bugfix: pango alias was not saved by database

GenSpectrum · Jul 24, 2023 · 33e925c · 33e925c
1 parent 3e848a5
commit 33e925c
Show file tree

Hide file tree

Showing 2 changed files with 20 additions and 0 deletions.
diff --git a/include/silo/storage/pango_lineage_alias.h b/include/silo/storage/pango_lineage_alias.h
@@ -7,6 +7,9 @@
 #include <unordered_set>
 #include <vector>
 
+#include <boost/serialization/unordered_map.hpp>
+#include <boost/serialization/vector.hpp>
+
 namespace silo {
 
 namespace common {
@@ -16,7 +19,16 @@ struct RawPangoLineage;
 }  // namespace common
 
 class PangoLineageAliasLookup {
+   friend class boost::serialization::access;
+
   private:
+   template <class Archive>
+   [[maybe_unused]] void serialize(Archive& archive, const uint32_t /* version */) {
+      // clang-format off
+      archive & alias_key;
+      // clang-format on
+   }
+
    std::unordered_map<std::string, std::vector<std::string>> alias_key;
 
   public:

diff --git a/src/silo/database.cpp b/src/silo/database.cpp
@@ -392,6 +392,10 @@ void Database::saveDatabaseState(const std::string& save_directory) {
    const std::string database_config_filename = save_directory + "database_config.yaml";
    database_config.writeConfig(database_config_filename);
 
+   std::ofstream alias_key_file(save_directory + "alias_key.silo");
+   ::boost::archive::binary_oarchive alias_key_archive(alias_key_file);
+   alias_key_archive << alias_key;
+
    std::ofstream partitions_file(save_directory + "partitions.silo");
    ::boost::archive::binary_oarchive partitions_archive(partitions_file);
    partitions_archive << partitions;
@@ -439,6 +443,10 @@ Database Database::loadDatabaseState(const std::string& save_directory) {
    database.database_config =
       silo::config::DatabaseConfigReader().readConfig(database_config_filename);
 
+   std::ifstream alias_key_file(save_directory + "alias_key.silo");
+   ::boost::archive::binary_iarchive alias_key_archive(alias_key_file);
+   alias_key_archive >> database.alias_key;
+
    SPDLOG_INFO("Loading partitions from {}", save_directory);
 
    std::ifstream partitions_file(save_directory + "partitions.silo");