From af71bd116d95aa917b602ed2f369214edc0b81e3 Mon Sep 17 00:00:00 2001
From: Rob Ashton <robertashton94@gmail.com>
Date: Fri, 6 Dec 2024 08:20:29 +0000
Subject: [PATCH 1/7] Add function to create datapack download standalone

---
 DESCRIPTION                       |   2 +-
 NEWS.md                           |   4 ++
 R/downloads.R                     |  32 +++++++++
 R/outputs.R                       |  35 +++++----
 inst/traduire/en-translation.json |   1 +
 inst/traduire/fr-translation.json |   1 +
 inst/traduire/pt-translation.json |   1 +
 tests/testthat/test-downloads.R   | 114 ++++++++++++++++++++++++++++++
 8 files changed, 174 insertions(+), 16 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index ddf5d2f8..9c093542 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: naomi
 Title: Naomi Model for Subnational HIV Estimates
-Version: 2.10.4
+Version: 2.10.5
 Authors@R:
     person(given = "Jeff",
            family = "Eaton",
diff --git a/NEWS.md b/NEWS.md
index 424d65fb..3a3f3839 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,7 @@
+# naomi 2.10.5
+
+* Add standalone datapack download so that users do not have to download zip and extract this manually.
+
 # naomi 2.10.4
 
 * If users upload multiple quarters in ART programme data, return only the last quarter per year for input comparison data.
diff --git a/R/downloads.R b/R/downloads.R
index 6216af85..848b8390 100644
--- a/R/downloads.R
+++ b/R/downloads.R
@@ -130,6 +130,34 @@ hintr_prepare_agyw_download <- function(output, pjnz,
   )
 }
 
+#' Prepare Datapack download
+#'
+#' @param output hintr output object
+#' @param path Path to save output file
+#' @param vmmc_file Optional file object, with path, filename and hash for
+#'   VMMC input
+#'
+#' @return Path to output file and metadata for file
+#' @export
+hintr_prepare_datapack_download <- function(output,
+                                            path = tempfile(fileext = ".csv"),
+                                            vmmc_file = NULL) {
+  assert_model_output_version(output)
+  progress <- new_simple_progress()
+  progress$update_progress("PROGRESS_DOWNLOAD_SPECTRUM")
+  model_output <- read_hintr_output(output$model_output_path)
+  options <- yaml::read_yaml(text = model_output$info$options.yml)
+  list(
+    path = save_output_datapack(path, model_output$output_package,
+                                vmmc_file$path),
+    metadata = list(
+      description = build_datapack_description(options),
+      areas = options$area_scope,
+      type = "datapack"
+    )
+  )
+}
+
 build_output_description <- function(options) {
   build_description(t_("DOWNLOAD_OUTPUT_DESCRIPTION"), options)
 }
@@ -146,6 +174,10 @@ build_agyw_tool_description <- function(options) {
   build_description(t_("DOWNLOAD_AGYW_DESCRIPTION"), options)
 }
 
+build_datapack_description <- function(options) {
+  build_description(t_("DOWNLOAD_DATAPACK_DESCRIPTION"), options)
+}
+
 build_description <- function(type_text, options) {
   write_options <- function(name, value) {
     sprintf("%s - %s", name, value)
diff --git a/R/outputs.R b/R/outputs.R
index 8e04f485..d910915c 100644
--- a/R/outputs.R
+++ b/R/outputs.R
@@ -193,7 +193,7 @@ extract_indicators <- function(naomi_fit, naomi_mf, na.rm = FALSE) {
                          "anc_tested_neg_t4_out" = "anc_tested_neg",
                          "anc_rho_t4_out" = "anc_prevalence",
                          "anc_alpha_t4_out" = "anc_art_coverage")
-  
+
 
   indicator_anc_est_t1 <- Map(get_est, names(indicators_anc_t1), indicators_anc_t1,
                               naomi_mf$calendar_quarter1, list(naomi_mf$mf_anc_out))
@@ -886,6 +886,23 @@ save_output_spectrum <- function(path, naomi_output, notes = NULL,
               export_datapack = TRUE)
 }
 
