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Port comprehensive test assertions from Python vitessce for hierarchical coordination APIs
Co-authored-by: keller-mark <7525285+keller-mark@users.noreply.github.com>
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‎tests/testthat/test-config.R‎

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@@ -528,3 +528,367 @@ test_that("VitessceConfig add_meta_coordination", {
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expect_true("metaCoordinationScopes" %in% names(vc_list$coordinationSpace))
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expect_true("metaCoordinationScopesBy" %in% names(vc_list$coordinationSpace))
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})
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test_that("VitessceConfig add_coordination_by_dict with hierarchical structure", {
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vc <- VitessceConfig$new(schema_version = "1.0.16", name = "Test config")
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# Test complex hierarchical coordination using available coordination types
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# Simulate the Python test structure with R-compatible types
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scopes <- vc$add_coordination_by_dict(list(
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spatialLayers = CL(list(
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list(
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geneFilter = list("BRCA1", "TP53"),
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spatialZoom = 2.5,
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cellFilter = CL(list(
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list(
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spatialTargetX = 100,
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cellSetColor = list(255, 0, 0)
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),
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list(
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spatialTargetX = 200,
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cellSetColor = list(0, 255, 0)
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)
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))
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)
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))
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))
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vc_list <- vc$to_list()
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# Check that the hierarchical structure was created
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expect_true("spatialLayers" %in% names(vc_list$coordinationSpace))
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expect_true("geneFilter" %in% names(vc_list$coordinationSpace))
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expect_true("spatialZoom" %in% names(vc_list$coordinationSpace))
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expect_true("cellFilter" %in% names(vc_list$coordinationSpace))
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expect_true("spatialTargetX" %in% names(vc_list$coordinationSpace))
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expect_true("cellSetColor" %in% names(vc_list$coordinationSpace))
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# Check that dummy values were set for list types
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spatial_layers_scope <- names(vc_list$coordinationSpace$spatialLayers)[1]
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expect_equal(vc_list$coordinationSpace$spatialLayers[[spatial_layers_scope]], jsonlite::unbox("__dummy__"))
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# Check that regular values were set correctly
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zoom_scope <- names(vc_list$coordinationSpace$spatialZoom)[1]
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expect_equal(vc_list$coordinationSpace$spatialZoom[[zoom_scope]], jsonlite::unbox(2.5))
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# Check gene filter list
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gene_scope <- names(vc_list$coordinationSpace$geneFilter)[1]
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expect_equal(vc_list$coordinationSpace$geneFilter[[gene_scope]], list("BRCA1", "TP53"))
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# Check spatial target values
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x_scopes <- names(vc_list$coordinationSpace$spatialTargetX)
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expect_length(x_scopes, 2)
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expect_equal(vc_list$coordinationSpace$spatialTargetX[[x_scopes[1]]], jsonlite::unbox(100))
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expect_equal(vc_list$coordinationSpace$spatialTargetX[[x_scopes[2]]], jsonlite::unbox(200))
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# Check color values
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color_scopes <- names(vc_list$coordinationSpace$cellSetColor)
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expect_length(color_scopes, 2)
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expect_equal(vc_list$coordinationSpace$cellSetColor[[color_scopes[1]]], list(255, 0, 0))
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expect_equal(vc_list$coordinationSpace$cellSetColor[[color_scopes[2]]], list(0, 255, 0))
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})
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test_that("VitessceConfig add_and_use_coordination_by_dict", {
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vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config")
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dataset <- vc$add_dataset(name = "My dataset")
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# Add coordination first
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color_scope_list <- vc$add_coordination("cellSetColor")
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color_scope <- color_scope_list[[1]]
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color_scope$set_value(list(255, 0, 0))
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# Add hierarchical coordination using available R types
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scopes <- vc$add_coordination_by_dict(list(
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spatialLayers = CL(list(
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list(
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geneFilter = list("GENE1", "GENE2"),
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spatialZoom = 1.5,
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cellFilter = CL(list(
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list(
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spatialTargetX = 0,
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cellSetColor = list(0, 255, 0)
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),
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list(
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spatialTargetX = 1,
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cellSetColor = list(0, 0, 255)
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)
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))
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)
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)),
