handle if HLL file was deleted or corrupted

seqan · Aug 17, 2023 · b8e067a · b8e067a
1 parent f234a3b
commit b8e067a
Showing 1 changed file with 22 additions and 8 deletions.
diff --git a/include/chopper/sketch/toolbox.hpp b/include/chopper/sketch/toolbox.hpp
@@ -9,6 +9,7 @@
 #include <robin_hood.h>
 
 #include <chopper/sketch/hyperloglog.hpp>
+#include "execute.hpp"
 
 namespace chopper::sketch
 {
@@ -106,11 +107,21 @@ class toolbox
         std::sort(positions.begin(), positions.end(), cardinality_compare);
     }
 
+
+    static void read_hll_files_into(std::filesystem::path const & hll_dir,
+                                    std::vector<std::string> const & target_filenames,
+                                    std::vector<hyperloglog> & target)
+    {
+        chopper::configuration config; // Create default configuration
+        read_hll_files_into(hll_dir, target_filenames, target, config);
+    }
+
     /*!\brief Restore the HLL sketches from the files in hll_dir and target_filenames into target container.
     */
     static void read_hll_files_into(std::filesystem::path const & hll_dir,
                                     std::vector<std::string> const & target_filenames,
-                                    std::vector<hyperloglog> & target)
+                                    std::vector<hyperloglog> & target,
+                                    chopper::configuration & config)
     {
         assert(std::filesystem::exists(hll_dir) && !std::filesystem::is_empty(hll_dir)); // checked in chopper_layout
 
@@ -120,18 +131,21 @@ class toolbox
         {
             for (auto const & filename : target_filenames)
             {
-                if (std::filesystem::path(filename).extension() != ".empty_bin")
-                { //Myrthe
+                if (std::filesystem::path(filename).extension() != ".empty_bin") { //Myrthe
 
                     std::filesystem::path path = hll_dir / std::filesystem::path(filename).stem();
                     path += ".hll";
                     std::ifstream hll_fin(path, std::ios::binary);
+                    try {
+                        if (!hll_fin.good())
+                            throw std::runtime_error{"Could not open file " + path.string()};
 
-                    if (!hll_fin.good())
-                        throw std::runtime_error{"Could not open file " + path.string()};
-
-                    // the sketch bits will be automatically read from the files
-                    target.emplace_back().restore(hll_fin);
+                        target.emplace_back().restore(hll_fin);                        // the sketch bits will be automatically read from the files
+                    }
+                    catch (std::runtime_error const & ) {
+                        auto filename_input = std::vector<std::string> {filename};
+                        chopper::sketch::execute(config, filename_input, target);
+                    }
                 }
             }
         }