Nothing
testthat::test_that("merge_selectors makes no changes when single selector is provided", {
x1 <- list(
dataname = "ADSL",
filters = NULL,
select = utils::head(letters, 3),
keys = c("STUDYID", "USUBJID"),
reshape = FALSE,
internal_id = "test1"
)
testthat::expect_identical(
merge_selectors(list(x1)),
list(list(x1), c("test1" = "test1"))
)
})
testthat::test_that(
desc = "merge selectors combines two selectors into one if dataname, filters, keys, reshape are identical",
code = {
x1 <- list(
dataname = "ADSL",
filters = NULL,
select = utils::head(letters, 3),
keys = c("STUDYID", "USUBJID"),
reshape = FALSE,
internal_id = "test1"
)
x2 <- list(
dataname = "ADSL",
filters = NULL,
select = utils::tail(letters, 3),
keys = c("STUDYID", "USUBJID"),
reshape = FALSE,
internal_id = "test2"
)
testthat::expect_equal(
merge_selectors(list(x1, x2)),
list(
list(
list(
dataname = "ADSL",
filters = NULL,
select = c(utils::head(letters, 3), utils::tail(letters, 3)),
keys = c("STUDYID", "USUBJID"),
reshape = FALSE,
internal_id = "test1"
)
),
c("test1" = "test1", "test2" = "test1")
)
)
}
)
testthat::test_that("merge selectors combines two selectorsdespite duplicated internal_id", {
x1 <- list(
dataname = "ADSL",
filters = NULL,
select = utils::head(letters, 3),
keys = c("STUDYID", "USUBJID"),
reshape = FALSE,
internal_id = "test1"
)
x2 <- list(
dataname = "ADSL",
filters = NULL,
select = utils::tail(letters, 3),
keys = c("STUDYID", "USUBJID"),
reshape = FALSE,
internal_id = "test1"
)
testthat::expect_equal(
merge_selectors(list(x1, x2)),
list(
list(
list(
dataname = "ADSL",
filters = NULL,
select = c(utils::head(letters, 3), utils::tail(letters, 3)),
keys = c("STUDYID", "USUBJID"),
reshape = FALSE,
internal_id = "test1"
)
),
c("test1" = "test1", "test1" = "test1")
)
)
})
testthat::test_that("Two pairs of selectors combined into two selectors", {
x1 <- list(
dataname = "ADSL",
filters = NULL,
select = utils::head(letters, 3),
keys = c("STUDYID", "USUBJID"),
reshape = FALSE,
internal_id = "test1"
)
x2 <- list(
dataname = "ADLB",
filters = NULL,
select = utils::head(letters, 3),
keys = c("STUDYID", "USUBJID"),
reshape = FALSE,
internal_id = "test2"
)
x3 <- list(
dataname = "ADSL",
filters = NULL,
select = tail(letters, 3),
keys = c("STUDYID", "USUBJID"),
reshape = FALSE,
internal_id = "test3"
)
x4 <- list(
dataname = "ADLB",
filters = NULL,
select = utils::tail(letters, 3),
keys = c("STUDYID", "USUBJID"),
reshape = FALSE,
internal_id = "test4"
)
testthat::expect_equal(
merge_selectors(list(x1, x2, x3, x4)),
list(
list(
within(x1, {
select <- c("a", "b", "c", "x", "y", "z")
}),
within(x2, {
select <- c("a", "b", "c", "x", "y", "z")
})
),
c("test1" = "test1", "test2" = "test2", "test3" = "test1", "test4" = "test2")
)
)
})
testthat::test_that("merge does not merge when reshape differs", {
x1 <- list(
dataname = "ADSL",
filters = NULL,
select = utils::head(letters, 3),
keys = c("STUDYID", "USUBJID"),
reshape = FALSE,
internal_id = "test1"
)
x2 <- list(
dataname = "ADSL",
filters = NULL,
select = utils::tail(letters, 3),
keys = c("STUDYID", "USUBJID"),
reshape = TRUE,
internal_id = "test2"
)
testthat::expect_equal(
merge_selectors(list(x1, x2)),
list(
list(x1, x2),
c("test1" = "test1", "test2" = "test2")
)
)
})
testthat::test_that("merge does not merge when filters differs", {
x1 <- list(
dataname = "ADSL",
filters = NULL,
select = utils::head(letters, 3),
keys = c("STUDYID", "USUBJID"),
reshape = TRUE,
internal_id = "test1"
)
x2 <- list(
dataname = "ADSL",
filters = list(list(columns = "a", selected = list("1", "2"))),
select = utils::tail(letters, 3),
keys = c("STUDYID", "USUBJID"),
reshape = FALSE,
internal_id = "test2"
)
testthat::expect_equal(
merge_selectors(list(x1, x2)),
list(
list(x1, x2),
c("test1" = "test1", "test2" = "test2")
)
)
})
testthat::test_that("get_merge_key_pair works", {