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cellHighlight = CL(list(
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list(
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geneSelection = list("GENE3"),
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spatialTargetY = 10,
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cellSetColor = color_scope
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)
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))
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))
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spatial_view <- vc$add_view("spatial", dataset = dataset)
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spatial_view$use_coordination_by_dict(scopes)
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vc_list <- vc$to_list()
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# Check dataset
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expect_equal(vc_list$datasets[[1]]$uid, "A")
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expect_equal(vc_list$datasets[[1]]$name, "My dataset")
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# Check coordination space structure
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expect_true("dataset" %in% names(vc_list$coordinationSpace))
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expect_true("spatialLayers" %in% names(vc_list$coordinationSpace))
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expect_true("geneFilter" %in% names(vc_list$coordinationSpace))
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expect_true("spatialZoom" %in% names(vc_list$coordinationSpace))
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expect_true("cellFilter" %in% names(vc_list$coordinationSpace))
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expect_true("spatialTargetX" %in% names(vc_list$coordinationSpace))
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expect_true("spatialTargetY" %in% names(vc_list$coordinationSpace))
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expect_true("cellSetColor" %in% names(vc_list$coordinationSpace))
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expect_true("cellHighlight" %in% names(vc_list$coordinationSpace))
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expect_true("geneSelection" %in% names(vc_list$coordinationSpace))
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# Check specific values
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expect_equal(vc_list$coordinationSpace$dataset[["A"]], jsonlite::unbox("A"))
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# Check that spatial layers has dummy value
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spatial_layers_scope <- names(vc_list$coordinationSpace$spatialLayers)[1]
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expect_equal(vc_list$coordinationSpace$spatialLayers[[spatial_layers_scope]], jsonlite::unbox("__dummy__"))
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# Check zoom value
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zoom_scope <- names(vc_list$coordinationSpace$spatialZoom)[1]
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expect_equal(vc_list$coordinationSpace$spatialZoom[[zoom_scope]], jsonlite::unbox(1.5))
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# Check that color scope value is shared
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color_scopes <- names(vc_list$coordinationSpace$cellSetColor)
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expect_true(any(sapply(color_scopes, function(scope) {
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identical(vc_list$coordinationSpace$cellSetColor[[scope]], list(255, 0, 0))
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})))
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# Check layout - view should use the scopes
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expect_equal(vc_list$layout[[1]]$component, "spatial")
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expect_true("dataset" %in% names(vc_list$layout[[1]]$coordinationScopes))
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expect_equal(vc_list$layout[[1]]$coordinationScopes$dataset, "A")
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})
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test_that("VitessceConfig use_meta_complex_coordination", {
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vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config")
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dataset <- vc$add_dataset(name = "My dataset")
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# Create complex hierarchical coordination structure
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scopes <- vc$add_coordination_by_dict(list(
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spatialLayers = CL(list(
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list(
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geneFilter = list("GENE_A", "GENE_B"),
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spatialZoom = 2.0,
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cellFilter = CL(list(
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list(
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spatialTargetX = 0,
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cellSetColor = list(255, 0, 0)
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),
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list(
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spatialTargetX = 1,
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cellSetColor = list(0, 255, 0)
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)
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))
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)
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)),
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cellHighlight = CL(list(
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list(
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geneSelection = list("GENE_C"),
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spatialTargetY = 5,
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cellSetColor = list(255, 0, 0)
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)
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))
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))
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meta_coordination_scope <- vc$add_meta_coordination()
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meta_coordination_scope$use_coordination_by_dict(scopes)
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spatial_view <- vc$add_view("spatial", dataset = dataset)
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lc_view <- vc$add_view("layerController", dataset = dataset)
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spatial_view$use_meta_coordination(meta_coordination_scope)
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lc_view$use_meta_coordination(meta_coordination_scope)
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vc_list <- vc$to_list()
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# Check basic structure
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expect_equal(vc_list$version, "1.0.16")
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expect_equal(vc_list$name, "My config")
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expect_equal(vc_list$datasets[[1]]$uid, "A")
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expect_equal(vc_list$datasets[[1]]$name, "My dataset")
