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', $this->principalData); View::render('footer'); }
function getUpdate($sqlDataArray = array()) { if (isset($sqlDataArray['info_update_id'])) { $this->sql = 'SELECT info_update_title, info_update_id, info_update_content, info_update_date FROM info_update WHERE info_update_id = :info_update_id'; } else { $this->sql = 'SELECT info_update_title, info_update_id, info_update_date FROM info_update'; } $this->results = $this->db->select($this->sql, $sqlDataArray); $this->resultsQuantity = count($this->results); foreach ($this->results as $key => $footerData) { $this->results[$key]['info_update_title_url'] = Helpers::filterUrl($this->results[$key]['info_update_title']); $this->results[$key]['info_update_date'] = Dates::convertDate($this->results[$key]['info_update_date']); } if ($this->resultsQuantity > 0) { return $this->results; } else { FlashMessages::setFlashMessage('noresult', '<b>Not Found!</b><br />Update information you are looking for does not exist.'); } }
function searchCache($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 $this->results; } else { FlashMessages::setFlashMessage('noresult', '<b>Zero Results!</b><br />None of your cache search results was found.'); } }
function getBrowseCluster($sqlDataArray = array()) { $this->sqlAllResults = 'SELECT cluster_code FROM cluster'; $this->allResults = $this->db->select($this->sqlAllResults, $sqlDataArray); $this->results['quantityAllCluster'] = count($this->allResults); $this->sql = 'SELECT cluster_code, cluster_chromosome, cluster_start, cluster_end FROM cluster LIMIT :initialItem, :maximumQuantity'; $this->results['clusterList'] = $this->db->select($this->sql, $sqlDataArray); $this->results['totalPages'] = ceil($this->results['quantityAllCluster'] / $sqlDataArray['maximumQuantity']); if ($this->results['quantityAllCluster'] > 0) { return $this->results; } else { FlashMessages::setFlashMessage('noresult', '<b>Zero Results!</b><br />None cluster was found in database.'); } }
function searchList($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', $this->principalData); View::render('footer'); }
public function checkFormToken($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, $redirectTime); } }
function alignament($paramOne = null) { $this->actualPage = FormElements::filterString($paramOne); $this->model->quantityCacheSearch(); $this->model->BreadCumbs(); $this->sqlDataArray = array('alignament_id' => $this->actualPage); $this->resultInformation = $this->model->getInformation($this->sqlDataArray, 'alignament'); $this->resultPirna = $this->model->getPirna($this->sqlDataArray); if (FlashMessages::hasFlashMessage()) { $this->principalData['FlashMessage'] = FlashMessages::displayFlashMessage(); } else { $this->principalData['alignamentInfo'] = $this->resultInformation; $this->principalData['quantityPirna'] = $this->resultPirna['quantityPirna']; if ($this->principalData['quantityPirna'] > 0) { $this->principalData['listPirnaTwo'] = $this->resultPirna['listPirnaTwo']; $this->principalData['tabActive'] = $this->resultPirna['tabActive']; $this->principalData['contentTabActive'] = $this->resultPirna['contentTabActive']; } } View::setHeaderVars('title', 'Alignament Information'); View::setHeaderVars('specificKeywords', ''); View::setHeaderVars('description', ''); View::setHeaderVars('cannonicalUrl', ''); View::setHeaderVars('robots', 'index, follow'); View::render('header'); View::render('information/alignament', $this->principalData); View::render('footer-clean'); }
function cluster($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', $this->principalData); View::render('footer-clean'); }
