public function deleteSpecies($tid)
{
if (is_numeric($tid)) {
$sql = 'UPDATE taxa t SET t.SecurityStatus = 0 WHERE (t.tid = ' . $tid . ')';
//echo $sql;
$this->con->query($sql);
//Update specimen records
$sql2 = 'UPDATE omoccurrences o INNER JOIN taxstatus ts1 ON o.tidinterpreted = ts1.tid ' . 'INNER JOIN taxstatus ts2 ON ts1.tidaccepted = ts2.tidaccepted ' . 'INNER JOIN taxa t ON ts2.tid = t.tid ' . 'SET o.LocalitySecurity = 0 ' . 'WHERE (t.tid = ' . $tid . ')';
//echo $sql2; exit;
$this->con->query($sql2);
$occurUtil = new OccurrenceUtilities();
$occurUtil->protectGloballyRareSpecies();
}
}
public function getComments($collid, $start, $limit, $tsStart, $tsEnd, $uid, $rs)
{
$retArr = array();
if ($collid) {
$sqlBase = 'FROM omoccurcomments c INNER JOIN omoccurrences o ON c.occid = o.occid ' . 'WHERE o.collid = ' . $collid;
if ($uid) {
$sqlBase .= ' AND uid = ' . $uid;
}
if (is_numeric($rs)) {
$sqlBase .= ' AND reviewstatus = ' . $rs;
}
if ($tsStart) {
$tsStartStr = OccurrenceUtilities::formatDate($tsStart);
if ($tsStartStr) {
$sqlBase .= ' AND initialtimestamp >= ' . $tsStartStr;
}
}
if ($tsEnd) {
$tsEndStr = OccurrenceUtilities::formatDate($tsEnd);
if ($tsEndStr) {
$sqlBase .= ' AND initialtimestamp < ' . $tsEndStr;
}
}
//Get count
$sqlCnt = 'SELECT count(c.comid) as cnt ' . $sqlBase;
$rsCnt = $this->conn->query($sqlCnt);
while ($rCnt = $rsCnt->fetch_object()) {
$retArr['cnt'] = $rCnt->cnt;
}
$rsCnt->free();
//Get records
$sql = 'SELECT c.comid, c.occid, c.comment, c.uid, c.reviewstatus, c.parentcomid, c.initialtimestamp ' . $sqlBase . ' ORDER BY initialtimestamp DESC LIMIT ' . $start . ',' . $limit;
//echo $sql; exit;
$rs = $this->conn->query($sql);
while ($r = $rs->fetch_object()) {
$retArr[$r->comid]['str'] = $r->comment;
$retArr[$r->comid]['occid'] = $r->occid;
$retArr[$r->comid]['uid'] = $r->uid;
$retArr[$r->comid]['rs'] = $r->reviewstatus;
$retArr[$r->comid]['ts'] = $r->initialtimestamp;
}
$rs->free();
}
return $retArr;
}
private function DateFromOneLine($Field, $L, $Partial = false)
{
//Checks several formats
$RomanMonths = array("I" => "Jan", "II" => "Feb", "III" => "Mar", "IV" => "Apr", "V" => "May", "VI" => "Jun", "VII" => "Jul", "VIII" => "Aug", "IX" => "Sep", "X" => "Oct", "XI" => "Nov", "XII" => "Dec");
$match = array();
$RealVDate = "";
$VDate = "";
$TempString = $this->LabelLines[$L];
//Reformat expressions like: "23 de abril de 1956" to "23 abril 1956"
$TempString = preg_replace("((\\d{1,2})\\sde\\s({$this->PregMonths})[\\sde]{0,3}\\s(\\d{2,4}))", "\$1 \$2 \$5", $TempString);
//echo "Getting date from {$this->LabelLines[$L]}<br>";
if ($Partial) {
$Preg = "(\\b{$this->PregMonths}\\s*(\\b[0-9]{1,4}\\b))i";
} else {
$Preg = "((\\b[0-9]{1,4}\\b)\\s*{$this->PregMonths}[.,]*\\s*(\\b[0-9]{1,4}\\b))i";
}
$Found = preg_match($Preg, $TempString, $match);
if ($Found !== 1) {
//Format April 21, 1929
$Preg = "({$this->PregMonths}[.\\s]*(\\b[0-9]{1,4}\\b)[.,]*\\s*(\\b[0-9]{1,4}\\b)\\s*)i";
$Found = preg_match($Preg, $TempString, $match);
if ($Found) {
$VDate = $match[2] . " " . $match[3] . ", " . $match[4];
$RealVDate = $match[0];
}
}
if ($Found !== 1) {
//Format April, 1929
$Preg = "({$this->PregMonths}[.,]?\\s*(\\b[0-9]{1,4}\\b)\\s*)i";
$Found = preg_match($Preg, $TempString, $match);
}
if ($Found !== 0) {
if ($VDate == "") {
$VDate = $match[0];
$RealVDate = $VDate;
}
}
if ($Found == 0) {
//Roman numeral for month
$Preg = "(([0-9]+[ ./-]{1,2})([IVX]+)([ ./-]{1,2}[0-9]+))i";
$Found = preg_match($Preg, $TempString, $match);
if ($Found > 0) {
$Month = $RomanMonths[strtoupper($match[2])];
$VDate = trim($match[1], " .-") . "-" . $Month . "-" . trim($match[3], " .-");
$RealVDate = $match[0];
}
}
if ($Found == 0) {
//Day-AlphaMonth-Year
$Preg = "(([0-9]+[ ./-]{1,2}){$this->PregMonths}([ ./-]{1,2}[0-9]{2,4}))i";
$Found = preg_match($Preg, $TempString, $match);
if ($Found > 0) {
//$this->printr($match,"Day-Month-Year");
$VDate = trim(str_replace("-", " ", $match[0]));
$RealVDate = $match[0];
}
}
if ($Found == 0) {
// day-month-year all numeric
//echo "Checking $TempString: <br>";
$Preg = "(\\b([0-9]{1,2})[ ./-]+([0-9]{1,2})[ ./-]+([0-9]{2,4})\\b)";
$Found = preg_match($Preg, $TempString, $match);
if ($Found !== 0) {
//echo "Found {$match[0]}<br>";
$VDate = $match[0];
$RealVDate = $VDate;
}
}
if ($Found == 0) {
$Preg = "(\\b(19[0-9]{2,2}|20[01][0-9])\\b)";
$Found = preg_match($Preg, $TempString, $match);
if ($Found !== 0) {
//echo "Found {$match[0]}<br>";
$VDate = $match[0];
$RealVDate = $VDate;
}
}
if ($Found !== 0) {
$FrenchMonths = array("janvier", "febrier", "mars", "avril", "mai", "juin", "juillet", "aout", "septembre", "octobre", "novembre", "decembre");
