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

#include <OpenMS/FORMAT/OMSFileStore.h>

Inheritance diagram for OMSFileStore:

Collaboration 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...

void	store (const ConsensusMap &consensus)
	Write data from a ConsensusMap 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	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	createTable_ (const String &name, const String &definition, bool may_exist=false)
	Helper function to create a database table. More...

void	createTableDataValue_DataType_ ()
	Create a database table for the data types used in DataValue. More...

void	createTableCVTerm_ ()
	Create a database table (and prepare a query) for storing CV terms. More...

void	createTableMetaInfo_ (const String &parent_table, const String &key_column="id")
	Create a database table (and prepare a query) for storing meta values. More...

void	storeVersionAndDate_ ()
	Store version information and current date/time in the database. More...

Key	storeCVTerm_ (const CVTerm &cv_term)
	Store a CV term in the database. More...

void	storeMetaInfo_ (const MetaInfoInterface &info, const String &parent_table, Key parent_id)
	Store meta values (associated with one object) in the database. More...

template<class MetaInfoInterfaceContainer , class DBKeyTable >
void	storeMetaInfos_ (const MetaInfoInterfaceContainer &container, const String &parent_table, const DBKeyTable &db_keys)
	Store meta values (for all objects in a container) in the database. More...

Helper functions for storing identification data
Store score type information from IdentificationData in the database
void	storeScoreTypes_ (const IdentificationData &id_data)

void	storeInputFiles_ (const IdentificationData &id_data)
	Store input file information from IdentificationData in the database. More...

void	storeProcessingSoftwares_ (const IdentificationData &id_data)
	Store information on data processing software from IdentificationData in the database. More...

void	storeDBSearchParams_ (const IdentificationData &id_data)
	Store sequence database search parameters from IdentificationData in the database. More...

void	storeProcessingSteps_ (const IdentificationData &id_data)
	Store information on data processing steps from IdentificationData in the database. More...

void	storeObservations_ (const IdentificationData &id_data)
	Store information on observations (e.g. spectra) from IdentificationData in the database. More...

void	storeParentSequences_ (const IdentificationData &id_data)
	Store information on parent sequences (e.g. proteins) from IdentificationData in the database. More...

void	storeParentGroupSets_ (const IdentificationData &id_data)
	Store information on parent group sets (e.g. protein groups) from IdentificationData in the database. More...

void	storeIdentifiedCompounds_ (const IdentificationData &id_data)
	Store information on identified compounds from IdentificationData in the database. More...

void	storeIdentifiedSequences_ (const IdentificationData &id_data)
	Store information on identified sequences (peptides or oligonucleotides) from IdentificationData in the database. More...

void	storeAdducts_ (const IdentificationData &id_data)
	Store information on adducts from IdentificationData in the database. More...

void	storeObservationMatches_ (const IdentificationData &id_data)
	Store information on observation matches (e.g. PSMs) from IdentificationData in the database. More...

void	createTableMoleculeType_ ()
	Create a database table for molecule types (proteins, compounds, RNA) More...

void	createTableAppliedProcessingStep_ (const String &parent_table)
	Create a database table for storing processing metadata. More...

void	storeAppliedProcessingStep_ (const IdentificationData::AppliedProcessingStep &step, Size step_order, const String &parent_table, Key parent_id)
	Store processing metadata for a particular class (stored in `parent_table`) in the database. More...

void	createTableIdentifiedMolecule_ ()
	Create a database table for storing identified molecules (peptides, compounds, oligonucleotides) More...

Key	getDatabaseKey_ (const IdentificationData::IdentifiedMolecule &molecule_var)
	Return the database key used for an identified molecule (peptide, compound or oligonucleotide) More...

void	createTableParentMatches_ ()
	Create a database table for storing parent matches (e.g. proteins for a peptide) More...

void	storeParentMatches_ (const IdentificationData::ParentMatches &matches, Key molecule_id)
	Store information on parent matches in the database. More...

template<class ScoredProcessingResultContainer , class DBKeyTable >
void	storeScoredProcessingResults_ (const ScoredProcessingResultContainer &container, const String &parent_table, const DBKeyTable &db_keys)
	Store metadata on scores/processing steps (for all objects in a container) in the database. More...

