feat(silo): try to serialize phylo_tree

Author: anna-parker

src/silo/common/phylo_tree.cpp

@@ -5,9 +5,16 @@
 
 #include <nlohmann/json.hpp>
 
+#include <boost/serialization/export.hpp>
+#include <boost/serialization/optional.hpp>
+#include <boost/serialization/shared_ptr.hpp>
+#include <boost/serialization/vector.hpp>
+
 #include "silo/preprocessing/preprocessing_exception.h"
 #include "silo/query_engine/batched_bitmap_reader.h"
 
+BOOST_CLASS_EXPORT(silo::common::TreeNode)
+
 namespace silo::common {
 using silo::common::TreeNodeId;
 

src/silo/common/phylo_tree.h

@@ -22,6 +22,20 @@ class TreeNode {
 
    bool isLeaf() { return children.empty(); }
    bool rowIndexExists() const { return row_index.has_value(); }
+
+   virtual ~TreeNode() = default;
+
+   friend class boost::serialization::access;
+   template <class Archive>
+   [[maybe_unused]] void serialize(Archive& archive, const uint32_t /* version */) {
+      // clang-format off
+    archive & node_id;
+    archive & row_index;
+    archive & children;
+    archive & parent;
+    archive & depth;
+      // clang-format on
+   }
 };
 
 class PhyloTree {
@@ -50,6 +64,14 @@ class PhyloTree {
    roaring::Roaring getDescendants(const TreeNodeId& node_id);
 
    roaring::Roaring getDescendants(const std::string& node_label);
+
+   friend class boost::serialization::access;
+   template <class Archive>
+   [[maybe_unused]] void serialize(Archive& archive, const uint32_t /* version */) {
+      // clang-format off
+      archive & nodes;
+      // clang-format on
+   }
 };
 
 }  // namespace silo::common

src/silo/storage/column/string_column.h

@@ -117,8 +117,7 @@ template <class Archive>
 ) {
    ar & object.column_name;
    ar & object.dictionary;
-   // TODO(#815) add serialization function for phylo_tree
-   // ar & object.phylo_tree;
+   ar & object.phylo_tree;
 }
 }  // namespace boost::serialization
 
@@ -132,20 +131,18 @@ template <class Archive>
 ) {
    std::string column_name;
    silo::common::BidirectionalMap<std::string> dictionary;
-   // TODO(#815) add serialization function for phylo_tree
-   // std::optional<silo::common::PhyloTree> phylo_tree;
+   std::optional<silo::common::PhyloTree> phylo_tree;
    ar & column_name;
    ar & dictionary;
-   // ar & phylo_tree;
-   //   if(phylo_tree.has_value()){
-   //      object = std::make_shared<silo::storage::column::StringColumnMetadata>(
-   //         std::move(column_name), std::move(dictionary), std::move(phylo_tree)
-   //      );
-   //   }
-   //   else{
-   object = std::make_shared<silo::storage::column::StringColumnMetadata>(
-      std::move(column_name), std::move(dictionary)
-   );
-   //   }
+   ar & phylo_tree;
+   if (phylo_tree.has_value()) {
+      object = std::make_shared<silo::storage::column::StringColumnMetadata>(
+         std::move(column_name), std::move(dictionary), std::move(phylo_tree.value())
+      );
+   } else {
+      object = std::make_shared<silo::storage::column::StringColumnMetadata>(
+         std::move(column_name), std::move(dictionary)
+      );
+   }
 }
 }  // namespace boost::serialization