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fix expect_s3_class() tests #182

Merged
merged 11 commits into from
Dec 18, 2024
Merged

fix expect_s3_class() tests #182

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44cded7
avoid false-positives with s3 class checking
zkamvar Dec 13, 2024
76aad73
fix broken s3 expectation
zkamvar Dec 13, 2024
6daac36
clarify s3 checks for metadata schema match
zkamvar Dec 13, 2024
d4ef68f
update checks for check_tbl_values_required
zkamvar Dec 13, 2024
9eb39b6
fix check_tbl_spl_compound_tid expectation
zkamvar Dec 13, 2024
5ed5ae7
clean up remaining s3 expectations
zkamvar Dec 13, 2024
bf49461
skip lint for temporary skip directive
zkamvar Dec 13, 2024
9375c5c
Fix test file and remove test skip. Resolves #183
annakrystalli Dec 17, 2024
5a4404a
Remove trailing zeros from config.
annakrystalli Dec 17, 2024
cf93413
Apply suggestions from code review
zkamvar Dec 18, 2024
1268425
Merge pull request #184 from hubverse-org/ak/update-check-expectation…
zkamvar Dec 18, 2024
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4 changes: 2 additions & 2 deletions tests/testthat/test-check_file_exists.R
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Original file line number Diff line number Diff line change
Expand Up @@ -4,13 +4,13 @@ test_that("check_file_exists works", {

expect_s3_class(
check_file_exists(file_path, hub_path),
c("check_success", "rlang_message", "message", "condition")
c("check_success")
)

file_path <- "team1-goodmodel/2022-10-15-team1-goodmodel.csv"
expect_s3_class(
check_file_exists(file_path, hub_path),
c("check_error", "rlang_message", "message", "condition")
c("check_error")
)

expect_error(
Expand Down
4 changes: 2 additions & 2 deletions tests/testthat/test-check_file_n.R
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Original file line number Diff line number Diff line change
Expand Up @@ -8,15 +8,15 @@ test_that("check_file_n works", {
file_path = "team1-goodmodel/2022-10-08-team1-goodmodel.csv",
hub_path
),
c("check_success", "rlang_message", "message", "condition")
c("check_success")
)

expect_s3_class(
check_file_n(
file_path = "team1-goodmodel/2022-10-08-team1-goodmodel.parquet",
hub_path
),
c("check_failure", "hub_check", "rlang_error", "error", "condition")
c("check_failure")
)

expect_snapshot(
Expand Down
2 changes: 1 addition & 1 deletion tests/testthat/test-check_file_read.R
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,6 @@ test_that("check_file_read works", {
hub_path = hub_path
)
),
c("check_error", "hub_check", "rlang_error", "error", "condition")
c("check_error")
)
})
6 changes: 3 additions & 3 deletions tests/testthat/test-check_metadata_file_exists.R
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Original file line number Diff line number Diff line change
Expand Up @@ -3,23 +3,23 @@ test_that("check_metadata_file_exists works", {

expect_s3_class(
check_metadata_file_exists(hub_path, "hub-baseline.yml"),
c("check_success", "rlang_message", "message", "condition")
c("check_success")
)
expect_snapshot(
check_metadata_file_exists(hub_path, "hub-baseline.yml")
)

expect_s3_class(
check_metadata_file_exists(hub_path = "random_path", "hub-baseline.yml"),
c("check_error", "rlang_error", "error", "condition")
c("check_error")
)
expect_snapshot(
check_metadata_file_exists(hub_path = "random_path", "hub-baseline.yml")
)

expect_s3_class(
check_metadata_file_exists(hub_path = hub_path, "random_path"),
c("check_error", "rlang_error", "error", "condition")
c("check_error")
)
expect_snapshot(
check_metadata_file_exists(hub_path = hub_path, "random_path")
Expand Down
6 changes: 3 additions & 3 deletions tests/testthat/test-check_metadata_file_ext.R
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Original file line number Diff line number Diff line change
@@ -1,23 +1,23 @@
test_that("check_metadata_file_ext works", {
expect_s3_class(
check_metadata_file_ext("hub-baseline.yml"),
c("check_success", "rlang_message", "message", "condition")
c("check_success")
)
expect_snapshot(
check_metadata_file_ext("hub-baseline.yml")
)

expect_s3_class(
check_metadata_file_ext("hub-baseline.yaml"),
c("check_success", "rlang_message", "message", "condition")
c("check_success")
)
expect_snapshot(
check_metadata_file_ext("hub-baseline.yaml")
)

