Trim punctuation from a string
| static public trimPunctuation ( $string ) : string | ||
| $string | string input string | |
| return | string | the trimmed string |
/**
* @copydoc Filter::process()
* @param $isbn string
* @return MetadataDescription a looked up citation description
* or null if the filter fails
*/
function &process($isbn)
{
$nullVar = null;
// Instantiate the web service request
$lookupParams = array('access_key' => $this->getApiKey(), 'index1' => 'isbn', 'results' => 'details,authors', 'value1' => $isbn);
// Call the web service
if (is_null($resultDOM =& $this->callWebService(ISBNDB_WEBSERVICE_URL, $lookupParams))) {
return $nullVar;
}
// Transform and pre-process the web service result
if (is_null($metadata =& $this->transformWebServiceResults($resultDOM, dirname(__FILE__) . DIRECTORY_SEPARATOR . 'isbndb.xsl'))) {
return $nullVar;
}
// Extract place and publisher from the combined entry.
$metadata['publisher-loc'] = PKPString::trimPunctuation(PKPString::regexp_replace('/^(.+):.*/', '\\1', $metadata['place-publisher']));
$metadata['publisher-name'] = PKPString::trimPunctuation(PKPString::regexp_replace('/.*:([^,]+),?.*/', '\\1', $metadata['place-publisher']));
unset($metadata['place-publisher']);
// Reformat the publication date
$metadata['date'] = PKPString::regexp_replace('/^[^\\d{4}]+(\\d{4}).*/', '\\1', $metadata['date']);
// Clean non-numerics from ISBN
$metadata['isbn'] = PKPString::regexp_replace('/[^\\dX]*/', '', $isbn);
// Set the publicationType
$metadata['[@publication-type]'] = NLM30_PUBLICATION_TYPE_BOOK;
return $this->getNlm30CitationDescriptionFromMetadataArray($metadata);
}
/**
* @covers PKPString::trimPunctuation
*/
public function testTrimPunctuation()
{
$trimmedChars = array(' ', ',', '.', ';', ':', '!', '?', '(', ')', '[', ']', '\\', '/');
foreach ($trimmedChars as $trimmedChar) {
self::assertEquals('trim.med', PKPString::trimPunctuation($trimmedChar . 'trim.med' . $trimmedChar));
}
}
/**
* Converts a string with a single person
* to an NLM name description.
*
* TODO: add initials from all given names to initials
* element
*
* @param $personString string
* @param $title boolean true to parse for title
* @param $degrees boolean true to parse for degrees
* @return MetadataDescription an NLM name description or null
* if the string could not be converted
*/
function &_parsePersonString($personString, $title, $degrees)
{
// Expressions to parse person strings, ported from CiteULike person
// plugin, see http://svn.citeulike.org/svn/plugins/person.tcl
static $personRegex = array('title' => '(?:His (?:Excellency|Honou?r)\\s+|Her (?:Excellency|Honou?r)\\s+|The Right Honou?rable\\s+|The Honou?rable\\s+|Right Honou?rable\\s+|The Rt\\.? Hon\\.?\\s+|The Hon\\.?\\s+|Rt\\.? Hon\\.?\\s+|Mr\\.?\\s+|Ms\\.?\\s+|M\\/s\\.?\\s+|Mrs\\.?\\s+|Miss\\.?\\s+|Dr\\.?\\s+|Sir\\s+|Dame\\s+|Prof\\.?\\s+|Professor\\s+|Doctor\\s+|Mister\\s+|Mme\\.?\\s+|Mast(?:\\.|er)?\\s+|Lord\\s+|Lady\\s+|Madam(?:e)?\\s+|Priv\\.-Doz\\.