| static public strtolower ( $string ) : string | ||
| $string | string Input string | |
| return | string | Lower case version of input string |
/**
* 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 $keywords;
}
/**
* Query parsing helper routine.
* Returned structure is based on that used by the Search::QueryParser Perl module.
*/
function _parseQueryInternal($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;
}
/**
* 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;
}
/**
* 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');
}
/**
* 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, $this, '_returnSimpleAuthorFromRow');
}
/**
* @copydoc PKPPubIdPlugin::getPubId()
*/
function getPubId($pubObject)
{
// Get the pub id type
$pubIdType = $this->getPubIdType();
// If we already have an assigned pub id, use it.
$storedPubId = $pubObject->getStoredPubId($pubIdType);
if ($storedPubId) {
return $storedPubId;
}
// Determine the type of the publishing object.
$pubObjectType = $this->getPubObjectType($pubObject);
// Initialize variables for publication objects.
$submission = $pubObjectType == 'Submission' ? $pubObject : null;
$representation = $pubObjectType == 'Representation' ? $pubObject : null;
$submissionFile = $pubObjectType == 'SubmissionFile' ? $pubObject : null;
// Get the context id.
if ($pubObjectType == 'Submission') {
$contextId = $pubObject->getContextId();
} else {
// Retrieve the submission.
assert(is_a($pubObject, 'Representation') || is_a($pubObject, 'SubmissionFile'));
$submissionDao = Application::getSubmissionDAO();
$submission = $submissionDao->getById($pubObject->getSubmissionId(), null, true);
if (!$submission) {
return null;
}
// Now we can identify the context.
$contextId = $submission->getContextId();
}
// Check the context
$context = $this->getContext($contextId);
if (!$context) {
return null;
}
$contextId = $context->getId();
// Check whether pub ids are enabled for the given object type.
$objectTypeEnabled = $this->isObjectTypeEnabled($pubObjectType, $contextId);
if (!$objectTypeEnabled) {
return null;
}
// Retrieve the pub id prefix.
$pubIdPrefix = $this->getSetting($contextId, $this->getPrefixFieldName());
if (empty($pubIdPrefix)) {
return null;
}
// Generate the pub id suffix.
$suffixFieldName = $this->getSuffixFieldName();
$suffixGenerationStrategy = $this->getSetting($contextId, $suffixFieldName);
switch ($suffixGenerationStrategy) {
case 'customId':
$pubIdSuffix = $pubObject->getData($suffixFieldName);
break;
case 'pattern':
$suffixPatternsFieldNames = $this->getSuffixPatternsFieldNames();
$pubIdSuffix = $this->getSetting($contextId, $suffixPatternsFieldNames[$pubObjectType]);
// %p - press initials
$pubIdSuffix = PKPString::regexp_replace('/%p/', PKPString::strtolower($context->getAcronym($context->getPrimaryLocale())), $pubIdSuffix);
// %x - custom identifier
if ($pubObject->getStoredPubId('publisher-id')) {
$pubIdSuffix = PKPString::regexp_replace('/%x/', $pubObject->getStoredPubId('publisher-id'), $pubIdSuffix);
}
if ($submission) {
// %m - monograph id
$pubIdSuffix = PKPString::regexp_replace('/%m/', $submission->getId(), $pubIdSuffix);
}
if ($representation) {
// %f - publication format id
$pubIdSuffix = PKPString::regexp_replace('/%f/', $representation->getId(), $pubIdSuffix);
}
if ($submissionFile) {
// %s - file id
$pubIdSuffix = PKPString::regexp_replace('/%s/', $submissionFile->getFileId(), $pubIdSuffix);
}
break;
default:
$pubIdSuffix = PKPString::strtolower($context->getAcronym($context->getPrimaryLocale()));
if ($submission) {
$pubIdSuffix .= '.' . $submission->getId();
}
if ($representation) {
$pubIdSuffix .= '.' . $representation->getId();
}
if ($submissionFile) {
$pubIdSuffix .= '.' . $submissionFile->getFileId();
}
}
if (empty($pubIdSuffix)) {
return null;
}
// Costruct the pub id from prefix and suffix.
$pubId = $this->constructPubId($pubIdPrefix, $pubIdSuffix, $contextId);
return $pubId;
}
/**
* Handle incoming requests/notifications
* @param $args array
* @param $request PKPRequest
*/
function handle($args, $request)
{
$templateMgr = TemplateManager::getManager($request);
$journal = $request->getJournal();
if (!$journal) {
return parent::handle($args, $request);
}
// Just in case we need to contact someone
import('lib.pkp.classes.mail.MailTemplate');
// Prefer technical support contact
$contactName = $journal->getSetting('supportName');
$contactEmail = $journal->getSetting('supportEmail');
if (!$contactEmail) {
// Fall back on primary contact
$contactName = $journal->getSetting('contactName');
$contactEmail = $journal->getSetting('contactEmail');
}
$mail = new MailTemplate('PAYPAL_INVESTIGATE_PAYMENT');
$mail->setReplyTo(null);
$mail->addRecipient($contactEmail, $contactName);
$paymentStatus = $request->getUserVar('payment_status');
switch (array_shift($args)) {
case 'ipn':
// Build a confirmation transaction.
