naomi-agyw-tool-integration

DESCRIPTION

@@ -22,7 +22,7 @@ Imports:
     glue,
     ids,
     jsonlite (>= 1.2.2),
-    naomi (>= 2.9.23),
+    naomi (>= 2.9.24),
     naomi.options (>= 1.1.0),
     porcelain (>= 0.1.8),
     R6,
@@ -48,7 +48,6 @@ Suggests:
     tidyselect,
     withr
 Remotes:
-    mrc-ide/geojsonio,
     mrc-ide/rrq,
     mrc-ide/mockr
 Config/testthat/edition: 3

R/downloads.R

@@ -29,8 +29,8 @@ download <- function(model_output, type, path_results, input, language = NULL) {
       add_state_json(out$path, input$state)
     }
   } else if (type == "agyw") {
-    out <- naomi::hintr_prepare_agyw_download(model_output, input$pjnz,
-                                              download_path)
+    out <- naomi::hintr_prepare_shipp_download(model_output, input$pjnz$path,
+                                               download_path)
   } else {
     func <- switch(type,
                    coarse_output = naomi::hintr_prepare_coarse_age_group_download,

R/endpoints.R

@@ -411,13 +411,13 @@ download_result <- function(queue) {
                          coarse_output = "coarse-output",
                          summary = "summary-report",
                          comparison = "comparison-report",
-                         agyw = "AGYW")
+                         shipp = "SHIPP")
       ext <- switch(res$metadata$type,
                     spectrum = ".zip",
                     coarse_output = ".zip",
                     summary = ".html",
                     comparison = ".html",
-                    agyw = ".xlsx")
+                    shipp = ".xlsx")
       bytes <- readBin(res$path, "raw", n = file.size(res$path))
       bytes <- porcelain::porcelain_add_headers(bytes, list(
         "Content-Disposition" = build_content_disp_header(res$metadata$areas,

R/payload_helpers.R

@@ -1,6 +1,7 @@
 # nocov start
 # These are test helpers so skipping coverage checks, they should not
 # be used by anything in the package
+
 #' Build JSON from template and a set of params
 #'
 #' @param template Template JSON of payload

docker/build

@@ -28,7 +28,7 @@ ENTRYPOINT [ "/bin/bash", "-l", "-c" ]
 EOF
 
 rm -rf naomi
-git clone https://github.com/mrc-ide/naomi
+git clone --single-branch --branch agyw-tool-integration https://github.com/mrc-ide/naomi
 
 if [ -z $NAOMI_SHA ]; then
     git -C $PACKAGE_ROOT/naomi checkout $NAOMI_SHA

scripts/run_model

@@ -1,4 +1,5 @@
 #!/usr/bin/env Rscript
+
 "Run a model and save outputs at specified paths
 Usage:
   run_model (--model-payload=<model-payload> --calibrate-payload=<calibrate-payload> --download-payload=<download-payload> --model-output-path=<output-path> --calibrate-output-path=<calibrate-output-path> --calibrate-plot-path=<calibrate-plot-path> --spectrum-path=<spectrum-path> --coarse-output-path=<coarse-output-path> --summary-report-path=<summary-report-path> --agyw-path=<agyw-path>)
@@ -70,12 +71,27 @@ message(sprintf("Saving coarse output at %s",
 
 summary_report <- naomi::hintr_prepare_summary_report_download(
   calibrated, dat$summary_report_path)
+
 message(sprintf("Saving summary report at %s",
                 normalizePath(dat$summary_report_path, mustWork = TRUE)))
 
+# Create dummy data
+# Create naomi outputs with "MWI_demo" iso3 to align with testing data in
+# naomi.resources
+output <- naomi::read_hintr_output(calibrated$model_output_path)
+
+if(output$output_package$fit$model_options$area_scope == "MWI"){
+
+  agyw_test_outputs <- naomi:::make_shipp_testfiles(calibrated)
+
+} else {
+
+  agyw_test_outputs <- calibrated
+
+}
 
-agyw_tool <- naomi::hintr_prepare_agyw_download(calibrated,
-                                                model_payload$data$pjnz,
-                                                dat$agyw_path)
+agyw_tool <- naomi::hintr_prepare_shipp_download(agyw_test_outputs,
+                                                 model_payload$data$pjnz$path,
+                                                 dat$agyw_path)
 message(sprintf("Saving AGYW tool at %s",
                 normalizePath(dat$agyw_path, mustWork = TRUE)))

tests/testthat/helper-queue.R

@@ -88,6 +88,12 @@ test_queue_result <- function(model = mock_model, calibrate = mock_calibrate,
   )
 }
 
+add_queue_result <- function(queue, res) {
+  new_id <- queue$submit(quote(identity(res)))
+  queue$queue$task_wait(new_id)
+  new_id
+}
+
 prerun_inputs <- list(
   pjnz = "testdata/Malawi2019.PJNZ",
   population = "testdata/population.csv",

tests/testthat/test-01-endpoints-download.R

@@ -851,20 +851,24 @@ test_that("comparison report download errors for old model output", {
     "Model output out of date please re-run model and try again."))
 })
 
-test_that("api can create agyw download", {
+test_that("api can create agyw/shipp download", {
   test_redis_available()
   test_mock_model_available()
   q <- test_queue_result()
   api <- api_build(q$queue)
 
+  res <- q$queue$result(q$calibrate_id)
+  agyw_result <- naomi:::make_shipp_testfiles(res)
+  agyw_result_id <- add_queue_result(q$queue, agyw_result)
+
   ## Prepare body
   payload <- setup_payload_download_request(include_notes = FALSE,
                                             include_state = FALSE,
                                             include_pjnz = TRUE)
 
   ## Submit download request
   submit <- api$request("POST",
-                        paste0("/download/submit/agyw/", q$calibrate_id),
+                        paste0("/download/submit/agyw/", agyw_result_id),
                         body = payload)
   submit_body <- jsonlite::fromJSON(submit$body)
   expect_equal(submit$status, 200)
@@ -890,7 +894,7 @@ test_that("api can create agyw download", {
   expect_equal(res$status, 200)
   expect_equal(res$headers$`Content-Type`, "application/octet-stream")
   expect_match(res$headers$`Content-Disposition`,
-               'attachment; filename="MWI_AGYW_\\d+-\\d+.xlsx"')
+               'attachment; filename="MWI_SHIPP_\\d+-\\d+.xlsx"')
   ## Size of bytes is close to expected
   size <- length(res$body)
   expect_equal(res$headers$`Content-Length`, size)
@@ -902,7 +906,7 @@ test_that("api can create agyw download", {
   expect_equal(head_res$status, 200)
   expect_equal(head_res$headers$`Content-Type`, "application/octet-stream")
   expect_match(head_res$headers$`Content-Disposition`,
-               'attachment; filename="MWI_AGYW_\\d+-\\d+.xlsx"')
+               'attachment; filename="MWI_SHIPP_\\d+-\\d+.xlsx"')
   expect_equal(head_res$headers$`Content-Length`, size)
   ## Plumber uses an empty string to represent an empty body
   expect_null(head_res$body)