\\s+)+', 'degrees' => '(,\\s+(?:[A-Z\\.]+))+', 'initials' => '(?:(?:[A-Z]\\.){1,3}[A-Z]\\.?)|(?:(?:[A-Z]\\.\\s){1,3}[A-Z]\\.?)|(?:[A-Z]{1,4})|(?:(?:[A-Z]\\.-?){1,4})|(?:(?:[A-Z]\\.-?){1,3}[A-Z]\\.?)|(?:(?:[A-Z]-){1,3}[A-Z])|(?:(?:[A-Z]\\s){1,3}[A-Z]\\.?)|(?:(?:[A-Z]-){1,3}[A-Z]\\.?)', 'prefix' => 'Dell(?:[a|e])?(?:\\s|$)|Dalle(?:\\s|$)|D[a|e]ll\'(?:\\s|$)|Dela(?:\\s|$)|Del(?:\\s|$)|[Dd]e(?:\\s|$)(?:La(?:\\s|$)|Los(?:\\s|$))?|[Dd]e(?:\\s|$)|[Dd][a|i|u](?:\\s|$)|L[a|e|o](?:\\s|$)|[D|L|O]\'|St\\.?(?:\\s|$)|San(?:\\s|$)|[Dd]en(?:\\s|$)|[Vv]on(?:\\s|$)(?:[Dd]er(?:\\s|$))?|(?:[Ll][ea](?:\\s|$))?[Vv]an(?:\\s|$)(?:[Dd]e(?:n|r)?(?:\\s|$))?', 'givenName' => '(?:[^ \\t\\n\\r\\f\\v,.;()]{2,}|[^ \\t\\n\\r\\f\\v,.;()]{2,}\\-[^ \\t\\n\\r\\f\\v,.;()]{2,})');
// The expressions for given name, suffix and surname are the same
$personRegex['surname'] = $personRegex['suffix'] = $personRegex['givenName'];
$personRegex['double-surname'] = "(?:" . $personRegex['surname'] . "\\s)*" . $personRegex['surname'];
// Shortcut for prefixed surname
$personRegexPrefixedSurname = "(?P<prefix>(?:" . $personRegex['prefix'] . ")?)(?P<surname>" . $personRegex['surname'] . ")";
$personRegexPrefixedDoubleSurname = "(?P<prefix>(?:" . $personRegex['prefix'] . ")?)(?P<surname>" . $personRegex['double-surname'] . ")";
// Instantiate the target person description
$personDescription = new MetadataDescription('lib.pkp.plugins.metadata.nlm30.schema.Nlm30NameSchema', $this->_assocType);
// Clean the person string
$personString = trim($personString);
// 1. Extract title and degree from the person string and use this as suffix
$suffixString = '';
$results = array();
if ($title && PKPString::regexp_match_get('/^(' . $personRegex['title'] . ')/i', $personString, $results)) {
$suffixString = trim($results[1], ',:; ');
$personString = PKPString::regexp_replace('/^(' . $personRegex['title'] . ')/i', '', $personString);
}
if ($degrees && PKPString::regexp_match_get('/(' . $personRegex['degrees'] . ')$/i', $personString, $results)) {
$degreesArray = explode(',', trim($results[1], ','));
foreach ($degreesArray as $key => $degree) {
$degreesArray[$key] = PKPString::trimPunctuation($degree);
}
$suffixString .= ' - ' . implode('; ', $degreesArray);
$personString = PKPString::regexp_replace('/(' . $personRegex['degrees'] . ')$/i', '', $personString);
}
if (!empty($suffixString)) {
$personDescription->addStatement('suffix', $suffixString);
}
// Space initials when followed by a given name or last name.
$personString = PKPString::regexp_replace('/([A-Z])\\.([A-Z][a-z])/', '\\1. \\2', $personString);
// 2. Extract names and initials from the person string
// The parser expressions are ordered by specificity. The most specific expressions
// come first. Only if these specific expressions don't work will we turn to less
// specific ones. This avoids parsing errors. It also explains why we don't use the
// ?-quantifier for optional elements like initials or middle name where they could
// be misinterpreted.
