| static public regexp_replace ( $pattern, $replacement, $subject, $limit ) : mixed | ||
| $pattern | string Regular expression | |
| $replacement | string String to replace matches in $subject with | |
| $subject | string String to apply regular expression to | |
| $limit | int Number of replacements to perform, maximum, or -1 for no limit. | |
| return | mixed | |
/**
* Display user login form.
* Redirect to user index page if user is already validated.
*/
function index($args, $request)
{
$this->setupTemplate($request);
if (Validation::isLoggedIn()) {
$this->sendHome($request);
}
if (Config::getVar('security', 'force_login_ssl') && $request->getProtocol() != 'https') {
// Force SSL connections for login
$request->redirectSSL();
}
$sessionManager = SessionManager::getManager();
$session = $sessionManager->getUserSession();
$templateMgr = TemplateManager::getManager($request);
// If the user wasn't expecting a login page, i.e. if they're new to the
// site and want to submit a paper, it helps to explain why they need to
// register.
if ($request->getUserVar('loginMessage')) {
$templateMgr->assign('loginMessage', $request->getUserVar('loginMessage'));
}
$templateMgr->assign('username', $session->getSessionVar('username'));
$templateMgr->assign('remember', $request->getUserVar('remember'));
$templateMgr->assign('source', $request->getUserVar('source'));
$templateMgr->assign('showRemember', Config::getVar('general', 'session_lifetime') > 0);
// For force_login_ssl with base_url[...]: make sure SSL used for login form
$loginUrl = $this->_getLoginUrl($request);
if (Config::getVar('security', 'force_login_ssl')) {
$loginUrl = PKPString::regexp_replace('/^http:/', 'https:', $loginUrl);
}
$templateMgr->assign('loginUrl', $loginUrl);
$templateMgr->display('frontend/pages/userLogin.tpl');
}
/**
* @copydoc Filter::process()
* @param $citationString string
* @return MetadataDescription
*/
function &process(&$input)
{
$nullVar = null;
$queryParams = array('demo' => '3', 'textlines' => $input);
// Parscit web form - the result is (mal-formed) HTML
if (is_null($result = $this->callWebService(PARSCIT_WEBSERVICE, $queryParams, XSL_TRANSFORMER_DOCTYPE_STRING, 'POST'))) {
return $nullVar;
}
$result = html_entity_decode($result);
// Detect errors.
if (!PKPString::regexp_match('/.*<algorithm[^>]+>.*<\\/algorithm>.*/s', $result)) {
$translationParams = array('filterName' => $this->getDisplayName());
$this->addError(__('submission.citations.filter.webserviceResultTransformationError', $translationParams));
return $nullVar;
}
// Screen-scrape the tagged portion and turn it into XML.
$xmlResult = PKPString::regexp_replace('/.*<algorithm[^>]+>(.*)<\\/algorithm>.*/s', '\\1', $result);
$xmlResult = PKPString::regexp_replace('/&/', '&', $xmlResult);
// Transform the result into an array of meta-data.
if (is_null($metadata = $this->transformWebServiceResults($xmlResult, dirname(__FILE__) . DIRECTORY_SEPARATOR . 'parscit.xsl'))) {
return $nullVar;
}
// Extract a publisher from the place string if possible.
$metadata =& $this->fixPublisherNameAndLocation($metadata);
return $this->getNlm30CitationDescriptionFromMetadataArray($metadata);
}
/**
* @copydoc Filter::process()
* @param $isbn string
* @return MetadataDescription a looked up citation description
* or null if the filter fails
*/
function &process($isbn)
{
$nullVar = null;
// Instantiate the web service request
$lookupParams = array('access_key' => $this->getApiKey(), 'index1' => 'isbn', 'results' => 'details,authors', 'value1' => $isbn);
// Call the web service
if (is_null($resultDOM =& $this->callWebService(ISBNDB_WEBSERVICE_URL, $lookupParams))) {
return $nullVar;
}
// Transform and pre-process the web service result
if (is_null($metadata =& $this->transformWebServiceResults($resultDOM, dirname(__FILE__) . DIRECTORY_SEPARATOR . 'isbndb.xsl'))) {
return $nullVar;
}
// Extract place and publisher from the combined entry.
$metadata['publisher-loc'] = PKPString::trimPunctuation(PKPString::regexp_replace('/^(.+):.*/', '\\1', $metadata['place-publisher']));
$metadata['publisher-name'] = PKPString::trimPunctuation(PKPString::regexp_replace('/.*:([^,]+),?.*/', '\\1', $metadata['place-publisher']));
unset($metadata['place-publisher']);
// Reformat the publication date
$metadata['date'] = PKPString::regexp_replace('/^[^\\d{4}]+(\\d{4}).*/', '\\1', $metadata['date']);
// Clean non-numerics from ISBN
$metadata['isbn'] = PKPString::regexp_replace('/[^\\dX]*/', '', $isbn);
// Set the publicationType
$metadata['[@publication-type]'] = NLM30_PUBLICATION_TYPE_BOOK;
return $this->getNlm30CitationDescriptionFromMetadataArray($metadata);
}
/**
* 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;
}
/**
* Format XML for single DC element.
* @param $propertyName string
* @param $value array
* @param $multilingual boolean optional
*/
function formatElement($propertyName, $values, $multilingual = false)
{
if (!is_array($values)) {
$values = array($values);
}
// Translate the property name to XML syntax.
$openingElement = str_replace(array('[@', ']'), array(' ', ''), $propertyName);
$closingElement = PKPString::regexp_replace('/\\[@.*/', '', $propertyName);
// Create the actual XML entry.
$response = '';
foreach ($values as $key => $value) {
if ($multilingual) {
$key = str_replace('_', '-', $key);
assert(is_array($value));
foreach ($value as $subValue) {
if ($key == METADATA_DESCRIPTION_UNKNOWN_LOCALE) {
$response .= "\t<{$openingElement}>" . OAIUtils::prepOutput($subValue) . "</{$closingElement}>\n";
} else {
$response .= "\t<{$openingElement} xml:lang=\"{$key}\">" . OAIUtils::prepOutput($subValue) . "</{$closingElement}>\n";
}
}
} else {
assert(is_scalar($value));
$response .= "\t<{$openingElement}>" . OAIUtils::prepOutput($value) . "</{$closingElement}>\n";
}
}
return $response;
}
/**
* @see Filter::process()
* @param $input string
* @return mixed array
*/
function &process(&$input)
{
// The default implementation assumes that raw citations are
// separated with line endings.
// 1) Remove empty lines and normalize line endings.
$input = PKPString::regexp_replace('/[\\r\\n]+/s', "\n", $input);
// 2) Remove trailing/leading line breaks.
$input = trim($input, "\n");
// 3) Break up at line endings.
if (empty($input)) {
$citations = array();
} else {
$citations = explode("\n", $input);
}
// 4) Remove numbers from the beginning of each citation.
foreach ($citations as $index => $citation) {
$citations[$index] = PKPString::regexp_replace('/^\\s*[\\[#]?[0-9]+[.)\\]]?\\s*/', '', $citation);
}
return $citations;
}
/**
* Display user login form.
