Graph manipulation in SQL databases utilities. More...

#include <aims/graph/qsqlgraphdatabase.h>

Collaboration diagram for aims::QSqlGraphDatabase:

[legend]

Classes
struct	CurrentGraphData
	This structure stores information needed to help and speed-up graph queries in SQL databases. More...

Public Types
typedef std::map< std::string, std::map< std::string, std::vector< std::string > > >	Syntax

Public Member Functions
	QSqlGraphDatabase ()

	~QSqlGraphDatabase ()

void	setUrl (const std::string &url, carto::Object header=carto::none())
	Set the database address, and parse it. More...

bool	open ()
	Actually open the database connection. More...

bool	open (const std::string &user, const std::string &password)

void	close ()
	Close the connection. After this call, queries cannot be done. More...

QSqlQuery	exec (const std::string &query) const
	Shortcut to the Qt QSqlDatabase exec() query for SQL code. More...

QSqlError	lastError () const
	Shortcut to the Qt QSqlDatabase lastError() call for SQL code. More...

std::string	hostname () const
	Address of the database (may be a local file for SQLite) More...

QSqlDatabase &	database () const
	Qt database. More...

carto::Object	header ()
	The header stores information about how to open the database, and possibly an initial selection query, to restrict to a given single graph, especially for Reader<Graph> operations. More...

carto::Object	parsedUrl ()
	Decomposed URL. More...

void	setHeader (carto::Object hdr)

bool	readSchema ()
	Read the database schema (or syntax) from the SQL database. More...

void	sqlAttributes (const GraphObject &el, std::map< std::string, std::string > &atts, bool addinherited=true, const std::string &assyntax=std::string()) const
	Build an attributes/value list from a graph element according to the database schema, in a SQL-compatible way. More...

void	sqlAttributesAsStrings (const GraphObject &el, std::string &names, std::string &values, bool first=true, bool addinherited=true) const
	Same as sqlAttributes but fills two strings for attributes names and values, as needed for SQL insert queries. More...

void	insertOrUpdateVertex (Vertex *vert, CurrentGraphData &data)
	Store a graph vertex into the database, or updates it if it already exists. More...

void	insertOrUpdateEdge (Edge *v, CurrentGraphData &data)
	Store a graph edge into the database, or updates it if it already exists. More...

std::list< carto::rc_ptr< Graph > >	partialReadFromVertexQuery (const std::string &sqlquery, std::list< CurrentGraphData > &graphsinfo, bool allownewgraphs=true)
	Reads information from a given SQL selection query, and fills graph/vertices information from it. More...

std::list< carto::rc_ptr< Graph > >	partialReadFromEdgeQuery (const std::string &sqlquery, std::list< CurrentGraphData > &graphsinfo, bool allownewgraphs=true)
	Reads information from a given SQL selection query, and fills edge information from it. More...

void	updateElement (const GraphObject &el, int eid)
	Store in the database the attributes of an existing element (graph, vertex or edge) More...

void	fillGraphData (CurrentGraphData &data, Graph &g, int geid=-1)
	Fills the CurrentGraphData structure using database information (performs appropriate queries) More...

void	updateVertexIndexMap (CurrentGraphData &data)
	Fills the CurrentGraphData vertexindex2eid map. More...

void	updateEdgeIndexMap (CurrentGraphData &data)
	Fills the CurrentGraphData edgeindex2eid map. More...

void	updateVertexMap (CurrentGraphData &data)
	Fills the CurrentGraphData vertexeid map. More...

void	updateEdgeMap (CurrentGraphData &data)
	Fills the CurrentGraphData edgeeid map. More...

void	readElementAttributes (GraphObject &, const std::list< std::string > &attributes, QSqlQuery &query, int eid)
	Set the element attributes contained in the query result. More...

void	readElementAttributes (GraphObject &item, const std::list< std::string > &attributes, const std::vector< QVariant > &query, int i)
	Set the element attributes contained in the query result, but read from an already filled vector of QVariant instrad of directly the SQL query result. More...

void	readElementAttributes (GraphObject &item, QSqlQuery &query, const std::map< std::string, std::vector< std::string > > &vatts, int i)
	read/set all the attributes of the given element, which must have all been queried in the attributes map order. More...

void	readGraphAttributes (Graph &g, int eid)

void	readGraphAttributes (std::list< CurrentGraphData > &graphsinfo)

Public Attributes
carto::rc_ptr< Syntax >	attributesSyntax
	Database schema syntax: supported attributes (database columns) for each element type. More...

std::map< std::string, std::list< std::string > >	syntaxInheritance
	Database schema syntax: elements types inheritance. More...

