/**
* Installs filter template entries into the filters table.
* FIXME: Move this to plug-in installation when moving filters to plug-ins, see #5157.
*/
function installFilterTemplates()
{
// Filters are supported on PHP5+ only.
if (!checkPhpVersion('5.0.0')) {
return true;
}
$filterDao =& DAORegistry::getDAO('FilterDAO');
$filtersToBeInstalled = array('lib.pkp.classes.citation.lookup.crossref.CrossrefNlmCitationSchemaFilter', 'lib.pkp.classes.citation.lookup.pubmed.PubmedNlmCitationSchemaFilter', 'lib.pkp.classes.citation.lookup.worldcat.WorldcatNlmCitationSchemaFilter', 'lib.pkp.classes.citation.parser.freecite.FreeciteRawCitationNlmCitationSchemaFilter', 'lib.pkp.classes.citation.parser.paracite.ParaciteRawCitationNlmCitationSchemaFilter', 'lib.pkp.classes.citation.parser.parscit.ParscitRawCitationNlmCitationSchemaFilter', 'lib.pkp.classes.citation.parser.regex.RegexRawCitationNlmCitationSchemaFilter', 'lib.pkp.classes.citation.output.abnt.NlmCitationSchemaAbntFilter', 'lib.pkp.classes.citation.output.apa.NlmCitationSchemaApaFilter', 'lib.pkp.classes.citation.output.mla.NlmCitationSchemaMlaFilter', 'lib.pkp.classes.citation.output.vancouver.NlmCitationSchemaVancouverFilter', 'lib.pkp.classes.importexport.nlm.PKPSubmissionNlmXmlFilter');
import('lib.pkp.classes.citation.output.PlainTextReferencesListFilter');
foreach ($filtersToBeInstalled as $filterToBeInstalled) {
// Instantiate filter.
$filter =& instantiate($filterToBeInstalled, 'Filter');
// Install citation output filters as non-configurable site-wide filter instances.
if (is_a($filter, 'NlmCitationSchemaCitationOutputFormatFilter') || is_a($filter, 'PKPSubmissionNlmXmlFilter')) {
$filter->setIsTemplate(false);
// Check whether the filter instance has been
// installed before.
$existingFilters =& $filterDao->getObjectsByClass($filterToBeInstalled, 0, false);
// Install other filter as configurable templates.
} else {
$filter->setIsTemplate(true);
// Check whether the filter template has been
// installed before.
$existingFilters =& $filterDao->getObjectsByClass($filterToBeInstalled, 0, true);
}
// Guarantee idempotence.
if ($existingFilters->getCount()) {
continue;
}
// Install the filter or template.
$filterDao->insertObject($filter, 0);
// If this is a citation output filter then also install a corresponding references list filter.
if (is_a($filter, 'NlmCitationSchemaCitationOutputFormatFilter')) {
// Only Vancouver Style listings require numerical ordering.
if (is_a($filter, 'NlmCitationSchemaVancouverFilter')) {
$ordering = REFERENCES_LIST_ORDERING_NUMERICAL;
} else {
$ordering = REFERENCES_LIST_ORDERING_ALPHABETICAL;
}
// Instantiate the filter.
$referencesListFilter = new PlainTextReferencesListFilter($filter->getDisplayName(), $filter->getClassName(), $ordering);
$referencesListFilter->setIsTemplate(false);
// Install the filter.
$filterDao->insertObject($referencesListFilter, 0);
unset($referencesListFilter);
}
unset($filter);
}
// Composite filters are more complex to install because they
// need to be constructed first:
// 1) Check and install the ISBNdb filter template.
