add all possible API search queries

DESCRIPTION

@@ -23,7 +23,8 @@ Imports:
 Suggests: 
     covr,
     httpuv,
-    spelling
+    spelling,
+    tibble
 Encoding: UTF-8
 LazyData: true
 Language: en-GB

R/icd_search.R

@@ -2,10 +2,16 @@
 #' Search the foundation component of the ICD-11
 #'
 #' @param base_url The base URL of the API. Default uses the WHO API server at
-#'   https://id.who.int/icd/entity
-#' @param client The OAuth2 client produced through a call to `icd_oauth_client()`
+#'   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 q String. Text to be searched. Having the character `%` at the end will
-#'   be regarded as a wild card for that word
+#'   be regarded as a wild card for that word.
+#' @param subtree A string or vector of strings of URIs. If provided, the
+#'   search will be performed on the entities provided and their descendants.
+#' @param chapter A string or vector of strings of chapter codes
+#'   eg: c("01", "02") When provided, the search will be performed only on
+#'   these chapters.
 #' @param flexisearch Logical. Default is FALSE. Changes the search mode to
 #'   flexible search. In the regular search mode, the Coding Tool will only give
 #'   you results that contain all of the words that you've used in your search.
@@ -15,16 +21,24 @@
 #'   that are typed. It would still try to find the best matching phrase but
 #'   there may be words in your search that are not matched at all. It is
 #'   recommended to use flexible search only when regular search does not
-#'   provide a result
+#'   provide a result.
 #' @param flat Logical. Default is FALSE. If set to true the search result
 #'   entities are provided in a nested data structure representing the
-#'   ICD-11 hierarchy. Otherwise they are listed as flat list of matches
+#'   ICD-11 hierarchy. Otherwise they are listed as flat list of matches.
+#' @param properties A string or a vector of strings for the properties to be
+#'   searched. By default the system  searches, *"Title"*, *"Synonyms"*, and
+#'   *"FullySpecifiedName"*. The valid values that could be used are: *Title"*,
+#'   *"Synonym"*, *"NarrowerTerm"*, *"FullySpecifiedName"*, *"Definition"*, and
+#'   *"Exclusion"*.
+#' @param release A string specifying the release version of the Foundation to
+#'   search from. If not specified, defaults to the latest release version. See
+#'   the available versions with `icd_versions`.
 #' @param highlight Logical. Default is FALSE. If set to FALSE the search result
 #'   highlighting is turned off and the results don't contain special tags for
-#'   highlighting where the results are found within the text
+#'   highlighting where the results are found within the text.
 #' @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`
+#'   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
@@ -36,36 +50,83 @@
 #' @examples
 #' icd_search_foundation(q = "cholera")
 #'
+#' @rdname icd_search
 #' @export
 #'
 
-icd_search_foundation <- function(base_url = "https://id.who.int/icd",
+icd_search_foundation <- function(base_url = "https://id.who.int",
                                   client = icd_oauth_client(),
-                                  q = NULL,
+                                  q,
+                                  subtree = NULL,
+                                  chapter = NULL,
                                   flexisearch = FALSE,
                                   flat = TRUE,
+                                  properties = NULL,
+                                  release = NULL,
                                   highlight = FALSE,
                                   api_version = c("v2", "v1"),
                                   language = "en") {
   ## Get API version to use ----
   api_version <- match.arg(api_version)
 
-  httr2::request(file.path(base_url, "entity/search")) |>
+  ## Make base request ----
+  req <- httr2::request(file.path(base_url, "icd/entity/search")) |>
+    httr2::req_url_query(q = q)
+
+  ## Add query components ----
+
+  ### Subtrees filter ----
+  if (!is.null(subtree)) {
+    req <- req |>
+      httr2::req_url_query(subtreesFilter = paste(subtree, collapse = ","))
+  }
+
+  ### Chapters filter ----
+  if (!is.null(chapter)) {
+    req <- req |>
+      httr2::req_url_query(chapterFilter = paste(chapter, collapse = ","))
+  }
+
+  ### Flexi search and flatResults component ----
+  req <- req |>
     httr2::req_url_query(
-      q = q,
       useFlexisearch = ifelse(flexisearch, "true", "false"),
-      flatResults = ifelse(flat, "true", "false"),
+      flatResults = ifelse(flat, "true", "false")
+    )
+
+  ### Properties ----
+  if (!is.null(properties)) {
+    req <- req |>
+      httr2::req_url_query(
+        propertiesToBeSearched = paste(properties, collapse = ",")
+      )
+  }
+
+  ### Release ID ----
+  if (!is.null(release)) {
+    req <- req |>
+      httr2::req_url_query(releaseId = release)
+  }
+
+  ### Highlighting ----
+  req <- req |>
+    httr2::req_url_query(
       highlightingEnabled = ifelse(highlight, "true", "false")
-    ) |>
+    )
+
+  ## Add headers ----
+  req <- req |>
     httr2::req_headers(
       Accept = "application/json",
       "API-Version" = api_version,
       "Accept-Language" = language
     ) |>
+    ## Authenticate ----
     httr2::req_oauth_client_credentials(
       client = client,
       scope = "icdapi_access"
     ) |>
+    ## Perform request ----
     httr2::req_perform()
 }
 

R/utils.R

@@ -0,0 +1,6 @@
+#'
+#'
+#'
+#'
+#'
+#'

data-raw/icd_linearization_tables.R

@@ -38,6 +38,9 @@ icd11_linearization_mms$Version <- header_values |>
   (\(x) x[2:3])() |>
   paste(collapse = ":")
 
+icd11_linearization_mms <- icd11_linearization_mms |>
+  tibble::tibble()
+
 usethis::use_data(icd11_linearization_mms, overwrite = TRUE, compress = "xz")
 
 ### Simple Table MMS ----
@@ -60,4 +63,7 @@ icd11_simple_table_mms <- read_xlsx(
   sheet = 1, data_only = TRUE
 )
 
+icd11_simple_table_mms |>
+  tibble::tibble()
+
 usethis::use_data(icd11_simple_table_mms, overwrite = TRUE, compress = "xz")

inst/WORDLIST

@@ -6,21 +6,25 @@ ClassKind
 CodeFactor
 Codecov
 DepthInKind
+FullySpecifiedName
 GroupingX
 ICF
 IsLeaf
 IsResidual
 Lifecycle
 LinearizationMiniOutput
+NarrowerTerm
 OAuth
 ORCID
 PrimaryLocation
 RC
 SimpleTabulation
 SupportedClassifications
+URIs
 WIP
 api
 depthinkind
+eg
 es
 etc
 fileName