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/* @source ensdatabaseconnection **********************************************
**
** Ensembl Database Connection functions
**
** @author Copyright (C) 1999 Ensembl Developers
** @author Copyright (C) 2006 Michael K. Schuster
** @version $Revision: 1.37 $
** @modified $Date: 2013/02/17 13:02:40 $ by $Author: mks $
** @modified $Date: 2013/02/17 13:02:40 $ by $Author: mks $
**
** This library is free software; you can redistribute it and/or
** modify it under the terms of the GNU Lesser General Public
** License as published by the Free Software Foundation; either
** version 2.1 of the License, or (at your option) any later version.
**
** This library is distributed in the hope that it will be useful,
** but WITHOUT ANY WARRANTY; without even the implied warranty of
** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
** Lesser General Public License for more details.
**
** You should have received a copy of the GNU Lesser General Public
** License along with this library; if not, write to the Free Software
** Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
** MA 02110-1301, USA.
**
******************************************************************************/
/* ========================================================================= */
/* ============================= include files ============================= */
/* ========================================================================= */
#include "ensdatabaseconnection.h"
/* ========================================================================= */
/* =============================== constants =============================== */
/* ========================================================================= */
/* ========================================================================= */
/* =========================== global variables ============================ */
/* ========================================================================= */
/* ========================================================================= */
/* ============================= private data ============================== */
/* ========================================================================= */
/* ========================================================================= */
/* =========================== private constants =========================== */
/* ========================================================================= */
/* ========================================================================= */
/* =========================== private variables =========================== */
/* ========================================================================= */
/* ========================================================================= */
/* =========================== private functions =========================== */
/* ========================================================================= */
/* ========================================================================= */
/* ======================= All functions by section ======================== */
/* ========================================================================= */
/* @filesection ensdatabaseconnection *****************************************
**
** @nam1rule ens Function belongs to the Ensembl library
**
******************************************************************************/
/* @datasection [EnsPDatabaseconnection] Ensembl Database Connection **********
**
** @nam2rule Databaseconnection Functions for manipulating
** Ensembl Database Connection objects
**
** @cc Bio::EnsEMBL::DBSQL::DBConnection
** @cc CVS Revision: 1.79
** @cc CVS Tag: branch-ensembl-68
**
** NOTE: The Perl API also supports the ORACLE, ODBC and Sybase SQL client
** libraries.
******************************************************************************/
/* @section constructors ******************************************************
**
** All constructors return a new Ensembl Database Connection by pointer.
** It is the responsibility of the user to first destroy any previous
** Database Connection. The target pointer does not need to be initialised to
** NULL, but it is good programming practice to do so anyway.
**
** @fdata [EnsPDatabaseconnection]
**
** @nam3rule New Constructor
** @nam4rule Cpy Constructor with existing object
** @nam4rule Ini Constructor with initial values
** @nam4rule Ref Constructor by incrementing the reference counter
** @nam4rule Url Constructor with a Uniform Resource Locator
**
** @argrule Cpy dbc [EnsPDatabaseconnection] Ensembl Database Connection
** @argrule Cpy database [AjPStr] SQL database name (optional)
** @argrule Ini client [AjESqlconnectionClient] AJAX SQL Connection client
** @argrule Ini user [AjPStr] User name
** @argrule Ini password [AjPStr] Password
** @argrule Ini host [AjPStr] Host name or IP address
** @argrule Ini port [AjPStr] Host TCP/IP port
** @argrule Ini socketfile [AjPStr] UNIX socket file
** @argrule Ini database [AjPStr] SQL database name
** @argrule Ini dbctimeout [ajuint]
** Timeout in seconds for idle, non-interactive connections
** @argrule Ref dbc [EnsPDatabaseconnection] Ensembl Database Connection
** @argrule Url url [const AjPStr] Uniform Resource Locator
**
** @valrule * [EnsPDatabaseconnection] Ensembl Database Connection or NULL
**
** @fcategory new
******************************************************************************/
/* @func ensDatabaseconnectionNewCpy ******************************************
