[r] Add four add_new_* setters to CollectionBase (#1091)

apis/r/R/SOMACollectionBase.R

@@ -12,7 +12,7 @@ SOMACollectionBase <- R6::R6Class(
     #'
     #' @param uri URI of the TileDB group
     #' @param platform_config Optional storage-engine specific configuration
-    #' @param ctx optional tiledb context
+    #' @param ctx Optional TileDB context
     initialize = function(uri, platform_config = NULL, ctx = NULL) {
       super$initialize(uri, platform_config, ctx)
     },
@@ -42,6 +42,48 @@ SOMACollectionBase <- R6::R6Class(
     #' @returns SOMA object.
     get = function(name) {
       super$get(name)
+    },
+
+    #' @description Add a new SOMA collection to this collection. (lifecycle: experimental)
+    #' @param object SOMA collection object.
+    #' @param key The key to be added.
+    add_new_collection = function(object, key) {
+      # TODO: Check that object is a collection
+      super$set(object, key)
+    },
+
+    #' @description Add a new SOMA dataframe to this collection. (lifecycle: experimental)
+    #' @param key The key to be added.
+    #' @param schema Arrow schema argument passed on to DataFrame$create()
+    #' @param index_column_names Index column names passed on to DataFrame$create()
+    add_new_dataframe = function(key, schema, index_column_names) {
+      ## TODO: Check argument validity
+      ## TODO: platform_config ?
+      ndf <- SOMADataFrame$new( file.path(self$uri, key) )
+      ndf$create(schema, index_column_names)
+      super$set(ndf, key)
+    },
+
+    #' @description Add a new SOMA DenseNdArray to this collection. (lifecycle: experimental)
+    #' @param key The key to be added.
+    #' @param type an [Arrow type][arrow::data-type] defining the type of each
+    #' element in the array.
+    #' @param shape a vector of integers defining the shape of the array.
+    add_new_dense_ndarray = function(key, type, shape) {
+      ndarr <- SOMADenseNDArray$new( file.path(self$uri, key) )
+      ndarr$create(type, shape)
+      super$set(ndarr, key)
+    },
+
+    #' @description Add a new SOMA SparseNdArray to this collection. (lifecycle: experimental)
+    #' @param key The key to be added.
+    #' @param type an [Arrow type][arrow::data-type] defining the type of each
+    #' element in the array.
+    #' @param shape a vector of integers defining the shape of the array.
+    add_new_sparse_ndarray = function(key, type, shape) {
+      ndarr <- SOMASparseNDArray$new( file.path(self$uri, key) )
+      ndarr$create(type, shape)
+      super$set(ndarr, key)
     }
 
   ),

apis/r/tests/testthat/test-SOMACollection.R

@@ -27,4 +27,28 @@ test_that("SOMACollection basics", {
 
   readback_dataframe <- readback_collection$get("sdf")
   expect_is(readback_dataframe, "SOMADataFrame")
+
+  # Add the collection to the collection
+  collection$add_new_collection(collection, "collection")
+  collection2 <- collection$get("collection")
+  expect_true(collection2$soma_type == "SOMACollection")
+  expect_true(collection2$exists())
+  df2 <- collection2$get("sdf")
+  ## -- uri differs by "./" so cannot compare R6 objects directly
+  expect_equal(readback_dataframe$object[], df2$object[])
+
+  # Add new dataframe to the collection
+  collection$add_new_dataframe("new_df", create_arrow_schema(), "foo")
+  df3 <- collection$get("new_df")
+  expect_true(df3$soma_type == "SOMADataFrame")
+
+  # Add new DenseNdArray to the collection
+  collection$add_new_dense_ndarray("nd_d_arr", arrow::int32(), shape = c(10, 5))
+  arr <- collection$get("nd_d_arr")
+  expect_true(arr$soma_type == "SOMADenseNDArray")
+
+  # Add new SparseNdArray to the collection
+  collection$add_new_sparse_ndarray("nd_s_arr", arrow::int32(), shape = c(10, 5))
+  arr <- collection$get("nd_s_arr")
+  expect_true(arr$soma_type == "SOMASparseNDArray")
 })