--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/map_geographical_coverage.R	Tue Oct 15 20:33:32 2024 +0000
@@ -0,0 +1,64 @@
+#From https://github.com/TanguyGen/metaCure/blob/main/R/eml_down.R
+#Modified by Seguineau Pauline (2024-10-15)
+library(dplyr)
+library(xslt)
+library(xml2)
+library(mapview)
+library(leaflet)
+
+args = commandArgs(trailingOnly=TRUE) 
+if (length(args)==0)
+{
+    stop("This tool needs at least one argument")
+}else{
+    data <- args[1]
+}
+
+#' map_geographical_coverage
+#'Make a map from EML
+#' @param eml Metadata using EML standard in XML format
+#'
+#' @return A map
+#' @export
+
+map_geographical_coverage <- function(eml){
+  name <- xml2::xml_find_all(eml, "//geographicCoverage/geographicDescription")
+  name <- unlist(xml2::as_list(name))
+
+  west <- xml2::xml_find_all(eml, "//geographicCoverage/boundingCoordinates/westBoundingCoordinate")
+  west <- as.numeric(unlist(xml2::as_list(west)))
+
+  east <- xml2::xml_find_all(eml, "//geographicCoverage/boundingCoordinates/eastBoundingCoordinate")
+  east <- as.numeric(unlist(xml2::as_list(east)))
+
+  north <- xml2::xml_find_all(eml, "//geographicCoverage/boundingCoordinates/northBoundingCoordinate")
+  north <- as.numeric(unlist(xml2::as_list(north)))
+
+  south <- xml2::xml_find_all(eml, "//geographicCoverage/boundingCoordinates/southBoundingCoordinate")
+  south <- as.numeric(unlist(xml2::as_list(south)))
+
+  geo_info <- data.frame(name = name, west = west, east = east, south = south, north = north)
+
+  map <- leaflet(geo_info) %>%
+         addProviderTiles("CartoDB.Positron")  
+  
+  for (i in 1:nrow(geo_info)) {
+    if (geo_info$west[i]==geo_info$east[i] && geo_info$south[i]==geo_info$north[i]){
+      map <- map %>% addCircles(lng = geo_info$west[i] , lat= geo_info$south[i], fillColor = "transparent" ) %>% addScaleBar()}
+   
+     else if(geo_info$west[i]!=geo_info$east[i] && geo_info$south[i]!=geo_info$north[i]){
+      map <- map %>% addRectangles(lng1 = geo_info$west[i], lat1 = geo_info$south[i], 
+                                   lng2 = geo_info$east[i], lat2 = geo_info$north[i], fillColor = "transparent") %>% addScaleBar()}
+    }
+   mapview::mapshot(map, file = "map.png",remove_controls = c("zoomControl", "layersControl", "homeButton","drawToolbar", "easyButton"))
+}
+
+doc <- read_xml(data)
+
+if (is.na(xml2::xml_find_first(doc, "//geographicCoverage"))){
+   mes = "No geographic coverage found, skipping geographic coverage step."
+   mes
+}else{
+ map_geographical_coverage(doc)
+}
+