/**
* 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
$cleanText = String::regexp_replace('/[!"\\#\\$%\'\\(\\)\\.\\?@\\[\\]\\^`\\{\\}~]/', '', $cleanText);
$cleanText = String::regexp_replace('/[\\+,:;&\\/<=>\\|\\\\]/', ' ', $cleanText);
$cleanText = String::regexp_replace('/[\\*]/', $allowWildcards ? '%' : ' ', $cleanText);
$cleanText = String::strtolower($cleanText);
// Split into words
$words = String::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[$k]) && String::strlen($k) >= $minLength && !is_numeric($k)) {
$keywords[] = String::substr($k, 0, SEARCH_KEYWORD_MAX_LENGTH);
}
}
return $keywords;
}
/**
* @see PKPPlugin::getName()
*/
function getName()
{
// Lazy load enabled plug-ins always use the plugin's class name
// as plug-in name. Legacy plug-ins will override this method so
// this implementation is backwards compatible.
// NB: strtolower is required for PHP4 compatibility.
return String::strtolower(get_class($this));
}
/**
* 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 = String::strtolower(__('search.operator.not'));
$andOperator = String::strtolower(__('search.operator.and'));
$orOperator = String::strtolower(__('search.operator.or'));
while ($pos < $total) {
if (!empty($signTokens[$pos])) {
$sign = $signTokens[$pos];
} else {
if (empty($sign)) {
$sign = '+';
}
}
$token = String::strtolower($tokens[$pos++]);
switch ($token) {
case $notOperator:
$sign = '-';
break;
case ')':
return $return;
case '(':
$token = $this->_parseQueryInternal($signTokens, $tokens, $pos, $total);
default:
$postBool = '';
if ($pos < $total) {
$peek = String::strtolower($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;
}
/**
* Return an HTML-formatted citation. Default implementation displays
* an HTML-based citation using the citation.tpl template in the plugin
* path.
* @param $paper object
*/
function cite(&$paper)
{
$loweredTitle = String::strtolower($paper->getLocalizedTitle());
$apaCapitalized = String::ucfirst($loweredTitle);
HookRegistry::register('Template::RT::CaptureCite', array(&$this, 'displayCitation'));
$templateMgr =& TemplateManager::getManager();
$templateMgr->assign_by_ref('citationPlugin', $this);
$templateMgr->assign('apaCapitalized', $apaCapitalized);
$templateMgr->display('rt/captureCite.tpl');
}
function _handleOcsUrl($matchArray)
{
$url = $matchArray[2];
$anchor = null;
if (($i = strpos($url, '#')) !== false) {
$anchor = substr($url, $i + 1);
$url = substr($url, 0, $i);
}
$urlParts = explode('/', $url);
if (isset($urlParts[0])) {
switch (String::strtolower($urlParts[0])) {
case 'conference':
$url = Request::url(isset($urlParts[1]) ? $urlParts[1] : Request::getRequestedConferencePath(), null, null, null, null, null, $anchor);
break;
case 'paper':
if (isset($urlParts[1])) {
$url = Request::url(null, null, 'paper', 'view', $urlParts[1], null, $anchor);
}
break;
case 'schedConf':
if (isset($urlParts[1])) {
$schedConfDao =& DAORegistry::getDAO('SchedConfDAO');
$conferenceDao =& DAORegistry::getDAO('ConferenceDAO');
$thisSchedConf =& $schedConfDao->getSchedConfByPath($urlParts[1]);
if (!$thisSchedConf) {
break;
}
$thisConference =& $conferenceDao->getConference($thisSchedConf->getConferenceId());
$url = Request::url($thisConference->getPath(), $thisSchedConf->getPath(), null, null, null, null, $anchor);
} else {
$url = Request::url(null, null, 'schedConfs', 'current', null, null, $anchor);
}
break;
case 'suppfile':
if (isset($urlParts[1]) && isset($urlParts[2])) {
$url = Request::url(null, null, 'paper', 'downloadSuppFile', array($urlParts[1], $urlParts[2]), null, $anchor);
}
break;
case 'sitepublic':
array_shift($urlParts);
import('file.PublicFileManager');
$publicFileManager = new PublicFileManager();
$url = Request::getBaseUrl() . '/' . $publicFileManager->getSiteFilesPath() . '/' . implode('/', $urlParts) . ($anchor ? '#' . $anchor : '');
break;
case 'public':
array_shift($urlParts);
$schedConf =& Request::getSchedConf();
import('file.PublicFileManager');
$publicFileManager = new PublicFileManager();
$url = Request::getBaseUrl() . '/' . $publicFileManager->getSchedConfFilesPath($schedConf->getId()) . '/' . implode('/', $urlParts) . ($anchor ? '#' . $anchor : '');
break;
}
}
return $matchArray[1] . $url . $matchArray[3];
}
/**
