foreach ($ids as $reference_id) {
echo $reference_id . "\n";
$specimens = specimens_from_db($reference_id);
if (count($specimens) == 0) {
$specimens = specimens_from_reference($reference_id);
}
echo "Specimens:\n";
print_r($specimens);
$nm = bhl_names_in_reference_by_page($reference_id);
$nm->names;
// Get majority rule taxon (what paper is about)
$tags = array();
foreach ($nm->names as $name) {
$tags[] = $name->namestring;
}
$paths = get_paths($tags);
$majority_rule = majority_rule_path($paths);
$expanded = expand_path($majority_rule);
print_r($expanded);
// OK, now match...
foreach ($specimens as $specimen) {
//$go = false;
$go = true;
$code = $specimen->code;
if (preg_match('/^AMNH /', $code)) {
if (in_array('Amphibia', $expanded)) {
$code = str_replace('AMNH ', 'AMNH A-', $code);
}
if (in_array('Reptilia', $expanded)) {
$code = str_replace('AMNH ', 'AMNH R-', $code);
}
function get_paths($path)
{
global $server, $size, $max_size;
$list = $server->parse_raw_list($path);
if (!$list) {
return array();
}
$items = array();
foreach ($list as $v) {
if ($v['type'] != 'file') {
if ($v['name'] == '.' or $v['name'] == '..') {
continue;
}
$size += $v['size'];
if ($size > $max_size) {
return false;
}
$arr = get_paths($path . $v['name'] . '/');
$items = array_merge($items, $arr);
} else {
$items[] = $path . $v['name'];
}
}
return $items;
}
function DisplayJson()
{
$j = reference_to_mendeley($this->object);
// Array of BHL pages
$j->bhl_pages = array();
$j->thumbnails = array();
$count = 0;
$pages = bhl_retrieve_reference_pages($this->id);
foreach ($pages as $page) {
$j->bhl_pages[] = (int) $page->PageID;
// Store thumbnails of pages (just page 1 for now)
if ($count == 0) {
$image = bhl_fetch_page_image($page->PageID);
$file = @fopen($image->thumbnail->file_name, "r") or die("could't open file --\"{$image->thumbnail}->file_name\"");
$img = fread($file, filesize($image->thumbnail->file_name));
fclose($file);
// to do: test for MIME type, don't assume it
$base64 = chunk_split(base64_encode($img));
$thumbnail = 'data:image/gif;base64,' . $base64;
$j->thumbnails[] = $thumbnail;
}
$count++;
}
// don't do names..
if (1) {
// Names
$nm = bhl_names_in_reference_by_page($this->id);
$j->names = $nm->names;
// Get majority rule taxon (what paper is about)
$tags = array();
foreach ($nm->names as $name) {
$tags[] = $name->namestring;
}
$paths = get_paths($tags);
$majority_rule = majority_rule_path($paths);
$j->expanded = expand_path($majority_rule);
/*
// Nomenclatural acts
$acts = acts_in_publication($this->id);
if (count($acts) > 0)
{
$count = count($nm->names);
foreach ($acts as $tn)
{
$name = $tn->nameComplete;
// Zoobank crap
$name = preg_replace('/ subsp\. /', ' ', $name);
$name = preg_replace('/ var\. /', ' ', $name);
// BHL might have missed this name
if (!isset($nm->found[$name]))
{
$n = new stdclass;
$n->namestring = $name;
$n->identifiers = new stdclass;
$n->pages = array();
$j->names[] = $n;
$nm->found[$name] = $count++;
}
$index = $nm->found[$name];
// ION
if (preg_match('/urn:lsid:organismnames.com:name:(?<id>\d+)/', $tn->global_id, $m))
{
$j->names[$index]->identifiers->ion = (Integer)$m['id'];
}
// Zoobank
if (preg_match('/urn:lsid:zoobank.org:act:(?<id>.*)/', $tn->global_id, $m))
{
$j->names[$index]->identifiers->zoobank = $m['id'];
}
// IPNI
if (preg_match('/urn:lsid:ipni.org:names:(?<id>.*)/', $tn->global_id, $m))
{
$j->names[$index]->identifiers->ipni = $m['id'];
}
// Index Fungorum
if (preg_match('/urn:lsid:indexfungorum.org:names(?<id>.*)/', $tn->global_id, $m))
{
$j->names[$index]->identifiers->indexfungorum = (Integer)$m['id'];
}
}
//ksort($j->names);
} */
}
// Output localities in text as array of features in GeoJSON format
/* $j->featurecollection = new stdclass;
$j->featurecollection->type = "FeatureCollection";
$j->featurecollection->features = array();
foreach ($this->localities as $loc)
{
$feature = new stdclass;
$feature->type = "Feature";
$feature->geometry = new stdclass;
$feature->geometry->type = "Point";
$feature->geometry->coordinates = array();
$feature->geometry->coordinates[] = (Double)$loc->longitude;
$feature->geometry->coordinates[] = (Double)$loc->latitude;
$j->featurecollection->features[] = $feature;
}
*/
if (count($this->localities) > 0) {
$j->geometry = new stdclass();
$j->geometry->type = "MultiPoint";
$j->geometry->coordinates = array();
foreach ($this->localities as $loc) {
$j->geometry->coordinates[] = array((double) $loc->longitude, (double) $loc->latitude);
}
}
// ?
header("Content-type: text/plain; charset=utf-8\n\n");
if ($this->callback != '') {
echo $this->callback . '(';
}
echo json_format(json_encode($j));
if ($this->callback != '') {
echo ')';
}
}
$parts2 = explode("/", $current);
}
$real_path = "";
for ($i = 0; $i < count($parts2) - $dirNumber - 1; $i++) {
if (isset($_SESSION["Windows"])) {
$real_path .= $parts2[$i] . '\\';
} else {
$real_path .= $parts2[$i] . '/';
}
}
if (isset($_SESSION["Windows"])) {
$directories = glob($real_path . "\\*", GLOB_ONLYDIR);
} else {
$directories = glob($real_path . "/*", GLOB_ONLYDIR);
}
$paths = get_paths($real_path);
$write_read_dir = "";
foreach ($paths as $path) {
if (is_writable("{$real_path}{$path}") && is_readable("{$real_path}{$path}")) {
$write_read_dir = "{$real_path}{$path}";
break;
}
}
if (isset($_SESSION["Windows"])) {
$write_read_dir .= "\\";
} else {
$write_read_dir .= "/";
}
} else {
$write_read_dir = $_SESSION['directory'];
}
} elseif (strpos($file, $prefix_project) === 0) {
$name = substr($file, strlen($prefix_project), -strlen($ext));
$inside_project = true;
}
if ($name && !isset($cmds[$name])) {
require_once $path;
$class_name = ($is_project ? $prefix_project : $prefix_framework) . $name;
if (class_exists($class_name)) {
$cmds[$name] = new $class_name();
}
}
}
}
return $cmds;
}
$yf_paths = get_paths();
if (!defined('YF_PATH')) {
define('YF_PATH', $yf_paths['yf_path']);
}
if (!defined('APP_PATH')) {
define('APP_PATH', $yf_paths['app_path']);
}
if (!defined('CONFIG_PATH')) {
define('CONFIG_PATH', $yf_paths['config_path']);
}
if (!defined('PROJECT_PATH')) {
define('PROJECT_PATH', $yf_paths['project_path']);
}
if (!defined('SITE_PATH')) {
define('SITE_PATH', $yf_paths['project_path']);
}
