[basedb-cvs] basedb/www bioassay.inc.php,1.34,1.35 bioassayset.inc.php,1.26,1.27 job.inc.php,1.37,1.38 mysql.inc.php,1.15,1.16 pgsql.inc.php,1.11,1.12 program.inc.php,1.22,1.23 raw.inc.php,1.36,1.37 trans_create.phtml,1.23,1.24

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

Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv23080

Modified Files:
	bioassay.inc.php bioassayset.inc.php job.inc.php mysql.inc.php 
	pgsql.inc.php program.inc.php raw.inc.php trans_create.phtml 
Log Message:
More PostgreSQL stuff

Index: bioassay.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/bioassay.inc.php,v
retrieving revision 1.34
retrieving revision 1.35
diff -C2 -d -r1.34 -r1.35
*** bioassay.inc.php	9 Sep 2002 10:56:08 -0000	1.34
--- bioassay.inc.php	10 Sep 2002 10:57:41 -0000	1.35
***************
*** 433,438 ****
  			"m.species, m.`clusterId`, bad.molecule, bad.position AS position, ".
  			"$dia $ecol ".
! 			"FROM $config[dbDynamic]BioAssayData$this->experiment bad ".
! 			$search->getExtraTables()." $ljoin ".
  			"WHERE ".db_true()." ".
  			$search->getWhere()." ".$search->getExtraWhere().
--- 433,438 ----
  			"m.species, m.`clusterId`, bad.molecule, bad.position AS position, ".
  			"$dia $ecol ".
! 			"FROM $config[dbDynamic]BioAssayData$this->experiment bad $ljoin ".
! 			$search->getExtraTables()." ".
  			"WHERE ".db_true()." ".
  			$search->getWhere()." ".$search->getExtraWhere().
***************
*** 475,480 ****
  
  		$query = "SELECT DISTINCT bad.molecule ".
! 			"FROM $config[dbDynamic]BioAssayData$this->experiment bad ".
! 			$search->getExtraTables()." $ljoin ".
  			"WHERE ".db_true()." ".$search->getWhere()." ".
  			$search->getExtraWhere()." $ob";
--- 475,480 ----
  
  		$query = "SELECT DISTINCT bad.molecule ".
! 			"FROM $config[dbDynamic]BioAssayData$this->experiment bad $ljoin ".
! 			$search->getExtraTables()." ".
  			"WHERE ".db_true()." ".$search->getWhere()." ".
  			$search->getExtraWhere()." $ob";
***************
*** 591,597 ****
  
  		$query = "SELECT ba.id, $sel $xf ".
! 			"FROM $config[dbDynamic]BioAssayData$expid bad ".
  			$search->getExtraTables()." ".
- 			"$ljoin ".
  			"WHERE bad.molecule = $molecule ".
  			$search->getWhere()." ".$search->getExtraWhere()." ";
--- 591,596 ----
  
  		$query = "SELECT ba.id, $sel $xf ".
! 			"FROM $config[dbDynamic]BioAssayData$expid bad $ljoin ".
  			$search->getExtraTables()." ".
  			"WHERE bad.molecule = $molecule ".
  			$search->getWhere()." ".$search->getExtraWhere()." ";
***************
*** 881,889 ****
  		$ob = $search->makeOrderBy($sortfields);
  
! 		$query = "SELECT rba.name as rawname, ba.* ".
  			"FROM BioAssay ba ".
  			"LEFT JOIN RawBioAssay rba ON rba.id = ba.`rawBioAssay` ".
  			"WHERE ba.`bioAssaySet` = $setid ".$search->getWhere()." ".
! 			"GROUP BY ba.id $ob ".$search->makeLimit();
  
  		$arr = array();
--- 880,888 ----
  		$ob = $search->makeOrderBy($sortfields);
  
! 		$query = "SELECT ba.*, rba.name as rawname ".
  			"FROM BioAssay ba ".
  			"LEFT JOIN RawBioAssay rba ON rba.id = ba.`rawBioAssay` ".
  			"WHERE ba.`bioAssaySet` = $setid ".$search->getWhere()." ".
! 			"$ob ".$search->makeLimit();
  
  		$arr = array();
***************
*** 944,948 ****
  		$query = "INSERT INTO $config[dbDynamic]BioAssayData$this->experiment ".
  			"(`bioAssay`, position, molecule, intensity1, intensity2, ratio) ".
! 			"SELECT $this->id, position, molecule, $i1, $i2, ($i1) / ($i2) ".
  			"FROM RawBioAssayData WHERE `rawBioAssay` = $this->rawBioAssay";
  		if(!query($query)) return false;
--- 943,948 ----
  		$query = "INSERT INTO $config[dbDynamic]BioAssayData$this->experiment ".
  			"(`bioAssay`, position, molecule, intensity1, intensity2, ratio) ".
! 			"SELECT $this->id, position, molecule, $i1, $i2, ".
! 			"CASE WHEN $i1 > 0 AND $i2 > 0 THEN ($i1)/($i2) ELSE -1 END ".
  			"FROM RawBioAssayData WHERE `rawBioAssay` = $this->rawBioAssay";
  		if(!query($query)) return false;