* Redirect to user index page if user is already validated.
*/
function index($args, $request)
{
$this->setupTemplate($request);
if (Validation::isLoggedIn()) {
$this->sendHome($request);
}
if (Config::getVar('security', 'force_login_ssl') && $request->getProtocol() != 'https') {
// Force SSL connections for login
$request->redirectSSL();
}
$sessionManager = SessionManager::getManager();
$session = $sessionManager->getUserSession();
$templateMgr = TemplateManager::getManager($request);
$templateMgr->assign(array('loginMessage' => $request->getUserVar('loginMessage'), 'username' => $session->getSessionVar('username'), 'remember' => $request->getUserVar('remember'), 'source' => $request->getUserVar('source'), 'showRemember' => Config::getVar('general', 'session_lifetime') > 0));
// For force_login_ssl with base_url[...]: make sure SSL used for login form
$loginUrl = $this->_getLoginUrl($request);
if (Config::getVar('security', 'force_login_ssl')) {
$loginUrl = PKPString::regexp_replace('/^http:/', 'https:', $loginUrl);
}
$templateMgr->assign('loginUrl', $loginUrl);
$templateMgr->display('frontend/pages/userLogin.tpl');
}
/**
* @see Form::fetch()
*/
function fetch($request)
{
$templateMgr = TemplateManager::getManager($request);
// The form description depends on the current state
// of the selection process: do we select a filter template
// or configure the settings of a selected template?
$filter =& $this->getFilter();
if (is_a($filter, 'Filter')) {
$displayName = $filter->getDisplayName();
$templateMgr->assign('filterDisplayName', $displayName);
if (count($filter->getSettings())) {
// We need a filter specific translation key so that we
// can explain the filter's configuration options.
// We use the display name to generate such a key as this
// is probably easiest for translators to understand.
// This also has the advantage that we can explain
// composite filters individually.
// FIXME: When we start to translate display names then
// please make sure that you use the en-US key for this
// processing. Alternatively we might want to introduce
// an alphanumeric "filter key" to the filters table.
$filterKey = PKPString::regexp_replace('/[^a-zA-Z0-9]/', '', $displayName);
$filterKey = strtolower(substr($filterKey, 0, 1)) . substr($filterKey, 1);
$formDescriptionKey = $this->getDescription() . '.' . $filterKey;
} else {
$formDescriptionKey = $this->getDescription() . 'Confirm';
}
} else {
$templateMgr->assign('filterDisplayName', '');
$formDescriptionKey = $this->getDescription() . 'Template';
}
$templateMgr->assign('formTitle', $this->getTitle());
$templateMgr->assign('formDescription', $formDescriptionKey);
return parent::fetch($request);
}
/**
* Converts a string with a single person
* to an NLM name description.
*
* TODO: add initials from all given names to initials
* element
*
* @param $personString string
* @param $title boolean true to parse for title
* @param $degrees boolean true to parse for degrees
* @return MetadataDescription an NLM name description or null
* if the string could not be converted
*/
function &_parsePersonString($personString, $title, $degrees)
{
// Expressions to parse person strings, ported from CiteULike person
// plugin, see http://svn.citeulike.org/svn/plugins/person.tcl
static $personRegex = array('title' => '(?:His (?:Excellency|Honou?r)\\s+|Her (?:Excellency|Honou?r)\\s+|The Right Honou?rable\\s+|The Honou?rable\\s+|Right Honou?rable\\s+|The Rt\\.? Hon\\.?\\s+|The Hon\\.?\\s+|Rt\\.? Hon\\.?\\s+|Mr\\.?\\s+|Ms\\.?\\s+|M\\/s\\.?\\s+|Mrs\\.?\\s+|Miss\\.?\\s+|Dr\\.?\\s+|Sir\\s+|Dame\\s+|Prof\\.?\\s+|Professor\\s+|Doctor\\s+|Mister\\s+|Mme\\.?\\s+|Mast(?:\\.|er)?\\s+|Lord\\s+|Lady\\s+|Madam(?:e)?\\s+|Priv\\.-Doz\\.\\s+)+', 'degrees' => '(,\\s+(?:[A-Z\\.]+))+', 'initials' => '(?:(?:[A-Z]\\.){1,3}[A-Z]\\.?)|(?:(?:[A-Z]\\.\\s){1,3}[A-Z]\\.?)|(?:[A-Z]{1,4})|(?:(?:[A-Z]\\.-?){1,4})|(?:(?:[A-Z]\\.-?){1,3}[A-Z]\\.?)|(?:(?:[A-Z]-){1,3}[A-Z])|(?:(?:[A-Z]\\s){1,3}[A-Z]\\.?)|(?:(?:[A-Z]-){1,3}[A-Z]\\.?)', 'prefix' => 'Dell(?:[a|e])?(?:\\s|$)|Dalle(?:\\s|$)|D[a|e]ll\'(?:\\s|$)|Dela(?:\\s|$)|Del(?:\\s|$)|[Dd]e(?:\\s|$)(?:La(?:\\s|$)|Los(?:\\s|$))?|[Dd]e(?:\\s|$)|[Dd][a|i|u](?:\\s|$)|L[a|e|o](?:\\s|$)|[D|L|O]\'|St\\.?(?:\\s|$)|San(?:\\s|$)|[Dd]en(?:\\s|$)|[Vv]on(?:\\s|$)(?:[Dd]er(?:\\s|$))?|(?:[Ll][ea](?:\\s|$))?[Vv]an(?:\\s|$)(?:[Dd]e(?:n|r)?(?:\\s|$))?', 'givenName' => '(?:[^ \\t\\n\\r\\f\\v,.;()]{2,}|[^ \\t\\n\\r\\f\\v,.;()]{2,}\\-[^ \\t\\n\\r\\f\\v,.;()]{2,})');
// The expressions for given name, suffix and surname are the same
$personRegex['surname'] = $personRegex['suffix'] = $personRegex['givenName'];
$personRegex['double-surname'] = "(?:" . $personRegex['surname'] . "\\s)*" . $personRegex['surname'];
// Shortcut for prefixed surname
$personRegexPrefixedSurname = "(?P<prefix>(?:" . $personRegex['prefix'] . ")?)(?P<surname>" . $personRegex['surname'] . ")";
$personRegexPrefixedDoubleSurname = "(?P<prefix>(?:" . $personRegex['prefix'] . ")?)(?P<surname>" . $personRegex['double-surname'] . ")";
// Instantiate the target person description
$personDescription = new MetadataDescription('lib.pkp.plugins.metadata.nlm30.schema.Nlm30NameSchema', $this->_assocType);
// Clean the person string
$personString = trim($personString);
// 1. Extract title and degree from the person string and use this as suffix
$suffixString = '';
$results = array();
if ($title && PKPString::regexp_match_get('/^(' . $personRegex['title'] . ')/i', $personString, $results)) {
$suffixString = trim($results[1], ',:; ');
$personString = PKPString::regexp_replace('/^(' . $personRegex['title'] . ')/i', '', $personString);
}
if ($degrees && PKPString::regexp_match_get('/(' . $personRegex['degrees'] . ')$/i', $personString, $results)) {
$degreesArray = explode(',', trim($results[1], ','));
foreach ($degreesArray as $key => $degree) {
$degreesArray[$key] = PKPString::trimPunctuation($degree);
}
$suffixString .= ' - ' . implode('; ', $degreesArray);
$personString = PKPString::regexp_replace('/(' . $personRegex['degrees'] . ')$/i', '', $personString);
}
if (!empty($suffixString)) {
$personDescription->addStatement('suffix', $suffixString);
}
// Space initials when followed by a given name or last name.
