if (preg_match('/^CAS-SU /', $code)) {
$go = true;
$code = str_replace('CAS-SU ', 'CAS ', $code);
}
if ($go) {
$url = 'http://iphylo.org/~rpage/phyloinformatics/services/get_gbif_occurrence.php?code=' . rawurlencode($code);
echo $url . "\n";
$json = get($url);
//echo $json;
$hits = json_decode($json);
print_r($hits);
// score match
$hit = 0;
foreach ($hits->occurrences as $occurrenceID => $occurrence) {
// cache
store_specimen($occurrence);
if (in_array($occurrence->class, $expanded)) {
echo $occurrence->class . "\n";
$hit = $occurrenceID;
}
}
if ($hit != 0) {
echo "===hit===\n";
echo $specimen->code . "\n";
print_r($hits->occurrences->{$hit});
// Update Database
$sql = "UPDATE rdmp_reference_specimen_joiner SET occurrenceID=" . $hits->occurrences->{$hit}->occurrenceID . " WHERE reference_id=" . $reference_id . " AND code=" . $db->qstr($specimen->code);
echo $sql . "\n";
$result = $db->Execute($sql);
if ($result == false) {
die("failed [" . __FILE__ . ":" . __LINE__ . "]: " . $sql);
function get_specimen($institutionCode, $collectionCode, $catalogNumber, &$item)
{
$id = find_specimen($institutionCode, $collectionCode, $catalogNumber);
if ($id == 0) {
$s = new DiGIRProvider('');
//echo "$institutionCode, $collectionCode, $catalogNumber\n";
// Some collections don't have a collection code,
// or need other fixes
switch ($institutionCode) {
case 'SAMA':
$collectionCode = '';
break;
case 'KUNHM':
$institutionCode = 'KU';
break;
default:
break;
}
$data = $s->Get2($institutionCode, $collectionCode, $catalogNumber);
//print_r($data);
if (isset($data->record)) {
foreach ($data->record as $d) {
$d = $s->post_process($d);
// We may have to reverse extract collection code
/* $d->institutionCode = $institutionCode;
$d->collectionCode = $collectionCode;
$d->catalogNumber = $catalogNumber; */
$cCode = $d->collectionCode;
if ($cCode == '') {
if (preg_match('/(.*):(?<collectionCode>.*):(.*)/', $d->guid, $matches)) {
$d->collectionCode = $matches['collectionCode'];
}
switch ($institutionCode) {
case 'CAS':
if ($collectionCode == 'Herps') {
$d->collectionCode = $collectionCode;
if (preg_match('/CAS::(?<id>\\d+)/', $d->guid, $m)) {
$d->guid = 'CAS:Herps:' . $m['id'];
}
}
break;
default:
break;
}
} else {
// We have a collection code, but we might need to fix it...
switch ($institutionCode) {
case 'CAS':
if ($d->collectionCode == 'ORN') {
$d->collectionCode = 'Birds';
}
break;
case 'KU':
if ($d->collectionCode == 'KUH') {
$d->collectionCode = 'Herps';
}
break;
default:
break;
}
}
$bci = $s->GetBci($d->institutionCode, $d->collectionCode, $d->catalogNumber);
if ($bci != '') {
$d->bci = $bci;
}
//print_r($d);
$id = store_specimen($d);
$item = $d;
}
}
} else {
$json = retrieve_specimen_json($id);
$item = json_decode($json);
}
return $id;
}
$xml_doc = new DOMDocument();
$xml_doc->loadXML($xml);
$json = $xp->transformToXML($xml_doc);
//echo $json;
$json = str_replace("\n\"", "\"", $json);
$data = json_decode($json);
//print_r($data);
if (isset($data->status)) {
if ($data->status == 'ok') {
$state = 200;
$data->record[0]->bci = 'urn:lsid:biocol.org:col:35143';
$data->record[0]->title = 'CASENT' . $id;
}
}
if ($state == 200) {
store_specimen($data->record[0]);
$item = $data->record[0];
}
}
}
}
switch ($state) {
case 404:
ob_start();
header('HTTP/1.1 404 Not Found');
header('Status: 404 Not Found');
$_SERVER['REDIRECT_STATUS'] = 404;
break;
case 400:
ob_start();
header('HTTP/1.0 400');