$VDate = str_replace($FrenchMonths, $RomanMonths, $VDate);
//Converts french dates to English (Using the same Roman Numeral conversion array)
$OU = new OccurrenceUtilities();
$FormattedDate = $OU->formatDate($VDate);
if ($FormattedDate != "") {
$FoundYear = preg_match("((\\d{4,4})\\-)", $FormattedDate, $match);
//$this->printr($match,"FormattedDate");
if ($match[1] > 2020 || $match[1] < 1700) {
return false;
}
$this->AddToResults($Field, $FormattedDate, $L);
if ($RealVDate != "") {
$VDate = $RealVDate;
}
$this->LabelLines[$L] = str_replace($VDate, "", $this->LabelLines[$L]);
if ($Field == "eventDate") {
$this->AddToResults("verbatimEventDate", $VDate, $L);
}
$this->RemoveStartWords($L, $Field);
return true;
}
}
return;
}
<?php
date_default_timezone_set('America/Phoenix');
require_once '../../config/symbini.php';
require_once $serverRoot . '/classes/OccurrenceUtilities.php';
$assocHandler = new OccurrenceUtilities();
$assocHandler->buildAssociatedTaxaIndex(1);
private function formatDate($inDate)
{
$retDate = OccurrenceUtilities::formatDate($inDate);
return $retDate;
}
public static function parseVerbatimCoordinates($inStr, $target = '')
{
$retArr = array();
if (strpos($inStr, ' to ')) {
return $retArr;
}
if (strpos($inStr, ' betw ')) {
return $retArr;
}
//Get rid of curly quotes
$search = array("’", "‘", "`", "”", "“");
$replace = array("'", "'", "'", '"', '"');
$inStr = str_replace($search, $replace, $inStr);
//Try to parse lat/lng
$latDeg = 'null';
$latMin = 0;
$latSec = 0;
$latNS = 'N';
$lngDeg = 'null';
$lngMin = 0;
$lngSec = 0;
$lngEW = 'W';
//Grab lat deg and min
if (!$target || $target == 'LL') {
if (preg_match('/([\\sNSns]{0,1})(-?\\d{1,2}\\.{1}\\d+)\\D{0,1}\\s{0,1}([NSns]{0,1})\\D{0,1}([\\sEWew]{1})(-?\\d{1,4}\\.{1}\\d+)\\D{0,1}\\s{0,1}([EWew]{0,1})\\D*/', $inStr, $m)) {
//Decimal degree format
$retArr['lat'] = $m[2];
$retArr['lng'] = $m[5];
$latDir = $m[3];
if (!$latDir && $m[1]) {
$latDir = trim($m[1]);
}
if ($retArr['lat'] > 0 && $latDir && ($latDir == 'S' || $latDir == 's')) {
$retArr['lat'] = -1 * $retArr['lat'];
}
$lngDir = $m[6];
if (!$lngDir && $m[4]) {
$lngDir = trim($m[4]);
}
if ($retArr['lng'] > 0 && $latDir && ($lngDir == 'W' || $lngDir == 'w')) {
$retArr['lng'] = -1 * $retArr['lng'];
}
} elseif (preg_match('/(\\d{1,2})\\D{1,3}\\s{0,2}(\\d{1,2}\\.{0,1}\\d*)[\'m]{1}(.*)/i', $inStr, $m)) {
//DMS format
$latDeg = $m[1];
$latMin = $m[2];
$leftOver = str_replace("''", '"', trim($m[3]));
//Grab lat NS and lng EW
if (stripos($inStr, 'N') === false && strpos($inStr, 'S') !== false) {
$latNS = 'S';
}
if (stripos($inStr, 'W') === false && stripos($inStr, 'E') !== false) {
$lngEW = 'E';
}
//Grab lat sec
if (preg_match('/^(\\d{1,2}\\.{0,1}\\d*)["s]{1}(.*)/i', $leftOver, $m)) {
$latSec = $m[1];
if (count($m) > 2) {
$leftOver = trim($m[2]);
}
}
//Grab lng deg and min
if (preg_match('/(\\d{1,3})\\D{1,3}\\s{0,2}(\\d{1,2}\\.{0,1}\\d*)[\'m]{1}(.*)/i', $leftOver, $m)) {
$lngDeg = $m[1];
$lngMin = $m[2];
$leftOver = trim($m[3]);
//Grab lng sec
if (preg_match('/^(\\d{1,2}\\.{0,1}\\d*)["s]{1}(.*)/i', $leftOver, $m)) {
$lngSec = $m[1];
if (count($m) > 2) {
$leftOver = trim($m[2]);
}
}
if (is_numeric($latDeg) && is_numeric($latMin) && is_numeric($lngDeg) && is_numeric($lngMin)) {
if ($latDeg < 90 && $latMin < 60 && $lngDeg < 180 && $lngMin < 60) {
$latDec = $latDeg + $latMin / 60 + $latSec / 3600;
$lngDec = $lngDeg + $lngMin / 60 + $lngSec / 3600;
if ($latNS == 'S') {
$latDec = -$latDec;
}
if ($lngEW == 'W') {
$lngDec = -$lngDec;
}
$retArr['lat'] = round($latDec, 6);
$retArr['lng'] = round($lngDec, 6);
}
}
}
}
}
if (!$target && !$retArr || $target == 'UTM') {
//UTM parsing
$d = '';
if (preg_match('/NAD\\s*27/i', $inStr)) {
$d = 'NAD27';
}
if (preg_match('/\\D*(\\d{1,2}\\D{0,1})\\s+(\\d{6,7})E\\s+(\\d{7})N/i', $inStr, $m)) {
$z = $m[1];
$e = $m[2];
$n = $m[3];
if ($n && $e && $z) {
$llArr = OccurrenceUtilities::convertUtmToLL($e, $n, $z, $d);
if (isset($llArr['lat'])) {
$retArr['lat'] = $llArr['lat'];
}
if (isset($llArr['lng'])) {
$retArr['lng'] = $llArr['lng'];
}
}
} elseif (preg_match('/UTM/', $inStr) || preg_match('/\\d{1,2}[\\D\\s]+\\d{6,7}[\\D\\s]+\\d{6,7}/', $inStr)) {
//UTM
$z = '';
$e = '';
$n = '';
if (preg_match('/^(\\d{1,2}\\D{0,1})[\\s\\D]+/', $inStr, $m)) {
$z = $m[1];
}
if (!$z && preg_match('/[\\s\\D]+(\\d{1,2}\\D{0,1})$/', $inStr, $m)) {
$z = $m[1];
}
if (!$z && preg_match('/[\\s\\D]+(\\d{1,2}\\D{0,1})[\\s\\D]+/', $inStr, $m)) {
$z = $m[1];
}
if ($z) {
if (preg_match('/(\\d{6,7})E{1}[\\D\\s]+(\\d{7})N{1}/i', $inStr, $m)) {
$e = $m[1];