* 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 == '' || String::strpos(String::strtolower(serialize($plugin)), String::strtolower($search)) !== false)) {
$plugins[] = $plugin;
}
}
return $plugins;
}
function _handleOjsUrl($matchArray)
{
$url = $matchArray[2];
$anchor = null;
if (($i = strpos($url, '#')) !== false) {
$anchor = substr($url, $i + 1);
$url = substr($url, 0, $i);
}
$urlParts = explode('/', $url);
if (isset($urlParts[0])) {
switch (String::strtolower($urlParts[0])) {
case 'journal':
$url = Request::url(isset($urlParts[1]) ? $urlParts[1] : Request::getRequestedJournalPath(), null, null, null, null, $anchor);
break;
case 'article':
if (isset($urlParts[1])) {
$url = Request::url(null, 'article', 'view', $urlParts[1], null, $anchor);
}
break;
case 'issue':
if (isset($urlParts[1])) {
$url = Request::url(null, 'issue', 'view', $urlParts[1], null, $anchor);
} else {
$url = Request::url(null, 'issue', 'current', null, null, $anchor);
}
break;
case 'suppfile':
if (isset($urlParts[1]) && isset($urlParts[2])) {
$url = Request::url(null, 'article', 'downloadSuppFile', array($urlParts[1], $urlParts[2]), null, $anchor);
}
break;
case 'sitepublic':
array_shift($urlParts);
import('file.PublicFileManager');
$publicFileManager =& new PublicFileManager();
$url = Request::getBaseUrl() . '/' . $publicFileManager->getSiteFilesPath() . '/' . implode('/', $urlParts) . ($anchor ? '#' . $anchor : '');
break;
case 'public':
array_shift($urlParts);
$journal =& Request::getJournal();
import('file.PublicFileManager');
$publicFileManager =& new PublicFileManager();
$url = Request::getBaseUrl() . '/' . $publicFileManager->getJournalFilesPath($journal->getJournalId()) . '/' . implode('/', $urlParts) . ($anchor ? '#' . $anchor : '');
break;
}
}
return $matchArray[1] . $url . $matchArray[3];
}
/**
* 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)) {
$params[] = String::strtolower($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 journals are returned.
* @param $journalId int
* @param $initial An initial the last names must begin with
* @param $rangeInfo Range information
* @param $includeEmail Whether or not to include the email in the select distinct
* @return array Authors ordered by sequence
*/
function getAuthorsAlphabetizedByJournal($journalId = null, $initial = null, $rangeInfo = null, $includeEmail = false)
{
$params = array('affiliation', AppLocale::getPrimaryLocale(), 'affiliation', AppLocale::getLocale());
if (isset($journalId)) {
$params[] = $journalId;
}
if (isset($initial)) {
$params[] = String::strtolower($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 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) ? 'a.context_id = ? 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');
}
/**
* 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)
{
$authors = array();
$params = array('affiliation', Locale::getPrimaryLocale(), 'affiliation', Locale::getLocale());
if (isset($pressId)) {
$params[] = $pressId;
}
if (isset($initial)) {
$params[] = String::strtolower($initial) . '%';
$initialSql = ' AND LOWER(ma.last_name) LIKE LOWER(?)';
} else {
$initialSql = '';
}
$result =& $this->retrieveRange('SELECT DISTINCT
CAST(\'\' AS CHAR) AS url,
0 AS author_id,
0 AS submission_id,
CAST(\'\' AS CHAR) AS email,
0 AS primary_contact,
0 AS seq,
ma.first_name AS first_name,
ma.middle_name AS middle_name,
ma.last_name AS last_name,
asl.setting_value AS affiliation_l,
asl.locale,
aspl.setting_value AS affiliation_pl,
aspl.locale AS primary_locale,
ma.country
FROM authors ma
LEFT JOIN author_settings aspl ON (aa.author_id = aspl.author_id AND aspl.setting_name = ? AND aspl.locale = ?)
LEFT JOIN author_settings asl ON (aa.author_id = asl.author_id AND asl.setting_name = ? AND asl.locale = ?)
LEFT JOIN monographs a ON (ma.submission_id = a.monograph_id)
WHERE a.status = ' . STATUS_PUBLISHED . ' ' . (isset($pressId) ? 'AND a.press_id = ? ' : '') . '
AND (ma.last_name IS NOT NULL AND ma.last_name <> \'\')' . $initialSql . '
ORDER BY ma.last_name, ma.first_name', $params, $rangeInfo);
$returner = new DAOResultFactory($result, $this, '_returnAuthorFromRow');
return $returner;
}
/**
* @see PubIdPlugin::getPubId()
*/
function getPubId($monograph, $preview = false)
{
// Determine the type of the publishing object.