$req = 'cmd=_notify-validate';
if (get_magic_quotes_gpc()) {
foreach ($_POST as $key => $value) {
$req .= '&' . urlencode(stripslashes($key)) . '=' . urlencode(stripslashes($value));
}
} else {
foreach ($_POST as $key => $value) {
$req .= '&' . urlencode($key) . '=' . urlencode($value);
}
}
// Create POST response
$ch = curl_init();
curl_setopt($ch, CURLOPT_URL, $this->getSetting($journal->getId(), 'paypalurl'));
curl_setopt($ch, CURLOPT_RETURNTRANSFER, 1);
curl_setopt($ch, CURLOPT_POST, 1);
curl_setopt($ch, CURLOPT_HTTPHEADER, array('User-Agent: PKP PayPal Service', 'Content-Type: application/x-www-form-urlencoded', 'Content-Length: ' . strlen($req)));
curl_setopt($ch, CURLOPT_POSTFIELDS, $req);
$ret = curl_exec($ch);
$curlError = curl_error($ch);
curl_close($ch);
// Check the confirmation response and handle as necessary.
if (strcmp($ret, 'VERIFIED') == 0) {
switch ($paymentStatus) {
case 'Completed':
$payPalDao = DAORegistry::getDAO('PayPalDAO');
$transactionId = $request->getUserVar('txn_id');
if ($payPalDao->transactionExists($transactionId)) {
// A duplicate transaction was received; notify someone.
$mail->assignParams(array('journalName' => $journal->getLocalizedName(), 'postInfo' => print_r($_POST, true), 'additionalInfo' => "Duplicate transaction ID: {$transactionId}", 'serverVars' => print_r($_SERVER, true)));
$mail->send();
exit;
} else {
// New transaction succeeded. Record it.
$payPalDao->insertTransaction($transactionId, $request->getUserVar('txn_type'), PKPString::strtolower($request->getUserVar('payer_email')), PKPString::strtolower($request->getUserVar('receiver_email')), $request->getUserVar('item_number'), $request->getUserVar('payment_date'), $request->getUserVar('payer_id'), $request->getUserVar('receiver_id'));
$queuedPaymentId = $request->getUserVar('custom');
import('classes.payment.ojs.OJSPaymentManager');
$ojsPaymentManager = new OJSPaymentManager($request);
// Verify the cost and user details as per PayPal spec.
$queuedPayment =& $ojsPaymentManager->getQueuedPayment($queuedPaymentId);
if (!$queuedPayment) {
// The queued payment entry is missing. Complain.
$mail->assignParams(array('journalName' => $journal->getLocalizedName(), 'postInfo' => print_r($_POST, true), 'additionalInfo' => "Missing queued payment ID: {$queuedPaymentId}", 'serverVars' => print_r($_SERVER, true)));
$mail->send();
exit;
}
//NB: if/when paypal subscriptions are enabled, these checks will have to be adjusted
// because subscription prices may change over time
$queuedAmount = $queuedPayment->getAmount();
$grantedAmount = $request->getUserVar('mc_gross');
$queuedCurrency = $queuedPayment->getCurrencyCode();
$grantedCurrency = $request->getUserVar('mc_currency');
$grantedEmail = PKPString::strtolower($request->getUserVar('receiver_email'));
$queuedEmail = PKPString::strtolower($this->getSetting($journal->getId(), 'selleraccount'));
if ($queuedAmount != $grantedAmount && $queuedAmount > 0 || $queuedCurrency != $grantedCurrency || $grantedEmail != $queuedEmail) {
// The integrity checks for the transaction failed. Complain.
$mail->assignParams(array('journalName' => $journal->getLocalizedName(), 'postInfo' => print_r($_POST, true), 'additionalInfo' => "Granted amount: {$grantedAmount}\n" . "Queued amount: {$queuedAmount}\n" . "Granted currency: {$grantedCurrency}\n" . "Queued currency: {$queuedCurrency}\n" . "Granted to PayPal account: {$grantedEmail}\n" . "Configured PayPal account: {$queuedEmail}", 'serverVars' => print_r($_SERVER, true)));
$mail->send();
exit;
}
// Update queued amount if amount set by user (e.g. donation)
if ($queuedAmount == 0 && $grantedAmount > 0) {
$queuedPaymentDao = DAORegistry::getDAO('QueuedPaymentDAO');
$queuedPayment->setAmount($grantedAmount);
$queuedPayment->setCurrencyCode($grantedCurrency);
$queuedPaymentDao->updateQueuedPayment($queuedPaymentId, $queuedPayment);
}
// Fulfill the queued payment.
if ($ojsPaymentManager->fulfillQueuedPayment($request, $queuedPayment, $this->getName())) {
exit;
}
// If we're still here, it means the payment couldn't be fulfilled.
