3.1.1 Release: Merge Hotfix branch into Master (#1747)

* Occurrence Mapping: Adjust SQL to relax enforcement of link to taxon thesaurus, thus to include records with coordinates but lacking thesaurus relationship * Styling: Various styling, spacing, and display adjustments * Occurrence search: add type attribute to buttons to avoid defaulting as submit buttons * Occurrence Profile: Fix error triggered when otherCatalogNumbers are used to create backlink to original snapshot record within external institution web resource * Occurrence editing functions -- Fix fatal error triggered by cloning an occurrence record with the create association option selected -- Fix fatal error triggered when quick association feature is activated within occurrence editor -- Fix fatal error when deleting an occurrence when the occurrence was previously deleted (e.g. record already in omoccurarchive) -- Adjust occurrence restore option to dynamically determine associationType when restoring a record that was deleted prior to this field being added as a required input -- If resource association does not have an objectID, use url as the display text * Taxonomy editor: bug fix triggered by adding a child directly to the root node of the thesaurus (e.g. kingdom) * Scientific name parsing utility functions: Integrate cleanInfra function directly into code. It served no purpose being separate, and was also causing a bug where parent authors were being incorrectly merged with insfraspecific authors --------- Co-authored-by: Katie Pearson <[email protected]> Co-authored-by: Mark <[email protected]> Co-authored-by: MuchQuak <[email protected]> Co-authored-by: Logan Wilt <[email protected]>
BioKIC · Sep 26, 2024 · 697749d · 697749d
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Showing 21 changed files with 172 additions and 147 deletions.
diff --git a/api/app/Helpers/TaxonomyHelper.php b/api/app/Helpers/TaxonomyHelper.php
@@ -126,7 +126,19 @@ public static function parseScientificName($inStr, $conn = null, $rankId = 0, $k
 					//cycles through the final terms to evaluate and extract infraspecific data
 					while($sciStr = array_shift($sciNameArr)){
 						if($testArr = self::cleanInfra($sciStr)){
-							self::setInfraNode($sciStr, $sciNameArr, $retArr, $authorArr, $testArr['infra']);
+							if($sciNameArr){
+								$infraStr = array_shift($sciNameArr);
+								if(preg_match('/^[a-z]{3,}$/', $infraStr)){
+									$retArr['unitind3'] = $testArr['infra'];
+									$retArr['unitname3'] = $infraStr;
+									unset($authorArr);
+									$authorArr = array();
+								}
+								else{
+									$authorArr[] = $sciStr;
+									$authorArr[] = $infraStr;
+								}
+							}
 						}
 						elseif($kingdomName == 'Animalia' && !$retArr['unitname3'] && ($rankId == 230 || preg_match('/^[a-z]{3,}$/',$sciStr) || preg_match('/^[A-Z]{3,}$/',$sciStr))){
 							$retArr['unitind3'] = '';
@@ -246,22 +258,6 @@ public static function cleanInfra($testStr){
 		return $retArr;
 	}
 
-	private static function setInfraNode($sciStr, &$sciNameArr, &$retArr, &$authorArr, $rankTag){
-		if($sciNameArr){
-			$infraStr = array_shift($sciNameArr);
-			if(preg_match('/^[a-z]{3,}$/', $infraStr)){
-				$retArr['unitind3'] = $rankTag;
-				$retArr['unitname3'] = $infraStr;
-				unset($authorArr);
-				$authorArr = array();
-			}
-			else{
-				$authorArr[] = $sciStr;
-				$authorArr[] = $infraStr;
-			}
-		}
-	}
-
 	//Taxonomic indexing functions
 	public static function rebuildHierarchyEnumTree($conn = null){
 		$status = true;

diff --git a/classes/DwcArchiverOccurrence.php b/classes/DwcArchiverOccurrence.php
@@ -498,11 +498,9 @@ public function getAssociationStr($occid, $associationType = null){
 	private function getAssociationJSON($occid) {
 
