From 9ad7f1361b89ead2774794b8cab29aa37cd05b8d Mon Sep 17 00:00:00 2001
From: Elie Ker Arno <earnaud@outlook.com>
Date: Thu, 16 Jul 2020 14:01:47 +0200
Subject: [PATCH] Refactoring #5

---
 .RData                         | Bin 2876 -> 48 bytes
 DESCRIPTION                    |   2 +-
 R/eal_2_DataFiles.R            |  20 +-
 R/eal_3_Attributes.R           |   6 +-
 R/eal_3_attributeInput.R       | 168 ++++++-------
 R/eal_4_CatVars.R              |   3 +-
 R/eal_5_GeoCovInput.R          | 193 ++++++++-------
 R/eal_5_geographicCoverage.R   |   4 -
 R/eal_6_taxonomicCoverage.R    |   3 -
 R/eal_7_personnel.R            | 430 ++++++++++++++++-----------------
 R/eal_8_misc.R                 |   2 +-
 R/eal_8_miscellaneous.R        |  79 +++---
 R/fill-module.R                |  26 +-
 R/fill_pages.R                 |  34 ++-
 R/{headerScript.R => header.R} |  36 ++-
 R/runMetashark.R               |  37 +--
 R/server.R                     |  15 +-
 R/ui.R                         |  59 +++--
 man/runMetashark.Rd            |   8 +-
 19 files changed, 564 insertions(+), 561 deletions(-)
 rename R/{headerScript.R => header.R} (92%)

diff --git a/.RData b/.RData
index 339a67021dc804db47f54ed44eee539c028f0a41..1103bfcb6150a6ca2949ccf3881ab18fa491af33 100644
GIT binary patch
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zcmb2|=3oE=X6~X+gJ)e2k`fXU(h|~`lfo1xH=3Fp@x9J;;s-m!lXooK3P6PbQ)&+M

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diff --git a/DESCRIPTION b/DESCRIPTION
index 9e98025..026ad16 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -50,7 +50,7 @@ Imports:
 Remotes:
     ThinkR-open/tagsinput,
     ropenscilabs/emldown
-RoxygenNote: 7.1.0
+RoxygenNote: 7.1.1
 URL: https://github.com/earnaud/MetaShARK-v2.git
 BugReports: https://github.com/earnaud/MetaShARK-v2.git/issues
 Suggests: 
diff --git a/R/eal_2_DataFiles.R b/R/eal_2_DataFiles.R
index d359c90..796b105 100644
--- a/R/eal_2_DataFiles.R
+++ b/R/eal_2_DataFiles.R
@@ -3,8 +3,6 @@
 #' 
 #' @noRd
 DataFilesUI <- function(id, main.env) {
-  ns <- NS(id)
-  
   return(
     fluidPage(
       tags$b("Disclaimers:"),
@@ -147,7 +145,7 @@ DataFiles <- function(id, main.env) {
             df$name,
             function(label) {
               # Variable initialization
-              id <- match(label, df$name)
+              .id <- match(label, df$name)
               xls.warning <- if (grepl("xlsx?$", label)) {
                 tags$div(
                   "Only the first sheet of Excel files will be read.",
@@ -159,7 +157,7 @@ DataFiles <- function(id, main.env) {
               
               # Output
               collapsibleUI(
-                id = ns(id),
+                id = NS(id, .id),
                 label = label,
                 hidden = FALSE,
                 class = "inputBox",
@@ -168,7 +166,7 @@ DataFiles <- function(id, main.env) {
                     column(
                       6,
                       textInput(
-                        ns(paste0(id, "-dataName")),
+                        NS(id, paste0(.id, "-dataName")),
                         "Data table name",
                         value = label
                       )
@@ -176,7 +174,7 @@ DataFiles <- function(id, main.env) {
                     column(
                       6,
                       URL_Input_UI(
-                        ns(paste0(id, "-dataURL")),
+                        NS(id, paste0(.id, "-dataURL")),
                         label = "Data remote location"
                       )
                     ),
@@ -186,7 +184,7 @@ DataFiles <- function(id, main.env) {
                     column(
                       12,
                       textAreaInput(
-                        ns(paste0(id, "-dataDesc")),
+                        NS(id, paste0(.id, "-dataDesc")),
                         "Data Table Description",
                         value = paste("Content of", label),
                         width = "100%"
@@ -209,9 +207,9 @@ DataFiles <- function(id, main.env) {
           any(grepl("dataURL", names(input))) ||
           any(grepl("dataDesc", names(input)))
       )
-      sapply(rv$data.files$name, function(id) {
-        collapsible(id)
-        ind <- match(id, rv$data.files$name)
+      sapply(rv$data.files$name, function(.id) {
+        collapsible(.id)
+        ind <- match(.id, rv$data.files$name)
         
         # Data name
         observeEvent(input[[paste0(ind, "-dataName")]],
@@ -266,7 +264,7 @@ DataFiles <- function(id, main.env) {
         tags$p(
           utils::object.size(files.size),
           if (files.size >= files.size.max) {
-            paste("Max. recommended:", utils::object.size(files.size.max))
+            paste("Max. recommended:", utils:::format.object_size(files.size.max))
           } else {
             NULL
           },
diff --git a/R/eal_3_Attributes.R b/R/eal_3_Attributes.R
index 4eed1e6..3882e3d 100644
--- a/R/eal_3_Attributes.R
+++ b/R/eal_3_Attributes.R
@@ -298,7 +298,7 @@ Attributes <- function(id, main.env) {
                           
                           # GUI
                           attributeInputUI(
-                            ns(inputId),
+                            NS(id, inputId),
                             colname,
                             saved.value,
                             main.env$FORMATS,
@@ -311,7 +311,7 @@ Attributes <- function(id, main.env) {
                         # Preview ====
                         h4("Preview:"),
                         tableOutput(
-                          ns(paste0(
+                          NS(id, paste0(
                             "preview-", 
                             colnames(rv$current.preview)[row.index]
                           ))
@@ -320,7 +320,7 @@ Attributes <- function(id, main.env) {
                         # Annotate ====
                         # tags$div(
                         #   annotateUI(
-                        #     ns(paste(
+                        #     NS(id, paste(
                         #       "annotate",
                         #       isolate(rv$current.file),
                         #       row.index,
diff --git a/R/eal_3_attributeInput.R b/R/eal_3_attributeInput.R
index 0c155d4..b1f0ea4 100644
--- a/R/eal_3_attributeInput.R
+++ b/R/eal_3_attributeInput.R
@@ -4,19 +4,19 @@ attributeInputUI <- function(id, colname, value, formats, rv) {
   
   ui <- switch(colname,
     attributeDefinition = textAreaInput(
-      ns(colname),
+      NS(id, colname),
       value = value,
       withRedStar("Describe the attribute")
     ),
     class = selectInput(
-      ns(colname),
+      NS(id, colname),
       "Dectected class (change if misdetected)",
       choices = c("numeric", "character", "Date", "categorical"),
       selected = value
     ),
     unit = {
       tmp <- selectInput(
-        ns(colname),
+        NS(id, colname),
         withRedStar("Select an unit"),
         rv$units.list,
         selected = if (isTruthy(value)) value
@@ -29,7 +29,7 @@ attributeInputUI <- function(id, colname, value, formats, rv) {
     },
     dateTimeFormatString = {
       tmp <- selectInput( # TODO better hour format
-        ns(colname),
+        NS(id, colname),
         withRedStar("Select a date format"),
         unique(c(value, formats$DATE)),
         selected = value
@@ -41,12 +41,12 @@ attributeInputUI <- function(id, colname, value, formats, rv) {
       }
     },
     missingValueCode = textInput(
-      ns(colname),
+      NS(id, colname),
       "Code for missing value (max 1 word)",
       value = value
     ),
     missingValueCodeExplanation = textAreaInput(
-      ns(colname),
+      NS(id, colname),
       "Explain Missing Values",
       value = value
     ),
@@ -58,88 +58,88 @@ attributeInputUI <- function(id, colname, value, formats, rv) {
 
