public static function display($title)
{
$cache = $GLOBALS['okwCache'];
$html = '';
$titleArray = explode(':', $title);
$ontAbbr = $titleArray[0];
$termID = str_replace(' ', '_', $titleArray[1]);
$ontology = new OntologyData($ontAbbr);
$term = $ontology->parseTermByID($termID);
if (!empty($cache['hierarchy']) || !empty($cache['axiom']['subclassof']) || !empty($cache['axiom']['equivalent'])) {
$html .= self::printPageSidebar($ontology, $term, $cache);
}
if ($ontology->existClass($term->iri) || !empty($cache['annotation'])) {
$html .= self::printPageHeader($ontology, $term, $cache);
}
return DisplayHelper::tidyHTML($html);
}
protected static function describeFieldHTML($perm, $term)
{
$types = $GLOBALS['okwRDFConfig']['type'];
$html = '<table id="okw-describe-main" class="main">';
$html .= '<tr><td><label id="okw-describe-label" class="term-label"><strong>Label: </strong></label>';
$html .= '<input id="okw-describe-label-input" class="term-input-label" name="term-label" value="';
$html .= $term->label;
$html .= '"></td>';
$html .= '<td><label id="okw-describe-iri" class="term-iri"><strong>IRI: </strong></label>';
$html .= '<input id="okw-describe-iri-input" class="term-input-iri" name="term-iri" value="';
$html .= $term->iri;
if ($perm == FormEditAction::ONTOLOGY_MASTER) {
$html .= '"></td>';
} else {
$html .= '" readonly></td>';
}
$html .= '<td><label id="okw-describe-type" class="type"><strong>Type: </strong></label>';
if ($perm == FormEditAction::ONTOLOGY_MASTER) {
$html .= '<select id="okw-describe-type-select" class="term-select-type" name="term-type">';
} else {
$html .= '<select id="okw-describe-type-select" class="term-select-type" name="term-type" disabled>';
}
foreach ($types as $type) {
$typeLabel = DisplayHelper::getShortTerm($type);
$html .= '<option value="';
$html .= $type;
if ($typeLabel == $term->type) {
$html .= '" selected>';
} else {
$html .= '">';
}
$html .= $typeLabel;
$html .= '</option>';
}
$html .= '</select></td>';
$html .= '</tr></table>';
return $html;
}
public static function extractSupClass($params, $ontology)
{
$options = array();
$valids = array();
$invalids = array();
$supClasses = array();
foreach ($params as $param) {
$index = uniqid();
$pair = explode('=', $param, 2);
if (count($pair) == 2) {
$name = $pair[0];
$name = preg_replace('/[\\s]*(<!--.*?(?=-->)-->)[\\s]*/', '', $name);
$name = strtolower(trim($name));
$value = $pair[1];
$value = preg_replace('/[\\s]*(<!--.*?(?=-->)-->)[\\s]*/', '', $value);
$value = trim($value);
$options[$index][] = $name;
$options[$index][] = $value;
if ($name == 'subclassof') {
if (strtolower($value) == 'thing') {
$supClassIRI = $GLOBALS['okwRDFConfig']['Thing'];
$valids[$index]['iri'] = $supClassIRI;
$valids[$index]['id'] = DisplayHelper::getShortTerm($supClassIRI);
$valids[$index]['title'] = DisplayHelper::getShortTerm($supClassIRI);
} else {
$supClassIRI = $ontology->convertToIRI($value);
$term = $ontology->parseTermByIRI($supClassIRI);
if (!is_null($term)) {
$title = $ontology->getOntAbbr() . ':' . $term->id;
if (OntologyValidator::isExistTitleText($title)) {