$n = $m[2];
} elseif (preg_match('/E{1}(\\d{6,7})[\\D\\s]+N{1}(\\d{7})/i', $inStr, $m)) {
$e = $m[1];
$n = $m[2];
} elseif (preg_match('/(\\d{7})N{1}[\\D\\s]+(\\d{6,7})E{1}/i', $inStr, $m)) {
$e = $m[2];
$n = $m[1];
} elseif (preg_match('/N{1}(\\d{7})[\\D\\s]+E{1}(\\d{6,7})/i', $inStr, $m)) {
$e = $m[2];
$n = $m[1];
} elseif (preg_match('/(\\d{6})[\\D\\s]+(\\d{7})/', $inStr, $m)) {
$e = $m[1];
$n = $m[2];
} elseif (preg_match('/(\\d{7})[\\D\\s]+(\\d{6})/', $inStr, $m)) {
$e = $m[2];
$n = $m[1];
}
if ($e && $n) {
$llArr = OccurrenceUtilities::convertUtmToLL($e, $n, $z, $d);
if (isset($llArr['lat'])) {
$retArr['lat'] = $llArr['lat'];
}
if (isset($llArr['lng'])) {
$retArr['lng'] = $llArr['lng'];
}
}
}
}
}
//Clean
if ($retArr) {
if ($retArr['lat'] < -90 || $retArr['lat'] > 90) {
return;
}
if ($retArr['lng'] < -180 || $retArr['lng'] > 180) {
return;
}
}
return $retArr;
}
public static function convertUtmToLL($e, $n, $z, $d)
{
return OccurrenceUtilities::convertUtmToLL($e, $n, $z, $d);
}
private function cleanHouse($collList)
{
$this->logOrEcho('Updating collection statistics...', 1);
$occurUtil = new OccurrenceUtilities();
$this->logOrEcho('General cleaning...', 2);
$collString = implode(',', $collList);
if (!$occurUtil->generalOccurrenceCleaning($collString)) {
$errorArr = $occurUtil->getErrorArr();
foreach ($errorArr as $errorStr) {
$this->logOrEcho($errorStr, 1);
}
}
$this->logOrEcho('Protecting sensitive species...', 2);
if (!$occurUtil->protectRareSpecies()) {
$errorArr = $occurUtil->getErrorArr();
foreach ($errorArr as $errorStr) {
$this->logOrEcho($errorStr, 1);
}
}
if ($collList) {
$this->logOrEcho('Updating collection statistics...', 2);
foreach ($collList as $collid) {
if (!$occurUtil->updateCollectionStats($collid)) {
$errorArr = $occurUtil->getErrorArr();
foreach ($errorArr as $errorStr) {
$this->logOrEcho($errorStr, 1);
}
}
}
}
$this->logOrEcho('Populating global unique identifiers (GUIDs) for all records...', 2);
$uuidManager = new UuidFactory();
$uuidManager->setSilent(1);
$uuidManager->populateGuids();
}
private function updateCollectionStats()
{
if ($this->dbMetadata) {
//Do some more cleaning of the data after it haas been indexed in the omoccurrences table
$occurUtil = new OccurrenceUtilities();
$this->logOrEcho('Cleaning house...');
if (!$occurUtil->generalOccurrenceCleaning()) {
$errorArr = $occurUtil->getErrorArr();
foreach ($errorArr as $errorStr) {
$this->logOrEcho($errorStr, 1);
}
}
$this->logOrEcho('Protecting sensitive species...');
if (!$occurUtil->protectRareSpecies()) {
$errorArr = $occurUtil->getErrorArr();
foreach ($errorArr as $errorStr) {
$this->logOrEcho($errorStr, 1);
}
}
$this->logOrEcho('Updating statistics...');
foreach ($this->collProcessedArr as $collid) {
if (!$occurUtil->updateCollectionStats($collid)) {
$errorArr = $occurUtil->getErrorArr();
foreach ($errorArr as $errorStr) {
$this->logOrEcho($errorStr, 1);
}
}
}
$this->logOrEcho('Populating global unique identifiers (GUIDs) for all records...');
$uuidManager = new UuidFactory();
$uuidManager->setSilent(1);
$uuidManager->populateGuids();
}
$this->logOrEcho("Stats update completed");
}
public function setDwcArr($dwcObj)
{
$recArr = json_decode($dwcObj, true);
if ($recArr) {
$recArr = array_change_key_case($recArr);
//Translate fields
foreach ($this->fieldTranslation as $otherName => $symbName) {
if (array_key_exists($otherName, $recArr) && !array_key_exists($symbName, $recArr)) {
$recArr[$symbName] = $recArr[$otherName];
unset($recArr[$otherName]);
}
}
//Filter out unapproved fields
$recArr = array_intersect_key($recArr, array_flip($this->approvedFields));
$this->dwcArr = OccurrenceUtilities::occurrenceArrayCleaning($recArr);
if ($this->dwcArr) {
return true;
}
}
return false;
}
public function batchUpdateStatistics($collId)
{
echo 'Updating collection statistics...';
echo '<ul>';
//echo '<li>General cleaning in preparation for collecting stats... </li>';
flush();
ob_flush();
$occurUtil = new OccurrenceUtilities();
//$occurUtil->generalOccurrenceCleaning();
$sql = 'SELECT collid, collectionname FROM omcollections WHERE collid IN(' . $collId . ') ';
//echo $sql;
$rs = $this->conn->query($sql);
while ($r = $rs->fetch_object()) {
echo '<li style="margin-left:15px;">Cleaning statistics for: ' . $r->collectionname . '</li>';
flush();
ob_flush();
$occurUtil->updateCollectionStats($r->collid, true);
}
$rs->free();
echo '<li>Statistics update complete!</li>';
echo '</ul>';
flush();
ob_flush();
}
public function getHierarchyEntries($id, $includeSynonyms = true, $includeCommonNames = true, $includeParents = true)
{
