ArrowIOHelpers.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Timo Sachsenberg $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/config.h>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/DATASTRUCTURES/StringUtils.h>
#include <OpenMS/FORMAT/MSExperimentArrowExport.h>  // for ParquetWriteConfig
 
#include <cstdint>
#include <map>
#include <memory>
#include <string>
#include <utility>
#include <unordered_set>
#include <vector>
 
// Forward declarations
namespace arrow
{
  class Array;
  class KeyValueMetadata;
  class Table;
}
 
namespace OpenMS
{
class ConsensusMap;
class MetaInfoInterface;
namespace MS1LabelState { struct Keys; }
 
namespace ArrowIOHelpers
{
  OPENMS_DLLAPI std::string generateUuidV4();
 
  OPENMS_DLLAPI Size tableRowCount(const std::shared_ptr<arrow::Table>& table);
 
  OPENMS_DLLAPI bool writeTableToParquet(
    const std::shared_ptr<arrow::Table>& table,
    const std::string& filename,
    const ParquetWriteConfig& config = ParquetWriteConfig{});
 
  OPENMS_DLLAPI bool concatenateAndWriteToParquet(
    const std::vector<std::shared_ptr<arrow::Table>>& tables,
    const std::string& filename,
    const ParquetWriteConfig& config = ParquetWriteConfig{},
    const std::shared_ptr<const arrow::KeyValueMetadata>& metadata = nullptr);
 
  // ---------------------------------------------------------------------------
  // QPX file metadata
  // ---------------------------------------------------------------------------
 
  OPENMS_DLLAPI std::shared_ptr<const arrow::KeyValueMetadata> qpxFileMetadata(
    const std::string& file_type,
    const ParquetWriteConfig& config = ParquetWriteConfig{},
    const std::map<std::string, std::string>& extra = {});
 
  OPENMS_DLLAPI std::string qpxScanFormat(const std::string& native_id);
 
  OPENMS_DLLAPI std::string qpxScanFormat(const std::vector<std::string>& native_ids);
 
  OPENMS_DLLAPI std::string qpxRunFileName(const std::string& ms_run_path);
 
  OPENMS_DLLAPI std::vector<Int32> qpxScanComponents(const std::string& spectrum_reference);
 
  struct OPENMS_DLLAPI QPXRunFileNameKeys
  {
    QPXRunFileNameKeys();
    UInt reference_file_name;
    UInt run_file_name;
  };
 
  OPENMS_DLLAPI std::string qpxPsmRunFileName(const MetaInfoInterface& hit,
                                              const MetaInfoInterface& identification,
                                              const std::string& resolved_run_file,
                                              const QPXRunFileNameKeys& keys);
 
  OPENMS_DLLAPI bool qpxWarnOnRunNameCollisions(
    const std::string& context,
    const std::vector<std::string>& ms_run_paths);
 
 
  OPENMS_DLLAPI std::string qpxIntensityLabel(
    const std::string& column_label,
    const std::string& channel_name);
 
  OPENMS_DLLAPI std::map<std::uint64_t, std::string> qpxIntensityLabels(
    const ConsensusMap& cmap);
 
  OPENMS_DLLAPI bool qpxIsCanonicalIntensityLabel(const std::string& label);
 
  OPENMS_DLLAPI std::vector<std::pair<std::string, std::string>> qpxCvParams(const MetaInfoInterface& hit);
 
  OPENMS_DLLAPI std::vector<std::pair<std::string, std::string>> qpxCvParams(const MetaInfoInterface& hit,
                                                                              const MS1LabelState::Keys& keys);
 
  // ---------------------------------------------------------------------------
  // Read helpers
  // ---------------------------------------------------------------------------
 
  OPENMS_DLLAPI std::shared_ptr<arrow::Array> getColumn(
    const std::shared_ptr<arrow::Table>& table,
    const std::string& name,
    bool required = true);
 
  OPENMS_DLLAPI std::string getStringValue(
    const std::shared_ptr<arrow::Array>& array,
    int64_t row);
 
  OPENMS_DLLAPI double getDoubleValue(
    const std::shared_ptr<arrow::Array>& array,
    int64_t row,
    double default_val = 0.0);
 
  OPENMS_DLLAPI float getFloatValue(
    const std::shared_ptr<arrow::Array>& array,
    int64_t row,
    float default_val = 0.0f);
 
  OPENMS_DLLAPI int32_t getInt32Value(
    const std::shared_ptr<arrow::Array>& array,
    int64_t row,
    int32_t default_val = 0);
 
  OPENMS_DLLAPI int64_t getInt64Value(
    const std::shared_ptr<arrow::Array>& array,
    int64_t row,
    int64_t default_val = 0);
 
  OPENMS_DLLAPI bool getBoolValue(
    const std::shared_ptr<arrow::Array>& array,
    int64_t row,
    bool default_val = false);
 
  OPENMS_DLLAPI bool isNull(
    const std::shared_ptr<arrow::Array>& array,
    int64_t row);
 
  OPENMS_DLLAPI void readMetaValues(
    const std::shared_ptr<arrow::Array>& array,
    int64_t row,
    MetaInfoInterface& target,
    const std::unordered_set<std::string>& excluded_keys = {});
}
 
} // namespace OpenMS