comment" %in% unlist(credentials$privileges[user$role], use.name = FALSE)) addCommentUI(id = ns("add_comment")),
+              if ("general_comment" %in% unlist(credentials$privileges[user$role], use.names = FALSE)) addCommentUI(id = ns("add_comment")),
               viewCommentsUI(id = ns("view_comments")))),
           id = id
         )
diff --git a/R/mod_reportPreview.R b/R/mod_reportPreview.R
index a78aa7717..652943946 100644
--- a/R/mod_reportPreview.R
+++ b/R/mod_reportPreview.R
@@ -82,7 +82,7 @@ reportPreviewServer <- function(id, selected_pkg, maint_metrics, com_metrics,
             
             br(), br(),
             
-            if ("overall_comment" %in% unlist(credentials$privileges[user$role], use.name = FALSE)) 
+            if ("overall_comment" %in% unlist(credentials$privileges[user$role], use.names = FALSE)) 
               div(id = NS(id, "pkg-summary-grp"),
                   # Compose pkg summary - either disabled, enabled, or pre-populated
                   uiOutput(NS(id, "pkg_summary_ui")),
diff --git a/R/mod_reweightView.R b/R/mod_reweightView.R
index 4cba4e44b..4602b3b0c 100644
--- a/R/mod_reweightView.R
+++ b/R/mod_reweightView.R
@@ -46,7 +46,7 @@ reweightViewServer <- function(id, user, decision_list, credentials) {
       )
     
     observeEvent(input$update_weight, {
-      req("weight_adjust" %in% unlist(credentials$privileges[user$role], use.name = FALSE))
+      req("weight_adjust" %in% unlist(credentials$privileges[user$role], use.names = FALSE))
       curr_new_wts(save$data %>%
                      dplyr::mutate(new_weight = ifelse(name == isolate(input$metric_name),
                                                        isolate(input$metric_weight), new_weight)))
@@ -184,7 +184,7 @@ reweightViewServer <- function(id, user, decision_list, credentials) {
     
     # Update metric weight dropdown so that it matches the metric name.
     observeEvent(input$metric_name, {
-      req("weight_adjust" %in% unlist(credentials$privileges[user$role], use.name = FALSE))
+      req("weight_adjust" %in% unlist(credentials$privileges[user$role], use.names = FALSE))
       
       shinyjs::disable("update_weight")
       updateNumericInput(session, "metric_weight",
@@ -199,14 +199,14 @@ reweightViewServer <- function(id, user, decision_list, credentials) {
     # Note that another of the observeEvents will update the metric weight after
     # the selected metric name is updated.
     observeEvent(input$weights_table_rows_selected, {
-      req("weight_adjust" %in% unlist(credentials$privileges[user$role], use.name = FALSE))
+      req("weight_adjust" %in% unlist(credentials$privileges[user$role], use.names = FALSE))
       updateSelectInput(session, "metric_name",
                         selected = curr_new_wts()$name[input$weights_table_rows_selected])
     })
     
     # Save new weight into db.
     observeEvent(input$update_pkg_risk, {
-      req("weight_adjust" %in% unlist(credentials$privileges[user$role], use.name = FALSE))
+      req("weight_adjust" %in% unlist(credentials$privileges[user$role], use.names = FALSE))
       
       # if you the user goes input$back2dash, then when they return to the 
       if(n_wts_chngd() == 0){
@@ -243,7 +243,7 @@ reweightViewServer <- function(id, user, decision_list, credentials) {
     
     # Upon confirming the risk re-calculation
     observeEvent(input$confirm_update_risk, {
-      req("weight_adjust" %in% unlist(credentials$privileges[user$role], use.name = FALSE))
+      req("weight_adjust" %in% unlist(credentials$privileges[user$role], use.names = FALSE))
       removeModal()
       
       session$userData$trigger_events[["reset_pkg_upload"]] <- session$userData$trigger_events[["reset_pkg_upload"]] + 1
diff --git a/R/mod_sidebar.R b/R/mod_sidebar.R
index 1f4356eea..24548c84a 100644
--- a/R/mod_sidebar.R
+++ b/R/mod_sidebar.R
@@ -224,7 +224,7 @@ sidebarServer <- function(id, user, uploaded_pkgs, credentials) {
     
     # Update db if comment is submitted.
     observeEvent(input$submit_overall_comment, {
-      req("overall_comment" %in% unlist(credentials$privileges[user$role], use.name = FALSE))
+      req("overall_comment" %in% unlist(credentials$privileges[user$role], use.names = FALSE))
       
       current_comment <- trimws(input$overall_comment)
       
