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[TEST] add tests for new input/output functions
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@eseiler
eseiler committed Aug 28, 2023
1 parent 9d3ec6f commit aa8008e
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1 change: 1 addition & 0 deletions test/api/CMakeLists.txt
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Expand Up @@ -7,6 +7,7 @@

include (add_subdirectories)

add_api_test (config_test.cpp)
add_api_test (input_functor_test.cpp)

add_subdirectories ()
181 changes: 181 additions & 0 deletions test/api/config_test.cpp
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#include <gtest/gtest.h> // for Test, TestInfo, EXPECT_EQ, Message, TEST, TestPartResult

#include <cstddef> // for size_t
#include <sstream> // for operator<<, char_traits, basic_ostream, basic_stringstream, strings...
#include <string> // for allocator, string
#include <string_view> // for operator<<
#include <vector> // for vector

#include <chopper/configuration.hpp> // for config
#include <chopper/layout/input.hpp>

chopper::configuration generate_config()
{
chopper::configuration config{};

config.data_file = "/path/to/data.file";
config.sketch_directory = "/path/to/sketch/directory";
config.k = 20;
config.disable_sketch_output = true;
config.precomputed_files = true;
config.output_filename = "file.layout";
config.determine_best_tmax = true;
config.force_all_binnings = true;
config.output_verbose_statistics = true;

config.hibf_config.number_of_user_bins = 123456789;
config.hibf_config.number_of_hash_functions = 4;
config.hibf_config.maximum_false_positive_rate = 0.0001;
config.hibf_config.threads = 31;
config.hibf_config.sketch_bits = 8;
config.hibf_config.tmax = 128;
config.hibf_config.alpha = 1.0;
config.hibf_config.max_rearrangement_ratio = 0.333;
config.hibf_config.disable_estimate_union = true;
config.hibf_config.disable_rearrangement = false;
config.hibf_config.disable_cutoffs = false;

return config;
}

namespace chopper
{

bool operator==(chopper::configuration const & lhs, chopper::configuration const & rhs)
{
return lhs.data_file == rhs.data_file && //
lhs.debug == rhs.debug && //
lhs.sketch_directory == rhs.sketch_directory && //
lhs.k == rhs.k && //
lhs.disable_sketch_output == rhs.disable_sketch_output && //
lhs.precomputed_files == rhs.precomputed_files && //
lhs.output_filename == rhs.output_filename && //
lhs.determine_best_tmax == rhs.determine_best_tmax && //
lhs.force_all_binnings == rhs.force_all_binnings && //
lhs.hibf_config.number_of_user_bins == rhs.hibf_config.number_of_user_bins && //
lhs.hibf_config.number_of_hash_functions == rhs.hibf_config.number_of_hash_functions && //
lhs.hibf_config.maximum_false_positive_rate == rhs.hibf_config.maximum_false_positive_rate && //
lhs.hibf_config.threads == rhs.hibf_config.threads && //
lhs.hibf_config.sketch_bits == rhs.hibf_config.sketch_bits && //
lhs.hibf_config.tmax == rhs.hibf_config.tmax && //
lhs.hibf_config.alpha == rhs.hibf_config.alpha && //
lhs.hibf_config.max_rearrangement_ratio == rhs.hibf_config.max_rearrangement_ratio && //
lhs.hibf_config.disable_estimate_union == rhs.hibf_config.disable_estimate_union && //
lhs.hibf_config.disable_rearrangement == rhs.hibf_config.disable_rearrangement && //
lhs.hibf_config.disable_cutoffs == rhs.hibf_config.disable_cutoffs;
}

} // namespace chopper

static constexpr std::string_view config_string_view{"@CHOPPER_CONFIG\n"
"@{\n"
"@ \"chopper_config\": {\n"
"@ \"version\": 2,\n"
"@ \"data_file\": {\n"
"@ \"value0\": \"/path/to/data.file\"\n"
"@ },\n"
"@ \"debug\": false,\n"
"@ \"sketch_directory\": {\n"
"@ \"value0\": \"/path/to/sketch/directory\"\n"
"@ },\n"
"@ \"k\": 20,\n"
"@ \"disable_sketch_output\": true,\n"
"@ \"precomputed_files\": true,\n"
"@ \"output_filename\": {\n"
"@ \"value0\": \"file.layout\"\n"
"@ },\n"
"@ \"determine_best_tmax\": true,\n"
"@ \"force_all_binnings\": true\n"
"@ }\n"
"@}\n"
"@CHOPPER_CONFIG_END\n"
"@HIBF_CONFIG\n"
"@{\n"
"@ \"hibf_config\": {\n"
"@ \"version\": 1,\n"
"@ \"number_of_user_bins\": 123456789,\n"
"@ \"number_of_hash_functions\": 4,\n"
"@ \"maximum_false_positive_rate\": 0.0001,\n"
"@ \"threads\": 31,\n"
"@ \"sketch_bits\": 8,\n"
"@ \"tmax\": 128,\n"
"@ \"alpha\": 1.0,\n"
"@ \"max_rearrangement_ratio\": 0.333,\n"
"@ \"disable_estimate_union\": true,\n"
"@ \"disable_rearrangement\": false,\n"
"@ \"disable_cutoffs\": false\n"
"@ }\n"
"@}\n"
"@HIBF_CONFIG_END\n"};