**
** Construct an Ensembl Database Connection on an already existing connection.
** Optionally, a database name may be provided to connect to a different
** database on the same SQL server using the same SQL account information.
**
** @cc Bio::EnsEMBL::DBSQL::DBConnection::new
** @param [u] dbc [EnsPDatabaseconnection] Ensembl Database Connection
** @param [uN] database [AjPStr] SQL database name (optional)
**
** @return [EnsPDatabaseconnection] Ensembl Database Connection or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
EnsPDatabaseconnection ensDatabaseconnectionNewCpy(
EnsPDatabaseconnection dbc,
AjPStr database)
{
EnsPDatabaseconnection pthis = NULL;
if (!dbc)
return NULL;
if (ajDebugTest("ensDatabaseconnectionNewCpy"))
{
ajDebug("ensDatabaseconnectionNewCpy\n"
" dbc %p\n"
" database '%S'\n",
dbc,
database);
ensDatabaseconnectionTrace(dbc, 1);
}
AJNEW0(pthis);
pthis->Sqlconnectionclient = dbc->Sqlconnectionclient;
if (dbc->Username)
pthis->Username = ajStrNewRef(dbc->Username);
if (dbc->Password)
pthis->Password = ajStrNewRef(dbc->Password);
if (dbc->Hostname)
pthis->Hostname = ajStrNewRef(dbc->Hostname);
if (dbc->Hostport)
pthis->Hostport = ajStrNewRef(dbc->Hostport);
if (dbc->Socketfile)
pthis->Socketfile = ajStrNewRef(dbc->Socketfile);
if (database && ajStrGetLen(database))
pthis->Databasename = ajStrNewRef(database);
else
{
if (dbc->Databasename)
pthis->Databasename = ajStrNewRef(dbc->Databasename);
}
pthis->Timeout = dbc->Timeout;
pthis->Use = 1U;
return pthis;
}
/* @func ensDatabaseconnectionNewIni ******************************************
**
** Constructor for an Ensembl Database Connection with initial values.
**
** @cc Bio::EnsEMBL::DBSQL::DBConnection::new
** @param [u] client [AjESqlconnectionClient] AJAX SQL Connection client
** @param [uN] user [AjPStr] User name
** @param [uN] password [AjPStr] Password
** @param [uN] host [AjPStr] Host name or IP address
** @param [uN] port [AjPStr] Host TCP/IP port
** @param [uN] socketfile [AjPStr] UNIX socket file
** @param [uN] database [AjPStr] SQL database name
** @param [rN] dbctimeout [ajuint]
** Timeout in seconds for idle, non-interactive connections
**
** @return [EnsPDatabaseconnection] Ensembl Database Connection or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
EnsPDatabaseconnection ensDatabaseconnectionNewIni(
AjESqlconnectionClient client,
AjPStr user,
AjPStr password,
AjPStr host,
AjPStr port,
AjPStr socketfile,
AjPStr database,
ajuint dbctimeout)
{
EnsPDatabaseconnection dbc = NULL;
if (!client)
return NULL;
if (ajDebugTest("ensDatabaseconnectionNewIni"))
ajDebug("ensDatabaseconnectionNewIni\n"
" client %d\n"
" user '%S'\n"
" password '***'\n"
" host '%S'\n"
" port '%S'\n"
" socketfile '%S'\n"
" database '%S'\n"
" dbctimeout %u\n",
client,
user,
host,
port,
socketfile,
database,
dbctimeout);
AJNEW0(dbc);
dbc->Sqlconnectionclient = client;
if (user)
dbc->Username = ajStrNewRef(user);
if (password)
dbc->Password = ajStrNewRef(password);
if (host)
dbc->Hostname = ajStrNewRef(host);
if (port)
dbc->Hostport = ajStrNewRef(port);
if (socketfile)
dbc->Socketfile = ajStrNewRef(socketfile);
if (database)
dbc->Databasename = ajStrNewRef(database);
dbc->Timeout = dbctimeout;
dbc->Use = 1U;
return dbc;
}
/* @func ensDatabaseconnectionNewRef ******************************************
**
** Ensembl Object referencing function, which returns a pointer to the
** Ensembl Object passed in and increases its reference count.
**
** @param [u] dbc [EnsPDatabaseconnection] Ensembl Database Connection
**
** @return [EnsPDatabaseconnection] Ensembl Database Connection
**
** @release 6.3.0
** @@
******************************************************************************/
EnsPDatabaseconnection ensDatabaseconnectionNewRef(EnsPDatabaseconnection dbc)
{
if (!dbc)
return NULL;
dbc->Use++;
return dbc;
}
/* @func ensDatabaseconnectionNewUrl ******************************************
**
** Construct an Ensembl Database Connection from a Uniform Resource Locator
** with the following schema where brackets indicate optional components.
**
** client://username[:password]@host[:port][/databasename]
**
** The following URL would be an example for the public Ensembl MySQL instance.
**
** mysql://anonymous@ensembldb.ensembl.org:5306/
**
** @cc Bio::EnsEMBL::DBSQL::DBConnection::*
** @param [r] url [const AjPStr] Uniform Resource Locator
**
** @return [EnsPDatabaseconnection] Ensembl Database Connection or NULL
**
** @release 6.3.0
** @@
******************************************************************************/
EnsPDatabaseconnection ensDatabaseconnectionNewUrl(const AjPStr url)
{
AjPRegexp urlre = NULL;
AjESqlconnectionClient eclient = ajESqlconnectionClientNULL;
EnsPDatabaseconnection dbc = NULL;
AjPStr client = NULL;
AjPStr user = NULL;
AjPStr password = NULL;
AjPStr host = NULL;
AjPStr port = NULL;
AjPStr database = NULL;
if (ajDebugTest("ensDatabaseconnectionNewUrl"))
ajDebug("ensDatabaseconnectionNewUrl\n"
" url '%S'\n",
url);
if ((url == NULL) || (ajStrGetLen(url) == 0))
return NULL;
urlre = ajRegCompC("([^:]+)://(?:([^@:]+)(?:\\:([^@]*))?@)?"
