public static function fromJSON($filename)
{
$jc = new JobConfiguration();
try {
if (!file_exists($filename) || !is_readable($filename)) {
throw new Exception('JSON template file does not exist or is not readable.');
}
$json = file_get_contents($filename);
if (!($arr = json_decode($json, true))) {
throw new Exception('JSON incorrectly formatted');
}
$jc->content = $arr;
return $jc;
} catch (Exception $e) {
Log::debug("{$e} - using empty JobConf");
return $jc;
}
}
public function createAnnotationVectorRelEx()
{
try {
// AMT
if (isset($this->content['Q1text'])) {
$ans = str_replace(" ", "_", rtrim($this->content['Q1text']));
$ans = str_replace("[DIAGNOSED_BY_TEST_OR_DRUG]", "[DIAGNOSE_BY_TEST_OR_DRUG]", $ans);
if ($ans == '') {
return null;
}
// throw new Exception('Answer is empty.');
$ans = str_replace("]_[", "]*[", $ans);
$ans = explode('*', $ans);
// CF
} elseif (isset($this->content['step_1_select_the_valid_relations'])) {
if (is_array($this->content['step_1_select_the_valid_relations'])) {
$ans = $this->content['step_1_select_the_valid_relations'];
} else {
$ans = str_replace("\n", "_", rtrim($this->content['step_1_select_the_valid_relations']));
$ans = str_replace("\r", "_", $ans);
$ans = str_replace("]_[", "]*[", $ans);
$ans = explode('*', $ans);
}
} else {
throw new Exception('Can\'t determine if it\'s CF or AMT.');
}
/* if(in_array("[NONE]", $ans)){
if(count($ans)>1)
throw new Exception('Worker selected none but also other relations.');
if(empty($this->content['Q2b']))
throw new Exception('Worker selected [NONE] but gave no explanation.');
} elseif(empty($this->content['Q2a'])){
throw new Exception('Worker selected a relation but didn\'t hightlight words');
}*/
$dic = array("[TREATS]" => in_array("[TREATS]", $ans) ? 1 : 0, "[CAUSES]" => in_array("[CAUSES]", $ans) ? 1 : 0, "[PREVENTS]" => in_array("[PREVENTS]", $ans) ? 1 : 0, "[IS_A]" => in_array("[IS_A]", $ans) ? 1 : 0, "[OTHER]" => in_array("[OTHER]", $ans) ? 1 : 0, "[NONE]" => in_array("[NONE]", $ans) ? 1 : 0, "[PART_OF]" => in_array("[PART_OF]", $ans) ? 1 : 0, "[DIAGNOSE_BY_TEST_OR_DRUG]" => in_array("[DIAGNOSE_BY_TEST_OR_DRUG]", $ans) ? 1 : 0, "[ASSOCIATED_WITH]" => in_array("[ASSOCIATED_WITH]", $ans) ? 1 : 0, "[SIDE_EFFECT]" => in_array("[SIDE_EFFECT]", $ans) ? 1 : 0, "[SYMPTOM]" => in_array("[SYMPTOM]", $ans) ? 1 : 0, "[LOCATION]" => in_array("[LOCATION]", $ans) ? 1 : 0, "[MANIFESTATION]" => in_array("[MANIFESTATION]", $ans) ? 1 : 0, "[CONTRAINDICATES]" => in_array("[CONTRAINDICATES]", $ans) ? 1 : 0);
// We decided to give the spammers just empty vectors.
/* foreach($ans as $a){
if(!in_array($a, array_keys($dic)))
throw new Exception("Answer $a not in annotationVector.");
}
if(!in_array(1, $dic)){
throw new Exception('AnnotationVector EMPTY');
}*/
return array('extraction' => $dic);
} catch (Exception $e) {
echo $e->getMessage();
Log::debug($e->getMessage());
return null;
}
}
/**
* In case of exception: undo everything.
* @throws Exception if even the undo isn't working.
*/
private function undoCreation($ids, $error = null)
{
// TODO use platformjobid.
Log::debug("Attempting to delete jobs from crowdsourcing platform.");
try {
$this->getPlatform()->undoCreation($ids);
} catch (Exception $e) {
// This is bad.
if ($error) {
$orige = $error->getMessage();
} else {
$orige = 'None.';
}
$newe = $e->getMessage();
throw new Exception("WARNING. There was an error in uploading the jobs. We could not undo all the steps. \n\t\t\t\tPlease check the platforms manually and delete any uploaded jobs.\n\t\t\t\t<br>Initial exception: {$orige}\n\t\t\t\t<br>Deletion error: {$newe}\n\t\t\t\t<br>Please contact an administrator.");
Log::warning("Couldn't delete jobs. Please manually check the platforms and database.\r\nInitial exception: {$orige}\n\t\t\t\t\r\nDeletion error: {$newe}\r\nActivity: {$this->activityURI}\r\nJob ID's: " . json_encode($ids));
}
}