$personString = PKPString::regexp_replace('/([A-Z])\\.([A-Z][a-z])/', '\\1. \\2', $personString);
// 2. Extract names and initials from the person string
// The parser expressions are ordered by specificity. The most specific expressions
// come first. Only if these specific expressions don't work will we turn to less
// specific ones. This avoids parsing errors. It also explains why we don't use the
// ?-quantifier for optional elements like initials or middle name where they could
// be misinterpreted.
$personExpressions = array('/^' . $personRegexPrefixedSurname . '$/i', '/^(?P<initials>' . $personRegex['initials'] . ')\\s' . $personRegexPrefixedSurname . '$/', '/^' . $personRegexPrefixedSurname . ',?\\s(?P<initials>' . $personRegex['initials'] . ')$/', '/^' . $personRegexPrefixedDoubleSurname . ',\\s(?P<givenName>' . $personRegex['givenName'] . ')\\s(?P<initials>' . $personRegex['initials'] . ')$/', '/^(?P<givenName>' . $personRegex['givenName'] . ')\\s(?P<initials>' . $personRegex['initials'] . ')\\s' . $personRegexPrefixedSurname . '$/', '/^' . $personRegexPrefixedDoubleSurname . ',\\s(?P<givenName>(?:' . $personRegex['givenName'] . '\\s)+)(?P<initials>' . $personRegex['initials'] . ')$/', '/^(?P<givenName>(?:' . $personRegex['givenName'] . '\\s)+)(?P<initials>' . $personRegex['initials'] . ')\\s' . $personRegexPrefixedSurname . '$/', '/^' . $personRegexPrefixedDoubleSurname . ',(?P<givenName>(?:\\s' . $personRegex['givenName'] . ')+)$/', '/^(?P<givenName>(?:' . $personRegex['givenName'] . '\\s)+)' . $personRegexPrefixedSurname . '$/', '/^\\s*(?P<surname>' . $personRegex['surname'] . ')(?P<suffix>(?:\\s+' . $personRegex['suffix'] . ')?)\\s*,\\s*(?P<initials>(?:' . $personRegex['initials'] . ')?)\\s*\\((?P<givenName>(?:\\s*' . $personRegex['givenName'] . ')+)\\s*\\)\\s*(?P<prefix>(?:' . $personRegex['prefix'] . ')?)$/', '/^(?P<givenName>' . $personRegex['givenName'] . ')\\.(?P<surname>' . $personRegex['double-surname'] . ')$/', '/^(?P<surname>.*)$/');
$results = array();
foreach ($personExpressions as $expressionId => $personExpression) {
if ($nameFound = PKPString::regexp_match_get($personExpression, $personString, $results)) {
// Given names
if (!empty($results['givenName'])) {
// Split given names
$givenNames = explode(' ', trim($results['givenName']));
foreach ($givenNames as $givenName) {
$personDescription->addStatement('given-names', $givenName);
unset($givenName);
}
}
// Initials (will also be saved as given names)
if (!empty($results['initials'])) {
$results['initials'] = str_replace(array('.', '-', ' '), array('', '', ''), $results['initials']);
for ($initialNum = 0; $initialNum < PKPString::strlen($results['initials']); $initialNum++) {
$initial = $results['initials'][$initialNum];
$personDescription->addStatement('given-names', $initial);
unset($initial);
}
}
// Surname
if (!empty($results['surname'])) {
// Correct all-upper surname
if (strtoupper($results['surname']) == $results['surname']) {
$results['surname'] = ucwords(strtolower($results['surname']));
}
$personDescription->addStatement('surname', $results['surname']);
}
// Prefix/Suffix
foreach (array('prefix', 'suffix') as $propertyName) {
if (!empty($results[$propertyName])) {
$results[$propertyName] = trim($results[$propertyName]);
$personDescription->addStatement($propertyName, $results[$propertyName]);
}
}
break;
}
}
return $personDescription;
}
/**
* Create and return an issue node, either as work or as manifestation.
* @param $doc DOMDocument
* @param $pubObject Issue
* @return DOMElement
*/
function createIssueNode($doc, $pubObject)
{
$deployment = $this->getDeployment();
$context = $deployment->getContext();
$cache = $deployment->getCache();
$plugin = $deployment->getPlugin();
$request = Application::getRequest();
$router = $request->getRouter();
$issueNodeName = $this->isWork($context, $plugin) ? 'DOISerialIssueWork' : 'DOISerialIssueVersion';
$issueNode = $doc->createElementNS($deployment->getNamespace(), $issueNodeName);
// Notification type (mandatory)
$doi = $pubObject->getStoredPubId('doi');
$registeredDoi = $pubObject->getData('medra::registeredDoi');
assert(empty($registeredDoi) || $registeredDoi == $doi);
$notificationType = empty($registeredDoi) ? O4DOI_NOTIFICATION_TYPE_NEW : O4DOI_NOTIFICATION_TYPE_UPDATE;
$issueNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'NotificationType', $notificationType));
// DOI (mandatory)
$issueNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'DOI', htmlspecialchars($doi, ENT_COMPAT, 'UTF-8')));
// DOI URL (mandatory)
$url = $router->url($request, $context->getPath(), 'article', 'view', $pubObject->getBestIssueId(), null, null, true);
if ($plugin->isTestMode($context)) {
// Change server domain for testing.
$url = PKPString::regexp_replace('#://[^\\s]+/index.php#', '://example.com/index.php', $url);
}
$issueNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'DOIWebsiteLink', $url));
// DOI strucural type
$structuralType = $this->isWork($context, $plugin) ? 'Abstraction' : 'DigitalFixation';
$issueNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'DOIStructuralType', $structuralType));
// Registrant (mandatory)
$issueNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'RegistrantName', htmlspecialchars($plugin->getSetting($context->getId(), 'registrantName'), ENT_COMPAT, 'UTF-8')));
// Registration authority (mandatory)
$issueNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'RegistrationAuthority', 'mEDRA'));
// Work/ProductIdentifier - proprietary ID
$pubObjectProprietaryId = $context->getId() . '-' . $pubObject->getId();
$workOrProduct = $this->isWork($context, $plugin) ? 'Work' : 'Product';
$issueNode->appendChild($this->createIdentifierNode($doc, $workOrProduct, O4DOI_ID_TYPE_PROPRIETARY, $pubObjectProprietaryId));
// Issue/journal and object locale precedence.
