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author | Daniel Baumann <daniel.baumann@progress-linux.org> | 2024-04-21 11:54:28 +0000 |
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committer | Daniel Baumann <daniel.baumann@progress-linux.org> | 2024-04-21 11:54:28 +0000 |
commit | e6918187568dbd01842d8d1d2c808ce16a894239 (patch) | |
tree | 64f88b554b444a49f656b6c656111a145cbbaa28 /src/arrow/r/tests/testthat/test-dataset.R | |
parent | Initial commit. (diff) | |
download | ceph-upstream/18.2.2.tar.xz ceph-upstream/18.2.2.zip |
Adding upstream version 18.2.2.upstream/18.2.2
Signed-off-by: Daniel Baumann <daniel.baumann@progress-linux.org>
Diffstat (limited to 'src/arrow/r/tests/testthat/test-dataset.R')
-rw-r--r-- | src/arrow/r/tests/testthat/test-dataset.R | 696 |
1 files changed, 696 insertions, 0 deletions
diff --git a/src/arrow/r/tests/testthat/test-dataset.R b/src/arrow/r/tests/testthat/test-dataset.R new file mode 100644 index 000000000..4403b479a --- /dev/null +++ b/src/arrow/r/tests/testthat/test-dataset.R @@ -0,0 +1,696 @@ +# 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_available("dataset") + +library(dplyr, warn.conflicts = FALSE) + +dataset_dir <- make_temp_dir() +hive_dir <- make_temp_dir() +ipc_dir <- make_temp_dir() + +test_that("Setup (putting data in the dir)", { + if (arrow_with_parquet()) { + dir.create(file.path(dataset_dir, 1)) + dir.create(file.path(dataset_dir, 2)) + write_parquet(df1, file.path(dataset_dir, 1, "file1.parquet")) + write_parquet(df2, file.path(dataset_dir, 2, "file2.parquet")) + expect_length(dir(dataset_dir, recursive = TRUE), 2) + + dir.create(file.path(hive_dir, "subdir", "group=1", "other=xxx"), recursive = TRUE) + dir.create(file.path(hive_dir, "subdir", "group=2", "other=yyy"), recursive = TRUE) + write_parquet(df1, file.path(hive_dir, "subdir", "group=1", "other=xxx", "file1.parquet")) + write_parquet(df2, file.path(hive_dir, "subdir", "group=2", "other=yyy", "file2.parquet")) + expect_length(dir(hive_dir, recursive = TRUE), 2) + } + + # Now, an IPC format dataset + dir.create(file.path(ipc_dir, 3)) + dir.create(file.path(ipc_dir, 4)) + write_feather(df1, file.path(ipc_dir, 3, "file1.arrow")) + write_feather(df2, file.path(ipc_dir, 4, "file2.arrow")) + expect_length(dir(ipc_dir, recursive = TRUE), 2) +}) + +test_that("IPC/Feather format data", { + ds <- open_dataset(ipc_dir, partitioning = "part", format = "feather") + expect_r6_class(ds$format, "IpcFileFormat") + expect_r6_class(ds$filesystem, "LocalFileSystem") + expect_identical(names(ds), c(names(df1), "part")) + expect_identical(dim(ds), c(20L, 7L)) + + expect_equal( + ds %>% + select(string = chr, integer = int, part) %>% + filter(integer > 6 & part == 3) %>% + collect() %>% + summarize(mean = mean(integer)), + df1 %>% + select(string = chr, integer = int) %>% + filter(integer > 6) %>% + summarize(mean = mean(integer)) + ) + + # Collecting virtual partition column works + expect_equal( + ds %>% arrange(part) %>% pull(part), + c(rep(3, 10), rep(4, 10)) + ) +}) + +expect_scan_result <- function(ds, schm) { + sb <- ds$NewScan() + expect_r6_class(sb, "ScannerBuilder") + expect_equal(sb$schema, schm) + + sb$Project(c("chr", "lgl")) + sb$Filter(Expression$field_ref("dbl") == 8) + scn <- sb$Finish() + expect_r6_class(scn, "Scanner") + + tab <- scn$ToTable() + expect_r6_class(tab, "Table") + + expect_equal( + as.data.frame(tab), + df1[8, c("chr", "lgl")] + ) +} + +test_that("URI-decoding with directory partitioning", { + root <- make_temp_dir() + fmt <- FileFormat$create("feather") + fs <- LocalFileSystem$create() + selector <- FileSelector$create(root, recursive = TRUE) + dir1 <- file.path(root, "2021-05-04 00%3A00%3A00", "%24") + dir.create(dir1, recursive = TRUE) + write_feather(df1, file.path(dir1, "data.feather")) + + partitioning <- DirectoryPartitioning$create( + schema(date = timestamp(unit = "s"), string = utf8()) + ) + factory <- FileSystemDatasetFactory$create( + fs, selector, NULL, fmt, + partitioning = partitioning + ) + schm <- factory$Inspect() + ds <- factory$Finish(schm) + expect_scan_result(ds, schm) + + partitioning <- DirectoryPartitioning$create( + schema(date = timestamp(unit = "s"), string = utf8()), + segment_encoding = "none" + ) + factory <- FileSystemDatasetFactory$create( + fs, selector, NULL, fmt, + partitioning = partitioning + ) + schm <- factory$Inspect() + expect_error(factory$Finish(schm), "Invalid: error parsing") + + partitioning_factory <- DirectoryPartitioningFactory$create( + c("date", "string") + ) + factory <- FileSystemDatasetFactory$create( + fs, selector, NULL, fmt, partitioning_factory + ) + schm <- factory$Inspect() + ds <- factory$Finish(schm) + # Can't directly inspect partition expressions, so do it implicitly via scan + expect_equal( + ds %>% + filter(date == "2021-05-04 00:00:00", string == "$") %>% + select(int) %>% + collect(), + df1 %>% select(int) %>% collect() + ) + + partitioning_factory <- DirectoryPartitioningFactory$create( + c("date", "string"), + segment_encoding = "none" + ) + factory <- FileSystemDatasetFactory$create( + fs, selector, NULL, fmt, partitioning_factory + ) + schm <- factory$Inspect() + ds <- factory$Finish(schm) + expect_equal( + ds %>% + filter(date == "2021-05-04 00%3A00%3A00", string == "%24") %>% + select(int) %>% + collect(), + df1 %>% select(int) %>% collect() + ) +}) + +test_that("URI-decoding with hive partitioning", { + root <- make_temp_dir() + fmt <- FileFormat$create("feather") + fs <- LocalFileSystem$create() + selector <- FileSelector$create(root, recursive = TRUE) + dir1 <- file.path(root, "date=2021-05-04 00%3A00%3A00", "string=%24") + dir.create(dir1, recursive = TRUE) + write_feather(df1, file.path(dir1, "data.feather")) + + partitioning <- hive_partition( + date = timestamp(unit = "s"), string = utf8() + ) + factory <- FileSystemDatasetFactory$create( + fs, selector, NULL, fmt, + partitioning = partitioning + ) + ds <- factory$Finish(schm) + expect_scan_result(ds, schm) + + partitioning <- hive_partition( + date = timestamp(unit = "s"), string = utf8(), segment_encoding = "none" + ) + factory <- FileSystemDatasetFactory$create( + fs, selector, NULL, fmt, + partitioning = partitioning + ) + expect_error(factory$Finish(schm), "Invalid: error parsing") + + partitioning_factory <- hive_partition() + factory <- FileSystemDatasetFactory$create( + fs, selector, NULL, fmt, partitioning_factory + ) + schm <- factory$Inspect() + ds <- factory$Finish(schm) + # Can't directly inspect partition expressions, so do it implicitly via scan + expect_equal( + ds %>% + filter(date == "2021-05-04 00:00:00", string == "$") %>% + select(int) %>% + collect(), + df1 %>% select(int) %>% collect() + ) + + partitioning_factory <- hive_partition(segment_encoding = "none") + factory <- FileSystemDatasetFactory$create( + fs, selector, NULL, fmt, partitioning_factory + ) + schm <- factory$Inspect() + ds <- factory$Finish(schm) + expect_equal( + ds %>% + filter(date == "2021-05-04 00%3A00%3A00", string == "%24") %>% + select(int) %>% + collect(), + df1 %>% select(int) %>% collect() + ) +}) + +# Everything else below here is using parquet files +skip_if_not_available("parquet") + +files <- c( + file.path(dataset_dir, 1, "file1.parquet", fsep = "/"), + file.path(dataset_dir, 2, "file2.parquet", fsep = "/") +) + +test_that("Simple interface for datasets", { + ds <- open_dataset(dataset_dir, partitioning = schema(part = uint8())) + expect_r6_class(ds$format, "ParquetFileFormat") + expect_r6_class(ds$filesystem, "LocalFileSystem") + expect_r6_class(ds, "Dataset") + expect_equal( + ds %>% + select(chr, dbl) %>% + filter(dbl > 7 & dbl < 53L) %>% # Testing the auto-casting of scalars + collect() %>% + arrange(dbl), + rbind( + df1[8:10, c("chr", "dbl")], + df2[1:2, c("chr", "dbl")] + ) + ) + + expect_equal( + ds %>% + select(string = chr, integer = int, part) %>% + filter(integer > 6 & part == 1) %>% # 6 not 6L to test autocasting + collect() %>% + summarize(mean = mean(integer)), + df1 %>% + select(string = chr, integer = int) %>% + filter(integer > 6) %>% + summarize(mean = mean(integer)) + ) + + # Collecting virtual partition column works + expect_equal( + ds %>% arrange(part) %>% pull(part), + c(rep(1, 10), rep(2, 10)) + ) +}) + +test_that("dim method returns the correct number of rows and columns", { + ds <- open_dataset(dataset_dir, partitioning = schema(part = uint8())) + expect_identical(dim(ds), c(20L, 7L)) +}) + + +test_that("dim() correctly determine numbers of rows and columns on arrow_dplyr_query object", { + ds <- open_dataset(dataset_dir, partitioning = schema(part = uint8())) + + expect_identical( + ds %>% + filter(chr == "a") %>% + dim(), + c(2L, 7L) + ) + expect_equal( + ds %>% + select(chr, fct, int) %>% + dim(), + c(20L, 3L) + ) + expect_identical( + ds %>% + select(chr, fct, int) %>% + filter(chr == "a") %>% + dim(), + c(2L, 3L) + ) +}) + +test_that("Simple interface for datasets (custom ParquetFileFormat)", { + ds <- open_dataset(dataset_dir, + partitioning = schema(part = uint8()), + format = FileFormat$create("parquet", dict_columns = c("chr")) + ) + expect_type_equal(ds$schema$GetFieldByName("chr")$type, dictionary()) +}) + +test_that("Hive partitioning", { + ds <- open_dataset(hive_dir, partitioning = hive_partition(other = utf8(), group = uint8())) + expect_r6_class(ds, "Dataset") + expect_equal( + ds %>% + filter(group == 2) %>% + select(chr, dbl) %>% + filter(dbl > 7 & dbl < 53) %>% + collect() %>% + arrange(dbl), + df2[1:2, c("chr", "dbl")] + ) +}) + +test_that("input validation", { + expect_error( + open_dataset(hive_dir, hive_partition(other = utf8(), group = uint8())) + ) +}) + +test_that("Partitioning inference", { + # These are the same tests as above, just using the *PartitioningFactory + ds1 <- open_dataset(dataset_dir, partitioning = "part") + expect_identical(names(ds1), c(names(df1), "part")) + expect_equal( + ds1 %>% + select(string = chr, integer = int, part) %>% + filter(integer > 6 & part == 1) %>% + collect() %>% + summarize(mean = mean(integer)), + df1 %>% + select(string = chr, integer = int) %>% + filter(integer > 6) %>% + summarize(mean = mean(integer)) + ) + + ds2 <- open_dataset(hive_dir) + expect_identical(names(ds2), c(names(df1), "group", "other")) + expect_equal( + ds2 %>% + filter(group == 2) %>% + select(chr, dbl) %>% + filter(dbl > 7 & dbl < 53) %>% + collect() %>% + arrange(dbl), + df2[1:2, c("chr", "dbl")] + ) +}) + +test_that("Dataset with multiple file formats", { + skip("https://issues.apache.org/jira/browse/ARROW-7653") + ds <- open_dataset(list( + open_dataset(dataset_dir, format = "parquet", partitioning = "part"), + open_dataset(ipc_dir, format = "arrow", partitioning = "part") + )) + expect_identical(names(ds), c(names(df1), "part")) + expect_equal( + ds %>% + filter(int > 6 & part %in% c(1, 3)) %>% + select(string = chr, integer = int) %>% + collect(), + df1 %>% + select(string = chr, integer = int) %>% + filter(integer > 6) %>% + rbind(., .) # Stack it twice + ) +}) + +test_that("Creating UnionDataset", { + ds1 <- open_dataset(file.path(dataset_dir, 1)) + ds2 <- open_dataset(file.path(dataset_dir, 2)) + union1 <- open_dataset(list(ds1, ds2)) + expect_r6_class(union1, "UnionDataset") + expect_equal( + union1 %>% + select(chr, dbl) %>% + filter(dbl > 7 & dbl < 53L) %>% # Testing the auto-casting of scalars + collect() %>% + arrange(dbl), + rbind( + df1[8:10, c("chr", "dbl")], + df2[1:2, c("chr", "dbl")] + ) + ) + + # Now with the c() method + union2 <- c(ds1, ds2) + expect_r6_class(union2, "UnionDataset") + expect_equal( + union2 %>% + select(chr, dbl) %>% + filter(dbl > 7 & dbl < 53L) %>% # Testing the auto-casting of scalars + collect() %>% + arrange(dbl), + rbind( + df1[8:10, c("chr", "dbl")], + df2[1:2, c("chr", "dbl")] + ) + ) + + # Confirm c() method error handling + expect_error(c(ds1, 42), "character") +}) + +test_that("map_batches", { + skip("map_batches() is broken (ARROW-14029)") + ds <- open_dataset(dataset_dir, partitioning = "part") + expect_equal( + ds %>% + filter(int > 5) %>% + select(int, lgl) %>% + map_batches(~ summarize(., min_int = min(int))), + tibble(min_int = c(6L, 101L)) + ) +}) + +test_that("partitioning = NULL to ignore partition information (but why?)", { + ds <- open_dataset(hive_dir, partitioning = NULL) + expect_identical(names(ds), names(df1)) # i.e. not c(names(df1), "group", "other") +}) + +test_that("head/tail", { + # head/tail with no query are still deterministic order + ds <- open_dataset(dataset_dir) + expect_equal(as.data.frame(head(ds)), head(df1)) + expect_equal( + as.data.frame(head(ds, 12)), + rbind(df1, df2[1:2, ]) + ) + + expect_equal(as.data.frame(tail(ds)), tail(df2)) + expect_equal( + as.data.frame(tail(ds, 12)), + rbind(df1[9:10, ], df2) + ) +}) + +test_that("Dataset [ (take by index)", { + ds <- open_dataset(dataset_dir) + # Taking only from one file + expect_equal( + as.data.frame(ds[c(4, 5, 9), 3:4]), + df1[c(4, 5, 9), 3:4] + ) + # Taking from more than one + expect_equal( + as.data.frame(ds[c(4, 5, 9, 12, 13), 3:4]), + rbind(df1[c(4, 5, 9), 3:4], df2[2:3, 3:4]) + ) + # Taking out of order + expect_equal( + as.data.frame(ds[c(4, 13, 9, 12, 5), ]), + rbind( + df1[4, ], + df2[3, ], + df1[9, ], + df2[2, ], + df1[5, ] + ) + ) + + # Take from a query + ds2 <- ds %>% + filter(int > 6) %>% + select(int, lgl) + expect_equal( + as.data.frame(ds2[c(2, 