/**
* Process data
*
* @return void
*/
protected function _process()
{
// New project?
$new = $this->model->exists() ? false : true;
// Are we in setup?
$setup = $new || $this->model->inSetup() ? true : false;
// Incoming
$private = Request::getInt('private', 1);
// Save section
switch ($this->section) {
case 'describe':
case 'info':
// Incoming
$name = trim(Request::getVar('name', '', 'post'));
$title = trim(Request::getVar('title', '', 'post'));
$name = preg_replace('/ /', '', $name);
$name = strtolower($name);
// Clean up title from any scripting
$title = preg_replace('/\\s+/', ' ', $title);
$title = $this->_txtClean($title);
// Check incoming data
if ($setup && $new && !$this->model->check($name, $this->model->get('id'))) {
$this->setError(Lang::txt('COM_PROJECTS_ERROR_NAME_INVALID_OR_EMPTY'));
return false;
} elseif (!$title) {
$this->setError(Lang::txt('COM_PROJECTS_ERROR_TITLE_SHORT_OR_EMPTY'));
return false;
}
if ($this->model->exists()) {
$this->model->set('modified', Date::toSql());
$this->model->set('modified_by', User::get('id'));
} else {
$this->model->set('alias', $name);
$this->model->set('created', Date::toSql());
$this->model->set('created_by_user', User::get('id'));
$this->model->set('owned_by_group', $this->_gid);
$this->model->set('owned_by_user', User::get('id'));
$this->model->set('private', $this->config->get('privacy', 1));
}
$this->model->set('title', \Hubzero\Utility\String::truncate($title, 250));
$this->model->set('about', trim(Request::getVar('about', '', 'post', 'none', 2)));
$this->model->set('type', Request::getInt('type', 1, 'post'));
// save advanced permissions
if (isset($_POST['private'])) {
$this->model->set('private', $private);
}
if ($setup && !$this->model->exists()) {
// Copy params from default project type
$objT = $this->model->table('Type');
$this->model->set('params', $objT->getParams($this->model->get('type')));
}
// Save changes
if (!$this->model->store()) {
$this->setError($this->model->getError());
return false;
}
// Save owners for new projects
if ($new) {
$this->_identifier = $this->model->get('alias');
// Group owners
$objO = $this->model->table('Owner');
if ($this->_gid) {
if (!$objO->saveOwners($this->model->get('id'), User::get('id'), 0, $this->_gid, 0, 1, 1, '', $split_group_roles = 0)) {
$this->setError(Lang::txt('COM_PROJECTS_ERROR_SAVING_AUTHORS') . ': ' . $objO->getError());
return false;
}
// Make sure project creator is manager
$objO->reassignRole($this->model->get('id'), $users = array(User::get('id')), 0, 1);
} elseif (!$objO->saveOwners($this->model->get('id'), User::get('id'), User::get('id'), $this->_gid, 1, 1, 1)) {
$this->setError(Lang::txt('COM_PROJECTS_ERROR_SAVING_AUTHORS') . ': ' . $objO->getError());
return false;
}
}
break;
case 'team':
if ($new) {
return false;
}
// Save team
$content = Event::trigger('projects.onProject', array($this->model, 'save', array('team')));
if (isset($content[0]) && $this->next == $this->section) {
if (isset($content[0]['msg']) && !empty($content[0]['msg'])) {
$this->_setNotification($content[0]['msg']['message'], $content[0]['msg']['type']);
}
}
break;
case 'settings':
if ($new) {
return false;
}
// Save privacy
if (isset($_POST['private'])) {
$this->model->set('private', $private);
// Save changes
if (!$this->model->store()) {
$this->setError($this->model->getError());
return false;
}
}
// Save params
$incoming = Request::getVar('params', array());
if (!empty($incoming)) {
foreach ($incoming as $key => $value) {
$this->model->saveParam($key, $value);