$journalLocalePrecedence = $objectLocalePrecedence = $this->getObjectLocalePrecedence($context, null, null);
// Serial Publication (mandatory)
$issueNode->appendChild($this->createSerialPublicationNode($doc, $journalLocalePrecedence, O4DOI_EPUB_FORMAT_HTML));
// Journal Issue (mandatory)
$issueId = $pubObject->getId();
if (!$cache->isCached('issues', $issueId)) {
$cache->add($pubObject, null);
}
$issueNode->appendChild($this->createJournalIssueNode($doc, $pubObject, $journalLocalePrecedence));
// Object Description 'OtherText'
$descriptions = $this->getTranslationsByPrecedence($pubObject->getDescription(null), $objectLocalePrecedence);
foreach ($descriptions as $locale => $description) {
$issueNode->appendChild($this->createOtherTextNode($doc, $locale, $description));
}
// 4) issue (as-work and as-manifestation):
// related works:
// - includes articles-as-work
$articleDao = DAORegistry::getDAO('PublishedArticleDAO');
/* @var $articleDao PublishedArticleDAO */
$articlesByIssue = $articleDao->getPublishedArticles($issueId);
$galleyDao = DAORegistry::getDAO('ArticleGalleyDAO');
/* @var $galleyDao ArticleGalleyDAO */
$galleysByIssue = array();
foreach ($articlesByIssue as $relatedArticle) {
$articleProprietaryId = $context->getId() . '-' . $pubObject->getId() . '-' . $relatedArticle->getId();
$relatedArticleIds = array(O4DOI_ID_TYPE_PROPRIETARY => $articleProprietaryId);
$doi = $relatedArticle->getStoredPubId('doi');
if (!empty($doi)) {
$relatedArticleIds[O4DOI_ID_TYPE_DOI] = $doi;
}
$issueNode->appendChild($this->createRelatedNode($doc, 'Work', O4DOI_RELATION_INCLUDES, $relatedArticleIds));
// Collect galleys by issue
$galleysByArticle = $galleyDao->getBySubmissionId($relatedArticle->getId())->toArray();
$galleysByIssue = array_merge($galleysByIssue, $galleysByArticle);
unset($relatedArticle, $relatedArticleIds);
}
// related products:
// - includes articles-as-manifestation
foreach ($galleysByIssue as $relatedGalley) {
$galleyProprietaryId = $context->getId() . '-' . $pubObject->getId() . '-' . $relatedGalley->getSubmissionId() . '-g' . $relatedGalley->getId();
$relatedGalleyIds = array(O4DOI_ID_TYPE_PROPRIETARY => $galleyProprietaryId);
$doi = $relatedGalley->getStoredPubId('doi');
if (!empty($doi)) {
$relatedGalleyIds[O4DOI_ID_TYPE_DOI] = $doi;
}
$issueNode->appendChild($this->createRelatedNode($doc, 'Product', O4DOI_RELATION_INCLUDES, $relatedGalleyIds));
unset($relatedGalley, $relatedGalleyIds);
}
return $issueNode;
}
/**
* Mark an object as "registered"
* by saving it's DOI to the object's
* "registeredDoi" setting.
* We prefix the setting with the plug-in's
* id so that we do not get name clashes
* when several DOI registration plug-ins
* are active at the same time.
* @parem $request Request
* @param $object Issue|PublishedArticle|ArticleGalley
* @parem $testPrefix string
*/
function markRegistered($request, $object, $testPrefix)
{
$registeredDoi = $object->getPubId('doi');
assert(!empty($registeredDoi));
if ($this->isTestMode($request)) {
$registeredDoi = PKPString::regexp_replace('#^[^/]+/#', $testPrefix . '/', $registeredDoi);
}
$this->saveRegisteredDoi($object, $registeredDoi);
}
/**
* Retrieve the DOI of an object. The DOI will be
* patched if we are in test mode.
* @param $object Issue|PublishedArticle|ArticleGalley
* @return string
*/
function _getDoi(&$object)
{
$doi = $object->getPubId('doi');
if (!empty($doi) && $this->getTestMode()) {
$doi = PKPString::regexp_replace('#^[^/]+/#', MEDRA_WS_TESTPREFIX . '/', $doi);
}
return $doi;
}
/**
* Strip SQL comments from SQL string.
* @param $sql string
*/
function stripComments(&$sql)
{
$sql = trim(PKPString::regexp_replace(sprintf('/^\\s*%s(.*)$/m', $this->commentDelim), '', $sql));
}
/**
* Translate query keywords.
* @param $searchPhrase string
* @return The translated search phrase.
*/
function _translateSearchPhrase($searchPhrase, $backwards = false)
{
static $queryKeywords;
if (is_null($queryKeywords)) {
// Query keywords.
$queryKeywords = array(PKPString::strtoupper(__('search.operator.not')) => 'NOT', PKPString::strtoupper(__('search.operator.and')) => 'AND', PKPString::strtoupper(__('search.operator.or')) => 'OR');
}
if ($backwards) {
$translationTable = array_flip($queryKeywords);
} else {
$translationTable = $queryKeywords;
}
// Translate the search phrase.
foreach ($translationTable as $translateFrom => $translateTo) {
$searchPhrase = PKPString::regexp_replace("/(^|\\s){$translateFrom}(\\s|\$)/i", "\\1{$translateTo}\\2", $searchPhrase);
}
return $searchPhrase;
}
/**
* Suggest a username given the first and last names.
* @return string
*/
static function suggestUsername($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 . $i;
}
/**
* @see PubIdPlugin::getPubId()
*/
function getPubId($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;
}
/**
* Take an NLM preliminary meta-data array and fix publisher-loc
* and publisher-name entries:
* - If there is a location but no name then try to extract a
* publisher name from the location string.
* - Make sure that location and name are not the same.
* - Copy institution to publisher if no publisher is set,
* otherwise leave the institution.
* @param $metadata array
* @return array
*/
function &fixPublisherNameAndLocation(&$metadata)
{
if (isset($metadata['publisher-loc'])) {
// Extract publisher-name from publisher-loc if we don't have a
// publisher-name in the parsing result.
if (empty($metadata['publisher-name'])) {
$metadata['publisher-name'] = PKPString::regexp_replace('/.*:([^,]+),?.*/', '\\1', $metadata['publisher-loc']);
}
// Remove publisher-name from publisher-loc
$metadata['publisher-loc'] = PKPString::regexp_replace('/^(.+):.*/', '\\1', $metadata['publisher-loc']);
// Check that publisher-name and location are not the same
if (!empty($metadata['publisher-name']) && $metadata['publisher-name'] == $metadata['publisher-loc']) {
unset($metadata['publisher-name']);
}
}
// Copy the institution property (if any) as the publisher-name
if (isset($metadata['institution']) && (!isset($metadata['publisher-name']) || empty($metadata['publisher-name']))) {
$metadata['publisher-name'] = $metadata['institution'];
}
// Clean the result
foreach (array('publisher-name', 'publisher-loc') as $publisherProperty) {
if (isset($metadata[$publisherProperty])) {
$metadata[$publisherProperty] = PKPString::trimPunctuation($metadata[$publisherProperty]);
}
}
return $metadata;
}
/**
* Take a citation string and clean/normalize it
* @param $citationString string
* @return string
*/
function _cleanCitationString($citationString)
{
// 1) If the string contains non-UTF8 characters, convert it to UTF-8
if (Config::getVar('i18n', 'charset_normalization') && !PKPString::utf8_compliant($citationString)) {
$citationString = PKPString::utf8_normalize($citationString);
}
// 2) Strip slashes and whitespace
$citationString = trim(stripslashes($citationString));
// 3) Normalize whitespace
$citationString = PKPString::regexp_replace('/[\\s]+/', ' ', $citationString);
return $citationString;
}
/**
* Sanitize a value to be used in a file path.
