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Merge pull request #49 from BioKIC/master
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Hotfix 2024 05 22 (BioKIC#1374)
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@egbot
egbot authored Jun 12, 2024
2 parents 36036a5 + f5defa0 commit f1143eb
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Showing 4 changed files with 72 additions and 75 deletions.
18 changes: 10 additions & 8 deletions classes/ChecklistVoucherManager.php
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Original file line number Diff line number Diff line change
Expand Up @@ -58,13 +58,15 @@ public function renameTaxon($targetTid, $rareLocality = ''){
$statusStr = false;
if(is_numeric($targetTid)){
$clTaxaID = $this->getClTaxaID($this->tid);
$sql = 'UPDATE fmchklsttaxalink SET TID = '.$targetTid.' WHERE (clTaxaID = '.$clTaxaID.')';
//First transfer taxa that
$sql = 'UPDATE IGNORE fmchklsttaxalink SET TID = '.$targetTid.' WHERE (clTaxaID = '.$clTaxaID.')';
if($this->conn->query($sql)){
$this->tid = $targetTid;
$this->taxonName = '';
$statusStr = true;
}
else{
if(!$this->conn->affected_rows){
//Transferred failed due to target name already exiting within checklist
$sqlTarget = 'SELECT clTaxaID, Habitat, Abundance, Notes, internalnotes, source, Nativity FROM fmchklsttaxalink WHERE (tid = '.$targetTid.') AND (clid = '.$this->clid.')';
$rsTarget = $this->conn->query($sqlTarget);
if($row = $rsTarget->fetch_object()){
Expand Down Expand Up @@ -93,12 +95,12 @@ public function renameTaxon($targetTid, $rareLocality = ''){
$sqlSourceCl = 'SELECT Habitat, Abundance, Notes, internalnotes, source, Nativity FROM fmchklsttaxalink WHERE (clTaxaID = '.$clTaxaID.')';
$rsSourceCl = $this->conn->query($sqlSourceCl);
if($row = $rsSourceCl->fetch_object()){
$habitatSource = $this->cleanInStr($row->Habitat);
$abundSource = $this->cleanInStr($row->Abundance);
$notesSource = $this->cleanInStr($row->Notes);
$internalNotesSource = $this->cleanInStr($row->internalnotes);
$sourceSource = $this->cleanInStr($row->source);
$nativeSource = $this->cleanInStr($row->Nativity);
$habitatSource = $row->Habitat;
$abundSource = $row->Abundance;
$notesSource = $row->Notes;
$internalNotesSource = $row->internalnotes;
$sourceSource = $row->source;
$nativeSource = $row->Nativity;
}
$rsSourceCl->free();
//Transfer source chklsttaxalink data to target record
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6 changes: 3 additions & 3 deletions classes/ImageLocalProcessor.php
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Original file line number Diff line number Diff line change
Expand Up @@ -998,17 +998,17 @@ private function databaseImage($imgArr){
}
if($this->conn->query('DELETE FROM images WHERE imgid = '.$r->imgid)){
//Remove images
$urlPath = current(parse_url($r->url, PHP_URL_PATH));
$urlPath = parse_url($r->url, PHP_URL_PATH);
if($urlPath && strpos($urlPath, $this->imgUrlBase) === 0){
$wFile = str_replace($this->imgUrlBase,$this->targetPathBase,$urlPath);
if(file_exists($wFile) && is_writable($wFile)) unlink($wFile);
}
$urlTnPath = current(parse_url($r->thumbnailUrl, PHP_URL_PATH));
$urlTnPath = parse_url($r->thumbnailUrl, PHP_URL_PATH);
if($urlTnPath && strpos($urlTnPath, $this->imgUrlBase) === 0){
$wFile = str_replace($this->imgUrlBase,$this->targetPathBase,$urlTnPath);
if(file_exists($wFile) && is_writable($wFile)) unlink($wFile);
}
$urlLgPath = current(parse_url($r->originalUrl, PHP_URL_PATH));
$urlLgPath = parse_url($r->originalUrl, PHP_URL_PATH);
if($urlLgPath && strpos($urlLgPath, $this->imgUrlBase) === 0){
$wFile = str_replace($this->imgUrlBase,$this->targetPathBase,$urlLgPath);
