context("get-num-files.R")
manifest <- tibble::tribble(
~path, ~specimenID,
"a/a", "a",
"a/b", "b",
"a/c", "c"
)
view1 <- tibble::tribble(
~metadataType, ~file_data,
"manifest", manifest,
"assay", NA,
"biospecimen", NA,
"individual", NA
)
view2 <- tibble::tribble(
~metadataType, ~file_data,
"assay", NA,
NA, NA,
"manifest", manifest,
"biospecimen", NA
)
view3 <- tibble::tribble(
~metadataType, ~file_data,
"assay", NA,
NA, NA,
NA, NA,
"manifest", manifest,
)
view4 <- tibble::tribble(
~metadataType, ~file_data,
NA, NA,
)
test_that("num_meta_files returns correct number", {
res1 <- num_meta_files(view1)
res2 <- num_meta_files(view2)
res3 <- num_meta_files(view3)
res4 <- num_meta_files(view4)
expect_equal(res1, 4)
expect_equal(res2, 3)
expect_equal(res3, 2)
expect_equal(res4, 0)
})
test_that("num_manifest_files returns correct number", {
res1 <- num_manifest_files(view1)
res2 <- num_manifest_files(view4)
expect_equal(res1, 3)
expect_equal(res2, 0)
})
test_that("num_doc_files returns correct number", {
res1 <- num_doc_files(view1)
res2 <- num_doc_files(view2)
res3 <- num_doc_files(view3)
res4 <- num_doc_files(view4)
expect_equal(res1, 0)
expect_equal(res2, 1)
expect_equal(res3, 2)
expect_equal(res4, 1)
})
context("get-num-ids.R")
assay <- tibble::tribble(
~specimenID,
"sa",
"sb",
"sc"
)
biospecimen <- tibble::tribble(
~specimenID, ~individualID,
"sa", "ia",
"sb", "ib",
"sc", "ic",
"sd", "id"
)
individual <- tibble::tribble(
~individualID,
"ia",
"ib",
"ic",
"id"
)
manifest <- tibble::tribble(
~specimenID, ~individualID,
"sa", "ia",
"sb", "ib",
"sc", "ic",
"sd", "id",
"se", "ie"
)
manifest_duplicates <- tibble::tribble(
~specimenID, ~individualID,
"sa", "ia",
"sb", "ib",
"sc", "ic",
"sa", "ia",
"sb", "ib",
"sc", "ic"
)
study_view <- tibble::tribble(
~metadataType, ~file_data,
"manifest", manifest,
"individual", individual,
"biospecimen", biospecimen,
"assay", assay
)
study_view_duplicates <- tibble::tribble(
~metadataType, ~file_data,
"manifest", manifest_duplicates,
"individual", individual,
"biospecimen", biospecimen,
"assay", assay
)
study_view_missing <- tibble::tribble(
~metadataType, ~file_data,
"individual", individual,
"biospecimen", biospecimen,
"assay", assay
)
test_that("num_individuals returns correct number", {
res1 <- num_individuals(study_view)
res2 <- num_individuals(study_view_duplicates)
res3 <- num_individuals(study_view_missing)
expect_equal(res1, 5)
expect_equal(res2, 4)
expect_equal(res2, 4)
})
test_that("num_individuals returns 0 if files not present", {
view <- tibble::tribble(
~metadataType, ~file_data,
"assay", assay
)
res1 <- num_individuals(view)
expect_equal(res1, 0)
})
test_that("num_individuals doesn't break if $individualID missing", {
manifest_no_ind <- tibble::tribble(
~specimenID,
"sa",
"sb",
"sc",
"sd",
"se"
)
view <- tibble::tribble(
~metadataType, ~file_data,
"manifest", manifest_no_ind,
"individual", individual,
"biospecimen", biospecimen,
"assay", assay
)
res1 <- num_individuals(view)
expect_equal(res1, 4)
})
test_that("num_specimens returns correct number", {
res1 <- num_specimens(study_view)
res2 <- num_specimens(study_view_duplicates)
res3 <- num_specimens(study_view_missing)
expect_equal(res1, 5)
expect_equal(res2, 4)
expect_equal(res3, 4)
})
test_that("num_specimens returns 0 if files not present", {
view <- tibble::tribble(
~metadataType, ~file_data,
"individual", individual,
)
res1 <- num_specimens(view)
expect_equal(res1, 0)
})
test_that("num_specimens doesn't break if $specimenID missing", {
manifest_no_sid <- tibble::tribble(
~individualID,
"ia",
"ib",
"ic",
"id"
)
view <- tibble::tribble(
~metadataType, ~file_data,
"manifest", manifest_no_sid,
"individual", individual,
"biospecimen", biospecimen,
"assay", assay
)
res1 <- num_specimens(view)
expect_equal(res1, 4)
})
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.