$alreadyInstalled = false;
$existingTemplatesFactory =& $filterDao->getObjectsByClass('lib.pkp.classes.filter.GenericSequencerFilter', 0, true);
$existingTemplates =& $existingTemplatesFactory->toArray();
foreach ($existingTemplates as $existingTemplate) {
$subFilters =& $existingTemplate->getFilters();
if (count($subFilters) != 2) {
continue;
}
if (!(isset($subFilters[1]) && is_a($subFilters[1], 'IsbndbNlmCitationSchemaIsbnFilter'))) {
continue;
}
if (!(isset($subFilters[2]) && is_a($subFilters[2], 'IsbndbIsbnNlmCitationSchemaFilter'))) {
continue;
}
$alreadyInstalled = true;
break;
}
if (!$alreadyInstalled) {
// Instantiate the filter as a configurable template.
$isbndbTransformation = array('metadata::lib.pkp.classes.metadata.nlm.NlmCitationSchema(CITATION)', 'metadata::lib.pkp.classes.metadata.nlm.NlmCitationSchema(CITATION)');
import('lib.pkp.classes.filter.GenericSequencerFilter');
$isbndbFilter = new GenericSequencerFilter('ISBNdb', $isbndbTransformation);
$isbndbFilter->setIsTemplate(true);
// Instantiate and add the NLM-to-ISBN filter.
import('lib.pkp.classes.citation.lookup.isbndb.IsbndbNlmCitationSchemaIsbnFilter');
$nlmToIsbnFilter = new IsbndbNlmCitationSchemaIsbnFilter();
$isbndbFilter->addFilter($nlmToIsbnFilter);
// Instantiate and add the ISBN-to-NLM filter.
import('lib.pkp.classes.citation.lookup.isbndb.IsbndbIsbnNlmCitationSchemaFilter');
$isbnToNlmFilter = new IsbndbIsbnNlmCitationSchemaFilter();
$isbndbFilter->addFilter($isbnToNlmFilter);
// Add the settings mapping.
$isbndbFilter->setSettingsMapping(array('apiKey' => array('seq' . $nlmToIsbnFilter->getSeq() . '_apiKey', 'seq' . $isbnToNlmFilter->getSeq() . '_apiKey'), 'isOptional' => array('seq' . $nlmToIsbnFilter->getSeq() . '_isOptional', 'seq' . $isbnToNlmFilter->getSeq() . '_isOptional')));
// Persist the composite filter.
$filterDao->insertObject($isbndbFilter, 0);
}
// 3) Check and install the NLM XML 2.3 output filter.
$alreadyInstalled = false;
$existingTemplatesFactory =& $filterDao->getObjectsByClass('lib.pkp.classes.filter.GenericSequencerFilter', 0, false);
$existingTemplates =& $existingTemplatesFactory->toArray();
foreach ($existingTemplates as $existingTemplate) {
$subFilters =& $existingTemplate->getFilters();
if (count($subFilters) != 2) {
continue;
}
if (!(isset($subFilters[1]) && is_a($subFilters[1], 'PKPSubmissionNlmXmlFilter'))) {
continue;
}
if (!(isset($subFilters[2]) && is_a($subFilters[2], 'XSLTransformationFilter'))) {
continue;
}
$alreadyInstalled = true;
break;
}
if (!$alreadyInstalled) {
// Instantiate the filter as a non-configurable filter instance.
$nlm23Transformation = array('class::lib.pkp.classes.submission.Submission', 'xml::*');
$nlm23Filter = new GenericSequencerFilter('NLM Journal Publishing V2.3 ref-list', $nlm23Transformation);
$nlm23Filter->setIsTemplate(false);
// Instantiate and add the NLM 3.0 export filter.
import('lib.pkp.classes.importexport.nlm.PKPSubmissionNlmXmlFilter');
$nlm30Filter = new PKPSubmissionNlmXmlFilter();
$nlm23Filter->addFilter($nlm30Filter);
// Instantiate, configure and add the NLM 3.0 to 2.3 downgrade XSL transformation.
import('lib.pkp.classes.xslt.XSLTransformationFilter');
$downgradeFilter = new XSLTransformationFilter('NLM 3.0 to 2.3 ref-list downgrade', array('xml::*', 'xml::*'));
$downgradeFilter->setXSLFilename('lib/pkp/classes/importexport/nlm/nlm-ref-list-30-to-23.xsl');
$nlm23Filter->addFilter($downgradeFilter);
// Persist the composite filter.
