GenSpectrum · Taepper · Apr 7, 2026 · Mar 31, 2026
diff --git a/documentation/api.md b/documentation/api.md
@@ -57,8 +57,7 @@ Returns metadata about the loaded database.
   "version": "0.1.0",
   "sequenceCount": 100,
   "horizontalBitmapsSize": 5594,
-  "verticalBitmapsSize": 28102,
-  "numberOfPartitions": 1
+  "verticalBitmapsSize": 28102
 }
 ```
 
@@ -68,7 +67,6 @@ Returns metadata about the loaded database.
 | `sequenceCount` | Total number of sequences in the database |
 | `horizontalBitmapsSize` | Size of horizontal bitmap indexes (bytes) |
 | `verticalBitmapsSize` | Size of vertical bitmap indexes (bytes) |
-| `numberOfPartitions` | Number of table partitions |
 
 ---
 

diff --git a/documentation/data_directories.md b/documentation/data_directories.md
@@ -11,13 +11,11 @@ output/
   1700000000/
     data_version.silo
     database_schema.silo
-    default/
-      ...  (partition data)
+    default.silo
   1700100000/
     data_version.silo
     database_schema.silo
-    default/
-      ...
+    default.silo
 ```
 
 ### data_version.silo format

diff --git a/endToEndTests/test/info.test.js b/endToEndTests/test/info.test.js
@@ -19,7 +19,6 @@ describe('The /info endpoint', () => {
           sequenceCount: 100,
           horizontalBitmapsSize: 5595,
           verticalBitmapsSize: 28102,
-          numberOfPartitions: 1,
         });
       });
   });

diff --git a/src/silo/api/lineage_definition_handler.cpp b/src/silo/api/lineage_definition_handler.cpp
@@ -44,8 +44,7 @@ void LineageDefinitionHandler::get(
       throw BadRequest("The column {} is not of type indexed-string.", column_name);
    }
    auto* metadata =
-      table->second->schema
-         ->getColumnMetadata<storage::column::IndexedStringColumnPartition>(column_name)
+      table->second->schema->getColumnMetadata<storage::column::IndexedStringColumn>(column_name)
          .value();
    if (!metadata->lineage_tree.has_value()) {
       throw BadRequest("The column {} does not have a lineageIndex defined.", column_name);

diff --git a/src/silo/append/database_inserter.cpp b/src/silo/append/database_inserter.cpp
@@ -52,7 +52,7 @@ std::expected<simdjson::ondemand::value, std::string> findFieldManual(
 
 std::expected<simdjson::ondemand::value, std::string> findFieldWithFallbacks(
    simdjson::ondemand::object& object,
-   const TablePartitionInserter::SniffedField& sniffed_field
+   const TableInserter::SniffedField& sniffed_field
 ) {
    simdjson::ondemand::value column_value;
    auto error = object.find_field(sniffed_field.escaped_key).get(column_value);
@@ -108,10 +108,11 @@ std::expected<simdjson::ondemand::object, std::string> iterateToObject(
 
 }  // namespace
 
-std::expected<std::vector<TablePartitionInserter::SniffedField>, std::string>
-TablePartitionInserter::sniffFieldOrder(simdjson::ondemand::document_reference ndjson_line) const {
+std::expected<std::vector<TableInserter::SniffedField>, std::string> TableInserter::sniffFieldOrder(
+   simdjson::ondemand::document_reference ndjson_line
+) const {
    std::vector<SniffedField> order_in_json_line;
-   auto columns_in_table = table_partition->columns.metadata;
+   auto columns_in_table = table->columns.metadata;
    ASSIGN_OR_RAISE(auto object, iterateToObject(ndjson_line));
    for (auto maybe_field : object) {
       ASSIGN_OR_RAISE_SIMDJSON(
@@ -161,64 +162,46 @@ TablePartitionInserter::sniffFieldOrder(simdjson::ondemand::document_reference n
    return order_in_json_line;
 }
 