if(file_exists($wFile) && is_writable($wFile)) unlink($wFile);
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121 changes: 58 additions & 63 deletions classes/OccurrenceMapManager.php
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Original file line number Diff line number Diff line change
Expand Up @@ -63,31 +63,29 @@ public function getCoordinateMap($start, $limit){
if(is_numeric($start) && $limit){
$sql .= "LIMIT ".$start.",".$limit;
}
//echo "<div>SQL: ".$sql."</div>"; exit;
//echo '//SQL: ' . $sql;
$result = $this->conn->query($sql);
$color = 'e69e67';
$occidArr = array();
while($row = $result->fetch_object()){
if(($row->DecimalLongitude <= 180 && $row->DecimalLongitude >= -180) && ($row->DecimalLatitude <= 90 && $row->DecimalLatitude >= -90)){
$occidArr[] = $row->occid;
$collName = $row->CollectionName;
$tidInterpreted = $this->htmlEntities($row->tidinterpreted);
$latLngStr = $row->DecimalLatitude.",".$row->DecimalLongitude;
$coordArr[$collName][$row->occid]["llStr"] = $latLngStr;
$coordArr[$collName][$row->occid]["collid"] = $this->htmlEntities($row->collid);
//$tidcode = strtolower(str_replace(" ", "",$tidInterpreted.$row->sciname));
//$tidcode = preg_replace( "/[^A-Za-z0-9 ]/","",$tidcode);
//$coordArr[$collName][$occId]["ns"] = $this->htmlEntities($tidcode);
$coordArr[$collName][$row->occid]["tid"] = $tidInterpreted;
$coordArr[$collName][$row->occid]["fam"] = ($row->family?strtoupper($row->family):'undefined');
$coordArr[$collName][$row->occid]["sn"] = $row->sciname;
$coordArr[$collName][$row->occid]["id"] = $this->htmlEntities($row->identifier);
//$coordArr[$collName][$occId]["icode"] = $this->htmlEntities($row->institutioncode);
//$coordArr[$collName][$occId]["ccode"] = $this->htmlEntities($row->collectioncode);
//$coordArr[$collName][$occId]["cn"] = $this->htmlEntities($row->catalognumber);
//$coordArr[$collName][$occId]["ocn"] = $this->htmlEntities($row->othercatalognumbers);
$coordArr[$collName]["c"] = $color;
}
$occidArr[] = $row->occid;
$collName = $row->CollectionName;
$tidInterpreted = $this->htmlEntities($row->tidinterpreted);
$latLngStr = $row->DecimalLatitude.",".$row->DecimalLongitude;
$coordArr[$collName][$row->occid]["llStr"] = $latLngStr;
$coordArr[$collName][$row->occid]["collid"] = $this->htmlEntities($row->collid);
//$tidcode = strtolower(str_replace(" ", "",$tidInterpreted.$row->sciname));
//$tidcode = preg_replace( "/[^A-Za-z0-9 ]/","",$tidcode);
//$coordArr[$collName][$occId]["ns"] = $this->htmlEntities($tidcode);
$coordArr[$collName][$row->occid]["tid"] = $tidInterpreted;
$coordArr[$collName][$row->occid]["fam"] = ($row->family?strtoupper($row->family):'undefined');
$coordArr[$collName][$row->occid]["sn"] = $row->sciname;
$coordArr[$collName][$row->occid]["id"] = $this->htmlEntities($row->identifier);
//$coordArr[$collName][$occId]["icode"] = $this->htmlEntities($row->institutioncode);
//$coordArr[$collName][$occId]["ccode"] = $this->htmlEntities($row->collectioncode);
//$coordArr[$collName][$occId]["cn"] = $this->htmlEntities($row->catalognumber);
//$coordArr[$collName][$occId]["ocn"] = $this->htmlEntities($row->othercatalognumbers);
$coordArr[$collName]["c"] = $color;
}
$statsManager->recordAccessEventByArr($occidArr, 'map');
if(array_key_exists('undefined',$coordArr)){
Expand All @@ -105,44 +103,41 @@ public function getMappingData($recLimit, $extraFieldArr = null){
$coordArr = array();
if($this->sqlWhere){
$statsManager = new OccurrenceAccessStats();
$sql = 'SELECT DISTINCT o.occid, CONCAT_WS(" ",o.recordedby,IFNULL(o.recordnumber,o.eventdate)) AS collector, o.sciname, o.tidinterpreted, '.
