/**
* Issue master DOI for tool resources if does not exist
*
* @param object $job \Components\Cron\Models\Job
* @return boolean
*/
public function issueResourceMasterDoi(\Components\Cron\Models\Job $job)
{
$database = App::get('db');
$config = Component::params('com_publications');
// Is config to issue master DOI turned ON?
if (!$config->get('master_doi')) {
return true;
}
// Get all tool resources without master DOI
$sql = "SELECT r.id, r.created_by, v.id as tool_version_id,\n\t\t\t\tv.toolid, v.toolname, v.title, v.description,\n\t\t\t\tv.instance, v.revision, v.released\n\t\t\t\tFROM #__resources AS r, #__tool_version AS v\n\t\t\t\tWHERE r.published=1\n\t\t\t\tAND r.type=7\n\t\t\t\tAND r.standalone=1\n\t\t\t\tAND r.alias=v.toolname\n\t\t\t\tAND v.state=1\n\t\t\t\tAND (r.master_doi IS NULL OR r.master_doi=0)\n\t\t\t\tGROUP BY r.id\n\t\t\t\tORDER BY v.title, v.toolname, v.revision DESC";
$database->setQuery($sql);
if (!($rows = $database->loadObjectList())) {
// No applicable results
return true;
}
// Includes
require_once PATH_CORE . DS . 'components' . DS . 'com_resources' . DS . 'tables' . DS . 'resource.php';
include_once PATH_CORE . DS . 'components' . DS . 'com_publications' . DS . 'models' . DS . 'doi.php';
// Get DOI service
$doiService = new \Components\Publications\Models\Doi();
// Is service enabled?
if (!$doiService->on() || !$doiService->_configs->livesite) {
return true;
}
// Go through records
foreach ($rows as $row) {
// Reset metadata
$doiService->reset();
// Map data
$pubYear = $row->released && $row->released != '0000-00-00 00:00:00' ? gmdate('Y', strtotime($row->released)) : gmdate('Y');
$doiService->set('pubYear', $pubYear);
$doiService->mapUser($row->created_by, array(), 'creator');
$doiService->set('resourceType', 'Software');
$doiService->set('title', htmlspecialchars(stripslashes($row->title)));
$doiService->set('url', $doiService->_configs->livesite . DS . 'resources' . DS . $row->toolname . DS . 'main');
// Register DOI
$masterDoi = $doiService->register();
// Save with publication record
$resource = new \Components\Resources\Tables\Resource($database);
if ($masterDoi && $resource->load($row->id)) {
$resource->master_doi = strtoupper($masterDoi);
$resource->store();
}
}
return true;
}
/**
* Approve publication
*
* @return void
*/
public function approveTask()
{
// Incoming
$pid = $this->_id ? $this->_id : Request::getInt('id', 0);
$vid = Request::getInt('vid', 0);
// Load publication model
$this->_pub = new \Components\Publications\Models\Publication($pid, NULL, $vid);
if (!$this->_pub->exists()) {
throw new Exception(Lang::txt('COM_PUBLICATIONS_NOT_FOUND'), 404);
}
// Check authorization
if (!$this->_pub->access('curator')) {
if (User::isGuest()) {
$this->_msg = Lang::txt('COM_PUBLICATIONS_CURATION_LOGIN');
$this->_login();
return;
}
throw new Exception(Lang::txt('COM_PUBLICATIONS_CURATION_ERROR_UNAUTHORIZED'), 403);
}
$this->_pub->version->set('state', 1);
$this->_pub->version->set('accepted', Date::toSql());
$this->_pub->version->set('reviewed', Date::toSql());
$this->_pub->version->set('reviewed_by', User::get('id'));
// Archive (mkAIP) if no grace period and not previously archived
if (!$this->getError() && !$this->config->get('graceperiod', 0) && $this->_pub->version->doi && \Components\Publications\Helpers\Utilities::mkAip($this->_pub->version) && !$this->_pub->archived()) {
$this->_pub->version->set('archived', Date::toSql());
}
// Set curation
$this->_pub->setCuration();
$curation = json_encode($this->_pub->_curationModel->_manifest);
