create wrappers for icd-10 api endpoints

DESCRIPTION

@@ -3,11 +3,13 @@ Type: Package
 Title: Interface to the International Classification of Diseases (ICD) API
 Version: 0.0.0.9000
 Authors@R: c(
-    person("Anita", "Makori", email = "",
-           role = c("aut", "cph")),
+    person("Anita", "Makori", role = c("aut", "cph")),
     person("Ernest", "Guevarra", 
            comment = c(ORCID = "0000-0002-4887-4415"), 
-           email = "[email protected]", role = c("aut", "cre", "cph")))
+           email = "[email protected]", role = c("aut", "cre", "cph")),
+    person("Sanjeev", "Pugazhendhi", role = c("ths", "rev")),
+    person("Williams", "Udoh Ituen-Umanah", role = "rev"),
+    person("Proochista", "Ariana", role = c("rev", "cph")))
 Description: The International Classification of Diseases (ICD) serves a broad 
     range of uses globally and provides critical knowledge on the extent, causes 
     and consequences of human disease and death worldwide via data that is 
@@ -34,7 +36,7 @@ LazyData: true
 Language: en-GB
 RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)
-URL: https://oxford-ihtm.io/codigo/,https://github.com/OxfordIHTM/codigo
+URL: https://oxford-ihtm.io/codigo/, https://github.com/OxfordIHTM/codigo
 BugReports: https://github.com/OxfordIHTM/codigo/issues
 Config/testthat/edition: 3
 VignetteBuilder: knitr

NAMESPACE

@@ -1,5 +1,9 @@
 # Generated by roxygen2: do not edit by hand
 
+export(icd_10_get_chapters)
+export(icd_10_get_info)
+export(icd_10_get_release_by_category)
+export(icd_10_get_releases)
 export(icd_authenticate)
 export(icd_autocode)
 export(icd_autocode_foundation)

R/icd_10_get.R

@@ -0,0 +1,186 @@
+#'
+#' Get available ICD-10 releases
+#'
+#' @param release A string specifying the release version of ICD-10 to search
+#'   from. If not specified, defaults to the latest release version. See
+#'   the available versions with `icd_versions`.
+#' @param api_version Version of the API. Possible values are `v1` or `v2`.
+#'   For example, if you provide value v2, the API will respond in the format of
+#'   the version 2 of the API. Default is `v2`.
+#' @param language ICD-API is multi-lingual. By changing this header, you may
+#'   make the API respond in different languages. Languages will be available as
+#'   the translations of ICD-11 completes. The values are language codes such as
+#'   en, es, zh, etc. Depending on the `release_id` specified, the available
+#'   languages will vary. Default is English ("en"). Note that language support
+#'   for ICD-10 is limited to English (`en`).
+#' @param category ICD-10 category code or for blocks, the code range.
+#' @param base_url The base URL of the API. Default uses the WHO API server at
+#'   https://id.who.int. If you are using a locally deployed server or hosting
+#'   your own ICD API server, you should specify the URL of your instance here.
+#' @param client The OAuth2 client produced through a call to
+#'   `icd_oauth_client()`.
+#' @param scope Scopes to be requested from the resource owner. Default is
+#'   *"icdapi_access"* as specified in the ICD API documentation.
+#'
+#' @returns A list with information on specified ICD 10 parameters
+#'
+#' @examples
+#' icd_10_get_releases()
+#' icd_10_get_chapters()
+#' icd_10_get_release_by_category(category = "A00")
+#' icd_10_get_release_by_category(category = "A00-A09")
+#' icd_10_get_info(category = "A00")
+#' icd_10_get_info(category = "A00-A09")
+#'
+#' @rdname icd_10_get
+#' @export
+#'
+#'
+
+icd_10_get_releases <- function(api_version = c("v2", "v1"),
+                                base_url = "https://id.who.int",
+                                client = icd_oauth_client(),
+                                scope = "icdapi_access") {
+  ## Get API version to use ----
+  api_version <- match.arg(api_version)
+
+  ## Make base request ----
+  req <- httr2::request(base_url) |>
+    httr2::req_url_path("icd/release/10") |>
+    httr2::req_headers(
+      Accept = "application/json",
+      "API-Version" = api_version,
+      "Accept-Language" = "en"
+    )
+
+  ## Authenticate and perform request ----
+  resp <- req |>
+    icd_authenticate(client = client, scope = scope) |>
+    httr2::req_perform() |>
+    httr2::resp_body_json()
+
+  ## Return response ----
+  resp
+}
+
+
+#'
+#' @rdname icd_10_get
+#' @export
+#'
+
+icd_10_get_chapters <- function(release = NULL,
+                                api_version = c("v2", "v1"),
+                                language = "en",
+                                base_url = "https://id.who.int",
+                                client = icd_oauth_client(),
+                                scope = "icdapi_access") {
+  ## Get API version to use ----
+  api_version <- match.arg(api_version)
+
+  ## Check release identifier ----
+  if (!is.null(release))
+    icd_check_release(release)
+  else
+    release <- icd_get_releases(icd = "icd10", latest = TRUE) |> dplyr::pull()
+
+  ## Check language ----
+  if (!is.null(language))
+    icd_check_language(release = release, language = language)
+
+  ## Make base request ----
+  req <- httr2::request(base_url) |>
+    httr2::req_url_path("icd/release/10", release) |>
+    httr2::req_headers(
+      Accept = "application/json",
+      "API-Version" = api_version,
+      "Accept-Language" = language
+    )
+
+  ## Authenticate and perform request ----
+  resp <- req |>
+    icd_authenticate(client = client, scope = scope) |>
+    httr2::req_perform() |>
+    httr2::resp_body_json()
+
+  ## Return response ----
+  resp
+}
+
+
+#'
+#' @rdname icd_10_get
+#' @export
+#'
+
+icd_10_get_release_by_category <- function(category,
+                                           api_version = c("v2", "v1"),
+                                           base_url = "https://id.who.int",
+                                           client = icd_oauth_client(),
+                                           scope = "icdapi_access") {
+  ## Get API version to use ----
+  api_version <- match.arg(api_version)
+
+  ## Make base request ----
+  req <- httr2::request(base_url) |>
+    httr2::req_url_path("icd/release/10", category) |>
+    httr2::req_headers(
+      Accept = "application/json",
+      "API-Version" = api_version,
+      "Accept-Language" = "en"
+    )
+
+  ## Authenticate and perform request ----
+  resp <- req |>
+    icd_authenticate(client = client, scope = scope) |>
+    httr2::req_perform() |>
+    httr2::resp_body_json()
+
+  ## Return response ----
+  resp
+}
+
+
+#'
+#' @rdname icd_10_get
+#' @export
+#'
+
+icd_10_get_info <- function(release = NULL,
+                            category,
+                            api_version = c("v2", "v1"),
+                            language = "en",
+                            base_url = "https://id.who.int",
+                            client = icd_oauth_client(),
+                            scope = "icdapi_access") {
+  ## Get API version to use ----
+  api_version <- match.arg(api_version)
+
+  ## Check release identifier ----
+  if (!is.null(release))
+    icd_check_release(release)
+  else
+    release <- icd_get_releases(icd = "icd10", latest = TRUE) |> dplyr::pull()
+
+  ## Check language ----
+  if (!is.null(language))
+    icd_check_language(release = release, language = language)
+
+  ## Make base request ----
+  req <- httr2::request(base_url) |>
+    httr2::req_url_path("icd/release/10", release, category) |>
+    httr2::req_headers(
+      Accept = "application/json",
+      "API-Version" = api_version,
+      "Accept-Language" = language
+    )
+
+  ## Authenticate and perform request ----
+  resp <- req |>
+    icd_authenticate(client = client, scope = scope) |>
+    httr2::req_perform() |>
+    httr2::resp_body_json()
+
+  ## Return response ----
+  resp
+}

