function information($paramOne = null)
{
$this->updateItem = FormElements::filterString($paramOne);
$this->model->quantityCacheSearch();
$this->model->breadCumbs();
$this->model->footerFaq();
$this->model->footerSystemUpdate();
if ($this->updateItem != null) {
$this->sqlDataArray = array('info_update_id' => $this->updateItem);
$this->updateData = $this->model->getUpdate($this->sqlDataArray);
if (FlashMessages::hasFlashMessage()) {
$this->principalData['FlashMessage'] = FlashMessages::displayFlashMessage();
} else {
$this->principalData['updateData'] = $this->updateData[0];
$this->principalData['updateItem'] = true;
}
} else {
$this->updateData = $this->model->getUpdate();
if (FlashMessages::hasFlashMessage()) {
$this->principalData['FlashMessage'] = FlashMessages::displayFlashMessage();
} else {
$this->principalData['updateData'] = $this->updateData;
$this->principalData['updateItem'] = false;
}
}
View::setHeaderVars('title', 'Update Information');
View::setHeaderVars('specificKeywords', '');
View::setHeaderVars('description', '');
View::setHeaderVars('cannonicalUrl', '');
View::setHeaderVars('robots', 'noindex, nofollow');
View::render('header');
View::render('update/index', $this->principalData);
View::render('footer');
}
function archive($paramOne = 'pirna', $paramTwo = null, $paramThree = null)
{
$this->actualPage = FormElements::filterString($paramOne);
$this->dataType = FormElements::filterString($paramTwo);
$this->archiveExtension = FormElements::filterString($paramThree);
$this->model->quantityCacheSearch();
$this->model->BreadCumbs();
$this->model->footerFaq();
$this->model->footerSystemUpdate();
$this->principalData['downloadPage'] = false;
if (!empty($this->dataType) && !empty($this->archiveExtension)) {
$this->principalData['downloadPage'] = true;
}
$this->principalData['activeDownloadPirna'] = '';
$this->principalData['activeDownloadDataset'] = '';
$this->principalData['activeDownloadAlignament'] = '';
$this->principalData['activeDownloadCluster'] = '';
if ($this->actualPage === 'pirna') {
$this->model->generateLog('download pirna', 'download', '400');
$this->principalData['activeDownloadPirna'] = 'class="active"';
$this->temporaryTitle = 'piRNA';
$this->principalData['sizeHsaFile'] = Files::getFileSize('downloads/pirna/hsa-pirna-list.txt');
$this->principalData['downloadType'] = 'pirna/hsa-pirna-list';
$this->cannonicalUrl = URL . 'download/archive/pirna';
} elseif ($this->actualPage === 'dataset') {
$this->model->generateLog('download dataset', 'download', '420');
$this->principalData['activeDownloadDataset'] = 'class="active"';
$this->temporaryTitle = 'Dataset';
$this->principalData['sizeHsaFile'] = Files::getFileSize('downloads/dataset/hsa-dataset-list.txt');
$this->principalData['downloadType'] = 'dataset/hsa-dataset-list';
$this->cannonicalUrl = '';
} elseif ($this->actualPage === 'alignament') {
$this->model->generateLog('download alignament', 'download', '440');
$this->principalData['activeDownloadAlignament'] = 'class="active"';
$this->temporaryTitle = 'Alignament';
$this->principalData['sizeHsaFile'] = Files::getFileSize('downloads/alignament/hsa-alignament-list.txt');
$this->principalData['downloadType'] = 'alignament/hsa-alignament-list';
$this->cannonicalUrl = '';
} elseif ($this->actualPage === 'cluster') {
$this->model->generateLog('download cluster', 'download', '430');
$this->principalData['activeDownloadCluster'] = 'class="active"';
$this->temporaryTitle = 'Cluster';
$this->principalData['sizeHsaFile'] = Files::getFileSize('downloads/cluster/hsa-cluster-list.txt');
$this->principalData['downloadType'] = 'cluster/hsa-cluster-list';
