/**
* Display the form.
*/
function display()
{
$journal =& Request::getJournal();
$user =& Request::getUser();
$templateMgr =& TemplateManager::getManager();
// Get sections for this journal
$sectionDao =& DAORegistry::getDAO('SectionDAO');
// If this user is a section editor or an editor, they are allowed
// to submit to sections flagged as "editor-only" for submissions.
// Otherwise, display only sections they are allowed to submit to.
$roleDao =& DAORegistry::getDAO('RoleDAO');
$isEditor = $roleDao->roleExists($journal->getId(), $user->getId(), ROLE_ID_EDITOR) || $roleDao->roleExists($journal->getId(), $user->getId(), ROLE_ID_SECTION_EDITOR);
// Set up required Payment Related Information
import('payment.ojs.OJSPaymentManager');
$paymentManager =& OJSPaymentManager::getManager();
if ($paymentManager->submissionEnabled() || $paymentManager->fastTrackEnabled() || $paymentManager->publicationEnabled()) {
$templateMgr->assign('authorFees', true);
$completedPaymentDAO =& DAORegistry::getDAO('OJSCompletedPaymentDAO');
$articleId = $this->articleId;
if ($paymentManager->submissionEnabled()) {
$templateMgr->assign_by_ref('submissionPayment', $completedPaymentDAO->getSubmissionCompletedPayment($journal->getId(), $articleId));
}
if ($paymentManager->fastTrackEnabled()) {
$templateMgr->assign_by_ref('fastTrackPayment', $completedPaymentDAO->getFastTrackCompletedPayment($journal->getId(), $articleId));
}
}
$templateMgr->assign('sectionOptions', array('0' => Locale::translate('author.submit.selectSection')) + $sectionDao->getSectionTitles($journal->getId(), !$isEditor));
parent::display();
}
/**
* Display the form.
*/
function display()
{
$conference =& Request::getConference();
$schedConf =& Request::getSchedConf();
$user =& Request::getUser();
$templateMgr =& TemplateManager::getManager();
// Get tracks for this conference
$trackDao = DAORegistry::getDAO('TrackDAO');
// If this user is a track director or a director, they are
// allowed to submit to tracks flagged as "director-only" for
// submissions. Otherwise, display only tracks they are allowed
// to submit to.
$roleDao = DAORegistry::getDAO('RoleDAO');
$isDirector = $roleDao->userHasRole($conference->getId(), $schedConf->getId(), $user->getId(), ROLE_ID_DIRECTOR) || $roleDao->userHasRole($conference->getId(), $schedConf->getId(), $user->getId(), ROLE_ID_TRACK_DIRECTOR) || $roleDao->userHasRole($conference->getId(), 0, $user->getId(), ROLE_ID_DIRECTOR) || $roleDao->userHasRole($conference->getId(), 0, $user->getId(), ROLE_ID_TRACK_DIRECTOR);
$templateMgr->assign('trackOptions', array('0' => __('author.submit.selectTrack')) + $trackDao->getTrackTitles($schedConf->getId(), !$isDirector));
$paperTypeDao = DAORegistry::getDAO('PaperTypeDAO');
$sessionTypes = $paperTypeDao->getPaperTypes($schedConf->getId());
$templateMgr->assign('sessionTypes', $sessionTypes->toArray());
// Provide available submission languages. (Convert the array
// of locale symbolic names xx_XX into an associative array
// of symbolic names => readable names.)
$supportedSubmissionLocales = $conference->getSetting('supportedSubmissionLocales');
if (empty($supportedSubmissionLocales)) {
$supportedSubmissionLocales = array($conference->getPrimaryLocale());
}
$templateMgr->assign('supportedSubmissionLocaleNames', array_flip(array_intersect(array_flip(AppLocale::getAllLocales()), $supportedSubmissionLocales)));
parent::display();
}
/**
* Display the form.
*/
function display()
{
$templateMgr =& TemplateManager::getManager();
// Get supplementary files for this article
$suppFileDao =& DAORegistry::getDAO('SuppFileDAO');
$templateMgr->assign_by_ref('suppFiles', $suppFileDao->getSuppFilesByArticle($this->articleId));
parent::display();
}
/**
* Display the form.
*/
function display()
{
$templateMgr =& TemplateManager::getManager();
$countryDao =& DAORegistry::getDAO('CountryDAO');
$countries =& $countryDao->getCountries();
$templateMgr->assign_by_ref('countries', $countries);
parent::display();
}
/**
* Display the form.
*/
function display()
{
$templateMgr =& TemplateManager::getManager();
// Get supplementary files for this paper
$paperFileDao = DAORegistry::getDAO('PaperFileDAO');
if ($this->paper->getSubmissionFileId() != null) {
$templateMgr->assign_by_ref('submissionFile', $paperFileDao->getPaperFile($this->paper->getSubmissionFileId()));
}
parent::display();
}
/**
* Display the form.
*/
function display()
{
$templateMgr =& TemplateManager::getManager();
// Get supplementary files for this article
$articleFileDao =& DAORegistry::getDAO('ArticleFileDAO');
if ($this->article->getSubmissionFileId() != null) {
$templateMgr->assign_by_ref('submissionFile', $articleFileDao->getArticleFile($this->article->getSubmissionFileId()));
}
parent::display();
}
/**
* Display the form.
*/
function display()
{
$templateMgr =& TemplateManager::getManager();
$typeOptions = array("author.submit.suppFile.summary" => "author.submit.suppFile.summary", "author.submit.suppFile.grantRequest" => "author.submit.suppFile.grantRequest", "author.submit.suppFile.informedConsent" => "author.submit.suppFile.informedConsent", "author.submit.suppFile.minutes" => "author.submit.suppFile.minutes", "author.submit.suppFile.proofOfPayment" => "author.submit.suppFile.proofOfPayment", "author.submit.suppFile.funding" => "author.submit.suppFile.funding", "author.submit.suppFile.cv" => "author.submit.suppFile.cv", "author.submit.suppFile.questionnaire" => "author.submit.suppFile.questionnaire", "author.submit.suppFile.proofOfRegistration" => "author.submit.suppFile.proofOfRegistration", "author.submit.suppFile.otherErcDecision" => "author.submit.suppFile.otherErcDecision", "author.submit.suppFile.amendment" => "author.submit.suppFile.amendment", "common.other" => "common.other");
$templateMgr->assign('typeOptions', $typeOptions);
// Get supplementary files for this article
$suppFileDao =& DAORegistry::getDAO('SuppFileDAO');
$templateMgr->assign_by_ref('suppFiles', $suppFileDao->getSuppFilesByArticle($this->articleId));
parent::display();
}
/**
* Display the form.
*/
function display()
{
$templateMgr =& TemplateManager::getManager();
// Get paper file for this paper
$paperFileDao =& DAORegistry::getDAO('PaperFileDAO');
$paperFiles =& $paperFileDao->getPaperFilesByPaper($this->paperId);
$templateMgr->assign_by_ref('files', $paperFiles);
$templateMgr->assign_by_ref('conference', Request::getConference());
parent::display();
}
/**
* Display the form.
*/
function display()
{
$templateMgr =& TemplateManager::getManager();
// Get supplementary files for this article
$suppFileDao =& DAORegistry::getDAO('SuppFileDAO');
$templateMgr->assign_by_ref('suppFiles', $suppFileDao->getSuppFilesByArticle($this->articleId));
//%CBP% get required sections
$CBPPlatformDao =& DAORegistry::getDAO('CBPPlatformDAO');
$article = $this->article->_data;
$templateMgr->assign_by_ref('requiredSections', $CBPPlatformDao->getRequiredSections($article['journalId'], "author"));
parent::display();
}
/**
* Display the form.
*/
function display()
{
$templateMgr =& TemplateManager::getManager();
// Get supplementary files for this article
$articleFileDao =& DAORegistry::getDAO('ArticleFileDAO');
if ($this->article->getSubmissionFileId() != null) {
$templateMgr->assign_by_ref('submissionFile', $articleFileDao->getArticleFile($this->article->getSubmissionFileId()));
}
//Get comments, if any, for this article
//Updated by: AIM
//Last updated: June 21, 2011
$articleCommentsDao =& DAORegistry::getDAO('ArticleCommentDAO');
$articleComments = $articleCommentsDao->getArticleComments($this->articleId);
if (!empty($articleComments)) {
$templateMgr->assign_by_ref('articleComments', $articleComments);
}
parent::display();
}
/**
* Display the form.
*/
function display()
{
$conference =& Request::getConference();
$schedConf =& Request::getSchedConf();
$user =& Request::getUser();
$templateMgr =& TemplateManager::getManager();
// Get tracks for this conference
$trackDao =& DAORegistry::getDAO('TrackDAO');
// If this user is a track director or a director, they are
// allowed to submit to tracks flagged as "director-only" for
// submissions. Otherwise, display only tracks they are allowed
// to submit to.
$roleDao =& DAORegistry::getDAO('RoleDAO');
$isDirector = $roleDao->roleExists($conference->getId(), $schedConf->getId(), $user->getId(), ROLE_ID_DIRECTOR) || $roleDao->roleExists($conference->getId(), $schedConf->getId(), $user->getId(), ROLE_ID_TRACK_DIRECTOR) || $roleDao->roleExists($conference->getId(), 0, $user->getId(), ROLE_ID_DIRECTOR) || $roleDao->roleExists($conference->getId(), 0, $user->getId(), ROLE_ID_TRACK_DIRECTOR);
$templateMgr->assign('trackOptions', array('0' => Locale::translate('author.submit.selectTrack')) + $trackDao->getTrackTitles($schedConf->getId(), !$isDirector));
$paperTypeDao =& DAORegistry::getDAO('PaperTypeDAO');
$sessionTypes = $paperTypeDao->getPaperTypes($schedConf->getId());
$templateMgr->assign('sessionTypes', $sessionTypes->toArray());
parent::display();
}
/**
* Display the form.
*/
function display()
{
$journal =& $this->request->getJournal();
$user =& $this->request->getUser();
$templateMgr =& TemplateManager::getManager();
// Get sections for this journal
$sectionDao =& DAORegistry::getDAO('SectionDAO');
// If this user is a section editor or an editor, they are
// allowed to submit to sections flagged as "editor-only" for
// submissions. Otherwise, display only sections they are
// allowed to submit to.
$roleDao =& DAORegistry::getDAO('RoleDAO');
$isEditor = $roleDao->userHasRole($journal->getId(), $user->getId(), ROLE_ID_EDITOR) || $roleDao->userHasRole($journal->getId(), $user->getId(), ROLE_ID_SECTION_EDITOR);
$templateMgr->assign('sectionOptions', array('0' => __('author.submit.selectSection')) + $sectionDao->getSectionTitles($journal->getId(), !$isEditor));
// Set up required Payment Related Information
import('classes.payment.ojs.OJSPaymentManager');
$paymentManager = new OJSPaymentManager($this->request);
if ($paymentManager->submissionEnabled() || $paymentManager->fastTrackEnabled() || $paymentManager->publicationEnabled()) {
$templateMgr->assign('authorFees', true);
$completedPaymentDao =& DAORegistry::getDAO('OJSCompletedPaymentDAO');
$articleId = $this->articleId;
if ($paymentManager->submissionEnabled()) {
$templateMgr->assign_by_ref('submissionPayment', $completedPaymentDao->getSubmissionCompletedPayment($journal->getId(), $articleId));
}
if ($paymentManager->fastTrackEnabled()) {
$templateMgr->assign_by_ref('fastTrackPayment', $completedPaymentDao->getFastTrackCompletedPayment($journal->getId(), $articleId));
}
}
// Provide available submission languages. (Convert the array
// of locale symbolic names xx_XX into an associative array
// of symbolic names => readable names.)
$supportedSubmissionLocales = $journal->getSetting('supportedSubmissionLocales');
if (empty($supportedSubmissionLocales)) {
$supportedSubmissionLocales = array($journal->getPrimaryLocale());
}
$templateMgr->assign('supportedSubmissionLocaleNames', array_flip(array_intersect(array_flip(AppLocale::getAllLocales()), $supportedSubmissionLocales)));
parent::display();
}
/**
* Save changes to article.
* @param $request Request
* @return int the article ID
*/
function execute()
{
$articleDao =& DAORegistry::getDAO('ArticleDAO');
$authorDao =& DAORegistry::getDAO('AuthorDAO');
$article =& $this->article;
// Retrieve the previous citation list for comparison.