function getInformation($sqlDataArray = array(), $type = null) { if ($type === 'pirna') { $this->sql = 'SELECT pirna_code, pirna_access, pirna_organism, pirna_sequence, pirna_feedback_agree, pirna_feedback_disagree FROM pirna WHERE pirna_code = :pirna_code'; $this->results['pirnaData'] = $this->db->select($this->sql, $sqlDataArray, false); $this->resultsQuantity = count($this->results); $this->sql = 'SELECT COUNT(rel_alignament_pirna.id) AS qttAlignaments FROM rel_alignament_pirna INNER JOIN rel_alignament_build ON rel_alignament_pirna.pirna_code = :pirna_code AND rel_alignament_pirna.alignament_id = rel_alignament_build.alignament_id AND rel_alignament_build.build_code = "hg38"'; $this->results['qttAlignamentsFirst'] = $this->db->select($this->sql, $sqlDataArray, false); $this->sql = 'SELECT COUNT(rel_alignament_pirna.id) AS qttAlignaments FROM rel_alignament_pirna INNER JOIN rel_alignament_build ON rel_alignament_pirna.pirna_code = :pirna_code AND rel_alignament_pirna.alignament_id = rel_alignament_build.alignament_id AND rel_alignament_build.build_code = "hg19"'; $this->results['qttAlignamentsSecond'] = $this->db->select($this->sql, $sqlDataArray, false); $this->sql = 'SELECT COUNT(DISTINCT target.target_id) AS qttTargets FROM target INNER JOIN rel_alignament_pirna ON rel_alignament_pirna.pirna_code = :pirna_code INNER JOIN alignament ON rel_alignament_pirna.alignament_id = alignament.alignament_id AND alignament.alignament_chromosome = target.target_chromosome AND alignament.alignament_start >= target.target_start AND alignament.alignament_end <= target.target_end AND alignament.alignament_strand = target.target_strand '; $this->results['qttTargets'] = $this->db->select($this->sql, $sqlDataArray, false); $this->sql = 'SELECT alignament.alignament_chromosome FROM alignament INNER JOIN rel_alignament_pirna ON rel_alignament_pirna.pirna_code = :pirna_code INNER JOIN rel_alignament_build ON rel_alignament_build.alignament_id = rel_alignament_pirna.alignament_id AND rel_alignament_build.alignament_id = alignament.alignament_id AND rel_alignament_build.build_code = "hg38" GROUP BY alignament.alignament_chromosome '; $this->results['qttChromosomesFirst'] = $this->db->select($this->sql, $sqlDataArray); $this->sql = 'SELECT alignament.alignament_chromosome FROM alignament INNER JOIN rel_alignament_pirna ON rel_alignament_pirna.pirna_code = :pirna_code INNER JOIN rel_alignament_build ON rel_alignament_build.alignament_id = rel_alignament_pirna.alignament_id AND rel_alignament_build.alignament_id = alignament.alignament_id AND rel_alignament_build.build_code = "hg19" GROUP BY alignament.alignament_chromosome '; $this->results['qttChromosomesSecond'] = $this->db->select($this->sql, $sqlDataArray); $this->sql = 'SELECT COUNT(alignament.alignament_strand) AS qttAlignaments FROM alignament INNER JOIN rel_alignament_pirna ON rel_alignament_pirna.pirna_code = :pirna_code AND rel_alignament_pirna.alignament_id = alignament.alignament_id AND alignament.alignament_strand = "p" '; $this->results['qttAlignamentsSense'] = $this->db->select($this->sql, $sqlDataArray, false); $this->sql = 'SELECT COUNT(alignament.alignament_strand) AS qttAlignaments FROM alignament INNER JOIN rel_alignament_pirna ON rel_alignament_pirna.pirna_code = :pirna_code AND rel_alignament_pirna.alignament_id = alignament.alignament_id AND alignament.alignament_strand = "m" '; $this->results['qttAlignamentsAntisense'] = $this->db->select($this->sql, $sqlDataArray, false); $this->sql = 'SELECT COUNT(DISTINCT rel_alignament_cluster.cluster_code) AS qttCluster FROM rel_alignament_cluster INNER JOIN rel_alignament_pirna ON rel_alignament_pirna.pirna_code = :pirna_code AND rel_alignament_pirna.alignament_id = rel_alignament_cluster.alignament_id '; $this->results['qttCluster'] = $this->db->select($this->sql, $sqlDataArray, false); $this->sql = 'SELECT COUNT(DISTINCT comment_id) AS qttComments FROM rel_comment_pirna WHERE pirna_code = :pirna_code'; $this->results['qttComments'] = $this->db->select($this->sql, $sqlDataArray, false); if ($this->resultsQuantity > 0) { return $this->results; } else { FlashMessages::setFlashMessage('noresult', '<b>Not Found!