context("dataset")
test_that("datasets can be listed", {
ds_1 <- datasets
expect_s3_class(ds_1, "DataSet")
expect_s3_class(ds_1, "json_vec")
expect_gte(length(ds_1), 1L)
for (i in seq_along(ds_1)) {
expect_s3_class(ds_1[[i]], "DataSet")
expect_s3_class(ds_1[[i]], "json_class")
expect_true(has_fields(ds_1[[i]], "retrievedConnections"))
expect_identical(ds_1[[i]][["retrievedConnections"]], list())
}
check_skip()
ds_2 <- list_datasets(tok, samples[c(1, 2)])
expect_s3_class(ds_2, "DataSet")
expect_s3_class(ds_2, "json_vec")
expect_gte(length(ds_2), length(ds_1))
for (i in seq_along(ds_2)) {
expect_s3_class(ds_2[[i]], "DataSet")
expect_s3_class(ds_2[[i]], "json_class")
expect_true(has_fields(ds_2[[i]], "retrievedConnections"))
expect_identical(ds_2[[i]][["retrievedConnections"]], list())
}
ds_3 <- list_datasets(tok, samples[[1]], "all")
expect_s3_class(ds_3, "DataSet")
expect_s3_class(ds_3, "json_vec")
expect_gte(length(ds_3), length(ds_1))
for (i in seq_along(ds_3)) {
expect_s3_class(ds_3[[i]], "DataSet")
expect_s3_class(ds_3[[i]], "json_class")
expect_true(has_fields(ds_3[[i]], "retrievedConnections"))
expect_identical(ds_3[[i]][["retrievedConnections"]],
list("PARENTS", "CHILDREN"))
}
ds_1 <- list_datasets(tok, experiments[[1]])
expect_s3_class(ds_1, "DataSet")
expect_s3_class(ds_1, "json_vec")
expect_gte(length(ds_1), 1L)
for (i in seq_along(ds_1)) {
expect_s3_class(ds_1[[i]], "DataSet")
expect_s3_class(ds_1[[i]], "json_class")
expect_true(has_fields(ds_1[[i]], "retrievedConnections"))
expect_identical(ds_1[[i]][["retrievedConnections"]], list())
}
ds_2 <- list_datasets(tok, experiments[c(1, 2)])
expect_s3_class(ds_2, "DataSet")
expect_s3_class(ds_2, "json_vec")
expect_gte(length(ds_2), length(ds_1))
for (i in seq_along(ds_2)) {
expect_s3_class(ds_2[[i]], "DataSet")
expect_s3_class(ds_2[[i]], "json_class")
expect_true(has_fields(ds_2[[i]], "retrievedConnections"))
expect_identical(ds_2[[i]][["retrievedConnections"]], list())
}
ds_3 <- list_datasets(tok, experiments[[1]], "all")
expect_s3_class(ds_3, "DataSet")
expect_s3_class(ds_3, "json_vec")
expect_gte(length(ds_3), length(ds_1))
for (i in seq_along(ds_3)) {
expect_s3_class(ds_3[[i]], "DataSet")
expect_s3_class(ds_3[[i]], "json_class")
expect_true(has_fields(ds_3[[i]], "retrievedConnections"))
expect_identical(ds_3[[i]][["retrievedConnections"]],
list("PARENTS", "CHILDREN"))
}
codes <- sapply(ds_3, `[[`, "code")
ds_1 <- list_datasets(tok, codes[1])
expect_s3_class(ds_1, "DataSet")
expect_s3_class(ds_1, "json_class")
expect_true(has_fields(ds_1, "retrievedConnections"))
expect_identical(ds_1[["retrievedConnections"]], list())
ds_2 <- list_datasets(tok, codes[c(1, 2)])
expect_s3_class(ds_2, "DataSet")
expect_s3_class(ds_2, "json_vec")
expect_length(ds_2, 2L)
for (i in seq_along(ds_2)) {
expect_s3_class(ds_2[[i]], "DataSet")
expect_s3_class(ds_2[[i]], "json_class")
expect_true(has_fields(ds_2[[i]], "retrievedConnections"))
expect_identical(ds_2[[i]][["retrievedConnections"]], list())
}
ds_3 <- list_datasets(tok, codes[1], "all")
expect_s3_class(ds_3, "DataSet")
expect_s3_class(ds_3, "json_class")
expect_gte(length(ds_3), 1L)
expect_true(has_fields(ds_3, "retrievedConnections"))
