nealrichardson commented on a change in pull request #10780: URL: https://github.com/apache/arrow/pull/10780#discussion_r675991803
########## File path: r/tests/testthat/test-duckdb.R ########## @@ -0,0 +1,188 @@ +# Licensed to the Apache Software Foundation (ASF) under one +# or more contributor license agreements. See the NOTICE file +# distributed with this work for additional information +# regarding copyright ownership. The ASF licenses this file +# to you under the Apache License, Version 2.0 (the +# "License"); you may not use this file except in compliance +# with the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, +# software distributed under the License is distributed on an +# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +# KIND, either express or implied. See the License for the +# specific language governing permissions and limitations +# under the License. + +skip_if_not_installed("duckdb", minimum_version = "0.2.8") +skip_if_not_installed("dbplyr") +library(duckdb) +library(dplyr) + +test_that("to_duckdb", { + ds <- InMemoryDataset$create(example_data) + + expect_identical( + ds %>% + to_duckdb() %>% + collect() %>% + # factors don't roundtrip + select(!fct), + select(example_data, !fct) + ) + + expect_identical( + ds %>% + select(int, lgl, dbl) %>% + to_duckdb() %>% + group_by(lgl) %>% + summarise(mean_int = mean(int, na.rm = TRUE), mean_dbl = mean(dbl, na.rm = TRUE)) %>% + collect(), + tibble::tibble( + lgl = c(TRUE, NA, FALSE), + mean_int = c(3, 6.25, 8.5), + mean_dbl = c(3.1, 6.35, 6.1) + ) + ) + + # can group_by before the to_duckdb + expect_identical( + ds %>% + select(int, lgl, dbl) %>% + group_by(lgl) %>% + to_duckdb() %>% + summarise(mean_int = mean(int, na.rm = TRUE), mean_dbl = mean(dbl, na.rm = TRUE)) %>% + collect(), + tibble::tibble( + lgl = c(TRUE, NA, FALSE), + mean_int = c(3, 6.25, 8.5), + mean_dbl = c(3.1, 6.35, 6.1) + ) + ) +}) + +test_that("summarise(..., .engine)", { + ds <- InMemoryDataset$create(example_data) + expect_identical( + ds %>% + select(int, lgl, dbl) %>% + group_by(lgl) %>% + summarise( + mean_int = mean(int, na.rm = TRUE), + mean_dbl = mean(dbl, na.rm = TRUE), + .engine = "duckdb" + ) %>% + collect(), + tibble::tibble( + lgl = c(TRUE, NA, FALSE), + mean_int = c(3, 6.25, 8.5), + mean_dbl = c(3.1, 6.35, 6.1) + ) + ) +}) + +# The next set of tests use an already-extant connection to test features of +# persistence and querying against the table without using the `tbl` itself, so +# we need to create a connection separate from the ephemeral one that is made +# with arrow_duck_connection() +con <- dbConnect(duckdb::duckdb()) +dbExecute(con, "PRAGMA threads=2") + +# write one table to the connection so it is kept open +DBI::dbWriteTable(con, "mtcars", mtcars) + +test_that("Joining, auto-cleanup", { + ds <- InMemoryDataset$create(example_data) + + table_one_name <- "my_arrow_table_1" + table_one <- to_duckdb(ds, con = con, table_name = table_one_name) + table_two_name <- "my_arrow_table_2" + table_two <- to_duckdb(ds, con = con, table_name = table_two_name) + + res <- dbGetQuery( + con, + paste0( + "SELECT * FROM ", table_one_name, + " INNER JOIN ", table_two_name, + " ON ", table_one_name, ".int = ", table_two_name, ".int" + ) + ) + expect_identical(dim(res), c(9L, 14L)) + + # clean up cleans up the tables + expect_true(all(c(table_one_name, table_two_name) %in% DBI::dbListTables(con))) + rm(table_one, table_two) + gc() + expect_false(any(c(table_one_name, table_two_name) %in% DBI::dbListTables(con))) +}) + +test_that("Joining, auto-cleanup disabling", { + ds <- InMemoryDataset$create(example_data) + + table_three_name <- "my_arrow_table_3" + table_three <- to_duckdb(ds, con = con, table_name = table_three_name, auto_disconnect = FALSE) + + # clean up does *not* clean these tables + expect_true(table_three_name %in% DBI::dbListTables(con)) + rm(table_three) + gc() + # but because we aren't auto_disconnecting then we still have this table. + expect_true(table_three_name %in% DBI::dbListTables(con)) +}) + +test_that("to_duckdb with a table", { + tab <- Table$create(example_data) + + expect_identical( + tab %>% + to_duckdb() %>% + group_by(int > 4) %>% + summarise( + int_mean = mean(int, na.rm = TRUE), + dbl_mean = mean(dbl, na.rm = TRUE) + ) %>% + collect(), + tibble::tibble( + "int > 4" = c(FALSE, NA, TRUE), + int_mean = c(2, NA, 7.5), + dbl_mean = c(2.1, 4.1, 7.3) + ) + ) +}) + +test_that("to_duckdb passing a connection", { + ds <- InMemoryDataset$create(example_data) + + con_separate <- dbConnect(duckdb::duckdb()) + # we always want to test in parallel + dbExecute(con_separate, "PRAGMA threads=2") + + # create a table to join to that we know is in our con_separate + new_df <- data.frame( + int = 1:10, + char = letters[26:17] + ) + DBI::dbWriteTable(con_separate, "separate_join_table", new_df) + + table_four <- ds %>% + select(int, lgl, dbl) %>% + to_duckdb(con = con_separate) + table_four_name <- table_four$ops$x + + result <- DBI::dbGetQuery( + con_separate, + paste0( + "SELECT * FROM ", table_four_name, + " INNER JOIN separate_join_table ", + "ON separate_join_table.int = ", table_four_name, ".int" + ) + ) + + expect_identical(dim(result), c(9L, 5L)) + expect_identical(result$char, new_df[new_df$int != 4, ]$char) + + dbDisconnect(con_separate, shutdown = TRUE) +}) + +dbDisconnect(con, shutdown = TRUE) Review comment: Should we put these dbDisconnects in an `on.exit()` up by their corresponding dbConnects? ########## File path: r/R/duckdb.R ########## @@ -0,0 +1,115 @@ +# Licensed to the Apache Software Foundation (ASF) under one +# or more contributor license agreements. See the NOTICE file +# distributed with this work for additional information +# regarding copyright ownership. The ASF licenses this file +# to you under the Apache License, Version 2.0 (the +# "License"); you may not use this file except in compliance +# with the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, +# software distributed under the License is distributed on an +# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +# KIND, either express or implied. See the License for the +# specific language governing permissions and limitations +# under the License. + +#' Create a (virtual) DuckDB table from an Arrow object +#' +#' This will do the necessary configuration to create a (virtual) table in DuckDB +#' that is backed by the Arrow object given. No data is copied or modified until +#' `collect()` or `compute()` are called or a query is run against the table. +#' +#' The result is a dbplyr-compatible object that can be used in d(b)plyr pipelines. +#' +#' Alternatively, one can pass the argument `.engine = "duckdb"` to `summarise()` +#' that starts with an Arrow object to use DuckDB to calculate the summarization +#' step. Internally, this calls `to_duckdb()` with all of the default argument +#' values. +#' +#' @param .data the Arrow object (e.g. Dataset, Table) to use for the DuckDB table +#' @param con a DuckDB connection to use (default will create one and store it +#' in `options("arrow_duck_con")`) +#' @param table_name a name to use in DuckDB for this object. The default is a +#' unique string `"arrow_"` followed by numbers. +#' @param auto_disconnect should the table be automatically cleaned up when the +#' resulting object is removed (and garbage collected)? Default: `TRUE` +#' +#' @return A `tbl` of the new table in DuckDB +#' +#' @name to_duckdb +#' @export +#' @examplesIf arrow_with_dataset() && requireNamespace("duckdb", quietly = TRUE) && requireNamespace("dplyr", quietly = TRUE) +#' library(dplyr) +#' +#' ds <- InMemoryDataset$create(mtcars) +#' +#' ds %>% +#' filter(mpg < 30) %>% +#' to_duckdb() %>% +#' group_by(cyl) %>% +#' summarize(mean_mpg = mean(mpg, na.rm = TRUE)) +#' +#' # the same query can be simplified using .engine = "duckdb" +#' ds %>% +#' filter(mpg < 30) %>% +#' group_by(cyl) %>% +#' summarize(mean_mpg = mean(mpg, na.rm = TRUE), .engine = "duckdb") +#' +to_duckdb <- function(.data, + con = arrow_duck_connection(), + table_name = unique_arrow_tablename(), + auto_disconnect = TRUE) { + .data <- arrow_dplyr_query(.data) + duckdb::duckdb_register_arrow(con, table_name, .data) + + tbl <- tbl(con, table_name) + groups <- dplyr::groups(.data) + if (length(groups)) { + tbl <- dplyr::group_by(tbl, groups) + } + + if (auto_disconnect) { + # this will add the correct connection disconnection when the tbl is gced. + # we should probably confirm that this use of src$disco is kosher. + tbl$src$disco <- duckdb_disconnector(con, table_name) + } + + tbl +} + +arrow_duck_connection <- function() { + con <- getOption("arrow_duck_con") + if (is.null(con) || !DBI::dbIsValid(con)) { Review comment: The null check seems like it should be unnecessary (should we make a PR to DBI?) ``` > DBI::dbIsValid(NULL) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘dbIsValid’ for signature ‘"NULL"’ ``` -- This is an automated message from the Apache Git Service. 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