$filterDao->insertObject($nlm23Filter, 0);
}
return true;
}
/**
* Takes the raw xml result of a web service and
* transforms it via XSL to a (preliminary) XML similar
* to NLM which is then re-encoded into an array. Finally
* some typical post-processing is performed.
* FIXME: Rewrite parser/lookup filter XSL to produce real NLM
* element-citation XML and factor this code into an NLM XML to
* NLM description filter.
* @param $xmlResult string or DOMDocument
* @param $xslFileName string
* @return array a metadata array
*/
function &transformWebServiceResults(&$xmlResult, $xslFileName)
{
// Send the result through the XSL to generate a (preliminary) NLM XML.
$xslFilter = new XSLTransformationFilter(PersistableFilter::tempGroup('xml::*', 'xml::*'), 'Web Service Transformation');
$xslFilter->setXSLFilename($xslFileName);
$xslFilter->setResultType(XSL_TRANSFORMER_DOCTYPE_DOM);
$preliminaryNlm30DOM =& $xslFilter->execute($xmlResult);
if (is_null($preliminaryNlm30DOM) || is_null($preliminaryNlm30DOM->documentElement)) {
$translationParams = array('filterName' => $this->getDisplayName());
$this->addError(__('submission.citations.filter.webserviceResultTransformationError', $translationParams));
$nullVar = null;
return $nullVar;
}
// Transform the result to an array.
$xmlHelper = new XMLHelper();
$preliminaryNlm30Array = $xmlHelper->xmlToArray($preliminaryNlm30DOM->documentElement);
$preliminaryNlm30Array =& $this->postProcessMetadataArray($preliminaryNlm30Array);
return $preliminaryNlm30Array;
}
/**
* @covers Nlm30Nlm23CrosswalkFilter
*/
public function testExecute()
{
$this->markTestSkipped('Weird class interaction with ControlledVocabEntryDAO leads to failure');
// Instantiate test meta-data for a citation. This must use the complete
// available schema (although in practice this doesn't make sense) so that
// we can make sure all tags are correctly converted.
import('lib.pkp.classes.metadata.MetadataDescription');
$nameSchemaName = 'lib.pkp.plugins.metadata.nlm30.schema.Nlm30NameSchema';
$nameDescription = new MetadataDescription($nameSchemaName, ASSOC_TYPE_AUTHOR);
$nameDescription->addStatement('given-names', $value = 'Peter');
$nameDescription->addStatement('given-names', $value = 'B');
$nameDescription->addStatement('surname', $value = 'Bork');
$nameDescription->addStatement('prefix', $value = 'Mr.');
$nameDescription->addStatement('suffix', $value = 'Jr');
$citationSchemaName = 'lib.pkp.plugins.metadata.nlm30.schema.Nlm30CitationSchema';
$citationDescription = new MetadataDescription($citationSchemaName, ASSOC_TYPE_CITATION);
$citationDescription->addStatement('person-group[@person-group-type="author"]', $nameDescription);
$citationDescription->addStatement('person-group[@person-group-type="editor"]', $nameDescription);
$citationDescription->addStatement('article-title', $value = 'PHPUnit in a nutshell', 'en_US');
$citationDescription->addStatement('source', $value = 'PHPUnit in a nutshell', 'en_US');
$citationDescription->addStatement('date', $value = '2009-08-17');
$citationDescription->addStatement('date-in-citation[@content-type="access-date"]', $value = '2009-08');
$citationDescription->addStatement('issue', $value = 5);
$citationDescription->addStatement('volume', $value = 6);
$citationDescription->addStatement('season', $value = 'Summer');
$citationDescription->addStatement('chapter-title', $value = 'Introduction');
$citationDescription->addStatement('edition', $value = '2nd edition');
