RMD check passing

DESCRIPTION

@@ -15,11 +15,15 @@ Depends:
     R (>= 4.2)
 Imports: 
     arrow,
+    DBI,
+    RSQLite,
     dplyr,
     glue,
     jsonlite,
     nhdplusTools,
     sf
+Suggests:
+    testthat
 License: GPL (>= 3)
 Encoding: UTF-8
 LazyData: true

R/find_origin.R

@@ -22,6 +22,8 @@ findOrigin <- function(
   nldi_feature = NULL,
   xy = NULL
 ) {
+
+  hf_id <- hydroseq <- poi_id <- toid <- topo <- vpuid <- NULL
   # Capture arguments
   .args <- c(as.list(environment()))
 
@@ -98,6 +100,7 @@ findOriginQuery.hf_id <- function(id, network, ...) {
 #' @method findOriginQuery comid
 #' @keywords internal
 findOriginQuery.comid <- function(comid, network, ...) {
+  hf_id <- NULL
   arrow::open_dataset(network) |>
     dplyr::filter(hf_id == !!comid)
 }

R/find_origin_gpkg.R

@@ -1,5 +1,5 @@
 #' Find Origin From ID
-#' @param network a URI to a network-formatted Arrow dataset
+#' @param gpkg a local geopackages file path
 #' @inheritParams get_subset
 #' @return data.frame
 #' @export
@@ -13,6 +13,8 @@ findOriginGPKG <- function(
     nldi_feature = NULL,
     xy = NULL
 ) {
+
+  hf_id <- hydroseq <- poi_id <- toid <- topo <- vpuid <- NULL
   # Capture arguments
   .args <- c(as.list(environment()))
 
@@ -56,7 +58,7 @@ findOriginGPKG <- function(
 
 
 #' S3 method for dispatching on query type
-#' @return Arrow Table/Deferred connection
+#' @return SQLite connection
 #' @keywords internal
 findOriginQueryGPKG <- function(id, gpkg, ...) {
   if (!inherits(gpkg, "character")) {
@@ -89,6 +91,7 @@ findOriginQueryGPKG.hf_id <- function(id, gpkg, ...) {
 #' @method findOriginQuery comid
 #' @keywords internal
 findOriginQueryGPKG.comid <- function(comid, gpkg, ...) {
+  hf_id <- NULL
   as_sqlite(gpkg, "network") |>
     dplyr::filter(hf_id == !!comid)
 }

R/get_subset.R

@@ -1,13 +1,17 @@
 na.omit = function(x){ x[!is.na(x)] }
 
 #' Extract Data from Arrow Stores
-#' @inheritParams get_subset
 #' @param hook a local or s3 hydrofabric directory
+#' @param vpu an optional VPU to quicken search
+#' @param ids all identifiers to extract
+#' @param lyrs hydrofabric layers to subset
+#' @param outfile a path to write resulting geopackage
 #' @return list or file path
 #' @export
 
 extract_arrow_data = function(hook, vpu, ids, lyrs, outfile = NULL){
 
+  vpuid <- poi_id <-  NULL
   hydrofabric = list()
 
   for(i in 1:length(lyrs)){
@@ -58,13 +62,17 @@ extract_arrow_data = function(hook, vpu, ids, lyrs, outfile = NULL){
 
 
 #' Extract Data from Arrow Stores
-#' @inheritParams get_subset
-#' @param hook a local or s3 hydrofabric directory
+#' @param gpkg a local gpkg file
+#' @param vpu an optional VPU to quicken search
+#' @param ids all identifiers to extract
+#' @param lyrs hydrofabric layers to subset
+#' @param outfile a path to write resulting geopackage
 #' @return list or file path
 #' @export
 
 extract_gpkg_data = function(gpkg, vpu, ids, lyrs, outfile = NULL){
 
+  vpuid <- poi_id <-  NULL
   hydrofabric = list()
 
   for(i in 1:length(lyrs)){
@@ -114,7 +122,6 @@ extract_gpkg_data = function(gpkg, vpu, ids, lyrs, outfile = NULL){
 }
 
 
-
 #' @title Build a hydrofabric subset
 #' @param id hydrofabric id. datatype: string / vector of strings e.g., 'wb-10026' or c('wb-10026', 'wb-10355') 
 #' @param comid NHDPlusV2 COMID. datatype: int / vector of int e.g., 61297116 or c(61297116 , 6129261) 
@@ -125,6 +132,7 @@ extract_gpkg_data = function(gpkg, vpu, ids, lyrs, outfile = NULL){
 #' @param type hydrofabric type
 #' @param hf_version hydrofabric version
 #' @param source hydrofabric source (local root directory or s3 link)
+#' @param gpkg a local gpkg file
 #' @param outfile If gpkg file path is provided, data will be written to a file.
 #' @param lyrs layers to extract
 #' @param domain hydrofabric domain
@@ -163,6 +171,7 @@ get_subset = function(id           = NULL,
     }
   }
 
+  hf_id <- vpuid <-  NULL
   hook      <- glue("{source}/v{hf_version}/{type}/{domain}")
 
   if(!is.null(gpkg)){

tests/testthat/test-origin.R

@@ -1,6 +1,11 @@
 #x network  <- '/Users/mjohnson/hydrofabric/v2.2/reference/conus_network'
 network  <- 's3://lynker-spatial/hydrofabric/v2.2/reference/conus_network'
 
+test =  arrow %>% 
+  filter(hl_uri == "gages-06752260") %>% 
+  collect()
+
+
 test_that("Test ID", {
   ido = findOrigin(network, id = test$id)
   expect_equal(ido$id, 2899997)
@@ -46,8 +51,6 @@ test_that("Test XY", {
 #x network  <- '/Users/mjohnson/hydrofabric/v2.2/reference/conus_network'
 gpkg  <- conus_gpkg
 
-read_sf(ne)
-
 test =  as_sqlite(gpkg, "network") %>% 
   filter(hl_uri == "gages-06752260") %>% 
   collect()