// If grant information changed
if ($key == 'grant_status') {
// Meta data for comment
$meta = '<meta>' . Date::of('now')->toLocal('M d, Y') . ' - ' . User::get('name') . '</meta>';
$cbase = $this->model->get('admin_notes');
$cbase .= '<nb:sponsored>' . Lang::txt('COM_PROJECTS_PROJECT_MANAGER_GRANT_INFO_UPDATE') . $meta . '</nb:sponsored>';
$this->model->set('admin_notes', $cbase);
// Save admin notes
if (!$this->model->store()) {
$this->setError($this->model->getError());
return false;
}
$admingroup = $this->config->get('ginfo_group', '');
if (\Hubzero\User\Group::getInstance($admingroup)) {
$admins = Helpers\Html::getGroupMembers($admingroup);
// Send out email to admins
if (!empty($admins)) {
Helpers\Html::sendHUBMessage($this->_option, $this->model, $admins, Lang::txt('COM_PROJECTS_EMAIL_ADMIN_REVIEWER_NOTIFICATION'), 'projects_new_project_admin', 'admin', Lang::txt('COM_PROJECTS_PROJECT_MANAGER_GRANT_INFO_UPDATE'), 'sponsored');
}
}
}
}
}
break;
}
}
/**
* Archive publications beyond grace period
*
* @param object $job \Components\Cron\Models\Job
* @return boolean
*/
public function runMkAip(\Components\Cron\Models\Job $job)
{
$database = \App::get('db');
$config = Component::params('com_publications');
require_once PATH_CORE . DS . 'components' . DS . 'com_publications' . DS . 'helpers' . DS . 'utilities.php';
require_once PATH_CORE . DS . 'components' . DS . 'com_publications' . DS . 'tables' . DS . 'version.php';
require_once PATH_CORE . DS . 'components' . DS . 'com_projects' . DS . 'helpers' . DS . 'html.php';
// Check that mkAIP script exists
if (!\Components\Publications\Helpers\Utilities::archiveOn()) {
return;
}
// Check for grace period
$gracePeriod = $config->get('graceperiod', 0);
if (!$gracePeriod) {
// If no grace period, this cron is unnecessary (archived as approval)
return;
}
$aipBasePath = trim($config->get('aip_path', NULL), DS);
$aipBasePath = $aipBasePath && is_dir(DS . $aipBasePath) ? DS . $aipBasePath : NULL;
// Check for base path
if (!$aipBasePath) {
$this->setError('Missing archival base directory');
return;
}
// Get all unarchived publication versions
$query = "SELECT V.*, C.id as id, V.id as version_id ";
$query .= " FROM #__publication_versions as V, #__publications as C ";
$query .= " WHERE C.id=V.publication_id AND V.state=1 ";
$query .= " AND V.doi IS NOT NULL ";
$query .= " AND V.accepted IS NOT NULL AND V.accepted !='0000-00-00 00:00:00' ";
$query .= " AND (V.archived IS NULL OR V.archived ='0000-00-00 00:00:00') ";
$database->setQuery($query);
if (!($rows = $database->loadObjectList())) {
return true;
}
// Start email message
$subject = Lang::txt('Update on recently archived publications');
$body = Lang::txt('The following publications passed the grace period and were archived:') . "\n";
$aipGroup = $config->get('aip_group');
$counter = 0;
foreach ($rows as $row) {
// Grace period unexpired?
$monthFrom = Date::of($row->accepted . '+1 month')->toSql();
if (strtotime($monthFrom) > strtotime(Date::of('now'))) {
continue;
}
// Load version
$pv = new \Components\Publications\Tables\Version($database);
if (!$pv->load($row->version_id)) {
continue;
}
// Create aip path
$doiParts = explode('/', $row->doi);
$aipName = count($doiParts) > 1 ? $doiParts[0] . '__' . $doiParts[1] : '';
// Archival package exists?
if ($aipBasePath && $aipName && is_dir($aipBasePath . DS . $aipName)) {
// Save approved date and archive date
$pv->archived = $pv->accepted;
$pv->store();
// Do not overwrite existing archives !!
