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') {
$occUtil = new OccurrenceUtilities();
$occUtil->protectStateRareSpecies();
}
} else {
$this->errorStr = 'ERROR: unable to locate scientific name column';
}
return $successCnt;
}