Detailed Description

Graph manipulation in SQL databases utilities.

A QSqlGraphDatabase instance stores the database connection, and caches several needed information on the database, amongst which the database schema (elements inheritance and attributes).

It is useful to facilitate IO for graphs in SQL databases. It is used by Reader<Graph> and Writer<Graph> for database formats. It can also be used to perform partial reading on multiple graphs:

(the example is in python language, it is just a bit clearer)

from soma import aims
from soma.aims import aimsgui
 
db = aims.QSqlGraphDatabase()
db.setUrl( '/tmp/morphee2.sqlite' )
db.open()
db.readSchema()
lg = aims.aimsguisip.list_CurrentGraphData()
ng = db.partialReadFromVertexQuery( 'SELECT fold.eid, fold.graph, ' \
  'fold.graph_index, fold.name, fold.label, class.class_name FROM fold ' \
  'JOIN class ON class.eid=fold.eid WHERE fold.name=\'ventricle_left\'',
  lg )

Definition at line 73 of file qsqlgraphdatabase.h.

Member Typedef Documentation

◆ Syntax

typedef std::map<std::string, std::map<std::string, std::vector<std::string> > > aims::QSqlGraphDatabase::Syntax

Definition at line 77 of file qsqlgraphdatabase.h.

Constructor & Destructor Documentation

◆ QSqlGraphDatabase()

aims::QSqlGraphDatabase::QSqlGraphDatabase ( )

◆ ~QSqlGraphDatabase()

aims::QSqlGraphDatabase::~QSqlGraphDatabase ( )

Member Function Documentation

◆ close()

void aims::QSqlGraphDatabase::close ( )

Close the connection. After this call, queries cannot be done.

◆ database()

QSqlDatabase & aims::QSqlGraphDatabase::database ( ) const

inline

Qt database.

Definition at line 302 of file qsqlgraphdatabase.h.

Referenced by exec(), and lastError().

◆ exec()

QSqlQuery aims::QSqlGraphDatabase::exec ( const std::string & query ) const

inline

Shortcut to the Qt QSqlDatabase exec() query for SQL code.

Definition at line 326 of file qsqlgraphdatabase.h.

References database().

◆ fillGraphData()

void aims::QSqlGraphDatabase::fillGraphData	(	CurrentGraphData &	data,
		Graph &	g,
		int	geid = `-1`
	)

Fills the CurrentGraphData structure using database information (performs appropriate queries)

◆ header()

carto::Object aims::QSqlGraphDatabase::header ( )

inline

The header stores information about how to open the database, and possibly an initial selection query, to restrict to a given single graph, especially for Reader<Graph> operations.

Definition at line 308 of file qsqlgraphdatabase.h.

◆ hostname()

std::string aims::QSqlGraphDatabase::hostname ( ) const

inline

Address of the database (may be a local file for SQLite)

Definition at line 320 of file qsqlgraphdatabase.h.

◆ insertOrUpdateEdge()

void aims::QSqlGraphDatabase::insertOrUpdateEdge	(	Edge *	v,
		CurrentGraphData &	data
	)

Store a graph edge into the database, or updates it if it already exists.

◆ insertOrUpdateVertex()

void aims::QSqlGraphDatabase::insertOrUpdateVertex	(	Vertex *	vert,
		CurrentGraphData &	data
	)

Store a graph vertex into the database, or updates it if it already exists.

◆ lastError()

QSqlError aims::QSqlGraphDatabase::lastError ( ) const

inline

Shortcut to the Qt QSqlDatabase lastError() call for SQL code.

Definition at line 332 of file qsqlgraphdatabase.h.

References database().

◆ open() [1/2]

bool aims::QSqlGraphDatabase::open ( )

Actually open the database connection.

◆ open() [2/2]

bool aims::QSqlGraphDatabase::open	(	const std::string &	user,
		const std::string &	password
	)

◆ parsedUrl()

carto::Object aims::QSqlGraphDatabase::parsedUrl ( )

inline

Decomposed URL.

Definition at line 314 of file qsqlgraphdatabase.h.

