/**
* Display user login form.
* Redirect to user index page if user is already validated.
*/
function index($args, $request)
{
$this->setupTemplate($request);
if (Validation::isLoggedIn()) {
$this->sendHome($request);
}
if (Config::getVar('security', 'force_login_ssl') && $request->getProtocol() != 'https') {
// Force SSL connections for login
$request->redirectSSL();
}
$sessionManager = SessionManager::getManager();
$session = $sessionManager->getUserSession();
$templateMgr = TemplateManager::getManager($request);
// If the user wasn't expecting a login page, i.e. if they're new to the
// site and want to submit a paper, it helps to explain why they need to
// register.
if ($request->getUserVar('loginMessage')) {
$templateMgr->assign('loginMessage', $request->getUserVar('loginMessage'));
}
$templateMgr->assign('username', $session->getSessionVar('username'));
$templateMgr->assign('remember', $request->getUserVar('remember'));
$templateMgr->assign('source', $request->getUserVar('source'));
$templateMgr->assign('showRemember', Config::getVar('general', 'session_lifetime') > 0);
// For force_login_ssl with base_url[...]: make sure SSL used for login form
$loginUrl = $this->_getLoginUrl($request);
if (Config::getVar('security', 'force_login_ssl')) {
$loginUrl = PKPString::regexp_replace('/^http:/', 'https:', $loginUrl);
}
$templateMgr->assign('loginUrl', $loginUrl);
$templateMgr->display('frontend/pages/userLogin.tpl');
}
/**
* Generate a filename for a library file.
* @param $type int LIBRARY_FILE_TYPE_...
* @param $originalFileName string
* @return string
*/
function generateFileName($type, $originalFileName)
{
$libraryFileDao = DAORegistry::getDAO('LibraryFileDAO');
$suffix = $this->getFileSuffixFromType($type);
$ext = $this->getExtension($originalFileName);
$truncated = $this->truncateFileName($originalFileName, 127 - PKPString::strlen($suffix) - 1);
$baseName = PKPString::substr($truncated, 0, PKPString::strpos($originalFileName, $ext) - 1);
// Try a simple syntax first
$fileName = $baseName . '-' . $suffix . '.' . $ext;
if (!$libraryFileDao->filenameExists($this->contextId, $fileName)) {
return $fileName;
}
for ($i = 1;; $i++) {
$fullSuffix = $suffix . '-' . $i;
//truncate more if necessary
$truncated = $this->truncateFileName($originalFileName, 127 - PKPString::strlen($fullSuffix) - 1);
// get the base name and append the suffix
$baseName = PKPString::substr($truncated, 0, PKPString::strpos($originalFileName, $ext) - 1);
//try the following
$fileName = $baseName . '-' . $fullSuffix . '.' . $ext;
if (!$libraryFileDao->filenameExists($this->contextId, $fileName)) {
return $fileName;
}
}
}
/**
* Format XML for single DC element.
* @param $propertyName string
* @param $value array
* @param $multilingual boolean optional
*/
function formatElement($propertyName, $values, $multilingual = false)
{
if (!is_array($values)) {
$values = array($values);
}
// Translate the property name to XML syntax.
$openingElement = str_replace(array('[@', ']'), array(' ', ''), $propertyName);
$closingElement = PKPString::regexp_replace('/\\[@.*/', '', $propertyName);
// Create the actual XML entry.
$response = '';
foreach ($values as $key => $value) {
if ($multilingual) {
$key = str_replace('_', '-', $key);
assert(is_array($value));
foreach ($value as $subValue) {
if ($key == METADATA_DESCRIPTION_UNKNOWN_LOCALE) {
$response .= "\t<{$openingElement}>" . OAIUtils::prepOutput($subValue) . "</{$closingElement}>\n";
} else {
$response .= "\t<{$openingElement} xml:lang=\"{$key}\">" . OAIUtils::prepOutput($subValue) . "</{$closingElement}>\n";
}
}
} else {
assert(is_scalar($value));
$response .= "\t<{$openingElement}>" . OAIUtils::prepOutput($value) . "</{$closingElement}>\n";
}
}
return $response;
}
/**
* Split a string into a clean array of keywords
* @param $text string
* @param $allowWildcards boolean
* @return array of keywords
*/
static function filterKeywords($text, $allowWildcards = false)
{
$minLength = Config::getVar('search', 'min_word_length');
$stopwords = self::_loadStopwords();
// Join multiple lines into a single string
if (is_array($text)) {
$text = join("\n", $text);
}
$cleanText = Core::cleanVar($text);
// Remove punctuation
$cleanText = PKPString::regexp_replace('/[!"\\#\\$%\'\\(\\)\\.\\?@\\[\\]\\^`\\{\\}~]/', '', $cleanText);
$cleanText = PKPString::regexp_replace('/[\\+,:;&\\/<=>\\|\\\\]/', ' ', $cleanText);
$cleanText = PKPString::regexp_replace('/[\\*]/', $allowWildcards ? '%' : ' ', $cleanText);
$cleanText = PKPString::strtolower($cleanText);
// Split into words
$words = PKPString::regexp_split('/\\s+/', $cleanText);
// FIXME Do not perform further filtering for some fields, e.g., author names?
// Remove stopwords
$keywords = array();
foreach ($words as $k) {
if (!isset($stopwords[$k]) && PKPString::strlen($k) >= $minLength && !is_numeric($k)) {
$keywords[] = PKPString::substr($k, 0, SEARCH_KEYWORD_MAX_LENGTH);
}
}
return $keywords;
}
/**
* @see TypeDescription::parseTypeName()
*/
function parseTypeName($typeName)
{
// Standard validators are based on string input.
parent::parseTypeName('string');
// Split the type name into validator name and arguments.
$typeNameParts = explode('(', $typeName, 2);
switch (count($typeNameParts)) {
case 1:
// no argument
$this->_validatorArgs = '';
break;
case 2:
// parse arguments (no UTF8-treatment necessary)
if (substr($typeNameParts[1], -1) != ')') {
return false;
}
// FIXME: Escape for PHP code inclusion?
$this->_validatorArgs = substr($typeNameParts[1], 0, -1);
break;
}
// Validator name must start with a lower case letter
// and may contain only alphanumeric letters.
if (!PKPString::regexp_match('/^[a-z][a-zA-Z0-9]+$/', $typeNameParts[0])) {
return false;
}
// Translate the validator name into a validator class name.