$mail->assignParams(array('journalName' => $journal->getLocalizedName(), 'postInfo' => print_r($_POST, true), 'additionalInfo' => "Queued payment ID {$queuedPaymentId} could not be fulfilled.", 'serverVars' => print_r($_SERVER, true)));
$mail->send();
}
exit;
case 'Pending':
// Ignore.
exit;
default:
// An unhandled payment status was received; notify someone.
$mail->assignParams(array('journalName' => $journal->getLocalizedName(), 'postInfo' => print_r($_POST, true), 'additionalInfo' => "Payment status: {$paymentStatus}", 'serverVars' => print_r($_SERVER, true)));
$mail->send();
exit;
}
} else {
// An unknown confirmation response was received; notify someone.
$mail->assignParams(array('journalName' => $journal->getLocalizedName(), 'postInfo' => print_r($_POST, true), 'additionalInfo' => "Confirmation return: {$ret}\nCURL error: {$curlError}", 'serverVars' => print_r($_SERVER, true)));
$mail->send();
exit;
}
case 'cancel':
Handler::setupTemplate();
$templateMgr->assign(array('currentUrl' => $request->url(null, 'index'), 'pageTitle' => 'plugins.paymethod.paypal.purchase.cancelled.title', 'message' => 'plugins.paymethod.paypal.purchase.cancelled', 'backLink' => $request->getUserVar('ojsReturnUrl'), 'backLinkLabel' => 'common.continue'));
$templateMgr->display('frontend/pages/message.tpl');
exit;
}
parent::handle($args, $request);
// Don't know what to do with it
}
/**
* @see PubIdPlugin::getPubId()
*/
function getPubId($pubObject, $preview = false)
{
$urn = $pubObject->getStoredPubId($this->getPubIdType());
if (!$urn) {
// Determine the type of the publishing object
$pubObjectType = $this->getPubObjectType($pubObject);
// Initialize variables for publication objects
$issue = $pubObjectType == 'Issue' ? $pubObject : null;
$article = $pubObjectType == 'Article' ? $pubObject : null;
$galley = $pubObjectType == 'Galley' ? $pubObject : null;
// Get the journal id of the object
if (in_array($pubObjectType, array('Issue', 'Article'))) {
$journalId = $pubObject->getJournalId();
} else {
// Retrieve the published article
assert(is_a($pubObject, 'SubmissionFile'));
$articleDao = DAORegistry::getDAO('ArticleDAO');
$article = $articleDao->getById($pubObject->getArticleId(), null, true);
if (!$article) {
return null;
}
// Now we can identify the journal
$journalId = $article->getJournalId();
}
// get the journal
$journal = $this->getJournal($journalId);
if (!$journal) {
return null;
}
$journalId = $journal->getId();
// Check whether URNs are enabled for the given object type
$urnEnabled = $this->getSetting($journalId, "enable{$pubObjectType}URN") == '1';
if (!$urnEnabled) {
return null;
}
// Retrieve the issue
if (!is_a($pubObject, 'Issue')) {
assert(!is_null($article));
$issueDao = DAORegistry::getDAO('IssueDAO');
$issue = $issueDao->getIssueByArticleId($article->getId(), $journal->getId());
}
// Retrieve the URN prefix
$urnPrefix = $this->getSetting($journal->getId(), 'urnPrefix');
if (empty($urnPrefix)) {
return null;
}
// Generate the URN suffix
$urnSuffixSetting = $this->getSetting($journal->getId(), 'urnSuffix');
switch ($urnSuffixSetting) {
case 'publisherId':
$urnSuffix = (string) call_user_func_array(array($pubObject, "getBest{$pubObjectType}Id"), array(&$journal));
// When the suffix equals the object's ID then
// require an object-specific prefix to be sure that the suffix is unique
if ($pubObjectType != 'Article' && $urnSuffix === (string) $pubObject->getId()) {
$urnSuffix = strtolower_codesafe($pubObjectType[0]) . $urnSuffix;
}
if (!empty($urnSuffix)) {
$urn = $urnPrefix . $urnSuffix;
if ($this->getSetting($journal->getId(), 'checkNo')) {
$urn .= $this->_calculateCheckNo($urn);
}
}
break;
case 'customIdentifier':
$urnSuffix = $pubObject->getData('urnSuffix');
if (!empty($urnSuffix)) {
$urn = $urnPrefix . $urnSuffix;
}
break;
case 'pattern':
$urnSuffix = $this->getSetting($journal->getId(), "urn{$pubObjectType}SuffixPattern");
// %j - journal initials
$urnSuffix = PKPString::regexp_replace('/%j/', PKPString::strtolower($journal->getAcronym($journal->getPrimaryLocale())), $urnSuffix);
// %x - custom identifier
if ($pubObject->getStoredPubId('publisher-id')) {
$urnSuffix = PKPString::regexp_replace('/%x/', $pubObject->getStoredPubId('publisher-id'), $urnSuffix);
}
if ($issue) {
// %v - volume number
$urnSuffix = PKPString::regexp_replace('/%v/', $issue->getVolume(), $urnSuffix);
