function Harvest()
{
$xml = get($this->url);
//echo $xml;
// Convert Mycobank RSS to JSON
$xp = new XsltProcessor();
$xsl = new DomDocument();
$xsl->load('xsl/rss2.xsl');
$xp->importStylesheet($xsl);
// replace carriage returns and end of lines, which break JSON
$xml = str_replace("\n", " ", $xml);
$xml = str_replace("\r", " ", $xml);
$xml_doc = new DOMDocument();
$xml_doc->loadXML($xml);
$json = $xp->transformToXML($xml_doc);
//echo $json;
$obj = json_decode($json);
//print_r($obj);
// Extract details
foreach ($obj->items as $i) {
$item = new stdclass();
$item->links = array();
$item->link = $i->link;
$item->description = $i->description;
$item->id = $i->link;
// Mycobank ID
$id = $i->link;
$id = str_replace('http://www.mycobank.org/MycoTaxo.aspx?Link=T&Rec=', '', $id);
// Dates
if (preg_match('/<br>Date of deposit:\\s*(?<date>(.*))<br>/', $i->description, $matches)) {
//print_r($matches);
$item->created = date("Y-m-d H:i:s", strtotime($matches['date']));
$item->updated = $item->created;
}
$have_literature = false;
// Taxon name
if (preg_match('/<a href=(.*)><i>(?<name>(.*))<\\/i><\\/a>/', $i->description, $matches)) {
$item->title = $matches['name'];
//print_r($matches);
// Index Fungorum search...
$url = 'http://www.indexfungorum.org/IXFWebService/Fungus.asmx/NameSearch?SearchText=' . str_replace(' ', '%20', $matches['name']) . '&AnywhereInText=false&MaxNumber=1';
//echo $url . "\n";
$xml = get($url);
//echo $xml;
$dom = new DOMDocument();
$dom->loadXML($xml);
$xpath = new DOMXPath($dom);
$record_id = 0;
$nodeCollection = $xpath->query("//NewDataSet/IndexFungorum/RECORD_x0020_NUMBER");
foreach ($nodeCollection as $node) {
// We have this name in Index Fungorum...
$record_id = $node->firstChild->nodeValue;
$lsid = 'urn:lsid:indexfungorum.org:names:' . $record_id;
// Store LSID
array_push($item->links, array('lsid' => $lsid));
$item->description .= '<br/><a href="http://bioguid.info/' . $lsid . '">' . $lsid . '</a>';
// Get bibliographic details
$rdf = ResolveGuid($lsid);
//echo $rdf;
$url = 'http://bioguid.info/openurl?genre=article';
$d = new DOMDocument();
$d->loadXML($rdf);
$xpath = new DOMXPath($d);
$n = $xpath->query("//tpub:title");
foreach ($n as $n2) {
$url .= '&title=' . $n2->firstChild->nodeValue;
}
$n = $xpath->query("//tpub:volume");
foreach ($n as $n2) {
$url .= '&volume=' . $n2->firstChild->nodeValue;
}
$n = $xpath->query("//tpub:pages");
foreach ($n as $n2) {
$url .= '&pages=' . $n2->firstChild->nodeValue;
}
$n = $xpath->query("//tpub:year");
foreach ($n as $n2) {
$url .= '&date=' . $n2->firstChild->nodeValue;
}
$url .= '&display=json';
//echo $url;
$ref = json_decode(get($url));
if ($ref->status == 'ok') {
$have_literature = true;
if (isset($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' => $ref->pmid));
}
if (isset($ref->hdl)) {
array_push($item->links, array('hdl' => $ref->hdl));
$item->description .= '<br/><a href="http://hdl.handle.net/' . $ref->hdl . '">doi:' . $ref->hdl . '</a>';
}
if (isset($ref->url)) {
array_push($item->links, array('url' => $ref->url));
$item->description .= '<br/><a href="' . $ref->url . '">' . $ref->url . '</a>';
}
} else {
// No joy...
