public function testNativeDoiImport()
{
$testfile = 'tests/functional/plugins/importexport/native/testissue.xml';
$args = array('import', $testfile, 'test', 'admin');
$result = $this->executeCli('NativeImportExportPlugin', $args);
self::assertRegExp('/##plugins.importexport.native.import.success.description##/', $result);
$daos = array('Issue' => 'IssueDAO', 'PublishedArticle' => 'PublishedArticleDAO', 'Galley' => 'ArticleGalleyDAO');
$articleId = null;
foreach ($daos as $objectType => $daoName) {
$dao = DAORegistry::getDAO($daoName);
$pubObject = call_user_func(array($dao, "get{$objectType}ByPubId"), 'doi', $this->expectedDois[$objectType]);
self::assertNotNull($pubObject, "Error while testing {$objectType}: object or DOI has not been imported.");
$pubObjectByURN = call_user_func(array($dao, "get{$objectType}ByPubId"), 'other::urn', $this->expectedURNs[$objectType]);
self::assertNotNull($pubObjectByURN, "Error while testing {$objectType}: object or URN has not been imported.");
if ($objectType == 'PublishedArticle') {
$articleId = $pubObject->getId();
}
}
// Trying to import the same file again should lead to an error.
$args = array('import', $testfile, 'test', 'admin');
$result = $this->executeCli('NativeImportExportPlugin', $args);
self::assertRegExp('/##plugins.importexport.native.import.error.duplicatePubId##/', $result);
// Delete inserted article files from the filesystem.
$request = $application->getRequest();
$context = $request->getContext();
import('lib.pkp.classes.file.SubmissionFileManager');
$submissionFileManager = new SubmissionFileManager($context->getId(), $articleId);
$submissionFileManager->rmtree($submissionFileManager->getBasePath());
}
/**
* Fix broken submission filenames (bug #8461)
* @param $upgrade Upgrade
* @param $params array
* @param $dryrun boolean True iff only a dry run (displaying rather than executing changes) should be done.
* @return boolean
*/
function fixFilenames($upgrade, $params, $dryrun = false)
{
$pressDao = DAORegistry::getDAO('PressDAO');
$submissionDao = DAORegistry::getDAO('MonographDAO');
$submissionFileDao = DAORegistry::getDAO('SubmissionFileDAO');
DAORegistry::getDAO('GenreDAO');
// Load constants
$siteDao = DAORegistry::getDAO('SiteDAO');
/* @var $siteDao SiteDAO */
$site = $siteDao->getSite();
$adminEmail = $site->getLocalizedContactEmail();
import('lib.pkp.classes.file.SubmissionFileManager');
$contexts = $pressDao->getAll();
while ($context = $contexts->next()) {
$submissions = $submissionDao->getByPressId($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() . $submissionFile->_fileStageToPath($submissionFile->getFileStage()) . '/';
$globPattern = $submissionFile->getSubmissionId() . '-' . '*' . '-' . $submissionFile->getFileId() . '-' . $submissionFile->getRevision() . '-' . $submissionFile->getFileStage() . '-' . date('Ymd', strtotime($submissionFile->getDateUploaded())) . '.' . strtolower_codesafe($submissionFile->getExtension());
$matchedResults = glob($basePath . $globPattern);
if (count($matchedResults) > 1) {
error_log("Duplicate potential files for \"{$globPattern}\"!", 1, $adminEmail);
continue;
}
if (count($matchedResults) == 1) {
// 1 result matched.
$discoveredFilename = array_shift($matchedResults);
if ($dryrun) {
echo "Need to rename \"{$discoveredFilename}\" to \"{$generatedFilename}\".\n";
} else {
rename($discoveredFilename, $basePath . $generatedFilename);
}
} else {
// 0 results matched.
error_log("Unable to find a match for \"{$globPattern}\".\n", 1, $adminEmail);
continue;
}
}
}
}
return true;
}
/**
* Delete a submission by ID.
* @param $submissionId int
*/
function deleteById($submissionId)
{
// Delete submission files.