$citationDescription->addStatement('series', $value = 7);
$citationDescription->addStatement('supplement', $value = 'Summer Special');
$citationDescription->addStatement('conf-date', $value = '2009-08-17');
$citationDescription->addStatement('conf-loc', $value = 'Helsinki');
$citationDescription->addStatement('conf-name', $value = 'PHPUnit Hackfest');
$citationDescription->addStatement('conf-sponsor', $value = 'Basti himself');
$citationDescription->addStatement('institution', $value = 'PKP');
$citationDescription->addStatement('fpage', $value = 9);
$citationDescription->addStatement('lpage', $value = 312);
$citationDescription->addStatement('size', $value = 320);
$citationDescription->addStatement('publisher-loc', $value = 'Vancouver');
$citationDescription->addStatement('publisher-name', $value = 'SFU');
$citationDescription->addStatement('isbn', $value = '123456789');
$citationDescription->addStatement('issn[@pub-type="ppub"]', $value = '987654321');
$citationDescription->addStatement('issn[@pub-type="epub"]', $value = '111111111');
$citationDescription->addStatement('pub-id[@pub-id-type="doi"]', $value = '10420/39406');
$citationDescription->addStatement('pub-id[@pub-id-type="publisher-id"]', $value = 'xyz');
$citationDescription->addStatement('pub-id[@pub-id-type="coden"]', $value = 'abc');
$citationDescription->addStatement('pub-id[@pub-id-type="sici"]', $value = 'def');
$citationDescription->addStatement('pub-id[@pub-id-type="pmid"]', $value = '999999');
$citationDescription->addStatement('uri', $value = 'http://phpunit.org/nutshell');
$citationDescription->addStatement('comment', $value = 'just nonsense');
$citationDescription->addStatement('annotation', $value = 'more nonsense');
$citationDescription->addStatement('[@publication-type]', $value = 'conf-proc');
$citation =& $this->getCitation($citationDescription);
// Persist one copy of the citation for testing.
$citationDao =& $this->getCitationDao();
$citation->setSeq(1);
$citation->setCitationState(CITATION_APPROVED);
$citationId = $citationDao->insertObject($citation);
self::assertTrue(is_numeric($citationId));
self::assertTrue($citationId > 0);
// Construct the expected output.
$expectedOutput = '';
// Prepare NLM 3.0 input.
$mockSubmission =& $this->getTestSubmission();
import('lib.pkp.plugins.metadata.nlm30.filter.PKPSubmissionNlm30XmlFilter');
$nlm30Filter = new PKPSubmissionNlm30XmlFilter(PersistableFilter::tempGroup('class::lib.pkp.classes.submission.Submission', 'xml::*'));
$nlm30Xml = $nlm30Filter->execute($mockSubmission);
// Test the downgrade filter.
import('lib.pkp.classes.xslt.XSLTransformationFilter');
// FIXME: Add NLM 2.3 and 3.0 tag set schema validation as soon as we implement the full tag set, see #5648.
$downgradeFilter = new XSLTransformationFilter(PersistableFilter::tempGroup('xml::*', 'xml::*'), 'NLM 3.0 to 2.3 ref-list downgrade');
$downgradeFilter->setXSLFilename('lib/pkp/plugins/metadata/nlm30/filter/nlm30-to-23-ref-list.xsl');
$nlm30Xml = $downgradeFilter->execute($nlm30Xml);
self::assertXmlStringEqualsXmlFile('./lib/pkp/tests/plugins/metadata/nlm30/filter/sample-nlm23-citation.xml', $nlm30Xml);
}
/**
* Takes the raw xml result of a web service and
* transforms it via XSL to a (preliminary) XML similar
* to NLM which is then re-encoded into an array. Finally
* some typical post-processing is performed.
* FIXME: Rewrite parser/lookup filter XSL to produce real NLM
* element-citation XML and factor this code into an NLM XML to
* NLM description filter.