testthat::expect_identical(
get_merge_key_pair(
list(
dataname = "ADSL",
filters = NULL,
select = utils::head(letters, 3),
keys = c("STUDYID", "USUBJID"),
reshape = FALSE,
internal_id = "test1"
),
list(
dataname = "ADSL",
filters = NULL,
select = utils::tail(letters, 3),
keys = c("STUDYID", "USUBJID"),
reshape = FALSE,
internal_id = "test2"
),
c("STUDYID", "USUBJID")
),
rlang::set_names(c("STUDYID", "USUBJID"))
)
# this is useful when merging two subsets of long datasets -> value columns next to each other
# subtract from keys single filter on "from" selector
testthat::expect_identical(
get_merge_key_pair(
list(
dataname = "ADRS",
filters = list(list(columns = "PARAMCD", selected = "OS", multiple = FALSE)),
select = utils::head(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = FALSE,
internal_id = "test1"
),
list(
dataname = "ADRS",
filters = NULL,
select = utils::tail(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = FALSE,
internal_id = "test2"
),
c("STUDYID", "USUBJID", "PARAMCD", "AVISIT")
),
rlang::set_names(setdiff(c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"), "PARAMCD"))
)
# ignore "to" selector's filter
testthat::expect_identical(
get_merge_key_pair(
list(
dataname = "ADRS",
filters = NULL,
select = utils::head(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = FALSE,
internal_id = "test1"
),
list(
dataname = "ADRS",
filters = list(list(columns = "PARAMCD", selected = "OS", multiple = FALSE)),
select = utils::tail(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = FALSE,
internal_id = "test2"
),
c("STUDYID", "USUBJID", "PARAMCD", "AVISIT")
),
rlang::set_names(c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"))
)
# subtract from keys single filter on "from" selector
testthat::expect_identical(
get_merge_key_pair(
list(
dataname = "ADRS",
filters = list(list(columns = "PARAMCD", selected = "OS", multiple = FALSE)),
select = utils::head(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = FALSE,
internal_id = "test1"
),
list(
dataname = "ADRS",
filters = list(list(columns = "PARAMCD", selected = "OS", multiple = FALSE)),
select = utils::tail(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = FALSE,
internal_id = "test2"
),
c("STUDYID", "USUBJID", "PARAMCD", "AVISIT")
),
rlang::set_names(setdiff(c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"), "PARAMCD"))
)
# subtract if multiple filter and single selection
testthat::expect_identical(
get_merge_key_pair(
list(
dataname = "ADRS",
filters = list(list(columns = "PARAMCD", selected = "OS", multiple = TRUE)),
select = utils::head(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = FALSE,
internal_id = "test1"
),
list(
dataname = "ADRS",
filters = list(list(columns = "PARAMCD", selected = "OS", multiple = FALSE)),
select = utils::tail(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = FALSE,
internal_id = "test2"
),
c("STUDYID", "USUBJID", "PARAMCD", "AVISIT")
),
rlang::set_names(setdiff(c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"), "PARAMCD"))
)
# ignore if multiple filter with multiple selection
testthat::expect_identical(
get_merge_key_pair(
list(
dataname = "ADRS",
filters = list(list(columns = "PARAMCD", selected = c("OS", "PFS"), multiple = TRUE)),
select = utils::head(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = FALSE,
internal_id = "test1"
),
list(
dataname = "ADRS",
filters = list(list(columns = "PARAMCD", selected = c("OS", "PFS"), multiple = FALSE)),
select = utils::tail(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = FALSE,
internal_id = "test2"
),
c("STUDYID", "USUBJID", "PARAMCD", "AVISIT")
),
rlang::set_names(c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"))
)
# subtract only keys filter cols
testthat::expect_identical(
get_merge_key_pair(
list(
dataname = "ADRS",
filters = list(
