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basic::database Namespace Reference

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...
 
bool find_cache_file (std::string const &cache_file, bool dir_only)
 Does cache file (absolute path) exist? if dir_only is true, will return true if the cache file could be created. More...
 
std::string full_cache_name (std::string const &short_name, std::string const &source_file, bool for_writing)
 Get the (absolute) path to a given cached file. If source_file is given, it's the full path to the source database file that's being cached. If for_writing is true, will only check that the given file would be creatable. Will return an empty string if it can't find a cache file. 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

Definition at line 24 of file DatabaseSessionLoader.fwd.hh.

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

Definition at line 22 of file DatabaseSessionLoader.fwd.hh.

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

Definition at line 25 of file DatabaseSessionOptions.fwd.hh.

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

Definition at line 23 of file DatabaseSessionOptions.fwd.hh.

Function Documentation

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

Definition at line 522 of file sql_utils.cc.

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.

Definition at line 269 of file sql_utils.cc.

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().

bool basic::database::find_cache_file ( std::string const &  cache_file,
bool  dir_only 
)

Does cache file (absolute path) exist? if dir_only is true, will return true if the cache file could be created.

Definition at line 116 of file open.cc.

References utility::file::create_directory_recursive(), utility::file::create_temp_filename(), basic::Tracer::Debug, utility::file::file_delete(), utility::file::file_exists(), utility::file::FileName::path(), TR(), and basic::Tracer::TracerProxy::visible().

Referenced by full_cache_name().

std::string basic::database::full_cache_name ( std::string const &  short_name,
std::string const &  source_file,
bool  for_writing 
)

Get the (absolute) path to a given cached file. If source_file is given, it's the full path to the source database file that's being cached. If for_writing is true, will only check that the given file would be creatable. Will return an empty string if it can't find a cache file.

Definition at line 151 of file open.cc.

References utility::file::FileName::bare_name(), find_cache_file(), option, options, app.surface_docking.surface_docking::path, utility::file::FileName::path(), and utility::options::OptionKeys::options::user.

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

Full-path database file name.

Definition at line 95 of file open.cc.

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

Referenced by make_scorefxn(), and 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.

Definition at line 88 of file sql_utils.cc.

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

Referenced by DatabaseIOBenchmark::setUp().

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.

Definition at line 101 of file sql_utils.cc.

References utility::sql_database::database_mode_from_name(), get_db_session(), contacts::mode, 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 
)

Definition at line 117 of file sql_utils.cc.

References utility::sql_database::database_mode_from_name(), get_db_session(), contacts::mode, 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 
)

Definition at line 135 of file sql_utils.cc.

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 
)

Definition at line 149 of file sql_utils.cc.

References db_partition_from_options(), utility::sql_database::DatabaseSessionManager::get_instance(), utility::sql_database::DatabaseSessionManager::get_session_mysql(), utility::sql_database::DatabaseSessionManager::get_session_postgres(), utility::sql_database::DatabaseSessionManager::get_session_sqlite3(), utility::sql_database::DatabaseMode::mysql, utility::sql_database::name_from_database_mode(), option, options, utility::sql_database::DatabaseMode::postgres, utility::sql_database::DatabaseMode::sqlite3, TR(), utility::options::OptionKeys::options::user, utility_exit_with_message, and basic::Tracer::Warning.

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 
)

Definition at line 542 of file sql_utils.cc.

References utility::sql_database::DatabaseMode::mysql, utility::sql_database::name_from_database_mode(), utility::sql_database::DatabaseMode::postgres, app.delta_score_per_mutation::res, 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 
)

Definition at line 706 of file sql_utils.cc.

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

Definition at line 55 of file open.cc.