'o.decimallatitude, o.decimallongitude, o.catalognumber, o.othercatalognumbers, c.institutioncode, c.collectioncode, c.colltype ';
$sql = 'SELECT DISTINCT o.occid, CONCAT_WS(" ",o.recordedby,IFNULL(o.recordnumber,o.eventdate)) AS collector, o.sciname, o.tidinterpreted,
o.decimallatitude, o.decimallongitude, o.catalognumber, o.othercatalognumbers, c.institutioncode, c.collectioncode, c.colltype ';
if(isset($extraFieldArr) && is_array($extraFieldArr)){
foreach($extraFieldArr as $fieldName){
$sql .= ", o.".$fieldName." ";
$sql .= ', o.' . $fieldName . ' ';
}
}
$sql .= 'FROM omoccurrences o INNER JOIN omcollections c ON o.collid = c.collid ';
$sql .= $this->getTableJoins($this->sqlWhere);
$sql .= $this->sqlWhere;
$sql .= 'AND (o.decimallatitude BETWEEN -90 AND 90) AND (o.decimallongitude BETWEEN -180 AND 180) ';
if(is_numeric($start) && $recLimit && is_numeric($recLimit)) $sql .= "LIMIT ".$start.",".$recLimit;
//echo "<div>SQL: ".$sql."</div>";
//echo '<div>SQL: ' . $sql . '</div>';
$rs = $this->conn->query($sql);
$occidArr = array();
while($r = $rs->fetch_assoc()){
if(($r['decimallongitude'] <= 180 && $r['decimallongitude'] >= -180) && ($r['decimallatitude'] <= 90 && $r['decimallatitude'] >= -90)){
$sciname = $r['sciname'];
if(!$sciname) $sciname = 'undefined';
$coordArr[$sciname][$r['occid']]['instcode'] = $r['institutioncode'];
if($r['collectioncode']) $coordArr[$sciname][$r['occid']]['collcode'] = $r['collectioncode'];
$collType = 'obs';
if(stripos($r['colltype'],'specimen')) $collType = 'spec';
$coordArr[$sciname][$r['occid']]['colltype'] = $collType;
if($r['catalognumber']) $coordArr[$sciname][$r['occid']]['catnum'] = $r['catalognumber'];
if($r['othercatalognumbers']) $coordArr[$sciname][$r['occid']]['ocatnum'] = $r['othercatalognumbers'];
if($r['tidinterpreted']) $coordArr[$sciname]['tid'] = $r['tidinterpreted'];
$coordArr[$sciname][$r['occid']]['collector'] = $r['collector'];
$coordArr[$sciname][$r['occid']]['lat'] = $r['decimallatitude'];
$coordArr[$sciname][$r['occid']]['lng'] = $r['decimallongitude'];
if(isset($extraFieldArr) && is_array($extraFieldArr)){
reset($extraFieldArr);
foreach($extraFieldArr as $fieldName){
if(isset($r[$fieldName])) $coordArr[$sciname][$r['occid']][$fieldName] = $r[$fieldName];
}
$sciname = $r['sciname'];
if(!$sciname) $sciname = 'undefined';
$coordArr[$sciname][$r['occid']]['instcode'] = $r['institutioncode'];
if($r['collectioncode']) $coordArr[$sciname][$r['occid']]['collcode'] = $r['collectioncode'];
$collType = 'obs';
if(stripos($r['colltype'],'specimen')) $collType = 'spec';
$coordArr[$sciname][$r['occid']]['colltype'] = $collType;
if($r['catalognumber']) $coordArr[$sciname][$r['occid']]['catnum'] = $r['catalognumber'];
if($r['othercatalognumbers']) $coordArr[$sciname][$r['occid']]['ocatnum'] = $r['othercatalognumbers'];
if($r['tidinterpreted']) $coordArr[$sciname]['tid'] = $r['tidinterpreted'];
$coordArr[$sciname][$r['occid']]['collector'] = $r['collector'];
$coordArr[$sciname][$r['occid']]['lat'] = $r['decimallatitude'];
$coordArr[$sciname][$r['occid']]['lng'] = $r['decimallongitude'];
if(isset($extraFieldArr) && is_array($extraFieldArr)){
reset($extraFieldArr);
foreach($extraFieldArr as $fieldName){
if(isset($r[$fieldName])) $coordArr[$sciname][$r['occid']][$fieldName] = $r[$fieldName];
}
$occidArr[] = $r['occid'];
}
$occidArr[] = $r['occid'];
}
$rs->free();
$statsManager->recordAccessEventByArr($occidArr, 'map');
Expand Down Expand Up @@ -210,9 +205,9 @@ public function getRecordCnt(){