$personExpressions = array('/^' . $personRegexPrefixedSurname . '$/i', '/^(?P<initials>' . $personRegex['initials'] . ')\\s' . $personRegexPrefixedSurname . '$/', '/^' . $personRegexPrefixedSurname . ',?\\s(?P<initials>' . $personRegex['initials'] . ')$/', '/^' . $personRegexPrefixedDoubleSurname . ',\\s(?P<givenName>' . $personRegex['givenName'] . ')\\s(?P<initials>' . $personRegex['initials'] . ')$/', '/^(?P<givenName>' . $personRegex['givenName'] . ')\\s(?P<initials>' . $personRegex['initials'] . ')\\s' . $personRegexPrefixedSurname . '$/', '/^' . $personRegexPrefixedDoubleSurname . ',\\s(?P<givenName>(?:' . $personRegex['givenName'] . '\\s)+)(?P<initials>' . $personRegex['initials'] . ')$/', '/^(?P<givenName>(?:' . $personRegex['givenName'] . '\\s)+)(?P<initials>' . $personRegex['initials'] . ')\\s' . $personRegexPrefixedSurname . '$/', '/^' . $personRegexPrefixedDoubleSurname . ',(?P<givenName>(?:\\s' . $personRegex['givenName'] . ')+)$/', '/^(?P<givenName>(?:' . $personRegex['givenName'] . '\\s)+)' . $personRegexPrefixedSurname . '$/', '/^\\s*(?P<surname>' . $personRegex['surname'] . ')(?P<suffix>(?:\\s+' . $personRegex['suffix'] . ')?)\\s*,\\s*(?P<initials>(?:' . $personRegex['initials'] . ')?)\\s*\\((?P<givenName>(?:\\s*' . $personRegex['givenName'] . ')+)\\s*\\)\\s*(?P<prefix>(?:' . $personRegex['prefix'] . ')?)$/', '/^(?P<givenName>' . $personRegex['givenName'] . ')\\.(?P<surname>' . $personRegex['double-surname'] . ')$/', '/^(?P<surname>.*)$/');
$results = array();
foreach ($personExpressions as $expressionId => $personExpression) {
if ($nameFound = PKPString::regexp_match_get($personExpression, $personString, $results)) {
// Given names
if (!empty($results['givenName'])) {
// Split given names
$givenNames = explode(' ', trim($results['givenName']));
foreach ($givenNames as $givenName) {
$personDescription->addStatement('given-names', $givenName);
unset($givenName);
}
}
// Initials (will also be saved as given names)
if (!empty($results['initials'])) {
$results['initials'] = str_replace(array('.', '-', ' '), array('', '', ''), $results['initials']);
for ($initialNum = 0; $initialNum < PKPString::strlen($results['initials']); $initialNum++) {
$initial = $results['initials'][$initialNum];
$personDescription->addStatement('given-names', $initial);
unset($initial);
}
}
// Surname
if (!empty($results['surname'])) {
// Correct all-upper surname
if (strtoupper($results['surname']) == $results['surname']) {
$results['surname'] = ucwords(strtolower($results['surname']));
}
$personDescription->addStatement('surname', $results['surname']);
}
// Prefix/Suffix
foreach (array('prefix', 'suffix') as $propertyName) {
if (!empty($results[$propertyName])) {
$results[$propertyName] = trim($results[$propertyName]);
$personDescription->addStatement($propertyName, $results[$propertyName]);
}
}
break;
}
}
return $personDescription;
}
/**
* Recursively trim punctuation from a metadata array.
* @param $metadataArray array
*/
function &_recursivelyTrimPunctuation(&$metadataArray)
{
assert(is_array($metadataArray));
foreach ($metadataArray as $metadataKey => $metadataValue) {
// If we find an array then we'll recurse
if (is_array($metadataValue)) {
$metadataArray[$metadataKey] = $this->_recursivelyTrimPunctuation($metadataValue);
}
// String scalars will be trimmed
if (is_string($metadataValue)) {
$metadataArray[$metadataKey] = PKPString::trimPunctuation($metadataValue);
}
// All other value types (i.e. integers, composite values, etc.)
// will be ignored.
}
return $metadataArray;
}
/**
* @copydoc Filter::process()
* @param $input string
* @return MetadataDescription
*/
function &process(&$input)
{
$citationString =& $input;
$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
$citationString = PKPString::utf8_to_ascii($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 $nullVar;
}
if (Config::getVar('i18n', 'charset_normalization') == 'On' && !PKPString::utf8_compliant($xmlResult)) {
$xmlResult = PKPString::utf8_normalize($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'])) {
$metadata['authors'] = PKPString::trimPunctuation($metadata['authors']);
$metadata['authors'] = PKPString::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] = PKPString::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'])) {
$metadata['genre'] = OPENURL10_GENRE_ARTICLE;
}
// Handle title, chapter and publication depending on
// the (inferred) genre. Also instantiate the target schema.