@@ -277,7 +277,7 @@ sidebarServer <- function(id, user, uploaded_pkgs, credentials) {
     observeEvent(input$submit_overall_comment_yes, {
 
       req(selected_pkg$name)
-      req("overall_comment" %in% unlist(credentials$privileges[user$role], use.name = FALSE))
+      req("overall_comment" %in% unlist(credentials$privileges[user$role], use.names = FALSE))
 
       dbUpdate(
           "UPDATE comments
@@ -334,7 +334,7 @@ sidebarServer <- function(id, user, uploaded_pkgs, credentials) {
     observeEvent(req(input$select_ver, session$userData$trigger_events$reset_sidebar), {
       if (input$select_pkg != "-" && input$select_ver != "-" &&
           (rlang::is_empty(selected_pkg$decision) || is.na(selected_pkg$decision)) &&
-          "overall_comment" %in% unlist(credentials$privileges[user$role], use.name = FALSE)) {
+          "overall_comment" %in% unlist(credentials$privileges[user$role], use.names = FALSE)) {
         shinyjs::enable("overall_comment")
         shinyjs::enable("submit_overall_comment")
         
@@ -345,7 +345,7 @@ sidebarServer <- function(id, user, uploaded_pkgs, credentials) {
     }, ignoreInit = TRUE)
     
     observeEvent(req(input$select_ver, session$userData$trigger_events$reset_sidebar), {
-      req("final_decision" %in% unlist(credentials$privileges[user$role], use.name = FALSE))
+      req("final_decision" %in% unlist(credentials$privileges[user$role], use.names = FALSE))
 
       if (input$select_pkg != "-" && input$select_ver != "-" &&
           (rlang::is_empty(selected_pkg$decision) || is.na(selected_pkg$decision))) {
@@ -363,7 +363,7 @@ sidebarServer <- function(id, user, uploaded_pkgs, credentials) {
 
       if (!(input$select_pkg == "-" && input$select_ver == "-" ||
           (rlang::is_empty(selected_pkg$decision) || is.na(selected_pkg$decision))) &&
-          "revert_decision" %in% unlist(credentials$privileges[user$role], use.name = FALSE)) {
+          "revert_decision" %in% unlist(credentials$privileges[user$role], use.names = FALSE)) {
         shinyjs::hide("submit_decision")
       } else {
         shinyjs::show("submit_decision")
@@ -375,7 +375,7 @@ sidebarServer <- function(id, user, uploaded_pkgs, credentials) {
     output$reset_decision_ui <- renderUI({
       req(user$role)
       req(credentials$privileges)
-      req("revert_decision" %in% unlist(credentials$privileges[user$role], use.name = FALSE))
+      req("revert_decision" %in% unlist(credentials$privileges[user$role], use.names = FALSE))
       req(!(input$select_pkg == "-" && input$select_ver == "-" ||
             (rlang::is_empty(selected_pkg$decision) || is.na(selected_pkg$decision))))
       
@@ -385,7 +385,7 @@ sidebarServer <- function(id, user, uploaded_pkgs, credentials) {
     # Show a confirmation modal when submitting a decision.
     observeEvent(input$submit_decision, {
       req(input$decision)
-      req("final_decision" %in% unlist(credentials$privileges[user$role], use.name = FALSE))
+      req("final_decision" %in% unlist(credentials$privileges[user$role], use.names = FALSE))
       
       showModal(modalDialog(
         size = "l",
@@ -412,7 +412,7 @@ sidebarServer <- function(id, user, uploaded_pkgs, credentials) {
     # Show a confirmation modal when resetting a decision
     observeEvent(input$reset_decision, {
       req(input$decision)
-      req("revert_decision" %in% unlist(credentials$privileges[user$role], use.name = FALSE))
+      req("revert_decision" %in% unlist(credentials$privileges[user$role], use.names = FALSE))
       
       showModal(modalDialog(
         size = "l",
@@ -440,7 +440,7 @@ sidebarServer <- function(id, user, uploaded_pkgs, credentials) {
     
