context("createResourcesPageArtifacts")
studyPersonnel <- readRDS("datasets/ResourcesPageMock.studyPersonnel.rds")
assayTimepoint <- readRDS("datasets/ResourcesPageMock.assayTimepoint.rds")
studyOverview <- readRDS("datasets/ResourcesPageMock.studyOverview.rds")
validStudies <- readRDS("datasets/ResourcesPageMock.validStudies.rds")
test_that("makeStudyStats", {
ISR_inits <- readRDS("datasets/parseLogsToISRInitsOutput.rds")
UI <- readRDS("datasets/parseLogsToUIStudyViews.rds")
res <- ImmuneSpaceCron:::makeStudyStats(ISR_inits, UI)
expectedCols <- c("Date", "study", "studyId", "ISR_connections", "UI_pageviews", "total_views")
expect_equivalent(colnames(res), expectedCols)
types <- unname(sapply(res, typeof))
expectedTypes <- c("double", "character", "double", "double", "double", "double")
expect_equivalent(types, expectedTypes)
expect_true(all(grepl("SDY\\d{2,4}", res$study)))
expect_true(nrow(res) == 21)
})
test_that("mungePIData", {
res <- ImmuneSpaceCron:::mungePIData(studyPersonnel, validStudies$Name)
expect_true(all.equal(colnames(res), c("role_in_study", "study", "person_accession")))
types <- unname(sapply(res, typeof))
expect_equivalent(types, c("character", "character", "character"))
expect_true(nrow(res) > 100)
expect_true(all(!is.na(res$study)))
expect_true(all(grepl("SDY\\d{2,4}", res$study)))
})
test_that("mungeStudyOverviewData", {
res <- ImmuneSpaceCron:::mungeStudyOverviewData(studyOverview, validStudies$Name)
expectedCols <- c(
"study", "actual_enrollment", "clinical_trial", "condition_studied",
"maximum_age", "minimum_age", "sponsoring_organization", "initial_data_release_date"
)
expect_equivalent(colnames(res), expectedCols)
types <- unname(sapply(res, typeof))
expectedTypes <- c(
"character", "integer", "character", "character",
"character", "character", "character", "double"
)
expect_equivalent(types, expectedTypes)
expect_true(nrow(res) > 100)
expect_true(all(!is.na(res$study)))
})
test_that("mungeAssayTimepointData", {
res <- ImmuneSpaceCron:::mungeAssayTimepointData(assayTimepoint)
expectedCols <- c(
"ParticipantId", "Name", "Label", "Timepoint",
"Features", "study", "name_timepoint", "count"
)
expect_equivalent(colnames(res), expectedCols)
types <- unname(sapply(res, typeof))
expectedTypes <- c(
"character", "character", "character", "character",
"integer", "character", "character", "double"
)
expect_equivalent(types, expectedTypes)
expect_true(nrow(res) > 1000)
expect_true(all(!is.na(res$study)))
expect_true(all(grepl("SDY\\d{2,4}", res$study)))
})
test_that("mergeStudyMetaData", {
assayTimepoint <- ImmuneSpaceCron:::mungeAssayTimepointData(assayTimepoint)
studyOverview <- ImmuneSpaceCron:::mungeStudyOverviewData(studyOverview, validStudies$Name)
studyPersonnel <- ImmuneSpaceCron:::mungePIData(studyPersonnel, validStudies$Name)
res <- ImmuneSpaceCron:::mergeStudyMetaData(
valid = validStudies,
pi = studyPersonnel,
study = studyOverview,
at = assayTimepoint
)
sdyOverviewCols <- c(
"person_accession", "actual_enrollment", "clinical_trial", "condition_studied",
"maximum_age", "minimum_age", "sponsoring_organization", "initial_data_release_date"
)
expect_true(all(sdyOverviewCols %in% colnames(res)))
expect_true(any(grepl("neut_ab_titer", colnames(res))))
expect_true(nrow(res) == nrow(studyOverview))
elisa <- res[, grep("elisa", colnames(res))]
expect_equivalent(range(elisa), c(0, 1))
expect_true(all(grepl("SDY\\d{2,4}", rownames(res))))
})
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