TEST(config_test, write_to)
{
chopper::configuration const config{generate_config()};

std::stringstream ss{};
config.write_to(ss);

EXPECT_EQ(ss.str(), config_string_view);
}

TEST(config_test, read_from)
{
std::string config_string{config_string_view};
std::stringstream ss{config_string};

chopper::configuration config;
config.read_from(ss);

EXPECT_EQ(config, generate_config());
}

TEST(config_test, read_from_with_more_meta)
{
std::string config_string{"@blah some other stuff\n"
"@blah some other stuff\n"
"@blah some other stuff\n"
"@blah some other stuff\n"
"@blah some other stuff\n"};
config_string += config_string_view;
std::stringstream ss{config_string};

chopper::configuration config;
config.read_from(ss);

EXPECT_EQ(config, generate_config());
}

// Easier to do in the config_test because of existing helper functions
TEST(input, read_layout_file)
{
std::string config_string{"@CHOPPER_USER_BINS\n"
"@0 file1.fa\n"
"@1 file2.fa\n"
"@2 path/to/file3.fa\n"
"@3 file4.fastq\n"
"@CHOPPER_USER_BINS_END\n"};
config_string += config_string_view;

{
seqan::hibf::layout::layout hibf_layout{};
hibf_layout.top_level_max_bin_id = 42u;
std::stringstream config_out{};
hibf_layout.write_to(config_out);
config_string += config_out.str();
}

std::stringstream ss{config_string};

auto [filenames, config, layout] = chopper::layout::read_layout_file(ss);

std::vector<std::vector<std::string>> const expected_filenames{{"file1.fa"},
{"file2.fa"},
{"path/to/file3.fa"},
{"file4.fastq"}};

EXPECT_EQ(filenames, expected_filenames);
EXPECT_EQ(config, generate_config());
EXPECT_EQ(layout.top_level_max_bin_id, 42u);
EXPECT_TRUE(layout.max_bins.empty());
EXPECT_TRUE(layout.user_bins.empty());
}
1 change: 1 addition & 0 deletions test/api/layout/CMakeLists.txt
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Expand Up @@ -17,3 +17,4 @@ target_use_datasources (execute_with_estimation_test FILES seq3.fa)
target_use_datasources (execute_with_estimation_test FILES small.fa)

add_api_test (hibf_statistics_test.cpp)
add_api_test (user_bin_io_test.cpp)
45 changes: 45 additions & 0 deletions test/api/layout/user_bin_io_test.cpp
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#include <gtest/gtest.h> // for Test, TestInfo, EXPECT_EQ, Message, TEST, TestPartResult

#include <cstddef> // for size_t
#include <sstream> // for operator<<, char_traits, basic_ostream, basic_stringstream, strings...
#include <string> // for allocator, string
#include <string_view> // for operator<<
#include <vector> // for vector

#include <chopper/layout/input.hpp>
#include <chopper/layout/output.hpp>

TEST(output, user_bins)
{
std::vector<std::string> const filenames{"file1.fa", "file2.fa", "path/to/file3.fa", "file4.fastq"};

std::stringstream ss{};
chopper::layout::write_user_bins_to(filenames, ss);

std::string const expected{"@CHOPPER_USER_BINS\n"
"@0 file1.fa\n"
"@1 file2.fa\n"
"@2 path/to/file3.fa\n"
"@3 file4.fastq\n"
"@CHOPPER_USER_BINS_END\n"};

EXPECT_EQ(ss.str(), expected);
}

TEST(input, user_bins)
{
std::stringstream ss{"@CHOPPER_USER_BINS\n"
"@0 file1.fa\n"
"@1 file2.fa\n"
"@2 path/to/file3.fa\n"
"@3 file4.fastq\n"
"@CHOPPER_USER_BINS_END\n"};

std::vector<std::vector<std::string>> filenames = chopper::layout::read_filenames_from(ss);
std::vector<std::vector<std::string>> const expected{{"file1.fa"},
{"file2.fa"},
{"path/to/file3.fa"},
{"file4.fastq"}};

EXPECT_EQ(filenames, expected);
}

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