[basedb-cvs] basedb/include/classes bioassay.inc.php,1.31,1.32 bioassayset.inc.php,1.21,1.22 jobhandler.inc.php,1.9,1.10

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

Update of /cvsroot/basedb/basedb/include/classes
In directory sc8-pr-cvs1:/tmp/cvs-serv7133/classes

Modified Files:
	bioassay.inc.php bioassayset.inc.php jobhandler.inc.php 
Log Message:
Added import and display of extra bioassayset float columns

Index: bioassay.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/bioassay.inc.php,v
retrieving revision 1.31
retrieving revision 1.32
diff -C2 -d -r1.31 -r1.32
*** bioassay.inc.php	3 Feb 2003 20:13:17 -0000	1.31
--- bioassay.inc.php	11 Feb 2003 14:43:06 -0000	1.32
***************
*** 708,712 ****
  		{
  			$xct = $xctables[$arr["valueType"]];
! 			$tn = "xc_$xid";
  			$tables[$tn] = array(
  				"$config[dbDynamic]BioAssayExtra$xct$expid $tn",
--- 708,712 ----
  		{
  			$xct = $xctables[$arr["valueType"]];
! 			$tn = "baef_$xid";
  			$tables[$tn] = array(
  				"$config[dbDynamic]BioAssayExtra$xct$expid $tn",

Index: bioassayset.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/bioassayset.inc.php,v
retrieving revision 1.21
retrieving revision 1.22
diff -C2 -d -r1.21 -r1.22
*** bioassayset.inc.php	10 Feb 2003 08:40:42 -0000	1.21
--- bioassayset.inc.php	11 Feb 2003 14:43:08 -0000	1.22
***************
*** 154,158 ****
  		if(!$this->extraColumns)
  			$this->extraColumns = ExtraDataColumn::getBriefForSet($this->id);
! 		return $this->hasExtraColumns;
  	}
  
--- 154,158 ----
  		if(!$this->extraColumns)
  			$this->extraColumns = ExtraDataColumn::getBriefForSet($this->id);
! 		return $this->extraColumns;
  	}
  
***************
*** 169,172 ****
--- 169,176 ----
  		$this->intensityMeasure = $val;
  	}
+ 	function setHasExtraColumns($val)
+ 	{
+ 		$this->hasExtraColumns = $val ? 1 : 0;
+ 	}
  
  	// Adds another extra data column for this bioassayset.
***************
*** 709,716 ****
  		for($i = 1; $i <= $channels; $i++)
  			$columns[] = "intensity$i";
! 		if(!db_tabfile_load($fname, $table, $columns))
  			return false;
  		return $this->updateGeneTable(false);
  	}
  }
  
--- 713,731 ----
  		for($i = 1; $i <= $channels; $i++)
  			$columns[] = "intensity$i";
! 		if(db_tabfile_load($fname, $table, $columns) < 1)
  			return false;
  		return $this->updateGeneTable(false);
  	}
+ 
+ 	function importExtraFloats($fname)
+ 	{
+ 		global $config;
+ 		$table = "$config[dbDynamic]BioAssayExtraFloat$this->experiment";
+ 		$columns = array("bioAssay", "position", "extraDataColumn",
+ 			"extraValue");
+ 		if(db_tabfile_load($fname, $table, $columns) < 1)
+ 			return false;
+ 		return true;
+ 	}
  }
  
***************
*** 948,957 ****
  		for(reset($arr), $i = 0; list($id, $a) = each($arr); $i++)
  		{
! 			$expr[] = array("_xc_$id", $types[$a["valueType"]],
! 				"%%.extraValue", $a["name"]);
! 			Search::bindExpressionToTable($expr[$i], "xc_$id");
  		}
  		return $expr;
  	}
  }
  
--- 963,976 ----
  		for(reset($arr), $i = 0; list($id, $a) = each($arr); $i++)
  		{
! 			$name = $a["name"];
! 			$expr[] = array("_xc_".printable($name), $types[$a["valueType"]],
! 				"%%.extraValue", $name);
! 			$tname = "baef_$id";
! 			$comm = "[Extra]";
! 			Search::bindExpressionToTable($expr[$i], $tname, $comm);
  		}
  		return $expr;
  	}
+ 
  }
  

Index: jobhandler.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/jobhandler.inc.php,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** jobhandler.inc.php	10 Feb 2003 08:40:45 -0000	1.9
--- jobhandler.inc.php	11 Feb 2003 14:43:10 -0000	1.10
***************
*** 358,361 ****
--- 358,370 ----
  			unset($parents);
  		}
+ 
+ 		// Find the ids of the extra float columns
+ 		for(reset($extraFloats); list($ef) = each($extraFloats); )
+ 		{
+ 			$efid = ExtraDataColumn::getIdFromNameAndType($ef, 0, true);
+ 			if(!$efid)
+ 				return "Can't create extra float column '$ef'\n";
[...117 lines suppressed...]
+ 			unlink($tempfileextra);
  			return "assayImporter returned $rc: ".implode("\n", $res);
  		}
! 		$ok = $set->importBASEfile($tempfile2, $channels);
  		unlink($tempfile2);
! 		if(!$ok)
! 		{
! 			unlink($tempfileextra);
  			return "Failed to import assay data into database";
+ 		}
+ 
+ 		if($extraFloats)
+ 			$ok = $set->importExtraFloats($tempfileextra);
+ 		else
+ 			$ok = true;
+ 		unlink($tempfileextra);
+ 		if(!$ok)
+ 			return "Failed to import extra float columns into database";
  		return "";
  	}