// %i - issue number
$urnSuffix = PKPString::regexp_replace('/%i/', $issue->getNumber(), $urnSuffix);
// %Y - year
$urnSuffix = PKPString::regexp_replace('/%Y/', $issue->getYear(), $urnSuffix);
}
if ($article) {
// %a - article id
$urnSuffix = PKPString::regexp_replace('/%a/', $article->getId(), $urnSuffix);
// %p - page number
if ($article->getPages()) {
$urnSuffix = PKPString::regexp_replace('/%p/', $article->getPages(), $urnSuffix);
}
}
if ($galley) {
// %g - galley id
$urnSuffix = PKPString::regexp_replace('/%g/', $galley->getId(), $urnSuffix);
}
if (!empty($urnSuffix)) {
$urn = $urnPrefix . $urnSuffix;
if ($this->getSetting($journal->getId(), 'checkNo')) {
$urn .= $this->_calculateCheckNo($urn);
}
}
break;
default:
$urnSuffix = PKPString::strtolower($journal->getAcronym($journal->getPrimaryLocale()));
if ($issue) {
$urnSuffix .= '.v' . $issue->getVolume() . 'i' . $issue->getNumber();
} else {
$urnSuffix .= '.v%vi%i';
}
if ($article) {
$urnSuffix .= '.' . $article->getId();
}
if ($galley) {
$urnSuffix .= '.g' . $galley->getId();
}
$urn = $urnPrefix . $urnSuffix;
if ($this->getSetting($journal->getId(), 'checkNo')) {
$urn .= $this->_calculateCheckNo($urn);
}
}
if ($urn && !$preview) {
$this->setStoredPubId($pubObject, $pubObjectType, $urn);
}
}
return $urn;
}
/**
* @function abntDateFormatWithDay Format date taking in consideration ABNT month abbreviations
* @param $string string
* @return string
*/
function abntDateFormatWithDay($string)
{
if (is_numeric($string)) {
// it is a numeric string, we handle it as timestamp
$timestamp = (int) $string;
} else {
$timestamp = strtotime($string);
}
$format = "%d %B %Y";
if (PKPString::strlen(strftime("%B", $timestamp)) > 4) {
$format = "%d %b. %Y";
}
return PKPString::strtolower(strftime($format, $timestamp));
}
/**
* Fills the given citation object with
* meta-data retrieved from PubMed.
* @param $pmid string
* @return MetadataDescription
*/
function &_lookup($pmid)
{
$nullVar = null;
// Use eFetch to get XML metadata for the given PMID
$lookupParams = array('db' => 'pubmed', 'mode' => 'xml', 'tool' => 'pkp-wal', 'id' => $pmid);
if (!is_null($this->getEmail())) {
$lookupParams['email'] = $this->getEmail();
}
// Call the eFetch URL and get an XML result
if (is_null($resultDOM = $this->callWebService(PUBMED_WEBSERVICE_EFETCH, $lookupParams))) {
return $nullVar;
}
$articleTitleNodes = $resultDOM->getElementsByTagName('ArticleTitle');
$articleTitleFirstNode = $articleTitleNodes->item(0);
$medlineTaNodes = $resultDOM->getElementsByTagName('MedlineTA');
$medlineTaFirstNode = $medlineTaNodes->item(0);
$metadata = array('pub-id[@pub-id-type="pmid"]' => $pmid, 'article-title' => $articleTitleFirstNode->textContent, 'source' => $medlineTaFirstNode->textContent);
$volumeNodes = $resultDOM->getElementsByTagName('Volume');
$issueNodes = $resultDOM->getElementsByTagName('Issue');
if ($volumeNodes->length > 0) {
$volumeFirstNode = $volumeNodes->item(0);
}
$metadata['volume'] = $volumeFirstNode->textContent;
if ($issueNodes->length > 0) {
$issueFirstNode = $issueNodes->item(0);
}
$metadata['issue'] = $issueFirstNode->textContent;
// Get list of author full names
foreach ($resultDOM->getElementsByTagName("Author") as $authorNode) {
if (!isset($metadata['person-group[@person-group-type="author"]'])) {
$metadata['person-group[@person-group-type="author"]'] = array();
}
// Instantiate an NLM name description
$authorDescription = new MetadataDescription('lib.pkp.plugins.metadata.nlm30.schema.Nlm30NameSchema', ASSOC_TYPE_AUTHOR);
// Surname
$lastNameNodes = $authorNode->getElementsByTagName('LastName');
$lastNameFirstNode = $lastNameNodes->item(0);
$authorDescription->addStatement('surname', $lastNameFirstNode->textContent);
// Given names
$givenNamesString = '';
$firstNameNodes = $authorNode->getElementsByTagName('FirstName');
if ($firstNameNodes->length > 0) {
$firstNameFirstNode = $firstNameNodes->item(0);
$givenNamesString = $firstNameFirstNode->textContent;
} else {
$foreNameNodes = $authorNode->getElementsByTagName('ForeName');
if ($foreNameNodes->length > 0) {
$foreNameFirstNode = $foreNameNodes->item(0);
$givenNamesString = $foreNameFirstNode->textContent;
}
}
if (!empty($givenNamesString)) {
foreach (explode(' ', $givenNamesString) as $givenName) {
$authorDescription->addStatement('given-names', PKPString::trimPunctuation($givenName));