 		// Build SQL to find any associations for the occurrence record passed with occid
-		$sql = 'SELECT occid, occidAssociate, relationship, subType, identifier,' .
-			'basisOfRecord, resourceUrl, verbatimSciname, locationOnHost ' .
-			'FROM omoccurassociations ' .
-			'WHERE (occid = ' . $occid . ' OR occidAssociate = ' . $occid . ') ';
-
+		$sql = 'SELECT occid, associationType, occidAssociate, relationship, subType, identifier, basisOfRecord, resourceUrl, verbatimSciname, locationOnHost 
+			FROM omoccurassociations 
+			WHERE (occid = ' . $occid . ' OR occidAssociate = ' . $occid . ') ';
 		if ($rs = $this->conn->query($sql)) {
 
 			// No associations, so just return an empty string, and quit the function

diff --git a/classes/OccurrenceAssociations.php b/classes/OccurrenceAssociations.php
@@ -164,9 +164,9 @@ private function parseAssocSpecies($assocSpeciesStr,$occid){
 
 	private function databaseAssocSpecies($assocArr, $occid){
 		if($assocArr){
-			$sql = 'INSERT INTO omoccurassociations(occid, verbatimsciname, relationship) VALUES';
+			$sql = 'INSERT INTO omoccurassociations(occid, associationType, verbatimsciname, relationship) VALUES';
 			foreach($assocArr as $aStr){
-				$sql .= '('.$occid.',"'.$this->conn->real_escape_string($aStr).'","associatedSpecies"), ';
+				$sql .= '('.$occid.', "observational", "'.$this->conn->real_escape_string($aStr).'","associatedSpecies"), ';
 			}
 			$sql = trim($sql,', ');
 			//echo $sql; exit;

diff --git a/classes/OccurrenceEditorManager.php b/classes/OccurrenceEditorManager.php
@@ -1016,7 +1016,7 @@ public function editOccurrence($postArr, $editorStatus){
 							if($postArr['host']) $sqlHost = 'UPDATE omoccurassociations SET verbatimsciname = "'.$postArr['host'].'" WHERE associd = '.$postArr['hostassocid'].' ';
 							else $sqlHost = 'DELETE FROM omoccurassociations WHERE associd = '.$postArr['hostassocid'].' ';
 						}
-						else $sqlHost = 'INSERT INTO omoccurassociations(occid,relationship,verbatimsciname) VALUES('.$this->occid.',"host","'.$postArr['host'].'")';
+						else $sqlHost = 'INSERT INTO omoccurassociations(occid,associationType,relationship,verbatimsciname) VALUES('.$this->occid.',"observational","host","'.$postArr['host'].'")';
 						$this->conn->query($sqlHost);
 					}
 					//Update occurrence record
@@ -1341,7 +1341,8 @@ public function addOccurrence($postArr){
 				}
 				//Deal with host data
 				if(array_key_exists('host',$postArr)){
