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

#include <OpenMS/FORMAT/OMSFileStore.h>

Inheritance diagram for OMSFileStore:

Public Types
using	Key = int64_t
	< Type used for database keys More...

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

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

	~OMSFileStore ()
	Destructor. More...

void	store (const IdentificationData &id_data)
	Write data from an IdentificationData object to database. More...

void	store (const FeatureMap &features)
	Write data from a FeatureMap object to database. 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	storeVersionAndDate_ ()

void	storeScoreTypes_ (const IdentificationData &id_data)

void	storeInputFiles_ (const IdentificationData &id_data)

void	storeProcessingSoftwares_ (const IdentificationData &id_data)

void	storeDBSearchParams_ (const IdentificationData &id_data)

void	storeProcessingSteps_ (const IdentificationData &id_data)

void	storeObservations_ (const IdentificationData &id_data)

void	storeParentSequences_ (const IdentificationData &id_data)

void	storeParentGroupSets_ (const IdentificationData &id_data)

void	storeIdentifiedCompounds_ (const IdentificationData &id_data)

void	storeIdentifiedSequences_ (const IdentificationData &id_data)

void	storeAdducts_ (const IdentificationData &id_data)

void	storeObservationMatches_ (const IdentificationData &id_data)

void	storeFeatures_ (const FeatureMap &features)

void	createTable_ (const String &name, const String &definition, bool may_exist=false)

void	createTableMoleculeType_ ()

void	createTableDataValue_DataType_ ()

void	createTableCVTerm_ ()

Key	storeCVTerm_ (const CVTerm &cv_term)

void	createTableMetaInfo_ (const String &parent_table, const String &key_column="id")

void	storeMetaInfo_ (const MetaInfoInterface &info, const String &parent_table, Key parent_id)

void	createTableAppliedProcessingStep_ (const String &parent_table)

void	storeAppliedProcessingStep_ (const IdentificationData::AppliedProcessingStep &step, Size step_order, const String &parent_table, Key parent_id)

void	createTableIdentifiedMolecule_ ()

Key	getDatabaseKey_ (const IdentificationData::IdentifiedMolecule &molecule_var)

void	createTableParentMatches_ ()

void	storeParentMatches_ (const IdentificationData::ParentMatches &matches, Key molecule_id)

template<class MetaInfoInterfaceContainer , class DBKeyTable >
void	storeMetaInfos_ (const MetaInfoInterfaceContainer &container, const String &parent_table, const DBKeyTable &db_keys)

template<class ScoredProcessingResultContainer , class DBKeyTable >
void	storeScoredProcessingResults_ (const ScoredProcessingResultContainer &container, const String &parent_table, const DBKeyTable &db_keys)

void	storeFeature_ (const FeatureMap &features)

void	storeFeatureAndSubordinates_ (const Feature &feature, int &feature_id, int parent_id)

template<class FeatureContainer , class Predicate >
bool	anyFeaturePredicate_ (const FeatureContainer &features, const Predicate &pred)
	check whether a predicate is true for any feature (or subordinate thereof) in a container More...

void	storeMapMetaData_ (const FeatureMap &features)

void	storeDataProcessing_ (const FeatureMap &features)

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

std::map< std::string, std::unique_ptr< SQLite::Statement > >	prepared_queries_
	prepared queries for inserting data into different tables More...

std::map< const IdentificationData::ScoreType *, Key >	score_type_keys_

std::map< const IdentificationData::InputFile *, Key >	input_file_keys_

std::map< const IdentificationData::ProcessingSoftware *, Key >	processing_software_keys_

std::map< const IdentificationData::ProcessingStep *, Key >	processing_step_keys_

std::map< const IdentificationData::DBSearchParam *, Key >	search_param_keys_

std::map< const IdentificationData::Observation *, Key >	observation_keys_

std::map< const IdentificationData::ParentSequence *, Key >	parent_sequence_keys_

std::map< const IdentificationData::ParentGroupSet *, Key >	parent_grouping_keys_

std::map< const IdentificationData::IdentifiedCompound *, Key >	identified_compound_keys_

std::map< const IdentificationData::IdentifiedPeptide *, Key >	identified_peptide_keys_

std::map< const IdentificationData::IdentifiedOligo *, Key >	identified_oligo_keys_

std::map< const AdductInfo *, Key >	adduct_keys_

std::map< const IdentificationData::ObservationMatch *, Key >	observation_match_keys_

std::map< const DataProcessing *, Key >	feat_processing_keys_

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 storing .oms files (SQLite format)

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

Member Typedef Documentation

◆ Key

using Key = int64_t

< Type used for database keys

Constructor & Destructor Documentation

◆ OMSFileStore()

OMSFileStore	(	const String &	filename,
		LogType	log_type
	)

Constructor.