"([^:/]+)(?:\\:)?(\\d+)?(?:\\/(\\w+))?");
if (ajRegExec(urlre, url))
{
client = ajStrNew();
user = ajStrNew();
password = ajStrNew();
host = ajStrNew();
port = ajStrNew();
database = ajStrNew();
ajRegSubI(urlre, 1, &client);
ajRegSubI(urlre, 2, &user);
ajRegSubI(urlre, 3, &password);
ajRegSubI(urlre, 4, &host);
ajRegSubI(urlre, 5, &port);
ajRegSubI(urlre, 6, &database);
eclient = ajSqlconnectionClientFromStr(client);
if (!eclient)
ajDebug("ensDatabaseconnectionNewUrl encountered "
"unexpected string '%S' in the "
"client part of the URL '%S'.\n",
client, url);
dbc = ensDatabaseconnectionNewIni(eclient,
user,
password,
host,
port,
(AjPStr) NULL,
database,
0);
ajStrDel(&client);
ajStrDel(&user);
ajStrDel(&password);
ajStrDel(&host);
ajStrDel(&port);
ajStrDel(&database);
}
ajRegFree(&urlre);
return dbc;
}
/* @section destructors *******************************************************
**
** Destruction destroys all internal data structures and frees the memory
** allocated for an Ensembl Database Connection object.
**
** @fdata [EnsPDatabaseconnection]
**
** @nam3rule Del Destroy (free) an Ensembl Database Connection
**
** @argrule * Pdbc [EnsPDatabaseconnection*]
** Ensembl Database Connection address
**
** @valrule * [void]
**
** @fcategory delete
******************************************************************************/
/* @func ensDatabaseconnectionDel *********************************************
**
** Default destructor for an Ensembl Database Connection.
**
** Before freeing memory, the AJAX SQL Connection to the SQL RDBMS instance
** is dropped.
**
** @param [d] Pdbc [EnsPDatabaseconnection*]
** Ensembl Database Connection address
**
** @return [void]
**
** @release 6.2.0
** @@
******************************************************************************/
void ensDatabaseconnectionDel(EnsPDatabaseconnection *Pdbc)
{
EnsPDatabaseconnection pthis = NULL;
if (!Pdbc)
return;
#if defined(AJ_DEBUG) && AJ_DEBUG >= 1
if (ajDebugTest("ensDatabaseconnectionDel"))
{
ajDebug("ensDatabaseconnectionDel\n"
" *Pdbc %p\n",
*Pdbc);
ensDatabaseconnectionTrace(*Pdbc, 1);
}
#endif /* defined(AJ_DEBUG) && AJ_DEBUG >= 1 */
if (!(pthis = *Pdbc) || --pthis->Use)
{
*Pdbc = NULL;
return;
}
ajSqlconnectionDel(&pthis->Sqlconnection);
ajStrDel(&pthis->Username);
ajStrDel(&pthis->Password);
ajStrDel(&pthis->Hostname);
ajStrDel(&pthis->Hostport);
ajStrDel(&pthis->Socketfile);
ajStrDel(&pthis->Databasename);
ajMemFree((void **) Pdbc);
return;
