81 lines
1.9 KiB
R
81 lines
1.9 KiB
R
# simpleobismapsCCP.R
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# Simple example for CCP integration
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#
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# Author: Giancarlo Panichi
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###############################################################################
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library(robis)
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library(ggplot2)
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library(rgeos)
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library(stringr)
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library(utils)
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createplot <- function(sname,usedPolygon){
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result = tryCatch({
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result=paste("/ccp_data/maps/",sname,".png",sep="")
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wktP <-readWKT(usedPolygon)
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print(wktP@bbox)
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#By scientific name and geometry
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y=occurrence(sname, geometry = usedPolygon)
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occplot<-map_ggplot(y, color = "#ff3399")+coord_sf(xlim = wktP@bbox[1,], ylim = wktP@bbox[2,])
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ggsave(result, plot = occplot)
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}, warning = function(w) {
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print(w)
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}, error = function(e) {
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print(e)
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}, finally = {
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print(paste(sname,"done.", sep=" "))
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})
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}
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readfile <- function(filename, usedPolygon) {
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con = file(filename, "r")
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while ( TRUE ) {
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line = readLines(con, n = 1)
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line = str_trim(line)
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if ( length(line) == 0 ) {
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break
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}
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print(line)
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createplot(line, usedPolygon)
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}
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close(con)
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}
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checkmapsfolder <- function(){
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if (!dir.exists("/ccp_data/maps")){
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dir.create("/ccp_data/maps")
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}else{
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print("maps dir exists")
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}
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}
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#url="https://data.d4science.net/Y8WK"
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#usedPolygon="POLYGON((-5.657713322217344 45.88175260533238,38.99072417778265 45.88175260533238,38.99072417778265 29.60135866020714,-5.657713322217344 29.60135866020714,-5.657713322217344 45.88175260533238))"
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main <- function(){
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args = commandArgs(trailingOnly=TRUE)
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print(args)
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if (length(args)<=1) {
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stop("At least two arguments must be supplied", call.=FALSE)
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}
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filename="fishScientificName.csv"
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url=args[1]
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usedPolygon=args[2]
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mapszip="/ccp_data/maps.zip"
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download.file(url, filename)
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checkmapsfolder()
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readfile(filename,usedPolygon)
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zip(zipfile = mapszip, files = "/ccp_data/maps")
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unlink("/ccp_data/maps",recursive = TRUE)
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}
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main()
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