//http://eol.org/api/docs/hierarchy_entries
//http://eol.org/api/hierarchy_entries/1.0/52595368.json?common_names=true&synonyms=true&cache_ttl=
$taxonArr = array();
if ($id) {
//Get taxonomy
$url = 'http://eol.org/api/hierarchy_entries/1.0/' . $id . '.json?common_names=' . ($includeCommonNames ? 'true' : 'false') . '&synonyms=' . ($includeSynonyms ? 'true' : 'false');
//echo $url; exit;
if ($fh = fopen($url, 'r')) {
$content = "";
while ($line = fread($fh, 1024)) {
$content .= trim($line);
}
fclose($fh);
//Process return
$eolObj = json_decode($content);
if ($eolObj->scientificName) {
$taxonArr = OccurrenceUtilities::parseScientificName($eolObj->scientificName);
$taxonArr['scientificName'] = $eolObj->scientificName;
$taxonArr['taxonRank'] = $eolObj->taxonRank;
if (isset($eolObj->nameAccordingTo)) {
$taxonArr['source'] = $eolObj->nameAccordingTo[0];
}
if (isset($eolObj->source)) {
$taxonArr['sourceURL'] = $eolObj->source;
}
//Add synonyms
if ($includeSynonyms) {
$synonyms = $eolObj->synonyms;
foreach ($synonyms as $synObj) {
$taxonArr['syns'][] = array('scientificName' => $synObj->scientificName, 'synreason' => $synObj->taxonomicStatus);
}
}
//Add vernaculars
if ($includeCommonNames) {
$vernacularNames = $eolObj->vernacularNames;
foreach ($vernacularNames as $vernObj) {
if (in_array($vernObj->language, $this->targetLanguages)) {
$taxonArr['verns'][] = array('language' => $vernObj->language, 'vernacularName' => $vernObj->vernacularName);
}
}
}
//Process ancestors
if ($eolObj->ancestors && $eolObj->parentNameUsageID) {
$ancArr = array_reverse((array) $eolObj->ancestors);
$parArr = $this->getParentArray($ancArr, $eolObj->parentNameUsageID);
if ($parArr) {
$taxonArr['parent'] = $parArr;
}
}
$taxonArr['id'] = $id;
}
} else {
$this->errorStr = 'ERROR opening EOL hierarchy url: ' . $url;
}
} else {
$this->errorStr = "Input ID is null";
return false;
}
return $taxonArr;
}
public function parseSciName($scientificName, $rankId = 0)
{
//Converts scinetific name with author embedded into separate fields
$retArr = array();
$retArr = OccurrenceUtilities::parseScientificName($scientificName, $rankId);
return $retArr;
}
private function getSqlFragments($recMap, $fieldMap)
{
$sqlFields = '';
$sqlValues = '';
foreach ($recMap as $symbField => $valueStr) {
if (substr($symbField, 0, 8) != 'unmapped') {
$sqlFields .= ',' . $symbField;
$valueStr = $this->encodeString($valueStr);
$valueStr = $this->cleanInStr($valueStr);
//Load data
$type = '';
$size = 0;
if (array_key_exists($symbField, $fieldMap)) {
if (array_key_exists('type', $fieldMap[$symbField])) {
$type = $fieldMap[$symbField]["type"];
}
if (array_key_exists('size', $fieldMap[$symbField])) {
$size = $fieldMap[$symbField]["size"];
}
}
switch ($type) {
case "numeric":
if (is_numeric($valueStr)) {
$sqlValues .= "," . $valueStr;
} elseif (is_numeric(str_replace(',', "", $valueStr))) {
$sqlValues .= "," . str_replace(',', "", $valueStr);
} else {
$sqlValues .= ",NULL";
}
break;
case "decimal":
if (strpos($valueStr, ',')) {
$sqlValues = str_replace(',', '', $valueStr);
}
if ($valueStr && $size && strpos($size, ',') !== false) {
$tok = explode(',', $size);
$m = $tok[0];
$d = $tok[1];
if ($m && $d) {
$dec = substr($valueStr, strpos($valueStr, '.'));
if (strlen($dec) > $d) {
$valueStr = round($valueStr, $d);
}
$rawLen = strlen(str_replace(array('-', '.'), '', $valueStr));
if ($rawLen > $m) {
if (strpos($valueStr, '.') !== false) {
$decLen = strlen(substr($valueStr, strpos($valueStr, '.')));
if ($decLen < $rawLen - $m) {
$valueStr = '';
} else {
$valueStr = round($valueStr, $decLen - ($rawLen - $m));
}
} else {
$valueStr = '';
}
}
}
}
if (is_numeric($valueStr)) {
$sqlValues .= "," . $valueStr;
} else {
$sqlValues .= ",NULL";
}
break;
case "date":
$dateStr = OccurrenceUtilities::formatDate($valueStr);
if ($dateStr) {
$sqlValues .= ',"' . $dateStr . '"';
} else {
$sqlValues .= ",NULL";
}
break;
default:
//string
if ($size && strlen($valueStr) > $size) {
$valueStr = substr($valueStr, 0, $size);
}
if (substr($valueStr, -1) == "\\") {
$valueStr = rtrim($valueStr, "\\");
}
if ($valueStr) {
$sqlValues .= ',"' . $valueStr . '"';
} else {
$sqlValues .= ",NULL";
}
}
}
}
return array('fieldstr' => $sqlFields, 'valuestr' => $sqlValues);
}
public function uploadCsvList($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 $successCnt;
}
public static function occurrenceArrayCleaning($recMap)
{
//Trim all field values
foreach ($recMap as $k => $v) {
$recMap[$k] = trim($v);
}
//Date cleaning
if (isset($recMap['eventdate']) && $recMap['eventdate']) {
if (is_numeric($recMap['eventdate'])) {
