jidea-136 use iso3 codes as country ids (#28)

* use iso3 codes as country ids * use iso in test and do not require name match in gdp fetch * default country to THA * use setNames sensibly when getting hospital capacity Co-authored-by: Rich FitzJohn <r.fitzjohn@imperial.ac.uk> --------- Co-authored-by: Rich FitzJohn <r.fitzjohn@imperial.ac.uk>
jameel-institute · Oct 21, 2024 · d260cf9 · d260cf9
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: daedalus.api
 Title: Serve the 'daedalus' model via an API
-Version: 0.0.5
+Version: 0.0.7
 Authors@R: c(
     person("Pratik", "Gupte", , "p.gupte24@imperial.ac.uk", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-5294-7819")),
@@ -12,7 +12,7 @@ License: MIT + file LICENSE
 URL: https://github.com/jameel-institute/daedalus.api
 BugReports: https://github.com/jameel-institute/daedalus.api/issues
 Imports: 
-    daedalus (>= 0.0.17),
+    daedalus (>= 0.0.19),
     docopt,
     dplyr,
     jsonlite,

diff --git a/R/api.R b/R/api.R
@@ -58,11 +58,11 @@ metadata <- function() {
 
   # Set available countries from daedalus package
   # JIDEA-62: use the right version of daedalus/model
-  # we will get ISO ids from daedalus when available
   country_names <- daedalus::country_names
+  country_codes <- daedalus::country_codes_iso3c
 
-  country_options <- lapply(country_names, function(country) {
-    get_option(country, country)
+  country_options <- lapply(seq_along(country_names), function(idx) {
+    get_option(country_codes[[idx]], country_names[[idx]])
   })
   country_idx <- match("country", param_ids)
   response$parameters[[country_idx]]$options <- country_options
@@ -84,9 +84,10 @@ metadata <- function() {
   step <- response$parameters[[hospital_capacity_idx]]$step
   # setNames to get json object not array
   hospital_capacities <- lapply(
-    setNames(country_names, country_names),
-    function(country) {
-      default <- daedalus::daedalus_country(country)$hospital_capacity
+    setNames(country_names, country_codes),
+    function(country_name) {
+      default <- daedalus::daedalus_country(country_name)$hospital_capacity
+
       get_hospital_capacity_range(default, step)
   })
 

diff --git a/R/util.R b/R/util.R
@@ -119,17 +119,14 @@ get_nested_costs <- function(raw_costs) {
 #'
 #' @description Convert daily GVA values to annual GDP values.
 #'
-#' @param x A string giving a country name from among `daedalus::country_names`.
+#' @param x A string giving a country name from among `daedalus::country_names`
+#' or an ISO2 code from among `daedalus::country_codes_iso2c` or an ISO3 code
+#' from among `daedalus::country_codes_iso3c`.
 #'
 #' @return A single number value for the annual GDP of a country in terms of
 #' million dollars. Values are in 2018 terms.
 #' @keyword internal
 get_annual_gdp <- function(x) {
-  stopifnot(
-    "`x` must be a string giving a country name from `daedalus::country_names" =
-      is.character(x) && x %in% daedalus::country_names
-  )
-
   n_days <- 365
 
   x <- daedalus::daedalus_country(x)

diff --git a/inst/json/metadata_0.1.0.json b/inst/json/metadata_0.1.0.json
@@ -6,7 +6,7 @@
       "label": "Country",
       "description": "Select a country to set model parameters for country-specific demographic, patterns of social mixing and economic data",
       "parameterType": "globeSelect",
-      "defaultOption": "Thailand",
+      "defaultOption": "THA",
       "ordered": false,
       "options": null
     },

diff --git a/tests/testthat/test-endpoints.R b/tests/testthat/test-endpoints.R
@@ -53,26 +53,27 @@ test_that("Can get metadata", {
   )
   country_idx <- match("country", expected_parameters)
   country_options <- params[[country_idx]]$options
-  daedalus_countries <- daedalus::country_names
+  daedalus_country_codes <- daedalus::country_codes_iso3c
   # expect country ids to match those from daedalus
   expect_identical(
     vapply(country_options, function(option) {
         option$id
     }, character(1)),
-    daedalus_countries
+    daedalus_country_codes
   )
   # expect country labels to match those from daedalus
+  daedalus_country_names <- daedalus::country_names
   expect_identical(
     vapply(country_options, function(option) {
       option$label
     }, character(1)),
-    daedalus_countries
+    daedalus_country_names
   )
-  expect_identical(params[[country_idx]]$defaultOption, "Thailand")
+  expect_identical(params[[country_idx]]$defaultOption, "THA")
   hosp_cap_idx <- match("hospital_capacity", expected_parameters)
   update_values <- res$data$parameters[[hosp_cap_idx]]$updateNumericFrom$values
-  expect_named(update_values, daedalus_countries)
-  for (country in daedalus_countries) {
+  expect_named(update_values, daedalus_country_codes)
+  for (country in daedalus_country_codes) {
     values <- update_values[[country]]
     expect_identical(values$min %% 100, 0)
     expect_identical(values$default %% 100, 0)

diff --git a/tests/testthat/test-zzz-e2e.R b/tests/testthat/test-zzz-e2e.R
@@ -38,7 +38,7 @@ test_that("can run model, get status and results", {
   data <- list(
     modelVersion = "0.0.2",
     parameters = list(
-      country = "United Kingdom",
+      country = "GBR",
       pathogen = "sars_cov_1",
       response = "economic_closures",
       vaccine = "low",

diff --git a/tests/testthat/test_model_run.R b/tests/testthat/test_model_run.R
@@ -21,7 +21,7 @@ test_that("can run model and return results", {
   mockery::stub(model_run, "get_annual_gdp", mock_get_gdp)
 
   parameters <- list(
-    country = "Canada",
+    country = "CAN",
     pathogen = "influenza_1918",
     response = "elimination",
     vaccine = "high",
@@ -31,7 +31,7 @@ test_that("can run model and return results", {
 
   expect_identical(
     mockery::mock_args(mock_daedalus)[[1]],
-    list("Canada",
+    list("CAN",
          "influenza_1918",
          response_strategy = "elimination",
          response_threshold = 4500,