switch ($metadata['genre']) {
case OPENURL10_GENRE_BOOK:
case OPENURL10_GENRE_BOOKITEM:
case OPENURL10_GENRE_REPORT:
case OPENURL10_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']);
}
$openurl10SchemaName = 'lib.pkp.plugins.metadata.openurl10.schema.Openurl10BookSchema';
$openurl10SchemaClass = 'Openurl10BookSchema';
break;
case OPENURL10_GENRE_ARTICLE:
case OPENURL10_GENRE_JOURNAL:
case OPENURL10_GENRE_ISSUE:
case OPENURL10_GENRE_CONFERENCE:
case OPENURL10_GENRE_PROCEEDING:
case OPENURL10_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']);
}
$openurl10SchemaName = 'lib.pkp.plugins.metadata.openurl10.schema.Openurl10JournalSchema';
$openurl10SchemaClass = 'Openurl10JournalSchema';
break;
}
// Instantiate an OpenURL description
$openurl10Description = new MetadataDescription($openurl10SchemaName, ASSOC_TYPE_CITATION);
$openurl10Schema = new $openurl10SchemaClass();
// Map the ParaCite result to OpenURL
foreach ($metadata as $paraciteElementName => $paraciteValue) {
if (!empty($paraciteValue)) {
// Trim punctuation
if (is_string($paraciteValue)) {
$paraciteValue = PKPString::trimPunctuation($paraciteValue);
}
// Transfer the value to the OpenURL result array
assert(array_key_exists($paraciteElementName, $metadataMapping));
$openurl10PropertyName = $metadataMapping[$paraciteElementName];
if (!is_null($openurl10PropertyName) && $openurl10Schema->hasProperty($openurl10PropertyName)) {
if (is_array($paraciteValue)) {
foreach ($paraciteValue as $singleValue) {
$success = $openurl10Description->addStatement($openurl10PropertyName, $singleValue);
assert($success);
}
} else {
$success = $openurl10Description->addStatement($openurl10PropertyName, $paraciteValue);
assert($success);
}
}
}
}
// Crosswalk to NLM
$crosswalkFilter = new Openurl10Nlm30CitationSchemaCrosswalkFilter();
$nlm30Description =& $crosswalkFilter->execute($openurl10Description);
assert(is_a($nlm30Description, 'MetadataDescription'));
// Add 'rest_text' as NLM comment (if given)
if (isset($metadata['rest_text'])) {
$nlm30Description->addStatement('comment', PKPString::trimPunctuation($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.
$nlm30Description->setDisplayName($this->getDisplayName());
$nlm30Description->setSequence($this->getSequence());
return $nlm30Description;
}
/**
* @copydoc Filter::process()
* @param $input string
* @return MetadataDescription
*/
function &process(&$input)
{
$citationString =& $input;
// Initialize the parser result array
$matches = array();
$metadata = array();
// Parse out any embedded URLs
$urlPattern = '(<?(https?://([-\\w\\.]+)+(:\\d+)?(/([\\w/_\\.,]*(\\?[^\\s>]+)?)?)?)>?)';
if (PKPString::regexp_match_get($urlPattern, $citationString, $matches)) {
// Assume that the URL is a link to the resource.
$metadata['uri'] = $matches[1];
// Remove the URL from the citation string
$citationString = PKPString::regexp_replace($urlPattern, '', $citationString);
// If the URL is a link to PubMed, save the PMID
$pmIdExpressions = array('/list_uids=(?P<pmId>\\d+)/i', '/pubmed.*details_term=(?P<pmId>\\d+)/i', '/pubmedid=(?P<pmId>\\d+)/i');
foreach ($pmIdExpressions as $pmIdExpression) {
if (PKPString::regexp_match_get($pmIdExpression, $matches[1], $pmIdMatches)) {
$metadata['pub-id[@pub-id-type="pmid"]'] = $pmIdMatches['pmId'];
break;
}
}
}
// Parse out an embedded PMID and remove from the citation string
$pmidPattern = '/pmid:?\\s*(\\d+)/i';
if (PKPString::regexp_match_get($pmidPattern, $citationString, $matches)) {
$metadata['pub-id[@pub-id-type="pmid"]'] = $matches[1];
$citationString = PKPString::regexp_replace($pmidPattern, '', $citationString);
}
// Parse out an embedded DOI and remove it from the citation string