$this->cannonicalUrl = '';
}
$this->principalData['downloadTitle'] = $this->temporaryTitle;
View::setHeaderVars('title', 'Download ' . $this->temporaryTitle);
View::setHeaderVars('specificKeywords', DEFAULT_KEYWORDS . ', piRNA download, dataset download, alignament download');
View::setHeaderVars('description', 'Download piRNA sequences, alignaments or full datasets');
View::setHeaderVars('cannonicalUrl', $this->cannonicalUrl);
View::setHeaderVars('robots', 'index, follow');
View::render('header');
View::render('download/index', $this->principalData);
View::render('footer');
}
function searchCache($sqlDataArray = array())
{
if (isset($_COOKIE['pirna_db_cache_search'])) {
$this->rawData = explode('@', FormElements::filterString($_COOKIE['pirna_db_cache_search']));
$quantity = count($this->rawData);
for ($num = 0; $num < $quantity; ++$num) {
$this->temporaryData[$num] = explode('|', $this->rawData[$num]);
}
if ($sqlDataArray['cache_type'] === 'pirna') {
$tempNumber = 0;
for ($num = 0; $num < $quantity; ++$num) {
if ($this->temporaryData[$num][1] === 'pirna') {
$this->results[$tempNumber]['cacheDate'] = Dates::convertDate($this->temporaryData[$num][0]);
$this->results[$tempNumber]['cacheUrl'] = 'pirna/1?pirna_code=' . $this->temporaryData[$num][3];
$this->results[$tempNumber]['cacheUrl'] .= '&pirna_organism=' . $this->temporaryData[$num][5];
$this->results[$tempNumber]['cacheQuery'] = 'piRNA Code = ' . $this->temporaryData[$num][3];
$this->results[$tempNumber]['cacheQuery'] .= ' & piRNA Organism = ' . $this->temporaryData[$num][5];
++$tempNumber;
}
}
} elseif ($sqlDataArray['cache_type'] === 'alignament') {
$tempNumber = 0;
for ($num = 0; $num < $quantity; ++$num) {
if ($this->temporaryData[$num][1] === 'alignament') {
$this->results[$tempNumber]['cacheDate'] = Dates::convertDate($this->temporaryData[$num][0]);
$this->results[$tempNumber]['cacheUrl'] = 'alignament/1?alignament_chromosome=' . $this->temporaryData[$num][3];
$this->results[$tempNumber]['cacheUrl'] .= '&alignament_start=' . $this->temporaryData[$num][5];
$this->results[$tempNumber]['cacheUrl'] .= '&alignament_end=' . $this->temporaryData[$num][7];
$this->results[$tempNumber]['cacheQuery'] = 'Chromosome = ' . $this->temporaryData[$num][3];
$this->results[$tempNumber]['cacheQuery'] .= ' & Start = ' . $this->temporaryData[$num][5];
$this->results[$tempNumber]['cacheQuery'] .= ' & End = ' . $this->temporaryData[$num][7];
++$tempNumber;
}
}
} elseif ($sqlDataArray['cache_type'] === 'cluster') {
$tempNumber = 0;
for ($num = 0; $num < $quantity; ++$num) {
if ($this->temporaryData[$num][1] === 'cluster') {
$this->results[$tempNumber]['cacheDate'] = Dates::convertDate($this->temporaryData[$num][0]);
$this->results[$tempNumber]['cacheUrl'] = 'cluster/1?cluster_chromosome=' . $this->temporaryData[$num][3] . '&cluster_start=' . $this->temporaryData[$num][5] . '&cluster_end=' . $this->temporaryData[$num][7];
$this->results[$tempNumber]['cacheQuery'] = 'Chromosome = ' . $this->temporaryData[$num][3] . ' & Start = ' . $this->temporaryData[$num][5] . ' & End = ' . $this->temporaryData[$num][7];
++$tempNumber;
}
}
}
}
$this->quantityResults = count($this->results);
if ($this->quantityResults > 0) {
return $this->results;
} else {
FlashMessages::setFlashMessage('noresult', '<b>Zero Results!</b><br />None of your cache search results was found.');
}
}
function informations($paramOne = 'pirna')
{
$this->actualPage = FormElements::filterString($paramOne);
$this->model->quantityCacheSearch();
$this->model->breadCumbs();
$this->model->footerFaq();
$this->model->footerSystemUpdate();
