Before v1

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: bedbaser
 Title: A BEDbase client
-Version: 0.0.0.9000
+Version: 0.0.9000
 Authors@R: 
     person("Jennifer", "Wokaty", , "[email protected]",
            role = c("aut", "cre"))
@@ -12,13 +12,13 @@ Imports:
     AnVIL,
     BiocFileCache,
     dplyr,
-    glue,
     httr,
     purrr,
     rtracklayer,
     R.utils,
     stringr,
     tibble,
+    tools,
     utils
 Suggests:
     BiocStyle,

NAMESPACE

@@ -2,16 +2,15 @@
 
 export(.BEDbase)
 export(BEDbase)
+export(bb_search)
 export(download_file)
 export(get_rec_type)
-export(search_bedbase)
 exportClasses(BEDbase)
 exportMethods(bb_beds_in_bedset)
 exportMethods(bb_count)
 exportMethods(bb_genomes)
 exportMethods(bb_metadata)
 exportMethods(bb_records)
-exportMethods(get_bb_service_info)
 importFrom(AnVIL,Service)
 importFrom(BiocFileCache,BiocFileCache)
 importFrom(BiocFileCache,bfcadd)
@@ -20,7 +19,6 @@ importFrom(BiocFileCache,bfcneedsupdate)
 importFrom(BiocFileCache,bfcquery)
 importFrom(BiocFileCache,bfcrpath)
 importFrom(dplyr,bind_rows)
-importFrom(glue,glue)
 importFrom(httr,content)
 importFrom(httr2,req_perform)
 importFrom(httr2,request)
@@ -34,6 +32,7 @@ importFrom(stringr,str_detect)
 importFrom(stringr,str_split_1)
 importFrom(tibble,as_tibble)
 importFrom(tibble,tibble)
+importFrom(tools,R_user_dir)
 importFrom(utils,URLencode)
 importFrom(utils,download.file)
 importFrom(utils,tail)

R/bedbaser.R

@@ -82,10 +82,10 @@ setMethod(
     function(x, rec_type = c("bed", "bedset")) {
         rec_type <- match.arg(rec_type)
         if (rec_type == "bed")
-            response <- x$get_bed_genome_assemblies_bed_genomes_get()
+            resp <- x$get_bed_genome_assemblies_bed_genomes_get()
         else
-            response <- x$get_bedset_genome_assemblies_bedset_genomes_get()
-        genome_list <- content(response)
+            resp <- x$get_bedset_genome_assemblies_bedset_genomes_get()
+        genome_list <- content(resp)
         genome_tibble <- tibble()
         if (length(genome_list)) {
             cnames <- names(genome_list[[1]])
@@ -120,10 +120,10 @@ setMethod(
     function(x, id, rec_type = c("bed", "bedset")) {
         rec_type <- match.arg(rec_type)
         if (rec_type == "bed")
-            response <- x$get_bed_metadata_bed__bed_id__metadata_get(id)
+            resp <- x$get_bed_metadata_bed__bed_id__metadata_get(id)
         else
-            response <- x$get_bedset_metadata_bedset__bedset_id__metadata_get(id)
-        record <- content(response)
+            resp <- x$get_bedset_metadata_bedset__bedset_id__metadata_get(id)
+        record <- content(resp)
         record$metadata
     }
 )
@@ -138,9 +138,10 @@ setGeneric(name = "bb_records",
 #' Note: how to get next page token
 #'
 #' @param rec_type character() bed or bedset
-#' @param limit integer() maximum records
-#' @param token integer() next page of records
+#' @param limit integer() (defaults to NULL) maximum records
+#' @param token integer() (defaults to NULL) page token of records
 #'
+#' @importFrom httr content
 #' @importFrom purrr map_dfr set_names
 #' @importFrom tibble tibble as_tibble
 #'
@@ -156,11 +157,11 @@ setMethod(
     function(x, rec_type = c("bed", "bedset"), limit = NULL, token = NULL) {
         rec_type <- match.arg(rec_type)
         if (rec_type == "bed")
-            response <- x$list_beds_bed_list_get(limit=limit, token=token)
+            resp <- x$list_beds_bed_list_get(limit=limit, token=token)
         else
-            response <- x$list_bedsets_bedset_list_get(limit=limit, token=token)
+            resp <- x$list_bedsets_bedset_list_get(limit=limit, token=token)
         records_tibble <- tibble()
-        records_list <- content(response)
+        records_list <- content(resp)
         if (length(records_list)) {
             cnames <- names(records_list$records[[1]])
             records_tibble <- records_list$records |>
@@ -178,6 +179,8 @@ setGeneric(name = "bb_beds_in_bedset",
 #'
 #' @param rec_id integer() BEDset record identifier
 #'
+#' @importFrom httr content
+#'
 #' @return list() BED record identifiers
 #'
 #' @examples
@@ -190,33 +193,40 @@ setMethod(
     function(x, rec_id) {
         response <-
             x$get_bedfiles_in_bedset_bedset__bedset_id__bedfiles_get(rec_id)
-        records <- content(response)
+        records <- content(resp)
         unlist(records$bedfile_metadata, use.names = FALSE)
     }
 )
 
+setGeneric(name = "bb_search",
+           def = function(x, query, limit = NULL, offset = NULL) {
+               standardGeneric("bb_search")
+})
+
 #' Search BEDbase
 #'
-#' @param keywords character() keyword to search for
-#' @param limit integer() maximum number of results to include
-#' @param quiet logical() (default FALSE) display message
+#' @param query character() keywords to search
+#' @param limit integer() (defaults to NULL) maximum number of results
+#' @param offset integer() (defaults to NULL) page offset of results
 #'
 #' @importFrom dplyr bind_rows
-#' @importFrom glue glue
-#' @importFrom httr2 req_perform request resp_body_json
+#' @importFrom httr content
 #' @importFrom tibble as_tibble
 #' @importFrom utils URLencode
 #'
 #' @return tibble()
 #'
 #' @examples
-#' search_bedbase("excluderanges")
+#' client <- BEDbase()
+#' bb_search(client, "excluderanges")
 #'
 #' @export
-search_bedbase <- function(keywords, limit, quiet = FALSE) {
-    encoded_keywords <- URLencode(keywords, reserved = TRUE)
-    url <- glue("search/bed/{encoded_keywords}?limit={limit}")
-    results <- query_bedbase(url, quiet)
+bb_search <- function(x, query, limit = NULL, offset = NULL) {
+    encoded_query <- URLencode(query, reserved = TRUE)
+    resp <- x$text_to_bed_search_search_bed__query__get(encoded_query,
+                                                        limit = limit,
+                                                        offset = offset)
+    results <- content(resp)
     if (!length(results))
         return(results)
     metadata <- tibble()
@@ -249,7 +259,6 @@ search_bedbase <- function(keywords, limit, quiet = FALSE) {
 #' @param quiet logical() (default FALSE) display message
 #'
 #' @importFrom BiocFileCache bfcrpath
-#' @importFrom glue glue
 #' @importFrom httr2 req_perform request resp_body_json
 #' @importFrom stringr str_split_1
 #' @importFrom utils download.file tail
@@ -265,9 +274,9 @@ download_file <- function(rec_id, file_type = c("bytes", "thumbnail"),
     obj_id <- make_obj_id(rec_id)
     stopifnot(acc_id %in% get_access_ids(obj_id, TRUE))
     file_type <- match.arg(file_type)
-    url <- glue("objects/{obj_id}/access/{acc_id}")
+    url <- paste0("objects/", obj_id, "/access/", acc_id)
     if (file_type == "thumbnail")
-        url <- glue("{url}/{file_type}")
+        url <- paste(url, file_type, sep="/")
     download_url <- query_bedbase(url, quiet)
     .download_and_cache(download_url, quiet)
 }

R/cache.R

@@ -1,8 +1,9 @@
 #' Get the cache
 #'
-#' Note: This function is described in BiocFileCache
+#' This function is described in the BiocFileCache vignette.
 #'
 #' @importFrom BiocFileCache BiocFileCache
+#' @importFrom tools R_user_dir
 #'
 #' @return BiocFileCache object
 #'
@@ -11,20 +12,19 @@
 #'
 #' @noRd
 .get_cache <- function() {
-    bfc <- tools::R_user_dir("bedbaser", which="cache")
+    bfc <- R_user_dir("bedbaser", which="cache")
     BiocFileCache(bfc)
 }
 
 #' Retrieve path from cache or download file and cache
 #'
-#' Note: This function is described in BiocFileCache
+#' This function is described in the BiocFileCache vignette.
 #'
 #' @param url character() remote resource
 #' @param quiet logical() display message
 #'
 #' @importFrom BiocFileCache BiocFileCache bfcadd bfcdownload bfcneedsupdate
 #'     bfcquery bfcrpath
-#' @importFrom glue glue
 #' @importFrom rlang inform
 #'
 #' @return filepath character()
@@ -37,7 +37,7 @@
     rid <- bfcquery(bfc, url)$rid
     if (!length(rid)) {
         if (!quiet)
-            inform(glue("Downloading {url} ..."))
+            inform(paste("Downloading", url, "..."))
         rid <- names(bfcadd(bfc, url))
     }
     if (!isFALSE(bfcneedsupdate(bfc, rid)))

R/utils.R

@@ -2,7 +2,6 @@
 #'
 #' @param id character() BEDbase identifier
 #'
-#' @importFrom glue glue
 #' @importFrom rlang abort
 #' @importFrom stringr regex str_detect
 #'
@@ -20,7 +19,7 @@ get_rec_type <- function(id) {
     else if (str_detect(id, regex("^[:alnum:]+$")))
         rec_type <- "object"
     else
-        abort(glue("Unknown record identifier: {id}"))
+        abort(paste("Unknown record identifier:", id))
     rec_type
 }
 
@@ -32,15 +31,13 @@ get_rec_type <- function(id) {
 #' @param rec_type character() (default bed) BEDbase record type
 #' @param result_id character() (default bedfile) BEDbase result identifier
 #'
-#' @importFrom glue glue
-#'
 #' @return String
 #'
 #' @examples
 #' obj_id <- make_obj_id("eaf9ee97241f300f1c7e76e1f945141f")
 make_obj_id <- function(rec_id, rec_type = "bed", result_id = "bedfile")
 {
-    glue("{rec_type}.{rec_id}.{result_id}")
+    paste(rec_type, rec_id, result_id, sep =".")
 }
 
 #' Get valid access identifiers
@@ -63,24 +60,3 @@ get_access_ids <- function(obj_id, quiet = FALSE) {
     }
     access_methods
 }
-
-setGeneric(name = "get_bb_service_info",
-           def = function(x) { standardGeneric("get_bb_service_info") })
-
-#' Get service information
-#'
-#' @importFrom httr content
-#'
-#' @return list() service info, such as version
-#'
-#' @examples
-#' bb <- BEDbase()
-#' get_bb_service_info(bb)
-#'
-#' @export
-setMethod(
-    "get_bb_service_info", "BEDbase",
-    function(x) {
-        content(x$service_info_service_info_get())
-    }
-)