$doiPattern = '/doi:?\\s*(\\S+)/i';
if (PKPString::regexp_match_get($doiPattern, $citationString, $matches)) {
$metadata['pub-id[@pub-id-type="doi"]'] = $matches[1];
$citationString = PKPString::regexp_replace($doiPattern, '', $citationString);
}
// Parse out the access date if we have one and remove it from the citation string
$accessDatePattern = '/accessed:?\\s*([\\s\\w]+)/i';
if (PKPString::regexp_match_get($accessDatePattern, $citationString, $matches)) {
$metadata['access-date'] = $matches[1];
$citationString = PKPString::regexp_replace($accessDatePattern, '', $citationString);
}
// Clean out square brackets
$citationString = PKPString::regexp_replace('/\\[(\\s*(pubmed|medline|full text)\\s*)*]/i', '', $citationString);
// Book citation
$unparsedTail = '';
if (PKPString::regexp_match_get("/\\s*(?P<authors>[^\\.]+)\\.\\s*(?P<source>.*?)\\s*(?P<publisherLoc>[^\\.]*):\\s*(?P<publisherName>[^:]*?);\\s*(?P<date>\\d\\d\\d\\d.*?)(?P<tail>.*)/", $citationString, $matches)) {
$metadata['[@publication-type]'] = NLM30_PUBLICATION_TYPE_BOOK;
$metadata['author'] = $matches['authors'];
$metadata['source'] = $matches['source'];
$metadata['publisher-loc'] = $matches['publisherLoc'];
$metadata['publisher-name'] = $matches['publisherName'];
$metadata['date'] = $matches['date'];
$unparsedTail = $matches['tail'];
// Journal citation
} elseif (PKPString::regexp_match_get("/\\s*(?P<authors>[^\\.]+)\\.\\s*(?P<titleSource>.*)\\s*(?P<date>\\d\\d\\d\\d.*?);(?P<volumeAndIssue>[^:]+):(?P<tail>.*)/", $citationString, $matches)) {
$metadata['[@publication-type]'] = NLM30_PUBLICATION_TYPE_JOURNAL;
$metadata['author'] = $matches['authors'];
$titleSource = array();
if (PKPString::regexp_match_get("/(.*[\\.!\\?])(.*)/", trim($matches['titleSource'], " ."), $titleSource)) {
$metadata['article-title'] = $titleSource[1];
$metadata['source'] = $titleSource[2];
}
$metadata['date'] = $matches['date'];
$volumeAndIssue = array();
if (PKPString::regexp_match_get("/([^\\(]+)(\\(([^\\)]+)\\))?/", $matches['volumeAndIssue'], $volumeAndIssue)) {
$metadata['volume'] = $volumeAndIssue[1];
if (isset($volumeAndIssue[3])) {
$metadata['issue'] = $volumeAndIssue[3];
}
}
$unparsedTail = $matches['tail'];
// Web citation with or without authors
} elseif (PKPString::regexp_match_get("/\\s*(?P<citationSource>.*?)\\s*URL:\\s*(?P<tail>.*)/", $citationString, $matches)) {
$unparsedTail = $matches['tail'];
$citationParts = explode(".", trim($matches['citationSource'], '. '));
switch (count($citationParts)) {
case 0:
// This case should never occur...
assert(false);
break;
case 1:
// Assume this to be a title for the web site.
$metadata['article-title'] = $citationParts[0];
break;
case 2:
// Assume the format: Authors. Title.
$metadata['author'] = $citationParts[0];
$metadata['article-title'] = $citationParts[1];
break;
default:
// Assume the format: Authors. Article Title. Journal Title.
$metadata['author'] = array_shift($citationParts);
// The last part is assumed to be the journal title
$metadata['source'] = array_pop($citationParts);
// Everything in between is assumed to belong to the article title
$metadata['article-title'] = implode('.', $citationParts);
}
}
// TODO: Handle in-ref titles, eg. with editor lists
// Extract page numbers if possible
$pagesPattern = "/^[:p\\.\\s]*(?P<fpage>[Ee]?\\d+)(-(?P<lpage>\\d+))?/";
if (!empty($unparsedTail) && PKPString::regexp_match_get($pagesPattern, $unparsedTail, $matches)) {
$metadata['fpage'] = $matches['fpage'];
if (isset($matches['lpage'])) {
$metadata['lpage'] = $matches['lpage'];
}
// Add the unparsed part of the citation string as a comment so it doesn't get lost.
