function index()
{
if (isset($_POST['submit'])) {
$this->model->loginAdmin();
}
$this->principalData['formToken'] = FormElements::formToken();
$this->principalData['logged'] = Session::getSession('logged');
if (FlashMessages::hasFlashMessage()) {
$this->principalData['FlashMessage'] = FlashMessages::displayFlashMessage();
}
View::setHeaderVars('title', 'Administration Home');
View::render('sidebar-admin');
View::render('administration/index', $this->principalData);
}
public function checkFormToken($formToken = null, $redirectTo = 'index', $redirectTime = 5)
{
if ($formToken != Session::getSession('formToken')) {
Session::unsetSession('formToken');
FlashMessages::setFlashMessage('warning', '<b>Form Authentication Error!</b><br />You Will be Redirected in 5 Seconds.');
FlashMessages::redirectFlashMessage($redirectTo, $redirectTime);
}
}
function searchCluster($sqlDataArray = array())
{
if (isset($_POST['search'])) {
$this->dataArray = array('cluster_chromosome' => FormElements::getPostInteger('inputSearchChromosome', true), 'cluster_start' => FormElements::getPostInteger('inputSearchStart', true), 'cluster_end' => FormElements::getPostInteger('inputSearchEnd', true));
$this->formToken = FormElements::getPostString('token', true);
parent::checkFormRequired($this->dataArray);
parent::checkFormToken($this->formToken, 'search/cluster');
} elseif (isset($_GET['cluster_chromosome']) && isset($_GET['cluster_start']) && isset($_GET['cluster_end'])) {
$this->dataArray = array('cluster_chromosome' => FormElements::filterInteger($_GET['cluster_chromosome'], true), 'cluster_start' => FormElements::filterInteger($_GET['cluster_start'], true), 'cluster_end' => FormElements::filterInteger($_GET['cluster_end'], true));
}
if (!in_array('errorRequiredField', $this->dataArray) && (isset($_GET['cluster_chromosome']) || $this->formToken === Session::getSession('formToken')) && !FlashMessages::hasFlashMessage()) {
$cookieData = date('Y-m-d') . '|cluster|' . 'cluster_chromosome|' . $this->dataArray['cluster_chromosome'] . '|cluster_start|' . $this->dataArray['cluster_start'] . '|cluster_end|' . $this->dataArray['cluster_end'];
if (isset($_COOKIE['pirna_db_cache_search'])) {
$newData = $_COOKIE['pirna_db_cache_search'] . '@' . $cookieData;
} else {
$newData = $cookieData;
}
setcookie('pirna_db_cache_search', $newData, time() + 86400 * 30 * 30, '/');
Session::unsetSession('formToken');
$this->sqlAllResults = 'SELECT cluster_code,
cluster_chromosome,
cluster_start,
cluster_end
FROM cluster
WHERE cluster_chromosome = ' . $this->dataArray['cluster_chromosome'] . ' AND
cluster_start >= ' . $this->dataArray['cluster_start'] . ' AND
cluster_end <= ' . $this->dataArray['cluster_end'];
$this->allResults = $this->db->select($this->sqlAllResults);
$this->results[0] = count($this->allResults);
$this->results[1] = ceil($this->results[0] / $sqlDataArray['maximumQuantity']);
$this->sql = 'SELECT cluster_code,
cluster_chromosome,
cluster_start,
cluster_end
FROM cluster
WHERE cluster_chromosome = ' . $this->dataArray['cluster_chromosome'] . ' AND
cluster_start >= ' . $this->dataArray['cluster_start'] . ' AND
cluster_end <= ' . $this->dataArray['cluster_end'] . '
LIMIT :initialItem, :maximumQuantity';
$this->results[2] = $this->db->select($this->sql, $sqlDataArray);
$this->results[3] = '?cluster_chromosome=' . $this->dataArray['cluster_chromosome'] . '&' . 'cluster_start=' . $this->dataArray['cluster_start'] . '&' . 'cluster_end=' . $this->dataArray['cluster_end'];
if ($this->results[0] > 0) {
return $this->results;
} else {
FlashMessages::setFlashMessage('noresult', '<b>Not Found!</b><br />None cluster was found using your query..');
}
}
}
function addDataset()
{
$isGeo = FormElements::getPostString('isGeoAddDataset', true);
$dataset_reference = FormElements::getPostString('referenceAddDataset', false);
$this->table = 'dataset';
