test_that("summariseChecks works", {
  resultList <- list()

  # create input data
  ingredientConceptIds <- c("1125315", "1139042")
  ingredients <- c("acetaminophen", "acetylcysteine")
  resultList$conceptSummary <- data.frame(ingredient = ingredients,
                                          ingredient_concept_id = ingredientConceptIds,
                                          dose_form = c("injection", NA),
                                          n_records = c(123, 299),
                                          n_patients = c(123, 200))
  resultList$drugRoutesOverall <-  data.frame(route_type = c("Route1", "Route2", "Route3"),
                                              route_type_id = c(1, 2, 3),
                                              n_records = c(1, 2, 5))
  resultList$drugTypesOverall <- data.frame(drug_type = c("Type1", "Type2", "Type3"),
                                            drug_type_id = c(1, 2, 3),
                                            n_records = c(1, 2, 0))
  resultList$drugExposureDurationOverall <- data.frame(ingredient_concept_id = ingredientConceptIds,
                                                       n_negative_days = c(10, 20),
                                                       proportion_negative_days = c(0.1, 0.2),
                                                       median_drug_exposure_days = c(5, 6),
                                                       q05_drug_exposure_days = c(1, 2),
                                                       q95_drug_exposure_days = c(15, 19))
  resultList$drugDose <- data.frame(ingredient_concept_id = c(rep("1125315",12),rep("1139042",12)),
                                    ingredient = c(rep("Acetaminophen",12),rep("Acetylcysteine",12)),
                                    group_name = c(rep("ingredient_name",24)),
                                    strata_name = c(rep(c(rep("overall",6),rep("unit",6)),2)),
                                    strata_level = c(rep(c(rep("NA",6),rep("milligram",6)),2)),
                                    variable_name = c(rep(c("number_records",rep("daily_dose",5)),4)),
                                    estimate_name = c(rep(c("count","count_missing","percentage_missing",
                                                      "q05","median","q95"),4)),
                                    estimate_type = c(rep(c("integer","integer","percentage",
                                                            "numeric","numeric","numeric"),4)),
                                    estimate_value = c(10,5,50,2,6,10,8,2,0.25,1,2,4,
                                                       10,1,0.1,2,4,8,5,1,0.2,1,5,10))
  resultList$drugQuantity <- data.frame(ingredient_concept_id = ingredientConceptIds,
                                        median_drug_exposure_quantity = c(10, 12),
                                        q05_drug_exposure_quantity = c(1, 2),
                                        q95_drug_exposure_quantity = c(15, 19))

  result <- DrugExposureDiagnostics:::summariseChecks(resultList)

  expect_equal(
    names(result),
    c("ingredient", "ingredient_concept_id", "n_records", "n_patients",
      "proportion_of_records_by_drug_type",
      "proportion_of_records_by_route_type",
      "proportion_of_records_with_dose_form",
      "n_dose_and_missingness",
      "median_daily_dose_q05_q95",
      "median_quantity_q05_q95",
      "median_drug_exposure_days_q05_q95",
      "proportion_of_records_with_negative_drug_exposure_days"))


  expect_equal(result$ingredient, ingredients)
  expect_equal(result$ingredient_concept_id, ingredientConceptIds)
  expect_equal(result$n_records, c(123, 299))
  expect_equal(unique(result$proportion_of_records_by_drug_type), c("Type1 (1, 33.3%);Type2 (2, 66.7%);Type3 (0, 0%)"))
  expect_equal(unique(result$proportion_of_records_by_route_type), c("Route1 (1, 12.5%);Route2 (2, 25%);Route3 (5, 62.5%)"))
  expect_equal(result$proportion_of_records_with_dose_form, c("123 (100%)", "0 (0%)"))
  expect_equal(result$median_daily_dose_q05_q95, c("6 (2-10) [milligram]", "4 (2-8) [milligram]"))
  expect_equal(result$median_quantity_q05_q95, c("10 (1-15)", "12 (2-19)"))
  expect_equal(result$median_drug_exposure_days_q05_q95, c("5 (1-15)", "6 (2-19)"))
  expect_equal(result$proportion_of_records_with_negative_drug_exposure_days, c("10 (10%)", "20 (20%)"))
})

test_that("summariseChecks partial inputs: summary, quantity and dose", {
  resultList <- list()