$this->principalData['activeAboutPirna'] = '';
$this->principalData['activeAboutDatabase'] = '';
$this->principalData['activeAboutDataset'] = '';
$this->principalData['activeAboutReference'] = '';
$this->principalData['activeAboutStatistics'] = '';
if ($this->actualPage === 'database') {
$this->sqlDataArray = array('text_type' => 'database');
$this->temporaryTitle = 'Database';
$this->principalData['activeAboutDatabase'] = 'class="active"';
} elseif ($this->actualPage === 'dataset') {
$this->sqlDataArray = array('text_type' => 'dataset');
$this->temporaryTitle = 'Dataset';
$this->principalData['activeAboutDataset'] = 'class="active"';
} elseif ($this->actualPage === 'reference') {
$this->sqlDataArray = array('text_type' => 'reference');
$this->temporaryTitle = 'Reference';
$this->principalData['activeAboutReference'] = 'class="active"';
} elseif ($this->actualPage === 'statistics') {
$this->temporaryTitle = 'Statistics';
$this->principalData['activeAboutStatistics'] = 'class="active"';
} else {
$this->sqlDataArray = array('text_type' => 'pirna');
$this->temporaryTitle = 'piRNA';
$this->principalData['activeAboutPirna'] = 'class="active"';
}
if ($this->actualPage === 'statistics') {
$this->aboutData = $this->model->getAboutStatistics();
$this->principalData['aboutDataTitle'] = $this->temporaryTitle;
$this->principalData['aboutData'] = $this->aboutData;
} else {
$this->aboutData = $this->model->getAboutInformation($this->sqlDataArray);
$this->principalData['aboutDataTitle'] = $this->temporaryTitle;
$this->principalData['aboutData'] = $this->aboutData['text_content'];
}
View::setHeaderVars('title', 'About ' . $this->temporaryTitle);
View::setHeaderVars('specificKeywords', DEFAULT_KEYWORDS . ' ,about pirna, about database, about dataset, about');
View::setHeaderVars('description', 'Informations about piRNAs, origin, functions, database and datasets');
View::setHeaderVars('cannonicalUrl', '');
View::setHeaderVars('robots', 'noindex, nofollow');
View::render('header');
View::render('about/index', $this->principalData);
View::render('footer');
}
function informations($paramOne = 'pirna')
{
$this->actualPage = FormElements::filterString($paramOne);
$this->model->quantityCacheSearch();
$this->model->BreadCumbs();
$this->model->footerFaq();
$this->model->footerSystemUpdate();
$this->principalData['activeFaqPirna'] = '';
$this->principalData['activeFaqDatabase'] = '';
$this->principalData['activeFaqDataset'] = '';
$this->principalData['activeFaqLogs'] = '';
if ($this->actualPage === 'pirna') {
$this->principalData['activeFaqPirna'] = 'class="active"';
$this->sqlDataArray = array('faq_type' => '1');
$this->temporaryTitle = 'piRNA';
$this->cannonicalUrl = URL . 'faq/informations/pirna';
} elseif ($this->actualPage === 'database') {
$this->principalData['activeFaqDatabase'] = 'class="active"';
$this->sqlDataArray = array('faq_type' => '2');
$this->temporaryTitle = 'Database';
$this->cannonicalUrl = '';
} elseif ($this->actualPage === 'dataset') {
$this->principalData['activeFaqDataset'] = 'class="active"';
$this->sqlDataArray = array('faq_type' => '3');
$this->temporaryTitle = 'Dataset';
$this->cannonicalUrl = '';
} elseif ($this->actualPage === 'logs') {
$this->principalData['activeFaqLogs'] = 'class="active"';
$this->sqlDataArray = array('faq_type' => '4');
$this->temporaryTitle = 'Logs';
$this->cannonicalUrl = '';
}
$this->faqData = $this->model->getFaqData($this->sqlDataArray);
$this->principalData['faqTitle'] = $this->temporaryTitle;
$this->principalData['faqData'] = $this->faqData;
$this->principalData['faqType'] = $this->actualPage;
