library(testthat)
test_that("Record keeping of single type tasks", {
rkf <- tempfile()
sql1 <- "SELECT * FROM my_table WHERE x = 1;"
checksum1 <- CohortDiagnostics:::computeChecksum(sql1)
expect_true(
CohortDiagnostics:::isTaskRequired(
cohortId = 1,
runSql = TRUE,
checksum = checksum1,
recordKeepingFile = rkf
)
)
CohortDiagnostics:::recordTasksDone(
cohortId = 1,
runSql = TRUE,
checksum = checksum1,
recordKeepingFile = rkf
)
expect_false(
CohortDiagnostics:::isTaskRequired(
cohortId = 1,
runSql = TRUE,
checksum = checksum1,
recordKeepingFile = rkf
)
)
sql2 <- "SELECT * FROM my_table WHERE x = 2;"
checksum2 <- CohortDiagnostics:::computeChecksum(sql2)
expect_true(
CohortDiagnostics:::isTaskRequired(
cohortId = 2,
runSql = TRUE,
checksum = checksum2,
recordKeepingFile = rkf
)
)
CohortDiagnostics:::recordTasksDone(
cohortId = 2,
runSql = TRUE,
checksum = checksum2,
recordKeepingFile = rkf
)
sql1a <- "SELECT * FROM my_table WHERE x = 1 AND y = 2;"
checksum1a <- CohortDiagnostics:::computeChecksum(sql1a)
expect_true(
CohortDiagnostics:::isTaskRequired(
cohortId = 1,
runSql = TRUE,
checksum = checksum1a,
recordKeepingFile = rkf
)
)
CohortDiagnostics:::recordTasksDone(
cohortId = 1,
runSql = TRUE,
checksum = checksum1a,
recordKeepingFile = rkf
)
expect_false(
CohortDiagnostics:::isTaskRequired(
cohortId = 1,
runSql = TRUE,
checksum = checksum1a,
recordKeepingFile = rkf
)
)
unlink(rkf)
})
test_that("Record keeping of multiple type tasks", {
rkf <- tempfile()
sql1 <- "SELECT * FROM my_table WHERE x = 1;"
checksum1 <- CohortDiagnostics:::computeChecksum(sql1)
expect_true(
CohortDiagnostics:::isTaskRequired(
cohortId = 1,
task = "Run SQL",
checksum = checksum1,
recordKeepingFile = rkf
)
)
CohortDiagnostics:::recordTasksDone(
cohortId = 1,
task = "Run SQL",
checksum = checksum1,
recordKeepingFile = rkf
)
expect_false(
CohortDiagnostics:::isTaskRequired(
cohortId = 1,
task = "Run SQL",
checksum = checksum1,
recordKeepingFile = rkf
)
)
sql2 <- "SELECT * FROM my_table WHERE x = 1 AND y = 1;"
checksum2 <- CohortDiagnostics:::computeChecksum(sql2)
expect_true(
CohortDiagnostics:::isTaskRequired(
cohortId = 1,
comparatorId = 2,
task = "Compare cohorts",
checksum = checksum2,
recordKeepingFile = rkf
)
)
CohortDiagnostics:::recordTasksDone(
cohortId = 1,
comparatorId = 2,
task = "Compare cohorts",
checksum = checksum2,
recordKeepingFile = rkf
)
expect_false(
CohortDiagnostics:::isTaskRequired(
cohortId = 1,
task = "Run SQL",
checksum = checksum1,
recordKeepingFile = rkf
)
)
sql2a <- "SELECT * FROM my_table WHERE x = 1 AND y = 2 AND z = 3;"
checksum2a <- CohortDiagnostics:::computeChecksum(sql2a)
expect_true(
CohortDiagnostics:::isTaskRequired(
cohortId = 1,
comparatorId = 2,
task = "Compare cohorts",
checksum = checksum2a,
recordKeepingFile = rkf
)
)
CohortDiagnostics:::recordTasksDone(
cohortId = 1,
comparatorId = 2,
task = "Compare cohorts",
checksum = checksum2a,
recordKeepingFile = rkf
)
expect_false(
CohortDiagnostics:::isTaskRequired(
cohortId = 1,
comparatorId = 2,
task = "Compare cohorts",
checksum = checksum2a,
recordKeepingFile = rkf
)
)
unlink(rkf)
})