$pubObjectType = $this->getPubObjectType($monograph);
// Get the press id of the object.
if (in_array($pubObjectType, array('Monograph', 'PublishedMonograph'))) {
$pressId = $monograph->getContextId();
} else {
return null;
}
$press = $this->_getPress($pressId);
if (!$press) {
return null;
}
$pressId = $press->getId();
// If we already have an assigned URN, use it.
$storedURNDNB = $monograph->getStoredPubId('urn');
if ($storedURNDNB) {
return $storedURNDNB;
}
// Retrieve the URN prefix.
$urnPrefix = $this->getSetting($pressId, 'urnDNBPrefix');
if (empty($urnPrefix)) {
return null;
}
// Generate the URN suffix.
$urnSuffixGenerationStrategy = $this->getSetting($pressId, 'urnDNBSuffix');
switch ($urnSuffixGenerationStrategy) {
case 'pattern':
$urnSuffix = $this->getSetting($pressId, "urnDNBSuffixPattern");
// %p - press initials
$urnSuffix = String::regexp_replace('/%p/', String::strtolower($press->getPath()), $urnSuffix);
if ($monograph) {
// %m - monograph id
$urnSuffix = String::regexp_replace('/%m/', $monograph->getId(), $urnSuffix);
}
break;
default:
$urnSuffix = '-' . String::strtolower($press->getPath());
if ($monograph) {
$urnSuffix .= '.' . $monograph->getId();
}
}
if (empty($urnSuffix)) {
return null;
}
// Join prefix and suffix.
$urn = $urnPrefix . $urnSuffix;
if (!$preview) {
// Save the generated URN.
$this->setStoredPubId($monograph, $pubObjectType, $urn);
}
return $urn . $this->_calculateUrnCheckNo($urn);
}
/**
* If $value is found in the mapping, return the mapped value; otherwise
* return $value untouched. The comparison ignores case and white-
* space.
* @param $value string
* @return string
*/
function mapLanguage($value)
{
$cache =& $this->_getMapCache();
if ($newValue = $cache->get(String::strtolower(trim($value)))) {
return $newValue;
}
return $value;
}
/**
* Get a DOI for this article.
*/
function getDOI()
{
// If we already have an assigned DOI, use it.
$storedDOI = $this->getStoredDOI();
if ($storedDOI) {
return $storedDOI;
}
// Otherwise, create a new one.
$journalId = $this->getJournalId();
// Get the Journal object (optimized)
$journal =& Request::getJournal();
if (!$journal || $journal->getId() != $journalId) {
unset($journal);
$journalDao =& DAORegistry::getDAO('JournalDAO');
$journal =& $journalDao->getJournal($journalId);
}
if (($doiPrefix = $journal->getSetting('doiPrefix')) == '') {
return null;
}
$doiSuffixSetting = $journal->getSetting('doiSuffix');
// Get the issue
$issueDao =& DAORegistry::getDAO('IssueDAO');
$issue =& $issueDao->getIssueById($this->getIssueId(), $this->getJournalId(), true);
if (!$issue || !$journal || $journal->getId() != $issue->getJournalId()) {
return null;
}
switch ($doiSuffixSetting) {
case 'customIdentifier':
$doi = $doiPrefix . '/' . $this->getBestArticleId();
break;
case 'pattern':
$suffixPattern = $journal->getSetting('doiSuffixPattern');
// %j - journal initials
$suffixPattern = String::regexp_replace('/%j/', String::strtolower($journal->getLocalizedSetting('initials')), $suffixPattern);
// %v - volume number
$suffixPattern = String::regexp_replace('/%v/', $issue->getVolume(), $suffixPattern);
// %i - issue number
$suffixPattern = String::regexp_replace('/%i/', $issue->getNumber(), $suffixPattern);
// %Y - year
$suffixPattern = String::regexp_replace('/%Y/', $issue->getYear(), $suffixPattern);
// %a - article id
$suffixPattern = String::regexp_replace('/%a/', $this->getArticleId(), $suffixPattern);
// %p - page number
$suffixPattern = String::regexp_replace('/%p/', $this->getPages(), $suffixPattern);
$doi = $doiPrefix . '/' . $suffixPattern;
break;
default:
$doi = $doiPrefix . '/' . String::strtolower($journal->getLocalizedSetting('initials')) . '.v' . $issue->getVolume() . 'i' . $issue->getNumber() . '.' . $this->getArticleId();
}
// Save the generated DOI
$this->setStoredDOI($doi);
$articleDao =& DAORegistry::getDAO('ArticleDAO');
$articleDao->changeDOI($this->getId(), $doi);
return $doi;
}
/**
* 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.
$userInput = String::substr($userInput, 0, -String::strlen($facetPrefix));
switch ($fieldName) {
case 'query':
// The 'query' filter goes agains 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';
}
$facetPrefixLc = String::strtolower($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 = $facetPrefix . String::substr($termSuggestion, String::strlen($facetPrefix));
}
$suggestions[] = $userInput . $termSuggestion;
}
return $suggestions;
}
/**
* 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 journals are returned.
