PHP retrieve_specimen_json Examples

Example #1

File: digir.php Project: rdmpage/bioguid

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;
}

Example #2

File: tapir.php Project: rdmpage/bioguid

        case 'rdf':
            $format = $_GET['format'];
            break;
        default:
            $format = 'html';
            break;
    }
}
//$id = '0100367';
$state = 404;
// not found
if ($id != '') {
    $guid = 'antweb:casent' . $id;
    $specimen_id = find_specimen_from_guid($guid);
    if ($specimen_id != 0) {
        $json = retrieve_specimen_json($specimen_id);
        $item = json_decode($json);
        $state = 200;
    } else {
        $url = 'http://www.antweb.org/tapirlink/www/tapir.php/antweb?op=search&start=0&limit=1&template=http://bioguid.info/tapir/dwc_catalog_number.xml&name=casent' . $id;
        $xml = get($url);
        if ($xml != '') {
            $xp = new XsltProcessor();
            $xsl = new DomDocument();
            $xsl->load('xsl/tapir2json.xsl');
            $xp->importStylesheet($xsl);
            $xml_doc = new DOMDocument();
            $xml_doc->loadXML($xml);
            $json = $xp->transformToXML($xml_doc);
            //echo $json;
            $json = str_replace("\n\"", "\"", $json);