$this->_validatorClassName = 'Validator' . PKPString::ucfirst($typeNameParts[0]);
return true;
}
/**
* @copydoc Filter::process()
* @param $citationString string
* @return MetadataDescription
*/
function &process(&$input)
{
$nullVar = null;
$queryParams = array('demo' => '3', 'textlines' => $input);
// Parscit web form - the result is (mal-formed) HTML
if (is_null($result = $this->callWebService(PARSCIT_WEBSERVICE, $queryParams, XSL_TRANSFORMER_DOCTYPE_STRING, 'POST'))) {
return $nullVar;
}
$result = html_entity_decode($result);
// Detect errors.
if (!PKPString::regexp_match('/.*<algorithm[^>]+>.*<\\/algorithm>.*/s', $result)) {
$translationParams = array('filterName' => $this->getDisplayName());
$this->addError(__('submission.citations.filter.webserviceResultTransformationError', $translationParams));
return $nullVar;
}
// Screen-scrape the tagged portion and turn it into XML.
$xmlResult = PKPString::regexp_replace('/.*<algorithm[^>]+>(.*)<\\/algorithm>.*/s', '\\1', $result);
$xmlResult = PKPString::regexp_replace('/&/', '&', $xmlResult);
// Transform the result into an array of meta-data.
if (is_null($metadata = $this->transformWebServiceResults($xmlResult, dirname(__FILE__) . DIRECTORY_SEPARATOR . 'parscit.xsl'))) {
return $nullVar;
}
// Extract a publisher from the place string if possible.
$metadata =& $this->fixPublisherNameAndLocation($metadata);
return $this->getNlm30CitationDescriptionFromMetadataArray($metadata);
}
/**
* @copydoc Form::display
*/
function display($request = null, $template = null)
{
import('lib.pkp.classes.xslt.XSLTransformer');
$templateMgr = TemplateManager::getManager($request);
$templateMgr->assign(array('localeOptions' => $this->supportedLocales, 'localesComplete' => $this->localesComplete, 'clientCharsetOptions' => $this->supportedClientCharsets, 'connectionCharsetOptions' => $this->supportedConnectionCharsets, 'databaseCharsetOptions' => $this->supportedDatabaseCharsets, 'allowFileUploads' => get_cfg_var('file_uploads') ? __('common.yes') : __('common.no'), 'maxFileUploadSize' => get_cfg_var('upload_max_filesize'), 'databaseDriverOptions' => $this->checkDBDrivers(), 'supportsMBString' => PKPString::hasMBString() ? __('common.yes') : __('common.no'), 'phpIsSupportedVersion' => version_compare(PHP_REQUIRED_VERSION, PHP_VERSION) != 1, 'xslEnabled' => XSLTransformer::checkSupport(), 'xslRequired' => REQUIRES_XSL, 'phpRequiredVersion' => PHP_REQUIRED_VERSION, 'phpVersion' => PHP_VERSION));
parent::display();
}
/**
* Assign parameters to template
* @param $paramArray array
*/
function assignParams($paramArray = array())
{
$submission = $this->submission;
$application = PKPApplication::getApplication();
$request = $application->getRequest();
parent::assignParams(array_merge(array('submissionTitle' => strip_tags($submission->getLocalizedTitle()), 'submissionId' => $submission->getId(), 'submissionAbstract' => PKPString::html2text($submission->getLocalizedAbstract()), 'authorString' => strip_tags($submission->getAuthorString())), $paramArray));
}
/**
* @copydoc Filter::process()
* @param $isbn string
* @return MetadataDescription a looked up citation description
* or null if the filter fails
*/
function &process($isbn)
{
$nullVar = null;
// Instantiate the web service request
$lookupParams = array('access_key' => $this->getApiKey(), 'index1' => 'isbn', 'results' => 'details,authors', 'value1' => $isbn);
// Call the web service
if (is_null($resultDOM =& $this->callWebService(ISBNDB_WEBSERVICE_URL, $lookupParams))) {
return $nullVar;
}
// Transform and pre-process the web service result
if (is_null($metadata =& $this->transformWebServiceResults($resultDOM, dirname(__FILE__) . DIRECTORY_SEPARATOR . 'isbndb.xsl'))) {
return $nullVar;
}
// Extract place and publisher from the combined entry.
$metadata['publisher-loc'] = PKPString::trimPunctuation(PKPString::regexp_replace('/^(.+):.*/', '\\1', $metadata['place-publisher']));
$metadata['publisher-name'] = PKPString::trimPunctuation(PKPString::regexp_replace('/.*:([^,]+),?.*/', '\\1', $metadata['place-publisher']));
unset($metadata['place-publisher']);
// Reformat the publication date
$metadata['date'] = PKPString::regexp_replace('/^[^\\d{4}]+(\\d{4}).*/', '\\1', $metadata['date']);
// Clean non-numerics from ISBN
$metadata['isbn'] = PKPString::regexp_replace('/[^\\dX]*/', '', $isbn);
// Set the publicationType
$metadata['[@publication-type]'] = NLM30_PUBLICATION_TYPE_BOOK;
return $this->getNlm30CitationDescriptionFromMetadataArray($metadata);
}
/**
* Get the chapter full title (with title and subtitle).
* @return string
*/
function getLocalizedFullTitle()
{
$fullTitle = $this->getLocalizedTitle();
if ($subtitle = $this->getLocalizedSubtitle()) {
$fullTitle = PKPString::concatTitleFields(array($fullTitle, $subtitle));
}
return $fullTitle;
}
/**
* Query parsing helper routine.
* Returned structure is based on that used by the Search::QueryParser Perl module.
*/
function _parseQueryInternal($signTokens, $tokens, &$pos, $total)
{
$return = array('+' => array(), '' => array(), '-' => array());
$postBool = $preBool = '';
$submissionSearchIndex = new SubmissionSearchIndex();
$notOperator = PKPString::strtolower(__('search.operator.not'));
$andOperator = PKPString::strtolower(__('search.operator.and'));
$orOperator = PKPString::strtolower(__('search.operator.or'));
while ($pos < $total) {
if (!empty($signTokens[$pos])) {
$sign = $signTokens[$pos];
} else {
if (empty($sign)) {
$sign = '+';
}
}
$token = PKPString::strtolower($tokens[$pos++]);
switch ($token) {
case $notOperator:
$sign = '-';
break;
case ')':
return $return;
case '(':
$token = $this->_parseQueryInternal($signTokens, $tokens, $pos, $total);
default:
$postBool = '';
if ($pos < $total) {
$peek = PKPString::strtolower($tokens[$pos]);
if ($peek == $orOperator) {
$postBool = 'or';
$pos++;
} else {
if ($peek == $andOperator) {
$postBool = 'and';
$pos++;
}
}
}
$bool = empty($postBool) ? $preBool : $postBool;
$preBool = $postBool;
if ($bool == 'or') {
$sign = '';
}
if (is_array($token)) {
$k = $token;
} else {
$k = $submissionSearchIndex->filterKeywords($token, true);
}
if (!empty($k)) {
$return[$sign][] = $k;
}
$sign = '';
break;
}
}
return $return;
}
/**
* @see OAIMetadataFormat#toXml
*/
function toXml(&$record, $format = null)
{
$article = $record->getData('article');
$journal = $record->getData('journal');
$templateMgr = TemplateManager::getManager();
$templateMgr->assign(array('journal' => $journal, 'article' => $article, 'issue' => $record->getData('issue'), 'section' => $record->getData('section')));
$subjects = array_merge_recursive($this->stripAssocArray((array) $article->getDiscipline(null)), $this->stripAssocArray((array) $article->getSubject(null)));
$templateMgr->assign(array('subject' => isset($subjects[$journal->getPrimaryLocale()]) ? $subjects[$journal->getPrimaryLocale()] : '', 'abstract' => PKPString::html2text($article->getAbstract($article->getLocale())), 'language' => AppLocale::get3LetterIsoFromLocale($article->getLocale())));
return $templateMgr->fetch(dirname(__FILE__) . '/record.tpl');
}
/**
* Retrieve the export as an XML string.
