Merge pull request #1179 from BioKIC/master

Hotfix 2024 08 07 (#1606)
BioKIC · Aug 12, 2024 · b9e54ce · b9e54ce
2 parents 8a03036 + 49ec39d
commit b9e54ce
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Showing 15 changed files with 141 additions and 78 deletions.
diff --git a/classes/GlossaryManager.php b/classes/GlossaryManager.php
@@ -578,7 +578,7 @@ public function getTaxonSources($tidStr = ''){
 
 	public function addSource($pArr){
 		$status = true;
-		if(is_numeric($pArr['tid'])){
+		if($pArr['tid'] && is_numeric($pArr['tid'])){
 			$terms = $this->cleanInStr($pArr['contributorTerm']);
 			$images = $this->cleanInStr($pArr['contributorImage']);
 			$translator = $this->cleanInStr($pArr['translator']);

diff --git a/classes/OccurrenceCleaner.php b/classes/OccurrenceCleaner.php
@@ -45,7 +45,7 @@ public function getDuplicateCatalogNumber($type, $start, $limit = 500){
 		}
 		$rs->free();
 
-		$retArr = array();
+		$stagingArr = array();
 		if($dupArr){
 			$sqlFrag = '';
 			if($type=='cat'){
@@ -54,13 +54,15 @@ public function getDuplicateCatalogNumber($type, $start, $limit = 500){
 			else{
 				$sqlFrag = 'occid, otherCatalogNumbers, otherCatalogNumbers AS dupid FROM omoccurrences WHERE collid = '.$this->collid.' AND otherCatalogNumbers IN("'.implode('","', $dupArr).'") ORDER BY otherCatalogNumbers';
 			}
-			$retArr = $this->getDuplicates($sqlFrag);
+			$stagingArr = $this->getDuplicates($sqlFrag);
 		}
 
 		if($type=='other' && count($dupArr) < $limit){
-			$retArr = array_merge($retArr, $this->setAdditionalIdentifiers($cnt, ($limit - count($dupArr))));
+			$stagingArr = array_merge($stagingArr, $this->setAdditionalIdentifiers($cnt, ($limit - count($dupArr))));
 		}
 
+		//Replace catalog number keys with renumbered numeric keys, thus avoid unusual characters interferring with naming form target element
+		$retArr = array_values($stagingArr);
 		return $retArr;
 	}
 
@@ -152,7 +154,7 @@ private function getDuplicates($sqlFragment){
 			$sqlFragment;
 		$rs = $this->conn->query($sql);
 		while($row = $rs->fetch_assoc()){
-			$retArr[$row['dupid']][$row['occid']] = array_change_key_case($row);
+			$retArr[strtolower($row['dupid'])][$row['occid']] = array_change_key_case($row);
 		}
 		$rs->free();
 		return $retArr;
@@ -162,6 +164,7 @@ public function mergeDupeArr($occidArr){
 		$status = true;
 		$this->verboseMode = 2;
 		$editorManager = new OccurrenceEditorManager($this->conn);
+		$editorManager->setCollId($this->collid);
 		foreach($occidArr as $target => $occArr){
 			$mergeArr = array($target);
 			foreach($occArr as $source){

diff --git a/classes/SpecUploadBase.php b/classes/SpecUploadBase.php
@@ -896,9 +896,7 @@ protected function transferOccurrences(){
 			$this->outputMsg('<li>Transferring edits to versioning tables...</li>');
 			$this->versionExternalEdits();
 		}
-		elseif($this->collMetadataArr['managementtype'] == 'Live Data' && $this->uploadType != $this->RESTOREBACKUP){
-			$this->versionInternalEdits();
-		}
+		$this->versionInternalEdits();
 		$transactionInterval = 1000;
 		$this->outputMsg('<li>Updating existing records in batches of '.$transactionInterval.'... </li>');
 		//Grab specimen intervals for updating records in batches
@@ -1003,23 +1001,25 @@ protected function transferOccurrences(){
 
 	private function versionInternalEdits(){
 		if($this->versionDataEdits){
-			$sqlFrag = '';
-			$excludedFieldArr = array('dateentered','observeruid');
-			foreach($this->targetFieldArr as $field){
-				if(!in_array($field, $excludedFieldArr)) $sqlFrag .= ',u.'.$field.',o.'.$field.' as old_'.$field;
-			}
-			$sql = 'SELECT o.occid'.$sqlFrag.' FROM omoccurrences o INNER JOIN uploadspectemp u ON o.occid = u.occid WHERE o.collid IN('.$this->collId.') AND u.collid IN('.$this->collId.')';
-			$rs = $this->conn->query($sql);
-			while($r = $rs->fetch_assoc()){
+			if($this->collMetadataArr['managementtype'] == 'Live Data' && $this->uploadType != $this->RESTOREBACKUP){
+				$sqlFrag = '';
+				$excludedFieldArr = array('dateentered','observeruid');
 				foreach($this->targetFieldArr as $field){
-					if(in_array($field, $excludedFieldArr)) continue;
-					if($r[$field] != $r['old_'.$field]){
-						if($this->uploadType == $this->SKELETAL && $r['old_'.$field]) continue;
-						$this->insertOccurEdit($r['occid'], $field, $r[$field], $r['old_'.$field]);
+					if(!in_array($field, $excludedFieldArr)) $sqlFrag .= ',u.'.$field.',o.'.$field.' as old_'.$field;
+				}
+				$sql = 'SELECT o.occid'.$sqlFrag.' FROM omoccurrences o INNER JOIN uploadspectemp u ON o.occid = u.occid WHERE o.collid IN('.$this->collId.') AND u.collid IN('.$this->collId.')';
+				$rs = $this->conn->query($sql);
+				while($r = $rs->fetch_assoc()){
+					foreach($this->targetFieldArr as $field){
+						if(in_array($field, $excludedFieldArr)) continue;
+						if($r[$field] != $r['old_'.$field]){
+							if($this->uploadType == $this->SKELETAL && $r['old_'.$field]) continue;
+							$this->insertOccurEdit($r['occid'], $field, $r[$field], $r['old_'.$field]);
+						}
 					}
 				}
+				$rs->free();
 			}
-			$rs->free();
 		}
 	}
 

diff --git a/classes/TaxonomyEditorManager.php b/classes/TaxonomyEditorManager.php
@@ -1,6 +1,8 @@
 <?php
 include_once($SERVER_ROOT.'/classes/Manager.php');
-include_once($SERVER_ROOT.'/content/lang/classes/TaxonomyEditorManager.'.$LANG_TAG.'.php');
+if($LANG_TAG == 'en' || !file_exists($SERVER_ROOT . '/content/lang/classes/TaxonomyEditorManager.' . $LANG_TAG . '.php'))
+	include_once($SERVER_ROOT . '/content/lang/classes/TaxonomyEditorManager.en.php');
+else include_once($SERVER_ROOT . '/content/lang/classes/TaxonomyEditorManager.' . $LANG_TAG . '.php');
 
 class TaxonomyEditorManager extends Manager{
 
@@ -680,6 +682,14 @@ public function verifyDeleteTaxon(){
 		}
 		$rs->free();
 
+		//Taxon maps
+		$sql ='SELECT COUNT(mid) AS cnt FROM taxamaps WHERE tid = '.$this->tid;
+		$rs = $this->conn->query($sql);
+		while($r = $rs->fetch_object()){
+			$retArr['map'] = $r->cnt;
+		}
+		$rs->free();
+
 		//Vernaculars
 		$sql ='SELECT vernacularname FROM taxavernaculars WHERE tid = '.$this->tid;
 		$rs = $this->conn->query($sql);
@@ -750,6 +760,10 @@ public function transferResources($targetTid){
 			$sql ='UPDATE IGNORE images SET tid = '.$targetTid.' WHERE occid IS NULL AND tid = '.$this->tid;
 			if(!$this->conn->query($sql)) $this->warningArr[] = (isset($this->langArr['ERROR_TRANSFER_IMGS'])?$this->langArr['ERROR_TRANSFER_IMGS']:'ERROR transferring image links').' ('.$this->conn->error.')';
 
+			//Taxon maps
+			$sql ='UPDATE IGNORE taxamaps SET mid = '.$targetTid.' WHERE tid = '.$this->tid;
+			if(!$this->conn->query($sql)) $this->warningArr[] = $this->langArr['ERROR_TRANSFER_MAPS'] . ' (' . $this->conn->error . ')';
+
 			//Vernaculars
 			$sql ='UPDATE IGNORE taxavernaculars SET tid = '.$targetTid.' WHERE tid = '.$this->tid;
 			if(!$this->conn->query($sql)) $this->warningArr[] = (isset($this->langArr['ERROR_TRANSFER_VERNACULARS'])?$this->langArr['ERROR_TRANSFER_VERNACULARS']:'ERROR transferring vernaculars').' ('.$this->conn->error.')';
@@ -800,6 +814,10 @@ public function deleteTaxon(){
 		if(!$this->conn->query($sql)) $this->warningArr[] = 'ERROR deleting remaining links in deleteTaxon method ('.$this->conn->error.')';
 		*/
 
+		//Taxon maps
+		$sql ='DELETE FROM taxamaps WHERE tid = '.$this->tid;
+		if(!$this->conn->query($sql)) $this->warningArr[] = $this->langArr['ERROR_DEL_MAPS'] . ' (' . $this->conn->error . ')';
+
 		//Vernaculars
 		$sql ='DELETE FROM taxavernaculars WHERE tid = '.$this->tid;
 		if(!$this->conn->query($sql)) $this->warningArr[] = (isset($this->langArr['ERROR_DEL_VERNACULARS'])?$this->langArr['ERROR_DEL_VERNACULARS']:'ERROR deleting vernaculars in deleteTaxon method').' ('.$this->conn->error.')';

diff --git a/collections/admin/specuploadmap.php b/collections/admin/specuploadmap.php
@@ -627,13 +627,15 @@ function pkChanged(selObj){
 								</ul>
 								<?php
 							}
-							$versionCheckedStr = '';
-							if($isLiveData) $versionCheckedStr = 'checked';
+							if($isLiveData){
+								?>
+								<div style="margin:10px 0px;">
+									<input name="versiondata" type="checkbox" value="1">
+									<?php echo (isset($LANG['VERSION_DATA_CHANGES'])?$LANG['VERSION_DATA_CHANGES']:'Version data changes'); ?>
+								</div>
+								<?php
+							}
 							?>
-							<div style="margin:10px 0px;">
-								<input name="versiondata" type="checkbox" value="1" <?php echo $versionCheckedStr; ?> />
-								<?php echo (isset($LANG['VERSION_DATA_CHANGES'])?$LANG['VERSION_DATA_CHANGES']:'Version data changes'); ?>
-							</div>
 							<div style="margin:10px 0px;">
 								<input name="verifyimages" type="checkbox" value="1" />
 								<?php echo (isset($LANG['VER_LINKS_MEDIA'])?$LANG['VER_LINKS_MEDIA']:'Verify image links from associatedMedia field'); ?>

diff --git a/collections/cleaning/duplicatesearch.php b/collections/cleaning/duplicatesearch.php
@@ -96,6 +96,9 @@ function batchSwitchTargetSpecimens(cbElem){
 	</script>
 </head>
 <body style="margin-left:10px; width: 100%">
+	<?php
+	include($SERVER_ROOT . '/includes/header.php');
+	?>
 	<div class='navpath' style="margin:10px">
 		<a href="../../index.php"><?php echo $LANG['HOME']; ?></a> &gt;&gt;
 		<a href="../misc/collprofiles.php?collid=<?php echo $collid; ?>&emode=1"><?php echo $LANG['COL_MAN']; ?></a> &gt;&gt;
@@ -122,7 +125,7 @@ function batchSwitchTargetSpecimens(cbElem){
 								$href = 'duplicatesearch.php?collid='.$collid.'&action='.$action.'&start='.($start+$limit);
 								echo '<div style="float:right;"><a href="'.$href.'"><b>'.$LANG['NEXT'].' '.$limit.' '.$LANG['RECORDS'].' &gt;&gt;</b></a></div>';
 							}
-							echo '<div style="float:left;margin-bottom:4px;margin-left:15px;"><input name="action" type="submit" value="Merge Duplicate Records" /></div>';
+							echo '<div style="float:left;margin-bottom:4px;margin-left:15px;"><button name="action" type="submit" value="mergeDuplicates">' . $LANG['MERGE_DUPES'] . '</button></div>';
 							echo '<div style="float:left;margin-left:15px;"><b>'.($start+1).' '.$LANG['TO'].' '.($start+$recCnt).' '.$LANG['DUP_CLUSTERS'].' </b></div>';
 							?>
 						</div>
@@ -177,7 +180,7 @@ function batchSwitchTargetSpecimens(cbElem){
 							</table>
 						</div>
 						<div style="margin:15px;">
-							<button name="action" type="submit" value="Merge Duplicate Records"><?php echo $LANG['MERGE_DUPES']; ?></button>
+							<button name="action" type="submit" value="mergeDuplicates"><?php echo $LANG['MERGE_DUPES']; ?></button>
 						</div>
 					</form>
 					<?php
@@ -190,7 +193,7 @@ function batchSwitchTargetSpecimens(cbElem){
 					<?php
 				}
 			}
-			elseif($action == 'Merge Duplicate Records'){
+			elseif($action == 'mergeDuplicates'){
 				?>
 				<ul>
 					<li><?php echo $LANG['DUPE_MERGING_STARTED']; ?></li>
@@ -199,7 +202,7 @@ function batchSwitchTargetSpecimens(cbElem){
 					foreach($_POST['dupid'] as $v){
 						$vArr = explode('|',$v);
 						if(count($vArr) > 1){
-							$target = $_POST['dup'.str_replace(' ', '_', $vArr[0]).'target'];
+							$target = $_POST['dup' . $vArr[0] . 'target'];
 							if($target != $vArr[1]) $dupArr[$target][] = $vArr[1];
 						}
 					}
@@ -229,5 +232,8 @@ function batchSwitchTargetSpecimens(cbElem){
 		}
 		?>
 	</div>
+	<?php
+	include($SERVER_ROOT . '/includes/footer.php');
+	?>
 </body>
 </html>
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');
-$CODE_VERSION = '3.0.33';
+$CODE_VERSION = '3.0.34';
 
 if(!isset($CLIENT_ROOT) && isset($clientRoot)) $CLIENT_ROOT = $clientRoot;
 if(substr($CLIENT_ROOT,-1) == '/') $CLIENT_ROOT = substr($CLIENT_ROOT,0,strlen($CLIENT_ROOT)-1);

diff --git a/content/lang/classes/TaxonomyEditorManager.en.php b/content/lang/classes/TaxonomyEditorManager.en.php
@@ -22,6 +22,7 @@
 $LANG['WARNING_UPDATE_IMAGES'] = 'WARNING: Taxon loaded into taxa, but occurrence images must be updated with matching name';
 $LANG['ERROR_INSERT'] = 'ERROR inserting new taxon';
 $LANG['ERROR_TRANSFER_IMGS'] = 'ERROR transferring image links';
+$LANG['ERROR_TRANSFER_MAPS'] = 'ERROR transferring taxon map links';
 $LANG['ERROR_TRANSFER_VERNACULARS'] = 'ERROR transferring vernaculars';
 $LANG['ERROR_TRANSFER_TAXADESC'] = 'ERROR transferring taxadescblocks';
 $LANG['ERROR_TRANSFER_CHECKLIST'] = 'ERROR transferring checklist links';
@@ -33,6 +34,7 @@
 $LANG['ERROR_TRANSFER_SYN'] = 'ERROR transferring synonyms taxa';
 $LANG['ERROR_TRANSFER_TAXENUMTREE'] = 'ERROR resetting taxaEnumTree index';
 $LANG['ERROR_SETTING_NULL'] = 'ERROR setting tid to NULL for occurrence images in deleteTaxon method';
+$LANG['ERROR_DEL_MAPS'] = 'ERROR deleting taxon maps wtihin deleteTaxon method';
 $LANG['ERROR_DEL_VERNACULARS'] = 'ERROR deleting vernaculars in deleteTaxon method';
 $LANG['ERROR_DEL_TAXDESC'] = 'ERROR deleting taxa description blocks in deleteTaxon method';
 $LANG['ERROR_TIDINT_NULL'] = 'ERROR setting tidinterpreted to NULL in deleteTaxon method';