Helper functions for storing (consensus) feature data
Create a table for storing feature information
void	createTableBaseFeature_ (bool with_metainfo, bool with_idmatches)

void	storeBaseFeature_ (const BaseFeature &feature, int feature_id, int parent_id)
	Store information on a feature in the database. More...

void	storeFeatures_ (const FeatureMap &features)
	Store information on features from a feature map in the database. More...

void	storeFeatureAndSubordinates_ (const Feature &feature, int &feature_id, int parent_id)
	Store a feature (incl. its subordinate features) in the database. More...

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...

template<class MapType >
void	storeMapMetaData_ (const MapType &features, const String &experiment_type="")
	Store feature/consensus map meta data in the database. More...

void	storeDataProcessing_ (const std::vector< DataProcessing > &data_processing)
	Store information on data processing from a feature/consensus map in the database. More...

void	storeConsensusFeatures_ (const ConsensusMap &consensus)
	Store information on consensus features from a consensus map in the database. More...

void	storeConsensusColumnHeaders_ (const ConsensusMap &consensus)
	Store information on column headers from a consensus map in the database. More...

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
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

Helper function to create a database table.

Parameters

name	Name of the new table
definition	Table definition in SQL
may_exist	If true, the table may already exist (otherwise this is an error)

◆ createTableAppliedProcessingStep_()

void createTableAppliedProcessingStep_ ( const String & parent_table )

private

Create a database table for storing processing metadata.

Referenced by OMSFileStore::storeScoredProcessingResults_().

◆ createTableBaseFeature_()

void createTableBaseFeature_	(	bool	with_metainfo,
		bool	with_idmatches
	)

private

◆ createTableCVTerm_()

void createTableCVTerm_ ( )

private

Create a database table (and prepare a query) for storing CV terms.

◆ createTableDataValue_DataType_()

void createTableDataValue_DataType_ ( )

private

Create a database table for the data types used in DataValue.

◆ createTableIdentifiedMolecule_()

void createTableIdentifiedMolecule_ ( )

private

Create a database table for storing identified molecules (peptides, compounds, oligonucleotides)

◆ createTableMetaInfo_()

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

private

Create a database table (and prepare a query) for storing meta values.

Referenced by OMSFileStore::storeMetaInfos_().

◆ createTableMoleculeType_()

void createTableMoleculeType_ ( )

private

Create a database table for molecule types (proteins, compounds, RNA)

◆ createTableParentMatches_()

void createTableParentMatches_ ( )

private

Create a database table for storing parent matches (e.g. proteins for a peptide)

◆ getDatabaseKey_()

Key getDatabaseKey_ ( const IdentificationData::IdentifiedMolecule & molecule_var )

private

Return the database key used for an identified molecule (peptide, compound or oligonucleotide)

◆ store() [1/3]

void store ( const ConsensusMap & consensus )

Write data from a ConsensusMap object to database.

◆ store() [2/3]

void store ( const FeatureMap & features )

Write data from a FeatureMap object to database.

◆ store() [3/3]

void store ( const IdentificationData & id_data )

Write data from an IdentificationData object to database.

◆ storeAdducts_()

void storeAdducts_ ( const IdentificationData & id_data )

private

Store information on adducts from IdentificationData in the database.

◆ storeAppliedProcessingStep_()

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

private

Store processing metadata for a particular class (stored in parent_table) in the database.

Referenced by OMSFileStore::storeScoredProcessingResults_().

◆ storeBaseFeature_()

void storeBaseFeature_	(	const BaseFeature &	feature,
		int	feature_id,
		int	parent_id
	)

private

Store information on a feature in the database.

◆ storeConsensusColumnHeaders_()

void storeConsensusColumnHeaders_ ( const ConsensusMap & consensus )

private

Store information on column headers from a consensus map in the database.

