[basedb-cvs] basedb/www bioassay.inc.php,1.33,1.34 bioassayset.inc.php,1.25,1.26 common.inc.php,1.18,1.19 experiment.inc.php,1.48,1.49 mysql.inc.php,1.11,1.12 pgsql.inc.php,1.7,1.8 plot.inc.php,1.20,1.21

[<tr...@us...>]

Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv19503

Modified Files:
	bioassay.inc.php bioassayset.inc.php common.inc.php 
	experiment.inc.php mysql.inc.php pgsql.inc.php plot.inc.php 
Log Message:
Turned dynamic database into table name prefix

Index: bioassay.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/bioassay.inc.php,v
retrieving revision 1.33
retrieving revision 1.34
diff -C2 -d -r1.33 -r1.34
*** bioassay.inc.php	9 Sep 2002 06:29:34 -0000	1.33
--- bioassay.inc.php	9 Sep 2002 10:56:08 -0000	1.34
***************
*** 75,79 ****
  			return false;
  
! 		$query = "DELETE FROM $config[dbDynamic].BioAssayData$this->experiment ".
  			"WHERE `bioAssay` = $this->id";
  		query($query);
--- 75,79 ----
  			return false;
  
! 		$query = "DELETE FROM $config[dbDynamic]BioAssayData$this->experiment ".
  			"WHERE `bioAssay` = $this->id";
[...197 lines suppressed...]
  			"SELECT $this->id, position, molecule, $i1, $i2, ($i1) / ($i2) ".
--- 942,946 ----
  		}
  
! 		$query = "INSERT INTO $config[dbDynamic]BioAssayData$this->experiment ".
  			"(`bioAssay`, position, molecule, intensity1, intensity2, ratio) ".
  			"SELECT $this->id, position, molecule, $i1, $i2, ($i1) / ($i2) ".
***************
*** 1053,1057 ****
  
  		$query = "SELECT $xc AS `A`, $yc AS `B`, $extra ".
! 			"FROM $config[dbDynamic].BioAssayData$this->experiment bad ".
  			$sea->getExtraTables()." ".
  			"WHERE bad.`bioAssay` = $this->id ".$sea->getExtraWhere()." ".
--- 1053,1057 ----
  
  		$query = "SELECT $xc AS `A`, $yc AS `B`, $extra ".
! 			"FROM $config[dbDynamic]BioAssayData$this->experiment bad ".
  			$sea->getExtraTables()." ".
  			"WHERE bad.`bioAssay` = $this->id ".$sea->getExtraWhere()." ".

Index: bioassayset.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/bioassayset.inc.php,v
retrieving revision 1.25
retrieving revision 1.26
diff -C2 -d -r1.25 -r1.26
*** bioassayset.inc.php	8 Sep 2002 22:38:08 -0000	1.25
--- bioassayset.inc.php	9 Sep 2002 10:56:08 -0000	1.26
***************
*** 96,103 ****
  		$query = "DELETE FROM BioAssaySetCreation WHERE `bioAssaySet` = $id";
  		query($query);
! 		$query = "DELETE FROM $config[dbDynamic].BioAssaySetGene$expid ".
  			"WHERE `bioAssaySet` = $id";
  		query($query);
! 		$query = "DELETE FROM $config[dbDynamic].BioAssaySetPosGene$expid ".
  			"WHERE `bioAssaySet` = $id";
  		query($query);
--- 96,103 ----
  		$query = "DELETE FROM BioAssaySetCreation WHERE `bioAssaySet` = $id";
[...222 lines suppressed...]
  			"SELECT STRAIGHT_JOIN $this->id, bad.position, bad.molecule, COUNT(*) ".
--- 641,645 ----
  		// appear in.
  		$query = "INSERT INTO ".
! 			"$config[dbDynamic]BioAssaySetPosGene$this->experiment ".
  			"(`bioAssaySet`, position, molecule, cnt) ".
  			"SELECT STRAIGHT_JOIN $this->id, bad.position, bad.molecule, COUNT(*) ".
***************
*** 678,682 ****
  	{
  		global $config;
! 		$table = "$config[dbDynamic].BioAssayData$this->experiment";
  		$columns = array("bioAssay", "position", "molecule", "intensity1",
  			"intensity2", "ratio");
--- 680,684 ----
  	{
  		global $config;
! 		$table = "$config[dbDynamic]BioAssayData$this->experiment";
  		$columns = array("bioAssay", "position", "molecule", "intensity1",
  			"intensity2", "ratio");

Index: common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/common.inc.php,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** common.inc.php	8 Sep 2002 13:18:33 -0000	1.18
--- common.inc.php	9 Sep 2002 10:56:08 -0000	1.19
***************
*** 26,29 ****
--- 26,30 ----
  	require_once("display.inc.php");
  	require_once("getconfig.inc.php");
+ 	require_once("db.inc.php");
  
  	if(!isset($config) || !is_array($config))
***************
*** 49,52 ****
--- 50,57 ----
  	unset($cfgvars);
  	unset($v);
+ 
+ 	// The name of the dynamic database has to be turned into something
+ 	// that can be put in an SQL statement as the prefix of a table name.
+ 	db_dynamic_db_prepare($config["dbDynamic"]);
  
