Merge pull request #761 from pharmaR/bm-752

`bm-752` Adds 'About' tab
pharmaR · Apr 15, 2024 · 1619e2b · 1619e2b
2 parents 0ad3888 + 0133a7a
commit 1619e2b
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: riskassessment
 Title: A web app designed to interface with the `riskmetric` package
-Version: 3.0.0.9017
+Version: 3.0.0.9018
 Authors@R: c( 
-    person("Aaron", "Clark", role = c("aut", "cre"), email = "aaron.clark@biogen.com"),
+    person("Aaron", "Clark", role = c("aut", "cre"), email = "clark.aaronchris@gmail.com"),
     person("Robert", "Krajcik", role = "aut", email = "robert.krajcik@biogen.com"),
     person("Jeff", "Thompson", role = "aut", email = "jeff.thompson51317@gmail.com"),
     person("Lars", "Andersen", role = "aut", email = "lars.andersen@boehringer-ingelheim.com"),

diff --git a/NAMESPACE b/NAMESPACE
@@ -132,6 +132,7 @@ importFrom(sortable,sortable_js)
 importFrom(sortable,sortable_js_capture_input)
 importFrom(sortable,sortable_options)
 importFrom(stats,lm)
+importFrom(stats,na.omit)
 importFrom(stats,predict)
 importFrom(stringr,regex)
 importFrom(stringr,str_extract)
@@ -144,6 +145,7 @@ importFrom(tools,Rd2HTML)
 importFrom(tools,package_dependencies)
 importFrom(utils,adist)
 importFrom(utils,available.packages)
+importFrom(utils,capture.output)
 importFrom(utils,download.file)
 importFrom(utils,getParseData)
 importFrom(utils,head)

diff --git a/NEWS.md b/NEWS.md
@@ -17,6 +17,7 @@
 * Utilize `{archive}` to parse DESCRIPTION file in package upload process
 * Incorporates table to show reverse dependencies included in the database
 * updated manifest file and deployments article
+* Adds about page to help users understand the project a little more, providing useful resources and attribution
 
 # riskassessment 3.0.0
 

diff --git a/R/app_server.R b/R/app_server.R
@@ -77,6 +77,10 @@ app_server <- function(input, output, session) {
                   value = "admin-mode-tab",
                   h2("Administrative Tools & Options", align = "center", `padding-bottom`="20px"),
                   br(),
+
+                  fluidRow(
+                    column(
+                      width = 10, offset = 1,
                   tabsetPanel(
                     id = "credentials",
                     if (res_auth$admin)
@@ -102,6 +106,7 @@ app_server <- function(input, output, session) {
                       title = "Assessment Reweighting",
                       reweightViewUI("reweightInfo")
                     )
+                  ))
                   ),
                   tags$script(HTML("document.getElementById('admin-add_user').style.width = 'auto';"))
                 ))
@@ -210,12 +215,14 @@ app_server <- function(input, output, session) {
   })
 
   observeEvent(input$apptabs, {
-    req(input$apptabs %in% c("risk-assessment-tab", "database-tab"))
+    req(input$apptabs %in% c("about-tab", "database-tab"))
     session$userData$trigger_events$update_report_pref_inclusions <- session$userData$trigger_events$update_report_pref_inclusions + 1
   })
 
-  # Load server of the assessment criteria module.
-  assessmentInfoServer("assessmentInfo", metric_weights = metric_weights)
+
+
+  # Load server of the about tab module
+  aboutInfoServer("aboutInfo", metric_weights)
 
   # Load server of the database view module.
   #parentSession <- .subset2(session, "parent")

diff --git a/R/app_ui.R b/R/app_ui.R
@@ -13,7 +13,7 @@ app_ui <- function(request) {
 
     theme = app_theme(), # defined in data-raw/interanl-data.R
 
-    div(id = "raa-logo", shiny::a(img(src="www/raa-alt-image-lt-ug2.png"), href = "https://pharmar.github.io/riskassessment/", target="_blank")),
+    div(id = "raa-logo", shiny::a(img(src="www/images/raa-alt-image-lt-ug2.png"), href = "https://pharmar.github.io/riskassessment/", target="_blank")),
 
     tabsetPanel(
       id = "apptabs",
@@ -98,13 +98,17 @@ app_ui <- function(request) {
         value = "database-tab"
       ),
 