}
/* @section member retrieval **************************************************
**
** Functions for returning members of an Ensembl Database Connection object.
**
** @fdata [EnsPDatabaseconnection]
**
** @nam3rule Get Return Database Connection attribute(s)
** @nam4rule Autodisconnect Return the auto disconnect flag
** @nam4rule Databasename Return the database name
** @nam4rule Hostname Return the host name
** @nam4rule Hostport Return host port
** @nam4rule Password Return the password
** @nam4rule Socketfile Return the UNIX socket file
** @nam4rule Sqlconnection Return the AJAX SQL Connection
** @nam4rule Sqlconnectionclient Return the AJAX SQL Connection client
** @nam4rule Timeout Return the timeout
** @nam4rule Username Return the user name
**
** @argrule * dbc [const EnsPDatabaseconnection] Ensembl Database Connection
**
** @valrule Autodisconnect [AjBool] Auto disconnect flag or ajFalse
** @valrule Databasename [AjPStr] Database name or NULL
** @valrule Hostname [AjPStr] Host name or NULL
** @valrule Hostport [AjPStr] Host port or NULL
** @valrule Password [AjPStr] Password or NULL
** @valrule Socketfile [AjPStr] UNIX socket file or NULL
** @valrule Sqlconnection [AjPSqlconnection] AJAX SQL Connection or NULL
** @valrule Sqlconnectionclient [AjESqlconnectionClient]
** AJAX SQL Connection Client enumeration or ajESqlconnectionClientNULL
** @valrule Timeout [ajuint] Timeout or 0U
** @valrule Username [AjPStr] User name or NULL
**
** @fcategory use
******************************************************************************/
/* @func ensDatabaseconnectionGetAutodisconnect *******************************
**
** Get the auto disconnect member of an Ensembl Database Connection.
**
** @cc Bio::EnsEMBL::DBSQL::DBConnection::disconnect_when_inactive
** @param [r] dbc [const EnsPDatabaseconnection] Ensembl Database Connection
**
** @return [AjBool] Auto disconnect or ajFalse
** ajTrue: The Ensembl Database Connection will automatically
** disconnect, i.e. delete the AJAX SQL Connection,
** if no AJAX SQL Statement is active.
** ajFalse: No automatic disconnects will occur.
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensDatabaseconnectionGetAutodisconnect(
const EnsPDatabaseconnection dbc)
{
return (dbc) ? dbc->Autodisconnect : ajFalse;
}
/* @func ensDatabaseconnectionGetDatabasename *********************************
**
** Get the database name member of an Ensembl Database Connection.
**
** @cc Bio::EnsEMBL::DBSQL::DBConnection::dbname
** @param [r] dbc [const EnsPDatabaseconnection] Ensembl Database Connection
**
** @return [AjPStr] Database name or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
AjPStr ensDatabaseconnectionGetDatabasename(
const EnsPDatabaseconnection dbc)
{
return (dbc) ? dbc->Databasename : NULL;
}
/* @func ensDatabaseconnectionGetHostname *************************************
**
** Get the host name member of an Ensembl Database Connection.
**
** @cc Bio::EnsEMBL::DBSQL::DBConnection::host
** @param [r] dbc [const EnsPDatabaseconnection] Ensembl Database Connection
**
** @return [AjPStr] Host name or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
AjPStr ensDatabaseconnectionGetHostname(
const EnsPDatabaseconnection dbc)
{
return (dbc) ? dbc->Hostname : NULL;
}
/* @func ensDatabaseconnectionGetHostport *************************************
**
** Get the host port member of an Ensembl Database Connection.
**
** @cc Bio::EnsEMBL::DBSQL::DBConnection::port
** @param [r] dbc [const EnsPDatabaseconnection] Ensembl Database Connection
**
** @return [AjPStr] Host port or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
AjPStr ensDatabaseconnectionGetHostport(
const EnsPDatabaseconnection dbc)
{
return (dbc) ? dbc->Hostport : NULL;
}
/* @func ensDatabaseconnectionGetPassword *************************************
**
** Get the password member of an Ensembl Database Connection.
**
** @cc Bio::EnsEMBL::DBSQL::DBConnection::password
** @param [r] dbc [const EnsPDatabaseconnection] Ensembl Database Connection
**
** @return [AjPStr] Password or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
AjPStr ensDatabaseconnectionGetPassword(
const EnsPDatabaseconnection dbc)
{
return (dbc) ? dbc->Password : NULL;
}
/* @func ensDatabaseconnectionGetSocketfile ***********************************
**
** Get the UNIX socket file member of an Ensembl Database Connection.
**
** @param [r] dbc [const EnsPDatabaseconnection] Ensembl Database Connection
**
** @return [AjPStr] UNIX socket file or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
AjPStr ensDatabaseconnectionGetSocketfile(
const EnsPDatabaseconnection dbc)
{
return (dbc) ? dbc->Socketfile : NULL;
}
/* @func ensDatabaseconnectionGetSqlconnection ********************************
**
** Get the AJAX SQL Connection member of an Ensembl Database Connection.
**
** @param [r] dbc [const EnsPDatabaseconnection] Ensembl Database Connection
**
** @return [AjPSqlconnection] AJAX SQL Connection or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
AjPSqlconnection ensDatabaseconnectionGetSqlconnection(
const EnsPDatabaseconnection dbc)
{
return (dbc) ? dbc->Sqlconnection : NULL;
}
/* @func ensDatabaseconnectionGetSqlconnectionclient **************************
**
** Get the AJAX SQL Connection Client enumeration member of an
** Ensembl Database Connection.
**
** @cc Bio::EnsEMBL::DBSQL::DBConnection::driver
** @param [r] dbc [const EnsPDatabaseconnection] Ensembl Database Connection
**
** @return [AjESqlconnectionClient]
** AJAX SQL Connection Client enumeration or ajESqlconnectionClientNULL
**
** @release 6.4.0
** @@
******************************************************************************/
AjESqlconnectionClient ensDatabaseconnectionGetSqlconnectionclient(
const EnsPDatabaseconnection dbc)
{
return (dbc) ? dbc->Sqlconnectionclient : ajESqlconnectionClientNULL;