$submission = $this->getById($submissionId);
assert(is_a($submission, 'Submission'));
import('lib.pkp.classes.file.SubmissionFileManager');
$submissionFileManager = new SubmissionFileManager($submission->getContextId(), $submission->getId());
$submissionFileManager->rmtree($submissionFileManager->getBasePath());
$this->authorDao->deleteBySubmissionId($submissionId);
$reviewRoundDao = DAORegistry::getDAO('ReviewRoundDAO');
$reviewRoundDao->deleteBySubmissionId($submissionId);
$editDecisionDao = DAORegistry::getDAO('EditDecisionDAO');
$editDecisionDao->deleteDecisionsBySubmissionId($submissionId);
$reviewAssignmentDao = DAORegistry::getDAO('ReviewAssignmentDAO');
$reviewAssignmentDao->deleteBySubmissionId($submissionId);
// Signoff DAOs
$signoffDao = DAORegistry::getDAO('SignoffDAO');
$submissionFileSignoffDao = DAORegistry::getDAO('SubmissionFileSignoffDAO');
// Delete Signoffs associated with a submission file of this submission.
$submissionFileSignoffs = $submissionFileSignoffDao->getAllBySubmission($submissionId);
while ($signoff = $submissionFileSignoffs->next()) {
$signoffDao->deleteObject($signoff);
}
// Delete the Signoffs associated with the submission itself.
$submissionSignoffs = $signoffDao->getAllByAssocType(ASSOC_TYPE_SUBMISSION, $submissionId);
while ($signoff = $submissionSignoffs->next()) {
$signoffDao->deleteObject($signoff);
}
// Delete the stage assignments.
$stageAssignmentDao = DAORegistry::getDAO('StageAssignmentDAO');
$stageAssignments = $stageAssignmentDao->getBySubmissionAndStageId($submissionId);
while ($stageAssignment = $stageAssignments->next()) {
$stageAssignmentDao->deleteObject($stageAssignment);
}
// N.B. Files must be deleted after signoffs to identify submission file signoffs.
// Delete submission files.
$submissionFileDao = DAORegistry::getDAO('SubmissionFileDAO');
/* @var $submissionFileDao SubmissionFileDAO */
$submissionFileDao->deleteAllRevisionsBySubmissionId($submissionId);
$noteDao = DAORegistry::getDAO('NoteDAO');
$noteDao->deleteByAssoc(ASSOC_TYPE_SUBMISSION, $submissionId);
$submissionCommentDao = DAORegistry::getDAO('SubmissionCommentDAO');
$submissionCommentDao->deleteBySubmissionId($submissionId);
// Delete any outstanding notifications for this submission
$notificationDao = DAORegistry::getDAO('NotificationDAO');
$notificationDao->deleteByAssoc(ASSOC_TYPE_SUBMISSION, $submissionId);
$submissionEventLogDao = DAORegistry::getDAO('SubmissionEventLogDAO');
$submissionEventLogDao->deleteByAssoc(ASSOC_TYPE_SUBMISSION, $submissionId);
$submissionEmailLogDao = DAORegistry::getDAO('SubmissionEmailLogDAO');
$submissionEmailLogDao->deleteByAssoc(ASSOC_TYPE_SUBMISSION, $submissionId);
// Delete controlled vocab lists assigned to this submission
$submissionKeywordDao = DAORegistry::getDAO('SubmissionKeywordDAO');
$submissionKeywordVocab = $submissionKeywordDao->getBySymbolic(CONTROLLED_VOCAB_SUBMISSION_KEYWORD, ASSOC_TYPE_SUBMISSION, $submissionId);
if (isset($submissionKeywordVocab)) {
$submissionKeywordDao->deleteObject($submissionKeywordVocab);
}
$submissionDisciplineDao = DAORegistry::getDAO('SubmissionDisciplineDAO');
$submissionDisciplineVocab = $submissionDisciplineDao->getBySymbolic(CONTROLLED_VOCAB_SUBMISSION_DISCIPLINE, ASSOC_TYPE_SUBMISSION, $submissionId);
if (isset($submissionDisciplineVocab)) {