if ($recMap['eventdate'] > 2100 && $recMap['eventdate'] < 45000) {
//Date field was converted to Excel's numeric format (number of days since 01/01/1900)
$recMap['eventdate'] = date('Y-m-d', mktime(0, 0, 0, 1, $recMap['eventdate'] - 1, 1900));
} elseif ($recMap['eventdate'] > 2200000 && $recMap['eventdate'] < 2500000) {
//Date is in the Gregorian format
$dArr = explode('/', jdtogregorian($recMap['eventdate']));
$recMap['eventdate'] = $dArr[2] . '-' . $dArr[0] . '-' . $dArr[1];
} elseif ($recMap['eventdate'] > 19000000) {
//Format: 20120101 = 2012-01-01
$recMap['eventdate'] = substr($recMap['eventdate'], 0, 4) . '-' . substr($recMap['eventdate'], 4, 2) . '-' . substr($recMap['eventdate'], 6, 2);
}
} else {
//Make sure event date is a valid format or drop into verbatimEventDate
$dateStr = OccurrenceUtilities::formatDate($recMap['eventdate']);
if ($dateStr) {
if ($recMap['eventdate'] != $dateStr && (!array_key_exists('verbatimeventdate', $recMap) || !$recMap['verbatimeventdate'])) {
$recMap['verbatimeventdate'] = $recMap['eventdate'];
}
$recMap['eventdate'] = $dateStr;
} else {
if (!array_key_exists('verbatimeventdate', $recMap) || !$recMap['verbatimeventdate']) {
$recMap['verbatimeventdate'] = $recMap['eventdate'];
}
unset($recMap['eventdate']);
}
}
}
if (array_key_exists('latestdatecollected', $recMap) && $recMap['latestdatecollected'] && is_numeric($recMap['latestdatecollected'])) {
if ($recMap['latestdatecollected'] > 2100 && $recMap['latestdatecollected'] < 45000) {
//Date field was converted to Excel's numeric format (number of days since 01/01/1900)
$recMap['latestdatecollected'] = date('Y-m-d', mktime(0, 0, 0, 1, $recMap['latestdatecollected'] - 1, 1900));
} elseif ($recMap['latestdatecollected'] > 2200000 && $recMap['latestdatecollected'] < 2500000) {
$dArr = explode('/', jdtogregorian($recMap['latestdatecollected']));
$recMap['latestdatecollected'] = $dArr[2] . '-' . $dArr[0] . '-' . $dArr[1];
} elseif ($recMap['latestdatecollected'] > 19000000) {
$recMap['latestdatecollected'] = substr($recMap['latestdatecollected'], 0, 4) . '-' . substr($recMap['latestdatecollected'], 4, 2) . '-' . substr($recMap['latestdatecollected'], 6, 2);
}
}
if (array_key_exists('verbatimeventdate', $recMap) && $recMap['verbatimeventdate'] && is_numeric($recMap['verbatimeventdate']) && $recMap['verbatimeventdate'] > 2100 && $recMap['verbatimeventdate'] < 45000) {
//Date field was converted to Excel's numeric format (number of days since 01/01/1900)
$recMap['verbatimeventdate'] = date('Y-m-d', mktime(0, 0, 0, 1, $recMap['verbatimeventdate'] - 1, 1900));
}
if (array_key_exists('dateidentified', $recMap) && $recMap['dateidentified'] && is_numeric($recMap['dateidentified']) && $recMap['dateidentified'] > 2100 && $recMap['dateidentified'] < 45000) {
//Date field was converted to Excel's numeric format (number of days since 01/01/1900)
$recMap['dateidentified'] = date('Y-m-d', mktime(0, 0, 0, 1, $recMap['dateidentified'] - 1, 1900));
}
//If month, day, or year are text, avoid SQL error by converting to numeric value
if (array_key_exists('year', $recMap) || array_key_exists('month', $recMap) || array_key_exists('day', $recMap)) {
$y = array_key_exists('year', $recMap) ? $recMap['year'] : '00';
$m = array_key_exists('month', $recMap) ? $recMap['month'] : '00';
$d = array_key_exists('day', $recMap) ? $recMap['day'] : '00';
$vDate = trim($y . '-' . $m . '-' . $d, '- ');
if (isset($recMap['day']) && !is_numeric($recMap['day'])) {
if (!array_key_exists('verbatimeventdate', $recMap) || !$recMap['verbatimeventdate']) {
$recMap['verbatimeventdate'] = $vDate;
}
unset($recMap['day']);
$d = '00';
}
if (isset($recMap['year']) && !is_numeric($recMap['year'])) {
if (!array_key_exists('verbatimeventdate', $recMap) || !$recMap['verbatimeventdate']) {
$recMap['verbatimeventdate'] = $vDate;
}
unset($recMap['year']);
}
if (isset($recMap['month']) && $recMap['month'] && !is_numeric($recMap['month'])) {
if (strlen($recMap['month']) > 2) {
$monAbbr = strtolower(substr($recMap['month'], 0, 3));
if (array_key_exists($monAbbr, OccurrenceUtilities::$monthNames)) {
$recMap['month'] = OccurrenceUtilities::$monthNames[$monAbbr];
$recMap['eventdate'] = OccurrenceUtilities::formatDate(trim($y . '-' . $recMap['month'] . '-' . ($d ? $d : '00'), '- '));
} else {
if (!array_key_exists('verbatimeventdate', $recMap) || !$recMap['verbatimeventdate']) {
$recMap['verbatimeventdate'] = $vDate;
}
unset($recMap['month']);
}
} else {
if (!array_key_exists('verbatimeventdate', $recMap) || !$recMap['verbatimeventdate']) {
$recMap['verbatimeventdate'] = $vDate;
}
unset($recMap['month']);