* @param $pluginUrl string the url to be requested for export.
* @param $postParams array additional post parameters
* @return string
*/
protected function getXmlOnExport($pluginUrl, $postParams = array())
{
// Prepare HTTP session.
$curlCh = curl_init();
curl_setopt($curlCh, CURLOPT_POST, true);
// Create a cookie file (required for log-in).
$cookies = tempnam(sys_get_temp_dir(), 'curlcookies');
// Log in.
$loginUrl = $this->baseUrl . '/index.php/test/login/signIn';
// Bug #8518 safety work-around
if ($this->password[0] == '@') {
die('CURL parameters may not begin with @.');
}
$loginParams = array('username' => 'admin', 'password' => $this->password);
curl_setopt($curlCh, CURLOPT_URL, $loginUrl);
curl_setopt($curlCh, CURLOPT_POSTFIELDS, $loginParams);
curl_setopt($curlCh, CURLOPT_COOKIEJAR, $cookies);
self::assertTrue(curl_exec($curlCh));
// Request export document.
$exportUrl = $this->baseUrl . '/index.php/test/manager/importexport/plugin/' . $pluginUrl;
curl_setopt($curlCh, CURLOPT_URL, $exportUrl);
// Bug #8518 safety work-around
foreach ($postParams as $paramValue) {
if ($paramValue[0] == '@') {
die('CURL parameters may not begin with @.');
}
}
curl_setopt($curlCh, CURLOPT_POSTFIELDS, $postParams);
curl_setopt($curlCh, CURLOPT_HTTPHEADER, array('Accept: application/xml, application/x-gtar, */*'));
curl_setopt($curlCh, CURLOPT_RETURNTRANSFER, true);
curl_setopt($curlCh, CURLOPT_HEADER, true);
$response = curl_exec($curlCh);
do {
list($header, $response) = explode("\r\n\r\n", $response, 2);
} while (PKPString::regexp_match('#HTTP/.*100#', $header));
// Check whether we got a tar file.
if (PKPString::regexp_match('#Content-Type: application/x-gtar#', $header)) {
// Save the data to a temporary file.
$tempfile = tempnam(sys_get_temp_dir(), 'tst');
file_put_contents($tempfile, $response);
// Recursively extract tar file.
$result = $this->extractTarFile($tempfile);
unlink($tempfile);
} else {
$matches = null;
PKPString::regexp_match_get('#filename="([^"]+)"#', $header, $matches);
self::assertTrue(isset($matches[1]));
$result = array($matches[1] => $response);
}
// Destroy HTTP session.
curl_close($curlCh);
unlink($cookies);
return $result;
}
/**
* Get the series full title (with title and subtitle).
* @return string
*/
function getLocalizedFullTitle()
{
$fullTitle = null;
if ($prefix = $this->getLocalizedPrefix()) {
$fullTitle = $prefix . ' ';
}
$fullTitle .= $this->getLocalizedTitle();
if ($subtitle = $this->getLocalizedSubtitle()) {
$fullTitle = PKPString::concatTitleFields(array($fullTitle, $subtitle));
}
return $fullTitle;
}
/**
* Extracts variables for a given column from a data element
* so that they may be assigned to template before rendering.
* @param $row GridRow
* @param $column GridColumn
* @return array
*/
function getTemplateVarsFromRowColumn($row, $column)
{
$element =& $row->getData();
$columnId = $column->getId();
assert(!empty($columnId));
switch ($columnId) {
case 'url':
return array('label' => '<a href="' . PKPString::stripUnsafeHtml($element['url']) . '" target="_blank">' . PKPString::stripUnsafeHtml($element['url']) . '</a>');
case 'shares':
return array('label' => $element['shares']);
}
}
/**
* Get a set of GalleryPlugin objects describing the available
* compatible plugins in their newest versions.
* @param $application PKPApplication
* @param $category string Optional category name to use as filter
* @param $search string Optional text to use as filter
* @return array GalleryPlugin objects
*/
function getNewestCompatible($application, $category = null, $search = null)
{
$doc = $this->_getDocument();
$plugins = array();
foreach ($doc->getElementsByTagName('plugin') as $element) {
$plugin = $this->_compatibleFromElement($element, $application);
// May be null if no compatible version exists; also
// apply search filters if any supplied.
if ($plugin && ($category == '' || $plugin->getCategory() == $category) && ($search == '' || PKPString::strpos(PKPString::strtolower(serialize($plugin)), PKPString::strtolower($search)) !== false)) {
$plugins[] = $plugin;
}
}
return $plugins;
}
/**
* Extract and validate a plugin (prior to installation)
* @param $filePath string Full path to plugin archive
* @param $originalFileName string Original filename of plugin archive
* @return string|null Extracted plugin path on success; null on error
*/
function extractPlugin($filePath, $originalFileName, &$errorMsg)
{
$fileManager = new FileManager();
// tar archive basename (less potential version number) must
// equal plugin directory name and plugin files must be in a
// directory named after the plug-in (potentially with version)
$matches = array();
PKPString::regexp_match_get('/^[a-zA-Z0-9]+/', basename($originalFileName, '.tar.gz'), $matches);
$pluginShortName = array_pop($matches);
if (!$pluginShortName) {
$errorMsg = __('manager.plugins.invalidPluginArchive');
$fileManager->deleteFile($filePath);
return null;
}
// Create random dirname to avoid symlink attacks.
