Hotfix 2023 06 19 (BioKIC#518)

* Taxonomy Harvesting minor adjustments - Check resources before interpretation and again after interpretation - If name is matched within one recourse, skip the unnecessary step to check other resources - Synchronize display text * Refactor ImageLocalProcessor and resolve various bugs - Provide support for input file to include medium and thumbnail image derivatives - Expand Image Map processing to allow mapping file to include any images table field name - Expand images insert function to handle any valid field found within images table - Merge duplicate actions into shared private functions - MD5 hash large version of image input file, but don't overwrite hash if supplied by source, unless image is not modified by upload scripts - Handle BOM characters at start of csv file. - Trim header elements for testing column names. - Enforce default action of accepting derivative urls supplied within a csv image map file - Improve uriExists function - Make sure to remove staging images * Occurrence Public Display page - Allow occurrence archive (deleted occurrences) to be searchable by GUID (occurrenceID, recordID), thus reporting when a record is deleted * Checklist multi-polygon map Issue - Multipolygons defined within a checklist fail to map within both simple and dynamic maps * Suppress geo ref index during stats update * Occurrence Reviewer bug - Fix for field name and start and end date filter variables failing to be carried forward when advancing to pages beyond 1000 records BioKIC#335 * Collection metadata editor bug - Reset contact array to ensure that JSON string is standardized as a non-associated array Resolves issue: BioKIC#487 --------- Co-authored-by: Greg Post <[email protected]>
cdtyrrell · Jun 22, 2023 · deb6549 · deb6549
1 parent f55bc39
commit deb6549
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Showing 13 changed files with 492 additions and 421 deletions.
diff --git a/checklists/checklistmap.php b/checklists/checklistmap.php
@@ -67,33 +67,34 @@ function initialize(){
 					}
 				}
 			}
-			//Check for and add checklist polygon
 			$clMeta = $clManager->getClMetaData();
 			if($clMeta['footprintwkt']){
-				?>
-				var polyPointArr = [];
-				<?php
-				$footPrintWkt = $clMeta['footprintwkt'];
-				if(substr($footPrintWkt, 0, 7) == 'POLYGON'){
-					$footPrintWkt = substr($footPrintWkt, 10, -2);
-					$pointArr = explode(',', $footPrintWkt);
-					foreach($pointArr as $pointStr){
-						$llArr = explode(' ', trim($pointStr));
-						if($llArr[0] > 90 || $llArr[0] < -90) break;
+				//Add checklist polygon
+				$wkt = $clMeta['footprintwkt'];
+				if(substr($wkt,0,7) == 'POLYGON') $wkt = substr($wkt,7);
+				else if(substr($wkt,0,12) == 'MULTIPOLYGON') $wkt = substr($wkt,12);
+				$coordArr = explode('),(', $wkt);
+				foreach($coordArr as $k => $polyFrag){
+					if($pointArr = explode(',', trim($polyFrag,' (),'))){
+						echo 'var polyPointArr'.$k.' = [];';
+						foreach($pointArr as $pointStr){
+							$llArr = explode(' ', trim($pointStr));
+							if($llArr[0] > 90 || $llArr[0] < -90) break;
+							?>
+							var polyPt = new google.maps.LatLng(<?php echo $llArr[0].','.$llArr[1]; ?>);
+							polyPointArr<?php echo $k; ?>.push(polyPt);
+							llBounds.extend(polyPt);
+							<?php
+						}
 						?>
-						var polyPt = new google.maps.LatLng(<?php echo $llArr[0].','.$llArr[1]; ?>);
-						polyPointArr.push(polyPt);
-						llBounds.extend(polyPt);
+						var footPoly<?php echo $k; ?> = new google.maps.Polygon({
+							paths: polyPointArr<?php echo $k; ?>,
+							strokeWeight: 2,
+							fillOpacity: 0.4,
+							map: map
+						});
 						<?php
 					}
-					?>
-					var footPoly = new google.maps.Polygon({
-						paths: polyPointArr,
-						strokeWeight: 2,
-						fillOpacity: 0.4,
-						map: map
-					});
-					<?php
 				}
 			}
 			?>