$submissionDisciplineDao->deleteObject($submissionDisciplineVocab);
}
$submissionAgencyDao = DAORegistry::getDAO('SubmissionAgencyDAO');
$submissionAgencyVocab = $submissionAgencyDao->getBySymbolic(CONTROLLED_VOCAB_SUBMISSION_AGENCY, ASSOC_TYPE_SUBMISSION, $submissionId);
if (isset($submissionAgencyVocab)) {
$submissionAgencyDao->deleteObject($submissionAgencyVocab);
}
$submissionLanguageDao = DAORegistry::getDAO('SubmissionLanguageDAO');
$submissionLanguageVocab = $submissionLanguageDao->getBySymbolic(CONTROLLED_VOCAB_SUBMISSION_LANGUAGE, ASSOC_TYPE_SUBMISSION, $submissionId);
if (isset($submissionLanguageVocab)) {
$submissionLanguageDao->deleteObject($submissionLanguageVocab);
}
$submissionSubjectDao = DAORegistry::getDAO('SubmissionSubjectDAO');
$submissionSubjectVocab = $submissionSubjectDao->getBySymbolic(CONTROLLED_VOCAB_SUBMISSION_SUBJECT, ASSOC_TYPE_SUBMISSION, $submissionId);
if (isset($submissionSubjectVocab)) {
$submissionSubjectDao->deleteObject($submissionSubjectVocab);
}
$this->update('DELETE FROM submission_settings WHERE submission_id = ?', (int) $submissionId);
$this->update('DELETE FROM submissions WHERE submission_id = ?', (int) $submissionId);
}
/**
* Return a context-aware file path.
*/
function getFilePath()
{
// Get the context ID
$submissionDao = Application::getSubmissionDAO();
$submission = $submissionDao->getById($this->getSubmissionId());
if (!$submission) {
return null;
}
$contextId = $submission->getContextId();
unset($submission);
// Construct the file path
import('lib.pkp.classes.file.SubmissionFileManager');
$submissionFileManager = new SubmissionFileManager($contextId, $this->getSubmissionId());
return $submissionFileManager->getBasePath() . $this->_fileStageToPath($this->getFileStage()) . '/' . $this->getServerFileName();
}
/**
* Delete a submission by ID.
* @param $submissionId int
*/
function deleteById($submissionId)
{
// Delete submission files.
$submission = $this->getById($submissionId);
assert(is_a($submission, 'Submission'));
// 'deleteAllRevisionsBySubmissionId' has to be called before 'rmtree'
// because SubmissionFileDaoDelegate::deleteObjects checks the file
// and returns false if the file is not there, which makes the foreach loop in
// PKPSubmissionFileDAO::_deleteInternally not run till the end.
$submissionFileDao = DAORegistry::getDAO('SubmissionFileDAO');
/* @var $submissionFileDao SubmissionFileDAO */
$submissionFileDao->deleteAllRevisionsBySubmissionId($submissionId);
import('lib.pkp.classes.file.SubmissionFileManager');
$submissionFileManager = new SubmissionFileManager($submission->getContextId(), $submission->getId());
$submissionFileManager->rmtree($submissionFileManager->getBasePath());
$this->authorDao->deleteBySubmissionId($submissionId);
$reviewRoundDao = DAORegistry::getDAO('ReviewRoundDAO');
$reviewRoundDao->deleteBySubmissionId($submissionId);
$editDecisionDao = DAORegistry::getDAO('EditDecisionDAO');
$editDecisionDao->deleteDecisionsBySubmissionId($submissionId);
$reviewAssignmentDao = DAORegistry::getDAO('ReviewAssignmentDAO');
$reviewAssignmentDao->deleteBySubmissionId($submissionId);
// Delete the queries associated with a submission
$queryDao = DAORegistry::getDAO('QueryDAO');
$queryDao->deleteByAssoc(ASSOC_TYPE_SUBMISSION, $submissionId);
// Delete the stage assignments.
