tests/testthat/test-feature.R

In ropensci/infx: OpenBIS API Access to the InfectX Data Repository

context("list features")

test_that("features and feature codes can be listed", {

  check_skip()

  refs <- list_references(tok, plates[[1]], type = "feature")
  wells <- json_vec(
    json_class(wellRow = 1L, wellColumn = 1L, class = "WellPosition"),
    json_class(wellRow = 1L, wellColumn = 2L, class = "WellPosition")
  )

  feat_1 <- list_features(tok, refs[[1]])
  expect_s3_class(feat_1, "FeatureInformation")
  expect_s3_class(feat_1, "json_vec")
  expect_gte(length(feat_1), 1L)
  for (i in seq_along(feat_1)) {
    expect_s3_class(feat_1[[i]], "FeatureInformation")
    expect_s3_class(feat_1[[i]], "json_class")
  }

  feat_2 <- list_features(tok, refs[1:2])
  expect_s3_class(feat_2, "FeatureInformation")
  expect_s3_class(feat_2, "json_vec")
  expect_gte(length(feat_2), length(feat_1))
  for (i in seq_along(feat_2)) {
    expect_s3_class(feat_2[[i]], "FeatureInformation")
    expect_s3_class(feat_2[[i]], "json_class")
  }

  expect_identical(list_features(tok, refs[[1]], wells[[1]]),
                   feat_1)
  expect_identical(list_features(tok, refs[[1]], wells),
                   feat_1)
  expect_identical(list_features(tok, refs[1:2], wells[[1]]),
                   feat_2)
  expect_identical(list_features(tok, refs[1:2], wells),
                   feat_2)

  expect_identical(list_feature_codes(tok, refs[[1]]),
                   lapply(feat_1, `[[`, "code"))
  expect_identical(list_feature_codes(tok, refs[1:2]),
                   lapply(feat_2, `[[`, "code"))
})

test_that("features can be fetched", {

  check_skip()

  refs <- list_references(tok, plates[[1]], type = "feature")
  feats <- list_features(tok, refs[[1]])

  codes <- sapply(feats, `[[`, "code")

  feat_data_11 <- fetch_features(tok, refs[[1]], codes[1])
  expect_s3_class(feat_data_11, "FeatureVectorDataset")
  expect_s3_class(feat_data_11, "json_class")
  expect_true(has_fields(feat_data_11, "dataset", "featureVectors"))
  expect_s3_class(feat_data_11[["dataset"]], "FeatureVectorDatasetReference")
  expect_s3_class(feat_data_11[["dataset"]], "json_class")
  expect_length(feat_data_11[["featureVectors"]], 384L)
  expect_s3_class(feat_data_11[["featureVectors"]], "FeatureVector")
  expect_s3_class(feat_data_11[["featureVectors"]], "json_vec")
  for (i in seq_along(feat_data_11[["featureVectors"]])) {
    expect_s3_class(feat_data_11[["featureVectors"]][[i]], "FeatureVector")
    expect_s3_class(feat_data_11[["featureVectors"]][[i]], "json_class")
    expect_true(has_fields(feat_data_11[["featureVectors"]][[i]], "values"))
    expect_length(feat_data_11[["featureVectors"]][[i]][["values"]], 1L)
  }

  feat_data_12 <- fetch_features(tok, refs[[1]], codes[1:2])
  expect_s3_class(feat_data_12, "FeatureVectorDataset")
  expect_s3_class(feat_data_12, "json_class")
  expect_true(has_fields(feat_data_12, "dataset", "featureVectors"))
  expect_s3_class(feat_data_12[["dataset"]], "FeatureVectorDatasetReference")
  expect_s3_class(feat_data_12[["dataset"]], "json_class")
  expect_length(feat_data_12[["featureVectors"]], 384L)
  expect_s3_class(feat_data_12[["featureVectors"]], "FeatureVector")
  expect_s3_class(feat_data_12[["featureVectors"]], "json_vec")
  for (i in seq_along(feat_data_12[["featureVectors"]])) {
    expect_s3_class(feat_data_12[["featureVectors"]][[i]], "FeatureVector")
    expect_s3_class(feat_data_12[["featureVectors"]][[i]], "json_class")
    expect_true(has_fields(feat_data_12[["featureVectors"]][[i]], "values"))
    expect_length(feat_data_12[["featureVectors"]][[i]][["values"]], 2L)
  }

  feat_data_1 <- fetch_features(tok, refs[[1]])
  expect_s3_class(feat_data_1, "FeatureVectorDataset")
  expect_s3_class(feat_data_1, "json_class")
  expect_true(has_fields(feat_data_1, "dataset", "featureVectors"))
  expect_s3_class(feat_data_1[["dataset"]], "FeatureVectorDatasetReference")
  expect_s3_class(feat_data_1[["dataset"]], "json_class")
  expect_length(feat_data_1[["featureVectors"]], 384L)
  expect_s3_class(feat_data_1[["featureVectors"]], "FeatureVector")
  expect_s3_class(feat_data_1[["featureVectors"]], "json_vec")
  for (i in seq_along(feat_data_1[["featureVectors"]])) {
    expect_s3_class(feat_data_1[["featureVectors"]][[i]], "FeatureVector")
    expect_s3_class(feat_data_1[["featureVectors"]][[i]], "json_class")
    expect_true(has_fields(feat_data_1[["featureVectors"]][[i]], "values"))
    expect_length(feat_data_1[["featureVectors"]][[i]][["values"]],
                  length(codes))
  }

  well_pos <- lapply(feat_data_11[["featureVectors"]], `[[`, "wellPosition")
  refs_well <- json_vec(
    json_class(datasetCode = refs[[1]][["datasetCode"]],
               datastoreServerUrl = refs[[1]][["datastoreServerUrl"]],
               plate = refs[[1]][["plate"]],
               experimentIdentifier = refs[[1]][["experimentIdentifier"]],
               plateGeometry = refs[[1]][["plateGeometry"]],
               registrationDate = refs[[1]][["registrationDate"]],
               properties = refs[[1]][["properties"]],
               wellPosition = well_pos[[1]],
               class = "FeatureVectorDatasetWellReference"),
    json_class(datasetCode = refs[[1]][["datasetCode"]],
               datastoreServerUrl = refs[[1]][["datastoreServerUrl"]],
               plate = refs[[1]][["plate"]],
               experimentIdentifier = refs[[1]][["experimentIdentifier"]],
               plateGeometry = refs[[1]][["plateGeometry"]],
               registrationDate = refs[[1]][["registrationDate"]],
               properties = refs[[1]][["properties"]],
               wellPosition = well_pos[[2]],
               class = "FeatureVectorDatasetWellReference"))

  feat_data_11 <- fetch_features(tok, refs_well[[1]], codes[1])
  expect_s3_class(feat_data_11, "FeatureVectorWithDescription")
  expect_s3_class(feat_data_11, "json_class")
  expect_true(has_fields(feat_data_11, c("values", "datasetWellReference")))
  expect_s3_class(feat_data_11[["datasetWellReference"]],
                  "FeatureVectorDatasetWellReference")
  expect_s3_class(feat_data_11[["datasetWellReference"]], "json_class")
  expect_length(feat_data_11[["values"]], 1L)

  expect_identical(fetch_features(tok, refs[[1]], codes[1], well_pos[[1]]),
                   feat_data_11)

  feat_data_12 <- fetch_features(tok, refs_well[[1]], codes[1:2])
  expect_s3_class(feat_data_12, "FeatureVectorWithDescription")
  expect_s3_class(feat_data_12, "json_class")
  expect_true(has_fields(feat_data_12, c("values", "datasetWellReference")))
  expect_s3_class(feat_data_12[["datasetWellReference"]],
                  "FeatureVectorDatasetWellReference")
  expect_s3_class(feat_data_12[["datasetWellReference"]], "json_class")
  expect_length(feat_data_12[["values"]], 2L)

  expect_identical(fetch_features(tok, refs[[1]], codes[1:2], well_pos[[1]]),
                   feat_data_12)

  feat_data_1 <- fetch_features(tok, refs_well[[1]])
  expect_s3_class(feat_data_1, "FeatureVectorWithDescription")
  expect_s3_class(feat_data_1, "json_class")
  expect_true(has_fields(feat_data_1, c("values", "datasetWellReference")))
  expect_s3_class(feat_data_1[["datasetWellReference"]],
                  "FeatureVectorDatasetWellReference")
  expect_s3_class(feat_data_1[["datasetWellReference"]], "json_class")
  expect_length(feat_data_1[["values"]], length(codes))