* @param $xmlResult string or DOMDocument
* @param $xslFileName string
* @return array a metadata array
*/
function &transformWebServiceResults(&$xmlResult, $xslFileName)
{
// Send the result through the XSL to generate a (preliminary) NLM XML.
$xslFilter = new XSLTransformationFilter();
$xslFilter->setXSLFilename($xslFileName);
$xslFilter->setResultType(XSL_TRANSFORMER_DOCTYPE_DOM);
$preliminaryNlmDOM =& $xslFilter->execute($xmlResult);
if (is_null($preliminaryNlmDOM)) {
return $preliminaryNlmDOM;
}
// Transform the result to an array.
$xmlHelper = new XMLHelper();
$preliminaryNlmArray = $xmlHelper->xmlToArray($preliminaryNlmDOM->documentElement);
$preliminaryNlmArray =& $this->postProcessMetadataArray($preliminaryNlmArray);
return $preliminaryNlmArray;
}
/**
* @see OAIMetadataFormat#toXml
* TODO:
* <copyright-holder>
* In Isabelle's mapping document:
* Article order in the issue's Table of Contents
*/
function toXml(&$record, $format = null)
{
$article =& $record->getData('article');
$journal =& $record->getData('journal');
$section =& $record->getData('section');
$issue =& $record->getData('issue');
$galleys =& $record->getData('galleys');
$articleId = $article->getId();
// Cache issue ordering information.
static $issueId;
static $sectionSeq;
if (!isset($issueId) || $issueId != $issue->getId()) {
$sectionDao =& DAORegistry::getDAO('SectionDAO');
$issueId = $issue->getId();
$sections =& $sectionDao->getSectionsForIssue($issueId);
$sectionSeq = array();
$i = 0;
foreach ($sections as $thisSection) {
$sectionSeq[$thisSection->getSectionId()] = $i++;
}
unset($sections);
}
$abbreviation = $journal->getLocalizedSetting('abbreviation');
$printIssn = $journal->getSetting('printIssn');
$onlineIssn = $journal->getSetting('onlineIssn');
$primaryLocale = $journal->getPrimaryLocale();
$publisherInstitution = $journal->getSetting('publisherInstitution');
$datePublished = $article->getDatePublished();
if (!$datePublished) {
$datePublished = $issue->getDatePublished();
}
if ($datePublished) {
$datePublished = strtotime($datePublished);
}
$response = "<article\n" . "\txmlns=\"http://dtd.nlm.nih.gov/publishing/2.3\"\n" . "\txmlns:xlink=\"http://www.w3.org/1999/xlink\"\n" . "\txmlns:mml=\"http://www.w3.org/1998/Math/MathML\"\n" . "\txmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"\n" . "\txsi:schemaLocation=\"http://dtd.nlm.nih.gov/publishing/2.3\n" . "\thttp://dtd.nlm.nih.gov/publishing/2.3/xsd/journalpublishing.xsd\"\n" . (($s = $section->getSectionIdentifyType()) != '' ? "\tarticle-type=\"" . htmlspecialchars(Core::cleanVar($s)) . "\"" : '') . "\txml:lang=\"" . strtoupper(substr($primaryLocale, 0, 2)) . "\">\n" . "\t<front>\n" . "\t\t<journal-meta>\n" . "\t\t\t<journal-id journal-id-type=\"other\">" . htmlspecialchars(Core::cleanVar(($s = Config::getVar('oai', 'nlm_journal_id')) != '' ? $s : $journal->getPath())) . "</journal-id>\n" . "\t\t\t<journal-title>" . htmlspecialchars(Core::cleanVar($journal->getJournalTitle())) . "</journal-title>\n";
// Include translated journal titles
foreach ($journal->getTitle(null) as $locale => $title) {
if ($locale == $primaryLocale) {
continue;
}
$response .= "\t\t\t<trans-title xml:lang=\"" . strtoupper(substr($locale, 0, 2)) . "\">" . htmlspecialchars(Core::cleanVar($title)) . "</trans-title>\n";
}