-std::expected<void, std::string> TablePartitionInserter::insert(
+std::expected<void, std::string> TableInserter::insert(
    simdjson::ondemand::document_reference ndjson_line,
-   const std::vector<TablePartitionInserter::SniffedField>& field_order_hint
+   const std::vector<TableInserter::SniffedField>& field_order_hint
 ) const {
-   EVOBENCH_SCOPE_EVERY(20, "TablePartitionInserter", "insert");
+   EVOBENCH_SCOPE_EVERY(20, "TableInserter", "insert");
    ASSIGN_OR_RAISE(auto object, iterateToObject(ndjson_line));
    for (const auto& sniffed_field : field_order_hint) {
       ASSIGN_OR_RAISE(auto column_value, findFieldWithFallbacks(object, sniffed_field));
-      auto success_or_error = table_partition->columns.addJsonValueToColumn(
-         sniffed_field.column_identifier, column_value
-      );
+      auto success_or_error =
+         table->columns.addJsonValueToColumn(sniffed_field.column_identifier, column_value);
       if (!success_or_error.has_value()) {
          return success_or_error;
       }
    }
-   table_partition->sequence_count++;
+   table->sequence_count++;
    return {};
 }
 
-TablePartitionInserter::Commit TablePartitionInserter::commit() const {
-   table_partition->finalize();
-   table_partition->validate();
-   return Commit{};
-}
-
-TablePartitionInserter TableInserter::openNewPartition() const {
-   if (table->getNumberOfPartitions() == 0) {
-      return TablePartitionInserter{table->addPartition()};
-   }
-   return TablePartitionInserter{table->getPartition(0)};
-}
-
-TablePartitionInserter TableInserter::openLastPartition() const {
-   if (table->getNumberOfPartitions() == 0) {
-      return openNewPartition();
-   }
-   return TablePartitionInserter{table->getPartition(table->getNumberOfPartitions() - 1)};
-}
-
 TableInserter::Commit TableInserter::commit() const {
    try {
+      table->finalize();
       table->validate();
       return Commit{};
    } catch (const silo::schema::DuplicatePrimaryKeyException& exception) {
       throw silo::append::AppendException(exception.what());
    }
 }
 
-TablePartitionInserter::Commit appendDataToTablePartition(
-   const TablePartitionInserter& partition_inserter,
+TableInserter::Commit appendDataToTable(
+   std::shared_ptr<silo::storage::Table> table,
    NdjsonLineReader& input_data
 ) {
-   EVOBENCH_SCOPE("TablePartitionInserter", "appendDataToTablePartition");
+   EVOBENCH_SCOPE("TableInserter", "appendDataToTable");
+   const TableInserter table_inserter(std::move(table));
+
    size_t line_count = 0;
 
    bool first_line = true;
 
-   std::vector<TablePartitionInserter::SniffedField> sniffed_field_order;
+   std::vector<TableInserter::SniffedField> sniffed_field_order;
    for (auto [json_obj_or_error, raw_line] : input_data) {
       simdjson::ondemand::document_reference ndjson_line;
       auto error = json_obj_or_error.get(ndjson_line);
@@ -231,7 +214,7 @@ TablePartitionInserter::Commit appendDataToTablePartition(
       }
 
       if (first_line) {
-         auto sniffed_field_order_or_error = partition_inserter.sniffFieldOrder(ndjson_line);
+         auto sniffed_field_order_or_error = table_inserter.sniffFieldOrder(ndjson_line);
          if (!sniffed_field_order_or_error.has_value()) {
             throw AppendException{
                "{} - current line: {}", sniffed_field_order_or_error.error(), raw_line
@@ -241,7 +224,7 @@ TablePartitionInserter::Commit appendDataToTablePartition(
          first_line = false;
       }
 
-      auto maybe_error = partition_inserter.insert(ndjson_line, sniffed_field_order);
+      auto maybe_error = table_inserter.insert(ndjson_line, sniffed_field_order);
       if (!maybe_error.has_value()) {
          throw AppendException{"{} - current line: {}", maybe_error.error(), raw_line};
       }
@@ -252,20 +235,6 @@ TablePartitionInserter::Commit appendDataToTablePartition(
       }
    }
 