expect_identical(ds_3[["retrievedConnections"]], list("PARENTS", "CHILDREN"))
})
test_that("dataset references can be listed", {
check_skip()
mat <- material_id(c(3832L, 2475L), mode = "screening")
ds_1 <- list_references(tok, mat[[1]], exp_ids[[1]])
expect_identical(ds_1, list())
ds_1 <- list_references(tok, mat[[2]], exp_ids[[1]])
expect_s3_class(ds_1, "PlateWellReferenceWithDatasets")
expect_s3_class(ds_1, "json_vec")
expect_gte(length(ds_1), 1L)
for (i in seq_along(ds_1)) {
expect_s3_class(ds_1[[i]], "PlateWellReferenceWithDatasets")
expect_s3_class(ds_1[[i]], "json_class")
expect_true(has_fields(ds_1[[i]], c("imageDatasetReferences",
"featureVectorDatasetReferences")))
expect_s3_class(ds_1[[i]][["imageDatasetReferences"]],
"ImageDatasetReference")
expect_s3_class(ds_1[[i]][["imageDatasetReferences"]], "json_class")
expect_s3_class(ds_1[[i]][["featureVectorDatasetReferences"]],
"FeatureVectorDatasetReference")
expect_s3_class(ds_1[[i]][["featureVectorDatasetReferences"]],
"json_vec")
for (j in seq_along(ds_1[[i]][["featureVectorDatasetReferences"]])) {
expect_s3_class(ds_1[[i]][["featureVectorDatasetReferences"]][[j]],
"FeatureVectorDatasetReference")
expect_s3_class(ds_1[[i]][["featureVectorDatasetReferences"]][[j]],
"json_class")
}
}
ds_2 <- list_references(tok, mat[1:2], exp_ids[[1]])
expect_s3_class(ds_2, "PlateWellReferenceWithDatasets")
expect_s3_class(ds_2, "json_vec")
expect_gte(length(ds_2), length(ds_1))
for (i in seq_along(ds_2)) {
expect_s3_class(ds_2[[i]], "PlateWellReferenceWithDatasets")
expect_s3_class(ds_2[[i]], "json_class")
expect_true(has_fields(ds_2[[i]], c("imageDatasetReferences",
"featureVectorDatasetReferences")))
expect_s3_class(ds_2[[i]][["imageDatasetReferences"]],
"ImageDatasetReference")
expect_s3_class(ds_2[[i]][["imageDatasetReferences"]], "json_class")
expect_s3_class(ds_2[[i]][["featureVectorDatasetReferences"]],
"FeatureVectorDatasetReference")
expect_s3_class(ds_2[[i]][["featureVectorDatasetReferences"]],
"json_vec")
for (j in seq_along(ds_2[[i]][["featureVectorDatasetReferences"]])) {
expect_s3_class(ds_2[[i]][["featureVectorDatasetReferences"]][[j]],
"FeatureVectorDatasetReference")
expect_s3_class(ds_2[[i]][["featureVectorDatasetReferences"]][[j]],
"json_class")
}
}
ds_1 <- list_references(tok, samples[[1]])
expect_s3_class(ds_1, "ImageDatasetReference")
expect_s3_class(ds_1, "json_class")
expect_true(has_fields(ds_1, c("plate", "experimentIdentifier",
"plateGeometry")))
expect_s3_class(ds_1[["plate"]], "PlateIdentifier")
expect_s3_class(ds_1[["plate"]], "json_class")
expect_s3_class(ds_1[["experimentIdentifier"]], "ExperimentIdentifier")
expect_s3_class(ds_1[["experimentIdentifier"]], "json_class")
expect_s3_class(ds_1[["plateGeometry"]], "Geometry")
expect_s3_class(ds_1[["plateGeometry"]], "json_class")
ds_2 <- list_references(tok, samples[1:2])
expect_s3_class(ds_2, "ImageDatasetReference")
expect_s3_class(ds_2, "json_vec")
expect_length(ds_2, 2L)
for (i in seq_along(ds_2)) {
expect_s3_class(ds_2[[i]], "ImageDatasetReference")
expect_s3_class(ds_2[[i]], "json_class")
expect_true(has_fields(ds_2, c("plate", "experimentIdentifier",
"plateGeometry")))