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# Check coordination space
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expect_true("dataset" %in% names(vc_list$coordinationSpace))
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expect_true("spatialLayers" %in% names(vc_list$coordinationSpace))
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expect_true("geneFilter" %in% names(vc_list$coordinationSpace))
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expect_true("spatialZoom" %in% names(vc_list$coordinationSpace))
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expect_true("cellFilter" %in% names(vc_list$coordinationSpace))
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expect_true("spatialTargetX" %in% names(vc_list$coordinationSpace))
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expect_true("spatialTargetY" %in% names(vc_list$coordinationSpace))
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expect_true("cellSetColor" %in% names(vc_list$coordinationSpace))
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expect_true("cellHighlight" %in% names(vc_list$coordinationSpace))
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expect_true("geneSelection" %in% names(vc_list$coordinationSpace))
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expect_true("metaCoordinationScopes" %in% names(vc_list$coordinationSpace))
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expect_true("metaCoordinationScopesBy" %in% names(vc_list$coordinationSpace))
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# Check meta coordination structure
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meta_scope_names <- names(vc_list$coordinationSpace$metaCoordinationScopes)
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expect_length(meta_scope_names, 1)
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meta_scope_content <- vc_list$coordinationSpace$metaCoordinationScopes[[meta_scope_names[1]]]
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expect_true("spatialLayers" %in% names(meta_scope_content))
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expect_true("cellHighlight" %in% names(meta_scope_content))
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# Check that views use meta coordination
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expect_equal(vc_list$layout[[1]]$component, "spatial")
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expect_true("metaCoordinationScopes" %in% names(vc_list$layout[[1]]$coordinationScopes))
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expect_true("metaCoordinationScopesBy" %in% names(vc_list$layout[[1]]$coordinationScopes))
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expect_equal(vc_list$layout[[2]]$component, "layerController")
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expect_true("metaCoordinationScopes" %in% names(vc_list$layout[[2]]$coordinationScopes))
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expect_true("metaCoordinationScopesBy" %in% names(vc_list$layout[[2]]$coordinationScopes))
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})
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test_that("VitessceConfig link_views_by_dict complex hierarchical", {
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vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config")
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dataset <- vc$add_dataset(name = "My dataset")
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spatial_view <- vc$add_view("spatial", dataset = dataset)
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lc_view <- vc$add_view("layerController", dataset = dataset)
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# Use complex hierarchical coordination linking
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vc$link_views_by_dict(list(spatial_view, lc_view), list(
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spatialLayers = CL(list(
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list(
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geneFilter = list("GENE_1", "GENE_2"),
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spatialZoom = 3.0,
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cellFilter = CL(list(
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list(
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spatialTargetX = 0,
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cellSetColor = list(255, 0, 0)
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),
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list(
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spatialTargetX = 1,
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cellSetColor = list(0, 255, 0)
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)
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))
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)
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)),
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cellHighlight = CL(list(
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list(
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geneSelection = list("GENE_3"),
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spatialTargetY = 0,
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cellSetColor = list(255, 0, 0)
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)
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))
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))
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vc_list <- vc$to_list()
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# Check structure matches expected format
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expect_equal(vc_list$version, "1.0.16")
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expect_equal(vc_list$name, "My config")
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expect_equal(vc_list$datasets[[1]]$uid, "A")
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expect_equal(vc_list$datasets[[1]]$name, "My dataset")
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# Check coordination space contains all expected types
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expect_true("dataset" %in% names(vc_list$coordinationSpace))
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expect_true("spatialLayers" %in% names(vc_list$coordinationSpace))
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expect_true("geneFilter" %in% names(vc_list$coordinationSpace))
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expect_true("spatialZoom" %in% names(vc_list$coordinationSpace))
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expect_true("cellFilter" %in% names(vc_list$coordinationSpace))
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expect_true("spatialTargetX" %in% names(vc_list$coordinationSpace))
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expect_true("spatialTargetY" %in% names(vc_list$coordinationSpace))
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expect_true("cellSetColor" %in% names(vc_list$coordinationSpace))
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expect_true("cellHighlight" %in% names(vc_list$coordinationSpace))
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expect_true("geneSelection" %in% names(vc_list$coordinationSpace))
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expect_true("metaCoordinationScopes" %in% names(vc_list$coordinationSpace))