  expect_identical(fetch_features(tok, refs[[1]], wells = well_pos[[1]]),
                   feat_data_1)

  feat_data_21 <- fetch_features(tok, refs_well, codes[1])
  expect_s3_class(feat_data_21, "FeatureVectorWithDescription")
  expect_s3_class(feat_data_21, "json_vec")
  expect_length(feat_data_21, 2L)
  for (i in seq_along(feat_data_21)) {
    expect_s3_class(feat_data_21[[i]], "FeatureVectorWithDescription")
    expect_s3_class(feat_data_21[[i]], "json_class")
    expect_true(has_fields(feat_data_21[[i]], c("values",
                                                "datasetWellReference")))
    expect_s3_class(feat_data_21[[i]][["datasetWellReference"]],
                    "FeatureVectorDatasetWellReference")
    expect_s3_class(feat_data_21[[i]][["datasetWellReference"]], "json_class")
    expect_length(feat_data_21[[i]][["values"]], 1L)
  }

  expect_identical(fetch_features(tok, refs[[1]], codes[1], well_pos[1:2]),
                   feat_data_21)

  feat_data_22 <- fetch_features(tok, refs_well, codes[1:2])
  expect_s3_class(feat_data_22, "FeatureVectorWithDescription")
  expect_s3_class(feat_data_22, "json_vec")
  expect_length(feat_data_22, 2L)
  for (i in seq_along(feat_data_22)) {
    expect_s3_class(feat_data_22[[i]], "FeatureVectorWithDescription")
    expect_s3_class(feat_data_22[[i]], "json_class")
    expect_true(has_fields(feat_data_22[[i]], "values"))
    expect_true(has_fields(feat_data_22[[i]], c("values",
                                                "datasetWellReference")))
    expect_s3_class(feat_data_22[[i]][["datasetWellReference"]],
                    "FeatureVectorDatasetWellReference")
    expect_s3_class(feat_data_22[[i]][["datasetWellReference"]], "json_class")
    expect_length(feat_data_22[[i]][["values"]], 2L)
  }

  expect_identical(fetch_features(tok, refs[[1]], codes[1:2], well_pos[1:2]),
                   feat_data_22)

  feat_data_12 <- fetch_features(tok, refs_well[[1]], codes[1:2])
  expect_s3_class(feat_data_12, "FeatureVectorWithDescription")
  expect_s3_class(feat_data_12, "json_class")
  expect_true(has_fields(feat_data_12, c("values", "datasetWellReference")))
  expect_s3_class(feat_data_12[["datasetWellReference"]],
                  "FeatureVectorDatasetWellReference")
  expect_s3_class(feat_data_12[["datasetWellReference"]], "json_class")
  expect_length(feat_data_12[["values"]], 2L)

  expect_identical(fetch_features(tok, refs[[1]], codes[1:2], well_pos[[1]]),
                   feat_data_12)
})

test_that("feature dataset refs can be converted", {

  check_skip()

  refs <- list_references(tok, plates[[1]], type = "feature")
  wells <- json_vec(
    json_class(wellRow = 1L, wellColumn = 1L, class = "WellPosition"),
    json_class(wellRow = 1L, wellColumn = 2L, class = "WellPosition")
  )

  fields <- c("datasetCode", "datastoreServerUrl", "plate",
              "experimentIdentifier", "plateGeometry", "registrationDate",
              "properties", "wellPosition")

  well_ref_11 <- feat_ds_well_ref(refs[[1]], wells[[1]])
  expect_s3_class(well_ref_11, "FeatureVectorDatasetWellReference")
  expect_s3_class(well_ref_11, "json_class")
  expect_true(has_fields(well_ref_11, fields))
  expect_s3_class(well_ref_11[["plate"]], "PlateIdentifier")
  expect_s3_class(well_ref_11[["plate"]], "json_class")
  expect_s3_class(well_ref_11[["experimentIdentifier"]],
                  "ExperimentIdentifier")
  expect_s3_class(well_ref_11[["experimentIdentifier"]], "json_class")
  expect_s3_class(well_ref_11[["plateGeometry"]], "Geometry")
  expect_s3_class(well_ref_11[["plateGeometry"]], "json_class")
  expect_s3_class(well_ref_11[["wellPosition"]], "WellPosition")
  expect_s3_class(well_ref_11[["wellPosition"]], "json_class")