5), ]), + rbind( + df1[8, c("int", "lgl")], + df2[1, c("int", "lgl")] + ) + ) +}) + +test_that("Dataset and query print methods", { + ds <- open_dataset(hive_dir) + expect_output( + print(ds), + paste( + "FileSystemDataset with 2 Parquet files", + "int: int32", + "dbl: double", + "lgl: bool", + "chr: string", + "fct: dictionary<values=string, indices=int32>", + "ts: timestamp[us, tz=UTC]", + "group: int32", + "other: string", + sep = "\n" + ), + fixed = TRUE + ) + expect_type(ds$metadata, "list") + q <- select(ds, string = chr, lgl, integer = int) + expect_output( + print(q), + paste( + "Dataset (query)", + "string: string", + "lgl: bool", + "integer: int32", + "", + "See $.data for the source Arrow object", + sep = "\n" + ), + fixed = TRUE + ) + expect_output( + print(q %>% filter(integer == 6) %>% group_by(lgl)), + paste( + "Dataset (query)", + "string: string", + "lgl: bool", + "integer: int32", + "", + "* Filter: (int == 6)", + "* Grouped by lgl", + "See $.data for the source Arrow object", + sep = "\n" + ), + fixed = TRUE + ) +}) + +test_that("Scanner$ScanBatches", { + ds <- open_dataset(ipc_dir, format = "feather") + batches <- ds$NewScan()$Finish()$ScanBatches() + table <- Table$create(!!!batches) + expect_equal(as.data.frame(table), rbind(df1, df2)) + + batches <- ds$NewScan()$UseAsync(TRUE)$Finish()$ScanBatches() + table <- Table$create(!!!batches) + expect_equal(as.data.frame(table), rbind(df1, df2)) +}) + +test_that("Scanner$ToRecordBatchReader()", { + ds <- open_dataset(dataset_dir, partitioning = "part") + scan <- ds %>% + filter(part == 1) %>% + select(int, lgl) %>% + filter(int > 6) %>% + Scanner$create() + reader <- scan$ToRecordBatchReader() + expect_r6_class(reader, "RecordBatchReader") + expect_identical( + as.data.frame(reader$read_table()), + df1[df1$int > 6, c("int", "lgl")] + ) +}) + +test_that("Scanner$create() filter/projection pushdown", { + ds <- open_dataset(dataset_dir, partitioning = "part") + + # the standard to compare all Scanner$create()s against + scan_one <- ds %>% + filter(int > 7 & dbl < 57) %>% + select(int, dbl, lgl) %>% + mutate(int_plus = int + 1, dbl_minus = dbl - 1) %>% + Scanner$create() + + # select a column in projection + scan_two <- ds %>% + filter(int > 7 & dbl < 57) %>% + # select an extra column, since we are going to + select(int, dbl, lgl, chr) %>% + mutate(int_plus = int + 1, dbl_minus = dbl - 1) %>% + Scanner$create(projection = c("int", "dbl", "lgl", "int_plus", "dbl_minus")) + expect_identical( + as.data.frame(scan_one$ToRecordBatchReader()$read_table()), + as.data.frame(scan_two$ToRecordBatchReader()$read_table()) + ) + + # adding filters to Scanner$create + scan_three <- ds %>% + filter(int > 7) %>% + select(int, dbl, lgl) %>% + mutate(int_plus = int + 1, dbl_minus = dbl - 1) %>% + Scanner$create( + filter = Expression$create("less", Expression$field_ref("dbl"), Expression$scalar(57)) + ) + expect_identical( + as.data.frame(scan_one$ToRecordBatchReader()$read_table()), + as.data.frame(scan_three$ToRecordBatchReader()$read_table()) + ) + + expect_error( + ds %>% + select(int, dbl, lgl) %>% + Scanner$create(projection = "not_a_col"), + # Full message is "attempting to project with unknown columns" >= 4.0.0, but + # prior versions have a less nice "all(projection %in% names(proj)) is not TRUE" + "project" + ) + + expect_error( + ds %>% + select(int, dbl, lgl) %>% + Scanner$create(filter = list("foo", "bar")), + "filter expressions must be either an expression or a list of expressions" + ) +}) + +test_that("Assembling a Dataset manually and getting a Table", { + fs <- LocalFileSystem$create() + selector <- FileSelector$create(dataset_dir, recursive = TRUE) + partitioning <- DirectoryPartitioning$create(schema(part = double())) + + fmt <- FileFormat$create("parquet") + factory <- FileSystemDatasetFactory$create(fs, selector, NULL, fmt, partitioning = partitioning) + expect_r6_class(factory, "FileSystemDatasetFactory") + + schm <- factory$Inspect() + expect_r6_class(schm, "Schema") + + phys_schm <- ParquetFileReader$create(files[1])$GetSchema() + expect_equal(names(phys_schm), names(df1)) + expect_equal(names(schm), c(names(phys_schm), "part")) + + child <- factory$Finish(schm) + expect_r6_class(child, "FileSystemDataset") + expect_r6_class(child$schema, "Schema") + expect_r6_class(child$format, "ParquetFileFormat") + expect_equal(names(schm), names(child$schema)) + expect_equal(child$files, files) + + ds <- Dataset$create(list(child), schm) + expect_scan_result(ds, schm) +}) + +test_that("Assembling multiple DatasetFactories with DatasetFactory", { + factory1 <- dataset_factory(file.path(dataset_dir, 1), format = "parquet") + expect_r6_class(factory1, "FileSystemDatasetFactory") + factory2 <- dataset_factory(file.path(dataset_dir, 2), format = "parquet") + expect_r6_class(factory2, "FileSystemDatasetFactory") + + factory <- DatasetFactory$create(list(factory1, factory2)) + expect_r6_class(factory, "DatasetFactory") + + schm <- factory$Inspect() + expect_r6_class(schm, "Schema") + + phys_schm <- ParquetFileReader$create(files[1])$GetSchema() + expect_equal(names(phys_schm), names(df1)) + + ds <- factory$Finish(schm) + expect_r6_class(ds, "UnionDataset") + expect_r6_class(ds$schema, "Schema") + expect_equal(names(schm), names(ds$schema)) + expect_equal(unlist(map(ds$children, ~ .$files)), files) + + expect_scan_result(ds, schm) +}) + +# see https://issues.apache.org/jira/browse/ARROW-11328 +test_that("Collecting zero columns from a dataset doesn't return entire dataset", { + tmp <- tempfile() + write_dataset(mtcars, tmp, format = "parquet") + expect_equal( + open_dataset(tmp) %>% select() %>% collect() %>% dim(), + c(32, 0) + ) +}) + + +test_that("dataset RecordBatchReader to C-interface to arrow_dplyr_query", { + ds <- open_dataset(ipc_dir, partitioning = "part", format = "feather") + + # export the RecordBatchReader via the C-interface + stream_ptr <- allocate_arrow_array_stream() + scan <- Scanner$create(ds) + reader <- scan$ToRecordBatchReader() + reader$export_to_c(stream_ptr) + + # then import it and check that the roundtripped value is the same + circle <- RecordBatchStreamReader$import_from_c(stream_ptr) + + # create an arrow_dplyr_query() from the recordbatch reader + reader_adq <- arrow_dplyr_query(circle) + + # TODO: ARROW-14321 should be able to arrange then collect + tab_from_c_new <- reader_adq %>% + filter(int < 8, int > 55) %>% + mutate(part_plus = part + 6) %>% + collect() + expect_equal( + tab_from_c_new %>% + arrange(dbl), + ds %>% + filter(int < 8, int > 55) %>% + mutate(part_plus = part + 6) %>% + collect() %>% + arrange(dbl) + ) + + # must clean up the pointer or we leak + delete_arrow_array_stream(stream_ptr) +}) |