+save_output_datapack <- function(path, naomi_output, vmmc_path = NULL) {
+  if (!is.null(vmmc_path)) {
+    ## Skip the first row, the file has two rows of headers
+    vmmc_datapack_raw <- openxlsx::read.xlsx(vmmc_path, sheet = "Datapack inputs",
+                                             startRow = 2)
+    vmmc_datapack <- transform_dmppt2(vmmc_datapack_raw)
+  } else {
+    vmmc_datapack <- NULL
+  }
+
+  write_datapack_csv(naomi_output = naomi_output,
+                     path = path,
+                     psnu_level = naomi_output$fit$model_options$psnu_level,
+                     dmppt2_output = vmmc_datapack)
+}
+
+
 #' Save outputs to zip file
 #'
 #' @param naomi_output Naomi output object
@@ -994,20 +1011,8 @@ save_output <- function(filename, dir,
   }
 
   if (export_datapack) {
-
-    if (!is.null(vmmc_path)) {
-      ## Skip the first row, the file has two rows of headers
-      vmmc_datapack_raw <- openxlsx::read.xlsx(vmmc_path, sheet = "Datapack inputs",
-                                               startRow = 2)
-      vmmc_datapack <- transform_dmppt2(vmmc_datapack_raw)
-    } else {
-      vmmc_datapack <- NULL
-    }
-
-    write_datapack_csv(naomi_output = naomi_output,
-                       path = PEPFAR_DATAPACK_FILENAME,   # global defined in R/pepfar-datapack.R
-                       psnu_level = naomi_output$fit$model_options$psnu_level,
-                       dmppt2_output = vmmc_datapack)
+    # PEPFAR_DATAPACK_FILENAME global defined in R/pepfar-datapack.R
+    save_output_datapack(PEPFAR_DATAPACK_FILENAME, naomi_output, vmmc_path)
   }
 
