/**
* @covers OpenUrlNlmCitationSchemaCrosswalkFilter
* @covers OpenUrlCrosswalkFilter
*/
public function testExecute()
{
$openUrlDescription = $this->getTestOpenUrlDescription();
$nlmDescription = $this->getTestNlmDescription();
// Properties that are not part of the OpenURL
// description must be removed from the NLM description
// before we compare the two.
self::assertTrue($nlmDescription->removeStatement('person-group[@person-group-type="editor"]'));
self::assertTrue($nlmDescription->removeStatement('source', 'de_DE'));
self::assertTrue($nlmDescription->removeStatement('article-title', 'de_DE'));
self::assertTrue($nlmDescription->removeStatement('publisher-loc'));
self::assertTrue($nlmDescription->removeStatement('publisher-name'));
self::assertTrue($nlmDescription->removeStatement('pub-id[@pub-id-type="doi"]'));
self::assertTrue($nlmDescription->removeStatement('pub-id[@pub-id-type="pmid"]'));
self::assertTrue($nlmDescription->removeStatement('uri'));
self::assertTrue($nlmDescription->removeStatement('comment'));
self::assertTrue($nlmDescription->removeStatement('annotation'));
$filter = new OpenUrlNlmCitationSchemaCrosswalkFilter();
self::assertEquals($nlmDescription, $filter->execute($openUrlDescription));
}
/**
* @see Filter::process()
* @param $citationString string
* @return MetadataDescription
*/
function &process($citationString)
{
$nullVar = null;
// Check the availability of perl
$perlCommand = Config::getVar('cli', 'perl');
if (empty($perlCommand) || !file_exists($perlCommand)) {
return $nullVar;
}
// Convert to ASCII - Paracite doesn't handle UTF-8 well
$citationString = String::utf8_to_ascii($citationString);
// Call the paracite parser
$wrapperScript = dirname(__FILE__) . DIRECTORY_SEPARATOR . 'paracite.pl';
$paraciteCommand = $perlCommand . ' ' . escapeshellarg($wrapperScript) . ' ' . $this->getCitationModule() . ' ' . escapeshellarg($citationString);
$xmlResult = shell_exec($paraciteCommand);
if (empty($xmlResult)) {
return $nullVar;
}
if (Config::getVar('i18n', 'charset_normalization') == 'On' && !String::utf8_compliant($xmlResult)) {
$xmlResult = String::utf8_normalize($xmlResult);
}
// Create a temporary DOM document
$resultDOM = new DOMDocument();
$resultDOM->recover = true;
$resultDOM->loadXML($xmlResult);
// Extract the parser results as an array
$xmlHelper = new XMLHelper();
$metadata = $xmlHelper->xmlToArray($resultDOM->documentElement);
// We have to merge subtitle and title as neither OpenURL
// nor NLM can handle subtitles.
if (isset($metadata['subtitle'])) {
$metadata['title'] .= '. ' . $metadata['subtitle'];
unset($metadata['subtitle']);
}
// Break up the authors field
if (isset($metadata['authors'])) {
$metadata['authors'] = String::trimPunctuation($metadata['authors']);
$metadata['authors'] = String::iterativeExplode(array(':', ';'), $metadata['authors']);
}
// Convert pages to integers
foreach (array('spage', 'epage') as $pageProperty) {
if (isset($metadata[$pageProperty])) {
$metadata[$pageProperty] = (int) $metadata[$pageProperty];
}
}
// Convert titles to title case
foreach (array('title', 'chapter', 'publication') as $titleProperty) {
if (isset($metadata[$titleProperty])) {
$metadata[$titleProperty] = String::titleCase($metadata[$titleProperty]);
}
}
// Map ParaCite results to OpenURL - null means
// throw the value away.