expect_s3_class(ds_2[[i]][["plate"]], "PlateIdentifier")
expect_s3_class(ds_2[[i]][["plate"]], "json_class")
expect_s3_class(ds_2[[i]][["experimentIdentifier"]],
"ExperimentIdentifier")
expect_s3_class(ds_2[[i]][["experimentIdentifier"]], "json_class")
expect_s3_class(ds_2[[i]][["plateGeometry"]], "Geometry")
expect_s3_class(ds_2[[i]][["plateGeometry"]], "json_class")
}
ds_1 <- list_references(tok, plates[[1]])
expect_s3_class(ds_1, "ImageDatasetReference")
expect_s3_class(ds_1, "json_class")
expect_true(has_fields(ds_1, c("plate", "experimentIdentifier",
"plateGeometry")))
expect_s3_class(ds_1[["plate"]], "PlateIdentifier")
expect_s3_class(ds_1[["plate"]], "json_class")
expect_s3_class(ds_1[["experimentIdentifier"]], "ExperimentIdentifier")
expect_s3_class(ds_1[["experimentIdentifier"]], "json_class")
expect_s3_class(ds_1[["plateGeometry"]], "Geometry")
expect_s3_class(ds_1[["plateGeometry"]], "json_class")
ds_2 <- list_references(tok, plates[1:2])
expect_s3_class(ds_2, "ImageDatasetReference")
expect_s3_class(ds_2, "json_vec")
expect_length(ds_2, 2L)
for (i in seq_along(ds_2)) {
expect_s3_class(ds_2[[i]], "ImageDatasetReference")
expect_s3_class(ds_2[[i]], "json_class")
expect_true(has_fields(ds_2, c("plate", "experimentIdentifier",
"plateGeometry")))
expect_s3_class(ds_2[[i]][["plate"]], "PlateIdentifier")
expect_s3_class(ds_2[[i]][["plate"]], "json_class")
expect_s3_class(ds_2[[i]][["experimentIdentifier"]],
"ExperimentIdentifier")
expect_s3_class(ds_2[[i]][["experimentIdentifier"]], "json_class")
expect_s3_class(ds_2[[i]][["plateGeometry"]], "Geometry")
expect_s3_class(ds_2[[i]][["plateGeometry"]], "json_class")
}
plate_ids <- as_plate_id(plates)
expect_identical(list_references(tok, plate_ids[[1]]), ds_1)
expect_identical(list_references(tok, plate_ids[1:2]), ds_2)
expect_identical(list_references(tok, plate_meta[[1]]), ds_1)
expect_identical(list_references(tok, plate_meta[1:2]), ds_2)
ds_1 <- list_references(tok, plates[[1]], type = "feature")
expect_s3_class(ds_1, "FeatureVectorDatasetReference")
expect_s3_class(ds_1, "json_vec")
expect_gte(length(ds_1), 1L)
for (i in seq_along(ds_1)) {
expect_s3_class(ds_1[[i]], "FeatureVectorDatasetReference")
expect_s3_class(ds_1[[i]], "json_class")
}
dsids <- list_dataset_ids(tok, sapply(ds_2, `[[`, "datasetCode"))
ds_1 <- list_references(tok, dsids[[1]], channels = "DAPI")
expect_s3_class(ds_1, "MicroscopyImageReference")
expect_s3_class(ds_1, "json_vec")
expect_length(ds_1, 9L)
for (i in seq_along(ds_1)) {
expect_s3_class(ds_1[[i]], "MicroscopyImageReference")
expect_s3_class(ds_1[[i]], "json_class")
}
ds_2 <- list_references(tok, dsids[1:2], channels = "DAPI")
expect_s3_class(ds_2, "MicroscopyImageReference")
expect_s3_class(ds_2, "json_vec")
expect_length(ds_2, 18L)
for (i in seq_along(ds_2)) {
expect_s3_class(ds_2[[i]], "MicroscopyImageReference")
expect_s3_class(ds_2[[i]], "json_class")
}
ds_3 <- list_references(tok, dsids[[1]], channels = c("DAPI", "GFP"))
expect_s3_class(ds_3, "MicroscopyImageReference")
expect_s3_class(ds_3, "json_vec")
expect_length(ds_3, 18L)
for (i in seq_along(ds_3)) {
expect_s3_class(ds_3[[i]], "MicroscopyImageReference")