* @param $journalId int
* @param $initial An initial the last names must begin with
* @return array Authors ordered by sequence
*/
function &getAuthorsAlphabetizedByJournal($journalId = null, $initial = null, $rangeInfo = null)
{
$authors = array();
$params = array();
$locale = Locale::getLocale();
$params[] = 'firstName';
$params[] = $locale;
$params[] = 'lastName';
$params[] = $locale;
$params[] = 'middleName';
$params[] = $locale;
$params[] = 'affiliation';
$params[] = $locale;
if (isset($journalId)) {
$params[] = $journalId;
}
if (isset($initial)) {
$params[] = String::strtolower($initial) . '%';
$initialSql = ' AND LOWER(aal.setting_value) LIKE LOWER(?)';
} else {
$initialSql = '';
}
// Opatan Inc. : joined with article_author_settings to provide setting_value of author firstName
$result =& $this->retrieveRange('SELECT DISTINCT
CAST(\'\' AS CHAR(1)) AS url,
0 AS author_id,
0 AS article_id,
CAST(\'\' AS CHAR(1)) AS email,
0 AS primary_contact,
0 AS seq,
aaf.setting_value AS first_name,
aam.setting_value AS middle_name,
aal.setting_value AS last_name,
aaaf.setting_value AS affiliation,
aa.country
FROM article_authors aa
LEFT JOIN article_author_settings aaf ON (aa.author_id = aaf.author_id AND aaf.setting_name = ? AND aaf.locale = ?)
LEFT JOIN article_author_settings aal ON (aa.author_id = aal.author_id AND aal.setting_name = ? AND aal.locale = ?)
LEFT JOIN article_author_settings aam ON (aa.author_id = aam.author_id AND aam.setting_name = ? AND aam.locale = ?)
LEFT JOIN article_author_settings aaaf ON (aa.author_id = aaaf.author_id AND aaaf.setting_name = ? AND aaaf.locale = ?),
articles a,
published_articles pa,
issues i
WHERE i.issue_id = pa.issue_id
AND i.published = 1
AND aa.article_id = a.article_id ' . (isset($journalId) ? 'AND a.journal_id = ? ' : '') . '
AND pa.article_id = a.article_id
AND a.status = ' . STATUS_PUBLISHED . '
AND (aal.setting_value IS NOT NULL AND aal.setting_value <> \'\')' . $initialSql . '
ORDER BY last_name, first_name', empty($params) ? false : $params, $rangeInfo);
$returner =& new DAOResultFactory($result, $this, '_returnAuthorFromRow');
return $returner;
}
/**
* 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"
$componentId = str_replace('.', '-', String::strtolower(String::substr($componentId, 0, -7)));
$this->setId($componentId);
} else {
assert(is_a($router, 'PKPPageRouter'));
$this->setId($router->getRequestedPage($request));
}
}
/**
* 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) {
$authorDescription->addStatement('given-names', String::trimPunctuation($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 (String::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) {
$lPage = (int) (String::substr($pages['fpage'], 0, -String::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 $publicationType) {
// The vast majority of items on PubMed are articles so catch these...
if (String::strpos(String::strtolower($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) {
$attributes .= String::strtolower($attribute->textContent) . ' / ';
}
// Only add links to open access resources
if (String::strpos($attributes, "subscription") === false && String::strpos($attributes, "membership") === false && String::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 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
* @param $disallowRepeatedEmail Whether or not to include duplicated emails in the array
* @return array Authors ordered by sequence
*/
function &getAuthorsAlphabetizedByJournal($journalId = null, $initial = null, $rangeInfo = null, $includeEmail = false, $disallowRepeatedEmail = false)
{
$authors = array();
$params = array('affiliation', AppLocale::getPrimaryLocale(), 'affiliation', AppLocale::getLocale());
if (isset($journalId)) {
$params[] = $journalId;
}
$params[] = AUTHOR_TOC_DEFAULT;
$params[] = AUTHOR_TOC_SHOW;
if (isset($initial)) {
$params[] = String::strtolower($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,
CASE WHEN asl.setting_value = \'\' THEN NULL ELSE SUBSTRING(asl.setting_value FROM 1 FOR 255) END AS affiliation_l,
CASE WHEN asl.setting_value = \'\' THEN NULL ELSE asl.locale END AS locale,
CASE WHEN aspl.setting_value = \'\' THEN NULL ELSE SUBSTRING(aspl.setting_value FROM 1 FOR 255) END AS affiliation_pl,
CASE WHEN aspl.setting_value = \'\' THEN NULL ELSE aspl.locale END AS primary_locale,
CASE WHEN aa.country = \'\' THEN NULL ELSE aa.country END AS 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 = ?)