}
}
// Suffix
$suffixNodes = $authorNode->getElementsByTagName('Suffix');
if ($suffixNodes->length > 0) {
$suffixFirstNode = $suffixNodes->item(0);
$authorDescription->addStatement('suffix', $suffixFirstNode->textContent);
}
// Include collective names
// FIXME: This corresponds to an NLM-citation <collab> tag and should be part of the Metadata implementation
/*if ($resultDOM->getElementsByTagName("CollectiveName")->length > 0 && $authorNode->getElementsByTagName("CollectiveName")->item(0)->textContent != '') {
}*/
$metadata['person-group[@person-group-type="author"]'][] =& $authorDescription;
unset($authorDescription);
}
// Extract pagination
$medlinePgnNodes = $resultDOM->getElementsByTagName('MedlinePgn');
$medlinePgnFirstNode = $medlinePgnNodes->item(0);
if (PKPString::regexp_match_get("/^[:p\\.\\s]*(?P<fpage>[Ee]?\\d+)(-(?P<lpage>\\d+))?/", $medlinePgnFirstNode->textContent, $pages)) {
$fPage = (int) $pages['fpage'];
$metadata['fpage'] = $fPage;
if (!empty($pages['lpage'])) {
$lPage = (int) $pages['lpage'];
// Deal with shortcuts like '382-7'
if ($lPage < $fPage) {
$lPage = (int) (PKPString::substr($pages['fpage'], 0, -PKPString::strlen($pages['lpage'])) . $pages['lpage']);
}
$metadata['lpage'] = $lPage;
}
}
// Get publication date (can be in several places in PubMed).
$dateNode = null;
$articleDateNodes = $resultDOM->getElementsByTagName('ArticleDate');
if ($articleDateNodes->length > 0) {
$dateNode = $articleDateNodes->item(0);
} else {
$pubDateNodes = $resultDOM->getElementsByTagName('PubDate');
if ($pubDateNodes->length > 0) {
$dateNode = $pubDateNodes->item(0);
}
}
// Retrieve the data parts and assemble date.
if (!is_null($dateNode)) {
$publicationDate = '';
$requiresNormalization = false;
foreach (array('Year' => 4, 'Month' => 2, 'Day' => 2) as $dateElement => $padding) {
$dateElementNodes = $dateNode->getElementsByTagName($dateElement);
if ($dateElementNodes->length > 0) {
if (!empty($publicationDate)) {
$publicationDate .= '-';
}
$dateElementFirstNode = $dateElementNodes->item(0);
$datePart = str_pad($dateElementFirstNode->textContent, $padding, '0', STR_PAD_LEFT);
if (!is_numeric($datePart)) {
$requiresNormalization = true;
}
$publicationDate .= $datePart;
} else {
break;
}
}
// Normalize the date to NLM standard if necessary.
if ($requiresNormalization) {
$dateFilter = new DateStringNormalizerFilter();
$publicationDate = $dateFilter->execute($publicationDate);
}
if (!empty($publicationDate)) {
$metadata['date'] = $publicationDate;
}
}
// Get publication type
$publicationTypeNodes = $resultDOM->getElementsByTagName('PublicationType');
if ($publicationTypeNodes->length > 0) {
foreach ($publicationTypeNodes as $publicationType) {
// The vast majority of items on PubMed are articles so catch these...
if (PKPString::strpos(PKPString::strtolower($publicationType->textContent), 'article') !== false) {
$metadata['[@publication-type]'] = NLM30_PUBLICATION_TYPE_JOURNAL;
break;
}
}
}
// Get DOI if it exists
$articleIdNodes = $resultDOM->getElementsByTagName('ArticleId');
foreach ($articleIdNodes as $idNode) {
if ($idNode->getAttribute('IdType') == 'doi') {
$metadata['pub-id[@pub-id-type="doi"]'] = $idNode->textContent;
}
}
// Use eLink utility to find fulltext links
$lookupParams = array('dbfrom' => 'pubmed', 'cmd' => 'llinks', 'tool' => 'pkp-wal', 'id' => $pmid);
if (!is_null($resultDOM = $this->callWebService(PUBMED_WEBSERVICE_ELINK, $lookupParams))) {
// Get a list of possible links
foreach ($resultDOM->getElementsByTagName("ObjUrl") as $linkOut) {
$attributes = '';
foreach ($linkOut->getElementsByTagName("Attribute") as $attribute) {
$attributes .= PKPString::strtolower($attribute->textContent) . ' / ';
}
// Only add links to open access resources
if (PKPString::strpos($attributes, "subscription") === false && PKPString::strpos($attributes, "membership") === false && PKPString::strpos($attributes, "fee") === false && $attributes != "") {
$urlNodes = $linkOut->getElementsByTagName('Url');
$urlFirstNode = $urlNodes->item(0);
$links[] = $urlFirstNode->textContent;
}
}
// Take the first link if we have any left (presumably pubmed returns them in preferential order)
if (isset($links[0])) {
$metadata['uri'] = $links[0];
}
}
return $this->getNlm30CitationDescriptionFromMetadataArray($metadata);
}
/**
* Retrieve auto-suggestions from the faceting service.