 #' @import shiny
 #' @importFrom shinyjs show hide
-attributeInput <- function(input, output, session,
-  rv, row.index, colname, obs, curt) {
-  ns <- session$ns
-  
-  obs[[ns(colname)]] <- observeEvent(input[[colname]],
-    {
-      req(input[[colname]])
-      
-      .val <- input[[colname]]
-      
-      # Class ====
-      if (colname == "class") {
-        # Date
-        date.id <- "dateTimeFormatString"
-        if (input[[colname]] == "Date") {
-          isolate(rv$current.table[row.index, "unit"] <- input[[date.id]])
-          shinyjs::show(date.id)
-        } else {
-          isolate(rv$current.table[row.index, "dateTimeFormatString"] <- "")
-          shinyjs::hide(date.id)
-        }
+attributeInput <- function(id, rv, row.index, colname, obs, curt){
+  moduleServer(id, function(input, output, session) {
+    
+    obs[[NS(id, colname)]] <- observeEvent(input[[colname]],
+      {
+        req(input[[colname]])
         
-        # Unit
-        unit.id <- "unit"
-        if (input[[colname]] == "numeric") {
-          isolate(rv$current.table[row.index, "unit"] <- input[[unit.id]])
-          shinyjs::show(unit.id)
-        } else {
-          isolate(rv$current.table[row.index, "unit"] <- "")
-          shinyjs::hide(unit.id)
-        }
-      }
-      # Missing Value Code ====
-      if (colname == "missingValueCode") { # input: missing Value code
-        if (grepl(".+ +.*", input[[colname]])) {
-          .val <- strsplit(gsub("^ +", "", .val), split = " ")[[1]][1]
+        .val <- input[[colname]]
+        
+        # Class ====
+        if (colname == "class") {
+          # Date
+          date.id <- "dateTimeFormatString"
+          if (input[[colname]] == "Date") {
+            isolate(rv$current.table[row.index, "unit"] <- input[[date.id]])
+            shinyjs::show(date.id)
+          } else {
+            isolate(rv$current.table[row.index, "dateTimeFormatString"] <- "")
+            shinyjs::hide(date.id)
+          }
           
-          updateTextInput(
-            session,
-            colname,
-            value = .val
-          )
-          showNotification(
-            id = session$NS(id, "mvc_update"),
-            ui = HTML("<code>missingValueCode</code> fields are limited to a
-              <b>single word.</b>"),
-            duration = 3,
-            type = "warning"
-          )
+          # Unit
+          unit.id <- "unit"
+          if (input[[colname]] == "numeric") {
+            isolate(rv$current.table[row.index, "unit"] <- input[[unit.id]])
+            shinyjs::show(unit.id)
+          } else {
+            isolate(rv$current.table[row.index, "unit"] <- "")
+            shinyjs::hide(unit.id)
+          }
         }
-      }
-      # Units ====
-      if (grepl("unit", ns(colname))) {
-        # Trigger CU
-        if (input[[colname]] == "custom" &&
-            isFALSE(rv$modal.on)) {
-          curt$trigger()
+        # Missing Value Code ====
+        if (colname == "missingValueCode") { # input: missing Value code
+          if (grepl(".+ +.*", input[[colname]])) {
+            .val <- strsplit(gsub("^ +", "", .val), split = " ")[[1]][1]
+            
+            updateTextInput(
+              session,
+              colname,
+              value = .val
+            )
+            showNotification(
+              id = session$NS(id, "mvc_update"),
+              ui = HTML("<code>missingValueCode</code> fields are limited to a
+              <b>single word.</b>"),
+              duration = 3,
+              type = "warning"
+            )
+          }
         }
-        
-        if (isFALSE(input[[colname]] %in% rv$units.list)) {
-          .cu <- rv$current.table[row.index, colname]
-          if (.cu %in% rv$cu.table$id) {
-            .ind <- which(rv$cu.table$id == .cu)
-            rv$cu.table$id <- rv$cu.table$id[-.ind]
+        # Units ====
+        if (grepl("unit", NS(id, colname))) {
+          # Trigger CU
+          if (input[[colname]] == "custom" &&
+              isFALSE(rv$modal.on)) {
+            curt$trigger()
+          }
+          
+          if (isFALSE(input[[colname]] %in% rv$units.list)) {
+            .cu <- rv$current.table[row.index, colname]
+            if (.cu %in% rv$cu.table$id) {
+              .ind <- which(rv$cu.table$id == .cu)
+              rv$cu.table$id <- rv$cu.table$id[-.ind]
+            }
           }
         }
-      }
-      
-      # Set values ====
-      if(
-        (colname == "unit" && 
-            rv$current.table[row.index, "class"] != "numeric") ||
-          (colname == "dateTimeFormatString" && 
-              rv$current.table[row.index, "class"] != "Date")
-      )
-        .val <- ""
-      rv$current.table[row.index, colname] <- .val
-      rv$tables[[rv$current.file]] <- rv$current.table
-    },
-    label = ns(colname)
-  )
-  
-  # Output ----
-  return(obs)
+        
+        # Set values ====
+        if(
+          (colname == "unit" && 
+              rv$current.table[row.index, "class"] != "numeric") ||
+            (colname == "dateTimeFormatString" && 
+                rv$current.table[row.index, "class"] != "Date")
+        )
+          .val <- ""
+        rv$current.table[row.index, colname] <- .val
+        rv$tables[[rv$current.file]] <- rv$current.table
+      },
+      label = NS(id, colname)
+    )
+    
+    # Output ----
+    return(obs)
+  })
 }
\ No newline at end of file
diff --git a/R/eal_4_CatVars.R b/R/eal_4_CatVars.R
index 0417133..ee523fd 100644
--- a/R/eal_4_CatVars.R
+++ b/R/eal_4_CatVars.R
@@ -48,7 +48,6 @@ CatVarsUI <- function(id, main.env) {
 CatVars <- function(id, main.env) {
   moduleServer(id, function(input, output, session){
     save.variable <- main.env$save.variable
-    ns <- session$ns
     
     # variables initialization ----
     rv <- reactiveValues(
@@ -113,7 +112,7 @@ CatVars <- function(id, main.env) {
                 )
                 