</b><br />piRNA you are looking for does not exist.'); } } elseif ($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 = :dataset_id'; $this->results = $this->db->select($this->sql, $sqlDataArray); $this->resultsQuantity = count($this->results); $this->results['geoInformation']['noResult'] = true; $this->results['isGeo'] = false; if (substr($this->results[0]['dataset_sample'], 0, 3) === 'GSM') { $this->results['isGeo'] = true; $url = 'http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=' . $this->results[0]['dataset_sample'] . '&targ=self&form=xml&view=quick'; $geoHeaders = get_headers($url); $geoHeadersStatus = substr($geoHeaders[0], 9, 3); if ($geoHeadersStatus === '200') { $geoInformation = file_get_contents($url); preg_match('/<Person>([a-zA-Z<>\\/0-9 ]{1,})<\\/Person>/U', $geoInformation, $tempAuthorName); if (!empty($tempAuthorName[0])) { $tempAuthorName[0] = preg_replace('/(<\\/Person>)/U', '', $tempAuthorName[0]); $tempAuthorName[0] = preg_replace('/(<[a-zA-Z]{1,}>)/U', '', $tempAuthorName[0]); $tempAuthorName[0] = preg_replace('/(<\\/[a-zA-Z]{1,}>)/U', '; ', $tempAuthorName[0]); $tempAuthorName[0] = rtrim($tempAuthorName[0], '; '); } preg_match('/<Laboratory>(.*)<\\/Laboratory>/U', $geoInformation, $tempLaboratoryName); preg_match('/<Department>(.*)<\\/Department>/U', $geoInformation, $tempDepartamentName); preg_match('/<Organization>(.*)<\\/Organization>/U', $geoInformation, $tempOrganizationName); preg_match('/<Platform iid="([a-zA-Z0-9]{1,})">/U', $geoInformation, $tempPlatformId); preg_match('/<Title>(.*)<\\/Title>/U', $geoInformation, $tempTitleDataset); preg_match('/<Type>(.*)<\\/Type>/U', $geoInformation, $tempTypeDataset); preg_match('/<Treatment-Protocol>(.*)<\\/Treatment-Protocol>/s', $geoInformation, $tempTreatmentProtocol); preg_match('/<Growth-Protocol>(.*)<\\/Growth-Protocol>/s', $geoInformation, $tempGrowthProtocol); preg_match('/<Molecule>(.*)<\\/Molecule>/U', $geoInformation, $tempMolecule); preg_match('/<Extract-Protocol>(.*)<\\/Extract-Protocol>/s', $geoInformation, $tempExtractProtocol); preg_match('/<Label-Protocol>(.*)<\\/Label-Protocol>/s', $geoInformation, $tempLabelProtocol); preg_match('/<Hybridization-Protocol>(.*)<\\/Hybridization-Protocol>/s', $geoInformation, $tempHybridizationProtocol); preg_match('/<Scan-Protocol>(.*)<\\/Scan-Protocol>/s', $geoInformation, $tempScanProtocol); preg_match('/<Description>(.*)<\\/Description>/Us', $geoInformation, $tempDescription); preg_match('/<Data-Processing>(.*)<\\/Data-Processing>/s', $geoInformation, $tempDataProcessing); $this->results['geoInformation']['author'] = isset($tempAuthorName[0]) ? $tempAuthorName[0] : ''; $this->results['geoInformation']['laboratory'] = isset($tempLaboratoryName[1]) ? $tempLaboratoryName[1] : ''; $this->results['geoInformation']['departament'] = isset($tempDepartamentName[1]) ? $tempDepartamentName[1] : ''; $this->results['geoInformation']['organization'] = isset($tempOrganizationName[1]) ? $tempOrganizationName[1] : ''; $this->results['geoInformation']['platform'] = isset($tempPlatformId[1]) ? $tempPlatformId[1] : ''; $this->results['geoInformation']['title'] = isset($tempTitleDataset[1]) ? $tempTitleDataset[1] : ''; $this->results['geoInformation']['type'] = isset($tempTypeDataset[1]) ? $tempTypeDataset[1] : ''; $this->results['geoInformation']['treatmentProtocol'] = isset($tempTreatmentProtocol[1]) ? $tempTreatmentProtocol[1] : ''; $this->results['geoInformation']['growthProtocol'] = isset($tempGrowthProtocol[1]) ? $tempGrowthProtocol[1] : ''; $this->results['geoInformation']['molecule'] = isset($tempMolecule[1]) ? $tempMolecule[1] : ''; $this->results['geoInformation']['extractProtocol'] = isset($tempExtractProtocol[1]) ? $tempExtractProtocol[1