  	// This appeared before we had chosen the name 'BASE'. It used to be in

Index: experiment.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/experiment.inc.php,v
retrieving revision 1.48
retrieving revision 1.49
diff -C2 -d -r1.48 -r1.49
*** experiment.inc.php	9 Sep 2002 06:33:50 -0000	1.48
--- experiment.inc.php	9 Sep 2002 10:56:08 -0000	1.49
***************
*** 88,96 ****
  			{
  				if(!db_table_copy("TemplateBioAssayData",
! 						"$config[dbDynamic].BioAssayData$this->id") ||
  					!db_table_copy("TemplateBioAssaySetGene",
! 						"$config[dbDynamic].BioAssaySetGene$this->id") ||
  					!db_table_copy("TemplateBioAssaySetPosGene",
! 						"$config[dbDynamic].BioAssaySetPosGene$this->id"))
  				{
  					if(!$this->remove())
--- 88,96 ----
  			{
  				if(!db_table_copy("TemplateBioAssayData",
! 						"$config[dbDynamic]BioAssayData$this->id") ||
  					!db_table_copy("TemplateBioAssaySetGene",
! 						"$config[dbDynamic]BioAssaySetGene$this->id") ||
  					!db_table_copy("TemplateBioAssaySetPosGene",
! 						"$config[dbDynamic]BioAssaySetPosGene$this->id"))
  				{
  					if(!$this->remove())
***************
*** 114,120 ****
  			return false;
  
! 		db_table_drop("$config[dbDynamic].BioAssayData$id");
! 		db_table_drop("$config[dbDynamic].BioAssaySetGene$id");
! 		db_table_drop("$config[dbDynamic].BioAssaySetPosGene$id");
  		return true;
  	}
--- 114,120 ----
  			return false;
  
! 		db_table_drop("$config[dbDynamic]BioAssayData$id");
! 		db_table_drop("$config[dbDynamic]BioAssaySetGene$id");
! 		db_table_drop("$config[dbDynamic]BioAssaySetPosGene$id");
  		return true;
  	}

Index: mysql.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/mysql.inc.php,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** mysql.inc.php	9 Sep 2002 06:39:01 -0000	1.11
--- mysql.inc.php	9 Sep 2002 10:56:08 -0000	1.12
***************
*** 275,277 ****
--- 275,284 ----
  }
  
+ function db_dynamic_db_prepare(&$dyn)
+ {
+ 	// MySQL can access a table in another database as database.table,
+ 	// so we just append a '.' to the database name.
+ 	$dyn .= ".";
+ }
+ 
  ?>

Index: pgsql.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/pgsql.inc.php,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** pgsql.inc.php	9 Sep 2002 06:39:01 -0000	1.7
--- pgsql.inc.php	9 Sep 2002 10:56:08 -0000	1.8
***************
*** 339,341 ****
--- 339,353 ----
  }
  
+ function db_dynamic_db_prepare(&$dyn)
+ {
+ 	// PostgreSQL can only access tables in one database at a time,
+ 	// so we turn this into a prefix for the table name. As there's
+ 	// (by default) a 31-character limit on table names, we need to
+ 	// make sure that the name doesn't get to long. The longest table
+ 	// name we can expect is BioAssaySetPosGene[0-9]{10}, which has
+ 	// 28 characters. Although having 10^9 Experiments seems a bit odd,
+ 	// we play it safe and limit the prefix to 2 chars plus underscore.
+ 	$dyn = substr($dyn, 0, 2)."_";
+ }
+ 
  ?>

Index: plot.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/plot.inc.php,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** plot.inc.php	8 Sep 2002 22:38:08 -0000	1.20
--- plot.inc.php	9 Sep 2002 10:56:08 -0000	1.21
***************
*** 435,439 ****
  
  		if($a1->type == "v")
! 			$table1 = "$config[dbDynamic].BioAssayData".$a1->vset->getExperiment()." t1";
  		else $table1 = "RawBioAssayData t1";
  		if($a1->type == $a2->type && $a1->id == $a2->id)
--- 435,439 ----
  
  		if($a1->type == "v")
! 			$table1 = "$config[dbDynamic]BioAssayData".$a1->vset->getExperiment()." t1";
  		else $table1 = "RawBioAssayData t1";
  		if($a1->type == $a2->type && $a1->id == $a2->id)
***************
*** 465,469 ****
  		{
  			if($a2->type == "v")
! 				$table2 = "$config[dbDynamic].BioAssayData".$a2->vset->getExperiment()." t2";
  			else $table2 = "RawBioAssayData t2";
  
--- 465,469 ----
  		{
  			if($a2->type == "v")
! 				$table2 = "$config[dbDynamic]BioAssayData".$a2->vset->getExperiment()." t2";
  			else $table2 = "RawBioAssayData t2";