                 textAreaInput(
-                  ns(input.id),
+                  NS(id, input.id),
                   cod,
                   value = rv[[file.name]]$CatVars %>%
                     dplyr::filter(attributeName == attribute, code == cod) %>%
diff --git a/R/eal_5_GeoCovInput.R b/R/eal_5_GeoCovInput.R
index 8a705c7..207d56c 100644
--- a/R/eal_5_GeoCovInput.R
+++ b/R/eal_5_GeoCovInput.R
@@ -3,10 +3,8 @@
 #' 
 #' @noRd
 GeoCovInputUI <- function(id, site.id, rmv.id, default = NULL) {
-  ns <- NS(id)
-
   div.id <- id
-
+  
   if (!is.null(default)) {
     default <- as.vector(default)
     def.site <- default["geographicDescription"]
@@ -24,7 +22,7 @@ GeoCovInputUI <- function(id, site.id, rmv.id, default = NULL) {
     def.lat <- c(-45, 45)
     def.lon <- c(-90, 90)
   }
-
+  
   tags$div(
     id = site.id,
     fluidRow(
@@ -33,7 +31,7 @@ GeoCovInputUI <- function(id, site.id, rmv.id, default = NULL) {
       column(
         1,
         actionButton(
-          ns(rmv.id),
+          NS(id, rmv.id),
           "",
           icon("trash"),
           class = "danger"
@@ -44,7 +42,7 @@ GeoCovInputUI <- function(id, site.id, rmv.id, default = NULL) {
       column(
         6,
         sliderInput(
-          ns(paste0("lat_", site.id)),
+          NS(id, paste0("lat_", site.id)),
           tags$h4("Latitude"),
           min = -90, max = 90,
           value = def.lat,
@@ -58,7 +56,7 @@ GeoCovInputUI <- function(id, site.id, rmv.id, default = NULL) {
       column(
         6,
         sliderInput(
-          ns(paste0("lon_", site.id)),
+          NS(id, paste0("lon_", site.id)),
           tags$h4("Longitude"),
           min = -180, max = 180,
           value = def.lon,
@@ -79,85 +77,86 @@ GeoCovInputUI <- function(id, site.id, rmv.id, default = NULL) {
 #' @importFrom shinyjs onclick
 #' 
 #' @noRd
-GeoCovInput <- function(input, output, session,
-                        rv, rmv.id, site.id, ref) {
-
-  # Metadata acquisition ----
-  local.rv <- reactiveValues(
-    id = ref,
-    geographicDescription = "",
-    northBoundingCoordinate = 0,
-    southBoundingCoordinate = 0,
-    eastBoundingCoordinate = 0,
-    westBoundingCoordinate = 0
-  )
-
-  # site description
-  observeEvent(input$site_description,
-    {
-      req(input$site_description)
-      local.rv$geographicDescription <- input$site_description
-    },
-    priority = 1
-  )
-  
-  # latitude
-  observeEvent(input[[paste0("lat_", site.id)]],
-    {
-      req(input[[paste0("lat_", site.id)]])
-      local.rv$northBoundingCoordinate <- max(input[[paste0("lat_", site.id)]])
-      local.rv$southBoundingCoordinate <- min(input[[paste0("lat_", site.id)]])
-    },
-    priority = 1
-  )
-  
-  # longitude
-  observeEvent(input[[paste0("lon_", site.id)]],
-    {
-      req(input[[paste0("lon_", site.id)]])
-      local.rv$eastBoundingCoordinate <- max(input[[paste0("lon_", site.id)]])
-      local.rv$westBoundingCoordinate <- min(input[[paste0("lon_", site.id)]])
-    },
-    priority = 1
-  )
-
-  # Metadata save ----
-  observeEvent(
-    {
-      input$site_description
-      input[[paste0("lat_", site.id)]]
-      input[[paste0("lon_", site.id)]]
-    },
-    {
-      # Fetch correct index
+GeoCovInput <- function(id, rv, rmv.id, site.id, ref) {
+  moduleServer(id, function(input, output, session) {
+    
+    # Metadata acquisition ----
+    local.rv <- reactiveValues(
+      id = ref,
+      geographicDescription = "",
+      northBoundingCoordinate = 0,
+      southBoundingCoordinate = 0,
+      eastBoundingCoordinate = 0,
+      westBoundingCoordinate = 0
+    )
+    
+    # site description
+    observeEvent(input$site_description,
+      {
+        req(input$site_description)
+        local.rv$geographicDescription <- input$site_description
+      },
+      priority = 1
+    )
+    
+    # latitude
+    observeEvent(input[[paste0("lat_", site.id)]],
+      {
+        req(input[[paste0("lat_", site.id)]])
+        local.rv$northBoundingCoordinate <- max(input[[paste0("lat_", site.id)]])
+        local.rv$southBoundingCoordinate <- min(input[[paste0("lat_", site.id)]])
+      },
+      priority = 1
+    )
+    
+    # longitude
+    observeEvent(input[[paste0("lon_", site.id)]],
+      {
+        req(input[[paste0("lon_", site.id)]])
+        local.rv$eastBoundingCoordinate <- max(input[[paste0("lon_", site.id)]])
+        local.rv$westBoundingCoordinate <- min(input[[paste0("lon_", site.id)]])
+      },
+      priority = 1
+    )
+    
+    # Metadata save ----
+    observeEvent(
+      {
+        input$site_description
+        input[[paste0("lat_", site.id)]]
+        input[[paste0("lon_", site.id)]]
+      },
+      {
+        # Fetch correct index
+        ind <- match(ref, rv$id)
+        if (is.na(ind)) {
+          ind <- length(rv$id) + 1
+        }
+        
+        # print values into rv at selected index
+        .actual.values <- printReactiveValues(local.rv)
+        rv$id <- c(rv$id, .actual.values["id"])
+        .actual.values <- .actual.values[names(.actual.values) != "id"]
+        rv$coordinates[ind, ] <- .actual.values[colnames(rv$coordinates)]
+      },
+      ignoreInit = TRUE,
+      priority = 0
+    )
+    
+    # Remove UI ----
+    shinyjs::onclick(rmv.id, {
+      # remove the UI
+      removeUI(selector = paste0("#", site.id), immediate = TRUE)
+      
+      # unload the UI
       ind <- match(ref, rv$id)
-      if (is.na(ind)) {
-        ind <- length(rv$id) + 1
-      }
-
-      # print values into rv at selected index
-      .actual.values <- printReactiveValues(local.rv)
-      rv$id <- c(rv$id, .actual.values["id"])
-      .actual.values <- .actual.values[names(.actual.values) != "id"]
-      rv$coordinates[ind, ] <- .actual.values[colnames(rv$coordinates)]
-    },
-    ignoreInit = TRUE,
-    priority = 0
-  )
-
-  # Remove UI ----
-  shinyjs::onclick(rmv.id, {
-    # remove the UI
-    removeUI(selector = paste0("#", site.id), immediate = TRUE)
-
-    # unload the UI
-    ind <- match(ref, rv$id)
-    rv$coordinates <- rv$coordinates[-ind, ]
-    rv$id <- rv$id[-ind]
+      rv$coordinates <- rv$coordinates[-ind, ]
+      rv$id <- rv$id[-ind]
+    })
+    
+    # Output ----
+    return(rv)
   })
-
-  # Output ----
-  return(rv)
 }
 
 #' @importFrom dplyr bind_rows
@@ -166,22 +165,22 @@ GeoCovInput <- function(input, output, session,
 #' @noRd
 insertGeoCovInput <- function(id, rv, ns, default = NULL) {
   # !!! warning: rv = rv$custom here !!!
-
+  
   # initialize IDs ----
   div.id <- id
   site.id <- paste0("site_", div.id)
   rmv.id <- paste0("rmv_", div.id)
-
+  
   # Proper module server ----
   # create the UI
   new.ui <- GeoCovInputUI(ns(div.id), site.id, rmv.id, default = default)
-
+  
   # insert the UI
   insertUI(selector = "#inserthere", ui = new.ui)
-
+  
   # create the server
   rv <- GeoCovInput(div.id, rv, rmv.id, site.id, id)
-
+  
   # Output ----
   return(rv)
 }
@@ -204,7 +203,7 @@ extractCoordinates <- function(
     coord.cols <- printReactiveValues(rv$columns$lon)
     coord.tags <- c("E", "W")
   }
-
+  
   # Extract proper coordinates
   coordinates <- files.data[[coord.cols["file"]]][[coord.cols["col"]]] %>% # uniformize decimal separators
     sapply(.,
@@ -216,7 +215,7 @@ extractCoordinates <- function(
   coordinates <- coordinates[coord.index] %>% 
     unname %>% 
     as.numeric
-
+  
   if(!is.data.frame(coordinates))
     coordinates <- data.frame(
       coordinates, stringsAsFactors = FALSE
@@ -227,21 +226,21 @@ extractCoordinates <- function(
     coordinates <- coordinates[, 1:2]
   if (dim(coordinates)[2] == 1)
     coordinates <- cbind(coordinates, coordinates)
-
+  
   if (dim(coordinates)[2] <= 2 && dim(coordinates)[2] > 0) {
     # assign West and East / North and South to columns
     coordinates[
       coordinates[, 1] <= coordinates[, 2],
-    ] <- rev(coordinates[
-      coordinates[, 1] <= coordinates[, 2],
-    ])
-
+      ] <- rev(coordinates[
+        coordinates[, 1] <= coordinates[, 2],
+        ])
+    
     colnames(coordinates) <- coord.tags
     if (all(coordinates[, 1] <= coordinates[, 2])) {
       colnames(coordinates) <- rev(coord.tags)
     }
   }
-
+  
   return(
     list(
       coordinates = coordinates,
diff --git a/R/eal_5_geographicCoverage.R b/R/eal_5_geographicCoverage.R
index 543bf8c..63f2597 100644
--- a/R/eal_5_geographicCoverage.R
+++ b/R/eal_5_geographicCoverage.R
@@ -3,8 +3,6 @@
 #' 
 #' @noRd
 GeoCovUI <- function(id, main.env) {
-  ns <- NS(id)
-
   return(
     fluidPage(
       fluidRow(
@@ -78,8 +76,6 @@ GeoCovUI <- function(id, main.env) {
 GeoCov <- function(id, main.env) {
   moduleServer(id, function(input, output, session){
     save.variable <- main.env$save.variable
-  ns <- session$ns
-  
   # Variable initialization ----
 