diff --git a/classes/ImageLocalProcessor.php b/classes/ImageLocalProcessor.php
diff --git a/classes/OccurrenceCollectionProfile.php b/classes/OccurrenceCollectionProfile.php
@@ -516,7 +516,7 @@ public function updateStatistics($verbose = false){
 			ob_flush();
 		}
 		$occurMaintenance->generalOccurrenceCleaning();
-		$occurMaintenance->batchUpdateGeoreferenceIndex();
+		//$occurMaintenance->batchUpdateGeoreferenceIndex();
 		if($verbose){
 			echo '<li>Updating statistics...</li>';
 			flush();

diff --git a/classes/OccurrenceIndividual.php b/classes/OccurrenceIndividual.php
@@ -968,21 +968,35 @@ public function getChecklists($clidExcludeArr){
 		return $returnArr;
 	}
 
-	public function checkArchive(){
+	public function checkArchive($guid){
 		$retArr = array();
+		$archiveObject = '';
+		$notes = '';
+		$sql = 'SELECT archiveobj, remarks FROM omoccurarchive ';
 		if($this->occid){
-			$sql = 'SELECT archiveobj, remarks FROM omoccurarchive WHERE occid = '.$this->occid;
-			if($rs = $this->conn->query($sql)){
-				if($r = $rs->fetch_object()){
-					$retArr['obj'] = json_decode($r->archiveobj, true);
-					$retArr['notes'] = $r->remarks;
-				}
-				$rs->free();
+			$sql .= 'WHERE occid = ?';
+			if($stmt = $this->conn->prepare($sql)){
+				$stmt->bind_param('i', $this->occid);
+				$stmt->execute();
+				$stmt->bind_result($archiveObject, $notes);
+				$stmt->fetch();
+				$stmt->close();
 			}
-			else{
-				trigger_error('ERROR checking archive: '.$this->conn->error,E_USER_WARNING);
+		}
+		if(!$retArr && $guid){
+			$sql .= 'WHERE (occurrenceid = ?) OR (recordID = ?) ';
+			if($stmt = $this->conn->prepare($sql)){
+				$stmt->bind_param('ss', $guid, $guid);
+				$stmt->execute();
+				$stmt->bind_result($archiveObject, $notes);
+				$stmt->fetch();
+				$stmt->close();
 			}
 		}
+		if($archiveObject){
+			$retArr['obj'] = json_decode($archiveObject, true);
+			$retArr['notes'] = $notes;
+		}
 		return $retArr;
 	}
 

