/**
* Display list of people in the selected role.
* @param $args array first parameter is the role ID to display
*/
function people($args, &$request)
{
$this->validate();
$this->setupTemplate($request, true);
$roleDao = DAORegistry::getDAO('RoleDAO');
if ($request->getUserVar('roleSymbolic') != null) {
$roleSymbolic = $request->getUserVar('roleSymbolic');
} else {
$roleSymbolic = isset($args[0]) ? $args[0] : 'all';
}
if ($roleSymbolic != 'all' && String::regexp_match_get('/^(\\w+)s$/', $roleSymbolic, $matches)) {
$roleId = $roleDao->getRoleIdFromPath($matches[1]);
if ($roleId == null) {
$request->redirect(null, null, 'all');
}
$roleName = $roleDao->getRoleName($roleId, true);
} else {
$roleId = 0;
$roleName = 'admin.people.allUsers';
}
$sort = $request->getUserVar('sort');
$sort = isset($sort) ? $sort : 'name';
$sortDirection = $request->getUserVar('sortDirection');
$templateMgr =& TemplateManager::getManager($request);
$searchType = null;
$searchMatch = null;
$search = $request->getUserVar('search');
$searchInitial = $request->getUserVar('searchInitial');
if (isset($search)) {
$searchType = $request->getUserVar('searchField');
$searchMatch = $request->getUserVar('searchMatch');
} else {
if (isset($searchInitial)) {
$searchInitial = String::strtoupper($searchInitial);
$searchType = USER_FIELD_INITIAL;
$search = $searchInitial;
}
}
$rangeInfo = $this->getRangeInfo($request, 'users');
$users = $roleDao->getUsersByRoleId($roleId, $searchType, $search, $searchMatch, $rangeInfo, $sort, $sortDirection);
$templateMgr->assign('roleId', $roleId);
$templateMgr->assign('currentUrl', $request->url(null, 'people', 'all'));
$templateMgr->assign('roleName', $roleName);
$templateMgr->assign_by_ref('users', $users);
$templateMgr->assign_by_ref('thisUser', $request->getUser());
$templateMgr->assign('searchField', $searchType);
$templateMgr->assign('searchMatch', $searchMatch);
$templateMgr->assign('search', $search);
$templateMgr->assign('searchInitial', $request->getUserVar('searchInitial'));
$fieldOptions = array(USER_FIELD_FIRSTNAME => 'user.firstName', USER_FIELD_LASTNAME => 'user.lastName', USER_FIELD_USERNAME => 'user.username', USER_FIELD_INTERESTS => 'user.interests', USER_FIELD_EMAIL => 'user.email');
$templateMgr->assign('fieldOptions', $fieldOptions);
$role =& $roleDao->newDataObject();
$role->setId($roleId);
$templateMgr->assign('rolePath', $role->getPath());
$templateMgr->assign('alphaList', explode(' ', __('common.alphaList')));
$templateMgr->assign('roleSymbolic', $roleSymbolic);
$templateMgr->assign('sort', $sort);
$templateMgr->assign('sortDirection', $sortDirection);
$templateMgr->display('admin/people/enrollment.tpl');
}
/**
* Submit a submission.
*/
protected function submitSubmission()
{
$this->logAuthorIn();
$submissionPage = self::$baseUrl . '/index.php/publicknowledge/submission/wizard/';
//
// First submission page.
//
$this->verifyAndOpen($submissionPage . '1');
$this->waitForElementPresent('css=button.submitFormButton');
$this->doActionsOnStep1();
// Accept submission conditions.
$checkboxId = 0;
while ($this->isElementPresent("checklist-{$checkboxId}")) {
$this->check("checklist-{$checkboxId}");
$checkboxId++;
}
$this->clickAndWait('css=button.submitFormButton');
//
// Second submission page.
//
$this->waitForLocation($submissionPage . '2*');
$this->waitForElementPresent('css=div.plupload_buttons');
// We should now have the submission ID in the URL.
$url = $this->getLocation();
$matches = null;
String::regexp_match_get('/submissionId=([0-9]+)#/', $url, $matches);
self::assertTrue(count($matches) == 2);
$submissionId = $matches[1];
self::assertTrue(is_numeric($submissionId));
$submissionId = (int) $submissionId;
// Close the upload file modal.
$this->click('id=cancelButton');
// Save the second step without uploading a file.
$this->waitForElementNotPresent('css=div.plupload_buttons');
$this->waitForElementPresent($selector = '//button[contains(., \'Save and continue\')]');
$this->click($selector);
//
// Third submission page.
//
$this->waitForElementPresent('css=button.submitFormButton');
$title = 'test book';
$this->waitForElementPresent("css=[id^=title]");
$this->type("css=[id^=title]", $title);
$this->verifyElementPresent('css=iframe[id^=abstract]');
if ($this->verified()) {
// TinyMCE hack.
$jsScript = "selenium.browserbot.getCurrentWindow().document" . ".querySelector('iframe[id^=abstract]').contentDocument.body.innerHTML = " . "'{$title} abstract'";
$this->getEval($jsScript);
} else {
$this->type('css=[id^=abstract]', $title . ' abstract');
}
$this->click("css=#submitStep3Form .submitFormButton");
$this->waitForElementPresent($selector = 'link=OK');
$this->click($selector);
$authorDashboardLink = self::$baseUrl . '/index.php/publicknowledge/authorDashboard/submission/' . $submissionId;
$this->waitForElementPresent("css=a[href='" . $authorDashboardLink . "']");
$this->assertTrue(is_int($submissionId));
return $submissionId;
}
/**
* Retrieve the export as an XML string.
* @param $pluginUrl string the url to be requested for export.
* @param $postParams array additional post parameters
* @return string
*/
protected function getXmlOnExport($pluginUrl, $postParams = array())
{
// Prepare HTTP session.
$curlCh = curl_init();
curl_setopt($curlCh, CURLOPT_POST, true);
// Create a cookie file (required for log-in).
$cookies = tempnam(sys_get_temp_dir(), 'curlcookies');
// Log in.
$loginUrl = $this->baseUrl . '/index.php/test/login/signIn';
// Bug #8518 safety work-around
if ($this->password[0] == '@') {
die('CURL parameters may not begin with @.');
}
$loginParams = array('username' => 'admin', 'password' => $this->password);
curl_setopt($curlCh, CURLOPT_URL, $loginUrl);
curl_setopt($curlCh, CURLOPT_POSTFIELDS, $loginParams);
curl_setopt($curlCh, CURLOPT_COOKIEJAR, $cookies);
self::assertTrue(curl_exec($curlCh));
// Request export document.
$exportUrl = $this->baseUrl . '/index.php/test/manager/importexport/plugin/' . $pluginUrl;
curl_setopt($curlCh, CURLOPT_URL, $exportUrl);
// Bug #8518 safety work-around
foreach ($postParams as $paramValue) {
if ($paramValue[0] == '@') {
die('CURL parameters may not begin with @.');
}
}
curl_setopt($curlCh, CURLOPT_POSTFIELDS, $postParams);
curl_setopt($curlCh, CURLOPT_HTTPHEADER, array('Accept: application/xml, application/x-gtar, */*'));
curl_setopt($curlCh, CURLOPT_RETURNTRANSFER, true);
curl_setopt($curlCh, CURLOPT_HEADER, true);
$response = curl_exec($curlCh);
do {
list($header, $response) = explode("\r\n\r\n", $response, 2);
} while (String::regexp_match('#HTTP/.*100#', $header));
// Check whether we got a tar file.
if (String::regexp_match('#Content-Type: application/x-gtar#', $header)) {
// Save the data to a temporary file.
$tempfile = tempnam(sys_get_temp_dir(), 'tst');
file_put_contents($tempfile, $response);
// Recursively extract tar file.
$result = $this->extractTarFile($tempfile);
unlink($tempfile);
} else {
$matches = null;
String::regexp_match_get('#filename="([^"]+)"#', $header, $matches);
self::assertTrue(isset($matches[1]));
$result = array($matches[1] => $response);
}
// Destroy HTTP session.
curl_close($curlCh);
unlink($cookies);
return $result;
}
/**
* Extract and validate a plugin (prior to installation)
* @param $filePath string Full path to plugin archive
* @param $originalFileName string Original filename of plugin archive
* @return string|null Extracted plugin path on success; null on error
*/
function extractPlugin($filePath, $originalFileName, &$errorMsg)
{
// tar archive basename (less potential version number) must
// equal plugin directory name and plugin files must be in a
// directory named after the plug-in (potentially with version)
$matches = array();
String::regexp_match_get('/^[a-zA-Z0-9]+/', basename($originalFileName, '.tar.gz'), $matches);
$pluginShortName = array_pop($matches);
if (!$pluginShortName) {
$errorMsg = __('manager.plugins.invalidPluginArchive');
return null;
}
// Create random dirname to avoid symlink attacks.
$pluginExtractDir = dirname($filePath) . DIRECTORY_SEPARATOR . $pluginShortName . substr(md5(mt_rand()), 0, 10);
mkdir($pluginExtractDir);
// Test whether the tar binary is available for the export to work
$tarBinary = Config::getVar('cli', 'tar');
if (!empty($tarBinary) && file_exists($tarBinary)) {
exec($tarBinary . ' -xzf ' . escapeshellarg($filePath) . ' -C ' . escapeshellarg($pluginExtractDir));
} else {
$errorMsg = __('manager.plugins.tarCommandNotFound');
}
if (empty($errorMsg)) {
// Look for a directory named after the plug-in's short
// (alphanumeric) name within the extracted archive.
if (is_dir($tryDir = $pluginExtractDir . '/' . $pluginShortName)) {
return $tryDir;
// Success
}
// Failing that, look for a directory named after the
// archive. (Typically also contains the version number
// e.g. with github generated release archives.)
String::regexp_match_get('/^[a-zA-Z0-9.-]+/', basename($originalFileName, '.tar.gz'), $matches);
if (is_dir($tryDir = $pluginExtractDir . '/' . array_pop($matches))) {
// We found a directory named after the archive
// within the extracted archive. (Typically also
// contains the version number, e.g. github
// generated release archives.)
return $tryDir;
}
$errorMsg = __('manager.plugins.invalidPluginArchive');
}
return null;
}
/**
* Normalize incoming date string.
* @see Filter::process()
* @param $input string
* @return string
*/
function &process(&$input)
{
// FIXME: We have to i18nize this when expanding citation parsing to other languages
static $monthNames = array('Jan' => '01', 'Feb' => '02', 'Mar' => '03', 'Apr' => '04', 'May' => '05', 'Jun' => '06', 'Jul' => '07', 'Aug' => '08', 'Sep' => '09', 'Oct' => '10', 'Nov' => '11', 'Dec' => '12');
$dateExpressions = array('/(?P<year>\\d{4})-(?P<month>\\d{2})-(?P<day>\\d{2})/', '/(?P<year>\\d{4})\\s*(?P<monthName>[a-z]\\w+)?\\s*(?P<day>\\d+)?/i');
$normalizedDate = null;
foreach ($dateExpressions as $dateExpression) {
if (String::regexp_match_get($dateExpression, $input, $parsedDate)) {
if (isset($parsedDate['year'])) {
$normalizedDate = $parsedDate['year'];
$month = '';
if (isset($parsedDate['monthName'])) {
$monthName = substr($parsedDate['monthName'], 0, 3);
if (isset($monthNames[$monthName])) {
// Convert the month name to a two digit numeric month representation
// before adding it to the normalized date string.
$month = $monthNames[$monthName];
}
}
if (isset($parsedDate['month'])) {
$monthInt = (int) $parsedDate['month'];
if ($monthInt >= 1 && $monthInt <= 12) {
$month = str_pad((string) $monthInt, 2, '0', STR_PAD_LEFT);
}
}
if (!empty($month)) {
$normalizedDate .= '-' . $month;
if (isset($parsedDate['day'])) {
$normalizedDate .= '-' . str_pad($parsedDate['day'], 2, '0', STR_PAD_LEFT);
}
}
}
if (!empty($normalizedDate)) {
break;
}
}
}
return $normalizedDate;
}
/**
* Submit a new test article.
* @param $title string
* @return integer the id of the new article
*/
protected function submitArticle($title = 'Editing test article')
{
// We need to be logged in to submit an article.
$this->logIn();
$submissionPage = $this->baseUrl . '/index.php/lucene-test/author/submit/';
//
// First submission page.
//
$this->verifyAndOpen($submissionPage . '1');
$this->waitForElementPresent('css=input.defaultButton');
// Set Section.
$this->select('sectionId', 'value=3');
// Accept submission conditions.
$checkboxId = 1;
while ($this->isElementPresent("checklist-{$checkboxId}")) {
$this->check("checklist-{$checkboxId}");
$checkboxId++;
}
// Submit first submission page.
$this->clickAndWait('css=input.defaultButton');
//
// Second submission page.
//
$this->waitForLocation($submissionPage . '2*');
$this->waitForElementPresent('css=input.defaultButton');
// We should now have the article ID in the URL.
$url = $this->getLocation();
$matches = null;
String::regexp_match_get('/articleId=([0-9]+)/', $url, $matches);
self::assertTrue(count($matches) == 2);
$articleId = $matches[1];
self::assertTrue(is_numeric($articleId));
$articleId = (int) $articleId;
// Submit the second submission page.
$this->clickAndWait('css=input.defaultButton');
$this->waitForConfirmation('*Are you sure you wish to continue*');
//
// Third submission page.
//
$this->waitForLocation($submissionPage . '3*');
$this->waitForElementPresent('css=input.defaultButton');
// Fill in article metadata.
$this->type('authors-0-firstName', 'Arthur');
$this->type('authors-0-lastName', 'McAutomatic');
$this->type('title', $title);
$this->verifyElementPresent('id=abstract_ifr');
if ($this->verified()) {
// TinyMCE hack.
$jsScript = "selenium.browserbot.getCurrentWindow().document" . ".getElementById('abstract_ifr').contentDocument.body.innerHTML = " . "'{$title} abstract'";
$this->getEval($jsScript);
} else {
$this->type('abstract', $title . ' abstract');
}
// Submit metadata.
$this->clickAndWait('css=input.defaultButton');
//
// Fourth and fifth submission page.
//
$this->waitForLocation($submissionPage . '4*');
$this->waitForElementPresent('css=input.defaultButton');
// Do not upload any supplementary file and continue.
$this->clickAndWait('css=input.defaultButton');
$this->waitForLocation($submissionPage . '5*');
$this->waitForElementPresent('css=input.defaultButton');
// Confirm the submission.
$this->clickAndWait('css=input.defaultButton');
return $articleId;
}
/**
* Allow the Journal Manager to merge user accounts, including attributed articles etc.
*/
function mergeUsers($args)
{
parent::validate();
parent::setupTemplate(true);
$roleDao =& DAORegistry::getDAO('RoleDAO');
$userDao =& DAORegistry::getDAO('UserDAO');
$journal =& Request::getJournal();
$journalId = $journal->getJournalId();
$templateMgr =& TemplateManager::getManager();
$oldUserId = Request::getUserVar('oldUserId');
$newUserId = Request::getUserVar('newUserId');
// Ensure that we have administrative priveleges over the specified user(s).
if (!empty($oldUserId) && !Validation::canAdminister($journalId, $oldUserId) || !empty($newUserId) && !Validation::canAdminister($journalId, $newUserId)) {
$templateMgr->assign('pageTitle', 'manager.people');
$templateMgr->assign('errorMsg', 'manager.people.noAdministrativeRights');
$templateMgr->assign('backLink', Request::url(null, null, 'people', 'all'));
$templateMgr->assign('backLinkLabel', 'manager.people.allUsers');
return $templateMgr->display('common/error.tpl');
}
if (!empty($oldUserId) && !empty($newUserId)) {
// Both user IDs have been selected. Merge the accounts.
$articleDao =& DAORegistry::getDAO('ArticleDAO');
foreach ($articleDao->getArticlesByUserId($oldUserId) as $article) {
$article->setUserId($newUserId);
$articleDao->updateArticle($article);
unset($article);
}
$commentDao =& DAORegistry::getDAO('CommentDAO');
foreach ($commentDao->getCommentsByUserId($oldUserId) as $comment) {
$comment->setUserId($newUserId);
$commentDao->updateComment($comment);
unset($comment);
}
$articleNoteDao =& DAORegistry::getDAO('ArticleNoteDAO');
$articleNotes =& $articleNoteDao->getArticleNotesByUserId($oldUserId);
while ($articleNote =& $articleNotes->next()) {
$articleNote->setUserId($newUserId);
$articleNoteDao->updateArticleNote($articleNote);
unset($articleNote);
}
$editAssignmentDao =& DAORegistry::getDAO('EditAssignmentDAO');
$editAssignments =& $editAssignmentDao->getEditAssignmentsByUserId($oldUserId);
while ($editAssignment =& $editAssignments->next()) {
$editAssignment->setEditorId($newUserId);
$editAssignmentDao->updateEditAssignment($editAssignment);
unset($editAssignment);
}
$editorSubmissionDao =& DAORegistry::getDAO('EditorSubmissionDAO');
$editorSubmissionDao->transferEditorDecisions($oldUserId, $newUserId);
$reviewAssignmentDao =& DAORegistry::getDAO('ReviewAssignmentDAO');
foreach ($reviewAssignmentDao->getReviewAssignmentsByUserId($oldUserId) as $reviewAssignment) {
$reviewAssignment->setReviewerId($newUserId);
$reviewAssignmentDao->updateReviewAssignment($reviewAssignment);
unset($reviewAssignment);
}
$copyeditorSubmissionDao =& DAORegistry::getDAO('CopyeditorSubmissionDAO');
$copyeditorSubmissions =& $copyeditorSubmissionDao->getCopyeditorSubmissionsByCopyeditorId($oldUserId);
while ($copyeditorSubmission =& $copyeditorSubmissions->next()) {
$copyeditorSubmission->setCopyeditorId($newUserId);
$copyeditorSubmissionDao->updateCopyeditorSubmission($copyeditorSubmission);
unset($copyeditorSubmission);
}
$layoutEditorSubmissionDao =& DAORegistry::getDAO('LayoutEditorSubmissionDAO');
$layoutEditorSubmissions =& $layoutEditorSubmissionDao->getSubmissions($oldUserId);
while ($layoutEditorSubmission =& $layoutEditorSubmissions->next()) {
$layoutAssignment =& $layoutEditorSubmission->getLayoutAssignment();
$layoutAssignment->setEditorId($newUserId);
$layoutEditorSubmissionDao->updateSubmission($layoutEditorSubmission);
unset($layoutAssignment);
unset($layoutEditorSubmission);
}
$proofreaderSubmissionDao =& DAORegistry::getDAO('ProofreaderSubmissionDAO');
$proofreaderSubmissions =& $proofreaderSubmissionDao->getSubmissions($oldUserId);
while ($proofreaderSubmission =& $proofreaderSubmissions->next()) {
$proofAssignment =& $proofreaderSubmission->getProofAssignment();
$proofAssignment->setProofreaderId($newUserId);
$proofreaderSubmissionDao->updateSubmission($proofreaderSubmission);
unset($proofAssignment);
unset($proofreaderSubmission);
}
$articleEmailLogDao =& DAORegistry::getDAO('ArticleEmailLogDAO');
$articleEmailLogDao->transferArticleLogEntries($oldUserId, $newUserId);
$articleEventLogDao =& DAORegistry::getDAO('ArticleEventLogDAO');
$articleEventLogDao->transferArticleLogEntries($oldUserId, $newUserId);
$articleCommentDao =& DAORegistry::getDAO('ArticleCommentDAO');
foreach ($articleCommentDao->getArticleCommentsByUserId($oldUserId) as $articleComment) {
$articleComment->setAuthorId($newUserId);
$articleCommentDao->updateArticleComment($articleComment);
unset($articleComment);
}
$accessKeyDao =& DAORegistry::getDAO('AccessKeyDAO');
$accessKeyDao->transferAccessKeys($oldUserId, $newUserId);
// Delete the old user and associated info.
$sessionDao =& DAORegistry::getDAO('SessionDAO');
$sessionDao->deleteSessionsByUserId($oldUserId);
$subscriptionDao =& DAORegistry::getDAO('SubscriptionDAO');
$subscriptionDao->deleteSubscriptionsByUserId($oldUserId);
$temporaryFileDao =& DAORegistry::getDAO('TemporaryFileDAO');
$temporaryFileDao->deleteTemporaryFilesByUserId($oldUserId);
$notificationStatusDao =& DAORegistry::getDAO('NotificationStatusDAO');
$notificationStatusDao->deleteNotificationStatusByUserId($oldUserId);
$userSettingsDao =& DAORegistry::getDAO('UserSettingsDAO');
$userSettingsDao->deleteSettings($oldUserId);
$groupMembershipDao =& DAORegistry::getDAO('GroupMembershipDAO');
$groupMembershipDao->deleteMembershipByUserId($oldUserId);
$sectionEditorsDao =& DAORegistry::getDAO('SectionEditorsDAO');
$sectionEditorsDao->deleteEditorsByUserId($oldUserId);
// Transfer old user's roles
$roles =& $roleDao->getRolesByUserId($oldUserId);
foreach ($roles as $role) {
if (!$roleDao->roleExists($role->getJournalId(), $newUserId, $role->getRoleId())) {
$role->setUserId($newUserId);
$roleDao->insertRole($role);
}
}
$roleDao->deleteRoleByUserId($oldUserId);
$userDao->deleteUserById($oldUserId);
Request::redirect(null, 'manager');
}
if (!empty($oldUserId)) {
// Get the old username for the confirm prompt.
$oldUser =& $userDao->getUser($oldUserId);
$templateMgr->assign('oldUsername', $oldUser->getUsername());
unset($oldUser);
}
// The manager must select one or both IDs.
if (Request::getUserVar('roleSymbolic') != null) {
$roleSymbolic = Request::getUserVar('roleSymbolic');
} else {
$roleSymbolic = isset($args[0]) ? $args[0] : 'all';
}
if ($roleSymbolic != 'all' && String::regexp_match_get('/^(\\w+)s$/', $roleSymbolic, $matches)) {
$roleId = $roleDao->getRoleIdFromPath($matches[1]);
if ($roleId == null) {
Request::redirect(null, null, null, 'all');
}
$roleName = $roleDao->getRoleName($roleId, true);
} else {
$roleId = 0;
$roleName = 'manager.people.allUsers';
}
$searchType = null;
$searchMatch = null;
$search = Request::getUserVar('search');
$searchInitial = Request::getUserVar('searchInitial');
if (isset($search)) {
$searchType = Request::getUserVar('searchField');
$searchMatch = Request::getUserVar('searchMatch');
} else {
if (isset($searchInitial)) {
$searchInitial = String::strtoupper($searchInitial);
$searchType = USER_FIELD_INITIAL;
$search = $searchInitial;
}
}
$rangeInfo = Handler::getRangeInfo('users');
if ($roleId) {
$users =& $roleDao->getUsersByRoleId($roleId, $journalId, $searchType, $search, $searchMatch, $rangeInfo);
$templateMgr->assign('roleId', $roleId);
} else {
$users =& $roleDao->getUsersByJournalId($journalId, $searchType, $search, $searchMatch, $rangeInfo);
}
$templateMgr->assign('currentUrl', Request::url(null, null, 'people', 'all'));
$templateMgr->assign('helpTopicId', 'journal.managementPages.mergeUsers');
$templateMgr->assign('roleName', $roleName);
$templateMgr->assign_by_ref('users', $users);
$templateMgr->assign_by_ref('thisUser', Request::getUser());
$templateMgr->assign('isReviewer', $roleId == ROLE_ID_REVIEWER);
$templateMgr->assign('searchField', $searchType);
$templateMgr->assign('searchMatch', $searchMatch);
$templateMgr->assign('search', $search);
$templateMgr->assign('searchInitial', Request::getUserVar('searchInitial'));
if ($roleId == ROLE_ID_REVIEWER) {
$reviewAssignmentDao =& DAORegistry::getDAO('ReviewAssignmentDAO');
$templateMgr->assign('rateReviewerOnQuality', $journal->getSetting('rateReviewerOnQuality'));
$templateMgr->assign('qualityRatings', $journal->getSetting('rateReviewerOnQuality') ? $reviewAssignmentDao->getAverageQualityRatings($journalId) : null);
}
$templateMgr->assign('fieldOptions', array(USER_FIELD_FIRSTNAME => 'user.firstName', USER_FIELD_LASTNAME => 'user.lastName', USER_FIELD_USERNAME => 'user.username', USER_FIELD_EMAIL => 'user.email', USER_FIELD_INTERESTS => 'user.interests'));
$templateMgr->assign('alphaList', explode(' ', Locale::translate('common.alphaList')));
$templateMgr->assign('oldUserId', $oldUserId);
$templateMgr->assign('rolePath', $roleDao->getRolePath($roleId));
$templateMgr->assign('roleSymbolic', $roleSymbolic);
$templateMgr->display('manager/people/selectMergeUser.tpl');
}
/**
* @see Validator::isValid()
* @param $value mixed
* @return boolean
*/
function isValid($value)
{
return (bool) String::regexp_match_get($this->_regExp, $value, $this->_matches);
}
/**
* Allow the Site Administrator to merge user accounts, including attributed monographs etc.
*/
function mergeUsers($args)
{
$this->validate();
$this->setupTemplate(true);
$userGroupDao =& DAORegistry::getDAO('UserGroupDAO');
$userDao =& DAORegistry::getDAO('UserDAO');
$signoffDao =& DAORegistry::getDAO('SignoffDAO');
$templateMgr =& TemplateManager::getManager();
$oldUserId = Request::getUserVar('oldUserId');
$newUserId = Request::getUserVar('newUserId');
if (!empty($oldUserId) && !empty($newUserId)) {
// Both user IDs have been selected. Merge the accounts.
$monographDao =& DAORegistry::getDAO('MonographDAO');
foreach ($monographDao->getMonographsByUserId($oldUserId) as $monograph) {
$monograph->setUserId($newUserId);
$monographDao->updateMonograph($monograph);
unset($monograph);
}
$commentDao =& DAORegistry::getDAO('CommentDAO');
foreach ($commentDao->getCommentsByUserId($oldUserId) as $comment) {
$comment->setUserId($newUserId);
$commentDao->updateComment($comment);
unset($comment);
}
$monographNoteDao =& DAORegistry::getDAO('MonographNoteDAO');
$monographNotes =& $monographNoteDao->getMonographNotesByUserId($oldUserId);
while ($monographNote =& $monographNotes->next()) {
$monographNote->setUserId($newUserId);
$monographNoteDao->updateMonographNote($monographNote);
unset($monographNote);
}
$stageSignoffs =& $signoffDao->getByUserId($oldUserId);
while ($stageSignoff =& $stageSignoffs->next()) {
$stageSignoff->setUserId($newUserId);
$signoffDao->updateObject($stageSignoff);
unset($stageSignoff);
}
$editorSubmissionDao =& DAORegistry::getDAO('EditorSubmissionDAO');
$editorSubmissionDao->transferEditorDecisions($oldUserId, $newUserId);
$reviewAssignmentDao =& DAORegistry::getDAO('ReviewAssignmentDAO');
foreach ($reviewAssignmentDao->getByUserId($oldUserId) as $reviewAssignment) {
$reviewAssignment->setReviewerId($newUserId);
$reviewAssignmentDao->updateObject($reviewAssignment);
unset($reviewAssignment);
}
$layoutEditorSubmissionDao =& DAORegistry::getDAO('LayoutEditorSubmissionDAO');
$layoutEditorSubmissions =& $layoutEditorSubmissionDao->getSubmissions($oldUserId);
while ($layoutEditorSubmission =& $layoutEditorSubmissions->next()) {
$layoutAssignment =& $layoutEditorSubmission->getLayoutAssignment();
$layoutAssignment->setEditorId($newUserId);
$layoutEditorSubmissionDao->updateSubmission($layoutEditorSubmission);
unset($layoutAssignment);
unset($layoutEditorSubmission);
}
$monographEmailLogDao =& DAORegistry::getDAO('MonographEmailLogDAO');
$monographEmailLogDao->changeUser($oldUserId, $newUserId);
$monographEventLogDao =& DAORegistry::getDAO('MonographEventLogDAO');
$monographEventLogDao->changeUser($oldUserId, $newUserId);
$monographCommentDao =& DAORegistry::getDAO('MonographCommentDAO');
foreach ($monographCommentDao->getMonographCommentsByUserId($oldUserId) as $monographComment) {
$monographComment->setAuthorId($newUserId);
$monographCommentDao->updateMonographComment($monographComment);
unset($monographComment);
}
$accessKeyDao =& DAORegistry::getDAO('AccessKeyDAO');
$accessKeyDao->transferAccessKeys($oldUserId, $newUserId);
// Delete the old user and associated info.
$sessionDao =& DAORegistry::getDAO('SessionDAO');
$sessionDao->deleteSessionsByUserId($oldUserId);
$temporaryFileDao =& DAORegistry::getDAO('TemporaryFileDAO');
$temporaryFileDao->deleteTemporaryFilesByUserId($oldUserId);
$notificationStatusDao =& DAORegistry::getDAO('NotificationStatusDAO');
$notificationStatusDao->deleteNotificationStatusByUserId($oldUserId);
$userSettingsDao =& DAORegistry::getDAO('UserSettingsDAO');
$userSettingsDao->deleteSettings($oldUserId);
$groupMembershipDao =& DAORegistry::getDAO('GroupMembershipDAO');
$groupMembershipDao->deleteMembershipByUserId($oldUserId);
$seriesEditorsDao =& DAORegistry::getDAO('SeriesEditorsDAO');
$seriesEditorsDao->deleteEditorsByUserId($oldUserId);
// Transfer old user's roles
$userGroups =& $userGroupDao->getByUserId($oldUserId);
while (!$userGroups->eof()) {
$userGroup =& $userGroups->next();
if (!$userGroupDao->userInGroup($userGroup->getContextId(), $newUserId, $userGroup->getId())) {
$userGroupDao->assignUserToGroup($newUserId, $userGroup->getId());
}
unset($userGroup);
}
$userGroupDao->deleteAssignmentsByUserId($oldUserId);
$userDao->deleteUserById($oldUserId);
Request::redirect(null, 'admin', 'mergeUsers');
}
if (!empty($oldUserId)) {
// Get the old username for the confirm prompt.
$oldUser =& $userDao->getUser($oldUserId);
$templateMgr->assign('oldUsername', $oldUser->getUsername());
unset($oldUser);
}
// The administrator must select one or both IDs.
if (Request::getUserVar('roleSymbolic') != null) {
$roleSymbolic = Request::getUserVar('roleSymbolic');
} else {
$roleSymbolic = isset($args[0]) ? $args[0] : 'all';
}
if ($roleSymbolic != 'all' && String::regexp_match_get('/^(\\w+)s$/', $roleSymbolic, $matches)) {
$roleId = $roleDao->getRoleIdFromPath($matches[1]);
if ($roleId == null) {
Request::redirect(null, null, null, 'all');
}
$roleName = $roleDao->getRoleName($roleId, true);
} else {
$roleId = 0;
$roleName = 'admin.mergeUsers.allUsers';
}
$searchType = null;
$searchMatch = null;
$search = Request::getUserVar('search');
$searchInitial = Request::getUserVar('searchInitial');
if (!empty($search)) {
$searchType = Request::getUserVar('searchField');
$searchMatch = Request::getUserVar('searchMatch');
} else {
if (!empty($searchInitial)) {
$searchInitial = String::strtoupper($searchInitial);
$searchType = USER_FIELD_INITIAL;
$search = $searchInitial;
}
}
$rangeInfo = Handler::getRangeInfo('users');
if ($roleId) {
$users =& $roleDao->getUsersByRoleId($roleId, null, $searchType, $search, $searchMatch, $rangeInfo);
$templateMgr->assign('roleId', $roleId);
} else {
$users =& $userDao->getUsersByField($searchType, $searchMatch, $search, true, $rangeInfo);
}
$templateMgr->assign('currentUrl', Request::url(null, null, 'mergeUsers'));
$templateMgr->assign('helpTopicId', 'site.administrativeFunctions');
$templateMgr->assign('roleName', $roleName);
$templateMgr->assign_by_ref('users', $users);
$templateMgr->assign_by_ref('thisUser', Request::getUser());
$templateMgr->assign('isReviewer', $roleId == ROLE_ID_REVIEWER);
$templateMgr->assign('searchField', $searchType);
$templateMgr->assign('searchMatch', $searchMatch);
$templateMgr->assign('search', $search);
$templateMgr->assign('searchInitial', Request::getUserVar('searchInitial'));
$templateMgr->assign('fieldOptions', array(USER_FIELD_FIRSTNAME => 'user.firstName', USER_FIELD_LASTNAME => 'user.lastName', USER_FIELD_USERNAME => 'user.username', USER_FIELD_EMAIL => 'user.email', USER_FIELD_INTERESTS => 'user.interests'));
$templateMgr->assign('alphaList', explode(' ', Locale::translate('common.alphaList')));
$templateMgr->assign('oldUserId', $oldUserId);
$templateMgr->assign('rolePath', $roleDao->getRolePath($roleId));
$templateMgr->assign('roleSymbolic', $roleSymbolic);
$templateMgr->display('admin/selectMergeUser.tpl');
}
/**
* @see OAIMetadataFormat#toXml
* TODO:
* <copyright-holder>
* In Isabelle's mapping document:
* Article order in the issue's Table of Contents
*/
function toXml(&$record, $format = null)
{
$article =& $record->getData('article');
$journal =& $record->getData('journal');
$section =& $record->getData('section');
$issue =& $record->getData('issue');
$galleys =& $record->getData('galleys');
$articleId = $article->getId();
// Cache issue ordering information.
static $issueId;
static $sectionSeq;
if (!isset($issueId) || $issueId != $issue->getId()) {
$sectionDao =& DAORegistry::getDAO('SectionDAO');
$issueId = $issue->getId();
$sections =& $sectionDao->getSectionsForIssue($issueId);
$sectionSeq = array();
$i = 0;
foreach ($sections as $thisSection) {
$sectionSeq[$thisSection->getSectionId()] = $i++;
}
unset($sections);
}
$abbreviation = $journal->getLocalizedSetting('abbreviation');
$printIssn = $journal->getSetting('printIssn');
$onlineIssn = $journal->getSetting('onlineIssn');
$primaryLocale = $journal->getPrimaryLocale();
$publisherInstitution = $journal->getSetting('publisherInstitution');
$datePublished = strtotime($article->getDatePublished());
$response = "<article\n" . "\txmlns=\"http://dtd.nlm.nih.gov/publishing/2.3\"\n" . "\txmlns:xlink=\"http://www.w3.org/1999/xlink\"\n" . "\txmlns:mml=\"http://www.w3.org/1998/Math/MathML\"\n" . "\txmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"\n" . "\txsi:schemaLocation=\"http://dtd.nlm.nih.gov/publishing/2.3\n" . "\thttp://dtd.nlm.nih.gov/publishing/2.3/xsd/journalpublishing.xsd\"\n" . (($s = $section->getSectionIdentifyType()) != '' ? "\tarticle-type=\"" . htmlspecialchars(Core::cleanVar($s)) . "\"" : '') . "\txml:lang=\"" . strtoupper(substr($primaryLocale, 0, 2)) . "\">\n" . "\t<front>\n" . "\t\t<journal-meta>\n" . "\t\t\t<journal-id journal-id-type=\"other\">" . htmlspecialchars(Core::cleanVar(($s = Config::getVar('oai', 'nlm_journal_id')) != '' ? $s : $journal->getPath())) . "</journal-id>\n" . "\t\t\t<journal-title>" . htmlspecialchars(Core::cleanVar($journal->getJournalTitle())) . "</journal-title>\n";
// Include translated journal titles
foreach ($journal->getTitle(null) as $locale => $title) {
if ($locale == $primaryLocale) {
continue;
}
$response .= "\t\t\t<trans-title xml:lang=\"" . strtoupper(substr($locale, 0, 2)) . "\">" . htmlspecialchars(Core::cleanVar($title)) . "</trans-title>\n";
}
$response .= (!empty($onlineIssn) ? "\t\t\t<issn pub-type=\"epub\">" . htmlspecialchars(Core::cleanVar($onlineIssn)) . "</issn>" : '') . (!empty($printIssn) ? "\t\t\t<issn pub-type=\"ppub\">" . htmlspecialchars(Core::cleanVar($printIssn)) . "</issn>" : '') . ($publisherInstitution != '' ? "\t\t\t<publisher><publisher-name>" . htmlspecialchars(Core::cleanVar($publisherInstitution)) . "</publisher-name></publisher>\n" : '') . "\t\t</journal-meta>\n" . "\t\t<article-meta>\n" . "\t\t\t<article-id pub-id-type=\"other\">" . htmlspecialchars(Core::cleanVar($article->getBestArticleId())) . "</article-id>\n" . (($s = $article->getDOI()) != '' ? "\t\t\t<article-id pub-id-type=\"doi\">" . htmlspecialchars(Core::cleanVar($s)) . "</article-id>\n" : '') . "\t\t\t<article-categories><subj-group subj-group-type=\"heading\"><subject>" . htmlspecialchars(Core::cleanVar($section->getSectionTitle())) . "</subject></subj-group></article-categories>\n" . "\t\t\t<title-group>\n" . "\t\t\t\t<article-title>" . htmlspecialchars(Core::cleanVar(strip_tags($article->getArticleTitle()))) . "</article-title>\n";
// Include translated journal titles
foreach ($article->getTitle(null) as $locale => $title) {
if ($locale == $primaryLocale) {
continue;
}
$response .= "\t\t\t\t<trans-title xml:lang=\"" . strtoupper(substr($locale, 0, 2)) . "\">" . htmlspecialchars(Core::cleanVar(strip_tags($title))) . "</trans-title>\n";
}
$response .= "\t\t\t</title-group>\n" . "\t\t\t<contrib-group>\n";
// Include authors
foreach ($article->getAuthors() as $author) {
$response .= "\t\t\t\t<contrib " . ($author->getPrimaryContact() ? 'corresp="yes" ' : '') . "contrib-type=\"author\">\n" . "\t\t\t\t\t<name name-style=\"western\">\n" . "\t\t\t\t\t\t<surname>" . htmlspecialchars(Core::cleanVar($author->getLastName())) . "</surname>\n" . "\t\t\t\t\t\t<given-names>" . htmlspecialchars(Core::cleanVar($author->getFirstName()) . (($s = $author->getMiddleName()) != '' ? " {$s}" : '')) . "</given-names>\n" . "\t\t\t\t\t</name>\n" . (($s = $author->getAffiliation()) != '' ? "\t\t\t\t\t<aff>" . htmlspecialchars(Core::cleanVar($s)) . "</aff>\n" : '') . "\t\t\t\t\t<email>" . htmlspecialchars(Core::cleanVar($author->getEmail())) . "</email>\n" . (($s = $author->getUrl()) != '' ? "\t\t\t\t\t<uri>" . htmlspecialchars(Core::cleanVar($s)) . "</uri>\n" : '') . "\t\t\t\t</contrib>\n";
}
// Include editorships (optimized)
$response .= $this->getEditorialInfo($journal->getId());
$response .= "\t\t\t</contrib-group>\n" . "\t\t\t<pub-date pub-type=\"epub\">\n" . "\t\t\t\t<day>" . strftime('%d', $datePublished) . "</day>\n" . "\t\t\t\t<month>" . strftime('%m', $datePublished) . "</month>\n" . "\t\t\t\t<year>" . strftime('%Y', $datePublished) . "</year>\n" . "\t\t\t</pub-date>\n" . ($issue->getShowYear() ? "\t\t\t<pub-date pub-type=\"collection\"><year>" . htmlspecialchars(Core::cleanVar($issue->getYear())) . "</year></pub-date>\n" : '') . ($issue->getShowVolume() ? "\t\t\t<volume>" . htmlspecialchars(Core::cleanVar($issue->getVolume())) . "</volume>\n" : '') . ($issue->getShowNumber() ? "\t\t\t<issue seq=\"" . htmlspecialchars(Core::cleanVar($sectionSeq[$section->getId()] * 100 + $article->getSeq())) . "\">" . htmlspecialchars(Core::cleanVar($issue->getNumber())) . "</issue>\n" : '') . "\t\t\t<issue-id pub-id-type=\"other\">" . htmlspecialchars(Core::cleanVar($issue->getBestIssueId())) . "</issue-id>\n" . ($issue->getShowTitle() ? "\t\t\t<issue-title>" . htmlspecialchars(Core::cleanVar($issue->getIssueTitle())) . "</issue-title>\n" : '');
// Include page info, if available and parseable.
$matches = null;
if (String::regexp_match_get('/^[Pp][Pp]?[.]?[ ]?(\\d+)$/', $article->getPages(), $matches)) {
$matchedPage = htmlspecialchars(Core::cleanVar($matches[1]));
$response .= "\t\t\t\t<fpage>{$matchedPage}</fpage><lpage>{$matchedPage}</lpage>\n";
$pageCount = 1;
} elseif (String::regexp_match_get('/^[Pp][Pp]?[.]?[ ]?(\\d+)[ ]?-[ ]?([Pp][Pp]?[.]?[ ]?)?(\\d+)$/', $article->getPages(), $matches)) {
$matchedPageFrom = htmlspecialchars(Core::cleanVar($matches[1]));
$matchedPageTo = htmlspecialchars(Core::cleanVar($matches[3]));
$response .= "\t\t\t\t<fpage>{$matchedPageFrom}</fpage>\n" . "\t\t\t\t<lpage>{$matchedPageTo}</lpage>\n";
$pageCount = $matchedPageTo - $matchedPageFrom + 1;
}
$response .= "\t\t\t<permissions>\n" . (($s = $journal->getLocalizedSetting('copyrightNotice')) != '' ? "\t\t\t\t<copyright-statement>" . htmlspecialchars(Core::cleanVar($s)) . "</copyright-statement>\n" : '') . "\t\t\t\t<copyright-year>" . strftime('%Y', $datePublished) . "</copyright-year>\n" . "\t\t\t</permissions>\n" . "\t\t\t<self-uri xlink:href=\"" . htmlspecialchars(Core::cleanVar(Request::url($journal->getPath(), 'article', 'view', $article->getBestArticleId()))) . "\" />\n";
// Include galley links
foreach ($article->getGalleys() as $galley) {
$response .= "\t\t\t<self-uri content-type=\"" . htmlspecialchars(Core::cleanVar($galley->getFileType())) . "\" xlink:href=\"" . htmlspecialchars(Core::cleanVar(Request::url($journal->getPath(), 'article', 'view', array($article->getBestArticleId(), $galley->getId())))) . "\" />\n";
}
// Include abstract(s)
$abstract = htmlspecialchars(Core::cleanVar(strip_tags($article->getArticleAbstract())));
if (!empty($abstract)) {
$abstract = "<p>{$abstract}</p>";
// $abstract = '<p>' . String::regexp_replace('/\n+/', '</p><p>', $abstract) . '</p>';
$response .= "\t\t\t<abstract xml:lang=\"" . strtoupper(substr($primaryLocale, 0, 2)) . "\">{$abstract}</abstract>\n";
}
if (is_array($article->getAbstract(null))) {
foreach ($article->getAbstract(null) as $locale => $abstract) {
if ($locale == $primaryLocale || empty($abstract)) {
continue;
}
$abstract = htmlspecialchars(Core::cleanVar(strip_tags($abstract)));
if (empty($abstract)) {
continue;
}
$abstract = "<p>{$abstract}</p>";
//$abstract = '<p>' . String::regexp_replace('/\n+/', '</p><p>', $abstract) . '</p>';
$response .= "\t\t\t<abstract-trans xml:lang=\"" . strtoupper(substr($locale, 0, 2)) . "\">{$abstract}</abstract-trans>\n";
}
}
$subjects = array();
if (is_array($article->getSubject(null))) {
foreach ($article->getSubject(null) as $locale => $subject) {
$s = array_map('trim', explode(';', Core::cleanVar($subject)));
if (!empty($s)) {
$subjects[$locale] = $s;
}
}
}
if (!empty($subjects)) {
foreach ($subjects as $locale => $s) {
$response .= "\t\t\t<kwd-group xml:lang=\"" . strtoupper(substr($locale, 0, 2)) . "\">\n";
foreach ($s as $subject) {
$response .= "\t\t\t\t<kwd>" . htmlspecialchars($subject) . "</kwd>\n";
}
$response .= "\t\t\t</kwd-group>\n";
}
}
$response .= (isset($pageCount) ? "\t\t\t<counts><page-count count=\"" . (int) $pageCount . "\" /></counts>\n" : '') . "\t\t</article-meta>\n" . "\t</front>\n";
// Include body text (for search indexing only)
import('search.ArticleSearchIndex');
$text = '';
$galleys = $article->getGalleys();
// Give precedence to HTML galleys, as they're quickest to parse
usort($galleys, create_function('$a, $b', 'return $a->isHtmlGalley()?-1:1;'));
// Determine any access limitations. If there are, do not
// provide the full-text.
import('issue.IssueAction');
$subscriptionRequired = IssueAction::subscriptionRequired($issue);
$isSubscribedDomain = IssueAction::subscribedDomain($journal, $issue->getId(), $article->getId());
if (!$subscriptionRequired || $isSubscribedDomain) {
foreach ($galleys as $galley) {
$parser =& SearchFileParser::fromFile($galley);
if ($parser && $parser->open()) {
while (($s = $parser->read()) !== false) {
$text .= $s;
}
$parser->close();
}
if ($galley->isHtmlGalley()) {
$text = strip_tags($text);
}
unset($galley);
// Use the first parseable galley.
if (!empty($text)) {
break;
}
}
}
if (!empty($text)) {
$response .= "\t<body><p>" . htmlspecialchars(Core::cleanVar(Core::cleanVar($text))) . "</p></body>\n";
}
$response .= "</article>";
return $response;
}
/**
* Allow the Site Administrator to merge user accounts.
*/
function mergeUsers($args)
{
$this->validate();
$this->setupTemplate(true);
$roleDao =& DAORegistry::getDAO('RoleDAO');
$userDao =& DAORegistry::getDAO('UserDAO');
$templateMgr =& TemplateManager::getManager();
$oldUserIds = (array) Request::getUserVar('oldUserIds');
$newUserId = Request::getUserVar('newUserId');
if (!empty($oldUserIds) && !empty($newUserId)) {
import('user.UserAction');
foreach ($oldUserIds as $oldUserId) {
UserAction::mergeUsers($oldUserId, $newUserId);
}
Request::redirect(null, null, 'admin', 'mergeUsers');
}
// The administrator must select one or both IDs.
if (Request::getUserVar('roleSymbolic') != null) {
$roleSymbolic = Request::getUserVar('roleSymbolic');
} else {
$roleSymbolic = isset($args[0]) ? $args[0] : 'all';
}
if ($roleSymbolic != 'all' && String::regexp_match_get('/^(\\w+)s$/', $roleSymbolic, $matches)) {
$roleId = $roleDao->getRoleIdFromPath($matches[1]);
if ($roleId == null) {
Request::redirect(null, null, null, null, 'all');
}
$roleName = $roleDao->getRoleName($roleId, true);
} else {
$roleId = 0;
$roleName = 'admin.mergeUsers.allUsers';
}
$searchType = null;
$searchMatch = null;
$search = Request::getUserVar('search');
$searchInitial = Request::getUserVar('searchInitial');
if (!empty($search)) {
$searchType = Request::getUserVar('searchField');
$searchMatch = Request::getUserVar('searchMatch');
} elseif (!empty($searchInitial)) {
$searchInitial = String::strtoupper($searchInitial);
$searchType = USER_FIELD_INITIAL;
$search = $searchInitial;
}
$rangeInfo =& Handler::getRangeInfo('users', array($roleId, (string) $search, (string) $searchMatch, (string) $searchType));
if ($roleId) {
while (true) {
$users =& $roleDao->getUsersByRoleId($roleId, null, null, $searchType, $search, $searchMatch, $rangeInfo);
if ($users->isInBounds()) {
break;
}
unset($rangeInfo);
$rangeInfo =& $users->getLastPageRangeInfo();
unset($users);
}
$templateMgr->assign('roleId', $roleId);
} else {
while (true) {
$users =& $userDao->getUsersByField($searchType, $searchMatch, $search, true, $rangeInfo);
if ($users->isInBounds()) {
break;
}
unset($rangeInfo);
$rangeInfo =& $users->getLastPageRangeInfo();
unset($users);
}
}
$templateMgr->assign('currentUrl', Request::url(null, null, 'admin', 'mergeUsers'));
$templateMgr->assign('helpTopicId', 'site.administrativeFunctions');
$templateMgr->assign('roleName', $roleName);
$templateMgr->assign_by_ref('users', $users);
$templateMgr->assign_by_ref('thisUser', Request::getUser());
$templateMgr->assign('isReviewer', $roleId == ROLE_ID_REVIEWER);
$templateMgr->assign('searchField', $searchType);
$templateMgr->assign('searchMatch', $searchMatch);
$templateMgr->assign('search', $search);
$templateMgr->assign('searchInitial', Request::getUserVar('searchInitial'));
if ($roleId == ROLE_ID_REVIEWER) {
$reviewAssignmentDao =& DAORegistry::getDAO('ReviewAssignmentDAO');
$templateMgr->assign('rateReviewerOnQuality', $conference->getSetting('rateReviewerOnQuality'));
$templateMgr->assign('qualityRatings', $conference->getSetting('rateReviewerOnQuality') ? $reviewAssignmentDao->getAverageQualityRatings($conference->getId()) : null);
}
$templateMgr->assign('fieldOptions', array(USER_FIELD_FIRSTNAME => 'user.firstName', USER_FIELD_LASTNAME => 'user.lastName', USER_FIELD_USERNAME => 'user.username', USER_FIELD_EMAIL => 'user.email', USER_FIELD_INTERESTS => 'user.interests'));
$templateMgr->assign('alphaList', explode(' ', Locale::translate('common.alphaList')));
$templateMgr->assign('oldUserIds', $oldUserIds);
$templateMgr->assign('rolePath', $roleDao->getRolePath($roleId));
$templateMgr->assign('roleSymbolic', $roleSymbolic);
$templateMgr->display('admin/selectMergeUser.tpl');
}
/**
* Authenticate against the AnthroNET portal.
* @return String the auth token if successful
*/
function _doAuthenticate()
{
// Build the multipart SOAP message from scratch.
$journal =& Request::getJournal();
$ofrPlugin =& $this->_getObjectsForReviewPlugin();
$soapMessage = '<soapenv:Envelope xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/" xmlns:ns="http://www.avectra.com/2005/">
<soapenv:Header />
<soapenv:Body>
<ns:Authenticate>
<ns:userName>' . $ofrPlugin->getSetting($journal->getId(), 'anthroNetUsername') . '</ns:userName>
<ns:password><![CDATA[' . $ofrPlugin->getSetting($journal->getId(), 'anthroNetPassword') . ']]></ns:password>
</ns:Authenticate>
</soapenv:Body>
</soapenv:Envelope>';
// Prepare HTTP session.
$curlCh = curl_init();
curl_setopt($curlCh, CURLOPT_RETURNTRANSFER, true);
curl_setopt($curlCh, CURLOPT_POST, true);
// Set up SSL.
curl_setopt($curlCh, CURLOPT_SSL_VERIFYPEER, false);
curl_setopt($curlCh, CURLOPT_HTTP_VERSION, CURL_HTTP_VERSION_1_1);
// Make SOAP request.
curl_setopt($curlCh, CURLOPT_URL, $ofrPlugin->getSetting($journal->getId(), 'anthroNetSoapURL'));
$extraHeaders = array('Host: avectra.aaanet.org', 'SOAPAction: "http://www.avectra.com/2005/Authenticate"', 'Content-Type: text/xml;charset=UTF-8');
curl_setopt($curlCh, CURLOPT_HTTPHEADER, $extraHeaders);
curl_setopt($curlCh, CURLOPT_POSTFIELDS, $soapMessage);
$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) {
$result = 'OJS-OFR: Expected string response.';
}
if ($result === true && ($status = curl_getinfo($curlCh, CURLINFO_HTTP_CODE)) != OFR_WS_RESPONSE_OK) {
$result = 'OJS-OFR: Expected ' . OFR_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();
String::regexp_match_get('#<Token>([^<]*)</Token>#', $response, $matches);
if (!empty($matches)) {
$result = $matches[1];
} else {
$result = 'OFR: ' . $status . ' - ' . $matches[1];
}
} else {
$result = 'OJS-OFR: Expected string response.';
}
return $result;
}
/**
* Processes form-submitted addresses for inclusion in
* the recipient list
* @param $currentList array Current recipient/cc/bcc list
* @param $newAddresses array "Raw" form parameter for additional addresses
*/
function &processAddresses($currentList, &$newAddresses)
{
foreach ($newAddresses as $newAddress) {
$regs = array();
// Match the form "My Name <*****@*****.**>"
if (String::regexp_match_get('/^([^<>' . "\n" . ']*[^<> ' . "\n" . '])[ ]*<(?P<email>' . PCRE_EMAIL_ADDRESS . ')>$/i', $newAddress, $regs)) {
$currentList[] = array('name' => $regs[1], 'email' => $regs['email']);
} elseif (String::regexp_match_get('/^<?(?P<email>' . PCRE_EMAIL_ADDRESS . ')>?$/i', $newAddress, $regs)) {
$currentList[] = array('name' => '', 'email' => $regs['email']);
} elseif ($newAddress != '') {
$this->errorMessages[] = array('type' => MAIL_ERROR_INVALID_EMAIL, 'address' => $newAddress);
}
}
return $currentList;
}
/**
* Handle fetch requests for this plugin.
*/
function fetch($args, $request)
{
if (!$this->getEnabled()) {
return false;
}
$scheme = array_shift($args);
switch ($scheme) {
case 'doi':
$doi = implode('/', $args);
$journal =& $request->getJournal();
$publishedArticleDao =& DAORegistry::getDAO('PublishedArticleDAO');
$articles =& $publishedArticleDao->getPublishedArticlesByDOI($doi, $journal ? $journal->getId() : null);
while ($article =& $articles->next()) {
$request->redirect(null, 'article', 'view', $article->getBestArticleId());
}
break;
case 'vnp':
// Volume, number, page
// Volume, number, page
case 'ynp':
// Volume, number, year, page
// This can only be used from within a journal context
$journal =& Request::getJournal();
if (!$journal) {
break;
}
if ($scheme == 'vnp') {
$volume = (int) array_shift($args);
$year = null;
} elseif ($scheme == 'ynp') {
$year = (int) array_shift($args);
$volume = null;
}
$number = array_shift($args);
$page = (int) array_shift($args);
$issueDao =& DAORegistry::getDAO('IssueDAO');
$issues =& $issueDao->getPublishedIssuesByNumber($journal->getId(), $volume, $number, $year);
// Ensure only one issue matched, and fetch it.
$issue =& $issues->next();
if (!$issue || $issues->next()) {
break;
}
unset($issues);
$publishedArticleDao =& DAORegistry::getDAO('PublishedArticleDAO');
$articles =& $publishedArticleDao->getPublishedArticles($issue->getId());
foreach ($articles as $article) {
// Look for the correct page in the list of articles.
$matches = null;
if (String::regexp_match_get('/^[Pp][Pp]?[.]?[ ]?(\\d+)$/', $article->getPages(), $matches)) {
$matchedPage = $matches[1];
if ($page == $matchedPage) {
Request::redirect(null, 'article', 'view', $article->getBestArticleId());
}
}
if (String::regexp_match_get('/^[Pp][Pp]?[.]?[ ]?(\\d+)[ ]?-[ ]?([Pp][Pp]?[.]?[ ]?)?(\\d+)$/', $article->getPages(), $matches)) {
$matchedPageFrom = $matches[1];
$matchedPageTo = $matches[3];
if ($page >= $matchedPageFrom && ($page < $matchedPageTo || $page == $matchedPageTo && ($matchedPageFrom = $matchedPageTo))) {
Request::redirect(null, 'article', 'view', $article->getBestArticleId());
}
}
unset($article);
}
}
// Failure.
header("HTTP/1.0 500 Internal Server Error");
$templateMgr =& TemplateManager::getManager();
Locale::requireComponents(array(LOCALE_COMPONENT_APPLICATION_COMMON));
$templateMgr->assign('message', 'plugins.gateways.resolver.errors.errorMessage');
$templateMgr->display('common/message.tpl');
exit;
}
/**
* 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);
}
/**
* Given a locale string, get the list of parameter references of the
* form {$myParameterName}.
* @param $source string
* @return array
*/
function getParameterNames($source)
{
$matches = null;
String::regexp_match_get('/({\\$[^}]+})/', $source, $matches);
array_shift($matches);
// Knock the top element off the array
return $matches;
}
/**
* 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_SSLVERSION, 3);
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();
String::regexp_match_get('#<faultstring>([^<]*)</faultstring>#', $response, $matches);
if (empty($matches)) {
if ($attachment) {
assert(String::regexp_match('#<returnCode>success</returnCode>#', $response));
} else {
$parts = explode("\r\n\r\n", $response);
$result = array_pop($parts);
$result = String::regexp_replace('/>[^>]*$/', '>', $result);
}
} else {
$result = 'mEDRA: ' . $status . ' - ' . $matches[1];
}
} else {
$result = 'OJS-mEDRA: Expected string response.';
}
return $result;
}
/**
* 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 && String::regexp_match_get('/^(' . $personRegex['title'] . ')/i', $personString, $results)) {
$suffixString = trim($results[1], ',:; ');
$personString = String::regexp_replace('/^(' . $personRegex['title'] . ')/i', '', $personString);
}
if ($degrees && String::regexp_match_get('/(' . $personRegex['degrees'] . ')$/i', $personString, $results)) {
$degreesArray = explode(',', trim($results[1], ','));
foreach ($degreesArray as $key => $degree) {
$degreesArray[$key] = String::trimPunctuation($degree);
}
$suffixString .= ' - ' . implode('; ', $degreesArray);
$personString = String::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 = String::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 = String::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; $initialNum < String::strlen($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;
}
/**
* @see Filter::process()
* @param $citationString string
* @return MetadataDescription
*/
function &process($citationString)
{
// Initialize the parser result array
$matches = array();
$metadata = array();
// Parse out any embedded URLs
$urlPattern = '(<?(https?://([-\\w\\.]+)+(:\\d+)?(/([\\w/_\\.,]*(\\?[^\\s>]+)?)?)?)>?)';
if (String::regexp_match_get($urlPattern, $citationString, $matches)) {
// Assume that the URL is a link to the resource.
$metadata['uri'] = $matches[1];
// Remove the URL from the citation string
$citationString = String::regexp_replace($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 $pmIdExpression) {
if (String::regexp_match_get($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
$pmidPattern = '/pmid:?\\s*(\\d+)/i';
if (String::regexp_match_get($pmidPattern, $citationString, $matches)) {
$metadata['pub-id[@pub-id-type="pmid"]'] = $matches[1];
$citationString = String::regexp_replace($pmidPattern, '', $citationString);
}
// Parse out an embedded DOI and remove it from the citation string
$doiPattern = '/doi:?\\s*(\\S+)/i';
if (String::regexp_match_get($doiPattern, $citationString, $matches)) {
$metadata['pub-id[@pub-id-type="doi"]'] = $matches[1];
$citationString = String::regexp_replace($doiPattern, '', $citationString);
}
// Parse out the access date if we have one and remove it from the citation string
$accessDatePattern = '/accessed:?\\s*([\\s\\w]+)/i';
if (String::regexp_match_get($accessDatePattern, $citationString, $matches)) {
$metadata['access-date'] = $matches[1];
$citationString = String::regexp_replace($accessDatePattern, '', $citationString);
}
// Clean out square brackets
$citationString = String::regexp_replace('/\\[(\\s*(pubmed|medline|full text)\\s*)*]/i', '', $citationString);
// Book citation
$unparsedTail = '';
if (String::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 (String::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'];
$titleSource = array();
if (String::regexp_match_get("/(.*[\\.!\\?])(.*)/", trim($matches['titleSource'], " ."), $titleSource)) {
$metadata['article-title'] = $titleSource[1];
$metadata['source'] = $titleSource[2];
}
$metadata['date'] = $matches['date'];
$volumeAndIssue = array();
if (String::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 (String::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) && String::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.
$comment = String::trimPunctuation(String::regexp_replace($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);
}
/**
* Decompress uploaded plugin and install in the correct plugin directory.
* @param $function string type of operation to perform after upload ('upgrade' or 'install')
* @param $category string the category of the uploaded plugin (upgrade only)
* @param $plugin string the name of the uploaded plugin (upgrade only)
*/
function uploadPlugin($function, $category = null, $plugin = null)
{
$this->validate();
$templateMgr =& TemplateManager::getManager();
$this->setupTemplate(true);
$templateMgr->assign('error', false);
$templateMgr->assign('uploaded', false);
$templateMgr->assign('path', $function);
$errorMsg = '';
if (Request::getUserVar('uploadPlugin')) {
import('classes.file.TemporaryFileManager');
$temporaryFileManager = new TemporaryFileManager();
$user =& Request::getUser();
} else {
$errorMsg = 'manager.plugins.fileSelectError';
}
if (empty($errorMsg)) {
if ($temporaryFile = $temporaryFileManager->handleUpload('newPlugin', $user->getId())) {
// tar archive basename (less potential version number) must equal plugin directory name
// and plugin files must be in a directory named after the plug-in.
$matches = array();
String::regexp_match_get('/^[a-zA-Z0-9]+/', basename($temporaryFile->getOriginalFileName(), '.tar.gz'), $matches);
$pluginName = array_pop($matches);
// Create random dirname to avoid symlink attacks.
$pluginDir = dirname($temporaryFile->getFilePath()) . DIRECTORY_SEPARATOR . $pluginName . substr(md5(mt_rand()), 0, 10);
mkdir($pluginDir);
} else {
$errorMsg = 'manager.plugins.uploadError';
}
}
if (empty($errorMsg)) {
// Test whether the tar binary is available for the export to work
$tarBinary = Config::getVar('cli', 'tar');
if (!empty($tarBinary) && file_exists($tarBinary)) {
exec($tarBinary . ' -xzf ' . escapeshellarg($temporaryFile->getFilePath()) . ' -C ' . escapeshellarg($pluginDir));
} else {
$errorMsg = 'manager.plugins.tarCommandNotFound';
}
}
if (empty($errorMsg)) {
// We should now find a directory named after the
// plug-in within the extracted archive.
$pluginDir .= DIRECTORY_SEPARATOR . $pluginName;
if (is_dir($pluginDir)) {
if ($function == 'install') {
$this->installPlugin($pluginDir, $templateMgr);
} else {
if ($function == 'upgrade') {
$this->upgradePlugin($pluginDir, $templateMgr, $category, $plugin);
}
}
} else {
$errorMsg = 'manager.plugins.invalidPluginArchive';
}
}
if (!empty($errorMsg)) {
$templateMgr->assign('error', true);
$templateMgr->assign('message', $errorMsg);
}
$templateMgr->display('manager/plugins/managePlugins.tpl');
}
/**
* 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, $citationDescription);
}
/**
* Allow the Conference Manager to merge user accounts, including attributed papers etc.
*/
function mergeUsers($args)
{
$this->validate();
$this->setupTemplate(true);
$roleDao =& DAORegistry::getDAO('RoleDAO');
$userDao =& DAORegistry::getDAO('UserDAO');
$conference =& Request::getConference();
$schedConf =& Request::getSchedConf();
$schedConfId = isset($schedConf) ? $schedConf->getId() : null;
$templateMgr =& TemplateManager::getManager();
$oldUserIds = (array) Request::getUserVar('oldUserIds');
$newUserId = Request::getUserVar('newUserId');
// Ensure that we have administrative priveleges over the specified user(s).
$canAdministerAll = true;
foreach ($oldUserIds as $oldUserId) {
if (!Validation::canAdminister($conference->getId(), $oldUserId)) {
$canAdministerAll = false;
}
}
if (!empty($oldUserIds) && !$canAdministerAll || !empty($newUserId) && !Validation::canAdminister($conference->getId(), $newUserId)) {
$templateMgr->assign('pageTitle', 'manager.people');
$templateMgr->assign('errorMsg', 'manager.people.noAdministrativeRights');
$templateMgr->assign('backLink', Request::url(null, null, null, 'people', 'all'));
$templateMgr->assign('backLinkLabel', 'manager.people.allUsers');
return $templateMgr->display('common/error.tpl');
}
if (!empty($oldUserIds) && !empty($newUserId)) {
import('classes.user.UserAction');
foreach ($oldUserIds as $oldUserId) {
UserAction::mergeUsers($oldUserId, $newUserId);
}
Request::redirect(null, null, 'manager');
}
// The manager must select one or both IDs.
if (Request::getUserVar('roleSymbolic') != null) {
$roleSymbolic = Request::getUserVar('roleSymbolic');
} else {
$roleSymbolic = isset($args[0]) ? $args[0] : 'all';
}
if ($roleSymbolic != 'all' && String::regexp_match_get('/^(\\w+)s$/', $roleSymbolic, $matches)) {
$roleId = $roleDao->getRoleIdFromPath($matches[1]);
if ($roleId == null) {
Request::redirect(null, null, null, null, 'all');
}
$roleName = $roleDao->getRoleName($roleId, true);
} else {
$roleId = 0;
$roleName = 'manager.people.allUsers';
}
$sort = Request::getUserVar('sort');
$sort = isset($sort) ? $sort : 'name';
$sortDirection = Request::getUserVar('sortDirection');
$searchType = null;
$searchMatch = null;
$search = Request::getUserVar('search');
$searchInitial = Request::getUserVar('searchInitial');
if (!empty($search)) {
$searchType = Request::getUserVar('searchField');
$searchMatch = Request::getUserVar('searchMatch');
} elseif (!empty($searchInitial)) {
$searchInitial = String::strtoupper($searchInitial);
$searchType = USER_FIELD_INITIAL;
$search = $searchInitial;
}
$rangeInfo =& Handler::getRangeInfo('users', array($roleId, (string) $search, (string) $searchMatch, (string) $searchType));
if ($roleId) {
while (true) {
$users =& $roleDao->getUsersByRoleId($roleId, $conference->getId(), $schedConfId, $searchType, $search, $searchMatch, $rangeInfo, $sort);
if ($users->isInBounds()) {
break;
}
unset($rangeInfo);
$rangeInfo =& $users->getLastPageRangeInfo();
unset($users);
}
$templateMgr->assign('roleId', $roleId);
} else {
while (true) {
$users =& $roleDao->getUsersByConferenceId($conference->getId(), $searchType, $search, $searchMatch, $rangeInfo, $sort);
if ($users->isInBounds()) {
break;
}
unset($rangeInfo);
$rangeInfo =& $users->getLastPageRangeInfo();
unset($users);
}
}
$templateMgr->assign('currentUrl', Request::url(null, null, null, 'people', 'all'));
$templateMgr->assign('helpTopicId', 'conference.users.mergeUsers');
$templateMgr->assign('roleName', $roleName);
$templateMgr->assign_by_ref('users', $users);
$templateMgr->assign_by_ref('thisUser', Request::getUser());
$templateMgr->assign('isReviewer', $roleId == ROLE_ID_REVIEWER);
$templateMgr->assign('searchField', $searchType);
$templateMgr->assign('searchMatch', $searchMatch);
$templateMgr->assign('search', $search);
$templateMgr->assign('searchInitial', Request::getUserVar('searchInitial'));
if ($roleId == ROLE_ID_REVIEWER) {
$reviewAssignmentDao =& DAORegistry::getDAO('ReviewAssignmentDAO');
$templateMgr->assign('rateReviewerOnQuality', $conference->getSetting('rateReviewerOnQuality'));
$templateMgr->assign('qualityRatings', $conference->getSetting('rateReviewerOnQuality') ? $reviewAssignmentDao->getAverageQualityRatings($conference->getId()) : null);
}
$templateMgr->assign('fieldOptions', array(USER_FIELD_FIRSTNAME => 'user.firstName', USER_FIELD_LASTNAME => 'user.lastName', USER_FIELD_USERNAME => 'user.username', USER_FIELD_EMAIL => 'user.email', USER_FIELD_INTERESTS => 'user.interests'));
$templateMgr->assign('alphaList', explode(' ', Locale::translate('common.alphaList')));
$templateMgr->assign('oldUserIds', $oldUserIds);
$templateMgr->assign('rolePath', $roleDao->getRolePath($roleId));
$templateMgr->assign('roleSymbolic', $roleSymbolic);
$templateMgr->assign('sort', $sort);
$templateMgr->assign('sortDirection', $sortDirection);
$templateMgr->display('manager/people/selectMergeUser.tpl');
}
/**
* Convert a Windows path to a cygwin path.
* @param string $path Windows path
* @return string Cygwin path.
*/
function cygwinConversion($path)
{
$path = str_replace('\\', '/', $path);
$matches = null;
String::regexp_match_get('/^([A-Z]):/i', $path, $matches);
if (isset($matches[1]) && strlen($matches[1]) === 1) {
$path = String::regexp_replace('/^[A-Z]:/i', '/cygdrive/' . strtolower($matches[1]), $path);
}
return $path;
}
