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 $status;
}
public function uploadCsvList($hasHeader, $thesId)
{
set_time_limit(300);
ini_set("max_input_time", 300);
ini_set('auto_detect_line_endings', true);
$successCnt = 0;
$fh = fopen($_FILES['uploadfile']['tmp_name'], 'r') or die("Can't open file. File may be too large. Try uploading file in sections.");
$headerArr = array();
if ($hasHeader) {
$headerData = fgetcsv($fh);
foreach ($headerData as $k => $v) {
$vStr = strtolower($v);
$vStr = str_replace(array(" ", ".", "_"), "", $vStr);
$vStr = str_replace(array("scientificnamewithauthor", "scientificname", "taxa", "species", "taxon"), "sciname", $vStr);
$headerArr[$vStr] = $k;
}
} else {
$headerArr["sciname"] = 0;
}
if (array_key_exists("sciname", $headerArr)) {
$cnt = 0;
ob_flush();
flush();
$taxUtil = new TaxonomyUtilities();
while ($valueArr = fgetcsv($fh)) {
$tid = 0;
$rankId = 0;
$sciName = "";
$family = "";
$sciNameStr = $this->cleanInStr($valueArr[$headerArr["sciname"]]);
$noteStr = '';
if ($sciNameStr) {
$sciNameArr = $taxUtil->parseSciName($sciNameStr);
//Check name is in taxa table and grab tid if it is
$sql = "";
if ($thesId && is_numeric($thesId)) {
$sql = 'SELECT t2.tid, ts.family, t2.rankid ' . 'FROM (taxa t INNER JOIN taxstatus ts ON t.tid = ts.tid) ' . 'INNER JOIN taxa t2 ON ts.tidaccepted = t2.tid ' . 'WHERE (ts.taxauthid = ' . $thesId . ') ';
} else {
$sql = 'SELECT t.tid, ts.family, t.rankid ' . 'FROM taxa t INNER JOIN taxstatus ts ON t.tid = ts.tid ' . 'WHERE ts.taxauthid = 1 ';
}
$cleanSciName = $this->encodeString($sciNameArr['sciname']);
$sql .= 'AND (t.sciname IN("' . $sciNameStr . '"' . ($cleanSciName ? ',"' . $cleanSciName . '"' : '') . '))';
$rs = $this->conn->query($sql);
if ($rs) {
if ($row = $rs->fetch_object()) {
$tid = $row->tid;
$family = $row->family;
$rankId = $row->rankid;
}
$rs->free();
}
//Load taxon into checklist
if ($tid) {
if ($rankId >= 180) {
$sqlInsert = '';
$sqlValues = '';
if (array_key_exists('family', $headerArr) && ($valueArr[$headerArr['family']] && strtolower($family) != strtolower($valueArr[$headerArr['family']]))) {
$sqlInsert .= ',familyoverride';
$sqlValues .= ',"' . $this->cleanInStr($valueArr[$headerArr['family']]) . '"';
}
if (array_key_exists('habitat', $headerArr) && $valueArr[$headerArr['habitat']]) {
$sqlInsert .= ',habitat';
$sqlValues .= ',"' . $this->cleanInStr($valueArr[$headerArr['habitat']]) . '"';
}
if (array_key_exists('abundance', $headerArr) && $valueArr[$headerArr['abundance']]) {
$sqlInsert .= ',abundance';
$sqlValues .= ',"' . $this->cleanInStr($valueArr[$headerArr['abundance']]) . '"';
}
if ($noteStr || array_key_exists('notes', $headerArr) && $valueArr[$headerArr['notes']]) {
if (array_key_exists('notes', $headerArr) && $valueArr[$headerArr['notes']]) {
if ($noteStr) {
$noteStr .= '; ';
}
$noteStr .= $valueArr[$headerArr['notes']];
}
$sqlInsert .= ',notes';
$sqlValues .= ',"' . $this->cleanInStr($noteStr) . '"';
}
$sql = 'INSERT INTO fmchklsttaxalink (tid,clid' . $sqlInsert . ') VALUES (' . $tid . ', ' . $this->clid . $sqlValues . ')';
//echo $sql;
if ($this->conn->query($sql)) {
$successCnt++;
} else {
$this->errorArr[] = $sciNameStr . " (TID = {$tid}) failed to load<br />Error msg: " . $this->conn->error;
//echo $sql."<br />";
}
} else {
$this->errorArr[] = $sciNameStr . " failed to load (taxon must be of genus, species, or infraspecific ranking)";
}
} else {
$this->problemTaxa[] = $cleanSciName;
//$statusStr = $sciNameStr." failed to load (misspelled or not yet in taxonomic thesaurus)";
//$failCnt++;
}
$cnt++;
if ($cnt % 500 == 0) {
echo '<li style="margin-left:10px;">' . $cnt . ' taxa loaded</li>';
ob_flush();
flush();
}
}
}
fclose($fh);
if ($cnt && $this->clMeta['type'] == 'rarespp') {
$occurMain = new OccurrenceMaintenance($this->conn);
$occurMain->protectStateRareSpecies();