Deletes the output file if it exists, then creates an SQLite database in its place. Opens the database and configures it for fast writing.

Parameters

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

Exceptions

Exception::FailedAPICall Database cannot be opened

◆ ~OMSFileStore()

~OMSFileStore ( )

Destructor.

Closes the connection to the database file.

Member Function Documentation

◆ anyFeaturePredicate_()

bool anyFeaturePredicate_	(	const FeatureContainer &	features,
		const Predicate &	pred
	)

inlineprivate

check whether a predicate is true for any feature (or subordinate thereof) in a container

◆ createTable_()

void createTable_	(	const String &	name,
		const String &	definition,
		bool	may_exist = `false`
	)

private

◆ createTableAppliedProcessingStep_()

void createTableAppliedProcessingStep_ ( const String & parent_table )

private

Referenced by OMSFileStore::storeScoredProcessingResults_().

◆ createTableCVTerm_()

void createTableCVTerm_ ( )

private

◆ createTableDataValue_DataType_()

void createTableDataValue_DataType_ ( )

private

◆ createTableIdentifiedMolecule_()

void createTableIdentifiedMolecule_ ( )

private

◆ createTableMetaInfo_()

void createTableMetaInfo_	(	const String &	parent_table,
		const String &	key_column = `"id"`
	)

private

Referenced by OMSFileStore::storeMetaInfos_().

◆ createTableMoleculeType_()

void createTableMoleculeType_ ( )

private

◆ createTableParentMatches_()

void createTableParentMatches_ ( )

private

◆ getDatabaseKey_()

Key getDatabaseKey_ ( const IdentificationData::IdentifiedMolecule & molecule_var )

private

◆ store() [1/2]

void store ( const IdentificationData & id_data )

Write data from an IdentificationData object to database.

◆ store() [2/2]

void store ( const FeatureMap & features )

Write data from a FeatureMap object to database.

◆ storeAdducts_()

void storeAdducts_ ( const IdentificationData & id_data )

private

◆ storeAppliedProcessingStep_()

void storeAppliedProcessingStep_	(	const IdentificationData::AppliedProcessingStep &	step,
		Size	step_order,
		const String &	parent_table,
		Key	parent_id
	)

private

Referenced by OMSFileStore::storeScoredProcessingResults_().

◆ storeCVTerm_()

Key storeCVTerm_ ( const CVTerm & cv_term )

private

◆ storeDataProcessing_()

void storeDataProcessing_ ( const FeatureMap & features )

private

◆ storeDBSearchParams_()

void storeDBSearchParams_ ( const IdentificationData & id_data )

private

◆ storeFeature_()

void storeFeature_ ( const FeatureMap & features )

private

◆ storeFeatureAndSubordinates_()

void storeFeatureAndSubordinates_	(	const Feature &	feature,
		int &	feature_id,
		int	parent_id
	)

private

◆ storeFeatures_()

void storeFeatures_ ( const FeatureMap & features )

private

◆ storeIdentifiedCompounds_()

void storeIdentifiedCompounds_ ( const IdentificationData & id_data )

private

◆ storeIdentifiedSequences_()

void storeIdentifiedSequences_ ( const IdentificationData & id_data )

private

◆ storeInputFiles_()

void storeInputFiles_ ( const IdentificationData & id_data )

private

◆ storeMapMetaData_()

void storeMapMetaData_ ( const FeatureMap & features )

private

◆ storeMetaInfo_()

void storeMetaInfo_	(	const MetaInfoInterface &	info,
		const String &	parent_table,
		Key	parent_id
	)

private

Referenced by OMSFileStore::storeMetaInfos_().

◆ storeMetaInfos_()

void storeMetaInfos_	(	const MetaInfoInterfaceContainer &	container,
		const String &	parent_table,
		const DBKeyTable &	db_keys
	)

inlineprivate

References OMSFileStore::createTableMetaInfo_(), and OMSFileStore::storeMetaInfo_().

Referenced by OMSFileStore::storeScoredProcessingResults_().