 
diff --git a/inst/traduire/en-translation.json b/inst/traduire/en-translation.json
index 8d65b654..78f07efd 100644
--- a/inst/traduire/en-translation.json
+++ b/inst/traduire/en-translation.json
@@ -274,6 +274,7 @@
     "DOWNLOAD_SUMMARY_DESCRIPTION": "Naomi summary report uploaded from Naomi web app",
     "DOWNLOAD_COMPARISON_DESCRIPTION": "Naomi comparison report uploaded from Naomi web app",
     "DOWNLOAD_AGYW_DESCRIPTION": "Naomi AGYW tool uploaded from Naomi web app",
+    "DOWNLOAD_DATAPACK_DESCRIPTION": "Naomi datapack output uploaded from Naomi web app",
     "NUMBER_ON_ART": "Number on ART",
     "NUMBER_ON_ART_DESC": "Number on ART description",
     "POPULATION_PROPORTION": "Population proportion",
diff --git a/inst/traduire/fr-translation.json b/inst/traduire/fr-translation.json
index 6d785c48..60c7d9e2 100644
--- a/inst/traduire/fr-translation.json
+++ b/inst/traduire/fr-translation.json
@@ -271,6 +271,7 @@
     "DOWNLOAD_OUTPUT_DESCRIPTION": "Paquet Naomi téléchargée depuis l'application web Naomi",
     "DOWNLOAD_SUMMARY_DESCRIPTION": "Rapport de synthèse Naomi téléchargé depuis l'application web Naomi",
     "DOWNLOAD_COMPARISON_DESCRIPTION": "Rapport de comparaison Naomi téléchargé à partir de l'application web Naomi",
+    "DOWNLOAD_DATAPACK_DESCRIPTION": "Sortie du datapack Naomi téléchargée depuis l'application web Naomi",
     "NUMBER_ON_ART": "Nombre de personnes sous TARV",
     "NUMBER_ON_ART_DESC": "Number on ART description",
     "POPULATION_PROPORTION": "Proportion de la population",
diff --git a/inst/traduire/pt-translation.json b/inst/traduire/pt-translation.json
index effd3d56..3b5622cb 100644
--- a/inst/traduire/pt-translation.json
+++ b/inst/traduire/pt-translation.json
@@ -271,6 +271,7 @@
     "DOWNLOAD_OUTPUT_DESCRIPTION": "Pacote Naomi descarregado a partir da aplicação web Naomi",
     "DOWNLOAD_SUMMARY_DESCRIPTION": "Relatório de síntese da Naomi carregado da aplicação web Naomi",
     "DOWNLOAD_COMPARISON_DESCRIPTION": "Relatório de comparação Naomi carregado a partir da aplicação web Naomi",
+    "DOWNLOAD_DATAPACK_DESCRIPTION": "Saída do Naomi datapack carregada a partir da aplicação web Naomi",
     "NUMBER_ON_ART": "Nombre de personnes sous TARV",
     "NUMBER_ON_ART_DESC": "Number on ART description",
     "POPULATION_PROPORTION": "Proporção da população",
diff --git a/tests/testthat/test-downloads.R b/tests/testthat/test-downloads.R
index 7f46686f..17b4f1ff 100644
--- a/tests/testthat/test-downloads.R
+++ b/tests/testthat/test-downloads.R
@@ -227,3 +227,117 @@ test_that("output description is translated", {
   expect_match(text, paste0("Paquet Naomi téléchargée depuis l'application ",
                             "web Naomi\\n\\nPérimètre de zone - MWI\\n.+"))
 })
+
+test_that("spectrum download can be created", {
+  mock_new_simple_progress <- mockery::mock(MockSimpleProgress$new())
+  notes <- "these are my\nmultiline notes"
+  with_mock(new_simple_progress = mock_new_simple_progress, {
+    messages <- naomi_evaluate_promise(
+      out <- hintr_prepare_spectrum_download(a_hintr_output_calibrated,
+                                             notes = notes))
+  })
+  expect_true(file.exists(out$path))
+
+  expect_type(out$metadata$description, "character")
+  expect_length(out$metadata$description, 1)
+  expect_equal(out$metadata$areas, "MWI")
+
+  tmp <- tempfile()
+  info <- naomi_info(format_data_input(a_hintr_data), a_hintr_options)
+  info_names <- paste0("info/", names(info))
+  unzip(out$path, exdir = tmp, files = info_names)
+  expect_equal(dir(tmp), "info")
+  expect_equal(dir(file.path(tmp, "info")), names(info))
+
+
+  ## # UNAIDS Navigator Checklist checks
+  navigator_checklist <- utils::read.csv(unz(out$path, "info/unaids_navigator_checklist.csv"))
+
+
+  expect_equal(names(navigator_checklist),
+               c("NaomiCheckPermPrimKey", "NaomiCheckDes", "TrueFalse"))
+
+  checklist_primkeys <- c( "ART_is_Spectrum","ANC_is_Spectrum","Package_created",
+                           "Package_has_all_data","Opt_recent_qtr","Opt_future_proj_qtr",
+                           "Opt_area_ID_selected","Opt_calendar_survey_match","Opt_recent_survey_only",
+                           "Opt_ART_coverage","Opt_ANC_data","Opt_ART_data",
+                           "Opt_ART_attendance_yes","Model_fit","Cal_Population",
+                           "Cal_PLHIV","Cal_ART","Cal_KOS",
+                           "Cal_new_infections","Cal_method" )
+  expect_equal(navigator_checklist$NaomiCheckPermPrimKey, checklist_primkeys)
+  expect_true(all(navigator_checklist$TrueFalse %in% c(TRUE, FALSE)))
+  ## Check tradiure translation hooks worked
+  expect_true("Calibration - method is logistic" %in% navigator_checklist$NaomiCheckDes)
+
+
+  outputs <- read_output_package(out$path)
+  expect_true(
+    all(c("area_level", "area_level_label", "area_id", "area_name", "parent_area_id",
+          "spectrum_region_code", "area_sort_order", "geometry") %in%
+          names(outputs$meta_area))
+  )
+
+  tmpf <- tempfile()
+  unzip(out$path, "boundaries.geojson", exdir = tmpf)
+  output_boundaries <- sf::read_sf(file.path(tmpf, "boundaries.geojson"))
+
+  ## Column 'name' added in boundaries.geojson during save_output() for Spectrum
+  expect_true(
+    all(c("area_level", "area_level_label", "area_id", "area_name", "parent_area_id",
+          "spectrum_region_code", "area_sort_order", "name", "geometry") %in%
+          names(output_boundaries))
+  )
+
+  ## Progress messages printed
+  expect_length(messages$progress, 1)
+  expect_equal(messages$progress[[1]]$message,
+               "Generating output zip download")
+
+  ## Notes are saved
+  t <- tempfile()
+  unzip(out$path, "notes.txt", exdir = t)
+  saved_notes <- readLines(file.path(t, "notes.txt"))
+  expect_equal(saved_notes, c("these are my", "multiline notes"))
+})
+
+test_that("datapack download can be created", {
+  mock_new_simple_progress <- mockery::mock(MockSimpleProgress$new())
+  with_mock(new_simple_progress = mock_new_simple_progress, {
+    messages <- naomi_evaluate_promise(
+      out <- hintr_prepare_datapack_download(a_hintr_output_calibrated))
+  })
+  expect_true(file.exists(out$path))
+
+  expect_type(out$metadata$description, "character")
+  expect_length(out$metadata$description, 1)
+  expect_equal(out$metadata$areas, "MWI")
+
+  datapack <- utils::read.csv(out$path)
+
+  expect_true("psnu_uid" %in% colnames(datapack))
+  expect_true(!any(is.na(datapack)))
+  ## Simple smoke test that we have some indicator code
+  expect_true("HIV_PREV.T_1" %in% datapack$indicator_code)
+})
+
+test_that("datapack download can include vmmc data", {
+  mock_new_simple_progress <- mockery::mock(MockSimpleProgress$new())
+  vmmc_file <- list(path = file.path("testdata", "vmmc.xlsx"),
+                    hash = "123",
+                    filename = "vmmc.xlsx")
+  testthat::with_mocked_bindings(
+    messages <- naomi_evaluate_promise(
+      out <- hintr_prepare_datapack_download(a_hintr_output_calibrated,
+                                             vmmc_file = vmmc_file)
+    ),
+    new_simple_progress = mock_new_simple_progress
+  )
+  expect_true(file.exists(out$path))
+
+  datapack <- utils::read.csv(out$path)
+
+  expect_true("psnu_uid" %in% colnames(datapack))
+  expect_true(!any(is.na(datapack)))
+  expect_true(all(c("VMMC_CIRC_SUBNAT.T_1", "VMMC_TOTALCIRC_SUBNAT.T_1") %in%
+                    datapack$indicator_code))
+})

