Namespaces
	insert_statement_generator

	schema_generator

Classes
class	DatabaseSessionLoader

class	DatabaseSessionLoaderCreator

class	DatabaseSessionOptions

class	DatabaseSessionOptionsCreator

Typedefs
typedef utility::pointer::shared_ptr < DatabaseSessionLoader >	DatabaseSessionLoaderOP

typedef utility::pointer::shared_ptr < DatabaseSessionLoader const >	DatabaseSessionLoaderCOP

typedef utility::pointer::shared_ptr < DatabaseSessionOptions >	DatabaseSessionOptionsOP

typedef utility::pointer::shared_ptr < DatabaseSessionOptions const >	DatabaseSessionOptionsCOP

Functions
static thread_local basic::Tracer	TR ("basic.io.database")

bool	open (utility::io::izstream &db_stream, std::string const &db_file, bool warn)
	Open a database file on a provided stream. More...

std::string	full_name (std::string const &db_file, bool warn)
	Full-path database file name. More...

static thread_local basic::Tracer	TR ("basic.database.sql_utils")

sessionOP	get_db_session ()
	Aquire a database session using the command line options transaction type is set to standard. More...

sessionOP	get_db_session (std::string const &db_name, std::string const &pq_schema="")
	Aquire a database session using the command line parameters For postgres databases, the pq_schema acts like a namespace in the database. Transaction type set to standard. More...

sessionOP	get_db_session (string const &db_name, TransactionMode::e transaction_mode, Size chunk_size, string const &pq_schema)

utility::sql_database::sessionOP	get_db_session (utility::sql_database::DatabaseMode::e db_mode, std::string const &db_name, std::string const &pq_schema)

sessionOP	get_db_session (DatabaseMode::e db_mode, TransactionMode::e transaction_mode, Size chunk_size, string const &db_name, string const &pq_schema)

platform::SSize	db_partition_from_options (DatabaseMode::e db_mode)
	@ More...

platform::SSize	resolve_db_partition (bool partition_by_mpi_process, platform::SSize manual_partition=-1)
	Returns partition identifer from mpi rank if in partitioned database mode, or valid manual partition, otherwise -1. More...

statement	safely_prepare_statement (string const &statement_string, sessionOP db_session)

void	safely_write_to_database (statement &statement)

result	safely_read_from_database (statement &statement)

bool	table_exists (sessionOP db_session, string const &table_name)

void	check_statement_sanity (string sql)

void	insert_or_ignore (string table_name, std::vector< string > column_names, std::vector< string > values, sessionOP db_session)

void	write_schema_to_database (string schema_str, sessionOP db_session)

void	set_cache_size (sessionOP db_session, Size cache_size)

std::string	make_compound_statement (std::string const &table_name, std::vector< std::string > const &column_names, platform::Size const &row_count)

utility::sql_database::sessionOP	parse_database_connection (utility::tag::TagCOP tag)

utility::sql_database::sessionOP	get_db_session (std::string const &db_name, utility::sql_database::TransactionMode::e transaction_mode, platform::Size chunk_size, std::string const &pq_schema="")
	Aquire a database session using the command line parameters For postgres databases, the pq_schema acts like a namespace in the database. More...

utility::sql_database::sessionOP	get_db_session (utility::sql_database::DatabaseMode::e db_mode, utility::sql_database::TransactionMode::e transaction_mode, platform::Size chunk_size, std::string const &db_name, std::string const &pq_schema="")
	Aquire a database session using the command line parameters For postgres databases, the pq_schema acts like a namespace in the database. More...

cppdb::statement	safely_prepare_statement (std::string const &statement_string, utility::sql_database::sessionOP db_session)

void	safely_write_to_database (cppdb::statement &statement)

cppdb::result	safely_read_from_database (cppdb::statement &statement)

void	insert_or_ignore (std::string table_name, std::vector< std::string > column_names, std::vector< std::string > values, utility::sql_database::sessionOP db_session)

bool	table_exists (utility::sql_database::sessionOP db_session, std::string const &table_name)

void	set_cache_size (utility::sql_database::sessionOP db_session, platform::Size cache_size)
	set the number of 1kb pages to use for cache More...

void	write_schema_to_database (std::string schema, utility::sql_database::sessionOP db_session)

Typedef Documentation

typedef utility::pointer::shared_ptr< DatabaseSessionLoader const > basic::database::DatabaseSessionLoaderCOP

typedef utility::pointer::shared_ptr< DatabaseSessionLoader > basic::database::DatabaseSessionLoaderOP

typedef utility::pointer::shared_ptr< DatabaseSessionOptions const > basic::database::DatabaseSessionOptionsCOP

typedef utility::pointer::shared_ptr< DatabaseSessionOptions > basic::database::DatabaseSessionOptionsOP

Function Documentation

void basic::database::check_statement_sanity ( string sql )

References utility_exit_with_message.

