Partial update branch by pulling in master bug fixes (#523)

* Occurrence Taxon Indexing adjustments

- Refactor OccurrenceMaintenance class to consolidate occurrence indexing tools into single set of functions
- Isolate general occurrence cleaning SQL statements from taxon indexing SQL
- Extend occurrence-taxon indexing to accommodate a matching hierarchy that involves taxon author, subgeneric formats, etc
- Refactor occurrence statistic function

* Taxonomic function adjustments

- Remove occurrence cleaning and occurrence-taxon indexing functions in preference to identical functions within OccurrenceMaintenance class (consolidate functions)

* Taxonomic Harvester bug

- Fix Catalog of Life API import issue where in certain situation species names are duplicated with one containing imbedded subgeneric name and the other not

* Resolve COL Taxonomy Harvesting discrepancies

- Include taxonRank within the ranking algorithm to get a correct match on subgenera search
- Condense translateColNode algorithm into a single function that can translate both api and webservice formats
- Various adjustments to subgeneric formatting

* Update code version

* Hotfix 2023-05-25 (#488)

* Taxon Profile display bug - Ensure the taxadescrblock field take precedence

* GeoLocate CoGe bug fix - path correction for temp staging area

* Hotfix: Occurrence upload, Key editor, Taxon Profile

- Resolve issue with occurrence-taxon indexing code
- Only build sciname from taxon units if all units are mapped
- Resolve issue with ID Key editor not displaying characters that are not grouped
-Taxon Profile insert issue

* Hotfix 2023 06 03 (#508)

* Occurrence Upload adjustment
    - Trim off delimiters that are left on the beginning or end of filter string to ensure that null values are not included
* Collection Listing bug fix
    - Collection categories failing to be persist
* Occurrence Image Submissions issue resolution
    - Set default image sort order to 40 for observations to ensure that preserved specimen images do not take precedence
* Image Processing bug
    - collection identifier (collid) failed to be passed to statistics update function
* Resolve Taxonomy Harvester issues
    - Improve TROPICOS method of matching on infraspecific taxa
    - Improve close match suggestions

* Update .gitignore

* Hotfix 2023 06 19 (#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
#335

* Collection metadata editor bug

- Reset contact array to ensure that JSON string is standardized as a non-associated array
Resolves issue: #487

---------

Co-authored-by: Greg Post <[email protected]>

---------

Co-authored-by: Greg Post <[email protected]>

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
 				}
 			}
 			?>

classes/ChecklistVoucherReport.php

@@ -271,8 +271,6 @@ private function getMissingTaxaBaseSql($sqlFrag){
 	public function getMissingProblemTaxa(){
 		$retArr = Array();
 		if($sqlFrag = $this->getSqlFrag()){
-			//Make sure tidinterpreted are valid
-			//$this->conn->query('UPDATE omoccurrences o INNER JOIN taxa t ON o.sciname = t.sciname SET o.tidinterpreted = t.tid WHERE o.tidinterpreted IS NULL');
 			//Grab records
 			$sql = 'SELECT DISTINCT o.occid, c.institutioncode, c.collectioncode, o.catalognumber, o.sciname, o.recordedby, o.recordnumber, o.eventdate, '.
 				'CONCAT_WS("; ",o.country, o.stateprovince, o.county, o.locality) as locality '.

classes/ImageProcessor.php

@@ -347,7 +347,7 @@ public function loadFileData($postArr){
 				$occurMain = new OccurrenceMaintenance($this->conn);
 
 				$this->logOrEcho('Updating statistics...');
-				if(!$occurMain->updateCollectionStats($this->collid)){
+				if(!$occurMain->updateCollectionStatsBasic($this->collid)){
 					$errorArr = $occurMain->getErrorArr();
 					foreach($errorArr as $errorStr){
 						$this->logOrEcho($errorStr,1);
@@ -545,7 +545,8 @@ private function cleanHouse($collList){
 		/*
 		$this->logOrEcho('General cleaning...',2);
 		$collString = implode(',',$collList);
-		if(!$occurMain->generalOccurrenceCleaning($collString)){
+		$occurMain->setCollidStr($collString);
+		if(!$occurMain->generalOccurrenceCleaning()){
 			$errorArr = $occurMain->getErrorArr();
 			foreach($errorArr as $errorStr){
 				$this->logOrEcho($errorStr,1);
@@ -559,7 +560,7 @@ private function cleanHouse($collList){
 		if($collList){
 			$this->logOrEcho('Updating collection statistics...',2);
 			foreach($collList as $collid){
-				if(!$occurMain->updateCollectionStats($collid)){
+				if(!$occurMain->updateCollectionStatsBasic($collid)){
 					$errorArr = $occurMain->getErrorArr();
 					foreach($errorArr as $errorStr){
 						$this->logOrEcho($errorStr,1);

