Merge pull request #310 from mrc-ide/mrc-2727

Update programme test data to include vls indicators
mrc-ide · Nov 10, 2021 · bc8ea2c · bc8ea2c
2 parents bffa1a2 + 7b513f7
commit bc8ea2c
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Showing 10 changed files with 1,087 additions and 519 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -22,7 +22,7 @@ Imports:
     ids,
     jsonlite (>= 1.2.2),
     lgr,
-    naomi (>= 2.5.7),
+    naomi (>= 2.5.8),
     porcelain (>= 0.1.6),
     R6,
     redux,

diff --git a/R/metadata.R b/R/metadata.R
@@ -32,7 +32,11 @@ build_indicator_metadata <- function(metadata) {
     colour = scalar(metadata$colour),
     invert_scale = scalar(metadata$invert_scale),
     scale = scalar(metadata$scale),
-    accuracy = scalar(metadata$accuracy),
+    accuracy = if (is.na(metadata$accuracy)) {
+      json_null()
+    } else {
+      scalar(metadata$accuracy)
+    },
     format = scalar(metadata$format)
   )
 }

diff --git a/tests/testthat/integration-server.R b/tests/testthat/integration-server.R
@@ -88,7 +88,7 @@ test_that("validate programme", {
                c("age", "calendar_quarter", "indicators"))
   expect_length(response$data$filters$age, 2)
   expect_length(response$data$filters$calendar_quarter, 8)
-  expect_length(response$data$filters$indicators, 1)
+  expect_length(response$data$filters$indicators, 4)
 })
 
 test_that("validate ANC", {

diff --git a/tests/testthat/test-endpoints-validate-survey-and-programme.R b/tests/testthat/test-endpoints-validate-survey-and-programme.R
@@ -113,10 +113,19 @@ test_that("possible filters are returned for data", {
   expect_equal(response$filters$calendar_quarter[[1]]$id, scalar("CY2018Q4"))
   expect_equal(response$filters$calendar_quarter[[1]]$label, scalar("December 2018"))
 
-  expect_length(response$filters$indicators, 1)
+  expect_length(response$filters$indicators, 4)
   expect_equal(response$filters$indicators[[1]]$id, scalar("art_current"))
   expect_equal(response$filters$indicators[[1]]$label,
                scalar("ART number (attending)"))
+  expect_equal(response$filters$indicators[[2]]$id, scalar("art_new"))
+  expect_equal(response$filters$indicators[[2]]$label,
+               scalar("ART new"))
+  expect_equal(response$filters$indicators[[3]]$id, scalar("vls_tested"))
+  expect_equal(response$filters$indicators[[3]]$label,
+               scalar("VLS tested"))
+  expect_equal(response$filters$indicators[[4]]$id, scalar("vls_suppressed"))
+  expect_equal(response$filters$indicators[[4]]$label,
+               scalar("VLS tests suppressed"))
 
 
   input <- validate_programme_survey_input(
@@ -176,3 +185,22 @@ test_that("possible filters are returned for data", {
   expect_equal(response$filters$indicators[[4]]$label,
                scalar("Viral load suppression"))
 })
+
+test_that("filters not returned if indicator missing from input data", {
+  input <- validate_programme_survey_input(
+    file.path("testdata", "programme_no_vls.csv"),
+    "programme",
+    file.path("testdata", "malawi.geojson"))
+  response <- validate_survey_programme(input)
+
+  expect_equal(names(response$filters),
+               c("age", "calendar_quarter", "indicators"))
+
+  expect_length(response$filters$indicators, 2)
+  expect_equal(response$filters$indicators[[1]]$id, scalar("art_current"))
+  expect_equal(response$filters$indicators[[1]]$label,
+               scalar("ART number (attending)"))
+  expect_equal(response$filters$indicators[[2]]$id, scalar("art_new"))
+  expect_equal(response$filters$indicators[[2]]$label,
+               scalar("ART new"))
+})
diff --git a/tests/testthat/test-filters.R b/tests/testthat/test-filters.R
@@ -211,9 +211,15 @@ test_that("can get indicator filters for programme data", {
   programme <- read_csv(programme_path, header = TRUE)
   filters <- get_indicator_filters(programme, "programme")
 