Referenced by basic::resource_manager::locator::DatabaseResourceLocator::parse_my_tag().

platform::SSize basic::database::db_partition_from_options ( DatabaseMode::e db_mode )

@

Returns partition identifer if in partitioned database mode, otherwise -1.

References utility::sql_database::DatabaseMode::mysql, option, options, utility::sql_database::DatabaseMode::postgres, resolve_db_partition(), utility::sql_database::DatabaseMode::sqlite3, utility::options::OptionKeys::options::user, and utility_exit_with_message.

Referenced by get_db_session().

std::string basic::database::full_name	(	std::string const &	db_file,
		bool	warn
	)

Full-path database file name.

References utility::file::file_exists(), name, option, options, and basic::Warning().

Referenced by open().

utility::sql_database::sessionOP basic::database::get_db_session	(	std::string const &	db_name,
		utility::sql_database::TransactionMode::e	transaction_mode,
		platform::Size	chunk_size,
		std::string const &	pq_schema = `""`
	)

Aquire a database session using the command line parameters For postgres databases, the pq_schema acts like a namespace in the database.

utility::sql_database::sessionOP basic::database::get_db_session	(	utility::sql_database::DatabaseMode::e	db_mode,
		utility::sql_database::TransactionMode::e	transaction_mode,
		platform::Size	chunk_size,
		std::string const &	db_name,
		std::string const &	pq_schema = `""`
	)

Aquire a database session using the command line parameters For postgres databases, the pq_schema acts like a namespace in the database.

utility::sql_database::sessionOP basic::database::get_db_session ( )

Aquire a database session using the command line options transaction type is set to standard.

References get_db_session(), option, options, and utility::sql_database::TransactionMode::standard.

utility::sql_database::sessionOP basic::database::get_db_session	(	string const &	db_name,
		string const &	pq_schema
	)

Aquire a database session using the command line parameters For postgres databases, the pq_schema acts like a namespace in the database. Transaction type set to standard.

References utility::sql_database::database_mode_from_name(), get_db_session(), option, options, and utility::sql_database::TransactionMode::standard.

sessionOP basic::database::get_db_session	(	string const &	db_name,
		TransactionMode::e	transaction_mode,
		Size	chunk_size,
		string const &	pq_schema
	)

References utility::sql_database::database_mode_from_name(), get_db_session(), option, and options.

utility::sql_database::sessionOP basic::database::get_db_session	(	utility::sql_database::DatabaseMode::e	db_mode,
		std::string const &	db_name,
		std::string const &	pq_schema
	)

References get_db_session(), and utility::sql_database::TransactionMode::standard.

sessionOP basic::database::get_db_session	(	DatabaseMode::e	db_mode,
		TransactionMode::e	transaction_mode,
		Size	chunk_size,
		string const &	db_name,
		string const &	pq_schema
	)

Referenced by get_db_session().

void basic::database::insert_or_ignore	(	std::string	table_name,
		std::vector< std::string >	column_names,
		std::vector< std::string >	values,
		utility::sql_database::sessionOP	db_session
	)

void basic::database::insert_or_ignore	(	string	table_name,
		std::vector< string >	column_names,
		std::vector< string >	values,
		sessionOP	db_session
	)

References utility::sql_database::DatabaseMode::mysql, utility::sql_database::name_from_database_mode(), utility::sql_database::DatabaseMode::postgres, safely_prepare_statement(), safely_read_from_database(), safely_write_to_database(), utility::sql_database::DatabaseMode::sqlite3, and utility_exit_with_message.

std::string basic::database::make_compound_statement	(	std::string const &	table_name,
		std::vector< std::string > const &	column_names,
		platform::Size const &	row_count
	)

References utility::join().

Referenced by basic::database::insert_statement_generator::InsertGenerator::write_to_database(), basic::database::insert_statement_generator::InsertGenerator::write_to_database_chunked(), and basic::database::insert_statement_generator::InsertGenerator::write_to_database_sequential().

bool basic::database::open	(	utility::io::izstream &	db_stream,
		std::string const &	db_file,
		bool	warn = `true`
	)

Open a database file on a provided stream.

