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JATS2Citation.php
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JATS2Citation.php
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<?php
/**
* Extract metadata from XML JATS and return an HTML string ready for citation.
*
* Example:
*
* $file = 'https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0055937&type=manuscript';
* $J2C = new JATS2Citation();
* $res = $J2C->make_citation($file);
* print $res;
*
* @todo: a Formatter class for the output can be useful.
*
*/
class JATS2Citation {
/**
* For future implementation of different output formats.
*/
const SCHEMA_HTML_DEFAULT = 'default';
/**
* The maximum number of authors allowed.
* More authors will be cited as "et al".
* Set 0 for no limits.
*
* @var int
*/
private $max_authors = 5;
/**
* Set the maximum number of authors in citation.
* Set 0 for no limits.
*
* @param int $n
*/
public function set_max_authors($n) {
$this->max_authors = (int) $n;
}
/**
* Get the maximum number of allowed authors.
*
* @return int
*/
public function get_max_authors() {
return $this->max_authors;
}
/**
* Make the citation.
*
* @param string $fpath The XML path. Can be local or remote file (url)
* @param string $formatter For further development.
* @todo An implementation of formatter can be useful.
*
* @return string
*/
public function make_citation($fpath, $formatter=self::SCHEMA_HTML_DEFAULT) {
$doc = new DomDocument();
$doc->load($fpath);
$x = new DomXPath($doc);
$xp['title'] = $x->query('/article/front/article-meta/title-group/article-title/text()')[0]->textContent;
$xp['journal'] = $x->query('/article/front/journal-meta/journal-title-group/journal-title/text()')[0]->nodeValue;
$xp['volume'] = $x->query('/article/front/article-meta/volume/text()')[0]->nodeValue;
$xp['issue'] = $x->query('/article/front/article-meta/issue/text()')[0]->nodeValue ?? null;
$xp['eloc'] = $x->query('/article/front/article-meta/elocation-id/text()')[0]->nodeValue;
$xp['doi'] = $x->query('/article/front/article-meta/article-id[@pub-id-type="doi"]/text()')[0]->nodeValue;
$xp['pub_year']= $x->query('//pub-date[@pub-type="epub"]/year/text()')[0]->nodeValue;
$_xp['surname'] = $x->query('/article/front/article-meta/contrib-group/contrib/name/surname/text()');
$_xp['gname'] = $x->query('/article/front/article-meta/contrib-group/contrib/name/given-names/text()');
$xp['authors'] = $this->_make_authors_string($_xp['surname'], $_xp['gname']);
$format_string = $this->formatter($formatter, $xp);
return $format_string;
}
/**
* For futher development.
*
* @param string $schema
* @param array $xp
* @return string
*/
private function formatter($schema, array $xp) {
switch($schema) {
case self::SCHEMA_HTML_DEFAULT :
default :
return $this->_formatter_standard($xp);
}
}
/**
* Format the citation as HTML, following the PLoS rules.
*
* @param array $xp
* @return string
*/
private function _formatter_standard(array $xp) {
$url_doi = '<a href="https://doi.org/' . $xp['doi'].'" class="cit-url" rel="nofollow">'.'https://doi.org/' . $xp['doi'].'</a>';
$citation = $xp['authors'] . ' (' . $xp['pub_year'] .') '
. $xp['title'] . '. '
. $xp['journal'] .' '
. $xp['volume'];
$citation.= (!empty($xp['issue'])) ? '('. $xp['issue'] . '): ' : '';
$citation.= $xp['eloc'] . '. ' . $url_doi;
return $citation;
}
/**
* Get the first letters of the author's name
* @param string $given_names
* @return string
*/
private function _get_first_letters($given_names) {
$words = explode(" ", trim($given_names));
$acronym = "";
foreach ($words as $w) {
if(preg_match('/[\w]/', $w[0])) {
$acronym .= $w[0];
}
}
return $acronym;
}
/**
* Create the authors' list.
*
* @param DOMNodeList $_snames
* @param DOMNodeList $_gnames
* @return string
*/
private function _make_authors_string(DOMNodeList $_snames, DOMNodeList $_gnames) {
$authors = '';
if(count($_snames) == 0) {
return '';
}
foreach ($_snames as $entry) {
$surnames[] = $entry->nodeValue;
}
foreach ($_gnames as $entry) {
$gnames[] = $entry->nodeValue;
}
for($i=0; $i<count($surnames); $i++) {
$authors.=$surnames[$i].' '.$this->_get_first_letters($gnames[$i]).", ";
if($this->max_authors > 0 && ($i+1 == $this->max_authors)) {
$authors.= 'et al.';
break;
}
}
if(substr($authors, -2, 2) == ', ') {
$authors = substr($authors, 0, -2);
}
return $authors;
}
}