◆ storeObservationMatches_()

void storeObservationMatches_ ( const IdentificationData & id_data )

private

◆ storeObservations_()

void storeObservations_ ( const IdentificationData & id_data )

private

◆ storeParentGroupSets_()

void storeParentGroupSets_ ( const IdentificationData & id_data )

private

◆ storeParentMatches_()

void storeParentMatches_	(	const IdentificationData::ParentMatches &	matches,
		Key	molecule_id
	)

private

◆ storeParentSequences_()

void storeParentSequences_ ( const IdentificationData & id_data )

private

◆ storeProcessingSoftwares_()

void storeProcessingSoftwares_ ( const IdentificationData & id_data )

private

◆ storeProcessingSteps_()

void storeProcessingSteps_ ( const IdentificationData & id_data )

private

◆ storeScoredProcessingResults_()

void storeScoredProcessingResults_	(	const ScoredProcessingResultContainer &	container,
		const String &	parent_table,
		const DBKeyTable &	db_keys
	)

inlineprivate

References OMSFileStore::createTableAppliedProcessingStep_(), OMSFileStore::storeAppliedProcessingStep_(), and OMSFileStore::storeMetaInfos_().

◆ storeScoreTypes_()

void storeScoreTypes_ ( const IdentificationData & id_data )

private

◆ storeVersionAndDate_()

void storeVersionAndDate_ ( )

private

Member Data Documentation

◆ adduct_keys_

std::map<const AdductInfo*, Key> adduct_keys_

private

◆ db_

std::unique_ptr<SQLite::Database> db_

private

The database connection (read/write)

◆ feat_processing_keys_

std::map<const DataProcessing*, Key> feat_processing_keys_

private

◆ identified_compound_keys_

std::map<const IdentificationData::IdentifiedCompound*, Key> identified_compound_keys_

private

◆ identified_oligo_keys_

std::map<const IdentificationData::IdentifiedOligo*, Key> identified_oligo_keys_

private

◆ identified_peptide_keys_

std::map<const IdentificationData::IdentifiedPeptide*, Key> identified_peptide_keys_

private

◆ input_file_keys_

std::map<const IdentificationData::InputFile*, Key> input_file_keys_

private

◆ observation_keys_

std::map<const IdentificationData::Observation*, Key> observation_keys_

private

◆ observation_match_keys_

std::map<const IdentificationData::ObservationMatch*, Key> observation_match_keys_

private

◆ parent_grouping_keys_

std::map<const IdentificationData::ParentGroupSet*, Key> parent_grouping_keys_

private

◆ parent_sequence_keys_

std::map<const IdentificationData::ParentSequence*, Key> parent_sequence_keys_

private

◆ prepared_queries_

std::map<std::string, std::unique_ptr<SQLite::Statement> > prepared_queries_

private

prepared queries for inserting data into different tables

◆ processing_software_keys_

std::map<const IdentificationData::ProcessingSoftware*, Key> processing_software_keys_

private

◆ processing_step_keys_

std::map<const IdentificationData::ProcessingStep*, Key> processing_step_keys_

private

◆ score_type_keys_

std::map<const IdentificationData::ScoreType*, Key> score_type_keys_

private

◆ search_param_keys_

std::map<const IdentificationData::DBSearchParam*, Key> search_param_keys_

private

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Key

Constructor & Destructor Documentation

◆ OMSFileStore()

◆ ~OMSFileStore()

Member Function Documentation

◆ anyFeaturePredicate_()

◆ createTable_()

◆ createTableAppliedProcessingStep_()

◆ createTableCVTerm_()

◆ createTableDataValue_DataType_()

◆ createTableIdentifiedMolecule_()

◆ createTableMetaInfo_()

◆ createTableMoleculeType_()

◆ createTableParentMatches_()

◆ getDatabaseKey_()

◆ store() [1/2]

◆ store() [2/2]

◆ storeAdducts_()

◆ storeAppliedProcessingStep_()

◆ storeCVTerm_()

◆ storeDataProcessing_()

◆ storeDBSearchParams_()

◆ storeFeature_()

◆ storeFeatureAndSubordinates_()

◆ storeFeatures_()

◆ storeIdentifiedCompounds_()

◆ storeIdentifiedSequences_()

◆ storeInputFiles_()

◆ storeMapMetaData_()

◆ storeMetaInfo_()

◆ storeMetaInfos_()

◆ storeObservationMatches_()

◆ storeObservations_()

◆ storeParentGroupSets_()

◆ storeParentMatches_()

◆ storeParentSequences_()

◆ storeProcessingSoftwares_()

◆ storeProcessingSteps_()

◆ storeScoredProcessingResults_()

◆ storeScoreTypes_()

◆ storeVersionAndDate_()

Member Data Documentation

◆ adduct_keys_

◆ db_

◆ feat_processing_keys_

◆ identified_compound_keys_

◆ identified_oligo_keys_

◆ identified_peptide_keys_

◆ input_file_keys_

◆ observation_keys_

◆ observation_match_keys_

◆ parent_grouping_keys_

◆ parent_sequence_keys_

◆ prepared_queries_

◆ processing_software_keys_

◆ processing_step_keys_

◆ score_type_keys_

◆ search_param_keys_