     # Update database info after decision is submitted.
     observeEvent(input$submit_confirmed_decision, {
-      req("final_decision" %in% unlist(credentials$privileges[user$role], use.name = FALSE))
+      req("final_decision" %in% unlist(credentials$privileges[user$role], use.names = FALSE))
       
       dbUpdate("UPDATE package
           SET decision_id = {match(input$decision, golem::get_golem_options(\"decision_categories\"))}, decision_by = {user$name}, decision_date = {get_Date()}
@@ -462,7 +462,7 @@ sidebarServer <- function(id, user, uploaded_pkgs, credentials) {
     })
     
     observeEvent(input$reset_confirmed_decision, {
-      req("revert_decision" %in% unlist(credentials$privileges[user$role], use.name = FALSE))
+      req("revert_decision" %in% unlist(credentials$privileges[user$role], use.names = FALSE))
       
       dbUpdate("UPDATE package
           SET decision_id = NULL, decision_by = '', decision_date = NULL
diff --git a/R/mod_uploadPackage.R b/R/mod_uploadPackage.R
index 0516aa4e8..6e9fc63d4 100644
--- a/R/mod_uploadPackage.R
+++ b/R/mod_uploadPackage.R
@@ -94,7 +94,7 @@ uploadPackageServer <- function(id, user, auto_list, credentials, parent) {
       req(user$role)
       req(credentials$privileges)
       
-      if ("add_package" %in% unlist(credentials$privileges[user$role], use.name = FALSE)) {
+      if ("add_package" %in% unlist(credentials$privileges[user$role], use.names = FALSE)) {
         shinyjs::enable("pkg_lst")
         shinyjs::enable("add_pkgs")
         shinyjs::enable("uploaded_file")
@@ -108,7 +108,7 @@ uploadPackageServer <- function(id, user, auto_list, credentials, parent) {
     })
 
     output$upload_format_lnk <- renderUI({
-      req("add_package" %in% unlist(credentials$privileges[user$role], use.name = FALSE))
+      req("add_package" %in% unlist(credentials$privileges[user$role], use.names = FALSE))
       
       actionLink(NS(id, "upload_format"), "View Sample Dataset")
     })
@@ -119,9 +119,9 @@ uploadPackageServer <- function(id, user, auto_list, credentials, parent) {
       
       dplyr::bind_rows(
         upload_pkg,
-        if ("add_package" %in% unlist(credentials$privileges[user$role], use.name = FALSE)) upload_pkg_add,
-        if ("delete_package" %in% unlist(credentials$privileges[user$role], use.name = FALSE)) upload_pkg_delete,
-        if ("auto_decision_adjust" %in% unlist(credentials$privileges[user$role], use.name = FALSE)) upload_pkg_dec_adj,
+        if ("add_package" %in% unlist(credentials$privileges[user$role], use.names = FALSE)) upload_pkg_add,
+        if ("delete_package" %in% unlist(credentials$privileges[user$role], use.names = FALSE)) upload_pkg_delete,
+        if ("auto_decision_adjust" %in% unlist(credentials$privileges[user$role], use.names = FALSE)) upload_pkg_dec_adj,
         if (nrow(uploaded_pkgs()) > 0) upload_pkg_comp
       )
     })
@@ -165,7 +165,7 @@ uploadPackageServer <- function(id, user, auto_list, credentials, parent) {
     output$rem_pkg_div <- renderUI({
       req(user$role)
       req(credentials$privileges)
-      req("delete_package" %in% unlist(credentials$privileges[user$role], use.name = FALSE))
+      req("delete_package" %in% unlist(credentials$privileges[user$role], use.names = FALSE))
       
       session$onFlushed(function() {
         shinyjs::runjs(glue::glue('$("#{NS(id, "rem_pkg_btn")}").css("margin-top", $("#{NS(id, "rem_pkg_lst")}-label")[0].scrollHeight + .5*parseFloat(getComputedStyle(document.documentElement).fontSize))'))
@@ -246,7 +246,7 @@ uploadPackageServer <- function(id, user, auto_list, credentials, parent) {
     })
     
     observeEvent(input$rem_pkg_btn, {
-      req("delete_package" %in% unlist(credentials$privileges[user$role], use.name = FALSE)) 
+      req("delete_package" %in% unlist(credentials$privileges[user$role], use.names = FALSE)) 
       
       np <- length(input$rem_pkg_lst)
       uploaded_packages <-
diff --git a/R/mod_user_roles.R b/R/mod_user_roles.R
index 1ec407d9e..05c8b75b4 100644
--- a/R/mod_user_roles.R
+++ b/R/mod_user_roles.R
@@ -323,7 +323,7 @@ mod_user_roles_server <- function(id, user, credentials){
     })
     
     observeEvent(input$submit_changes, {
-      req("admin" %in% unlist(credentials$privileges[user$role], use.name = FALSE))
+      req("admin" %in% unlist(credentials$privileges[user$role], use.names = FALSE))
       
       chng_lst <- dplyr::filter(role_changes(), paste(old_role) != paste(new_role))
       purrr::pmap(chng_lst, function(old_role, new_role) {