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

Referenced by tools.DoxygenExtractorPyPP.doxygen_doc_extractor::__call__(), toolbox.load_ligand::add_cid_to_database(), loadPDB::addasa(), app.surface_docking.append_data::append_constraints(), app.surface_docking.append_data::append_hbonds(), app.surface_docking.append_data::append_rmsd(), app.surface_docking.append_data::append_scores(), BuildBindings::buildModule_All(), app.pyrosetta_toolkit.window_modules.ligand_ncaa_ptm_manager.ligand_ncaa_ptm_manager.Properties::check_if_on_by_default(), toolbox.cleaning::cleanATOM(), toolbox::cleanATOM(), options.KeepSameFile::close(), compare_times::compare_times(), ContactMap::ContactMap(), app.pyrosetta_toolkit.modules.tools.output::convert_PDBLIST_to_sqlite3db(), app.pyrosetta_toolkit.modules.ScoreAnalysis.ScoreAnalysis::copy_results(), app.pyrosetta_toolkit.modules.ScoreAnalysis.ScoreAnalysis::copy_results2(), app.pyrosetta_toolkit.modules.tools.output::extract_pdbs_from_sqlite3db(), fcn(), app.pyrosetta_toolkit.window_main.IO.GUIInput.GUIInput::fetch_pdb(), exclude::finalize(), exclude::finalize2(), exclude::finalize_old(), loadPDB::generate_one_model(), toolbox.generate_resfile::generate_resfile_from_pose(), toolbox::generate_resfile_from_pose(), demo.D050_Packer_task::generate_resfile_from_pose(), BuildPackagedBindings.ModuleBuilder::generateBindings(), tools.dox_extract.dox_extract::getDoxygenComment(), app.pyrosetta_toolkit.window_modules.scorefunction.ScoreFxnControl.ScoreFxnControl::getRefs(), IO::load(), app.surface_docking.surf_param::load(), PhiPsi::load(), app.surface_docking.constraints::load_constraints(), toolbox.rcsb::load_fasta_from_rcsb(), compare_times::load_files(), toolbox.load_ligand::load_from_pubchem(), toolbox.rcsb::load_from_rcsb(), toolbox::load_from_rcsb(), app.pyrosetta_toolkit.window_main.IO.GUIInput.GUIInput::load_loop(), app.pyrosetta_toolkit.window_main.IO.GUIInput.GUIInput::load_param_list(), app.pyrosetta_toolkit.window_main.IO.SessionIO.SessionIO::load_params(), load_range(), app.pyrosetta_toolkit.modules.DesignBreakdown.DesignBreakdown::load_sequences(), app.pyrosetta_toolkit.window_main.IO.SessionIO.SessionIO::load_session(), app.pyrosetta_toolkit.window_modules.options_system.OptionSystemManager.OptionSystemManager::load_settings(), loadPDB::loadProt(), best_ifaceE::main(), get_scores::main(), prune_atdiff_top5pct::main(), PlotSurfaceContactMap::MAIN(), make_amb_constr::main(), sidechain_cst_3::main(), PhiPsi::MAIN(), arls_impl::main(), app.surface_docking.constraints::make_ads_disulf(), app.pyrosetta_toolkit.modules.tools.output::make_PDBLIST(), app.pyrosetta_toolkit.modules.tools.output::make_PDBLIST_recursively(), app.pyrosetta_toolkit.modules.DesignBreakdown.DesignBreakdown::output_basic_table(), app.pyrosetta_toolkit.modules.DesignBreakdown.DesignBreakdown::output_prettytable(), src::output_scorefile(), calccontacts.contactProtein::outputMap(), calccontacts.contactProtein::outputProfile(), extract_scores_and_constraints::parse(), ObjexxFCL::process_file(), app.pyrosetta_toolkit.modules.ScoreAnalysis.ScoreAnalysis::read_FASC(), app.pyrosetta_toolkit.modules.PythonPDB.PythonPDB::read_file_and_replace_b_factors(), app.pyrosetta_toolkit.modules.SQLPDB.SQLPDB::read_pdb_into_database_flat(), app.pyrosetta_toolkit.modules.PythonPDB.PythonPDB::read_pdb_into_map(), app.pyrosetta_toolkit.modules.ScoreAnalysis.ScoreAnalysis::read_PDBList(), app.pyrosetta_toolkit.window_modules.ligand_ncaa_ptm_manager.ligand_ncaa_ptm_manager.Properties::read_properties(), app.pyrosetta_toolkit.modules.ScoreAnalysis.ScoreAnalysis::read_SC(), app.pyrosetta_toolkit.modules.tools.analysis::readFASC(), basic::sampling::orientations::QuaternionGridManager::request_by_name(), app.pyrosetta_toolkit.window_modules.clean_pdb.FixPDBWindow.FixPDBWindow::runFixPDB(), app.pyrosetta_toolkit.modules.tools.output::save_basic_blueprint(), app.pyrosetta_toolkit.modules.SQLPDB.PDB_database::save_cur_as_pdb(), app.pyrosetta_toolkit.modules.tools.output::save_FASTA(), app.pyrosetta_toolkit.modules.tools.output::save_FASTA_PDBLIST(), app.pyrosetta_toolkit.modules.tools.output::save_loop_file(), app.pyrosetta_toolkit.modules.tools.output::save_param_path_list(), app.pyrosetta_toolkit.modules.PythonPDB.PythonPDB::save_PDB(), app.pyrosetta_toolkit.modules.tools.output::save_resfile_w_designdic(), app.pyrosetta_toolkit.window_main.IO.SessionIO.SessionIO::save_session(), app.pyrosetta_toolkit.window_modules.options_system.OptionSystemManager.OptionSystemManager::save_settings(), app.pyrosetta_toolkit.window_modules.scorefunction.ScoreFxnControl.ScoreFxnControl::saveAS(), app.pyrosetta_toolkit.window_modules.scorefunction.ScoreFxnControl.ScoreFxnControl::saveDefaults(), app.pyrosetta_toolkit.modules.tools.output::saveSeqFile(), app.pyrosetta_toolkit.window_modules.scorefunction.ScoreFxnControl.ScoreFxnControl::saveToWD(), demo.D090_Ala_scan::scanning(), demo.D090_Ala_scan::scanning_analysis(), app.pyrosetta_toolkit.modules.tools.output::score_PDBLIST(), src.PyJobDistributor::start_decoy(), arls_impl::write_if_not_exists(), app.pyrosetta_toolkit.modules.ScoreAnalysis.ScoreAnalysis::write_score_vs_rmsd_to_txt(), and loadPDB::writeToPDB().

