005 switch to using httr2

.Rbuildignore

@@ -9,3 +9,4 @@
 ^pkgdown$
 ^\.travis\.yml$
 ^\.github$
+^tmp$

.gitignore

@@ -5,3 +5,4 @@
 inst/doc
 docs/
 docs
+tmp/

DESCRIPTION

@@ -49,11 +49,13 @@ Imports:
     memoise,
     httr2,
     tidyjson,
-    tibblify
+    tibblify,
+    testthat
 Suggests: 
     knitr,
     rmarkdown
 VignetteBuilder: knitr
 URL: https://github.com/patterninstitute/ensemblr, https://www.pattern.institute/ensemblr/
 BugReports: https://github.com/patterninstitute/ensemblr/issues
 Config/Needs/website: patterninstitute/chic
+Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -1,33 +1,77 @@
 # Generated by roxygen2: do not edit by hand
 
 export("%>%")
+export(._get_divisions)
+export(._get_rest_version)
+export(._get_software_version)
+export(._get_variation_sources)
 export(genomic_range)
+export(get_alignment_by_region)
 export(get_analyses)
+export(get_analysis_info)
 export(get_assemblies)
+export(get_assembly_info)
+export(get_biotypes)
+export(get_biotypes_by_name)
+export(get_biotypes_groups)
+export(get_cafe_genetree_by_id)
+export(get_cafe_genetree_by_species_id)
+export(get_cafe_genetree_by_symbol)
+export(get_compara_methods)
+export(get_compara_species_sets)
+export(get_comparas)
+export(get_consequence_types)
 export(get_cytogenetic_bands)
+export(get_data)
+export(get_data_version2)
 export(get_data_versions)
 export(get_divisions)
+export(get_eg_version)
 export(get_ensembl_genomes_version)
+export(get_external_dbs)
+export(get_genetree_by_id)
+export(get_genetree_by_species_id)
+export(get_genetree_by_symbol)
+export(get_genome_info)
+export(get_genome_info_by_accession)
+export(get_genome_info_by_assembly)
+export(get_genome_info_by_division)
+export(get_genome_info_by_taxonomy)
+export(get_homology_by_species_id)
+export(get_homology_by_symbol)
 export(get_id)
 export(get_individuals)
 export(get_karyotypes)
+export(get_ld_by_variant)
+export(get_ld_values_by_region)
 export(get_ld_variants_by_pair)
 export(get_ld_variants_by_pair_combn)
 export(get_ld_variants_by_range)
 export(get_ld_variants_by_window)
+export(get_pairwise_ld_values)
+export(get_population_individuals)
 export(get_populations)
+export(get_region_info)
 export(get_rest_version)
+export(get_rest_version2)
 export(get_software_version)
+export(get_software_version2)
 export(get_species)
+export(get_species_info)
+export(get_species_populations)
 export(get_toplevel_sequence_info)
 export(get_toplevel_sequences)
 export(get_variant_consequences)
 export(get_variation_sources)
 export(get_versioning)
+export(get_versioning2)
 export(get_xrefs_by_ensembl_id)
 export(get_xrefs_by_gene)
+export(get_xrefs_by_id)
+export(get_xrefs_by_name)
+export(get_xrefs_by_symbol)
 export(is_ensembl_reachable)
+export(ping_service)
 importFrom(magrittr,"%>%")
-importFrom(memoise,memoise)
 importFrom(rlang,.data)
 importFrom(tibble,tibble)

R/analysis.R

@@ -1,7 +1,8 @@
 analysis_tbl <- function(
-    species_name = character(),
-    database = character(),
-    analysis = character()) {
+  species_name = character(),
+  database = character(),
+  analysis = character()
+) {
   tbl <- tibble::tibble(
     species_name = species_name,
     database = database,
@@ -11,14 +12,13 @@ analysis_tbl <- function(
 }
 
 json_list_to_analysis_tbl <- function(species_name, json_list) {
+
   tbl <- purrr::imap_dfr(
     json_list,
-    .f = ~ analysis_tbl(
-      species_name = species_name,
-      database = .x,
-      analysis = .y
+    .f = ~ analysis_tbl(species_name = species_name,
+                        database = .x,
+                        analysis = .y)
     )
-  )
 
