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

#include <OpenMS/FORMAT/OMSFileLoad.h>

Inheritance diagram for OMSFileLoad:

Collaboration 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	load (ConsensusMap &consensus)
	Load data from database and populate a ConsensusMap 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	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging. 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 (UInt64 bytes_processed=0) const

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

Private Member Functions
void	loadScoreTypes_ (IdentificationData &id_data)
	Load information on score type from the database into IdentificationData. More...

void	loadInputFiles_ (IdentificationData &id_data)
	Load information on input files from the database into IdentificationData. More...

void	loadProcessingSoftwares_ (IdentificationData &id_data)
	Load information on data processing software from the database into IdentificationData. More...

void	loadDBSearchParams_ (IdentificationData &id_data)
	Load information on sequence database search parameters from the database into IdentificationData. More...

void	loadProcessingSteps_ (IdentificationData &id_data)
	Load information on data processing steps from the database into IdentificationData. More...

void	loadObservations_ (IdentificationData &id_data)
	Load information on observations (e.g. spectra) from the database into IdentificationData. More...

void	loadParentSequences_ (IdentificationData &id_data)
	Load information on parent sequences (e.g. proteins) from the database into IdentificationData. More...

void	loadParentGroupSets_ (IdentificationData &id_data)
	Load information on parent group sets (e.g. protein groups) from the database into IdentificationData. More...

void	loadIdentifiedCompounds_ (IdentificationData &id_data)
	Load information on identified compounds from the database into IdentificationData. More...

void	loadIdentifiedSequences_ (IdentificationData &id_data)
	Load information on identified sequences (peptides or oligonucleotides) from the database into IdentificationData. More...

void	loadAdducts_ (IdentificationData &id_data)
	Load information on adducts from the database into IdentificationData. More...

void	loadObservationMatches_ (IdentificationData &id_data)
	Load information on observation matches (e.g. PSMs) from the database into IdentificationData. More...

template<class MapType >
String	loadMapMetaDataTemplate_ (MapType &features)
	Helper function for loading meta data on feature/consensus maps from the database. More...

void	loadMapMetaData_ (FeatureMap &features)
	Load feature map meta data from the database. More...

void	loadMapMetaData_ (ConsensusMap &consensus)
	Load consensus map meta data from the database. More...

void	loadDataProcessing_ (std::vector< DataProcessing > &data_processing)
	Load information on data processing for feature/consensus maps from the database. More...

void	loadFeatures_ (FeatureMap &features)
	Load information on features from the database into a feature map. More...

Feature	loadFeatureAndSubordinates_ (SQLite::Statement &query_feat, SQLite::Statement &query_meta, SQLite::Statement &query_match, SQLite::Statement &query_hull)
	Generate a feature (incl. subordinate features) from data returned by SQL queries. More...

void	loadConsensusColumnHeaders_ (ConsensusMap &consensus)
	Load consensus map column headers from the database. More...

void	loadConsensusFeatures_ (ConsensusMap &consensus)
	Load information on consensus features from the database into a consensus map. More...

BaseFeature	makeBaseFeature_ (int id, SQLite::Statement &query_feat, SQLite::Statement &query_meta, SQLite::Statement &query_match)
	Generate a BaseFeature (parent class) from data returned by SQL queries. More...

void	prepareQueriesBaseFeature_ (SQLite::Statement &query_meta, SQLite::Statement &query_match)
	Prepare SQL queries for loading (meta) data on BaseFeatures from the database. More...

bool	prepareQueryMetaInfo_ (SQLite::Statement &query, const String &parent_table)
	Prepare SQL query for loading meta values associated with a particular class (stored in `parent_table`) More...

void	handleQueryMetaInfo_ (SQLite::Statement &query, MetaInfoInterface &info, Key parent_id)
	Store results from an SQL query on meta values in a MetaInfoInterface(-derived) object. More...

