Helper class for loading .oms files (SQLite format) More...

#include <OpenMS/FORMAT/OMSFileLoad.h>

Inheritance diagram for OMSFileLoad:

Public Types
using	Key = OMSFileStore::Key
	Type used for database keys. More...

Public Types inherited from ProgressLogger
enum	LogType { CMD, GUI, NONE }
	Possible log types. More...

Public Member Functions
	OMSFileLoad (const String &filename, LogType log_type)
	Constructor. More...

	~OMSFileLoad ()
	Destructor. More...

void	load (IdentificationData &id_data)
	Load data from database and populate an IdentificationData object. More...

void	load (FeatureMap &features)
	Load data from database and populate a FeatureMap object. More...

void	exportToJSON (std::ostream &output)
	Export database contents in JSON format, write to stream. More...

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...

virtual	~ProgressLogger ()
	Destructor. More...

	ProgressLogger (const ProgressLogger &other)
	Copy constructor. More...

ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator. More...

void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE! More...

LogType	getLogType () const
	Returns the type of progress log being used. More...

void	startProgress (SignedSize begin, SignedSize end, const String &label) const
	Initializes the progress display. More...

void	setProgress (SignedSize value) const
	Sets the current progress. More...

void	endProgress () const
	Ends the progress display. More...

void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

Private Member Functions
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)

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)

Static Private Member Functions
static DataValue	makeDataValue_ (const SQLite::Statement &query)

Private Attributes
std::unique_ptr< SQLite::Database >	db_
	The database connection (read) More...

int	version_number_
	schema version number More...

QString	subquery_score_
	query for score types used in JSON export More...

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_

Static Private Attributes
static std::map< QString, QString >	export_order_by_

Additional Inherited Members
Static Protected Member Functions inherited from ProgressLogger
static String	logTypeToFactoryName_ (LogType type)
	Return the name of the factory product used for this log type. More...

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

Helper class for loading .oms files (SQLite format)

This class encapsulates the SQLite database stored in a .oms file and allows to load data from it.

Member Typedef Documentation

◆ Key

using Key = OMSFileStore::Key

Type used for database keys.

Constructor & Destructor Documentation

◆ OMSFileLoad()

OMSFileLoad	(	const String &	filename,
		LogType	log_type
	)

Constructor.

Opens the connection to the database file (in read-only mode).

Parameters

filename	Path to the .oms input file (SQLite database)
log_type	Type of logging to use

Exceptions

Exception::FailedAPICall Database cannot be opened

◆ ~OMSFileLoad()

~OMSFileLoad ( )

Destructor.

Closes the connection to the database file.

Member Function Documentation

◆ createView_()

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

private

◆ exportTableToJSON_()

QJsonArray exportTableToJSON_	(	const QString &	table,
		const QString &	order_by
	)

private

◆ exportToJSON()

void exportToJSON ( std::ostream & output )

Export database contents in JSON format, write to stream.

◆ handleQueryAppliedProcessingStep_()

void handleQueryAppliedProcessingStep_	(	SQLite::Statement &	query,
		IdentificationDataInternal::ScoredProcessingResult &	result,
		Key	parent_id
	)

private

◆ handleQueryMetaInfo_()

void handleQueryMetaInfo_	(	SQLite::Statement &	query,
		MetaInfoInterface &	info,
		Key	parent_id
	)

private

◆ handleQueryParentMatch_()

void handleQueryParentMatch_	(	SQLite::Statement &	query,
		IdentificationData::ParentMatches &	parent_matches,
		Key	molecule_id
	)

private

◆ handleQueryPeakAnnotation_()

void handleQueryPeakAnnotation_	(	SQLite::Statement &	query,
		IdentificationData::ObservationMatch &	match,
		Key	parent_id
	)

private

◆ load() [1/2]

void load ( IdentificationData & id_data )

Load data from database and populate an IdentificationData object.

◆ load() [2/2]

void load ( FeatureMap & features )

Load data from database and populate a FeatureMap object.