-      tabPanel(
-        title = "Assessment Criteria",
-        icon = icon("circle-info"),
-        assessmentInfoUI("assessmentInfo"),
-        value = "assessment-criteria-tab"
-      )
-    ),
+
+    tabPanel(
+      title = "About",
+      icon = icon("circle-info"),
+      aboutInfoUI("aboutInfo"),
+      value = "about-tab"
+    )
+
+
+
+     ),
 
     wellPanel(
       id = "footer",

diff --git a/R/global.R b/R/global.R
@@ -63,13 +63,15 @@ utils::globalVariables(
     'old_role',
     'package',
     'Package',
+    'path',
     'Published',
     'Role',
     'role',
     'row_n',
     'rpt_choices',
     'score',
     'setNames',
+    'size',
     'status',
     'succ_icon',
     'text',

diff --git a/R/mod_aboutInfo.R b/R/mod_aboutInfo.R
@@ -0,0 +1,152 @@
+#' UI for 'About' Module
+#' 
+#' @param id a module id name
+#' 
+#' @importFrom DT dataTableOutput
+#' 
+#' @keywords internal
+#' 
+aboutInfoUI <- function(id) {
+  fluidPage(
+    fluidRow(
+      column(
+        width = 10, offset = 1,
+        h2("About", align = "center", `padding-bottom`="20px"),
+        br(),
+        # Assessment criteria sub-tab
+        tabsetPanel(
+          tabPanel(
+            title = "Assessment Criteria",
+            icon = icon("circle-info"),
+            br(),
+            fluidRow(
+              column(
+                width = 10, offset = 1,
+            assessmentInfoUI(NS(id,"assessmentInfo"))  # call assessment module UI
+               ))
+            ),
+        # Contacts sub-tab  
+          tabPanel(
+            title = "Contact",
+            icon = icon("envelope"),
+
+            # contacts description.
+            br(),
+            h2("Contact", align = "center", `padding-bottom`="20px"),
+            br(),
+            fluidRow(
+              column(
+                width = 10, offset = 1,
+            br(),
+            shiny::HTML(
+               "<h3><i class='fa fa-github' aria-hidden='true'></i> Report Issues </h3>
+                <p> To propose new features or report a bug, please review our open issues first on our 
+                <a target='_blank' href='https://github.com/pharmaR/riskassessment/issues' > GitHub page</a>. If your topic hasn't been addressed, we highly encourage you to <a target='_blank' href='https://github.com/pharmaR/riskassessment/issues/new' >open a new issue</a>!</p>
+                <br>
+                <br>
+                
+                <h3><i class='fa fa-coffee' aria-hidden='true'></i> Development Team </h3> 
+                <p> Most all inquiries should flow through the GitHub page reference above (start there), but you may reach out to the lead developer at any time, especially if you would like to start contributing to the project!</p>
+                <br>
+                <ul>  
+                  <li>Aaron Clark [ <a href= 'mailto:clark.aaronchris@gmail.com?subject={riskassessment} inquiry'> Send Email </a> ] </li>
+                </ul> 
+                <br>                           
+                
+                <h3><img src='www/images/R_validation_hub_logo.png' alt='R Validation Hub Logo' style = 'height:50px;padding-right:8px;'>R Validation Hub </h3>
+                <p> To learn more about the work and initiatives of R Validation Hub, please visit <a target='_blank' href= 'https://www.pharmar.org/about/'> 
+                                            https://www.pharmar.org/about/</a>. </p>  ")
+          ))
+          ),
+        # Contributors sub-tab
+          tabPanel(
+            title = "Contributors and Companies",
+            icon = icon("address-card"),
+
+            br(),
+            h2("Contributors and Companies", align = "center", `padding-bottom`="20px"),
+            br(),
+            fluidRow(
+              column(
+                width = 10, offset = 1,
+            br(),
+            shiny::HTML(
+               "<h3> Official Workstream of the <a target='_blank' href='https://www.pharmar.org/'>R Validation Hub</a>.
+                <br/>Sponsored by the <a target='_blank' href='https://www.r-consortium.org//'>R Consortium</a></h3>
+                <br>
+                <img src='www/images/pharmaRlogo_large.png' alt='R Validation Hub Logo' style = 'height:130px;padding-right:50px;padding-top:15px;padding-bottom:15px;'>  
+                <img src='www/images/rc_logo.png' alt = 'ProCogia logo' style='height:130px;padding-top:15px;padding-bottom:15px;'> 
+                <br>
+                
+                <br>
+                <h3> Collaborative Deployment hosted by <a target='_blank' href='https://procogia.com/'> ProCogia </a> </h3>
+                <br>
+                <img src='www/images/procogia_logo.png' alt = 'ProCogia logo' style='height:100px'> 