' . ($disallowRepeatedEmail ? " LEFT JOIN authors aa2 ON (aa.email=aa2.email AND aa.author_id < aa2.author_id) " : "") . '
JOIN articles a ON (a.article_id = aa.submission_id AND a.status = ' . STATUS_PUBLISHED . ')
JOIN published_articles pa ON (pa.article_id = a.article_id)
JOIN issues i ON (pa.issue_id = i.issue_id AND i.published = 1)
JOIN sections s ON (a.section_id = s.section_id)
JOIN journals j ON (a.journal_id = j.journal_id)
WHERE ' . (isset($journalId) ? 'a.journal_id = ?' : 'j.enabled = 1') . '
AND (aa.last_name IS NOT NULL AND aa.last_name <> \'\')
AND ((s.hide_author = 0 AND a.hide_author = ?) OR a.hide_author = ?)
' . ($disallowRepeatedEmail ? ' AND aa2.email IS NULL ' : '') . $initialSql . '
ORDER BY aa.last_name, aa.first_name', $params, $rangeInfo);
$returner = new DAOResultFactory($result, $this, '_returnSimpleAuthorFromRow');
return $returner;
}
/**
* @see PubIdPlugin::getPubId()
*/
function getPubId($pubObject, $preview = false)
{
// Determine the type of the publishing object.
$pubObjectType = $this->getPubObjectType($pubObject);
// Initialize variables for publication objects.
$publicationFormat = $pubObjectType == 'PublicationFormat' ? $pubObject : null;
$monograph = $pubObjectType == 'Monograph' ? $pubObject : null;
// Get the press id of the object.
if (in_array($pubObjectType, array('PublicationFormat', 'Monograph'))) {
$pressId = $pubObject->getContextId();
} else {
return null;
}
$press = $this->_getPress($pressId);
if (!$press) {
return null;
}
$pressId = $press->getId();
// If we already have an assigned DOI, use it.
$storedDOI = $pubObject->getStoredPubId('doi');
if ($storedDOI) {
return $storedDOI;
}
// Retrieve the DOI prefix.
$doiPrefix = $this->getSetting($pressId, 'doiPrefix');
if (empty($doiPrefix)) {
return null;
}
// Generate the DOI suffix.
$doiSuffixGenerationStrategy = $this->getSetting($pressId, 'doiSuffix');
switch ($doiSuffixGenerationStrategy) {
case 'customId':
$doiSuffix = $pubObject->getData('doiSuffix');
break;
case 'pattern':
$doiSuffix = $this->getSetting($pressId, "doi{$pubObjectType}SuffixPattern");
// %p - press initials
$doiSuffix = String::regexp_replace('/%p/', String::strtolower($press->getPath()), $doiSuffix);
if ($publicationFormat) {
// %m - monograph id, %f - publication format id
$doiSuffix = String::regexp_replace('/%m/', $publicationFormat->getMonographId(), $doiSuffix);
$doiSuffix = String::regexp_replace('/%f/', $publicationFormat->getId(), $doiSuffix);
}
if ($monograph) {
// %m - monograph id
$doiSuffix = String::regexp_replace('/%m/', $monograph->getId(), $doiSuffix);
}
break;
default:
$doiSuffix = String::strtolower($press->getPath());
if ($publicationFormat) {
$doiSuffix .= '.' . $publicationFormat->getMonographId();
$doiSuffix .= '.' . $publicationFormat->getId();
}
if ($monograph) {
$doiSuffix .= '.' . $monograph->getId();
}
}
if (empty($doiSuffix)) {
return null;
}
// Join prefix and suffix.
$doi = $doiPrefix . '/' . $doiSuffix;
if (!$preview) {
// Save the generated DOI.
$this->setStoredPubId($pubObject, $pubObjectType, $doi);
}
return $doi;
}
/**
* @see PubIdPlugin::getPubId()
*/
function getPubId(&$pubObject, $preview = false)
{
$doi = null;
if (!$this->isExcluded($pubObject)) {
// 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;
$suppFile = $pubObjectType == 'SuppFile' ? $pubObject : null;
// Get the journal id of the object.
if (in_array($pubObjectType, array('Issue', 'Article'))) {
$journalId = $pubObject->getJournalId();
} else {
// Retrieve the published article.