test_that("Record keeping of multiple tasks at once", {
rkf <- tempfile()
task <- dplyr::tibble(
cohortId = c(1, 2),
sql = c(
"SELECT * FROM my_table WHERE x = 1;",
"SELECT * FROM my_table WHERE x = 2;"
)
)
task$checksum <- CohortDiagnostics:::computeChecksum(task$sql)
expect_true(
CohortDiagnostics:::isTaskRequired(
cohortId = task$cohortId[1],
checksum = task$checksum[1],
recordKeepingFile = rkf
)
)
CohortDiagnostics:::recordTasksDone(
cohortId = task$cohortId,
checksum = task$checksum,
recordKeepingFile = rkf
)
expect_false(
CohortDiagnostics:::isTaskRequired(
cohortId = task$cohortId[1],
checksum = task$checksum[1],
recordKeepingFile = rkf
)
)
expect_false(
CohortDiagnostics:::isTaskRequired(
cohortId = task$cohortId[2],
checksum = task$checksum[2],
recordKeepingFile = rkf
)
)
task <- dplyr::tibble(
cohortId = c(1, 2, 3),
sql = c(
"SELECT * FROM my_table WHERE x = 3;",
"SELECT * FROM my_table WHERE x = 4;",
"SELECT * FROM my_table WHERE x = 5;"
)
)
task$checksum <- CohortDiagnostics:::computeChecksum(task$sql)
expect_true(
CohortDiagnostics:::isTaskRequired(
cohortId = task$cohortId[1],
checksum = task$checksum[1],
recordKeepingFile = rkf
)
)
tasks <-
CohortDiagnostics:::getRequiredTasks(
cohortId = task$cohortId,
checksum = task$checksum,
recordKeepingFile = rkf
)
expect_equal(nrow(tasks), 3)
CohortDiagnostics:::recordTasksDone(
cohortId = task$cohortId,
checksum = task$checksum,
recordKeepingFile = rkf
)
expect_false(
CohortDiagnostics:::isTaskRequired(
cohortId = task$cohortId[1],
checksum = task$checksum[1],
recordKeepingFile = rkf
)
)
expect_false(
CohortDiagnostics:::isTaskRequired(
cohortId = task$cohortId[2],
checksum = task$checksum[2],
recordKeepingFile = rkf
)
)
expect_false(
CohortDiagnostics:::isTaskRequired(
cohortId = task$cohortId[3],
checksum = task$checksum[3],
recordKeepingFile = rkf
)
)
tasks <-
CohortDiagnostics:::getRequiredTasks(
cohortId = task$cohortId[2],
checksum = task$checksum[2],
recordKeepingFile = rkf
)
expect_equal(nrow(tasks), 0)
unlink(rkf)
})
test_that("Incremental save", {
tmpFile <- tempfile()
data <- dplyr::tibble(
cohortId = c(1, 1, 2, 2, 3),
count = c(100, 200, 300, 400, 500)
)
CohortDiagnostics:::saveIncremental(data, tmpFile, cohortId = c(1, 2, 3))
newData <- dplyr::tibble(
cohortId = c(1, 2, 2),
count = c(600, 700, 800)
)
CohortDiagnostics:::saveIncremental(newData, tmpFile, cohortId = c(1, 2))
goldStandard <- dplyr::tibble(
cohortId = c(3, 1, 2, 2),
count = c(500, 600, 700, 800)
)
expect_equal(
readr::read_csv(
tmpFile,
col_types = readr::cols(),
guess_max = min(1e7)
),
goldStandard,
ignore_attr = TRUE
)
unlink(tmpFile)
})
test_that("Incremental save with empty key", {
tmpFile <- tempfile()
data <- dplyr::tibble(
cohortId = c(1, 1, 2, 2, 3),
count = c(100, 200, 300, 400, 500)
)
CohortDiagnostics:::saveIncremental(data, tmpFile, cohortId = c(1, 2, 3))
newData <- dplyr::tibble()
CohortDiagnostics:::saveIncremental(newData, tmpFile, cohortId = c())
expect_equal(
readr::read_csv(
tmpFile,
col_types = readr::cols(),
guess_max = min(1e7)
),
data,
ignore_attr = TRUE
)
unlink(tmpFile)
})
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