diff --git a/classes/OccurrenceMapManager.php b/classes/OccurrenceMapManager.php
@@ -294,35 +294,32 @@ public function createShape(){
 		if($this->getSearchTerm('polycoords')){
 			$wkt = $this->getSearchTerm('polycoords');
 			if(substr($wkt,0,7) == 'POLYGON') $wkt = substr($wkt,7);
-			$wkt = trim($wkt,' (),');
-			$coordArr = explode(',',$wkt);
-			if($coordArr){
-				$shapeBounds = 'var queryShapeBounds = new google.maps.LatLngBounds();';
-				$queryShape = 'var queryPolygon = new google.maps.Polygon({';
-				$points = '';
-				foreach($coordArr as $k => $ptStr){
-					$ptArr = explode(' ',$ptStr);
-					$points .= ',new google.maps.LatLng('.$ptArr[0].', '.$ptArr[1].')';
-					$shapeBounds .= 'queryShapeBounds.extend(new google.maps.LatLng('.$ptArr[0].', '.$ptArr[1].'));';
+			else if(substr($wkt,0,12) == 'MULTIPOLYGON') $wkt = substr($wkt,12);
+			$coordArr = explode('),(', $wkt);
+			$shapeBounds = 'var queryShapeBounds = new google.maps.LatLngBounds();'."\n";
+			foreach($coordArr as $k => $polyFrag){
+				if($pointArr = explode(',', trim($polyFrag,' (),'))){
+					$queryShape .= 'var queryPolygon'.$k.' = new google.maps.Polygon({';
+					$points = '';
+					foreach($pointArr as $ptStr){
+						$ptArr = explode(' ',$ptStr);
+						$points .= ',new google.maps.LatLng('.$ptArr[0].', '.$ptArr[1].')';
+						$shapeBounds .= 'queryShapeBounds.extend(new google.maps.LatLng('.$ptArr[0].', '.$ptArr[1].'));'."\n";
+					}
+					$queryShape .= 'paths: ['.substr($points,1).'],';
+					$queryShape .= $properties;
+					$queryShape .= 'queryPolygon'.$k.'.type = "polygon";';
+					$queryShape .= 'google.maps.event.addListener(queryPolygon'.$k.', "click", function() { setSelection(queryPolygon'.$k.');});';
+					$queryShape .= 'google.maps.event.addListener(queryPolygon'.$k.', "dragend", function() { setSelection(queryPolygon'.$k.');});';
+					$queryShape .= 'google.maps.event.addListener(queryPolygon'.$k.'.getPath(), "insert_at", function() { setSelection(queryPolygon'.$k.');});';
+					$queryShape .= 'google.maps.event.addListener(queryPolygon'.$k.'.getPath(), "remove_at", function() { setSelection(queryPolygon'.$k.');});';
+					$queryShape .= 'google.maps.event.addListener(queryPolygon'.$k.'.getPath(), "set_at", function() { setSelection(queryPolygon'.$k.');});';
+					$queryShape .= 'setSelection(queryPolygon'.$k.');';
 				}
-				$queryShape .= 'paths: ['.substr($points,1).'],';
-				$queryShape .= $properties;
-				$queryShape .= "queryPolygon.type = 'polygon';";
-				$queryShape .= "google.maps.event.addListener(queryPolygon, 'click', function() {";
-				$queryShape .= 'setSelection(queryPolygon);});';
-				$queryShape .= "google.maps.event.addListener(queryPolygon, 'dragend', function() {";
-				$queryShape .= 'setSelection(queryPolygon);});';
-				$queryShape .= "google.maps.event.addListener(queryPolygon.getPath(), 'insert_at', function() {";
-				$queryShape .= 'setSelection(queryPolygon);});';
-				$queryShape .= "google.maps.event.addListener(queryPolygon.getPath(), 'remove_at', function() {";
-				$queryShape .= 'setSelection(queryPolygon);});';
-				$queryShape .= "google.maps.event.addListener(queryPolygon.getPath(), 'set_at', function() {";
-				$queryShape .= 'setSelection(queryPolygon);});';
-				$queryShape .= 'setSelection(queryPolygon);';
-				$queryShape .= $shapeBounds;
-				$queryShape .= 'map.fitBounds(queryShapeBounds);';
-				$queryShape .= 'map.panToBounds(queryShapeBounds);';
 			}
+			$queryShape .= $shapeBounds;
+			$queryShape .= 'map.fitBounds(queryShapeBounds);';
+			$queryShape .= 'map.panToBounds(queryShapeBounds);'."\n";
 		}
 		return $queryShape;
 	}

diff --git a/classes/OmCollections.php b/classes/OmCollections.php
@@ -214,15 +214,19 @@ public function deleteContact($index){
 	}
 
 	private function updateContactJson($contactArr){
+		$status = false;
 		if($this->collid){
-			$sql = 'UPDATE omcollections SET contactJson = "'.$this->cleanInStr(json_encode($contactArr)).'" WHERE collid = '.$this->collid;
-			if(!$this->conn->query($sql)){
-				$this->errorMessage = 'ERROR updating contact: '.$this->conn->error;
-				return false;
+			$contactStr = json_encode(array_values($contactArr));
+			$sql = 'UPDATE omcollections SET contactJson = ? WHERE collid = '.$this->collid;
+			if($stmt = $this->conn->prepare($sql)){
+				$stmt->bind_param('s', $contactStr);
+				$stmt->execute();
+				if($stmt->affected_rows) $status = true;
+				elseif($stmt->error) $this->errorMessage = $stmt->error;
+				$stmt->close();
 			}
-			return true;
 		}
-		return false;
+		return $status;
 	}
 
