feat: log databaseConfig and preprocessingConfig

include/silo/config/database_config.h

@@ -5,6 +5,8 @@
 #include <string>
 #include <vector>
 
+#include <fmt/core.h>
+
 namespace silo::config {
 
 enum class ValueType { STRING, PANGOLINEAGE, DATE, INT, FLOAT };
@@ -36,4 +38,20 @@ struct DatabaseConfig {
 };
 }  // namespace silo::config
 
+template <>
+struct [[maybe_unused]] fmt::formatter<silo::config::DatabaseConfig> : fmt::formatter<std::string> {
+   [[maybe_unused]] static auto format(
+      const silo::config::DatabaseConfig& database_config,
+      format_context& ctx
+   ) -> decltype(ctx.out());
+};
+
+template <>
+struct [[maybe_unused]] fmt::formatter<silo::config::DatabaseSchema> : fmt::formatter<std::string> {
+   [[maybe_unused]] static auto format(
+      const silo::config::DatabaseSchema& database_schema,
+      format_context& ctx
+   ) -> decltype(ctx.out());
+};
+
 #endif  // SILO_INCLUDE_SILO_CONFIG_DATABASECONFIG_H_

src/silo/config/database_config.cpp

@@ -67,4 +67,29 @@ std::optional<DatabaseMetadata> DatabaseConfig::getMetadata(const std::string& n
    return *element;
 }
 
-}  // namespace silo::config
+}  // namespace silo::config
+
+[[maybe_unused]] auto fmt::formatter<silo::config::DatabaseConfig>::format(
+   const silo::config::DatabaseConfig& database_config,
+   fmt::format_context& ctx
+) -> decltype(ctx.out()) {
+   return format_to(
+      ctx.out(),
+      "DatabaseConfig[default_nucleotide_sequence: {}, schema: {}",
+      database_config.default_nucleotide_sequence,
+      database_config.schema
+   );
+}
+
+[[maybe_unused]] auto fmt::formatter<silo::config::DatabaseSchema>::format(
+   const silo::config::DatabaseSchema& database_schema,
+   fmt::format_context& ctx
+) -> decltype(ctx.out()) {
+   return format_to(
+      ctx.out(),
+      "DatabaseSchema[instance_name: {}, primary_key: {}, partition_by: {}]",
+      database_schema.instance_name,
+      database_schema.primary_key,
+      database_schema.partition_by
+   );
+}

src/silo/database.cpp

@@ -448,6 +448,8 @@ void Database::preprocessing(
    const config::DatabaseConfig& database_config_
 ) {
    database_config = database_config_;
+   SPDLOG_DEBUG("preprocessing - using database config: {}", database_config);
+   SPDLOG_DEBUG("preprocessing - using preprocessing config: {}", preprocessing_config);
 
    SPDLOG_INFO("preprocessing - validate metadata file against config");
    preprocessing::MetadataValidator().validateMedataFile(

src/silo/preprocessing/metadata.cpp

@@ -5,13 +5,15 @@
 #include <ostream>
 #include <string>
 
+#include <spdlog/spdlog.h>
 #include <boost/algorithm/string/join.hpp>
 
 #include "silo/preprocessing/preprocessing_exception.h"
 
 namespace silo::preprocessing {
 
 csv::CSVReader buildReader(const std::filesystem::path& metadata_path) {
+   SPDLOG_INFO("Reading metadata file: {}", metadata_path.string());
    try {
       csv::CSVFormat format;
       format.delimiter('\t');