}
}
if ($vDate && (!array_key_exists('eventdate', $recMap) || !$recMap['eventdate'])) {
$recMap['eventdate'] = OccurrenceUtilities::formatDate($vDate);
}
}
//eventDate NULL && verbatimEventDate NOT NULL && year NOT NULL
if ((!array_key_exists('eventdate', $recMap) || !$recMap['eventdate']) && array_key_exists('verbatimeventdate', $recMap) && $recMap['verbatimeventdate'] && (!array_key_exists('year', $recMap) || !$recMap['year'])) {
$dateStr = OccurrenceUtilities::formatDate($recMap['verbatimeventdate']);
if ($dateStr) {
$recMap['eventdate'] = $dateStr;
}
}
if (isset($recMap['recordnumberprefix']) && $recMap['recordnumberprefix'] || isset($recMap['recordnumbersuffix']) && $recMap['recordnumbersuffix']) {
$recNumber = $recMap['recordnumber'];
if (isset($recMap['recordnumberprefix']) && $recMap['recordnumberprefix']) {
$recNumber = $recMap['recordnumberprefix'] . '-' . $recNumber;
}
if (isset($recMap['recordnumbersuffix']) && $recMap['recordnumbersuffix']) {
if (is_numeric($recMap['recordnumbersuffix']) && $recMap['recordnumber']) {
$recNumber .= '-';
}
$recNumber .= $recMap['recordnumbersuffix'];
}
$recMap['recordnumber'] = $recNumber;
}
//If lat or long are not numeric, try to make them so
if (array_key_exists('decimallatitude', $recMap) || array_key_exists('decimallongitude', $recMap)) {
$latValue = array_key_exists('decimallatitude', $recMap) ? $recMap['decimallatitude'] : '';
$lngValue = array_key_exists('decimallongitude', $recMap) ? $recMap['decimallongitude'] : '';
if ($latValue && !is_numeric($latValue) || $lngValue && !is_numeric($lngValue)) {
$llArr = OccurrenceUtilities::parseVerbatimCoordinates(trim($latValue . ' ' . $lngValue), 'LL');
if (array_key_exists('lat', $llArr) && array_key_exists('lng', $llArr)) {
$recMap['decimallatitude'] = $llArr['lat'];
$recMap['decimallongitude'] = $llArr['lng'];
} else {
unset($recMap['decimallatitude']);
unset($recMap['decimallongitude']);
}
$vcStr = '';
if (array_key_exists('verbatimcoordinates', $recMap) && $recMap['verbatimcoordinates']) {
$vcStr .= $recMap['verbatimcoordinates'] . '; ';
}
$vcStr .= $latValue . ' ' . $lngValue;
if (trim($vcStr)) {
$recMap['verbatimcoordinates'] = trim($vcStr);
}
}
}
//Transfer verbatim Lat/Long to verbatim coords
if (isset($recMap['verbatimlatitude']) || isset($recMap['verbatimlongitude'])) {
if (isset($recMap['verbatimlatitude']) && isset($recMap['verbatimlongitude'])) {
if (!isset($recMap['decimallatitude']) || !isset($recMap['decimallongitude'])) {
if (is_numeric($recMap['verbatimlatitude']) && is_numeric($recMap['verbatimlongitude'])) {
if ($recMap['verbatimlatitude'] > -90 && $recMap['verbatimlatitude'] < 90 && $recMap['verbatimlongitude'] > -180 && $recMap['verbatimlongitude'] < 180) {
$recMap['decimallatitude'] = $recMap['verbatimlatitude'];
$recMap['decimallongitude'] = $recMap['verbatimlongitude'];
}
} else {
//Attempt to extract decimal lat/long
$coordArr = OccurrenceUtilities::parseVerbatimCoordinates($recMap['verbatimlatitude'] . ' ' . $recMap['verbatimlongitude'], 'LL');
if ($coordArr) {
if (array_key_exists('lat', $coordArr)) {
$recMap['decimallatitude'] = $coordArr['lat'];
}
if (array_key_exists('lng', $coordArr)) {
$recMap['decimallongitude'] = $coordArr['lng'];
}
}
}
}
}
//Place into verbatim coord field
$vCoord = isset($recMap['verbatimcoordinates']) ? $recMap['verbatimcoordinates'] : '';
if ($vCoord) {
$vCoord .= '; ';
}
if (stripos($vCoord, $recMap['verbatimlatitude']) === false && stripos($vCoord, $recMap['verbatimlongitude']) === false) {
$recMap['verbatimcoordinates'] = $vCoord . $recMap['verbatimlatitude'] . ', ' . $recMap['verbatimlongitude'];
}
}
//Transfer DMS to verbatim coords
if (isset($recMap['latdeg']) && $recMap['latdeg'] && isset($recMap['lngdeg']) && $recMap['lngdeg']) {
//Attempt to create decimal lat/long
if (is_numeric($recMap['latdeg']) && is_numeric($recMap['lngdeg']) && (!isset($recMap['decimallatitude']) || !isset($recMap['decimallongitude']))) {
$latDec = $recMap['latdeg'];
if (isset($recMap['latmin']) && $recMap['latmin'] && is_numeric($recMap['latmin'])) {
$latDec += $recMap['latmin'] / 60;
}
if (isset($recMap['latsec']) && $recMap['latsec'] && is_numeric($recMap['latsec'])) {
$latDec += $recMap['latsec'] / 3600;
}
if (stripos($recMap['latns'], 's') === 0 && $latDec > 0) {
$latDec *= -1;
}
$lngDec = $recMap['lngdeg'];
if (isset($recMap['lngmin']) && $recMap['lngmin'] && is_numeric($recMap['lngmin'])) {
$lngDec += $recMap['lngmin'] / 60;
}
if (isset($recMap['lngsec']) && $recMap['lngsec'] && is_numeric($recMap['lngsec'])) {
$lngDec += $recMap['lngsec'] / 3600;
}