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.

Definition at line 733 of file sql_utils.cc.

References utility::options::OptionKeys::options::all, utility::sql_database::TransactionMode::chunk, utility::sql_database::database_mode_from_name(), utility::sql_database::DatabaseSessionManager::get_db_session(), utility::sql_database::DatabaseSessionManager::get_instance(), contacts::mode, utility::sql_database::DatabaseMode::mysql, utility::sql_database::name_from_database_mode(), utility::sql_database::name_from_transaction_mode(), utility::sql_database::TransactionMode::none, option, options, app.surface_docking.surface_docking::path, utility::sql_database::DatabaseMode::postgres, resolve_db_partition(), utility::sql_database::DatabaseMode::sqlite3, utility::sql_database::TransactionMode::standard, TR(), utility::sql_database::transaction_mode_from_name(), utility::options::OptionKeys::options::user, and utility_exit_with_message.

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.

Definition at line 314 of file sql_utils.cc.

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 
)

Definition at line 333 of file sql_utils.cc.

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)

Definition at line 418 of file sql_utils.cc.

References option, options, numeric::random::rg(), BuildBindings::Sleep(), 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)

Definition at line 354 of file sql_utils.cc.

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 
)

Definition at line 688 of file sql_utils.cc.

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 
)

Definition at line 473 of file sql_utils.cc.

References utility::sql_database::DatabaseMode::mysql, utility::sql_database::DatabaseMode::postgres, app.delta_score_per_mutation::res, 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 find_cache_file(), and 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 
)

Definition at line 663 of file sql_utils.cc.

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

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