fix #234 fix ecoengine bug in bbox usage

use wellknown instead of wicket for doing wkt manipulation #235

Author: sckott

DESCRIPTION

@@ -8,7 +8,7 @@ Description: A programmatic interface to many species occurrence data sources,
     System ('OBIS'), and Atlas of Living Australia ('ALA'). Includes
     functionality for retrieving species occurrence data, and combining
     those data.
-Version: 1.1.0
+Version: 1.1.1.91
 License: MIT + file LICENSE
 Authors@R: 
     c(person(given = "Scott", family = "Chamberlain",
@@ -40,13 +40,14 @@ Imports:
     jsonlite (>= 1.4),
     data.table (>= 1.9.6),
     tibble (>= 1.2),
-    wicket (>= 0.4.0)
+    wellknown
 Suggests:
     testthat,
     knitr,
     rmarkdown,
     taxize (>= 0.8.4),
     vcr
+Remotes: ropensci/wellknown
 RoxygenNote: 7.1.1
 X-schema.org-applicationCategory: Biodiversity
 X-schema.org-keywords: specimens, API, web-services, occurrences, species, taxonomy, GBIF, INAT, BISON, Vertnet, eBird, Ecoengine, iDigBio, OBIS, ALA

R/handle_sp.R

@@ -33,7 +33,6 @@
 # row.names=row.names(sppoly)))
 # handle_sp(sppoly_df)
 # handle_sp(sppoly_df, group = FALSE)[[1]]
-
-handle_sp <- function(spobj, group = TRUE) { # nocov start
-  wicket::sp_convert(spobj, group = group)
-} # nocov end
+# handle_sp <- function(spobj, group = TRUE) { # nocov start
+#   wicket::sp_convert(spobj, group = group)
+# } # nocov end

R/occ_funs.R

@@ -145,7 +145,8 @@ strip_classes <- function(x, z) {
 occ_geom <- function(x) {
   if (!is.null(x)) {
     if (inherits(x, c('SpatialPolygons', 'SpatialPolygonsDataFrame'))) {
-      x <- as.list(handle_sp(x))
+      # x <- as.list(handle_sp(x))
+      stop("'sp' classes no longer supported; convert to sf")
     }
     if (inherits(x, c('sf', 'sfc', 'sfg', 'POLYGON', 'MULTIPOLYGON'))) {
       x <- strip_classes(x, c("XY", "data.frame", "sfc_POLYGON"))

R/plugins.r

@@ -116,7 +116,7 @@ foo_ecoengine <- function(sources, query, limit, page, geometry, has_coords,
                                               collapse = " "))) {
         paste0(wkt2bbox(geometry), collapse = ",")
       } else {
-        geometry
+        paste0(geometry, collapse = ",")
       }
     }
     if (!is.null(date)) {

R/wkt_bbox.R

@@ -55,10 +55,10 @@ bbox2wkt <- function(minx=NA, miny=NA, maxx=NA, maxy=NA, bbox=NULL) {
   )
 }
 
-#' @param wkt A Well Known Text object.
+#' @param wkt A Well Known Text string
 #' @export
 #' @family bbox
 #' @rdname bbox2wkt
-wkt2bbox <- function(wkt){
-  wicket::wkt_bounding(wkt)
+wkt2bbox <- function(wkt) {
+  wellknown::wkt_bounding(wkt)
 }

R/wkt_vis.r

@@ -36,8 +36,10 @@ wkt_vis <- function(x, zoom = 6, maptype = "terrain", browse = TRUE) {
   stopifnot(!is.null(x))
   stopifnot(is.character(x))
   x <- gsub("\n|\n\\s+", "", strtrim(x))
-  out <- wicket::wkt_coords(x)
-  centroid <- wicket::wkt_centroid(x)
+  # out <- wicket::wkt_coords(x)
+  out <- wellknown::wkt_coords(x)
+  # centroid <- wicket::wkt_centroid(x)
+  centroid <- wellknown::wkt_centroid(x)
   dfs <- unname(lapply(split(out, out$ring), function(z) {
     unname(
       apply(z, 1, function(x) {
@@ -66,8 +68,9 @@ map_header <- '
 <meta charset=utf-8 />
 <title>spocc WKT Viewer</title>
 <meta name="viewport" content="initial-scale=1,maximum-scale=1,user-scalable=no" />
-<script src="https://api.tiles.mapbox.com/mapbox.js/v3.0.1/mapbox.js"></script>
-<link href="https://api.tiles.mapbox.com/mapbox.js/v3.0.1/mapbox.css" rel="stylesheet" />
+<script src="https://api.mapbox.com/mapbox.js/v3.3.1/mapbox.js"></script>
+<link href="https://api.mapbox.com/mapbox.js/v3.3.1/mapbox.css" rel="stylesheet" />
+
 <style>
   body { margin:0; padding:0; }
   #map { position:absolute; top:0; bottom:0; width:100%; }