$stageAssignmentDao = DAORegistry::getDAO('StageAssignmentDAO');
$stageAssignments = $stageAssignmentDao->getBySubmissionAndStageId($submissionId);
while ($stageAssignment = $stageAssignments->next()) {
$stageAssignmentDao->deleteObject($stageAssignment);
}
$noteDao = DAORegistry::getDAO('NoteDAO');
$noteDao->deleteByAssoc(ASSOC_TYPE_SUBMISSION, $submissionId);
$submissionCommentDao = DAORegistry::getDAO('SubmissionCommentDAO');
$submissionCommentDao->deleteBySubmissionId($submissionId);
// Delete any outstanding notifications for this submission
$notificationDao = DAORegistry::getDAO('NotificationDAO');
$notificationDao->deleteByAssoc(ASSOC_TYPE_SUBMISSION, $submissionId);
$submissionEventLogDao = DAORegistry::getDAO('SubmissionEventLogDAO');
$submissionEventLogDao->deleteByAssoc(ASSOC_TYPE_SUBMISSION, $submissionId);
$submissionEmailLogDao = DAORegistry::getDAO('SubmissionEmailLogDAO');
$submissionEmailLogDao->deleteByAssoc(ASSOC_TYPE_SUBMISSION, $submissionId);
// Delete controlled vocab lists assigned to this submission
$submissionKeywordDao = DAORegistry::getDAO('SubmissionKeywordDAO');
$submissionKeywordVocab = $submissionKeywordDao->getBySymbolic(CONTROLLED_VOCAB_SUBMISSION_KEYWORD, ASSOC_TYPE_SUBMISSION, $submissionId);
if (isset($submissionKeywordVocab)) {
$submissionKeywordDao->deleteObject($submissionKeywordVocab);
}
$submissionDisciplineDao = DAORegistry::getDAO('SubmissionDisciplineDAO');
$submissionDisciplineVocab = $submissionDisciplineDao->getBySymbolic(CONTROLLED_VOCAB_SUBMISSION_DISCIPLINE, ASSOC_TYPE_SUBMISSION, $submissionId);
if (isset($submissionDisciplineVocab)) {
$submissionDisciplineDao->deleteObject($submissionDisciplineVocab);
}
$submissionAgencyDao = DAORegistry::getDAO('SubmissionAgencyDAO');
$submissionAgencyVocab = $submissionAgencyDao->getBySymbolic(CONTROLLED_VOCAB_SUBMISSION_AGENCY, ASSOC_TYPE_SUBMISSION, $submissionId);
if (isset($submissionAgencyVocab)) {
$submissionAgencyDao->deleteObject($submissionAgencyVocab);
}
$submissionLanguageDao = DAORegistry::getDAO('SubmissionLanguageDAO');
$submissionLanguageVocab = $submissionLanguageDao->getBySymbolic(CONTROLLED_VOCAB_SUBMISSION_LANGUAGE, ASSOC_TYPE_SUBMISSION, $submissionId);
if (isset($submissionLanguageVocab)) {
$submissionLanguageDao->deleteObject($submissionLanguageVocab);
}
$submissionSubjectDao = DAORegistry::getDAO('SubmissionSubjectDAO');
$submissionSubjectVocab = $submissionSubjectDao->getBySymbolic(CONTROLLED_VOCAB_SUBMISSION_SUBJECT, ASSOC_TYPE_SUBMISSION, $submissionId);
if (isset($submissionSubjectVocab)) {
$submissionSubjectDao->deleteObject($submissionSubjectVocab);
}
$this->update('DELETE FROM submission_settings WHERE submission_id = ?', (int) $submissionId);
$this->update('DELETE FROM submissions WHERE submission_id = ?', (int) $submissionId);
}
/**
* Migrate submission filenames from OJS 2.x
* @param $upgrade Upgrade
* @param $params array
* @return boolean
*/
function migrateFiles($upgrade, $params)
{
$journalDao = DAORegistry::getDAO('JournalDAO');
$submissionDao = DAORegistry::getDAO('ArticleDAO');
$submissionFileDao = DAORegistry::getDAO('SubmissionFileDAO');
DAORegistry::getDAO('GenreDAO');
// Load constants
$siteDao = DAORegistry::getDAO('SiteDAO');
/* @var $siteDao SiteDAO */
$site = $siteDao->getSite();
$adminEmail = $site->getLocalizedContactEmail();
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 = $submissionFile->getSubmissionId() . '-' . $submissionFile->getFileId() . '-' . $submissionFile->getRevision() . '-' . '??' . '.' . strtolower_codesafe($submissionFile->getExtension());
$matchedResults = array_merge(glob($basePath . '*/*/' . $globPattern), glob($basePath . '*/' . $globPattern));
if (count($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;
}