$valids[$index]['iri'] = $supClassIRI;
$valids[$index]['id'] = $ontology->convertToID($supClassIRI);
$valids[$index]['title'] = $ontology->convertToTitle($supClassIRI);
} else {
$invalids[$index] = self::ERROR_INVALID_TERM;
}
} else {
$invalids[$index] = self::ERROR_INVALID_TERM;
}
}
} else {
$invalids[$index] = self::ERROR_INVALID_MAGICWORD;
}
} else {
$options[$index][] = $param;
$invalids[$index] = self::ERROR_EXCESS_INPUT;
}
}
return array($options, $valids, $invalids);
}
public function parseTermHierarchy($term, $pathType, $supClass = null)
{
/*if ( !is_object( $term ) ) {
$term = $this->parseTermByIRI( $term );
}*/
$hierarchy = array();
$supClasses = array();
$sibClasses = array();
$subClasses = array();
$hasChild = array();
if (!preg_match('/http:\\/\\/.+/', $supClass)) {
$tmpClass = $this->convertToIRI(array($supClass));
$supClass = $tmpClass[0];
}
$supClassResults = $this->rdf->getTransitiveSupClass($this->graph, $pathType, $term->iri, $supClass);
if (!empty($supClassResults)) {
foreach ($supClassResults as $supClassResult) {
foreach ($supClassResult as $supClassIRI => $supClassLabel) {
if ($supClassLabel != '') {
$supClasses[$supClassIRI] = $supClassLabel;
} else {
$supClasses[$supClassIRI] = DisplayHelper::getShortTerm($supClassIRI);
}
}
if (!empty($supClasses)) {
$tmpClasses = $supClasses;
end($tmpClasses);
$supClass = key($tmpClasses);
$sibClassResult = $this->rdf->getSubClass($this->graph, $supClass);
unset($sibClassResult[$term->iri]);
foreach ($sibClassResult as $sibClassIRI => $sibClassObject) {
$sibClasses[$sibClassIRI] = $sibClassObject->label;
if ($sibClassObject->hasChild) {
$hasChild[$sibClassIRI] = true;
} else {
$hasChild[$sibClassIRI] = false;
}
}
}
$subClassResult = $this->rdf->getSubClass($this->graph, $term->iri);
foreach ($subClassResult as $subClassIRI => $subClassObject) {
$subClasses[$subClassIRI] = $subClassObject->label;
if ($subClassObject->hasChild) {
$hasChild[$subClassIRI] = true;
} else {
$hasChild[$subClassIRI] = false;
}
}
$hierarchy[] = array('path' => $supClasses, 'supClass' => $supClass, 'sibClasses' => $sibClasses, 'subClasses' => $subClasses, 'hasChild' => $hasChild);
}
} else {
$subClassResult = $this->rdf->getSubClass($this->graph, $term->iri);
foreach ($subClassResult as $subClassIRI => $subClassObject) {
$subClasses[$subClassIRI] = $subClassObject->label;
if ($subClassObject->hasChild) {
$hasChild[$subClassIRI] = true;
} else {
$hasChild[$subClassIRI] = false;
}
}
$hierarchy[] = array('path' => null, 'supClass' => null, 'sibClasses' => null, 'subClasses' => $subClasses, 'hasChild' => $hasChild);
}
return $hierarchy;
}
public static function parseSearchResult($keywords, $graph, $searchResult)
{
$match = array();
$terms = array();
$count = 0;
# IRI Match
$results1 = array();
foreach ($searchResult as $result) {
if (preg_match_all('/([a-zA-Z]+)[:_]([a-zA-Z]*)[:_]?(\\d+)/', $keywords, $matches, PREG_SET_ORDER)) {
if ($matches[0][2] == '') {
$searchTermURL = 'http://purl.obolibrary.org/obo/' . $matches[0][1] . '_' . $matches[0][3];
} else {