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expect_true("metaCoordinationScopesBy" %in% names(vc_list$coordinationSpace))
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# Check specific values
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zoom_scope <- names(vc_list$coordinationSpace$spatialZoom)[1]
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expect_equal(vc_list$coordinationSpace$spatialZoom[[zoom_scope]], jsonlite::unbox(3.0))
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gene_filter_scope <- names(vc_list$coordinationSpace$geneFilter)[1]
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expect_equal(vc_list$coordinationSpace$geneFilter[[gene_filter_scope]], list("GENE_1", "GENE_2"))
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# Check that both views use meta coordination
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expect_equal(vc_list$layout[[1]]$component, "spatial")
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expect_true("metaCoordinationScopes" %in% names(vc_list$layout[[1]]$coordinationScopes))
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expect_true("metaCoordinationScopesBy" %in% names(vc_list$layout[[1]]$coordinationScopes))
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expect_equal(vc_list$layout[[2]]$component, "layerController")
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expect_true("metaCoordinationScopes" %in% names(vc_list$layout[[2]]$coordinationScopes))
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expect_true("metaCoordinationScopesBy" %in% names(vc_list$layout[[2]]$coordinationScopes))
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})
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test_that("VitessceConfig link_views_by_dict with scope_prefix", {
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vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config")
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dataset <- vc$add_dataset(name = "My dataset")
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spatial_view <- vc$add_view("spatial", dataset = dataset)
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lc_view <- vc$add_view("layerController", dataset = dataset)
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# Test with scope prefix like Python test
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vc$link_views_by_dict(list(spatial_view, lc_view), list(
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spatialLayers = CL(list(
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list(
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spatialZoom = 1.0,
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cellFilter = CL(list(
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list(
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spatialTargetX = 0,
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cellSetColor = list(255, 0, 0)
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),
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list(
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spatialTargetX = 1,
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cellSetColor = list(0, 255, 0)
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)
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))
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)
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))
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), scope_prefix = "SOME_PREFIX_")
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vc_list <- vc$to_list()
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# Check structure
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expect_equal(vc_list$version, "1.0.16")
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expect_equal(vc_list$name, "My config")
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expect_equal(vc_list$datasets[[1]]$uid, "A")
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expect_equal(vc_list$datasets[[1]]$name, "My dataset")
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# Check coordination space with prefixes
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expect_true("dataset" %in% names(vc_list$coordinationSpace))
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expect_true("spatialLayers" %in% names(vc_list$coordinationSpace))
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expect_true("spatialZoom" %in% names(vc_list$coordinationSpace))
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expect_true("cellFilter" %in% names(vc_list$coordinationSpace))
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expect_true("spatialTargetX" %in% names(vc_list$coordinationSpace))
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expect_true("cellSetColor" %in% names(vc_list$coordinationSpace))
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expect_true("metaCoordinationScopes" %in% names(vc_list$coordinationSpace))
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expect_true("metaCoordinationScopesBy" %in% names(vc_list$coordinationSpace))
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# Check that scope names use the prefix
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spatial_layers_scopes <- names(vc_list$coordinationSpace$spatialLayers)
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expect_true(any(grepl("^SOME_PREFIX_", spatial_layers_scopes)))
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zoom_scopes <- names(vc_list$coordinationSpace$spatialZoom)
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expect_true(any(grepl("^SOME_PREFIX_", zoom_scopes)))
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x_target_scopes <- names(vc_list$coordinationSpace$spatialTargetX)
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expect_true(any(grepl("^SOME_PREFIX_", x_target_scopes)))
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color_scopes <- names(vc_list$coordinationSpace$cellSetColor)
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expect_true(any(grepl("^SOME_PREFIX_", color_scopes)))
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# Check meta coordination scope names use prefix
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meta_scopes <- names(vc_list$coordinationSpace$metaCoordinationScopes)
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expect_true(any(grepl("^SOME_PREFIX_", meta_scopes)))
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# Check that views use the prefixed meta coordination
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expect_equal(vc_list$layout[[1]]$component, "spatial")
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expect_true("metaCoordinationScopes" %in% names(vc_list$layout[[1]]$coordinationScopes))
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meta_scope_used <- vc_list$layout[[1]]$coordinationScopes$metaCoordinationScopes[1]
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expect_true(grepl("^SOME_PREFIX_", meta_scope_used))
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expect_equal(vc_list$layout[[2]]$component, "layerController")
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expect_true("metaCoordinationScopes" %in% names(vc_list$layout[[2]]$coordinationScopes))
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meta_scope_used_2 <- vc_list$layout[[2]]$coordinationScopes$metaCoordinationScopes[1]
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expect_true(grepl("^SOME_PREFIX_", meta_scope_used_2))
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})

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