$comment = PKPString::trimPunctuation(PKPString::regexp_replace($pagesPattern, '', $unparsedTail));
if (!empty($comment)) {
$metadata['comment'] = $comment;
}
}
// Make the meta-data fully NLM citation compliant
$metadata =& $this->postProcessMetadataArray($metadata);
// Create the NLM citation description
return $this->getNlm30CitationDescriptionFromMetadataArray($metadata);
}
/**
* Fills the given citation object with
* meta-data retrieved from PubMed.
* @param $pmid string
* @return MetadataDescription
*/
function &_lookup($pmid)
{
$nullVar = null;
// Use eFetch to get XML metadata for the given PMID
$lookupParams = array('db' => 'pubmed', 'mode' => 'xml', 'tool' => 'pkp-wal', 'id' => $pmid);
if (!is_null($this->getEmail())) {
$lookupParams['email'] = $this->getEmail();
}
// Call the eFetch URL and get an XML result
if (is_null($resultDOM = $this->callWebService(PUBMED_WEBSERVICE_EFETCH, $lookupParams))) {
return $nullVar;
}
$articleTitleNodes = $resultDOM->getElementsByTagName('ArticleTitle');
$articleTitleFirstNode = $articleTitleNodes->item(0);
$medlineTaNodes = $resultDOM->getElementsByTagName('MedlineTA');
$medlineTaFirstNode = $medlineTaNodes->item(0);
$metadata = array('pub-id[@pub-id-type="pmid"]' => $pmid, 'article-title' => $articleTitleFirstNode->textContent, 'source' => $medlineTaFirstNode->textContent);
$volumeNodes = $resultDOM->getElementsByTagName('Volume');
$issueNodes = $resultDOM->getElementsByTagName('Issue');
if ($volumeNodes->length > 0) {
$volumeFirstNode = $volumeNodes->item(0);
}
$metadata['volume'] = $volumeFirstNode->textContent;
if ($issueNodes->length > 0) {
$issueFirstNode = $issueNodes->item(0);
}
$metadata['issue'] = $issueFirstNode->textContent;
// Get list of author full names
foreach ($resultDOM->getElementsByTagName("Author") as $authorNode) {
if (!isset($metadata['person-group[@person-group-type="author"]'])) {
$metadata['person-group[@person-group-type="author"]'] = array();
}
// Instantiate an NLM name description
$authorDescription = new MetadataDescription('lib.pkp.plugins.metadata.nlm30.schema.Nlm30NameSchema', ASSOC_TYPE_AUTHOR);
// Surname
$lastNameNodes = $authorNode->getElementsByTagName('LastName');
$lastNameFirstNode = $lastNameNodes->item(0);
$authorDescription->addStatement('surname', $lastNameFirstNode->textContent);
// Given names
$givenNamesString = '';
$firstNameNodes = $authorNode->getElementsByTagName('FirstName');
if ($firstNameNodes->length > 0) {
$firstNameFirstNode = $firstNameNodes->item(0);
$givenNamesString = $firstNameFirstNode->textContent;
} else {
$foreNameNodes = $authorNode->getElementsByTagName('ForeName');
if ($foreNameNodes->length > 0) {
$foreNameFirstNode = $foreNameNodes->item(0);
$givenNamesString = $foreNameFirstNode->textContent;
}
}
if (!empty($givenNamesString)) {
foreach (explode(' ', $givenNamesString) as $givenName) {
$authorDescription->addStatement('given-names', PKPString::trimPunctuation($givenName));
}
}
// Suffix
$suffixNodes = $authorNode->getElementsByTagName('Suffix');
if ($suffixNodes->length > 0) {
$suffixFirstNode = $suffixNodes->item(0);
$authorDescription->addStatement('suffix', $suffixFirstNode->textContent);
}
// Include collective names
// FIXME: This corresponds to an NLM-citation <collab> tag and should be part of the Metadata implementation
/*if ($resultDOM->getElementsByTagName("CollectiveName")->length > 0 && $authorNode->getElementsByTagName("CollectiveName")->item(0)->textContent != '') {
}*/
$metadata['person-group[@person-group-type="author"]'][] =& $authorDescription;
unset($authorDescription);
}
// Extract pagination
$medlinePgnNodes = $resultDOM->getElementsByTagName('MedlinePgn');
$medlinePgnFirstNode = $medlinePgnNodes->item(0);
if (PKPString::regexp_match_get("/^[:p\\.\\s]*(?P<fpage>[Ee]?\\d+)(-(?P<lpage>\\d+))?/", $medlinePgnFirstNode->textContent, $pages)) {
$fPage = (int) $pages['fpage'];
$metadata['fpage'] = $fPage;
if (!empty($pages['lpage'])) {
$lPage = (int) $pages['lpage'];
// Deal with shortcuts like '382-7'
if ($lPage < $fPage) {
$lPage = (int) (PKPString::substr($pages['fpage'], 0, -PKPString::strlen($pages['lpage'])) . $pages['lpage']);
}
$metadata['lpage'] = $lPage;
}
}
// Get publication date (can be in several places in PubMed).
