First commit

.Rbuildignore

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

.Rhistory

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+golem::fill_desc(
+pkg_name = "MetaShARK", # The Name of the package containing the App
+pkg_title = "metashark", # The Title of the package containing the App
+pkg_description = "MetaShARK is a Shiny application allowing its
+user to fill metadata for a given ecological
+dataset of his owns. The data description relies
+on Ecological Metadata Language (EML).", # The Description of the package containing the App
+author_first_name = "Elie", # Your First Name
+author_last_name = "ARNAUD",  # Your Last Name
+author_email = "[email protected]",   # Your Email
+repo_url = "https://github.com/earnaud/MetaShARK.git" # The (optional) URL of the GitHub Repo
+)
+getwd()
+golem::set_golem_options()
+usethis::use_readme_rmd( open = FALSE )
+{usethis}
+usethis
+## 1.3 - Add a data-raw folder
+##
+## If you have data in your package
+usethis::use_data_raw( name = "resources", open = FALSE ) # Change "my_dataset"
+usethis::use_data_rax
+usethis::use_data_raw
+golem::use_recommended_tests
+normalizePath
+interactive()
+golem::use_recommended_tests()
+golem::use_recommended_deps()
+# Add helper functions
+golem::use_utils_ui()
+golem::use_utils_server()
+# You're now set!
+# go to dev/02_dev.R
+rstudioapi::navigateToFile( "dev/02_dev.R" )
+## 2.1 Add modules
+##
+golem::add_module( name = "modules/my_first_module" ) # Name of the module
+## 3.1 Vignette
+usethis::use_vignette("MetaShARK")
+# You're now set!
+# go to dev/03_deploy.R
+rstudioapi::navigateToFile("dev/03_deploy.R")
+# You're now set!
+# go to dev/03_deploy.R
+rstudioapi::navigateToFile("dev/03_deploy.R")
+install.packages("rhub")
+devtools::test()
+#' Run the Shiny Application
+#'
+#' @export
+#' @importFrom shiny shinyApp
+#' @importFrom golem with_golem_options
+run_app <- function(...) {
+with_golem_options(
+app = shinyApp(ui = app_ui, server = app_server),
+golem_opts = list(...)
+)
+}
+run_app()
+test_check("MetaShARK")
+library(testthat)
+library(MetaShARK)
+test_check("MetaShARK")
+run_app()
+MetaShARK::runMetashark
+source('~/Softwares/MetaShARK/R/run_app.R')
+library(MetaShARK)
+#' Run the Shiny Application
+#'
+#' @export
+#' @importFrom shiny shinyApp
+#' @importFrom golem with_golem_options
+runMetashark <- function(...) {
+with_golem_options(
+app = shinyApp(ui = app_ui, server = app_server),
+golem_opts = list(...)
+)
+}
+library(MetaShARK)
+library(MetaShARK)
+MetaShARK::run_app()
+getwd()
+build(,)
+build
+build()
+document_and_reload()
+runMetashark()
+document_and_reload()
+document_and_reload()
+runMetashark()
+runMetashark()
+document_and_reload()
+runMetashark()
+document_and_reload()
+runMetashark()
+?golem_add_external_resources
+?golem::golem_add_external_resources
+golem::golem_add_external_resources
+library(golem)
+golem::golem_add_external_resources
+getwd()
+document_and_reload
+document_and_reload()
+runMetashark()
+document_and_reload()
+runMetashark()
+document_and_reload()
+runMetashark()
+document_and_reload()
+runMetashark()
+?runMetashark
+document_and_reload()
+?runMetashark
+document_and_reload()
+library(golem)
+document_and_reload()
+runMetashark()
+document_and_reload()
+data()
+??build
+getwd()
+document_and_reload
+load_all()
+??load_all
+devtools::load_all()
+devtools::load_all()
+test <- readRDS("resources/backboneGuideline.RData")
+getwd()
+backboneGuideline <- test
+usethis::use_data(backboneGuideline)
+docGuideline <- readRDS("resources/docGuideline.RData"); usethis::use_data(docGuideline)
+systemGuideline <- readRDS("resources/systemGuideline.RData"); usethis::use_data(systemGuideline)
+rm(list = ls())
+devtools::load_all()
+runMetashark()
+devtools::load_all()
+runMetashark()
+devtools::load_all()
+runMetashark()
+devtools::load_all()
+runMetashark()