//$curation = $this->_pub->masterType()->curation;
// Get manifest version
$versionNumber = $this->_pub->_curationModel->checkCurationVersion();
// Store curation manifest
$this->_pub->version->set('curation', $curation);
$this->_pub->version->set('curation_version_id', $versionNumber);
if (!$this->_pub->version->store()) {
throw new Exception(Lang::txt('PLG_PROJECTS_PUBLICATIONS_PUBLICATION_FAILED'), 403);
}
// Get DOI service
$doiService = new \Components\Publications\Models\Doi($this->_pub);
if ($this->_pub->version->doi) {
$doiService->update($this->_pub->version->doi, true);
}
// Mark as curated
$this->_pub->saveParam('curated', 1);
// On after status change
$this->onAfterStatusChange();
$message = $this->getError() ? $this->getError() : Lang::txt('COM_PUBLICATIONS_CURATION_SUCCESS_APPROVED');
$class = $this->getError() ? 'error' : 'success';
// Redirect to main listing
App::redirect(Route::url('index.php?option=' . $this->_option . '&controller=curation'), $message, $class);
return;
}
/**
* Change publication status
*
* @return string
*/
public function publishDraft()
{
// Incoming
$pid = $this->_pid ? $this->_pid : Request::getInt('pid', 0);
$confirm = Request::getInt('confirm', 0);
$version = Request::getVar('version', 'dev');
$agree = Request::getInt('agree', 0);
$pubdate = Request::getVar('publish_date', '', 'post');
$submitter = Request::getInt('submitter', $this->_uid, 'post');
$notify = 1;
$block = Request::getVar('section', '');
$blockId = Request::getInt('step', 0);
$element = Request::getInt('element', 0);
// Check permission
if (!$this->model->access('content')) {
throw new Exception(Lang::txt('ALERTNOTAUTH'), 403);
return;
}
// Load review step
if (!$confirm && $this->_task != 'revert') {
$this->_task = 'review';
return $this->editDraft();
}
// Load publication model
$pub = new \Components\Publications\Models\Publication($pid, $version);
// Error loading publication record
if (!$pub->exists()) {
\Notify::message(Lang::txt('PLG_PROJECTS_PUBLICATIONS_PUBLICATION_NOT_FOUND'), 'error', 'projects');
App::redirect(Route::url($pub->link('editbase')));
return;
}
// Agreement to terms is required
if ($confirm && !$agree) {
\Notify::message(Lang::txt('PLG_PROJECTS_PUBLICATIONS_PUBLICATION_REVIEW_AGREE_TERMS_REQUIRED'), 'error', 'projects');
App::redirect(Route::url($pub->link('editversion') . '&action=' . $this->_task));
return;
}
// Check against quota
if ($this->_overQuota()) {
\Notify::message(Lang::txt('PLG_PROJECTS_PUBLICATIONS_PUBLICATION_NO_DISK_SPACE'), 'error', 'projects');
App::redirect(Route::url($pub->link('editversion') . '&action=' . $this->_task));
return;
}
// Set curation
$pub->setCuration();
// Require DOI?
$requireDoi = isset($pub->_curationModel->_manifest->params->require_doi) ? $pub->_curationModel->_manifest->params->require_doi : 0;
// Make sure the publication belongs to the project
if (!$pub->belongsToProject($this->model->get('id'))) {
Notify::message(Lang::txt('PLG_PROJECTS_PUBLICATIONS_ERROR_PROJECT_ASSOC'), 'error', 'projects');
App::redirect(Route::url($this->model->link('publications')));
return;
}
// Check that version label was not published before
$used_labels = $pub->version->getUsedLabels($pid, $version);
if (!$pub->version->version_label || in_array($pub->version->version_label, $used_labels)) {
$this->setError(Lang::txt('PLG_PROJECTS_PUBLICATIONS_PUBLICATION_VERSION_LABEL_USED'));
}
// Is draft complete?
if (!$pub->curation('complete') && $this->_task != 'revert') {
$this->setError(Lang::txt('PLG_PROJECTS_PUBLICATIONS_PUBLICATION_NOT_ALLOWED'));
}
// Is revert allowed?