◆ storeConsensusFeatures_()

void storeConsensusFeatures_ ( const ConsensusMap & consensus )

private

Store information on consensus features from a consensus map in the database.

◆ storeCVTerm_()

Key storeCVTerm_ ( const CVTerm & cv_term )

private

Store a CV term in the database.

◆ storeDataProcessing_()

void storeDataProcessing_ ( const std::vector< DataProcessing > & data_processing )

private

Store information on data processing from a feature/consensus map in the database.

◆ storeDBSearchParams_()

void storeDBSearchParams_ ( const IdentificationData & id_data )

private

Store sequence database search parameters from IdentificationData in the database.

◆ storeFeatureAndSubordinates_()

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

private

Store a feature (incl. its subordinate features) in the database.

◆ storeFeatures_()

void storeFeatures_ ( const FeatureMap & features )

private

Store information on features from a feature map in the database.

◆ storeIdentifiedCompounds_()

void storeIdentifiedCompounds_ ( const IdentificationData & id_data )

private

Store information on identified compounds from IdentificationData in the database.

◆ storeIdentifiedSequences_()

void storeIdentifiedSequences_ ( const IdentificationData & id_data )

private

Store information on identified sequences (peptides or oligonucleotides) from IdentificationData in the database.

◆ storeInputFiles_()

void storeInputFiles_ ( const IdentificationData & id_data )

private

Store input file information from IdentificationData in the database.

◆ storeMapMetaData_()

void storeMapMetaData_	(	const MapType &	features,
		const String &	experiment_type = `""`
	)

private

Store feature/consensus map meta data in the database.

◆ storeMetaInfo_()

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

private

Store meta values (associated with one object) in the database.

Referenced by OMSFileStore::storeMetaInfos_().

◆ storeMetaInfos_()

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

inlineprivate

Store meta values (for all objects in a container) in the database.

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

Referenced by OMSFileStore::storeScoredProcessingResults_().

◆ storeObservationMatches_()

void storeObservationMatches_ ( const IdentificationData & id_data )

private

Store information on observation matches (e.g. PSMs) from IdentificationData in the database.

◆ storeObservations_()

void storeObservations_ ( const IdentificationData & id_data )

private

Store information on observations (e.g. spectra) from IdentificationData in the database.

◆ storeParentGroupSets_()

void storeParentGroupSets_ ( const IdentificationData & id_data )

private

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

◆ storeParentMatches_()

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

private

Store information on parent matches in the database.

◆ storeParentSequences_()

void storeParentSequences_ ( const IdentificationData & id_data )

private

Store information on parent sequences (e.g. proteins) from IdentificationData in the database.

◆ storeProcessingSoftwares_()

void storeProcessingSoftwares_ ( const IdentificationData & id_data )

private

Store information on data processing software from IdentificationData in the database.

◆ storeProcessingSteps_()

void storeProcessingSteps_ ( const IdentificationData & id_data )

private

Store information on data processing steps from IdentificationData in the database.

◆ storeScoredProcessingResults_()

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

inlineprivate

Store metadata on scores/processing steps (for all objects in a container) in the database.

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

◆ storeScoreTypes_()

void storeScoreTypes_ ( const IdentificationData & id_data )

private

◆ storeVersionAndDate_()

void storeVersionAndDate_ ( )

private

Store version information and current date/time in the database.

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_()

◆ createTableBaseFeature_()

◆ createTableCVTerm_()

◆ createTableDataValue_DataType_()

◆ createTableIdentifiedMolecule_()

◆ createTableMetaInfo_()

◆ createTableMoleculeType_()

◆ createTableParentMatches_()

◆ getDatabaseKey_()

◆ store() [1/3]

◆ store() [2/3]

◆ store() [3/3]

◆ storeAdducts_()

◆ storeAppliedProcessingStep_()

◆ storeBaseFeature_()

◆ storeConsensusColumnHeaders_()

◆ storeConsensusFeatures_()

◆ storeCVTerm_()

◆ storeDataProcessing_()

◆ storeDBSearchParams_()

◆ 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_