classes/KeyEditorManager.php

@@ -23,8 +23,7 @@ public function __destruct(){
 	public function setTid($t){
 		if(is_numeric($t)){
 			$this->tid = $t;
-			$sql = "SELECT t.SciName, ts.ParentTID, t.RankId ".
-				"FROM taxa t INNER JOIN taxstatus ts ON t.tid = ts.tid WHERE ts.taxauthid = 1 AND (t.TID = ".$this->tid.')';
+			$sql = 'SELECT t.SciName, ts.ParentTID, t.RankId FROM taxa t INNER JOIN taxstatus ts ON t.tid = ts.tid WHERE ts.taxauthid = 1 AND (t.TID = '.$this->tid.')';
 			$result = $this->conn->query($sql);
 			if($row = $result->fetch_object()){
 				$this->taxonName = $row->SciName;
@@ -81,9 +80,9 @@ private function setCharList(){
 		$parentStr = implode(',',$this->getParentArr($this->tid));
 		$sql = 'SELECT c.CharName, c.CID, ch.headingname, dep.CIDDependance, dep.CSDependance '.
 			'FROM kmcharacters c INNER JOIN kmchartaxalink ctl ON c.CID = ctl.CID '.
-			'INNER JOIN kmcharheading ch ON c.hid = ch.hid '.
+			'LEFT JOIN kmcharheading ch ON c.hid = ch.hid '.
 			'LEFT JOIN kmchardependance dep ON c.CID = dep.CID '.
-			'WHERE (ch.language = "English") AND (c.CID Not In (SELECT DISTINCT chartl.CID FROM kmchartaxalink chartl WHERE (chartl.TID In ('.$parentStr.')) AND (chartl.Relation="exclude"))) '.
+			'WHERE (ch.language IS NULL OR ch.language = "English") AND (c.CID Not In (SELECT DISTINCT chartl.CID FROM kmchartaxalink chartl WHERE (chartl.TID In ('.$parentStr.')) AND (chartl.Relation="exclude"))) '.
 			'AND (c.chartype = "UM" Or c.chartype="OM") AND (ctl.TID In ('.$parentStr.')) AND (ctl.Relation="include") '.
 			'ORDER BY ch.SortSequence,c.SortSequence';
 		//echo $sql;

classes/OccurrenceCollectionProfile.php

@@ -507,20 +507,22 @@ public function getBasicStats(){
 
 	public function updateStatistics($verbose = false){
 		$occurMaintenance = new OccurrenceMaintenance();
+		$occurMaintenance->setCollidStr($this->collid);
 		if($verbose){
 			echo '<ul>';
 			$occurMaintenance->setVerbose(true);
 			echo '<li>General cleaning in preparation for collecting stats...</li>';
 			flush();
 			ob_flush();
 		}
-		$occurMaintenance->generalOccurrenceCleaning($this->collid);
+		$occurMaintenance->generalOccurrenceCleaning();
+		//$occurMaintenance->batchUpdateGeoreferenceIndex();
 		if($verbose){
 			echo '<li>Updating statistics...</li>';
 			flush();
 			ob_flush();
 		}
-		$occurMaintenance->updateCollectionStats($this->collid, true);
+		$occurMaintenance->updateCollectionStatsFull();
 		if($verbose){
 			echo '<li>Finished updating collection statistics</li>';
 			flush();
@@ -602,7 +604,8 @@ public function batchUpdateStatistics($collId){
 				echo '<li style="margin-left:15px;">Cleaning statistics for: '.$r->collectionname.'</li>';
 				flush();
 				ob_flush();
-				$occurMaintenance->updateCollectionStats($r->collid, true);
+				$occurMaintenance->setCollidStr($r->collid);
+				$occurMaintenance->updateCollectionStatsFull();
 			}
 			$rs->free();
 			echo '<li>Statistics update complete!</li>';

classes/OccurrenceEditorImages.php

@@ -401,6 +401,7 @@ public function addImage($postArr){
 		if(array_key_exists('copyright',$postArr)) $imgManager->setCopyright($postArr['copyright']);
 		if(array_key_exists('notes',$postArr)) $imgManager->setNotes($postArr['notes']);
 		if(array_key_exists('sortoccurrence',$postArr)) $imgManager->setSortOccurrence($postArr['sortoccurrence']);
+		if(strpos($this->collMap['colltype'], 'Observations') !== false)  $imgManager->setSortSeq(40);
 
 		$sourceImgUri = $postArr['imgurl'];
 		if($sourceImgUri){

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;
 	}