}
/* @func ensDatabaseconnectionGetTimeout **************************************
**
** Get the timeout member of an Ensembl Database Connection.
**
** @cc Bio::EnsEMBL::DBSQL::DBConnection::timeout
** @param [r] dbc [const EnsPDatabaseconnection] Ensembl Database Connection
**
** @return [ajuint] Timeout or 0U
**
** @release 6.4.0
** @@
******************************************************************************/
ajuint ensDatabaseconnectionGetTimeout(
const EnsPDatabaseconnection dbc)
{
return (dbc) ? dbc->Timeout : 0U;
}
/* @func ensDatabaseconnectionGetUsername *************************************
**
** Get the user name member of an Ensembl Database Connection.
**
** @cc Bio::EnsEMBL::DBSQL::DBConnection::username
** @param [r] dbc [const EnsPDatabaseconnection] Ensembl Database Connection
**
** @return [AjPStr] User name or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
AjPStr ensDatabaseconnectionGetUsername(
const EnsPDatabaseconnection dbc)
{
return (dbc) ? dbc->Username : NULL;
}
/* @section member assignment *************************************************
**
** Functions for assigning members of an Ensembl Database Connection object.
**
** @fdata [EnsPDatabaseconnection]
**
** @nam3rule Set Set one member of an Ensembl Database Connection
** @nam4rule Autodisconnect Set the automatic disconnect flag
**
** @argrule * dbc [EnsPDatabaseconnection] Ensembl Database Connection object
** @argrule Autodisconnect autodisconnect [AjBool] Auto disconnect flag
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory modify
******************************************************************************/
/* @func ensDatabaseconnectionSetAutodisconnect *******************************
**
** Set the auto disconnect member of an Ensembl Database Connection.
**
** @cc Bio::EnsEMBL::DBSQL::DBConnection::disconnect_when_inactive
** @param [u] dbc [EnsPDatabaseconnection] Ensembl Database Connection
** @param [r] autodisconnect [AjBool] Auto disconnect flag
**
** ajTrue: The Ensembl Database Connection will automatically
** disconnect, i.e. delete the AJAX SQL Connection,
** if no AJAX SQL Statement is active.
**
** ajFalse: No automatic disconnects will occur.
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensDatabaseconnectionSetAutodisconnect(
EnsPDatabaseconnection dbc,
AjBool autodisconnect)
{
if (!dbc)
return ajFalse;
dbc->Autodisconnect = autodisconnect;
return ajTrue;
}
/* @section debugging *********************************************************
**
** Functions for reporting of an Ensembl Database Connection object.
**
** @fdata [EnsPDatabaseconnection]
**
** @nam3rule Trace Report Ensembl Database Connection members to debug file
**
** @argrule Trace dbc [const EnsPDatabaseconnection] Ensembl Database
** Connection
** @argrule Trace level [ajuint] Indentation level
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory misc
******************************************************************************/
/* @func ensDatabaseconnectionTrace *******************************************
**
** Trace an Ensembl Database Connection.
**
** @param [r] dbc [const EnsPDatabaseconnection] Ensembl Database Connection
** @param [r] level [ajuint] Indentation level
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensDatabaseconnectionTrace(const EnsPDatabaseconnection dbc,
ajuint level)
{
AjPStr indent = NULL;
if (!dbc)
return ajFalse;
indent = ajStrNew();
ajStrAppendCountK(&indent, ' ', level * 2);
ajDebug("%SensDatabaseconnectionTrace %p\n"
"%S Sqlconnection %p\n"
"%S Sqlconnectionclient '%s'\n"
"%S Username '%S'\n"
"%S Password '***'\n"
"%S Hostname '%S'\n"
"%S Hostport '%S'\n"
"%S Socketfile '%S'\n"
"%S Databasename '%S'\n"
"%S Use %u\n",
indent, dbc,
indent, dbc->Sqlconnection,
indent, ajSqlconnectionClientToChar(dbc->Sqlconnectionclient),
indent, dbc->Username,
indent,
indent, dbc->Hostname,
indent, dbc->Hostport,
indent, dbc->Socketfile,
indent, dbc->Databasename,
indent, dbc->Use);
ajSqlconnectionTrace(dbc->Sqlconnection, level + 1);
ajStrDel(&indent);
return ajTrue;