$previousRawCitationList = $article->getCitations();
// Update article
$article->setTitle($this->getData('title'), null);
// Localized
$article->setAbstract($this->getData('abstract'), null);
// Localized
$article->setDiscipline($this->getData('discipline'), null);
// Localized
$article->setSubjectClass($this->getData('subjectClass'), null);
// Localized
$article->setSubject($this->getData('subject'), null);
// Localized
$article->setCoverageGeo($this->getData('coverageGeo'), null);
// Localized
$article->setCoverageChron($this->getData('coverageChron'), null);
// Localized
$article->setCoverageSample($this->getData('coverageSample'), null);
// Localized
$article->setType($this->getData('type'), null);
// Localized
$article->setLanguage($this->getData('language'));
$article->setSponsor($this->getData('sponsor'), null);
// Localized
$article->setCitations($this->getData('citations'));
if ($article->getSubmissionProgress() <= $this->step) {
$article->stampStatusModified();
$article->setSubmissionProgress($this->step + 1);
}
// Update authors
$authors = $this->getData('authors');
for ($i = 0, $count = count($authors); $i < $count; $i++) {
if ($authors[$i]['authorId'] > 0) {
// Update an existing author
$author =& $authorDao->getAuthor($authors[$i]['authorId'], $article->getId());
$isExistingAuthor = true;
} else {
// Create a new author
$author = new Author();
$isExistingAuthor = false;
}
if ($author != null) {
$author->setSubmissionId($article->getId());
$author->setFirstName($authors[$i]['firstName']);
$author->setMiddleName($authors[$i]['middleName']);
$author->setLastName($authors[$i]['lastName']);
$author->setAffiliation($authors[$i]['affiliation'], null);
$author->setCountry($authors[$i]['country']);
$author->setEmail($authors[$i]['email']);
$author->setData('orcid', $authors[$i]['orcid']);
$author->setUrl($authors[$i]['url']);
if (array_key_exists('competingInterests', $authors[$i])) {
$author->setCompetingInterests($authors[$i]['competingInterests'], null);
}
$author->setBiography($authors[$i]['biography'], null);
$author->setPrimaryContact($this->getData('primaryContact') == $i ? 1 : 0);
$author->setSequence($authors[$i]['seq']);
HookRegistry::call('Author::Form::Submit::AuthorSubmitStep3Form::Execute', array(&$author, &$authors[$i]));
if ($isExistingAuthor) {
$authorDao->updateAuthor($author);
} else {
$authorDao->insertAuthor($author);
}
}
unset($author);
}
// Remove deleted authors
$deletedAuthors = preg_split('/:/', $this->getData('deletedAuthors'), -1, PREG_SPLIT_NO_EMPTY);
for ($i = 0, $count = count($deletedAuthors); $i < $count; $i++) {
$authorDao->deleteAuthorById($deletedAuthors[$i], $article->getId());
}
parent::execute();
// Save the article
$articleDao->updateArticle($article);
// Update references list if it changed.
$citationDao =& DAORegistry::getDAO('CitationDAO');
$rawCitationList = $article->getCitations();
if ($previousRawCitationList != $rawCitationList) {
$citationDao->importCitations($this->request, ASSOC_TYPE_ARTICLE, $article->getId(), $rawCitationList);
}
return $this->articleId;
}
/**
* Save changes to article.
* @param $request Request
* @return int the article ID
*/
function execute(&$request)
{
$articleDao =& DAORegistry::getDAO('ArticleDAO');
$article =& $this->article;
$articleContact = new ArticleContact();
$articleContact->setArticleId($article->getId());
$articleContact->setPQName($this->getData('pqName'));
$articleContact->setPQAffiliation($this->getData('pqAffiliation'));
$articleContact->setPQAddress($this->getData('pqAddress'));
$articleContact->setPQCountry($this->getData('pqCountry'));
$articleContact->setPQPhone($this->getData('pqPhone'));
$articleContact->setPQFax($this->getData('pqFax'));
$articleContact->setPQEmail($this->getData('pqEmail'));
$articleContact->setSQName($this->getData('sqName'));
$articleContact->setSQAffiliation($this->getData('sqAffiliation'));
$articleContact->setSQAddress($this->getData('sqAddress'));
$articleContact->setSQCountry($this->getData('sqCountry'));
$articleContact->setSQPhone($this->getData('sqPhone'));
$articleContact->setSQFax($this->getData('sqFax'));
$articleContact->setSQEmail($this->getData('sqEmail'));
$article->setArticleContact($articleContact);
//update step
if ($article->getSubmissionProgress() <= $this->step) {
$article->stampStatusModified();
$article->setSubmissionProgress($this->step + 1);
} elseif ($article->getSubmissionProgress() == 9) {
$article->setSubmissionProgress(8);
}
parent::execute();
// Save the article
$articleDao->updateArticle($article);
return $this->articleId;
}
/**
* Save changes to article.
* @param $request Request
* @return int the article ID
*/
function execute(&$request)
{
$articleDao =& DAORegistry::getDAO('ArticleDAO');
$article =& $this->article;
$articleSitesData = $this->getData('articleSites');
$articleSites = $article->getArticleSites();
import('classes.journal.TrialSite');
import('classes.article.ArticleSite');
// Remove deleted article sites
foreach ($articleSites as $articleSite) {
$isPresent = false;
foreach ($articleSitesData as $articleSiteData) {
if (!empty($articleSiteData['id'])) {
if ($articleSite->getId() == $articleSiteData['id']) {
$isPresent = true;
}
}
}
if (!$isPresent) {
$article->removeArticleSite($articleSite->getId());
}
unset($isPresent);
unset($articleSite);
}
// Update / Insters article sites
foreach ($articleSitesData as $articleSiteData) {
if (isset($articleSiteData['id'])) {
$articleSite = $article->getArticleSite($articleSiteData['id']);
$isExistingSite = true;
} else {
$articleSite = new ArticleSite();
$isExistingSite = false;
}
$articleSite->setArticleId($article->getId());
if ($articleSiteData['siteSelect'] == "OTHER") {
$trialSite = new TrialSite();
$trialSite->setName($articleSiteData['siteName']);
$trialSite->setAddress($articleSiteData['siteAddress']);
$trialSite->setCity($articleSiteData['siteCity']);
$trialSite->setRegion($articleSiteData['siteRegion']);
$trialSite->setLicensure($articleSiteData['siteLicensure']);
$trialSite->setAccreditation($articleSiteData['siteAccreditation']);
$articleSite->setSiteId($this->trialSiteDao->insertTrialSite($trialSite));
} else {
$articleSite->setSiteId($articleSiteData['siteSelect']);
}
$articleSite->setAuthority($articleSiteData['authority']);
$articleSite->setERCId($articleSiteData['erc']);
$articleSite->setPrimaryPhone($articleSiteData['primaryPhone']);
$articleSite->setSecondaryPhone($articleSiteData['secondaryPhone']);
$articleSite->setFax($articleSiteData['fax']);
$articleSite->setEmail($articleSiteData['email']);
$articleSite->setSubjectsNumber($articleSiteData['subjectsNumber']);
$investigatorsData = $articleSiteData['investigators'];
$investigators = $articleSite->getInvestigators();
// Remove deleted investigators
foreach ($investigators as $investigator) {
$isPresent = false;
foreach ($investigatorsData as $investigatorData) {
if (!empty($investigatorData['id'])) {
if ($investigator->getId() == $investigatorData['id']) {
$isPresent = true;
}
}
}
if (!$isPresent) {
$articleSite->removeInvestigator($investigator->getId());
}
unset($isPresent);
unset($investigator);
}
// Update / Insert Investigators
$investigatorIterator = 1;
foreach ($investigatorsData as $investigatorData) {
if (isset($investigatorData['id'])) {
$investigator = $articleSite->getInvestigator($investigatorData['id']);
} else {
$investigator = new Author();
}
if ($isExistingSite) {
$investigator->setSiteId($articleSite->getId());
}
if ($investigatorIterator == 1) {
$investigator->setPrimaryContact(1);
}
$investigator->setSequence($investigatorIterator);
$investigator->setFirstName($investigatorData['firstName']);
$investigator->setLastName($investigatorData['lastName']);
$investigator->setExpertise($investigatorData['expertise']);
$investigator->setPrimaryPhoneNumber($investigatorData['iPrimaryPhone']);
$investigator->setSecondaryPhoneNumber($investigatorData['iSecondaryPhone']);
$investigator->setFaxNumber($investigatorData['iFax']);
$investigator->setEmail($investigatorData['iEmail']);
$articleSite->addInvestigator($investigator);
$investigatorIterator++;
}
$article->addArticleSite($articleSite);
}
//update step
if ($article->getSubmissionProgress() <= $this->step) {
$article->stampStatusModified();
$article->setSubmissionProgress($this->step + 1);
} elseif ($article->getSubmissionProgress() == 9) {
$article->setSubmissionProgress(8);
}
parent::execute();
// Save the article
$articleDao->updateArticle($article);
return $this->articleId;
}
/**
* Display the form.
*/
function display()
{
$templateMgr =& TemplateManager::getManager();
$countryDao =& DAORegistry::getDAO('CountryDAO');
$countries =& $countryDao->getCountries();
$templateMgr->assign_by_ref('countries', $countries);
if (Request::getUserVar('addAuthor') || Request::getUserVar('delAuthor') || Request::getUserVar('moveAuthor')) {
$templateMgr->assign('scrollToAuthor', true);
}
$schedConf =& Request::getSchedConf();
$reviewMode = $this->paper->getReviewMode();
$templateMgr->assign('collectAbstracts', $reviewMode != REVIEW_MODE_PRESENTATIONS_ALONE);
parent::display();
}
/**
* Display the form.