◆ partialReadFromEdgeQuery()

std::list<carto::rc_ptr<Graph> > aims::QSqlGraphDatabase::partialReadFromEdgeQuery	(	const std::string &	sqlquery,
		std::list< CurrentGraphData > &	graphsinfo,
		bool	allownewgraphs = `true`
	)

Reads information from a given SQL selection query, and fills edge information from it.

The SQL query is executed as is, and must include eid, vertex1 and vertex2 from edges.

It is also strongly advised to also get the class_name column from the class table (via a JOIN in the SQL query) because it avoids individual queries for it in each edge, and if possible the graph eid (via a JOIN on the vertices in ths SQL query).

Referenced graphs /vertices are queried and added to the CurrentGraphData list if allownewgraphs is true, otherwise edges belonging to an "unknown" graph are dropped.

Returns: a list of new graphs which have been allocated if allownewgraphs is true. New graphs must be deleted when not needed any longer.

for instance:

// graphs will be queried separately
ng = db.partialReadFromEdgeQuery( 'SELECT cortical.eid,
cortical.vertex1, cortical.vertex2, cortical.size, class.class_name FROM
cortical JOIN class ON class.eid=cortical.eid WHERE cortical.size > 50',
lg )
 
// here graph info is part of the same query
ng = db.partialReadFromEdgeQuery( 'SELECT cortical.eid,
cortical.vertex1, cortical.vertex2, cortical.size, class.class_name,
_Vertex.graph FROM cortical JOIN class, _Vertex ON
class.eid=cortical.eid AND _Vertex.eid=cortical.vertex1 WHERE
cortical.size > 50', lg )

◆ partialReadFromVertexQuery()

std::list<carto::rc_ptr<Graph> > aims::QSqlGraphDatabase::partialReadFromVertexQuery	(	const std::string &	sqlquery,
		std::list< CurrentGraphData > &	graphsinfo,
		bool	allownewgraphs = `true`
	)

Reads information from a given SQL selection query, and fills graph/vertices information from it.

The SQL query is executed as is, and must include eid and graph columns from vertices.

It is also strongly advised to also get the class_name column from the class table (via a JOIN in the SQL query) because it avoids individual queries for it in each vertex.

Referenced graphs are queried and added to the CurrentGraphData list if allownewgraphs is true, otherwise vertices belonging to an "unknown" graph are dropped.

Returns: a list of new graphs which have been allocated if allownewgraphs is true. New graphs must be deleted when not needed any longer.

for instance:

// classes will be queried separately
ng = db.partialReadFromVertexQuery( 'SELECT fold.eid, fold.graph,
  fold.graph_index, fold.name, fold.label, class.class_name FROM fold
  JOIN class ON class.eid=fold.eid WHERE fold.name=\'ventricle_left\'',
  lg );
 
// here classes are part of the same query, which will avoid
// additional queries
ng = db.partialReadFromVertexQuery( 'SELECT fold.eid, fold.graph,
  fold.graph_index, fold.name, fold.label, class.class_name FROM fold
  JOIN class ON class.eid=fold.eid', lg );

◆ readElementAttributes() [1/3]

void aims::QSqlGraphDatabase::readElementAttributes	(	GraphObject &	,
		const std::list< std::string > &	attributes,
		QSqlQuery &	query,
		int	eid
	)

Set the element attributes contained in the query result.

◆ readElementAttributes() [2/3]

void aims::QSqlGraphDatabase::readElementAttributes	(	GraphObject &	item,
		const std::list< std::string > &	attributes,
		const std::vector< QVariant > &	query,
		int	i
	)

Set the element attributes contained in the query result, but read from an already filled vector of QVariant instrad of directly the SQL query result.

◆ readElementAttributes() [3/3]

void aims::QSqlGraphDatabase::readElementAttributes	(	GraphObject &	item,
		QSqlQuery &	query,
		const std::map< std::string, std::vector< std::string > > &	vatts,
		int	i
	)

read/set all the attributes of the given element, which must have all been queried in the attributes map order.

Parameters

i	is the index in the query of the first attribute

◆ readGraphAttributes() [1/2]

void aims::QSqlGraphDatabase::readGraphAttributes	(	Graph &	g,
		int	eid
	)

◆ readGraphAttributes() [2/2]

void aims::QSqlGraphDatabase::readGraphAttributes ( std::list< CurrentGraphData > & graphsinfo )

◆ readSchema()

bool aims::QSqlGraphDatabase::readSchema ( )

Read the database schema (or syntax) from the SQL database.