From 937554391247c6a1b77d9822bca656eba141a3eb Mon Sep 17 00:00:00 2001
From: Rob Ashton <robertashton94@gmail.com>
Date: Fri, 6 Dec 2024 10:56:01 +0000
Subject: [PATCH 2/7] Regen docs

---
 NAMESPACE                              |  1 +
 man/hintr_prepare_datapack_download.Rd | 26 ++++++++++++++++++++++++++
 2 files changed, 27 insertions(+)
 create mode 100644 man/hintr_prepare_datapack_download.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 2bd06c28..a5e29c55 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -50,6 +50,7 @@ export(hintr_comparison_plot)
 export(hintr_prepare_agyw_download)
 export(hintr_prepare_coarse_age_group_download)
 export(hintr_prepare_comparison_report_download)
+export(hintr_prepare_datapack_download)
 export(hintr_prepare_spectrum_download)
 export(hintr_prepare_summary_report_download)
 export(hintr_run_model)
diff --git a/man/hintr_prepare_datapack_download.Rd b/man/hintr_prepare_datapack_download.Rd
new file mode 100644
index 00000000..1e55dfa3
--- /dev/null
+++ b/man/hintr_prepare_datapack_download.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/downloads.R
+\name{hintr_prepare_datapack_download}
+\alias{hintr_prepare_datapack_download}
+\title{Prepare Datapack download}
+\usage{
+hintr_prepare_datapack_download(
+  output,
+  path = tempfile(fileext = ".csv"),
+  vmmc_file = NULL
+)
+}
+\arguments{
+\item{output}{hintr output object}
+
+\item{path}{Path to save output file}
+
+\item{vmmc_file}{Optional file object, with path, filename and hash for
+VMMC input}
+}
+\value{
+Path to output file and metadata for file
+}
+\description{
+Prepare Datapack download
+}

From 9f4de2cb0ad22aa8e732872f8bcbed59c042375f Mon Sep 17 00:00:00 2001
From: Rob Ashton <robertashton94@gmail.com>
Date: Mon, 9 Dec 2024 19:24:36 +0000
Subject: [PATCH 3/7] Return datapack download as an xlsx file

---
 R/downloads.R                   | 18 ++++++++++--
 R/outputs.R                     | 15 ++++++----
 R/pepfar-datapack.R             | 52 ++++++++++++++++++++++++++-------
 tests/testthat/test-downloads.R | 14 +++++++--
 4 files changed, 79 insertions(+), 20 deletions(-)