From f1693cec5bb542841aaf75a07e63cb80ce76078b Mon Sep 17 00:00:00 2001
From: Jeff Thompson <85879620+Jeff-Thompson12@users.noreply.github.com>
Date: Tue, 27 Feb 2024 09:41:39 -0500
Subject: [PATCH 11/22] Add words to global variables list

---
 R/global.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/R/global.R b/R/global.R
index dc673cdb3..cffa1c1bc 100644
--- a/R/global.R
+++ b/R/global.R
@@ -42,6 +42,7 @@ utils::globalVariables(
     'downloads',
     'ea_v',
     'estimate',
+    'explore_metrics',
     'func',
     'have_changed',
     'Last modified',
@@ -69,6 +70,7 @@ utils::globalVariables(
     'rpt_choices',
     'score',
     'setNames',
+    'status',
     'succ_icon',
     'text',
     'token',

From af64b38446e542e4e4d5899e0896d8e4f53e80a8 Mon Sep 17 00:00:00 2001
From: Jeff Thompson <85879620+Jeff-Thompson12@users.noreply.github.com>
Date: Tue, 27 Feb 2024 09:42:30 -0500
Subject: [PATCH 12/22] Add files to ignore in R build

---
 .Rbuildignore | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.Rbuildignore b/.Rbuildignore
index d5e53830d..0d44e7371 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -25,3 +25,5 @@ _\.new\.png$
 ^source$
 ^revdep
 ^revdep$
+^manifest\.json$
+^\.rscignore$

From 2ac14127e0198b2f9f3a11e5f30c132117c69f86 Mon Sep 17 00:00:00 2001
From: Jeff Thompson <85879620+Jeff-Thompson12@users.noreply.github.com>
Date: Tue, 27 Feb 2024 09:57:08 -0500
Subject: [PATCH 13/22] Don't export `add_buttons_to_table()`

---
 NAMESPACE | 1 -
 R/utils.R | 1 -
 2 files changed, 2 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 3d978267f..a73fff296 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,6 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-export(add_buttons_to_table)
 export(app_theme)
 export(build_comm_plotly)
 export(generate_comm_data)
diff --git a/R/utils.R b/R/utils.R
index d923168ef..1ca07fbf5 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -638,7 +638,6 @@ datatable_custom <- function(
 #' @param ... For future expansions. Currently not in use. 
 #'
 #' @return A data frame with a button in each table row. 
-#' @export
 #'
 #' @examples 
 #' add_buttons_to_table(mtcars[, 1:5], "button_id", "click me") |> 

From 18bfe7570ebe179fb0a7fe5ece521f81edd59937 Mon Sep 17 00:00:00 2001
From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com>
Date: Mon, 1 Apr 2024 11:04:27 -0400
Subject: [PATCH 14/22] Add function to retrieve dependency info

---
 R/utils_get_db.R | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

diff --git a/R/utils_get_db.R b/R/utils_get_db.R
index 2a49f3aa4..9bc0e4d7e 100644
--- a/R/utils_get_db.R
+++ b/R/utils_get_db.R
@@ -14,13 +14,15 @@
 #' @returns a data frame
 #'
 #' @noRd
-dbSelect <- function(query, db_name = golem::get_golem_options('assessment_db_name'), .envir = parent.frame()){
+dbSelect <- function(query, db_name = golem::get_golem_options('assessment_db_name'), .envir = parent.frame(), params = NULL){
   errFlag <- FALSE
   con <- DBI::dbConnect(RSQLite::SQLite(), db_name)
   
   tryCatch(
     expr = {
       rs <- DBI::dbSendQuery(con, glue::glue_sql(query, .envir = .envir, .con = con))
+      if (!is.null(params))
+        DBI::dbBind(rs, params)
     },
     warning = function(warn) {
       message <- glue::glue("warning:\n {query} \nresulted in\n {warn}")
@@ -315,6 +317,19 @@ get_assess_blob <- function(pkg_name, db_name = golem::get_golem_options('assess
   purrr::pmap_dfc(db_table, function(name, encode) {dplyr::tibble(unserialize(encode)) %>% purrr::set_names(name)}) 
 }
 