View::setHeaderVars('title', 'FAQ/Help ' . $this->temporaryTitle);
View::setHeaderVars('specificKeywords', DEFAULT_KEYWORDS . ', faq pirna, help pirna, faq, help');
View::setHeaderVars('description', 'Questions and step-by-step about functions of database');
View::setHeaderVars('cannonicalUrl', $this->cannonicalUrl);
View::setHeaderVars('robots', 'index, follow');
View::render('header');
View::render('faq/index', $this->principalData);
View::render('footer');
}
function searchList($paramOne = null)
{
$this->actualPage = FormElements::filterString($paramOne);
$this->model->quantityCacheSearch();
$this->model->breadCumbs();
$this->model->footerFaq();
$this->model->footerSystemUpdate();
$this->principalData['activeCachePirna'] = '';
$this->principalData['activeCacheAlignament'] = '';
$this->principalData['activeCacheCluster'] = '';
if ($this->actualPage === 'pirna') {
$this->sqlDataArray = array('cache_type' => 'pirna');
$this->principalData['activeCachePirna'] = 'class="active"';
$this->temporaryTitle = 'piRNA';
} elseif ($this->actualPage === 'alignament') {
$this->sqlDataArray = array('cache_type' => 'alignament');
$this->principalData['activeCacheAlignament'] = 'class="active"';
$this->temporaryTitle = 'Alignament';
} elseif ($this->actualPage === 'cluster') {
$this->sqlDataArray = array('cache_type' => 'cluster');
$this->principalData['activeCacheCluster'] = 'class="active"';
$this->temporaryTitle = 'Cluster';
}
$this->cacheData = $this->model->searchCache($this->sqlDataArray);
if (FlashMessages::hasFlashMessage()) {
$this->principalData['FlashMessage'] = FlashMessages::displayFlashMessage();
} else {
$this->principalData['cacheData'] = $this->cacheData;
}
View::setHeaderVars('title', $this->temporaryTitle . ' Results Cache');
View::setHeaderVars('specificKeywords', DEFAULT_KEYWORDS . ', cache results, search pirna cache');
View::setHeaderVars('description', 'Stored piRNA search');
View::setHeaderVars('cannonicalUrl', '');
View::setHeaderVars('robots', 'noindex, nofollow');
View::render('header');
View::render('cache/index', $this->principalData);
View::render('footer');
}
function loadMoreComments($paramOne = null, $paramTwo = null)
{
$maximumQuantity = FormElements::filterInteger($paramTwo, true) + 1;
$this->sqlDataArray = array('pirnaCode' => FormElements::filterString($paramOne, true), 'initialItem' => 0, 'maximumQuantity' => $maximumQuantity);
$this->principalData = $this->model->loadMoreComments($this->sqlDataArray);
View::render('information/morecomments', $this->principalData);
}
function cluster($paramOne = 1)
{
$this->model->quantityCacheSearch();
$this->model->BreadCumbs();
$this->actualPage = FormElements::filterString($paramOne);
$this->principalData['resultPage'] = false;
if (isset($_POST['search']) || isset($_GET['cluster_chromosome']) && isset($_GET['cluster_start']) && isset($_GET['cluster_end'])) {
$this->principalData['resultPage'] = true;
$this->initialResult = ($this->actualPage - 1) * $this->resultsPerPage;
$this->sqlDataArray = array('initialItem' => $this->initialResult, 'maximumQuantity' => $this->resultsPerPage);
$this->searchResults = $this->model->searchCluster($this->sqlDataArray);
if (FlashMessages::hasFlashMessage()) {
$this->principalData['FlashMessage'] = FlashMessages::displayFlashMessage();
} else {
$this->principalData['resultCount'] = $this->searchResults[0];
$this->principalData['totalPages'] = $this->searchResults[1];
$this->principalData['resultSearch'] = $this->searchResults[2];
$this->principalData['resultQuery'] = $this->searchResults[3];
$this->temporaryPagination = $this->model->pagination($this->actualPage, $this->searchResults[1]);