] : ''; $this->results['geoInformation']['labelProtocol'] = isset($tempLabelProtocol[1]) ? $tempLabelProtocol[1] : ''; $this->results['geoInformation']['hybridizationProtocol'] = isset($tempHybridizationProtocol[1]) ? $tempHybridizationProtocol[1] : ''; $this->results['geoInformation']['scanProtocol'] = isset($tempScanProtocol[1]) ? $tempScanProtocol[1] : ''; $this->results['geoInformation']['description'] = isset($tempDescription[1]) ? $tempDescription[1] : ''; $this->results['geoInformation']['dataProcessing'] = isset($tempDataProcessing[1]) ? $tempDataProcessing[1] : ''; $this->results['geoInformation']['noResult'] = false; } } if ($this->resultsQuantity > 0) { return $this->results; } else { FlashMessages::setFlashMessage('noresult', '<b>Not Found!</b><br />Dataset you are looking for does not exist.'); } } elseif ($type === 'cluster') { $this->sql = 'SELECT cluster_code, cluster_chromosome, cluster_start, cluster_end FROM cluster WHERE cluster_code = :cluster_code'; $this->results = $this->db->select($this->sql, $sqlDataArray); $this->resultsQuantity = count($this->results); if ($this->resultsQuantity > 0) { return $this->results[0]; } else { FlashMessages::setFlashMessage('noresult', '<b>Not Found!</b><br />Cluster you are looking for does not exist.'); } } elseif ($type === 'alignament') { $this->sql = 'SELECT alignament_id, alignament_chromosome, alignament_start, alignament_end, alignament_strand FROM alignament WHERE alignament_id = :alignament_id'; $this->results = $this->db->select($this->sql, $sqlDataArray); $this->results[0]['alignament_strand'] = Helpers::changeStrandIcon($this->results[0]['alignament_strand']); $this->resultsQuantity = count($this->results); if ($this->resultsQuantity > 0) { return $this->results[0]; } else { FlashMessages::setFlashMessage('noresult', '<b>Not Found!</b><br />The alignament you are looking for does not exist.'); } } }
function searchCluster($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 $this->results; } else { FlashMessages::setFlashMessage('noresult', '<b>Not Found!</b><br />None cluster was found using your query..'); } } }
function createInfo($paramOne = null) { $this->model->checkLogged(); if ($paramOne === 'faq') { if (isset($_POST['submit'])) { $this->model->sendCreateInfo('faq'); } $this->principalData['formToken'] = FormElements::formToken(); if (FlashMessages::hasFlashMessage()) { $this->principalData['FlashMessage'] = FlashMessages::displayFlashMessage(); } View::setHeaderVars('title', 'Admin'); View::render('sidebar-admin'); View::render('administration/createinfofaq', $this->principalData); } elseif ($paramOne === 'article') { if (isset($_POST['submit'])) { $this->model->sendCreateInfo('article'); } $this->principalData['formToken'] = FormElements::formToken(); if (FlashMessages::hasFlashMessage()) { $this->principalData['FlashMessage'] = FlashMessages::displayFlashMessage(); } View::setHeaderVars('title', 'Admin'); View::render('sidebar-admin'); View::render('administration/createinfoarticle', $this->principalData); } elseif ($paramOne === 'informations') { if (isset($_POST['submit'])) { $this->model->sendCreateInfo('informations'); } $this->principalData['formToken'] = FormElements::formToken(); if (FlashMessages::hasFlashMessage()) { $this->principalData['FlashMessage'] = FlashMessages::displayFlashMessage(); } View::setHeaderVars('title', 'Admin'); View::render('sidebar-admin'); View::render('administration/createinfoinformations', $this->principalData); } elseif ($paramOne === 'update') { if (isset($_POST['submit'])) { $this->model->sendCreateInfo('update'); } $this->principalData['formToken'] = FormElements::formToken(); if (FlashMessages::hasFlashMessage()) { $this->principalData['FlashMessage'] = FlashMessages::displayFlashMessage(); } View::setHeaderVars('title', 'Admin'); View::render('sidebar-admin'); View::render('administration/createinfoupdate', $this->principalData); } }
