Minor polishing edits

GenSpectrum · Dec 15, 2023 · 37a1294 · 37a1294
1 parent 7f57c4c
commit 37a1294
Show file tree

Hide file tree

Showing 10 changed files with 21 additions and 54 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -81,13 +81,13 @@ target_link_libraries(
         silo
         PUBLIC
         ${Boost_LIBRARIES}
-        TBB::tbb
+        ${duckdb_LIBRARIES}
+        nlohmann_json::nlohmann_json
         ${roaring_LIBRARIES}
         ${spdlog_LIBRARIES}
+        TBB::tbb
         ${yaml-cpp_LIBRARIES}
-        nlohmann_json::nlohmann_json
         zstd::libzstd_static
-        ${duckdb_LIBRARIES}
 )
 
 add_executable(siloApi src/silo_api/api.cpp ${SRC_SILO_API})

diff --git a/include/silo/preprocessing/preprocessor.h b/include/silo/preprocessing/preprocessor.h
@@ -17,8 +17,8 @@ class Preprocessor {
 
   public:
    Preprocessor(
-      const preprocessing::PreprocessingConfig& preprocessing_config,
-      const config::DatabaseConfig& database_config
+      const preprocessing::PreprocessingConfig preprocessing_config,
+      const config::DatabaseConfig database_config
    );
 
    Database preprocess();

diff --git a/include/silo/storage/build_exception.h b/include/silo/storage/build_exception.h
diff --git a/include/silo/zstdfasta/zstdfasta_table_reader.h b/include/silo/zstdfasta/zstdfasta_table_reader.h
@@ -27,7 +27,7 @@ class ZstdFastaTableReader {
    std::unique_ptr<silo::ZstdDecompressor> decompressor;
    size_t current_row;
 
-   std::string DEBUG_dictionary;
+   // std::string DEBUG_dictionary;
 
    std::string genome_buffer;
 

diff --git a/src/silo/preprocessing/preprocessor.cpp b/src/silo/preprocessing/preprocessor.cpp
@@ -22,11 +22,11 @@
 namespace silo::preprocessing {
 
 Preprocessor::Preprocessor(
-   const preprocessing::PreprocessingConfig& preprocessing_config,
-   const config::DatabaseConfig& database_config
+   const preprocessing::PreprocessingConfig preprocessing_config,
+   const config::DatabaseConfig database_config
 )
-    : preprocessing_config(preprocessing_config),
-      database_config(database_config),
+    : preprocessing_config(std::move(preprocessing_config)),
+      database_config(std::move(database_config)),
       preprocessing_db(preprocessing_config.getPreprocessingDatabaseLocation().value_or(":memory:")
       ) {}
 
@@ -225,7 +225,7 @@ from metadata_table;
       "select 0::bigint as partition_id, metadata_table.*\n"
       "from metadata_table;"
    );
-};
+}
 
 void Preprocessor::createSequenceViews(const ReferenceGenomes& reference_genomes) {
    std::string order_by_select =

diff --git a/src/silo/preprocessing/sequence_info.cpp b/src/silo/preprocessing/sequence_info.cpp
@@ -1,6 +1,5 @@
 #include "silo/preprocessing/sequence_info.h"
 
-#include <boost/algorithm/string/join.hpp>
 #include <duckdb.hpp>
 
 #include "silo/preprocessing/preprocessing_database.h"

diff --git a/src/silo/storage/build_exception.cpp b/src/silo/storage/build_exception.cpp
diff --git a/src/silo/storage/column/pango_lineage_column.cpp b/src/silo/storage/column/pango_lineage_column.cpp
@@ -30,15 +30,7 @@ void PangoLineageColumnPartition::insert(const common::RawPangoLineage& value) {
 }
 
 void PangoLineageColumnPartition::insertNull() {
-   const common::UnaliasedPangoLineage resolved_lineage = alias_key.unaliasPangoLineage({""});
-   for (const auto& parent_lineage : resolved_lineage.getParentLineages()) {
-      (void)lookup.getOrCreateId(parent_lineage);
-   }
-   const Idx value_id = lookup.getOrCreateId(resolved_lineage);
-   const size_t row_number = value_ids.size();
-   value_ids.push_back(value_id);
-   indexed_values[value_id].add(row_number);
-   insertSublineageValues(resolved_lineage, row_number);
+   insert({""});
 }
 
 void PangoLineageColumnPartition::insertSublineageValues(

diff --git a/src/silo/zstdfasta/zstdfasta_table_reader.cpp b/src/silo/zstdfasta/zstdfasta_table_reader.cpp
@@ -24,8 +24,7 @@ silo::ZstdFastaTableReader::ZstdFastaTableReader(
       table_name(table_name),
       where_clause(where_clause),
       order_by_clause(order_by_clause),
-      decompressor(std::make_unique<ZstdDecompressor>(compression_dict)),
-      DEBUG_dictionary(compression_dict) {
+      decompressor(std::make_unique<ZstdDecompressor>(compression_dict)) {
    SPDLOG_TRACE("Initializing ZstdFastaTableReader for table {}", table_name);
    genome_buffer.resize(compression_dict.size());
    reset();

diff --git a/src/silo/zstdfasta/zstdfasta_table_reader.test.cpp b/src/silo/zstdfasta/zstdfasta_table_reader.test.cpp
@@ -18,8 +18,8 @@ TEST(ZstdFastaTableReader, correctlyReadsZstdFastaTableFromFastaFile) {
 
    silo::FastaReader file_reader(file_path);
 
-   duckdb::DuckDB duckDB(nullptr);
-   duckdb::Connection connection(duckDB);
+   duckdb::DuckDB duck_db(nullptr);
+   duckdb::Connection connection(duck_db);
 
    silo::ZstdFastaTable::generate(connection, "test", file_reader, "ACGT");
 
@@ -47,8 +47,8 @@ TEST(ZstdFastaTableReader, correctlyReadsZstdFastaTableFromZstdFastaFile) {
 
    silo::ZstdFastaReader file_reader(file_path, "ACGT");
 
-   duckdb::DuckDB duckDB(nullptr);
-   duckdb::Connection connection(duckDB);
+   duckdb::DuckDB duck_db(nullptr);
+   duckdb::Connection connection(duck_db);
 
    silo::ZstdFastaTable::generate(connection, "test", file_reader);
 
@@ -76,8 +76,8 @@ TEST(ZstdFastaTableReader, correctlySortsZstdFastaTableFromFastaFile) {
 
    silo::FastaReader file_reader(file_path);
 
-   duckdb::DuckDB duckDB(nullptr);
-   duckdb::Connection connection(duckDB);
+   duckdb::DuckDB duck_db(nullptr);
+   duckdb::Connection connection(duck_db);
 
    silo::ZstdFastaTable::generate(connection, "test", file_reader, "ACGT");
 
@@ -105,8 +105,8 @@ TEST(ZstdFastaTableReader, correctlySortsZstdFastaTableFromZstdFastaFile) {
 
    silo::ZstdFastaReader file_reader(file_path, "ACGT");
 
-   duckdb::DuckDB duckDB(nullptr);
-   duckdb::Connection connection(duckDB);
+   duckdb::DuckDB duck_db(nullptr);
+   duckdb::Connection connection(duck_db);
 
    silo::ZstdFastaTable::generate(connection, "test", file_reader);