   # Reactive Values
diff --git a/R/eal_6_taxonomicCoverage.R b/R/eal_6_taxonomicCoverage.R
index 044ddd1..e79225d 100644
--- a/R/eal_6_taxonomicCoverage.R
+++ b/R/eal_6_taxonomicCoverage.R
@@ -3,8 +3,6 @@
 #' 
 #' @noRd
 TaxCovUI <- function(id, main.env) {
-  ns <- NS(id)
-  
   return(
     fluidPage(
       fluidRow(
@@ -33,7 +31,6 @@ TaxCovUI <- function(id, main.env) {
 TaxCov <-function(id, main.env) {
   moduleServer(id, function(input, output, session){
     save.variable <- main.env$save.variable
-    ns <- session$ns
     
     # Variable Initialization ----
     rv <- reactiveValues(
diff --git a/R/eal_7_personnel.R b/R/eal_7_personnel.R
index b157c84..96cd3a3 100644
--- a/R/eal_7_personnel.R
+++ b/R/eal_7_personnel.R
@@ -186,7 +186,7 @@ insertPersonnelInput <- function(id, rv, ns, main.env, role = NULL, saved = NULL
   # Proper module server ----
   # insert new UI
   newUI <- PersonnelModUI(
-    ns(id), div.id, site.id, rmv.id,
+    NS(id, id), div.id, site.id, rmv.id,
     role = role, saved = saved
   )
   insertUI(
@@ -211,7 +211,6 @@ insertPersonnelInput <- function(id, rv, ns, main.env, role = NULL, saved = NULL
 #' @noRd
 PersonnelModUI <- function(id, div.id, site.id, rmv.id,
   role = NULL, saved = NULL) {
-  ns <- NS(id)
   
   value <- if (checkTruth(saved)) {
     saved[saved$id == div.id, ]
@@ -289,7 +288,7 @@ PersonnelModUI <- function(id, div.id, site.id, rmv.id,
           column(1,
             if (is.null(role)) {
               actionButton(
-                ns(rmv.id),
+                NS(id, rmv.id),
                 "",
                 icon("trash"),
                 class = "danger"
@@ -389,243 +388,244 @@ PersonnelModUI <- function(id, div.id, site.id, rmv.id,
 #' @importFrom stringr str_extract
 #' 
 #' @noRd
-PersonnelMod <- function(input, output, session, main.env,
-  rv, rmv.id, site.id, ref, role = NULL, saved = NULL) {
-  ns <- session$ns
-  
-  # Variable initialization ----
-  if (!is.null(saved)) {
-    value <- saved[saved$id == ref, ]
-  } else {
-    value <- NULL
-  }
-  
-  local.rv <- reactiveValues(
-    id = ref,
-    # Basic Identity
-    givenName = if (!is.null(value)) value$givenName else character(),
-    middleInitial = if (!is.null(value)) value$middleInitial else character(),
-    surName = if (!is.null(value)) value$surName else character(),
-    # Contact
-    organizationName = if (!is.null(value)) value$organizationName else character(),
-    electronicMailAddress = if (!is.null(value)) value$electronicMailAddress else character(),
-    # Personnel information
-    userId = if (!is.null(value)) value$userId else character(),
-    role = if (!is.null(role)) role else if (!is.null(value)) value$role else character(),
-    `role-other` = if (!is.null(role)) role else if (!is.null(value)) value$`role-other` else character(),
-    # Project information
-    projectTitle = if (!is.null(value)) value$projectTitle else NA,
-    fundingAgency = if (!is.null(value)) value$fundingAgency else NA,
-    fundingNumber = if (!is.null(value)) value$fundingNumber else NA
-  )
-  
-  # * Basic Identity ----
-  name.pattern <- main.env$PATTERNS$name
-  
-  observeEvent(input$givenName, {
-    local.rv$givenName <- if (grepl(name.pattern, input$givenName)) {
-      input$givenName
-    }
-  })
-  
-  observeEvent(input$middleInitial, {
-    local.rv$middleInitial <- input$middleInitial
-  })
-  
-  observeEvent(input$surName, {
-    local.rv$surName <- if (grepl(name.pattern, input$surName)) {
-      input$surName
-    }
-  })
-  
-  # * Contact ----
-  mail.pattern <- main.env$PATTERNS$email
-  
-  observeEvent(input$organizationName, {
-    local.rv$organizationName <- input$organizationName
-  })
-  
-  observeEvent(input$electronicMailAddress, {
-    local.rv$electronicMailAddress <- if (grepl(mail.pattern, input$electronicMailAddress)) {
-      input$electronicMailAddress
-    }
-  })
-  
-  # * (ORCID) Personnel identification ----
-  orcid.pattern <- main.env$PATTERNS$ORCID
-  
-  observeEvent(input$userId, {
-    req(input$userId)
-    local.rv$userId <- input$userId
+PersonnelMod <- function(id, main.env, rv, rmv.id, site.id, ref, role = NULL, saved = NULL) {
+  moduleServer(id, function(input, output, session){
+    ns <- session$ns
     
-    if (grepl(orcid.pattern, input$userId)) {
-      local.rv$userId <- stringr::str_extract(local.rv$userId, orcid.pattern)
-      updateTextInput(
-        session = session,
-        inputId = "userId",
-        value = local.rv$userId
-      )
+    # Variable initialization ----
+    if (!is.null(saved)) {
+      value <- saved[saved$id == ref, ]
+    } else {
+      value <- NULL
     }
     
-    orcid.connect <- try(
-      rorcid::as.orcid(
-        local.rv$userId #TODO ORCID auth % snake
-      )
+    local.rv <- reactiveValues(
+      id = ref,
+      # Basic Identity
+      givenName = if (!is.null(value)) value$givenName else character(),
+      middleInitial = if (!is.null(value)) value$middleInitial else character(),
+      surName = if (!is.null(value)) value$surName else character(),
+      # Contact
+      organizationName = if (!is.null(value)) value$organizationName else character(),
+      electronicMailAddress = if (!is.null(value)) value$electronicMailAddress else character(),
+      # Personnel information
+      userId = if (!is.null(value)) value$userId else character(),
+      role = if (!is.null(role)) role else if (!is.null(value)) value$role else character(),
+      `role-other` = if (!is.null(role)) role else if (!is.null(value)) value$`role-other` else character(),
+      # Project information
+      projectTitle = if (!is.null(value)) value$projectTitle else NA,
+      fundingAgency = if (!is.null(value)) value$fundingAgency else NA,
+      fundingNumber = if (!is.null(value)) value$fundingNumber else NA
     )
     