}
} else {
$this->errorStr = 'ERROR: unable to locate scientific name column';
}
return $successCnt;
}
<?php
include_once '../../config/symbini.php';
include_once $SERVER_ROOT . '/classes/TaxonomyUtilities.php';
if (!$SYMB_UID) {
header('Location: ../../profile/index.php?refurl=../taxa/admin/taxonomymaintenance.php?' . $_SERVER['QUERY_STRING']);
}
$action = array_key_exists("action", $_REQUEST) ? $_REQUEST["action"] : "";
$taxonManager = new TaxonomyUtilities();
$isEditor = false;
if ($isAdmin || array_key_exists("Taxonomy", $userRights)) {
$isEditor = true;
}
if ($isEditor) {
if ($action == 'buildenumtree') {
if ($taxonManager->buildHierarchyEnumTree()) {
$statusStr = 'SUCCESS building Taxonomic Index';
} else {
$statusStr = 'ERROR building Taxonomic Index: ' . $taxonManager->getErrorMessage();
}
} elseif ($action == 'rebuildenumtree') {
if ($taxonManager->rebuildHierarchyEnumTree()) {
$statusStr = 'SUCCESS building Taxonomic Index';
} else {
$statusStr = 'ERROR building Taxonomic Index: ' . $taxonManager->getErrorMessage();
}
}
}
?>
<html>
<head>
public function getDynamicTreePath()
{
$retArr = array();
$tid = '';
$acceptedTid = '';
//Temporary code: check to make sure taxaenumtree is populated
//This code can be removed somewhere down the line
$sqlTest = 'SELECT tid FROM taxaenumtree LIMIT 1';
$rsTest = $this->conn->query($sqlTest);
if (!$rsTest->num_rows) {
echo '<div style="color:red;margin:30px;">';
echo 'NOTICE: Building new taxonomic hierarchy table (taxaenumtree).<br/>';
echo 'This may take a few minutes, but only needs to be done once.<br/>';
echo 'Do not terminate this process early.';
echo '</div>';
ob_flush();
flush();
$taxMainObj = new TaxonomyUtilities();
$taxMainObj->buildHierarchyEnumTree();
}
$rsTest->free();
//Get target taxa (we don't want children and parents of non-accepted taxa, so we'll get those later)
if ($this->targetStr) {
$sql1 = 'SELECT DISTINCT t.tid, ts.tidaccepted ' . 'FROM taxa t LEFT JOIN taxstatus ts ON t.tid = ts.tid ' . 'LEFT JOIN taxstatus ts1 ON t.tid = ts1.tidaccepted ' . 'LEFT JOIN taxa t1 ON ts1.tid = t1.tid ' . 'WHERE (ts.taxauthid = 1 OR ts.taxauthid IS NULL) AND (ts1.taxauthid = 1 OR ts1.taxauthid IS NULL) ';
if (is_numeric($this->targetStr)) {
$sql1 .= 'AND (t.tid IN(' . implode(',', $this->targetStr) . ') OR (ts1.tid = ' . $this->targetStr . '))';
} else {
$sql1 .= 'AND ((t.sciname = "' . $this->targetStr . '") OR (t1.sciname = "' . $this->targetStr . '"))';
}
//echo "<div>".$sql1."</div>";
$rs1 = $this->conn->query($sql1);
while ($row1 = $rs1->fetch_object()) {
if ($rs1->num_rows == 1) {
$tid = $row1->tid;
} elseif ($row1->tid != $row1->tidaccepted) {
$tid = $row1->tid;
$acceptedTid = $row1->tidaccepted;
}
}
$rs1->free();
if ($tid) {
$i = 1;
$prevTid = '';
$retArr[0] = 'root';
$sql2 = 'SELECT t.RankId, te.parenttid, ts.tidaccepted, ts.parenttid AS par2 ' . 'FROM (taxa t LEFT JOIN taxaenumtree te ON t.TID = te.parenttid) ' . 'LEFT JOIN taxstatus ts ON te.parenttid = ts.tid ' . 'WHERE te.TID = ' . ($acceptedTid ? $acceptedTid : $tid) . ' AND te.taxauthid = 1 AND ts.taxauthid = 1 ' . 'ORDER BY t.RankId ';
//echo "<div>".$sql2."</div>";
$rs2 = $this->conn->query($sql2);
while ($row2 = $rs2->fetch_object()) {
if (!$prevTid || $row2->par2 == $prevTid) {
$retArr[$i] = $row2->tidaccepted;
$prevTid = $row2->tidaccepted;
} else {
$sql3 = 'SELECT tid ' . 'FROM taxstatus ' . 'WHERE parenttid = ' . $prevTid . ' AND taxauthid = 1 ' . 'AND tid IN(SELECT parenttid FROM taxaenumtree WHERE tid = ' . $tid . ' AND taxauthid = 1) ';
//echo "<div>".$sql3."</div>";
$rs3 = $this->conn->query($sql3);
while ($row3 = $rs3->fetch_object()) {
$retArr[$i] = $row3->tid;
$prevTid = $row3->tid;
}
$rs3->free();
}
$i++;
}
if ($acceptedTid) {
$retArr[$i] = $acceptedTid;
$i++;
}
$retArr[$i] = $tid;
$rs2->free();
}
}
return $retArr;
}