-  expect_length(filters, 1)
+  expect_length(filters, 4)
   expect_equal(filters[[1]]$id, scalar("art_current"))
   expect_equal(filters[[1]]$label, scalar("ART number (attending)"))
+  expect_equal(filters[[2]]$id, scalar("art_new"))
+  expect_equal(filters[[2]]$label, scalar("ART new"))
+  expect_equal(filters[[3]]$id, scalar("vls_tested"))
+  expect_equal(filters[[3]]$label, scalar("VLS tested"))
+  expect_equal(filters[[4]]$id, scalar("vls_suppressed"))
+  expect_equal(filters[[4]]$label, scalar("VLS tests suppressed"))
 })
 
 test_that("can get indicator filters for anc data", {

diff --git a/tests/testthat/test-metadata.R b/tests/testthat/test-metadata.R
@@ -17,6 +17,17 @@ test_that("can build metadata response", {
                scalar("ANC HIV prevalence"))
   expect_equal(metadata$anc$choropleth$indicators[[2]]$name,
                scalar("ANC prior ART coverage"))
+  expect_length(metadata$programme$choropleth$indicators, 4)
+  programme_indicators <- metadata$programme$choropleth$indicators
+  expect_equal(programme_indicators[[1]]$indicator, scalar("art_current"))
+  expect_equal(programme_indicators[[1]]$name,
+               scalar("ART number (attending)"))
+  expect_equal(programme_indicators[[2]]$indicator, scalar("art_new"))
+  expect_equal(programme_indicators[[2]]$name, scalar("ART new"))
+  expect_equal(programme_indicators[[3]]$indicator, scalar("vls_tested"))
+  expect_equal(programme_indicators[[3]]$name, scalar("VLS tested"))
+  expect_equal(programme_indicators[[4]]$indicator, scalar("vls_suppressed"))
+  expect_equal(programme_indicators[[4]]$name, scalar("VLS tests suppressed"))
 })
 
 test_that("error thrown when metadata contains conflicting information", {

diff --git a/tests/testthat/test-time-series.R b/tests/testthat/test-time-series.R
@@ -14,7 +14,7 @@ test_that("get_programme_time_series returns data and columns", {
   expect_equal(columns[[1]]$id, scalar("plot_type"))
   expect_equal(columns[[1]]$column_id, scalar("plot"))
   expect_equal(columns[[1]]$label, scalar("Plot type"))
-  expect_length(columns[[1]]$values, 5)
+  expect_length(columns[[1]]$values, 20)
   expect_setequal(names(columns[[1]]$values[[1]]),
                   c("id", "label", "description"))
   expect_equal(columns[[2]]$id, scalar("area_level"))

diff --git a/tests/testthat/test-validate-inputs.R b/tests/testthat/test-validate-inputs.R
@@ -106,9 +106,17 @@ test_that("do_validate_programme validates programme file", {
   expect_equal(data$filters$calendar_quarter[[1]]$id, scalar("CY2018Q4"))
   expect_equal(data$filters$calendar_quarter[[1]]$label, scalar("December 2018"))
 
-  expect_length(data$filters$indicators, 1)
+  expect_length(data$filters$indicators, 4)
   expect_equal(data$filters$indicators[[1]]$id, scalar("art_current"))
-  expect_equal(data$filters$indicators[[1]]$label, scalar("ART number (attending)"))
+  expect_equal(data$filters$indicators[[1]]$label,
+               scalar("ART number (attending)"))
+  expect_equal(data$filters$indicators[[2]]$id, scalar("art_new"))
+  expect_equal(data$filters$indicators[[2]]$label, scalar("ART new"))
+  expect_equal(data$filters$indicators[[3]]$id, scalar("vls_tested"))
+  expect_equal(data$filters$indicators[[3]]$label, scalar("VLS tested"))
+  expect_equal(data$filters$indicators[[4]]$id, scalar("vls_suppressed"))
+  expect_equal(data$filters$indicators[[4]]$label,
+               scalar("VLS tests suppressed"))
 })
 
 test_that("do_validate_anc validates ANC file and gets data for plotting", {