+get_dep_blob <- function(pkg_lst, db_name = golem::get_golem_options('assessment_db_name')) {
+  db_table <- dbSelect("SELECT package.name, metric.name metric, package_metrics.encode FROM package 
+                       INNER JOIN package_metrics ON package.id = package_metrics.package_id
+                       INNER JOIN metric ON package_metrics.metric_id = metric.id
+                       WHERE metric.name IN ('dependencies', 'suggests') AND package.name = $pkg_name", 
+                       db_name = db_name,
+                       params = list(pkg_name = unlist(pkg_lst)))
+  
+  db_table %>% 
+    dplyr::mutate(encode = purrr::map(encode, ~ unserialize(.x)[[1]])) %>% 
+    tidyr::pivot_wider(names_from = metric, values_from = encode)
+}
+
 
 #' Get Dependency Pkg Versions and Scores
 #'

From b0366be3648139b9e902dc55abe3b4bf77d43d84 Mon Sep 17 00:00:00 2001
From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com>
Date: Mon, 1 Apr 2024 13:19:42 -0400
Subject: [PATCH 15/22] incorporate `get_dep_blob()` into `get_assess_blob`

---
 R/utils_get_db.R | 34 ++++++++++++++++++----------------
 1 file changed, 18 insertions(+), 16 deletions(-)

diff --git a/R/utils_get_db.R b/R/utils_get_db.R
index 9bc0e4d7e..fea3cfd0f 100644
--- a/R/utils_get_db.R
+++ b/R/utils_get_db.R
@@ -302,32 +302,34 @@ get_metric_weights <- function(db_name = golem::get_golem_options('assessment_db
 #'
 #' Retrieves metric name and current weight from metric table
 #' 
-#' @param pkg_name character name of the package
+#' @param pkg_lst character name of the package
 #' @param db_name character name (and file path) of the database
+#' @param metric_lst character name of metric
 #'
 #' @returns a data frame
 #' @noRd
-get_assess_blob <- function(pkg_name, db_name = golem::get_golem_options('assessment_db_name')) {
-  db_table <- dbSelect("SELECT metric.name, package_metrics.encode FROM package 
-                       INNER JOIN package_metrics ON package.id = package_metrics.package_id
-                       INNER JOIN metric ON package_metrics.metric_id = metric.id
-                       WHERE package.name = {pkg_name}", 
-                       db_name = db_name)
+#' 
+#' @import dplyr
+#' @importFrom purrr map pmap_dfc reduce
+get_assess_blob <- function(pkg_lst, db_name = golem::get_golem_options('assessment_db_name'),
+                            metric_lst = NA) {
+  if (length(pkg_lst) == 0) return(list())
   
-  purrr::pmap_dfc(db_table, function(name, encode) {dplyr::tibble(unserialize(encode)) %>% purrr::set_names(name)}) 
-}
-
-get_dep_blob <- function(pkg_lst, db_name = golem::get_golem_options('assessment_db_name')) {
   db_table <- dbSelect("SELECT package.name, metric.name metric, package_metrics.encode FROM package 
                        INNER JOIN package_metrics ON package.id = package_metrics.package_id
                        INNER JOIN metric ON package_metrics.metric_id = metric.id
-                       WHERE metric.name IN ('dependencies', 'suggests') AND package.name = $pkg_name", 
+                       WHERE package.name = $pkg_name AND metric.name = COALESCE($metric_name, metric.name)", 
                        db_name = db_name,
-                       params = list(pkg_name = unlist(pkg_lst)))
+                       params = list(pkg_name = rep(pkg_lst, each = length(metric_lst)),
+                                     metric_name = rep(metric_lst, length(pkg_lst))))
   
-  db_table %>% 
-    dplyr::mutate(encode = purrr::map(encode, ~ unserialize(.x)[[1]])) %>% 
-    tidyr::pivot_wider(names_from = metric, values_from = encode)
+  # This approach was used to avoid adding a dependency on tidyr to use pivot_wider
+  purrr::map(pkg_lst, ~ 
+               db_table %>% 
+               dplyr::filter(name == .x) %>% 
+               purrr::pmap_dfc(function(name, metric, encode) {dplyr::tibble(!!metric := unserialize(encode))}) %>%
+               dplyr::mutate(name = .x, .before = 0)) %>%
+    purrr::reduce(dplyr::bind_rows)
 }
 
 

