Merge pull request #30 from BioKIC/master

Update to BioKIC/Symbiota v3.0.13
BioKIC · Sep 1, 2023 · 84baa3e · 84baa3e
2 parents f709f0f + 38e3c36
commit 84baa3e
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Showing 78 changed files with 1,388 additions and 1,101 deletions.
diff --git a/admin/schemamanager.php b/admin/schemamanager.php
@@ -53,6 +53,8 @@
 							$schemaManager->setPort($port);
 							$schemaManager->setUsername($username);
 							$schemaManager->installPatch();
+							$verHistory = $schemaManager->getVersionHistory();
+							$curentVersion = $schemaManager->getCurrentVersion();
 						}
 						?>
 					</fieldset>

diff --git a/checklists/checklist.php b/checklists/checklist.php
@@ -107,18 +107,14 @@
 		if($clid) echo 'var clid = '.$clid.';'."\n";
 		echo 'var taxaCount = '.count($taxaArray).';'."\n";
 		?>
-		$( function() {
-			$( document ).tooltip();
-		} );
-
 		function changeImageSource(elem){
 			let f = document.optionform;
 			if(elem.id == "vi_voucher") f.voucherimages.value = "1";
 			else f.voucherimages.value = "0";
 			f.submit();
 		}
 	</script>
-	<script type="text/javascript" src="../js/symb/checklists.checklist.js?ver=3"></script>
+	<script type="text/javascript" src="../js/symb/checklists.checklist.js?ver=4"></script>
 	<style type="text/css">
 		<?php
 		if($printMode){

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/checklists/rpc/searchsuggest.php b/checklists/rpc/searchsuggest.php
@@ -1,13 +1,13 @@
 <?php
 include_once('../../config/symbini.php');
 include_once($SERVER_ROOT.'/classes/ChecklistManager.php');
-header("Content-Type: text/html; charset=".$CHARSET);
+header('Content-Type: text/html; charset='.$CHARSET);
 
 $clid = $_REQUEST['clid'];
 $term = $_REQUEST['term'];
 $deep = (isset($_REQUEST['deep'])?$_REQUEST['deep']:0);
 
 $clManager = new ChecklistManager();
-$retArr = $clManager->getTaxonSearch($term,$clid,$deep);
+$retArr = $clManager->getTaxonSearch($term, $clid, $deep);
 echo json_encode($retArr);
 ?>
diff --git a/classes/ChecklistManager.php b/classes/ChecklistManager.php
@@ -329,11 +329,16 @@ private function setImages(){
 		if($this->taxaList){
 			$matchedArr = array();
 			if($this->limitImagesToVouchers){
+				$clidStr = $this->clid;
+				if($this->childClidArr){
+					$clidStr .= ','.implode(',',array_keys($this->childClidArr));
+				}
 				$sql = 'SELECT i.tid, i.url, i.thumbnailurl, i.originalurl
 					FROM images i INNER JOIN omoccurrences o ON i.occid = o.occid
 					INNER JOIN fmvouchers v ON o.occid = v.occid
 					INNER JOIN fmchklsttaxalink cl ON v.clTaxaID = cl.clTaxaID
-					WHERE (cl.clid = 2) AND (i.tid IN('.implode(',',array_keys($this->taxaList)).'))';
+					WHERE (cl.clid = '.$clidStr.') AND (i.tid IN('.implode(',',array_keys($this->taxaList)).'))
+					ORDER BY i.sortOccurrence, i.sortSequence';
 				$matchedArr = $this->setImageSubset($sql);
 			}
 			if($missingArr = array_diff(array_keys($this->taxaList),$matchedArr)){
@@ -346,7 +351,7 @@ private function setImages(){
 				$matchedArr = $this->setImageSubset($sql);
 				if($missingArr = array_diff(array_keys($this->taxaList),$matchedArr)){
 					//Get children images
-					$sql = 'SELECT i2.tid, i.url, i.thumbnailurl FROM images i INNER JOIN '.
+					$sql = 'SELECT DISTINCT i2.tid, i.url, i.thumbnailurl FROM images i INNER JOIN '.
 						'(SELECT ts1.parenttid AS tid, SUBSTR(MIN(CONCAT(LPAD(i.sortsequence,6,"0"),i.imgid)),7) AS imgid '.
 						'FROM taxstatus ts1 INNER JOIN taxstatus ts2 ON ts1.tidaccepted = ts2.tidaccepted '.
 						'INNER JOIN images i ON ts2.tid = i.tid '.
@@ -361,7 +366,6 @@ private function setImages(){
 	private function setImageSubset($sql){
 		$matchTidArr = array();
 		if($this->taxaList){
-			//echo $sql;
 			$rs = $this->conn->query($sql);
 			while($r = $rs->fetch_object()){
 				if(!in_array($r->tid,$matchTidArr)){

