OMSFileLoad.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Hendrik Weisser $
// $Authors: Hendrik Weisser, Chris Bielow $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/METADATA/ID/IdentificationData.h>
#include <OpenMS/FORMAT/OMSFileStore.h>
 
#include <QtCore/QJsonArray> // for JSON export
 
namespace SQLite
{
  class Database;
} // namespace SQLite
 
namespace OpenMS
{
  class FeatureMap;
  class ConsensusMap;
 
  namespace Internal
  {
    class OMSFileLoad: public ProgressLogger
    {
    public:
      using Key = OMSFileStore::Key; 
 
      OMSFileLoad(const String& filename, LogType log_type);
 
      ~OMSFileLoad();
 
      void load(IdentificationData& id_data);
 
      void load(FeatureMap& features);
 
      void load(ConsensusMap& consensus);
 
      void exportToJSON(std::ostream& output);
 
    private:
      static bool isEmpty_(const SQLite::Statement& query);
 
      static DataValue makeDataValue_(const SQLite::Statement& query);
 
      // static CVTerm loadCVTerm_(int id);
 
      void loadScoreTypes_(IdentificationData& id_data);
 
      void loadInputFiles_(IdentificationData& id_data);
 
      void loadProcessingSoftwares_(IdentificationData& id_data);
 
      void loadDBSearchParams_(IdentificationData& id_data);
 
      void loadProcessingSteps_(IdentificationData& id_data);
 
      void loadObservations_(IdentificationData& id_data);
 
      void loadParentSequences_(IdentificationData& id_data);
 
      void loadParentGroupSets_(IdentificationData& id_data);
 
      void loadIdentifiedCompounds_(IdentificationData& id_data);
 
      void loadIdentifiedSequences_(IdentificationData& id_data);
 
      void loadAdducts_(IdentificationData& id_data);
 
      void loadObservationMatches_(IdentificationData& id_data);
 
      template <class MapType> String loadMapMetaDataTemplate_(MapType& features);
 
      void loadMapMetaData_(FeatureMap& features);
 
      void loadMapMetaData_(ConsensusMap& consensus);
 
      void loadDataProcessing_(std::vector<DataProcessing>& data_processing);
 
      void loadFeatures_(FeatureMap& features);
 
      Feature loadFeatureAndSubordinates_(SQLite::Statement& query_feat,
                                          SQLite::Statement& query_meta,
                                          SQLite::Statement& query_match,
                                          SQLite::Statement& query_hull);
 
      void loadConsensusColumnHeaders_(ConsensusMap& consensus);
 
      void loadConsensusFeatures_(ConsensusMap& consensus);
 
      BaseFeature makeBaseFeature_(int id, SQLite::Statement& query_feat,
                                   SQLite::Statement& query_meta,
                                   SQLite::Statement& query_match);
 
      void prepareQueriesBaseFeature_(SQLite::Statement& query_meta,
                                      SQLite::Statement& query_match);
 
      bool prepareQueryMetaInfo_(SQLite::Statement& query, const String& parent_table);
 
      void handleQueryMetaInfo_(SQLite::Statement& query, MetaInfoInterface& info,
                                Key parent_id);
 
      bool prepareQueryAppliedProcessingStep_(SQLite::Statement& query,
                                              const String& parent_table);
 
      void handleQueryAppliedProcessingStep_(
        SQLite::Statement& query,
        IdentificationDataInternal::ScoredProcessingResult& result,
        Key parent_id);
 
      void handleQueryParentMatch_(
        SQLite::Statement& query, IdentificationData::ParentMatches& parent_matches,
        Key molecule_id);
 
      void handleQueryPeakAnnotation_(
        SQLite::Statement& query, IdentificationData::ObservationMatch& match,
        Key parent_id);
 
      QJsonArray exportTableToJSON_(const QString& table, const QString& order_by);
 
      std::unique_ptr<SQLite::Database> db_;
 
      int version_number_; 
 
      QString subquery_score_; 
 
      // mappings between database keys and loaded data:
      std::unordered_map<Key, IdentificationData::ScoreTypeRef> score_type_refs_;
      std::unordered_map<Key, IdentificationData::InputFileRef> input_file_refs_;
      std::unordered_map<Key, IdentificationData::ProcessingSoftwareRef> processing_software_refs_;
      std::unordered_map<Key, IdentificationData::ProcessingStepRef> processing_step_refs_;
      std::unordered_map<Key, IdentificationData::SearchParamRef> search_param_refs_;
      std::unordered_map<Key, IdentificationData::ObservationRef> observation_refs_;
      std::unordered_map<Key, IdentificationData::ParentSequenceRef> parent_sequence_refs_;
      std::unordered_map<Key, IdentificationData::IdentifiedMolecule> identified_molecule_vars_;
      std::unordered_map<Key, IdentificationData::ObservationMatchRef> observation_match_refs_;
      std::unordered_map<Key, IdentificationData::AdductRef> adduct_refs_;
 
      // mapping: table name -> ordering critera (for JSON export)
      // @TODO: could use 'unordered_map' here, but would need to specify hash function for 'QString'
      static std::map<QString, QString> export_order_by_;
    };
  }
}