Index: bioassayset.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/bioassayset.inc.php,v
retrieving revision 1.26
retrieving revision 1.27
diff -C2 -d -r1.26 -r1.27
*** bioassayset.inc.php	9 Sep 2002 10:56:08 -0000	1.26
--- bioassayset.inc.php	10 Sep 2002 10:57:41 -0000	1.27
***************
*** 81,85 ****
  		$expid = $this->experiment;
  
! 		$query = "SELECT id FROM BioAssay WHERE bioAssaySet = $id";
  		$rc = true;
  		if(!($res = query($query)))
--- 81,85 ----
  		$expid = $this->experiment;
  
! 		$query = "SELECT id FROM BioAssay WHERE `bioAssaySet` = $id";
  		$rc = true;
  		if(!($res = query($query)))
***************
*** 199,203 ****
  		$id = (int)$id;
  		$query = "SELECT 1 FROM BioAssaySet ".
! 			"WHERE id = $id && experiment = ".(int)$expid;
  		$res = query($query);
  		if(db_num_rows($res)) return true;
--- 199,203 ----
  		$id = (int)$id;
  		$query = "SELECT 1 FROM BioAssaySet ".
! 			"WHERE id = $id AND experiment = ".(int)$expid;
  		$res = query($query);
  		if(db_num_rows($res)) return true;
***************
*** 631,635 ****
  			"$config[dbDynamic]BioAssaySetGene$this->experiment ".
  			"(`bioAssaySet`, molecule, cnt) ".
! 			"SELECT STRAIGHT_JOIN $this->id, bad.molecule, COUNT(DISTINCT ba.id) ".
  			"FROM BioAssay ba, $datatable bad ".
  			"WHERE ba.`bioAssaySet` = $this->id AND bad.`bioAssay` = ba.id ".
--- 631,636 ----
  			"$config[dbDynamic]BioAssaySetGene$this->experiment ".
  			"(`bioAssaySet`, molecule, cnt) ".
! 			"SELECT ".db_straight_join()." $this->id, ".
! 			"bad.molecule, COUNT(DISTINCT ba.id) ".
  			"FROM BioAssay ba, $datatable bad ".
  			"WHERE ba.`bioAssaySet` = $this->id AND bad.`bioAssay` = ba.id ".
***************
*** 643,647 ****
  			"$config[dbDynamic]BioAssaySetPosGene$this->experiment ".
  			"(`bioAssaySet`, position, molecule, cnt) ".
! 			"SELECT STRAIGHT_JOIN $this->id, bad.position, bad.molecule, COUNT(*) ".
  			"FROM BioAssay ba, $datatable bad ".
  			"WHERE ba.`bioAssaySet` = $this->id AND bad.`bioAssay` = ba.id ".
--- 644,649 ----
  			"$config[dbDynamic]BioAssaySetPosGene$this->experiment ".
  			"(`bioAssaySet`, position, molecule, cnt) ".
! 			"SELECT ".db_straight_join()." $this->id, ".
! 			"bad.position, bad.molecule, COUNT(*) ".
  			"FROM BioAssay ba, $datatable bad ".
  			"WHERE ba.`bioAssaySet` = $this->id AND bad.`bioAssay` = ba.id ".

Index: job.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/job.inc.php,v
retrieving revision 1.37
retrieving revision 1.38
diff -C2 -d -r1.37 -r1.38
*** job.inc.php	10 Sep 2002 09:29:44 -0000	1.37
--- job.inc.php	10 Sep 2002 10:57:41 -0000	1.38
***************
*** 38,43 ****
  		$this->experiment = (int)$experiment;
  		$this->transformation = (int)$transformation;
! 		$this->startTime = $startTime;
! 		$this->endTime = $endTime;
  		$this->status = $status;
  		$this->program = (int)$program;
--- 38,43 ----
  		$this->experiment = (int)$experiment;
  		$this->transformation = (int)$transformation;
! 		$this->startTime = strtodate($startTime);
! 		$this->endTime = strtodate($endTime);
  		$this->status = $status;
  		$this->program = (int)$program;
***************
*** 229,238 ****
  	function setStartTime($val)
  	{
! 		$this->startTime = $val;
  		$this->saveVar("startTime", $val);
  	}
  	function setEndTime($val)
  	{
! 		$this->endTime = $val;
  		$this->saveVar("endTime", $val);
  	}
--- 229,238 ----
  	function setStartTime($val)
  	{
! 		$this->startTime = strtodate($val);
  		$this->saveVar("startTime", $val);
  	}
  	function setEndTime($val)
  	{
! 		$this->endTime = strtodate($val);
  		$this->saveVar("endTime", $val);
  	}