From a2e54d72ba477a20d16aaccacdbe23c652986d75 Mon Sep 17 00:00:00 2001
From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com>
Date: Mon, 1 Apr 2024 13:26:37 -0400
Subject: [PATCH 16/22] Only pull needed metric blobs

---
 R/mod_packageDependencies.R | 2 +-
 R/utils_build_cards.R       | 2 +-
 R/utils_get_db.R            | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/mod_packageDependencies.R b/R/mod_packageDependencies.R
index 4f2991343..cf909ef2e 100644
--- a/R/mod_packageDependencies.R
+++ b/R/mod_packageDependencies.R
@@ -57,7 +57,7 @@ packageDependenciesServer <- function(id, selected_pkg, user, parent) {
       req(selected_pkg$name() != "-")
       req(tabready() == 1L)
       
-      get_assess_blob(selected_pkg$name())
+      get_assess_blob(selected_pkg$name(), metric_lst = c("dependencies", "suggests", "reverse_dependencies"))
     })
     
     observeEvent(list(pkgref(), toggled()), {
diff --git a/R/utils_build_cards.R b/R/utils_build_cards.R
index bf8252596..c4dd4b667 100644
--- a/R/utils_build_cards.R
+++ b/R/utils_build_cards.R
@@ -147,7 +147,7 @@ build_comm_cards <- function(data){
   
   
   # get reverse dependency info
-  rev_deps <- get_assess_blob(data$id[1])$reverse_dependencies[[1]]
+  rev_deps <- get_assess_blob(data$id[1], metric_lst = "reverse_dependencies")$reverse_dependencies[[1]]
   
   comm_rev <- comm %>% filter(name == "reverse_dependencies")
   # new
diff --git a/R/utils_get_db.R b/R/utils_get_db.R
index fea3cfd0f..6ecb376cc 100644
--- a/R/utils_get_db.R
+++ b/R/utils_get_db.R
@@ -231,7 +231,7 @@ get_metric_data <- function(pkg_name, metric_class = 'maintenance', db_name = go
 #' @noRd
 get_depends_data <- function(pkg_name, db_name = golem::get_golem_options('assessment_db_name')){
   
-  pkgref <- get_assess_blob(pkg_name, db_name)
+  pkgref <- get_assess_blob(pkg_name, db_name, metric_lst = "dependencies")
   
   if(suppressWarnings(is.null(nrow(pkgref$dependencies[[1]])) || nrow(pkgref$dependencies[[1]]) == 0)) {
     dplyr::tibble(package = character(0), type = character(0), name = character(0))

From e08fefda389d9c4d2ec9cdc97a8ed674de76998f Mon Sep 17 00:00:00 2001
From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com>
Date: Mon, 1 Apr 2024 14:42:50 -0400
Subject: [PATCH 17/22] Use Suggests toggle

---
 R/mod_packageDependencies.R | 26 +++++++++++++++++++++++---
 R/utils_get_db.R            |  2 +-
 2 files changed, 24 insertions(+), 4 deletions(-)

diff --git a/R/mod_packageDependencies.R b/R/mod_packageDependencies.R
index cf909ef2e..a4364eee0 100644
--- a/R/mod_packageDependencies.R
+++ b/R/mod_packageDependencies.R
@@ -155,11 +155,31 @@ packageDependenciesServer <- function(id, selected_pkg, user, parent) {
         mutate(Actions = if_else(!name %in% session$userData$loaded2_db()$name, gsub("fas fa-arrow-right fa-regular", "fas fa-upload fa-solid", Actions), Actions))
     })
     
-    table_revdeps_local <- reactive({
+    revdeps_local <- reactive({
       df <- session$userData$loaded2_db()
       req(df, df$name)
-      with(df, df[name %in% revdeps(),]) |> 
-      add_buttons_to_table(ns("go_to_revdep"))
+      req(revdeps())
+      
+      revdeps <-
+        df %>%
+        dplyr::filter(name %in% revdeps()) %>%
+        dplyr::pull(name) %>%
+        get_assess_blob(metric_lst = "suggests")
+      
+      if (nrow(revdeps) == 0) return(dplyr::left_join(bind_rows(revdeps, list(suggests = logical())), df, by = "name"))
+      
+      revdeps %>%
+        dplyr::mutate(suggests = purrr::map_lgl(suggests, ~ selected_pkg$name() %in% .x$package)) %>%
+        dplyr::left_join(df, by = "name")
+    })
+    
+    table_revdeps_local <- reactive({
+      req(revdeps_local())
+      
+      revdeps_local() %>%
+        dplyr::filter(toggled() == 1L | !suggests) %>%
+        dplyr::select(-suggests) %>%
+        add_buttons_to_table(ns("go_to_revdep"))
     })
     
