function uploadBiocaseFile($db, $xml, $reindex = FALSE, $diagnostics = FALSE, $resourceid = FALSE)
{
$doc = new DOMDocument();
$doc->loadXML($xml);
//get config
$config = array();
$config['core'] = array();
$handle = fopen('config/config_avh_db_core.csv', 'r');
while (!feof($handle)) {
$config['core'][] = fgetcsv($handle);
}
fclose($handle);
$config['extension'] = array();
$handle = fopen('config/config_avh_db_extension.csv', 'r');
while (!feof($handle)) {
$config['extension'][] = fgetcsv($handle);
}
fclose($handle);
if ($diagnostics && $resourceid) {
$diag = new BiocaseDiagnostic($db, $doc, $resourceid);
$diag->diagnose();
}
$data = array();
$dehispidator = new Hispid5ToCsv();
$data['core'] = $dehispidator->parseHISPID5($doc);
$data['extension'] = $dehispidator->DeterminationHistory($doc);
$upload = new AvhDb($db, $data, $config);
$upload->uploadCoreData($reindex);
}
public function harvest()
{
$biocase = new BioCase($this->resourceurl, $this->resourcedsa, $this->resourceschema);
$result = $biocase->biocaseCount();
$doc = new DOMDocument('1.0', 'UTF-8');
$doc->loadXML($result);
$list = $doc->getElementsByTagName('count');
$recordCount = $list->item(0)->nodeValue;
if ($recordCount) {
fwrite($this->log, date('Y-m-d H:i:s') . "\t" . str_pad($this->resource . ':', 6, ' ', STR_PAD_RIGHT) . "\t" . $recordCount . "\n");
$offset = $this->offset;
$date = date('Y-m-d');
//get config
$config = array();
$config['core'] = array();
$handle = fopen('config/config_avh_db_core.csv', 'r');
while (!feof($handle)) {
$config['core'][] = fgetcsv($handle);
}
fclose($handle);
$config['extension'] = array();
$handle = fopen('config/config_avh_db_extension.csv', 'r');
while (!feof($handle)) {
$config['extension'][] = fgetcsv($handle);
}
fclose($handle);
while ($offset <= $recordCount) {
$biocase = new BioCase($this->resourceurl, $this->resourcedsa, $this->resourceschema, $this->resourcelastupdated, $offset, $this->limit);
$xml = $biocase->bulkHarvest();
$filename = 'xml/' . $this->resource . '_' . $date . '_' . str_pad($offset, 7, '0', STR_PAD_LEFT) . '.xml';
file_put_contents($filename, $xml);
$doc = new DOMDocument('1.0', 'UTF-8');
$doc->loadXML($xml);
$diag = new BiocaseDiagnostic($this->db, $doc, $this->resourceid);
$diag->diagnose();
if ($this->resource == 'AD') {
$doc = new DOMDocument('1.0', 'UTF-8');
$xml = substr($xml, strpos($xml, '<DataSet>'));
$xml = substr($xml, 0, strpos($xml, '</DataSet>') + strlen('</DataSets>'));
$doc->loadXML($xml);
}
$data = array();
$dehispidator = new Hispid5ToCsv();
$data['core'] = $dehispidator->parseHISPID5($doc);
$data['extension'] = $dehispidator->DeterminationHistory($doc);
$upload = new AvhDb($this->db, $data, $config);
$upload->uploadCoreData(TRUE);
$upload->uploadExtensionData();
$offset += $this->limit;
}
$select = "SELECT MAX(modified) FROM core WHERE \"institutionCode\"=?";
$selStmt = $this->db->prepare($select);
$selStmt->execute(array($this->resource));
$r = $selStmt->fetch(PDO::FETCH_NUM);
$lastModified = $r[0];
$update = "UPDATE resource\n SET date_last_queried=?\n WHERE resource_id=?";
$updStmt = $this->db->prepare($update);
$updStmt->execute(array($lastModified, $this->resourceid));
} else {
fwrite($this->log, date('Y-m-d H:i:s') . "\t" . str_pad($this->resource . ':', 6, ' ', STR_PAD_RIGHT) . "\t0\n");
}
}