}
/* @section test **************************************************************
**
** Functions for testing Ensembl Database Connection objects
**
** @fdata [EnsPDatabaseconnection]
**
** @nam3rule Is Ensembl Database Connection has a property
** @nam4rule Connected Test whether an active AJAX SQL Connection exists
**
** @argrule * dbc [const EnsPDatabaseconnection] Ensembl Database Connection
**
** @valrule Connected [AjBool] ajTrue if connected
**
** @fcategory use
******************************************************************************/
/* @func ensDatabaseconnectionIsConnected *************************************
**
** Test whether an Ensembl Database Connection has an active
** AJAX SQL Connection assigned.
**
** @cc Bio::EnsEMBL::DBSQL::DBConnection::connected
** @param [r] dbc [const EnsPDatabaseconnection] Ensembl Database Connection
**
** @return [AjBool] ajTrue if the Ensembl Database Connection has an active
** AJAX SQL Connection assigned
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensDatabaseconnectionIsConnected(const EnsPDatabaseconnection dbc)
{
return (dbc && dbc->Sqlconnection) ? ajTrue : ajFalse;
}
/* @section comparison ********************************************************
**
** Functions for comparing Ensembl Database Connections
**
** @fdata [EnsPDatabaseconnection]
**
** @nam3rule Match Compare two Ensembl Database Connections
**
** @argrule * dbc1 [const EnsPDatabaseconnection] Ensembl Database Connection
** @argrule * dbc2 [const EnsPDatabaseconnection] Ensembl Database Connection
**
** @valrule * [AjBool] ajTrue on success
**
** @fcategory use
******************************************************************************/
/* @func ensDatabaseconnectionMatch *******************************************
**
** Tests for matching two Ensembl Database Connections.
**
** @cc Bio::EnsEMBL::DBSQL::DBConnection::equals
** @param [r] dbc1 [const EnsPDatabaseconnection] Ensembl Database Connection
** @param [r] dbc2 [const EnsPDatabaseconnection] Ensembl Database Connection
**
** @return [AjBool] ajTrue if the Ensembl Database Connection objects match
**
** @release 6.2.0
** @@
** The comparison is based on initial pointer equality and if that fails a
** direct comparison of Ensembl Database Connection members.
******************************************************************************/
AjBool ensDatabaseconnectionMatch(const EnsPDatabaseconnection dbc1,
const EnsPDatabaseconnection dbc2)
{
if (!dbc1)
return ajFalse;
if (!dbc2)
return ajFalse;
if (dbc1 == dbc2)
return ajTrue;
/*
** The AJAX SQL Connection is not tested as it can be disconnected at any
** time and the database name is most likely to be different and
** therefore tested first. String matches are rather expensive...
*/
if (!ajStrMatchS(dbc1->Databasename, dbc2->Databasename))
return ajFalse;
if (!ajStrMatchS(dbc1->Username, dbc2->Username))
return ajFalse;
if (!ajStrMatchS(dbc1->Password, dbc2->Password))
return ajFalse;
if (!ajStrMatchS(dbc1->Hostname, dbc2->Hostname))
return ajFalse;
if (!ajStrMatchS(dbc1->Hostport, dbc2->Hostport))
return ajFalse;
if (!ajStrMatchS(dbc1->Socketfile, dbc2->Socketfile))
return ajFalse;
if (dbc1->Sqlconnectionclient != dbc2->Sqlconnectionclient)
return ajFalse;
return ajTrue;
}
/* @section connection ********************************************************
**
** Functions for connecting and disconnecting Ensembl Database Connections
**
** @fdata [EnsPDatabaseconnection]
**
** @nam3rule Connect Connect an Ensembl Database Connection
** @nam3rule Disconnect Disconnect an Ensembl Database Connection
**
** @argrule * dbc [EnsPDatabaseconnection] Ensembl Database Connection
**
** @valrule * [AjBool] True on success, ajFalse otherwise
**
** @fcategory use
******************************************************************************/
/* @func ensDatabaseconnectionConnect *****************************************
**
** Connect an Ensembl Database Connection to the specified SQL database.
**
** @cc Bio::EnsEMBL::DBSQL::DBConnection::connect
** @param [u] dbc [EnsPDatabaseconnection] Ensembl Database Connection
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensDatabaseconnectionConnect(EnsPDatabaseconnection dbc)
{
AjPSqlstatement sqls = NULL;
AjPStr statement = NULL;
if (!dbc)
return ajFalse;
if (dbc->Sqlconnection)
return ajTrue;
if (ajDebugTest("ensDatabaseconnectionConnect"))
ajDebug("ensDatabaseconnectionConnect\n"
" dbc %p\n",
dbc);
dbc->Sqlconnection = ajSqlconnectionNewData(dbc->Sqlconnectionclient,
dbc->Username,
dbc->Password,
dbc->Hostname,
dbc->Hostport,
dbc->Socketfile,
dbc->Databasename);
if (!dbc->Sqlconnection)
{
ajWarn("Could not establish an SQL connection for user '%S' "
"to host '%S' at port '%S' for database '%S'.\n",
dbc->Username,
dbc->Hostname,
dbc->Hostport,
dbc->Databasename);
return ajFalse;
}
/* NOTE: Setting a connection timeout is MySQL-specific for the moment. */
if ((dbc->Timeout > 0)
&&
(dbc->Sqlconnectionclient == ajESqlconnectionClientMySQL))
{
statement = ajFmtStr("SET SESSION wait_timeout=%u", dbc->Timeout);
sqls = ajSqlstatementNewRun(dbc->Sqlconnection, statement);
ajSqlstatementDel(&sqls);
ajStrDel(&statement);
}
return ajTrue;