$revertAllowed = $this->_pubconfig->get('graceperiod', 0);
if ($revertAllowed && $pub->version->state == 1 && $pub->version->accepted && $pub->version->accepted != '0000-00-00 00:00:00') {
$monthFrom = Date::of($pub->version->accepted . '+1 month')->toSql();
if (strtotime($monthFrom) < strtotime(Date::of())) {
$revertAllowed = 0;
}
}
// Embargo?
if ($pubdate) {
$pubdate = $this->_parseDate($pubdate);
$tenYearsFromNow = Date::of(strtotime("+10 years"))->toSql();
// Stop if more than 10 years from now
if ($pubdate > $tenYearsFromNow) {
$this->setError(Lang::txt('PLG_PROJECTS_PUBLICATIONS_PUBLICATION_ERROR_EMBARGO'));
}
}
// Contact info is required for repositories
if ($pub->config()->get('repository')) {
$contact = Request::getVar('contact', array(), 'post');
if (!$contact || empty($contact)) {
$this->setError(Lang::txt('PLG_PROJECTS_PUBLICATIONS_PUBLICATION_ERROR_CONTACT_INFO_MISSING'));
}
$db = \App::get('db');
foreach ($contact as $key) {
$author = new \Components\Publications\Tables\Author($db);
if (!$author->load($key)) {
$this->setError(Lang::txt('PLG_PROJECTS_PUBLICATIONS_PUBLICATION_ERROR_CONTACT_NOT_FOUND'));
continue;
}
$author->repository_contact = 1;
if (!$author->store()) {
$this->setError(Lang::txt('PLG_PROJECTS_PUBLICATIONS_PUBLICATION_ERROR_CONTACT_NOT_SAVED'));
}
}
}
// Main version?
$main = $this->_task == 'republish' ? $pub->version->main : 1;
$main_vid = $pub->version->getMainVersionId($pid);
// current default version
// Save version before changes
$originalStatus = $pub->version->state;
// Checks
if ($this->_task == 'republish' && $pub->version->state != 0) {
// Can only re-publish unpublished version
$this->setError(Lang::txt('PLG_PROJECTS_PUBLICATIONS_PUBLICATION_CANNOT_REPUBLISH'));
} elseif ($this->_task == 'revert' && $pub->version->state != 5 && !$revertAllowed) {
// Can only revert a pending resource
$this->setError(Lang::txt('PLG_PROJECTS_PUBLICATIONS_PUBLICATION_CANNOT_REVERT'));
}
// On error
if ($this->getError()) {
\Notify::message($this->getError(), 'error', 'projects');
App::redirect(Route::url($pub->link('editversion') . '&action=' . $this->_task));
return;
}
// Determine state
$state = 5;
// Default - pending approval
if ($this->_task == 'share' || $this->_task == 'revert') {
$state = 4;
// No approval needed
} elseif ($this->_task == 'republish') {
$state = 1;
// No approval needed
} else {
$pub->version->set('submitted', Date::toSql());
// Save submitter
$pa = new \Components\Publications\Tables\Author($this->_database);
$pa->saveSubmitter($pub->version->id, $submitter, $this->model->get('id'));
if ($this->_pubconfig->get('autoapprove') == 1) {
$state = 1;
} else {
$apu = $this->_pubconfig->get('autoapproved_users');
$apu = explode(',', $apu);
$apu = array_map('trim', $apu);
if (in_array(User::get('username'), $apu)) {
// Set status to published
$state = 1;
} else {
// Set status to pending review (submitted)
$state = 5;
}
}
}
// Save state
$pub->version->set('state', $state);
$pub->version->set('main', $main);
if ($this->_task != 'revert') {
$publishedUp = $this->_task == 'republish' ? $pub->version->published_up : Date::toSql();
$publishedUp = $pubdate ? $pubdate : $publishedUp;
$pub->version->set('rating', '0.0');
$pub->version->set('published_up', $publishedUp);
