Specimen Upload

- Integrate omoccuridentifiers table into specimen upload option to match on other identifiers
BioKIC · Jan 11, 2022 · cce3f21 · cce3f21
1 parent d83b5e5
commit cce3f21
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Showing 4 changed files with 74 additions and 60 deletions.
diff --git a/classes/OccurrenceSesar.php b/classes/OccurrenceSesar.php
@@ -713,6 +713,19 @@ public function syncIGSN($occid,$catalogNumber,$igsn){
 			}
 			$rs->free();
 
+			$sql = 'SELECT identifierValue FROM omoccuridentifiers WHERE occid = '.$occid;
+			$rs = $this->conn->query($sql);
+			while($r = $rs->fetch_object()){
+				if($r->identifierValue != $catalogNumber && $r->identifierValue != $catalogNumber){
+					$retArr['errCode'] = 2;
+					$catNum = $r->identifierValue;
+					if(isset($retArr['catNum'])) $catNum .= ', '.$retArr['catNum'];
+					$retArr['catNum'] = $catNum;
+					$ok = false;
+				}
+			}
+			$rs->free();
+
 			if($ok){
 				$sqlUpdate = 'UPDATE omoccurrences SET occurrenceid = "'.$this->cleanInStr($igsn).'" WHERE occid = '.$occid;
 				if($this->conn->query($sqlUpdate)){

diff --git a/classes/OccurrenceSupport.php b/classes/OccurrenceSupport.php
@@ -123,30 +123,21 @@ public function getOccurrenceList($collid, $catalogNumber, $otherCatalogNumbers,
 		$retArr = Array();
 		if(!$catalogNumber && !$otherCatalogNumbers && !$recordedBy && !$recordNumber) return $retArr;
 		$sqlWhere = "";
-		if($collid){
-			$sqlWhere .= "AND (o.collid = ".$collid.") ";
-		}
-		if($catalogNumber){
-			$sqlWhere .= 'AND (o.catalognumber = "'.$catalogNumber.'") ';
-		}
-		if($otherCatalogNumbers){
-			$sqlWhere .= 'AND (o.othercatalognumbers = "'.$otherCatalogNumbers.'") ';
-		}
+		if($collid) $sqlWhere .= "AND (o.collid = ".$collid.") ";
+		if($catalogNumber) $sqlWhere .= 'AND (o.catalognumber = "'.$catalogNumber.'") ';
+		if($otherCatalogNumbers) $sqlWhere .= 'AND (o.othercatalognumbers = "'.$otherCatalogNumbers.'" OR i.identifiervalue = "'.$otherCatalogNumbers.'") ';
 		if($recordedBy){
 			if(strlen($recordedBy) < 4 || in_array(strtolower($recordedBy),array('best','little'))){
 				//Need to avoid FULLTEXT stopwords interfering with return
 				$sqlWhere .= 'AND (o.recordedby LIKE "%'.$recordedBy.'%") ';
 			}
-			else{
-				$sqlWhere .= 'AND (MATCH(f.recordedby) AGAINST("'.$recordedBy.'")) ';
-			}
-		}
-		if($recordNumber){
-			$sqlWhere .= 'AND (o.recordnumber = "'.$recordNumber.'") ';
+			else $sqlWhere .= 'AND (MATCH(f.recordedby) AGAINST("'.$recordedBy.'")) ';
 		}
-		$sql = 'SELECT o.occid, o.recordedby, o.recordnumber, o.eventdate, CONCAT_WS("; ",o.stateprovince, o.county, o.locality) AS locality '.
-			'FROM omoccurrences o LEFT JOIN omoccurrencesfulltext f ON o.occid = f.occid '.
-			'WHERE '.substr($sqlWhere,4);
+		if($recordNumber) $sqlWhere .= 'AND (o.recordnumber = "'.$recordNumber.'") ';
+		$sql = 'SELECT o.occid, o.recordedby, o.recordnumber, o.eventdate, CONCAT_WS("; ",o.stateprovince, o.county, o.locality) AS locality
+			FROM omoccurrences o LEFT JOIN omoccurrencesfulltext f ON o.occid = f.occid ';
+		if($otherCatalogNumbers) $sql .= 'LEFT JOIN omoccuridentifiers i ON o.occid = i.occid ';
+		$sql .= 'WHERE '.substr($sqlWhere,4);
 		//echo $sql;
 		$rs = $this->conn->query($sql);
 		while($row = $rs->fetch_object()){