diff --git a/classes/ChecklistVoucherAdmin.php b/classes/ChecklistVoucherAdmin.php
@@ -354,7 +354,7 @@ public function linkVouchers($occidArr){
 		return $statusCnt;
 	}
 
-	public function linkVoucher($taxa, $occid, $morphoSpecies=''){
+	public function linkVoucher($taxa, $occid, $morphoSpecies = '', $editorNotes = null, $notes = null){
 		$status = false;
 		if($this->voucherIsLinked($occid)){
 			$this->errorMessage = 'voucherAlreadyLinked';
@@ -364,7 +364,7 @@ public function linkVoucher($taxa, $occid, $morphoSpecies=''){
 		$clTaxaID = $this->getClTaxaID($taxa, $morphoSpecies);
 		if(!$clTaxaID) $clTaxaID = $this->insertChecklistTaxaLink($taxa);
 		if($clTaxaID){
-			$status = $this->insertVoucher($clTaxaID, $occid);
+			$status = $this->insertVoucher($clTaxaID, $occid, $editorNotes, $notes);
 		}
 		return $status;
 	}
@@ -495,6 +495,22 @@ private function transferVouchers($target, $source){
 		return $status;
 	}
 
+	public function deleteVoucher($voucherID){
+		$status = false;
+		if(is_numeric($voucherID)){
+			$sql = 'DELETE FROM fmvouchers WHERE (voucherID = ?)';
+			if($stmt = $this->conn->prepare($sql)) {
+				$stmt->bind_param('i', $voucherID);
+				$stmt->execute();
+				if($stmt->affected_rows) $status = true;
+				elseif($stmt->error) $this->errorMessage = 'ERROR deleting vouchers: '.$stmt->error;
+				$stmt->close();
+			}
+			else $this->errorMessage = 'ERROR preparing statement for voucher deletion: '.$this->conn->error;
+		}
+		return $status;
+	}
+
 	//Misc support and data functions
 	protected function getClTaxaID($tid, $morphoSpecies = ''){
 		$clTaxaID = 0;

diff --git a/classes/ChecklistVoucherManager.php b/classes/ChecklistVoucherManager.php
@@ -258,22 +258,6 @@ private function addVoucherRecord($vOccId, $vNotes, $vEditNotes){
 		return false;
 	}
 
-	public function deleteVoucher($voucherID){
-		$status = false;
-		if(is_numeric($voucherID)){
-			$sql = 'DELETE FROM fmvouchers WHERE (voucherID = ?)';
-			if($stmt = $this->conn->prepare($sql)) {
-				$stmt->bind_param('i', $voucherID);
-				$stmt->execute();
-				if($stmt->affected_rows) $status = true;
-				elseif($stmt->error) $this->errorMessage = 'ERROR deleting vouchers: '.$stmt->error;
-				$stmt->close();
-			}
-			else $this->errorMessage = 'ERROR preparing statement for voucher deletion: '.$this->conn->error;
-		}
-		return $status;
-	}
-
 	//Setters and getters
 	public function setTid($t){
 		if(is_numeric($t)){