diff --git a/R/downloads.R b/R/downloads.R
index 848b8390..9f125ad8 100644
--- a/R/downloads.R
+++ b/R/downloads.R
@@ -140,16 +140,28 @@ hintr_prepare_agyw_download <- function(output, pjnz,
 #' @return Path to output file and metadata for file
 #' @export
 hintr_prepare_datapack_download <- function(output,
-                                            path = tempfile(fileext = ".csv"),
+                                            path = tempfile(fileext = ".xlsx"),
                                             vmmc_file = NULL) {
   assert_model_output_version(output)
   progress <- new_simple_progress()
   progress$update_progress("PROGRESS_DOWNLOAD_SPECTRUM")
+
+  if (!grepl("\\.xlsx$", path, ignore.case = TRUE)) {
+    path <- paste0(path, ".xlsx")
+  }
+
   model_output <- read_hintr_output(output$model_output_path)
   options <- yaml::read_yaml(text = model_output$info$options.yml)
+  vmmc_datapack <- datapack_read_vmmc(vmmc_file$path)
+  datapack_output <- build_datapack_output(
+    model_output$output_package,
+    model_output$output_package$fit$model_options$psnu_level,
+    vmmc_datapack)
+  datapack_metadata <- build_datapack_metadata(model_output$output_package)
+  writexl::write_xlsx(list(data = datapack_output, metadata = datapack_metadata),
+                      path = path)
   list(
-    path = save_output_datapack(path, model_output$output_package,
-                                vmmc_file$path),
+    path = path,
     metadata = list(
       description = build_datapack_description(options),
       areas = options$area_scope,
diff --git a/R/outputs.R b/R/outputs.R
index d910915c..e81bfddf 100644
--- a/R/outputs.R
+++ b/R/outputs.R
@@ -887,6 +887,15 @@ save_output_spectrum <- function(path, naomi_output, notes = NULL,
 }
 
 save_output_datapack <- function(path, naomi_output, vmmc_path = NULL) {
+  vmmc_datapack <- datapack_read_vmmc(vmmc_path)
+
+  write_datapack_csv(naomi_output = naomi_output,
+                     path = path,
+                     psnu_level = naomi_output$fit$model_options$psnu_level,
+                     dmppt2_output = vmmc_datapack)
+}
+
+datapack_read_vmmc <- function(vmmc_path) {
   if (!is.null(vmmc_path)) {
     ## Skip the first row, the file has two rows of headers
     vmmc_datapack_raw <- openxlsx::read.xlsx(vmmc_path, sheet = "Datapack inputs",
@@ -895,11 +904,7 @@ save_output_datapack <- function(path, naomi_output, vmmc_path = NULL) {
   } else {
     vmmc_datapack <- NULL
   }
-
-  write_datapack_csv(naomi_output = naomi_output,
-                     path = path,
-                     psnu_level = naomi_output$fit$model_options$psnu_level,
-                     dmppt2_output = vmmc_datapack)
+  vmmc_datapack
 }
 
 
diff --git a/R/pepfar-datapack.R b/R/pepfar-datapack.R
index d808b69a..84479c93 100644
--- a/R/pepfar-datapack.R
+++ b/R/pepfar-datapack.R
@@ -31,12 +31,19 @@ write_datapack_csv <- function(naomi_output,
                                psnu_level = NULL,
                                dmppt2_output = NULL) {
 
-  stopifnot(inherits(naomi_output, "naomi_output"))
-
   if (!grepl("\\.csv$", path, ignore.case = TRUE)) {
     path <- paste0(path, ".csv")
   }
 
+  datapack <- build_datapack_output(naomi_output, psnu_level, dmppt2_output)
+  naomi_write_csv(datapack, path)
+
+  path
+}
+
+build_datapack_output <- function(naomi_output, psnu_level, dmppt2_output) {
+  stopifnot(inherits(naomi_output, "naomi_output"))
+
   datapack_indicator_map <- naomi_read_csv(system_file("datapack", "datapack_indicator_mapping.csv"))
   datapack_age_group_map <- naomi_read_csv(system_file("datapack", "datapack_age_group_mapping.csv"))
   datapack_sex_map <- naomi_read_csv(system_file("datapack", "datapack_sex_mapping.csv"))
@@ -73,7 +80,7 @@ write_datapack_csv <- function(naomi_output,
     dplyr::rename(
       indicator_code = datapack_indicator_code,
       dataelement_uid = datapack_indicator_id,
-      ) %>%
+    ) %>%
     dplyr::select(indicator, indicator_code, dataelement_uid, is_integer, calendar_quarter)
 