-					$sql = 'INSERT INTO omoccurassociations(occid,relationship,verbatimsciname) VALUES('.$this->occid.',"host","'.$this->cleanInStr($postArr['host']).'")';
+					$sql = 'INSERT INTO omoccurassociations(occid, associationType, relationship, verbatimsciname) 
+						VALUES('.$this->occid.', "observational", "host", "'.$this->cleanInStr($postArr['host']).'")';
 					if(!$this->conn->query($sql)){
 						$status .= '(WARNING adding host: '.$this->conn->error.') ';
 					}
@@ -1551,7 +1552,7 @@ public function deleteOccurrence($delOccid){
 				$archiveArr['dateDeleted'] = date('r').' by '.$USER_DISPLAY_NAME;
 				$archiveObj = json_encode($archiveArr);
 				$stage = 'Create Archive';
-				$sqlArchive = 'INSERT INTO omoccurarchive(archiveobj, occid, catalogNumber, occurrenceID, recordID) '.
+				$sqlArchive = 'REPLACE INTO omoccurarchive(archiveobj, occid, catalogNumber, occurrenceID, recordID) '.
 					'VALUES ("'.$this->cleanInStr($this->encodeStrTargeted($archiveObj,'utf8',$CHARSET)).'", '.$delOccid.','.
 					(isset($archiveArr['catalogNumber']) && $archiveArr['catalogNumber']?'"'.$this->cleanInStr($archiveArr['catalogNumber']).'"':'NULL').', '.
 					(isset($archiveArr['occurrenceID']) && $archiveArr['occurrenceID']?'"'.$this->cleanInStr($archiveArr['occurrenceID']).'"':'NULL').', '.
@@ -1620,10 +1621,14 @@ public function cloneOccurrence($postArr){
 				if($sourceOccid != $this->occid && !in_array($this->occid,$retArr)){
 					$retArr[$this->occid] = $this->occid;
 					if(isset($postArr['assocrelation']) && $postArr['assocrelation']){
-						$sql = 'INSERT INTO omoccurassociations(occid, occidAssociate, relationship,createdUid) '.
-							'values('.$this->occid.','.$sourceOccid.',"'.$postArr['assocrelation'].'",'.$GLOBALS['SYMB_UID'].') ';
-						if(!$this->conn->query($sql)){
-							$this->errorArr[] = $LANG['ERROR_ADDING_REL'].': '.$this->conn->error;
+						$sql = 'INSERT INTO omoccurassociations(occid, associationType, occidAssociate, relationship,createdUid) VALUES(?, "internalOccurrence", ?, ?, ?) ';
+						if($stmt = $this->conn->prepare($sql)){
+							$stmt->bind_param('iisi', $this->occid, $sourceOccid, $postArr['assocrelation'], $GLOBALS['SYMB_UID']);
+							$stmt->execute();
+							if($stmt->error){
+								$this->errorArr[] = $LANG['ERROR_ADDING_REL'].': '.$this->conn->error;
+							}
+							$stmt->close();
 						}
 					}
 					if(isset($postArr['carryoverimages']) && $postArr['carryoverimages']){