$pluginExtractDir = dirname($filePath) . DIRECTORY_SEPARATOR . $pluginShortName . substr(md5(mt_rand()), 0, 10);
mkdir($pluginExtractDir);
// Test whether the tar binary is available for the export to work
$tarBinary = Config::getVar('cli', 'tar');
if (!empty($tarBinary) && file_exists($tarBinary)) {
exec($tarBinary . ' -xzf ' . escapeshellarg($filePath) . ' -C ' . escapeshellarg($pluginExtractDir));
} else {
$errorMsg = __('manager.plugins.tarCommandNotFound');
}
$fileManager->deleteFile($filePath);
if (empty($errorMsg)) {
// Look for a directory named after the plug-in's short
// (alphanumeric) name within the extracted archive.
if (is_dir($tryDir = $pluginExtractDir . '/' . $pluginShortName)) {
return $tryDir;
// Success
}
// Failing that, look for a directory named after the
// archive. (Typically also contains the version number
// e.g. with github generated release archives.)
PKPString::regexp_match_get('/^[a-zA-Z0-9.-]+/', basename($originalFileName, '.tar.gz'), $matches);
if (is_dir($tryDir = $pluginExtractDir . '/' . array_pop($matches))) {
// We found a directory named after the archive
// within the extracted archive. (Typically also
// contains the version number, e.g. github
// generated release archives.)
return $tryDir;
}
$errorMsg = __('manager.plugins.invalidPluginArchive');
}
$fileManager->rmtree($pluginExtractDir);
return null;
}
/**
* Get cell actions associated with this row/column combination
* @param $row GridRow
* @param $column GridColumn
* @return array an array of LinkAction instances
*/
function getCellActions($request, $row, $column, $position = GRID_ACTION_POSITION_DEFAULT)
{
assert($column->getId() == 'task');
$templateMgr = TemplateManager::getManager($request);
$notification = $row->getData();
$contextDao = Application::getContextDAO();
$context = $contextDao->getById($notification->getContextId());
$notificationMgr = new NotificationManager();
$router = $request->getRouter();
$templateMgr->assign(array('notificationMgr' => $notificationMgr, 'notification' => $notification, 'context' => $context, 'notificationObjectTitle' => $this->_getTitle($notification), 'message' => PKPString::stripUnsafeHtml($notificationMgr->getNotificationMessage($request, $notification))));
// See if we're working in a multi-context environment
$user = $request->getUser();
$contextDao = Application::getContextDAO();
$contexts = $contextDao->getAvailable($user ? $user->getId() : null)->toArray();
$templateMgr->assign('isMultiContext', count($contexts) > 1);
return array(new LinkAction('details', new AjaxAction($router->url($request, null, null, 'markRead', null, array('redirect' => 1, 'selectedElements' => array($notification->getId())))), $templateMgr->fetch('controllers/grid/tasks/task.tpl')));
}
/**
* Display the form.
*/
function display()
{
$templateMgr = TemplateManager::getManager($this->_request);
$templateMgr->assign('localeOptions', $this->supportedLocales);
$templateMgr->assign('localesComplete', $this->localesComplete);
$templateMgr->assign('clientCharsetOptions', $this->supportedClientCharsets);
$templateMgr->assign('connectionCharsetOptions', $this->supportedConnectionCharsets);
$templateMgr->assign('databaseCharsetOptions', $this->supportedDatabaseCharsets);
$templateMgr->assign('allowFileUploads', get_cfg_var('file_uploads') ? __('common.yes') : __('common.no'));
$templateMgr->assign('maxFileUploadSize', get_cfg_var('upload_max_filesize'));
$templateMgr->assign('databaseDriverOptions', $this->checkDBDrivers());
$templateMgr->assign('supportsMBString', PKPString::hasMBString() ? __('common.yes') : __('common.no'));
$templateMgr->assign('phpIsSupportedVersion', version_compare(PHP_REQUIRED_VERSION, PHP_VERSION) != 1);
import('lib.pkp.classes.xslt.XSLTransformer');
$templateMgr->assign('xslEnabled', XSLTransformer::checkSupport());
$templateMgr->assign('xslRequired', REQUIRES_XSL);
$templateMgr->assign('phpRequiredVersion', PHP_REQUIRED_VERSION);
$templateMgr->assign('phpVersion', PHP_VERSION);
parent::display();
}
/**
* @see Filter::process()
* @param $input string
* @return mixed array
*/
function &process(&$input)
{
// The default implementation assumes that raw citations are
// separated with line endings.
// 1) Remove empty lines and normalize line endings.
$input = PKPString::regexp_replace('/[\\r\\n]+/s', "\n", $input);
// 2) Remove trailing/leading line breaks.
$input = trim($input, "\n");
// 3) Break up at line endings.
if (empty($input)) {
$citations = array();
} else {
$citations = explode("\n", $input);
}
// 4) Remove numbers from the beginning of each citation.
foreach ($citations as $index => $citation) {
$citations[$index] = PKPString::regexp_replace('/^\\s*[\\[#]?[0-9]+[.)\\]]?\\s*/', '', $citation);
}
return $citations;
}
/**
* @copydoc NotificationManagerDelegate::getNotificationMessage()
*/
public function getNotificationMessage($request, $notification)
{
assert($notification->getAssocType() == ASSOC_TYPE_QUERY);
$queryDao = DAORegistry::getDAO('QueryDAO');
$query = $queryDao->getById($notification->getAssocId());
$headNote = $query->getHeadNote();
assert($headNote);
switch ($notification->getType()) {
case NOTIFICATION_TYPE_NEW_QUERY:
$user = $headNote->getUser();
return __('submission.query.new', array('creatorName' => $user->getFullName(), 'noteContents' => substr(PKPString::html2text($headNote->getContents()), 0, 200), 'noteTitle' => substr($headNote->getTitle(), 0, 200)));
case NOTIFICATION_TYPE_QUERY_ACTIVITY:
$notes = $query->getReplies(null, NOTE_ORDER_ID, SORT_DIRECTION_DESC);
$latestNote = $notes->next();
$user = $latestNote->getUser();
$notes->close();
return __('submission.query.activity', array('responderName' => $user->getFullName(), 'noteContents' => substr(PKPString::html2text($latestNote->getContents()), 0, 200), 'noteTitle' => substr($headNote->getTitle(), 0, 200)));
default:
assert(false);
}
}
/**
* @covers PKPString::diff
*/
public function testDiff()
{
// Test two strings that have common substrings.
$originalString = 'The original string.';
$editedString = 'The edited original.';
$expectedDiff = array(array(0 => 'The'), array(1 => ' edited'), array(0 => ' original'), array(-1 => ' string'), array(0 => '.'));
$resultDiff = PKPString::diff($originalString, $editedString);
self::assertEquals($expectedDiff, $resultDiff);
// Test two completely different strings.