$this->dataArray = array('dataset_sample' => FormElements::getPostString('sampleAddDataset', true), 'dataset_serie' => FormElements::getPostString('serieAddDataset', true), 'dataset_organism' => FormElements::getPostString('organismAddDataset', false), 'dataset_development_stage' => FormElements::getPostString('developmentStageAddDataset', false), 'dataset_method' => FormElements::getPostString('methodAddDataset', false), 'dataset_tissue' => FormElements::getPostString('tissueAddDataset', false));
if ($isGeo === 'another') {
$this->dataArray['dataset_sample'] = 'Supplementary ' . $dataset_reference;
$this->dataArray['dataset_serie'] = '';
}
$this->formToken = FormElements::getPostString('token', true);
if (in_array('errorRequiredField', $this->dataArray)) {
FlashMessages::setFlashMessage('error', '<b>Error Required Field!</b><br />Please Check the Information Sent.');
}
if ($this->formToken != Session::getSession('formToken')) {
Session::unsetSession('formToken');
FlashMessages::setFlashMessage('warning', '<b>Form Authentication Error!</b><br />You Will be Redirected in 5 Seconds.');
FlashMessages::redirectFlashMessage('administration/adddataset', 5);
}
if ($isGeo != 'another') {
$this->sql = 'SELECT dataset_id
FROM dataset
WHERE dataset_sample = "' . $this->dataArray['dataset_sample'] . '"';
$this->results['datasetAlreadyExists'] = count($this->db->select($this->sql));
} else {
$this->results['datasetAlreadyExists'] === 0;
}
if (!in_array('errorRequiredField', $this->dataArray) && $this->formToken === Session::getSession('formToken') && !FlashMessages::hasFlashMessage() && $this->results['datasetAlreadyExists'] <= 0) {
Session::unsetSession('formToken');
$this->resultsDelete = $this->db->insert($this->table, $this->dataArray);
$this->sql = 'SELECT reference_id
FROM reference
WHERE reference_code = "' . $dataset_reference . '"';
$this->results['referenceAlreadyExists'] = $this->db->select($this->sql);
if (count($this->results['referenceAlreadyExists']) > 0) {
$this->table = 'rel_dataset_reference';
$this->dataArray = array('reference_id' => $this->results['referenceAlreadyExists'][0]['reference_id'], 'dataset_id' => $this->resultsDelete);
$this->resultsAddReference = $this->db->insert($this->table, $this->dataArray);
} else {
$pubMedReferenceInfo = file_get_contents('http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=' . $dataset_reference);
preg_match('/<Item Name="PubDate" Type="Date">([0-9]{4})/U', $pubMedReferenceInfo, $tempDateData);
preg_match('/<Item Name="Source" Type="String">(.*)<\\/Item>/U', $pubMedReferenceInfo, $tempSourceData);
preg_match_all('/<Item Name="Author" Type="String">([a-zA-Z ]{1,})<\\/Item>/U', $pubMedReferenceInfo, $tempAuthorData);
preg_match('/<Item Name="Title" Type="String">(.*)<\\/Item>/U', $pubMedReferenceInfo, $tempTitleData);
$author = '';
foreach ($tempAuthorData[0] as $authorData) {
$author .= strip_tags($authorData) . '; ';
}
$author = rtrim($author, '; ');
$this->table = 'reference';
$this->dataArray = array('reference_code' => $dataset_reference, 'reference_title' => strip_tags($tempTitleData[0]), 'reference_author' => $author, 'reference_journal' => strip_tags($tempSourceData[0]), 'reference_date' => strip_tags($tempDateData[0]));
$this->resultsAddReference = $this->db->insert($this->table, $this->dataArray);
$this->table = 'rel_dataset_reference';
$this->dataArray = array('reference_id' => $this->resultsAddReference, 'dataset_id' => $this->resultsDelete);
$this->resultsAddReference = $this->db->insert($this->table, $this->dataArray);
}
if (count($this->resultsDelete) === 1) {
FlashMessages::setFlashMessage('success', '<b>Success!</b><br />Create Succesfully.');
} else {
FlashMessages::setFlashMessage('error', '<b>Error!</b><br />Create Unsuccesfully.');
}
} else {
FlashMessages::setFlashMessage('error', '<b>Error!</b><br />Create Unsuccesfully.');
}
}