expect_s3_class(ds_3[[i]], "json_class")
}
# check Dataset
expect_equivalent(list_references(tok,
list_datasets(tok,
ds_1[[1]][["datasetCode"]]),
channels = "DAPI"), ds_1)
# check MicroscopyImageReference
expect_equivalent(list_references(tok, ds_1[[1]], channels = "DAPI"), ds_1)
# check ImageDatasetReference
expect_equivalent(list_references(tok, list_references(tok, plates[[1]]),
channels = "DAPI"), ds_1)
well_pos <- as_json_vec(lapply(wells[1:2], `[[`, "wellPosition"))
ds_1 <- list_references(tok, dsids[[1]], wells = well_pos[[1]],
channels = "DAPI")
expect_s3_class(ds_1, "PlateImageReference")
expect_s3_class(ds_1, "json_vec")
expect_length(ds_1, 9L)
for (i in seq_along(ds_1)) {
expect_s3_class(ds_1[[i]], "PlateImageReference")
expect_s3_class(ds_1[[i]], "json_class")
}
ds_2 <- list_references(tok, dsids[[1]], wells = well_pos, channels = "DAPI")
expect_s3_class(ds_2, "PlateImageReference")
expect_s3_class(ds_2, "json_vec")
expect_length(ds_2, 18L)
for (i in seq_along(ds_2)) {
expect_s3_class(ds_2[[i]], "PlateImageReference")
expect_s3_class(ds_2[[i]], "json_class")
}
ds_3 <- list_references(tok, dsids[[1]], wells = well_pos[[1]],
channels = c("DAPI", "GFP"))
expect_s3_class(ds_3, "PlateImageReference")
expect_s3_class(ds_3, "json_vec")
expect_length(ds_3, 18L)
for (i in seq_along(ds_3)) {
expect_s3_class(ds_3[[i]], "PlateImageReference")
expect_s3_class(ds_3[[i]], "json_class")
}
})
test_that("dataset types can be listed", {
check_skip()
ds_types <- list_dataset_types(tok)
expect_s3_class(ds_types, "DataSetType")
expect_s3_class(ds_types, "json_vec")
expect_gte(length(ds_types), 1L)
for (i in seq_along(ds_types)) {
expect_s3_class(ds_types[[i]], "DataSetType")
expect_s3_class(ds_types[[i]], "json_class")
}
})
test_that("dataset ids can be listed", {
check_skip()
codes <- dataset_code(datasets)
dsid_1 <- list_dataset_ids(tok, codes[[1]])
expect_s3_class(dsid_1, "DatasetIdentifier")
expect_s3_class(dsid_1, "json_class")
expect_true(has_fields(dsid_1, c("datasetCode", "datastoreServerUrl",
"permId")))
expect_is(dsid_1[["datasetCode"]], "character")
expect_is(dsid_1[["datastoreServerUrl"]], "character")
expect_is(dsid_1[["permId"]], "character")
dsid_2 <- list_dataset_ids(tok, codes[1:2])
expect_s3_class(dsid_2, "DatasetIdentifier")
expect_s3_class(dsid_2, "json_vec")
expect_length(dsid_2, 2L)
for (i in seq_along(dsid_2)) {
expect_s3_class(dsid_2[[i]], "DatasetIdentifier")
expect_s3_class(dsid_2[[i]], "json_class")
expect_true(has_fields(dsid_2[[i]], c("datasetCode", "datastoreServerUrl",
"permId")))
expect_is(dsid_2[[i]][["datasetCode"]], "character")
expect_is(dsid_2[[i]][["datastoreServerUrl"]], "character")
expect_is(dsid_2[[i]][["permId"]], "character")
}
expect_identical(list_dataset_ids(tok, datasets[[1]]), dsid_1)
expect_identical(list_dataset_ids(tok, datasets[1:2]), dsid_2)
})
test_that("dataset codes can be extracted", {
check_skip()
codes <- dataset_code(datasets)
expect_is(codes, "character")
expect_length(codes, length(datasets))
codes <- dataset_code(list_dataset_ids(tok, codes[1:2]))
expect_is(codes, "character")
expect_length(codes, 2L)
})
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