     # Create metric grid card.
diff --git a/R/utils_get_db.R b/R/utils_get_db.R
index 6ecb376cc..353e0bd19 100644
--- a/R/utils_get_db.R
+++ b/R/utils_get_db.R
@@ -313,7 +313,7 @@ get_metric_weights <- function(db_name = golem::get_golem_options('assessment_db
 #' @importFrom purrr map pmap_dfc reduce
 get_assess_blob <- function(pkg_lst, db_name = golem::get_golem_options('assessment_db_name'),
                             metric_lst = NA) {
-  if (length(pkg_lst) == 0) return(list())
+  if (length(pkg_lst) == 0) return(dplyr::tibble(name = character()))
   
   db_table <- dbSelect("SELECT package.name, metric.name metric, package_metrics.encode FROM package 
                        INNER JOIN package_metrics ON package.id = package_metrics.package_id

From 7e4dad6b60d87cf5b30000296cf05e538ef4bb0e Mon Sep 17 00:00:00 2001
From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com>
Date: Mon, 1 Apr 2024 14:50:58 -0400
Subject: [PATCH 18/22] Update UI layout

---
 R/mod_packageDependencies.R | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/R/mod_packageDependencies.R b/R/mod_packageDependencies.R
index a4364eee0..daec438d4 100644
--- a/R/mod_packageDependencies.R
+++ b/R/mod_packageDependencies.R
@@ -234,27 +234,27 @@ packageDependenciesServer <- function(id, selected_pkg, user, parent) {
               fluidRow(
                 column(
                   width = 8,
-                    DT::renderDataTable(server = FALSE, {
+                  DT::renderDataTable(server = FALSE, {
                     datatable_custom(data_table())                      
-                    }),
-                  br(), br(),  
-                  h4(glue::glue("Reverse Dependencies available in database: {nrow(table_revdeps_local()) %||% 0}"), style = "text-align: left;"),
-                  br(), 
-                  DT::renderDataTable({
-                    datatable_custom(
-                      table_revdeps_local(), 
-                      colnames = c("Package", "Version", "Score", "Review Package"),
-                      hide_names = NULL
-                    )
                   })
                 )
               ), 
               br(), br(),
-              h4(glue::glue("All reverse Dependencies: {length(revdeps())}"), style = "text-align: left;"),
+              h3(glue::glue("All reverse Dependencies: {length(revdeps())}"), style = "text-align: left;"),
               br(),
               fluidRow(
                 column(
                   width = 8,
+                  h4(glue::glue("Reverse Dependencies available in database: {nrow(table_revdeps_local()) %||% 0}"), style = "text-align: left;"),
+                  br(), 
+                  DT::renderDataTable({
+                    datatable_custom(
+                      table_revdeps_local(), 
+                      colnames = c("Package", "Version", "Score", "Review Package"),
+                      hide_names = NULL
+                    )
+                  }),
+                  br(), br(),
                   wellPanel(
                     renderText(revdeps() %>% sort()),
                     style = "max-height: 500px; overflow: auto"

From 8ad0cb656c4a0f266796036b49c25d5a486df6df Mon Sep 17 00:00:00 2001
From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com>
Date: Mon, 1 Apr 2024 15:03:27 -0400
Subject: [PATCH 19/22] Update NEWS

---
 DESCRIPTION | 2 +-
 NEWS.md     | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 7c1397df0..3b2a1d3ba 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: riskassessment
 Title: A web app designed to interface with the `riskmetric` package
-Version: 3.0.0.9015
+Version: 3.0.0.9016
 Authors@R: c( 
     person("Aaron", "Clark", role = c("aut", "cre"), email = "aaron.clark@biogen.com"),
     person("Robert", "Krajcik", role = "aut", email = "robert.krajcik@biogen.com"),
diff --git a/NEWS.md b/NEWS.md
index 157457efe..93a65ba58 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -15,6 +15,7 @@
 * Move package upload process to a function
 * Updated logo in reports to lighter version to match application UI
 * Utilize `{archive}` to parse DESCRIPTION file in package upload process
+* Incorporates table to show reverse dependencies included in the database
 