}
}
/* if (!$have_literature)
{
// Get from Mycobank, doesn't seem to work when I try and havest with CURL :(
echo "Get lit\n";
// Get literature from Mycobank
// 1. Get Mycobank web page
$url = $item->link;
$html = get($url);
echo "html=" . $html . "\n";
echo "link=" . $item->link . "\n";
if (preg_match("/<A href='MycoBiblio.aspx\?Link=T&Rec=(.*)'\s+/", $html, $matches))
{
print_r($matches);
}
}
*/
$this->StoreFeedItem($item);
}
}
}
function Harvest()
{
global $debug;
//echo "|" . $this->url . "|";
//$html = get($this->url);
//echo $html;
$url = 'http://www.ipni.org/ipni/advPlantNameSearch.do?find_family=' . $this->title . '&find_genus=&find_species=&find_infrafamily=&find_infragenus=&find_infraspecies=&find_authorAbbrev=&find_includePublicationAuthors=on&find_includePublicationAuthors=off&find_includeBasionymAuthors=on&find_includeBasionymAuthors=off&find_publicationTitle=&show_extras=on&find_geoUnit=&find_addedSince=' . ($d = date("Y-m-d", strtotime("now - 2 months")) . '&find_modifiedSince=&find_isAPNIRecord=on&find_isAPNIRecord=false&find_isGCIRecord=on&find_isGCIRecord=false&find_isIKRecord=on&find_isIKRecord=false&find_rankToReturn=all&output_format=delimited-minimal&find_sortByFamily=on&find_sortByFamily=off&query_type=by_query&back_page=plantsearch');
//echo $url;
$text = 'Id%Version%Family%Full name without family and authors%Authors
77096980-1%1.2%Begoniaceae%Begonia hekensis%D.C.Thomas
77097937-1%1.1%Begoniaceae%Begonia mysteriosa%L.Kollmann & A.P.Fontana
77096979-1%1.1%Begoniaceae%Begonia ozotothrix%D.C.Thomas';
$text = get($url);
$text = trim($text);
/*$text='Id%Version%Family%Full name without family and authors%Authors
60451177-2%1.1%Euphorbiaceae%Croton subgen. Geiseleria%(Klotzsch) A.Gray
77097911-1%1.1%Euphorbiaceae%Croton pallidulus var. glabrus%L.R.Lima
77097476-1%1.1%Euphorbiaceae%Euphorbia confinalis subsp. rhodesiaca%L.C.Leach
77097491-1%1.1%Euphorbiaceae%Euphorbia maryrichardsiae%G.Will.
77098208-1%1.2%Euphorbiaceae%Euphorbia ohiva%Swanepoel
60451526-2%1.1.2.1%Euphorbiaceae%Luntia%Neck. ex Raf.'; */
if ($debug) {
echo $url . "\n";
echo $text . "\n";
}
// Get array of individual lines
$lines = explode("\n", $text);
// Extract headings from first line
$parts = explode("%", $lines[0]);
$size = count($parts);
$heading = array();
for ($i = 0; $i < $size; $i++) {
$heading[$parts[$i]] = $i;
}
// Read each remaining line
$size = count($lines);
for ($i = 1; $i < $size; $i++) {
$parts = explode("%", $lines[$i]);
//print_r($parts);
$item = new stdclass();
//Add elements to the feed item
$lsid = 'urn:lsid:ipni.org:names:' . $parts[$heading["Id"]];
$item->title = $parts[$heading["Full name without family and authors"]];
$item->id = $lsid;
$item->link = 'http://www.ipni.org/ipni/idPlantNameSearch.do?id=' . $parts[$heading["Id"]];
$item->description = '<i>' . $parts[$heading["Full name without family and authors"]] . '</i> ' . $parts[$heading["Authors"]];
$item->description = str_replace('subsp.', '</i>subsp.<i>', $item->description);
$item->description = str_replace('var.', '</i>var.<i>', $item->description);
// Identifiers
$item->links = array();
// tag
// $parts[$heading["Family"]]
// retrieve metadata...
$rdf = ResolveGuid($lsid);
// Fix IPNI bug
$rdf = preg_replace('/ & /', ' & ', $rdf);
if ($debug) {
echo $rdf;
}
//echo $rdf;
// extract extra details...
$dom = new DOMDocument();
$dom->loadXML($rdf);
$xpath = new DOMXPath($dom);
$nodeCollection = $xpath->query("//tcom:publishedIn");
foreach ($nodeCollection as $node) {
$publishedIn = $node->firstChild->nodeValue;
$item->description .= '<br/>' . $publishedIn;
// Can we get any GUIDs for this...?
$matches = array();
if (parse_ipni_ref($publishedIn, $matches)) {
//print_r($matches);
// we parsed it OK, now find guid...
$url = 'http://bioguid.info/openurl/?genre=article';
$url .= '&title=' . urlencode($matches['journal']);
$url .= '&volume=' . $matches['volume'];
$url .= '&pages=' . $matches['page'];
$url .= '&display=json';
//echo $url;
$j = get($url);
$ref = json_decode($j);
//print_r($ref);
if ($ref->status == 'ok') {
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' => $ref->pmid));
}
if (isset($ref->hdl)) {
array_push($item->links, array('hdl' => $ref->hdl));
$item->description .= '<br/><a href="http://hdl.handle.net/' . $ref->hdl . '">doi:' . $ref->hdl . '</a>';
}
if (isset($ref->url)) {
array_push($item->links, array('url' => $ref->url));
$item->description .= '<br/><a href="' . $ref->url . '">' . $ref->url . '</a>';
}
} else {
// No guid found, but we did parse it OK...
}
} else {
// Don't understand this reference at all...
}
}
$nodeCollection = $xpath->query("//dcterms:created");
foreach ($nodeCollection as $node) {
$item->created = $node->firstChild->nodeValue;
}
$nodeCollection = $xpath->query("//dcterms:modified");
foreach ($nodeCollection as $node) {
$item->updated = $node->firstChild->nodeValue;
}
//print_r($item);
$this->StoreFeedItem($item);
}
}