bool	prepareQueryAppliedProcessingStep_ (SQLite::Statement &query, const String &parent_table)
	Prepare SQL query for loading processing metadata associated with a particular class (stored in `parent_table`) More...

void	handleQueryAppliedProcessingStep_ (SQLite::Statement &query, IdentificationDataInternal::ScoredProcessingResult &result, Key parent_id)
	Store results from an SQL query on processing metadata in a ScoredProcessingResult(-derived) object. More...

void	handleQueryParentMatch_ (SQLite::Statement &query, IdentificationData::ParentMatches &parent_matches, Key molecule_id)
	Store results from an SQL query on parent matches. More...

void	handleQueryPeakAnnotation_ (SQLite::Statement &query, IdentificationData::ObservationMatch &match, Key parent_id)
	Store results from an SQL query on peak annotations in an observation match. More...

QJsonArray	exportTableToJSON_ (const QString &table, const QString &order_by)
	Export the contents of a database table to JSON. More...

Static Private Member Functions
static bool	isEmpty_ (const SQLite::Statement &query)
	Does the `query` contain an empty SQL statement (signifying that it shouldn't be executed)? More...

static DataValue	makeDataValue_ (const SQLite::Statement &query)
	Generate a DataValue with information returned by an SQL query. More...

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
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

◆ exportTableToJSON_()

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

private

Export the contents of a database table to JSON.

◆ 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

Store results from an SQL query on processing metadata in a ScoredProcessingResult(-derived) object.

◆ handleQueryMetaInfo_()

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

private

Store results from an SQL query on meta values in a MetaInfoInterface(-derived) object.

◆ handleQueryParentMatch_()

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

private

Store results from an SQL query on parent matches.

◆ handleQueryPeakAnnotation_()

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

private

Store results from an SQL query on peak annotations in an observation match.

◆ isEmpty_()

static bool isEmpty_ ( const SQLite::Statement & query )

staticprivate

Does the query contain an empty SQL statement (signifying that it shouldn't be executed)?

◆ load() [1/3]

void load ( ConsensusMap & consensus )

Load data from database and populate a ConsensusMap object.

◆ load() [2/3]

void load ( FeatureMap & features )

Load data from database and populate a FeatureMap object.

◆ load() [3/3]

void load ( IdentificationData & id_data )

Load data from database and populate an IdentificationData object.

◆ loadAdducts_()

void loadAdducts_ ( IdentificationData & id_data )

private

Load information on adducts from the database into IdentificationData.

◆ loadConsensusColumnHeaders_()

void loadConsensusColumnHeaders_ ( ConsensusMap & consensus )

private

Load consensus map column headers from the database.

◆ loadConsensusFeatures_()

void loadConsensusFeatures_ ( ConsensusMap & consensus )

private

Load information on consensus features from the database into a consensus map.

◆ loadDataProcessing_()

void loadDataProcessing_ ( std::vector< DataProcessing > & data_processing )

private

Load information on data processing for feature/consensus maps from the database.

◆ loadDBSearchParams_()

void loadDBSearchParams_ ( IdentificationData & id_data )

private

Load information on sequence database search parameters from the database into IdentificationData.

◆ loadFeatureAndSubordinates_()

Feature loadFeatureAndSubordinates_	(	SQLite::Statement &	query_feat,
		SQLite::Statement &	query_meta,
		SQLite::Statement &	query_match,
		SQLite::Statement &	query_hull
	)

private

Generate a feature (incl. subordinate features) from data returned by SQL queries.

◆ loadFeatures_()

void loadFeatures_ ( FeatureMap & features )

private

Load information on features from the database into a feature map.

◆ loadIdentifiedCompounds_()

void loadIdentifiedCompounds_ ( IdentificationData & id_data )

private

Load information on identified compounds from the database into IdentificationData.

◆ loadIdentifiedSequences_()

void loadIdentifiedSequences_ ( IdentificationData & id_data )

private

Load information on identified sequences (peptides or oligonucleotides) from the database into IdentificationData.