expect_s3_class(
check_metadata_file_ext("hub-baseline.txt"),
c("check_error", "rlang_error", "error", "condition")
c("check_error")
)
expect_snapshot(
check_metadata_file_ext("hub-baseline.txt")
Expand Down
10 changes: 5 additions & 5 deletions tests/testthat/test-check_metadata_file_name.R
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ test_that("check_metadata_file_name works", {
file_path = "hub-baseline.yml",
hub_path = hub_path
),
c("check_success", "rlang_message", "message", "condition")
c("check_success")
)
expect_snapshot(
check_metadata_file_name(
Expand All @@ -20,7 +20,7 @@ test_that("check_metadata_file_name works", {
file_path = "hub-baseline-with-model_id.yml",
hub_path = hub_path
),
c("check_success", "rlang_message", "message", "condition")
c("check_success")
)
expect_snapshot(
check_metadata_file_name(
Expand All @@ -34,7 +34,7 @@ test_that("check_metadata_file_name works", {
file_path = "hub-baseline-with-wrong-model_id.yml",
hub_path = hub_path
),
c("check_error", "rlang_message", "message", "condition")
c("check_error")
)
expect_snapshot(
check_metadata_file_name(
Expand All @@ -48,7 +48,7 @@ test_that("check_metadata_file_name works", {
file_path = "hub-baseline-no-abbrs-or-model_id.yml",
hub_path = hub_path
),
c("check_error", "rlang_message", "message", "condition")
c("check_error")
)
expect_snapshot(
check_metadata_file_name(
Expand All @@ -62,7 +62,7 @@ test_that("check_metadata_file_name works", {
file_path = "team1-goodmodel.yaml",
hub_path = hub_path
),
c("check_success", "rlang_message", "message", "condition")
c("check_success")
)
expect_snapshot(
check_metadata_file_name(
Expand Down
4 changes: 2 additions & 2 deletions tests/testthat/test-check_metadata_matches_schema.R
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ test_that("check_metadata_matches_schema works", {
file_path = "hub-baseline.yml",
hub_path = hub_path
),
c("check_success", "rlang_message", "message", "condition")
c("check_success")
)
expect_snapshot(
check_metadata_matches_schema(
Expand All @@ -20,7 +20,7 @@ test_that("check_metadata_matches_schema works", {
file_path = "team1-goodmodel.yaml",
hub_path = hub_path
),
c("check_error", "rlang_message", "message", "condition")
c("check_error")
)
expect_snapshot(
check_metadata_matches_schema(
Expand Down
4 changes: 2 additions & 2 deletions tests/testthat/test-check_metadata_schema_exists.R
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,15 +3,15 @@ test_that("check_metadata_schema_exists works", {

expect_s3_class(
check_metadata_schema_exists(hub_path),
c("check_success", "rlang_message", "message", "condition")
c("check_success")
)
expect_snapshot(
check_metadata_schema_exists(hub_path)
)

expect_s3_class(
check_metadata_schema_exists(hub_path = "random_path"),
c("check_error", "rlang_error", "error", "condition")
c("check_error")
)
expect_snapshot(
check_metadata_schema_exists(hub_path = "random_path")
Expand Down
4 changes: 2 additions & 2 deletions tests/testthat/test-check_submission_metadata_file_exists.R
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ test_that("check_metadata_file_exists works", {
hub_path = hub_path,
file_path = "hub-baseline/2022-10-01-hub-baseline.csv"
),
c("check_success", "rlang_message", "message", "condition")
c("check_success")
)
expect_snapshot(
check_submission_metadata_file_exists(
Expand All @@ -20,7 +20,7 @@ test_that("check_metadata_file_exists works", {
hub_path = hub_path,
file_path = "random-model/2022-10-01-random-model.csv"
),
c("check_error", "rlang_error", "error", "condition")
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Good catch!

c("check_failure")
)
expect_snapshot(
check_submission_metadata_file_exists(
Expand Down
6 changes: 3 additions & 3 deletions tests/testthat/test-check_tbl_spl_compound_tid.R
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Original file line number Diff line number Diff line change
Expand Up @@ -29,11 +29,11 @@ test_that("check_tbl_spl_compound_tid works", {
# Ensure other checks pass
expect_s3_class(
check_tbl_spl_non_compound_tid(tbl_error, round_id, file_path, hub_path),
c("check_success", "hub_check", "rlang_message", "message", "condition")
c("check_success")
)
expect_s3_class(
check_tbl_spl_compound_tid(tbl_error, round_id, file_path, hub_path),
c("check_success", "hub_check", "rlang_message", "message", "condition")
check_tbl_spl_n(tbl_error, round_id, file_path, hub_path),
c("check_success")
)
})

Expand Down
4 changes: 2 additions & 2 deletions tests/testthat/test-check_tbl_spl_n.R
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Original file line number Diff line number Diff line change
Expand Up @@ -35,14 +35,14 @@ test_that("check_tbl_spl_n works", {
tbl_const_error, round_id,
file_path, hub_path
),
c("check_success", "hub_check", "rlang_message", "message", "condition")
c("check_success")
)
expect_s3_class(
check_tbl_spl_compound_tid(
tbl_const_error, round_id,
file_path, hub_path
),
c("check_success", "hub_check", "rlang_message", "message", "condition")
c("check_success")
)