$response .= (!empty($onlineIssn) ? "\t\t\t<issn pub-type=\"epub\">" . htmlspecialchars(Core::cleanVar($onlineIssn)) . "</issn>" : '') . (!empty($printIssn) ? "\t\t\t<issn pub-type=\"ppub\">" . htmlspecialchars(Core::cleanVar($printIssn)) . "</issn>" : '') . ($publisherInstitution != '' ? "\t\t\t<publisher><publisher-name>" . htmlspecialchars(Core::cleanVar($publisherInstitution)) . "</publisher-name></publisher>\n" : '') . "\t\t</journal-meta>\n" . "\t\t<article-meta>\n" . "\t\t\t<article-id pub-id-type=\"other\">" . htmlspecialchars(Core::cleanVar($article->getBestArticleId())) . "</article-id>\n" . (($s = $article->getDOI()) != '' ? "\t\t\t<article-id pub-id-type=\"doi\">" . htmlspecialchars(Core::cleanVar($s)) . "</article-id>\n" : '') . "\t\t\t<article-categories><subj-group subj-group-type=\"heading\"><subject>" . htmlspecialchars(Core::cleanVar($section->getSectionTitle())) . "</subject></subj-group></article-categories>\n" . "\t\t\t<title-group>\n" . "\t\t\t\t<article-title>" . htmlspecialchars(Core::cleanVar(strip_tags($article->getArticleTitle()))) . "</article-title>\n";
// Include translated journal titles
foreach ($article->getTitle(null) as $locale => $title) {
if ($locale == $primaryLocale) {
continue;
}
$response .= "\t\t\t\t<trans-title xml:lang=\"" . strtoupper(substr($locale, 0, 2)) . "\">" . htmlspecialchars(Core::cleanVar(strip_tags($title))) . "</trans-title>\n";
}
$response .= "\t\t\t</title-group>\n" . "\t\t\t<contrib-group>\n";
// Include authors
foreach ($article->getAuthors() as $author) {
$response .= "\t\t\t\t<contrib " . ($author->getPrimaryContact() ? 'corresp="yes" ' : '') . "contrib-type=\"author\">\n" . "\t\t\t\t\t<name name-style=\"western\">\n" . "\t\t\t\t\t\t<surname>" . htmlspecialchars(Core::cleanVar($author->getLastName())) . "</surname>\n" . "\t\t\t\t\t\t<given-names>" . htmlspecialchars(Core::cleanVar($author->getFirstName()) . (($s = $author->getMiddleName()) != '' ? " {$s}" : '')) . "</given-names>\n" . "\t\t\t\t\t</name>\n" . (($s = $author->getLocalizedAffiliation()) != '' ? "\t\t\t\t\t<aff>" . htmlspecialchars(Core::cleanVar($s)) . "</aff>\n" : '') . "\t\t\t\t\t<email>" . htmlspecialchars(Core::cleanVar($author->getEmail())) . "</email>\n" . (($s = $author->getUrl()) != '' ? "\t\t\t\t\t<uri>" . htmlspecialchars(Core::cleanVar($s)) . "</uri>\n" : '') . "\t\t\t\t</contrib>\n";
}
// Include editorships (optimized)
$response .= $this->getEditorialInfo($journal->getId());
$response .= "\t\t\t</contrib-group>\n";
if ($datePublished) {
$response .= "\t\t\t<pub-date pub-type=\"epub\">\n" . "\t\t\t\t<day>" . strftime('%d', $datePublished) . "</day>\n" . "\t\t\t\t<month>" . strftime('%m', $datePublished) . "</month>\n" . "\t\t\t\t<year>" . strftime('%Y', $datePublished) . "</year>\n" . "\t\t\t</pub-date>\n";
}
$response .= ($issue->getShowYear() ? "\t\t\t<pub-date pub-type=\"collection\"><year>" . htmlspecialchars(Core::cleanVar($issue->getYear())) . "</year></pub-date>\n" : '') . ($issue->getShowVolume() ? "\t\t\t<volume>" . htmlspecialchars(Core::cleanVar($issue->getVolume())) . "</volume>\n" : '') . ($issue->getShowNumber() ? "\t\t\t<issue seq=\"" . htmlspecialchars(Core::cleanVar($sectionSeq[$section->getId()] * 100 + $article->getSeq())) . "\">" . htmlspecialchars(Core::cleanVar($issue->getNumber())) . "</issue>\n" : '') . "\t\t\t<issue-id pub-id-type=\"other\">" . htmlspecialchars(Core::cleanVar($issue->getBestIssueId())) . "</issue-id>\n" . ($issue->getShowTitle() ? "\t\t\t<issue-title>" . htmlspecialchars(Core::cleanVar($issue->getIssueTitle())) . "</issue-title>\n" : '');
// Include page info, if available and parseable.