diff --git a/classes/OccurrenceIndividual.php b/classes/OccurrenceIndividual.php
@@ -413,14 +413,24 @@ private function setOccurrenceRelationships(){
 			}
 		}
 		if($relOccidArr){
-			$sql = 'SELECT o.occid, o.sciname,
-				CONCAT_WS("-",IFNULL(o.institutioncode, c.institutioncode), IFNULL(o.collectioncode, c.collectioncode)) as collcode, IFNULL(o.catalogNumber, o.otherCatalogNumbers) as catnum
+			$sql = 'SELECT o.occid, o.sciname, IFNULL(o.institutioncode, c.institutioncode) as instCode, IFNULL(o.collectioncode, c.collectioncode) as collCode, o.catalogNumber, o.occurrenceID, o.recordID
 				FROM omoccurrences o INNER JOIN omcollections c ON o.collid = c.collid
 				WHERE o.occid IN(' . implode(',', array_keys($relOccidArr)) . ')';
 			$rs = $this->conn->query($sql);
 			while($r = $rs->fetch_object()){
 				foreach($relOccidArr[$r->occid] as $targetAssocID){
-					$this->occArr['relation'][$targetAssocID]['objectID'] = $r->collcode . ':' . $r->catnum;
+					$objectID = $r->catalogNumber;
+					if($objectID) {
+						if(strpos($objectID, $r->instCode) === false){
+							//Append institution and collection code to catalogNumber, but only if it is not already included 
+							$collCode = $r->instCode;
+							if($r->collCode) $collCode .= '-' . $r->collCode;
+							$objectID = $collCode . ':' . $r->catalogNumber;
+						}
+					}
+					elseif($r->occurrenceID) $objectID = $r->occurrenceID;
+					else $objectID = $r->recordID;
+					$this->occArr['relation'][$targetAssocID]['objectID'] = $objectID;
 					$this->occArr['relation'][$targetAssocID]['sciname'] = $r->sciname;
 				}
 			}
@@ -545,26 +555,16 @@ private function setSource(){
 				$displayStr = $this->occArr['catalognumber'];
 			}
 			elseif(strpos($iUrl,'--OTHERCATALOGNUMBERS--') !== false && $this->occArr['othercatalognumbers']){
-				if(substr($this->occArr['othercatalognumbers'],0,1) == '{'){
-					if($this->occArr['othercatalognumbers']){
-						foreach($this->occArr['othercatalognumbers'] as $idKey => $idArr){
-							if(!$displayStr || $idKey == 'NEON sampleID' || $idKey == 'NEON sampleCode (barcode)'){
-								$displayStr = $idArr[0];
-								if($idKey == 'NEON sampleCode (barcode)') $iUrl = str_replace('sampleTag','barcode',$iUrl);
-								$indUrl = str_replace('--OTHERCATALOGNUMBERS--',$idArr[0],$iUrl);
-								if($idKey == 'NEON sampleCode (barcode)') break;
-							}
-						}
+				foreach($this->occArr['othercatalognumbers'] as $idArr){
+					$tagName = $idArr['name'];
+					$idValue = $idArr['value'];
+					if(!$displayStr || $tagName == 'NEON sampleID' || $tagName == 'NEON sampleCode (barcode)'){
+						$displayStr = $tagName;
+						if($tagName == 'NEON sampleCode (barcode)') $iUrl = str_replace('sampleTag','barcode',$iUrl);
+						$indUrl = str_replace('--OTHERCATALOGNUMBERS--', $idValue, $iUrl);
+						if($tagName == 'NEON sampleCode (barcode)') break;
 					}
 				}
-				else{
-					$ocn = str_replace($this->occArr['othercatalognumbers'], ',', ';');
-					$ocnArr = explode(';',$ocn);
-					$ocnValue = trim(array_pop($ocnArr));
-					if(stripos($ocnValue,':')) $ocnValue = trim(array_pop(explode(':',$ocnValue)));
-					$indUrl = str_replace('--OTHERCATALOGNUMBERS--',$ocnValue,$iUrl);
-					$displayStr = $ocnValue;
-				}
 			}
 			elseif(strpos($iUrl,'--OCCURRENCEID--') !== false && $this->occArr['occurrenceid']){
 				$indUrl = str_replace('--OCCURRENCEID--',$this->occArr['occurrenceid'],$iUrl);
@@ -1251,6 +1251,15 @@ public function restoreRecord(){
 				}
 				$rsAssoc->free();
 				foreach($recArr['assoc'] as $pk => $secArr){
+					if(empty($secArr['associationType'])){
+						if(!empty($secArr['occidAssociate'])) $secArr['associationType'] = 'internalOccurrence';
+						elseif(!empty($secArr['resourceUrl'])){
+							if(!empty($secArr['verbatimSciname'])) $secArr['associationType'] = 'externalOccurrence';
+							else $secArr['associationType'] = 'resource';
+						}
+						elseif(!empty($secArr['verbatimSciname'])) $secArr['associationType'] = 'observational';
+						else $secArr['associationType'] = 'resource';
+					}
 					$sql1 = 'INSERT INTO omoccurassociations(';
 					$sql2 = 'VALUES(';
 					foreach($secArr as $f => $v){