Index: mysql.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/mysql.inc.php,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** mysql.inc.php	10 Sep 2002 09:29:44 -0000	1.15
--- mysql.inc.php	10 Sep 2002 10:57:41 -0000	1.16
***************
*** 307,313 ****
  {
  	if($base)
! 		return "LOG($arg)/LOG($base)";
  	else
  		return "LOG($arg)";
  }
  
--- 307,318 ----
  {
  	if($base)
! 		return "(LOG($arg)/LOG($base))";
  	else
  		return "LOG($arg)";
+ }
+ 
+ function db_straight_join()
+ {
+ 	return "STRAIGHT_JOIN";
  }
  

Index: pgsql.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/pgsql.inc.php,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** pgsql.inc.php	10 Sep 2002 09:29:44 -0000	1.11
--- pgsql.inc.php	10 Sep 2002 10:57:41 -0000	1.12
***************
*** 394,401 ****
  {
  	if($base)
! 		$e = "LOG(".(float)$base.", float8($arg))";
  	else
  		$e = "LOG(float8($arg))";
  	return "CASE WHEN $arg > 0. THEN $e ELSE NULL END";
  }
  
--- 394,406 ----
  {
  	if($base)
! 		$e = "(LOG(float8($arg))/LOG($base.))";
  	else
  		$e = "LOG(float8($arg))";
  	return "CASE WHEN $arg > 0. THEN $e ELSE NULL END";
+ }
+ 
+ function db_straight_join()
+ {
+ 	return "";
  }
  

Index: program.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/program.inc.php,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -d -r1.22 -r1.23
*** program.inc.php	9 Sep 2002 06:29:34 -0000	1.22
--- program.inc.php	10 Sep 2002 10:57:41 -0000	1.23
***************
*** 167,171 ****
  	{
  		$query = "SELECT id, name FROM Program ".
! 			"WHERE `onServer` ORDER BY name";
  		$res = query($query);
  		$arr = array();
--- 167,171 ----
  	{
  		$query = "SELECT id, name FROM Program ".
! 			"WHERE `onServer` <> 0 ORDER BY name";
  		$res = query($query);
  		$arr = array();
***************
*** 185,189 ****
--- 185,193 ----
  		$arr = array();
  		while($row =& db_fetch_assoc($res))
+ //temp. fix for my dev database
+ {
+ $row["valueType"]=trim($row["valueType"]);
  			$arr[(int)$row["position"]] = $row;
+ }
  		return $arr;
  	}

Index: raw.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/raw.inc.php,v
retrieving revision 1.36
retrieving revision 1.37
diff -C2 -d -r1.36 -r1.37
*** raw.inc.php	10 Sep 2002 09:29:44 -0000	1.36
--- raw.inc.php	10 Sep 2002 10:57:41 -0000	1.37
***************
*** 484,488 ****
  				"FROM RawBioAssay r, LabeledExtract le, Extract e ".
  				"WHERE r.id = ".(int)$rawid." ".
! 				"AND le.id = r.`labeledCh`".($pos+1)." ".
  				"AND e.id = le.extract";
  			$res = query($query);
--- 484,488 ----
  				"FROM RawBioAssay r, LabeledExtract le, Extract e ".
  				"WHERE r.id = ".(int)$rawid." ".
! 				"AND le.id = r.`labeledCh".($pos+1)."` ".
  				"AND e.id = le.extract";
  			$res = query($query);

Index: trans_create.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/trans_create.phtml,v
retrieving revision 1.23
retrieving revision 1.24
diff -C2 -d -r1.23 -r1.24
*** trans_create.phtml	29 Aug 2002 16:51:34 -0000	1.23
--- trans_create.phtml	10 Sep 2002 10:57:41 -0000	1.24
***************
*** 181,184 ****
--- 181,186 ----
  			if(!$prog->read($i_prog))
  				$err = "No such plug-in";
+ 			else if(!$prog->getOnServer())
+ 				$err = "The selected plug-in has been disabled by the admin";
  		}
  		if(!$prog->getId()) $step = 0;
***************
*** 401,406 ****
  				if(!isset($ptypes[$type]))
  				{
! 					echo "<tr><td colspan=3>Unknown parameter ".
! 						"type '$type'</td></tr>\n";
  					continue;
  				}
--- 403,408 ----
  				if(!isset($ptypes[$type]))
  				{
! 					echo "<tr><td colspan=3>Unknown parameter type ".
! 						"'$type'</td></tr>\n";
  					continue;
  				}