$matches = null;
if (String::regexp_match_get('/^[Pp][Pp]?[.]?[ ]?(\\d+)$/', $article->getPages(), $matches)) {
$matchedPage = htmlspecialchars(Core::cleanVar($matches[1]));
$response .= "\t\t\t\t<fpage>{$matchedPage}</fpage><lpage>{$matchedPage}</lpage>\n";
$pageCount = 1;
} elseif (String::regexp_match_get('/^[Pp][Pp]?[.]?[ ]?(\\d+)[ ]?-[ ]?([Pp][Pp]?[.]?[ ]?)?(\\d+)$/', $article->getPages(), $matches)) {
$matchedPageFrom = htmlspecialchars(Core::cleanVar($matches[1]));
$matchedPageTo = htmlspecialchars(Core::cleanVar($matches[3]));
$response .= "\t\t\t\t<fpage>{$matchedPageFrom}</fpage>\n" . "\t\t\t\t<lpage>{$matchedPageTo}</lpage>\n";
$pageCount = $matchedPageTo - $matchedPageFrom + 1;
}
$response .= "\t\t\t<permissions>\n" . (($s = $journal->getLocalizedSetting('copyrightNotice')) != '' ? "\t\t\t\t<copyright-statement>" . htmlspecialchars(Core::cleanVar($s)) . "</copyright-statement>\n" : '') . ($datePublished ? "\t\t\t\t<copyright-year>" . strftime('%Y', $datePublished) . "</copyright-year>\n" : '') . "\t\t\t</permissions>\n" . "\t\t\t<self-uri xlink:href=\"" . htmlspecialchars(Core::cleanVar(Request::url($journal->getPath(), 'article', 'view', $article->getBestArticleId()))) . "\" />\n";
// Include galley links
foreach ($article->getGalleys() as $galley) {
$response .= "\t\t\t<self-uri content-type=\"" . htmlspecialchars(Core::cleanVar($galley->getFileType())) . "\" xlink:href=\"" . htmlspecialchars(Core::cleanVar(Request::url($journal->getPath(), 'article', 'view', array($article->getBestArticleId(), $galley->getId())))) . "\" />\n";
}
// Include abstract(s)
$abstract = htmlspecialchars(Core::cleanVar(strip_tags($article->getArticleAbstract())));
if (!empty($abstract)) {
$abstract = "<p>{$abstract}</p>";
// $abstract = '<p>' . String::regexp_replace('/\n+/', '</p><p>', $abstract) . '</p>';
$response .= "\t\t\t<abstract xml:lang=\"" . strtoupper(substr($primaryLocale, 0, 2)) . "\">{$abstract}</abstract>\n";
}
if (is_array($article->getAbstract(null))) {
foreach ($article->getAbstract(null) as $locale => $abstract) {
if ($locale == $primaryLocale || empty($abstract)) {
continue;
}
$abstract = htmlspecialchars(Core::cleanVar(strip_tags($abstract)));
if (empty($abstract)) {
continue;
}
$abstract = "<p>{$abstract}</p>";
//$abstract = '<p>' . String::regexp_replace('/\n+/', '</p><p>', $abstract) . '</p>';
$response .= "\t\t\t<abstract-trans xml:lang=\"" . strtoupper(substr($locale, 0, 2)) . "\">{$abstract}</abstract-trans>\n";
}
}
$subjects = array();
if (is_array($article->getSubject(null))) {
foreach ($article->getSubject(null) as $locale => $subject) {
$s = array_map('trim', explode(';', Core::cleanVar($subject)));
if (!empty($s)) {
$subjects[$locale] = $s;
}
}
}
if (!empty($subjects)) {