$searchTermURL = 'http://purl.obolibrary.org/obo/' . $matches[0][2] . '_' . $matches[0][3];
}
$term = array_pop(preg_split('/[\\/#]/', $result['s']));
if ($searchTermURL == $result['s']) {
$count++;
$match[] = array('id' => DisplayHelper::encodeURL($term), 'iri' => $result['s'], 'label' => $result['o']);
$terms[$result['o']] = 1;
}
}
}
# Exact Match
$results2 = array();
foreach ($searchResult as $result) {
if (strtolower($result['o']) == strtolower($keywords)) {
$term = array_pop(preg_split('/[\\/#]/', $result['s']));
if (!isset($terms[$result['o']])) {
$count++;
$match[] = array('id' => DisplayHelper::encodeURL($term), 'iri' => $result['s'], 'label' => $result['o']);
$terms[$result['o']] = 1;
}
} else {
$results2[] = $result;
}
}
# Partial Match
$results3 = array();
foreach ($searchResult as $result) {
if ($count > 100) {
break;
}
if (strpos(strtolower($result['o']), strtolower($keywords)) === 0) {
$tokens = preg_split('/[\\/#]/', $result['s']);
$term = array_pop($tokens);
if (!isset($terms[$result['o']])) {
$count++;
$match[] = array('id' => DisplayHelper::encodeURL($term), 'iri' => $result['s'], 'label' => $result['o']);
$terms[$result['o']] = 1;
}
} else {
$results3[] = $result;
}
}
# Remaining Match (Regular Expression Match return by SPARQL)
foreach ($searchResult as $result) {
if ($count > 100) {
break;
}
$tokens = preg_split('/[\\/#]/', $result['s']);
$term = array_pop($tokens);
if (!isset($terms[$result['o']])) {
$count++;
$match[] = array('id' => DisplayHelper::encodeURL($term), 'iri' => $result['s'], 'label' => $result['o']);
$terms[$result['o']] = 1;
}
}
return $match;
}
protected static function printCreateForm($perm, $ontAbbr, $label, $ontologies, $magic)
{
$html = self::printFormHeader();
$html .= '<input id="okw-form-ontology" type="hidden" value="">';
$html .= CreateDescribeHTML::getHTML($perm, $label, $ontologies);
$html .= EditHierarchyHTML::getHTML();
$html .= EditAxiomHTML::getHTML($ontAbbr);
$html .= EditAnnotationHTML::getHTML($magic);
$html .= self::printFormBottom();
return DisplayHelper::tidyHTML($html);
}
/**
* Static function to generate Sub-Class Section HTML
*
* @param $subClasses
* @param $hasChild
* @return $html
*/
protected static function subClassSectionHTML($ontAbbr, $rootURL, $subClasses, $hasChild)
{
$subHasChildMax = $GLOBALS['okwHierarchyConfig']['subClassHasChildMax'];
$subNoChildMax = $GLOBALS['okwHierarchyConfig']['subClassNoChildMax'];
$html = '<!-- OKW Hierarchy Sub Class Opening -->';
$html .= '<ul>';
$noChildCount = 0;
$hasChildCount = 0;
$showMore = false;
foreach ($subClasses as $subClassIRI => $subClassLabel) {
if ($hasChildCount > $subHasChildMax && $noChildCount > $subNoChildMax) {
break;
}
if ($subClassLabel == '') {
$subClassLabel = DisplayHelper::getShortTerm($subClassIRI);
}
if ($hasChild[$subClassIRI] && $hasChildCount <= $subHasChildMax) {
$hasChildCount++;
$html .= '<li>+ ';
$html .= self::entitiyHTML('sub-term', $rootURL . $ontAbbr . ':' . DisplayHelper::getShortTerm($subClassIRI), $subClassLabel);
$html .= '</li>';
} elseif ($hasChildCount > $subHasChildMax) {
$showMore = true;
}