diff --git a/classes/OccurrenceMapManager.php b/classes/OccurrenceMapManager.php
@@ -59,7 +59,7 @@ public function getCoordinateMap($start, $limit){
 				'o.othercatalognumbers, c.institutioncode, c.collectioncode, c.CollectionName '.
 				'FROM omoccurrences o INNER JOIN omcollections c ON o.collid = c.collid ';
 
-			$this->sqlWhere .= 'AND ts.taxauthid = 1 ';
+			$this->sqlWhere .= 'AND (ts.taxauthid = 1 OR ts.taxauthid IS NULL) ';
 
 			$sql .= $this->getTableJoins($this->sqlWhere);
 
@@ -68,7 +68,6 @@ public function getCoordinateMap($start, $limit){
 			if(is_numeric($start) && $limit){
 				$sql .= "LIMIT ".$start.",".$limit;
 			}
-			//echo '//SQL: ' . $sql;
 			$result = $this->conn->query($sql);
 			$color = 'e69e67';
 			$occidArr = array();

diff --git a/classes/OmAssociations.php b/classes/OmAssociations.php
@@ -77,13 +77,13 @@ public function getAssociationArr($filter = null){
 			$rs = $this->conn->query($sql);
 			while($r = $rs->fetch_object()){
 				$prefix = '';
-				if(strpos($r->catalogNumber, $r->instCode) === false){
+				if($r->catalogNumber && strpos($r->catalogNumber, $r->instCode) === false){
 					$prefix = $r->instCode;
 					if($r->collCode) $prefix .= '-' . $r->collCode;
 					$prefix .= ':';
 				}
 				foreach($relOccidArr[$r->occid] as $targetAssocID){
-					$retArr[$targetAssocID]['object-catalogNumber'] = $prefix . $r->catalogNumber;
+					$retArr[$targetAssocID]['object-catalogNumber'] = $prefix . ($r->catalogNumber ?? 'not defined');
 					$retArr[$targetAssocID]['verbatimSciname'] = $r->sciname;
 				}
 			}

diff --git a/classes/OmDeterminations.php b/classes/OmDeterminations.php
@@ -13,8 +13,16 @@ class OmDeterminations extends Manager{
 
 	public function __construct($conn){
 		parent::__construct(null, 'write', $conn);
+		/*
+		 $this->fieldMap = array('identifiedBy' => 's', 'identifiedByAgentID' => 'i', 'identifiedByID' => 's', 'dateIdentified' => 's', 'dateIdentifiedInterpreted' => 's',
+		 'higherClassification' => 's', 'family' => 's', 'sciname' => 's', 'verbatimIdentification' => 's', 'scientificNameAuthorship' => 's', 'tidInterpreted' => 'i',
+		 'identificationUncertain' => 'i', 'identificationQualifier' => 's', 'genus' => 's', 'specificEpithet' => 's', 'verbatimTaxonRank' => 's', 'taxonRank' => 's',
+		 'infraSpecificEpithet' => 's', 'isCurrent' => 'i', 'printQueue' => 'i', 'appliedStatus' => 'i', 'securityStatus' => 'i', 'securityStatusReason' => 's',
+		 'detType' => 's', 'identificationReferences' => 's', 'identificationRemarks' => 's', 'taxonRemarks' => 's', 'identificationVerificationStatus' => 's',
+		 'taxonConceptID' => 's', 'sourceIdentifier' => 's', 'sortSequence' => 'i', 'recordID' => 's', 'createdUid' => 'i', 'modifiedUid' => 'i', 'dateLastModified' => 's');
+		 */
 		$this->schemaMap = array('identifiedBy' => 's', 'dateIdentified' => 's', 'higherClassification' => 's', 'family' => 's', 'sciname' => 's', 'verbatimIdentification' => 's',
-			'scientificNameAuthorship' => 's', 'identificationUncertain' => 'i', 'identificationQualifier' => 's', 'isCurrent' => 'i', 'printQueue' => 'i', 'appliedStatus' => 'i',
+			'scientificNameAuthorship' => 's', 'identificationQualifier' => 's', 'isCurrent' => 'i', 'printQueue' => 'i', 'appliedStatus' => 'i',
 			'securityStatus' => 'i', 'securityStatusReason' => 's', 'detType' => 's', 'identificationReferences' => 's', 'identificationRemarks' => 's', 'taxonRemarks' => 's',
 			'identificationVerificationStatus' => 's', 'taxonConceptID' => 's', 'sourceIdentifier' => 's', 'sortSequence' => 'i');
 	}

diff --git a/classes/SpecUploadBase.php b/classes/SpecUploadBase.php
@@ -1960,6 +1960,7 @@ protected function loadIdentificationRecord($recMap){
 				unset($recMap['taxonrank']);
 				unset($recMap['infraspecificepithet']);
 				//Try to get author, if it's not there
+				/*
 				if(!array_key_exists('scientificnameauthorship',$recMap) || !$recMap['scientificnameauthorship']){
 					//Parse scientific name to see if it has author imbedded
 					$parsedArr = OccurrenceUtilities::parseScientificName($recMap['sciname'],$this->conn);
@@ -1969,6 +1970,7 @@ protected function loadIdentificationRecord($recMap){
 						$recMap['sciname'] = trim($parsedArr['unitname1'].' '.$parsedArr['unitname2'].' '.$parsedArr['unitind3'].' '.$parsedArr['unitname3']);
 					}
 				}
+				*/
 				if(!isset($recMap['sciname']) || !$recMap['sciname']) return false;
 
