started harmo NCBI backbone

.gitignore

@@ -3,7 +3,7 @@ data/
 results/
 *-bkp/
 tmp/
-
+inst/data/
 
 ## Default R gitignore ---
 # History files

R/fct_dl_backbones.R

@@ -0,0 +1,18 @@
+
+
+
+## TEST
+path_bb <- "inst/data/backbones"
+
+# Read lines from NCBI data
+
+ncbi_url <- "https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump_archive/"
+
+ncbi_version <-  readLines(ncbi_url) |> stringr::str_extract('new\\_taxdump\\_2024\\-.[0-9]\\-.[0-9]') |> max(na.rm = T)
+
+dl_ncbi <- download.file(
+  url = paste0(ncbi_url, ncbi_version, ".zip"),
+  destfile = file.path(path_bb, paste0("NCBI-", ncbi_version, ".zip"))
+  )
+
+unzip(zipfile = file.path(path_bb, paste0("NCBI-", ncbi_version, ".zip")), exdir = path_bb)

R/mod_info_UI.R

@@ -9,9 +9,16 @@ mod_info_UI <- function(id){
   ns <- NS(id)
 
   ##
-  ## UI Elements ###############################################################
+  ## UI Content ################################################################
   ##
 
+  ## 4 cards
+  ## left width 4 and right width 8
+  ## right split top and bottom
+  ## right top split left 1/2 right 1/2
+
+
+  ## Left - Welcome -------------------------------------------------------------------
   card_left <- card(
     h1("Welcome"),
 
@@ -24,14 +31,14 @@ mod_info_UI <- function(id){
     ),
 
     p(
-      "you are using the package ", tags$code("speval"), "version: ",
+      "You are using the package ", tags$code("speval"), "version:",
       textOutput(outputId = ns("speval_version"), inline = TRUE), "."
     ),
 
     h4("What is ", tags$code("arena-helpers")),
     p(
       "This app is part of of a collection of tools designed to support Forest inventory related
-      activities and grouped under ", tags$code("arena-helpers")
+      activities and grouped under ", tags$code("arena-helpers"), "."
       ),
     br(),
     h4("Open Foris Arena ", tags$img(src="www/Arena-Logo.png", height = '30px')),
@@ -45,46 +52,71 @@ mod_info_UI <- function(id){
         .noWS = "before-end"
       ),
       " in particular support data analysis parts that cannot be embedded directly
-      to OF Arena "
+      to OF Arena."
     )
   )
 
-
-  ## Emission factors ----------------------------------------------------------
-  card_right_sub1 <- card(
-    p("Placeholder for content sub1"),
+  ## right top 1 - Instructions ------------------------------------------------
+  card_right_top1 <- card(
+    h5("Instructions"),
+    tags$ol(
+      tags$li('In the ', tags$b('Run Validation'), ' tab, upload a list of species name as a CSV file.'),
+      tags$li('The species names will be displayed and validation settings appear.'),
+      tags$li('Select the taxonomic backbones and the fuzzy matching functions.'),
+      tags$li('Select multicore to run the processes in parrallel (only useful if more than a few hundred names to validate).'),
+      tags$li('Select IUCN and follow instructions to add IUCN endangered species list to the analysis.')
+    ),
+  )
+  # It can be a one column file with header: "scientific_name"
+
+  ## right top 2 - Results -----------------------------------------------------
+  card_right_top2 <- card(
+    h5("Results"),
+    p("The app outputs a detailed table where the results of each backbone are given for each
+      species name with the fuzzy distance of the closest name found in the backbone, the
+      proposed accepted name and status of the input species if not an accepted name already."),
+    p("The apps also provides a table where a unique validated name is proposed for each input
+      species name. The selection process arbitrarily favors the Leipzig Catalogue of Vascular
+      Plants but should be crossed-checked carefully, especially if the proposed solution as a
+      low fuzzy score."),
+    p("Finally, the app provides a series of statistics on the valdiation process: number of
+      accepted names found, number of conflicts between taxonomic backbones, etc."
+    )
   )
 
-  card_right_sub2 <- card(
-    p("placeholder for content sub2")
+  ## Right bottom - Under the hood ---------------------------------------------
+  card_right_bot <- card(
+    h5("Under the hood"),
+    p("placeholder for more content")
   )
 
+  ## right top combine ---------------------------------------------------------
   card_right_top <- card(
-    card_header(bsicons::bs_icon("1-circle-fill", size = "1.5rem", class = "text-primary"), "Card right top"),
+    card_header(
+      h4(bsicons::bs_icon("1-circle-fill", size = "1.5rem", class = "text-primary"), "How to use the app")
+    ),
     layout_column_wrap(
       width = 1/2,
-      card_right_sub1,
-      card_right_sub2
+      card_right_top1,
+      card_right_top2
     )
   )
 
-  card_right_bot <- card(
-    p("placeholder for more content")
-  )
 
-  card_right <- card(
-    card_right_top,
-    card_right_bot
-  )
 
+  ##
+  ## UI elements order wrapped in a tagList() function #########################
+  ##
 
-  ## UI elements wrapped in a tagList() function
   tagList(
 
     layout_columns(
       col_widths = c(4, 8),
       card_left,
-      card_right
+      card(
+        card_right_top,
+        card_right_bot
+      )
     )
 
   ) ## END tagList