 
@@ -128,10 +135,10 @@ write_datapack_csv <- function(naomi_output,
       by = c("indicator", "calendar_quarter")
     ) %>%
     dplyr::filter(
-    (sex_naomi %in% datapack_sex_map$sex_naomi &
-       age_group %in% datapack_age_group_map$age_group |
-       sex_naomi == "both" & age_group == "Y000_999" & !anc_indicator |
-       sex_naomi == "female" & age_group == "Y015_049" & anc_indicator )
+      (sex_naomi %in% datapack_sex_map$sex_naomi &
+         age_group %in% datapack_age_group_map$age_group |
+         sex_naomi == "both" & age_group == "Y000_999" & !anc_indicator |
+         sex_naomi == "female" & age_group == "Y015_049" & anc_indicator )
     ) %>%
     dplyr::transmute(
       area_id,
@@ -176,7 +183,7 @@ write_datapack_csv <- function(naomi_output,
   dat <- dplyr::left_join(dat, psnu_map, by = "area_id")
   dat$psnu <- ifelse(is.na(dat$map_name), dat$area_name, dat$map_name)
 
-  datapack <- dat %>%
+  dat %>%
     dplyr::select(
       psnu,
       psnu_uid,
@@ -192,10 +199,35 @@ write_datapack_csv <- function(naomi_output,
       age_sex_rse,
       district_rse
     )
+}
 
-  naomi_write_csv(datapack, path)
+build_datapack_metadata <- function(naomi_output) {
+  meta_period <- get_period_metadata(
+    c(naomi_output$fit$model_options$calendar_quarter_t1,
+      naomi_output$fit$model_options$calendar_quarter_t2,
+      naomi_output$fit$model_options$calendar_quarter_t3,
+      naomi_output$fit$model_options$calendar_quarter_t4,
+      naomi_output$fit$model_options$calendar_quarter_t5))
+  info <- attr(naomi_output, "info")
+  inputs <- read.csv(text = info$inputs.csv, header = FALSE)
+
+  version <- data.frame("version", utils::packageVersion("naomi"))
+  all_data <- list(version, inputs)
+
+  max_cols <- max(vapply(all_data, ncol, numeric(1)))
+  col_names <- vapply(seq_len(max_cols), function(i) paste0("V", i), character(1))
+  empty_row <- data.frame(matrix("", ncol = max_cols, nrow = 1))
+  colnames(empty_row) <- col_names
+  all_data <- lapply(all_data, function(df) {
+    colnames(df) <- col_names[seq(1, ncol(df))]
+    if (ncol(df) < max_cols) {
+      df[, col_names[seq(ncol(df) + 1, max_cols)]] <- ""
+    }
+    df[] <- lapply(df, as.character)
+    rbind.data.frame(df, empty_row)
+  })
 
-  path
+  do.call(rbind.data.frame, all_data)
 }
 
 
diff --git a/tests/testthat/test-downloads.R b/tests/testthat/test-downloads.R
index 17b4f1ff..37fc7c8e 100644
--- a/tests/testthat/test-downloads.R
+++ b/tests/testthat/test-downloads.R
@@ -312,12 +312,17 @@ test_that("datapack download can be created", {
   expect_length(out$metadata$description, 1)
   expect_equal(out$metadata$areas, "MWI")
 
-  datapack <- utils::read.csv(out$path)
+  datapack <- readxl::read_xlsx(out$path, "data")
 
   expect_true("psnu_uid" %in% colnames(datapack))
   expect_true(!any(is.na(datapack)))
   ## Simple smoke test that we have some indicator code
   expect_true("HIV_PREV.T_1" %in% datapack$indicator_code)
+
+  metadata <- readxl::read_xlsx(out$path, "metadata")
+
+  expect_true(nrow(metadata) > 0)
+  expect_equal(as.character(metadata[1, 1]), "version")
 })
 
 test_that("datapack download can include vmmc data", {
@@ -334,10 +339,15 @@ test_that("datapack download can include vmmc data", {
   )
   expect_true(file.exists(out$path))
 
-  datapack <- utils::read.csv(out$path)
+  datapack <- readxl::read_xlsx(out$path, "data")
 
   expect_true("psnu_uid" %in% colnames(datapack))
   expect_true(!any(is.na(datapack)))
   expect_true(all(c("VMMC_CIRC_SUBNAT.T_1", "VMMC_TOTALCIRC_SUBNAT.T_1") %in%
                     datapack$indicator_code))
+
+  metadata <- readxl::read_xlsx(out$path, "metadata")
+
+  expect_true(nrow(metadata) > 0)
+  expect_equal(as.character(metadata[1, 1]), "version")
 })

From 2a3f62669ecdd6928ea93d134b39f21f4c2b4ba3 Mon Sep 17 00:00:00 2001
From: Rob Ashton <robertashton94@gmail.com>
Date: Tue, 10 Dec 2024 07:40:51 +0000
Subject: [PATCH 4/7] Add model fit and calibrate ids into the datapack
 download

