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 2002-2022.
//
// This software is released under a three-clause BSD license:
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//  * Redistributions in binary form must reproduce the above copyright
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//    documentation and/or other materials provided with the distribution.
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//    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.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// $Maintainer: Hendrik Weisser $
// $Authors: Hendrik Weisser, Chris Bielow $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/KERNEL/FeatureMap.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
{
  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 exportToJSON(std::ostream& output);

    private:
      // 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);

      void loadMapMetaData_(FeatureMap& features);

      void loadDataProcessing_(FeatureMap& features);

      void loadFeatures_(FeatureMap& features);

      Feature loadFeatureAndSubordinates_(SQLite::Statement& query_feat,
                                          std::optional<SQLite::Statement>& query_meta,
                                          std::optional<SQLite::Statement>& query_hull,
                                          std::optional<SQLite::Statement>& query_match);

      static DataValue makeDataValue_(const SQLite::Statement& query);

      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);

      void createView_(const String& name, const String& select);

      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_;
    };
  }
}