 	private function getContactArr(){
@@ -288,9 +292,8 @@ public function linkAddress($addIID){
 	public function removeAddress($removeIID){
 		$status = false;
 		if($this->collid && is_numeric($removeIID)){
-			$con = MySQLiConnectionFactory::getCon("write");
-			$sql = 'UPDATE omcollections SET iid = NULL '.
-				'WHERE collid = '.$this->collid.' AND iid = '.$removeIID;
+			$con = MySQLiConnectionFactory::getCon('write');
+			$sql = 'UPDATE omcollections SET iid = NULL WHERE collid = '.$this->collid.' AND iid = '.$removeIID;
 			if($con->query($sql)){
 				$status = true;
 			}

diff --git a/classes/TaxonomyCleaner.php b/classes/TaxonomyCleaner.php
@@ -94,27 +94,27 @@ public function analyzeTaxa($taxResource, $startIndex, $limit = 50){
 				$sciname = $r->sciname;
 				$tid = 0;
 				$manualCheck = true;
-				$taxonArr = TaxonomyUtilities::parseScientificName($r->sciname,$this->conn,0,$this->targetKingdomName);
-				if(isset($taxonArr['sciname']) && $taxonArr['sciname']){
-					$sciname = $taxonArr['sciname'];
-					if($sciname != $r->sciname){
-						$this->logOrEcho('Interpreted base name: <b>'.$sciname.'</b>',1);
-					}
-					$tid = $taxonHarvester->getTid($taxonArr);
-					if($tid && $this->autoClean){
-						$this->remapOccurrenceTaxon($this->collid, $r->sciname, $tid, (isset($taxonArr['identificationqualifier'])?$taxonArr['identificationqualifier']:''));
-						$this->logOrEcho('Taxon remapped to <b>'.$sciname.'</b>',1);
+				if($tid = $taxonHarvester->processSciname($sciname)){
+					$taxaAdded= true;
+					if($taxonHarvester->isFullyResolved()){
 						$manualCheck = false;
 					}
+					else{
+						$this->logOrEcho('Taxon not fully resolved...',1);
+					}
 				}
-				if(!$tid){
-					if($taxonHarvester->processSciname($sciname)){
-						$taxaAdded= true;
-						if($taxonHarvester->isFullyResolved()){
-							$manualCheck = false;
+				$taxonArr = TaxonomyUtilities::parseScientificName($r->sciname,$this->conn,0,$this->targetKingdomName);
+				if(!$tid && $this->autoClean){
+					if(isset($taxonArr['sciname']) && $taxonArr['sciname']){
+						$sciname = $taxonArr['sciname'];
+						if($sciname != $r->sciname){
+							$this->logOrEcho('Interpreted base name: <b>'.$sciname.'</b>',1);
 						}
-						else{
-							$this->logOrEcho('Taxon not fully resolved...',1);
+						$tid = $taxonHarvester->getTid($taxonArr);
+						if($tid){
+							$this->remapOccurrenceTaxon($this->collid, $r->sciname, $tid, (isset($taxonArr['identificationqualifier'])?$taxonArr['identificationqualifier']:''));
+							$this->logOrEcho('Taxon remapped to <b>'.$sciname.'</b>',1);
+							$manualCheck = false;
 						}
 					}
 				}
@@ -129,14 +129,14 @@ public function analyzeTaxa($taxResource, $startIndex, $limit = 50){
 						for($x=1; $x <= 3; $x++){
 							if(isset($taxonArr['unitname'.$x]) && $taxonArr['unitname'.$x]) $strTestArr[] = $taxonArr['unitname'.$x];
 						}
-						foreach($matchArr as $tid => $scinameMatch){
+						foreach($matchArr as $tidMatch => $scinameMatch){
 							$snTokens = explode(' ',$scinameMatch);
 							foreach($snTokens as $k => $v){
 								if(in_array($v, $strTestArr)) $snTokens[$k] = '<b>'.$v.'</b>';
 							}
 							$idQual = (isset($taxonArr['identificationqualifier'])?str_replace("'", '', $taxonArr['identificationqualifier']):'');
 							$echoStr = '<i>'.implode(' ',$snTokens).'</i> =&gt; <span class="hideOnLoad">wait for page to finish loading...</span><span class="displayOnLoad" style="display:none">'.
-								'<a href="#" onclick="return remappTaxon(\''.urlencode($r->sciname).'\','.$tid.',\''.$idQual.'\','.$itemCnt.')" style="color:blue"> remap to this taxon</a>'.
+								'<a href="#" onclick="return remappTaxon(\''.urlencode($r->sciname).'\','.$tidMatch.',\''.$idQual.'\','.$itemCnt.')" style="color:blue"> remap to this taxon</a>'.
 								'<span id="remapSpan-'.$itemCnt.'"></span></span>';
 							$this->logOrEcho($echoStr,2);
 							$itemCnt++;