continue;
}
// Run mkAIP and save archived date
if (\Components\Publications\Helpers\Utilities::mkAip($row)) {
$pv->archived = Date::toSql();
$pv->store();
$counter++;
$body .= $row->title . ' v.' . $row->version_label . ' (id #' . $row->id . ')' . "\n";
}
}
// Email update to admins
if ($counter > 0 && $aipGroup) {
// Set email config
$from = array('name' => Config::get('fromname') . ' ' . Lang::txt('Publications'), 'email' => Config::get('mailfrom'), 'multipart' => md5(date('U')));
$admins = \Components\Projects\Helpers\Html::getGroupMembers($aipGroup);
// Build message
if (!empty($admins)) {
foreach ($admins as $admin) {
// Get the user's account
$user = User::getInstance($admin);
if (!$user->get('id')) {
continue;
}
$message = new \Hubzero\Mail\Message();
$message->setSubject($subject)->addFrom($from['email'], $from['name'])->addTo($user->get('email'), $user->get('name'))->addHeader('X-Component', 'com_publications')->addHeader('X-Component-Object', 'publications');
$message->addPart($body, 'text/plain');
$message->send();
}
}
}
// All done
return true;
}
/**
* Process data
*
* @return void
*/
protected function _process()
{
// New project?
$new = $this->model->exists() ? false : true;
// Are we in setup?
$setup = $new || $this->model->inSetup() ? true : false;
// Incoming
$private = Request::getInt('private', 1);
// Save section
switch ($this->section) {
case 'describe':
case 'info':
case 'info_custom':
// Incoming
$name = trim(Request::getVar('name', '', 'post'));
$title = trim(Request::getVar('title', '', 'post'));
$name = preg_replace('/ /', '', $name);
$name = strtolower($name);
// Clean up title from any scripting
$title = preg_replace('/\\s+/', ' ', $title);
$title = $this->_txtClean($title);
// Check incoming data
if ($setup && $new && !$this->model->check($name, $this->model->get('id'))) {
$this->setError(Lang::txt('COM_PROJECTS_ERROR_NAME_INVALID_OR_EMPTY'));
return false;
} elseif (!$title) {
$this->setError(Lang::txt('COM_PROJECTS_ERROR_TITLE_SHORT_OR_EMPTY'));
return false;
}
if ($this->model->exists()) {
$this->model->set('modified', Date::toSql());
$this->model->set('modified_by', User::get('id'));
} else {
$this->model->set('alias', $name);
$this->model->set('created', Date::toSql());
$this->model->set('created_by_user', User::get('id'));
$this->model->set('owned_by_group', $this->_gid);
$this->model->set('owned_by_user', User::get('id'));
$this->model->set('private', $this->config->get('privacy', 1));
}
$this->model->set('title', \Hubzero\Utility\String::truncate($title, 250));
$this->model->set('about', trim(Request::getVar('about', '', 'post', 'none', 2)));
$this->model->set('type', Request::getInt('type', 1, 'post'));
// save advanced permissions
if (isset($_POST['private'])) {
$this->model->set('private', $private);
}
if ($setup && !$this->model->exists()) {
// Copy params from default project type
$objT = $this->model->table('Type');
$this->model->set('params', $objT->getParams($this->model->get('type')));
}
// Save changes
if (!$this->model->store()) {
$this->setError($this->model->getError());
return false;
}
// Save custom description
if ($this->section == 'info_custom') {
$newInfo = Request::getVar('description', array());
$projectID = $this->model->get('id');
$project = ProjectORM::one($this->model->get('id'));
$old = Description::collect($project->descriptions);
$formFields = array_merge($old, $newInfo);
$knownFields = Field::all()->rows()->toObject();
foreach ($knownFields as $kField) {
