add test_request parameter for selected endpoints

.gitignore

@@ -5,3 +5,5 @@ BEDbaseR.Rproj
 .httr-oauth
 /doc/
 /Meta/
+
+.DS_Store

R/bedbaser.R

@@ -292,6 +292,7 @@ bb_example <- function(bedbase, rec_type = c("bed", "bedset")) {
 #' @param id integer(1) record or object identifier
 #' @param full logical(1) (default \code{FALSE}) include full record with
 #' stats, files, and metadata
+#' @param test_request boolean() (default \code{FALSE}) internal parameter for testing purposes
 #'
 #' @return list() metadata
 #'
@@ -305,15 +306,16 @@ bb_example <- function(bedbase, rec_type = c("bed", "bedset")) {
 #' bb_metadata(bedbase, ex_bedset$id)
 #'
 #' @export
-bb_metadata <- function(bedbase, id, full = FALSE) {
+bb_metadata <- function(bedbase, id, full = FALSE, test_request = FALSE) {
     rsp <- bedbase$get_bed_metadata_v1_bed__bed_id__metadata_get(
         bed_id = id,
         full = full
     )
     if (rsp$status_code != 200) {
         rsp <- bedbase$get_bedset_metadata_v1_bedset__bedset_id__metadata_get(
             bedset_id = id,
-            full = full
+            full = full,
+            test_request = test_request,
         )
     }
     result <- httr::content(rsp)
@@ -379,6 +381,7 @@ bb_list_beds <- function(bedbase, genome = NULL, bed_compliance = NULL,
 #' @param query character() (default \code{""}) keyword
 #' @param limit integer(1) (default \code{1000}) maximum records
 #' @param offset integer(1) (default \code{0}) page token of records
+#' @param test_request boolean() (default \code{FALSE}) internal parameter for testing purposes
 #'
 #' @return [tibble][tibble::tibble] of BEDset records
 #'
@@ -387,11 +390,12 @@ bb_list_beds <- function(bedbase, genome = NULL, bed_compliance = NULL,
 #' bb_list_bedsets(bedbase)
 #'
 #' @export
-bb_list_bedsets <- function(bedbase, query = "", limit = 1000, offset = 0) {
+bb_list_bedsets <- function(bedbase, query = "", limit = 1000, offset = 0, test_request = FALSE) {
     rsp <- bedbase$list_bedsets_v1_bedset_list_get(
         query = query,
         limit = limit,
-        offset = offset
+        offset = offset,
+        test_request = test_request
     )
     recs <- httr::content(rsp)
     results <- tibble::tibble()
@@ -460,6 +464,7 @@ bb_beds_in_bedset <- function(bedbase, bedset_id) {
 #' @param assay character() (default NULL) assay to search
 #' @param limit integer(1) (default \code{10}) maximum number of results
 #' @param offset integer(1) (default \code{0}) page offset of results
+#' @param test_request boolean() (default \code{FALSE}) internal parameter for testing purposes
 #'
 #' @return [tibble][tibble::tibble] of results
 #'
@@ -469,7 +474,7 @@ bb_beds_in_bedset <- function(bedbase, bedset_id) {
 #'
 #' @export
 bb_bed_text_search <- function(bedbase, query, genome = NULL, assay = NULL,
-                               limit = 10, offset = 0) {
+                               limit = 10, offset = 0, test_request = FALSE) {
     query <- utils::URLencode(query, reserved = TRUE)
     if (!is.null(genome))
         genome <- utils::URLencode(genome, reserved = TRUE)
@@ -480,7 +485,8 @@ bb_bed_text_search <- function(bedbase, query, genome = NULL, assay = NULL,
         genome = genome,
         assay = assay,
         limit = limit,
-        offset = offset
+        offset = offset,
+        test_request = test_request
     )
     recs <- httr::content(rsp)
     results <- tibble::tibble()

inst/service/bedbase/README.md

@@ -26,3 +26,15 @@ Convert openapi.json from OpenAPI 3.1 to 3.0:
 Convert from OpenAPI 3.0 to Swagger 2.0:
 
     api-spec-converter -f openapi_3 -t swagger_2 openapi_3_0.json > api.yaml
+
+### Development Note:
+
+The following endpoints take a hidden parameter `test_request` for internal testing purposes:
+
+- bed_metadata
+- bed_text_to_bed_search
+- bedset_metadata
+- bed_set_search
+- downloading files
+
+The `test_request` is TRUE, the request will not be counted in statistics. 

inst/service/bedbase/api.yaml

@@ -369,6 +369,13 @@
             "name": "offset",
             "required": false,
             "type": "integer"
+          },
+          {
+            "default": false,
+            "in": "query",
+            "name": "test_request",
+            "required": false,
+            "type": "boolean"
           }
         ],
         "responses": {
@@ -532,6 +539,13 @@
             "in": "query",
             "name": "full",
             "required": false
+          },
+          {
+            "default": false,
+            "in": "query",
+            "name": "test_request",
+            "required": false,
+            "type": "boolean"
           }
         ],
         "responses": {
@@ -1031,6 +1045,13 @@
             "name": "offset",
             "required": false,
             "type": "integer"
+          },
+          {
+            "default": false,
+            "in": "query",
+            "name": "test_request",
+            "required": false,
+            "type": "boolean"
           }
         ],
         "responses": {
@@ -1109,6 +1130,13 @@
             "name": "full",
             "required": false,
             "type": "boolean"
+          },
+          {
+            "default": false,
+            "in": "query",
+            "name": "test_request",
+            "required": false,
+            "type": "boolean"
           }
         ],
         "responses": {
@@ -1390,6 +1418,13 @@
             "name": "file_path",
             "required": true,
             "type": "string"
+          },
+          {
+            "default": false,
+            "in": "query",
+            "name": "test_request",
+            "required": false,
+            "type": "boolean"
           }
         ],
         "responses": {

tests/testthat/test-bedbaser.R

@@ -18,14 +18,14 @@ test_that("bb_example has 'bed_ids' given rec_type 'bedset'", {
 })
 
 test_that("bb_metadata returns metadata for BEDs", {
-    ex_metadata <- httr::content(bedbase$get_bed_metadata_v1_bed__bed_id__metadata_get(ex_bed$id, TRUE))
-    bed_metadata <- bb_metadata(bedbase, ex_bed$id, TRUE)
+    ex_metadata <- httr::content(bedbase$get_bed_metadata_v1_bed__bed_id__metadata_get(ex_bed$id, TRUE, test_request = TRUE))
+    bed_metadata <- bb_metadata(bedbase, ex_bed$id, TRUE, test_request = TRUE)
     expect_identical(ex_metadata, bed_metadata)
 })
 
 test_that("bb_metadata returns metadata for BEDsets", {
-    ex_bedset_metadata <- httr::content(bedbase$get_bedset_metadata_v1_bedset__bedset_id__metadata_get(ex_bedset$id, TRUE))
-    bedset_metadata <- bb_metadata(bedbase, ex_bedset$id, TRUE)
+    ex_bedset_metadata <- httr::content(bedbase$get_bedset_metadata_v1_bedset__bedset_id__metadata_get(ex_bedset$id, TRUE, test_request = TRUE))
+    bedset_metadata <- bb_metadata(bedbase, ex_bedset$id, TRUE, test_request = TRUE)
     expect_identical(ex_bedset_metadata, bedset_metadata)
 })
 
@@ -49,13 +49,14 @@ test_that("bb_list_beds returns same number of results for the mm39 genome", {
 test_that("bb_list_bedsets returns same number for query 'alzheimer'", {
     bedsets_raw <- httr::content(bedbase$list_bedsets_v1_bedset_list_get(
         query = "alzheimer",
-        limit = 5000
+        limit = 5000,
+        test_request = TRUE
     ))
     bedsets_names_bed_ids_list <- lapply(bedsets_raw$results, `[`, c("id", "bed_ids"))
     bedsets_from_raw <- dplyr::bind_rows(bedsets_names_bed_ids_list) |>
         tidyr::unnest(cols = c(bed_ids))
     bedset_ids <- bedsets_from_raw$id |> unique()
-    bedsets <- bb_list_bedsets(bedbase, query = "alzheimer", limit = 5000)
+    bedsets <- bb_list_bedsets(bedbase, query = "alzheimer", limit = 5000, test_request = TRUE)
     expect_equal(bedset_ids, bedsets$id)
 })
 
@@ -82,14 +83,15 @@ test_that("bb_beds_in_bedset returns expected bed_ids", {
 })
 
 test_that("bb_bed_text_search returns results scored against the query", {
-    beds <- bb_bed_text_search(bedbase, "hg38") |>
+    beds <- bb_bed_text_search(bedbase, "hg38", test_request = TRUE) |>
         dplyr::arrange(id)
     ex_beds <- httr::content(bedbase$text_to_bed_search_v1_bed_search_text_get(
         query = "hg38",
         genome = NULL,
         assay = NULL,
         limit = 10,
-        offset = 0
+        offset = 0,
+        test_request = TRUE
     ))
     ex_beds <- purrr::map_depth(.x = ex_beds$results, 1, \(y) unlist(y)) |>
         dplyr::bind_rows() |>