+                <br>
+                
+                <br>
+                <h3> Current Contributors </h3>
+                <ul>
+                  <li> Aaron Clark, Arcus Biosciences </li>
+                  <li> Narayanan Iyer, Pfizer </li>
+                  <li> Robert Krajcik, Cytel </li>
+                  <li> Barbara Mikulasova, Katalyze Data </li>
+                  <li> Jeff Thompson, Arcus Biosciences </li>
+                </ul>
+                
+                <br>
+                
+                <h3> Past Contributors </h3>
+                
+                <ul>
+                  <li> Eduardo Almeida, Appsilon </li>
+                  <li> Lars Andersen, Boehringer Ingelheim </li>
+                  <li> Andrew Borgman, Biogen </li>
+                  <li> Maya Gans, Cytel </li>
+                  <li> Marly Gotti, Biogen </li>
+                  <li> Munshi Imran Hossain, Cytel </li>
+                  <li> Aravid Reddy Kallem, Fission Labs </li>
+                  <li> Scott Schumacker, Canary Medical </li>
+                </ul>
+                <br>
+                
+                <h3> Contributing Companies </h3>
+                
+                <img src='www/images/appsilon_logo.jpg' alt='Appsilon' style = 'height:100px;padding-right:40px;padding-top:15px;padding-bottom:15px;'> 
+                <img src='www/images/arcus_logo.png' alt='Arcus Biosciences' style = 'height:100px;padding-right:40px;padding-top:15px;padding-bottom:15px;'> 
+                <img src='www/images/bi_logo.png' alt='Boehringer Ingelheim' style = 'height:100px;padding-right:40px;padding-top:15px;padding-bottom:15px;'>
+                <img src='www/images/biogen_logo.jpg' alt='Biogen' style = 'height:100px;padding-right:40px;padding-top:15px;padding-bottom:15px;'>
+                <img src='www/images/cytel.png' alt='Cytel' style = 'height:100px;padding-right:40px;padding-top:15px;padding-bottom:15px;'>
+                <img src='www/images/fission_logo.png' alt='Fission Labs India Pvt Ltd' style = 'height:100px;padding-right:40px;padding-top:15px;padding-bottom:15px;'>
+                <img src='www/images/gcp_logo.png' alt='GCP-Service International' style = 'height:100px;padding-right:40px;padding-top:15px;padding-bottom:15px;'>
+                <img src='www/images/GSK_logo.jpg' alt='GSK' style = 'height:100px;padding-right:40px;padding-top:15px;padding-bottom:15px;'>
+                <img src='www/images/katalyzedata_logo.jpg' alt='Katalyze Data' style = 'height:100px;padding-right:40px;padding-top:15px;padding-bottom:15px;'>
+                <img src='www/images/merck_logo.png' alt='Merck' style = 'height:100px;padding-right:40px;padding-top:15px;padding-bottom:15px;'>
+                <img src='www/images/pfizer_logo.png' alt='Pfizer' style = 'height:100px;padding-right:40px;padding-top:15px;padding-bottom:15px;'>
+                <img src='www/images/roche_logo.png' alt='Roche' style = 'height:100px;padding-top:15px;padding-bottom:15px;'>
+                <br>
+                <br>
+                <br>
+                <br>
+               ")
+          ))
+          )
+        )
+      )))
+}
+
+#' Server Logic for 'About' Module
+#' 
+#' @param id a module id name
+#' @param metric_weights object outputted from reweightViewServer()
+#' 
+#' @keywords internal
+#' 
+aboutInfoServer <- function(id, metric_weights) {
+  moduleServer(id, function(input, output, session) {
+
+    # Load server of the assessment criteria module.
+    assessmentInfoServer("assessmentInfo", metric_weights = metric_weights) 
+
+  })
+}
diff --git a/R/mod_assessmentInfo.R b/R/mod_assessmentInfo.R
@@ -8,9 +8,9 @@
 #' 
 assessmentInfoUI <- function(id) {
   fluidPage(
-    fluidRow(
-      column(
-        width = 8, offset = 2,
+    # fluidRow(
+      # column(
+      #   width = 8, offset = 2,
         h2("Assessment Criteria Overview", align = "center", `padding-bottom`="20px"),
         br(),
         tabsetPanel(
@@ -19,7 +19,9 @@ assessmentInfoUI <- function(id) {
             h6("About Risk Calculation"),
             uiOutput(NS(id, "riskcalc_desc")),  # Maintenance metrics description.
             br(),
-            DT::dataTableOutput(NS(id, "riskcalc_weights_table"))
+            column(width = 8, #offset = 2,
+              DT::dataTableOutput(NS(id, "riskcalc_weights_table"))
+            )
           ),
           tabPanel(
             title = "Maintenance Metrics",
@@ -42,7 +44,8 @@ assessmentInfoUI <- function(id) {
             br(),
             DT::dataTableOutput(NS(id, "testing_table"))  # data table for testing metrics.
           )
-        ))))
+        # ))
+    ))
 }
 