function cluster($paramOne = 1) { $this->model->quantityCacheSearch(); $this->model->breadCumbs(); $this->actualPage = FormElements::filterInteger($paramOne); $this->initialResult = ($this->actualPage - 1) * $this->resultsPerPage; $this->sqlDataArray = array('initialItem' => $this->initialResult, 'maximumQuantity' => 5); $this->browseData = $this->model->getBrowseCluster($this->sqlDataArray); if (FlashMessages::hasFlashMessage()) { $this->principalData['FlashMessage'] = FlashMessages::displayFlashMessage(); } else { $this->principalData['countResults'] = $this->browseData['quantityAllCluster']; $this->principalData['browseData'] = $this->browseData['clusterList']; $this->principalData['totalPages'] = $this->browseData['totalPages']; $this->temporaryPagination = $this->model->pagination($this->actualPage, $this->browseData['totalPages']); $this->principalData['pagination'] = $this->temporaryPagination[0]; $this->principalData['activePagination'] = $this->temporaryPagination[1]; } if ($this->actualPage === 1) { $this->cannonicalUrl = URL . 'browse/cluster'; } else { $this->cannonicalUrl = ''; } $this->principalData['qttResultPage'] = $this->resultsPerPage; $this->principalData['activeBrowsePirna'] = ''; $this->principalData['activeBrowseDataset'] = ''; $this->principalData['activeBrowseCluster'] = 'class="active"'; View::setHeaderVars('title', 'Browse piRNA Clusters'); View::setHeaderVars('specificKeywords', DEFAULT_KEYWORDS . ', piRNA cluster List, piRNA cluster, browse piRNA cluster'); View::setHeaderVars('description', 'Browse all the piRNA clusters in the database'); View::setHeaderVars('cannonicalUrl', $this->cannonicalUrl); View::setHeaderVars('robots', 'index, follow'); View::render('header'); View::render('browse/cluster', $this->principalData); View::render('footer-clean'); }
function sendCreateInfo($type = null) { if ($type === 'faq') { $this->table = 'faq'; $this->dataArray = array('faq_title' => FormElements::getPostString('createFaqTitle', true), 'faq_content' => FormElements::getPostString('createFaqContent', true), 'faq_type' => FormElements::getPostString('createFaqType', true)); } elseif ($type === 'article') { $this->table = 'system_article'; $this->dataArray = array('article_title' => FormElements::getPostString('createArticleTitle', true), 'article_author' => FormElements::getPostString('createArticleAuthor', true), 'article_journal' => FormElements::getPostString('createArticleJournal', true), 'article_date' => FormElements::getPostString('createArticleDate', true), 'article_reference' => FormElements::getPostString('createArticleReference', true)); } elseif ($type === 'informations') { $this->table = 'general_text'; $this->dataArray = array('text_content' => FormElements::getPostString('createInformationsContent', true), 'text_type' => FormElements::getPostString('createInformationsType', true)); } elseif ($type === 'update') { $this->table = 'info_update'; $this->dataArray = array('info_update_title' => FormElements::getPostString('createUpdateTitle', true), 'info_update_content' => FormElements::getPostString('createUpdateContent', true)); } else { FlashMessages::setFlashMessage('error', '<b>Error!</b><br />This Section Does not Exists.'); } $this->formToken = FormElements::getPostString('token', true); parent::checkFormRequired($this->dataArray); parent::checkFormToken($this->formToken, 'administration/createinfo/' . $type); if (!FlashMessages::hasFlashMessage()) { Session::unsetSession('formToken'); $this->resultsDelete = $this->db->insert($this->table, $this->dataArray); if (count($this->resultsDelete) === 1) { FlashMessages::setFlashMessage('success', '<b>Success!</b><br />Succesfully Created.'); } else { FlashMessages::setFlashMessage('error', '<b>Error!</b><br />Unsuccesfully Created.'); } } }