diff --git a/classes/SpecUpload.php b/classes/SpecUpload.php
@@ -152,12 +152,12 @@ public function validateSecurityKey($k){
 			$sql = 'SELECT collid FROM omcollections WHERE securitykey = "'.$k.'"';
 			//echo $sql;
 			$rs = $this->conn->query($sql);
-	    	if($r = $rs->fetch_object()){
-	    		$this->setCollId($r->collid);
-	    	}
-	    	else{
-	    		return false;
-	    	}
+			if($r = $rs->fetch_object()){
+				$this->setCollId($r->collid);
+			}
+			else{
+				return false;
+			}
 			$rs->free();
 		}
 		elseif(!isset($this->collMetadataArr["securitykey"])){
@@ -246,7 +246,8 @@ private function getPendingImportSql($searchVariables){
 			if($searchVariables == 'matchappend'){
 				$sql = 'SELECT DISTINCT u.occid, u.dbpk, u.'.implode(',u.',$occFieldArr).' '.
 					'FROM uploadspectemp u INNER JOIN omoccurrences o ON u.collid = o.collid '.
-					'WHERE (u.collid IN('.$this->collId.')) AND (u.occid IS NULL) AND (u.catalogNumber = o.catalogNumber OR u.othercatalogNumbers = o.othercatalogNumbers) ';
+					'LEFT JOIN omoccuridentifiers i ON o.occid = i.occid '.
+					'WHERE (u.collid IN('.$this->collId.')) AND (u.occid IS NULL) AND (u.catalogNumber = o.catalogNumber OR u.othercatalogNumbers = o.othercatalogNumbers OR u.othercatalogNumbers = i.identifiervalue) ';
 			}
 			elseif($searchVariables == 'sync'){
 				$sql = 'SELECT DISTINCT u.occid, u.dbpk, u.'.implode(',u.',$occFieldArr).' '.
@@ -317,38 +318,38 @@ public function getUploadCount(){
 	}
 
 	//Profile management
-    public function readUploadParameters(){
-    	if($this->uspid){
+	public function readUploadParameters(){
+		if($this->uspid){
 			$sql = 'SELECT usp.collid, usp.title, usp.Platform, usp.server, usp.port, usp.Username, usp.Password, usp.SchemaName, '.
-	    		'usp.code, usp.path, usp.pkfield, usp.querystr, usp.cleanupsp, cs.uploaddate, usp.uploadtype '.
+				'usp.code, usp.path, usp.pkfield, usp.querystr, usp.cleanupsp, cs.uploaddate, usp.uploadtype '.
 				'FROM uploadspecparameters usp LEFT JOIN omcollectionstats cs ON usp.collid = cs.collid '.
-	    		'WHERE (usp.uspid = '.$this->uspid.')';
+				'WHERE (usp.uspid = '.$this->uspid.')';
 			//echo $sql;
 			$result = $this->conn->query($sql);
-	    	if($row = $result->fetch_object()){
-	    		if(!$this->collId) $this->collId = $row->collid;
-	    		$this->title = $row->title;
-	    		$this->platform = $row->Platform;
-	    		$this->server = $row->server;
-	    		$this->port = $row->port;
-	    		$this->username = $row->Username;
-	    		$this->password = $row->Password;
-	    		$this->schemaName = $row->SchemaName;
-	    		$this->code = $row->code;
-	    		if(!$this->path) $this->path = $row->path;
-	    		$this->pKField = strtolower($row->pkfield);
-	    		$this->queryStr = $row->querystr;
-	    		$this->storedProcedure = $row->cleanupsp;
-	    		$this->lastUploadDate = $row->uploaddate;
-	    		$this->uploadType = $row->uploadtype;
-	    		if(!$this->lastUploadDate) $this->lastUploadDate = date('Y-m-d H:i:s');
-	    	}
-	    	$result->free();
-    	}
-    }
-
-    public function editUploadProfile($profileArr){
-    	$sql = 'UPDATE uploadspecparameters SET title = "'.$this->cleanInStr($profileArr['title']).'"'.
+			if($row = $result->fetch_object()){
+				if(!$this->collId) $this->collId = $row->collid;
+				$this->title = $row->title;
+				$this->platform = $row->Platform;
+				$this->server = $row->server;
+				$this->port = $row->port;
+				$this->username = $row->Username;
+				$this->password = $row->Password;
+				$this->schemaName = $row->SchemaName;
+				$this->code = $row->code;
+				if(!$this->path) $this->path = $row->path;
+				$this->pKField = strtolower($row->pkfield);
+				$this->queryStr = $row->querystr;
+				$this->storedProcedure = $row->cleanupsp;
+				$this->lastUploadDate = $row->uploaddate;
+				$this->uploadType = $row->uploadtype;
+				if(!$this->lastUploadDate) $this->lastUploadDate = date('Y-m-d H:i:s');
+			}
+			$result->free();
+		}
+	}
+
+	public function editUploadProfile($profileArr){
+		$sql = 'UPDATE uploadspecparameters SET title = "'.$this->cleanInStr($profileArr['title']).'"'.
 			', platform = '.($profileArr['platform']?'"'.$profileArr['platform'].'"':'NULL').
 			', server = '.($profileArr['server']?'"'.$profileArr['server'].'"':'NULL').
 			', port = '.($profileArr['port']?$profileArr['port']:'NULL').
@@ -369,7 +370,7 @@ public function editUploadProfile($profileArr){
 		return true;
 	}
 
