fix(prepro): enforce exact match on file base stem when processing fr…

…om file, to resolve incorrect pairing of sequence/metadata resolves #607
GenSpectrum · Oct 10, 2024 · bd07da6 · bd07da6
1 parent bd86cc6
commit bd07da6
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Showing 2 changed files with 14 additions and 2 deletions.
diff --git a/include/silo/preprocessing/preprocessing_database.h b/include/silo/preprocessing/preprocessing_database.h
@@ -39,6 +39,8 @@ class PreprocessingDatabase {
 
    std::unique_ptr<duckdb::MaterializedQueryResult> query(std::string sql_query);
 
+   static std::string getBaseStem(const std::filesystem::path& file_path);
+
    ZstdTable generateSequenceTableViaFile(
       const std::string& table_name,
       const std::string& reference_sequence,

diff --git a/src/silo/preprocessing/preprocessing_database.cpp b/src/silo/preprocessing/preprocessing_database.cpp
@@ -127,15 +127,25 @@ preprocessing::Partitions PreprocessingDatabase::getPartitionDescriptor() {
    return preprocessing::Partitions(partitions);
 }
 
+std::string PreprocessingDatabase::getBaseStem(const std::filesystem::path& file_path) {
+   std::filesystem::path stem = file_path;
+   while (stem.has_extension()) {
+      stem = stem.stem();
+   }
+
+   return stem.stem().string();
+}
+
 ZstdTable PreprocessingDatabase::generateSequenceTableViaFile(
    const std::string& table_name,
    const std::string& reference_sequence,
    const std::filesystem::path& file_path
 ) {
-   const auto file_stem = file_path.stem().string();
+   const auto file_stem = getBaseStem(file_path);
    for (const auto& entry : std::filesystem::directory_iterator(file_path.parent_path())) {
+      const auto entry_stem = getBaseStem(entry.path());
       const auto entry_file_name = entry.path().filename().string();
-      if (!entry.is_regular_file() || !entry_file_name.starts_with(file_stem)) {
+      if (!entry.is_regular_file() || entry_stem != file_stem) {
          continue;
       }
       auto extensions = splitBy(entry_file_name, ".");