$originalString = 'abc';
$editedString = 'def';
$expectedDiff = array(array(-1 => 'abc'), array(1 => 'def'));
$resultDiff = PKPString::diff($originalString, $editedString);
self::assertEquals($expectedDiff, $resultDiff);
// A more realistic example from the citation editor use case
$originalString = 'Willinsky, B. (2006). The access principle: The case for open acces to research and scholarship. Cambridge, MA: MIT Press.';
$editedString = 'Willinsky, J. (2006). The access principle: The case for open access to research and scholarship. Cambridge, MA: MIT Press.';
$expectedDiff = array(array(0 => 'Willinsky, '), array(-1 => 'B'), array(1 => 'J'), array(0 => '. (2006). The access principle: The case for open acce'), array(1 => 's'), array(0 => 's to research and scholarship. Cambridge, MA: MIT Press.'));
$resultDiff = PKPString::diff($originalString, $editedString);
self::assertEquals($expectedDiff, $resultDiff);
}
/**
* Retrieve all published authors for a press in an associative array by
* the first letter of the last name, for example:
* $returnedArray['S'] gives array($misterSmithObject, $misterSmytheObject, ...)
* Keys will appear in sorted order. Note that if pressId is null,
* alphabetized authors for all presses are returned.
* @param $pressId int
* @param $initial An initial the last names must begin with
* @return array Authors ordered by sequence
*/
function getAuthorsAlphabetizedByPress($pressId = null, $initial = null, $rangeInfo = null)
{
$params = array('affiliation', AppLocale::getPrimaryLocale(), 'affiliation', AppLocale::getLocale());
if (isset($pressId)) {
$params[] = $pressId;
}
if (isset($initial)) {
$params[] = PKPString::strtolower($initial) . '%';
$initialSql = ' AND LOWER(a.last_name) LIKE LOWER(?)';
} else {
$initialSql = '';
}
$result = $this->retrieveRange('SELECT DISTINCT
CAST(\'\' AS CHAR) AS url,
a.author_id AS author_id,
a.submission_id AS submission_id,
CAST(\'\' AS CHAR) AS email,
0 AS primary_contact,
0 AS seq,
a.first_name AS first_name,
a.middle_name AS middle_name,
a.last_name AS last_name,
asl.setting_value AS affiliation_l,
asl.locale,
aspl.setting_value AS affiliation_pl,
aspl.locale AS primary_locale,
a.suffix AS suffix,
a.user_group_id AS user_group_id,
a.include_in_browse AS include_in_browse,
0 AS show_title,
a.country
FROM authors a
LEFT JOIN author_settings aspl ON (a.author_id = aspl.author_id AND aspl.setting_name = ? AND aspl.locale = ?)
LEFT JOIN author_settings asl ON (a.author_id = asl.author_id AND asl.setting_name = ? AND asl.locale = ?)
JOIN submissions s ON (a.submission_id = s.submission_id)
WHERE s.status = ' . STATUS_PUBLISHED . ' ' . (isset($pressId) ? 'AND s.context_id = ? ' : '') . '
AND (a.last_name IS NOT NULL AND a.last_name <> \'\')' . $initialSql . '
ORDER BY a.last_name, a.first_name', $params, $rangeInfo);
return new DAOResultFactory($result, $this, '_fromRow');
}
/**
* Display user login form.
* Redirect to user index page if user is already validated.
*/
function index($args, $request)
{
$this->setupTemplate($request);
if (Validation::isLoggedIn()) {
$this->sendHome($request);
}
if (Config::getVar('security', 'force_login_ssl') && $request->getProtocol() != 'https') {
// Force SSL connections for login
$request->redirectSSL();
}
$sessionManager = SessionManager::getManager();
$session = $sessionManager->getUserSession();
$templateMgr = TemplateManager::getManager($request);
$templateMgr->assign(array('loginMessage' => $request->getUserVar('loginMessage'), 'username' => $session->getSessionVar('username'), 'remember' => $request->getUserVar('remember'), 'source' => $request->getUserVar('source'), 'showRemember' => Config::getVar('general', 'session_lifetime') > 0));
// For force_login_ssl with base_url[...]: make sure SSL used for login form
$loginUrl = $this->_getLoginUrl($request);
if (Config::getVar('security', 'force_login_ssl')) {
$loginUrl = PKPString::regexp_replace('/^http:/', 'https:', $loginUrl);
}
$templateMgr->assign('loginUrl', $loginUrl);
$templateMgr->display('frontend/pages/userLogin.tpl');
}
/**
* @see FormValidator::isValid()
* Value is valid if it is empty and optional or meets the specified length requirements.
* @return boolean
*/
function isValid()
{
if ($this->isEmptyAndOptional()) {
return true;
} else {
$length = PKPString::strlen($this->getFieldValue());
switch ($this->_comparator) {
case '==':
return $length == $this->_length;
case '!=':
return $length != $this->_length;
case '<':
return $length < $this->_length;
case '>':
return $length > $this->_length;
case '<=':
return $length <= $this->_length;
case '>=':
return $length >= $this->_length;
}
return false;
}
}
/**
* Normalize incoming date string.
* @see Filter::process()
* @param $input string
* @return string
*/
function &process(&$input)
{
// FIXME: We have to i18nize this when expanding citation parsing to other languages
static $monthNames = array('Jan' => '01', 'Feb' => '02', 'Mar' => '03', 'Apr' => '04', 'May' => '05', 'Jun' => '06', 'Jul' => '07', 'Aug' => '08', 'Sep' => '09', 'Oct' => '10', 'Nov' => '11', 'Dec' => '12');
$dateExpressions = array('/(?P<year>\\d{4})-(?P<month>\\d{2})-(?P<day>\\d{2})/', '/(?P<year>\\d{4})(\\s|-)*(?P<monthName>[a-z]\\w+)?(\\s|-)*(?P<day>\\d+)?/i');
$normalizedDate = null;
foreach ($dateExpressions as $dateExpression) {
if (PKPString::regexp_match_get($dateExpression, $input, $parsedDate)) {
if (isset($parsedDate['year'])) {
$normalizedDate = $parsedDate['year'];
$month = '';
if (isset($parsedDate['monthName'])) {
$monthName = substr($parsedDate['monthName'], 0, 3);
if (isset($monthNames[$monthName])) {
// Convert the month name to a two digit numeric month representation.
$month = $monthNames[$monthName];
}
}
if (isset($parsedDate['month'])) {
// Convert month to a two digit representation.
$month = str_pad($parsedDate['month'], 2, '0', STR_PAD_LEFT);
}
if (!empty($month)) {
$normalizedDate .= '-' . $month;
if (isset($parsedDate['day'])) {
$normalizedDate .= '-' . str_pad($parsedDate['day'], 2, '0', STR_PAD_LEFT);
}
}
}
if (!empty($normalizedDate)) {
break;
}
}
}
return $normalizedDate;
}
/**
* @verbatim
* Helper method that configures and optionally
* installs a filter based on the given XML node
* which represents a <filter> element.
* @endverbatim
* @param $filterNode XMLNode
* @param $persist boolean whether to install the filter
* @return PersistableFilter the installed filter.