---
 R/downloads.R       |  6 ++++--
 R/pepfar-datapack.R | 10 ++++++++--
 2 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/R/downloads.R b/R/downloads.R
index 9f125ad8..2f3ee899 100644
--- a/R/downloads.R
+++ b/R/downloads.R
@@ -136,12 +136,14 @@ hintr_prepare_agyw_download <- function(output, pjnz,
 #' @param path Path to save output file
 #' @param vmmc_file Optional file object, with path, filename and hash for
 #'   VMMC input
+#' @param ids List of naomi web app queue ids for putting into metadata
 #'
 #' @return Path to output file and metadata for file
 #' @export
 hintr_prepare_datapack_download <- function(output,
                                             path = tempfile(fileext = ".xlsx"),
-                                            vmmc_file = NULL) {
+                                            vmmc_file = NULL,
+                                            ids = NULL) {
   assert_model_output_version(output)
   progress <- new_simple_progress()
   progress$update_progress("PROGRESS_DOWNLOAD_SPECTRUM")
@@ -157,7 +159,7 @@ hintr_prepare_datapack_download <- function(output,
     model_output$output_package,
     model_output$output_package$fit$model_options$psnu_level,
     vmmc_datapack)
-  datapack_metadata <- build_datapack_metadata(model_output$output_package)
+  datapack_metadata <- build_datapack_metadata(model_output$output_package, ids)
   writexl::write_xlsx(list(data = datapack_output, metadata = datapack_metadata),
                       path = path)
   list(
diff --git a/R/pepfar-datapack.R b/R/pepfar-datapack.R
index 84479c93..c5ddb66b 100644
--- a/R/pepfar-datapack.R
+++ b/R/pepfar-datapack.R
@@ -201,18 +201,24 @@ build_datapack_output <- function(naomi_output, psnu_level, dmppt2_output) {
     )
 }
 
-build_datapack_metadata <- function(naomi_output) {
+build_datapack_metadata <- function(naomi_output, ids) {
   meta_period <- get_period_metadata(
     c(naomi_output$fit$model_options$calendar_quarter_t1,
       naomi_output$fit$model_options$calendar_quarter_t2,
       naomi_output$fit$model_options$calendar_quarter_t3,
       naomi_output$fit$model_options$calendar_quarter_t4,
       naomi_output$fit$model_options$calendar_quarter_t5))
+
   info <- attr(naomi_output, "info")
   inputs <- read.csv(text = info$inputs.csv, header = FALSE)
 
   version <- data.frame("version", utils::packageVersion("naomi"))
-  all_data <- list(version, inputs)
+
+  if (!is.null(ids)) {
+    all_data <- list(version, ids, inputs, meta_period)
+  } else {
+    all_data <- list(version, inputs, meta_period)
+  }
 
   max_cols <- max(vapply(all_data, ncol, numeric(1)))
   col_names <- vapply(seq_len(max_cols), function(i) paste0("V", i), character(1))

From 53ceefc21e62aa3558796089bdab86f2237534c3 Mon Sep 17 00:00:00 2001
From: Rob Ashton <robertashton94@gmail.com>
Date: Tue, 10 Dec 2024 09:47:14 +0000
Subject: [PATCH 5/7] Update docs

---
 man/hintr_prepare_datapack_download.Rd | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/man/hintr_prepare_datapack_download.Rd b/man/hintr_prepare_datapack_download.Rd
index 1e55dfa3..44ee5c5f 100644
--- a/man/hintr_prepare_datapack_download.Rd
+++ b/man/hintr_prepare_datapack_download.Rd
@@ -6,8 +6,9 @@
 \usage{
 hintr_prepare_datapack_download(
   output,
-  path = tempfile(fileext = ".csv"),
-  vmmc_file = NULL
+  path = tempfile(fileext = ".xlsx"),
+  vmmc_file = NULL,
+  ids = NULL
 )
 }
 \arguments{
@@ -17,6 +18,8 @@ hintr_prepare_datapack_download(
 
 \item{vmmc_file}{Optional file object, with path, filename and hash for
 VMMC input}
+
+\item{ids}{List of naomi web app queue ids for putting into metadata}
 }
 \value{
 Path to output file and metadata for file

From c4fb54817ddfcfbafd4fa3725f051776aa821a3b Mon Sep 17 00:00:00 2001
From: Rob Ashton <robertashton94@gmail.com>
Date: Tue, 10 Dec 2024 10:17:38 +0000
Subject: [PATCH 6/7] Format the time point output differently