$this->principalData['pagination'] = $this->temporaryPagination[0];
$this->principalData['activePagination'] = $this->temporaryPagination[1];
}
} else {
$this->principalData['formToken'] = FormElements::formToken();
}
$this->principalData['qttResultPage'] = $this->resultsPerPage;
$this->cannonicalUrl = URL . 'search/cluster';
$this->principalData['activeSearchPirna'] = '';
$this->principalData['activeSearchAlignament'] = '';
$this->principalData['activeSearchCluster'] = 'class="active"';
View::setHeaderVars('title', 'Search Cluster');
View::setHeaderVars('specificKeywords', '');
View::setHeaderVars('description', '');
View::setHeaderVars('cannonicalUrl', $this->cannonicalUrl);
View::setHeaderVars('robots', 'noindex, nofollow');
View::render('header');
View::render('search/cluster', $this->principalData);
View::render('footer-clean');
}
function searchAlignament($sqlDataArray = array())
{
if (isset($_POST['search'])) {
$this->dataArray = array('alignament_chromosome' => FormElements::getPostInteger('inputSearchChromosome', true), 'alignament_start' => FormElements::getPostInteger('inputSearchStart', true), 'alignament_end' => FormElements::getPostInteger('inputSearchEnd', true), 'build_code' => FormElements::getPostString('inputSearchBuild', true));
$this->formToken = FormElements::getPostString('token', true);
parent::checkFormRequired($this->dataArray);
parent::checkFormToken($this->formToken, 'search/alignament');
} elseif (isset($_GET['alignament_chromosome']) && isset($_GET['alignament_start']) && isset($_GET['alignament_end'])) {
$this->dataArray = array('alignament_chromosome' => FormElements::filterInteger($_GET['alignament_chromosome'], true), 'alignament_start' => FormElements::filterInteger($_GET['alignament_start'], true), 'alignament_end' => FormElements::filterInteger($_GET['alignament_end'], true), 'build_code' => FormElements::filterString($_GET['build_code'], true));
}
if (!in_array('errorRequiredField', $this->dataArray) && (isset($_GET['alignament_chromosome']) || $this->formToken === Session::getSession('formToken')) && !FlashMessages::hasFlashMessage()) {
$cookieData = date('Y-m-d') . '|alignament|' . 'alignament_chromosome|' . $this->dataArray['alignament_chromosome'] . '|alignament_start|' . $this->dataArray['alignament_start'] . '|alignament_end|' . $this->dataArray['alignament_end'] . '|build_code|' . $this->dataArray['build_code'];
if (isset($_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 alignament.alignament_id,
alignament.alignament_chromosome,
alignament.alignament_start,
alignament.alignament_end,
alignament.alignament_strand
FROM alignament
INNER JOIN rel_alignament_build
ON rel_alignament_build.alignament_id = alignament.alignament_id
AND rel_alignament_build.build_code = :build_code
AND alignament.alignament_chromosome = :alignament_chromosome
AND alignament.alignament_start >= :alignament_start
AND alignament.alignament_end <= :alignament_end';
$this->allResults = $this->db->select($this->sqlAllResults, $this->dataArray);
$this->results[0] = count($this->allResults);
$this->results[1] = ceil($this->results[0] / $sqlDataArray['maximumQuantity']);
$this->sql = 'SELECT alignament.alignament_id,
alignament.alignament_chromosome,
alignament.alignament_start,
alignament.alignament_end,
alignament.alignament_strand
FROM rel_alignament_build
INNER JOIN alignament
ON rel_alignament_build.alignament_id = alignament.alignament_id
AND rel_alignament_build.build_code = :build_code
AND alignament.alignament_chromosome = :alignament_chromosome
AND alignament.alignament_start >= :alignament_start