$dateNode = null;
$articleDateNodes = $resultDOM->getElementsByTagName('ArticleDate');
if ($articleDateNodes->length > 0) {
$dateNode = $articleDateNodes->item(0);
} else {
$pubDateNodes = $resultDOM->getElementsByTagName('PubDate');
if ($pubDateNodes->length > 0) {
$dateNode = $pubDateNodes->item(0);
}
}
// Retrieve the data parts and assemble date.
if (!is_null($dateNode)) {
$publicationDate = '';
$requiresNormalization = false;
foreach (array('Year' => 4, 'Month' => 2, 'Day' => 2) as $dateElement => $padding) {
$dateElementNodes = $dateNode->getElementsByTagName($dateElement);
if ($dateElementNodes->length > 0) {
if (!empty($publicationDate)) {
$publicationDate .= '-';
}
$dateElementFirstNode = $dateElementNodes->item(0);
$datePart = str_pad($dateElementFirstNode->textContent, $padding, '0', STR_PAD_LEFT);
if (!is_numeric($datePart)) {
$requiresNormalization = true;
}
$publicationDate .= $datePart;
} else {
break;
}
}
// Normalize the date to NLM standard if necessary.
if ($requiresNormalization) {
$dateFilter = new DateStringNormalizerFilter();
$publicationDate = $dateFilter->execute($publicationDate);
}
if (!empty($publicationDate)) {
$metadata['date'] = $publicationDate;
}
}
// Get publication type
$publicationTypeNodes = $resultDOM->getElementsByTagName('PublicationType');
if ($publicationTypeNodes->length > 0) {
foreach ($publicationTypeNodes as $publicationType) {
// The vast majority of items on PubMed are articles so catch these...
if (PKPString::strpos(PKPString::strtolower($publicationType->textContent), 'article') !== false) {
$metadata['[@publication-type]'] = NLM30_PUBLICATION_TYPE_JOURNAL;
break;
}
}
}
// Get DOI if it exists
$articleIdNodes = $resultDOM->getElementsByTagName('ArticleId');
foreach ($articleIdNodes as $idNode) {
if ($idNode->getAttribute('IdType') == 'doi') {
$metadata['pub-id[@pub-id-type="doi"]'] = $idNode->textContent;
}
}
// Use eLink utility to find fulltext links
$lookupParams = array('dbfrom' => 'pubmed', 'cmd' => 'llinks', 'tool' => 'pkp-wal', 'id' => $pmid);
if (!is_null($resultDOM = $this->callWebService(PUBMED_WEBSERVICE_ELINK, $lookupParams))) {
// Get a list of possible links
foreach ($resultDOM->getElementsByTagName("ObjUrl") as $linkOut) {
$attributes = '';
foreach ($linkOut->getElementsByTagName("Attribute") as $attribute) {
$attributes .= PKPString::strtolower($attribute->textContent) . ' / ';
}
// Only add links to open access resources
if (PKPString::strpos($attributes, "subscription") === false && PKPString::strpos($attributes, "membership") === false && PKPString::strpos($attributes, "fee") === false && $attributes != "") {
$urlNodes = $linkOut->getElementsByTagName('Url');
$urlFirstNode = $urlNodes->item(0);
$links[] = $urlFirstNode->textContent;
}
}
// Take the first link if we have any left (presumably pubmed returns them in preferential order)
if (isset($links[0])) {
$metadata['uri'] = $links[0];
}
}
return $this->getNlm30CitationDescriptionFromMetadataArray($metadata);
}