-    if (
-      grepl(orcid.pattern, input$userId) &&
-        isTruthy(orcid.connect)
-    ) {
-      orcid <- local.rv$userId
-      orcid.info <- list()
-      
-      # names
-      orcid.info$names <- rorcid::orcid_person(orcid)[[orcid]]$name
-      if (isTruthy(unlist(orcid.info$names$`given-names`$value))) {
-        local.rv$givenName <- orcid.info$names$`given-names`$value
-        updateTextInput(session, "givenName", value = local.rv$givenName)
-      }
-      if (isTruthy(unlist(orcid.info$names$`family-name`$value))) {
-        local.rv$surName <- orcid.info$names$`family-name`$value
-        updateTextInput(session, "surName", value = local.rv$surName)
+    # * Basic Identity ----
+    name.pattern <- main.env$PATTERNS$name
+    
+    observeEvent(input$givenName, {
+      local.rv$givenName <- if (grepl(name.pattern, input$givenName)) {
+        input$givenName
       }
-      
-      # organization
-      orcid.info$employment <- rorcid::orcid_employments(orcid)[[orcid]]$`affiliation-group`$summaries[[1]]
-      if (isTruthy(unlist(orcid.info$employment$`employment-summary.organization.name`))) {
-        local.rv$organizationName <- orcid.info$employment$`employment-summary.organization.name`
-        updateTextInput(session, "organizationName", value = local.rv$organizationName)
+    })
+    
+    observeEvent(input$middleInitial, {
+      local.rv$middleInitial <- input$middleInitial
+    })
+    
+    observeEvent(input$surName, {
+      local.rv$surName <- if (grepl(name.pattern, input$surName)) {
+        input$surName
       }
-      if (is.null(role) &&
-          isTruthy(unlist(orcid.info$employment$`employment-summary.role-title`))) {
-        local.rv$role <- "(other)"
-        updateTextInput(session, "role", value = local.rv$role)
-        local.rv$`role-other` <- orcid.info$employment$`employment-summary.role-title`
-        updateTextInput(session, "role-other", value = local.rv$`role-other`)
+    })
+    
+    # * Contact ----
+    mail.pattern <- main.env$PATTERNS$email
+    
+    observeEvent(input$organizationName, {
+      local.rv$organizationName <- input$organizationName
+    })
+    
+    observeEvent(input$electronicMailAddress, {
+      local.rv$electronicMailAddress <- if (grepl(mail.pattern, input$electronicMailAddress)) {
+        input$electronicMailAddress
       }
+    })
+    
+    # * (ORCID) Personnel identification ----
+    orcid.pattern <- main.env$PATTERNS$ORCID
+    
+    observeEvent(input$userId, {
+      req(input$userId)
+      local.rv$userId <- input$userId
       
-      # email
-      orcid.info$email <- rorcid::orcid_email(orcid)[[orcid]]$email
-      if (isTruthy(unlist(orcid.info$email$email))) {
-        local.rv$electronicMailAddress <- orcid.info$email$email
-        updateTextInput(session, "electronicMailAddress", value = local.rv$electronicMailAddress)
+      if (grepl(orcid.pattern, input$userId)) {
+        local.rv$userId <- stringr::str_extract(local.rv$userId, orcid.pattern)
+        updateTextInput(
+          session = session,
+          inputId = "userId",
+          value = local.rv$userId
+        )
       }
       
-      # fundings
-      if (local.rv$role == "PI (principal investigator)") {
-        orcid.info$fundings <- rorcid::orcid_fundings(orcid)[[orcid]]$group$`funding-summary`[[1]]
-        if (isTruthy(unlist(orcid.info$fundings$`title.title.value`))) {
-          local.rv$projectTitle <- orcid.info$fundings$`title.title.value`
-          updateTextInput(session, "projectTitle", value = local.rv$projectTitle)
+      orcid.connect <- try(
+        rorcid::as.orcid(
+          local.rv$userId #TODO ORCID auth % snake
+        )
+      )
+      
+      if (
+        grepl(orcid.pattern, input$userId) &&
+          isTruthy(orcid.connect)
+      ) {
+        orcid <- local.rv$userId
+        orcid.info <- list()
+        
+        # names
+        orcid.info$names <- rorcid::orcid_person(orcid)[[orcid]]$name
+        if (isTruthy(unlist(orcid.info$names$`given-names`$value))) {
+          local.rv$givenName <- orcid.info$names$`given-names`$value
+          updateTextInput(session, "givenName", value = local.rv$givenName)
         }
-        if (isTruthy(unlist(orcid.info$fundings$`organization.name`))) {
-          local.rv$fundingAgency <- orcid.info$fundings$`organization.name`
-          updateTextInput(session, "fundingAgency", value = local.rv$fundingAgency)
+        if (isTruthy(unlist(orcid.info$names$`family-name`$value))) {
+          local.rv$surName <- orcid.info$names$`family-name`$value
+          updateTextInput(session, "surName", value = local.rv$surName)
         }
-        if (isTruthy(unlist(orcid.info$fundings$`put-code`))) {
-          local.rv$fundingNumber <- orcid.info$fundings$`put-code`
-          updateTextInput(session, "fundingNumber", value = local.rv$fundingNumber)
+        
+        # organization
+        orcid.info$employment <- rorcid::orcid_employments(orcid)[[orcid]]$`affiliation-group`$summaries[[1]]
+        if (isTruthy(unlist(orcid.info$employment$`employment-summary.organization.name`))) {
+          local.rv$organizationName <- orcid.info$employment$`employment-summary.organization.name`
+          updateTextInput(session, "organizationName", value = local.rv$organizationName)
         }
+        if (is.null(role) &&
+            isTruthy(unlist(orcid.info$employment$`employment-summary.role-title`))) {
+          local.rv$role <- "(other)"
+          updateTextInput(session, "role", value = local.rv$role)
+          local.rv$`role-other` <- orcid.info$employment$`employment-summary.role-title`
+          updateTextInput(session, "role-other", value = local.rv$`role-other`)
+        }
+        
+        # email
+        orcid.info$email <- rorcid::orcid_email(orcid)[[orcid]]$email
+        if (isTruthy(unlist(orcid.info$email$email))) {
+          local.rv$electronicMailAddress <- orcid.info$email$email
+          updateTextInput(session, "electronicMailAddress", value = local.rv$electronicMailAddress)
+        }
+        
+        # fundings
+        if (local.rv$role == "PI (principal investigator)") {
+          orcid.info$fundings <- rorcid::orcid_fundings(orcid)[[orcid]]$group$`funding-summary`[[1]]
+          if (isTruthy(unlist(orcid.info$fundings$`title.title.value`))) {
+            local.rv$projectTitle <- orcid.info$fundings$`title.title.value`
+            updateTextInput(session, "projectTitle", value = local.rv$projectTitle)
+          }
+          if (isTruthy(unlist(orcid.info$fundings$`organization.name`))) {
+            local.rv$fundingAgency <- orcid.info$fundings$`organization.name`
+            updateTextInput(session, "fundingAgency", value = local.rv$fundingAgency)
+          }
+          if (isTruthy(unlist(orcid.info$fundings$`put-code`))) {
+            local.rv$fundingNumber <- orcid.info$fundings$`put-code`
+            updateTextInput(session, "fundingNumber", value = local.rv$fundingNumber)
+          }
+        }
+      } else {
+        showNotification(
+          id = NS(id, "invalid_userid"),
+          "Input 'userId' is not a valid ORCID.",
+          type = "warning"
+        )
       }
-    } else {
-      showNotification(
-        id = NS(id, "invalid_userid"),
-        "Input 'userId' is not a valid ORCID.",
-        type = "warning"
+    })
+    
+    # * Project information ----
+    if (is.null(role)) {
+      observeEvent(
+        {
+          input$role
+          input$`role-other`
+        },
+        {
+          # custom role
+          if (input$role == "(other)") {
+            shinyjs::show("role-other")
+            local.rv$role <- input$`role-other`
+          } else {
+            shinyjs::hide("role-other")
+            local.rv$role <- input$role
+          }
+          # project
+          if (input$role == "PI (principal investigator)") {
+            shinyjs::show("projectTitle")
+            shinyjs::show("fundingAgency")
+            shinyjs::show("fundingNumber")
+          } else {
+            shinyjs::hide("projectTitle")
+            shinyjs::hide("fundingAgency")
+            shinyjs::hide("fundingNumber")
+          }
+        },
+        ignoreInit = FALSE
       )
-    }
-  })
-  
-  # * Project information ----
-  if (is.null(role)) {
-    observeEvent(
-      {
-        input$role
-        input$`role-other`
-      },
-      {
-        # custom role
-        if (input$role == "(other)") {
-          shinyjs::show("role-other")
-          local.rv$role <- input$`role-other`
-        } else {
-          shinyjs::hide("role-other")
-          local.rv$role <- input$role
+      
+      observeEvent(input$projectTitle, {
+        if (input$role == "PI (principal investigator)") {
+          local.rv$projectTitle <- input$projectTitle
+        }
+      })
+      
+      observeEvent(input$fundingAgency, {
+        if (input$role == "PI (principal investigator)") {
+          local.rv$fundingAgency <- input$fundingAgency
         }
-        # project
+      })
+      
+      observeEvent(input$fundingNumber, {
         if (input$role == "PI (principal investigator)") {
-          shinyjs::show("projectTitle")
-          shinyjs::show("fundingAgency")
-          shinyjs::show("fundingNumber")
-        } else {
-          shinyjs::hide("projectTitle")
-          shinyjs::hide("fundingAgency")
-          shinyjs::hide("fundingNumber")
+          local.rv$fundingNumber <- input$fundingNumber
         }
-      },
-      ignoreInit = FALSE
-    )
+      })
+    } else {
+      local.rv$role <- role
+      local.rv$projectTitle <- ""
+      local.rv$fundingAgency <- ""
+      local.rv$fundingNumber <- ""
+    }
     