*/
function display()
{
$article =& $this->article;
$sites = $article->getArticleSites();
$details = $article->getArticleDetails();
$drugs = $article->getArticleDrugs();
$CROs = $article->getArticleCROs();
$suppFileDao =& DAORegistry::getDAO('SuppFileDAO');
$trialSiteDao =& DAORegistry::getDAO('TrialSiteDAO');
$goToNextStep = true;
$impds = $suppFileDao->getSuppFilesByArticleAndType($this->articleId, SUPP_FILE_IMPD);
$approvalLetters = $suppFileDao->getSuppFilesByArticleAndType($this->articleId, SUPP_FILE_APPROVAL);
$informedConsents = $suppFileDao->getSuppFilesByArticleAndType($this->articleId, SUPP_FILE_CONSENT);
$labelss = $suppFileDao->getSuppFilesByArticleAndType($this->articleId, SUPP_FILE_LABELS);
$gmps = $suppFileDao->getSuppFilesByArticleAndType($this->articleId, SUPP_FILE_GMP);
$relatedPublications = $suppFileDao->getSuppFilesByArticleAndType($this->articleId, SUPP_FILE_PUBLICATIONS);
if (empty($impds) || empty($approvalLetters) || empty($informedConsents) || empty($labelss) || empty($gmps)) {
$goToNextStep = false;
}
$sitesList = array();
$sitesArray = array();
foreach ($sites as $site) {
$trialSite = $trialSiteDao->getTrialSiteById($site->getSiteId());
$endorsmentLetters = $suppFileDao->getSuppFilesByArticleTypeAndAssocId($this->articleId, SUPP_FILE_ENDORSMENT, $site->getId());
$CVs = $suppFileDao->getSuppFilesByArticleTypeAndAssocId($this->articleId, SUPP_FILE_CV, $site->getId());
if (empty($endorsmentLetters) || empty($CVs)) {
$goToNextStep = false;
}
$sitesList[$site->getId()] = $trialSite->getName();
$siteArray = array('name' => $trialSite->getName(), 'endorsmentLetters' => $endorsmentLetters, 'CVs' => $CVs);
array_push($sitesArray, $siteArray);
}
$CROsList = array();
$CROsArray = array();
if ($details->getCROInvolved() == ARTICLE_DETAIL_YES) {
foreach ($CROs as $CRO) {
$delegationLetters = $suppFileDao->getSuppFilesByArticleTypeAndAssocId($this->articleId, SUPP_FILE_DELEGATION, $CRO->getId());
if (empty($delegationLetters)) {
$goToNextStep = false;
}
$CROsList[$CRO->getId()] = $CRO->getName();
array_push($CROsArray, array('name' => $CRO->getName(), 'delegations' => $delegationLetters));
}
}
$showPolicies = false;
if ($details->getCompensationPolicy() == ARTICLE_DETAIL_YES) {
$showPolicies = true;
$policies = $suppFileDao->getSuppFilesByArticleAndType($this->articleId, SUPP_FILE_POLICY);
if (empty($policies)) {
$goToNextStep = false;
}
}
$drugsListForIB = array();
$drugsListForSMPC = array();
$drugsArray = array();
foreach ($drugs as $drug) {
$IB = false;
$classes = $drug->getClassesArray();
foreach ($classes as $class) {
if ($class == ARTICLE_DRUG_INFO_CLASS_IV) {
$SmPCs = $suppFileDao->getSuppFilesByArticleTypeAndAssocId($this->articleId, SUPP_FILE_SMPC, $drug->getId());
array_push($drugsArray, array('name' => $drug->getName(), 'ib' => false, 'smpcs' => $SmPCs));
$drugsListForSMPC[$drug->getId()] = $drug->getName();
if (empty($SmPCs)) {
$goToNextStep = false;
}
} else {
if (!$IB) {
$IBs = $suppFileDao->getSuppFilesByArticleTypeAndAssocId($this->articleId, SUPP_FILE_BROCHURE, $drug->getId());
array_push($drugsArray, array('name' => $drug->getName(), 'ib' => true, 'ibs' => $IBs));
$drugsListForIB[$drug->getId()] = $drug->getName();
if (empty($IBs)) {
$goToNextStep = false;
}
}
$IB = true;
}
}
}
$showAdvertisements = false;
if ($details->getAdvertisingScheme() == ARTICLE_DETAIL_YES) {
$showAdvertisements = true;
$advertisements = $suppFileDao->getSuppFilesByArticleAndType($this->articleId, SUPP_FILE_ADVERTISEMENT);
if (empty($advertisements)) {
$goToNextStep = false;
}
}
$templateMgr =& TemplateManager::getManager();
$templateMgr->assign('typeOptions', $suppFileDao->getTypeMap());
$templateMgr->assign_by_ref('impds', $impds);
$templateMgr->assign_by_ref('approvalLetters', $approvalLetters);
$templateMgr->assign_by_ref('informedConsents', $informedConsents);
$templateMgr->assign_by_ref('labelss', $labelss);
$templateMgr->assign_by_ref('gmps', $gmps);
$templateMgr->assign('sitesArray', $sitesArray);
$templateMgr->assign('sitesList', $sitesList);
$templateMgr->assign('drugsArray', $drugsArray);
$templateMgr->assign('drugsListForIB', $drugsListForIB);
$templateMgr->assign('drugsListForSMPC', $drugsListForSMPC);
$templateMgr->assign('showAdvertisements', $showAdvertisements);
$templateMgr->assign_by_ref('advertisements', $advertisements);
$templateMgr->assign('showPolicies', $showPolicies);
$templateMgr->assign_by_ref('policies', $policies);
$templateMgr->assign('CROsList', $CROsList);
$templateMgr->assign('CROsArray', $CROsArray);
$templateMgr->assign_by_ref('relatedPublications', $relatedPublications);
$templateMgr->assign('goToNextStep', $goToNextStep);
parent::display();
}
/**
* Display the form.
*/
function display()
{
$templateMgr =& TemplateManager::getManager();
//Opatan Inc. : Assign Abstract Minimum and Maximum Length
$journal =& Request::getJournal();
$journalSettingsDao =& DAORegistry::getDAO('JournalSettingsDAO');
$abstractMinimumLength =& $journalSettingsDao->getSetting($journal->getJournalId(), 'abstractMinimumLength');
$abstractMaximumLength =& $journalSettingsDao->getSetting($journal->getJournalId(), 'abstractMaximumLength');
if ($abstractMinimumLength) {
$templateMgr->assign('abstractMinimumLength', $abstractMinimumLength);
} else {
$abstractMinimumLength = 200;
$templateMgr->assign('abstractMinimumLength', $abstractMinimumLength);
}
if ($abstractMaximumLength) {
$templateMgr->assign('abstractMaximumLength', $abstractMaximumLength);
} else {
$abstractMaximumLength = 300;
$templateMgr->assign('abstractMaximumLength', $abstractMaximumLength);
}
if ($journalSettingsDao->getSetting($journal->getJournalId(), 'authorCanSpecifyReviewers')) {
$authorCanRecommend =& $journalSettingsDao->getSetting($journal->getJournalId(), 'authorCanSpecifyReviewers');
$reviewerIsOptional =& $journalSettingsDao->getSetting($journal->getJournalId(), 'reviewerIsOptional');
$numberOfReviewers =& $journalSettingsDao->getSetting($journal->getJournalId(), 'numberOfReviewers');
$num = array();
$count = 0;
$number = $numberOfReviewers;
while ($number) {
$num[] = ++$count;
$number--;
}
$templateMgr->assign('reviewerIsOptional', $reviewerIsOptional);
$templateMgr->assign('countOfReviewers', $numberOfReviewers);
$templateMgr->assign_by_ref('numberOfReviewers', $num);
$templateMgr->assign('authorCanSpecifyReviewers', $authorCanRecommend);
}
$countryDao =& DAORegistry::getDAO('CountryDAO');
$countries =& $countryDao->getCountries();
$templateMgr->assign_by_ref('countries', $countries);
// Get submission files for this article
$articleFileDao =& DAORegistry::getDAO('ArticleFileDAO');
if ($this->article->getSubmissionFileId() != null) {
$templateMgr->assign_by_ref('submissionFile', $articleFileDao->getArticleFile($this->article->getSubmissionFileId()));
}
// Get supplementary files for this article
$suppFileDao =& DAORegistry::getDAO('SuppFileDAO');
$templateMgr->assign_by_ref('suppFiles', $suppFileDao->getSuppFilesByArticle($this->articleId));
parent::display();
}
/**
* Save settings.
*/
function execute()
{
$articleDao = DAORegistry::getDAO('ArticleDAO');
$signoffDao = DAORegistry::getDAO('SignoffDAO');
$sectionEditorSubmissionDao = DAORegistry::getDAO('SectionEditorSubmissionDAO');
$application = PKPApplication::getApplication();
$request = $this->request;
$user = $request->getUser();
$router = $request->getRouter();
$journal = $router->getContext($request);
$article = $articleDao->newDataObject();
$article->setLocale($journal->getPrimaryLocale());
// FIXME in bug #5543
$article->setUserId($user->getId());
$article->setJournalId($journal->getId());
$article->setSectionId($this->getData('sectionId'));
$article->setLanguage($this->getData('language'));
$article->setTitle($this->getData('title'), null);
// Localized
$article->setAbstract($this->getData('abstract'), null);
// Localized
$article->setDiscipline($this->getData('discipline'), null);
// Localized
$article->setSubjectClass($this->getData('subjectClass'), null);
// Localized
$article->setSubject($this->getData('subject'), null);
// Localized
$article->setCoverageGeo($this->getData('coverageGeo'), null);
// Localized
$article->setCoverageChron($this->getData('coverageChron'), null);
// Localized
$article->setCoverageSample($this->getData('coverageSample'), null);
// Localized
$article->setType($this->getData('type'), null);
// Localized
$article->setSponsor($this->getData('sponsor'), null);
// Localized
$article->setCitations($this->getData('citations'));
$article->setPages($this->getData('pages'));
// Set some default values so the ArticleDAO doesn't complain when adding this article
$article->setDateSubmitted(Core::getCurrentDate());
$article->setStatus(STATUS_PUBLISHED);
$article->setSubmissionProgress(0);
$article->stampStatusModified();
$article->setCurrentRound(1);
$article->setFastTracked(1);
$article->setHideAuthor(0);
$article->setCommentsStatus(0);
// Insert the article to get it's ID
$articleDao->insertObject($article);
$articleId = $article->getId();
// Add authors
$authors = $this->getData('authors');
for ($i = 0, $count = count($authors); $i < $count; $i++) {
if ($authors[$i]['authorId'] > 0) {
// Update an existing author
$author =& $authorDao->getAuthor($authors[$i]['authorId'], $articleId);
$isExistingAuthor = true;
} else {
// Create a new author
$author = new Author();
$isExistingAuthor = false;
}
if ($author != null) {
$author->setSubmissionId($articleId);
$author->setFirstName($authors[$i]['firstName']);
$author->setMiddleName($authors[$i]['middleName']);
$author->setLastName($authors[$i]['lastName']);
if (array_key_exists('affiliation', $authors[$i])) {
$author->setAffiliation($authors[$i]['affiliation'], null);
}
$author->setCountry($authors[$i]['country']);
$author->setEmail($authors[$i]['email']);
$author->setUrl($authors[$i]['url']);
if (array_key_exists('competingInterests', $authors[$i])) {
$author->setCompetingInterests($authors[$i]['competingInterests'], null);
}
$author->setBiography($authors[$i]['biography'], null);
$author->setPrimaryContact($this->getData('primaryContact') == $i ? 1 : 0);
$author->setSequence($authors[$i]['seq']);
if ($isExistingAuthor == false) {
$authorDao = DAORegistry::getDAO('AuthorDAO');
/* @var $authorDao AuthorDAO */
$authorDao->insertObject($author);
}
}
}
// Add the submission files as galleys
import('lib.pkp.classes.file.TemporaryFileManager');
import('classes.file.ArticleFileManager');
$tempFileIds = $this->getData('tempFileId');
$temporaryFileManager = new TemporaryFileManager();
$articleFileManager = new ArticleFileManager($articleId);
$designatedPrimary = false;
foreach (array_keys($tempFileIds) as $locale) {
$temporaryFile = $temporaryFileManager->getFile($tempFileIds[$locale], $user->getId());
$fileId = null;
if ($temporaryFile) {
$fileId = $articleFileManager->temporaryFileToArticleFile($temporaryFile, SUBMISSION_FILE_SUBMISSION);
$fileType = $temporaryFile->getFileType();
if (strstr($fileType, 'html')) {
import('classes.article.ArticleHTMLGalley');
$galley = new ArticleHTMLGalley();
} else {
import('classes.article.ArticleGalley');
$galley = new ArticleGalley();
}
$galley->setArticleId($articleId);
$galley->setFileId($fileId);
$galley->setLocale($locale);
if ($galley->isHTMLGalley()) {
$galley->setLabel('HTML');
} else {
if (strstr($fileType, 'pdf')) {
$galley->setLabel('PDF');
} else {
if (strstr($fileType, 'postscript')) {
$galley->setLabel('Postscript');
} else {
if (strstr($fileType, 'xml')) {
$galley->setLabel('XML');
} else {
$galley->setLabel(__('common.untitled'));
}
}
}
}
$galleyDao = DAORegistry::getDAO('ArticleGalleyDAO');
$galleyDao->insertGalley($galley);
if (!$designatedPrimary) {
$article->setSubmissionFileId($fileId);
if ($locale == $journal->getPrimaryLocale()) {
// Used to make sure that *some* file
// is designated Review Version, but
// preferrably the primary locale.
$designatedPrimary = true;
}
}
}
// Update file search index
import('classes.search.ArticleSearchIndex');
$articleSearchIndex = new ArticleSearchIndex();
if (isset($galley)) {
$articleSearchIndex->articleFileChanged($galley->getArticleId(), SUBMISSION_SEARCH_GALLEY_FILE, $galley->getFileId());
}
$articleSearchIndex->articleChangesFinished();
}
// Designate this as the review version by default.
$authorSubmissionDao = DAORegistry::getDAO('AuthorSubmissionDAO');
$authorSubmission =& $authorSubmissionDao->getAuthorSubmission($articleId);
import('classes.submission.author.AuthorAction');
AuthorAction::designateReviewVersion($authorSubmission, true);
// Accept the submission
$sectionEditorSubmission =& $sectionEditorSubmissionDao->getSectionEditorSubmission($articleId);
$articleFileManager = new ArticleFileManager($articleId);
import('classes.submission.sectionEditor.SectionEditorAction');
assert(false);
// FIXME: $decisionLabels missing from call below.
SectionEditorAction::recordDecision($this->request, $sectionEditorSubmission, SUBMISSION_EDITOR_DECISION_ACCEPT);
import('classes.author.form.submit.AuthorSubmitForm');
AuthorSubmitForm::assignEditors($article);
$articleDao->updateObject($article);
// Add to end of editing queue
import('classes.submission.editor.EditorAction');
if (isset($galley)) {
EditorAction::expediteSubmission($article, $this->request);
}
if ($this->getData('destination') == "issue") {
// Add to an existing issue
$issueId = $this->getData('issueId');
$this->scheduleForPublication($articleId, $issueId);
}
// Import the references list.