* Removes any characters except alphanumeric characters, underscores, and dashes.
* @param $var string
* @return string
*/
static function cleanFileVar($var)
{
return PKPString::regexp_replace('/[^\\w\\-]/', '', $var);
}
/**
* Create an identifier element with the object's DOI.
* @param $object Issue|PublishedArticle|ArticleGalley
* @param $relationType string One of the DATACITE_RELTYPE_* constants.
* @return XMLNode|DOMImplementation|null Can be null if the given ID Type
* has not been assigned to the given object.
*/
function &_relatedIdentifierElement(&$object, $relationType)
{
$id = $object->getStoredPubId('doi');
if (empty($id)) {
return $nullVar;
$nullVar = null;
}
if ($this->getTestMode()) {
$id = PKPString::regexp_replace('#^[^/]+/#', DATACITE_API_TESTPREFIX . '/', $id);
}
return $this->createElementWithText('relatedIdentifier', $id, array('relatedIdentifierType' => DATACITE_IDTYPE_DOI, 'relationType' => $relationType));
}
/**
* Create a serial version node.
* @param $doc DOMDocument
* @param $issn string
* @param $productForm One of the O4DOI_PRODUCT_FORM_* constants
* @param $epubFormat O4DOI_EPUB_FORMAT_*
* @return DOMElement
*/
function createSerialVersionNode($doc, $issn, $productForm, $epubFormat = null)
{
$deployment = $this->getDeployment();
$context = $deployment->getContext();
$serialVersionNode = $doc->createElementNS($deployment->getNamespace(), 'SerialVersion');
// Proprietary Journal Identifier
if ($productForm == O4DOI_PRODUCT_FORM_ELECTRONIC) {
$serialVersionNode->appendChild($this->createIdentifierNode($doc, 'Product', O4DOI_ID_TYPE_PROPRIETARY, $context->getId()));
}
// ISSN
if (!empty($issn)) {
$issn = PKPString::regexp_replace('/[^0-9]/', '', $issn);
$serialVersionNode->appendChild($this->createIdentifierNode($doc, 'Product', O4DOI_ID_TYPE_ISSN, $issn));
}
// Product Form
$serialVersionNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'ProductForm', $productForm));
if ($productForm == O4DOI_PRODUCT_FORM_ELECTRONIC) {
// ePublication Format
if ($epubFormat) {
$serialVersionNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'EpubFormat', $epubFormat));
}
// ePublication Format Description
$serialVersionNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'EpubFormatDescription', 'Open Journal Systems (OJS)'));
}
return $serialVersionNode;
}
/**
* @copydoc Filter::process()
* @param $input string
* @return MetadataDescription
*/
function &process(&$input)
{
$citationString =& $input;
// Initialize the parser result array
$matches = array();
$metadata = array();
// Parse out any embedded URLs
$urlPattern = '(<?(https?://([-\\w\\.]+)+(:\\d+)?(/([\\w/_\\.,]*(\\?[^\\s>]+)?)?)?)>?)';
if (PKPString::regexp_match_get($urlPattern, $citationString, $matches)) {
// Assume that the URL is a link to the resource.
$metadata['uri'] = $matches[1];
// Remove the URL from the citation string
$citationString = PKPString::regexp_replace($urlPattern, '', $citationString);
// If the URL is a link to PubMed, save the PMID
$pmIdExpressions = array('/list_uids=(?P<pmId>\\d+)/i', '/pubmed.*details_term=(?P<pmId>\\d+)/i', '/pubmedid=(?P<pmId>\\d+)/i');
foreach ($pmIdExpressions as $pmIdExpression) {
if (PKPString::regexp_match_get($pmIdExpression, $matches[1], $pmIdMatches)) {
$metadata['pub-id[@pub-id-type="pmid"]'] = $pmIdMatches['pmId'];
break;
}
}
}
// Parse out an embedded PMID and remove from the citation string
$pmidPattern = '/pmid:?\\s*(\\d+)/i';
if (PKPString::regexp_match_get($pmidPattern, $citationString, $matches)) {
$metadata['pub-id[@pub-id-type="pmid"]'] = $matches[1];
$citationString = PKPString::regexp_replace($pmidPattern, '', $citationString);
}
// Parse out an embedded DOI and remove it from the citation string
$doiPattern = '/doi:?\\s*(\\S+)/i';
if (PKPString::regexp_match_get($doiPattern, $citationString, $matches)) {
$metadata['pub-id[@pub-id-type="doi"]'] = $matches[1];
$citationString = PKPString::regexp_replace($doiPattern, '', $citationString);
}
// Parse out the access date if we have one and remove it from the citation string
$accessDatePattern = '/accessed:?\\s*([\\s\\w]+)/i';
if (PKPString::regexp_match_get($accessDatePattern, $citationString, $matches)) {
$metadata['access-date'] = $matches[1];
$citationString = PKPString::regexp_replace($accessDatePattern, '', $citationString);
}
// Clean out square brackets
$citationString = PKPString::regexp_replace('/\\[(\\s*(pubmed|medline|full text)\\s*)*]/i', '', $citationString);
// Book citation
$unparsedTail = '';
if (PKPString::regexp_match_get("/\\s*(?P<authors>[^\\.]+)\\.\\s*(?P<source>.*?)\\s*(?P<publisherLoc>[^\\.]*):\\s*(?P<publisherName>[^:]*?);\\s*(?P<date>\\d\\d\\d\\d.*?)(?P<tail>.*)/", $citationString, $matches)) {
$metadata['[@publication-type]'] = NLM30_PUBLICATION_TYPE_BOOK;
$metadata['author'] = $matches['authors'];
$metadata['source'] = $matches['source'];
$metadata['publisher-loc'] = $matches['publisherLoc'];
$metadata['publisher-name'] = $matches['publisherName'];
$metadata['date'] = $matches['date'];
$unparsedTail = $matches['tail'];
// Journal citation
} elseif (PKPString::regexp_match_get("/\\s*(?P<authors>[^\\.]+)\\.\\s*(?P<titleSource>.*)\\s*(?P<date>\\d\\d\\d\\d.*?);(?P<volumeAndIssue>[^:]+):(?P<tail>.*)/", $citationString, $matches)) {
$metadata['[@publication-type]'] = NLM30_PUBLICATION_TYPE_JOURNAL;
$metadata['author'] = $matches['authors'];
$titleSource = array();
if (PKPString::regexp_match_get("/(.*[\\.!\\?])(.*)/", trim($matches['titleSource'], " ."), $titleSource)) {
$metadata['article-title'] = $titleSource[1];
$metadata['source'] = $titleSource[2];
}
$metadata['date'] = $matches['date'];
$volumeAndIssue = array();
if (PKPString::regexp_match_get("/([^\\(]+)(\\(([^\\)]+)\\))?/", $matches['volumeAndIssue'], $volumeAndIssue)) {
$metadata['volume'] = $volumeAndIssue[1];
if (isset($volumeAndIssue[3])) {
$metadata['issue'] = $volumeAndIssue[3];
}
}
$unparsedTail = $matches['tail'];
// Web citation with or without authors
} elseif (PKPString::regexp_match_get("/\\s*(?P<citationSource>.*?)\\s*URL:\\s*(?P<tail>.*)/", $citationString, $matches)) {
$unparsedTail = $matches['tail'];
$citationParts = explode(".", trim($matches['citationSource'], '. '));
switch (count($citationParts)) {
case 0:
// This case should never occur...
assert(false);
break;
case 1:
// Assume this to be a title for the web site.
