feat: format DatabaseConfig

Dockerfile_linter

@@ -14,7 +14,7 @@ RUN apt update \
     && add-apt-repository 'deb http://apt.llvm.org/jammy/  llvm-toolchain-jammy main' \
     && apt install -y clang-tidy-17
 
-RUN pip install conan==2.0.2
+RUN pip install conan==2.0.8
 
 COPY conanfile.py conanprofile.docker ./
 RUN mv conanprofile.docker conanprofile

include/silo/config/database_config.h

@@ -54,4 +54,21 @@ struct [[maybe_unused]] fmt::formatter<silo::config::DatabaseSchema> : fmt::form
    ) -> decltype(ctx.out());
 };
 
+template <>
+struct [[maybe_unused]] fmt::formatter<silo::config::DatabaseMetadata>
+    : fmt::formatter<std::string> {
+   [[maybe_unused]] static auto format(
+      const silo::config::DatabaseMetadata& database_metadata,
+      format_context& ctx
+   ) -> decltype(ctx.out());
+};
+
+template <>
+struct [[maybe_unused]] fmt::formatter<silo::config::ValueType> : fmt::formatter<std::string> {
+   [[maybe_unused]] static auto format(
+      const silo::config::ValueType& value_type,
+      format_context& ctx
+   ) -> decltype(ctx.out());
+};
+
 #endif  // SILO_INCLUDE_SILO_CONFIG_DATABASECONFIG_H_

src/silo/config/database_config.cpp

@@ -1,5 +1,6 @@
 #include "silo/config/database_config.h"
 
+#include <fmt/format.h>
 #include <algorithm>
 #include <iterator>
 #include <stdexcept>
@@ -75,7 +76,7 @@ std::optional<DatabaseMetadata> DatabaseConfig::getMetadata(const std::string& n
 ) -> decltype(ctx.out()) {
    return format_to(
       ctx.out(),
-      "DatabaseConfig[default_nucleotide_sequence: {}, schema: {}",
+      "{{ default_nucleotide_sequence: '{}', schema: {} }}",
       database_config.default_nucleotide_sequence,
       database_config.schema
    );
@@ -87,9 +88,42 @@ std::optional<DatabaseMetadata> DatabaseConfig::getMetadata(const std::string& n
 ) -> decltype(ctx.out()) {
    return format_to(
       ctx.out(),
-      "DatabaseSchema[instance_name: {}, primary_key: {}, partition_by: {}]",
+      "{{ instance_name: '{}', primary_key: '{}', partition_by: '{}', metadata: [{}] }}",
       database_schema.instance_name,
       database_schema.primary_key,
-      database_schema.partition_by
+      database_schema.partition_by,
+      fmt::join(database_schema.metadata, ",")
    );
-}
+}
+
+[[maybe_unused]] auto fmt::formatter<silo::config::DatabaseMetadata>::format(
+   const silo::config::DatabaseMetadata& database_metadata,
+   fmt::format_context& ctx
+) -> decltype(ctx.out()) {
+   return format_to(
+      ctx.out(),
+      "{{ name: '{}', type: '{}', generate_index: {} }}",
+      database_metadata.name,
+      database_metadata.type,
+      database_metadata.generate_index
+   );
+}
+
+[[maybe_unused]] auto fmt::formatter<silo::config::ValueType>::format(
+   const silo::config::ValueType& value_type,
+   fmt::format_context& ctx
+) -> decltype(ctx.out()) {
+   switch (value_type) {
+      case silo::config::ValueType::STRING:
+         return format_to(ctx.out(), "string");
+      case silo::config::ValueType::DATE:
+         return format_to(ctx.out(), "date");
+      case silo::config::ValueType::PANGOLINEAGE:
+         return format_to(ctx.out(), "pango_lineage");
+      case silo::config::ValueType::INT:
+         return format_to(ctx.out(), "int");
+      case silo::config::ValueType::FLOAT:
+         return format_to(ctx.out(), "float");
+   }
+   return format_to(ctx.out(), "unknown");
+}

src/silo/config/database_config_reader.cpp

@@ -4,6 +4,7 @@
 #include <string>
 #include <vector>
 
+#include <spdlog/spdlog.h>
 #include <yaml-cpp/yaml.h>
 
 #include "silo/config/database_config.h"
@@ -19,6 +20,9 @@ struct convert<silo::config::DatabaseConfig> {
       } else {
          config.default_nucleotide_sequence = "main";
       }
+
+      SPDLOG_TRACE("Resulting database config: {}", config);
+
       return true;
    }
 };
@@ -64,6 +68,7 @@ struct convert<silo::config::DatabaseMetadata> {
 
 namespace silo::config {
 DatabaseConfig DatabaseConfigReader::readConfig(const std::filesystem::path& config_path) const {
+   SPDLOG_INFO("Reading database config from {}", config_path.string());
    return YAML::LoadFile(config_path.string()).as<DatabaseConfig>();
 }
 }  // namespace silo::config

src/silo/database.cpp

@@ -448,8 +448,6 @@ 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(