  well_ref_12 <- feat_ds_well_ref(refs[[1]], wells)
  expect_s3_class(well_ref_12, "FeatureVectorDatasetWellReference")
  expect_s3_class(well_ref_12, "json_vec")
  expect_length(well_ref_12, 2L)
  for (i in seq_along(well_ref_12)) {
    expect_s3_class(well_ref_12[[i]], "FeatureVectorDatasetWellReference")
    expect_s3_class(well_ref_12[[i]], "json_class")
    expect_true(has_fields(well_ref_12[[i]], fields))
    expect_s3_class(well_ref_12[[i]][["plate"]], "PlateIdentifier")
    expect_s3_class(well_ref_12[[i]][["plate"]], "json_class")
    expect_s3_class(well_ref_12[[i]][["experimentIdentifier"]],
                    "ExperimentIdentifier")
    expect_s3_class(well_ref_12[[i]][["experimentIdentifier"]], "json_class")
    expect_s3_class(well_ref_12[[i]][["plateGeometry"]], "Geometry")
    expect_s3_class(well_ref_12[[i]][["plateGeometry"]], "json_class")
    expect_s3_class(well_ref_12[[i]][["wellPosition"]], "WellPosition")
    expect_s3_class(well_ref_12[[i]][["wellPosition"]], "json_class")
  }

  well_ref_21 <- feat_ds_well_ref(refs[1:2], wells[[1]])
  expect_s3_class(well_ref_21, "FeatureVectorDatasetWellReference")
  expect_s3_class(well_ref_21, "json_vec")
  expect_length(well_ref_21, 2L)
  for (i in seq_along(well_ref_21)) {
    expect_s3_class(well_ref_21[[i]], "FeatureVectorDatasetWellReference")
    expect_s3_class(well_ref_21[[i]], "json_class")
    expect_true(has_fields(well_ref_21[[i]], fields))
    expect_s3_class(well_ref_21[[i]][["plate"]], "PlateIdentifier")
    expect_s3_class(well_ref_21[[i]][["plate"]], "json_class")
    expect_s3_class(well_ref_21[[i]][["experimentIdentifier"]],
                    "ExperimentIdentifier")
    expect_s3_class(well_ref_21[[i]][["experimentIdentifier"]], "json_class")
    expect_s3_class(well_ref_21[[i]][["plateGeometry"]], "Geometry")
    expect_s3_class(well_ref_21[[i]][["plateGeometry"]], "json_class")
    expect_s3_class(well_ref_21[[i]][["wellPosition"]], "WellPosition")
    expect_s3_class(well_ref_21[[i]][["wellPosition"]], "json_class")
  }

  well_ref_22 <- feat_ds_well_ref(refs[1:2], wells)
  expect_s3_class(well_ref_22, "FeatureVectorDatasetWellReference")
  expect_s3_class(well_ref_22, "json_vec")
  expect_length(well_ref_22, 2L)
  for (i in seq_along(well_ref_22)) {
    expect_s3_class(well_ref_22[[i]], "FeatureVectorDatasetWellReference")
    expect_s3_class(well_ref_22[[i]], "json_class")
    expect_true(has_fields(well_ref_22[[i]], fields))
    expect_s3_class(well_ref_22[[i]][["plate"]], "PlateIdentifier")
    expect_s3_class(well_ref_22[[i]][["plate"]], "json_class")
    expect_s3_class(well_ref_22[[i]][["experimentIdentifier"]],
                    "ExperimentIdentifier")
    expect_s3_class(well_ref_22[[i]][["experimentIdentifier"]], "json_class")
    expect_s3_class(well_ref_22[[i]][["plateGeometry"]], "Geometry")
    expect_s3_class(well_ref_22[[i]][["plateGeometry"]], "json_class")
    expect_s3_class(well_ref_22[[i]][["wellPosition"]], "WellPosition")
    expect_s3_class(well_ref_22[[i]][["wellPosition"]], "json_class")
  }

  expect_error(feat_ds_well_ref(refs, wells))
})