list(columns = "SEX", selected = "F", multiple = FALSE),
list(columns = "PARAMCD", selected = "OS", multiple = FALSE),
list(columns = "RACE", selected = "ASIAN", multiple = FALSE)
),
select = utils::head(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = FALSE,
internal_id = "test1"
),
list(
dataname = "ADRS",
filters = NULL,
select = utils::tail(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = FALSE,
internal_id = "test2"
),
c("STUDYID", "USUBJID", "PARAMCD", "AVISIT")
),
rlang::set_names(setdiff(c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"), "PARAMCD"))
)
# do not subtract from primary key if not reshape and multiple filter column
testthat::expect_identical(
get_merge_key_pair(
list(
dataname = "ADRS",
filters = list(list(columns = "PARAMCD", selected = c("OS", "PFS"), multiple = TRUE)),
select = utils::head(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = FALSE,
internal_id = "test1"
),
list(
dataname = "ADRS",
filters = NULL,
select = utils::tail(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = FALSE,
internal_id = "test2"
),
c("STUDYID", "USUBJID", "PARAMCD", "AVISIT")
),
rlang::set_names(c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"))
)
testthat::expect_identical(
get_merge_key_pair(
list(
dataname = "ADRS",
filters = NULL,
select = utils::head(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = FALSE,
internal_id = "test1"
),
list(
dataname = "ADRS",
filters = list(list(columns = "PARAMCD", selected = c("OS", "PFS"), multiple = TRUE)),
select = utils::tail(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = FALSE,
internal_id = "test2"
),
c("STUDYID", "USUBJID", "PARAMCD", "AVISIT")
),
rlang::set_names(c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"))
)
testthat::expect_identical(
get_merge_key_pair(
list(
dataname = "ADRS",
filters = list(list(columns = "PARAMCD", selected = c("OS", "PFS"), multiple = TRUE)),
select = utils::head(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = FALSE,
internal_id = "test1"
),
list(
dataname = "ADRS",
filters = list(list(columns = "PARAMCD", selected = c("OS", "PFS"), multiple = TRUE)),
select = utils::tail(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = FALSE,
internal_id = "test2"
),
c("STUDYID", "USUBJID", "PARAMCD", "AVISIT")
),
rlang::set_names(c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"))
)
## reshape cases
# subtract by filter column on "from" selector
testthat::expect_identical(
get_merge_key_pair(
list(
dataname = "ADRS",
filters = list(
list(columns = "SEX", selected = "F", multiple = TRUE),
list(columns = "PARAMCD", selected = c("OS", "PFS"), multiple = TRUE),
list(columns = "RACE", selected = "ASIAN", multiple = TRUE)
),
select = utils::head(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = FALSE,
internal_id = "test1"
),
list(
dataname = "ADRS",
filters = NULL,
select = utils::tail(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = FALSE,
internal_id = "test2"
),
c("STUDYID", "USUBJID", "PARAMCD", "AVISIT")
),
rlang::set_names(c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"))
)
## reshape cases
# subtract by filter column on "from" selector
testthat::expect_identical(
get_merge_key_pair(
list(
dataname = "ADRS",
filters = list(list(columns = "PARAMCD", selected = "OS", multiple = TRUE)),
select = utils::head(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = TRUE,
internal_id = "test1"
),
list(
dataname = "ADRS",
filters = NULL,
select = utils::tail(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = TRUE,
internal_id = "test2"
),
c("STUDYID", "USUBJID", "PARAMCD", "AVISIT")
),
rlang::set_names(setdiff(c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"), "PARAMCD"))
)
# no changes because only "from" filter is used
testthat::expect_identical(
get_merge_key_pair(
list(
dataname = "ADRS",