$metadataMapping = array('genre' => 'genre', '_class' => null, 'any' => null, 'authors' => 'au', 'aufirst' => 'aufirst', 'aufull' => null, 'auinit' => 'auinit', 'aulast' => 'aulast', 'atitle' => 'atitle', 'cappublication' => null, 'captitle' => null, 'date' => 'date', 'epage' => 'epage', 'featureID' => null, 'id' => null, 'issue' => 'issue', 'jnl_epos' => null, 'jnl_spos' => null, 'match' => null, 'marked' => null, 'num_of_fig' => null, 'pages' => 'pages', 'publisher' => 'pub', 'publoc' => 'place', 'ref' => null, 'rest_text' => null, 'spage' => 'spage', 'targetURL' => 'url', 'text' => null, 'ucpublication' => null, 'uctitle' => null, 'volume' => 'volume', 'year' => 'date');
// Ignore 'year' if 'date' is set
if (isset($metadata['date'])) {
$metadataMapping['year'] = null;
}
// Set default genre
if (empty($metadata['genre'])) {
$metadata['genre'] = OPENURL_GENRE_ARTICLE;
}
// Handle title, chapter and publication depending on
// the (inferred) genre. Also instantiate the target schema.
switch ($metadata['genre']) {
case OPENURL_GENRE_BOOK:
case OPENURL_GENRE_BOOKITEM:
case OPENURL_GENRE_REPORT:
case OPENURL_GENRE_DOCUMENT:
$metadataMapping += array('publication' => 'btitle', 'chapter' => 'atitle');
if (isset($metadata['title'])) {
if (!isset($metadata['publication'])) {
$metadata['publication'] = $metadata['title'];
} elseif (!isset($metadata['chapter'])) {
$metadata['chapter'] = $metadata['title'];
}
unset($metadata['title']);
}
$openUrlSchemaName = 'lib.pkp.classes.metadata.openurl.OpenUrlBookSchema';
$openUrlSchemaClass = 'OpenUrlBookSchema';
break;
case OPENURL_GENRE_ARTICLE:
case OPENURL_GENRE_JOURNAL:
case OPENURL_GENRE_ISSUE:
case OPENURL_GENRE_CONFERENCE:
case OPENURL_GENRE_PROCEEDING:
case OPENURL_GENRE_PREPRINT:
default:
$metadataMapping += array('publication' => 'jtitle');
if (isset($metadata['title'])) {
if (!isset($metadata['publication'])) {
$metadata['publication'] = $metadata['title'];
} elseif (!isset($metadata['atitle'])) {
$metadata['atitle'] = $metadata['title'];
}
unset($metadata['title']);
}
$openUrlSchemaName = 'lib.pkp.classes.metadata.openurl.OpenUrlJournalSchema';
$openUrlSchemaClass = 'OpenUrlJournalSchema';
break;
}
// Instantiate an OpenURL description
$openUrlDescription = new MetadataDescription($openUrlSchemaName, ASSOC_TYPE_CITATION);
$openUrlSchema = new $openUrlSchemaClass();
// Map the ParaCite result to OpenURL
foreach ($metadata as $paraciteElementName => $paraciteValue) {
if (!empty($paraciteValue)) {
// Trim punctuation
if (is_string($paraciteValue)) {
$paraciteValue = String::trimPunctuation($paraciteValue);
}
// Transfer the value to the OpenURL result array
assert(array_key_exists($paraciteElementName, $metadataMapping));
$openUrlPropertyName = $metadataMapping[$paraciteElementName];
if (!is_null($openUrlPropertyName) && $openUrlSchema->hasProperty($openUrlPropertyName)) {
if (is_array($paraciteValue)) {
foreach ($paraciteValue as $singleValue) {
$success = $openUrlDescription->addStatement($openUrlPropertyName, $singleValue);
assert($success);
}
} else {
$success = $openUrlDescription->addStatement($openUrlPropertyName, $paraciteValue);
assert($success);
}
}
}
}
// Crosswalk to NLM
$crosswalkFilter = new OpenUrlNlmCitationSchemaCrosswalkFilter();
$nlmDescription =& $crosswalkFilter->execute($openUrlDescription);
assert(is_a($nlmDescription, 'MetadataDescription'));
// Add 'rest_text' as NLM comment (if given)
if (isset($metadata['rest_text'])) {
$nlmDescription->addStatement('comment', String::trimPunctuation($metadata['rest_text']));
}
// Set display name and sequence id in the meta-data description
// to the corresponding values from the filter. This is important
// so that we later know which result came from which filter.
$nlmDescription->setDisplayName($this->getDisplayName());
$nlmDescription->setSeq($this->getSeq());
return $nlmDescription;
}