Merge pull request #204 from GEO-BON/BII_fix

cropped raster by country for viewer, added link to valid country nam…

scripts/BII/BIIZonalStats.R

@@ -42,18 +42,20 @@ for(i in 1:length(collections_items)){
                            srs.cube = "EPSG:4326", layers=NULL, variable=NULL, spatial.res=0.08,
                             t0 = NULL, t1 = NULL, temporal.res = "P1D", aggregation = "mean",  resampling = "near") # load cube from loacFromStacFun
 
+  summary(dat_cube)
+  dat_cube <-  filter_geom(cube=dat_cube, geom=study_area$geometry, srs="EPSG:4326")
+
 raster_layers[[i]] <- dat_cube # add to a list of raster layers
 names(raster_layers)[i] <- ci[2]
-
+print(names(raster_layers))
 if(input$summary_statistic == "Mean"){
 stats_each <- gdalcubes::extract_geom(cube=dat_cube, sf=study_area, FUN=mean, reduce_time=TRUE)
 } else if(input$summary_statistic == "Median"){
   stats_each <- gdalcubes::extract_geom(cube=dat_cube, sf=study_area, FUN=median, reduce_time=TRUE)
 } else {
   stats_each <- gdalcubes::extract_geom(cube=dat_cube, sf=study_area, FUN=mode, reduce_time=TRUE)}
 print(stats_each)
-#stats_each$name <- ci[2]
-#stats_each <- as.data.frame(stats_each)
+
 stats_layer <- data.frame(name=ci[2], statistic=stats_each[1,2])
 stats_list[[i]] <- stats_layer
 }

scripts/data/getBoundingBox.R

@@ -4,7 +4,8 @@ library("rjson")
 library("sf")
 
 input <- fromJSON(file=file.path(outputFolder, "input.json"))
-
+
+output<- tryCatch({
 # define study area
 if (is.null(input$studyarea_file)){ # if there is no study area file input
   if (is.null(input$state)){ # if there is only a country input (no state) 
@@ -19,7 +20,7 @@ if (is.null(input$studyarea_file)){ # if there is no study area file input
 study_area_polygon<- sf::st_read(study_area)  # load study area as sf object
 print(st_crs(study_area_polygon))
 if(nrow(study_area_polygon)==0){
-  stop("Study area polygon does not exist. Check spelling of country and state names. Check if region contains protected areas")
+  stop("Study area polygon does not exist. Check spelling of country and state names.")
 }  # stop if object is empty
 
 # Save study area and protected area data
@@ -34,8 +35,7 @@ bbox <- st_transform(study_area_polygon, st_crs(4326))
 bbox<-unname(st_bbox(study_area_polygon))
 
 output <- list("bbox" = bbox, "study_area_polygon" = study_area_polygon_path)
-print(output)
-
+}, error = function(e) { list(error = conditionMessage(e)) })
 ### return outpu
 jsonData <- toJSON(output, indent=2)
 write(jsonData, file.path(outputFolder,"output.json"))

scripts/data/getBoundingBox.yml

@@ -1,18 +1,18 @@
 script: getBoundingBox.R
 name: Get bounding box
-description: "Extract items and calculate zonal statistics from various collections on the GEO BON Stac Catalog."
+description: "Exrtact the bounding box of a country or region of interest."
 author:
   - name: Jory Griffith
     identifier: https://orcid.org/0000-0001-6020-6690
 inputs:
   country:
     label: Country
-    description: Country of interest
+    description: Country of interest. For list of countries look here https://geoio.biodiversite-quebec.ca/docs#/default/validate_country_name_validate_country_name_get.
     type: text
     example: Colombia
   state:
     label: State/Province
-    description: State or province of interest (leave blank if you want the full country)
+    description: State or province of interest (leave blank if you want the full country). For list of accepted region names look here https://geoio.biodiversite-quebec.ca/docs#/default/validate_state_name_validate_state_name_get. 
     type: text
     example: Putumayo
   study_area_file: