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<?php
/**
* @file classes/install/Upgrade.inc.php
*
* Copyright (c) 2014-2020 Simon Fraser University
* Copyright (c) 2003-2020 John Willinsky
* Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
*
* @class Upgrade
* @ingroup install
*
* @brief Perform system upgrade.
*/
import('lib.pkp.classes.install.Installer');
define('OJS2_ROLE_ID_EDITOR', 0x00000100);
define('OJS2_ROLE_ID_SECTION_EDITOR', 0x00000200);
define('OJS2_ROLE_ID_LAYOUT_EDITOR', 0x00000300);
define('OJS2_ROLE_ID_COPYEDITOR', 0x00002000);
define('OJS2_ROLE_ID_PROOFREADER', 0x00003000);
class Upgrade extends Installer {
/**
* Constructor.
* @param $params array upgrade parameters
*/
function __construct($params, $installFile = 'upgrade.xml', $isPlugin = false) {
parent::__construct($installFile, $params, $isPlugin);
}
/**
* Returns true iff this is an upgrade process.
* @return boolean
*/
function isUpgrade() {
return true;
}
//
// Upgrade actions
//
/**
* Rebuild the search index.
* @return boolean
*/
function rebuildSearchIndex() {
$submissionSearchIndex = Application::getSubmissionSearchIndex();
$submissionSearchIndex->rebuildIndex();
return true;
}
/**
* Clear the CSS cache files (needed when changing LESS files)
* @return boolean
*/
function clearCssCache() {
$request = Application::get()->getRequest();
$templateMgr = TemplateManager::getManager($request);
$templateMgr->clearCssCache();
return true;
}
/**
* For 3.0.0 upgrade: Remove the review round and the review file if editor is not assigned.
* @return boolean
*/
function removeReviewEntries() {
import('lib.pkp.classes.file.SubmissionFileManager');
$submissionDao = DAORegistry::getDAO('SubmissionDAO'); /* @var $submissionDao SubmissionDAO */
// Get review file IDs to be removed (from articles that have no editor assigned)
$reviewFileResult = $submissionDao->retrieve('SELECT article_id, journal_id, review_file_id FROM articles WHERE article_id NOT IN (SELECT article_id FROM edit_assignments)');
while (!$reviewFileResult->EOF) {
$row = $reviewFileResult->GetRowAssoc(false);
$articleId = (int)$row['article_id'];
$journalId = (int)$row['journal_id'];
$fileId = (int)$row['review_file_id'];
// Delete the files in the files_dir:
$submissionFileManager = new SubmissionFileManager($journalId, $articleId);
$basePath = $submissionFileManager->getBasePath();
// Get all file revisions
$fileResult = $submissionDao->retrieve('SELECT file_id, revision, file_name FROM article_files WHERE file_id = ?', array($fileId));
while (!$fileResult->EOF) {
$fileRow = $fileResult->GetRowAssoc(false);
$globPattern = $fileRow['file_name'];
// Search for the file name in the appropriate journal and article folder of the files_dir
$pattern1 = glob($basePath . '*/*/' . $globPattern);
$pattern2 = glob($basePath . '*/' . $globPattern);
if (!is_array($pattern1)) $pattern1 = array();
if (!is_array($pattern2)) $pattern2 = array();
$matchedResults = array_merge($pattern1, $pattern2);
if (count($matchedResults)>1) {
// Too many filenames matched. Continue with the first; this is just a warning.
error_log("WARNING: Duplicate potential files for \"$globPattern\" in \"" . $submissionFileManager->getBasePath() . "\". Taking the first.");
} elseif (count($matchedResults)==0) {
// No filenames matched. Skip migrating.
error_log("WARNING: Unable to find a match for \"$globPattern\" in \"" . $submissionFileManager->getBasePath() . "\". Skipping this file.");
$fileResult->MoveNext();
continue;
}
$discoveredFilename = array_shift($matchedResults);
// If the file exists, delete it
if (file_exists($discoveredFilename)) {
unlink($discoveredFilename);
} else {
error_log("WARNING: File \"$discoveredFilename\" does not exist.");
$fileResult->MoveNext();
continue;
}
$fileResult->MoveNext();
}
$fileResult->Close();
// Delete the file entries in the DB
$submissionDao->update('DELETE FROM article_files WHERE file_id = ?', array($fileId));
// Set review_file_id to NULL
$submissionDao->update('UPDATE articles SET review_file_id=NULL WHERE review_file_id = ?', array($fileId));
// Delete the review round for that article
$submissionDao->update('DELETE FROM review_rounds WHERE submission_id = ?', array($articleId));
$reviewFileResult->MoveNext();
}
$reviewFileResult->Close();
return true;
}
/**
* For 3.0.0 upgrade: Convert string-field semi-colon separated metadata to controlled vocabularies.
* @return boolean
*/
function migrateArticleMetadata() {
$journalDao = DAORegistry::getDAO('JournalDAO'); /* @var $journalDao JournalDAO */
$submissionDao = DAORegistry::getDAO('SubmissionDAO'); /* @var $submissionDao SubmissionDAO */
// controlled vocabulary DAOs.
$submissionSubjectDao = DAORegistry::getDAO('SubmissionSubjectDAO'); /* @var $submissionSubjectDao SubmissionSubjectDAO */
$submissionKeywordDao = DAORegistry::getDAO('SubmissionKeywordDAO'); /* @var $submissionKeywordDao SubmissionKeywordDAO */
$submissionDisciplineDao = DAORegistry::getDAO('SubmissionDisciplineDAO'); /* @var $submissionDisciplineDao SubmissionDisciplineDAO */
$submissionAgencyDao = DAORegistry::getDAO('SubmissionAgencyDAO'); /* @var $submissionAgencyDao SubmissionAgencyDAO */
$submissionLanguageDao = DAORegistry::getDAO('SubmissionLanguageDAO'); /* @var $submissionLanguageDao SubmissionLanguageDAO */
$controlledVocabDao = DAORegistry::getDAO('ControlledVocabDAO'); /* @var $controlledVocabDao ControlledVocabDAO */
// check to see if there are any existing controlled vocabs for submissionAgency, submissionDiscipline, submissionSubject, or submissionLanguage.
// IF there are, this implies that this code has run previously, so return.
$vocabTestResult = $controlledVocabDao->retrieve('SELECT count(*) AS total FROM controlled_vocabs WHERE symbolic = \'submissionAgency\' OR symbolic = \'submissionDiscipline\' OR symbolic = \'submissionSubject\' OR symbolic = \'submissionKeyword\' OR symbolic = \'submissionLanguage\'');
$testRow = $vocabTestResult->GetRowAssoc(false);
if ($testRow['total'] > 0) return true;
$journals = $journalDao->getAll();
while ($journal = $journals->next()) {
// for languages, we depend on the journal locale settings since languages are not localized.
// Use Journal locales, or primary if no defined submission locales.
$supportedLocales = $journal->getSupportedSubmissionLocales();
if (empty($supportedLocales)) $supportedLocales = array($journal->getPrimaryLocale());
else if (!is_array($supportedLocales)) $supportedLocales = array($supportedLocales);
$result = $submissionDao->retrieve('SELECT a.submission_id FROM submissions a WHERE a.context_id = ?', array((int)$journal->getId()));
while (!$result->EOF) {
$row = $result->GetRowAssoc(false);
$articleId = (int)$row['submission_id'];
$settings = array();
$settingResult = $submissionDao->retrieve('SELECT setting_value, setting_name, locale FROM submission_settings WHERE submission_id = ? AND setting_value <> \'\' AND (setting_name = \'discipline\' OR setting_name = \'subject\' OR setting_name = \'subjectClass\' OR setting_name = \'sponsor\')', array((int)$articleId));
while (!$settingResult->EOF) {
$settingRow = $settingResult->GetRowAssoc(false);
$locale = $settingRow['locale'];
$settingName = $settingRow['setting_name'];
$settingValue = $settingRow['setting_value'];
$settings[$settingName][$locale] = $settingValue;
$settingResult->MoveNext();
}
$settingResult->Close();
$disciplines = $subjects = $keywords = $agencies = array();
if (array_key_exists('discipline', $settings)) {
$disciplineLocales = array_keys($settings['discipline']);
if (is_array($disciplineLocales)) {
foreach ($disciplineLocales as &$locale) {
$disciplines[$locale] = preg_split('/[,;:]/', $settings['discipline'][$locale]);
$disciplines[$locale] = array_map('trim', $disciplines[$locale]);
}
$submissionDisciplineDao->insertDisciplines($disciplines, $articleId, false, ASSOC_TYPE_SUBMISSION);
}
unset($disciplineLocales);
unset($disciplines);
}
if (array_key_exists('subjectClass', $settings)) {
$subjectLocales = array_keys($settings['subjectClass']);
if (is_array($subjectLocales)) {
foreach ($subjectLocales as &$locale) {
$subjects[$locale] = preg_split('/[,;:]/', $settings['subjectClass'][$locale]);
$subjects[$locale] = array_map('trim', $subjects[$locale]);
}
$submissionSubjectDao->insertSubjects($subjects, $articleId, false, ASSOC_TYPE_SUBMISSION);
}
unset($subjectLocales);
unset($subjects);
}
if (array_key_exists('subject', $settings)) {
$keywordLocales = array_keys($settings['subject']);
if (is_array($keywordLocales)) {
foreach ($keywordLocales as &$locale) {
$keywords[$locale] = preg_split('/[,;:]/', $settings['subject'][$locale]);
$keywords[$locale] = array_map('trim', $keywords[$locale]);
}
$submissionKeywordDao->insertKeywords($keywords, $articleId, false, ASSOC_TYPE_SUBMISSION);
}
unset($keywordLocales);
unset($keywords);
}
if (array_key_exists('sponsor', $settings)) {
$sponsorLocales = array_keys($settings['sponsor']);
if (is_array($sponsorLocales)) {
foreach ($sponsorLocales as &$locale) {
// note array name change. Sponsor -> Agency
$agencies[$locale] = preg_split('/[,;:]/', $settings['sponsor'][$locale]);
$agencies[$locale] = array_map('trim', $agencies[$locale]);
}
$submissionAgencyDao->insertAgencies($agencies, $articleId, false, ASSOC_TYPE_SUBMISSION);
}
unset($sponsorLocales);
unset($agencies);
}
// Localize the languages setting (which previously wasn't localized).
$languageResult = $submissionDao->retrieve('SELECT language FROM articles_migration WHERE article_id = ?', array((int)$articleId));
$languageRow = $languageResult->getRowAssoc(false);
$language = $languageRow['language'];
$languageResult->Close();
$languages = array();
foreach ($supportedLocales as &$locale) {
$languages[$locale] = preg_split('/[\s+;,]+/', $language);
$languages[$locale] = array_map('trim', $languages[$locale]);
}
$submissionLanguageDao->insertLanguages($languages, $articleId, false, ASSOC_TYPE_SUBMISSION);
$result->MoveNext();
}
$result->Close();
unset($supportedLocales);
unset($result);
unset($journal);
}
// delete old settings
$submissionDao->update('DELETE FROM submission_settings WHERE setting_name = \'discipline\' OR setting_name = \'subject\' OR setting_name = \'subjectClass\' OR setting_name = \'sponsor\'');
return true;
}
/**
* For 3.0.0 upgrade: Migrate the static user role structure to
* user groups and stage assignments.
* @return boolean
*/
function migrateUserRoles() {
// if there are any user_groups created, then this has already run. Return immediately in that case.
$userGroupDao = DAORegistry::getDAO('UserGroupDAO'); /* @var $userGroupDao UserGroupDAO */
$userGroupTest = $userGroupDao->retrieve('SELECT count(*) AS total FROM user_groups');
$testRow = $userGroupTest->GetRowAssoc(false);
if ($testRow['total'] > 0) return true;
// First, do Admins.
// create the admin user group.
$userGroupDao->update('INSERT INTO user_groups (context_id, role_id, is_default) VALUES (?, ?, ?)', array(CONTEXT_SITE, ROLE_ID_SITE_ADMIN, 1));
$userGroupId = $userGroupDao->getInsertId();
$userResult = $userGroupDao->retrieve('SELECT user_id FROM roles WHERE journal_id = ? AND role_id = ?', array(CONTEXT_SITE, ROLE_ID_SITE_ADMIN));
while (!$userResult->EOF) {
$row = $userResult->GetRowAssoc(false);
$userGroupDao->update('INSERT INTO user_user_groups (user_group_id, user_id) VALUES (?, ?)', array($userGroupId, (int) $row['user_id']));
$userResult->MoveNext();
}
// iterate through all journals and assign remaining users to their respective groups.
$journalDao = DAORegistry::getDAO('JournalDAO'); /* @var $journalDao JournalDAO */
$journals = $journalDao->getAll();
AppLocale::requireComponents(LOCALE_COMPONENT_APP_DEFAULT, LOCALE_COMPONENT_PKP_DEFAULT);
// fix stage id assignments for reviews. OJS hard coded *all* of these to '1' initially. Consider OJS reviews as external reviews.
$userGroupDao->update('UPDATE review_assignments SET stage_id = ?', array(WORKFLOW_STAGE_ID_EXTERNAL_REVIEW));
while ($journal = $journals->next()) {
// Install default user groups so we can assign users to them.
$userGroupDao->installSettings($journal->getId(), 'registry/userGroups.xml');
// Readers.
$group = $userGroupDao->getDefaultByRoleId($journal->getId(), ROLE_ID_READER);
$userResult = $journalDao->retrieve('SELECT user_id FROM roles WHERE journal_id = ? AND role_id = ?', array((int) $journal->getId(), ROLE_ID_READER));
while (!$userResult->EOF) {
$row = $userResult->GetRowAssoc(false);
$userGroupDao->assignUserToGroup($row['user_id'], $group->getId());
$userResult->MoveNext();
}
// Subscription Managers.
$group = $userGroupDao->getDefaultByRoleId($journal->getId(), ROLE_ID_SUBSCRIPTION_MANAGER);
$userResult = $journalDao->retrieve('SELECT user_id FROM roles WHERE journal_id = ? AND role_id = ?', array((int) $journal->getId(), ROLE_ID_SUBSCRIPTION_MANAGER));
while (!$userResult->EOF) {
$row = $userResult->GetRowAssoc(false);
$userGroupDao->assignUserToGroup($row['user_id'], $group->getId());
$userResult->MoveNext();
}
// Managers.
$group = $userGroupDao->getDefaultByRoleId($journal->getId(), ROLE_ID_MANAGER);
$userResult = $journalDao->retrieve('SELECT user_id FROM roles WHERE journal_id = ? AND role_id = ?', array((int) $journal->getId(), ROLE_ID_MANAGER));
while (!$userResult->EOF) {
$row = $userResult->GetRowAssoc(false);
$userGroupDao->assignUserToGroup($row['user_id'], $group->getId());
$userResult->MoveNext();
}
// Authors.
$authorGroup = $userGroupDao->getDefaultByRoleId($journal->getId(), ROLE_ID_AUTHOR);
$userResult = $journalDao->retrieve('SELECT user_id FROM roles WHERE journal_id = ? AND role_id = ?', array((int) $journal->getId(), ROLE_ID_AUTHOR));
while (!$userResult->EOF) {
$row = $userResult->GetRowAssoc(false);
$userGroupDao->assignUserToGroup($row['user_id'], $authorGroup->getId());
$userResult->MoveNext();
}
// Reviewers. All existing OJS reviewers get mapped to external reviewers.
// There should only be one user group with ROLE_ID_REVIEWER in the external review stage.
$userGroups = $userGroupDao->getUserGroupsByStage($journal->getId(), WORKFLOW_STAGE_ID_EXTERNAL_REVIEW, ROLE_ID_REVIEWER);
$reviewerUserGroup = null; // keep this in scope for later.
while ($group = $userGroups->next()) {
$reviewerUserGroup = $group;
$userResult = $journalDao->retrieve('SELECT user_id FROM roles WHERE journal_id = ? AND role_id = ?', array((int) $journal->getId(), ROLE_ID_REVIEWER));
while (!$userResult->EOF) {
$row = $userResult->GetRowAssoc(false);
$userGroupDao->assignUserToGroup($row['user_id'], $group->getId());
$userResult->MoveNext();
}
}
// regular Editors. NOTE: this involves a role id change from 0x100 to 0x10 (old OJS _EDITOR to PKP-lib _MANAGER).
$userGroups = $userGroupDao->getByRoleId($journal->getId(), ROLE_ID_MANAGER);
$editorUserGroup = null;
while ($group = $userGroups->next()) {
if ($group->getData('nameLocaleKey') == 'default.groups.name.editor') {
$editorUserGroup = $group; // stash for later.
$userResult = $journalDao->retrieve('SELECT user_id FROM roles WHERE journal_id = ? AND role_id = ?', array((int) $journal->getId(), OJS2_ROLE_ID_EDITOR));
while (!$userResult->EOF) {
$row = $userResult->GetRowAssoc(false);
$userGroupDao->assignUserToGroup($row['user_id'], $group->getId());
$userResult->MoveNext();
}
}
}
// Section Editors.
$sectionEditorGroup = $userGroupDao->getDefaultByRoleId($journal->getId(), ROLE_ID_SUB_EDITOR);
$userResult = $journalDao->retrieve('SELECT user_id FROM roles WHERE journal_id = ? AND role_id = ?', array((int) $journal->getId(), OJS2_ROLE_ID_SECTION_EDITOR));
while (!$userResult->EOF) {
$row = $userResult->GetRowAssoc(false);
$userGroupDao->assignUserToGroup($row['user_id'], $sectionEditorGroup->getId());
$userResult->MoveNext();
}
// Layout Editors. NOTE: this involves a role id change from 0x300 to 0x1001 (old OJS _LAYOUT_EDITOR to PKP-lib _ASSISTANT).
$userGroups = $userGroupDao->getByRoleId($journal->getId(), ROLE_ID_ASSISTANT);
$layoutEditorGroup = null;
while ($group = $userGroups->next()) {
if ($group->getData('nameLocaleKey') == 'default.groups.name.layoutEditor') {
$layoutEditorGroup = $group;
$userResult = $journalDao->retrieve('SELECT user_id FROM roles WHERE journal_id = ? AND role_id = ?', array((int) $journal->getId(), OJS2_ROLE_ID_LAYOUT_EDITOR));
while (!$userResult->EOF) {
$row = $userResult->GetRowAssoc(false);
$userGroupDao->assignUserToGroup($row['user_id'], $group->getId());
$userResult->MoveNext();
}
}
}
// Copyeditors. NOTE: this involves a role id change from 0x2000 to 0x1001 (old OJS _COPYEDITOR to PKP-lib _ASSISTANT).
$userGroups = $userGroupDao->getByRoleId($journal->getId(), ROLE_ID_ASSISTANT);
$copyEditorGroup = null;
while ($group = $userGroups->next()) {
if ($group->getData('nameLocaleKey') == 'default.groups.name.copyeditor') {
$copyEditorGroup = $group;
$userResult = $journalDao->retrieve('SELECT user_id FROM roles WHERE journal_id = ? AND role_id = ?', array((int) $journal->getId(), OJS2_ROLE_ID_COPYEDITOR));
while (!$userResult->EOF) {
$row = $userResult->GetRowAssoc(false);
$userGroupDao->assignUserToGroup($row['user_id'], $group->getId());
$userResult->MoveNext();
}
}
}
// Proofreaders. NOTE: this involves a role id change from 0x3000 to 0x1001 (old OJS _PROOFREADER to PKP-lib _ASSISTANT).
$userGroups = $userGroupDao->getByRoleId($journal->getId(), ROLE_ID_ASSISTANT);
$proofreaderGroup = null;
while ($group = $userGroups->next()) {
if ($group->getData('nameLocaleKey') == 'default.groups.name.proofreader') {
$proofreaderGroup = $group;
$userResult = $journalDao->retrieve('SELECT user_id FROM roles WHERE journal_id = ? AND role_id = ?', array((int) $journal->getId(), OJS2_ROLE_ID_PROOFREADER));
while (!$userResult->EOF) {
$row = $userResult->GetRowAssoc(false);
$userGroupDao->assignUserToGroup($row['user_id'], $group->getId());
$userResult->MoveNext();
}
}
}
// Now, migrate stage assignments. This code is based on the default stage assignments outlined in registry/userGroups.xml
$submissionDao = DAORegistry::getDAO('SubmissionDAO'); /* @var $submissionDao SubmissionDAO */
$stageAssignmentDao = DAORegistry::getDAO('StageAssignmentDAO'); /* @var $stageAssignmentDao StageAssignmentDAO */
$submissionResult = $submissionDao->retrieve('SELECT article_id, user_id FROM articles_migration WHERE journal_id = ?', array($journal->getId()));
$authorGroup = $userGroupDao->getDefaultByRoleId($journal->getId(), ROLE_ID_AUTHOR);
while (!$submissionResult->EOF) {
$submissionRow = $submissionResult->GetRowAssoc(false);
$submissionId = $submissionRow['article_id'];
$submissionUserId = $submissionRow['user_id'];
unset($submissionRow);
// Authors get access to all stages.
$stageAssignmentDao->build($submissionId, $authorGroup->getId(), $submissionUserId);
// update the user_group_id column in the authors table.
$userGroupDao->update('UPDATE authors SET user_group_id = ? WHERE submission_id = ?', array((int) $authorGroup->getId(), $submissionId));
// Journal Editors
// First, full editors.
$editorsResult = $stageAssignmentDao->retrieve('SELECT e.* FROM submissions s, edit_assignments e, users u, roles r WHERE r.user_id = e.editor_id AND r.role_id = ' .
OJS2_ROLE_ID_EDITOR . ' AND e.article_id = ? AND r.journal_id = s.context_id AND s.submission_id = e.article_id AND e.editor_id = u.user_id', array($submissionId));
while (!$editorsResult->EOF) {
$editorRow = $editorsResult->GetRowAssoc(false);
$stageAssignmentDao->build($submissionId, $editorUserGroup->getId(), $editorRow['editor_id']);
$editorsResult->MoveNext();
}
unset($editorsResult);
// Section Editors.
$editorsResult = $stageAssignmentDao->retrieve('SELECT e.* FROM submissions s LEFT JOIN edit_assignments e ON (s.submission_id = e.article_id) LEFT JOIN users u ON (e.editor_id = u.user_id)
LEFT JOIN roles r ON (r.user_id = e.editor_id AND r.role_id = ' . OJS2_ROLE_ID_EDITOR . ' AND r.journal_id = s.context_id) WHERE e.article_id = ? AND s.submission_id = e.article_id
AND r.role_id IS NULL', array($submissionId));
while (!$editorsResult->EOF) {
$editorRow = $editorsResult->GetRowAssoc(false);
$stageAssignmentDao->build($submissionId, $sectionEditorGroup->getId(), $editorRow['editor_id']);
$editorsResult->MoveNext();
}
unset($editorsResult);
// Copyeditors. Pull from the signoffs for SIGNOFF_COPYEDITING_INITIAL.
// there should only be one (or no) copyeditor for each submission.
$copyEditorResult = $stageAssignmentDao->retrieve('SELECT user_id FROM signoffs WHERE assoc_type = ? AND assoc_id = ? AND symbolic = ?',
array(ASSOC_TYPE_SUBMISSION, $submissionId, 'SIGNOFF_COPYEDITING_INITIAL'));
if ($copyEditorResult->NumRows() == 1) { // the signoff exists.
$copyEditorRow = $copyEditorResult->GetRowAssoc(false);
$copyEditorId = (int) $copyEditorRow['user_id'];
if ($copyEditorId > 0) { // there is a user assigned.
$stageAssignmentDao->build($submissionId, $copyEditorGroup->getId(), $copyEditorId);
}
}
// Layout editors. Pull from the signoffs for SIGNOFF_LAYOUT.
// there should only be one (or no) layout editor for each submission.
$layoutEditorResult = $stageAssignmentDao->retrieve('SELECT user_id FROM signoffs WHERE assoc_type = ? AND assoc_id = ? AND symbolic = ?',
array(ASSOC_TYPE_SUBMISSION, $submissionId, 'SIGNOFF_LAYOUT'));
if ($layoutEditorResult->NumRows() == 1) { // the signoff exists.
$layoutEditorRow = $layoutEditorResult->GetRowAssoc(false);
$layoutEditorId = (int) $layoutEditorRow['user_id'];
if ($layoutEditorId > 0) { // there is a user assigned.
$stageAssignmentDao->build($submissionId, $layoutEditorGroup->getId(), $layoutEditorId);
}
}
// Proofreaders. Pull from the signoffs for SIGNOFF_PROOFREADING_PROOFREADER.
// there should only be one (or no) layout editor for each submission.
$proofreaderResult = $stageAssignmentDao->retrieve('SELECT user_id FROM signoffs WHERE assoc_type = ? AND assoc_id = ? AND symbolic = ?',
array(ASSOC_TYPE_SUBMISSION, $submissionId, 'SIGNOFF_PROOFREADING_PROOFREADER'));
if ($proofreaderResult->NumRows() == 1) { // the signoff exists.
$proofreaderRow = $proofreaderResult->GetRowAssoc(false);
$proofreaderId = (int) $proofreaderRow['user_id'];
if ($proofreaderId > 0) { // there is a user assigned.
$stageAssignmentDao->build($submissionId, $proofreaderGroup->getId(), $proofreaderId);
}
}
$submissionResult->MoveNext();
}
}
return true;
}
/**
* For 3.0.0 upgrade. Genres are required to migrate files.
*/
function installDefaultGenres() {
$genreDao = DAORegistry::getDAO('GenreDAO'); /* @var $genreDao GenreDAO */
$siteDao = DAORegistry::getDAO('SiteDAO'); /* @var $siteDao SiteDAO */
$site = $siteDao->getSite();
$contextsResult = $genreDao->retrieve('SELECT journal_id FROM journals');
while (!$contextsResult->EOF) {
$row = $contextsResult->GetRowAssoc(false);
$genreDao->installDefaults($row['journal_id'], $site->getInstalledLocales());
$contextsResult->MoveNext();
}
return true;
}
/**
* For 2.4 upgrade: migrate COUNTER statistics to the metrics table.
*/
function migrateCounterPluginUsageStatistics() {
$metricsDao = DAORegistry::getDAO('MetricsDAO'); /* @var $metricsDao MetricsDAO */
$result = $metricsDao->retrieve('SELECT * FROM counter_monthly_log');
if ($result->EOF) return true;
$loadId = '3.0.0-upgrade-counter';
$metricsDao->purgeLoadBatch($loadId);
$fileTypeCounts = array(
'count_html' => STATISTICS_FILE_TYPE_HTML,
'count_pdf' => STATISTICS_FILE_TYPE_PDF,
'count_other' => STATISTICS_FILE_TYPE_OTHER
);
while(!$result->EOF) {
$row = $result->GetRowAssoc(false);
foreach ($fileTypeCounts as $countType => $fileType) {
$month = (string) $row['month'];
if (strlen($month) == 1) {
$month = '0' . $month;
}
if ($row[$countType]) {
$record = array(
'load_id' => $loadId,
'assoc_type' => ASSOC_TYPE_JOURNAL,
'assoc_id' => $row['journal_id'],
'metric_type' => 'ojs::legacyCounterPlugin',
'metric' => $row[$countType],
'file_type' => $fileType,
'month' => $row['year'] . $month
);
$metricsDao->insertRecord($record);
}
}
$result->MoveNext();
}
// Remove the plugin settings.
$metricsDao->update('DELETE FROM plugin_settings WHERE plugin_name = ?', array('counterplugin'), false);
return true;
}
/**
* For 2.4 upgrade: migrate Timed views statistics to the metrics table.
*/
function migrateTimedViewsUsageStatistics() {
$metricsDao = DAORegistry::getDAO('MetricsDAO'); /* @var $metricsDao MetricsDAO */
$result =& $metricsDao->retrieve('SELECT * FROM timed_views_log');
if ($result->EOF) return true;
$loadId = '3.0.0-upgrade-timedViews';
$metricsDao->purgeLoadBatch($loadId);
$plugin = PluginRegistry::getPlugin('generic', 'usagestatsplugin');
$plugin->import('UsageStatsTemporaryRecordDAO');
$tempStatsDao = new UsageStatsTemporaryRecordDAO();
$tempStatsDao->deleteByLoadId($loadId);
import('plugins.generic.usageStats.GeoLocationTool');
$geoLocationTool = new GeoLocationTool();
while(!$result->EOF) {
$row = $result->GetRowAssoc(false);
list($countryId, $cityName, $region) = $geoLocationTool->getGeoLocation($row['ip_address']);
if ($row['galley_id']) {
$assocType = ASSOC_TYPE_GALLEY;
$assocId = $row['galley_id'];
} else {
$assocType = ASSOC_TYPE_SUBMISSION;
$assocId = $row['submission_id'];
};
$day = date('Ymd', strtotime($row['date']));
$tempStatsDao->insert($assocType, $assocId, $day, strtotime($row['date']), $countryId, $region, $cityName, null, $loadId);
$result->MoveNext();
}
// Articles.
$params = array('ojs::timedViews', $loadId, ASSOC_TYPE_SUBMISSION);
$tempStatsDao->update(
'INSERT INTO metrics (load_id, metric_type, assoc_type, assoc_id, day, country_id, region, city, submission_id, metric, context_id, assoc_object_type, assoc_object_id)
SELECT tr.load_id, ?, tr.assoc_type, tr.assoc_id, tr.day, tr.country_id, tr.region, tr.city, tr.assoc_id, count(tr.metric), a.context_id, ' . ASSOC_TYPE_ISSUE . ', pa.issue_id
FROM usage_stats_temporary_records AS tr
LEFT JOIN submissions AS a ON a.submission_id = tr.assoc_id
LEFT JOIN published_submissions AS pa ON pa.submission_id = tr.assoc_id
WHERE tr.load_id = ? AND tr.assoc_type = ? AND a.context_id IS NOT NULL AND pa.issue_id IS NOT NULL
GROUP BY tr.assoc_type, tr.assoc_id, tr.day, tr.country_id, tr.region, tr.city, tr.file_type, tr.load_id', $params
);
// Galleys.
$params = array('ojs::timedViews', $loadId, ASSOC_TYPE_GALLEY);
$tempStatsDao->update(
'INSERT INTO metrics (load_id, metric_type, assoc_type, assoc_id, day, country_id, region, city, submission_id, metric, context_id, assoc_object_type, assoc_object_id)
SELECT tr.load_id, ?, tr.assoc_type, tr.assoc_id, tr.day, tr.country_id, tr.region, tr.city, ag.submission_id, count(tr.metric), a.context_id, ' . ASSOC_TYPE_ISSUE . ', pa.issue_id
FROM usage_stats_temporary_records AS tr
LEFT JOIN submission_galleys AS ag ON ag.galley_id = tr.assoc_id
LEFT JOIN submissions AS a ON a.submission_id = ag.submission_id
LEFT JOIN published_submissions AS pa ON pa.submission_id = ag.submission_id
WHERE tr.load_id = ? AND tr.assoc_type = ? AND a.context_id IS NOT NULL AND pa.issue_id IS NOT NULL
GROUP BY tr.assoc_type, tr.assoc_id, tr.day, tr.country_id, tr.region, tr.city, tr.file_type, tr.load_id', $params
);
$tempStatsDao->deleteByLoadId($loadId);
// Remove the plugin settings.
$metricsDao->update('DELETE FROM plugin_settings WHERE plugin_name = ?', array('timedviewplugin'), false);
return true;
}
/**
* For 2.4 upgrade: migrate OJS default statistics to the metrics table.
*/
function migrateDefaultUsageStatistics() {
$loadId = '3.0.0-upgrade-ojsViews';
$metricsDao = DAORegistry::getDAO('MetricsDAO'); /* @var $metricsDao MetricsDAO */
$insertIntoClause = 'INSERT INTO metrics (file_type, load_id, metric_type, assoc_type, assoc_id, submission_id, metric, context_id, assoc_object_type, assoc_object_id)';
$selectClause = null; // Conditionally set later
// Galleys.
$galleyUpdateCases = array(
array('fileType' => STATISTICS_FILE_TYPE_PDF, 'isHtml' => false, 'assocType' => ASSOC_TYPE_GALLEY),
array('fileType' => STATISTICS_FILE_TYPE_HTML, 'isHtml' => true, 'assocType' => ASSOC_TYPE_GALLEY),
array('fileType' => STATISTICS_FILE_TYPE_OTHER, 'isHtml' => false, 'assocType' => ASSOC_TYPE_GALLEY),
array('fileType' => STATISTICS_FILE_TYPE_PDF, 'assocType' => ASSOC_TYPE_ISSUE_GALLEY),
array('fileType' => STATISTICS_FILE_TYPE_OTHER, 'assocType' => ASSOC_TYPE_ISSUE_GALLEY),
);
foreach ($galleyUpdateCases as $case) {
$skipQuery = false;
if ($case['fileType'] == STATISTICS_FILE_TYPE_PDF) {
$pdfFileTypeWhereCheck = 'IN';
} else {
$pdfFileTypeWhereCheck = 'NOT IN';
}
$params = array($case['fileType'], $loadId, 'ojs::legacyDefault', $case['assocType']);
if ($case['assocType'] == ASSOC_TYPE_GALLEY) {
array_push($params, (int) $case['isHtml']);
$selectClause = ' SELECT ?, ?, ?, ?, ag.galley_id, ag.article_id, ag.views, a.context_id, ' . ASSOC_TYPE_ISSUE . ', pa.issue_id
FROM article_galleys_stats_migration as ag
LEFT JOIN submissions AS a ON ag.article_id = a.submission_id
LEFT JOIN published_submissions as pa on ag.article_id = pa.submission_id
LEFT JOIN submission_files as af on ag.file_id = af.file_id
WHERE a.submission_id is not null AND ag.views > 0 AND ag.html_galley = ?
AND af.file_type ';
} else {
if ($this->tableExists('issue_galleys_stats_migration')) {
$selectClause = 'SELECT ?, ?, ?, ?, ig.galley_id, 0, ig.views, i.journal_id, ' . ASSOC_TYPE_ISSUE . ', ig.issue_id
FROM issue_galleys_stats_migration AS ig
LEFT JOIN issues AS i ON ig.issue_id = i.issue_id
LEFT JOIN issue_files AS ifi ON ig.file_id = ifi.file_id
WHERE ig.views > 0 AND i.issue_id is not null AND ifi.file_type ';
} else {
// Upgrading from a version that
// didn't support issue galleys. Skip.
$skipQuery = true;
}
}
array_push($params, 'application/pdf', 'application/x-pdf', 'text/pdf', 'text/x-pdf');
if (!$skipQuery) {
$metricsDao->update($insertIntoClause . $selectClause . $pdfFileTypeWhereCheck . ' (?, ?, ?, ?)', $params, false);
}
}
// Published submissions.
$params = array(null, $loadId, 'ojs::legacyDefault', ASSOC_TYPE_SUBMISSION);
$metricsDao->update($insertIntoClause .
' SELECT ?, ?, ?, ?, pa.article_id, pa.article_id, pa.views, i.journal_id, ' . ASSOC_TYPE_ISSUE . ', pa.issue_id
FROM published_articles_stats_migration as pa
LEFT JOIN issues AS i ON pa.issue_id = i.issue_id
WHERE pa.views > 0 AND i.issue_id is not null;', $params, false);
// Set the site default metric type.
$siteDao = DAORegistry::getDAO('SiteDAO'); /* @var $siteDao SiteDAO */
$site = $siteDao->getSite();
$site->setData('defaultMetricType', METRIC_TYPE_COUNTER);
$siteDao->updateObject($site);
return true;
}
/**
* Synchronize the ASSOC_TYPE_SERIES constant to ASSOC_TYPE_SECTION defined in PKPApplication.
* @return boolean
*/
function syncSeriesAssocType() {
// Can be any DAO.
$dao =& DAORegistry::getDAO('UserDAO'); /* @var $dao DAO */
$tablesToUpdate = array(
'announcements',
'announcements_types',
'user_settings',
'notification',
'email_templates',
'email_templates_data',
'controlled_vocabs',
'event_log',
'email_log',
'metadata_descriptions',
'metrics',
'notes',
'item_views',
'data_object_tombstone_oai_set_objects');
foreach ($tablesToUpdate as $tableName) {
if ($this->tableExists($tableName)) {
$dao->update('UPDATE ' . $tableName . ' SET assoc_type = ' . ASSOC_TYPE_SECTION . ' WHERE assoc_type = ' . "'526'");
}
}
return true;
}
/**
* Modernize review form storage from OJS 2.x
* @return boolean
*/
function fixReviewForms() {
// 1. Review form possible options were stored with 'order'
// and 'content' attributes. Just store by content.
$reviewFormDao = DAORegistry::getDAO('ReviewFormDAO'); /* @var $reviewFormDao ReviewFormDAO */
$result = $reviewFormDao->retrieve(
'SELECT * FROM review_form_element_settings WHERE setting_name = ?',
'possibleResponses'
);
while (!$result->EOF) {
$row = $result->GetRowAssoc(false);
$options = unserialize($row['setting_value']);
$newOptions = array();
foreach ($options as $key => $option) {
$newOptions[$key] = $option['content'];
}
$row['setting_value'] = serialize($newOptions);
$reviewFormDao->Replace('review_form_element_settings', $row, array('review_form_element_id', 'locale', 'setting_name'));
$result->MoveNext();
}
$result->Close();
// 2. Responses were stored with indexes offset by 1. Fix.
import('lib.pkp.classes.reviewForm.ReviewFormElement'); // Constants
$result = $reviewFormDao->retrieve(
'SELECT rfe.element_type AS element_type,
rfr.response_value AS response_value,
rfr.review_id AS review_id,
rfe.review_form_element_id AS review_form_element_id
FROM review_form_responses rfr
JOIN review_form_elements rfe ON (rfe.review_form_element_id = rfr.review_form_element_id)
WHERE rfe.element_type IN (?, ?, ?)',
array(
REVIEW_FORM_ELEMENT_TYPE_CHECKBOXES,
REVIEW_FORM_ELEMENT_TYPE_RADIO_BUTTONS,
REVIEW_FORM_ELEMENT_TYPE_DROP_DOWN_BOX
)
);
while (!$result->EOF) {
$row = $result->GetRowAssoc(false);
$value = $row['response_value'];
switch ($row['element_type']) {
case REVIEW_FORM_ELEMENT_TYPE_CHECKBOXES:
// Stored as a serialized object.
$oldValue = unserialize($value);
$value = array();
foreach ($oldValue as $k => $v) {
$value[$k] = $v-1;
}
$value = serialize($value);
break;
case REVIEW_FORM_ELEMENT_TYPE_RADIO_BUTTONS:
case REVIEW_FORM_ELEMENT_TYPE_DROP_DOWN_BOX:
// Stored as a simple number.
$value-=1;
break;
}
$reviewFormDao->update(
'UPDATE review_form_responses SET response_value = ? WHERE review_id = ? AND review_form_element_id = ?',
array($value, $row['review_id'], $row['review_form_element_id'])
);
$result->MoveNext();
}
$result->Close();
return true;
}
/**
* Convert email templates to HTML.
* @return boolean True indicates success.
*/
function htmlifyEmailTemplates() {
$emailTemplateDao = DAORegistry::getDAO('EmailTemplateDAO'); /* @var $emailTemplateDao EmailTemplateDAO */
// Convert the email templates in email_templates_data to localized
$result = $emailTemplateDao->retrieve('SELECT * FROM email_templates_data');
while (!$result->EOF) {
$row = $result->getRowAssoc(false);
$emailTemplateDao->update(
'UPDATE email_templates_data
SET body = ?
WHERE email_key = ? AND
locale = ? AND
assoc_type = ? AND
assoc_id = ?',
array(
preg_replace('/{\$[a-zA-Z]+Url}/', '<a href="\0">\0</a>', nl2br($row['body'])),
$row['email_key'],
$row['locale'],
$row['assoc_type'],
$row['assoc_id']
)
);
$result->MoveNext();
}
$result->Close();
// Convert the email templates in email_templates_default_data to localized
$result = $emailTemplateDao->retrieve('SELECT * FROM email_templates_default_data');
while (!$result->EOF) {
$row = $result->getRowAssoc(false);
$emailTemplateDao->update(
'UPDATE email_templates_default_data
SET body = ?
WHERE email_key = ? AND
locale = ?',
array(
preg_replace('/{\$[a-zA-Z]+Url}/', '<a href="\0">\0</a>', nl2br($row['body'])),
$row['email_key'],
$row['locale'],
)
);
$result->MoveNext();
}
$result->Close();
return true;
}
/**
* For 2.4.6 upgrade: to enable localization of a CustomBlock,
* the blockContent values are converted from string to array (key: primary_language)
*/
function localizeCustomBlockSettings() {
$pluginSettingsDao = DAORegistry::getDAO('PluginSettingsDAO'); /* @var $pluginSettingsDao PluginSettingsDAO */
$journalDao = DAORegistry::getDAO('JournalDAO'); /* @var $journalDao JournalDAO */
$journals = $journalDao->getAll();
while ($journal = $journals->next()) {
$journalId = $journal->getId();
$primaryLocale = $journal->getPrimaryLocale();
$blocks = $pluginSettingsDao->getSetting($journalId, 'customblockmanagerplugin', 'blocks');
if ($blocks) foreach ($blocks as $block) {
$blockContent = $pluginSettingsDao->getSetting($journalId, $block, 'blockContent');
if (!is_array($blockContent)) {
$pluginSettingsDao->updateSetting($journalId, $block, 'blockContent', array($primaryLocale => $blockContent));
}
}
unset($journal);
}
return true;
}
/**
* Migrate submission filenames from OJS 2.x
* @param $upgrade Upgrade
* @param $params array
* @return boolean
*/
function migrateFiles($upgrade, $params) {
$journalDao = DAORegistry::getDAO('JournalDAO'); /* @var $journalDao JournalDAO */
$submissionDao = DAORegistry::getDAO('SubmissionDAO'); /* @var $submissionDao SubmissionDAO */
$submissionFileDao = DAORegistry::getDAO('SubmissionFileDAO'); /* @var $submissionFileDao SubmissionFileDAO */
DAORegistry::getDAO('GenreDAO'); // Load constants
$siteDao = DAORegistry::getDAO('SiteDAO'); /* @var $siteDao SiteDAO */
$site = $siteDao->getSite();
$adminEmail = $site->getLocalizedContactEmail();
// get file names form OJS 2.4.x table article_files i.e.
// from the temporary table article_files_migration
$ojs2FileNames = array();
$result = $submissionFileDao->retrieve('SELECT file_id, revision, file_name FROM article_files_migration');
while (!$result->EOF) {
$row = $result->GetRowAssoc(false);
$ojs2FileNames[$row['file_id']][$row['revision']] = $row['file_name'];
$result->MoveNext();
}
$result->Close();
import('lib.pkp.classes.file.SubmissionFileManager');
$contexts = $journalDao->getAll();
while ($context = $contexts->next()) {
$submissions = $submissionDao->getByContextId($context->getId());
while ($submission = $submissions->next()) {
$submissionFileManager = new SubmissionFileManager($context->getId(), $submission->getId());
$submissionFiles = $submissionFileDao->getBySubmissionId($submission->getId());
foreach ($submissionFiles as $submissionFile) {
$generatedFilename = $submissionFile->getServerFileName();
$basePath = $submissionFileManager->getBasePath();
$globPattern = $ojs2FileNames[$submissionFile->getFileId()][$submissionFile->getRevision()];
$pattern1 = glob($basePath . '*/*/' . $globPattern);
$pattern2 = glob($basePath . '*/' . $globPattern);
if (!is_array($pattern1)) $pattern1 = array();
if (!is_array($pattern2)) $pattern2 = array();
$matchedResults = array_merge($pattern1, $pattern2);
if (count($matchedResults)>1) {
// Too many filenames matched. Continue with the first; this is just a warning.
error_log("WARNING: Duplicate potential files for \"$globPattern\" in \"" . $submissionFileManager->getBasePath() . "\". Taking the first.");
} elseif (count($matchedResults)==0) {
// No filenames matched. Skip migrating.
error_log("WARNING: Unable to find a match for \"$globPattern\" in \"" . $submissionFileManager->getBasePath() . "\". Skipping this file.");
continue;
}
$discoveredFilename = array_shift($matchedResults);
$targetFilename = $basePath . $submissionFile->_fileStageToPath($submissionFile->getFileStage()) . '/' . $generatedFilename;
if (file_exists($targetFilename)) continue; // Skip existing files/links
if (!file_exists($path = dirname($targetFilename)) && !$submissionFileManager->mkdirtree($path)) {
error_log("Unable to make directory \"$path\"");
}
if (!rename($discoveredFilename, $targetFilename)) {
error_log("Unable to move \"$discoveredFilename\" to \"$targetFilename\".");
}
}
}
}
return true;
}
/**
* Set the missing uploader user id to a journal manager.
* @return boolean True indicates success.
*/
function setFileUploader() {
$journalDao = DAORegistry::getDAO('JournalDAO'); /* @var $journalDao JournalDAO */
$userGroupDao = DAORegistry::getDAO('UserGroupDAO'); /* @var $userGroupDao UserGroupDAO */
$submissionFileDao = DAORegistry::getDAO('SubmissionFileDAO'); /* @var $submissionFileDao SubmissionFileDAO */
$journalIterator = $journalDao->getAll();
$driver = $submissionFileDao->getDriver();
while ($journal = $journalIterator->next()) {
$managerUserGroup = $userGroupDao->getDefaultByRoleId($journal->getId(), ROLE_ID_MANAGER);
$managerUsers = $userGroupDao->getUsersById($managerUserGroup->getId(), $journal->getId());
$creatorUserId = $managerUsers->next()->getId();
switch ($driver) {
case 'mysql':
case 'mysqli':
$submissionFileDao->update('UPDATE submission_files sf, submissions s SET sf.uploader_user_id = ? WHERE sf.uploader_user_id IS NULL AND sf.submission_id = s.submission_id AND s.context_id = ?', array($creatorUserId, $journal->getId()));
break;
case 'postgres':
case 'postgres64':
case 'postgres7':
case 'postgres8':
case 'postgres9':
$submissionFileDao->update('UPDATE submission_files SET uploader_user_id = ? FROM submissions s WHERE submission_files.uploader_user_id IS NULL AND submission_files.submission_id = s.submission_id AND s.context_id = ?', array($creatorUserId, $journal->getId()));
break;
default: fatalError('Unknown database type!');
}
unset($managerUsers, $managerUserGroup);
}
return true;
}
/**
* Set the missing file names.
* @return boolean True indicates success.
*/
function setFileName() {
$journalDao = DAORegistry::getDAO('JournalDAO'); /* @var $journalDao JournalDAO */
$submissionDao = DAORegistry::getDAO('SubmissionDAO'); /* @var $submissionDao SubmissionDAO */
$submissionFileDao = DAORegistry::getDAO('SubmissionFileDAO'); /* @var $submissionFileDao SubmissionFileDAO */
$contexts = $journalDao->getAll();
while ($context = $contexts->next()) {
$submissions = $submissionDao->getByContextId($context->getId());
while ($submission = $submissions->next()) {
$submissionFiles = $submissionFileDao->getBySubmissionId($submission->getId());
foreach ($submissionFiles as $submissionFile) {
$reviewStage = $submissionFile->getFileStage() == SUBMISSION_FILE_REVIEW_FILE ||
$submissionFile->getFileStage() == SUBMISSION_FILE_REVIEW_ATTACHMENT ||
$submissionFile->getFileStage() == SUBMISSION_FILE_REVIEW_REVISION;
if (!$submissionFile->getName(AppLocale::getPrimaryLocale())) {
if ($reviewStage) {
$submissionFile->setName($submissionFile->_generateName(true), AppLocale::getPrimaryLocale());
} else {
$submissionFile->setName($submissionFile->_generateName(), AppLocale::getPrimaryLocale());
}
}
$submissionFileDao->updateObject($submissionFile);
}
}
}
return true;
}
/**
* Convert supplementary files to submission files.
* @return boolean True indicates success.
*/
function convertSupplementaryFiles() {
$genreDao = DAORegistry::getDAO('GenreDAO'); /* @var $genreDao GenreDAO */
$journalDao = DAORegistry::getDAO('JournalDAO'); /* @var $journalDao JournalDAO */
$submissionDao = DAORegistry::getDAO('SubmissionDAO'); /* @var $submissionDao SubmissionDAO */
$articleGalleyDao = DAORegistry::getDAO('ArticleGalleyDAO'); /* @var $articleGalleyDao ArticleGalleyDAO */
$userGroupDao = DAORegistry::getDAO('UserGroupDAO'); /* @var $userGroupDao UserGroupDAO */
$journal = null;
$submissionFileDao = DAORegistry::getDAO('SubmissionFileDAO'); /* @var $submissionFileDao SubmissionFileDAO */
$suppFilesResult = $submissionFileDao->retrieve('SELECT a.context_id, sf.* FROM article_supplementary_files sf, submissions a WHERE a.submission_id = sf.article_id'); // COMMENT_TYPE_EDITOR_DECISION
while (!$suppFilesResult->EOF) {
$row = $suppFilesResult->getRowAssoc(false);
$suppFilesResult->MoveNext();
if (!$journal || $journal->getId() != $row['context_id']) {
$journal = $journalDao->getById($row['context_id']);
$managerUserGroup = $userGroupDao->getDefaultByRoleId($journal->getId(), ROLE_ID_MANAGER);
$managerUsers = $userGroupDao->getUsersById($managerUserGroup->getId(), $journal->getId());
$managerUser = $managerUsers->next();
if (!$managerUser) fatalError('Journal ID ' . $journal->getId() . ' does not have any enrolled managers!');
$creatorUserId = $managerUser->getId();
}
$article = $submissionDao->getById($row['article_id']);
if (!$article) {
error_log('WARNING: Unable to fetch article for article_supplementary_files.supp_id = ' . $row['supp_id'] . '. Skipping.');
continue;
}
// if it is a remote supp file and article is published, convert it to a remote galley
if (!$row['file_id'] && $row['remote_url'] != '' && $article->getStatus() == STATUS_PUBLISHED) {
$remoteSuppFileSettingsResult = $submissionFileDao->retrieve('SELECT * FROM article_supp_file_settings WHERE supp_id = ? AND setting_value IS NOT NULL', array($row['supp_id']));
$extraRemoteGalleySettings = $remoteSuppFileTitle = array();
while (!$remoteSuppFileSettingsResult->EOF) {
$rsfRow = $remoteSuppFileSettingsResult->getRowAssoc(false);
$remoteSuppFileSettingsResult->MoveNext();
switch ($rsfRow['setting_name']) {
case 'title':
$remoteSuppFileTitle[$rsfRow['locale']] = $rsfRow['setting_value'];
break;
case 'pub-id::doi':
case 'pub-id::other::urn':
case 'pub-id::publisher-id':
case 'urnSuffix':
case 'doiSuffix':
case 'datacite::registeredDoi':
$extraRemoteGalleySettings[$rsfRow['setting_name']] = $rsfRow['setting_value'];
break;
default:
// other settings are not relevant for remote galleys
break;
}
}
$remoteSuppFileSettingsResult->Close();
// Converted from DAO call to raw SQL because submission_id is no longer available post-schema sync.
$articleGalleyDao->update(
'INSERT INTO submission_galleys (locale, submission_id, remote_url, label) VALUES (?, ?, ?, ?)',
array(
$article->getLocale(),
$article->getId(),
$row['remote_url'],
$remoteSuppFileTitle[$article->getLocale()],
)
);
$galleyId = $articleGalleyDao->getInsertId();
// Preserve extra settings. (Plugins may not be loaded, so other mechanisms might not work.)
foreach ($extraRemoteGalleySettings as $name => $value) {
$submissionFileDao->update(
'INSERT INTO submission_galley_settings (galley_id, setting_name, setting_value, setting_type) VALUES (?, ?, ?, ?)',
array(
$galleyId,
$name,
$value,
'string'
)
);
}
// continue with the next supp file
continue;
}
$genre = null;
switch ($row['type']) {
// author.submit.suppFile.dataAnalysis
case 'Análise de Dados':
case 'Análises de dados':
case 'Anàlisi de les dades':
case 'Analisi di dati':
case 'Analisis Data':
case 'Análisis de datos':
case 'Análisis de los datos':
case 'Analiza podataka':
case 'Analize de date':
case 'Analizy':
case 'Analyse de données':
case 'Analyse':
case 'Analys':
case 'Analýza dat':
case 'Dataanalyse':
case 'Data Analysis':
case 'Datenanalyse':
case 'Datu-analisia':
case 'Gegevensanalyse':
case 'Phân tích dữ liệu':
case 'Veri Analizi':
case 'آنالیز داده':
case 'تحليل بيانات':
case 'Ανάλυση δεδομένων':
case 'Анализа на податоци':
case 'Анализ данных':
case 'Аналіз даних':
case 'ഡേറ്റാ വിശകലനം':
case 'データ分析':
case '数据分析':
case '資料分析':
$genre = $genreDao->getByKey('DATAANALYSIS', $journal->getId());
break;
// author.submit.suppFile.dataSet
case 'Baza podataka':
case 'Conjunt de dades':
case 'Conjunto de Dados':
case 'Conjunto de datos':
case 'Conjuntos de datos':
case 'Conxuntos de dados':
case 'Datasæt':
case 'Data Set':
case 'Dataset':
case 'Datasett':
case 'Datensatz':
case 'Datový soubor':
case 'Datu multzoa':
case 'Ensemble de données':
case 'Forskningsdata':
case 'データセット':
case 'Set Data':
case 'Set di dati':
case 'Set podataka':
case 'Seturi de date':
case 'Tập hợp dữ liệu':
case 'Veri Seti':
case 'Zbiory danych':
case 'مجموعة بيانات':
case 'مجموعه ناده':
case 'Σύνολο δεδομένων':
case 'Збирка на податоци':
case 'Набір даних':
case 'Набор данных':
case 'ഡേറ്റാ സെറ്റ്':
case '数据集':
case '資料或數據組':
$genre = $genreDao->getByKey('DATASET', $journal->getId());
break;
// author.submit.suppFile.researchInstrument
case 'Araştırma Enstürmanları':
case 'Công cụ nghiên cứu':
case 'Forschungsinstrument':
case 'Forskningsinstrument':
case 'Herramienta de investigación':
case 'Ikerketa-tresna':
case 'Instrumen Riset':
case 'Instrument de cercetare':
case 'Instrument de recerca':
case 'Instrument de recherche':
case 'Instrumenti istraživanja':
case 'Instrumento de investigación':
case 'Instrumento de Pesquisa':
case 'Istraživački instrument':
case 'Narzędzie badawcze':
case 'Onderzoeksinstrument':
case 'Research Instrument':
case 'Strumento di ricerca':
case 'Výzkumný nástroj':
case 'ابزار پژوهشی':
case 'أداة بحث':
case 'Όργανο έρευνας':
case 'Дослідний інструмент':
case 'Инструмент исследования':
case 'Истражувачки инструмент':
case 'ഗവേഷണ ഉപകരണങ്ങള്':
case '研究方法或工具':
case '研究装置':
case '科研仪器':
$genre = $genreDao->getByKey('RESEARCHINSTRUMENT', $journal->getId());
break;
// author.submit.suppFile.researchMaterials
case 'Araştırma Materyalleri':
case 'Các tài liệu nghiên cứu':
case 'Documents de recherche':
case 'Forschungsmaterial':
case 'Forskningsmateriale':
case 'Forskningsmaterialer':
case 'Forskningsmaterial':
case 'Ikerketako materialak':
case 'Istraživački materijali':
case 'Istraživački materijal':
case 'Materiais de investigación':
case 'Material de Pesquisa':
case 'Materiale de cercetare':
case 'Materiales de investigación':
case 'Materiali di ricerca':
case 'Materials de recerca':
case 'Materiały badawcze':
case 'Materi/ Bahan Riset':
case 'Onderzoeksmaterialen':
case 'Research Materials':
case 'Výzkumné materiály':
case 'مواد بحث':
case 'مواد پژوهشی':
case 'Υλικά έρευνας':
case 'Дослідні матеріали':
case 'Истражувачки материјали':
case 'Материалы исследования':
case 'ഗവേഷണ സാമഗ്രികള്':
case '研究材料':
case '科研资料':
$genre = $genreDao->getByKey('RESEARCHMATERIALS', $journal->getId());
break;
// author.submit.suppFile.researchResults
case 'Araştırma Sonuçları':
case 'Forschungsergebnisse':
case 'Forskningsresultater':
case 'Forskningsresultat':
case 'Hasil Riset':
case 'Ikerketaren emaitza':
case 'Istraživački rezultati':
case 'Kết quả nghiên cứu':
case 'Onderzoeksresultaten':
case 'Research Results':
case 'Resultados de investigación':
case 'Resultados de la investigación':
case 'Resultados de Pesquisa':
case 'Resultats de la recerca':
case 'Résultats de recherche':
case 'Rezultate de cercetare':
case 'Rezultati istraživanja':
case 'Rezultaty z badań':
case 'Risultati di ricerca':
case 'Výsledky výzkumu':
case 'نتایج پژوهش':
case 'نتائج بحث':
case 'Αποτελέσματα έρευνας':
case 'Истражувачки резултати':
case 'Результати дослідження':
case 'Результаты исследования':
case 'ഗവേഷണ ഫലങ്ങള്':
case '研究結果':
case '科研结果':
$genre = $genreDao->getByKey('RESEARCHRESULTS', $journal->getId());
break;
// author.submit.suppFile.sourceText
case 'Brontekst':
case 'Iturburu-testua':
case 'Izvorni tekst':
case 'Källtext':
case 'Kaynak Metin':
case 'Kildetekst':
case 'ソーステキスト':
case 'Quellentext':
case 'Source Text':
case 'Teks Sumber':
case 'Tekst źródłowy':
case 'Testo della fonte':
case 'Texte source':
case 'Texte sursă':
case 'Texto fonte':
case 'Texto fuente':
case 'Texto Original':
case 'Text original':
case 'Văn bản (text) nguồn':
case 'Zdrojový text':
case 'متن منبع':
case 'نص مصدر':
case 'Πηγαίο κείμενο':
case 'Изворен текст':
case 'Исходный текст':
case 'Текст першоджерела':
case 'സോഴ്സ് ടെക്സ്റ്റ്':
case '來源文獻':
case '源文本':
$genre = $genreDao->getByKey('SOURCETEXTS', $journal->getId());
break;
// author.submit.suppFile.transcripts
case 'Afskrifter':
case 'Kopya / Suret':
case 'Lời thoại':
case 'Reproduktioner':
case 'Transcrição':
case 'Transcricións':
case 'Transcripciones':
case 'Transcripcions':
case 'Transcripties':
case 'Transcriptions':
case 'Transcripts':
case 'Transcripturi':
case 'Transkrip':
case 'Transkripsjoner':
case 'Transkripte':
case 'Transkripti':
case 'Transkript':
case 'Transkripty':
case 'Transkripzioak':
case 'Transkrypcje':
case 'Trascrizioni':
case 'رونوشت':
case 'نصوص':
case 'Καταγραφή':
case 'Стенограми':
case 'Транскрипти':
case 'Транскрипты':
case 'പകര്പ്പുകള്':
case '副本':
case '筆記録':
$genre = $genreDao->getByKey('TRANSCRIPTS', $journal->getId());
break;
default:
$genre = $genreDao->getByKey('OTHER', $journal->getId());
break;
}
assert(isset($genre));
// Set genres for files
$submissionFiles = $submissionFileDao->getAllRevisions($row['file_id']);
foreach ((array) $submissionFiles as $submissionFile) {
$submissionFile->setGenreId($genre->getId());
$submissionFile->setUploaderUserId($creatorUserId);
$fileStage = $article->getStatus() == STATUS_PUBLISHED ? SUBMISSION_FILE_PROOF : SUBMISSION_FILE_SUBMISSION;
$submissionFile->setFileStage($fileStage);
$submissionFileDao->updateObject($submissionFile);
}
// Reload the files now that they're cast; set metadata
$submissionFiles = $submissionFileDao->getAllRevisions($row['file_id']);
foreach ((array) $submissionFiles as $submissionFile) {
$suppFileSettingsResult = $submissionFileDao->retrieve('SELECT * FROM article_supp_file_settings WHERE supp_id = ? AND setting_value IS NOT NULL', array($row['supp_id']));
$extraSettings = $extraGalleySettings = array();
while (!$suppFileSettingsResult->EOF) {
$sfRow = $suppFileSettingsResult->getRowAssoc(false);
$suppFileSettingsResult->MoveNext();
switch ($sfRow['setting_name']) {
case 'creator':
$submissionFile->setCreator($sfRow['setting_value'], $sfRow['locale']);
break;
case 'description':
$submissionFile->setDescription($sfRow['setting_value'], $sfRow['locale']);
break;
case 'publisher':
$submissionFile->setPublisher($sfRow['setting_value'], $sfRow['locale']);
break;
case 'source':
$submissionFile->setSource($sfRow['setting_value'], $sfRow['locale']);
break;
case 'sponsor':
$submissionFile->setSponsor($sfRow['setting_value'], $sfRow['locale']);
break;
case 'subject':
$submissionFile->setSubject($sfRow['setting_value'], $sfRow['locale']);
break;
case 'title':
$submissionFile->setName($sfRow['setting_value'], $sfRow['locale']);
break;
case 'typeOther': break; // Discard (at least for now)
case 'excludeDoi': break; // Discard (no longer relevant)
case 'excludeURN': break; // Discard (no longer relevant)
case 'pub-id::doi':
case 'pub-id::other::urn':
case 'pub-id::publisher-id':
case 'urnSuffix':
case 'doiSuffix':
case 'datacite::registeredDoi':
$extraGalleySettings[$sfRow['setting_name']] = $sfRow['setting_value'];
break;
default:
error_log('Unknown supplementary file setting "' . $sfRow['setting_name'] . '"!');
break;
}
}
$suppFileSettingsResult->Close();
// Store the old supp ID so that we can redirect requests for old URLs.
$extraSettings['old-supp-id'] = $row['supp_id'];
$submissionFileDao->updateObject($submissionFile);
// Preserve extra settings. (Plugins may not be loaded, so other mechanisms might not work.)
foreach ($extraSettings as $name => $value) {
$submissionFileDao->update(
'INSERT INTO submission_file_settings (file_id, setting_name, setting_value, setting_type) VALUES (?, ?, ?, ?)',
array(
$submissionFile->getFileId(),
$name,
$value,
'string'
)
);
}
if ($article->getStatus() == STATUS_PUBLISHED) {
// Converted from DAO call to raw SQL because submission_id is no longer available post-schema sync.
$articleGalleyDao->update(
'INSERT INTO submission_galleys (locale, submission_id, file_id, label) VALUES (?, ?, ?, ?)',
array(
$article->getLocale(),
$article->getId(),
$submissionFile->getFileId(),
$submissionFile->getName($article->getLocale())
)
);
$galleyId = $articleGalleyDao->getInsertId();
// Preserve extra settings. (Plugins may not be loaded, so other mechanisms might not work.)
foreach ($extraGalleySettings as $name => $value) {
$submissionFileDao->update(
'INSERT INTO submission_galley_settings (galley_id, setting_name, setting_value, setting_type) VALUES (?, ?, ?, ?)',
array(
$galleyId,
$name,
$value,
'string'
)
);
}
}
}
}
$suppFilesResult->Close();
return true;
}
/**
* Provide supplementary files of active submissions for review.
* @return boolean True indicates success.
*/
function provideSupplementaryFilesForReview() {
$submissionFileDao = DAORegistry::getDAO('SubmissionFileDAO'); /* @var $submissionFileDao SubmissionFileDAO */
$reviewRoundDao = DAORegistry::getDAO('ReviewRoundDAO'); /* @var $reviewRoundDao ReviewRoundDAO */
$reviewAssignmentDao = DAORegistry::getDAO('ReviewAssignmentDAO'); /* @var $reviewAssignmentDao ReviewAssignmentDAO */
$reviewFilesDao = DAORegistry::getDAO('ReviewFilesDAO'); /* @var $reviewFilesDao ReviewFilesDAO */
import('lib.pkp.classes.file.SubmissionFileManager');
// Get supp files with show_reviewers = 1
// We cannot support/consider remote supp files
$suppFilesResult = $submissionFileDao->retrieve('SELECT a.context_id, sf.* FROM article_supplementary_files sf, submissions a WHERE a.submission_id = sf.article_id AND sf.file_id <> 0 AND sf.show_reviewers = 1 AND sf.remote_url IS NULL and sf.file_id in (select f.file_id from submission_files f)');
while (!$suppFilesResult->EOF) {
$suppFilesRow = $suppFilesResult->getRowAssoc(false);
$suppFilesResult->MoveNext();
$reviewRounds = $reviewRoundDao->getBySubmissionId($suppFilesRow['article_id'], WORKFLOW_STAGE_ID_EXTERNAL_REVIEW);
// If a review round exists
// copy the supp file to the submission review stage, add it to each existing review round, and as a review round file
if ($reviewRounds->getCount() != 0) {
$submissionFileManager = new SubmissionFileManager($suppFilesRow['context_id'], $suppFilesRow['article_id']);
// Retrieve the supp file last revision number, although they probably only have revision 1.
$revisionNumber = $submissionFileDao->getLatestRevisionNumber($suppFilesRow['file_id']);
// copy the supp file to the submission review stage
$fileDetails = $submissionFileManager->copyFileToFileStage($suppFilesRow['file_id'], $revisionNumber, SUBMISSION_FILE_REVIEW_FILE, null, true);
if ($fileDetails) {
list($newFileId, $newRevision) = $fileDetails;
while ($reviewRound = $reviewRounds->next()) {
// add it to the review round
$submissionFileDao->assignRevisionToReviewRound($newFileId, $newRevision, $reviewRound);
// Get all review assignments
$reviewAssignments = $reviewAssignmentDao->getBySubmissionId($suppFilesRow['article_id'], $reviewRound->getId(), WORKFLOW_STAGE_ID_EXTERNAL_REVIEW);
foreach ($reviewAssignments as $reviewAssignment) {
// add it to the review files
$reviewFilesDao->grant($reviewAssignment->getId(), $newFileId);
}
}
} else {
error_log('WARNING: Unable to copy article_suppementary_files entry with file_id ' . $suppFilesRow['file_id'] . ' to review stage! Skipping this file.');
}
}
}
$suppFilesResult->Close();
return true;
}
function _createQuery($stageId, $submissionId, $sequence, $title, $dateNotified = null) {
$queryDao = DAORegistry::getDAO('QueryDAO'); /* @var $queryDao QueryDAO */
$noteDao = DAORegistry::getDAO('NoteDAO'); /* @var $noteDao NoteDAO */
$query = $queryDao->newDataObject();
$query->setAssocType(ASSOC_TYPE_SUBMISSION);
$query->setAssocId($submissionId);
$query->setStageId($stageId);
$query->setSequence($sequence);
$queryDao->insertObject($query);
$headNote = $noteDao->newDataObject();
$headNote->setAssocType(ASSOC_TYPE_QUERY);
$headNote->setAssocId($query->getId());
$headNote->setTitle($title);
$headNote->setDateCreated($dateNotified?$dateNotified:time());
$headNote->setDateModified($dateNotified?$dateNotified:time());
$noteDao->insertObject($headNote);
return $query;
}
/**
* Convert signoffs to queries.
* @return boolean True indicates success.
*/
function convertQueries() {
$submissionFileDao = DAORegistry::getDAO('SubmissionFileDAO'); /* @var $submissionFileDao SubmissionFileDAO */
import('lib.pkp.classes.submission.SubmissionFile');
$signoffsResult = $submissionFileDao->retrieve('SELECT * FROM signoffs WHERE user_id IS NOT NULL AND user_id <> 0');
$queryDao = DAORegistry::getDAO('QueryDAO'); /* @var $queryDao QueryDAO */
$noteDao = DAORegistry::getDAO('NoteDAO'); /* @var $noteDao NoteDAO */
$userDao = DAORegistry::getDAO('UserDAO'); /* @var $userDao UserDAO */
$stageAssignmentDao = DAORegistry::getDAO('StageAssignmentDAO'); /* @var $stageAssignmentDao StageAssignmentDAO */
// Go through all signoffs and migrate them into queries.
$copyeditingQueries = $proofreadingQueries = $layoutQueries = array();
while (!$signoffsResult->EOF) {
$row = $signoffsResult->getRowAssoc(false);
$fileId = $row['file_id'];
$symbolic = $row['symbolic'];
$dateNotified = $row['date_notified']?strtotime($row['date_notified']):null;
$dateCompleted = $row['date_completed']?strtotime($row['date_completed']):null;
$userId = $row['user_id'];
$signoffId = $row['signoff_id'];
assert($row['assoc_type'] == ASSOC_TYPE_SUBMISSION); // Already changed from ASSOC_TYPE_ARTICLE
$assocId = $row['assoc_id'];
$signoffsResult->MoveNext();
// Stage 1. Create or look up the query object.
switch ($symbolic) {
case 'SIGNOFF_COPYEDITING_INITIAL':
case 'SIGNOFF_COPYEDITING_AUTHOR':
case 'SIGNOFF_COPYEDITING_FINAL':
if (isset($copyeditingQueries[$assocId])) $query = $copyeditingQueries[$assocId];
else {
$query = $copyeditingQueries[$assocId] = $this->_createQuery(WORKFLOW_STAGE_ID_EDITING, $assocId, 1, 'Copyediting', $dateNotified);
}
break;
case 'SIGNOFF_LAYOUT':
$query = $layoutQueries[$assocId] = $this->_createQuery(WORKFLOW_STAGE_ID_PRODUCTION, $assocId, 1, 'Layout Editing', $dateNotified);
break;
case 'SIGNOFF_PROOFREADING_AUTHOR':
case 'SIGNOFF_PROOFREADING_PROOFREADER':
case 'SIGNOFF_PROOFREADING_LAYOUT':
if (isset($proofreadingQueries[$assocId])) $query = $proofreadingQueries[$assocId];
else {
$query = $proofreadingQueries[$assocId] = $this->_createQuery(WORKFLOW_STAGE_ID_PRODUCTION, $assocId, 2, 'Proofreading', $dateNotified);
}
break;
}
assert(isset($query)); // We've created or looked up a query.
$assignedUserIds = array($userId);
foreach (array(ROLE_ID_MANAGER, ROLE_ID_SUB_EDITOR, ROLE_ID_ASSISTANT) as $roleId) {
$stageAssignments = $stageAssignmentDao->getBySubmissionAndRoleId($assocId, $roleId, $query->getStageId());
while ($stageAssignment = $stageAssignments->next()) {
$assignedUserIds[] = $stageAssignment->getUserId();
}
}
// Ensure that the necessary users are assigned to the query
foreach (array_unique($assignedUserIds) as $assignedUserId) {
if (count($queryDao->getParticipantIds($query->getId(), $assignedUserId))!=0) continue;
$queryDao->insertParticipant($query->getId(), $assignedUserId);
}
$submissionFiles = $submissionFileDao->getAllRevisions($fileId);
foreach((array) $submissionFiles as $submissionFile) {
$submissionFile->setAssocType(ASSOC_TYPE_NOTE);
$submissionFile->setAssocId($query->getHeadNote()->getId());
$submissionFile->setFileStage(SUBMISSION_FILE_QUERY);
$submissionFileDao->updateObject($submissionFile);
}
}
$signoffsResult->Close();
// Migrate related notes into the queries
$commentsResult = $submissionFileDao->retrieve('SELECT * FROM submission_comments WHERE comment_type IN (3, 4, 5)');
while (!$commentsResult->EOF) {
$row = $commentsResult->getRowAssoc(false);
$commentsResult->MoveNext();
$note = $noteDao->newDataObject();
$note->setAssocType(ASSOC_TYPE_QUERY);
$note->setDateCreated(strtotime($row['date_posted']));
$note->setDateModified(strtotime($row['date_modified']));
switch ($row['comment_type']) {
case 3: // COMMENT_TYPE_COPYEDIT
$note->setTitle('Copyediting');
if (!isset($copyeditingQueries[$row['submission_id']])) {
$copyeditingQueries[$row['submission_id']] = $this->_createQuery(WORKFLOW_STAGE_ID_EDITING, $row['submission_id'], 1, 'Copyediting');
}
$note->setAssocId($copyeditingQueries[$row['submission_id']]->getId());
break;
case 4: // COMMENT_TYPE_LAYOUT
$note->setTitle('Layout Editing');
if (!isset($layoutQueries[$row['submission_id']])) {
$layoutQueries[$row['submission_id']] = $this->_createQuery(WORKFLOW_STAGE_ID_PRODUCTION, $row['submission_id'], 1, 'Layout Editing');
}
$note->setAssocId($layoutQueries[$row['submission_id']]->getId());
break;
case 5: // COMMENT_TYPE_PROOFREAD
$note->setTitle('Proofreading');
if (!isset($proofreadingQueries[$row['submission_id']])) {
$proofreadingQueries[$row['submission_id']] = $this->_createQuery(WORKFLOW_STAGE_ID_PRODUCTION, $row['submission_id'], 2, 'Proofreading');
}
$note->setAssocId($proofreadingQueries[$row['submission_id']]->getId());
break;
}
$note->setContents(nl2br($row['comments']));
$note->setUserId($row['author_id']);
$noteDao->insertObject($note);
}
$commentsResult->Close();
$submissionFileDao->update('DELETE FROM submission_comments WHERE comment_type IN (3, 4, 5)'); // COMMENT_TYPE_EDITOR_DECISION
return true;
}
/**
* Convert editor decision notes to a query.
* @return boolean True indicates success.
*/
function convertEditorDecisionNotes() {
$noteDao = DAORegistry::getDAO('NoteDAO'); /* @var $noteDao NoteDAO */
$queryDao = DAORegistry::getDAO('QueryDAO'); /* @var $queryDao QueryDAO */
$stageAssignmentDao = DAORegistry::getDAO('StageAssignmentDAO'); /* @var $stageAssignmentDao StageAssignmentDAO */
$commentsResult = $noteDao->retrieve('SELECT sc.*, a.user_id FROM submission_comments sc, articles_migration a WHERE sc.submission_id = a.article_id AND sc.comment_type=2 ORDER BY sc.submission_id, sc.comment_id ASC'); // COMMENT_TYPE_EDITOR_DECISION
$submissionId = 0;
$query = null; // Avoid Scrutinizer warnings
while (!$commentsResult->EOF) {
$row = $commentsResult->getRowAssoc(false);
$commentsResult->MoveNext();
if ($submissionId != $row['submission_id']) {
$submissionId = $row['submission_id'];
$query = $queryDao->newDataObject();
$query->setAssocType(ASSOC_TYPE_SUBMISSION);
$query->setAssocId($submissionId);
$query->setStageId(WORKFLOW_STAGE_ID_EXTERNAL_REVIEW);
$query->setSequence(REALLY_BIG_NUMBER);
$queryDao->insertObject($query);
$queryDao->resequence(ASSOC_TYPE_SUBMISSION, $submissionId);
$assignedUserIds = array($row['user_id']);
foreach (array(ROLE_ID_MANAGER, ROLE_ID_SUB_EDITOR, ROLE_ID_ASSISTANT) as $roleId) {
$stageAssignments = $stageAssignmentDao->getBySubmissionAndRoleId($submissionId, $roleId, $query->getStageId());
while ($stageAssignment = $stageAssignments->next()) {
$assignedUserIds[] = $stageAssignment->getUserId();
}
}
// Ensure that the necessary users are assigned to the query
foreach (array_unique($assignedUserIds) as $assignedUserId) {
if (count($queryDao->getParticipantIds($query->getId(), $assignedUserId))!=0) continue;
$queryDao->insertParticipant($query->getId(), $assignedUserId);
}
}
$note = $noteDao->newDataObject();
$note->setAssocType(ASSOC_TYPE_QUERY);
$note->setAssocId($query->getId());
$note->setContents(nl2br($row['comments']));
$note->setTitle('Editor Decision');
$note->setDateCreated(strtotime($row['date_posted']));
$note->setDateModified(strtotime($row['date_modified']));
$note->setUserId($row['author_id']);
$noteDao->insertObject($note);
}
$commentsResult->Close();
$noteDao->update('DELETE FROM submission_comments WHERE comment_type=2'); // COMMENT_TYPE_EDITOR_DECISION
return true;
}
/**
* Convert comments to editors to queries.
* @return boolean True indicates success.
*/
function convertCommentsToEditor() {
$submissionDao = DAORegistry::getDAO('SubmissionDAO'); /* @var $submissionDao SubmissionDAO */
$stageAssignmetDao = DAORegistry::getDAO('StageAssignmentDAO'); /* @var $stageAssignmetDao StageAssignmentDAO */
$queryDao = DAORegistry::getDAO('QueryDAO'); /* @var $queryDao QueryDAO */
$noteDao = DAORegistry::getDAO('NoteDAO'); /* @var $noteDao NoteDAO */
$userGroupDao = DAORegistry::getDAO('UserGroupDAO'); /* @var $userGroupDao UserGroupDAO */
import('lib.pkp.classes.security.Role'); // ROLE_ID_...
$commentsResult = $submissionDao->retrieve(
'SELECT s.submission_id, s.context_id, s.comments_to_ed, s.date_submitted
FROM submissions_tmp s
WHERE s.comments_to_ed IS NOT NULL AND s.comments_to_ed != \'\''
);
while (!$commentsResult->EOF) {
$row = $commentsResult->getRowAssoc(false);
$comments_to_ed = PKPString::stripUnsafeHtml($row['comments_to_ed']);
if ($comments_to_ed != ""){
$userId = null;
$authorAssignmentsResult = $stageAssignmetDao->getBySubmissionAndRoleId($row['submission_id'], ROLE_ID_AUTHOR);
if ($authorAssignmentsResult->getCount() != 0) {
// We assume the results are ordered by stage_assignment_id i.e. first author assignemnt is first
$userId = $authorAssignmentsResult->next()->getUserId();
} else {
$managerUserGroup = $userGroupDao->getDefaultByRoleId($row['context_id'], ROLE_ID_MANAGER);
$managerUsers = $userGroupDao->getUsersById($managerUserGroup->getId(), $row['context_id']);
$userId = $managerUsers->next()->getId();
}
assert($userId);
$query = $queryDao->newDataObject();
$query->setAssocType(ASSOC_TYPE_SUBMISSION);
$query->setAssocId($row['submission_id']);
$query->setStageId(WORKFLOW_STAGE_ID_SUBMISSION);
$query->setSequence(REALLY_BIG_NUMBER);
$queryDao->insertObject($query);
$queryDao->resequence(ASSOC_TYPE_SUBMISSION, $row['submission_id']);
$queryDao->insertParticipant($query->getId(), $userId);
$queryId = $query->getId();
$note = $noteDao->newDataObject();
$note->setUserId($userId);
$note->setAssocType(ASSOC_TYPE_QUERY);
$note->setTitle('Comments for the Editor');
$note->setContents($comments_to_ed);
$note->setDateCreated(strtotime($row['date_submitted']));
$note->setDateModified(strtotime($row['date_submitted']));
$note->setAssocId($queryId);
$noteDao->insertObject($note);
}
$commentsResult->MoveNext();
}
$commentsResult->Close();
// remove temporary table
$submissionDao->update('DROP TABLE submissions_tmp');
return true;
}
/**
* Localize issue cover images.
* @return boolean True indicates success.
*/
function localizeIssueCoverImages() {
$issueDao = DAORegistry::getDAO('IssueDAO'); /* @var $issueDao IssueDAO */
$publicFileManager = new PublicFileManager();
// remove strange old cover images with array values in the DB - from 3.alpha or 3.beta?
$issueDao->update('DELETE FROM issue_settings WHERE setting_name = \'coverImage\' AND setting_type = \'object\'');
// remove empty 3.0 cover images
$issueDao->update('DELETE FROM issue_settings WHERE setting_name = \'coverImage\' AND locale = \'\' AND setting_value = \'\'');
$issueDao->update('DELETE FROM issue_settings WHERE setting_name = \'coverImageAltText\' AND locale = \'\' AND setting_value = \'\'');
// get cover image duplicates, from 2.4.x and 3.0
$result = $issueDao->retrieve(
'SELECT DISTINCT iss1.issue_id, iss1.setting_value, i.journal_id
FROM issue_settings iss1
LEFT JOIN issues i ON (i.issue_id = iss1.issue_id)
JOIN issue_settings iss2 ON (iss2.issue_id = iss1.issue_id AND iss2.setting_name = \'coverImage\')
WHERE iss1.setting_name = \'fileName\''
);
// remove the old 2.4.x cover images, for which a new cover image exists
while (!$result->EOF) {
$row = $result->GetRowAssoc(false);
$oldFileName = $row['setting_value'];
if ($publicFileManager->fileExists($publicFileManager->getContextFilesPath($row['journal_id']) . '/' . $oldFileName)) {
$publicFileManager->removeContextFile($row['journal_id'], $oldFileName);
}
$issueDao->update('DELETE FROM issue_settings WHERE issue_id = ? AND setting_name = \'fileName\' AND setting_value = ?', array((int) $row['issue_id'], $oldFileName));
$result->MoveNext();
}
$result->Close();
// retrieve names for unlocalized issue cover images
$result = $issueDao->retrieve(
'SELECT iss.issue_id, iss.setting_value, j.journal_id, j.primary_locale
FROM issue_settings iss, issues i, journals j
WHERE iss.setting_name = \'coverImage\' AND iss.locale = \'\'
AND i.issue_id = iss.issue_id AND j.journal_id = i.journal_id'
);
// for all unlocalized issue cover images
// rename (copy + remove) the cover images files in the public folder,
// considereing the locale (using the journal primary locale)
while (!$result->EOF) {
$row = $result->GetRowAssoc(false);
$oldFileName = $row['setting_value'];
$newFileName = str_replace('.', '_' . $row['primary_locale'] . '.', $oldFileName);
if ($publicFileManager->fileExists($publicFileManager->getContextFilesPath($row['journal_id']) . '/' . $oldFileName)) {
$publicFileManager->copyContextFile($row['journal_id'], $publicFileManager->getContextFilesPath($row['journal_id']) . '/' . $oldFileName, $newFileName);
$publicFileManager->removeContextFile($row['journal_id'], $oldFileName);
}
$result->MoveNext();
}
$result->Close();
$driver = $issueDao->getDriver();
switch ($driver) {
case 'mysql':
case 'mysqli':
// Update cover image names in the issue_settings table
$issueDao->update(
'UPDATE issue_settings iss, issues i, journals j
SET iss.locale = j.primary_locale, iss.setting_value = CONCAT(LEFT( iss.setting_value, LOCATE(\'.\', iss.setting_value) - 1 ), \'_\', j.primary_locale, \'.\', SUBSTRING_INDEX(iss.setting_value,\'.\',-1))
WHERE iss.setting_name = \'coverImage\' AND iss.locale = \'\' AND i.issue_id = iss.issue_id AND j.journal_id = i.journal_id'
);
// Update cover image alt texts in the issue_settings table
$issueDao->update(
'UPDATE issue_settings iss, issues i, journals j SET iss.locale = j.primary_locale WHERE iss.setting_name = \'coverImageAltText\' AND iss.locale = \'\' AND i.issue_id = iss.issue_id AND j.journal_id = i.journal_id'
);
break;
case 'postgres':
case 'postgres64':
case 'postgres7':
case 'postgres8':
case 'postgres9':
// Update cover image names in the issue_settings table
$issueDao->update(
'UPDATE issue_settings
SET locale = j.primary_locale, setting_value = REGEXP_REPLACE(issue_settings.setting_value, \'[\.]\', CONCAT(\'_\', j.primary_locale, \'.\'))
FROM issues i, journals j
WHERE issue_settings.setting_name = \'coverImage\' AND issue_settings.locale = \'\' AND i.issue_id = issue_settings.issue_id AND j.journal_id = i.journal_id'
);
// Update cover image alt texts in the issue_settings table
$issueDao->update(
'UPDATE issue_settings
SET locale = j.primary_locale
FROM issues i, journals j
WHERE issue_settings.setting_name = \'coverImageAltText\' AND issue_settings.locale = \'\' AND i.issue_id = issue_settings.issue_id AND j.journal_id = i.journal_id'
);
break;
default: fatalError('Unknown database type!');
}
$issueDao->flushCache();
return true;
}
/**
* Localize article cover images.
* @return boolean True indicates success.
*/
function localizeArticleCoverImages() {
$submissionDao = DAORegistry::getDAO('SubmissionDAO'); /* @var $submissionDao SubmissionDAO */
$publicFileManager = new PublicFileManager();
// remove strange old cover images with array values in the DB - from 3.alpha or 3.beta?
$submissionDao->update('DELETE FROM submission_settings WHERE setting_name = \'coverImage\' AND setting_type = \'object\'');
// remove empty 3.0 cover images
$submissionDao->update('DELETE FROM submission_settings WHERE setting_name = \'coverImage\' AND locale = \'\' AND setting_value = \'\'');
$submissionDao->update('DELETE FROM submission_settings WHERE setting_name = \'coverImageAltText\' AND locale = \'\' AND setting_value = \'\'');
// get cover image duplicates, from 2.4.x and 3.0
$result = $submissionDao->retrieve(
'SELECT DISTINCT ss1.submission_id, ss1.setting_value, s.context_id
FROM submission_settings ss1
LEFT JOIN submissions s ON (s.submission_id = ss1.submission_id)
JOIN submission_settings ss2 ON (ss2.submission_id = ss1.submission_id AND ss2.setting_name = \'coverImage\')
WHERE ss1.setting_name = \'fileName\''
);
// remove the old 2.4.x cover images, for which a new cover image exists
while (!$result->EOF) {
$row = $result->GetRowAssoc(false);
$submissionId = $row['submission_id'];
$oldFileName = $row['setting_value'];
if ($publicFileManager->fileExists($publicFileManager->getContextFilesPath($row['context_id']) . '/' . $oldFileName)) {
$publicFileManager->removeContextFile($row['journal_id'], $oldFileName);
}
$submissionDao->update('DELETE FROM submission_settings WHERE submission_id = ? AND setting_name = \'fileName\' AND setting_value = ?', array((int) $submissionId, $oldFileName));
$result->MoveNext();
}
$result->Close();
// retrieve names for unlocalized article cover images
$result = $submissionDao->retrieve(
'SELECT ss.submission_id, ss.setting_value, j.journal_id, j.primary_locale
FROM submission_settings ss, submissions s, journals j
WHERE ss.setting_name = \'coverImage\' AND ss.locale = \'\'
AND s.submission_id = ss.submission_id AND j.journal_id = s.context_id'
);
// for all unlocalized article cover images
// rename (copy + remove) the cover images files in the public folder,
// considereing the locale (using the journal primary locale)
while (!$result->EOF) {
$row = $result->GetRowAssoc(false);
$oldFileName = $row['setting_value'];
$newFileName = str_replace('.', '_' . $row['primary_locale'] . '.', $oldFileName);
if ($publicFileManager->fileExists($publicFileManager->getContextFilesPath($row['journal_id']) . '/' . $oldFileName)) {
$publicFileManager->copyContextFile($row['journal_id'], $publicFileManager->getContextFilesPath($row['journal_id']) . '/' . $oldFileName, $newFileName);
$publicFileManager->removeContextFile($row['journal_id'], $oldFileName);
}
$result->MoveNext();
}
$result->Close();
$driver = $submissionDao->getDriver();
switch ($driver) {
case 'mysql':
case 'mysqli':
// Update cover image names in the submission_settings table
$submissionDao->update(
'UPDATE submission_settings ss, submissions s, journals j
SET ss.locale = j.primary_locale, ss.setting_value = CONCAT(LEFT( ss.setting_value, LOCATE(\'.\', ss.setting_value) - 1 ), \'_\', j.primary_locale, \'.\', SUBSTRING_INDEX(ss.setting_value,\'.\',-1))
WHERE ss.setting_name = \'coverImage\' AND ss.locale = \'\' AND s.submission_id = ss.submission_id AND j.journal_id = s.context_id'
);
// Update cover image alt texts in the submission_settings table
$submissionDao->update(
'UPDATE submission_settings ss, submissions s, journals j
SET ss.locale = j.primary_locale
WHERE ss.setting_name = \'coverImageAltText\' AND ss.locale = \'\' AND s.submission_id = ss.submission_id AND j.journal_id = s.context_id'
);
break;
case 'postgres':
case 'postgres64':
case 'postgres7':
case 'postgres8':
case 'postgres9':
// Update cover image names in the submission_settings table
$submissionDao->update(
'UPDATE submission_settings
SET locale = j.primary_locale, setting_value = REGEXP_REPLACE(submission_settings.setting_value, \'[\.]\', CONCAT(\'_\', j.primary_locale, \'.\'))
FROM submissions s, journals j
WHERE submission_settings.setting_name = \'coverImage\' AND submission_settings.locale = \'\' AND s.submission_id = submission_settings.submission_id AND j.journal_id = s.context_id'
);
// Update cover image alt texts in the submission_settings table
$submissionDao->update(
'UPDATE submission_settings
SET locale = j.primary_locale
FROM submissions s, journals j
WHERE submission_settings.setting_name = \'coverImageAltText\' AND submission_settings.locale = \'\' AND s.submission_id = submission_settings.submission_id AND j.journal_id = s.context_id'
);
break;
default: fatalError('Unknown database type!');
}
$submissionDao->flushCache();
return true;
}
/**
* For 3.1.0 upgrade (#2467): In multi-journal upgrades from OJS 2.x, the
* user_group_id column in the authors table may be updated to point to
* user groups in other journals.
* @return boolean
*/
function fixAuthorGroup() {
$userGroupDao = DAORegistry::getDAO('UserGroupDAO'); /* @var $userGroupDao UserGroupDAO */
$result = $userGroupDao->retrieve(
'SELECT a.author_id, s.context_id FROM authors a JOIN submissions s ON (a.submission_id = s.submission_id) JOIN user_groups g ON (a.user_group_id = g.user_group_id) WHERE g.context_id <> s.context_id'
);
while (!$result->EOF) {
$row = $result->GetRowAssoc(false);
$authorGroup = $userGroupDao->getDefaultByRoleId($row['context_id'], ROLE_ID_AUTHOR);
if ($authorGroup) $userGroupDao->update('UPDATE authors SET user_group_id = ? WHERE author_id = ?', array((int) $authorGroup->getId(), $row['author_id']));
$result->MoveNext();
}
$result->Close();
return true;
}
/**
* For 3.0.0 - 3.0.2 upgrade: first part of the fix for the migrated reviewer files.
* The files are renamed and moved from 'review' to 'review/attachment' folder.
* @return boolean
*/
function moveReviewerFiles() {
$submissionFileDao = DAORegistry::getDAO('SubmissionFileDAO'); /* @var $submissionFileDao SubmissionFileDAO */
import('lib.pkp.classes.file.SubmissionFileManager');
// get reviewer file ids
$result = $submissionFileDao->retrieve(
'SELECT ra.review_id, ra.submission_id, ra.review_round_id, ra.review_id, ra.reviewer_file_id, s.context_id
FROM review_assignments ra, submissions s
WHERE ra.reviewer_file_id IS NOT NULL AND s.submission_id = ra.submission_id'
);
while (!$result->EOF) {
$row = $result->GetRowAssoc(false);
$submissionFileManager = new SubmissionFileManager($row['context_id'], $row['submission_id']);
$revisions = $submissionFileDao->getAllRevisions($row['reviewer_file_id']);
if (!empty($revisions)) {
foreach ($revisions as $revision) {
$wrongFilePath = $revision->getFilePath();
$revision->setFileStage(SUBMISSION_FILE_REVIEW_ATTACHMENT);
$newFilePath = $revision->getFilePath();
if (!file_exists($newFilePath)) {
if (!file_exists($path = dirname($newFilePath)) && !$submissionFileManager->mkdirtree($path)) {
error_log("ERROR: Unable to make directory \"$path\"");
}
if (!rename($wrongFilePath, $newFilePath)) {
error_log("ERROR: Unable to move \"$wrongFilePath\" to \"$newFilePath\".");
}
}
}
} else {
error_log('ERROR: Reviewer files with ID ' . $row['reviewer_file_id'] . ' from review assignment ' .$row['review_id'] . ' could not be found in the database table submission_files');
}
$result->MoveNext();
}
$result->Close();
return true;
}
/**
* For 2.4.x - 3.1.0 upgrade: remove cancelled review assignments.
* @return boolean
*/
function removeCancelledReviewAssignments() {
$reviewAssignmentDao = DAORegistry::getDAO('ReviewAssignmentDAO'); /* @var $reviewAssignmentDao ReviewAssignmentDAO */
// get cancelled review assignemnts
$result = $reviewAssignmentDao->retrieve('SELECT review_id FROM review_assignments_tmp');
while (!$result->EOF) {
$row = $result->GetRowAssoc(false);
$reviewAssignmentDao->deleteById($row['review_id']);
$result->MoveNext();
}
$result->Close();
// remove temporary table
$reviewAssignmentDao->update('DROP TABLE review_assignments_tmp');
// update log messages
$eventLogDao = DAORegistry::getDAO('SubmissionEventLogDAO'); /* @var $eventLogDao SubmissionEventLogDAO */
$eventLogDao->update('UPDATE event_log SET message = \'log.review.reviewCleared\' WHERE message = \'log.review.reviewCancelled\'');
return true;
}
/**
* For 2.4.x - 3.1.0 upgrade: concatenate removed journal setting fields into the new journal setting 'about'.
* @return boolean
*/
function concatenateIntoAbout() {
$journalDao = DAORegistry::getDAO('JournalDAO'); /* @var $journalDao JournalDAO */
$journalSettingsDao = DAORegistry::getDAO('JournalSettingsDAO'); /* @var $journalSettingsDao JournalSettingsDAO */
$journals = $journalDao->getAll();
while ($journal = $journals->next()) {
$settings = $journalSettingsDao->loadSettings($journal->getId());
$supportedFormLocales = $journal->getSupportedFormLocales();
$focusAndScope = $journalSettingsDao->getSetting($journal->getId(), 'focusScopeDesc');
$focusAndScope['localeKey'] = 'about.focusAndScope';
$reviewPolicy = $journalSettingsDao->getSetting($journal->getId(), 'reviewPolicy');
$reviewPolicy['localeKey'] = 'about.peerReviewProcess';
$pubFreqPolicy = $journalSettingsDao->getSetting($journal->getId(), 'pubFreqPolicy');
$pubFreqPolicy['localeKey'] = 'about.publicationFrequency';
$oaPolicy = array();
if ($journal->getSetting('publishingMode') == PUBLISHING_MODE_OPEN) {
$oaPolicy = $journalSettingsDao->getSetting($journal->getId(), 'openAccessPolicy');
$oaPolicy['localeKey'] = 'about.openAccessPolicy';
}
// the elements order accords to how they were displayed on the about page
$editorialPolicySettings = array(
'focusAndScope' => $focusAndScope,
'peerReviewProcess' => $reviewPolicy,
'publicationFrequency' => $pubFreqPolicy,
'openAccessPolicy' => $oaPolicy,
);
$customAboutItems = $journalSettingsDao->getSetting($journal->getId(), 'customAboutItems');
$sponsorNote = $journalSettingsDao->getSetting($journal->getId(), 'sponsorNote');
$sponsors = $journalSettingsDao->getSetting($journal->getId(), 'sponsors');
$contributorNote = $journalSettingsDao->getSetting($journal->getId(), 'contributorNote');
$contributorNote['localeKey'] = 'grid.contributor.title';
$contributors = $journalSettingsDao->getSetting($journal->getId(), 'contributors');
$history = $journalSettingsDao->getSetting($journal->getId(), 'history');
$history['localeKey'] = 'about.history';
// the elements order accords to how they were displayed on the about page
$otherSettings = array(
'sponsors' => $sponsorNote,
'contributors' => $contributorNote,
'history' => $history,
);
$aboutJournal = array();
foreach ($supportedFormLocales as $locale) {
AppLocale::requireComponents(LOCALE_COMPONENT_APP_COMMON, LOCALE_COMPONENT_PKP_GRID, $locale);
$aboutJournal[$locale] = '';
// concatenate editorial policies first
foreach ($editorialPolicySettings as $divId => $editorialPolicySetting) {
if (!empty($editorialPolicySetting[$locale])) {
$aboutJournal[$locale] .= '
<div id="'.$divId.'">
<h3>'.__($editorialPolicySetting['localeKey'], array(), $locale).'</h3>
<p>'.nl2br($editorialPolicySetting[$locale]).'</p>
</div>';
}
}
// concatenate then the custom about items
if (!empty($customAboutItems[$locale])) {
foreach ($customAboutItems[$locale] as $index => $customItem) {
if (!empty($customItem['title']) && !empty($customItem['content'])) {
$aboutJournal[$locale] .= '
<div id="custom-'.$index.'">
<h3>'.$customItem['title'].'</h3>
<p>'.nl2br($customItem['content']).'</p>
</div>';
}
}
}
// finally, concatenate the other settings
foreach ($otherSettings as $divId => $otherSetting) {
if ($divId == 'sponsors') {
if (!empty($otherSetting[$locale]) || !empty($sponsors)) {
$aboutJournal[$locale] .= '
<div id="'.$divId.'">
<h3>Sponsors</h3>'; // hard coded because the locale key does no exist any more
if (!empty($otherSetting[$locale])) {
$aboutJournal[$locale] .= '
<p>'.nl2br($otherSetting[$locale]).'</p>';
}
if (!empty($sponsors)) {
$aboutJournal[$locale] .= '<ul>';
foreach ($sponsors as $sponsor) {
$aboutJournal[$locale] .= '<li>';
if (!empty($sponsor['url'])) {
$aboutJournal[$locale] .= '
<a href="'.htmlspecialchars($sponsor['url']).'">'.htmlspecialchars($sponsor['institution']).'</a>';
} else {
$aboutJournal[$locale] .= htmlspecialchars($sponsor['institution']);
}
$aboutJournal[$locale] .= '</li>';
}
$aboutJournal[$locale] .= '</ul>';
}
$aboutJournal[$locale] .= '</div>';
}
} elseif ($divId == 'contributors') {
if (!empty($otherSetting[$locale]) || !empty($contributors)) {
$aboutJournal[$locale] .= '
<div id="'.$divId.'">
<h3>'.__($otherSetting['localeKey'], array(), $locale).'</h3>';
if (!empty($otherSetting[$locale])) {
$aboutJournal[$locale] .= '
<p>'.nl2br($otherSetting[$locale]).'</p>';
}
if (!empty($contributors)) {
$aboutJournal[$locale] .= '<ul>';
foreach ($contributors as $contributor) {
$aboutJournal[$locale] .= '<li>';
if (!empty($contributor['url'])) {
$aboutJournal[$locale] .= '
<a href="'.htmlspecialchars($contributor['url']).'">'.htmlspecialchars($contributor['name']).'</a>';
} else {
$aboutJournal[$locale] .= htmlspecialchars($contributor['name']);
}
$aboutJournal[$locale] .= '</li>';
}
$aboutJournal[$locale] .= '</ul>';
}
$aboutJournal[$locale] .= '</div>';
}
} else {
if (!empty($otherSetting[$locale])) {
$aboutJournal[$locale] .= '
<div id="'.$divId.'">
<h3>'.__($otherSetting['localeKey'], array(), $locale).'</h3>
<p>'.nl2br($otherSetting[$locale]).'</p>
</div>';
}
}
}
}
$journalSettingsDao->updateSetting($journal->getId(), 'about', $aboutJournal, 'string', true);
unset($journal);
}
return true;
}
/**
* For 2.4.x - 3.1.0 upgrade: concatenate editorialTeam and displayMembership page to new journal setting 'masthead'.
* @return boolean
*/
function concatenateIntoMasthead() {
$roles = array(OJS2_ROLE_ID_EDITOR, OJS2_ROLE_ID_SECTION_EDITOR, OJS2_ROLE_ID_LAYOUT_EDITOR, OJS2_ROLE_ID_COPYEDITOR, OJS2_ROLE_ID_PROOFREADER);
$localeKeys = array(
OJS2_ROLE_ID_EDITOR => array('user.role.editor', 'user.role.editors'),
OJS2_ROLE_ID_SECTION_EDITOR => array('user.role.subEditor', 'user.role.subEditors'),
OJS2_ROLE_ID_LAYOUT_EDITOR => array('user.role.layoutEditor', 'user.role.layoutEditors'),
OJS2_ROLE_ID_COPYEDITOR => array('user.role.copyeditor', 'user.role.copyeditors'),
OJS2_ROLE_ID_PROOFREADER => array('user.role.proofreader', 'user.role.proofreaders'),
);
$roleDao = DAORegistry::getDAO('RoleDAO'); /* @var $roleDao RoleDAO */
$userDao = DAORegistry::getDAO('UserDAO'); /* @var $userDao UserDAO */
$journalDao = DAORegistry::getDAO('JournalDAO'); /* @var $journalDao JournalDAO */
$journalSettingsDao = DAORegistry::getDAO('JournalSettingsDAO'); /* @var $journalSettingsDao JournalSettingsDAO */
$isoCodes = new \Sokil\IsoCodes\IsoCodesFactory();
$countries = array();
foreach ($isoCodes->getCountries() as $country) {
$countries[$country->getAlpha2()] = $country->getLocalName();
}
$journals = $journalDao->getAll();
while ($journal = $journals->next()) {
$settings = $journalSettingsDao->loadSettings($journal->getId());
if ($journalSettingsDao->getSetting($journal->getId(), 'boardEnabled')) {
// get all users by group ID
$groupUsers = array();
$groupPrimaryLocaleTitles = array();
// get groups sorted by context -- that accords to the order they are displayed on the about page
$dataSource = $roleDao->getDataSource();
$allGroupsResult = $roleDao->retrieve('SELECT * FROM ' . $dataSource->nameQuote . 'groups' . $dataSource->nameQuote . ' WHERE assoc_type = ? AND assoc_id = ? AND about_displayed = 1 ORDER BY context, seq', array((int) ASSOC_TYPE_JOURNAL, (int) $journal->getId()));
while (!$allGroupsResult->EOF) {
$groupRow = $allGroupsResult->getRowAssoc(false);
$groupMembershipsResult = $roleDao->retrieve('SELECT * FROM group_memberships WHERE group_id = ? AND about_displayed = 1 ORDER BY seq', $groupRow['group_id']);
while (!$groupMembershipsResult->EOF) {
$groupMembershipRow = $groupMembershipsResult->getRowAssoc(false);
$user = $userDao->getById($groupMembershipRow['user_id']);
if ($user) {
$groupUsers[$groupRow['group_id']][] = $user;
$groupPrimaryLocaleTitleResult = $roleDao->retrieve('SELECT setting_value FROM group_settings WHERE group_id = ? AND locale = ? AND setting_name = \'title\'', array((int) $groupRow['group_id'], $journal->getPrimaryLocale()));
$groupPrimaryLocaleTitle = $groupPrimaryLocaleTitleResult->getRowAssoc(false);
$groupPrimaryLocaleTitles[$groupRow['group_id']] = $groupPrimaryLocaleTitle['setting_value'];
}
$groupMembershipsResult->MoveNext();
}
$groupMembershipsResult->Close();
$allGroupsResult->MoveNext();
}
$allGroupsResult->Close();
} else {
// get all users by role ID
$roleUsers = array();
foreach ($roles as $roleId) {
$allUsersResult = $roleDao->retrieve('SELECT DISTINCT user_id FROM roles WHERE role_id = ? AND journal_id = ?', array((int) $roleId, (int) $journal->getId()));
while (!$allUsersResult->EOF) {
$allUsersRow = $allUsersResult->getRowAssoc(false);
$user = $userDao->getById($allUsersRow['user_id']);
if ($user) $roleUsers[$roleId][] = $user;
$allUsersResult->MoveNext();
}
$allUsersResult->Close();
}
}
$supportedFormLocales = $journal->getSupportedFormLocales();
$masthead = array();
foreach ($supportedFormLocales as $locale) {
AppLocale::requireComponents(LOCALE_COMPONENT_APP_COMMON, LOCALE_COMPONENT_PKP_USER, $locale);
$masthead[$locale] = '';
if ($journalSettingsDao->getSetting($journal->getId(), 'boardEnabled')) {
// The Editorial Team feature has been enabled.
// Generate information using Group data.
foreach ($groupUsers as $groupId => $usersArray) {
$groupTitleResult = $roleDao->retrieve('SELECT setting_value FROM group_settings WHERE group_id = ? AND locale = ? AND setting_name = \'title\'', array((int) $groupId, $locale));
if ($groupTitleResult->RecordCount() == 0) {
$groupTitle = $groupPrimaryLocaleTitles[$groupId];
} else {
$groupTitleRow = $groupTitleResult->getRowAssoc(false);
$groupTitle = $groupTitleRow['setting_value'];
}
$masthead[$locale] .= '<h4>'.$groupTitle.'</h4>';
foreach ($usersArray as $user) {
$masthead[$locale] .= '<p>'.htmlspecialchars($user->getFullName());
if ($user->getAffiliation($locale)) {
$masthead[$locale] .= ', '.htmlspecialchars($user->getAffiliation($locale));
}
if ($user->getCountry()) {
$masthead[$locale] .= ', '.htmlspecialchars($countries[$user->getCountry()]);
}
$masthead[$locale] .= '</p>';
}
}
if (!empty($masthead[$locale])) {
$masthead[$locale] = '<div id="group">' .$masthead[$locale] .'</div>';
}
} else {
// Don't use the Editorial Team feature. Generate
// Editorial Team information using Role info.
foreach ($roleUsers as $roleId => $usersArray) {
$masthead[$locale] .= '<div id="'.__($localeKeys[$roleId][1], array(), $locale).'">';
if (count($usersArray) == 1) {
$masthead[$locale] .= '<h3>'.__($localeKeys[$roleId][0], array(), $locale).'</h3>';
} else {
$masthead[$locale] .= '<h3>'.__($localeKeys[$roleId][1], array(), $locale).'</h3>';
}
foreach ($usersArray as $user) {
$masthead[$locale] .= '<p>'.htmlspecialchars($user->getFullName());
if ($user->getAffiliation($locale)) {
$masthead[$locale] .= ', '.htmlspecialchars($user->getAffiliation($locale));
}
if ($user->getCountry()) {
$masthead[$locale] .= ', '.htmlspecialchars($countries[$user->getCountry()]);
}
$masthead[$locale] .= '</p>';
}
$masthead[$locale] .= '</div>';
}
if (!empty($masthead[$locale])) {
$masthead[$locale] = '<div id="editorialTeam">' .$masthead[$locale] .'</div>';
}
}
}
$journalSettingsDao->updateSetting($journal->getId(), 'editorialTeam', $masthead, 'string', true);
unset($journal);
}
return true;
}
/**
* Fix galley image associations (https://github.com/pkp/pkp-lib/issues/2582)
* @return boolean
*/
function repairImageAssociations() {
$genreDao = DAORegistry::getDAO('GenreDAO'); /* @var $genreDao GenreDAO */
$submissionDao = DAORegistry::getDAO('SubmissionDAO'); /* @var $submissionDao SubmissionDAO */
$submissionFileDao = DAORegistry::getDAO('SubmissionFileDAO'); /* @var $submissionFileDao SubmissionFileDAO */
$result = $submissionFileDao->retrieve('SELECT df.file_id AS dependent_file_id, gf.file_id AS galley_file_id FROM submission_files df, submission_files gf, submission_html_galley_images i, submission_galleys g WHERE i.galley_id = g.galley_id AND g.file_id = gf.file_id AND i.file_id = df.file_id');
while (!$result->EOF) {
$row = $result->GetRowAssoc(false);
$submissionFiles = $submissionFileDao->getAllRevisions($row['dependent_file_id']);
foreach ((array) $submissionFiles as $submissionFile) {
if ($submissionFile->getFileStage() != SUBMISSION_FILE_PUBLIC) continue;
$submission = $submissionDao->getById($submissionFile->getSubmissionId());
$imageGenre = $genreDao->getByKey('IMAGE', $submission->getContextId());
$submissionFile->setFileStage(SUBMISSION_FILE_DEPENDENT);
$submissionFile->setAssocType(ASSOC_TYPE_SUBMISSION_FILE);
$submissionFile->setAssocId($row['galley_file_id']);
$submissionFile->setGenreId($imageGenre->getId());
$submissionFileDao->updateObject($submissionFile);
}
$result->MoveNext();
}
$submissionDao->update('DROP TABLE submission_html_galley_images');
return true;
}
/**
* For 2.4.x - 3.1.0 upgrade: repair already migrated keywords and subjects.
* @return boolean
*/
function repairKeywordsAndSubjects() {
$request = Application::get()->getRequest();
$site = $request->getSite();
$installedLocales = $site->getInstalledLocales();
$submissionSubjectDao = DAORegistry::getDAO('SubmissionSubjectDAO'); /* @var $submissionSubjectDao SubmissionSubjectDAO */
$submissionKeywordDao = DAORegistry::getDAO('SubmissionKeywordDAO'); /* @var $submissionKeywordDao SubmissionKeywordDAO */
$submissionSubjectEntryDao = DAORegistry::getDAO('SubmissionSubjectEntryDAO'); /* @var $submissionSubjectEntryDao SubmissionSubjectEntryDAO */
// insert and correct old keywords migration:
// get old keywords
$subjectsToKeep = array();
$oldKeywordsFound = false;
$result = $submissionKeywordDao->retrieve('SELECT * FROM submission_settings WHERE setting_name = \'subject\' AND setting_value <> \'\'');
if ($result->RecordCount() > 0) $oldKeywordsFound = true;
while (!$result->EOF) {
$row = $result->GetRowAssoc(false);
$submissionId = $row['submission_id'];
$locale = $row['locale'];
$oldKeywordsArray = preg_split('/[,;:]/', $row['setting_value']);
$oldKeywords = array_map('trim', $oldKeywordsArray);
// get current keywords
$newKeywords = array();
$newKeywordsArray = $submissionKeywordDao->getKeywords($submissionId, [$locale], ASSOC_TYPE_SUBMISSION);
if (array_key_exists($locale, $newKeywordsArray)) {
$newKeywords = array_map('trim', $newKeywordsArray[$locale]);
}
// get the difference and insert them
$keywordsToAdd = array_diff($oldKeywords, $newKeywords);
if (!empty($keywordsToAdd)) {
$submissionKeywordDao->insertKeywords(array($locale => $keywordsToAdd), $submissionId, false, ASSOC_TYPE_SUBMISSION);
}
// correct the old keywords migration:
// because the old keywords were already migrated as subjects earlier:
// get current subjects for all possible locales, in order to also
// consider locales other than old keywords locales (for example if added after the migration),
// in order not to remove those when inserting below
if (!array_key_exists($submissionId, $subjectsToKeep)) {
$newSubjectsArray = $submissionSubjectDao->getSubjects($submissionId, $installedLocales, ASSOC_TYPE_SUBMISSION);
$subjectsToKeep[$submissionId] = $newSubjectsArray;
}
// if subjects for the current locale exist
if (array_key_exists($locale, $subjectsToKeep[$submissionId])) {
// get current subjects for the current locale
$newSubjects = array_map('trim', $subjectsToKeep[$submissionId][$locale]);
// get the difference to keep only them
$subjectsToKeep[$submissionId][$locale] = array_diff($newSubjects, $oldKeywords);
}
$result->MoveNext();
}
$result->Close();
unset($newSubjects);
unset($newSubjectsArray);
// if old keywords were found, it means that this this function is executed for the first time
// i.e. the subjects should be corrected
if ($oldKeywordsFound) {
// insert the subjects that should be kept, overriding the existing ones
// also if they are empty, because then they should be deleted
foreach ($subjectsToKeep as $submissionId => $submissionSubjects) {
$submissionSubjectDao->insertSubjects($submissionSubjects, $submissionId, true, ASSOC_TYPE_SUBMISSION);
}
}
// insert old subjects
$result = $submissionKeywordDao->retrieve('SELECT * FROM submission_settings WHERE setting_name = \'subjectClass\' AND setting_value <> \'\'');
while (!$result->EOF) {
$row = $result->GetRowAssoc(false);
$submissionId = $row['submission_id'];
$locale = $row['locale'];
$oldSubjectsArray = preg_split('/[,;:]/', $row['setting_value']);
$oldSubjects = array_map('trim', $oldSubjectsArray);
// get current subjects
$newSubjects = array();
$newSubjectsArray = $submissionSubjectDao->getSubjects($submissionId, array($locale), ASSOC_TYPE_SUBMISSION);
if (array_key_exists($locale, $newSubjectsArray)) {
$newSubjects = array_map('trim', $newSubjectsArray[$locale]);
}
// get the difference and insert them
$subjectsToAdd = array_diff($oldSubjects, $newSubjects);
if (!empty($subjectsToAdd)) {
$submissionSubjectDao->insertSubjects(array($locale => $subjectsToAdd), $submissionId, false, ASSOC_TYPE_SUBMISSION);
}
$result->MoveNext();
}
$result->Close();
// delete old settings
$submissionKeywordDao->update('DELETE FROM submission_settings WHERE setting_name = \'discipline\' OR setting_name = \'subject\' OR setting_name = \'subjectClass\' OR setting_name = \'sponsor\'');
return true;
}
/**
* For 3.0.x - 3.1.0 upgrade: repair enabled plugin setting for site plugins.
* @return boolean
*/
function enabledSitePlugins() {
$allPlugins =& PluginRegistry::getAllPlugins();
$pluginSettings = DAORegistry::getDAO('PluginSettingsDAO');
foreach ($allPlugins as $plugin) {
if ($plugin->isSitePlugin()) {
$pluginName = strtolower_codesafe($plugin->getName());
if ($pluginName != 'customblockmanagerplugin') {
$result = $pluginSettings->update('DELETE FROM plugin_settings WHERE plugin_name = ? AND setting_name = \'enabled\' AND context_id <> 0', array($pluginName));
}
}
}
return true;
}
/**
* For 3.0.x - 3.1.0 upgrade: repair the file names in files_dir after the genres are fixed in the DB.
*
* NOTE: we can assume that the migrated file names to be fixed are with genre ID = 1, s. https://github.com/pkp/pkp-lib/issues/2506
*
* @return boolean
*/
function fixGenreIdInFileNames() {
$journalDao = DAORegistry::getDAO('JournalDAO'); /* @var $journalDao JournalDAO */
$genreDao = DAORegistry::getDAO('GenreDAO'); /* @var $genreDao GenreDAO */
$submissionDao = DAORegistry::getDAO('SubmissionDAO'); /* @var $submissionDao SubmissionDAO */
$submissionFileDao = DAORegistry::getDAO('SubmissionFileDAO'); /* @var $submissionFileDao SubmissionFileDAO */
import('lib.pkp.classes.file.SubmissionFileManager');
$contexts = $journalDao->getAll();
while ($context = $contexts->next()) {
$styleGenre = $genreDao->getByKey('STYLE', $context->getId());
$submissions = $submissionDao->getByContextId($context->getId());
while ($submission = $submissions->next()) {
$submissionFileManager = new SubmissionFileManager($context->getId(), $submission->getId());
$basePath = $submissionFileManager->getBasePath();
$submissionFiles = $submissionFileDao->getBySubmissionId($submission->getId());
foreach ($submissionFiles as $submissionFile) {
// Ignore files with style genre -- if they exist, they are corrected manually i.e.
// the moveCSSFiles function will do this, s. https://github.com/pkp/pkp-lib/issues/2758
if ($submissionFile->getGenreId() != $styleGenre->getId()) {
$generatedNewFilename = $submissionFile->getServerFileName();
$targetFilename = $basePath . $submissionFile->_fileStageToPath($submissionFile->getFileStage()) . '/' . $generatedNewFilename;
$timestamp = date('Ymd', strtotime($submissionFile->getDateUploaded()));
$wrongFileName = $submission->getId() . '-' . '1' . '-' . $submissionFile->getFileId() . '-' . $submissionFile->getRevision() . '-' . $submissionFile->getFileStage() . '-' . $timestamp . '.' . strtolower_codesafe($submissionFile->getExtension());
$sourceFilename = $basePath . $submissionFile->_fileStageToPath($submissionFile->getFileStage()) . '/' . $wrongFileName;
if (file_exists($targetFilename)) continue; // Skip existing files/links
if (!file_exists($path = dirname($targetFilename)) && !$submissionFileManager->mkdirtree($path)) {
error_log("Unable to make directory \"$path\"");
}
if (!rename($sourceFilename, $targetFilename)) {
error_log("Unable to move \"$sourceFilename\" to \"$targetFilename\".");
}
}
}
}
}
return true;
}
/**
* For 3.0.x - 3.1.0 upgrade: repair the migration of the HTML galley CSS files in the OJS files_dir.
*
* NOTE: submission_files table should be first fixed with the SQLs from GitHub Issue: https://github.com/pkp/pkp-lib/issues/2758
*
* @return boolean
*/
function moveCSSFiles() {
$journalDao = DAORegistry::getDAO('JournalDAO'); /* @var $journalDao JournalDAO */
$genreDao = DAORegistry::getDAO('GenreDAO'); /* @var $genreDao GenreDAO */
$submissionFileDao = DAORegistry::getDAO('SubmissionFileDAO'); /* @var $submissionFileDao SubmissionFileDAO */
import('lib.pkp.classes.file.FileManager');
import('lib.pkp.classes.file.SubmissionFileManager');
import('lib.pkp.classes.submission.SubmissionFile');
$journals = $journalDao->getAll();
while ($journal = $journals->next()) {
// Get style genre
$genre = $genreDao->getByKey('STYLE', $journal->getId());
// get CSS file names from the corrected submission_files table
$result = $submissionFileDao->retrieve('SELECT file_id, revision, original_file_name, date_uploaded, submission_id FROM submission_files WHERE file_stage = ? AND genre_id = ? AND assoc_type = ?',
array((int) SUBMISSION_FILE_DEPENDENT, (int) $genre->getId(), (int) ASSOC_TYPE_SUBMISSION_FILE));
while (!$result->EOF) {
$row = $result->GetRowAssoc(false);
// Get the wrong file name (after the 3.0.x migration)
// and the correct file name
$timestamp = date('Ymd', strtotime($row['date_uploaded']));
$fileManager = new FileManager();
$extension = $fileManager->parseFileExtension($row['original_file_name']);
$wrongServerName = $row['submission_id'] . '-' . '1' . '-' . $row['file_id'] . '-' . $row['revision'] . '-' . '1' . '-' . $timestamp . '.' . strtolower_codesafe($extension);
$newServerName = $row['submission_id'] . '-' . $genre->getId() . '-' . $row['file_id'] . '-' . $row['revision'] . '-' . SUBMISSION_FILE_DEPENDENT . '-' . $timestamp . '.' . strtolower_codesafe($extension);
// Get the old file path (after the 3.0.x migration, i.e. from OJS 2.4.x)
// and the correct file path
$submissionFileManager = new SubmissionFileManager($journal->getId(), $row['submission_id']);
$basePath = $submissionFileManager->getBasePath();
$sourceFilename = $basePath . 'public' . '/' . $wrongServerName;
$targetFilename = $basePath . 'submission/proof' . '/' . $newServerName;
// Move the file
if (!file_exists($targetFilename) && file_exists($sourceFilename)) {
if (!file_exists($path = dirname($targetFilename)) && !$submissionFileManager->mkdirtree($path)) {
error_log("Unable to make directory \"$path\"");
}
if (!rename($sourceFilename, $targetFilename)) {
error_log("Unable to move \"$sourceFilename\" to \"$targetFilename\".");
}
}
$result->MoveNext();
}
$result->Close();
unset($journal);
}
return true;
}
/**
* For 3.0.x - 3.1.1 upgrade: repair the migration of the supp files.
* @return boolean True indicates success.
*/
function repairSuppFilesFilestage() {
$submissionFileDao = DAORegistry::getDAO('SubmissionFileDAO'); /* @var $submissionFileDao SubmissionFileDAO */
import('lib.pkp.classes.submission.SubmissionFile');
import('lib.pkp.classes.file.SubmissionFileManager');
// get reviewer file ids
$result = $submissionFileDao->retrieve(
'SELECT ssf.*, s.context_id
FROM submission_supplementary_files ssf, submission_files sf, submissions s
WHERE sf.file_id = ssf.file_id AND sf.file_stage = ? AND sf.assoc_type = ? AND sf.revision = ssf.revision AND s.submission_id = sf.submission_id',
array((int)SUBMISSION_FILE_SUBMISSION, (int)ASSOC_TYPE_REPRESENTATION)
);
while (!$result->EOF) {
$row = $result->GetRowAssoc(false);
$submissionFileRevision = $submissionFileDao->getRevision($row['file_id'], $row['revision']);
$submissionFileManager = new SubmissionFileManager($row['context_id'], $submissionFileRevision->getSubmissionId());
$basePath = $submissionFileManager->getBasePath();
$generatedOldFilename = $submissionFileRevision->getServerFileName();
$oldFileName = $basePath . $submissionFileRevision->_fileStageToPath($submissionFileRevision->getFileStage()) . '/' . $generatedOldFilename;
$submissionFileRevision->setFileStage(SUBMISSION_FILE_PROOF);
$generatedNewFilename = $submissionFileRevision->getServerFileName();
$newFileName = $basePath . $submissionFileRevision->_fileStageToPath($submissionFileRevision->getFileStage()) . '/' . $generatedNewFilename;
if (!file_exists($newFileName)) {
if (!file_exists($path = dirname($newFileName)) && !$submissionFileManager->mkdirtree($path)) {
error_log("Unable to make directory \"$path\"");
}
if (!rename($oldFileName, $newFileName)) {
error_log("Unable to move \"$oldFileName\" to \"$newFileName\".");
} else {
$submissionFileDao->updateObject($submissionFileRevision);
}
}
$result->MoveNext();
}
$result->Close();
return true;
}
/**
* If StaticPages table exists we should port the data as NMIs
* @return boolean
*/
function migrateStaticPagesToNavigationMenuItems() {
if ($this->tableExists('static_pages')) {
$contextDao = Application::getContextDAO();
$navigationMenuItemDao = DAORegistry::getDAO('NavigationMenuItemDAO'); /* @var $navigationMenuItemDao NavigationMenuItemDAO */
import('plugins.generic.staticPages.classes.StaticPagesDAO');
$staticPagesDao = new StaticPagesDAO();
$contexts = $contextDao->getAll();
while ($context = $contexts->next()) {
$contextStaticPages = $staticPagesDao->getByContextId($context->getId())->toAssociativeArray();
foreach($contextStaticPages as $staticPage) {
$retNMIId = $navigationMenuItemDao->portStaticPage($staticPage);
if ($retNMIId) {
$staticPagesDao->deleteById($staticPage->getId());
} else {
error_log('WARNING: The StaticPage "' . $staticPage->getLocalizedTitle() . '" uses a path (' . $staticPage->getPath() . ') that conflicts with an existing Custom Navigation Menu Item path. Skipping this StaticPage.');
}
}
}
}
return true;
}
/**
* Migrate sr_SR locale to the new sr_RS@latin.
* @return boolean
*/
function migrateSRLocale() {
$oldLocale = 'sr_SR';
$newLocale = 'sr_RS@latin';
$oldLocaleStringLength = 's:5';
$journalSettingsDao = DAORegistry::getDAO('JournalSettingsDAO'); /* @var $journalSettingsDao JournalSettingsDAO */
// Check if the sr_SR is used, and if not do not run further
$srExistResult = $journalSettingsDao->retrieve('SELECT COUNT(*) FROM site WHERE installed_locales LIKE ?', array('%'.$oldLocale.'%'));
$srExist = $srExistResult->fields[0] ? true : false;
$srExistResult->Close();
if (!$srExist) return true;
// Consider all DB tables that have locale column:
$dbTables = array(
'announcement_settings', 'announcement_type_settings', 'author_settings', 'books_for_review_settings', 'citation_settings', 'controlled_vocab_entry_settings',
'data_object_tombstone_settings', 'email_templates_data', 'email_templates_default_data', 'external_feed_settings', 'filter_settings', 'genre_settings', 'group_settings',
'issue_galleys', 'issue_galley_settings', 'issue_settings', 'journal_settings', 'library_file_settings', 'metadata_description_settings',
'navigation_menu_item_assignment_settings', 'navigation_menu_item_settings', 'notification_settings', 'referral_settings',
'review_form_element_settings', 'review_form_settings', 'review_object_metadata_settings', 'review_object_type_settings', 'section_settings', 'site_settings',
'static_page_settings', 'submissions', 'submission_file_settings', 'submission_galleys', 'submission_galley_settings', 'submission_settings', 'subscription_type_settings',
'user_group_settings', 'user_settings',
);
foreach ($dbTables as $dbTable) {
if ($this->tableExists($dbTable)) {
$journalSettingsDao->update('UPDATE '.$dbTable.' SET locale = ? WHERE locale = ?', array($newLocale, $oldLocale));
}
}
// Consider other locale columns
$journalSettingsDao->update('UPDATE journals SET primary_locale = ? WHERE primary_locale = ?', array($newLocale, $oldLocale));
$journalSettingsDao->update('UPDATE site SET primary_locale = ? WHERE primary_locale = ?', array($newLocale, $oldLocale));
$journalSettingsDao->update('UPDATE site SET installed_locales = REPLACE(installed_locales, ?, ?)', array($oldLocale, $newLocale));
$journalSettingsDao->update('UPDATE site SET supported_locales = REPLACE(supported_locales, ?, ?)', array($oldLocale, $newLocale));
$journalSettingsDao->update('UPDATE users SET locales = REPLACE(locales, ?, ?)', array($oldLocale, $newLocale));
// journal_settings
// Consider array setting values from the setting names:
// supportedFormLocales, supportedLocales, supportedSubmissionLocales
$settingNames = "('supportedFormLocales', 'supportedLocales', 'supportedSubmissionLocales')";
// As a precaution use $oldLocaleStringLength, to exclude that the text contain the old locale string
$settingValueResult = $journalSettingsDao->retrieve('SELECT * FROM journal_settings WHERE setting_name IN ' .$settingNames .' AND setting_value LIKE ? AND setting_type = \'object\'', array('%' .$oldLocaleStringLength .':"' .$oldLocale .'%'));
while (!$settingValueResult->EOF) {
$row = $settingValueResult->getRowAssoc(false);
$arraySettingValue = $journalSettingsDao->getSetting($row['journal_id'], $row['setting_name']);
for($i = 0; $i < count($arraySettingValue); $i++) {
if ($arraySettingValue[$i] == $oldLocale) {
$arraySettingValue[$i] = $newLocale;
}
}
$journalSettingsDao->updateSetting($row['journal_id'], $row['setting_name'], $arraySettingValue);
$settingValueResult->MoveNext();
}
$settingValueResult->Close();
// Consider journal images
// Note that the locale column values are already changed above
$publicFileManager = new PublicFileManager();
$settingNames = "('homeHeaderLogoImage', 'homeHeaderTitleImage', 'homepageImage', 'journalFavicon', 'journalThumbnail', 'pageHeaderLogoImage', 'pageHeaderTitleImage')";
$settingValueResult = $journalSettingsDao->retrieve('SELECT * FROM journal_settings WHERE setting_name IN ' .$settingNames .' AND locale = ? AND setting_value LIKE ? AND setting_type = \'object\'', array($newLocale, '%' .$oldLocale .'%'));
while (!$settingValueResult->EOF) {
$row = $settingValueResult->getRowAssoc(false);
$arraySettingValue = $journalSettingsDao->getSetting($row['journal_id'], $row['setting_name'], $newLocale);
$oldUploadName = $arraySettingValue['uploadName'];
$newUploadName = str_replace('_'.$oldLocale.'.', '_'.$newLocale.'.', $oldUploadName);
if ($publicFileManager->fileExists($publicFileManager->getContextFilesPath($row['journal_id']) . '/' . $oldUploadName)) {
$publicFileManager->copyContextFile($row['journal_id'], $publicFileManager->getContextFilesPath($row['journal_id']) . '/' . $oldUploadName, $newUploadName);
$publicFileManager->removeContextFile($row['journal_id'], $oldUploadName);
}
$arraySettingValue['uploadName'] = $newUploadName;
$newArraySettingValue[$newLocale] = $arraySettingValue;
$journalSettingsDao->updateSetting($row['journal_id'], $row['setting_name'], $newArraySettingValue, 'object', true);
$settingValueResult->MoveNext();
}
$settingValueResult->Close();
// Consider issue cover images
// Note that the locale column values are already changed above
$settingValueResult = $journalSettingsDao->retrieve('SELECT a.*, b.journal_id FROM issue_settings a, issues b WHERE a.setting_name = \'fileName\' AND a.locale = ? AND a.setting_value LIKE ? AND a.setting_type = \'string\' AND b.issue_id = a.issue_id', array($newLocale, '%' .$oldLocale .'%'));
while (!$settingValueResult->EOF) {
$row = $settingValueResult->getRowAssoc(false);
$oldCoverImage = $row['setting_value'];
$newCoverImage = str_replace('_'.$oldLocale.'.', '_'.$newLocale.'.', $oldCoverImage);
if ($publicFileManager->fileExists($publicFileManager->getContextFilesPath($row['journal_id']) . '/' . $oldCoverImage)) {
$publicFileManager->copyContextFile($row['journal_id'], $publicFileManager->getContextFilesPath($row['journal_id']) . '/' . $oldCoverImage, $newCoverImage);
$publicFileManager->removeContextFile($row['journal_id'], $oldCoverImage);
}
$journalSettingsDao->update('UPDATE issue_settings SET setting_value = ? WHERE issue_id = ? AND setting_name = \'fileName\' AND locale = ?', array($newCoverImage, (int) $row['issue_id'], $newLocale));
$settingValueResult->MoveNext();
}
$settingValueResult->Close();
// Consider article cover images
// Note that the locale column values are already changed above
$settingValueResult = $journalSettingsDao->retrieve('SELECT a.*, b.context_id FROM submission_settings a, submissions b WHERE a.setting_name = \'fileName\' AND a.locale = ? AND a.setting_value LIKE ? AND b.submission_id = a.submission_id', array($newLocale, '%' .$oldLocale .'%'));
while (!$settingValueResult->EOF) {
$row = $settingValueResult->getRowAssoc(false);
$oldCoverImage = $row['setting_value'];
$newCoverImage = str_replace('_'.$oldLocale.'.', '_'.$newLocale.'.', $oldCoverImage);
if ($publicFileManager->fileExists($publicFileManager->getContextFilesPath($row['context_id']) . '/' . $oldCoverImage)) {
$publicFileManager->copyContextFile($row['context_id'], $publicFileManager->getContextFilesPath($row['context_id']) . '/' . $oldCoverImage, $newCoverImage);
$publicFileManager->removeContextFile($row['context_id'], $oldCoverImage);
}
$journalSettingsDao->update('UPDATE submission_settings SET setting_value = ? WHERE submission_id = ? AND setting_name = \'fileName\' AND locale = ?', array($newCoverImage, (int) $row['submission_id'], $newLocale));
$settingValueResult->MoveNext();
}
$settingValueResult->Close();
// plugin_settings
// Consider array setting values from the setting names:
// blockContent (from a custom block plugin), additionalInformation (from objects for review plugin)
$pluginSettingsDao = DAORegistry::getDAO('PluginSettingsDAO'); /* @var $pluginSettingsDao PluginSettingsDAO */
$settingNames = "('blockContent', 'additionalInformation')";
$settingValueResult = $pluginSettingsDao->retrieve('SELECT * FROM plugin_settings WHERE setting_name IN ' .$settingNames .' AND setting_value LIKE ?', array('%' .$oldLocaleStringLength .':"' .$oldLocale .'%'));
while (!$settingValueResult->EOF) {
$row = $settingValueResult->getRowAssoc(false);
$arraySettingValue = $pluginSettingsDao->getSetting($row['context_id'], $row['plugin_name'], $row['setting_name']);
$arraySettingValue[$newLocale] = $arraySettingValue[$oldLocale];
unset($arraySettingValue[$oldLocale]);
$pluginSettingsDao->updateSetting($row['context_id'], $row['plugin_name'], $row['setting_name'], $arraySettingValue);
$settingValueResult->MoveNext();
}
$settingValueResult->Close();
return true;
}
/**
* Migrate first and last user names as multilingual into the DB table user_settings.
* @return boolean
*/
function migrateUserAndAuthorNames() {
$userDao = DAORegistry::getDAO('UserDAO'); /* @var $userDao UserDAO */
import('lib.pkp.classes.identity.Identity'); // IDENTITY_SETTING_...
// the user names will be saved in the site's primary locale
$userDao->update("INSERT INTO user_settings (user_id, locale, setting_name, setting_value, setting_type) SELECT DISTINCT u.user_id, s.primary_locale, ?, u.first_name, 'string' FROM users_tmp u, site s", array(IDENTITY_SETTING_GIVENNAME));
$userDao->update("INSERT INTO user_settings (user_id, locale, setting_name, setting_value, setting_type) SELECT DISTINCT u.user_id, s.primary_locale, ?, u.last_name, 'string' FROM users_tmp u, site s", array(IDENTITY_SETTING_FAMILYNAME));
// the author names will be saved in the submission's primary locale
$userDao->update("INSERT INTO author_settings (author_id, locale, setting_name, setting_value, setting_type) SELECT DISTINCT a.author_id, s.locale, ?, a.first_name, 'string' FROM authors_tmp a, submissions s WHERE s.submission_id = a.submission_id", array(IDENTITY_SETTING_GIVENNAME));
$userDao->update("INSERT INTO author_settings (author_id, locale, setting_name, setting_value, setting_type) SELECT DISTINCT a.author_id, s.locale, ?, a.last_name, 'string' FROM authors_tmp a, submissions s WHERE s.submission_id = a.submission_id", array(IDENTITY_SETTING_FAMILYNAME));
// middle name will be migrated to the given name
// note that given names are already migrated to the settings table
$driver = $userDao->getDriver();
switch ($driver) {
case 'mysql':
case 'mysqli':
// the alias for _settings table cannot be used for some reason -- syntax error
$userDao->update("UPDATE user_settings, users_tmp u SET user_settings.setting_value = CONCAT(user_settings.setting_value, ' ', u.middle_name) WHERE user_settings.setting_name = ? AND u.user_id = user_settings.user_id AND u.middle_name IS NOT NULL AND u.middle_name <> ''", array(IDENTITY_SETTING_GIVENNAME));
$userDao->update("UPDATE author_settings, authors_tmp a SET author_settings.setting_value = CONCAT(author_settings.setting_value, ' ', a.middle_name) WHERE author_settings.setting_name = ? AND a.author_id = author_settings.author_id AND a.middle_name IS NOT NULL AND a.middle_name <> ''", array(IDENTITY_SETTING_GIVENNAME));
break;
case 'postgres':
case 'postgres64':
case 'postgres7':
case 'postgres8':
case 'postgres9':
$userDao->update("UPDATE user_settings SET setting_value = CONCAT(setting_value, ' ', u.middle_name) FROM users_tmp u WHERE user_settings.setting_name = ? AND u.user_id = user_settings.user_id AND u.middle_name IS NOT NULL AND u.middle_name <> ''", array(IDENTITY_SETTING_GIVENNAME));
$userDao->update("UPDATE author_settings SET setting_value = CONCAT(setting_value, ' ', a.middle_name) FROM authors_tmp a WHERE author_settings.setting_name = ? AND a.author_id = author_settings.author_id AND a.middle_name IS NOT NULL AND a.middle_name <> ''", array(IDENTITY_SETTING_GIVENNAME));
break;
default: fatalError('Unknown database type!');
}
// salutation and suffix will be migrated to the preferred public name
// user preferred public names will be inserted for each supported site locales
$siteDao = DAORegistry::getDAO('SiteDAO'); /* @var $siteDao SiteDAO */
$site = $siteDao->getSite();
$supportedLocales = $site->getSupportedLocales();
$userResult = $userDao->retrieve("
SELECT user_id, first_name, last_name, middle_name, salutation, suffix FROM users_tmp
WHERE (salutation IS NOT NULL AND salutation <> '') OR
(suffix IS NOT NULL AND suffix <> '')
");
while (!$userResult->EOF) {
$row = $userResult->GetRowAssoc(false);
$userId = $row['user_id'];
$firstName = $row['first_name'];
$lastName = $row['last_name'];
$middleName = $row['middle_name'];
$salutation = $row['salutation'];
$suffix = $row['suffix'];
foreach ($supportedLocales as $siteLocale) {
$preferredPublicName = ($salutation != '' ? "$salutation " : '') . "$firstName " . ($middleName != '' ? "$middleName " : '') . $lastName . ($suffix != '' ? ", $suffix" : '');
if (AppLocale::isLocaleWithFamilyFirst($siteLocale)) {
$preferredPublicName = "$lastName, " . ($salutation != '' ? "$salutation " : '') . $firstName . ($middleName != '' ? " $middleName" : '');
}
$params = array((int) $userId, $siteLocale, $preferredPublicName);
$userDao->update("INSERT INTO user_settings (user_id, locale, setting_name, setting_value, setting_type) VALUES (?, ?, 'preferredPublicName', ?, 'string')", $params);
}
$userResult->MoveNext();
}
$userResult->Close();
// author suffix will be migrated to the author preferred public name
// author preferred public names will be inserted for each journal supported locale
// get supported locales for all journals
$journalDao = DAORegistry::getDAO('JournalDAO'); /* @var $journalDao JournalDAO */
$journals = $journalDao->getAll();
$journalsSupportedLocales = array();
while ($journal = $journals->next()) {
$journalsSupportedLocales[$journal->getId()] = $journal->getSupportedLocales();
}
// get all authors with a suffix
$authorResult = $userDao->retrieve("
SELECT a.author_id, a.first_name, a.last_name, a.middle_name, a.suffix, j.journal_id FROM authors_tmp a
LEFT JOIN submissions s ON (s.submission_id = a.submission_id)
LEFT JOIN journals j ON (j.journal_id = s.context_id)
WHERE suffix IS NOT NULL AND suffix <> ''
");
while (!$authorResult->EOF) {
$row = $authorResult->GetRowAssoc(false);
$authorId = $row['author_id'];
$firstName = $row['first_name'];
$lastName = $row['last_name'];
$middleName = $row['middle_name'];
$suffix = $row['suffix'];
$journalId = $row['journal_id'];
$supportedLocales = $journalsSupportedLocales[$journalId];
foreach ($supportedLocales as $locale) {
$preferredPublicName = "$firstName " . ($middleName != '' ? "$middleName " : '') . $lastName . ($suffix != '' ? ", $suffix" : '');
if (AppLocale::isLocaleWithFamilyFirst($locale)) {
$preferredPublicName = "$lastName, " . $firstName . ($middleName != '' ? " $middleName" : '');
}
$params = array((int) $authorId, $locale, $preferredPublicName);
$userDao->update("INSERT INTO author_settings (author_id, locale, setting_name, setting_value, setting_type) VALUES (?, ?, 'preferredPublicName', ?, 'string')", $params);
}
$authorResult->MoveNext();
}
$authorResult->Close();
// remove temporary table
$siteDao->update('DROP TABLE users_tmp');
$siteDao->update('DROP TABLE authors_tmp');
return true;
}
/**
* Update assoc_id for assoc_type ASSOC_TYPE_SUBMISSION_FILE_COUNTER_OTHER = 531
* @return boolean True indicates success.
*/
function updateSuppFileMetrics() {
$submissionFileDao = DAORegistry::getDAO('SubmissionFileDAO'); /* @var $submissionFileDao SubmissionFileDAO */
$metricsDao = DAORegistry::getDAO('MetricsDAO'); /* @var $metricsDao MetricsDAO */
# Copy 531 assoc_type data to temp table
$result = $metricsDao->update(
'CREATE TABLE metrics_supp AS (SELECT * FROM metrics WHERE assoc_type = 531)'
);
# Fetch submission_file data with old-supp-id
$result = $submissionFileDao->retrieve(
'SELECT * FROM submission_file_settings WHERE setting_name = ?',
'old-supp-id'
);
# Loop through the data and save to temp table
while (!$result->EOF) {
$row = $result->GetRowAssoc(false);
# Use assoc_type 2531 to prevent collisions between old assoc_id and new assoc_id
$metricsDao->update(
'UPDATE metrics_supp SET assoc_id = ?, assoc_type = ? WHERE assoc_type = ? AND assoc_id = ?',
array((int) $row['file_id'], 2531, 531, (int) $row['setting_value'])
);
$result->MoveNext();
}
$result->Close();
# update temprorary 2531 values to 531 values
$metricsDao->update(
'UPDATE metrics_supp SET assoc_type = ? WHERE assoc_type = ?',
array(531, 2531)
);
# delete all existing 531 values from the actual metrics table
$metricsDao->update('DELETE FROM metrics WHERE assoc_type = 531');
# copy updated 531 values from metrics_supp to metrics table
$metricsDao->update('INSERT INTO metrics SELECT * FROM metrics_supp');
# Drop metrics_supp table
$metricsDao->update('DROP TABLE metrics_supp');
return true;
}
/**
* Add an entry for the site stylesheet to the site_settings database when it
* exists
*/
function migrateSiteStylesheet() {
$siteDao = DAORegistry::getDAO('SiteDAO'); /* @var $siteDao SiteDAO */
import('classes.file.PublicFileManager');
$publicFileManager = new PublicFileManager();
if (!file_exists($publicFileManager->getSiteFilesPath() . '/sitestyle.css')) {
return true;
}
$site = $siteDao->getSite();
$site->setData('styleSheet', 'sitestyle.css');
$siteDao->updateObject($site);
return true;
}
/**
* Copy a context's copyrightNotice to a new licenseTerms setting, leaving
* the copyrightNotice in place.
*/
function createLicenseTerms() {
$contextDao = Application::getContextDao();
$result = $contextDao->retrieve('SELECT * from ' . $contextDao->settingsTableName . " WHERE setting_name='copyrightNotice'");
while (!$result->EOF) {
$row = $result->getRowAssoc(false);
$contextDao->update('
INSERT INTO ' . $contextDao->settingsTableName . ' (
' . $contextDao->primaryKeyColumn . ',
locale,
setting_name,
setting_value
) VALUES (?, ?, ?, ?)',
[
$row[$contextDao->primaryKeyColumn],
$row['locale'],
'licenseTerms',
$row['setting_value'],
]
);
$result->MoveNext();
}
$result->Close();
return true;
}
/**
* Update permit_metadata_edit and can_change_metadata for user_groups and stage_assignments tables.
*
* @return boolean True indicates success.
*/
function changeUserRolesAndStageAssignmentsForStagePermitSubmissionEdit() {
$stageAssignmentDao = DAORegistry::getDAO('StageAssignmentDAO'); /** @var $stageAssignmentDao StageAssignmentDAO */
$userGroupDao = DAORegistry::getDAO('UserGroupDAO'); /** @var $userGroupDao UserGroupDAO */
$roles = UserGroupDAO::getNotChangeMetadataEditPermissionRoles();
$roleString = '(' . implode(",", $roles) . ')';
$userGroupDao->update('UPDATE user_groups SET permit_metadata_edit = 1 WHERE role_id IN ' . $roleString);
switch ($userGroupDao->getDriver()) {
case 'mysql':
case 'mysqli':
$stageAssignmentDao->update('UPDATE stage_assignments sa JOIN user_groups ug on sa.user_group_id = ug.user_group_id SET sa.can_change_metadata = 1 WHERE ug.role_id IN ' . $roleString);
break;
case 'postgres':
case 'postgres64':
case 'postgres7':
case 'postgres8':
case 'postgres9':
$stageAssignmentDao->update('UPDATE stage_assignments SET can_change_metadata=1 FROM stage_assignments sa JOIN user_groups ug ON (sa.user_group_id = ug.user_group_id) WHERE ug.role_id IN ' . $roleString);
break;
default: fatalError("Unknown database type!");
}
return true;
}
/**
* Update how submission cover images are stored
*
* Combines the coverImage and coverImageAltText settings in the
* submissions table into an assoc array stored under the coverImage
* setting.
*
* This will be migrated to the publication_settings table in
* 3.2.0_versioning.xml.
*/
function migrateSubmissionCoverImages() {
$coverImagesBySubmission = [];
$submissionDao = DAORegistry::getDAO('SubmissionDAO'); /* @var $submissionDao SubmissionDAO */
$result = $submissionDao->retrieve(
'SELECT * from submission_settings WHERE setting_name=\'coverImage\' OR setting_name=\'coverImageAltText\''
);
while (!$result->EOF) {
$row = $result->getRowAssoc(false);
$submissionId = $row['submission_id'];
if (empty($coverImagesBySubmission[$submissionId])) {
$coverImagesBySubmission[$submissionId] = [];
}
if ($row['setting_name'] === 'coverImage') {
$coverImagesBySubmission[$submissionId]['uploadName'] = $row['setting_value'];
$coverImagesBySubmission[$submissionId]['dateUploaded'] = Core::getCurrentDate();
} elseif ($row['setting_name'] === 'coverImageAltText') {
$coverImagesBySubmission[$submissionId]['altText'] = $row['setting_value'];
}
$result->MoveNext();
}
$result->Close();
foreach ($coverImagesBySubmission as $submissionId => $coverImagesBySubmission) {
$submissionDao->update(
'UPDATE submission_settings
SET setting_value = ?
WHERE submission_id = ? AND setting_name = ?',
[
serialize($coverImagesBySubmission),
$submissionId,
'coverImage',
]
);
}
return true;
}
}