-    observeEvent(input$projectTitle, {
-      if (input$role == "PI (principal investigator)") {
-        local.rv$projectTitle <- input$projectTitle
+    # Metadata save ----
+    observe({
+      req(
+        !is.null(role) ||
+          (any(grepl(rmv.id, names(input))) &&
+              input[[rmv.id]] < 1)
+      )
+      personnel <- isolate(rv$Personnel)
+      # Fetch correct index
+      ind <- if (ref %in% personnel$id) {
+        match(ref, personnel$id) # find its index
       }
-    })
-    
-    observeEvent(input$fundingAgency, {
-      if (input$role == "PI (principal investigator)") {
-        local.rv$fundingAgency <- input$fundingAgency
+      else {
+        dim(personnel)[1] + 1
       }
+      
+      # print values into rv at selected index
+      .values <- printReactiveValues(local.rv)
+      .values <- .values[colnames(personnel)]
+      .values[which(!sapply(.values, isTruthy))] <- ""
+      isolate(rv$Personnel[ind, ] <- .values)
     })
     
-    observeEvent(input$fundingNumber, {
-      if (input$role == "PI (principal investigator)") {
-        local.rv$fundingNumber <- input$fundingNumber
-      }
-    })
-  } else {
-    local.rv$role <- role
-    local.rv$projectTitle <- ""
-    local.rv$fundingAgency <- ""
-    local.rv$fundingNumber <- ""
-  }
-  
-  # Metadata save ----
-  observe({
-    req(
-      !is.null(role) ||
-        (any(grepl(rmv.id, names(input))) &&
-            input[[rmv.id]] < 1)
-    )
-    personnel <- isolate(rv$Personnel)
-    # Fetch correct index
-    ind <- if (ref %in% personnel$id) {
-      match(ref, personnel$id) # find its index
-    }
-    else {
-      dim(personnel)[1] + 1
+    # Remove UI ----
+    if (is.null(role)) {
+      observeEvent(input$rmv.id, {
+        # unload the RV
+        ind <- match(ref, rv$Personnel$id)
+        rv$Personnel <- rv$Personnel %>% slice(-ind)
+        
+        # remove the UI
+        removeUI(selector = paste0("#", site.id), immediate = TRUE)
+      })
     }
     
-    # print values into rv at selected index
-    .values <- printReactiveValues(local.rv)
-    .values <- .values[colnames(personnel)]
-    .values[which(!sapply(.values, isTruthy))] <- ""
-    isolate(rv$Personnel[ind, ] <- .values)
+    # Output ----
+    return(rv)
   })
-  
-  # Remove UI ----
-  if (is.null(role)) {
-    observeEvent(input$rmv.id, {
-      # unload the RV
-      ind <- match(ref, rv$Personnel$id)
-      rv$Personnel <- rv$Personnel %>% slice(-ind)
-      
-      # remove the UI
-      removeUI(selector = paste0("#", site.id), immediate = TRUE)
-    })
-  }
-  
-  # Output ----
-  return(rv)
 }
diff --git a/R/eal_8_misc.R b/R/eal_8_misc.R
index 74814a4..af97f6c 100644
--- a/R/eal_8_misc.R
+++ b/R/eal_8_misc.R
@@ -210,7 +210,7 @@ Misc <- function(id, main.env) {
             .val <- rv$keywords$keyword.thesaurus[kid]
             
             textInput(
-              ns(paste0("thesaurus-for-", keyword)),
+              NS(id, paste0("thesaurus-for-", keyword)),
               keyword,
               value = if (isTruthy(.val)) .val else ""
             )
diff --git a/R/eal_8_miscellaneous.R b/R/eal_8_miscellaneous.R
index bb5039f..005ef21 100644
--- a/R/eal_8_miscellaneous.R
+++ b/R/eal_8_miscellaneous.R
@@ -3,7 +3,7 @@
 #' 
 #' @noRd
 MiscellaneousUI <- function(id, help.label = NULL, value = "") {
-
+  
   fluidRow(
     # file selection
     column(
@@ -41,45 +41,44 @@ MiscellaneousUI <- function(id, help.label = NULL, value = "") {
 #' @importFrom shinyAce updateAceEditor
 #' 
 #' @noRd
-Miscellaneous <- function(input, output, session, save.variable, rv) {
-  # Variable initialization ----
-  ns <- session$ns
-
-  # Get content ----
-  rv$content <- markdownInput("content", preview = FALSE)
-
-  # Get file ----
-  observeEvent(input$file,
-    {
-      req(input$file)
-      rv$file <- input$file$datapath
-    },
-    priority = 1
-  )
-
-  observeEvent(input$file,
-    {
-      req(
-        isTruthy(input$file) ||
-          isTruthy(names(input))
-      )
-      updateAceEditor(
-        session,
-        "content-md",
-        value = readPlainText(rv$file)
-      )
-    },
-    priority = 0
-  )
-
-  # UI Verbose
-  output$selected <- renderText({
-    paste(
-      basename(rv$file),
-      "\n(in:", dirname(rv$file), ")"
+Miscellaneous <- function(id){
+  moduleServer(id, function(id, input, output, session, save.variable, rv) {
+    # Get content ----
+    rv$content <- markdownInput("content", preview = FALSE)
+    
+    # Get file ----
+    observeEvent(input$file,
+      {
+        req(input$file)
+        rv$file <- input$file$datapath
+      },
+      priority = 1
+    )
+    
+    observeEvent(input$file,
+      {
+        req(
+          isTruthy(input$file) ||
+            isTruthy(names(input))
+        )
+        updateAceEditor(
+          session,
+          "content-md",
+          value = readPlainText(rv$file)
+        )
+      },
+      priority = 0
     )
+    
+    # UI Verbose
+    output$selected <- renderText({
+      paste(
+        basename(rv$file),
+        "\n(in:", dirname(rv$file), ")"
+      )
+    })
+    
+    # Output ----
+    return(rv)
   })
-
-  # Output ----
-  return(rv)
 }
diff --git a/R/fill-module.R b/R/fill-module.R
index 8643994..e190673 100644
--- a/R/fill-module.R
+++ b/R/fill-module.R
@@ -36,7 +36,6 @@ fill <- function(id, main.env){
     steps <- isolate(main.env$VALUES$steps)
     
     # Wizard  ====
-    
     # pages change
     pagesServer(NS(id, "wizard"), steps)
     
@@ -50,9 +49,10 @@ fill <- function(id, main.env){
     Personnel("Personnel", main.env)
     Misc("Misc", main.env)
     MakeEML("MakeEML", main.env)
+  message(NS(id, "machin"))
     
-    # Navigation ----
     observeEvent(.EAL$page, {
+      # * Navigation ====
       # set EAL variables
       if(identical(.EAL$history, character())){
         .EAL$history <- main.env$VALUES$steps[1:.EAL$page]
@@ -100,11 +100,11 @@ fill <- function(id, main.env){
       
       updateTabsetPanel(session, "wizard", selected = steps[to])
       