   # Drop rows if all columns except species_name are NA
   return(tidyr::drop_na(tbl, -species_name))
@@ -54,6 +54,7 @@ get_analyses <- function(species_name,
                          verbose = FALSE,
                          warnings = TRUE,
                          progress_bar = TRUE) {
+
   # Assert species_name argument.
   assert_species_name(species_name)
   # Assert verbose argument.
@@ -67,8 +68,8 @@ get_analyses <- function(species_name,
   e <- urltools::url_encode
 
   resource_urls <- glue::glue(
-    "/info/analysis/",
-    "{e(species_name)}?"
+    '/info/analysis/',
+    '{e(species_name)}?'
   )
 
   # Usually we'd use purrr::map here but we opted for plyr::llply
@@ -89,13 +90,11 @@ get_analyses <- function(species_name,
     )
 
   # Only keep those responses that responded successfully, i.e. with status == "OK".
-  responses_ok <- purrr::keep(responses, ~ identical(.x$status, "OK"))
+  responses_ok <- purrr::keep(responses, ~ identical(.x$status, 'OK'))
 
   # If none of the responses were successful then return an empty linkage
   # disequilibrium tibble.
-  if (rlang::is_empty(responses_ok)) {
-    return(analysis_tbl())
-  }
+  if (rlang::is_empty(responses_ok)) return(analysis_tbl())
 
   tbl <- purrr::imap_dfr(
     .x = responses_ok,
@@ -106,4 +105,5 @@ get_analyses <- function(species_name,
   analysis <- rlang::expr(analysis)
 
   return(dplyr::arrange(tbl, species_name, !!database, !!analysis))
+
 }

R/api-versioning.R

@@ -0,0 +1,90 @@
+##----Re-wrote the already existing functions from `versioning.R`----
+
+#' Get REST API version
+#'
+#' Retrieve the version of the Ensembl REST API currently in use.
+#' The version format is `major.minor.point`.
+#' @return A numeric value representing the REST API version components:
+#' `major`, `minor`, and `point`.
+#' @source \url{https://github.com/Ensembl/ensembl-rest/wiki/API-Versioning}
+#' @examples
+#' \dontrun{
+#' rest_version <- get_rest_version()
+#' print(rest_version)
+#' }
+#' @export
+get_rest_version2 <- function() {
+  res <- "info/rest"
+  version <- ensemblr:::get(res)[[1]] |>
+    httr2::resp_body_json()
+  version$release
+}
+
+#' Get data version
+#'
+#' Retreive the version(s) of the Ensembl data that the REST API is accessing.
+#' @return A numeric value representing of data release version.
+#' @source \url{https://github.com/Ensembl/ensembl-rest/wiki/API-Versioning}
+#' @examples
+#' \dontrun{
+#' data_version <- get_data_version()
+#' print(data_version)
+#' }
+#' @export
+get_data_version2 <- function() {
+  res <- "info/data"
+  version <- ensemblr:::get(res)[[1]] |>
+    httr2::resp_body_json()
+  version$release |> as.numeric()
+}
+
+#' Get API software version
+#'
+#' Retreive the version of the Ensembl software the REST API is using.
+#' @return A numeric value representing the software version.
+#' @source \url{https://github.com/Ensembl/ensembl-rest/wiki/API-Versioning}
+#' @examples
+#' \dontrun{
+#' software_version <- get_software_version()
+#' print(software_version)
+#' }
+#' @export
+get_software_version2 <- function() {
+  res <- "info/software"
+  version <- ensemblr:::get(res)[[1]] |>
+    httr2::resp_body_json()
+  version$release |> as.numeric()
+}
+
+#' Get Ensembl REST versions
+#'
+#' Retreive the versions of the different entities involved in the
+#' REST API requests. When accessing the Ensembl REST API, you are actually
+#' accessing three interconnected entities:
+#' \itemize{
+#' \item Ensembl databases (\code{data}).
+#' \item Perl API (\code{software}).
+#' \item REST API (\code{rest}).
+#' }
+#' \figure{ensembl_api_versioning_wo_fonts.svg}
+#'
+#' @return A named list of three elements: \code{data}, \code{software} and
+#'   \code{rest}.
+#'
+#' @examples
+#' # Get the versions of the different entities involved in the REST API
+#' # requests.
+#' get_versioning()
+#'
+#' @export
+get_versioning2 <- function() {
+  data_version <- get_data_version2()
+  software_version <- get_software_version2()
+  rest_version <- get_rest_version2()
+
+  api_versions <- list(data = data_version,
+                       software = software_version,
+                       rest = rest_version)
+
+  return(api_versions)
+}