$citationDao = DAORegistry::getDAO('CitationDAO');
$rawCitationList = $article->getCitations();
$citationDao->importCitations($request, ASSOC_TYPE_ARTICLE, $articleId, $rawCitationList);
// Index article.
import('classes.search.ArticleSearchIndex');
$articleSearchIndex = new ArticleSearchIndex();
$articleSearchIndex->articleMetadataChanged($article);
$articleSearchIndex->articleChangesFinished();
}
/**
* Save changes to article.
* @param $request Request
* @return int the article ID
*/
function execute(&$request)
{
$articleDao =& DAORegistry::getDAO('ArticleDAO');
$article =& $this->article;
// Retrieve the previous citation list for comparison.
$previousRawCitationList = $article->getCitations();
///////////////////////////////////////////
////////////// Update Authors /////////////
///////////////////////////////////////////
$authors = $this->getData('authors');
for ($i = 0, $count = count($authors); $i < $count; $i++) {
if ($authors[$i]['authorId'] > 0) {
// Update an existing author
$author =& $article->getAuthor($authors[$i]['authorId']);
$isExistingAuthor = true;
} else {
// Create a new author
$author = new Author();
$isExistingAuthor = false;
}
if ($author != null) {
$author->setSubmissionId($article->getId());
if (isset($authors[$i]['firstName'])) {
$author->setFirstName($authors[$i]['firstName']);
}
if (isset($authors[$i]['middleName'])) {
$author->setMiddleName($authors[$i]['middleName']);
}
if (isset($authors[$i]['lastName'])) {
$author->setLastName($authors[$i]['lastName']);
}
if (isset($authors[$i]['affiliation'])) {
$author->setAffiliation($authors[$i]['affiliation']);
}
if (isset($authors[$i]['phone'])) {
$author->setPhoneNumber($authors[$i]['phone']);
}
if (isset($authors[$i]['email'])) {
$author->setEmail($authors[$i]['email']);
}
$author->setPrimaryContact($this->getData('primaryContact') == $i ? 1 : 0);
$author->setSequence($authors[$i]['seq']);
if ($isExistingAuthor == false) {
$article->addAuthor($author);
}
}
unset($author);
}
// Remove deleted authors
$deletedAuthors = explode(':', $this->getData('deletedAuthors'));
for ($i = 0, $count = count($deletedAuthors); $i < $count; $i++) {
$article->removeAuthor($deletedAuthors[$i]);
}
///////////////////////////////////////////
//////////// Update Abstract(s) ///////////
///////////////////////////////////////////
import('classes.article.ProposalAbstract');
$journal = Request::getJournal();
$abstracts = $this->getData('abstracts');
foreach ($journal->getSupportedLocaleNames() as $localeKey => $localeValue) {
if ($abstracts[$localeKey]['abstractId'] > 0) {
$abstract = $article->getAbstractByLocale($localeKey);
$isExistingAbstract = true;
} else {
$abstract = new ProposalAbstract();
$isExistingAbstract = false;
}
if ($abstract != null) {
$abstract->setArticleId($article->getId());
$abstract->setLocale($localeKey);
$abstract->setScientificTitle($abstracts[$localeKey]['scientificTitle']);
$abstract->setPublicTitle($abstracts[$localeKey]['publicTitle']);
$abstract->setBackground($abstracts[$localeKey]['background']);
$abstract->setObjectives($abstracts[$localeKey]['objectives']);
$abstract->setStudyMethods($abstracts[$localeKey]['studyMethods']);
$abstract->setExpectedOutcomes($abstracts[$localeKey]['expectedOutcomes']);
$abstract->setKeywords($abstracts[$localeKey]['keywords']);
if ($isExistingAbstract == false) {
$article->addAbstract($abstract);
}
}
unset($abstract);
}
///////////////////////////////////////////
///////// Update Proposal Details /////////
///////////////////////////////////////////
$proposalDetailsData = $this->getData('proposalDetails');
import('classes.article.ProposalDetails');
$proposalDetails = new ProposalDetails();
$institutionDao =& DAORegistry::getDAO('InstitutionDAO');
import('classes.journal.Institution');
$proposalDetails->setArticleId($article->getId());
$proposalDetails->setStudentResearch($proposalDetailsData['studentInitiatedResearch']);
$proposalDetails->setStartDate($proposalDetailsData['startDate']);
$proposalDetails->setEndDate($proposalDetailsData['endDate']);
if ($proposalDetailsData['keyImplInstitution'] == "OTHER") {
$institution = new Institution();
$institution->setInstitutionName($proposalDetailsData['otherInstitutionName']);
$institution->setInstitutionAcronym($proposalDetailsData['otherInstitutionAcronym']);
$institution->setInstitutionType($proposalDetailsData['otherInstitutionType']);
$institution->setInstitutionInternational($proposalDetailsData['international']);
if ($proposalDetailsData['international'] == INSTITUTION_NATIONAL) {
$institution->setInstitutionLocation($proposalDetailsData['locationCountry']);
} elseif ($proposalDetailsData['international'] == INSTITUTION_INTERNATIONAL) {
$institution->setInstitutionLocation($proposalDetailsData['locationInternational']);
}
$institutionId = $institutionDao->insertInstitution($institution);
$proposalDetails->setKeyImplInstitution($institutionId);
unset($institution);
} else {
$proposalDetails->setKeyImplInstitution($proposalDetailsData['keyImplInstitution']);
}
$proposalDetails->setMultiCountryResearch($proposalDetailsData['multiCountryResearch']);
if ($proposalDetailsData['multiCountryResearch'] == PROPOSAL_DETAIL_YES) {
$countriesArray = $proposalDetailsData['countries'];
$countries = implode(",", $countriesArray);
$proposalDetails->setCountries($countries);
}
$proposalDetails->setNationwide($proposalDetailsData['nationwide']);
if ($proposalDetailsData['nationwide'] != PROPOSAL_DETAIL_YES) {
$geoAreasArray = $proposalDetailsData['geoAreas'];
$proposalDetails->setGeoAreasFromArray($geoAreasArray);
}
$researchDomainsArray = $proposalDetailsData['researchDomains'];
$proposalDetails->setResearchDomainsFromArray($researchDomainsArray);
$researchFieldsArray = $proposalDetailsData['researchFields'];
foreach ($researchFieldsArray as $i => $field) {
if ($field == "OTHER") {
$otherField = $proposalDetailsData['otherResearchField'];
if ($otherField != "") {
$researchFieldsArray[$i] = "Other (" . $otherField . ")";
}
}
}
$proposalDetails->setResearchFieldsFromArray($researchFieldsArray);
$proposalDetails->setHumanSubjects($proposalDetailsData['withHumanSubjects']);
if ($proposalDetailsData['withHumanSubjects'] == PROPOSAL_DETAIL_YES) {
$proposalTypesArray = $proposalDetailsData['proposalTypes'];
foreach ($proposalTypesArray as $i => $type) {
if ($type == "OTHER") {
$otherType = $proposalDetailsData['otherProposalType'];
if ($otherType != "") {
$proposalTypesArray[$i] = "Other (" . $otherType . ")";
}
}
}
$proposalDetails->setProposalTypesFromArray($proposalTypesArray);
}
$proposalDetails->setDataCollection($proposalDetailsData['dataCollection']);
if ($proposalDetailsData['reviewedByOtherErc'] == PROPOSAL_DETAIL_YES) {
$proposalDetails->setCommitteeReviewed($proposalDetailsData['otherErcDecision']);
} else {
$proposalDetails->setCommitteeReviewed(PROPOSAL_DETAIL_NO);
}
// Update or insert student research
import('classes.article.StudentResearch');
$studentResearchInfo = new StudentResearch();
$studentResearchInfo->setArticleId($article->getId());
$studentResearchData = $this->getData('studentResearch');
$studentResearchInfo->setInstitution($studentResearchData['studentInstitution']);
$studentResearchInfo->setDegree($studentResearchData['academicDegree']);
$studentResearchInfo->setSupervisorName($studentResearchData['supervisorName']);
$studentResearchInfo->setSupervisorEmail($studentResearchData['supervisorEmail']);
$proposalDetails->setStudentResearchInfo($studentResearchInfo);
$article->setProposalDetails($proposalDetails);
///////////////////////////////////////////
//////// Update Sources of Monetary ///////
///////////////////////////////////////////
$sources = $article->getSources();
$sourcesData = $this->getData('sources');
//Remove sources
foreach ($sources as $source) {
$isPresent = false;
foreach ($sourcesData as $sourceData) {
if (!empty($sourceData['sourceId'])) {
if ($source->getSourceId() == $sourceData['sourceId']) {
$isPresent = true;
}
}
}
if (!$isPresent) {
$article->removeSource($source->getSourceId());
}
unset($source);
}
for ($i = 0, $count = count($sourcesData); $i < $count; $i++) {
if (!empty($sourcesData[$i]['sourceId'])) {
// Update an existing source
$source =& $article->getSource($sourcesData[$i]['sourceId']);
$isExistingSource = true;
} else {
// Create a new source
$source = new ProposalSource();
$isExistingSource = false;
}
if ($source != null) {
$source->setArticleId($article->getId());
if ($sourcesData[$i]['institution'] == "OTHER") {
$institution = new Institution();
$institution->setInstitutionName($sourcesData[$i]['otherInstitutionName']);
$institution->setInstitutionAcronym($sourcesData[$i]['otherInstitutionAcronym']);
$institution->setInstitutionType($sourcesData[$i]['otherInstitutionType']);
$institution->setInstitutionInternational($sourcesData[$i]['international']);
if ($sourcesData[$i]['international'] == INSTITUTION_NATIONAL) {
$institution->setInstitutionLocation($sourcesData[$i]['locationCountry']);
} elseif ($proposalDetailsData['international'] == INSTITUTION_INTERNATIONAL) {
$institution->setInstitutionLocation($sourcesData[$i]['locationInternational']);
}
$institutionId = $institutionDao->insertInstitution($institution);
$source->setInstitutionId($institutionId);
unset($institution);
} elseif ($sourcesData[$i]['institution'] == "KII") {
$source->setInstitutionId($proposalDetails->getKeyImplInstitution());
} else {
$source->setInstitutionId($sourcesData[$i]['institution']);
}
$source->setSourceAmount($sourcesData[$i]['amount']);
if (!$isExistingSource) {
$article->addSource($source);
}
}
unset($source);
}
///////////////////////////////////////////
///////////// Risk Assessment /////////////
///////////////////////////////////////////
import('classes.article.RiskAssessment');
$riskAssessment = new RiskAssessment();
$riskAssessmentData = $this->getData('riskAssessment');
$riskAssessment->setArticleId($article->getId());
$riskAssessment->setIdentityRevealed($riskAssessmentData['identityRevealed']);
$riskAssessment->setUnableToConsent($riskAssessmentData['unableToConsent']);
$riskAssessment->setUnder18($riskAssessmentData['under18']);
$riskAssessment->setDependentRelationship($riskAssessmentData['dependentRelationship']);
$riskAssessment->setEthnicMinority($riskAssessmentData['ethnicMinority']);
$riskAssessment->setImpairment($riskAssessmentData['impairment']);
$riskAssessment->setPregnant($riskAssessmentData['pregnant']);
$riskAssessment->setNewTreatment($riskAssessmentData['newTreatment']);
$riskAssessment->setBioSamples($riskAssessmentData['bioSamples']);
$riskAssessment->setExportHumanTissue($riskAssessmentData['exportHumanTissue']);
$riskAssessment->setExportReason($riskAssessmentData['exportReason']);
$riskAssessment->setRadiation($riskAssessmentData['radiation']);
$riskAssessment->setDistress($riskAssessmentData['distress']);
$riskAssessment->setInducements($riskAssessmentData['inducements']);
$riskAssessment->setSensitiveInfo($riskAssessmentData['sensitiveInfo']);
$riskAssessment->setReproTechnology($riskAssessmentData['reproTechnology']);
$riskAssessment->setGenetic($riskAssessmentData['genetic']);
$riskAssessment->setStemCell($riskAssessmentData['stemCell']);
$riskAssessment->setBiosafety($riskAssessmentData['biosafety']);
$riskAssessment->setRiskLevel($riskAssessmentData['riskLevel']);
$riskAssessment->setListRisks($riskAssessmentData['listRisks']);
$riskAssessment->setHowRisksMinimized($riskAssessmentData['howRisksMinimized']);
$riskAssessment->setRisksToTeam(isset($riskAssessmentData['risksToTeam']) ? 1 : 0);
$riskAssessment->setRisksToSubjects(isset($riskAssessmentData['risksToSubjects']) ? 1 : 0);
$riskAssessment->setRisksToCommunity(isset($riskAssessmentData['risksToCommunity']) ? 1 : 0);
$riskAssessment->setBenefitsToParticipants(isset($riskAssessmentData['benefitsToParticipants']) ? 1 : 0);
$riskAssessment->setKnowledgeOnCondition(isset($riskAssessmentData['knowledgeOnCondition']) ? 1 : 0);
$riskAssessment->setKnowledgeOnDisease(isset($riskAssessmentData['knowledgeOnDisease']) ? 1 : 0);
$riskAssessment->setMultiInstitutions($riskAssessmentData['multiInstitutions']);
$riskAssessment->setConflictOfInterest($riskAssessmentData['conflictOfInterest']);
$article->setRiskAssessment($riskAssessment);
//update step
if ($article->getSubmissionProgress() <= $this->step) {
$article->stampStatusModified();
$article->setSubmissionProgress($this->step + 1);
}
parent::execute();
// Save the article
$articleDao->updateArticle($article);
// Update references list if it changed.