-      # Modules helper ----
-      NSB$help <- modalDialog(
+      # * Helps ====
+      EAL$help <- modalDialog(
         title = paste0(.EAL$current, " - Help"),
         switch(.EAL$page,
-          # SelectDP
+          # ** SelectDP ====
           tagList(
             tags$p("This module allows you to manage your", tags$strong("data packages"), ".
             A data package (aka DP) is a collection of a dataset and its associated metadata
@@ -126,7 +126,7 @@ fill <- function(id, main.env){
             fields in further steps. You still will be able to edit them at your 
             convenience.")
           ),
-          # Data Files
+          # ** Data Files ====
           tagList(
             tags$p("This module allows you to load data files from the dataset you want to
             describe. Once uploaded, you can set:"),
@@ -141,7 +141,7 @@ fill <- function(id, main.env){
             tags$p("Recommended size per file is around 1 Gb. Such files and heavier ones might slow down the
             app.")
           ),
-          # Attributes
+          # ** Attributes  ====
           tagList(
             tags$p("This module allows you to describe precisely each attribute of each file. Some of these metadata
             are guessed from the data files. Such fields are annoted with a star (*).
@@ -180,12 +180,12 @@ fill <- function(id, main.env){
               tags$li(tags$i("Unit description:"), "some additional notes about the unit, how to compute it.")
             )
           ),
-          # Catvars
+          # ** Catvars ====
           tagList(
             tags$p("This module allows you to detail the categorical variables (class \"categorical\" in Attributes).
             For each variable, you will be able to detail each of its value by a short description.")
           ),
-          # Geocov
+          # ** Geocov ====
           tagList(
             tags$p("This module allows you to define the geographic area in which the data have been produced. 
             You have the choice between two methods to define geographic coverage:"),
@@ -204,14 +204,14 @@ fill <- function(id, main.env){
               )
             )
           ),
-          # Taxcov
+          # ** Taxcov ====
           tagList(
             tags$p("This module allows you to define the taxonomical coverage of the study. You will be asked to 
             select columns among your files containing the species name. Also, let the app know if the taxonomic
             coverage shall be written with scientific, common or both names. At last, select at least one taxonomic
             authority among the ones suggested."),
           ),
-          # Personnel
+          # ** Personnel ====
           tagList(
             tags$p("This module allows you to get a full list of the people who contributed to the creation of 
             this dataset. The recommended best practice is to", tags$b("use the ORCID"), "of a person. With 
@@ -227,7 +227,7 @@ fill <- function(id, main.env){
               tags$li("Custom: as the list of roles is not exhaustive, feel free to add any role you consider important.")
             )
           ),
-          # Misc
+          # ** Misc ====
           tagList(
             tags$p("This module allows you to define the last details of your data package. Note that you can write
             some of these metadata using the markdown syntax. Here are brief descriptions of the fields:"),
@@ -245,7 +245,7 @@ fill <- function(id, main.env){
               from GBIF-EML).")
             )
           ),
-          # Make EML
+          # ** Make EML ====
           tagList(
             tags$p("Here we are (well done) ! This is the final step to write EML. Just click the button and let the magic happen. If an 
             error occurs, this will be displayed to the screen. In this case, do not hesitate to get in touch with the dev team."),
diff --git a/R/fill_pages.R b/R/fill_pages.R
index 95ff7fb..143d2ac 100644
--- a/R/fill_pages.R
+++ b/R/fill_pages.R
@@ -61,6 +61,7 @@ pagesUI <- function(id, parent.id, main.env){
             saveButton(id),
             if (i != 2) prevTabButton(id, i),
             if (i != .nb) nextTabButton(id, i),
+            uiOutput(NS(id,"tag.list")),
             tags$hr(),
             actionButton(NS(id, "help"), "Help", icon("question-circle"))
           )
@@ -80,7 +81,7 @@ pagesUI <- function(id, parent.id, main.env){
 
 #' @noRd
 #' 
-#' utility function for pages
+#' @import shiny
 changePage <- function(from, to) {
   observeEvent(input[[paste(from, to, sep = "_")]], {
     EAL$page <- EAL$page + to - from
@@ -101,10 +102,13 @@ pagesServer <- function(id, steps) {
     
     ids <- seq_along(steps)
     lapply(ids[-1], function(i) onQuit(i)) # modules
-    lapply(ids[-1], function(i) onSave(i)) # modules
+    # lapply(ids[-1], function(i) onSave(i)) # modules -- managed into modules
     lapply(ids[-1], function(i) changePage(i, i-1)) # observers
     lapply(ids[-length(steps)], function(i) changePage(i, i+1)) # observers
     
+    # * Side UI ====
+    output$tag.list <- renderUI(EAL$tag.list)
+    
     # * Chain ====
     # output$chain <- renderUI({
     #   validate(
@@ -189,6 +193,10 @@ pagesServer <- function(id, steps) {
     #         EAL$.prev <- EAL$.prev + 1
     #     })
     #   })
+    # * Helps ====
+    observeEvent(input$help, {
+      showModal(EAL$help)
+    })
   })
 }
 
@@ -300,17 +308,17 @@ saveButton <- function(id) {
 #'
 #' @import shiny
 #' @importFrom shinyjs onclick disable enable
-onSave <- function(id,  main.env){
-  moduleServer(id, function(input, output, session) {
-    observeEvent(input$save,
-      {
-        req(input$save)
-        NSB$SAVE <- NSB$SAVE + 1
-      },
-      label = "NSB save"
-    )
-  })
-}
+# onSave <- function(id,  main.env){
+#   moduleServer(id, function(input, output, session) {
+#     observeEvent(input$save,
+#       {
+#         req(input$save)
+#         NSB$SAVE <- NSB$SAVE + 1
+#       },
+#       label = "NSB save"
+#     )
+#   })
+# }
 
 # * Previous ====
 
diff --git a/R/headerScript.R b/R/header.R
similarity index 92%
rename from R/headerScript.R
rename to R/header.R
index 1ffec95..d598262 100644
--- a/R/headerScript.R
+++ b/R/header.R
@@ -1,12 +1,3 @@
-#' @description Misc preparations commands
-#'
-#' @noRd
-.headerScript <- function() {
-  rm(list = ls())
-  options(shiny.reactlog = TRUE)
-  addResourcePath("media", system.file("media/", package = "MetaShARK"))
-}
-
 #' @importFrom fs path_home
 #' @importFrom dataone listFormats CNode
 #' @import shiny
@@ -17,16 +8,32 @@
 #' @importFrom jsonlite serializeJSON unserializeJSON read_json write_json
 #'
 #' @noRd
-.globalScript <- function(dev = FALSE) {
+.globalScript <- function(
+  args = list(
+    dev = FALSE, 
+    wip = FALSE
+  )
+) {
   
   # Environment setup ====
   main.env <- new.env()
   
   assign(
     "dev",
-    is.logical(dev) && !is.null(dev),
+    isTRUE(args$dev),
+    main.env
+  )
+  assign(
+    "wip",
+    isTRUE(args$wip),
     main.env
   )
+  assign(
+    "reactlog",
+    isTRUE(args$reactlog),
+    main.env
+  )
+  
   
   # Paths====
   wwwPaths <- system.file("resources", package = "MetaShARK") %>%
@@ -164,6 +171,7 @@
       current = character(), # last of history
       completed = FALSE,  # is current page completed?
       tag.list = tagList(), # side HTML tags to display
+      help = character(),
       .next = 0,
       .prev = 0
     ), 
@@ -190,5 +198,9 @@
   )
   