* @param $url string
* @param $searchRequest SolrSearchRequest
* @param $userInput string
* @param $fieldName string
* @return array The generated suggestions.
*/
function _getFacetingAutosuggestions($url, $searchRequest, $userInput, $fieldName)
{
// Remove special characters from the user input.
$searchTerms = strtr($userInput, '"()+-|&!', ' ');
// Cut off the last search term.
$searchTerms = explode(' ', $searchTerms);
$facetPrefix = array_pop($searchTerms);
if (empty($facetPrefix)) {
return array();
}
// Use the remaining search query to pre-filter
// facet results. This may be an invalid query
// but edismax will deal gracefully with syntax
// errors.
$userInput = PKPString::substr($userInput, 0, -PKPString::strlen($facetPrefix));
switch ($fieldName) {
case 'query':
// The 'query' filter goes against all fields.
$articleSearch = new ArticleSearch();
$solrFields = array_values($articleSearch->getIndexFieldMap());
break;
case 'indexTerms':
// The 'index terms' filter goes against keyword index fields.
$solrFields = array('discipline', 'subject', 'type', 'coverage');
break;
default:
// All other filters can be used directly.
$solrFields = array($fieldName);
}
$solrFieldString = implode('|', $solrFields);
$searchRequest->addQueryFieldPhrase($solrFieldString, $userInput);
// Construct the main query.
$params = $this->_getSearchQueryParameters($searchRequest);
if (!isset($params['q'])) {
// Use a catch-all query in case we have no limiting
// search.
$params['q'] = '*:*';
}
if ($fieldName == 'query') {
$params['facet.field'] = 'default_spell';
} else {
$params['facet.field'] = $fieldName . '_spell';
}
$facetPrefixLc = PKPString::strtolower($facetPrefix);
$params['facet.prefix'] = $facetPrefixLc;
// Make the request.
$response = $this->_makeRequest($url, $params);
if (!is_a($response, 'DOMXPath')) {
return array();
}
// Extract term suggestions.
$nodeList = $response->query('//lst[@name="facet_fields"]/lst/int/@name');
if ($nodeList->length == 0) {
return array();
}
$termSuggestions = array();
foreach ($nodeList as $childNode) {
$termSuggestions[] = $childNode->value;
}
// Add the term suggestion to the remaining user input.
$suggestions = array();
foreach ($termSuggestions as $termSuggestion) {
// Restore case if possible.
if (strpos($termSuggestion, $facetPrefixLc) === 0) {
$termSuggestion = $facetPrefix . PKPString::substr($termSuggestion, PKPString::strlen($facetPrefix));
}
$suggestions[] = $userInput . $termSuggestion;
}
return $suggestions;
}
/**
* Suggest a username given the first and last names.
* @return string
*/
static function suggestUsername($firstName, $lastName)
{
$initial = PKPString::substr($firstName, 0, 1);
$suggestion = PKPString::regexp_replace('/[^a-zA-Z0-9_-]/', '', PKPString::strtolower($initial . $lastName));
$userDao = DAORegistry::getDAO('UserDAO');
for ($i = ''; $userDao->userExistsByUsername($suggestion . $i); $i++) {
}
return $suggestion . $i;
}
/**
* Subclasses can override this method to configure the
* handler.
*
* NB: This method will be called after validation and
* authorization.
*
* @param $request PKPRequest
* @param $args array
*/
function initialize($request, $args = null)
{
// Set the controller id to the requested
// page (page routing) or component name
// (component routing) by default.
$router = $request->getRouter();
if (is_a($router, 'PKPComponentRouter')) {
$componentId = $router->getRequestedComponent($request);
// Create a somewhat compressed but still globally unique
// and human readable component id.
// Example: "grid.citation.CitationGridHandler"
// becomes "grid-citation-citationgrid"
$componentId = str_replace('.', '-', PKPString::strtolower(PKPString::substr($componentId, 0, -7)));
$this->setId($componentId);
} else {
assert(is_a($router, 'PKPPageRouter'));
$this->setId($router->getRequestedPage($request));
}
}
/**
* @copydoc PKPPubIdPlugin::getPubId()
*/
function getPubId($pubObject)
{
// Get the pub id type
$pubIdType = $this->getPubIdType();
// If we already have an assigned pub id, use it.
$storedPubId = $pubObject->getStoredPubId($pubIdType);
if ($storedPubId) {
return $storedPubId;
}
// Determine the type of the publishing object.
