public function saveColor()
{
try {
$model = new TypeInstance($this->data->idAnnotationStatus);
$model->setIdColor($this->data->idColor);
$model->save();
$this->renderPrompt('information', 'OK');
} catch (\Exception $e) {
$this->renderPrompt('error', $e->getMessage());
}
}
public function setIdAnnotationStatus($value)
{
if (substr($value, 0, 3) == 'ast') {
$as = new TypeInstance();
$filter = (object) ['entry' => $value];
$idStatus = $as->listAnnotationStatus($filter)->asQuery()->getResult()[0]['idAnnotationStatus'];
} else {
$idStatus = $value;
}
parent::setIdAnnotationStatus($idStatus);
}
public function setIdInstantiationTypeFromEntry($entry)
{
$ti = new TypeInstance();
$idInstantiationType = $ti->getIdInstantiationTypeByEntry($entry);
parent::setIdInstantiationType($idInstantiationType);
}
public function createFromFrame($idFrame)
{
$transaction = $this->beginTransaction();
try {
$frame = new Frame($idFrame);
$this->setEntry('tpl_' . strtolower(str_replace('frm_', '', $frame->getEntry())));
$this->save();
Base::createEntityRelation($this->getIdEntity(), 'rel_createdfrom', $frame->getIdEntity());
$fes = $frame->listFE()->asQuery()->asObjectArray();
$fe = new FrameElement();
foreach ($fes as $feData) {
$fe->setPersistent(false);
$feEntry = $this->getEntry() . '_' . $feData->entry;
$entry = new Entry();
$entry->cloneEntry($feData->entry, $feEntry);
$fe->setEntry($feData->entry);
$entity = new Entity();
$entity->setAlias($feEntry);
$entity->setType('FE');
$entity->save();
Base::createEntityRelation($entity->getId(), 'rel_elementof', $this->getIdEntity());
$coreType = new TypeInstance($feData->idCoreType);
Base::createEntityRelation($entity->getId(), 'rel_hastype', $coreType->getIdEntity());
$fe->setIdEntity($entity->getId());
$fe->setActive(true);
$fe->setIdColor($feData->idColor);
$fe->saveModel();
}
$transaction->commit();
} catch (\Exception $e) {
$transaction->rollback();
throw new \Exception($e->getMessage());
}
}
public function createFromData($fe)
{
$this->setPersistent(false);
$this->setEntry($fe->entry);
$this->setActive($fe->active);
$this->setIdEntity($fe->idEntity);
$this->setIdColor($fe->idColor);
$coreType = new TypeInstance();
$idCoreType = $coreType->getIdCoreTypeByEntry($fe->coreType);
$coreType->getById($idCoreType);
Base::createEntityRelation($fe->idEntity, 'rel_hastype', $coreType->getIdEntity());
parent::save();
}
public static function newFromProlucidSearchInstance($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");