AND alignament.alignament_end <= :alignament_end
LIMIT ' . $sqlDataArray['initialItem'] . ', ' . $sqlDataArray['maximumQuantity'];
$this->results[2] = $this->db->select($this->sql, $this->dataArray);
$this->results[3] = '?alignament_chromosome=' . $this->dataArray['alignament_chromosome'] . '&' . 'alignament_start=' . $this->dataArray['alignament_start'] . '&' . 'alignament_end=' . $this->dataArray['alignament_end'] . '&' . 'build_code=' . $this->dataArray['build_code'];
if ($this->results[0] > 0) {
return $this->results;
} else {
FlashMessages::setFlashMessage('noresult', '<b>Not Found!</b><br />None alignament was found using your query..');
}
}
}
function deleteInfo($paramOne = null, $paramTwo = null)
{
$this->model->checkLogged();
if ($paramOne === 'pirna' && isset($_POST['submit'])) {
$this->model->sendDeleteInfo('pirna', FormElements::filterString($paramTwo, true));
} elseif ($paramOne === 'dataset' && isset($_POST['submit'])) {
$this->model->sendDeleteInfo('dataset', FormElements::filterString($paramTwo, true));
} elseif ($paramOne === 'cluster' && isset($_POST['submit'])) {
$this->model->sendDeleteInfo('cluster', FormElements::filterString($paramTwo, true));
} elseif ($paramOne === 'reference' && isset($_POST['submit'])) {
$this->model->sendDeleteInfo('reference', FormElements::filterString($paramTwo, true));
} elseif ($paramOne === 'target' && isset($_POST['submit'])) {
$this->model->sendDeleteInfo('target', FormElements::filterString($paramTwo, true));
} elseif ($paramOne === 'faq' && isset($_POST['submit'])) {
$this->model->sendDeleteInfo('faq', FormElements::filterString($paramTwo, true));
} elseif ($paramOne === 'article' && isset($_POST['submit'])) {
$this->model->sendDeleteInfo('article', FormElements::filterString($paramTwo, true));
} elseif ($paramOne === 'informations' && isset($_POST['submit'])) {
$this->model->sendDeleteInfo('informations', FormElements::filterString($paramTwo, true));
} elseif ($paramOne === 'contact' && isset($_POST['submit'])) {
$this->model->sendDeleteInfo('contact', FormElements::filterString($paramTwo, true));
} elseif ($paramOne === 'update' && isset($_POST['submit'])) {
$this->model->sendDeleteInfo('update', FormElements::filterString($paramTwo, true));
} elseif ($paramOne === 'pirnacomment' && isset($_POST['submit'])) {
$this->model->sendDeleteInfo('pirnacomment', FormElements::filterString($paramTwo, true));
}
$this->principalData['formToken'] = FormElements::formToken();
if (FlashMessages::hasFlashMessage()) {
$this->principalData['FlashMessage'] = FlashMessages::displayFlashMessage();
}
$this->principalData['typeItem'] = $paramOne;
$this->principalData['idItem'] = $paramTwo;
View::setHeaderVars('title', 'Admin');
View::render('sidebar-admin');
View::render('administration/deleteinfo', $this->principalData);
}
function getInfo($sqlDataArray = array(), $type = null)
{
if ($type === 'pirna') {
$this->sql = 'SELECT pirna_code,
pirna_access,
pirna_sequence,
pirna_organism,
pirna_feedback_agree,
pirna_feedback_disagree
FROM pirna
WHERE pirna_code = :searchQuery';
$this->results['pirnaInfo'] = $this->db->select($this->sql, $sqlDataArray);
if (count($this->results['pirnaInfo']) > 0) {
$this->sql = 'SELECT alignament_id
FROM rel_alignament_pirna
WHERE pirna_code = :searchQuery';
$this->results['alignamentInfo'] = $this->db->select($this->sql, $sqlDataArray);
$quantity = count($this->results['alignamentInfo']);
for ($num = 0; $num < $quantity; ++$num) {
$this->sql = 'SELECT alignament_chromosome,
alignament_start,
alignament_end,
alignament_strand
FROM alignament
WHERE alignament_id = ' . $this->results['alignamentInfo'][$num]['alignament_id'];
