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thiloshonthiloshon
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Add checks
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-21
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12 files changed

+247
-21
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‎NAMESPACE

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@@ -4,6 +4,8 @@ export(get_dc_groups)
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export(get_dc_ids)
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export(mod_configure_checks_server)
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export(mod_configure_checks_ui)
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export(mod_perform_checks_server)
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export(mod_perform_checks_ui)
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export(run_app)
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import(bdchecks)
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import(bddwc.app)

‎R/app_server.R

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@@ -21,6 +21,16 @@ app_server <- function(input, output,session) {
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id = "bdChecksConfigure"
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)
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callModule(
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mod_perform_checks_server,
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id = "bdChecksPerform"
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)
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callModule(
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bddwc.app::mod_citation_server,
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id = "bdcite"
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)
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#------------- Modules --------------
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@@ -36,5 +46,15 @@ app_server <- function(input, output,session) {
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}
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})
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observeEvent(input$sideBar, {
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if(input$sideBar == "configure"){
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shinyjs::runjs("$grid.isotope('shuffle');")
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}
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})
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#------------- Events --------------
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}

‎R/app_ui.R

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@@ -1,8 +1,11 @@
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#' @import shiny shinydashboard mod_add_data_ui
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app_ui <- function() {
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dbHeader <- dashboardHeader()
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dbHeader$children[[2]]$children <- tags$img(src='www/bdchecks-logo.png',height='50',width='50')
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tagList(
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dashboardPage(
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dashboardHeader(title = "bdchecks"),
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dbHeader,
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dashboardSidebar(sidebarMenu(
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id = "sideBar",
@@ -15,10 +18,17 @@ app_ui <- function() {
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"Configure Cleaning",
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tabName = "configure",
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icon = icon("wrench")
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),
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menuItem(
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"Perform Cleaning",
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tabName = "clean",
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icon = icon("broom")
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),
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menuItem(
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"Cite Us",
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tabName = "cite",
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icon = icon("copyright")
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)
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# menuItem("Darwinize",
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# tabName = "darwinize",
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# icon = icon("blocks"))
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)),
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dashboardBody(
@@ -41,8 +51,22 @@ app_ui <- function() {
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tabItem("configure",
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fluidRow(
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div(mod_configure_checks_ui("bdChecksConfigure"))
45-
))
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column(12,
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h1("Select Checks to Perform"),
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br(),
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div(mod_configure_checks_ui("bdChecksConfigure"))
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)
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)),
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tabItem("clean",
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fluidRow(
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div(mod_perform_checks_ui("bdChecksPerform"))
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)),
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tabItem("cite",
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fluidRow(
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div(bddwc.app:: mod_citation_ui("bdcite"))
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))
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)
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)
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),

‎R/mod_configure_checks.R

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Original file line numberDiff line numberDiff line change
@@ -68,13 +68,13 @@ mod_configure_checks_ui <- function(id) {
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),
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fluidRow(
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div(class = "checksListTopic col-sm-4", p("Category of Quality Check: ")),
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div(class = "checksListTopic col-sm-4", p("Category of Check: ")),
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div(class = "checksListTitle col-sm-8",
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p(check@description$DarwinCoreClass))
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),
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fluidRow(
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div(class = "checksListTopic col-sm-4", p("DWC Field Targetted by Check: ")),
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div(class = "checksListTopic col-sm-4", p("DWC Field Targetted: ")),
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div(class = "checksListTitle col-sm-8",
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p(check@input$Target))
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),
@@ -96,7 +96,7 @@ mod_configure_checks_ui <- function(id) {
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12,
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fluidRow(column(
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6,
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5,
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div(
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p("Sort Checks By: "),
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class = "btn-group btn-group-justified",
@@ -148,11 +148,18 @@ mod_configure_checks_ui <- function(id) {
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)
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,
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column(
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3,
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2,
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p("Select None: "),
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checkboxInput(ns("showDetailed"), label = "", value = FALSE)
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),
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column(
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4,
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p("Next:"),
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actionButton("configureToPerform", "Perform Cleaning")
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)
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)),
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div(class = "grid", components)