filters = NULL,
select = utils::head(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = TRUE,
internal_id = "test1"
),
list(
dataname = "ADRS",
filters = list(list(columns = "PARAMCD", selected = "OS", multiple = TRUE)),
select = utils::tail(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = TRUE,
internal_id = "test2"
),
c("STUDYID", "USUBJID", "PARAMCD", "AVISIT")
),
rlang::set_names(c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"))
)
# subtract by filter column on "from" selector
testthat::expect_identical(
get_merge_key_pair(
list(
dataname = "ADRS",
filters = list(list(columns = "PARAMCD", selected = "OS", multiple = TRUE)),
select = utils::head(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = TRUE,
internal_id = "test1"
),
list(
dataname = "ADRS",
filters = list(list(columns = "PARAMCD", selected = "OS", multiple = TRUE)),
select = utils::tail(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = TRUE,
internal_id = "test2"
),
c("STUDYID", "USUBJID", "PARAMCD", "AVISIT")
),
rlang::set_names(setdiff(c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"), "PARAMCD"))
)
# subtract by filter key column on "from" selector
testthat::expect_identical(
get_merge_key_pair(
list(
dataname = "ADRS",
filters = list(
list(columns = "SEX", selected = "F", multiple = TRUE),
list(columns = "PARAMCD", selected = "OS", multiple = TRUE),
list(columns = "RACE", selected = "ASIAN", multiple = TRUE)
),
select = utils::head(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = TRUE,
internal_id = "test1"
),
list(
dataname = "ADRS",
filters = NULL,
select = utils::tail(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = TRUE,
internal_id = "test2"
),
c("STUDYID", "USUBJID", "PARAMCD", "AVISIT")
),
rlang::set_names(setdiff(c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"), "PARAMCD"))
)
testthat::expect_identical(
get_merge_key_pair(
list(
dataname = "ADLB",
filters = list(list(columns = "PARAMCD", selected = "ALT", multiple = FALSE)),
select = utils::head(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = FALSE,
internal_id = "test1"
),
list(
dataname = "ADLB",
filters = NULL,
select = utils::tail(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = FALSE,
internal_id = "test2"
),
c("STUDYID", "USUBJID", "PARAMCD", "AVISIT")
),
rlang::set_names(setdiff(c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"), "PARAMCD"))
)
})
testthat::test_that("get_merge_call", {
x <- list(
list(
dataname = "ADSL",
filters = NULL,
select = utils::head(letters, 3),
keys = c("STUDYID", "USUBJID"),
reshape = FALSE,
internal_id = "test1"
)
)
testthat::expect_identical(
get_merge_call(x),
list(quote(ANL <- ANL_1))
)
x <- list(
list(
dataname = "ADSL",
filters = NULL,
select = utils::head(letters, 3),
keys = c("STUDYID", "USUBJID"),
reshape = FALSE,
internal_id = "test1"
),
list(
dataname = "ADSL",
filters = NULL,
select = utils::tail(letters, 3),
keys = c("STUDYID", "USUBJID"),
reshape = FALSE,
internal_id = "test2"
)
)
jk <- teal.data::join_keys(teal.data::join_key("ADSL", "ADSL", c("STUDYID", "USUBJID")))
testthat::expect_identical(
get_merge_call(x, jk),
list(
quote(ANL <- ANL_1),
quote(ANL <- dplyr::full_join(ANL, ANL_2, by = c("STUDYID", "USUBJID")))
)
)
x <- list(
list(
dataname = "ADRS",
filters = NULL,
select = utils::head(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = FALSE,
internal_id = "test1"
),
list(
dataname = "ADRS",
filters = NULL,
select = utils::tail(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = FALSE,
internal_id = "test2"
)
)
jk <- teal.data::join_keys(teal.data::join_key("ADRS", "ADRS", c("STUDYID", "USUBJID", "PARAMCD", "AVISIT")))
testthat::expect_identical(
get_merge_call(x, jk),
list(
quote(ANL <- ANL_1),
quote(
ANL <- dplyr::full_join(ANL, ANL_2, by = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"))
)
)
)