$this->results['allAlignamentInfo'][] = $this->db->select($this->sql, $sqlDataArray);
}
$this->sql = 'SELECT reference_id
FROM rel_pirna_reference
WHERE pirna_code = :searchQuery';
$this->results['referenceInfo'] = $this->db->select($this->sql, $sqlDataArray);
$quantity = count($this->results['referenceInfo']);
for ($num = 0; $num < $quantity; ++$num) {
$this->sql = 'SELECT reference_id,
reference_code
FROM reference
WHERE reference_id = ' . $this->results['referenceInfo'][$num]['reference_id'];
$this->results['allReferenceInfo'][] = $this->db->select($this->sql, $sqlDataArray);
}
$this->sql = 'SELECT dataset_id
FROM rel_dataset_pirna
WHERE pirna_code = :searchQuery';
$this->results['datasetInfo'] = $this->db->select($this->sql, $sqlDataArray);
$quantity = count($this->results['datasetInfo']);
for ($num = 0; $num < $quantity; ++$num) {
$this->sql = 'SELECT dataset_id,
dataset_sample,
dataset_serie,
dataset_organism,
dataset_development_stage,
dataset_method,
dataset_tissue
FROM dataset
WHERE dataset_id = ' . $this->results['datasetInfo'][$num]['dataset_id'];
$this->results['allDatasetInfo'][] = $this->db->select($this->sql, $sqlDataArray);
}
return $this->results;
} else {
FlashMessages::setFlashMessage('noresult', '<b>Not Found!</b><br />0 Results are found using this query.');
}
} elseif ($type === 'dataset') {
$this->sql = 'SELECT dataset_id,
dataset_sample,
dataset_serie,
dataset_organism,
dataset_development_stage,
dataset_method,
dataset_tissue
FROM dataset
WHERE dataset_id = :searchQuery';
$this->results['datasetInfo'] = $this->db->select($this->sql, $sqlDataArray);
if (count($this->results['datasetInfo']) > 0) {
$this->sql = 'SELECT pirna_code
FROM rel_dataset_pirna
WHERE dataset_id = "' . $this->results['datasetInfo'][0]['dataset_id'] . '"';
$this->results['pirnaInfo'] = $this->db->select($this->sql);
return $this->results;
} else {
FlashMessages::setFlashMessage('noresult', '<b>Not Found!</b><br />0 Results are found using this query.');
}
} elseif ($type === 'cluster') {
$this->sql = 'SELECT cluster_code,
cluster_chromosome,
cluster_start,
cluster_end
FROM cluster
WHERE cluster_code = :searchQuery';
$this->results['clusterInfo'] = $this->db->select($this->sql, $sqlDataArray);
if (count($this->results['clusterInfo']) > 0) {
$this->sql = 'SELECT alignament_id
FROM rel_alignament_cluster
WHERE cluster_code = :searchQuery';
$this->results['pirnaInfo'] = $this->db->select($this->sql, $sqlDataArray);
$quantity = count($this->results['pirnaInfo']);
for ($num = 0; $num < $quantity; ++$num) {
$this->sql = 'SELECT pirna_code
FROM rel_alignament_pirna
WHERE alignament_id = ' . $this->results['pirnaInfo'][$num]['alignament_id'];
$this->results['pirnaList'][] = $this->db->select($this->sql, $sqlDataArray);
}
return $this->results;
} else {
FlashMessages::setFlashMessage('noresult', '<b>Not Found!</b><br />0 Results are found using this query.');
}
} elseif ($type === 'reference') {
$this->sql = 'SELECT reference_id,
reference_code
FROM reference
WHERE reference_id = :searchQuery';
$this->results['referenceInfo'] = $this->db->select($this->sql, $sqlDataArray);
if (count($this->results['referenceInfo']) > 0) {
$edit = file_get_contents('http://www.ncbi.nlm.nih.gov/pubmed/' . $this->results['referenceInfo'][0]['reference_code']);
preg_match('/<title>(.*)<\\/title>/s', $edit, $title);
preg_match('/<AbstractText>(.*)<\\/AbstractText>/s', $edit, $abstract);
preg_match('/<div class="auths">(.*).<\\/div><div class="afflist">/s', $edit, $authors);
$authors[0] = preg_replace('/<sup>([0-9])<\\/sup>/s', '', $authors[0]);