}
/* @func ensDatabaseconnectionDisconnect **************************************
**
** Disconnect an Ensembl Database Connection from its SQL database.
**
** This function will only disconnect, if no other AJAX SQL Statement holds a
** reference to the AJAX SQL Connection, i.e. no AJAX SQL Statement is active.
**
** @cc Bio::EnsEMBL::DBSQL::DBConnection::disconnect_if_idle
** @param [u] dbc [EnsPDatabaseconnection] Ensembl Database Connection
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensDatabaseconnectionDisconnect(EnsPDatabaseconnection dbc)
{
if (ajDebugTest("ensDatabaseconnectionDisconnect"))
{
ajDebug("ensDatabaseconnectionDisconnect\n"
" dbc %p\n",
dbc);
ensDatabaseconnectionTrace(dbc, 1);
}
if (!dbc)
return ajFalse;
if (!dbc->Sqlconnection)
return ajTrue;
/*
** Disconnect if no other AJAX SQL Statement has a reference to the
** AJAX SQL Connection, except this Ensembl Database Connection object.
*/
if (ajSqlconnectionGetUse(dbc->Sqlconnection) == 1)
ajSqlconnectionDel(&dbc->Sqlconnection);
return ajTrue;
}
/* @section convenience functions *********************************************
**
** Ensembl Database Connection convenience functions
**
** @fdata [EnsPDatabaseconnection]
**
** @nam3rule Escape Escape a string
** @nam4rule C Escape to an AJAX String
** @nam4rule S Escape to a C-type character string
** @nam3rule Sqlstatement AJAX SQL Statement
** @nam4rule Del Delete an AJAX SQL Statement
** @nam4rule New Run a new AJAX SQL statement
**
** @argrule * dbc [EnsPDatabaseconnection] Ensembl Database Connection
** @argrule EscapeC Ptxt [char**] Address of the (new) SQL-escaped C string
** @argrule EscapeC str [const AjPStr] AJAX String to be escaped
** @argrule EscapeS Pstr [AjPStr*] Address of the (new) SQL-escaped AJAX String
** @argrule EscapeS str [const AjPStr] AJAX String to be escaped
** @argrule SqlstatementDel Psqls [AjPSqlstatement*] AJAX SQL Statement address
** @argrule SqlstatementNew statement [const AjPStr] SQL statement
**
** @valrule EscapeC [AjBool] ajTrue upon success, ajFalse otherwise
** @valrule EscapeS [AjBool] ajTrue upon success, ajFalse otherwise
** @valrule SqlstatementDel [AjBool] ajTrue upon success, ajFalse otherwise
** @valrule SqlstatementNew [AjPSqlstatement] AJAX SQL Statement
**
** @fcategory use
******************************************************************************/
/* @func ensDatabaseconnectionEscapeC *****************************************
**
** Escape special characters in an AJAX String for use in an SQL statement,
** taking into account the current character set of the AJAX SQL Connection
** and return a C-type character string.
**
** The caller is responsible for deleting the escaped C-type character string.
**
** @param [u] dbc [EnsPDatabaseconnection] Ensembl Database Connection
** @param [wP] Ptxt [char**] Address of the (new) SQL-escaped C string
** @param [r] str [const AjPStr] AJAX String to be escaped
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensDatabaseconnectionEscapeC(EnsPDatabaseconnection dbc,
char **Ptxt,
const AjPStr str)
{
if (!dbc)
return ajFalse;
if (!Ptxt)
return ajFalse;
if (!str)
return ajFalse;
if (ajDebugTest("ensDatabaseconnectionEscapeC"))
{
ajDebug("ensDatabaseconnectionEscapeC\n"
" dbc %p\n"
" Ptxt %p\n"
" str '%S'\n",
dbc,
Ptxt,
str);
ensDatabaseconnectionTrace(dbc, 1);
}
if (!ensDatabaseconnectionIsConnected(dbc))
if (!ensDatabaseconnectionConnect(dbc))
return ajFalse;
return ajSqlconnectionEscapeC(dbc->Sqlconnection, Ptxt, str);
}
/* @func ensDatabaseconnectionEscapeS *****************************************
**
** Escape special characters in an AJAX String for use in an SQL statement,
** taking into account the current character set of the AJAX SQL Connection
** and return an AJAX String.
**
** The caller is responsible for deleting the escaped AJAX String.
**
** @param [u] dbc [EnsPDatabaseconnection] Ensembl Database Connection
** @param [wP] Pstr [AjPStr*] Address of the (new) SQL-escaped AJAX String
** @param [r] str [const AjPStr] AJAX String to be escaped
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensDatabaseconnectionEscapeS(EnsPDatabaseconnection dbc,
AjPStr *Pstr,
const AjPStr str)
{
if (!dbc)
return ajFalse;
if (!Pstr)
return ajFalse;
if (!str)
return ajFalse;
if (ajDebugTest("ensDatabaseconnectionEscapeS"))
{
ajDebug("ensDatabaseconnectionEscapeS\n"
" dbc %p\n"
" Pstr %p\n"
" str '%S'\n",
dbc,
Pstr,
str);
ensDatabaseconnectionTrace(dbc, 1);
}
if (!ensDatabaseconnectionIsConnected(dbc))
if (!ensDatabaseconnectionConnect(dbc))
return ajFalse;
return ajSqlconnectionEscapeS(dbc->Sqlconnection, Pstr, str);