diff --git a/classes/TaxonomyHarvester.php b/classes/TaxonomyHarvester.php
@@ -39,6 +39,7 @@ public function processSciname($term){
 			}
 			foreach($this->taxonomicResources as $authCode => $apiKey){
 				$newTid = $this->addSciname($taxonArr, $authCode);
+				if($newTid) break;
 			}
 		}
 		return $newTid;
@@ -228,7 +229,7 @@ private function addColTaxon($taxonArr){
 				}
 				else $this->logOrEcho('Targeted taxon return does not exist',2);
 			}
-			else $this->logOrEcho($sciName.' not found in CoL',2);
+			else $this->logOrEcho('Taxon not found',2);
 		}
 		else $this->logOrEcho('ERROR harvesting COL name: null input name',1);
 		return $tid;

diff --git a/collections/editor/editreviewer.php b/collections/editor/editreviewer.php
@@ -11,7 +11,7 @@
 $displayMode = array_key_exists('display', $_REQUEST) ? filter_var($_REQUEST['display'], FILTER_SANITIZE_NUMBER_INT) : '1';
 $faStatus = array_key_exists('fastatus', $_REQUEST) ? filter_var($_REQUEST['fastatus'], FILTER_SANITIZE_NUMBER_INT) : '';
 $frStatus = array_key_exists('frstatus', $_REQUEST)? filter_var($_REQUEST['frstatus'], FILTER_SANITIZE_STRING) : '1,2';
-$filterFieldName = array_key_exists('ffieldname', $_POST) ? filter_var($_POST['ffieldname'], FILTER_SANITIZE_STRING) : '';
+$filterFieldName = array_key_exists('ffieldname', $_REQUEST) ? filter_var($_REQUEST['ffieldname'], FILTER_SANITIZE_STRING) : '';
 $editor = array_key_exists('editor', $_REQUEST) ? filter_var($_REQUEST['editor'], FILTER_SANITIZE_STRING) : '';
 $queryOccid = array_key_exists('occid', $_REQUEST) ? filter_var($_REQUEST['occid'], FILTER_SANITIZE_NUMBER_INT) : '';
 $startDate = array_key_exists('startdate', $_REQUEST) ? filter_var($_REQUEST['startdate'], FILTER_SANITIZE_STRING) : '';
@@ -81,7 +81,8 @@
 
 $subCnt = $limitCnt*($pageNum + 1);
 if($subCnt > $recCnt) $subCnt = $recCnt;
-$navPageBase = 'editreviewer.php?collid='.$collid.'&display='.$displayMode.'&fastatus='.$faStatus.'&frstatus='.$frStatus.'&editor='.$editor.'&reccnt='.$recCnt;
+$navPageBase = 'editreviewer.php?collid='.$collid.'&display='.$displayMode.'&fastatus='.$faStatus.'&frstatus='.$frStatus.'&ffieldname='.$filterFieldName.
+	'&startdate='.$startDate.'&enddate='.$endDate.'&editor='.$editor.'&reccnt='.$recCnt;
 
 $navStr = '<div class="navbarDiv" style="float:right;">';
 if($pageNum) $navStr .= '<a href="'.$navPageBase.'&pagenum='.($pageNum-1).'&limitcnt='.$limitCnt.'" title="'.$LANG['PREVIOUS'].' '.$limitCnt.' '.$LANG['RECORDS1'].'">&lt;&lt;</a>';

diff --git a/collections/individual/index.php b/collections/individual/index.php
@@ -1395,7 +1395,7 @@ function initializeMap(){
 					<?php
 					ob_flush();
 					flush();
-					$rawArchArr = $indManager->checkArchive();
+					$rawArchArr = $indManager->checkArchive($guid);
 					if($rawArchArr && $rawArchArr['obj']){
 						$archArr = $rawArchArr['obj'];
 						if($isEditor){