$this->results['referenceTitle'] = FormElements::filterString($title[0]);
$this->results['referenceAbstract'] = FormElements::filterString($abstract[0]);
$this->results['referenceAuthors'] = FormElements::filterString($authors[0]);
return $this->results;
} else {
FlashMessages::setFlashMessage('noresult', '<b>Not Found!</b><br />0 Results are found using this query.');
}
} elseif ($type === 'target') {
$this->sql = 'SELECT target_id,
target_type,
target_name,
target_chromosome,
target_start,
target_end,
target_strand
FROM target
WHERE target_id = :searchQuery';
$this->results['targetInfo'] = $this->db->select($this->sql, $sqlDataArray);
if (count($this->results['targetInfo']) > 0) {
return $this->results;
} else {
FlashMessages::setFlashMessage('noresult', '<b>Not Found!</b><br />0 Results are found using this query.');
}
} elseif ($type === 'article') {
$this->sql = 'SELECT article_reference,
article_title,
article_author,
article_journal,
article_date
FROM system_article
WHERE article_reference = :searchQuery';
$this->results['articleInfo'] = $this->db->select($this->sql, $sqlDataArray);
if (count($this->results['articleInfo']) > 0) {
return $this->results;
} else {
FlashMessages::setFlashMessage('noresult', '<b>Not Found!</b><br />None article was found.');
}
} elseif ($type === 'faq') {
$this->sql = 'SELECT faq_id,
faq_title,
faq_content,
faq_date_update,
faq_type
FROM faq
WHERE faq_id = :searchQuery';
$this->results['faqInfo'] = $this->db->select($this->sql, $sqlDataArray);
$this->results['faqInfo'][0]['faq_date_update'] = Dates::convertDate($this->results['faqInfo'][0]['faq_date_update']);
if (count($this->results['faqInfo']) > 0) {
return $this->results;
} else {
FlashMessages::setFlashMessage('noresult', '<b>Not Found!</b><br />0 Results are found using this query.');
}
} elseif ($type === 'informations') {
$this->sql = 'SELECT text_id,
text_content,
text_type
FROM general_text
WHERE text_id = :searchQuery';
$this->results['informationsInfo'] = $this->db->select($this->sql, $sqlDataArray, false);
if (count($this->results['informationsInfo']) > 0) {
return $this->results;
} else {
FlashMessages::setFlashMessage('noresult', '<b>Not Found!</b><br />0 Results are found using this query.');
}
} elseif ($type === 'update') {
$this->sql = 'SELECT info_update_id,
info_update_title,
info_update_content,
info_update_date
FROM info_update
WHERE info_update_id = :searchQuery';
$this->results['updateInfo'] = $this->db->select($this->sql, $sqlDataArray, false);
if (count($this->results['updateInfo']) > 0) {
return $this->results;
} else {
FlashMessages::setFlashMessage('noresult', '<b>Not Found!</b><br />0 Results are found using this query.');
}
} elseif ($type === 'pirnaComment') {
$this->sql = 'SELECT comment_id,
comment_name,
comment_email,
comment_content,
comment_date,
comment_moderated
FROM comment
WHERE comment_id = :searchQuery';
$this->results['commentInfo'] = $this->db->select($this->sql, $sqlDataArray);
$this->sql = 'SELECT pirna_code
FROM rel_comment_pirna
WHERE comment_id = ' . $this->results['commentInfo'][0]['comment_id'];
$this->results['commentPirnaInfo'] = $this->db->select($this->sql, $sqlDataArray);
$this->results['commentInfo'][0]['comment_date'] = Dates::convertDate($this->results['commentInfo'][0]['comment_date']);
if (count($this->results['commentInfo']) > 0) {
return $this->results;
} else {
FlashMessages::setFlashMessage('noresult', '<b>Not Found!</b><br />0 Results are found using this query.');
}
} else {
FlashMessages::setFlashMessage('noresult', '<b>Not Found!</b><br />0 Results are found using this query.');
}
}