//SQL where functions
private function setGeoSqlWhere(){
global $USER_RIGHTS;
$sqlWhere = $this->getSqlWhere();
$sqlWhere .= ($sqlWhere?'AND ':'WHERE ').'((o.decimallatitude BETWEEN -90 AND 90) AND (o.decimallongitude BETWEEN -180 AND 180)) ';
if($this->searchTermArr){
$sqlWhere = $this->getSqlWhere();
$sqlWhere .= ($sqlWhere?'AND ':'WHERE ').'(o.DecimalLatitude IS NOT NULL AND o.DecimalLongitude IS NOT NULL) ';
if(array_key_exists('clid',$this->searchTermArr) && $this->searchTermArr['clid']){
if(isset($this->searchTermArr['cltype']) && $this->searchTermArr['cltype'] == 'all'){
$sqlWhere .= "AND (ST_Within(p.point,GeomFromText('".$this->getClFootprintWkt()." '))) ";
Expand All @@ -224,22 +219,22 @@ private function setGeoSqlWhere(){
elseif(array_key_exists("polycoords",$this->searchTermArr)){
$sqlWhere .= "AND (ST_Within(p.point,GeomFromText('".$this->searchTermArr["polycoords"]." '))) ";
}
//Check and exclude records with sensitive species protections
if(array_key_exists('SuperAdmin',$USER_RIGHTS) || array_key_exists('CollAdmin',$USER_RIGHTS) || array_key_exists('RareSppAdmin',$USER_RIGHTS) || array_key_exists('RareSppReadAll',$USER_RIGHTS)){
//Is global rare species reader, thus do nothing to sql and grab all records
}
elseif(isset($USER_RIGHTS['RareSppReader']) || isset($USER_RIGHTS['CollEditor'])){
$securityCollArr = array();
if(isset($USER_RIGHTS['CollEditor'])) $securityCollArr = $USER_RIGHTS['CollEditor'];
if(isset($USER_RIGHTS['RareSppReader'])) $securityCollArr = array_unique(array_merge($securityCollArr, $USER_RIGHTS['RareSppReader']));
$sqlWhere .= ' AND (o.CollId IN ('.implode(',',$securityCollArr).') OR (o.LocalitySecurity = 0 OR o.LocalitySecurity IS NULL)) ';
}
else{
$sqlWhere .= ' AND (o.LocalitySecurity = 0 OR o.LocalitySecurity IS NULL) ';
}
$this->sqlWhere = $sqlWhere;
//echo '<div style="margin-left:10px">sql: '.$this->sqlWhere.'</div>'; exit;
}
//Check and exclude records with sensitive species protections
if(array_key_exists('SuperAdmin',$USER_RIGHTS) || array_key_exists('CollAdmin',$USER_RIGHTS) || array_key_exists('RareSppAdmin',$USER_RIGHTS) || array_key_exists('RareSppReadAll',$USER_RIGHTS)){
//Is global rare species reader, thus do nothing to sql and grab all records
}
elseif(isset($USER_RIGHTS['RareSppReader']) || isset($USER_RIGHTS['CollEditor'])){
$securityCollArr = array();
if(isset($USER_RIGHTS['CollEditor'])) $securityCollArr = $USER_RIGHTS['CollEditor'];
if(isset($USER_RIGHTS['RareSppReader'])) $securityCollArr = array_unique(array_merge($securityCollArr, $USER_RIGHTS['RareSppReader']));
$sqlWhere .= ' AND (o.CollId IN ('.implode(',',$securityCollArr).') OR (o.LocalitySecurity = 0 OR o.LocalitySecurity IS NULL)) ';
}
else{
$sqlWhere .= ' AND (o.LocalitySecurity = 0 OR o.LocalitySecurity IS NULL) ';
}
$this->sqlWhere = $sqlWhere;
//echo '<div style="margin-left:10px">sql: '.$this->sqlWhere.'</div>'; exit;
}

//Shape functions
Expand Down
2 changes: 1 addition & 1 deletion config/symbbase.php
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
header('X-Frame-Options: DENY');
header('Cache-control: private'); // IE 6 FIX
date_default_timezone_set('America/Phoenix');
$CODE_VERSION = '3.0.30';
$CODE_VERSION = '3.0.31';

if(!isset($CLIENT_ROOT) && isset($clientRoot)) $CLIENT_ROOT = $clientRoot;
if(substr($CLIENT_ROOT,-1) == '/') $CLIENT_ROOT = substr($CLIENT_ROOT,0,strlen($CLIENT_ROOT)-1);
Expand Down

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