예제 #1
0
 /**
  * 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);
     }
 }
예제 #2
0
 /**
  * Internal function to return a risk assignment object from a row.
  * @param $row array
  * @return riskAssignment
  */
 function &_returnRiskAssessmentFromRow(&$row)
 {
     $riskAssessment = new RiskAssessment();
     $riskAssessment->setArticleId($row['article_id']);
     $riskAssessment->setIdentityRevealed($row['identity_revealed']);
     $riskAssessment->setUnableToConsent($row['unable_to_consent']);
     $riskAssessment->setUnder18($row['under_18']);
     $riskAssessment->setDependentRelationship($row['dependent_relationship']);
     $riskAssessment->setEthnicMinority($row['ethnic_minority']);
     $riskAssessment->setImpairment($row['mental_impairment']);
     $riskAssessment->setPregnant($row['pregnant']);
     $riskAssessment->setNewTreatment($row['new_treatment']);
     $riskAssessment->setBioSamples($row['biological_samples']);
     $riskAssessment->setExportHumanTissue($row['export_human_tissue']);
     $riskAssessment->setExportReason($row['export_reason']);
     $riskAssessment->setRadiation($row['ionizing_radiation']);
     $riskAssessment->setDistress($row['distress']);
     $riskAssessment->setInducements($row['inducements']);
     $riskAssessment->setSensitiveInfo($row['sensitive_information']);
     $riskAssessment->setReproTechnology($row['repro_technology']);
     $riskAssessment->setGenetic($row['genetic']);
     $riskAssessment->setStemCell($row['stem_cell']);
     $riskAssessment->setBiosafety($row['biosafety']);
     $riskAssessment->setRiskLevel($row['level_of_risk']);
     $riskAssessment->setListRisks($row['risks_list']);
     $riskAssessment->setHowRisksMinimized($row['risks_management']);
     $riskAssessment->setRisksToTeam($row['risks_to_team']);
     $riskAssessment->setRisksToSubjects($row['risks_to_subjects']);
     $riskAssessment->setRisksToCommunity($row['risks_to_community']);
     $riskAssessment->setBenefitsToParticipants($row['benefits_to_participants']);
     $riskAssessment->setKnowledgeOnCondition($row['knowledge_on_condition']);
     $riskAssessment->setKnowledgeOnDisease($row['knowledge_on_disease']);
     $riskAssessment->setMultiInstitutions($row['multi_institution']);
     $riskAssessment->setConflictOfInterest($row['conflict_of_interest']);
     HookRegistry::call('RiskAssessmentDAO::_returnRiskAssessmentFromRow', array(&$riskAssessment, &$row));
     return $riskAssessment;
 }