$pub->version->set('published_down', '');
}
$pub->version->set('modified', Date::toSql());
$pub->version->set('modified_by', $this->_uid);
// Issue DOI
if ($requireDoi > 0 && $this->_task == 'publish' && !$pub->version->doi) {
// Get DOI service
$doiService = new \Components\Publications\Models\Doi($pub);
$extended = $state == 5 ? false : true;
$doi = $doiService->register($extended, $state == 5 ? 'reserved' : 'public');
// Store DOI
if ($doi) {
$pub->version->set('doi', $doi);
}
// Can't proceed without a valid DOI
if (!$doi || $doiService->getError()) {
$this->setError(Lang::txt('PLG_PROJECTS_PUBLICATIONS_ERROR_DOI') . ' ' . $doiService->getError());
}
}
// Proceed if no error
if (!$this->getError()) {
if ($state == 1) {
// Get and save manifest and its version
$versionNumber = $pub->_curationModel->checkCurationVersion();
$pub->version->set('curation', json_encode($pub->_curationModel->_manifest));
$pub->version->set('curation_version_id', $versionNumber);
}
// Save data
if (!$pub->version->store()) {
throw new Exception(Lang::txt('PLG_PROJECTS_PUBLICATIONS_PUBLICATION_FAILED'), 403);
return;
}
// Remove main flag from previous default version
if ($main && $main_vid && $main_vid != $pub->version->get('id')) {
$pub->version->removeMainFlag($main_vid);
}
}
// OnAfterPublish
$this->onAfterChangeState($pub, $originalStatus);
// Redirect
App::redirect(Route::url($pub->link('editversion')));
return;
}
/**
* Issue master DOI for publications if does not exist
*
* @param $job \Components\Cron\Models\Job
* @return boolean
*/
public function issueMasterDoi(\Components\Cron\Models\Job $job)
{
$database = \App::get('db');
$config = Component::params('com_publications');
// Is config to issue master DOI turned ON?
if (!$config->get('master_doi')) {
return true;
}
// Get all publications without master DOI
$sql = "SELECT V.* FROM #__publication_versions as V, #__publications as C";
$sql .= " WHERE C.id=V.publication_id AND (C.master_doi IS NULL OR master_doi=0)";
$sql .= " AND V.state=1 GROUP BY C.id ORDER BY V.version_number ASC";
$database->setQuery($sql);
if (!($rows = $database->loadObjectList())) {
// No applicable results
return true;
}
include_once PATH_CORE . DS . 'components' . DS . 'com_publications' . DS . 'models' . DS . 'publication.php';
// Get DOI service
$doiService = new \Components\Publications\Models\Doi();
// Is service enabled?
if (!$doiService->on() || !$doiService->_configs->livesite) {
return true;
}
// Go through records
foreach ($rows as $row) {
// Load publication model
$model = new \Components\Publications\Models\Publication($row->publication_id, $row->id);
// Check to make sure we got result
if (!$model->exists()) {
continue;
}
// Map publication
$doiService->mapPublication($model);
// Build url
$pointer = $model->publication->alias ? $model->publication->alias : $model->publication->id;
$url = $doiService->_configs->livesite . DS . 'publications' . DS . $pointer . DS . 'main';
// Master DOI should link to /main
$doiService->set('url', $url);
// Register DOI
$masterDoi = $doiService->register();
// Save with publication record
if ($masterDoi) {
$model->publication->master_doi = strtoupper($masterDoi);
$model->publication->store();
}
}
return true;
}