$pubObjectType = $this->getPubObjectType($pubObject);
// Initialize variables for publication objects.
$issue = $pubObjectType == 'Issue' ? $pubObject : null;
$submission = $pubObjectType == 'Submission' ? $pubObject : null;
$representation = $pubObjectType == 'Representation' ? $pubObject : null;
$submissionFile = $pubObjectType == 'SubmissionFile' ? $pubObject : null;
// Get the context id.
if (in_array($pubObjectType, array('Issue', 'Submission'))) {
$contextId = $pubObject->getJournalId();
} else {
// Retrieve the submission.
assert(is_a($pubObject, 'Representation') || is_a($pubObject, 'SubmissionFile'));
$submissionDao = Application::getSubmissionDAO();
$submission = $submissionDao->getById($pubObject->getSubmissionId(), null, true);
if (!$submission) {
return null;
}
// Now we can identify the context.
$contextId = $submission->getJournalId();
}
// Check the context
$context = $this->getContext($contextId);
if (!$context) {
return null;
}
$contextId = $context->getId();
// Check whether pub ids are enabled for the given object type.
$objectTypeEnabled = $this->isObjectTypeEnabled($pubObjectType, $contextId);
if (!$objectTypeEnabled) {
return null;
}
// Retrieve the issue.
if (!is_a($pubObject, 'Issue')) {
assert(!is_null($submission));
$issueDao = DAORegistry::getDAO('IssueDAO');
/* @var $issueDao IssueDAO */
$issue = $issueDao->getIssueByArticleId($submission->getId(), $contextId);
}
if ($issue && $contextId != $issue->getJournalId()) {
return null;
}
// Retrieve the pub id prefix.
$pubIdPrefix = $this->getSetting($contextId, $this->getPrefixFieldName());
if (empty($pubIdPrefix)) {
return null;
}
// Generate the pub id suffix.
$suffixFieldName = $this->getSuffixFieldName();
$suffixGenerationStrategy = $this->getSetting($contextId, $suffixFieldName);
switch ($suffixGenerationStrategy) {
case 'customId':
$pubIdSuffix = $pubObject->getData($suffixFieldName);
break;
case 'pattern':
$suffixPatternsFieldNames = $this->getSuffixPatternsFieldNames();
$pubIdSuffix = $this->getSetting($contextId, $suffixPatternsFieldNames[$pubObjectType]);
// %j - journal initials
$pubIdSuffix = PKPString::regexp_replace('/%j/', PKPString::strtolower($context->getAcronym($context->getPrimaryLocale())), $pubIdSuffix);
// %x - custom identifier
if ($pubObject->getStoredPubId('publisher-id')) {
$pubIdSuffix = PKPString::regexp_replace('/%x/', $pubObject->getStoredPubId('publisher-id'), $pubIdSuffix);
}
if ($issue) {
// %v - volume number
$pubIdSuffix = PKPString::regexp_replace('/%v/', $issue->getVolume(), $pubIdSuffix);
// %i - issue number
$pubIdSuffix = PKPString::regexp_replace('/%i/', $issue->getNumber(), $pubIdSuffix);
// %Y - year
$pubIdSuffix = PKPString::regexp_replace('/%Y/', $issue->getYear(), $pubIdSuffix);
}
if ($submission) {
// %a - article id
$pubIdSuffix = PKPString::regexp_replace('/%a/', $submission->getId(), $pubIdSuffix);
// %p - page number
if ($submission->getPages()) {
$pubIdSuffix = PKPString::regexp_replace('/%p/', $submission->getPages(), $pubIdSuffix);
}
}
if ($representation) {
// %g - galley id
$pubIdSuffix = PKPString::regexp_replace('/%g/', $representation->getId(), $pubIdSuffix);
}
if ($submissionFile) {
// %f - file id
$pubIdSuffix = PKPString::regexp_replace('/%f/', $submissionFile->getFileId(), $pubIdSuffix);
}
break;
default:
$pubIdSuffix = PKPString::strtolower($context->getAcronym($context->getPrimaryLocale()));
if ($issue) {
$pubIdSuffix .= '.v' . $issue->getVolume() . 'i' . $issue->getNumber();
} else {
$pubIdSuffix .= '.v%vi%i';
}
if ($submission) {
$pubIdSuffix .= '.' . $submission->getId();
}
if ($representation) {
$pubIdSuffix .= '.g' . $representation->getId();
}
if ($submissionFile) {
$pubIdSuffix .= '.f' . $submissionFile->getFileId();
}
}
if (empty($pubIdSuffix)) {
return null;
}
// Costruct the pub id from prefix and suffix.
$pubId = $this->constructPubId($pubIdPrefix, $pubIdSuffix, $contextId);
return $pubId;
}
/**
* @see PubIdPlugin::getPubId()
*/
function getPubId($pubObject, $preview = false)
{
// Determine the type of the publishing object.
$pubObjectType = $this->getPubObjectType($pubObject);
// Initialize variables for publication objects.