   # output ====
-  return(main.env)
+  shinyOptions(main.env = main.env)
+  shinyOptions(shiny.reactlog = main.env$reactlog)
+  addResourcePath("media", system.file("media/", package = "MetaShARK"))
+  # return(main.env)
+  return(NULL)
 }
diff --git a/R/runMetashark.R b/R/runMetashark.R
index 9460507..d925241 100644
--- a/R/runMetashark.R
+++ b/R/runMetashark.R
@@ -1,15 +1,17 @@
 #' @title Run MetaShARK
 #'
-#' @description Main function for launching the MetaShARK application.
+#' @description
+#' Main function for launching the MetaShARK application.
 #'
 #' @usage
-#' runMetaShark(...)
+#' runMetashark(...)
 #'
 #' @param ...
 #' options to pass to the application, ignored if missing or mistyped.
 #' \describe{
-#'   \item{wip}{logical. Shows WIP parts of the app.}
-#'   \item{dev}{logical. Add development elements in the GUI.}
+#'   \item{wip}{logical. Shows WIP parts of the app. (default to FALSE)}
+#'   \item{dev}{logical. Add development elements in the GUI. (default to FALSE)}
+#'   \item{reactlog}{logical. Use reactlog? (default to TRUE)}
 #' }
 #'
 #' @details
@@ -18,10 +20,12 @@
 #' metadata. It uses the EML standard (cf. NCEAS work) to allow a full and
 #' precise description of input datasets.
 #'
+#' @author
+#' Elie Arnaud <elie.arnaud@mnhn.fr>
+#'
 #' @examples
 #' # run this to launch MetaShARK
 #' runMetashark()
-#' @author Elie Arnaud <elie.arnaud@mnhn.fr>
 #'
 #' @export
 #' @import shiny
@@ -29,18 +33,17 @@
 runMetashark <- function(...) {
   args <- list(...)
   args$dev <- isTRUE(args$dev)
-  args$main.env <- .globalScript(args$dev)
+  args$wip <- isTRUE(args$wip)
+  args$reactlog <- if(is.null(args$reactlog)) TRUE else isTRUE(args$reactlog)
   
-  app <- golem::with_golem_options(
-    shinyApp(
-      ui = .app_ui,
-      server = .app_server,
-      onStart = .headerScript
-    ),
-    golem_opts = c(args)
-  )
-
-  runApp(
-    appDir = app
+  .globalScript(args = args)
+  
+  .app <- shinyApp(
+    ui = appUI,
+    server = appServer
   )
+  
+  browser()
+  
+  runApp(.app)
 }
diff --git a/R/server.R b/R/server.R
index 1e038ca..4e1801c 100644
--- a/R/server.R
+++ b/R/server.R
@@ -4,14 +4,10 @@
 #' @importFrom shinyjs onclick
 #'
 #' @noRd
-.app_server <- function(input, output, session) {
-
-  # get app arguments
-  app.args <- golem::get_golem_options()
-  main.env <- app.args$main.env
-
-  # initialize global variables
-  save.variable <- NULL
+appServer <- function(input, output, session) {
+  message("server")
+  # get variables
+  main.env <- getShinyOption("main.env")
 
   if (main.env$dev) {
     shinyjs::onclick("dev",
@@ -28,11 +24,10 @@
     updateTabItems(session, "side_menu", "settings")
   })
 
-  settings("settings", main.env)
-
   ## modules called ----
   fill("fill", main.env)
   upload("upload", main.env)
   documentation("documentation")
   about("about")
+  settings("settings", main.env)
 }
diff --git a/R/ui.R b/R/ui.R
index 39a22bb..9d857d6 100644
--- a/R/ui.R
+++ b/R/ui.R
@@ -6,25 +6,23 @@
 #' @importFrom shinycssloaders withSpinner
 #'
 #' @noRd
-.app_ui <- function() {
-  
+appUI <- function() {
   # get app arguments
-  .app.args <- golem::get_golem_options()
-  dev <- .app.args$dev
-  main.env <- .app.args$main.env
-  wip <- .app.args$wip
+  main.env <- getShinyOption("main.env")
+  dev <- main.env$dev
+  wip <- main.env$wip
 
   # prepare variable
   .menu.width <- "250px"
 
-  # action
-  tagList(
+  # ui
+  fluidPage(
     includeCSS(system.file("app/www/styles.css", package = "MetaShARK")),
     shinyjs::useShinyjs(),
     # List the first level UI elements here
-    dashboardPage(
+    shinydashboard::dashboardPage(
       title = "MetaShARK",
-      dashboardHeader(
+      shinydashboard::dashboardHeader(
         tags$li(
           class = "dropdown", 
           actionLink("settings", "", icon("gear"))
@@ -37,26 +35,26 @@
         titleWidth = .menu.width
       ),
       ## Menus ----
-      dashboardSidebar(
-        sidebarMenu(
+      shinydashboard::dashboardSidebar(
+        shinydashboard::sidebarMenu(
           id = "side_menu",
-          menuItem("Welcome",
+          shinydashboard::menuItem("Welcome",
             tabName = "welcome",
             icon = icon("home")
           ),
-          menuItem("Fill in EML",
+          shinydashboard::menuItem("Fill in EML",
             tabName = "fill",
             icon = icon("file-import")
           ),
-          menuItem("Upload EML",
+          shinydashboard::menuItem("Upload EML",
             tabName = "upload",
             icon = icon("file-export")
           ),
-          menuItem("EML Documentation",
+          shinydashboard::menuItem("EML Documentation",
             tabName = "documentation",
             icon = icon("glasses")
           ),
-          menuItem("About MetaShARK",
+          shinydashboard::menuItem("About MetaShARK",
             tabName = "about",
             icon = icon("beer")
           ),
@@ -66,44 +64,41 @@
               icon = icon("gear")
             )
           ),
-          if (isolate(main.env$dev)) {
-            actionButton(
-              "dev", "DEV CHECK"
-            )
-          }
+          if (isolate(main.env$dev))
+            actionButton("dev", "DEV CHECK")
         ),
         width = .menu.width
       ), # end sidebar
       ## Content ----
-      dashboardBody(
+      shinydashboard::dashboardBody(
         tags$script(HTML("$('body').addClass('fixed');")),
-        tabItems(
-          tabItem(
+        shinydashboard::tabItems(
+          shinydashboard::tabItem(
             tabName = "welcome",
             welcomeUI("welcome", wip=wip)
           ),
-          tabItem(
+          shinydashboard::tabItem(
             tabName = "fill",
             fillUI("fill", main.env)
           ),
-          tabItem(
+          shinydashboard::tabItem(
             tabName = "upload",
             uploadUI("upload", main.env)
           ),
-          tabItem(
+          shinydashboard::tabItem(
             tabName = "documentation",
             docUI("documentation")
           ),
-          tabItem(
+          shinydashboard::tabItem(
             tabName = "about",
             aboutUI("about")
           ),
-          tabItem(
+          shinydashboard::tabItem(
             tabName = "settings",
-            settingsUI("settings", wip)
+            settingsUI("settings", wip=wip)
           )
         )
       )
     ) # end dashboard
-  ) # end taglist
+  ) # end fluidPage
 }
diff --git a/man/runMetashark.Rd b/man/runMetashark.Rd
index f3fcb40..d36027e 100644
--- a/man/runMetashark.Rd
+++ b/man/runMetashark.Rd
@@ -4,13 +4,14 @@
 \alias{runMetashark}
 \title{Run MetaShARK}
 \usage{
-runMetaShark(...)
+runMetashark(...)
 }
 \arguments{
 \item{...}{options to pass to the application, ignored if missing or mistyped.
 \describe{
-  \item{wip}{logical. Shows WIP parts of the app.}
-  \item{dev}{logical. Add development elements in the GUI.}
+  \item{wip}{logical. Shows WIP parts of the app. (default to FALSE)}
+  \item{dev}{logical. Add development elements in the GUI. (default to FALSE)}
+  \item{reactlog}{logical. Use reactlog? (default to TRUE)}
 }}
 }
 \description{
@@ -25,6 +26,7 @@ precise description of input datasets.
 \examples{
 # run this to launch MetaShARK
 runMetashark()
+
 }
 \author{
 Elie Arnaud <elie.arnaud@mnhn.fr>