$citationDao =& DAORegistry::getDAO('CitationDAO');
$rawCitationList = $article->getCitations();
if ($previousRawCitationList != $rawCitationList) {
$citationDao->importCitations($request, ASSOC_TYPE_ARTICLE, $article->getId(), $rawCitationList);
}
return $this->articleId;
}
/**
* Save changes to article.
* @return int the article ID
*/
function execute()
{
$articleDao =& DAORegistry::getDAO('ArticleDAO');
$authorDao =& DAORegistry::getDAO('AuthorDAO');
// Update article
$article =& $this->article;
$article->setTitle($this->getData('title'), null);
// Localized
$article->setAbstract($this->getData('abstract'), null);
// Localized
$article->setDiscipline($this->getData('discipline'), null);
// Localized
$article->setSubjectClass($this->getData('subjectClass'), null);
// Localized
$article->setSubject($this->getData('subject'), null);
// Localized
$article->setCoverageGeo($this->getData('coverageGeo'), null);
// Localized
$article->setCoverageChron($this->getData('coverageChron'), null);
// Localized
$article->setCoverageSample($this->getData('coverageSample'), null);
// Localized
$article->setType($this->getData('type'), null);
// Localized
$article->setLanguage($this->getData('language'));
$article->setSponsor($this->getData('sponsor'), null);
// Localized
$article->setCitations($this->getData('citations'));
if ($article->getSubmissionProgress() <= $this->step) {
$article->stampStatusModified();
$article->setSubmissionProgress($this->step + 1);
}
// Update authors
$authors = $this->getData('authors');
for ($i = 0, $count = count($authors); $i < $count; $i++) {
if ($authors[$i]['authorId'] > 0) {
// Update an existing author
$author =& $article->getAuthor($authors[$i]['authorId']);
$isExistingAuthor = true;
} else {
// Create a new author
$author = new Author();
$isExistingAuthor = false;
}
if ($author != null) {
$author->setArticleId($article->getId());
$author->setFirstName($authors[$i]['firstName']);
$author->setMiddleName($authors[$i]['middleName']);
$author->setLastName($authors[$i]['lastName']);
$author->setAffiliation($authors[$i]['affiliation']);
$author->setCountry($authors[$i]['country']);
$author->setEmail($authors[$i]['email']);
$author->setUrl($authors[$i]['url']);
if (array_key_exists('competingInterests', $authors[$i])) {
$author->setCompetingInterests($authors[$i]['competingInterests'], null);
}
$author->setBiography($authors[$i]['biography'], null);
$author->setPrimaryContact($this->getData('primaryContact') == $i ? 1 : 0);
$author->setSequence($authors[$i]['seq']);
if ($isExistingAuthor == false) {
$article->addAuthor($author);
}
}
unset($author);
}
// Remove deleted authors
$deletedAuthors = explode(':', $this->getData('deletedAuthors'));
for ($i = 0, $count = count($deletedAuthors); $i < $count; $i++) {
$article->removeAuthor($deletedAuthors[$i]);
}
parent::execute();
// Save the article
$articleDao->updateArticle($article);
return $this->articleId;
}
/**
* Save settings.
*/
function execute($editArticleId)
{
$this->editArticleID = $editArticleId;
$articleDao =& DAORegistry::getDAO('ArticleDAO');
$signoffDao =& DAORegistry::getDAO('SignoffDAO');
$sectionEditorSubmissionDao =& DAORegistry::getDAO('SectionEditorSubmissionDAO');
$application =& PKPApplication::getApplication();
$request =& $application->getRequest();
$user =& $request->getUser();
$router =& $request->getRouter();
$journal =& $router->getContext($request);
$article = new Article();
$article->setLocale($journal->getPrimaryLocale());
// FIXME in bug #5543
$article->setUserId($user->getId());
$article->setJournalId($journal->getId());
$article->setSectionId($this->getData('sectionId'));
$article->setLanguage(String::substr($journal->getPrimaryLocale(), 0, 2));
$article->setTitle($this->getData('title'), null);
// Localized
//add Original Journal to Abstract
$orig_journal = $this->getData('originalJournal');
$abstr = $this->getData('abstract');
foreach (array_keys($abstr) as $abs_key) {
$abstr[$abs_key] .= ' <p id="originalPub"> ' . $orig_journal . ' </p> ';
// $abstr[$abs_key] .= ' <p id="originalPub"> ' . $orig_journal[$abs_key]. ' </p> ';
//OriginalJournal in EditPlugin only a string and not an array...
$this->setData('abstract', $abstr);
}
$article->setAbstract($this->getData('abstract'), null);
// Localized
$article->setDiscipline($this->getData('discipline'), null);
// Localized
$article->setSubjectClass($this->getData('subjectClass'), null);
// Localized
$article->setSubject($this->getData('subject'), null);
// Localized
$article->setCoverageGeo($this->getData('coverageGeo'), null);
// Localized
$article->setCoverageChron($this->getData('coverageChron'), null);
// Localized
$article->setCoverageSample($this->getData('coverageSample'), null);
// Localized
$article->setType($this->getData('type'), null);
// Localized
$article->setSponsor($this->getData('sponsor'), null);
// Localized
$article->setCitations($this->getData('citations'));
$article->setPages($this->getData('pages'));
// Set some default values so the ArticleDAO doesn't complain when adding this article
$article->setDateSubmitted(Core::getCurrentDate());
$article->setStatus(STATUS_PUBLISHED);
$article->setSubmissionProgress(0);
$article->stampStatusModified();
$article->setCurrentRound(1);
$article->setFastTracked(1);
$article->setHideAuthor(0);
$article->setCommentsStatus(0);
// As article has an ID already set it
$article->setId($this->editArticleID);
$articleId = $this->editArticleID;
//delete prior Authors to prevent from double saving the same authors
$authorDao =& DAORegistry::getDAO('AuthorDAO');
$authorDao->deleteAuthorsByArticle($articleId);
// Add authors
$authors = $this->getData('authors');
for ($i = 0, $count = count($authors); $i < $count; $i++) {
if ($authors[$i]['authorId'] > 0) {
// Update an existing author
$author =& $article->getAuthor($authors[$i]['authorId']);
$isExistingAuthor = true;
} else {
// Create a new author
$author = new Author();
$isExistingAuthor = false;
}
if ($author != null) {
$author->setSubmissionId($articleId);
$author->setFirstName($authors[$i]['firstName']);
$author->setMiddleName($authors[$i]['middleName']);
$author->setLastName($authors[$i]['lastName']);
if (array_key_exists('affiliation', $authors[$i])) {
$author->setAffiliation($authors[$i]['affiliation'], null);
}
$author->setCountry($authors[$i]['country']);
$author->setEmail($authors[$i]['email']);
$author->setUrl($authors[$i]['url']);
if (array_key_exists('competingInterests', $authors[$i])) {
$author->setCompetingInterests($authors[$i]['competingInterests'], null);
}
$author->setBiography($authors[$i]['biography'], null);
$author->setPrimaryContact($this->getData('primaryContact') == $i ? 1 : 0);
$author->setSequence($authors[$i]['seq']);
if ($isExistingAuthor == false) {
$article->addAuthor($author);
}
}
}
// Check whether the user gave a handle and create a handleSubmissionFile in case
$submissionHandle = $this->getData('submissionHandle');
$handleSubmissionFileId;
$handleCheck = FALSE;
//import FileManager before creating files because otherwise naming of the copied files failes
import('classes.file.ArticleFileManager');
foreach (array_keys($submissionHandle) as $locale) {
if (!empty($submissionHandle[$locale])) {
$this->deleteOldFile("submission/original", $articleId);
// $this->deleteOldFile("submission/copyedit", $articleId);
$handleCheck = TRUE;
$handleSubmissionId = $this->createHandleTXTFile($submissionHandle[$locale], $articleId, 'submission');
$handleSubmissionPDFId = $this->createHandlePDF($submissionHandle[$locale], $articleId, 'submission');
//Add the handle submission files as galley
$this->setGalley($articleId, $handleSubmissionPDFId, $locale, 'application/pdf');
}
if ($handleCheck == TRUE) {
if ($locale == $journal->getPrimaryLocale()) {
$article->setSubmissionFileId($handleSubmissionPDFId);
$article->SetReviewFileId($handleSubmissionPDFId);
}
// Update file search index
import('classes.search.ArticleSearchIndex');
if (isset($galley)) {
ArticleSearchIndex::updateFileIndex($galley->getArticleId(), ARTICLE_SEARCH_GALLEY_FILE, $galley->getFileId());
}
}
}
// Add the submission files as galleys
import('classes.file.TemporaryFileManager');
import('classes.file.ArticleFileManager');
$tempFileIds = $this->getData('tempFileId');
$temporaryFileManager = new TemporaryFileManager();
$articleFileManager = new ArticleFileManager($articleId);
$tempFileCheck = FALSE;
foreach (array_keys($tempFileIds) as $locale) {
$temporaryFile = $temporaryFileManager->getFile($tempFileIds[$locale], $user->getId());
$fileId = null;
if ($temporaryFile) {
$this->deleteOldFile("submission/original", $articleId);
$this->deleteOldFile("submission/copyedit", $articleId);
$tempFileCheck = TRUE;
$fileId = $articleFileManager->temporaryFileToArticleFile($temporaryFile, ARTICLE_FILE_SUBMISSION);
$fileType = $temporaryFile->getFileType();
$this->setGalley($articleId, $fileId, $locale, $fileType);
// $galley =& $this->setGalley($articleId, $fileId, $locale, $fileType);
}
if ($tempFileCheck == TRUE) {
if ($locale == $journal->getPrimaryLocale()) {
$article->setSubmissionFileId($fileId);
$article->SetReviewFileId($fileId);
}
// Update file search index
import('classes.search.ArticleSearchIndex');
if (isset($galley)) {
ArticleSearchIndex::updateFileIndex($galley->getArticleId(), ARTICLE_SEARCH_GALLEY_FILE, $galley->getFileId());
}
}
}
//Check whether the user gave a handle and create handleSupplFile in case
$supplHandle = $this->getData('supplHandle');
$handleSuppFileId = null;
foreach (array_keys($supplHandle) as $locale) {
if (!empty($supplHandle[$locale])) {
$this->deleteOldFile("supp", $articleId);
$handleSuppFileId = $this->createHandleTXTFile($supplHandle[$locale], $articleId, 'supplementary');
$handleSupplPDFFileID = $this->createHandlePDF($submissionHandle[$locale], $articleId, 'supplementary');
}
}
//Add uploaded Supplementary file
$tempSupplFileIds = $this->getData('tempSupplFileId');
foreach (array_keys($tempSupplFileIds) as $locale) {
$temporaryFile = $temporaryFileManager->getFile($tempSupplFileIds[$locale], $user->getId());
$fileId = null;
if ($temporaryFile) {
$this->deleteOldFile("supp", $articleId);
$fileId = $articleFileManager->temporaryFileToArticleFile($temporaryFile, ARTICLE_FILE_SUPP);
$fileType = $temporaryFile->getFileType();
}
}
// Designate this as the review version by default.
