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 $this->results;
} else {
FlashMessages::setFlashMessage('noresult', '<b>Zero Results!</b><br />None of your cache search results was found.');
}
}
function getInfo($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.');
}
}