if (stripos($recMap['lngew'], 'e') === 0) {
$lngDec *= -1;
}
$recMap['decimallatitude'] = round($latDec, 6);
$recMap['decimallongitude'] = round($lngDec, 6);
}
//Place into verbatim coord field
$vCoord = isset($recMap['verbatimcoordinates']) ? $recMap['verbatimcoordinates'] : '';
if ($vCoord) {
$vCoord .= '; ';
}
$vCoord .= $recMap['latdeg'] . '° ';
if (isset($recMap['latmin']) && $recMap['latmin']) {
$vCoord .= $recMap['latmin'] . 'm ';
}
if (isset($recMap['latsec']) && $recMap['latsec']) {
$vCoord .= $recMap['latsec'] . 's ';
}
if (isset($recMap['latns'])) {
$vCoord .= $recMap['latns'] . '; ';
}
$vCoord .= $recMap['lngdeg'] . '° ';
if (isset($recMap['lngmin']) && $recMap['lngmin']) {
$vCoord .= $recMap['lngmin'] . 'm ';
}
if (isset($recMap['lngsec']) && $recMap['lngsec']) {
$vCoord .= $recMap['lngsec'] . 's ';
}
if (isset($recMap['lngew'])) {
$vCoord .= $recMap['lngew'];
}
$recMap['verbatimcoordinates'] = $vCoord;
}
/*
if(array_key_exists('verbatimcoordinates',$recMap) && $recMap['verbatimcoordinates'] && (!isset($recMap['decimallatitude']) || !isset($recMap['decimallongitude']))){
$coordArr = OccurrenceUtilities::parseVerbatimCoordinates($recMap['verbatimcoordinates']);
if($coordArr){
if(array_key_exists('lat',$coordArr)) $recMap['decimallatitude'] = $coordArr['lat'];
if(array_key_exists('lng',$coordArr)) $recMap['decimallongitude'] = $coordArr['lng'];
}
}
*/
//Convert UTM to Lat/Long
if (array_key_exists('utmnorthing', $recMap) && $recMap['utmnorthing'] || array_key_exists('utmeasting', $recMap) && $recMap['utmeasting']) {
$no = array_key_exists('utmnorthing', $recMap) ? $recMap['utmnorthing'] : '';
$ea = array_key_exists('utmeasting', $recMap) ? $recMap['utmeasting'] : '';
$zo = array_key_exists('utmzoning', $recMap) ? $recMap['utmzoning'] : '';
$da = array_key_exists('geodeticdatum', $recMap) ? $recMap['geodeticdatum'] : '';
if (!isset($recMap['decimallatitude']) || !isset($recMap['decimallongitude'])) {
if ($no && $ea && $zo) {
//Northing, easting, and zoning all had values
$llArr = OccurrenceUtilities::convertUtmToLL($ea, $no, $zo, $da);
if (isset($llArr['lat'])) {
$recMap['decimallatitude'] = $llArr['lat'];
}
if (isset($llArr['lng'])) {
$recMap['decimallongitude'] = $llArr['lng'];
}
} else {
//UTM was a single field which was placed in UTM northing field within uploadspectemp table
$coordArr = OccurrenceUtilities::parseVerbatimCoordinates(trim($zo . ' ' . $ea . ' ' . $no), 'UTM');
if ($coordArr) {
if (array_key_exists('lat', $coordArr)) {
$recMap['decimallatitude'] = $coordArr['lat'];
}
if (array_key_exists('lng', $coordArr)) {
$recMap['decimallongitude'] = $coordArr['lng'];
}
}
}
}
$vCoord = isset($recMap['verbatimcoordinates']) ? $recMap['verbatimcoordinates'] : '';
if (!($no && strpos($vCoord, $no))) {
$recMap['verbatimcoordinates'] = ($vCoord ? $vCoord . '; ' : '') . $zo . ' ' . $ea . 'E ' . $no . 'N';
}
}
//Transfer TRS to verbatim coords
if (isset($recMap['trstownship']) && $recMap['trstownship'] && isset($recMap['trsrange']) && $recMap['trsrange']) {
$vCoord = isset($recMap['verbatimcoordinates']) ? $recMap['verbatimcoordinates'] : '';
if ($vCoord) {
$vCoord .= '; ';
}
$vCoord .= (stripos($recMap['trstownship'], 't') === false ? 'T' : '') . $recMap['trstownship'] . ' ';
$vCoord .= (stripos($recMap['trsrange'], 'r') === false ? 'R' : '') . $recMap['trsrange'] . ' ';
if (isset($recMap['trssection'])) {
$vCoord .= (stripos($recMap['trssection'], 's') === false ? 'sec' : '') . $recMap['trssection'] . ' ';
}
if (isset($recMap['trssectiondetails'])) {
$vCoord .= $recMap['trssectiondetails'];
}
$recMap['verbatimcoordinates'] = trim($vCoord);
}
//Check to see if evelation are valid numeric values
if (isset($recMap['minimumelevationinmeters']) && $recMap['minimumelevationinmeters'] && !is_numeric($recMap['minimumelevationinmeters']) || isset($recMap['maximumelevationinmeters']) && $recMap['maximumelevationinmeters'] && !is_numeric($recMap['maximumelevationinmeters'])) {
$vStr = isset($recMap['verbatimelevation']) ? $recMap['verbatimelevation'] : '';
if (isset($recMap['minimumelevationinmeters']) && $recMap['minimumelevationinmeters']) {
$vStr .= ($vStr ? '; ' : '') . $recMap['minimumelevationinmeters'];
}
if (isset($recMap['maximumelevationinmeters']) && $recMap['maximumelevationinmeters']) {
$vStr .= '-' . $recMap['maximumelevationinmeters'];
}
$recMap['verbatimelevation'] = $vStr;
$recMap['minimumelevationinmeters'] = '';
$recMap['maximumelevationinmeters'] = '';
}
//Verbatim elevation
if (array_key_exists('verbatimelevation', $recMap) && $recMap['verbatimelevation'] && (!array_key_exists('minimumelevationinmeters', $recMap) || !$recMap['minimumelevationinmeters'])) {