/*$authorSubmissionDao =& DAORegistry::getDAO('AuthorSubmissionDAO');
$authorSubmission =& $authorSubmissionDao->getAuthorSubmission($articleId);
import('classes.submission.author.AuthorAction');
AuthorAction::designateReviewVersion($authorSubmission, true);
*/
// Accept the submission
/*$sectionEditorSubmission =& $sectionEditorSubmissionDao->getSectionEditorSubmission($articleId);
$articleFileManager = new ArticleFileManager($articleId);
$sectionEditorSubmission->setReviewFile($articleFileManager->getFile($article->getSubmissionFileId()));
import('classes.submission.sectionEditor.SectionEditorAction');
SectionEditorAction::recordDecision($sectionEditorSubmission, SUBMISSION_EDITOR_DECISION_ACCEPT);
*/
// Create signoff infrastructure
$copyeditInitialSignoff = $signoffDao->build('SIGNOFF_COPYEDITING_INITIAL', ASSOC_TYPE_ARTICLE, $articleId);
$copyeditAuthorSignoff = $signoffDao->build('SIGNOFF_COPYEDITING_AUTHOR', ASSOC_TYPE_ARTICLE, $articleId);
$copyeditFinalSignoff = $signoffDao->build('SIGNOFF_COPYEDITING_FINAL', ASSOC_TYPE_ARTICLE, $articleId);
$copyeditInitialSignoff->setUserId(0);
$copyeditAuthorSignoff->setUserId($user->getId());
$copyeditFinalSignoff->setUserId(0);
$signoffDao->updateObject($copyeditInitialSignoff);
$signoffDao->updateObject($copyeditAuthorSignoff);
$signoffDao->updateObject($copyeditFinalSignoff);
$layoutSignoff = $signoffDao->build('SIGNOFF_LAYOUT', ASSOC_TYPE_ARTICLE, $articleId);
$layoutSignoff->setUserId(0);
$signoffDao->updateObject($layoutSignoff);
$proofAuthorSignoff = $signoffDao->build('SIGNOFF_PROOFREADING_AUTHOR', ASSOC_TYPE_ARTICLE, $articleId);
$proofProofreaderSignoff = $signoffDao->build('SIGNOFF_PROOFREADING_PROOFREADER', ASSOC_TYPE_ARTICLE, $articleId);
$proofLayoutEditorSignoff = $signoffDao->build('SIGNOFF_PROOFREADING_LAYOUT', ASSOC_TYPE_ARTICLE, $articleId);
$proofAuthorSignoff->setUserId($user->getId());
$proofProofreaderSignoff->setUserId(0);
$proofLayoutEditorSignoff->setUserId(0);
$signoffDao->updateObject($proofAuthorSignoff);
$signoffDao->updateObject($proofProofreaderSignoff);
$signoffDao->updateObject($proofLayoutEditorSignoff);
import('classes.author.form.submit.AuthorSubmitForm');
AuthorSubmitForm::assignEditors($article);
$articleDao->updateArticle($article);
// Add to end of editing queue
import('classes.submission.editor.EditorAction');
if (isset($galley)) {
EditorAction::expediteSubmission($article);
}
// As the article already has an issue, just get it from database
$issueDao =& DAORegistry::getDAO('IssueDAO');
$issue =& $issueDao->getIssueByArticleId($this->editArticleID);
$issueId = $issue->getIssueId();
//$this->scheduleForPublication($articleId, $issueId);
// Index article.
import('classes.search.ArticleSearchIndex');
ArticleSearchIndex::indexArticleMetadata($article);
// Import the references list.
$citationDao =& DAORegistry::getDAO('CitationDAO');
$rawCitationList = $article->getCitations();
$citationDao->importCitations($request, ASSOC_TYPE_ARTICLE, $articleId, $rawCitationList);
}
/**
* Save changes to article.
* @param $request Request
* @return int the article ID
*/
function execute(&$request)
{
$articleDao =& DAORegistry::getDAO('ArticleDAO');
$articleDetailsDao =& DAORegistry::getDAO('ArticleDetailsDAO');
$institutionDao =& DAORegistry::getDAO('InstitutionDAO');
import('classes.journal.Institution');
$article =& $this->article;
$fundingSourcesData = $this->getData('fundingSources');
$fundingSources = $article->getArticleFundingSources();
$primarySponsorData = $this->getData('primarySponsor');
$secondarySponsorsData = $this->getData('secondarySponsors');
$secondarySponsors = $article->getArticleSecondarySponsors();
$details = $article->getArticleDetails();
$CROsData = $this->getData('CROs');
$CROs = $article->getArticleCROs();
$newInstitutions = array();
// Remove deleted funding sources
foreach ($fundingSources as $fundingSource) {
$isPresent = false;
foreach ($fundingSourcesData as $fundingSourceData) {
if (!empty($fundingSourceData['id'])) {
if ($fundingSource->getId() == $fundingSourceData['id']) {
$isPresent = true;
}
}
}
if (!$isPresent) {
$article->removeArticleFundingSource($fundingSource->getId());
}
unset($isPresent);
unset($fundingSource);
}
// Update / Insert funding sources
foreach ($fundingSourcesData as $fundingSourceData) {
if (isset($fundingSourceData['id'])) {
$articleSource = $article->getArticleFundingSource($fundingSourceData['id']);
} else {
$articleSource = new ArticleSponsor();
}
$articleSource->setArticleId($article->getId());
$articleSource->setType(ARTICLE_SPONSOR_TYPE_FUNDING);
if ($fundingSourceData['institutionId'] == 'OTHER') {
$institution = new Institution();
$institution->setInstitutionName($fundingSourceData['name']);
$institution->setInstitutionAcronym($fundingSourceData['acronym']);
$institution->setInstitutionType($fundingSourceData['type']);
$institution->setInstitutionInternational($fundingSourceData['location']);
if ($fundingSourceData['location'] == INSTITUTION_NATIONAL) {
$institution->setInstitutionLocation($fundingSourceData['locationCountry']);
} elseif ($fundingSourceData['location'] == INSTITUTION_INTERNATIONAL) {
$institution->setInstitutionLocation($fundingSourceData['locationInternational']);
}
$institutionId = $institutionDao->insertInstitution($institution);
$articleSource->setInstitutionId($institutionId);
$fundingSourceData['institutionId'] = $institutionId;
array_push($newInstitutions, $fundingSourceData);
unset($institution);
} else {
$articleSource->setInstitutionId($fundingSourceData['institutionId']);
}
$article->addArticleFundingSource($articleSource);
unset($articleSource);
}
if (isset($primarySponsorData['id'])) {
$primarySponsor = $article->getArticlePrimarySponsor();
} else {
$primarySponsor = new ArticleSponsor();
}
$primarySponsor->setArticleId($article->getId());
$primarySponsor->setType(ARTICLE_SPONSOR_TYPE_PRIMARY);
if ($primarySponsorData['institutionId'] == 'OTHER') {
$found = false;
foreach ($newInstitutions as $newInstitution) {
if ($newInstitution['name'] == $primarySponsorData['name'] || $newInstitution['acronym'] == $primarySponsorData['acronym']) {
$found = $newInstitution['institutionId'];
}
}
if (!$found) {
$institution = new Institution();
$institution->setInstitutionName($primarySponsorData['name']);
$institution->setInstitutionAcronym($primarySponsorData['acronym']);
$institution->setInstitutionType($primarySponsorData['type']);
$institution->setInstitutionInternational($primarySponsorData['location']);
if ($primarySponsorData['location'] == INSTITUTION_NATIONAL) {
$institution->setInstitutionLocation($primarySponsorData['locationCountry']);
} elseif ($primarySponsorData['location'] == INSTITUTION_INTERNATIONAL) {
$institution->setInstitutionLocation($primarySponsorData['locationInternational']);
}
$institutionId = $institutionDao->insertInstitution($institution);
$primarySponsor->setInstitutionId($institutionId);
$primarySponsorData['institutionId'] = $institutionId;
array_push($newInstitutions, $primarySponsorData);
unset($institution);
} else {
$primarySponsor->setInstitutionId($found);
}
} else {
$primarySponsor->setInstitutionId($primarySponsorData['institutionId']);
}
$article->setArticlePrimarySponsor($primarySponsor);
// Remove deleted secondary sponsors
foreach ($secondarySponsors as $secondarySponsor) {
$isPresent = false;
foreach ($secondarySponsorsData as $secondarySponsorData) {
if (!empty($secondarySponsorData['id'])) {
if ($secondarySponsor->getId() == $secondarySponsorData['id']) {
$isPresent = true;
}
}
}
if (!$isPresent) {
$article->removeArticleSecondarySponsor($secondarySponsor->getId());
}
unset($isPresent);
unset($secondarySponsor);
}
// Update / Insert secondary sponsors
foreach ($secondarySponsorsData as $secondarySponsorData) {
if (isset($secondarySponsorData['id'])) {
$secondarySponsor = $article->getArticleSecondarySponsor($secondarySponsorData['id']);
} else {
$secondarySponsor = new ArticleSponsor();
}
$secondarySponsor->setArticleId($article->getId());
$secondarySponsor->setType(ARTICLE_SPONSOR_TYPE_SECONDARY);
if ($secondarySponsorData['ssInstitutionId'] == 'OTHER') {
$found = false;
foreach ($newInstitutions as $newInstitution) {
if ($newInstitution['name'] == $secondarySponsorData['ssName'] || $newInstitution['acronym'] == $secondarySponsorData['ssAcronym']) {
$found = $newInstitution['institutionId'];
}
}
if (!$found) {
$institution = new Institution();
$institution->setInstitutionName($secondarySponsorData['ssName']);
$institution->setInstitutionAcronym($secondarySponsorData['ssAcronym']);
$institution->setInstitutionType($secondarySponsorData['ssType']);
$institution->setInstitutionInternational($secondarySponsorData['ssLocation']);
if ($secondarySponsorData['ssLocation'] == INSTITUTION_NATIONAL) {
$institution->setInstitutionLocation($secondarySponsorData['ssLocationCountry']);
} elseif ($secondarySponsorData['ssLocation'] == INSTITUTION_INTERNATIONAL) {
$institution->setInstitutionLocation($secondarySponsorData['ssLocationInternational']);
}
$institutionId = $institutionDao->insertInstitution($institution);
$secondarySponsor->setInstitutionId($institutionId);
$primarySponsorData['institutionId'] = $institutionId;
array_push($newInstitutions, array('institutionId' => $institutionId, 'name' => $secondarySponsorData['ssName'], 'acronym' => $secondarySponsorData['ssAcronym']));
unset($institution);
} else {
$secondarySponsor->setInstitutionId($found);
}
} else {
$secondarySponsor->setInstitutionId($secondarySponsorData['ssInstitutionId']);
}
$article->addArticleSecondarySponsor($secondarySponsor);
unset($secondarySponsor);
}
$details->setCROInvolved($this->getData('croInvolved'));
$articleDetailsDao->updateArticleDetails($details);
// Remove deleted CROs
foreach ($CROs as $CRO) {
$isPresent = false;
foreach ($CROsData as $CROData) {
if (!empty($CROData['id'])) {
if ($CRO->getId() == $CROData['id']) {
$isPresent = true;
}
}
}
if (!$isPresent) {
$article->removeArticleCRO($CRO->getId());
}
unset($isPresent);
unset($CRO);
}
// Update / Insert CROs
if ($details->getCROInvolved() == ARTICLE_DETAIL_YES) {
foreach ($CROsData as $CROData) {
if (isset($CROData['id'])) {
$CRO = $article->getArticleCRO($CROData['id']);
} else {
$CRO = new ArticleCRO();
}
$CRO->setArticleId($article->getId());
$CRO->setName($CROData['croName']);
$CRO->setInternational($CROData['croLocation']);
if ($CROData['croLocation'] == CRO_NATIONAL) {
$CRO->setLocation($CROData['croLocationCountry']);
} elseif ($CROData['croLocation'] == CRO_INTERNATIONAL) {
$CRO->setLocation($CROData['croLocationInternational']);
}
$CRO->setCity($CROData['city']);
$CRO->setAddress($CROData['address']);
$CRO->setPrimaryPhone($CROData['primaryPhone']);
$CRO->setSecondaryPhone($CROData['secondaryPhone']);
$CRO->setFax($CROData['fax']);
$CRO->setEmail($CROData['email']);
$article->addArticleCRO($CRO);
unset($CRO);
}
}
//update step
if ($article->getSubmissionProgress() <= $this->step) {
$article->stampStatusModified();
$article->setSubmissionProgress($this->step + 1);
} elseif ($article->getSubmissionProgress() == 9) {
$article->setSubmissionProgress(8);
}
parent::execute();
// Save the article
$articleDao->updateArticle($article);
return $this->articleId;
}
/**
* Save settings.
