function post_process($d)
{
// guid
$d->guid = $d->institutionCode . ':' . $d->collectionCode . ':' . $d->catalogNumber;
// Fix dates
if (isset($d->verbatimCollectingDate)) {
$date = format_date($d->verbatimCollectingDate);
if ('' != $date) {
$d->dateCollected = $date;
}
}
if (isset($d->dateLastModified)) {
$date = format_date($d->dateLastModified);
if ('' != $date) {
$d->dateModified = $date;
}
}
// Coordinates
// F**K! What are people doing!!!!!!!
// KU 289791 occurs three times in the same XML document, but worse the
// decimalLatitude and decimalLongtitude fields contain the degree symbol and hemisphere.
if (isset($d->latitude)) {
if (preg_match("/°N/", $d->latitude)) {
$d->latitude = str_replace("°N", "", $d->latitude);
}
if (preg_match("/°S/", $d->latitude)) {
$d->latitude = str_replace("°S", "", $d->latitude);
if ($d->latitude > 0) {
$d->latitude *= -1.0;
}
}
}
if (isset($d->longitude)) {
if (preg_match("/°E/", $d->longitude)) {
$d->longitude = str_replace("°E", "", $d->longitude);
}
if (preg_match("/°W/", $d->longitude)) {
$d->longitude = str_replace("°W", "", $d->longitude);
if ($d->longitude > 0) {
$d->longitude *= -1.0;
}
}
}
// Can't do this as loc can't be NULL
/* if (isset($d->longitude) && isset($d->latitude))
{
$d->loc = "GeomFromText('POINT(" . $d->longitude . " " . $d->latitude . ")')";
}
*/
// uBio name lookup
$name = '';
if (isset($d->organism)) {
$d->organism = trim($d->organism);
$name = $d->organism;
} else {
if (isset($d->genus)) {
$name = $d->genus;
if (isset($d->species)) {
$name .= ' ' . $d->species;
}
$d->organism = $name;
}
}
if ($name != '') {
$names = ubio_namebank_search_rest(trim($name), false, true);
// just take simple exact match
if (count($names) > 0) {
$d->namebankID = array();
foreach ($names as $n) {
array_push($d->namebankID, $n);
}
}
}
return $d;
}
<?php
require_once dirname(__FILE__) . '/ubios.php';
$name = '';
$namebankID = array();
if (isset($_GET['name'])) {
$name = $_GET['name'];
}
if ($name != '') {
$names = ubio_namebank_search_rest(trim($name), false, true);
// just take simple exact match
//print_r($names);
if (count($names) > 0) {
foreach ($names as $n) {
array_push($namebankID, $n);
}
}
}
echo json_encode($namebankID);
function gb_host(&$data)
{
if (isset($data->source->host)) {
$names = ubio_namebank_search_rest(trim($data->source->host), false, true);
// just take simple exact match
if (count($names) > 0) {
$data->source->host_namebankID = $names[0];
}
}
}
}
print_r($item);
$item_id = store_item($item);
// if ($item->pmid != '') exit();
//-----------------------------------------------------------------------------------------------
// Handle names
// keywords are taxon names uBio has extracted from articles/abstracts
foreach ($item->keywords as $k) {
echo $k, "\n";
}
// Do our thang
$annotations = extract_new_names(strip_tags($item->title), $item->keywords);
echo "Names--------------------\n";
print_r($annotations);
// store names
foreach ($annotations as $k => $v) {
// lookup name
$namebankID = 0;
$find = ubio_namebank_search_rest($k, false, true);
if (count($find) != 0) {
$namebankID = $find[0];
}
// store
echo $k . ' ' . $namebankID . ' ' . $v['rank'] . ' ' . $v['new'] . "\n";
store_one_name($k, $namebankID, $v['rank'], $v['new'], $item_id);
// join to source
}
$lineages = extract_lineages(strip_tags($item->title), $item->keywords);
echo "Lineages-----------------\n";
print_r($lineages);
}