This fills the attributesSyntax and syntaxInheritance fields.

◆ setHeader()

void aims::QSqlGraphDatabase::setHeader ( carto::Object hdr )

◆ setUrl()

void aims::QSqlGraphDatabase::setUrl	(	const std::string &	url,
		carto::Object	header = `carto::none()`
	)

Set the database address, and parse it.

Or it can be already parsed in an Object. Only after using this method, hostname(), header(), parsedUrl() and open() methods may be used.

The url may contain an initial selection query, to restrict to a given single graph, especially for Reader<Graph> operations.

db.setUrl( "/home/totor/mysqlgraphs.sqlite?Graph.uuid="

"'259049f8-e93c-095d-064f-fad19a73dc0a'" );

◆ sqlAttributes()

void aims::QSqlGraphDatabase::sqlAttributes	(	const GraphObject &	el,
		std::map< std::string, std::string > &	atts,
		bool	addinherited = `true`,
		const std::string &	assyntax = `std::string()`
	)		const

Build an attributes/value list from a graph element according to the database schema, in a SQL-compatible way.

◆ sqlAttributesAsStrings()

void aims::QSqlGraphDatabase::sqlAttributesAsStrings	(	const GraphObject &	el,
		std::string &	names,
		std::string &	values,
		bool	first = `true`,
		bool	addinherited = `true`
	)		const

Same as sqlAttributes but fills two strings for attributes names and values, as needed for SQL insert queries.

◆ updateEdgeIndexMap()

void aims::QSqlGraphDatabase::updateEdgeIndexMap ( CurrentGraphData & data )

Fills the CurrentGraphData edgeindex2eid map.

◆ updateEdgeMap()

void aims::QSqlGraphDatabase::updateEdgeMap ( CurrentGraphData & data )

Fills the CurrentGraphData edgeeid map.

◆ updateElement()

void aims::QSqlGraphDatabase::updateElement	(	const GraphObject &	el,
		int	eid
	)

Store in the database the attributes of an existing element (graph, vertex or edge)

◆ updateVertexIndexMap()

void aims::QSqlGraphDatabase::updateVertexIndexMap ( CurrentGraphData & data )

Fills the CurrentGraphData vertexindex2eid map.

◆ updateVertexMap()

void aims::QSqlGraphDatabase::updateVertexMap ( CurrentGraphData & data )

Fills the CurrentGraphData vertexeid map.

Member Data Documentation

◆ attributesSyntax

carto::rc_ptr<Syntax> aims::QSqlGraphDatabase::attributesSyntax

Database schema syntax: supported attributes (database columns) for each element type.

Definition at line 285 of file qsqlgraphdatabase.h.

◆ syntaxInheritance

std::map<std::string, std::list<std::string> > aims::QSqlGraphDatabase::syntaxInheritance

Database schema syntax: elements types inheritance.

Definition at line 287 of file qsqlgraphdatabase.h.

The documentation for this class was generated from the following file:

aims/graph/qsqlgraphdatabase.h

Classes

Public Types

Public Member Functions

Public Attributes

Detailed Description

Member Typedef Documentation

◆ Syntax

Constructor & Destructor Documentation

◆ QSqlGraphDatabase()

◆ ~QSqlGraphDatabase()

Member Function Documentation

◆ close()

◆ database()

◆ exec()

◆ fillGraphData()

◆ header()

◆ hostname()

◆ insertOrUpdateEdge()

◆ insertOrUpdateVertex()

◆ lastError()

◆ open() [1/2]

◆ open() [2/2]

◆ parsedUrl()

◆ partialReadFromEdgeQuery()

◆ partialReadFromVertexQuery()

◆ readElementAttributes() [1/3]

◆ readElementAttributes() [2/3]

◆ readElementAttributes() [3/3]

◆ readGraphAttributes() [1/2]

◆ readGraphAttributes() [2/2]

◆ readSchema()

◆ setHeader()

◆ setUrl()

◆ sqlAttributes()

◆ sqlAttributesAsStrings()

◆ updateEdgeIndexMap()

◆ updateEdgeMap()

◆ updateElement()

◆ updateVertexIndexMap()

◆ updateVertexMap()

Member Data Documentation

◆ attributesSyntax

◆ syntaxInheritance