$metadata['article-title'] = $citationParts[0];
break;
case 2:
// Assume the format: Authors. Title.
$metadata['author'] = $citationParts[0];
$metadata['article-title'] = $citationParts[1];
break;
default:
// Assume the format: Authors. Article Title. Journal Title.
$metadata['author'] = array_shift($citationParts);
// The last part is assumed to be the journal title
$metadata['source'] = array_pop($citationParts);
// Everything in between is assumed to belong to the article title
$metadata['article-title'] = implode('.', $citationParts);
}
}
// TODO: Handle in-ref titles, eg. with editor lists
// Extract page numbers if possible
$pagesPattern = "/^[:p\\.\\s]*(?P<fpage>[Ee]?\\d+)(-(?P<lpage>\\d+))?/";
if (!empty($unparsedTail) && PKPString::regexp_match_get($pagesPattern, $unparsedTail, $matches)) {
$metadata['fpage'] = $matches['fpage'];
if (isset($matches['lpage'])) {
$metadata['lpage'] = $matches['lpage'];
}
// Add the unparsed part of the citation string as a comment so it doesn't get lost.
$comment = PKPString::trimPunctuation(PKPString::regexp_replace($pagesPattern, '', $unparsedTail));
if (!empty($comment)) {
$metadata['comment'] = $comment;
}
}
// Make the meta-data fully NLM citation compliant
$metadata =& $this->postProcessMetadataArray($metadata);
// Create the NLM citation description
return $this->getNlm30CitationDescriptionFromMetadataArray($metadata);
}
/**
* Build the test file UI as understood by Selenium.
* @param string $fileFormat The test file format, e.g. "pdf".
* @return string
*/
private function _getTestFileUri($fileFormat)
{
$testFile = 'tests/functional/pages/editor/test-files/test-article.' . $fileFormat;
self::assertTrue(file_exists($testFile));
$testFile = realpath($testFile);
if (Core::isWindows()) {
$testFile = str_replace(DIRECTORY_SEPARATOR, '/', $testFile);
$testFile = PKPString::regexp_replace('%^[A-Z]:/%', '/', $testFile);
}
$testFile = 'file://' . $testFile;
return $testFile;
}
/**
* Create and return the article (as work or as manifestation) node.
* @param $doc DOMDocument
* @param $pubObject PublishedArticle|ArticleGalley
* @return DOMElement
*/
function createArticleNode($doc, $pubObject)
{
$deployment = $this->getDeployment();
$context = $deployment->getContext();
$cache = $deployment->getCache();
$plugin = $deployment->getPlugin();
$request = Application::getRequest();
$router = $request->getRouter();
assert(is_a($pubObject, 'PublishedArticle') && $this->isWork($context, $plugin) || is_a($pubObject, 'ArticleGalley') && !$this->isWork($context, $plugin));
if (is_a($pubObject, 'PublishedArticle')) {
$galley = null;
$article = $pubObject;
if (!$cache->isCached('articles', $article->getId())) {
$cache->add($article, null);
}
$articleNodeName = 'DOISerialArticleWork';
$workOrProduct = 'Work';
$epubFormat = O4DOI_EPUB_FORMAT_HTML;
} else {
$galley = $pubObject;
$galleyFile = $galley->getFile();
if ($cache->isCached('articles', $galley->getSubmissionId())) {
$article = $cache->get('articles', $galley->getSubmissionId());
} else {
$publishedArticleDao = DAORegistry::getDAO('PublishedArticleDAO');
/* @var $publishedArticleDao PublishedArticleDAO */
$article = $publishedArticleDao->getPublishedArticleByArticleId($galley->getSubmissionId());
if ($article) {
$cache->add($article, null);
}
}
$articleNodeName = 'DOISerialArticleVersion';
$workOrProduct = 'Product';
$epubFormat = null;
if ($galley->isPdfGalley()) {
$epubFormat = O4DOI_EPUB_FORMAT_PDF;
} else {
if ($galley->getRemoteURL() || $galleyFile->getFileType() == 'text/html') {
$epubFormat = O4DOI_EPUB_FORMAT_HTML;
}
}
}
$articleNode = $doc->createElementNS($deployment->getNamespace(), $articleNodeName);
// Notification type (mandatory)
$doi = $pubObject->getStoredPubId('doi');
$registeredDoi = $pubObject->getData('medra::registeredDoi');
assert(empty($registeredDoi) || $registeredDoi == $doi);
$notificationType = empty($registeredDoi) ? O4DOI_NOTIFICATION_TYPE_NEW : O4DOI_NOTIFICATION_TYPE_UPDATE;
$articleNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'NotificationType', $notificationType));
// DOI (mandatory)
$articleNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'DOI', $doi));
// DOI URL (mandatory)
$urlPath = $article->getBestArticleId();
if ($galley) {
$urlPath = array($article->getBestArticleId(), $galley->getBestGalleyId());
}
$url = $router->url($request, $context->getPath(), 'article', 'view', $urlPath);
if ($plugin->isTestMode($context)) {
// Change server domain for testing.
$url = PKPString::regexp_replace('#://[^\\s]+/index.php#', '://example.com/index.php', $url);
}
$articleNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'DOIWebsiteLink', $url));
// DOI strucural type
$articleNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'DOIStructuralType', $this->getDOIStructuralType()));
// Registrant (mandatory)
$articleNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'RegistrantName', $plugin->getSetting($context->getId(), 'registrantName')));
// Registration authority (mandatory)
$articleNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'RegistrationAuthority', 'mEDRA'));
// WorkIdentifier - proprietary ID
$pubObjectProprietaryId = $context->getId() . '-' . $article->getIssueId() . '-' . $article->getId();
if ($galley) {
$pubObjectProprietaryId .= '-g' . $galley->getId();
}
$articleNode->appendChild($this->createIdentifierNode($doc, $workOrProduct, O4DOI_ID_TYPE_PROPRIETARY, $pubObjectProprietaryId));
// Issue/journal locale precedence.
$journalLocalePrecedence = $this->getObjectLocalePrecedence($context, null, null);
// Serial Publication (mandatory)
$articleNode->appendChild($this->createSerialPublicationNode($doc, $journalLocalePrecedence, $epubFormat));
// Journal Issue (mandatory)
$issueId = $article->getIssueId();
if ($cache->isCached('issues', $issueId)) {
$issue = $cache->get('issues', $issueId);
} else {
$issueDao = DAORegistry::getDAO('IssueDAO');
/* @var $issueDao IssueDAO */
$issue = $issueDao->getById($issueId, $context->getId());
if ($issue) {
$cache->add($issue, null);
}
}
$articleNode->appendChild($this->createJournalIssueNode($doc, $issue, $journalLocalePrecedence));
// Object locale precedence.
$objectLocalePrecedence = $this->getObjectLocalePrecedence($context, $article, $galley);
// Content Item (mandatory for articles)
$articleNode->appendChild($this->createContentItemNode($doc, $issue, $article, $galley, $objectLocalePrecedence));
return $articleNode;
}
/**
* Do the actual web service request.
* @param $action string
* @param $arg string
* @param $attachment array
* @return boolean|string True for success, an error message otherwise.
*/
function _doRequest($action, $arg, $attachment = null)
{
// Build the multipart SOAP message from scratch.
$soapMessage = '<SOAP-ENV:Envelope xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/" ' . 'xmlns:med="http://www.medra.org">' . '<SOAP-ENV:Header/>' . '<SOAP-ENV:Body>' . "<med:{$action}>{$arg}</med:{$action}>" . '</SOAP-ENV:Body>' . '</SOAP-ENV:Envelope>';
$soapMessageId = $this->_getContentId($action);
if ($attachment) {
assert(count($attachment) == 1);
$request = "--MIME_boundary\r\n" . $this->_getMimePart($soapMessageId, $soapMessage) . "--MIME_boundary\r\n" . $this->_getMimePart(key($attachment), current($attachment)) . "--MIME_boundary--\r\n";
$contentType = 'multipart/related; type="text/xml"; boundary="MIME_boundary"';
} else {
$request = $soapMessage;
$contentType = 'text/xml';
}
// Prepare HTTP session.
$curlCh = curl_init();
curl_setopt($curlCh, CURLOPT_RETURNTRANSFER, true);
curl_setopt($curlCh, CURLOPT_POST, true);
// Set up basic authentication.
curl_setopt($curlCh, CURLOPT_HTTPAUTH, CURLAUTH_BASIC);
curl_setopt($curlCh, CURLOPT_USERPWD, $this->_auth);
// Set up SSL.
curl_setopt($curlCh, CURLOPT_SSL_VERIFYPEER, false);
// Make SOAP request.
curl_setopt($curlCh, CURLOPT_URL, $this->_endpoint);
$extraHeaders = array('SOAPAction: "' . $action . '"', 'Content-Type: ' . $contentType, 'UserAgent: OJS-mEDRA');
curl_setopt($curlCh, CURLOPT_HTTPHEADER, $extraHeaders);
curl_setopt($curlCh, CURLOPT_POSTFIELDS, $request);
$result = true;
$response = curl_exec($curlCh);
// We do not localize our error messages as they are all
// fatal errors anyway and must be analyzed by technical staff.
if ($response === false) {
$result = 'OJS-mEDRA: Expected string response.';
}
if ($result === true && ($status = curl_getinfo($curlCh, CURLINFO_HTTP_CODE)) != MEDRA_WS_RESPONSE_OK) {
$result = 'OJS-mEDRA: Expected ' . MEDRA_WS_RESPONSE_OK . ' response code, got ' . $status . ' instead.';
}
curl_close($curlCh);
// Check SOAP response by simple string manipulation rather
// than instantiating a DOM.
if (is_string($response)) {
$matches = array();
PKPString::regexp_match_get('#<faultstring>([^<]*)</faultstring>#', $response, $matches);
if (empty($matches)) {
if ($attachment) {
assert(PKPString::regexp_match('#<returnCode>success</returnCode>#', $response));
} else {
$parts = explode("\r\n\r\n", $response);
$result = array_pop($parts);
$result = PKPString::regexp_replace('/>[^>]*$/', '>', $result);
}
} else {
$result = 'mEDRA: ' . $status . ' - ' . $matches[1];
}
} else {
$result = 'OJS-mEDRA: Expected string response.';
}
return $result;
}
/**
* Saving object's DOI to the object's
* "registeredDoi" setting.
* We prefix the setting with the plugin's
* id so that we do not get name clashes
* when several DOI registration plug-ins
* are active at the same time.
* @param $context Context
* @param $object Issue|PublishedArticle|ArticleGalley
* @param $testPrefix string
*/
function saveRegisteredDoi($context, $object, $testPrefix = '10.1234')
{
$registeredDoi = $object->getStoredPubId('doi');
assert(!empty($registeredDoi));
if ($this->isTestMode($context)) {
$registeredDoi = PKPString::regexp_replace('#^[^/]+/#', $testPrefix . '/', $registeredDoi);
}
$object->setData($this->getPluginSettingsPrefix() . '::' . DOI_EXPORT_REGISTERED_DOI, $registeredDoi);
$this->updateObject($object);
}
/**
* Get the canonical URL of an object.
* @param $request Request
* @param $journal Journal
* @param $object Issue|PublishedArticle|ArticleGalley
*/
function _getObjectUrl($request, $journal, $object)
{
$router = $request->getRouter();
// Retrieve the article of article files.
if (is_a($object, 'SubmissionFile')) {
$articleId = $object->getArticleId();
$cache = $this->getCache();
if ($cache->isCached('articles', $articleId)) {
$article = $cache->get('articles', $articleId);
} else {
$articleDao = DAORegistry::getDAO('PublishedArticleDAO');
/* @var $articleDao PublishedArticleDAO */
$article = $articleDao->getPublishedArticleByArticleId($articleId, $journal->getId(), true);
}
assert(is_a($article, 'PublishedArticle'));
}
$url = null;
switch (true) {
case is_a($object, 'Issue'):
$url = $router->url($request, null, 'issue', 'view', $object->getBestIssueId($journal));
break;
case is_a($object, 'PublishedArticle'):
$url = $router->url($request, null, 'article', 'view', $object->getBestArticleId($journal));
break;
case is_a($object, 'ArticleGalley'):
$url = $router->url($request, null, 'article', 'view', array($article->getBestArticleId($journal), $object->getBestGalleyId($journal)));
break;
}
if ($this->isTestMode($request)) {
// Change server domain for testing.