$issue = $pubObjectType == 'Issue' ? $pubObject : null;
$article = $pubObjectType == 'Article' ? $pubObject : null;
$galley = $pubObjectType == 'Galley' ? $pubObject : null;
// Get the journal id of the object.
if (in_array($pubObjectType, array('Issue', 'Article'))) {
$journalId = $pubObject->getJournalId();
} else {
// Retrieve the published article.
assert(is_a($pubObject, 'ArticleGalley'));
$articleDao = DAORegistry::getDAO('PublishedArticleDAO');
/* @var $articleDao PublishedArticleDAO */
$article =& $articleDao->getPublishedArticleByArticleId($pubObject->getSubmissionId(), null, true);
if (!$article) {
return null;
}
// Now we can identify the journal.
$journalId = $article->getJournalId();
}
$journal = $this->getJournal($journalId);
if (!$journal) {
return null;
}
$journalId = $journal->getId();
// Check whether DOIs are enabled for the given object type.
$doiEnabled = $this->getSetting($journalId, "enable{$pubObjectType}Doi") == '1';
if (!$doiEnabled) {
return null;
}
// If we already have an assigned DOI, use it.
$storedDOI = $pubObject->getStoredPubId('doi');
if ($storedDOI) {
return $storedDOI;
}
// Retrieve the issue.
if (!is_a($pubObject, 'Issue')) {
assert(!is_null($article));
$issueDao = DAORegistry::getDAO('IssueDAO');
/* @var $issueDao IssueDAO */
$issue = $issueDao->getIssueByArticleId($article->getId(), $journal->getId());
}
if ($issue && $journalId != $issue->getJournalId()) {
return null;
}
// Retrieve the DOI prefix.
$doiPrefix = $this->getSetting($journalId, 'doiPrefix');
if (empty($doiPrefix)) {
return null;
}
// Generate the DOI suffix.
$doiSuffixGenerationStrategy = $this->getSetting($journalId, 'doiSuffix');
switch ($doiSuffixGenerationStrategy) {
case 'publisherId':
switch ($pubObjectType) {
case 'Issue':
$doiSuffix = (string) $pubObject->getBestIssueId($journal);
break;
case 'Article':
$doiSuffix = (string) $pubObject->getBestArticleId($journal);
break;
case 'Galley':
$doiSuffix = (string) $pubObject->getBestGalleyId($journal);
break;
default:
assert(false);
}
// When the suffix equals the object's ID then
// require an object-specific prefix to be sure that
// the suffix is unique.
if ($pubObjectType != 'Article' && $doiSuffix === (string) $pubObject->getId()) {
$doiSuffix = strtolower_codesafe($pubObjectType[0]) . $doiSuffix;
}
break;
case 'customId':
$doiSuffix = $pubObject->getData('doiSuffix');
break;
case 'pattern':
$doiSuffix = $this->getSetting($journalId, "doi{$pubObjectType}SuffixPattern");
// %j - journal initials
$doiSuffix = PKPString::regexp_replace('/%j/', PKPString::strtolower($journal->getAcronym($journal->getPrimaryLocale())), $doiSuffix);
// %x - custom identifier
if ($pubObject->getStoredPubId('publisher-id')) {
$doiSuffix = PKPString::regexp_replace('/%x/', $pubObject->getStoredPubId('publisher-id'), $doiSuffix);
}
if ($issue) {
// %v - volume number
$doiSuffix = PKPString::regexp_replace('/%v/', $issue->getVolume(), $doiSuffix);
// %i - issue number
$doiSuffix = PKPString::regexp_replace('/%i/', $issue->getNumber(), $doiSuffix);
// %Y - year
$doiSuffix = PKPString::regexp_replace('/%Y/', $issue->getYear(), $doiSuffix);
}
if ($article) {
// %a - article id
$doiSuffix = PKPString::regexp_replace('/%a/', $article->getId(), $doiSuffix);
// %p - page number
if ($article->getPages()) {
$doiSuffix = PKPString::regexp_replace('/%p/', $article->getPages(), $doiSuffix);
}
}
if ($galley) {
// %g - galley id
$doiSuffix = PKPString::regexp_replace('/%g/', $galley->getId(), $doiSuffix);
}
break;
default:
$doiSuffix = PKPString::strtolower($journal->getAcronym($journal->getPrimaryLocale()));
if ($issue) {
$doiSuffix .= '.v' . $issue->getVolume() . 'i' . $issue->getNumber();
} else {
$doiSuffix .= '.v%vi%i';
}
if ($article) {
$doiSuffix .= '.' . $article->getId();
}
if ($galley) {
$doiSuffix .= '.g' . $galley->getId();
}
}
if (empty($doiSuffix)) {
return null;
}
// Join prefix and suffix.
$doi = $doiPrefix . '/' . $doiSuffix;
if (!$preview) {
// Save the generated DOI.
$this->setStoredPubId($pubObject, $pubObjectType, $doi);
}
return $doi;
}