assert(is_a($pubObject, 'ArticleFile'));
$articleDao =& DAORegistry::getDAO('PublishedArticleDAO');
/* @var $articleDao PublishedArticleDAO */
$article =& $articleDao->getPublishedArticleByArticleId($pubObject->getArticleId(), 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(), $journal->getId(), true);
}
if ($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;
case 'SuppFile':
$doiSuffix = (string) $pubObject->getBestSuppFileId($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
$doiSuffix = String::regexp_replace('/%j/', String::strtolower($journal->getLocalizedSetting('initials', $journal->getPrimaryLocale())), $doiSuffix);
// %x - custom identifier
if ($pubObject->getStoredPubId('publisher-id')) {
$doiSuffix = String::regexp_replace('/%x/', $pubObject->getStoredPubId('publisher-id'), $doiSuffix);
}
if ($issue) {
// %v - volume number
$doiSuffix = String::regexp_replace('/%v/', $issue->getVolume(), $doiSuffix);
// %i - issue number
$doiSuffix = String::regexp_replace('/%i/', $issue->getNumber(), $doiSuffix);
// %Y - year
$doiSuffix = String::regexp_replace('/%Y/', $issue->getYear(), $doiSuffix);
}
if ($article) {
// %a - article id
$doiSuffix = String::regexp_replace('/%a/', $article->getId(), $doiSuffix);
// %p - page number
if ($article->getPages()) {
$doiSuffix = String::regexp_replace('/%p/', $article->getPages(), $doiSuffix);
}
}
if ($galley) {
// %g - galley id
$doiSuffix = String::regexp_replace('/%g/', $galley->getId(), $doiSuffix);
}
if ($suppFile) {
// %s - supp file id
$doiSuffix = String::regexp_replace('/%s/', $suppFile->getId(), $doiSuffix);
}
break;
default:
$doiSuffix = String::strtolower($journal->getLocalizedSetting('initials', $journal->getPrimaryLocale()));
if ($issue) {
$doiSuffix .= '.v' . $issue->getVolume() . 'i' . $issue->getNumber();
} else {
$doiSuffix .= '.v%vi%i';
}
if ($article) {
$doiSuffix .= '.' . $article->getId();
}
if ($galley) {
$doiSuffix .= '.g' . $galley->getId();
}
if ($suppFile) {
$doiSuffix .= '.s' . $suppFile->getId();
}
}
if (empty($doiSuffix)) {
return null;
}
// Join prefix and suffix.
$doi = $doiPrefix . '/' . $doiSuffix;
if (!$preview) {
// Save the generated DOI.
$this->setStoredPubId($pubObject, $pubObjectType, $doi);
}
}
return $doi;
}
/**
* Convert a string to proper title case
* @param $title string
* @return string
*/
function titleCase($title)
{
$smallWords = array('of', 'a', 'the', 'and', 'an', 'or', 'nor', 'but', 'is', 'if', 'then', 'else', 'when', 'at', 'from', 'by', 'on', 'off', 'for', 'in', 'out', 'over', 'to', 'into', 'with');
$words = explode(' ', $title);
foreach ($words as $key => $word) {
if ($key == 0 or !in_array(String::strtolower($word), $smallWords)) {
$words[$key] = ucfirst(String::strtolower($word));
} else {
$words[$key] = String::strtolower($word);
}
}
$newTitle = implode(' ', $words);
return $newTitle;
}
public function testStrtolowerWhenAllIsLowerCaseShouldReturnAllLower()
{
$expected = "dafiti";
$actual = String::strtolower("dafiti");
$this->assertEquals($expected, $actual);
}
/**
* Suggest a username given the first and last names.
* @return string
*/
function suggestUsername($firstName, $lastName)
{
$initial = String::substr($firstName, 0, 1);
$suggestion = String::regexp_replace('/[^a-zA-Z0-9_-]/', '', String::strtolower($initial . $lastName));
$userDao =& DAORegistry::getDAO('UserDAO');
for ($i = ''; $userDao->userExistsByUsername($suggestion . $i); $i++) {
}
return $suggestion . $i;
}
/**
* 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, $request->getUserVar('txn_type'), String::strtolower($request->getUserVar('payer_email')), String::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');
$grantedEmail = String::strtolower($request->getUserVar('receiver_email'));
$queuedEmail = String::strtolower($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
}
/**
* Convert a string to proper title case
* @param $title string
* @return string
*/
static function titleCase($title)
{
AppLocale::requireComponents(LOCALE_COMPONENT_PKP_COMMON);
$smallWords = explode(' ', __('common.titleSmallWords'));
$words = explode(' ', $title);
foreach ($words as $key => $word) {
if ($key == 0 or !in_array(String::strtolower($word), $smallWords)) {
$words[$key] = ucfirst(String::strtolower($word));
} else {
$words[$key] = String::strtolower($word);
}
}
$newTitle = implode(' ', $words);
return $newTitle;
}
/**
* 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 journals are returned.