 # riskassessment 3.0.0
 

From 15ed5c6a08ee072e52609173175a76a685f547d9 Mon Sep 17 00:00:00 2001
From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com>
Date: Mon, 1 Apr 2024 16:45:48 -0400
Subject: [PATCH 20/22] Fix error in determining dependencies

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

diff --git a/R/mod_packageDependencies.R b/R/mod_packageDependencies.R
index daec438d4..acc360e43 100644
--- a/R/mod_packageDependencies.R
+++ b/R/mod_packageDependencies.R
@@ -169,7 +169,7 @@ packageDependenciesServer <- function(id, selected_pkg, user, parent) {
       if (nrow(revdeps) == 0) return(dplyr::left_join(bind_rows(revdeps, list(suggests = logical())), df, by = "name"))
       
       revdeps %>%
-        dplyr::mutate(suggests = purrr::map_lgl(suggests, ~ selected_pkg$name() %in% .x$package)) %>%
+        dplyr::mutate(suggests = purrr::map_lgl(suggests, ~ any(grepl(selected_pkg$name(), .x$package)))) %>%
         dplyr::left_join(df, by = "name")
     })
     

From e19d05d6d4278e77034bae940a13c195029706a2 Mon Sep 17 00:00:00 2001
From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com>
Date: Mon, 1 Apr 2024 16:49:41 -0400
Subject: [PATCH 21/22] Repair test

---
 tests/testthat/test-packageDependencies.R | 25 +++++------------------
 1 file changed, 5 insertions(+), 20 deletions(-)

diff --git a/tests/testthat/test-packageDependencies.R b/tests/testthat/test-packageDependencies.R
index df99f56c1..bbb24f6c4 100644
--- a/tests/testthat/test-packageDependencies.R
+++ b/tests/testthat/test-packageDependencies.R
@@ -65,27 +65,11 @@ test_that(
       )
     )
     
-    test_db_loc <- system.file("testdata", "upload_format.database", 
-                               package = "riskassessment")
+    test_db_loc <- test_path("test-apps", "downloadHandler-app", 
+                                "dplyr_tidyr.sqlite")
     temp_db_loc <- withr::local_tempfile(fileext = ".database")
     file.copy(test_db_loc, temp_db_loc)
     
-    # because only the dplyr package is in the test dataset, we add one of its 
-    # known reverse dependencies:
-    withr::with_db_connection(
-      list(con = DBI::dbConnect(RSQLite::SQLite(), temp_db_loc)),
-      {
-        DBI::dbAppendTable(
-          con, 
-          "package", 
-          data.frame(
-            name = "dbplyr",
-            version = "1.0.0",
-            score = "0.32"
-          )
-        )
-      }
-    )
     # add test db location to the app session:
     app_session <- MockShinySession$new()
     app_session$options$golem_options <- list(
@@ -95,8 +79,9 @@ test_that(
     
     testServer(packageDependenciesServer, args = testargs,  {
       session$flushReact()
-      expect_true(all(c("plotly", "admiral", "dbplyr", "glue") %in% revdeps()))
-      expect_equal(table_revdeps_local()$name, "dbplyr")
+      session$setInputs(incl_suggests = TRUE)
+      expect_true(all(c("plotly", "admiral", "dbplyr", "glue", "tidyr") %in% revdeps()))
+      expect_equal(table_revdeps_local()$name, "tidyr")
       # the table contains an action button:
       expect_true(grepl('button id=\"button_1\"',table_revdeps_local()$Actions))
     },

From 2ba0df24e2d4c58fee7e21f84e4226f84922a432 Mon Sep 17 00:00:00 2001
From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com>
Date: Wed, 3 Apr 2024 14:48:17 -0400
Subject: [PATCH 22/22] Allow empty reverse dependency vector

---
 R/mod_packageDependencies.R | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/R/mod_packageDependencies.R b/R/mod_packageDependencies.R
index acc360e43..efadb7dba 100644
--- a/R/mod_packageDependencies.R
+++ b/R/mod_packageDependencies.R
@@ -158,8 +158,7 @@ packageDependenciesServer <- function(id, selected_pkg, user, parent) {
     revdeps_local <- reactive({
       df <- session$userData$loaded2_db()
       req(df, df$name)
-      req(revdeps())
-      
+
       revdeps <-
         df %>%
         dplyr::filter(name %in% revdeps()) %>%
@@ -193,7 +192,7 @@ packageDependenciesServer <- function(id, selected_pkg, user, parent) {
         showHelperMessage()
       } else {
         req(depends())
-        
+
         fluidPage(
           shiny::
             tagList(