function parse($config, $db)
{
require_once "libraries/parse_large_xml.php";
$folder = $config["dir"] . $config["pubmed_central_dir"];
if ($config["test"] === true) {
$folder = $config["test_dir"] . $config["pubmed_central_dir"];
}
$xml_parser = new XML_parser();
$scanned_directory = array_diff(scandir($folder), array('..', '.'));
if (!isset($scanned_directory)) {
echo "Warning: no files found in: " . $folder . '<br/>';
return;
}
$articles = array();
foreach ($scanned_directory as $file) {
// Open the file
if (($handle = @fopen($folder . "/" . $file, "r")) === false) {
echo "Error: file not found at: " . $folder . "/" . $file;
return;
}
// Get the nodestring incrementally from the xml file by defining a callback
$articles = $xml_parser->nodeStringFromXMLFile($handle, "<article", "</article>", $db, function ($xml_parser, $db, $nodeText) {
$simpleXML = simplexml_load_string($nodeText);
// Title
$title = "";
$result = $simpleXML->xpath('//title-group/article-title');
if (isset($result[0])) {
$title = (string) $result[0];
}
// Abstract
$abstract = "";
$result = $simpleXML->xpath('//abstract');
if (isset($result[0])) {
foreach ($result as $item) {
// Abstract contain HTML tags for some reason
// Revert to plain XML string
$xml = $item->asXML();
// Remove the tags
$no_tags = trim(strip_tags($xml));
// Remove any extra whitespace
$abstract .= ' ' . preg_replace('/(\\s)+/', ' ', $no_tags);
}
}
// Keywords
$keywords = array();
$result = $simpleXML->xpath('//kwd-group/kwd');
while (list(, $keyword) = each($result)) {
array_push($keywords, (string) $keyword);
}
// Journal-Title
$journal_title = "";
$result = $simpleXML->xpath('//journal-title');
if (isset($result[0])) {
$journal_title = (string) $result[0];
}
// Journal-ISO
$journal_iso = "";
$result = $simpleXML->xpath('//journal-meta/journal-id[@journal-id-type="iso-abbrev"]');
if (isset($result[0])) {
$journal_iso = (string) $result[0];
}
// ISSN
$issn = "";
$result = $simpleXML->xpath('//issn[@pub-type="ppub"]');
if (isset($result[0])) {
$issn = (string) $result[0];
}
// DOI
$doi = "";
$result = $simpleXML->xpath('//article-meta/article-id[@pub-id-type="doi"]');
if (isset($result[0])) {
$doi = (string) $result[0];
$pattern = '/[0-9\\.]+\\/.*/';
preg_match($pattern, $doi, $match);
if (count($match) > 0) {
$doi = $match[0];
} else {
$doi = "";
}
}
// Publication date
$day = "";
$result = $simpleXML->xpath('//pub-date/day');
if (isset($result[0])) {
$day = (string) $result[0];
}
$month = "";
$result = $simpleXML->xpath('//pub-date/month');
if (isset($result[0])) {
$month = (string) $result[0];
}
$year = "";
$result = $simpleXML->xpath('//pub-date/year');
if (isset($result[0])) {
$year = (string) $result[0];
}
return array("title" => $title, "abstract" => $abstract, "doi" => $doi, "journal_title" => $journal_title, "journal_iso" => $journal_iso, "journal_issn" => $issn, "day" => $day, "month" => $month, "year" => $year);
});
fclose($handle);
}
require_once "models/articles.php";
$article_model = new Articles();
foreach ($articles as $article) {
$article_model->insert($db, $article, 'pubmed_central');
}
}
function parse($config, $db)
{
$folder = $config["dir"] . $config["ovid_dir"];
if ($config["test"] === true) {
$folder = $config["test_dir"] . $config["ovid_dir"];
}
require_once "libraries/parse_large_xml.php";
$xml_parser = new XML_parser();
$scanned_directory = array_diff(scandir($folder), array('..', '.'));
if (!isset($scanned_directory)) {
echo "Warning: no files found in: " . $folder . '<br/>';
return;
}
require_once "models/articles.php";
$article_model = new Articles();
foreach ($scanned_directory as $file) {
// Open the XML
if (($handle = @fopen($folder . "/" . $file, "r")) === false) {
echo "Warning: XML file not found at: " . $folder . "/" . $file;
return;
}
// Get the nodestring incrementally from the xml file by defining a callback
$articles = $xml_parser->nodeStringFromXMLFile($handle, "<record ", "</record>", $db, function ($xml_parser, $db, $nodeText) {
$simpleXML = simplexml_load_string($nodeText);
if (!$simpleXML) {
echo $nodeText;
}
// Title
$title = "";
$result = $simpleXML->xpath('//F[@L="Title"]/D');
if (isset($result[0])) {
$title = (string) $result[0];
}
// Abstract
$abstract = "";
$result = $simpleXML->xpath('//F[@L="Abstract"]/D');
if (isset($result[0])) {
foreach ($result as $item) {
// Abstract contain HTML tags for some reason
// Revert to plain XML string
$xml = $item->asXML();
// Remove the tags
$no_tags = trim(strip_tags($xml));
// Remove any extra whitespace
$abstract .= ' ' . preg_replace('/(\\s)+/', ' ', $no_tags);
}
}
// Journal-Title
$journal_title = "";
$result = $simpleXML->xpath('//F[@L="Source"]/D');
if (isset($result[0])) {
$journal_title = substr($result[0]->asXML(), 12, strpos($result[0]->asXML(), '<T>') - 12);
}
// Journal-ISO
$journal_iso = "";
// $result = $simpleXML->xpath('//journal-meta/journal-id[@journal-id-type="iso-abbrev"]');
// if (isset($result[0])) {
// $journal_iso = (string) $result[0];
// }
// ISSN
$issn = "";
$result = $simpleXML->xpath('//F[@L="ISSN"]/D');
if (isset($result[0])) {
$issn = (string) $result[0];
}
// DOI
$doi = "";
$result = $simpleXML->xpath('//F[@L="Digital Object Identifier"]/D');
if (isset($result[0])) {
$doi = (string) $result[0];
$pattern = '/[0-9\\.]+\\/.*/';
preg_match($pattern, $doi, $match);
if (count($match) > 0) {
$doi = $match[0];
} else {
$doi = "";
}
}
// Publication date
$day = "";
$month = "";
$year = "";
$result = $simpleXML->xpath('//F[@L="Year of Publication"]/D');
if (isset($result[0])) {
$year = (string) $result[0];
} else {
$result = $simpleXML->xpath('//F[@L="Date of Publication"]/D');
if (isset($result[0])) {
$year = (string) $result[0];
$year = preg_replace('/[^\\d]/', '', $year);
$year = substr($year, -4);
}
}
return array("title" => $title, "abstract" => $abstract, "doi" => $doi, "journal_title" => $journal_title, "journal_iso" => $journal_iso, "journal_issn" => $issn, "day" => $day, "month" => $month, "year" => $year);
});
fclose($handle);
foreach ($articles as $article) {
$article_model->insert($db, $article, 'ovid');
}
}
}