diff --git a/collections/specprocessor/processor.php b/collections/specprocessor/processor.php
@@ -61,7 +61,7 @@
 				$specManager->setProjVariables($spprid);
 				if($action == 'Process Images'){
 					if($specManager->getProjectType() == 'iplant'){
-						$imageProcessor = new ImageProcessor($specManager->getConn());
+						$imageProcessor = new ImageProcessor();
 						echo '<ul>';
 						$imageProcessor->setLogMode(3);
 						$imageProcessor->setCollid($collid);
@@ -95,9 +95,9 @@
 						if($specManager->getLgMaxFileSize()) $imageProcessor->setLgFileSizeLimit($specManager->getLgMaxFileSize());
 						if($specManager->getJpgQuality()) $imageProcessor->setJpgQuality($specManager->getJpgQuality());
 						$imageProcessor->setUseImageMagick($specManager->getUseImageMagick());
-						$imageProcessor->setWebImg($_POST['webimg']);
-						$imageProcessor->setTnImg($_POST['createtnimg']);
-						$imageProcessor->setLgImg($_POST['createlgimg']);
+						$imageProcessor->setMedProcessingCode($_POST['webimg']);
+						$imageProcessor->setTnProcessingCode($_POST['createtnimg']);
+						$imageProcessor->setLgProcessingCode($_POST['createlgimg']);
 						$imageProcessor->setCreateNewRec($_POST['createnewrec']);
 						$imageProcessor->setImgExists($_POST['imgexists']);
 						$imageProcessor->setKeepOrig(0);
@@ -111,7 +111,7 @@
 				}
 				elseif($action == 'mapImageFile'){
 					//Process csv file with remote image urls
-					$imageProcessor = new ImageProcessor($specManager->getConn());
+					$imageProcessor = new ImageProcessor();
 					echo '<ul>';
 					$imageProcessor->setLogMode(3);
 					$imageProcessor->setCollid($collid);

diff --git a/collections/specprocessor/standalone_scripts/ImageBatchHandler.php b/collections/specprocessor/standalone_scripts/ImageBatchHandler.php
@@ -39,12 +39,9 @@
 if($lgFileSizeLimit) $imageProcessor->setLgFileSizeLimit($lgFileSizeLimit);
 $imageProcessor->setJpgQuality($jpgQuality);
 
-if(isset($webImg) && $webImg) $imageProcessor->setWebImg($webImg);
-elseif(isset($createWebImg) && $createWebImg) $imageProcessor->setCreateWebImg($createWebImg);
-if(isset($tnImg) && $tnImg) $imageProcessor->setTnImg($tnImg);
-elseif(isset($createTnImg) && $createTnImg) $imageProcessor->setCreateTnImg($createTnImg);
-if(isset($lgImg) && $lgImg) $imageProcessor->setLgImg($lgImg);
-elseif(isset($createLgImg) && $createLgImg) $imageProcessor->setCreateLgImg($createLgImg);
+if(isset($webImg) && $webImg) $imageProcessor->setMedProcessingCode($webImg);
+if(isset($tnImg) && $tnImg) $imageProcessor->setTnProcessingCode($tnImg);
+if(isset($lgImg) && $lgImg) $imageProcessor->setLgProcessingCode($lgImg);
 $imageProcessor->setKeepOrig($keepOrig);
 $imageProcessor->setCreateNewRec($createNewRec);
 if(isset($imgExists)) $imageProcessor->setImgExists($imgExists);

diff --git a/config/symbbase.php b/config/symbbase.php
@@ -2,7 +2,7 @@
 header('X-Frame-Options: DENY');
 header('Cache-control: private'); // IE 6 FIX
 date_default_timezone_set('America/Phoenix');
-$CODE_VERSION = '3.0.9';
+$CODE_VERSION = '3.0.10';
 
 if(!isset($CLIENT_ROOT) && isset($clientRoot)) $CLIENT_ROOT = $clientRoot;
 if(substr($CLIENT_ROOT,-1) == '/') $CLIENT_ROOT = substr($CLIENT_ROOT,0,strlen($CLIENT_ROOT)-1);