Merge pull request #9 from BioKIC/master

Merge BioKIC/Symbiota developments
BioKIC · May 31, 2023 · c3e49aa · c3e49aa
2 parents 9b0d12d + de15df7
commit c3e49aa
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Showing 17 changed files with 472 additions and 418 deletions.
diff --git a/classes/ChecklistVoucherReport.php b/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 '.

diff --git a/classes/ImageLocalProcessor.php b/classes/ImageLocalProcessor.php
@@ -1557,7 +1557,8 @@ private function updateCollectionStats(){
 
 			$this->logOrEcho('Cleaning house...');
 			$collString = implode(',',$this->collProcessedArr);
-			if(!$occurMain->generalOccurrenceCleaning($collString)){
+			$occurMain->setCollidStr($collString);
+			if(!$occurMain->generalOccurrenceCleaning()){
 				$errorArr = $occurMain->getErrorArr();
 				foreach($errorArr as $errorStr){
 					$this->logOrEcho($errorStr,1);
@@ -1570,7 +1571,8 @@ private function updateCollectionStats(){
 
 			$this->logOrEcho('Updating statistics...');
 			foreach($this->collProcessedArr as $collid){
-				if(!$occurMain->updateCollectionStats($collid)){
+				$occurMain->setCollidStr($collid);
+				if(!$occurMain->updateCollectionStatsBasic()){
 					$errorArr = $occurMain->getErrorArr();
 					foreach($errorArr as $errorStr){
 						$this->logOrEcho($errorStr,1);

diff --git a/classes/ImageProcessor.php b/classes/ImageProcessor.php
@@ -347,7 +347,8 @@ public function loadFileData($postArr){
 				$occurMain = new OccurrenceMaintenance($this->conn);
 
 				$this->logOrEcho('Updating statistics...');
-				if(!$occurMain->updateCollectionStats($this->collid)){
+				$occurMain->setCollidStr($this->collid);
+				if(!$occurMain->updateCollectionStatsBasic()){
 					$errorArr = $occurMain->getErrorArr();
 					foreach($errorArr as $errorStr){
 						$this->logOrEcho($errorStr,1);
@@ -545,7 +546,8 @@ 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 +561,8 @@ private function cleanHouse($collList){
 		if($collList){
 			$this->logOrEcho('Updating collection statistics...',2);
 			foreach($collList as $collid){
-				if(!$occurMain->updateCollectionStats($collid)){
+				$occurMain->setCollidStr($collid);
+				if(!$occurMain->updateCollectionStatsBasic()){
 					$errorArr = $occurMain->getErrorArr();
 					foreach($errorArr as $errorStr){
 						$this->logOrEcho($errorStr,1);

diff --git a/classes/OccurrenceCollectionProfile.php b/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>';