Add upto configure

Author: thiloshon

.Rbuildignore

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+^CODE_OF_CONDUCT\.md$
+^README\.Rmd$
+^.*\.Rproj$
+^\.Rproj\.user$
+^data-raw$
+dev_history.R
+^dev$
+$run_dev.*

CODE_OF_CONDUCT.md

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+# Contributor Code of Conduct
+
+As contributors and maintainers of this project, we pledge to respect all people who 
+contribute through reporting issues, posting feature requests, updating documentation,
+submitting pull requests or patches, and other activities.
+
+We are committed to making participation in this project a harassment-free experience for
+everyone, regardless of level of experience, gender, gender identity and expression,
+sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.
+
+Examples of unacceptable behavior by participants include the use of sexual language or
+imagery, derogatory comments or personal attacks, trolling, public or private harassment,
+insults, or other unprofessional conduct.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments,
+commits, code, wiki edits, issues, and other contributions that are not aligned to this 
+Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed 
+from the project team.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by 
+opening an issue or contacting one or more of the project maintainers.
+
+This Code of Conduct is adapted from the Contributor Covenant 
+(http://contributor-covenant.org), version 1.0.0, available at 
+http://contributor-covenant.org/version/1/0/0/

DESCRIPTION

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+Package: bdchecks.app
+Title: Graphical Interface for bdchecks App
+Version: 0.0.0.9000
+Authors@R: person('Thiloshon', 'Nagarajah', email = '[email protected]', role = c('cre', 'aut'))
+Description: Shiny App giving complete workflow to selectively perform datachecks.
+License: What license is it under?
+Encoding: UTF-8
+LazyData: true
+Imports: 
+    shiny,
+    golem,
+    htmltools
+RoxygenNote: 6.1.1
+URL: https://github.com/bd-R/bdchecks.app
+BugReports: https://github.com/bd-R/bdchecks.app/issues

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(get_dc_groups)
+export(get_dc_ids)
+export(mod_configure_checks_server)
+export(mod_configure_checks_ui)
+export(run_app)
+import(bdchecks)
+import(bddwc.app)
+import(mod_add_data_ui)
+import(shiny)
+import(shinydashboard)
+import(shinyjs)
+importFrom(glue,glue)
+importFrom(golem,with_golem_options)
+importFrom(htmltools,HTML)
+importFrom(htmltools,tagAppendAttributes)
+importFrom(htmltools,tagList)
+importFrom(htmltools,tags)
+importFrom(shiny,NS)
+importFrom(shiny,column)
+importFrom(shiny,shinyApp)
+importFrom(shiny,tagList)

R/app_server.R

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+#' @import shiny bddwc.app
+app_server <- function(input, output,session) {
+    
+    #------------- Data --------------
+    data_store <-
+        shiny::reactiveValues(
+            data_user = data.frame()
+        )
+    #------------- Data --------------
+    
+    
+    #------------- Modules --------------
+    data_store$data_user <-
+        callModule(
+            bddwc.app::mod_add_data_server,
+            id = "bdFileInput"
+        )
+    
+    callModule(
+        mod_configure_checks_server,
+        id = "bdChecksConfigure"
+    )
+    
+    #------------- Modules --------------
+    
+    
+    #------------- Events --------------
+    observeEvent(input$dataToDictionary, {
+        dat <- data_store$data_user
+        
+        if (length(dat()) == 0) {
+            showNotification("Please add data",
+                             duration = 6)
+        } else {
+            updateTabItems(session, "sideBar", "configure")
+        }
+    })
+    
+    #------------- Events --------------
+}

R/app_ui.R

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+#' @import shiny shinydashboard mod_add_data_ui
+app_ui <- function() {
+  tagList(
+    dashboardPage(
+    dashboardHeader(title = "bdchecks"),
+    
+    dashboardSidebar(sidebarMenu(
+      id = "sideBar",
+      menuItem(
+        "Add Data",
+        tabName = "add",
+        icon = icon("plus-circle")
+      ),
+      menuItem(
+        "Configure Cleaning",
+        tabName = "configure",
+        icon = icon("wrench")
+      )
+      # menuItem("Darwinize",
+      #          tabName = "darwinize",
+      #          icon = icon("blocks"))
+    )),
+    
+    dashboardBody(
+      # Leave this function for adding external resources
+      golem_add_external_resources(),
+      
+      tabItems(
+        # ------------- Add Data Module -------------------
+        tabItem("add",
+                fluidRow(
+                  div(bddwc.app::mod_add_data_ui("bdFileInput")),
+                  
+                  column(12,
+                         div(
+                           id = "dataToDictionaryDiv",
+                           tags$br(),
+                           actionButton("dataToDictionary", "Next: Configure Cleaning")
+                         ))
+                )),
+        
+        tabItem("configure",
+                fluidRow(
+                  div(mod_configure_checks_ui("bdChecksConfigure"))
+                  ))
+      )
+    )
+  ),
+  tags$script(src = "www/isotope.pkgd.min.js"),
+  tags$script(src="www/script.js"))
+}
+
+#' @import shiny shinyjs
+golem_add_external_resources <- function(){
+  
+  addResourcePath(
+    'www', system.file('app/www', package = 'bdchecks.app')
+  )
+ 
+  tags$head(
+    golem::activate_js(),
+    golem::favicon(),
+    useShinyjs(),
+    
+    tags$link(rel = "stylesheet", type = "text/css", href = "www/input.css"),
+    tags$link(rel = "stylesheet", type = "text/css", href = "www/style.css"),
+    tags$link(rel = "stylesheet", type = "text/css", href = "www/shuffle.css")
+  )
+}

R/bd_utils.R

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+#' @export 
+#' @import bdchecks
+get_dc_groups <- function(group){
+    dc_group <- lapply(bdchecks:::data.checks@dc_body, function(x) {
+        if (group == "DarwinCoreClass") {
+            data.frame(
+                DC = x@name,
+                group = gsub(" ", "_", x@description$DarwinCoreClass),
+                groupName = gsub("_", " ", x@description$DarwinCoreClass)
+            )
+        } else {
+            data.frame(
+                DC = x@name,
+                group = gsub(" ", "_", x@flags[[group]]),
+                groupName = gsub("_", " ", x@flags[[group]])
+            )
+        }
+    })
+    do.call(rbind, dc_group)
+}
+
+
+#' @export 
+#' @import bdchecks
+get_dc_ids <- function(){
+    return(names(bdchecks::data.checks@dc_body))
+}

R/golem_utils_server.R

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+# Inverted versions of in, is.null and is.na
+`%not_in%` <- Negate(`%in%`)
+
+not_null <- Negate(is.null)
+
+not_na <- Negate(is.na)
+
+# Removes the null from a vector
+drop_nulls <- function(x){
+  x[!sapply(x, is.null)]
+}
+
+# If x is null, return y, otherwise return x
+"%||%" <- function(x, y){
+  if (is.null(x)) {
+    y
+  } else {
+    x
+  }
+}
+# If x is NA, return y, otherwise return x
+"%|NA|%" <- function(x, y){
+  if (is.na(x)) {
+    y
+  } else {
+    x
+  }
+}
+
+# typing reactiveValues is too long
+rv <- shiny::reactiveValues
+rvtl <- shiny::reactiveValuesToList