Expand Down
4 changes: 2 additions & 2 deletions tests/testthat/test-check_tbl_spl_non_compound_tid.R
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Original file line number Diff line number Diff line change
Expand Up @@ -29,11 +29,11 @@ test_that("check_tbl_spl_non_compound_tid works", {
# Ensure other checks pass
expect_s3_class(
check_tbl_spl_compound_tid(tbl_error, round_id, file_path, hub_path),
c("check_success", "hub_check", "rlang_message", "message", "condition")
c("check_success")
)
expect_s3_class(
check_tbl_spl_n(tbl_error, round_id, file_path, hub_path),
c("check_success", "hub_check", "rlang_message", "message", "condition")
c("check_success")
)
})

Expand Down
4 changes: 2 additions & 2 deletions tests/testthat/test-check_tbl_values_required.R
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Original file line number Diff line number Diff line change
Expand Up @@ -140,7 +140,7 @@ test_that(

expect_s3_class(
check,
c("check_failure", "hub_check", "rlang_warning", "warning", "condition")
c("check_failure")
)

# Expect that values for output type IDs "0.1000000000000000055511",
Expand Down Expand Up @@ -177,7 +177,7 @@ test_that(
file_path = file_path,
hub_path = hub_path
),
c("check_success", "hub_check", "rlang_message", "message", "condition")
c("check_success")
)
}
)
Expand Down
4 changes: 2 additions & 2 deletions tests/testthat/test-new_hub_validations.R
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ test_that("new_hub_validations works", {
expect_snapshot(str(new_hub_validations()))
expect_s3_class(
new_hub_validations(),
c("hub_validations", "list")
c("hub_validations")
)


Expand All @@ -23,6 +23,6 @@ test_that("new_hub_validations works", {
file_exists = check_file_exists(file_path, hub_path),
file_name = check_file_name(file_path)
),
c("hub_validations", "list")
c("hub_validations")
)
})
2 changes: 1 addition & 1 deletion tests/testthat/test-validate_model_data.R
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ test_that("validate_model_data works", {
)
expect_s3_class(
validate_model_data(hub_path, file_path),
c("hub_validations", "list")
c("hub_validations")
)

expect_snapshot(
Expand Down
4 changes: 2 additions & 2 deletions tests/testthat/test-validate_model_file.R
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ test_that("validate_model_file works", {
validate_model_file(hub_path,
file_path = "team1-goodmodel/2022-10-08-team1-goodmodel.csv"
),
c("hub_validations", "list")
c("hub_validations")
)

# File with validation error
Expand All @@ -28,7 +28,7 @@ test_that("validate_model_file works", {
validate_model_file(hub_path,
file_path = "team1-goodmodel/2022-10-15-team1-goodmodel.csv"
),
c("hub_validations", "list")
c("hub_validations")
)
})

Expand Down
8 changes: 4 additions & 4 deletions tests/testthat/test-validate_model_metadata.R
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ test_that("validate_model_metadata works", {
)
expect_s3_class(
validate_model_metadata(hub_path, file_path),
c("hub_validations", "list")
c("hub_validations")
)

file_path <- "hub-baseline.yml"
Expand All @@ -20,7 +20,7 @@ test_that("validate_model_metadata works", {
)
expect_s3_class(
validate_model_metadata(hub_path, file_path),
c("hub_validations", "list")
c("hub_validations")
)

file_path <- "hub-baseline-no-abbrs-or-model_id.yml"
Expand All @@ -31,7 +31,7 @@ test_that("validate_model_metadata works", {
)
expect_s3_class(
validate_model_metadata(hub_path, file_path),
c("hub_validations", "list")
c("hub_validations")
)

file_path <- "2020-10-06-random-path.csv"
Expand All @@ -42,6 +42,6 @@ test_that("validate_model_metadata works", {
)
expect_s3_class(
validate_model_metadata(hub_path, file_path),
c("hub_validations", "list")
c("hub_validations")
)
})
10 changes: 5 additions & 5 deletions tests/testthat/test-validate_submission.R
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ test_that("validate_submission works", {
skip_submit_window_check = TRUE,
skip_check_config = TRUE
),
c("hub_validations", "list")
c("hub_validations")
)

# File with validation error ----
Expand All @@ -39,7 +39,7 @@ test_that("validate_submission works", {
skip_submit_window_check = TRUE,
skip_check_config = TRUE
),
c("hub_validations", "list")
c("hub_validations")
)

# Wrong submission location & missing data column (age_group)
Expand All @@ -58,7 +58,7 @@ test_that("validate_submission works", {
skip_submit_window_check = TRUE,
skip_check_config = TRUE
),
c("hub_validations", "list")
c("hub_validations")
)


Expand Down Expand Up @@ -88,7 +88,7 @@ test_that("validate_submission works", {
file_path = "team1-goodmodel/2022-10-08-team1-goodmodel.csv",
skip_submit_window_check = TRUE
),
c("hub_validations", "list")
c("hub_validations")
)
})

Expand Down Expand Up @@ -149,7 +149,7 @@ test_that("validate_submission fails when csv cannot be parsed according to sche
file_path = "hub-baseline/2023-05-01-hub-baseline.csv",
skip_submit_window_check = TRUE
)[["file_read"]],
c("check_error", "hub_check", "rlang_error", "error", "condition")
c("check_error")
)
})

Expand Down
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