 				if(!isset($recMap['identifiedby'])) $recMap['identifiedby'] = '';
@@ -2540,10 +2542,7 @@ protected function encodeString($inStr){
 					}
 				}
 				else{
-					if(mb_detect_encoding($inStr,'UTF-8,ISO-8859-1',true) == 'ISO-8859-1'){
-						$retStr = utf8_encode($inStr);
-						//$retStr = iconv("ISO-8859-1//TRANSLIT","UTF-8",$inStr);
-					}
+					$retStr = mb_convert_encoding($inStr, 'UTF-8', mb_detect_encoding($inStr));
 				}
 			}
 			elseif($this->targetCharset == "ISO-8859-1"){

diff --git a/classes/TaxonomyEditorManager.php b/classes/TaxonomyEditorManager.php
@@ -592,7 +592,7 @@ public function loadNewName($dataArr){
 				$sqlEnumTree = 'INSERT INTO taxaenumtree(tid,parenttid,taxauthid) '.
 					'SELECT '.$tid.' as tid, parenttid, taxauthid FROM taxaenumtree WHERE tid = '.$parTid;
 				if($this->conn->query($sqlEnumTree)){
-					$sqlEnumTree2 = 'INSERT INTO taxaenumtree(tid,parenttid,taxauthid) '.
+					$sqlEnumTree2 = 'INSERT IGNORE INTO taxaenumtree(tid,parenttid,taxauthid) '.
 						'VALUES ('.$tid.','.$parTid.','.$this->taxAuthId.')';
 					if(!$this->conn->query($sqlEnumTree2)){
 						echo (isset($this->langArr['WARNING_TAXAENUMTREE2'])?$this->langArr['WARNING_TAXAENUMTREE2']:'WARNING: Taxon loaded into taxa, but failed to populate taxaenumtree(2)').': '.$this->conn->error;

diff --git a/classes/TaxonomyUpload.php b/classes/TaxonomyUpload.php
@@ -955,17 +955,19 @@ public function getSourceArr(){
 		$sourceArr = array();
 		if(($fh = fopen($this->uploadTargetPath.$this->uploadFileName,'r')) !== FALSE){
 			$headerArr = fgetcsv($fh);
-			if(substr($headerArr[0], 0, 3) == chr(hexdec('EF')).chr(hexdec('BB')).chr(hexdec('BF'))){
-				//Remove UTF-8 BOM
-				$headerArr[0] = trim(substr($headerArr[0], 3), ' "');
-			}
-			foreach($headerArr as $field){
-				$fieldStr = trim($field);
-				if($fieldStr){
-					$sourceArr[] = $fieldStr;
+			if($headerArr){
+				if(substr($headerArr[0], 0, 3) == chr(hexdec('EF')).chr(hexdec('BB')).chr(hexdec('BF'))){
+					//Remove UTF-8 BOM
+					$headerArr[0] = trim(substr($headerArr[0], 3), ' "');
 				}
-				else{
-					break;
+				foreach($headerArr as $field){
+					$fieldStr = trim($field);
+					if($fieldStr){
+						$sourceArr[] = $fieldStr;
+					}
+					else{
+						break;
+					}
 				}
 			}
 		}

