tests/testthat/test-convert_bds_individual.R

In stefvanbuuren/minihealth: Mini Dossier for Individual Health Data

context("convert_bds_individual")

# test the empty object
js1 <- '{"OrganisatieCode":0,"ClientGegevens":{}}'
test_that("handles the empty individual object",
           expect_message(is.individual(convert_bds_individual(js1)),
                          "should have required property 'Elementen'"))

# test the minimal object
minimal <- new("individual", sex = "male", dob = as.Date("20181231", "%Y%m%d"))
js2 <- minihealth::convert_individual_bds(minimal)
test_that("handles the minimal individual object",
          expect_message(convert_bds_individual(js2),
                         "Missing 'Contactmomenten'",
                         fixed = TRUE))

# test the below minimal (without sex field)
below <- new("individual", dob = as.Date("20181231", "%Y%m%d"))
js3 <- minihealth::convert_individual_bds(below)
test_that("handles the below minimal object",
          expect_message(convert_bds_individual(js3),
                         "verplicht BDS nummer ontbreekt: 19"))

jtf <- system.file("extdata", "test", paste0("test", 1:24, ".json"), package = "jamestest")

test_that("test1.json (client3.json) passes convert_individual_bds()",
          expect_s4_class(convert_bds_individual(jtf[1]), "individual"))

test_that("test2.json (missing Referentie) PASSES",
          expect_s4_class(convert_bds_individual(jtf[2]), "individual"))

test_that("test3.json (missing OrganisatieCode) MESS",
          expect_message(convert_bds_individual(jtf[3]),
                       "should have required property 'OrganisatieCode'"))

test_that("test4.json (wrong type) MESS",
          expect_message(convert_bds_individual(jtf[4]),
                       ".OrganisatieCode should be integer"))

test_that("test5.json (missing ClientGegevens) MESS",
          expect_message(convert_bds_individual(jtf[5]),
                       "should have required property 'ClientGegevens'"))

test_that("test6.json (Missing ContactMomenten) MESS",
          expect_message(convert_bds_individual(jtf[6]),
                         "Missing 'Contactmomenten'",
                         fixed = TRUE))

test_that("test7.json (Missing Referentie & OrganisatieCode) MESS",
          expect_message(convert_bds_individual(jtf[7]),
                       "should have required property 'OrganisatieCode'"))

test_that("test8.json (Invalid JSON) ERROR",
          expect_error(convert_bds_individual(jtf[8]),
                         "lexical error: invalid char in json text."))

test_that("test9.json (Bdsnummer 19 missing) MESS",
          expect_message(convert_bds_individual(jtf[9]),
                         "verplicht BDS nummer ontbreekt: 19"))

test_that("test10.json (Bdsnummer 20 missing) MESS",
          expect_message(convert_bds_individual(jtf[10]),
                         "verplicht BDS nummer ontbreekt: 20"))

test_that("test11.json (Bdsnummer 82 missing) MESS",
          expect_message(convert_bds_individual(jtf[11]),
                         "BDS 82 (Zwangerschapsduur in dagen) heeft geen waarde",
                         fixed = TRUE))

test_that("test12.json (Bdsnummer 91 missing) PASSES",
          expect_silent(convert_bds_individual(jtf[12])))

test_that("test13.json (Bdsnummer 110 missing) MESS",
          expect_message(convert_bds_individual(jtf[13]),
                         "BDS 110 (Geboortegewicht in grammen: heeft geen waarde",
                         fixed = TRUE))

test_that("test14.json (empty file) ERROR",
          expect_error(convert_bds_individual(jtf[14]), "premature EOF"))

test_that("test15.json (Bdsnummer 19 numeric) MESS",
          expect_message(convert_bds_individual(jtf[15]),
                       '[{"bdsnummer":19,"description":"Sex of child","expected":"one of: 0, 1, 2, 3","supplied":"2","supplied_type":"numeric"},{"bdsnummer":62,"description":"Caretaker relation","expected":"one of: 01, 02, 03, 04, 05, 06, 07, 08, 98","supplied":"1","supplied_type":"numeric"}]'))

test_that("test16.json (Bdsnummer 20 numeric) PASSES",
          expect_silent(convert_bds_individual(jtf[16])))

test_that("test17.json (Bdsnummer 82 numeric) PASSES",
          expect_silent(convert_bds_individual(jtf[17])))

test_that("test18.json (Bdsnummer 91 numeric) MESS",
          expect_message(convert_bds_individual(jtf[18]),
                         '[{"bdsnummer":91,"description":"Smoking during pregnancy","expected":"one of: 1, 2, 99","supplied":"1","supplied_type":"numeric"}]'))

test_that("test19.json (Bdsnummer 110 numeric) PASSES",
          expect_silent(convert_bds_individual(jtf[19])))

test_that("test20.json (missing Groepen) MESS",
           expect_message(convert_bds_individual(jtf[20]),
                          "Missing 'ClientGegevens$Groepen'",
                          fixed = TRUE))

test_that("test21.json (minimal data) MESS",
          expect_message(convert_bds_individual(jtf[21]),
                         "Missing 'Contactmomenten'",
                         fixed = TRUE))

test_that("test22.json (gad (=49) out of range 50-350: set to NA)",
          expect_message(convert_bds_individual(jtf[22])))

test_that("test23.json (multiple messages) MESS",
          expect_message(convert_bds_individual(jtf[23])))

test_that("test24.json (new DDI fields) SILENT",
          expect_silent(convert_bds_individual(jtf[24])))

fn  <- system.file("extdata", "smocc", "Laura_S.json", package = "jamestest")
js  <- jsonlite::toJSON(jsonlite::fromJSON(fn), auto_unbox = TRUE)

test_that("Laura_S.json is silent with GA in days",
          expect_silent(convert_bds_individual(js)))

# 2 problematic json files identified by Allegro Sultum - Feb 2020
fn  <- system.file("extdata", "test", "not_a_vector.json", package = "jamestest")
js  <- jsonlite::toJSON(jsonlite::fromJSON(fn), auto_unbox = TRUE)

test_that("not_a_vector.json produces messages",
          expect_message(convert_bds_individual(js)))

# problematic json file http400.json identified by Allegro Sultum - Feb 2020
fn  <- system.file("extdata", "test", "http400.json", package = "jamestest")
js  <- jsonlite::toJSON(jsonlite::fromJSON(fn), auto_unbox = TRUE)

test_that("http400.json proceeds silent - no biological mother",
          expect_silent(convert_bds_individual(js)))

# test battery - comment out to activate
# path <- system.file("extdata", package = "jamestest")
# libs <- c("allegrosultum", "test", "smocc", "terneuzen", "preterm", "graham")
# for (lib in libs) {
#   files <- list.files(path = file.path(path, lib), pattern = ".json", full.names = TRUE)
#   for (file in files) {
#     cat("File ", file, "\n")
#     if (file == "/Users/buurensv/Library/R/4.0/library/jamestest/extdata/test/test14.json") next
#     if (file == "/Users/buurensv/Library/R/4.0/library/jamestest/extdata/test/test8.json") next
#     js  <- jsonlite::toJSON(jsonlite::fromJSON(file), auto_unbox = TRUE)
#     test_that(paste(file, "passes"), {
#       expect_silent(suppressMessages(convert_bds_individual(txt = js)))
#     })
#   }
# }

# Kevin S: Check D-score and DAZ
fn  <- system.file("extdata", "smocc", "Kevin_S.json", package = "jamestest")
js  <- jsonlite::toJSON(jsonlite::fromJSON(fn), auto_unbox = TRUE)

ind <- convert_bds_individual(js)