R/archive.R

@@ -1,13 +1,14 @@
 id_tbl <- function(
-    id = character(),
-    id_latest = character(),
-    type = character(),
-    id_version = integer(),
-    release = integer(),
-    is_current = logical(),
-    genome_assembly_name = character(),
-    peptide = character(),
-    possible_replacement = list()) {
+  id = character(),
+  id_latest = character(),
+  type = character(),
+  id_version = integer(),
+  release = integer(),
+  is_current = logical(),
+  genome_assembly_name = character(),
+  peptide = character(),
+  possible_replacement = list()
+) {
   tbl <- tibble::tibble(
     id = id,
     id_latest = id_latest,
@@ -24,16 +25,17 @@ id_tbl <- function(
 }
 
 json_list_to_id_tbl <- function(json_list) {
+
   tbl <- id_tbl(
-    id = purrr::pluck(json_list, "id", .default = NA_character_),
-    id_latest = purrr::pluck(json_list, "latest", .default = NA_character_),
-    type = purrr::pluck(json_list, "type", .default = NA_character_),
-    id_version = as.integer(purrr::pluck(json_list, "version", .default = NA_integer_)),
-    release = as.integer(purrr::pluck(json_list, "release", .default = NA_integer_)),
-    is_current = purrr::pluck(json_list, "is_current", .default = NA) == "1",
-    genome_assembly_name = purrr::pluck(json_list, "assembly", .default = NA_character_),
-    peptide = purrr::pluck(json_list, "peptide", .default = NA_character_),
-    possible_replacement = purrr::pluck(json_list, "possible_replacement", .default = list(character()))
+    id = purrr::pluck(json_list, 'id', .default = NA_character_),
+    id_latest = purrr::pluck(json_list, 'latest', .default = NA_character_),
+    type = purrr::pluck(json_list, 'type', .default = NA_character_),
+    id_version = as.integer(purrr::pluck(json_list, 'version', .default = NA_integer_)),
+    release = as.integer(purrr::pluck(json_list, 'release', .default = NA_integer_)),
+    is_current = purrr::pluck(json_list, 'is_current', .default = NA) == '1',
+    genome_assembly_name = purrr::pluck(json_list, 'assembly', .default = NA_character_),
+    peptide = purrr::pluck(json_list, 'peptide', .default = NA_character_),
+    possible_replacement = purrr::pluck(json_list, 'possible_replacement', .default = list(character()))
   )
 
   return(tbl)
@@ -71,13 +73,15 @@ json_list_to_id_tbl <- function(json_list) {
 #' }
 #'
 #' @examples
-#' get_id(c("ENSDARE00000830915", "ENSG00000248378", "ENSDART00000033574", "ENSP00000000233"))
+#' get_id(c('ENSDARE00000830915', 'ENSG00000248378', 'ENSDART00000033574', 'ENSP00000000233'))
 #'
 #' @export
 get_id <- function(id,
                    verbose = FALSE,
                    warnings = TRUE,
                    progress_bar = TRUE) {
+
+
   # Assert verbose argument.
   assertthat::assert_that(assertthat::is.flag(verbose))
   # Assert warnings argument.
@@ -89,8 +93,8 @@ get_id <- function(id,
   e <- urltools::url_encode
 
   resource_urls <- glue::glue(
-    "/archive/id/",
-    "{e(id)}?"
+    '/archive/id/',
+    '{e(id)}?'
   )
 
   # Usually we'd use purrr::map here but we opted for plyr::llply
@@ -111,13 +115,11 @@ get_id <- function(id,
     )
 
   # Only keep those responses that responded successfully, i.e. with status == "OK".
-  responses_ok <- purrr::keep(responses, ~ identical(.x$status, "OK"))
+  responses_ok <- purrr::keep(responses, ~ identical(.x$status, 'OK'))
 
   # If none of the responses were successful then return an empty linkage
   # disequilibrium tibble.
-  if (rlang::is_empty(responses_ok)) {
-    return(id_tbl())
-  }
+  if (rlang::is_empty(responses_ok)) return(id_tbl())
 
   return(
     purrr::imap_dfr(