man-roxygen/occ_egs.R

@@ -113,7 +113,7 @@
 #' occ(query='Accipiter striatus', from='gbif', geometry=c(-125.0,38.4,-121.8,40.9))
 #'
 #' ## Bounding box constraint with ecoengine
-#' ## Use this website: http://boundingbox.klokantech.com/ to quickly grab a bbox.
+#' ## Use this website: https://boundingbox.klokantech.com/ to quickly grab a bbox.
 #' ## Just set the format on the bottom left to CSV.
 #' occ(query='Accipiter striatus', from='ecoengine', limit=10,
 #'    geometry=c(-125.0,38.4,-121.8,40.9))
@@ -186,32 +186,6 @@
 #' (ids <- get_tsn('Accipiter striatus'))
 #' occ(ids = ids, from='bison', limit=20)
 #'
-#' # SpatialPolygons/SpatialPolygonsDataFrame integration
-#' library("sp")
-#' ## Single polygon in SpatialPolygons class
-#' one <- Polygon(cbind(c(91,90,90,91), c(30,30,32,30)))
-#' spone = Polygons(list(one), "s1")
-#' sppoly = SpatialPolygons(list(spone), as.integer(1))
-#' out <- occ(geometry = sppoly, limit=50)
-#' out$gbif$data
-#'
-#' ## Two polygons in SpatialPolygons class
-#' one <- Polygon(cbind(c(-121.0,-117.9,-121.0,-121.0), c(39.4, 37.1, 35.1, 39.4)))
-#' two <- Polygon(cbind(c(-123.0,-121.2,-122.3,-124.5,-123.5,-124.1,-123.0),
-#'                      c(44.8,42.9,41.9,42.6,43.3,44.3,44.8)))
-#' spone = Polygons(list(one), "s1")
-#' sptwo = Polygons(list(two), "s2")
-#' sppoly = SpatialPolygons(list(spone, sptwo), 1:2)
-#' out <- occ(geometry = sppoly, limit=50)
-#' out$gbif$data
-#'
-#' ## Two polygons in SpatialPolygonsDataFrame class
-#' sppoly_df <- SpatialPolygonsDataFrame(sppoly, 
-#'    data.frame(a=c(1,2), b=c("a","b"), c=c(TRUE,FALSE),
-#'    row.names=row.names(sppoly)))
-#' out <- occ(geometry = sppoly_df, limit=50)
-#' out$gbif$data
-#' 
 #' ## sf classes
 #' library("sp")
 #' library("sf")
@@ -323,12 +297,9 @@
 #' res$obis
 #' 
 #' ## Pass in spatial classes
-#' library("sp")
-#' one <- Polygon(cbind(c(45,30,30,45), c(35,35,30,30)))
-#' spone = Polygons(list(one), "s1")
-#' sppoly = SpatialPolygons(list(spone), as.integer(1))
-#' (res <- occ(from = 'obis', geometry = sppoly, limit = 50))
-#' ## Do paging
+#' ## sp classes no longer supported
+#' 
+#' ## Paging
 #' (res1 <- occ(query = 'Mola mola', from = 'obis', limit = 10))
 #' occ_ids <- res1$obis$data$Mola_mola$id
 #' (res2 <- occ(query = 'Mola mola', from = 'obis',

man-roxygen/occtemp.r

@@ -13,8 +13,8 @@
 #' @param start,page (integer) Record to start at or page to start at. See `Paging` in
 #' Details for how these parameters are used internally. Optional
 #' @param geometry (character or nmeric) One of a Well Known Text (WKT) object, a vector of
-#' length 4 specifying a bounding box, an sp object (SpatialPolygons or SpatialPolygonsDataFrame),
-#' or an sf object (sfg, sfc, or sf). This parameter searches for occurrences inside a
+#' length 4 specifying a bounding box, or an sf object (sfg, sfc, or sf). This parameter
+#' searches for occurrences inside a
 #' polygon - converted to a polygon from whatever user input is given. A WKT shape written as
 #' `POLYGON((30.1 10.1, 20 40, 40 40, 30.1 10.1))` would be queried as is,
 #' i.e. http://bit.ly/HwUSif. See Details for more examples of WKT objects. The format of a