$cache = false;
$source = explode(",", $source);
$db = select_source($source, $classification);
$header = TnrsAggregator::$field;
if (isset($count)) {
array_unshift($header, "ID");
}
$outfh = fopen($outfile, 'w') or die("can't open outputfile");
fputcsv($outfh, $header);
$handle = fopen($file, "r");
while (($field = fgetcsv($handle, 1000, ",")) !== FALSE) {
if (!isset($field[0]) || $field[0] == '') {
continue;
}
$ta = new TnrsAggregator($db);
$tm = new Taxamatch($db);
$tm->set('debug_flag', '');
$tm->set('output_type', '');
$tm->set('cache_flag', false);
$tm->set('cache_path', CACHE_PATH);
$tm->set('name_parser', NAME_PARSER);
$tm->set('chop_overload', CHOP_OVERLOAD);
$tm->set('parse_only', $parse_only);
$name = escapeshellarg($field[0]);
if ($tm->process($name, $search_mode, $cache) && !$parse_only) {
$tm->generateResponse($cache);
}
$ta->aggregate($tm);
$result = $ta->getData();
foreach ($result as $re) {
if (isset($count)) {
if ($output == 'xml') {
$data = $tm->getXML();
}
break;
case 'tnrs_taxamatch':
require_once 'classes/class.taxamatch.php';
require_once 'classes/class.tnrs_aggregator.php';
if ($cache) {
$output = 'rest';
}
$db = select_source($source, $classification);
$data = array();
$names = preg_split("/[\r\n;]+/u", $str);
if (is_array($names)) {
foreach ($names as $name) {
$tm = new Taxamatch($db);
$tm->set('debug_flag', $debug);
$tm->set('output_type', strtolower($output));
$tm->set('cache_flag', $authorities[$source]['cache_flag']);
$tm->set('cache_path', CACHE_PATH);
$tm->set('name_parser', NAME_PARSER);
$tm->set('chop_overload', CHOP_OVERLOAD);
$tm->set('parse_only', $parse_only);
if ($tm->process($name, $search_mode, $cache)) {
$tm->generateResponse($cache);
}
$ta = new TnrsAggregator($db);
$ta->aggregate($tm);
$data[] = $ta->getData();
}
}
/**
* This is the function that process the input csv file and does the work.
* @param string $output_type : output type
*/
public function process($output_type = 'file')
{
// Assign File
if (file_exists($this->data['input_file'])) {
$this->handle_input = fopen($this->data['input_file'], "r");
} else {
return false;
}
$this->handle_output = fopen($this->data['output_file'], "w");
// Build Header
$this->build_new_header();
// Writes column header in 1st row of output.
$this->write_header();
/**
* This will run through the whole data and build the Higer Taxa with
* parentID relationship to be used in the final species list.
*/
$db = select_source($this->data['source']);
$search_mode = 'normal';
while (($row = fgetcsv($this->handle_input, 100000, $this->file_delimiter)) !== FALSE) {
// Call taxamatch and process row
$tm = new Taxamatch($db);
if ($tm->process($row[$this->scientificNameIndex], $search_mode)) {
$tm->generateResponse($cache);
}
$data = $tm->getData('flat');
if (is_array($data)) {
foreach ($data as $r) {
fputcsv($this->handle_output, array_merge($row, $r), $this->file_delimiter);
}
}
}
fclose($this->handle_output);
fclose($this->handle_input);
}
$cmd = $_REQUEST['cmd'];
} else {
$cmd = 'search';
}
switch($cmd) {
case 'search_results':
$output = '';
$source = $_REQUEST['source'];
$searchtxt = $_REQUEST['search_txt'];
$search_mode = 'normal';
$debug = 0;
$db = select_source( $source );
$tm = new Taxamatch($db);
$tm->set('debug_flag',$debug);
$tm->set('output_type',strtolower($output));
if($tm->process($searchtxt , $search_mode, $cache )) {
$tm->generateResponse($cache);
}
$data = $tm->getData();
$debug = $tm->debug;
?>
<ul title="Results" class="panel" >
<div class="panel" title="Results" id="results" style="left: 0%;" selected="true">
<h2><?=$searchtxt ?></h2>