*/
function &configureFilter($filterNode, $persist = true)
{
// Install filters.
$filterDao = DAORegistry::getDAO('FilterDAO');
/* @var $filterDao FilterDAO */
$filterGroupSymbolic = $filterNode->getAttribute('inGroup');
$filterClassName = $filterNode->getAttribute('class');
$isTemplate = $filterNode->getAttribute('isTemplate');
// We have to include the filter class before going on
// so that all required constants are defined before they
// might be used in settings.
if (PKPString::regexp_match('/^[a-zA-Z0-9.]+$/', $filterClassName)) {
import($filterClassName);
}
// Go through the filter sub-nodes. This can be nested
// filters or filter settings.
$subNodes = $filterNode->getChildren();
$settings = array();
$subFilters = array();
foreach ($subNodes as $subNode) {
/* @var $subNode XMLNode */
switch ($subNode->getName()) {
case 'setting':
// Get the filter setting.
list($name, $value) = $this->getFilterSetting($subNode);
$settings[$name] = $value;
unset($name, $value);
break;
case 'filter':
// Recursively configure sub-filters.
$subFilter =& $this->configureFilter($subNode, false);
$subFilters[] =& $subFilter;
unset($subFilter);
break;
}
}
// We ensure idempotence of plug-in installation by checking
// for existing identical filters.
$similarFilterFactory =& $filterDao->getObjectsByGroupAndClass($filterGroupSymbolic, $filterClassName, 0, $isTemplate);
if ($similarFilterFactory->getCount() > 0) {
// 1) Find similar filters.
$similarFilters =& $similarFilterFactory->toArray();
// 2) Go through similar filters and eliminate them
// if they don't have the exact same settings.
foreach ($similarFilters as $index => $similarFilter) {
/* @var $similarFilter PersistableFilter */
if (!$this->compareFilters($similarFilter, $settings, $subFilters)) {
unset($similarFilters[$index]);
}
}
// There can be a maximum of exactly one identical transformation
// in the database otherwise we've somehow installed a duplicate filter.
$identicalFilters = count($similarFilters);
assert($identicalFilters <= 1);
// 3) If the filter has been installed before then return the existing filter.
if ($identicalFilters) {
$existingFilter = array_pop($similarFilters);
return $existingFilter;
}
}
// Configure (and optionally install) the filter.
$installedFilter = $filterDao->configureObject($filterClassName, $filterGroupSymbolic, $settings, $isTemplate, 0, $subFilters, $persist);
assert(is_a($installedFilter, 'PersistableFilter'));
return $installedFilter;
}
/**
* @see Validator::isValid()
* @param $value mixed
* @return boolean
*/
function isValid($value)
{
return (bool) PKPString::regexp_match_get($this->_regExp, $value, $this->_matches);
}
/**
* Retrieve all published authors for a journal in an associative array by
* the first letter of the last name, for example:
* $returnedArray['S'] gives array($misterSmithObject, $misterSmytheObject, ...)
* Keys will appear in sorted order. Note that if journalId is null,
* alphabetized authors for all enabled journals are returned.
* @param $journalId int Optional journal ID to restrict results to
* @param $initial An initial the last names must begin with
* @param $rangeInfo Range information
* @param $includeEmail Whether or not to include the email in the select distinct
* @return DAOResultFactory Authors ordered by sequence
*/
function getAuthorsAlphabetizedByJournal($journalId = null, $initial = null, $rangeInfo = null, $includeEmail = false)
{
$params = array('affiliation', AppLocale::getPrimaryLocale(), 'affiliation', AppLocale::getLocale());
if (isset($journalId)) {
$params[] = $journalId;
}
if (isset($initial)) {
$params[] = PKPString::strtolower($initial) . '%';
$initialSql = ' AND LOWER(aa.last_name) LIKE LOWER(?)';
} else {
$initialSql = '';
}
$result = $this->retrieveRange('SELECT DISTINCT
CAST(\'\' AS CHAR) AS url,
0 AS author_id,
0 AS submission_id,
' . ($includeEmail ? 'aa.email AS email,' : 'CAST(\'\' AS CHAR) AS email,') . '
0 AS primary_contact,
0 AS seq,
aa.first_name,
aa.middle_name,
aa.last_name,
SUBSTRING(asl.setting_value FROM 1 FOR 255) AS affiliation_l,
asl.locale,
SUBSTRING(aspl.setting_value FROM 1 FOR 255) AS affiliation_pl,
aspl.locale AS primary_locale,
aa.country
FROM authors aa
LEFT JOIN author_settings aspl ON (aa.author_id = aspl.author_id AND aspl.setting_name = ? AND aspl.locale = ?)
LEFT JOIN author_settings asl ON (aa.author_id = asl.author_id AND asl.setting_name = ? AND asl.locale = ?)
JOIN submissions a ON (a.submission_id = aa.submission_id AND a.status = ' . STATUS_PUBLISHED . ')
JOIN journals j ON (a.context_id = j.journal_id)
JOIN published_submissions pa ON (pa.submission_id = a.submission_id)
JOIN issues i ON (pa.issue_id = i.issue_id AND i.published = 1)
WHERE ' . (isset($journalId) ? 'j.journal_id = ?' : 'j.enabled = 1') . '
AND (aa.last_name IS NOT NULL AND aa.last_name <> \'\')' . $initialSql . '
ORDER BY aa.last_name, aa.first_name', $params, $rangeInfo);
return new DAOResultFactory($result, $this, '_returnSimpleAuthorFromRow');
}
/**
* @see OAIMetadataFormat#toXml
* TODO:
* <copyright-holder>
* In Isabelle's mapping document:
* Article order in the issue's Table of Contents
*/
function toXml(&$record, $format = null)
{
$article =& $record->getData('article');
$journal =& $record->getData('journal');
$section =& $record->getData('section');
$issue =& $record->getData('issue');
$galleys =& $record->getData('galleys');
$articleId = $article->getId();
// Cache issue ordering information.