diff --git a/classes/DwcArchiverCore.php b/classes/DwcArchiverCore.php
@@ -43,7 +43,7 @@ class DwcArchiverCore extends Manager{
 	private $includeDets = 1;
 	private $includeImgs = 1;
 	private $includeAttributes = 0;
-	private $includeMaterialSample = 0;		// 0 = off, 1 = on, 2 = active (activated within at least one collection)
+	private $includeMaterialSample = 0;
 	private $hasPaleo = false;
 	private $redactLocalities = 1;
 	private $rareReaderArr = array();
@@ -191,7 +191,6 @@ public function setCollArr($collTarget, $collType = ''){
 									if (isset($modArr['paleo']['status'])) $this->hasPaleo = true;
 									elseif (isset($modArr['matSample']['status'])){
 										$this->collArr[$r->collid]['matSample'] = 1;
-										$this->includeMaterialSample = 2;
 									}
 								}
 							}
@@ -1055,7 +1054,7 @@ private function writeMetaFile(){
 		}
 
 		//MaterialSample extension
-		if ($this->includeMaterialSample == 2 && isset($this->fieldArrMap['materialSample'])) {
+		if ($this->includeMaterialSample && isset($this->fieldArrMap['materialSample'])) {
 			$extElem3 = $newDoc->createElement('extension');
 			$extElem3->setAttribute('encoding', $this->charSetOut);
 			$extElem3->setAttribute('fieldsTerminatedBy', $this->delimiter);
@@ -1765,7 +1764,7 @@ private function writeOccurrenceFile(){
 
 				$batchOccidArr[] = $r['occid'];
 				if (count($batchOccidArr) > 1000) {
-					if ($this->includeMaterialSample == 2) $this->writeMaterialSampleData($materialSampleHandler, $batchOccidArr);
+					if ($this->includeMaterialSample) $this->writeMaterialSampleData($materialSampleHandler, $batchOccidArr);
 					if ($pubID && $portalManager) $portalManager->insertPortalOccurrences($pubID, $batchOccidArr);
 					unset($batchOccidArr);
 					$batchOccidArr = array();
@@ -1782,7 +1781,7 @@ private function writeOccurrenceFile(){
 			if ($batchOccidArr) {
 				if ($pubID && $portalManager) $portalManager->insertPortalOccurrences($pubID, $batchOccidArr);
 			}
-			if ($this->includeMaterialSample == 2){
+			if ($this->includeMaterialSample){
 				$this->writeMaterialSampleData($materialSampleHandler, $batchOccidArr);
 				$materialSampleHandler->__destruct();
 			}
@@ -1801,7 +1800,7 @@ private function writeOccurrenceFile(){
 			$this->logOrEcho($this->errorMessage);
 		}
 		$this->logOrEcho('Done! (' . date('h:i:s A') . ")\n");
-		if ($this->includeMaterialSample == 2) $this->logOrEcho('Material Sample extension file created (' . date('h:i:s A') . ')... ');
+		if ($this->includeMaterialSample) $this->logOrEcho('Material Sample extension file created (' . date('h:i:s A') . ')... ');
 		return $filePath;
 	}
 
@@ -2161,19 +2160,19 @@ public function setDelimiter($d){
 	}
 
 	public function setIncludeDets($includeDets){
-		$this->includeDets = $includeDets;
+		if($includeDets) $this->includeDets = true;
 	}
 
 	public function setIncludeImgs($includeImgs){
-		$this->includeImgs = $includeImgs;
+		if($includeImgs) $this->includeImgs = true;
 	}
 
 	public function setIncludeAttributes($include){
-		$this->includeAttributes = $include;
+		if($include) $this->includeAttributes = true;
 	}
 
 	public function setIncludeMaterialSample($include){
-		$this->includeMaterialSample = $include;
+		if($include) $this->includeMaterialSample = true;
 	}
 
 	public function hasAttributes(){