inst/shiny/bdclean/ui.R

In bdclean: A User-Friendly Biodiversity Data Cleaning App for the Inexperienced R User

suppressPackageStartupMessages(library(data.table))
suppressPackageStartupMessages(library(shiny))
suppressPackageStartupMessages(library(DT))
suppressPackageStartupMessages(library(shinyjs))
suppressPackageStartupMessages(library(shinydashboard))
suppressPackageStartupMessages(library(bdchecks))
suppressPackageStartupMessages(library(finch))
suppressPackageStartupMessages(library(leaflet))

source("functions.R")

shinyUI(dashboardPage(
    #Header Title
    dashboardHeader(title = "bdclean", dropdownMenuOutput("messageMenu")),
    
    # ------------- Sidebar  -------------------
    dashboardSidebar(
        sidebarMenu(
            id = "sideBar",
            menuItem(
                "Add Data",
                tabName = "add",
                icon = icon("plus-circle")
            ),
            menuItem(
                "Configure Cleaning",
                tabName = "configure",
                icon = icon("wrench")
            ),
            menuItem("Flag & Clean", tabName = "flag", icon = icon("flag")),
            menuItem(
                "Artifacts & Documentation",
                tabName = "document",
                icon = icon("file")
            ),
            menuItem("Citations", tabName = "citTab", icon = icon("bookmark"))
        )
    ),
    
    # ------------- End of Sidebar  -------------------
    
    dashboardBody(
        tags$head(
            tags$link(rel = "stylesheet", type = "text/css", href = "style.css"),
            tags$link(rel = "stylesheet", type = "text/css", href = "checkbox.css")
        ),
        useShinyjs(),
        tabItems(
            # ------------- Add Data Module -------------------
            tabItem("add",
                    fluidRow(column(
                        12,
                        h1("Add Occurrence Data"),
                        column(
                            3,
                            tabsetPanel(
                                type = "tabs",
                                
                                # ------------- DB Module -------------------
                                
                                tabPanel(
                                    "Download Data",
                                    div(class = "secondaryHeaders", h3("Option 01: From Online Database")),
                                    textInput(
                                        "scientificName",
                                        label = h3("Scientific Name:"),
                                        value = "Puma concolor"
                                    ),
                                    
                                    numericInput(
                                        "recordSize",
                                        label = h3("Record Size:"),
                                        value = 500
                                    ),
                                    
                                    selectInput(
                                        "hasCoords",
                                        label = h3("Records Filter:"),
                                        choices = list(
                                            "With Coordinates" = "1",
                                            "Without Coordinates" = "2",
                                            "No Filter" = "3"
                                        ),
                                        selected = 3
                                    ),
                                    
                                    radioButtons(
                                        "queryDB",
                                        label = h3("Online Database:"),
                                        choices = list(
                                            "GBIF (Global Biodiversity Information Facility)" = "gbif",
                                            "iDigBio (Integrated Digitized Biocollections)" = "idigbio",
                                            "EcoEngine (Berkeley Ecoinformatics Engine)" = "ecoengine",
                                            "Vertnet (Vertebrate Network)" = "vertnet",
                                            "BISON (Biodiversity Information Serving Our Nation)" = "bison",
                                            "iNaturalist" = "inat",
                                            "ALA (Atlas of Living Australia)" = "ala",
                                            "OBIS (Ocean Biogeographic Information System)" = "obis",
                                            "AntWeb" = "antweb"
                                        ),
                                        selected = "gbif"
                                    ),
                                    
                                    br(),
                                    div(
                                        id = "queryDatabaseDiv",
                                        class = "activeButton",
                                        actionButton("queryDatabase", "Query Database", icon("download"))
                                    ),
                                    br()
                                ),
                                
                                # ------------- End of DB Module -------------------
                                
                                # ------------- Local Disk Module -------------------
                                tabPanel(
                                    "Upload Data",
                                    div(class = "secondaryHeaders", h3("Option 02: From Local Disk")),
                                    div(
                                        id = "inputFileDiv",
                                        class = "activeButton",
                                        fileInput(
                                            "inputFile",
                                            label = h3("CSV / DWCA ZIP file input"),
                                            accept = c(
                                                "text/csv",
                                                "text/comma-separated-values,text/plain",
                                                ".csv",
                                                ".zip",
                                                "application/zip"
                                            )
                                        )
                                    )
                                ),
                                
                                checkboxInput("darwinizerControl",
                                              label = "Perform Header Cleaning",
                                              value = TRUE),
                                
                                helpText(
                                    "To manually edit or clean headers, use ",
                                    a("bdDwC", href = "https://github.com/bd-R/bdDwC"),
                                    " package."
                                ),
                                
                                
                                # ------------- End of Local Disk Module -------------------
                                
                                div(class = "progressStep", taskItem(
                                    value = 15, color = "orange",
                                    "Step 1 of 6"
                                ))
                                
                            ),
                            div(
                                id = "dataToConfigureDiv",
                                actionButton("dataToConfigure", "Next: Configure Cleaning")
                            )
                        ),
                        