* @param $journalId int
* @param $initial An initial the last names must begin with
* @return array Authors ordered by sequence
*/
function &getAuthorsAlphabetizedByJournal($journalId = null, $initial = null, $rangeInfo = null)
{
$authors = array();
$params = array();
if (isset($journalId)) {
$params[] = $journalId;
}
if (isset($initial)) {
$params[] = String::strtolower($initial) . '%';
$initialSql = ' AND LOWER(aa.last_name) LIKE LOWER(?)';
} else {
$initialSql = '';
}
$result =& $this->retrieveRange('SELECT DISTINCT
CAST(\'\' AS CHAR) AS url,
0 AS author_id,
0 AS article_id,
CAST(\'\' AS CHAR) AS email,
0 AS primary_contact,
0 AS seq,
aa.first_name AS first_name,
aa.middle_name AS middle_name,
aa.last_name AS last_name,
aa.affiliation AS affiliation,
aa.country
FROM article_authors aa,
articles a,
published_articles pa,
issues i
WHERE i.issue_id = pa.issue_id
AND i.published = 1
AND aa.article_id = a.article_id ' . (isset($journalId) ? 'AND a.journal_id = ? ' : '') . '
AND pa.article_id = a.article_id
AND a.status = ' . STATUS_PUBLISHED . '
AND (aa.last_name IS NOT NULL AND aa.last_name <> \'\')' . $initialSql . '
ORDER BY aa.last_name, aa.first_name', empty($params) ? false : $params, $rangeInfo);
$returner =& new DAOResultFactory($result, $this, '_returnAuthorFromRow');
return $returner;
}
/**
* @see PubIdPlugin::getPubId()
*/
function getPubId($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(), true);
}
// 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
$urnSuffix = String::regexp_replace('/%j/', String::strtolower($journal->getAcronym($journal->getPrimaryLocale())), $urnSuffix);
// %x - custom identifier
if ($pubObject->getStoredPubId('publisher-id')) {
$urnSuffix = String::regexp_replace('/%x/', $pubObject->getStoredPubId('publisher-id'), $urnSuffix);
}
if ($issue) {
// %v - volume number
$urnSuffix = String::regexp_replace('/%v/', $issue->getVolume(), $urnSuffix);
// %i - issue number
$urnSuffix = String::regexp_replace('/%i/', $issue->getNumber(), $urnSuffix);
// %Y - year
$urnSuffix = String::regexp_replace('/%Y/', $issue->getYear(), $urnSuffix);
}
if ($article) {
// %a - article id
$urnSuffix = String::regexp_replace('/%a/', $article->getId(), $urnSuffix);
// %p - page number
if ($article->getPages()) {
$urnSuffix = String::regexp_replace('/%p/', $article->getPages(), $urnSuffix);
}
}
if ($galley) {
// %g - galley id
$urnSuffix = String::regexp_replace('/%g/', $galley->getId(), $urnSuffix);
}
if (!empty($urnSuffix)) {
$urn = $urnPrefix . $urnSuffix;
if ($this->getSetting($journal->getId(), 'checkNo')) {
$urn .= $this->_calculateCheckNo($urn);
}
}
break;
default:
$urnSuffix = String::strtolower($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;
}
/**
* Retrieve all 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 journals are returned.
* duplicates of email are suppressed
* @param $journalId int
* @param $initial An initial the last names must begin with
* @param $rangeInfo Range information
* @param $includeEmail Whether or not to include the email in the select distinct
* @return array Authors ordered by sequence
*/
function &getAuthorsAlphabetized($initial = null, $rangeInfo = null, $includeEmail = false)
{
$params = array();
if (isset($initial)) {
$params[] = String::strtolower($initial) . '%';
$initialSql = ' AND LOWER(aa.last_name) LIKE LOWER(?)';
} else {
$initialSql = '';
}
$result =& $this->retrieveRange('SELECT aa.*
FROM authors aa
LEFT JOIN section_decisions sdec ON (aa.submission_id = sdec.article_id)
WHERE sdec.review_type = 1 AND (sdec.decision = 1
OR sdec.decision = 6
OR sdec.decision = 9) AND
(aa.last_name IS NOT NULL AND aa.last_name <> \'\')' . $initialSql . '
GROUP BY aa.email
ORDER BY aa.last_name, aa.first_name', $params, $rangeInfo);
$returner = new DAOResultFactory($result, $this, '_returnSimpleAuthorFromRow');
return $returner;
}
/**
* Scans topic xml files for keywords
* @param $mappingFile object The responsible mapping file
* @param $matchingTopics array stores topics that match the keyword
* @param $keyword string
* @param $dir string
* @param $file string
* @modifies $matchingTopics array by reference
*/
function scanTopic(&$mappingFile, &$matchingTopics, $keyword, $dir, $file)
{
if (preg_match('/^\\d{6,6}\\.xml$/', $file)) {
$topicId = $mappingFile->getTopicIdForFilename($dir . DIRECTORY_SEPARATOR . $file);
$topic =& $this->getTopic($topicId);
if ($topic) {
$numMatches = String::substr_count(String::strtolower($topic->getTitle()), $keyword);
foreach ($topic->getSections() as $section) {
$numMatches += String::substr_count(String::strtolower($section->getTitle()), $keyword);
$numMatches += String::substr_count(String::strtolower($section->getContent()), $keyword);
}
if ($numMatches > 0) {
$matchingTopics[($numMatches << 16) + count($matchingTopics)] = $topic;
}
}
}
}
/**
* Fills the given citation object with
* meta-data retrieved from PubMed.
