/**
* Save changes to article.
* @param $request PKPRequest
* @return int the article ID
*/
function execute(&$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);
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);
}
}
/**
* Internal function to return a Institution object from a row.
* @param $row array
* @return Section
*/
function &_returnInstitutionFromRow(&$row)
{
$institution = new Institution();
$institution->setInstitutionId($row['institution_id']);
$institution->setInstitutionType($row['type']);
$institution->setInstitutionInternational($row['international']);
$institution->setInstitutionLocation($row['location']);
$institution->setInstitutionName($row['name']);
$institution->setInstitutionAcronym($row['acronym']);
HookRegistry::call('InstitutionDAO::_returnInstitutionFromRow', array(&$institution, &$row));
return $institution;
}
/**
* 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 institution.
*/
function execute()
{
$institutionDao =& DAORegistry::getDAO('InstitutionDAO');
if (isset($this->institutionId)) {
$institution =& $institutionDao->getInstitutionById($this->institutionId);
}
if (!isset($institution)) {
$institution = new Institution();
}
$institution->setInstitutionName($this->getData('name'));
$institution->setInstitutionAcronym($this->getData('acronym'));
$international = $this->getData('international');
$institution->setInstitutionInternational($international);
if ($international == INSTITUTION_NATIONAL) {
$institution->setInstitutionLocation($this->getData('locationCountry'));
} elseif ($international == INSTITUTION_INTERNATIONAL) {
$institution->setInstitutionLocation($this->getData('locationInternational'));
}
$institution->setInstitutionType($this->getData('type'));
if ($institution->getInstitutionId() != null) {
$institutionDao->updateInstitution($institution);
} else {
$institutionDao->insertInstitution($institution);
}
}