static $issueId;
static $sectionSeq;
if (!isset($issueId) || $issueId != $issue->getId()) {
$sectionDao = DAORegistry::getDAO('SectionDAO');
$issueId = $issue->getId();
$sections = $sectionDao->getByIssueId($issueId);
$sectionSeq = array();
$i = 0;
foreach ($sections as $thisSection) {
$sectionSeq[$thisSection->getId()] = $i++;
}
unset($sections);
}
$abbreviation = $journal->getLocalizedSetting('abbreviation');
$printIssn = $journal->getSetting('printIssn');
$onlineIssn = $journal->getSetting('onlineIssn');
$primaryLocale = $article->getLanguage() != '' ? $article->getLanguage() : $journal->getPrimaryLocale();
$publisherInstitution = $journal->getSetting('publisherInstitution');
$datePublished = $article->getDatePublished();
if (!$datePublished) {
$datePublished = $issue->getDatePublished();
}
if ($datePublished) {
$datePublished = strtotime($datePublished);
}
$response = "<article\n" . "\txmlns=\"http://dtd.nlm.nih.gov/publishing/2.3\"\n" . "\txmlns:xlink=\"http://www.w3.org/1999/xlink\"\n" . "\txmlns:mml=\"http://www.w3.org/1998/Math/MathML\"\n" . "\txmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"\n" . "\txsi:schemaLocation=\"http://dtd.nlm.nih.gov/publishing/2.3\n" . "\thttp://dtd.nlm.nih.gov/publishing/2.3/xsd/journalpublishing.xsd\"\n" . (($s = $section->getLocalizedIdentifyType()) != '' ? "\tarticle-type=\"" . htmlspecialchars(Core::cleanVar($s)) . "\"" : '') . "\txml:lang=\"" . strtoupper(substr($primaryLocale, 0, 2)) . "\">\n" . "\t<front>\n" . "\t\t<journal-meta>\n" . "\t\t\t<journal-id journal-id-type=\"other\">" . htmlspecialchars(Core::cleanVar(($s = Config::getVar('oai', 'nlm_journal_id')) != '' ? $s : $journal->getPath())) . "</journal-id>\n" . "\t\t\t<journal-title>" . htmlspecialchars(Core::cleanVar($journal->getLocalizedName())) . "</journal-title>\n";
// Include translated journal titles
foreach ($journal->getName(null) as $locale => $title) {
if ($locale == $primaryLocale) {
continue;
}
$response .= "\t\t\t<trans-title xml:lang=\"" . strtoupper(substr($locale, 0, 2)) . "\">" . htmlspecialchars(Core::cleanVar($title)) . "</trans-title>\n";
}
$response .= (!empty($onlineIssn) ? "\t\t\t<issn pub-type=\"epub\">" . htmlspecialchars(Core::cleanVar($onlineIssn)) . "</issn>" : '') . (!empty($printIssn) ? "\t\t\t<issn pub-type=\"ppub\">" . htmlspecialchars(Core::cleanVar($printIssn)) . "</issn>" : '') . ($publisherInstitution != '' ? "\t\t\t<publisher><publisher-name>" . htmlspecialchars(Core::cleanVar($publisherInstitution)) . "</publisher-name></publisher>\n" : '') . "\t\t</journal-meta>\n" . "\t\t<article-meta>\n" . "\t\t\t<article-id pub-id-type=\"other\">" . htmlspecialchars(Core::cleanVar($article->getBestArticleId())) . "</article-id>\n" . (($s = $article->getPubId('doi')) ? "\t\t\t<article-id pub-id-type=\"doi\">" . htmlspecialchars(Core::cleanVar($s)) . "</article-id>\n" : '') . "\t\t\t<article-categories><subj-group subj-group-type=\"heading\"><subject>" . htmlspecialchars(Core::cleanVar($section->getLocalizedTitle())) . "</subject></subj-group></article-categories>\n" . "\t\t\t<title-group>\n" . "\t\t\t\t<article-title>" . htmlspecialchars(Core::cleanVar(strip_tags($article->getLocalizedTitle()))) . "</article-title>\n";
// Include translated journal titles
foreach ($article->getTitle(null) as $locale => $title) {
if ($locale == $primaryLocale) {
continue;
}
$response .= "\t\t\t\t<trans-title xml:lang=\"" . strtoupper(substr($locale, 0, 2)) . "\">" . htmlspecialchars(Core::cleanVar(strip_tags($title))) . "</trans-title>\n";
}
$response .= "\t\t\t</title-group>\n" . "\t\t\t<contrib-group>\n";
// Include authors
foreach ($article->getAuthors() as $author) {
$response .= "\t\t\t\t<contrib " . ($author->getPrimaryContact() ? 'corresp="yes" ' : '') . "contrib-type=\"author\">\n" . "\t\t\t\t\t<name name-style=\"western\">\n" . "\t\t\t\t\t\t<surname>" . htmlspecialchars(Core::cleanVar($author->getLastName())) . "</surname>\n" . "\t\t\t\t\t\t<given-names>" . htmlspecialchars(Core::cleanVar($author->getFirstName()) . (($s = $author->getMiddleName()) != '' ? " {$s}" : '')) . "</given-names>\n" . "\t\t\t\t\t</name>\n" . (($s = $author->getLocalizedAffiliation()) != '' ? "\t\t\t\t\t<aff>" . htmlspecialchars(Core::cleanVar($s)) . "</aff>\n" : '') . "\t\t\t\t\t<email>" . htmlspecialchars(Core::cleanVar($author->getEmail())) . "</email>\n" . (($s = $author->getUrl()) != '' ? "\t\t\t\t\t<uri>" . htmlspecialchars(Core::cleanVar($s)) . "</uri>\n" : '') . "\t\t\t\t</contrib>\n";
}
// Include editorships (optimized)
$response .= $this->getEditorialInfo($journal->getId());
$response .= "\t\t\t</contrib-group>\n";
if ($datePublished) {
$response .= "\t\t\t<pub-date pub-type=\"epub\">\n" . "\t\t\t\t<day>" . strftime('%d', $datePublished) . "</day>\n" . "\t\t\t\t<month>" . strftime('%m', $datePublished) . "</month>\n" . "\t\t\t\t<year>" . strftime('%Y', $datePublished) . "</year>\n" . "\t\t\t</pub-date>\n";
}
$response .= ($issue->getShowYear() ? "\t\t\t<pub-date pub-type=\"collection\"><year>" . htmlspecialchars(Core::cleanVar($issue->getYear())) . "</year></pub-date>\n" : '') . ($issue->getShowVolume() ? "\t\t\t<volume>" . htmlspecialchars(Core::cleanVar($issue->getVolume())) . "</volume>\n" : '') . ($issue->getShowNumber() ? "\t\t\t<issue seq=\"" . htmlspecialchars(Core::cleanVar($sectionSeq[$section->getId()] * 100 + $article->getSequence())) . "\">" . htmlspecialchars(Core::cleanVar($issue->getNumber())) . "</issue>\n" : '') . "\t\t\t<issue-id pub-id-type=\"other\">" . htmlspecialchars(Core::cleanVar($issue->getBestIssueId())) . "</issue-id>\n" . ($issue->getShowTitle() ? "\t\t\t<issue-title>" . htmlspecialchars(Core::cleanVar($issue->getLocalizedTitle())) . "</issue-title>\n" : '');
// Include page info, if available and parseable.