-    public function createUploadProfile($profileArr){
+	public function createUploadProfile($profileArr){
 		$sql = 'INSERT INTO uploadspecparameters(collid, uploadtype, title, platform, server, port, code, path, '.
 			'pkfield, username, password, schemaname, cleanupsp, querystr) VALUES ('.$this->collId.','.
 			$profileArr['uploadtype'].',"'.$this->cleanInStr($profileArr['title']).'",'.
@@ -394,7 +395,7 @@ public function createUploadProfile($profileArr){
 		}
 	}
 
-    public function deleteUploadProfile($uspid){
+	public function deleteUploadProfile($uspid){
 		$sql = 'DELETE FROM uploadspecparameters WHERE (uspid = '.$uspid.')';
 		if(!$this->conn->query($sql)){
 			$this->errorStr = '<div>Error Adding Upload Parameters: '.$this->conn->error.'</div><div>'.$sql.'</div>';

diff --git a/classes/SpecUploadBase.php b/classes/SpecUploadBase.php
@@ -547,12 +547,20 @@ protected function cleanUpload(){
 			}
 			if($this->matchOtherCatalogNumbers){
 				//Match records based on other Catalog Numbers fields
-				$sql2 = 'UPDATE uploadspectemp u INNER JOIN omoccurrences o ON (u.otherCatalogNumbers = o.otherCatalogNumbers) AND (u.collid = o.collid) '.
+				$sql2 = 'UPDATE uploadspectemp u INNER JOIN omoccurrences o ON u.collid = o.collid '.
 					'SET u.occid = o.occid '.
-					'WHERE (u.collid IN('.$this->collId.')) AND (u.occid IS NULL) AND (u.othercatalogNumbers IS NOT NULL) AND (o.othercatalogNumbers IS NOT NULL) ';
-				if($this->collMetadataArr['colltype'] == 'General Observations' && $this->observerUid) $sql .= ' AND o.observeruid = '.$this->observerUid;
+					'WHERE (u.collid IN('.$this->collId.')) AND (u.occid IS NULL) AND (u.otherCatalogNumbers = o.otherCatalogNumbers) ';
+				if($this->collMetadataArr['colltype'] == 'General Observations' && $this->observerUid) $sql2 .= ' AND o.observeruid = '.$this->observerUid;
 				if(!$this->conn->query($sql2)){
-					$this->outputMsg('<li><span style="color:red;">Warning: unable to match on other catalog numbers: '.$this->conn->error.'</span></li>');
+					$this->outputMsg('<li><span style="color:red;">Warning: unable to match on otherCatalogNumbers: '.$this->conn->error.'</span></li>');
+				}
+				$sql2b = 'UPDATE uploadspectemp u INNER JOIN omoccurrences o ON u.collid = o.collid '.
+				    'INNER JOIN omoccuridentifiers i ON o.occid = i.occid '.
+				 	'SET u.occid = o.occid '.
+					'WHERE (u.collid IN('.$this->collId.')) AND (u.occid IS NULL) AND (u.othercatalogNumbers = i.identifiervalue) ';
+				if($this->collMetadataArr['colltype'] == 'General Observations' && $this->observerUid) $sql2b .= ' AND o.observeruid = '.$this->observerUid;
+				if(!$this->conn->query($sql2b)){
+				    $this->outputMsg('<li><span style="color:red;">Warning: unable to match on omoccuridentifiers: '.$this->conn->error.'</span></li>');
 				}
 			}
 		}
@@ -703,7 +711,8 @@ public function getTransferReport(){
 			//Records that can be matched on Catalog Number, but will be appended
 			$sql = 'SELECT count(o.occid) AS cnt '.
 				'FROM uploadspectemp u INNER JOIN omoccurrences o ON u.collid = o.collid '.
-				'WHERE (u.collid IN('.$this->collId.')) AND (u.occid IS NULL) AND (u.catalogNumber = o.catalogNumber OR u.othercatalogNumbers = o.othercatalogNumbers) ';
+				'LEFT JOIN omoccuridentifiers i ON o.occid = i.occid '.
+				'WHERE (u.collid IN('.$this->collId.')) AND (u.occid IS NULL) AND (u.catalogNumber = o.catalogNumber OR u.othercatalogNumbers = o.othercatalogNumbers OR u.othercatalogNumbers = i.identifierValue) ';
 			$rs = $this->conn->query($sql);
 			if($r = $rs->fetch_object()){
 				$reportArr['matchappend'] = $r->cnt;