Does a database file exist?

Open a database file on a provided stream

References utility::io::izstream::clear(), utility::io::izstream::close(), full_name(), utility::io::izstream::good(), utility::io::izstream::open(), and TR().

Referenced by options.KeepSameFile::close(), and basic::sampling::orientations::QuaternionGridManager::request_by_name().

utility::sql_database::sessionOP basic::database::parse_database_connection ( utility::tag::TagCOP tag )

build database connection from options in a tag, this is useful make sure the fields for constructing a database connection are consistent across different tags.

Referenced by basic::database::DatabaseSessionOptions::parse_my_tag().

platform::SSize basic::database::resolve_db_partition	(	bool	partition_by_mpi_process,
		platform::SSize	manual_partition
	)

Returns partition identifer from mpi rank if in partitioned database mode, or valid manual partition, otherwise -1.

References utility::mpi_rank().

Referenced by db_partition_from_options(), and parse_database_connection().

cppdb::statement basic::database::safely_prepare_statement	(	std::string const &	statement_string,
		utility::sql_database::sessionOP	db_session
	)

statement basic::database::safely_prepare_statement	(	string const &	statement_string,
		sessionOP	db_session
	)

References basic::Tracer::Error, TR(), and utility_exit_with_message.

Referenced by insert_or_ignore(), basic::resource_manager::locator::DatabaseResourceLocator::locate_resource_stream(), set_cache_size(), table_exists(), basic::database::insert_statement_generator::InsertGenerator::write_to_database(), basic::database::insert_statement_generator::InsertGenerator::write_to_database_chunked(), and basic::database::insert_statement_generator::InsertGenerator::write_to_database_sequential().

cppdb::result basic::database::safely_read_from_database ( cppdb::statement & statement )

result basic::database::safely_read_from_database ( statement & statement )

References option, options, numeric::random::rg(), TR(), numeric::random::uniform(), and utility_exit_with_message.

Referenced by insert_or_ignore(), and basic::resource_manager::locator::DatabaseResourceLocator::locate_resource_stream().

void basic::database::safely_write_to_database ( cppdb::statement & statement )

void basic::database::safely_write_to_database ( statement & statement )

References utility_exit_with_message.

Referenced by insert_or_ignore(), set_cache_size(), write_schema_to_database(), basic::database::insert_statement_generator::InsertGenerator::write_to_database(), basic::database::insert_statement_generator::InsertGenerator::write_to_database_chunked(), and basic::database::insert_statement_generator::InsertGenerator::write_to_database_sequential().

void basic::database::set_cache_size	(	utility::sql_database::sessionOP	db_session,
		platform::Size	cache_size
	)

set the number of 1kb pages to use for cache

void basic::database::set_cache_size	(	sessionOP	db_session,
		Size	cache_size
	)

References utility::sql_database::name_from_database_mode(), safely_prepare_statement(), safely_write_to_database(), utility::sql_database::DatabaseMode::sqlite3, and TR().

bool basic::database::table_exists	(	utility::sql_database::sessionOP	db_session,
		std::string const &	table_name
	)

bool basic::database::table_exists	(	sessionOP	db_session,
		string const &	table_name
	)

References utility::sql_database::DatabaseMode::mysql, utility::sql_database::DatabaseMode::postgres, safely_prepare_statement(), utility::sql_database::DatabaseMode::sqlite3, and utility_exit_with_message.

Referenced by basic::database::schema_generator::Schema::check_table_and_perform_write().

static thread_local basic::Tracer basic::database::TR ( "basic.io.database" )

static

Referenced by open().

static thread_local basic::Tracer basic::database::TR ( "basic.database.sql_utils" )

static

Referenced by get_db_session(), parse_database_connection(), safely_prepare_statement(), safely_read_from_database(), set_cache_size(), and write_schema_to_database().

void basic::database::write_schema_to_database	(	std::string	schema,
		utility::sql_database::sessionOP	db_session
	)

void basic::database::write_schema_to_database	(	string	schema_str,
		sessionOP	db_session
	)

References basic::Tracer::Error, safely_write_to_database(), TR(), utility::trim(), and utility_exit.

Namespaces

Classes

Typedefs

Functions

Typedef Documentation

Function Documentation