-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #98 from OxfordIHTM/dev
create wrappers for icd-10 api endpoints
- Loading branch information
Showing
10 changed files
with
309 additions
and
7 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -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 | ||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
Oops, something went wrong.
Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters