Merge pull request #24 from BioKIC/master

Synchronize with BioKIC/Symbiota developments
BioKIC · Nov 9, 2023 · 61d7f0a · 61d7f0a
2 parents 874a3d5 + 5b8fe4b
commit 61d7f0a
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Showing 90 changed files with 1,257 additions and 1,124 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/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/checklists/vamissingtaxa.php b/checklists/vamissingtaxa.php
@@ -84,8 +84,8 @@
 							ksort($missingArr);
 							foreach($missingArr as $sciname => $sArr){
 								foreach($sArr as $occid => $oArr){
-									$sciStr = $sciname;
-									if($sciStr != $oArr['o_sn']) $sciStr .= ' (syn: '.$oArr['o_sn'].')';
+									$sciStr = $oArr['o_sn'];
+									if(strtolower($sciname) != strtolower($oArr['o_sn'])) $sciStr .= ' (='.$sciname.')';
 									echo '<tr>';
 									echo '<td><input name="occids[]" type="checkbox" value="'.$occid.'-'.$oArr['tid'].'" /></td>';
 									echo '<td><a href="../taxa/index.php?taxon='.$oArr['tid'].'" target="_blank">'.$sciStr.'</a></td>';

diff --git a/classes/ChecklistLoaderManager.php b/classes/ChecklistLoaderManager.php
@@ -40,7 +40,9 @@ public function uploadCsvList($thesId){
 			ob_flush();
 			flush();
 			while($valueArr = fgetcsv($fh)){
-				$sciNameStr = $this->cleanInStr($valueArr[$headerArr["sciname"]]);
+				//Remove UTF-8 NO-BREAK SPACE codepoints
+				$sciNameStr = str_replace(chr(194).chr(160), ' ', $valueArr[$headerArr['sciname']]);
+				$sciNameStr = $this->cleanInStr($sciNameStr);
 				if($sciNameStr){
 					$tid = 0;
 					$rankId = 0;
@@ -60,7 +62,7 @@ public function uploadCsvList($thesId){
 							'WHERE ts.taxauthid = 1 ';
 					}
 					$cleanSciName = $this->encodeString($sciNameArr['sciname']);
-					$sql .= 'AND (t.sciname IN("'.$sciNameStr.'"'.($cleanSciName?',"'.$cleanSciName.'"':'').'))';
+					$sql .= 'AND (t.sciname IN("'.$sciNameStr.'"'.($cleanSciName && $cleanSciName != $sciNameStr ?',"'.$cleanSciName.'"':'').'))';
 					$rs = $this->conn->query($sql);
 					if($rs){
 						while($row = $rs->fetch_object()){
@@ -106,7 +108,6 @@ public function uploadCsvList($thesId){
 							}
 
 							$sql = 'INSERT INTO fmchklsttaxalink (tid,clid'.$sqlInsert.') VALUES ('.$tid.', '.$this->clid.$sqlValues.')';
-							//echo $sql; exit;
 							if($this->conn->query($sql)){
 								$successCnt++;
 							}

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)){
 			$this->errorMessage = 'voucherAlreadyLinked';
@@ -364,23 +364,32 @@ public function linkVoucher($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;
 	}
 
 	public function linkTaxaVouchers($occidArr, $useCurrentTaxon = true, $linkVouchers = true){
-		$tidsUsed = array();
+		$tidMap = array();
 		foreach($occidArr as $v){
 			$vArr = explode('-',$v);
-			$tid = $vArr[1];
-			$occid = $vArr[0];
-			if(count($vArr) == 2 && is_numeric($occid) && is_numeric($tid)){
-				if($useCurrentTaxon) $tid = $this->getTidAccepted($tid);
-				if(!in_array($tid, $tidsUsed)){
-					//Add name to checklist
-					$clTaxaID = $this->insertChecklistTaxaLink($tid);
-					$tidsUsed[] = $tid;
+			if(count($vArr) == 2){
+				$tid = $vArr[1];
+				$occid = $vArr[0];
+				if(is_numeric($occid) && is_numeric($tid)){
+					$clTaxaID = 0;
+					if(isset($tidMap[$tid])) $clTaxaID = $tidMap[$tid];
+					else{
+						$clTaxaID = $this->getClTaxaID($tid);
+						if(!$clTaxaID){
+							if($useCurrentTaxon){
+								$tid = $this->getTidAccepted($tid);
+							}
+							//Add name to checklist
+							$clTaxaID = $this->insertChecklistTaxaLink($tid);
+						}
+						$tidMap[$tid] = $clTaxaID;
+					}
 					if($clTaxaID && $linkVouchers){
 						$this->insertVoucher($clTaxaID, $occid);
 					}
@@ -495,16 +504,39 @@ private function transferVouchers($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;
+		$resultTid = 0;
 		if(is_numeric($tid)){
-			$sql = 'SELECT clTaxaID FROM fmchklsttaxalink WHERE clid = ? AND tid = ? AND morphospecies = ?';
-			if($stmt = $this->conn->prepare($sql)) {
+			$sql = 'SELECT c.clTaxaID, c.tid
+				FROM fmchklsttaxalink c INNER JOIN taxstatus ts ON c.tid = ts.tid
+				INNER JOIN taxstatus ts2 ON ts.tidaccepted = ts2.tidaccepted
+				WHERE ts.taxAuthID = 1 AND ts2.taxAuthID = 1 AND c.clid = ? AND ts2.tid = ? AND c.morphospecies = ?';
+			if($stmt = $this->conn->prepare($sql)){
 				if($stmt->bind_param('iis', $this->clid, $tid, $morphoSpecies)){
 					$stmt->execute();
-					$stmt->bind_result($clTaxaID);
-					$stmt->fetch();
+					$stmt->bind_result($clTaxaID, $resultTid);
+					while($stmt->fetch()){
+						//If there are multiple accepted records, take preferrence to clTaxaID associated with the accepted taxon
+						if($tid == $resultTid) break;
+					}
 					$stmt->close();
 				}
 				else $this->errorMessage = 'ERROR binding params for getClTaxaID: '.$this->conn->error;

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/ChecklistVoucherReport.php b/classes/ChecklistVoucherReport.php
@@ -68,14 +68,15 @@ public function getNewVouchers($startLimit = 500, $includeAll = 1){
 		if($this->clid){
 			if($sqlFrag = $this->getSqlFrag()){
 				if($includeAll == 1 || $includeAll == 2){
-					$sql = 'SELECT DISTINCT cl.clTaxaID, TRIM(CONCAT_WS(" ",t.sciname,cl.morphoSpecies)) AS clsciname, o.occid, c.institutioncode, c.collectioncode, o.catalognumber, '.
-						'o.tidinterpreted, o.sciname, o.recordedby, o.recordnumber, o.eventdate, CONCAT_WS("; ",o.country, o.stateprovince, o.county, o.locality) as locality '.
-						'FROM omoccurrences o LEFT JOIN omcollections c ON o.collid = c.collid '.
-						'INNER JOIN taxstatus ts ON o.tidinterpreted = ts.tid '.
-						'INNER JOIN fmchklsttaxalink cl ON ts.tidaccepted = cl.tid '.
-						'INNER JOIN taxa t ON cl.tid = t.tid ';
+					$sql = 'SELECT DISTINCT cl.clTaxaID, TRIM(CONCAT_WS(" ",t.sciname,cl.morphoSpecies)) AS clsciname, o.occid, c.institutioncode, c.collectioncode, o.catalognumber,
+						o.tidinterpreted, o.sciname, o.recordedby, o.recordnumber, o.eventdate, CONCAT_WS("; ",o.country, o.stateprovince, o.county, o.locality) as locality
+						FROM omoccurrences o LEFT JOIN omcollections c ON o.collid = c.collid
+						INNER JOIN taxstatus ts ON o.tidinterpreted = ts.tid
+						INNER JOIN taxstatus ts2 ON ts.tidaccepted = ts2.tidaccepted
+						INNER JOIN fmchklsttaxalink cl ON ts2.tid = cl.tid
+						INNER JOIN taxa t ON cl.tid = t.tid ';
 					$sql .= $this->getTableJoinFrag($sqlFrag);
-					$sql .= 'WHERE ('.$sqlFrag.') AND (cl.clid = '.$this->clid.') AND (ts.taxauthid = 1) ';
+					$sql .= 'WHERE ('.$sqlFrag.') AND (cl.clid = '.$this->clid.') AND (ts.taxauthid = 1) AND (ts2.taxauthid = 1) ';
 					if($includeAll == 1){
 						$idStr = $this->getVoucherTidStr('tid');
 						if($idStr) $sql .= 'AND cl.tid NOT IN('.$idStr.') ';
@@ -85,12 +86,11 @@ public function getNewVouchers($startLimit = 500, $includeAll = 1){
 						if($idStr) $sql .= 'AND o.occid NOT IN('.$idStr.') ';
 					}
 					$sql .= 'ORDER BY ts.family, o.sciname LIMIT '.$startLimit.', 1000';
-					//echo '<div>'.$sql.'</div>';
 					$rs = $this->conn->query($sql);
 					while($r = $rs->fetch_object()){
 						$retArr[$r->clTaxaID][$r->occid]['tid'] = $r->tidinterpreted;
 						$sciName = $r->clsciname;
-						if($r->clsciname <> $r->sciname) $sciName .= '<br/>specimen id: '.$r->sciname;
+						if($r->clsciname <> $r->sciname) $sciName .= '<br/>[specimen id: '.$r->sciname.']';
 						$retArr[$r->clTaxaID][$r->occid]['sciname'] = $sciName;
 						$collCode = '';
 						if(!$r->catalognumber || strpos($r->catalognumber, $r->institutioncode) === false){

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(){

diff --git a/classes/DwcArchiverOccurrence.php b/classes/DwcArchiverOccurrence.php
@@ -321,7 +321,7 @@ public function getOccurrenceArr(){
 			elseif($this->schemaType == 'coge'){
 				$targetArr = array('id','basisOfRecord','institutionCode','collectionCode','catalogNumber','occurrenceID','family','scientificName','scientificNameAuthorship',
 					'kingdom','phylum','class','order','genus','specificEpithet','infraSpecificEpithet','recordedBy','recordNumber','eventDate','year','month','day','fieldNumber',
-					'locationID','continent','waterBody','islandGroup','island','country','stateProvince','county','municipality',
+					'eventID', 'locationID','continent','waterBody','islandGroup','island','country','stateProvince','county','municipality',
 					'locality','localitySecurity','geodeticDatum','decimalLatitude','decimalLongitude','verbatimCoordinates',
 					'minimumElevationInMeters','maximumElevationInMeters','verbatimElevation','maximumDepthInMeters','minimumDepthInMeters','establishmentMeans',
 					'occurrenceRemarks','dateEntered','dateLastModified','recordID','references','collID');