diff --git a/classes/TaxonomyUtilities.php b/classes/TaxonomyUtilities.php
@@ -42,7 +42,7 @@ public static function parseScientificName($inStr, $conn = null, $rankId = 0, $k
 			}
 			//Remove extra spaces
 			$inStr = preg_replace('/\s\s+/',' ',$inStr);
-
+			if(!$inStr) return $retArr;
 			$sciNameArr = explode(' ',trim($inStr));
 			$okToCloseConn = true;
 			if($conn !== null) $okToCloseConn = false;
@@ -127,7 +127,19 @@ public static function parseScientificName($inStr, $conn = null, $rankId = 0, $k
 					//cycles through the final terms to evaluate and extract infraspecific data
 					while($sciStr = array_shift($sciNameArr)){
 						if($testArr = self::cleanInfra($sciStr)){
-							self::setInfraNode($sciStr, $sciNameArr, $retArr, $authorArr, $testArr['infra']);
+							if($sciNameArr){
+								$infraStr = array_shift($sciNameArr);
+								if(preg_match('/^[a-z]{3,}$/', $infraStr)){
+									$retArr['unitind3'] = $testArr['infra'];
+									$retArr['unitname3'] = $infraStr;
+									unset($authorArr);
+									$authorArr = array();
+								}
+								else{
+									$authorArr[] = $sciStr;
+									$authorArr[] = $infraStr;
+								}
+							}
 						}
 						elseif($kingdomName == 'Animalia' && !$retArr['unitname3'] && ($rankId == 230 || preg_match('/^[a-z]{3,}$/',$sciStr) || preg_match('/^[A-Z]{3,}$/',$sciStr))){
 							$retArr['unitind3'] = '';
@@ -247,22 +259,6 @@ public static function cleanInfra($testStr){
 		return $retArr;
 	}
 
-	private static function setInfraNode($sciStr, &$sciNameArr, &$retArr, &$authorArr, $rankTag){
-		if($sciNameArr){
-			$infraStr = array_shift($sciNameArr);
-			if(preg_match('/^[a-z]{3,}$/', $infraStr)){
-				$retArr['unitind3'] = $rankTag;
-				$retArr['unitname3'] = $infraStr;
-				unset($authorArr);
-				$authorArr = array();
-			}
-			else{
-				$authorArr[] = $sciStr;
-				$authorArr[] = $infraStr;
-			}
-		}
-	}
-
 	//Taxonomic indexing functions
 	public static function rebuildHierarchyEnumTree($conn = null){
 		$status = true;

diff --git a/collections/admin/specuploadmap.php b/collections/admin/specuploadmap.php
@@ -587,9 +587,9 @@ function pkChanged(selObj){
 								<?php
 							}
 							?>
-							<button type="submit" name="action" value="Automap Fields" ><?php echo (isset($LANG['AUTOMAP']) ? $LANG['AUTOMAP'] : 'Automap Fields'); ?></button>
-							<button type="submit" name="action" value="Verify Mapping" ><?php echo (isset($LANG['VER_MAPPING']) ? $LANG['VER_MAPPING'] : 'Verify Mapping'); ?></button>
-							<button type="submit" name="action" value="saveMapping" onclick="return verifySaveMapping(this.form)" ><?php echo (isset($LANG['SAVE_MAP']) ? $LANG['SAVE_MAP'] : 'Save Mapping'); ?></button>
+							<button class="bottom-breathing-room-rel-sm" type="submit" name="action" value="Automap Fields" ><?php echo (isset($LANG['AUTOMAP']) ? $LANG['AUTOMAP'] : 'Automap Fields'); ?></button>
+							<button class="bottom-breathing-room-rel-sm" type="submit" name="action" value="Verify Mapping" ><?php echo (isset($LANG['VER_MAPPING']) ? $LANG['VER_MAPPING'] : 'Verify Mapping'); ?></button>
+							<button class="bottom-breathing-room-rel-sm" type="submit" name="action" value="saveMapping" onclick="return verifySaveMapping(this.form)" ><?php echo (isset($LANG['SAVE_MAP']) ? $LANG['SAVE_MAP'] : 'Save Mapping'); ?></button>
 							<span id="newProfileNameDiv" style="margin-left:15px;color:red;display:none">
 								<?php echo (isset($LANG['NEW_PROF_TITLE']) ? $LANG['NEW_PROF_TITLE'] : 'New profile title'); ?>:
 								<input type="text" name="profiletitle" style="width:300px" value="<?php echo $duManager->getTitle().'-'.date('Y-m-d'); ?>" />