.gitignore

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+inst/doc
+.Rproj.user

DESCRIPTION

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+Package: MetaShARK
+Title: metashark
+Version: 0.0.0.9000
+Authors@R: person('Elie', 'ARNAUD', email = '[email protected]', role = c('cre', 'aut'))
+Description: MetaShARK is a Shiny application allowing its
+                    user to fill metadata for a given ecological
+                    dataset of his owns. The data description relies
+                    on Ecological Metadata Language (EML).
+License: What license is it under?
+Encoding: UTF-8
+LazyData: true
+Imports: 
+    shiny,
+    golem,
+    processx,
+    attempt,
+    DT,
+    glue,
+    htmltools
+RoxygenNote: 6.1.1
+URL: https://github.com/earnaud/MetaShARK.git
+BugReports: https://github.com/earnaud/MetaShARK.git/issues
+Suggests: 
+    testthat,
+    knitr,
+    rmarkdown
+VignetteBuilder: knitr

MetaShARK.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+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,column)
+importFrom(shiny,shinyApp)

R/app_server.R

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+#' @import shiny
+.app_server <- function(input, output,session) {
+  ## DEV: do things by clicking a button
+  observeEvent(input$check,{
+    browser()
+  })
+
+  ## modules called ----
+  # welcome
+
+  # fill
+  # doc
+  # about
+}

R/app_ui.R

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+#' @import shiny shinyjs shinydashboard
+.app_ui <- function() {
+  global <- .globalScript()
+  print(global$a)
+
+  # prepare variable
+  menuWidth = "250px"
+
+  # action
+  tagList(
+    # Leave this function for adding external resources
+    .golem_add_external_resources(),
+    # List the first level UI elements here
+    dashboardPage(
+      title = "MetaShARK",
+      dashboardHeader(
+        title = span(imageOutput("metashark-logo", inline = TRUE), "MetaShARK"),
+        titleWidth = menuWidth
+      ),
+      ## Menus ----
+      dashboardSidebar(
+        useShinyjs(),
+        sidebarMenu(
+          menuItem("Welcome", tabName = "welcome", 
+                   icon = icon("home")),
+          menuItem("Fill in EML", tabName = "fill",
+                   icon = icon("file-import")),
+          menuItem("EML Documentation", tabName = "documentation",
+                   icon = icon("glasses")),
+          menuItem("About MetaShARK", tabName = "about",
+                   icon = icon("beer"))
+          ,actionButton("check","Dev Check")
+        ),
+        width = menuWidth
+      ), # end sidebar
+      ## Content ----
+      dashboardBody(
+        tabItems(
+          tabItem(tabName = "welcome",
+                  # welcomeUI(IM.welcome[1], IM = IM.welcome)),
+                  fluidPage(1)),
+          tabItem(tabName = "fill",
+                  # fillUI(IM.fill[1], IM = IM.fill)),
+                  fluidPage(2)),
+          tabItem(tabName = "documentation",
+                  # docUI(IM.doc[1], IM = IM.doc)),
+                  fluidPage(3)),
+          tabItem(tabName = "about",
+                  # aboutUI(IM.about[1], IM = IM.about))
+                  fluidPage(4))
+        )
+      ) # end body
+
+    ) # end dashboard
+
+  ) # end taglist
+
+}
+
+#' @import shiny
+.golem_add_external_resources <- function(){
+
+  addResourcePath(
+    'www', system.file('app/www', package = 'MetaShARK')
+  )
+
+  tags$head(
+    golem::activate_js(),
+    golem::favicon()
+    # Add here all the external resources
+    # If you have a custom.css in the inst/app/www
+    # Or for example, you can add shinyalert::useShinyalert() here
+    #tags$link(rel="stylesheet", type="text/css", href="www/custom.css")
+  )
+}

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