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 "";
}
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