$matches = null;
if (PKPString::regexp_match_get('/^[Pp][Pp]?[.]?[ ]?(\\d+)$/', $article->getPages(), $matches)) {
$matchedPage = htmlspecialchars(Core::cleanVar($matches[1]));
$response .= "\t\t\t\t<fpage>{$matchedPage}</fpage><lpage>{$matchedPage}</lpage>\n";
$pageCount = 1;
} elseif (PKPString::regexp_match_get('/^[Pp][Pp]?[.]?[ ]?(\\d+)[ ]?(-|–)[ ]?([Pp][Pp]?[.]?[ ]?)?(\\d+)$/', $article->getPages(), $matches)) {
$matchedPageFrom = htmlspecialchars(Core::cleanVar($matches[1]));
$matchedPageTo = htmlspecialchars(Core::cleanVar($matches[4]));
$response .= "\t\t\t\t<fpage>{$matchedPageFrom}</fpage>\n" . "\t\t\t\t<lpage>{$matchedPageTo}</lpage>\n";
$pageCount = $matchedPageTo - $matchedPageFrom + 1;
}
$response .= "\t\t\t<permissions>\n" . "\t\t\t\t<copyright-statement>" . htmlspecialchars(__('submission.copyrightStatement', array('copyrightYear' => $article->getCopyrightYear(), 'copyrightHolder' => $article->getLocalizedCopyrightHolder()))) . "</copyright-statement>\n" . ($datePublished ? "\t\t\t\t<copyright-year>" . $article->getCopyrightYear() . "</copyright-year>\n" : '') . "\t\t\t\t<license xlink:href=\"" . $article->getLicenseURL() . "\">\n" . (($s = Application::getCCLicenseBadge($article->getLicenseURL())) ? "\t\t\t\t\t<license-p>" . strip_tags($s) . "</license-p>\n" : '') . "\t\t\t\t</license>\n" . "\t\t\t</permissions>\n" . "\t\t\t<self-uri xlink:href=\"" . htmlspecialchars(Core::cleanVar(Request::url($journal->getPath(), 'article', 'view', $article->getBestArticleId()))) . "\" />\n";
// Include galley links
foreach ($article->getGalleys() as $galley) {
$response .= "\t\t\t<self-uri content-type=\"" . htmlspecialchars(Core::cleanVar($galley->getFileType())) . "\" xlink:href=\"" . htmlspecialchars(Core::cleanVar(Request::url($journal->getPath(), 'article', 'view', array($article->getBestArticleId(), $galley->getId())))) . "\" />\n";
}
// Include abstract(s)
$abstract = htmlspecialchars(Core::cleanVar(strip_tags($article->getLocalizedAbstract())));
if (!empty($abstract)) {
$abstract = "<p>{$abstract}</p>";
// $abstract = '<p>' . PKPString::regexp_replace('/\n+/', '</p><p>', $abstract) . '</p>';
$response .= "\t\t\t<abstract xml:lang=\"" . strtoupper(substr($primaryLocale, 0, 2)) . "\">{$abstract}</abstract>\n";
}
if (is_array($article->getAbstract(null))) {
foreach ($article->getAbstract(null) as $locale => $abstract) {
if ($locale == $primaryLocale || empty($abstract)) {
continue;
}
$abstract = htmlspecialchars(Core::cleanVar(strip_tags($abstract)));
if (empty($abstract)) {
continue;
}
$abstract = "<p>{$abstract}</p>";
//$abstract = '<p>' . PKPString::regexp_replace('/\n+/', '</p><p>', $abstract) . '</p>';
$response .= "\t\t\t<abstract-trans xml:lang=\"" . strtoupper(substr($locale, 0, 2)) . "\">{$abstract}</abstract-trans>\n";
}
}
$subjects = array();
if (is_array($article->getSubject(null))) {
foreach ($article->getSubject(null) as $locale => $subject) {
$s = array_map('trim', explode(';', Core::cleanVar($subject)));
if (!empty($s)) {
$subjects[$locale] = $s;
}
}
}
if (!empty($subjects)) {
foreach ($subjects as $locale => $s) {
$response .= "\t\t\t<kwd-group xml:lang=\"" . strtoupper(substr($locale, 0, 2)) . "\">\n";
foreach ($s as $subject) {
$response .= "\t\t\t\t<kwd>" . htmlspecialchars($subject) . "</kwd>\n";
}
$response .= "\t\t\t</kwd-group>\n";
}
}
$response .= (isset($pageCount) ? "\t\t\t<counts><page-count count=\"" . (int) $pageCount . "\" /></counts>\n" : '') . "\t\t</article-meta>\n" . "\t</front>\n";
// Include body text (for search indexing only)
import('classes.search.ArticleSearchIndex');
$text = '';
$galleys = $article->getGalleys();
// Give precedence to HTML galleys, as they're quickest to parse
usort($galleys, create_function('$a, $b', 'return $a->getFileType()==\'text/html\')?-1:1;'));
// Determine any access limitations. If there are, do not
// provide the full-text.
import('classes.issue.IssueAction');
$issueAction = new IssueAction();
$subscriptionRequired = $issueAction->subscriptionRequired($issue);
$isSubscribedDomain = $issueAction->subscribedDomain($journal, $issue->getId(), $article->getId());
if (!$subscriptionRequired || $isSubscribedDomain) {
foreach ($galleys as $galley) {
$parser =& SearchFileParser::fromFile($galley);
if ($parser && $parser->open()) {
while (($s = $parser->read()) !== false) {
$text .= $s;
}
$parser->close();
}
if ($galley->getFileType() == 'text/html') {
$text = strip_tags($text);
}
unset($galley);
// Use the first parseable galley.
if (!empty($text)) {
break;
}
}
}
if (!empty($text)) {
$response .= "\t<body><p>" . htmlspecialchars(Core::cleanVar(Core::cleanVar($text))) . "</p></body>\n";
}
// Add NLM citation info
$filterDao = DAORegistry::getDAO('FilterDAO');
/* @var $filterDao FilterDAO */
$nlmFilters = $filterDao->getObjectsByGroup('submission=>nlm23-article-xml');
assert(count($nlmFilters) == 1);
$nlmFilter = array_pop($nlmFilters);
$nlmXmlDom = new DOMDocument();
$nlmXmlDom->loadXML($nlmFilter->execute($article));
$documentElement =& $nlmXmlDom->documentElement;
// Work-around for hasChildNodes being stupid about whitespace.
$hasChildren = false;
if (isset($documentElement->childNodes)) {
foreach ($documentElement->childNodes as $c) {
if ($c->nodeType == XML_ELEMENT_NODE) {
$hasChildren = true;
}
}
}
// If there were any citations, include them.
if ($hasChildren) {
$innerXml = $nlmXmlDom->saveXML($documentElement);
$response .= "<back>{$innerXml}</back>\n";
}
$response .= "</article>";
return $response;
}