◆ loadAdducts_()

void loadAdducts_ ( IdentificationData & id_data )

private

◆ loadDataProcessing_()

void loadDataProcessing_ ( FeatureMap & features )

private

◆ loadDBSearchParams_()

void loadDBSearchParams_ ( IdentificationData & id_data )

private

◆ loadFeatureAndSubordinates_()

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

private

◆ loadFeatures_()

void loadFeatures_ ( FeatureMap & features )

private

◆ loadIdentifiedCompounds_()

void loadIdentifiedCompounds_ ( IdentificationData & id_data )

private

◆ loadIdentifiedSequences_()

void loadIdentifiedSequences_ ( IdentificationData & id_data )

private

◆ loadInputFiles_()

void loadInputFiles_ ( IdentificationData & id_data )

private

◆ loadMapMetaData_()

void loadMapMetaData_ ( FeatureMap & features )

private

◆ loadObservationMatches_()

void loadObservationMatches_ ( IdentificationData & id_data )

private

◆ loadObservations_()

void loadObservations_ ( IdentificationData & id_data )

private

◆ loadParentGroupSets_()

void loadParentGroupSets_ ( IdentificationData & id_data )

private

◆ loadParentSequences_()

void loadParentSequences_ ( IdentificationData & id_data )

private

◆ loadProcessingSoftwares_()

void loadProcessingSoftwares_ ( IdentificationData & id_data )

private

◆ loadProcessingSteps_()

void loadProcessingSteps_ ( IdentificationData & id_data )

private

◆ loadScoreTypes_()

void loadScoreTypes_ ( IdentificationData & id_data )

private

◆ makeDataValue_()

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

staticprivate

◆ prepareQueryAppliedProcessingStep_()

bool prepareQueryAppliedProcessingStep_	(	SQLite::Statement &	query,
		const String &	parent_table
	)

private

◆ prepareQueryMetaInfo_()

bool prepareQueryMetaInfo_	(	SQLite::Statement &	query,
		const String &	parent_table
	)

private

Member Data Documentation

◆ adduct_refs_

std::unordered_map<Key, IdentificationData::AdductRef> adduct_refs_

private

◆ db_

std::unique_ptr<SQLite::Database> db_

private

The database connection (read)

◆ export_order_by_

std::map<QString, QString> export_order_by_

staticprivate

◆ identified_molecule_vars_

std::unordered_map<Key, IdentificationData::IdentifiedMolecule> identified_molecule_vars_

private

◆ input_file_refs_

std::unordered_map<Key, IdentificationData::InputFileRef> input_file_refs_

private

◆ observation_match_refs_

std::unordered_map<Key, IdentificationData::ObservationMatchRef> observation_match_refs_

private

◆ observation_refs_

std::unordered_map<Key, IdentificationData::ObservationRef> observation_refs_

private

◆ parent_sequence_refs_

std::unordered_map<Key, IdentificationData::ParentSequenceRef> parent_sequence_refs_

private

◆ processing_software_refs_

std::unordered_map<Key, IdentificationData::ProcessingSoftwareRef> processing_software_refs_

private

◆ processing_step_refs_

std::unordered_map<Key, IdentificationData::ProcessingStepRef> processing_step_refs_

private

◆ score_type_refs_

std::unordered_map<Key, IdentificationData::ScoreTypeRef> score_type_refs_

private

◆ search_param_refs_

std::unordered_map<Key, IdentificationData::SearchParamRef> search_param_refs_

private

◆ subquery_score_

QString subquery_score_

private

query for score types used in JSON export

◆ version_number_

int version_number_

private

schema version number

Public Types

Public Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Key

Constructor & Destructor Documentation

◆ OMSFileLoad()

◆ ~OMSFileLoad()

Member Function Documentation

◆ createView_()

◆ exportTableToJSON_()

◆ exportToJSON()

◆ handleQueryAppliedProcessingStep_()

◆ handleQueryMetaInfo_()

◆ handleQueryParentMatch_()

◆ handleQueryPeakAnnotation_()

◆ load() [1/2]

◆ load() [2/2]

◆ loadAdducts_()

◆ loadDataProcessing_()

◆ loadDBSearchParams_()

◆ loadFeatureAndSubordinates_()

◆ loadFeatures_()

◆ loadIdentifiedCompounds_()

◆ loadIdentifiedSequences_()

◆ loadInputFiles_()

◆ loadMapMetaData_()

◆ loadObservationMatches_()

◆ loadObservations_()

◆ loadParentGroupSets_()

◆ loadParentSequences_()

◆ loadProcessingSoftwares_()

◆ loadProcessingSteps_()

◆ loadScoreTypes_()

◆ makeDataValue_()

◆ prepareQueryAppliedProcessingStep_()

◆ prepareQueryMetaInfo_()

Member Data Documentation

◆ adduct_refs_

◆ db_

◆ export_order_by_

◆ identified_molecule_vars_

◆ input_file_refs_

◆ observation_match_refs_

◆ observation_refs_

◆ parent_sequence_refs_

◆ processing_software_refs_

◆ processing_step_refs_

◆ score_type_refs_

◆ search_param_refs_

◆ subquery_score_

◆ version_number_