Hotfix 2024 08 07 (#1606)

Taxonomy Editor - Add taxamaps table to data remapping functions when taxon is deleted or remapped. Resolves [issue #1598](#1598) - Minor error fixes and adjustments to language file imports Glossary Management - Fix issue associated within new sources failing to save when displaying all terms without a taxon group selected. Resolves [issue #1584](#1584) - Display all source definitions when taxon group is not selected - Minor adjustments to language terms and misc code Occurrence Cleaner - duplicate merge tool - Replace catalog numbers as the unique identifier for duplicate cluster with numeric key, thus avoiding interference of target form element due to existence of space or period within catalog number. Resolves [issue #1471](#1471) - Internationize first submit button - Add header and footer to cleaning page Specimen Upload - Remove display of Data Versioning Checkbox option for snapshot datasets. Batch import data versioning is only available for live managed collections.
BioKIC · Aug 8, 2024 · 49ec39d · 49ec39d
1 parent 58a886e
commit 49ec39d
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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';