‎R/mod_perform_checks.R

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@@ -0,0 +1,132 @@
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# Module UI
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#' @title mod_perform_checks_ui and mod_perform_checks_server
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#' @description A shiny Module.
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#'
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#' @param id shiny id
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#' @param input internal
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#' @param output internal
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#' @param session internal
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#'
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#' @rdname mod_perform_checks
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#'
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#' @keywords internal
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#' @export
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#' @importFrom shiny NS tagList
16+
mod_perform_checks_ui <- function(id) {
17+
ns <- NS(id)
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tagList(column(12,
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div(
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h1("Perform Cleaning"),
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column(
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12,
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fluidRow(column(4,
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h4("Records Submitted", class = "control-header"),
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div(class = "control-header stats-green", textOutput(ns("total")))),
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column(4,
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h4("Data Checks Performed", class = "control-header"),
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div(class = "control-header stats-green", textOutput(ns("checks")))),
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column(4,
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h4("Records After Filtering", class = "control-header"),
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div(class = "control-header stats-green", textOutput(ns("filtered"))))),
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fluidRow(
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column(
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12,
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actionButton(ns("perform"), "Perform Data Checks", width = "14%"),
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actionButton("a", "Select All Passed Records", width = "14%"),
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actionButton("b", "Select All Failed Records", width = "14%"),
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actionButton("c", "Select All Missing Records", width = "14%"),
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actionButton("d", "Clear Selections", width = "14%"),
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actionButton("e", "Accept Selections", width = "14%"),
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actionButton("f", "Download Final Data", width = "14%")
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)
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),
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br(),
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column(
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12,
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DT::dataTableOutput(ns("summaryTable"))
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)
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)
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)))
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}
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# Module Server
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#' @rdname mod_perform_checks
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#' @export
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#' @keywords internal
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mod_perform_checks_server <- function(input, output, session) {
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ns <- session$ns
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summary <- data.frame()
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observeEvent(input$perform, {
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checks <-
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bdchecks::perform_dc(
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bdchecks::data_bats,
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c(
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"elevationOutOfRange",
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"eventDateInFuture",
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"monthInvalid",
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"occurrenceIdNotGuid",
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"dateIdentifiedInFuture",
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"dataGeneralised",
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"countryMismatch",
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"dateNull",
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"coordinatesZero"
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)
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)
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summary <<-
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bdchecks::summary_dc(checks, fancy = FALSE, filtering_dt = TRUE)
89+
})
90+
91+
output$summaryTable <- DT::renderDataTable(
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DT::datatable({
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input$perform
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summary
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},
96+
rownames = FALSE,
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options = list(pageLength = 100,
98+
columnDefs = list(
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list(className = "no_select",
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targets = 0:1)
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)),
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selection = list(target = "cell"),
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callback = DT::JS(
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"table.on('click', 'td.no_select', function() {
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var td = $(this), row = table.row(td.closest('tr'));
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if ($(td.node()).hasClass('selected')) {
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$(td.node()).removeClass('selected');
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}});"
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))
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)
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output$filtered <-
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renderText({
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69
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})
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output$total <-
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renderText({
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128
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})
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output$checks <-
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renderText({
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14
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})
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}
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## To be copied in the UI
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# mod_perform_checks_ui("perform_checks_ui_1")
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## To be copied in the server
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# callModule(mod_perform_checks_server, "perform_checks_ui_1")

‎dev/02_dev.R

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@@ -7,7 +7,7 @@
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## 2.1 Add modules
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##
10-
golem::add_module( name = "configure_checks" ) # Name of the module
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golem::add_module( name = "perform_checks" ) # Name of the module
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golem::add_module( name = "my_other_module" ) # Name of the module
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## 2.2 Add dependencies

‎inst/app/www/bdchecks-logo.png

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‎inst/app/www/favicon.ico

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‎inst/app/www/input.css

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@@ -62,8 +62,7 @@
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left: 0; top: 0;
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width: 1.8em; height: 1.8em;
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border: 2px solid #ccc;
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background: #fff;
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border-radius: 4px;
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background: transparent;
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box-shadow: inset 0 1px 3px rgba(0,0,0,.1);
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}
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position: absolute;
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font-size: 2.5em;
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line-height: 0.8;
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color: #09ad7e;
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color: orange;
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transition: all .2s;
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font-family: Helvetica, Arial, sans-serif;
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}

‎inst/app/www/script.js

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@@ -27,9 +27,7 @@ $('.btn-group').each( function( i, buttonGroup ) {
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});
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});
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30-
$(window).load(function() {
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setTimeout(
32-
function() {
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$grid.isotope('shuffle');
34-
}, 2000);
30+
$grid.on( 'click', '.element-item', function() {
31+
var checkbox = $("input:checkbox[value=" + this.getElementsByTagName("h4")[0].innerHTML + "]");
32+
checkbox.prop("checked", !checkbox.prop("checked"));
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});

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