diff --git a/content/lang/glossary/index.en.php b/content/lang/glossary/index.en.php
@@ -30,7 +30,8 @@
 $LANG['KEYWORD'] = 'with keyword ';
 $LANG['DISP_SRC'] = 'Display Sources';
 $LANG['ADD_SRC'] = 'Add Sources';
-$LANG['TAX_CONTR'] = 'Contributors for Taxonomic Group';
+$LANG['TAX_CONTR'] = 'Contributors for Taxonomic Group(s)';
+$LANG['SOURCE_SCINAME'] = 'Taxon';
 $LANG['TERM_CONTR'] = 'Terms and Definitions contributed by';
 $LANG['IMG_CONTR'] = 'Images contributed by';
 $LANG['TRANS_BY'] = 'Translations by';

diff --git a/content/lang/glossary/index.es.php b/content/lang/glossary/index.es.php
@@ -30,7 +30,8 @@
 $LANG['KEYWORD'] = 'con palabra clave';
 $LANG['DISP_SRC'] = 'Desplegar Fuentes';
 $LANG['ADD_SRC'] = 'Añadir Fuentes';
-$LANG['TAX_CONTR'] = 'Contribuyentes para Grupo Taxonómico';
+$LANG['TAX_CONTR'] = 'Contribuyentes para Grupo(s) Taxonómico(s)';
+$LANG['SOURCE_SCINAME'] = 'Taxon';
 $LANG['TERM_CONTR'] = 'Términos y Definiciones contribuídas por';
 $LANG['IMG_CONTR'] = 'Imágenes contribuídas por';
 $LANG['TRANS_BY'] = 'Traducciones por';

diff --git a/content/lang/taxa/taxonomy/taxonomydelete.en.php b/content/lang/taxa/taxonomy/taxonomydelete.en.php
@@ -18,6 +18,8 @@
 $LANG['WARNING'] = 'Warning';
 $LANG['IMGS_LINKED'] = 'images linked to this taxon';
 $LANG['NO_IMGS'] = 'no images linked to this taxon';
+$LANG['MAPS_LINKED'] = 'taxon maps linked to this taxon';
+$LANG['NO_MAPS'] = 'no taxon maps linked to this taxon';
 $LANG['VERNACULARS'] = 'Vernaculars';
 $LANG['LINKED_VERNACULAR'] = 'Warning, linked vernacular names';
 $LANG['NO_VERNACULAR'] = 'no vernacular names linked to this taxon';

diff --git a/content/lang/taxa/taxonomy/taxonomydelete.es.php b/content/lang/taxa/taxonomy/taxonomydelete.es.php
@@ -18,6 +18,8 @@
 $LANG['WARNING'] = 'Advertencia';
 $LANG['IMGS_LINKED'] = 'imágenes vinculadas a este taxón';
 $LANG['NO_IMGS'] = 'no hay imágenes vinculadas a este taxón';
+$LANG['MAPS_LINKED'] = 'mapas vinculadas a este taxón';
+$LANG['NO_MAPS'] = 'no hay mapas vinculadas a este taxón';
 $LANG['VERNACULARS'] = 'Nombres comunes';
 $LANG['LINKED_VERNACULAR'] = 'Advertencia, existen nombres comunes enlazados';
 $LANG['NO_VERNACULAR'] = 'no existen nombres comunes enlazados con este taxón';