$existingField = Description::all()->whereEquals('project_id', $this->model->get('id'))->whereEquals('description_key', $kField->name)->limit(1)->row();
if ($existingField->id != NULL) {
$existingField->set('description_value', $formFields[$kField->name]);
$existingField->set('ordering', $kField->ordering);
$existingField->save();
} else {
// Create a new field
$newField = new Description();
$newField->set('description_key', $kField->name)->set('description_value', $formFields[$kField->name])->set('project_id', $this->model->get('id'))->set('ordering', $kField->ordering);
if (!$newField->save()) {
$this->setError($newField->getError());
}
}
}
}
// Save owners for new projects
if ($new && $this->section != 'info_custom') {
$this->_identifier = $this->model->get('alias');
// Group owners
$objO = $this->model->table('Owner');
if ($this->_gid) {
// Only add the creator
// They'll choose if they want to sync the entire group or not in the next step
if (!$objO->saveOwners($this->model->get('id'), User::get('id'), User::get('id'), $this->_gid, 0, 1, 1, '', $split_group_roles = 0)) {
$this->setError(Lang::txt('COM_PROJECTS_ERROR_SAVING_AUTHORS') . ': ' . $objO->getError());
return false;
}
// Make sure project creator is manager
$objO->reassignRole($this->model->get('id'), $users = array(User::get('id')), 0, 1);
} elseif (!$objO->saveOwners($this->model->get('id'), User::get('id'), User::get('id'), $this->_gid, 1, 1, 1)) {
$this->setError(Lang::txt('COM_PROJECTS_ERROR_SAVING_AUTHORS') . ': ' . $objO->getError());
return false;
}
}
// Record activity
$this->model->recordActivity(Lang::txt('COM_PROJECTS_PROJECT_INFO_UPDATED'));
break;
case 'team':
if ($new) {
return false;
}
if ($this->model->groupOwner()) {
// Save group sync settings
$this->model->set('sync_group', Request::getInt('sync_group', 0, 'post'));
if (!$this->model->store()) {
$this->setError($this->model->getError());
return false;
}
// Are we syncing group membership?
if ($this->model->get('sync_group')) {
$objO = $this->model->table('Owner');
$objO->saveOwners($this->model->get('id'), User::get('id'), 0, $this->_gid, 0, 1, 1, '', $split_group_roles = 0);
}
}
// Save team
$content = Event::trigger('projects.onProject', array($this->model, 'save', array('team')));
if (isset($content[0]) && $this->next == $this->section) {
if (isset($content[0]['msg']) && !empty($content[0]['msg'])) {
$this->_setNotification($content[0]['msg']['message'], $content[0]['msg']['type']);
}
}
break;
case 'settings':
if ($new) {
return false;
}
// Save privacy
if (isset($_POST['private'])) {
$this->model->set('private', $private);
// Save changes
if (!$this->model->store()) {
$this->setError($this->model->getError());
return false;
}
}
// Save params
$incoming = Request::getVar('params', array());
if (!empty($incoming)) {
foreach ($incoming as $key => $value) {
$this->model->saveParam($key, $value);
$this->model->params->set($key, $value);
// If grant information changed
if ($key == 'grant_status') {
// Meta data for comment
$meta = '<meta>' . Date::of('now')->toLocal('M d, Y') . ' - ' . User::get('name') . '</meta>';
$cbase = $this->model->get('admin_notes');
$cbase .= '<nb:sponsored>' . Lang::txt('COM_PROJECTS_PROJECT_MANAGER_GRANT_INFO_UPDATE') . $meta . '</nb:sponsored>';
$this->model->set('admin_notes', $cbase);
// Save admin notes
if (!$this->model->store()) {
$this->setError($this->model->getError());
return false;
}
$admingroup = $this->config->get('ginfo_group', '');
if (\Hubzero\User\Group::getInstance($admingroup)) {
$admins = Helpers\Html::getGroupMembers($admingroup);
// Send out email to admins
if (!empty($admins)) {