$eArr = OccurrenceUtilities::parseVerbatimElevation($recMap['verbatimelevation']);
if ($eArr) {
if (array_key_exists('minelev', $eArr)) {
$recMap['minimumelevationinmeters'] = $eArr['minelev'];
if (array_key_exists('maxelev', $eArr)) {
$recMap['maximumelevationinmeters'] = $eArr['maxelev'];
}
}
}
}
//Deal with elevation when in two fields (number and units)
if (isset($recMap['elevationnumber']) && $recMap['elevationnumber']) {
$elevStr = $recMap['elevationnumber'] . $recMap['elevationunits'];
//Try to extract meters
$eArr = OccurrenceUtilities::parseVerbatimElevation($elevStr);
if ($eArr) {
if (array_key_exists('minelev', $eArr)) {
$recMap['minimumelevationinmeters'] = $eArr['minelev'];
if (array_key_exists('maxelev', $eArr)) {
$recMap['maximumelevationinmeters'] = $eArr['maxelev'];
}
}
}
if (!$eArr || !stripos($elevStr, 'm')) {
$vElev = isset($recMap['verbatimelevation']) ? $recMap['verbatimelevation'] : '';
if ($vElev) {
$vElev .= '; ';
}
$recMap['verbatimelevation'] = $vElev . $elevStr;
}
}
//Concatenate collectorfamilyname and collectorinitials into recordedby
if (isset($recMap['collectorfamilyname']) && $recMap['collectorfamilyname'] && (!isset($recMap['recordedby']) || !$recMap['recordedby'])) {
$recordedBy = $recMap['collectorfamilyname'];
if (isset($recMap['collectorinitials']) && $recMap['collectorinitials']) {
$recordedBy .= ', ' . $recMap['collectorinitials'];
}
$recMap['recordedby'] = $recordedBy;
//Need to add code that maps to collector table
}
if (array_key_exists("specificepithet", $recMap)) {
if ($recMap["specificepithet"] == 'sp.' || $recMap["specificepithet"] == 'sp') {
$recMap["specificepithet"] = '';
}
}
if (array_key_exists("taxonrank", $recMap)) {
$tr = strtolower($recMap["taxonrank"]);
if ($tr == 'species' || !$recMap["specificepithet"]) {
$recMap["taxonrank"] = '';
}
if ($tr == 'subspecies') {
$recMap["taxonrank"] = 'subsp.';
}
if ($tr == 'variety') {
$recMap["taxonrank"] = 'var.';
}
if ($tr == 'forma') {
$recMap["taxonrank"] = 'f.';
}
}
//Populate sciname if null
if (array_key_exists('sciname', $recMap) && $recMap['sciname']) {
if (substr($recMap['sciname'], -4) == ' sp.') {
$recMap['sciname'] = substr($recMap['sciname'], 0, -4);
}
if (substr($recMap['sciname'], -3) == ' sp') {
$recMap['sciname'] = substr($recMap['sciname'], 0, -3);
}
$recMap['sciname'] = str_replace(array(' ssp. ', ' ssp '), ' subsp. ', $recMap['sciname']);
$recMap['sciname'] = str_replace(' var ', ' var. ', $recMap['sciname']);
$pattern = '/\\b(cf\\.|cf|aff\\.|aff)\\s{1}/';
if (preg_match($pattern, $recMap['sciname'], $m)) {
$recMap['identificationqualifier'] = $m[1];
$recMap['sciname'] = preg_replace($pattern, '', $recMap['sciname']);
}
} else {
if (array_key_exists("genus", $recMap)) {
//Build sciname from individual units supplied by source
$sciName = $recMap["genus"];
if (array_key_exists("specificepithet", $recMap)) {
$sciName .= " " . $recMap["specificepithet"];
}
if (array_key_exists("taxonrank", $recMap)) {
$sciName .= " " . $recMap["taxonrank"];
}
if (array_key_exists("infraspecificepithet", $recMap)) {
$sciName .= " " . $recMap["infraspecificepithet"];
}
$recMap['sciname'] = trim($sciName);
} elseif (array_key_exists('scientificname', $recMap)) {
//Clean and parse scientific name
$parsedArr = OccurrenceUtilities::parseScientificName($recMap['scientificname']);
$scinameStr = '';
if (array_key_exists('unitname1', $parsedArr)) {
$scinameStr = $parsedArr['unitname1'];
if (!array_key_exists('genus', $recMap) || $recMap['genus']) {
$recMap['genus'] = $parsedArr['unitname1'];
}
}
if (array_key_exists('unitname2', $parsedArr)) {
$scinameStr .= ' ' . $parsedArr['unitname2'];
if (!array_key_exists('specificepithet', $recMap) || !$recMap['specificepithet']) {
$recMap['specificepithet'] = $parsedArr['unitname2'];
}
}
if (array_key_exists('unitind3', $parsedArr)) {
$scinameStr .= ' ' . $parsedArr['unitind3'];
if (!array_key_exists('taxonrank', $recMap) || !$recMap['taxonrank']) {
$recMap['taxonrank'] = $parsedArr['unitind3'];
}
}
if (array_key_exists('unitname3', $parsedArr)) {
$scinameStr .= ' ' . $parsedArr['unitname3'];
if (!array_key_exists('infraspecificepithet', $recMap) || !$recMap['infraspecificepithet']) {
$recMap['infraspecificepithet'] = $parsedArr['unitname3'];
}
}
if (array_key_exists('author', $parsedArr)) {
if (!array_key_exists('scientificnameauthorship', $recMap) || !$recMap['scientificnameauthorship']) {
$recMap['scientificnameauthorship'] = $parsedArr['author'];
}
}
$recMap['sciname'] = trim($scinameStr);
}
}
return $recMap;
}