---
 R/pepfar-datapack.R             | 16 +++++++++-------
 tests/testthat/test-downloads.R |  2 +-
 2 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/R/pepfar-datapack.R b/R/pepfar-datapack.R
index c5ddb66b..816d55d9 100644
--- a/R/pepfar-datapack.R
+++ b/R/pepfar-datapack.R
@@ -202,17 +202,19 @@ build_datapack_output <- function(naomi_output, psnu_level, dmppt2_output) {
 }
 
 build_datapack_metadata <- function(naomi_output, ids) {
-  meta_period <- get_period_metadata(
-    c(naomi_output$fit$model_options$calendar_quarter_t1,
-      naomi_output$fit$model_options$calendar_quarter_t2,
-      naomi_output$fit$model_options$calendar_quarter_t3,
-      naomi_output$fit$model_options$calendar_quarter_t4,
-      naomi_output$fit$model_options$calendar_quarter_t5))
+  cqs <- c(naomi_output$fit$model_options$calendar_quarter_t1,
+           naomi_output$fit$model_options$calendar_quarter_t2,
+           naomi_output$fit$model_options$calendar_quarter_t3,
+           naomi_output$fit$model_options$calendar_quarter_t4,
+           naomi_output$fit$model_options$calendar_quarter_t5)
+  meta_period <- data.frame(
+    c("Time point", "t1", "t2", "t3", "t4", "t5"), c("Quarter", cqs)
+  )
 
   info <- attr(naomi_output, "info")
   inputs <- read.csv(text = info$inputs.csv, header = FALSE)
 
-  version <- data.frame("version", utils::packageVersion("naomi"))
+  version <- data.frame("Version", utils::packageVersion("naomi"))
 
   if (!is.null(ids)) {
     all_data <- list(version, ids, inputs, meta_period)
diff --git a/tests/testthat/test-downloads.R b/tests/testthat/test-downloads.R
index 37fc7c8e..6562b223 100644
--- a/tests/testthat/test-downloads.R
+++ b/tests/testthat/test-downloads.R
@@ -349,5 +349,5 @@ test_that("datapack download can include vmmc data", {
   metadata <- readxl::read_xlsx(out$path, "metadata")
 
   expect_true(nrow(metadata) > 0)
-  expect_equal(as.character(metadata[1, 1]), "version")
+  expect_equal(as.character(metadata[1, 1]), "Version")
 })

From 782e6b80d8b87564c829ab0ba636cdbe85dbf814 Mon Sep 17 00:00:00 2001
From: Rob Ashton <robertashton94@gmail.com>
Date: Tue, 10 Dec 2024 15:08:16 +0000
Subject: [PATCH 7/7] Update version number label in datapack download and test

---
 R/pepfar-datapack.R             | 2 +-
 tests/testthat/test-downloads.R | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/pepfar-datapack.R b/R/pepfar-datapack.R
index 816d55d9..dd051d29 100644
--- a/R/pepfar-datapack.R
+++ b/R/pepfar-datapack.R
@@ -214,7 +214,7 @@ build_datapack_metadata <- function(naomi_output, ids) {
   info <- attr(naomi_output, "info")
   inputs <- read.csv(text = info$inputs.csv, header = FALSE)
 
-  version <- data.frame("Version", utils::packageVersion("naomi"))
+  version <- data.frame("Naomi Version", utils::packageVersion("naomi"))
 
   if (!is.null(ids)) {
     all_data <- list(version, ids, inputs, meta_period)
diff --git a/tests/testthat/test-downloads.R b/tests/testthat/test-downloads.R
index 6562b223..0849cdd2 100644
--- a/tests/testthat/test-downloads.R
+++ b/tests/testthat/test-downloads.R
@@ -322,7 +322,7 @@ test_that("datapack download can be created", {
   metadata <- readxl::read_xlsx(out$path, "metadata")
 
   expect_true(nrow(metadata) > 0)
-  expect_equal(as.character(metadata[1, 1]), "version")
+  expect_equal(as.character(metadata[1, 1]), "Naomi Version")
 })
 
 test_that("datapack download can include vmmc data", {
@@ -349,5 +349,5 @@ test_that("datapack download can include vmmc data", {
   metadata <- readxl::read_xlsx(out$path, "metadata")
 
   expect_true(nrow(metadata) > 0)
-  expect_equal(as.character(metadata[1, 1]), "Version")
+  expect_equal(as.character(metadata[1, 1]), "Naomi Version")
 })