  # create input data
  ingredientConceptIds <- c("1125315", "1139042")
  ingredients <- c("acetaminophen", "acetylcysteine")
  resultList$conceptSummary <- data.frame(ingredient = ingredients,
                                          ingredient_concept_id = ingredientConceptIds,
                                          dose_form = c("injection", NA),
                                          n_records = c(123, 299),
                                          n_patients = c(123, 200))
  resultList$drugDose <- data.frame(ingredient_concept_id = c(rep("1125315",12),rep("1139042",12)),
                                    ingredient = c(rep("Acetaminophen",12),rep("Acetylcysteine",12)),
                                    group_name = c(rep("ingredient_name",24)),
                                    strata_name = c(rep(c(rep("overall",6),rep("unit",6)),2)),
                                    strata_level = c(rep(c(rep("NA",6),rep("milligram",6)),2)),
                                    variable_name = c(rep(c("number_records",rep("daily_dose",5)),4)),
                                    estimate_name = c(rep(c("count","count_missing","percentage_missing",
                                                            "q05","median","q95"),4)),
                                    estimate_type = c(rep(c("integer","integer","percentage",
                                                            "numeric","numeric","numeric"),4)),
                                    estimate_value = c(10,5,50,2,6,10,8,2,0.25,1,2,4,
                                                       10,1,0.1,2,4,8,5,1,0.2,1,5,10))
  resultList$drugQuantity <- data.frame(ingredient_concept_id = ingredientConceptIds,
                                        median_drug_exposure_quantity = c(10, 12),
                                        q05_drug_exposure_quantity = c(1, 2),
                                        q95_drug_exposure_quantity = c(15, 19))

  result <- DrugExposureDiagnostics:::summariseChecks(resultList)

  expect_equal(
    names(result),
    c("ingredient", "ingredient_concept_id", "n_records", "n_patients",
      "proportion_of_records_with_dose_form",
      "n_dose_and_missingness",
      "median_daily_dose_q05_q95",
      "median_quantity_q05_q95"
    ))

  expect_equal(result$ingredient, ingredients)
  expect_equal(result$ingredient_concept_id, ingredientConceptIds)
  expect_equal(result$n_records, c(123, 299))
  expect_equal(result$proportion_of_records_with_dose_form, c("123 (100%)", "0 (0%)"))
  expect_equal(result$n_dose_and_missingness, c("10 (5, 50%)", "10 (1, 0.1%)"))
  expect_equal(result$median_daily_dose_q05_q95, c("6 (2-10) [milligram]", "4 (2-8) [milligram]"))
  expect_equal(result$median_quantity_q05_q95, c("10 (1-15)", "12 (2-19)"))
})

test_that("summariseChecks partial inputs: summary and quantity", {
  resultList <- list()

  # create input data
  ingredientConceptIds <- c("1125315", "1139042")
  ingredients <- c("acetaminophen", "acetylcysteine")
  resultList$conceptSummary <- data.frame(ingredient = ingredients,
                                          ingredient_concept_id = ingredientConceptIds,
                                          dose_form = c("injection", NA),
                                          n_records = c(123, 299),
                                          n_patients = c(123, 200))
  resultList$drugQuantity <- data.frame(ingredient_concept_id = ingredientConceptIds,
                                        median_drug_exposure_quantity = c(10, 12),
                                        q05_drug_exposure_quantity = c(1, 2),
                                        q95_drug_exposure_quantity = c(15, 19))

  result <- DrugExposureDiagnostics:::summariseChecks(resultList)

  expect_equal(
    names(result),
    c("ingredient", "ingredient_concept_id", "n_records", "n_patients",
      "proportion_of_records_with_dose_form",  "median_quantity_q05_q95"
    ))

  expect_equal(result$ingredient, ingredients)
  expect_equal(result$ingredient_concept_id, ingredientConceptIds)
  expect_equal(result$n_records, c(123, 299))
  expect_equal(result$proportion_of_records_with_dose_form, c("123 (100%)", "0 (0%)"))
})

test_that("summariseChecks empty/wrong inputs", {
  expect_error(summariseChecks(list()))
  expect_error(summariseChecks(NULL))
})

test_that("summariseChecks partial inputs with only empty ingredient: summary of missing and quantity and dose", {

  cdm <- mockDrugExposure()

  empty_ing <- executeChecks(cdm = cdm,  ingredients = c(36854851), checks = c("missing", "quantity", "dose", "diagnosticsSummary"))

  expect_equal(nrow(empty_ing$diagnosticsSummary), 0)

  DBI::dbDisconnect(attr(cdm, "dbcon"), shutdown = TRUE)
})

test_that("summariseChecks partial inputs with combination of not empty and empty ingredient: summary of missing and quantity and dose", {

  cdm <- mockDrugExposure()

  empty_ing <- executeChecks(cdm = cdm,  ingredients = c(1125315, 36854851), checks = c("missing", "quantity", "dose", "diagnosticsSummary"))

  expect_equal(empty_ing$diagnosticsSummary$ingredient, "acetaminophen")
  expect_equal(nrow(empty_ing$diagnosticsSummary), 1)

  DBI::dbDisconnect(attr(cdm, "dbcon"), shutdown = TRUE)
})

test_that("summariseChecks empty/wrong inputs", {
  expect_error(summariseChecks(list()))
  expect_error(summariseChecks(NULL))
})