*/
function execute()
{
$articleDao =& DAORegistry::getDAO('ArticleDAO');
$signoffDao =& DAORegistry::getDAO('SignoffDAO');
$sectionEditorSubmissionDao =& DAORegistry::getDAO('SectionEditorSubmissionDAO');
$application =& PKPApplication::getApplication();
$request =& $application->getRequest();
$user =& $request->getUser();
$router =& $request->getRouter();
$journal =& $router->getContext($request);
$article = new Article();
$article->setLocale($journal->getPrimaryLocale());
// FIXME in bug #5543
$article->setUserId($user->getId());
$article->setJournalId($journal->getId());
$article->setSectionId($this->getData('sectionId'));
$article->setLanguage(String::substr($journal->getPrimaryLocale(), 0, 2));
$article->setTitle($this->getData('title'), null);
// Localized
$article->setAbstract($this->getData('abstract'), null);
// Localized
$article->setDiscipline($this->getData('discipline'), null);
// Localized
$article->setSubjectClass($this->getData('subjectClass'), null);
// Localized
$article->setSubject($this->getData('subject'), null);
// Localized
$article->setCoverageGeo($this->getData('coverageGeo'), null);
// Localized
$article->setCoverageChron($this->getData('coverageChron'), null);
// Localized
$article->setCoverageSample($this->getData('coverageSample'), null);
// Localized
$article->setType($this->getData('type'), null);
// Localized
$article->setSponsor($this->getData('sponsor'), null);
// Localized
$article->setCitations($this->getData('citations'));
$article->setPages($this->getData('pages'));
// Set some default values so the ArticleDAO doesn't complain when adding this article
$article->setDateSubmitted(Core::getCurrentDate());
$article->setStatus(STATUS_PUBLISHED);
$article->setSubmissionProgress(0);
$article->stampStatusModified();
$article->setCurrentRound(1);
$article->setFastTracked(1);
$article->setHideAuthor(0);
$article->setCommentsStatus(0);
// Insert the article to get it's ID
$articleDao->insertArticle($article);
$articleId = $article->getId();
// Add authors
$authors = $this->getData('authors');
for ($i = 0, $count = count($authors); $i < $count; $i++) {
if ($authors[$i]['authorId'] > 0) {
// Update an existing author
$author =& $article->getAuthor($authors[$i]['authorId']);
$isExistingAuthor = true;
} else {
// Create a new author
$author = new Author();
$isExistingAuthor = false;
}
if ($author != null) {
$author->setSubmissionId($articleId);
$author->setFirstName($authors[$i]['firstName']);
$author->setMiddleName($authors[$i]['middleName']);
$author->setLastName($authors[$i]['lastName']);
if (array_key_exists('affiliation', $authors[$i])) {
$author->setAffiliation($authors[$i]['affiliation'], null);
}
$author->setCountry($authors[$i]['country']);
$author->setEmail($authors[$i]['email']);
$author->setUrl($authors[$i]['url']);
if (array_key_exists('competingInterests', $authors[$i])) {
$author->setCompetingInterests($authors[$i]['competingInterests'], null);
}
$author->setBiography($authors[$i]['biography'], null);
$author->setPrimaryContact($this->getData('primaryContact') == $i ? 1 : 0);
$author->setSequence($authors[$i]['seq']);
if ($isExistingAuthor == false) {
$article->addAuthor($author);
}
}
}
// Add the submission files as galleys
import('classes.file.TemporaryFileManager');
import('classes.file.ArticleFileManager');
$tempFileIds = $this->getData('tempFileId');
$temporaryFileManager = new TemporaryFileManager();
$articleFileManager = new ArticleFileManager($articleId);
foreach (array_keys($tempFileIds) as $locale) {
$temporaryFile = $temporaryFileManager->getFile($tempFileIds[$locale], $user->getId());
$fileId = null;
if ($temporaryFile) {
$fileId = $articleFileManager->temporaryFileToArticleFile($temporaryFile, ARTICLE_FILE_SUBMISSION);
$fileType = $temporaryFile->getFileType();
if (strstr($fileType, 'html')) {
import('classes.article.ArticleHTMLGalley');
$galley = new ArticleHTMLGalley();
} else {
import('classes.article.ArticleGalley');
$galley = new ArticleGalley();
}
$galley->setArticleId($articleId);
$galley->setFileId($fileId);
$galley->setLocale($locale);
if ($galley->isHTMLGalley()) {
$galley->setLabel('HTML');
} else {
if (strstr($fileType, 'pdf')) {
$galley->setLabel('PDF');
} else {
if (strstr($fileType, 'postscript')) {
$galley->setLabel('Postscript');
} else {
if (strstr($fileType, 'xml')) {
$galley->setLabel('XML');
} else {
$galley->setLabel(__('common.untitled'));
}
}
}
}
$galleyDao =& DAORegistry::getDAO('ArticleGalleyDAO');
$galleyDao->insertGalley($galley);
}
if ($locale == $journal->getPrimaryLocale()) {
$article->setSubmissionFileId($fileId);
$article->SetReviewFileId($fileId);
}
// Update file search index
import('classes.search.ArticleSearchIndex');
if (isset($galley)) {
ArticleSearchIndex::updateFileIndex($galley->getArticleId(), ARTICLE_SEARCH_GALLEY_FILE, $galley->getFileId());
}
}
// Designate this as the review version by default.
$authorSubmissionDao =& DAORegistry::getDAO('AuthorSubmissionDAO');
$authorSubmission =& $authorSubmissionDao->getAuthorSubmission($articleId);
import('classes.submission.author.AuthorAction');
AuthorAction::designateReviewVersion($authorSubmission, true);
// Accept the submission
$sectionEditorSubmission =& $sectionEditorSubmissionDao->getSectionEditorSubmission($articleId);
$articleFileManager = new ArticleFileManager($articleId);
$sectionEditorSubmission->setReviewFile($articleFileManager->getFile($article->getSubmissionFileId()));
import('classes.submission.sectionEditor.SectionEditorAction');
SectionEditorAction::recordDecision($sectionEditorSubmission, SUBMISSION_EDITOR_DECISION_ACCEPT);
// Create signoff infrastructure
$copyeditInitialSignoff = $signoffDao->build('SIGNOFF_COPYEDITING_INITIAL', ASSOC_TYPE_ARTICLE, $articleId);
$copyeditAuthorSignoff = $signoffDao->build('SIGNOFF_COPYEDITING_AUTHOR', ASSOC_TYPE_ARTICLE, $articleId);
$copyeditFinalSignoff = $signoffDao->build('SIGNOFF_COPYEDITING_FINAL', ASSOC_TYPE_ARTICLE, $articleId);
$copyeditInitialSignoff->setUserId(0);
$copyeditAuthorSignoff->setUserId($user->getId());
$copyeditFinalSignoff->setUserId(0);
$signoffDao->updateObject($copyeditInitialSignoff);
$signoffDao->updateObject($copyeditAuthorSignoff);
$signoffDao->updateObject($copyeditFinalSignoff);
$layoutSignoff = $signoffDao->build('SIGNOFF_LAYOUT', ASSOC_TYPE_ARTICLE, $articleId);
$layoutSignoff->setUserId(0);
$signoffDao->updateObject($layoutSignoff);
$proofAuthorSignoff = $signoffDao->build('SIGNOFF_PROOFREADING_AUTHOR', ASSOC_TYPE_ARTICLE, $articleId);
$proofProofreaderSignoff = $signoffDao->build('SIGNOFF_PROOFREADING_PROOFREADER', ASSOC_TYPE_ARTICLE, $articleId);
$proofLayoutEditorSignoff = $signoffDao->build('SIGNOFF_PROOFREADING_LAYOUT', ASSOC_TYPE_ARTICLE, $articleId);
$proofAuthorSignoff->setUserId($user->getId());
$proofProofreaderSignoff->setUserId(0);
$proofLayoutEditorSignoff->setUserId(0);
$signoffDao->updateObject($proofAuthorSignoff);
$signoffDao->updateObject($proofProofreaderSignoff);
$signoffDao->updateObject($proofLayoutEditorSignoff);
import('classes.author.form.submit.AuthorSubmitForm');
AuthorSubmitForm::assignEditors($article);
$articleDao->updateArticle($article);
// Add to end of editing queue
import('classes.submission.editor.EditorAction');
if (isset($galley)) {
EditorAction::expediteSubmission($article);
}
if ($this->getData('destination') == "issue") {
// Add to an existing issue
$issueId = $this->getData('issueId');
$this->scheduleForPublication($articleId, $issueId);
}
// Index article.
import('classes.search.ArticleSearchIndex');
ArticleSearchIndex::indexArticleMetadata($article);
// Import the references list.
$citationDao =& DAORegistry::getDAO('CitationDAO');
$rawCitationList = $article->getCitations();
$citationDao->importCitations($request, ASSOC_TYPE_ARTICLE, $articleId, $rawCitationList);
}
/**
* Save changes to article.