 #' Server Logic for 'Assessment Info' Module

diff --git a/R/mod_code_explorer.R b/R/mod_code_explorer.R
@@ -17,7 +17,8 @@ mod_code_explorer_ui <- function(id){
 #' 
 #' @importFrom tools Rd2HTML
 #' @importFrom purrr map_dfr
-#' @importFrom archive archive_read archive 
+#' @importFrom archive archive_read archive
+#' @importFrom utils capture.output
 mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(), creating_dir = reactiveVal(TRUE), user, credentials){
   moduleServer( id, function(input, output, session){
     ns <- session$ns
@@ -158,7 +159,7 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
                                    file = fp)
       Rdfile <-tools::parse_Rd(con)
       close(con)
-      HTML(paste0(capture.output(tools::Rd2HTML(Rdfile,
+      HTML(paste0(utils::capture.output(tools::Rd2HTML(Rdfile,
                                                package = c(selected_pkg$name(),
                                                            selected_pkg$version()), out = "")), collapse = "\n"))
     }) %>%

diff --git a/R/mod_code_explorer_utils.R b/R/mod_code_explorer_utils.R
@@ -42,6 +42,8 @@ get_exported_functions <- function(pkg_name, pkg_version) {
 #' @noRd
 #' 
 #' @importFrom utils getParseData
+#' @importFrom stats na.omit
+#' 
 get_parse_data <- function(type = c("test", "source"), pkgarchive, pkg_name, pkg_version, funcnames = NULL) {
 
   type <- match.arg(type)
@@ -52,7 +54,7 @@ get_parse_data <- function(type = c("test", "source"), pkgarchive, pkg_name, pkg
     ,
     source = file.path(glue::glue("{pkg_name}"), "R")
   )
-  filenames <- na.omit((str_extract(pkgarchive$path,paste0(dirpath, ".+\\.[R|r]$"))))
+  filenames <- stats::na.omit((str_extract(pkgarchive$path,paste0(dirpath, ".+\\.[R|r]$"))))
   dplyr::bind_rows(lapply(filenames, function(filename) {
     con <- archive::archive_read(file.path("tarballs",
                                            glue::glue("{pkg_name}_{pkg_version}.tar.gz")),
@@ -119,10 +121,11 @@ get_source_files <- function(funcname, parse_data) {
 #' @param funcname The name of the function to evaluate
 #' @param pkgArchive   The package directory
 #' 
+#' @importFrom stats na.omit
 #' @noRd
 get_man_files <- function(funcname, pkgarchive, pkg_name, pkg_version) {
 
-  man_files <- na.omit((str_extract(pkgarchive$path,
+  man_files <- stats::na.omit((str_extract(pkgarchive$path,
                                     paste(glue::glue("{pkg_name}"), "man", ".+\\.Rd$", sep ="/"))))
   funcname_regex <- 
     gsub("([.|()\\^{}+$*?]|\\[|\\])", "\\\\\\1", funcname) %>%

diff --git a/R/mod_databaseView.R b/R/mod_databaseView.R
@@ -20,11 +20,14 @@ databaseViewUI <- function(id) {
   tagList(
     h2("Database Overview", align = "center", `padding-bottom`="20px"),
     br(),
+    fluidRow(
+      column(
+        width = 10, offset = 1,
     tabsetPanel(
       tabPanel(
         "Uploaded Packages",
         column(
-          width = 8, offset = 2, align = "center",
+          width = 10, offset = 1, align = "center",
           tags$section(
             div(class = "box",
               div(class = "box-header",
@@ -90,6 +93,7 @@ databaseViewUI <- function(id) {
         ))
     )
   )
+  ))
 }
 
 #' Server logic for 'Database View' module

diff --git a/R/mod_introJS_utils_text.R b/R/mod_introJS_utils_text.R
@@ -23,8 +23,8 @@ sidebar_steps <-
 # appui tab widgets
 apptab_steps <- data.frame(
   element = c(
-    "[data-value=assessment-criteria-tab]", "[data-value=database-tab]"),
-  intro = c("Discover the package assessment process & criteria",
+    "[data-value=about-tab]", "[data-value=database-tab]"),
+  intro = c("Discover more about the project, including the package assessment process & how to contact the maintainers.",
             "Review the R packages that already exist in the database"),
   position = c(rep("bottom", 2))
 )