◆ loadInputFiles_()

void loadInputFiles_ ( IdentificationData & id_data )

private

Load information on input files from the database into IdentificationData.

◆ loadMapMetaData_() [1/2]

void loadMapMetaData_ ( ConsensusMap & consensus )

private

Load consensus map meta data from the database.

◆ loadMapMetaData_() [2/2]

void loadMapMetaData_ ( FeatureMap & features )

private

Load feature map meta data from the database.

◆ loadMapMetaDataTemplate_()

String loadMapMetaDataTemplate_ ( MapType & features )

private

Helper function for loading meta data on feature/consensus maps from the database.

◆ loadObservationMatches_()

void loadObservationMatches_ ( IdentificationData & id_data )

private

Load information on observation matches (e.g. PSMs) from the database into IdentificationData.

◆ loadObservations_()

void loadObservations_ ( IdentificationData & id_data )

private

Load information on observations (e.g. spectra) from the database into IdentificationData.

◆ loadParentGroupSets_()

void loadParentGroupSets_ ( IdentificationData & id_data )

private

Load information on parent group sets (e.g. protein groups) from the database into IdentificationData.

◆ loadParentSequences_()

void loadParentSequences_ ( IdentificationData & id_data )

private

Load information on parent sequences (e.g. proteins) from the database into IdentificationData.

◆ loadProcessingSoftwares_()

void loadProcessingSoftwares_ ( IdentificationData & id_data )

private

Load information on data processing software from the database into IdentificationData.

◆ loadProcessingSteps_()

void loadProcessingSteps_ ( IdentificationData & id_data )

private

Load information on data processing steps from the database into IdentificationData.

◆ loadScoreTypes_()

void loadScoreTypes_ ( IdentificationData & id_data )

private

Load information on score type from the database into IdentificationData.

◆ makeBaseFeature_()

BaseFeature makeBaseFeature_	(	int	id,
		SQLite::Statement &	query_feat,
		SQLite::Statement &	query_meta,
		SQLite::Statement &	query_match
	)

private

Generate a BaseFeature (parent class) from data returned by SQL queries.

◆ makeDataValue_()

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

staticprivate

Generate a DataValue with information returned by an SQL query.

◆ prepareQueriesBaseFeature_()

void prepareQueriesBaseFeature_	(	SQLite::Statement &	query_meta,
		SQLite::Statement &	query_match
	)

private

Prepare SQL queries for loading (meta) data on BaseFeatures from the database.

◆ prepareQueryAppliedProcessingStep_()

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

private

Prepare SQL query for loading processing metadata associated with a particular class (stored in parent_table)

◆ prepareQueryMetaInfo_()

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

private

Prepare SQL query for loading meta values associated with a particular class (stored in parent_table)

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

◆ exportTableToJSON_()

◆ exportToJSON()

◆ handleQueryAppliedProcessingStep_()

◆ handleQueryMetaInfo_()

◆ handleQueryParentMatch_()

◆ handleQueryPeakAnnotation_()

◆ isEmpty_()

◆ load() [1/3]

◆ load() [2/3]

◆ load() [3/3]

◆ loadAdducts_()

◆ loadConsensusColumnHeaders_()

◆ loadConsensusFeatures_()

◆ loadDataProcessing_()

◆ loadDBSearchParams_()

◆ loadFeatureAndSubordinates_()

◆ loadFeatures_()

◆ loadIdentifiedCompounds_()

◆ loadIdentifiedSequences_()

◆ loadInputFiles_()

◆ loadMapMetaData_() [1/2]

◆ loadMapMetaData_() [2/2]

◆ loadMapMetaDataTemplate_()

◆ loadObservationMatches_()

◆ loadObservations_()

◆ loadParentGroupSets_()

◆ loadParentSequences_()

◆ loadProcessingSoftwares_()

◆ loadProcessingSteps_()

◆ loadScoreTypes_()

◆ makeBaseFeature_()

◆ makeDataValue_()

◆ prepareQueriesBaseFeature_()

◆ 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_