}
/* @func ensDatabaseconnectionSqlstatementDel *********************************
**
** Delete an AJAX SQL Statement associated with an
** Ensembl Database Connection.
**
** @param [u] dbc [EnsPDatabaseconnection] Ensembl Database Connection
** @param [d] Psqls [AjPSqlstatement*] AJAX SQL Statement address
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.3.0
** @@
******************************************************************************/
AjBool ensDatabaseconnectionSqlstatementDel(
EnsPDatabaseconnection dbc,
AjPSqlstatement *Psqls)
{
if (!dbc)
return ajFalse;
if (!Psqls)
return ajFalse;
if (ajDebugTest("ensDatabaseconnectionSqlstatementDel"))
ajDebug("ensDatabaseconnectionSqlstatementDel\n"
" dbc %p\n"
" Psqls %p\n",
dbc,
Psqls);
ajSqlstatementDel(Psqls);
*Psqls = NULL;
if (dbc->Autodisconnect)
ensDatabaseconnectionDisconnect(dbc);
return ajTrue;
}
/* @func ensDatabaseconnectionSqlstatementNew *********************************
**
** Run an SQL statement against an Ensembl Database Connection.
**
** @cc Bio::EnsEMBL::DBSQL::DBConnection::prepare
** @cc Bio::EnsEMBL::DBSQL::DBConnection::do
** @param [u] dbc [EnsPDatabaseconnection] Ensembl Database Connection
** @param [r] statement [const AjPStr] SQL statement
**
** @return [AjPSqlstatement] AJAX SQL Statement
**
** @release 6.2.0
** @@
******************************************************************************/
AjPSqlstatement ensDatabaseconnectionSqlstatementNew(
EnsPDatabaseconnection dbc,
const AjPStr statement)
{
if (ajDebugTest("ensDatabaseconnectionSqlstatementNew"))
{
ajDebug("ensDatabaseconnectionSqlstatementNew\n"
" dbc %p\n"
" statement '%S'\n",
dbc,
statement);
ensDatabaseconnectionTrace(dbc, 1);
}
if (!dbc)
return NULL;
if (!ensDatabaseconnectionIsConnected(dbc))
if (!ensDatabaseconnectionConnect(dbc))
return NULL;
return ajSqlstatementNewRun(dbc->Sqlconnection, statement);
}
/* @section retrieval *********************************************************
**
** Ensembl Database Connection retrieval functions
**
** @fdata [EnsPDatabaseconnection]
**
** @nam3rule Fetch Fetch an object from an Ensembl Database Connection
** @nam4rule Url Fetch a Uniform Resource Locator representation
**
** @argrule * dbc [const EnsPDatabaseconnection] Ensembl Database Connection
** @argrule FetchUrl Purl [AjPStr*] Uniform Resource Locator
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory use
******************************************************************************/
/* @func ensDatabaseconnectionFetchUrl ****************************************
**
** Fetch a Uniform Resource Locator representation of an
** Ensembl Database Connection.
**
** NOTE: The URL contains the password in text form so fetching the URL is a
** security risk.
**
** The caller is responsible for deleting the AJAX String.
**
** @param [r] dbc [const EnsPDatabaseconnection] Ensembl Database Connection
** @param [wP] Purl [AjPStr*] Uniform Resource Locator
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensDatabaseconnectionFetchUrl(const EnsPDatabaseconnection dbc,
AjPStr *Purl)
{
if (!dbc)
return ajFalse;
if (!Purl)
return ajFalse;
if (*Purl)
ajStrAssignClear(Purl);
else
*Purl = ajStrNew();
if (dbc->Socketfile && ajStrGetLen(dbc->Socketfile))
{
ajStrAppendC(Purl, "file:///");
ajStrAppendS(Purl, dbc->Socketfile);
}
else
{
ajStrAppendC(Purl,
ajSqlconnectionClientToChar(dbc->Sqlconnectionclient));
ajStrAppendC(Purl, "://");
if ((dbc->Username != NULL) && (ajStrGetLen(dbc->Username) > 0))
{
ajStrAppendS(Purl, dbc->Username);
if ((dbc->Password != NULL) && (ajStrGetLen(dbc->Password) > 0))
{
ajStrAppendC(Purl, ":");
ajStrAppendS(Purl, dbc->Password);
}
ajStrAppendC(Purl, "@");
}
ajStrAppendS(Purl, dbc->Hostname);
if ((dbc->Hostport != NULL) && (ajStrGetLen(dbc->Hostport) > 0))
{
ajStrAppendC(Purl, ":");
ajStrAppendS(Purl, dbc->Hostport);
}
ajStrAppendC(Purl, "/");
if ((dbc->Databasename != NULL) && (ajStrGetLen(dbc->Databasename) > 0))
ajStrAppendS(Purl, dbc->Databasename);
}
return ajTrue;
}
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