From 3f5bf72ada1c9b99141a678e8b79ac9a9e3d75ce Mon Sep 17 00:00:00 2001
From: taepper <alexander.taepper@gmail.com>
Date: Tue, 8 Aug 2023 12:09:25 +0200
Subject: [PATCH] refactor: minor edits

---
 src/silo/database.test.cpp   |  2 +-
 src/silo/prepare_dataset.cpp | 15 +--------------
 2 files changed, 2 insertions(+), 15 deletions(-)

diff --git a/src/silo/database.test.cpp b/src/silo/database.test.cpp
index a76e23c2a..2eb9a0adb 100644
--- a/src/silo/database.test.cpp
+++ b/src/silo/database.test.cpp
@@ -31,7 +31,7 @@ TEST(DatabaseTest, shouldBuildDatabaseWithoutErrors) {
    EXPECT_EQ(simple_database_info.sequence_count, 100);
 }
 
-TEST(DatabaseTest, shouldBuildPartitionLessDatabaseWithoutErrors) {
+TEST(DatabaseTest, shouldSuccessfullyBuildDatabaseWithoutPartitionBy) {
    const silo::preprocessing::InputDirectory input_directory{"./testBaseData/"};
 
    auto config = silo::preprocessing::PreprocessingConfigReader().readConfig(
diff --git a/src/silo/prepare_dataset.cpp b/src/silo/prepare_dataset.cpp
index 56fa2cb41..ddc05deca 100644
--- a/src/silo/prepare_dataset.cpp
+++ b/src/silo/prepare_dataset.cpp
@@ -126,17 +126,6 @@ std::unordered_map<std::string, silo::preprocessing::PartitionChunk> partitionMe
    );
 }
 
-void copyMetadataFile(
-   csv::CSVReader& metadata_reader,
-   silo::preprocessing::MetadataWriter& metadata_writer
-) {
-   metadata_writer.writeHeader(metadata_reader);
-   for (auto& row : metadata_reader) {
-      std::this_thread::sleep_for(std::chrono::nanoseconds(2));
-      metadata_writer.writeRow(row);
-   }
-}
-
 std::unordered_map<silo::preprocessing::PartitionChunk, silo::ZstdFastaWriter>
 getSequenceWritersForChunks(
    const std::unordered_map<silo::preprocessing::PartitionChunk, std::filesystem::path>&
@@ -264,12 +253,10 @@ void silo::copyDataToPartitionDirectory(
    const ReferenceGenomes& reference_genomes
 ) {
    const std::filesystem::path metadata_filename = preprocessing_config.getMetadataInputFilename();
-   auto metadata_reader = preprocessing::MetadataReader(metadata_filename);
 
    auto metadata_partition_filename = preprocessing_config.getMetadataPartitionFilename(0, 0);
-   auto metadata_writer = preprocessing::MetadataWriter(metadata_partition_filename);
 
-   copyMetadataFile(metadata_reader.reader, metadata_writer);
+   std::filesystem::copy(metadata_filename, metadata_partition_filename);
 
    for (const auto& [nuc_name, reference_genome] : reference_genomes.raw_nucleotide_sequences) {
       const std::filesystem::path sequence_in_filename =