* @param $pmid string
* @param $citationDescription MetadataDescription
* @return MetadataDescription
*/
function &_lookup($pmid, &$citationDescription)
{
$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;
}
$metadata = array('pub-id[@pub-id-type="pmid"]' => $pmid, 'article-title' => $resultDOM->getElementsByTagName("ArticleTitle")->item(0)->textContent, 'source' => $resultDOM->getElementsByTagName("MedlineTA")->item(0)->textContent);
if ($resultDOM->getElementsByTagName("Volume")->length > 0) {
$metadata['volume'] = $resultDOM->getElementsByTagName("Volume")->item(0)->textContent;
}
if ($resultDOM->getElementsByTagName("Issue")->length > 0) {
$metadata['issue'] = $resultDOM->getElementsByTagName("Issue")->item(0)->textContent;
}
// get list of author full names
$nlmNameSchema = new NlmNameSchema();
foreach ($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
$authorDescription = new MetadataDescription($nlmNameSchema, ASSOC_TYPE_AUTHOR);
// Surname
$authorDescription->addStatement('surname', $authorNode->getElementsByTagName("LastName")->item(0)->textContent);
// Given names
$givenNamesString = '';
if ($authorNode->getElementsByTagName("FirstName")->length > 0) {
$givenNamesString = $authorNode->getElementsByTagName("FirstName")->item(0)->textContent;
} elseif ($authorNode->getElementsByTagName("ForeName")->length > 0) {
$givenNamesString = $authorNode->getElementsByTagName("ForeName")->item(0)->textContent;
}
if (!empty($givenNamesString)) {
foreach (explode(' ', $givenNamesString) as $givenName) {
$authorDescription->addStatement('given-names', String::trimPunctuation($givenName));
}
}
// Suffix
if ($authorNode->getElementsByTagName("Suffix")->length > 0) {
$authorDescription->addStatement('suffix', $authorNode->getElementsByTagName("Suffix")->item(0)->textContent);
}
// Include collective names
/*if ($resultDOM->getElementsByTagName("CollectiveName")->length > 0 && $authorNode->getElementsByTagName("CollectiveName")->item(0)->textContent != '') {
// FIXME: This corresponds to an NLM-citation <collab> tag and should be part of the Metadata implementation
}*/
$metadata['person-group[@person-group-type="author"]'][] =& $authorDescription;
unset($authorDescription);
}
// Extract pagination
if (String::regexp_match_get("/^[:p\\.\\s]*(?P<fpage>[Ee]?\\d+)(-(?P<lpage>\\d+))?/", $resultDOM->getElementsByTagName("MedlinePgn")->item(0)->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) {
$lPage = (int) (String::substr($pages['fpage'], 0, -String::strlen($pages['lpage'])) . $pages['lpage']);
}
$metadata['lpage'] = $lPage;
}
}
// Get publication date
// TODO: The publication date could be in multiple places
if ($resultDOM->getElementsByTagName("ArticleDate")->length > 0) {
$publicationDate = $resultDOM->getElementsByTagName("ArticleDate")->item(0)->getElementsByTagName("Year")->item(0)->textContent . '-' . $resultDOM->getElementsByTagName("ArticleDate")->item(0)->getElementsByTagName("Month")->item(0)->textContent . '-' . $resultDOM->getElementsByTagName("ArticleDate")->item(0)->getElementsByTagName("Day")->item(0)->textContent;
$metadata['date'] = $publicationDate;
}
// Get publication type
if ($resultDOM->getElementsByTagName("PublicationType")->length > 0) {
foreach ($resultDOM->getElementsByTagName("PublicationType") as $publicationType) {
// The vast majority of items on PubMed are articles so catch these...
if (String::strpos(String::strtolower($publicationType->textContent), 'article') !== false) {
$metadata['[@publication-type]'] = NLM_PUBLICATION_TYPE_JOURNAL;
break;
}
}
}
// Get DOI if it exists
foreach ($resultDOM->getElementsByTagName("ArticleId") 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) {
$attributes .= String::strtolower($attribute->textContent) . ' / ';
}
// Only add links to open access resources
if (String::strpos($attributes, "subscription") === false && String::strpos($attributes, "membership") === false && String::strpos($attributes, "fee") === false && $attributes != "") {
$links[] = $linkOut->getElementsByTagName("Url")->item(0)->textContent;
}
}
// Take the first link if we have any left (presumably pubmed returns them in preferential order)
if (isset($links[0])) {
$metadata['uri'] = $links[0];
}
}
return $this->addMetadataArrayToNlmCitationDescription($metadata, $citationDescription);
}