* @param $request Request
* @return int the article ID
*/
function execute(&$request)
{
$articleDao =& DAORegistry::getDAO('ArticleDAO');
$article =& $this->article;
///////////////////////
///// UPDATE TEXTS/////
///////////////////////
$journal = Request::getJournal();
$articleTexts = $this->getData('articleTexts');
foreach ($journal->getSupportedLocaleNames() as $localeKey => $localeValue) {
if ($articleTexts[$localeKey]['articleTextId'] > 0) {
$articleText = $article->getArticleTextByLocale($localeKey);
$isExistingArticleText = true;
} else {
$articleText = new ArticleText();
$isExistingArticleText = false;
}
if ($articleText != null) {
$articleText->setArticleId($article->getId());
$articleText->setLocale($localeKey);
$articleText->setScientificTitle($articleTexts[$localeKey]['scientificTitle']);
$articleText->setPublicTitle($articleTexts[$localeKey]['publicTitle']);
$articleText->setDescription($articleTexts[$localeKey]['description']);
$articleText->setKeyInclusionCriteria($articleTexts[$localeKey]['keyInclusionCriteria']);
$articleText->setKeyExclusionCriteria($articleTexts[$localeKey]['keyExclusionCriteria']);
$articleText->setRecruitmentInfo($articleTexts[$localeKey]['recruitmentInfo']);
if ($isExistingArticleText == false) {
$article->addArticleText($articleText);
}
}
unset($articleText);
}
///////////////////////////////////////////
/////////// Update secondary IDs //////////
///////////////////////////////////////////
$secIds = $article->getArticleSecIds();
$secIdsData = $this->getData('articleSecIds');
//Remove secondary IDs
foreach ($secIds as $secId) {
$isPresent = false;
foreach ($secIdsData as $secIdData) {
if (!empty($secIdData['articleSecIdId'])) {
if ($secId->getId() == $secIdData['articleSecIdId']) {
$isPresent = true;
}
}
}
if (!$isPresent) {
$article->removeArticleSecId($secId->getId());
}
unset($secId);
}
foreach ($secIdsData as $secIdData) {
if (!empty($secIdData['type']) && !empty($secIdData['id'])) {
if (!empty($secIdData['articleSecIdId'])) {
// Update an existing sec id
$secId =& $article->getArticleSecId($secIdData['articleSecIdId']);
} else {
// Create a new sec id
$secId = new ArticleSecId();
}
if ($secId != null) {
$secId->setArticleId($article->getId());
$secId->setType($secIdData['type']);
$secId->setSecId($secIdData['id']);
$article->addArticleSecId($secId);
}
unset($secId);
}
}
///////////////////////////////////////////
////////// Update Article Details /////////
///////////////////////////////////////////
$articlelDetailsData = $this->getData('articleDetails');
if ($article->getArticleDetails()) {
$articleDetails = $article->getArticleDetails();
} else {
$articleDetails = new ArticleDetails();
}
$articleDetails->setArticleId($article->getId());
$articleDetails->setProtocolVersion($articlelDetailsData['protocolVersion']);
$articleDetails->setTherapeuticArea($articlelDetailsData['therapeuticArea'], $articlelDetailsData['otherTherapeuticArea']);
$articleDetails->setHealthCondDiseaseFromArray($articlelDetailsData['healthConds']);
$articleDetails->setMinAgeNum($articlelDetailsData['minAgeNum']);
$articleDetails->setMinAgeUnit($articlelDetailsData['minAgeUnit']);
$articleDetails->setMaxAgeNum($articlelDetailsData['maxAgeNum']);
$articleDetails->setMaxAgeUnit($articlelDetailsData['maxAgeUnit']);
$articleDetails->setSex($articlelDetailsData['sex']);
$articleDetails->setHealthy($articlelDetailsData['healthy']);
$articleDetails->setLocaleSampleSize($articlelDetailsData['localeSampleSize']);
$articleDetails->setMultinational($articlelDetailsData['multinational']);
$articleDetails->setIntSampleSizeFromArray($articlelDetailsData['intSampleSize']);
$articleDetails->setStartDate($articlelDetailsData['startDate']);
$articleDetails->setEndDate($articlelDetailsData['endDate']);
$articleDetails->setRecruitmentStatus($articlelDetailsData['recruitStatus']);
$articleDetails->setAdvertisingScheme($articlelDetailsData['adScheme']);
$articleDetails->setCompensationPolicy($articlelDetailsData['compensationPolicy']);
$article->setArticleDetails($articleDetails);
///////////////////////////////////////////
////////// Update Article Purposes ////////
///////////////////////////////////////////
$purposesData = $this->getData('purposes');
$purposes = $article->getArticlePurposes();
//Remove deleted article purposes
foreach ($purposes as $purpose) {
$isPresent = false;
foreach ($purposesData as $purposeData) {
if (!empty($purposeData['id'])) {
if ($purpose->getId() == $purposeData['id']) {
$isPresent = true;
}
}
}
if (!$isPresent) {
$article->removeArticlePurpose($purpose->getId());
}
unset($purpose);
}
foreach ($purposesData as $purposeData) {
if (!empty($purposeData['interventional'])) {
if (!empty($purposeData['id'])) {
// Update an existing purpose
$purpose =& $article->getArticlePurpose($purposeData['id']);
} else {
// Create a new article purpose
$purpose = new ArticlePurpose();
}
if ($purpose != null) {
$purpose->setArticleId($article->getId());
if ($purposeData['interventional'] == ARTICLE_PURPOSE_TYPE_OBS) {
$purpose->setType(ARTICLE_PURPOSE_TYPE_OBS);
} else {
$purpose->setType($purposeData['type']);
}
$purpose->setCTPhase($purposeData['ctPhase']);
$purpose->setAllocation($purposeData['allocation']);
$purpose->setMasking($purposeData['masking']);
$purpose->setControl($purposeData['control']);
$purpose->setAssignment($purposeData['assignment']);
$purpose->setEndpoint($purposeData['endpoint']);
$article->addArticlePurpose($purpose);
}
unset($purpose);
}
}
///////////////////////////////////////////
////////// Update Article Outcomes ////////
///////////////////////////////////////////
$primaryOutcomesData = $this->getData('primaryOutcomes');
$secondaryOutcomesData = $this->getData('secondaryOutcomes');
$articlelOutcomes = $article->getArticleOutcomes();
//Remove outcomes
foreach ($articlelOutcomes as $articlelOutcome) {
$isPresent = false;
foreach ($primaryOutcomesData as $primaryOutcomeData) {
foreach ($journal->getSupportedLocaleNames() as $localeKey => $localeValue) {
if (!empty($primaryOutcomeData[$localeKey]['primaryOutcomeId'])) {
if ($articlelOutcome[$localeKey]->getId() == $primaryOutcomeData[$localeKey]['primaryOutcomeId']) {
$isPresent = true;
}
}
}
}
foreach ($secondaryOutcomesData as $secondaryOutcomeData) {
foreach ($journal->getSupportedLocaleNames() as $localeKey => $localeValue) {
if (!empty($secondaryOutcomeData[$localeKey]['secondaryOutcomeId'])) {
if ($articlelOutcome[$localeKey]->getId() == $secondaryOutcomeData[$localeKey]['secondaryOutcomeId']) {
$isPresent = true;
}
}
}
}
if (!$isPresent) {
foreach ($journal->getSupportedLocaleNames() as $localeKey => $localeValue) {
if (!empty($articlelOutcome[$localeKey])) {
$article->removeArticleOutcome($articlelOutcome[$localeKey]->getId());
}
}
}
unset($articlelOutcome);
}
foreach ($primaryOutcomesData as $poKey => $primaryOutcomeData) {
foreach ($journal->getSupportedLocaleNames() as $localeKey => $localeValue) {
if (!empty($primaryOutcomeData[$localeKey]['name']) && !empty($primaryOutcomeData[$localeKey]['measurement']) && !empty($primaryOutcomeData[$localeKey]['timepoint'])) {
if (!empty($primaryOutcomeData[$localeKey]['primaryOutcomeId'])) {
$primaryOutcome = $article->getArticleOutcome($primaryOutcomeData[$localeKey]['primaryOutcomeId']);
} else {
$primaryOutcome = new ArticleOutcome();
}
if ($primaryOutcome != null) {
$primaryOutcome->setArticleId($article->getId());
$primaryOutcome->setName($primaryOutcomeData[$localeKey]['name']);
$primaryOutcome->setLocale($localeKey);
$primaryOutcome->setType(ARTICLE_OUTCOME_PRIMARY);
$primaryOutcome->setMeasurement($primaryOutcomeData[$localeKey]['measurement']);
$primaryOutcome->setTimepoint($primaryOutcomeData[$localeKey]['timepoint']);
$article->addArticleOutcome($primaryOutcome);
}
unset($primaryOutcome);
}
}
}
foreach ($secondaryOutcomesData as $poKey => $secondaryOutcomeData) {
foreach ($journal->getSupportedLocaleNames() as $localeKey => $localeValue) {
if (!empty($secondaryOutcomeData[$localeKey]['name']) && !empty($secondaryOutcomeData[$localeKey]['measurement']) && !empty($secondaryOutcomeData[$localeKey]['timepoint'])) {
if (!empty($secondaryOutcomeData[$localeKey]['secondaryOutcomeId'])) {
$secondaryOutcome = $article->getArticleOutcome($secondaryOutcomeData[$localeKey]['secondaryOutcomeId']);
} else {
$secondaryOutcome = new ArticleOutcome();
}
if ($secondaryOutcome != null) {
$secondaryOutcome->setArticleId($article->getId());
$secondaryOutcome->setName($secondaryOutcomeData[$localeKey]['name']);
$secondaryOutcome->setLocale($localeKey);
$secondaryOutcome->setType(ARTICLE_OUTCOME_SECONDARY);
$secondaryOutcome->setMeasurement($secondaryOutcomeData[$localeKey]['measurement']);
$secondaryOutcome->setTimepoint($secondaryOutcomeData[$localeKey]['timepoint']);
$article->addArticleOutcome($secondaryOutcome);
}
unset($secondaryOutcome);
}
}
}
//update step
if ($article->getSubmissionProgress() <= $this->step) {
$article->stampStatusModified();
$article->setSubmissionProgress($this->step + 1);
} elseif ($article->getSubmissionProgress() == 9) {
$article->setSubmissionProgress(8);
}
parent::execute();
// Save the article
$articleDao->updateArticle($article);
return $this->articleId;
}
/**
* Validate the form
*/
function validate()
{
import('classes.payment.ojs.OJSPaymentManager');
$paymentManager =& OJSPaymentManager::getManager();
if ($paymentManager->submissionEnabled()) {
if (!parent::validate()) {
return false;
}
$journal =& Request::getJournal();
$journalId = $journal->getId();
$articleId = $this->articleId;
$user =& Request::getUser();
$completedPaymentDAO =& DAORegistry::getDAO('OJSCompletedPaymentDAO');
if ($completedPaymentDAO->hasPaidSubmission($journalId, $articleId)) {
return parent::validate();
} elseif (Request::getUserVar('qualifyForWaiver') && Request::getUserVar('commentsToEditor') != '') {
return parent::validate();
} elseif (Request::getUserVar('paymentSent')) {
return parent::validate();
} else {
$queuedPayment =& $paymentManager->createQueuedPayment($journalId, PAYMENT_TYPE_SUBMISSION, $user->getId(), $articleId, $journal->getSetting('submissionFee'));
$queuedPaymentId = $paymentManager->queuePayment($queuedPayment);
$paymentManager->displayPaymentForm($queuedPaymentId, $queuedPayment);
exit;
}
} else {
return parent::validate();
}
}
/**
* Save changes to article.
* @param $request Request
* @return int the article ID
*/
function execute(&$request)
{
$articleDao =& DAORegistry::getDAO('ArticleDAO');
$article =& $this->article;
$articleDrugsData = $this->getData('articleDrugs');
$articleDrugs = $article->getArticleDrugs();
// Remove deleted article drugs
foreach ($articleDrugs as $articleDrug) {
$isPresent = false;
foreach ($articleDrugsData as $articleDrugData) {
if (!empty($articleDrugData['id'])) {
if ($articleDrug->getId() == $articleDrugData['id']) {
$isPresent = true;
}
}
}
if (!$isPresent) {
$article->removeArticleDrug($articleDrug->getId());
}
unset($isPresent);
unset($articleDrug);
}
// Update article drugs
foreach ($articleDrugsData as $articleDrugData) {
if (isset($articleDrugData['id'])) {
$articleDrug = $article->getArticleDrug($articleDrugData['id']);
$isExistingDrug = true;
} else {
$articleDrug = new ArticleDrugInfo();
$isExistingDrug = false;
}
$articleDrug->setArticleId($article->getId());
$articleDrug->setType($articleDrugData['type']);
$articleDrug->setName($articleDrugData['name']);
$articleDrug->setBrandName($articleDrugData['brandName']);
$articleDrug->setAdministration($articleDrugData['administration']);
$articleDrug->setOtherAdministration($articleDrugData['otherAdministration']);
$articleDrug->setForm($articleDrugData['form']);
$articleDrug->setOtherForm($articleDrugData['otherForm']);
$articleDrug->setStrength($articleDrugData['strength']);
$articleDrug->setStorage($articleDrugData['storage']);
$articleDrug->setPharmaClass($articleDrugData['pharmaClass']);
$articleDrug->setClassesFromArray($articleDrugData['studyClasses']);
$articleDrug->setCountriesFromArray($articleDrugData['countries']);
$articleDrug->setDifferentConditionsOfUse($articleDrugData['conditionsOfUse']);
$articleDrug->setCPR($articleDrugData['cpr']);
$articleDrug->setDrugRegistrationNumber($articleDrugData['drugRegistrationNumber']);
$articleDrug->setImportedQuantity($articleDrugData['importedQuantity']);
$manufacturersData = $articleDrugData['manufacturers'];
$manufacturers = $articleDrug->getManufacturers();
// Remove deleted manufacturers
foreach ($manufacturers as $manufacturer) {
$isPresent = false;
foreach ($manufacturersData as $manufacturerData) {
if (!empty($manufacturerData['id'])) {
if ($manufacturer->getId() == $manufacturerData['id']) {
$isPresent = true;
}
}
}
if (!$isPresent) {
$articleDrug->removeManufacturer($manufacturer->getId());
}
unset($isPresent);
unset($manufacturer);
}
// Update manufacturers
foreach ($manufacturersData as $manufacturerData) {
if (isset($manufacturerData['id'])) {
$manufacturer = $articleDrug->getManufacturer($manufacturerData['id']);
} else {
$manufacturer = new ArticleDrugManufacturer();
}
if ($isExistingDrug) {
$manufacturer->setDrugId($articleDrug->getId());
}
$manufacturer->setName($manufacturerData['name']);
$manufacturer->setAddress($manufacturerData['address']);
$articleDrug->addManufacturer($manufacturer);
}
$article->addArticleDrug($articleDrug);
}
//update step
if ($article->getSubmissionProgress() <= $this->step) {
$article->stampStatusModified();
$article->setSubmissionProgress($this->step + 1);
} elseif ($article->getSubmissionProgress() == 9) {
$article->setSubmissionProgress(8);
}
parent::execute();
// Save the article
$articleDao->updateArticle($article);
return $this->articleId;
}