                        # ------------- Map / Table Module -------------------
                        column(9,
                               tabsetPanel(
                                   type = "tabs",
                                   tabPanel(
                                       "Map View",
                                       leafletOutput("mymap", height = "700"),
                                       absolutePanel(
                                           top = 60,
                                           right = 20,
                                           selectInput(
                                               "mapTexture",
                                               "Map Texture",
                                               choices = list(
                                                   "OpenStreetMap.Mapnik" = "OpenStreetMap.Mapnik",
                                                   "OpenStreetMap.BlackAndWhite" = "OpenStreetMap.BlackAndWhite",
                                                   "Stamen.Toner" = "Stamen.Toner",
                                                   "CartoDB.Positron" = "CartoDB.Positron",
                                                   "Esri.NatGeoWorldMap" = "Esri.NatGeoWorldMap",
                                                   "Stamen.Watercolor" = "Stamen.Watercolor",
                                                   "Stamen.Terrain" = "Stamen.Terrain",
                                                   "Esri.WorldImagery" = "Esri.WorldImagery",
                                                   "Esri.WorldTerrain" = "Esri.WorldTerrain"
                                               ),
                                               selected = "CartoDB.Positron"
                                           ),
                                           selectInput(
                                               "mapColor",
                                               "Points Color",
                                               choices = list(
                                                   "Red" = 'red',
                                                   "Green" = "green",
                                                   "Blue" = "blue",
                                                   "Black" = "black"
                                               )
                                           )
                                       )
                                   ),
                                   tabPanel("Table View",
                                            DT::dataTableOutput("inputDataTable"))
                               ))
                        
                        # ------------- End of Map/Table Module -------------------
                    ))),
            
            # -------------  End of Add Data Module -------------------
            
            # ------------- Cleaning Configuration Module -------------------
            
            tabItem("configure",
                    fluidRow(column(
                        12,
                        h1("Configure Cleaning"),
                        column(
                            12,
                            tabsetPanel(
                                type = "tabs",
                                tabPanel(
                                    "Option 01: Questionnaire ",
                                    div(class = "secondaryHeaders", h3("Option 01: Questionnaire")),
                                    helpText(
                                        "Note: If you have limited knowledge in Biodiversity data,
                                        this option is preferred.",
                                        "Answer a few questions and let bdclean take care of the cleaning."
                                    ),
                                    
                                    
                                    # -------------------------------
                                    
                                    uiOutput("questionnaire")
                                    
                                    # -------------------------------
                                ),
                                tabPanel(
                                    "Option 02: Customized Checks",
                                    div(class = "secondaryHeaders", h3("Option 02: Customized Checks")),
                                    helpText(
                                        "Note: Select the quality checks you prefer and
                                        continue cleaning with just those checks"
                                    ),
                                    
                                    # -------------------------------
                                    
                                    uiOutput("qualityChecks")
                                    
                                    # -------------------------------
                                    
                                    ),
                                
                                div(class = "progressStep", taskItem(
                                    value = 30, color = "green",
                                    "Step 2 of 6"
                                ))
                                ),
                            div(class = "completedButton", actionButton("configureToFlag", "Next: Flagging"))
                        )
                    ))),
            
            # ------------- End of Cleaning Configuration Module -------------------
            
            
            # ------------- Flagging Module -------------------
            
            tabItem("flag",
                    fluidRow(column(
                        12,
                        column(
                            12,
                            h1("Flag Data"),
                            br(),
                            h4("Input Data"),
                            div(
                                class = "center",
                                fluidRow(
                                    infoBox("# of Records", textOutput("inputDataRows"), icon = icon("list-ol")),
                                    infoBox(
                                        "# of Fields",
                                        textOutput("inputDataColumns"),
                                        icon = icon("th-list"),
                                        color = "purple"
                                    ),
                                    infoBox(
                                        "# of Unique Scientific Names",
                                        textOutput("inputDataSpecies"),
                                        icon = icon("paw"),
                                        color = "yellow"
                                    )
                                ),
                                
                                h4("Flag Settings"),
                                checkboxInput("missingCase", label = "Mark missing values as Fail", value = FALSE),
                                helpText(
                                    "Quality checks in bdclean check the validity of each records of the column it targets. If ticked, records with missing values will be considered as invalid record and will be removed. If not ticked, missing records will not be considered in the quality check, so, will remain in the cleaned data.
                                    "
                                ),
                                fluidRow(
                                    div(
                                        id = "flagButtonDiv",
                                        class = "completedButton",
                                        actionButton("flagButton", label = "Flag Data")
                                    )
                                    
                                ),
                                
                                div(class = "progressStep", taskItem(
                                    value = 45, color = "yellow",
                                    "Step 3 of 6"
                                ))
                                ),
                            br(),
                            
                            # -------------------------------
                            
                            uiOutput("flaggedContentUI"),
                            
                            uiOutput("cleanedResultsUI")
                            
                            # -------------------------------
                    )
                    ))),
            
            # ------------- End of Flagging Module -------------------
            
            # ------------- Documentation Module -------------------
            tabItem("document",
                    fluidRow(column(
                        12,
                        column(
                            12,
                            h1("Artifacts and Reports"),
                            br(),
                            selectInput(
                                "reportFormat",
                                "Report Type",
                                choices = list(
                                    "PDF" = "pdf_document",
                                    "HTML" = "html_document",
                                    "Word" = "word_document",
                                    "Markdown" = "md_document"
                                ),
                                selected = "pdf_document"
                            ),
                            
                            # -------------------------------
                            
                            uiOutput("documentContentUI")
                        )
                    )))
        )
        
        # ------------- End of Documentation Module -------------------
        
    )
))