public function analyzeTaxa($startIndex = 0, $limit = 50)
{
$status = true;
$this->logOrEcho("Starting taxa check ");
$sql = 'SELECT DISTINCT sciname, family ' . 'FROM omoccurrences ' . 'WHERE (collid = ' . $this->collid . ') AND (tidinterpreted IS NULL) AND (sciname IS NOT NULL) AND (sciname != "") ' . 'ORDER BY sciname ' . 'LIMIT ' . $startIndex . ',' . $limit;
if ($rs = $this->conn->query($sql)) {
//Check name through taxonomic resources
$taxUtil = new TaxonomyUtilities();
$taxUtil->setVerboseMode(2);
$this->setVerboseMode(2);
$nameCnt = 0;
while ($r = $rs->fetch_object()) {
$this->logOrEcho('Resolving ' . $r->sciname . ($r->family ? ' (' . $r->family . ')' : '') . '...');
$newTid = $taxUtil->addSciname($r->sciname, $r->family);
if (!$newTid) {
//Check for near match using SoundEx
$this->logOrEcho('Checking close matches in thesaurus...', 1);
$closeArr = $taxUtil->getSoundexMatch($r->sciname);
if (!$closeArr) {
$closeArr = $taxUtil->getCloseMatchEpithet($r->sciname);
}
if ($closeArr) {
$cnt = 0;
foreach ($closeArr as $tid => $sciname) {
$echoStr = '<i>' . $sciname . '</i> =><a href="#" onclick="remappTaxon(\'' . $r->sciname . '\',' . $tid . ',\'' . $sciname . '\')"> remap to this taxon</a>';
$this->logOrEcho($echoStr, 2);
$cnt++;
}
} else {
$this->logOrEcho('No close matches found', 1);
}
}
$nameCnt++;
}
$rs->free();
}
$this->linkNewTaxa();
$this->logOrEcho("Done with taxa check ");
return $status;
}