Helpers\Html::sendHUBMessage($this->_option, $this->model, $admins, Lang::txt('COM_PROJECTS_EMAIL_ADMIN_REVIEWER_NOTIFICATION'), 'projects_new_project_admin', 'admin', Lang::txt('COM_PROJECTS_PROJECT_MANAGER_GRANT_INFO_UPDATE'), 'sponsored');
}
}
}
}
// Record activity
$this->model->recordActivity(Lang::txt('COM_PROJECTS_PROJECT_SETTINGS_UPDATED'));
}
break;
}
}
/**
* Reviewers actions (sensitive data, sponsored research)
*
* @return void
*/
public function processTask()
{
// Incoming
$reviewer = Request::getWord('reviewer', '');
$action = Request::getVar('action', '');
$comment = Request::getVar('comment', '');
$approve = Request::getInt('approve', 0);
$filterby = Request::getVar('filterby', 'pending');
$notify = Request::getVar('notify', 0, 'post');
// Cannot proceed without project id/alias
if (!$this->model->exists() || $this->model->isDeleted()) {
throw new Exception(Lang::txt('COM_PROJECTS_PROJECT_NOT_FOUND'), 404);
return;
}
// Authorize
if (!$this->model->reviewerAccess($reviewer)) {
throw new Exception(Lang::txt('ALERTNOTAUTH'), 403);
return;
}
// Set the pathway
$this->_buildPathway();
// Set the page title
$this->_buildTitle();
// Get project params
$params = $this->model->params;
if ($action == 'save' && !$this->getError()) {
$cbase = $this->model->get('admin_notes');
// Meta data for comment
$meta = '<meta>' . Date::of('now')->toLocal('M d, Y') . ' - ' . User::get('name') . '</meta>';
// Save approval
if ($reviewer == 'sensitive') {
$approve = $approve == 1 && $this->model->get('state') == 5 ? 1 : 0;
// can only approve pending project
$state = $approve ? 1 : $this->model->get('state');
$this->model->set('state', $state);
} elseif ($reviewer == 'sponsored') {
$grant_agency = Request::getVar('grant_agency', '');
$grant_title = Request::getVar('grant_title', '');
$grant_PI = Request::getVar('grant_PI', '');
$grant_budget = Request::getVar('grant_budget', '');
$grant_approval = Request::getVar('grant_approval', '');
$rejected = Request::getVar('rejected', 0);
// New approval
if (trim($params->get('grant_approval')) == '' && trim($grant_approval) != '' && $params->get('grant_status') != 1 && $rejected != 1) {
// Increase
$approve = 1;
// Bump up quota
$premiumQuota = Helpers\Html::convertSize(floatval($this->config->get('premiumQuota', '30')), 'GB', 'b');
$this->model->saveParam('quota', $premiumQuota);
// Bump up publication quota
$premiumPubQuota = Helpers\Html::convertSize(floatval($this->config->get('premiumPubQuota', '10')), 'GB', 'b');
$this->model->saveParam('pubQuota', $premiumPubQuota);
}
// Reject
if ($rejected == 1 && $params->get('grant_status') != 2) {
$approve = 2;
}
$this->model->saveParam('grant_budget', $grant_budget);
$this->model->saveParam('grant_agency', $grant_agency);
$this->model->saveParam('grant_title', $grant_title);
$this->model->saveParam('grant_PI', $grant_PI);
$this->model->saveParam('grant_approval', $grant_approval);
if ($approve) {
$this->model->saveParam('grant_status', $approve);
}
}
// Save comment
if (trim($comment) != '') {
$comment = \Hubzero\Utility\String::truncate($comment, 500);
$comment = \Hubzero\Utility\Sanitize::stripAll($comment);
if (!$approve) {
$cbase .= '<nb:' . $reviewer . '>' . $comment . $meta . '</nb:' . $reviewer . '>';
}
}
if ($approve) {
if ($reviewer == 'sensitive') {
$cbase .= '<nb:' . $reviewer . '>' . Lang::txt('COM_PROJECTS_PROJECT_APPROVED_HIPAA');
$cbase .= trim($comment) != '' ? ' ' . $comment : '';
$cbase .= $meta . '</nb:' . $reviewer . '>';
}
if ($reviewer == 'sponsored') {
if ($approve == 1) {
