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pratikunterwegspratikunterwegs
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Add prelim tests with dummy test data
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‎tests/testthat/incoming_burden_estimates/file_dictionary.csv‎

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scenario_type,scenario_type_description,scenario,scenario_description,file
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disease-rout,Routine Only,disease-rout,disease-rout,no-vaccination.csv
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novac,No Vaccination,disease-no-vaccination,No vaccination,with-vaccination.csv

‎tests/testthat/incoming_burden_estimates/model_inputs/scenario.csv‎

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"scenario_type","scenario_type_description","scenario","scenario_description","coverage_set","gavi_support_level","source_from","disease","vaccine","activity_type","year","country","age_from","age_to","age_range_verbatim","target","coverage","gender","proportion_risk"
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"disease_rout","Routine Only","disease_rout","disease_rout","disease : disease , routine ,with: disease_rout","with","scenario_source","disease","disease","routine",2030,"RFP",0,0,"default routine age","NA",0.8,"Both",1
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"disease_rout","Routine Only","disease_rout","disease_rout","disease : disease , routine ,with: disease_rout","with","scenario_source","disease","disease","routine",2031,"RFP",0,0,"default routine age","NA",0.8,"Both",1
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"disease_rout","Routine Only","disease_rout","disease_rout","disease : disease , routine ,with: disease_rout","with","scenario_source","disease","disease","routine",2032,"RFP",0,0,"default routine age","NA",0.8,"Both",1
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"disease_rout","Routine Only","disease_rout","disease_rout","disease : disease , routine ,with: disease_rout","with","scenario_source","disease","disease","routine",2033,"RFP",0,0,"default routine age","NA",0.8,"Both",1
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"disease_rout","Routine Only","disease_rout","disease_rout","disease : disease , routine ,with: disease_rout","with","scenario_source","disease","disease","routine",2034,"RFP",0,0,"default routine age","NA",0.8,"Both",1
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"disease_rout","Routine Only","disease_rout","disease_rout","disease : disease , routine ,with: disease_rout","with","scenario_source","disease","disease","routine",2035,"RFP",0,0,"default routine age","NA",0.8,"Both",1
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"disease_rout","Routine Only","disease_rout","disease_rout","disease : disease , routine ,with: disease_rout","with","scenario_source","disease","disease","routine",2036,"RFP",0,0,"default routine age","NA",0.8,"Both",1
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"disease_rout","Routine Only","disease_rout","disease_rout","disease : disease , routine ,with: disease_rout","with","scenario_source","disease","disease","routine",2037,"RFP",0,0,"default routine age","NA",0.8,"Both",1
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"disease_rout","Routine Only","disease_rout","disease_rout","disease : disease , routine ,with: disease_rout","with","scenario_source","disease","disease","routine",2038,"RFP",0,0,"default routine age","NA",0.8,"Both",1
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"disease_rout","Routine Only","disease_rout","disease_rout","disease : disease , routine ,with: disease_rout","with","scenario_source","disease","disease","routine",2039,"RFP",0,0,"default routine age","NA",0.8,"Both",1
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"disease_rout","Routine Only","disease_rout","disease_rout","disease : disease , routine ,with: disease_rout","with","scenario_source","disease","disease","routine",2040,"RFP",0,0,"default routine age","NA",0.8,"Both",1

‎tests/testthat/test-burden_diagnostics.R‎

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test_that("`validate_file_dict_template()` works", {
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# set up local tempdir to test missing bad file error msg
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wd <- withr::local_tempdir()
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path_burden <- file.path(wd, "incoming_burden_estimates")
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dir.create(path_burden)
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file_dict <- file.path(path_burden, "file_dictionary.csv")
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dummy_data <- data.frame()
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readr::write_csv(dummy_data, file_dict)
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success_msg <- glue::glue(
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"(File dictionary found at)*({file_dict})*(no action needed)"
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)
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fail_msg <- "(File dictionary found)*(but it is not well formed)"
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expect_error(
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validate_file_dict_template(
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disease,
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path_burden
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),
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fail_msg
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)
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# check success segment
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path_burden <- test_path("incoming_burden_estimates")
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expect_message(
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validate_file_dict_template(
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disease,
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path_burden
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),
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success_msg
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)
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validate_file_dict_template(
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"dummy_disease",
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test_path("incoming_burden_estimates")
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)
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# TODO: check other branch of if-else ladder
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})
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test_that("`validate_complete_incoming_files()`", {
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# set up local tempdir with bad file dictionary to check errors
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wd <- withr::local_tempdir()
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path_burden <- file.path(wd, "incoming_burden_estimates")
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dir.create(path_burden)
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fail_msg <- "(Expected a file dictionary)*(but it was not found)"
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expect_error(
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validate_complete_incoming_files(path_burden),
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fail_msg
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)
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file_dict <- file.path(path_burden, "file_dictionary.csv")
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dummy_data <- make_novax_scenario("dummy_disease")
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dummy_data <- rbind(dummy_data, dummy_data)
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n_duplicates <- anyDuplicated(dummy_data)
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readr::write_csv(dummy_data, file_dict)
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fail_msg <- glue::glue(
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"(Expected)*(non-duplicate entries)*(found {n_duplicates} duplicated rows)"
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)
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expect_error(
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validate_complete_incoming_files(path_burden),
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fail_msg
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)
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# check error on duplicated filenames
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dummy_data <- readr::read_csv(
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test_path("incoming_burden_estimates", "file_dictionary.csv")
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)
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dummy_data$file <- "dummy_file.csv"
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readr::write_csv(dummy_data, file_dict)
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fail_msg <- "(Expected)*(non-duplicate scenario filenames)"
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expect_error(
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validate_complete_incoming_files(path_burden),
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fail_msg
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)
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# check error on missing scenario files
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dummy_data <- readr::read_csv(
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test_path("incoming_burden_estimates", "file_dictionary.csv")
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)
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readr::write_csv(dummy_data, file_dict)
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fail_msg <- "Expected as many scenario data files as scenarios"
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expect_error(
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validate_complete_incoming_files(path_burden),
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fail_msg
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)
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})

‎tests/testthat/test-helpers.R‎

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# Basic checks on internal functions. These are mostly checked via exported
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# functions for a smaller testing surface
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test_that("`make_novax_scenario()` works", {
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disease <- "dummy"
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expect_no_condition(
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make_novax_scenario(disease)
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)
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df <- make_novax_scenario(disease)
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expect_named(
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df,
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file_dict_colnames
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)
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})

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