public static function newFromProlucidSearchInstance($table, $inst)
{
global $toprundir;
$toprundir = "/tmp/";
$jobclus = new ProlucidJobCluster();
$jobclus->setEmail("*****@*****.**");
$fh = new FileHandler();
print "\nGenerating input files for [" . $inst->getName() . "]\n";
$exname = $inst->getPropertyValue("Experiment");
$ex = new TypeInstance("Experiment", $exname);
$ex->fetch($table);
$jobclus->setExperiment($ex);
// Set the experiment
$dbname = $inst->getPropertyValue("Protein_Database");
$db = new TypeInstance("Protein_Database", $dbname);
$db->fetch($table);
$dbfile = preg_replace("#http://DUMMYHOST.ROOTDIR/misc/MiniFileView.php/#", "", $db->getPropertyValue("File"));
$dbfile = $fh->getFilePath($dbfile);
$jobclus->setDatabaseFile($dbfile);
// Set the database
$jobclus->setSourceInstance($inst);
// Set the source instance
$jobclus->setSourceType("Prolucid_Search");
// Set the source type
$count = 1;
$jobname = $inst->getName() . "_LSF_Job_" . $count;
$jobinst = new TypeInstance("LSF_Job", $jobname);
while ($jobinst->exists($table)) {
$count++;
$jobname = $inst->getName() . "_LSF_Job_" . $count;
$jobinst = new TypeInstance("LSF_Job", $jobname);
}
$jobdir = $toprundir . $jobname . "/";
$outdir = $jobdir . "out";
$jobclus->setJobName($jobname);
// Set the job name
$jobclus->setRunDir($jobdir);
// Set the job directory
$jobclus->setOutDir($outdir);
// Set the output directory
return $jobclus;
}
<?php
$topdir = dirname(dirname(__FILE__));
error_reporting(E_ALL);
require_once "{$topdir}/GlobalConfig.php";
require_once "{$topdir}/plugins/HarvardSMLims/ProlucidJobCluster.php";
require_once "{$topdir}/datamodel/TestDB.php";
require_once "Test.php";
$tname = 'semantic_data';
$sqlfile = 'testdb_small.sql';
$sqlfile2 = getcwd() . '/prolucid.sql';
$test = new Test();
$testdb = new TestDB();
$test->result($testdb, "Created TestDB");
$testdb->load_sql($sqlfile2);
$test->result($testdb, "Loaded prolucid sql");
$table = $testdb->getTable();
$test->result($table, "Got Table");
$plinst = new TypeInstance("Prolucid_Search", "PRO00001");
$plinst->fetch($table);
print $plinst->printValues() . "\n";
$jobclus = ProlucidJobCluster::newFromProlucidSearchInstance($table, $plinst);
$jobclus->split();
$test->print_total("ProlucidJobCluster");