$cbase .= '<nb:' . $reviewer . '>' . Lang::txt('COM_PROJECTS_PROJECT_APPROVED_SPS') . ' ' . ucfirst(Lang::txt('COM_PROJECTS_APPROVAL_CODE')) . ': ' . $grant_approval;
$cbase .= trim($comment) != '' ? '. ' . $comment : '';
$cbase .= $meta . '</nb:' . $reviewer . '>';
} elseif ($approve == 2) {
$cbase .= '<nb:' . $reviewer . '>' . Lang::txt('COM_PROJECTS_PROJECT_REJECTED_SPS');
$cbase .= trim($comment) != '' ? ' ' . $comment : '';
$cbase .= $meta . '</nb:' . $reviewer . '>';
}
}
}
$this->model->set('admin_notes', $cbase);
// Save changes
if ($approve || $comment) {
if (!$this->model->store()) {
$this->setError($this->model->getError());
}
$admingroup = $reviewer == 'sensitive' ? $this->config->get('sdata_group', '') : $this->config->get('ginfo_group', '');
if (\Hubzero\User\Group::getInstance($admingroup)) {
$admins = Helpers\Html::getGroupMembers($admingroup);
$admincomment = $comment ? User::get('name') . ' ' . Lang::txt('COM_PROJECTS_SAID') . ': ' . $comment : '';
// Send out email to admins
if (!empty($admins)) {
Helpers\Html::sendHUBMessage($this->_option, $this->model, $admins, Lang::txt('COM_PROJECTS_EMAIL_ADMIN_REVIEWER_NOTIFICATION'), 'projects_new_project_admin', 'admin', $admincomment, $reviewer);
}
}
}
// Pass success or error message
if ($this->getError()) {
$this->_setNotification($this->getError(), 'error');
} else {
if ($approve) {
if ($reviewer == 'sensitive') {
$this->_setNotification(Lang::txt('COM_PROJECTS_PROJECT_APPROVED_HIPAA_MSG'));
// Send out emails to team members
$this->_notifyTeam();
}
if ($reviewer == 'sponsored') {
$notification = $approve == 2 ? Lang::txt('COM_PROJECTS_PROJECT_REJECTED_SPS_MSG') : Lang::txt('COM_PROJECTS_PROJECT_APPROVED_SPS_MSG');
$this->_setNotification($notification);
}
} elseif ($comment) {
$this->_setNotification(Lang::txt('COM_PROJECTS_REVIEWER_COMMENT_POSTED'));
}
// Add to project activity feed
if ($notify) {
$activity = '';
if ($approve && $reviewer == 'sponsored') {
$activity = $approve == 2 ? Lang::txt('COM_PROJECTS_PROJECT_REJECTED_SPS_ACTIVITY') : Lang::txt('COM_PROJECTS_PROJECT_APPROVED_SPS_ACTIVITY');
} elseif ($comment) {
$activity = Lang::txt('COM_PROJECTS_PROJECT_REVIEWER_COMMENTED');
}
if ($activity) {
$aid = $this->model->recordActivity($activity, $this->model->get('id'), '', '', 'admin', 0, 1, 1);
// Append comment to activity
if ($comment && $aid) {
$objC = new Tables\Comment($this->database);
$cid = $objC->addComment($aid, 'activity', $comment, User::get('id'), $aid, 1);
if ($cid) {
$caid = $this->model->recordActivity(Lang::txt('COM_PROJECTS_COMMENTED') . ' ' . Lang::txt('COM_PROJECTS_ON') . ' ' . Lang::txt('COM_PROJECTS_AN_ACTIVITY'), $cid, '', '', 'quote', 0, 1, 1);
if ($caid) {
$objC->storeCommentActivityId($cid, $caid);
}
}
}
}
}
}
// Go back to project listing
App::redirect(Route::url('index.php?option=' . $this->_option . '&task=browse&reviewer=' . $reviewer . '&filterby=' . $filterby));
return;
} else {
// Instantiate a new view
$this->view->setLayout('review');
// Output HTML
$this->view->reviewer = $reviewer;
$this->view->ajax = Request::getInt('ajax', 0);
$this->view->title = $this->title;
$this->view->option = $this->_option;
$this->view->model = $this->model;
$this->view->params = $params;
$this->view->config = $this->config;
$this->view->database = $this->database;
$this->view->action = $action;
$this->view->filterby = $filterby;
$this->view->uid = User::get('id');
$this->view->msg = $this->_getNotifications('success');
if ($this->getError()) {
$this->view->setError($this->getError());
}
$this->view->display();
}
}