README.Rmd

@@ -19,8 +19,8 @@ knitr::opts_chunk$set(
 [![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 [![R-CMD-check](https://github.com/OxfordIHTM/icd/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/OxfordIHTM/icd/actions/workflows/R-CMD-check.yaml)
-[![Codecov test coverage](https://codecov.io/gh/OxfordIHTM/codigo/branch/main/graph/badge.svg)](https://app.codecov.io/gh/OxfordIHTM/codigo?branch=main)
 [![test-coverage](https://github.com/OxfordIHTM/icd/actions/workflows/test-coverage.yaml/badge.svg)](https://github.com/OxfordIHTM/icd/actions/workflows/test-coverage.yaml)
+[![Codecov test coverage](https://codecov.io/gh/OxfordIHTM/codigo/branch/main/graph/badge.svg)](https://app.codecov.io/gh/OxfordIHTM/codigo?branch=main)
 [![CodeFactor](https://www.codefactor.io/repository/github/oxfordihtm/codigo/badge)](https://www.codefactor.io/repository/github/oxfordihtm/codigo)
 <!-- badges: end -->
 

README.md

@@ -11,9 +11,9 @@ public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostat
 [![Lifecycle:
 experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 [![R-CMD-check](https://github.com/OxfordIHTM/icd/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/OxfordIHTM/icd/actions/workflows/R-CMD-check.yaml)
+[![test-coverage](https://github.com/OxfordIHTM/icd/actions/workflows/test-coverage.yaml/badge.svg)](https://github.com/OxfordIHTM/icd/actions/workflows/test-coverage.yaml)
 [![Codecov test
 coverage](https://codecov.io/gh/OxfordIHTM/codigo/branch/main/graph/badge.svg)](https://app.codecov.io/gh/OxfordIHTM/codigo?branch=main)
-[![test-coverage](https://github.com/OxfordIHTM/icd/actions/workflows/test-coverage.yaml/badge.svg)](https://github.com/OxfordIHTM/icd/actions/workflows/test-coverage.yaml)
 [![CodeFactor](https://www.codefactor.io/repository/github/oxfordihtm/codigo/badge)](https://www.codefactor.io/repository/github/oxfordihtm/codigo)
 <!-- badges: end -->
 

data-raw/icd_mapping_tables.R

@@ -17,3 +17,8 @@ unzip(
   overwrite = TRUE,
   exdir = "data-raw/icd-mapping"
 )
+
+
+map_to_multiple <- read_xlsx(
+  file = "data-raw/icd-mapping/10To11MapToMultipleCategories.xlsx", sheeet = 1
+)

inst/WORDLIST

@@ -1,3 +1,4 @@
+Autocode
 Autocoding
 BlockId
 BrowserLink
@@ -18,6 +19,7 @@ IHTM
 IndexTerm
 IsLeaf
 IsResidual
+Ituen
 Lifecycle
 LinearizationMiniOutput
 NarrowerTerm
@@ -27,6 +29,8 @@ PrimaryLocation
 SimpleTabulation
 SupportedClassifications
 URIs
+Udoh
+Umanah
 WIP
 api
 autocode

pkgdown/_pkgdown.yml

@@ -66,6 +66,13 @@ reference:
     - icd_get_entity
     - icd_get_info
 
+  - title: Get ICD-10
+    contents:
+    - icd_10_get_releases
+    - icd_10_get_chapters
+    - icd_10_get_release_by_category
+    - icd_10_get_info
+
   - title: Structure
     contents:
     - icd_structure_foundation