-   return partition_inserter.commit();
-}
-
-TableInserter::Commit appendDataToTable(
-   std::shared_ptr<silo::storage::Table> table,
-   NdjsonLineReader& input_data
-) {
-   const TableInserter table_inserter(std::move(table));
-
-   // TODO(#738) make partition configurable
-   auto table_partition = table_inserter.openLastPartition();
-
-   appendDataToTablePartition(table_partition, input_data);
-
    return table_inserter.commit();
 }
 

diff --git a/src/silo/append/database_inserter.h b/src/silo/append/database_inserter.h
@@ -8,22 +8,21 @@
 
 #include "silo/append/ndjson_line_reader.h"
 #include "silo/storage/table.h"
-#include "silo/storage/table_partition.h"
 
 namespace silo::append {
 
-class TablePartitionInserter {
-   std::shared_ptr<storage::TablePartition> table_partition;
+class TableInserter {
+   std::shared_ptr<storage::Table> table;
 
   public:
    class Commit {
-      friend class TablePartitionInserter;
+      friend class TableInserter;
 
       Commit() = default;
    };
 
-   explicit TablePartitionInserter(std::shared_ptr<storage::TablePartition> table_partition)
-       : table_partition(std::move(table_partition)) {}
+   explicit TableInserter(std::shared_ptr<storage::Table> table)
+       : table(std::move(table)) {}
 
    struct SniffedField {
       silo::schema::ColumnIdentifier column_identifier;
@@ -47,34 +46,9 @@ class TablePartitionInserter {
    [[nodiscard]] Commit commit() const;
 };
 
-class TableInserter {
-   std::shared_ptr<storage::Table> table;
-
-  public:
-   class Commit {
-      friend class TableInserter;
-
-      Commit() = default;
-   };
-
-   explicit TableInserter(std::shared_ptr<storage::Table> table)
-       : table(std::move(table)) {}
-
-   [[nodiscard]] TablePartitionInserter openNewPartition() const;
-
-   [[nodiscard]] TablePartitionInserter openLastPartition() const;
-
-   [[nodiscard]] Commit commit() const;
-};
-
-TablePartitionInserter::Commit appendDataToTablePartition(
-   const TablePartitionInserter& partition_inserter,
-   NdjsonLineReader& input_data
-);
-
 TableInserter::Commit appendDataToTable(
    std::shared_ptr<silo::storage::Table> table,
    NdjsonLineReader& input_data
 );
 
-}  // namespace silo::append
+}  // namespace silo::append
diff --git a/src/silo/common/aa_symbols.h b/src/silo/common/aa_symbols.h
@@ -14,7 +14,7 @@ namespace silo {
 
 namespace storage::column {
 template <typename SymbolType>
-class SequenceColumnPartition;
+class SequenceColumn;
 }
 
 class AminoAcid {
@@ -52,7 +52,7 @@ class AminoAcid {
    };
 
    static constexpr schema::ColumnType COLUMN_TYPE = schema::ColumnType::AMINO_ACID_SEQUENCE;
-   using Column = storage::column::SequenceColumnPartition<AminoAcid>;
+   using Column = storage::column::SequenceColumn<AminoAcid>;
 
    static constexpr uint32_t COUNT = 28;
    static_assert(COUNT == static_cast<uint32_t>(Symbol::X) + 1);

diff --git a/src/silo/common/nucleotide_symbols.h b/src/silo/common/nucleotide_symbols.h
@@ -14,7 +14,7 @@ namespace silo {
 
 namespace storage::column {
 template <typename SymbolType>
-class SequenceColumnPartition;
+class SequenceColumn;
 }
 
 class Nucleotide {
@@ -40,7 +40,7 @@ class Nucleotide {
    };
 
    static constexpr schema::ColumnType COLUMN_TYPE = schema::ColumnType::NUCLEOTIDE_SEQUENCE;
-   using Column = storage::column::SequenceColumnPartition<Nucleotide>;
+   using Column = storage::column::SequenceColumn<Nucleotide>;
 
    static constexpr uint32_t COUNT = 16;
 

diff --git a/src/silo/common/serialization_version.txt b/src/silo/common/serialization_version.txt
@@ -1 +1 @@
-1774509839
+1774967790