if (!$hasChild[$subClassIRI] && $noChildCount <= $subNoChildMax) {
$noChildCount++;
$html .= '<li>- ';
$html .= self::entitiyHTML('sub-term', $rootURL . $ontAbbr . ':' . DisplayHelper::getShortTerm($subClassIRI), $subClassLabel);
$html .= '</li>';
} elseif ($noChildCount > $subNoChildMax) {
$showMore = true;
}
}
if ($showMore) {
#TODO: Modify add remaining terms as hiddenthat trigger base on display more checkbox
$html .= self::moreHTML('sub');
}
$html .= '</ul>';
$html .= '<!-- OKW Hierarchy Sub Class Closing -->';
return $html;
}
private function importAnnotationProperty($ontID, $options, $sql, $rdf, $graph)
{
$prefixNS = $GLOBALS['okwRDFConfig']['prefixNS'];
$iris = $rdf->getSubject($graph, $prefixNS['rdf'] . 'type', $prefixNS['owl'] . 'AnnotationProperty');
$iris = $rdf->getLabel($graph, $iris);
$annotations = array();
foreach ($iris as $iri => $label) {
if ($iri == $prefixNS['rdfs'] . 'label') {
continue;
}
$id = DisplayHelper::getShortTerm($iri);
$label = str_replace(' ', '_', $label);
$annotations[$id]['id'] = $id;
$annotations[$id]['iri'] = $iri;
$annotations[$id]['magicword'] = $label;
if (preg_match('/([\\w\\d]*)_[\\d]+/', $id, $match)) {
$annotations[$id]['ontology'] = $match[1];
if ($options['ontology_abbrv'] == $match[1]) {
$annotations[$id]['source'] = $options['ontology_url'];
}
}
}
$sql->insertAnnotationProperty($ontID, $annotations);
}
protected static function supClassAxiomHTML($ontAbbr, $rootURL, $ontology, $term, $related, $axioms)
{
$sql = new SQLStore(wfGetDB(DB_SLAVE));
$magics = $sql->getObjectMagicWords($ontAbbr);
$objects = array();
foreach ($magics as $magic => $iri) {
$objects[$magic] = $magic;
$objects[$iri] = $magic;
$objects[DisplayHelper::getShortTerm($iri)] = $magic;
}
$operations = $GLOBALS['okwRDFConfig']['restriction']['operation'];
$types = $GLOBALS['okwRDFConfig']['restriction']['type'];
$html .= <<<END
<!-- OKW SupClass Axiom Display Start -->
<div id="okw-axiom-supclass-heading" class="supclass-heading">SubClassOf Axiom</div>
<div id="okw-axiom-supclass-main" class="supclass-main">
<ul>
END;
foreach ($axioms as $axiom) {
$axiomHTML = '<li>';
$axiomArray = preg_split('/\\s|([()])/', $axiom, -1, PREG_SPLIT_NO_EMPTY | PREG_SPLIT_DELIM_CAPTURE);
foreach ($axiomArray as $word) {
if ($word == '') {
continue;
} else {
if (array_key_exists($word, $objects)) {
$objectLabel = $objects[$word];
$axiomHTML .= "<b>{$objectLabel}</b>";
} else {
if (array_key_exists($word, $types) || array_key_exists($word, $operations)) {
$axiomHTML .= " {$word} ";
} else {
if ($word == '(' || $word == ')') {
$axiomHTML .= $word;
} else {
$classIRI = $ontology->convertToIRI($word);
$classID = $related[$classIRI]->id;
$classLabel = $related[$classIRI]->label;
$axiomHTML .= <<<END
<a href="{$rootURL}{$ontAbbr}:{$classID}">{$classLabel}</a>
END;
}
}
}
}
}
$axiomHTML .= '</li>';
$html .= $axiomHTML;
}
$html .= <<<END
</ul></div>
<!-- OKW SupClass Axiom Display End -->
END;
return $html;
}
private static function doMap($term, $mapping)
{
if (array_key_exists($term, $mapping)) {
return $mapping[$term];
} else {
return DisplayHelper::getShortTerm($term);
}
}
