function fetch_one($id)
{
global $config;
$sequence = fetch_sequence($id);
//print_r($sequence);
}
$updated = $rss->appendChild($updated);
$value = $feed->createTextNode(date(DATE_ATOM));
$value = $updated->appendChild($value);
// id
$id = $feed->createElement('id');
$id = $rss->appendChild($id);
$id->appendChild($feed->createTextNode('urn:uuid:' . uuid()));
// author
$author = $feed->createElement('author');
$author = $rss->appendChild($author);
$name = $feed->createElement('name');
$name = $author->appendChild($name);
$name->appendChild($feed->createTextNode('Phyloinformatics'));
// Cache, store metadata, and make into RSS feed
foreach ($ids as $id) {
$obj = fetch_sequence($id);
//print_r($obj);
if (isset($obj->accession)) {
$item = new stdclass();
$item->links = array();
if (isset($obj->created)) {
$item->created = $obj->created;
}
if (isset($obj->updated)) {
$item->updated = $obj->updated;
}
if (isset($obj->source->latitude)) {
$item->latitude = $obj->source->latitude;
}
if (isset($obj->source->longitude)) {
$item->longitude = $obj->source->longitude;
function Harvest()
{
global $debug;
$xml = get($this->url);
//echo $xml;
$ids = array();
$dom = new DOMDocument();
$dom->loadXML($xml);
$xpath = new DOMXPath($dom);
$xpath_query = "//eSearchResult/IdList/Id";
$nodeCollection = $xpath->query($xpath_query);
foreach ($nodeCollection as $node) {
$id = $node->firstChild->nodeValue;
array_push($ids, $id);
}
//print_r($ids);
// Get GenBank records
// Cache, store metadata, and make into RSS feed
foreach ($ids as $id) {
$obj = fetch_sequence($id);
//print_r($obj);
if (isset($obj->accession)) {
$item = new stdclass();
$item->links = array();
if (isset($obj->created)) {
$item->created = $obj->created;
}
if (isset($obj->updated)) {
$item->updated = $obj->updated;
}
if (isset($obj->source->latitude)) {
$item->latitude = $obj->source->latitude;
}
if (isset($obj->source->longitude)) {
$item->longitude = $obj->source->longitude;
}
$item->title = $obj->accession;
$item->description = $obj->definition;
$item->link = 'http://www.ncbi.nlm.nih.gov/nuccore/' . $obj->gi;
$item->id = $item->link;
$item->description .= '<br/><a href="http://www.ncbi.nlm.nih.gov/nuccore/' . $obj->accession . '">' . $obj->accession . '</a>';
// Source taxon
$txid = $obj->source->tax_id;
array_push($item->links, array('taxon' => $txid));
$item->description .= '<br/><a href="http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=' . $txid . '">taxon:' . $txid . '</a>';
/*
$ref = $obj->references[0];
if (isset($ref->doi))
{
array_push($item->links, array('doi' => $ref->doi));
$item->description .= '<br/><a href="http://dx.doi.org/' . $ref->doi . '">doi:' . $ref->doi . '</a>';
}
if (isset($ref->pmid))
{
array_push($item->links, array('pmid' => $ref->pmid));
}
*/
//print_r($item);
// Store
$this->StoreFeedItem($item);
}
}
}