$url = PKPString::regexp_replace('#://[^\\s]+/index.php#', '://example.com/index.php', $url);
}
return $url;
}
/**
* Fills the given citation description with
* meta-data retrieved from Worldcat
* @param $oclcId string
* @return MetadataDescription
*/
function &_lookupWorldcat($oclcId)
{
$nullVar = null;
$lookupParams = array('wskey' => $this->getApiKey());
if (is_null($resultDOM = $this->callWebService(WORLDCAT_WEBSERVICE_EXTRACT . urlencode($oclcId), $lookupParams))) {
return $nullVar;
}
if (is_null($metadata = $this->transformWebServiceResults($resultDOM, dirname(__FILE__) . DIRECTORY_SEPARATOR . 'worldcat.xsl'))) {
return $nullVar;
}
// FIXME: Use MARC parsed author field in XSL rather than full name
// Clean non-numerics from ISBN
if (!empty($metadata['isbn'])) {
$metadata['isbn'] = PKPString::regexp_replace('/[^\\dX]*/', '', $metadata['isbn']);
}
// Clean non-numerics from issued date (year)
if (!empty($metadata['date'])) {
$metadata['date'] = PKPString::regexp_replace('/,.*/', ', ', $metadata['date']);
$metadata['date'] = PKPString::regexp_replace('/[^\\d{4}]/', '', $metadata['date']);
}
$citationDescription =& $this->getNlm30CitationDescriptionFromMetadataArray($metadata);
return $citationDescription;
}
/**
* @copydoc PKPPubIdPlugin::getPubId()
*/
function getPubId($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;
}
/**
* @see Filter::process()
* @param $pubObject Issue|PublishedArticle|ArticleGalley
* @return DOMDocument
*/
function &process(&$pubObject)
{
// Create the XML document
$doc = new DOMDocument('1.0', 'utf-8');
$doc->preserveWhiteSpace = false;
$doc->formatOutput = true;
$deployment = $this->getDeployment();
$context = $deployment->getContext();
$plugin = $deployment->getPlugin();
$cache = $plugin->getCache();
// Get all objects
$issue = $article = $galley = $galleyFile = null;
if (is_a($pubObject, 'Issue')) {
$issue = $pubObject;
if (!$cache->isCached('issues', $issue->getId())) {
$cache->add($issue, null);
}
} elseif (is_a($pubObject, 'PublishedArticle')) {
$article = $pubObject;
if (!$cache->isCached('articles', $article->getId())) {
$cache->add($article, null);
}
} elseif (is_a($pubObject, 'ArticleGalley')) {
$galley = $pubObject;
$galleyFile = $galley->getFile();
$articleId = $galley->getSubmissionId();
if ($cache->isCached('articles', $articleId)) {
$article = $cache->get('articles', $articleId);
} else {
$articleDao = DAORegistry::getDAO('PublishedArticleDAO');
/* @var $articleDao PublishedArticleDAO */
$article = $articleDao->getPublishedArticleByArticleId($pubObject->getSubmissionId(), $context->getId());
if ($article) {
$cache->add($article, null);
}
}
}
if (!$issue) {
$issueId = $article->getIssueId();
if ($cache->isCached('issues', $issueId)) {
$issue = $cache->get('issues', $issueId);
} else {
$issueDao = DAORegistry::getDAO('IssueDAO');
/* @var $issueDao IssueDAO */
$issue = $issueDao->getById($issueId, $context->getId());
if ($issue) {
$cache->add($issue, null);
}
}
}
// The publisher is required.
// Use the journal title as DataCite recommends for now.
$publisher = $this->getPrimaryTranslation($context->getName(null), $objectLocalePrecedence);
assert(!empty($publisher));
// The publication date is required.
$publicationDate = isset($article) ? $article->getDatePublished() : null;
if (empty($publicationDate)) {
$publicationDate = $issue->getDatePublished();
}
assert(!empty($publicationDate));
// Create the root node
$rootNode = $this->createRootNode($doc);
$doc->appendChild($rootNode);
// Identify the object locale.
$objectLocalePrecedence = $this->getObjectLocalePrecedence($context, $article, $galley);
// DOI (mandatory)
$doi = $pubObject->getStoredPubId('doi');
if ($plugin->isTestMode($context)) {
$doi = PKPString::regexp_replace('#^[^/]+/#', DATACITE_API_TESTPREFIX . '/', $doi);
}
$rootNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'identifier', htmlspecialchars($doi, ENT_COMPAT, 'UTF-8')));
$node->setAttribute('identifierType', DATACITE_IDTYPE_DOI);
// Creators (mandatory)
$rootNode->appendChild($this->createCreatorsNode($doc, $issue, $article, $galley, $galleyFile, $publisher, $objectLocalePrecedence));
// Title (mandatory)
$rootNode->appendChild($this->createTitlesNode($doc, $issue, $article, $galley, $galleyFile, $objectLocalePrecedence));
// Publisher (mandatory)
$rootNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'publisher', htmlspecialchars($publisher, ENT_COMPAT, 'UTF-8')));
// Publication Year (mandatory)
$rootNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'publicationYear', date('Y', strtotime($publicationDate))));
// Subjects
$subject = null;
if (!empty($galleyFile) && is_a($galleyFile, 'SupplementaryFile')) {
$subject = $this->getPrimaryTranslation($galleyFile->getSubject(null), $objectLocalePrecedence);
} elseif (!empty($article)) {
$subject = $this->getPrimaryTranslation($article->getSubject(null), $objectLocalePrecedence);
}
if (!empty($subject)) {
$subjectsNode = $doc->createElementNS($deployment->getNamespace(), 'subjects');
$subjectsNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'subject', htmlspecialchars($subject, ENT_COMPAT, 'UTF-8')));
$rootNode->appendChild($subjectsNode);
}
// Dates
$rootNode->appendChild($this->createDatesNode($doc, $issue, $article, $galley, $galleyFile, $publicationDate));
// Language
$rootNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'language', AppLocale::getIso1FromLocale($objectLocalePrecedence[0])));
// Resource Type
$resourceTypeNode = $this->createResourceTypeNode($doc, $issue, $article, $galley, $galleyFile);
if ($resourceTypeNode) {
$rootNode->appendChild($resourceTypeNode);
}
// Alternate Identifiers
$rootNode->appendChild($this->createAlternateIdentifiersNode($doc, $issue, $article, $galley));
// Related Identifiers
$relatedIdentifiersNode = $this->createRelatedIdentifiersNode($doc, $issue, $article, $galley);
if ($relatedIdentifiersNode) {
$rootNode->appendChild($relatedIdentifiersNode);
}
// Sizes
$sizesNode = $this->createSizesNode($doc, $issue, $article, $galley, $galleyFile);
if ($sizesNode) {
$rootNode->appendChild($sizesNode);
}
// Formats
if (!empty($galleyFile)) {
$format = $galleyFile->getFileType();
if (!empty($format)) {
$formatsNode = $doc->createElementNS($deployment->getNamespace(), 'formats');
$formatsNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'format', htmlspecialchars($format, ENT_COMPAT, 'UTF-8')));
$rootNode->appendChild($formatsNode);
}
}
// Rights
$rightsURL = $article ? $article->getLicenseURL() : $context->getSetting('licenseURL');
if (!empty($rightsURL)) {
$rightsNode = $doc->createElementNS($deployment->getNamespace(), 'rightsList');
$rightsNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'rights', htmlspecialchars(strip_tags(Application::getCCLicenseBadge($rightsURL)), ENT_COMPAT, 'UTF-8')));
$node->setAttribute('rightsURI', $rightsURL);
$rootNode->appendChild($rightsNode);
}
// Descriptions
$descriptionsNode = $this->createDescriptionsNode($doc, $issue, $article, $galley, $galleyFile, $objectLocalePrecedence);
if ($descriptionsNode) {
$rootNode->appendChild($descriptionsNode);
}
return $doc;
}