foreach ($subjects as $locale => $s) {
$response .= "\t\t\t<kwd-group xml:lang=\"" . strtoupper(substr($locale, 0, 2)) . "\">\n";
foreach ($s as $subject) {
$response .= "\t\t\t\t<kwd>" . htmlspecialchars($subject) . "</kwd>\n";
}
$response .= "\t\t\t</kwd-group>\n";
}
}
$response .= (isset($pageCount) ? "\t\t\t<counts><page-count count=\"" . (int) $pageCount . "\" /></counts>\n" : '') . "\t\t</article-meta>\n" . "\t</front>\n";
// Include body text (for search indexing only)
import('classes.search.ArticleSearchIndex');
$text = '';
$galleys = $article->getGalleys();
// Give precedence to HTML galleys, as they're quickest to parse
usort($galleys, create_function('$a, $b', 'return $a->isHtmlGalley()?-1:1;'));
// Determine any access limitations. If there are, do not
// provide the full-text.
import('classes.issue.IssueAction');
$subscriptionRequired = IssueAction::subscriptionRequired($issue);
$isSubscribedDomain = IssueAction::subscribedDomain($journal, $issue->getId(), $article->getId());
if (!$subscriptionRequired || $isSubscribedDomain) {
foreach ($galleys as $galley) {
$parser =& SearchFileParser::fromFile($galley);
if ($parser && $parser->open()) {
while (($s = $parser->read()) !== false) {
$text .= $s;
}
$parser->close();
}
if ($galley->isHtmlGalley()) {
$text = strip_tags($text);
}
unset($galley);
// Use the first parseable galley.
if (!empty($text)) {
break;
}
}
}
if (!empty($text)) {
$response .= "\t<body><p>" . htmlspecialchars(Core::cleanVar(Core::cleanVar($text))) . "</p></body>\n";
}
// Add NLM citation info
import('lib.pkp.classes.importexport.nlm.PKPSubmissionNlmXmlFilter');
$nlmFilter = new PKPSubmissionNlmXmlFilter();
$nlmXml = $nlmFilter->execute($article);
// Downgrade to an NLM 2.3 ref-list
import('lib.pkp.classes.xslt.XSLTransformationFilter');
$downgradeFilter = new XSLTransformationFilter('NLM 3.0 to 2.3 ref-list downgrade', array('xml::*', 'xml::*'));
$downgradeFilter->setXSLFilename('lib/pkp/classes/importexport/nlm/nlm-ref-list-30-to-23.xsl');
// To suppress the XML header, get the DOM and convert it to
// string explicitly. (Also check for empty node.)
$downgradeFilter->setResultType(XSL_TRANSFORMER_DOCTYPE_DOM);
$nlmXmlDom = $downgradeFilter->execute($nlmXml);
$documentElement =& $nlmXmlDom->documentElement;
// Work-around for hasChildNodes being stupid about whitespace.
$hasChildren = false;
if (isset($documentElement->childNodes)) {
foreach ($documentElement->childNodes as $c) {
if ($c->nodeType == XML_ELEMENT_NODE) {
$hasChildren = true;
}
}
}
// If there were any citations, include them.
if ($hasChildren) {
$nlmXml = $nlmXmlDom->saveXML($documentElement);
$response .= "<back>{$nlmXml}</back>\n";
}
$response .= "</article>";
return $response;
}
