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#107 adjust tests
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@edgar-manukyan
edgar-manukyan committed Dec 2, 2024
1 parent 66b6ae0 commit 11e9ebc
Showing 1 changed file with 16 additions and 6 deletions.
22 changes: 16 additions & 6 deletions tests/testthat/test-generate_code.R
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Original file line number Diff line number Diff line change
Expand Up @@ -2,12 +2,21 @@ test_that("generate_code works", {

# nolint start
spec <- tibble::tribble(
~study_number, ~raw_dataset, ~raw_dataset_label, ~raw_variable, ~raw_variable_label, ~raw_variable_ordinal, ~raw_variable_type, ~raw_data_format, ~study_specific, ~annotation_ordinal, ~mapping_is_dataset, ~annotation_text, ~target_sdtm_domain, ~target_sdtm_variable, ~target_sdtm_variable_role, ~target_sdtm_variable_codelist_code, ~target_sdtm_variable_controlled_terms_or_format, ~target_sdtm_variable_ordinal, ~origin, ~mapping_algorithm, ~entity_sub_algorithm, ~target_hardcoded_value, ~target_term_value, ~target_term_code, ~condition_ordinal, ~condition_group_ordinal, ~condition_add_raw_dat, ~condition_add_tgt_dat, ~condition_left_raw_dataset, ~condition_left_raw_variable, ~condition_left_sdtm_domain, ~condition_left_sdtm_variable, ~condition_operator, ~condition_right_text_value, ~condition_right_sdtm_domain, ~condition_right_sdtm_variable, ~condition_right_raw_dataset, ~condition_right_raw_variable, ~condition_next_logical_operator, ~merge_type, ~merge_left, ~merge_right, ~merge_condition, ~unduplicate_keys, ~groupby_keys, ~target_resource_raw_dataset, ~target_resource_raw_variable,
"lp_study", "cm_raw_data", "Concomitant Medications", "IT.CMTRT", "var label", "3", "Text", "$200", "FALSE", "1", "FALSE", "CM.CMTRT", "CM", "CMTRT", "Topic Variable", NA, NA, "10", "CRF", "assign_no_ct", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
"lp_study", "cm_raw_data", "Concomitant Medications", "IT.CMINDC", "var label", "4", "Text", "$100", "FALSE", "1", "FALSE", "CM.CMINDC", "CM", "CMINDC", "Record Qualifier", NA, NA, "19", "CRF", "assign_no_ct", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA
)
~study_number, ~raw_dataset, ~raw_dataset_label, ~raw_variable, ~raw_variable_label, ~raw_variable_ordinal, ~raw_variable_type, ~raw_data_format, ~raw_fmt, ~raw_unk, ~study_specific, ~annotation_ordinal, ~mapping_is_dataset, ~annotation_text, ~target_sdtm_domain, ~target_sdtm_variable, ~target_sdtm_variable_role, ~target_sdtm_variable_codelist_code, ~target_sdtm_variable_controlled_terms_or_format, ~target_sdtm_variable_ordinal, ~origin, ~mapping_algorithm, ~entity_sub_algorithm, ~target_hardcoded_value, ~target_term_value, ~target_value, ~target_term_code, ~condition_ordinal, ~condition_group_ordinal, ~condition_add_raw_dat, ~condition_add_tgt_dat, ~condition_left_raw_dataset, ~condition_left_raw_variable, ~condition_left_sdtm_domain, ~condition_left_sdtm_variable, ~condition_operator, ~condition_right_text_value, ~condition_right_sdtm_domain, ~condition_right_sdtm_variable, ~condition_right_raw_dataset, ~condition_right_raw_variable, ~condition_next_logical_operator, ~merge_type, ~merge_left, ~merge_right, ~merge_condition, ~unduplicate_keys, ~groupby_keys, ~target_resource_raw_dataset, ~target_resource_raw_variable,
"lp_study", "cm_raw_data", "Concomitant Medications", "IT.CMTRT", "var label", "3", "Text", "$200", NA, NA, "FALSE", "1", "FALSE", "CM.CMTRT", "CM", "CMTRT", "Topic Variable", NA, NA, "10", "CRF", "assign_no_ct", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
"lp_study", "cm_raw_data", "Concomitant Medications", "IT.CMINDC", "var label", "4", "Text", "$100", NA, NA, "FALSE", "1", "FALSE", "CM.CMINDC", "CM", "CMINDC", "Record Qualifier", NA, NA, "19", "CRF", "assign_no_ct", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA
)
# nolint end

# Convert all NA to NA_character_
spec <- spec |>
dplyr::mutate(
dplyr::across(
.cols = dplyr::everything(),
.fns = ~dplyr::if_else(is.na(.x), NA_character_, .x)
)
)

domain <- "cm"

temp_dir <- tempdir()
Expand All @@ -19,7 +28,8 @@ test_that("generate_code works", {
generate_code(spec, domain, out_dir)
observed <- readLines(file.path(out_dir, paste0(domain, "_sdtm_oak_code.R")))

expect_true(identical(length(observed), 10L))
expect_true(grepl("CMTRT", observed[3]))
expect_true(length(observed) > 10L)
expect_true(grepl("generate_oak_id_vars", observed) |> any())
expect_true(grepl("assign_no_ct", observed) |> any())
})
})

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