Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Hotfix 2024 05 22 (#1374) #487

Merged
merged 1 commit into from
May 30, 2024
Merged

Hotfix 2024 05 22 (#1374) #487

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
18 changes: 10 additions & 8 deletions classes/ChecklistVoucherManager.php
View file
Open in desktop
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;
}
$rsSourceCl->free();
//Transfer source chklsttaxalink data to target record
Expand Down
6 changes: 3 additions & 3 deletions classes/ImageLocalProcessor.php
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -998,17 +998,17 @@ private function databaseImage($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($wFile);
Expand Down
121 changes: 58 additions & 63 deletions classes/OccurrenceMapManager.php
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -63,31 +63,29 @@ public function getCoordinateMap($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
View file
Open in desktop
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