x <- list(
list(
dataname = "ADSL",
filters = NULL,
select = utils::head(letters, 3),
keys = c("STUDYID", "USUBJID"),
reshape = FALSE,
internal_id = "test1"
),
list(
dataname = "ADRS",
filters = NULL,
select = utils::head(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = FALSE,
internal_id = "test2"
),
list(
dataname = "ADRS",
filters = NULL,
select = utils::tail(letters, 3),
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
reshape = FALSE,
internal_id = "test3"
)
)
jk <- teal.data::join_keys(
teal.data::join_key("ADSL", "ADSL", c("STUDYID", "USUBJID")),
teal.data::join_key("ADSL", "ADRS", c("STUDYID", "USUBJID")),
teal.data::join_key("ADRS", "ADRS", c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"))
)
testthat::expect_identical(
get_merge_call(x, jk),
list(
quote(ANL <- ANL_1),
quote(ANL <- dplyr::full_join(ANL, ANL_2, by = c("STUDYID", "USUBJID"))),
quote(
ANL <- dplyr::full_join(ANL, ANL_3, by = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"))
)
)
)
})
testthat::test_that("get_relabel_call", {
# removes duplicates by name (duplicated variables)
testthat::expect_identical(
get_relabel_call(c(
AGE = "Age",
SEX = "Sex",
AVAL = "Continuous Variable",
AGE = "Age",
SEX2 = "Sex",
AVAL = "Continuous Variable2"
)),
as.call(
parse(
text =
'teal.data::col_relabel(
AGE = "Age",
SEX = "Sex",
AVAL = "Continuous Variable",
SEX2 = "Sex")',
keep.source = FALSE
)
)[[1]]
)
# empty vector
testthat::expect_identical(
get_relabel_call(character(0)),
NULL
)
# unnamed vector
testthat::expect_identical(
get_relabel_call(c("a", "b")),
NULL
)
})
testthat::test_that("are_all_keys_provided returns TRUE if merged_selector_list has a single element", {
merged_selector_list_mock <- list(list(dataname = "dataset1"))
testthat::expect_true(are_needed_keys_provided(NULL, merged_selector_list_mock))
})
testthat::test_that(
"are_all_keys_provided returns FALSE if slices come from the same dataset and the dataset has no join_keys",
code = {
merged_selector_list_mock <- list(
list(dataname = "dataset1"),
list(dataname = "dataset1")
)
join_keys <- teal.data::join_keys()
testthat::expect_false(are_needed_keys_provided(join_keys, merged_selector_list_mock))
}
)
testthat::test_that(
"are_all_keys_provided returns TRUE if two slices come from the same dataset and the dataset has the join keys",
code = {
merged_selector_list_mock <- list(
list(dataname = "dataset1"),
list(dataname = "dataset1")
)
join_keys <- teal.data::join_keys(
teal.data::join_key("dataset1", "dataset1", c("key" = "key"))
)
testthat::expect_true(are_needed_keys_provided(join_keys, merged_selector_list_mock))
}
)
testthat::test_that("are_all_keys_provided returns TRUE if no slices are passed", {
testthat::expect_true(are_needed_keys_provided(list(), list()))
})
testthat::test_that(
"are_all_keys_provided returns TRUE if three slices from different datasets are provided and have the join keys",
code = {
merged_selector_list_mock <- list(
list(dataname = "dataset1"),
list(dataname = "dataset2"),
list(dataname = "dataset3")
)
join_keys <- teal.data::join_keys(
teal.data::join_key("dataset1", "dataset2", c("key" = "key")),
teal.data::join_key("dataset2", "dataset3", c("key" = "key")),
teal.data::join_key("dataset1", "dataset3", c("key" = "key"))
)
testthat::expect_true(are_needed_keys_provided(join_keys, merged_selector_list_mock))
}
)
testthat::test_that("validate_keys_sufficient returns TRUE for empty inputs", {
testthat::expect_true(validate_keys_sufficient(list(), list()))
})
testthat::test_that("validate_keys_sufficient raises an error for two slices with no join keys", {
merged_selector_list_mock <- list(
list(dataname = "dataset1"),
list(dataname = "dataset2")
)
testthat::expect_error(validate_keys_sufficient(list(), merged_selector_list_mock))
})
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