public static function parseScientificName($inStr)
{
return OccurrenceUtilities::parseScientificName($inStr);
}
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 $taxonArr;
}
protected function loadIdentificationRecord($recMap)
{
if ($recMap) {
//coreId should go into dbpk
if (isset($recMap['coreid']) && !isset($recMap['dbpk'])) {
$recMap['dbpk'] = $recMap['coreid'];
unset($recMap['coreid']);
}
//Import record only if required fields have data (coreId and a scientificName)
if (isset($recMap['dbpk']) && $recMap['dbpk'] && (isset($recMap['sciname']) || isset($recMap['genus']))) {
//Do some cleaning
//Populate sciname if null
if (!array_key_exists('sciname', $recMap) || !$recMap['sciname']) {
if (array_key_exists("genus", $recMap)) {
//Build sciname from individual units supplied by source
$sciName = $recMap["genus"];
if (array_key_exists("specificepithet", $recMap) && $recMap["specificepithet"]) {
$sciName .= " " . $recMap["specificepithet"];
}
if (array_key_exists("taxonrank", $recMap) && $recMap["taxonrank"]) {
$sciName .= " " . $recMap["taxonrank"];
}
if (array_key_exists("infraspecificepithet", $recMap) && $recMap["infraspecificepithet"]) {
$sciName .= " " . $recMap["infraspecificepithet"];
}
$recMap['sciname'] = trim($sciName);
}
}
//Try to get author, if it's not there
if (!array_key_exists('scientificnameauthorship', $recMap) || !$recMap['scientificnameauthorship']) {
//Parse scientific name to see if it has author imbedded
$parsedArr = OccurrenceUtilities::parseScientificName($recMap['sciname']);
if (array_key_exists('author', $parsedArr)) {
$recMap['scientificnameauthorship'] = $parsedArr['author'];
//Load sciname from parsedArr since if appears that author was embedded
$recMap['sciname'] = trim($parsedArr['unitname1'] . ' ' . $parsedArr['unitname2'] . ' ' . $parsedArr['unitind3'] . ' ' . $parsedArr['unitname3']);
}
}
$sqlFragments = $this->getSqlFragments($recMap, $this->identFieldMap);
if ($recMap['identifiedby'] || $recMap['dateidentified']) {
if (!$recMap['identifiedby']) {
$recMap['identifiedby'] = 'not specified';
}
if (!$recMap['dateidentified']) {
$recMap['dateidentified'] = 'not specified';
}
$sql = 'INSERT INTO uploaddetermtemp(collid' . $sqlFragments['fieldstr'] . ') ' . 'VALUES(' . $this->collId . $sqlFragments['valuestr'] . ')';
//echo "<div>SQL: ".$sql."</div>"; exit;
if ($this->conn->query($sql)) {
$this->identTransferCount++;
if ($this->identTransferCount % 1000 == 0) {
$this->outputMsg('<li style="margin-left:10px;">Count: ' . $this->identTransferCount . '</li>');
}
ob_flush();
flush();
} else {
$this->outputMsg("<li>FAILED adding indetification history record #" . $this->identTransferCount . "</li>");
$this->outputMsg("<li style='margin-left:10px;'>Error: " . $this->conn->error . "</li>");
$this->outputMsg("<li style='margin:0px 0px 10px 10px;'>SQL: {$sql}</li>");
}
}
}
}
}
public function parseSciName($scientificName, $rankId = 0)
{
//Converts scinetific name with author embedded into separate fields
$retArr = array();
$retArr = OccurrenceUtilities::parseScientificName($scientificName, $rankId);
return $retArr;
}
public static function occurrenceArrayCleaning($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;
}
