Improve Schema management workflow

- Add try/catch to db_connection file and connection test within Manager class that reports when connection to database fails (e.g. no connection, authentication issue, etc) - Sitemap adjustments that automatically forwards user to schema manager whenever schema is missing (e.g. fresh install). - Add backward ticks to all table and stored procedure names within schema files so that installation logger is able to properly report table name within logs - Misc adjustments to schema manager to improved output reports - Add message to schema manager that warns user when log directories are not writable by web user (e.g. apache) - Only check users accessibility settings if they are logged in to the portal
BioKIC · Aug 23, 2024 · c54952e · c54952e
1 parent 7391079
commit c54952e
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Showing 10 changed files with 118 additions and 94 deletions.
diff --git a/admin/schemamanager.php b/admin/schemamanager.php
@@ -28,7 +28,7 @@
 			label{ font-weight:bold; }
 			fieldset{ padding: 15px }
 			fieldset legend{ font-weight:bold; }
-			.info-div{ margin:10px 5px; }
+			.info-div{ margin:5px 5px 20px 5px; }
 			.form-section{ margin: 5px 10px; }
 			button{ margin: 15px; }
 		</style>
@@ -87,8 +87,22 @@
 					?>
 					<fieldset style="width:800px">
 						<legend>Database Schema Assistant</legend>
-						<div class="info-div">Enter login criteria for database user that has full DDL privileges (e.g. create/alter tables, routines, indexes, etc.).<br>
-						We recommend creating a backup of the database before applying any database patches.</div>
+						<div class="info-div">
+							Enter login for database user who has full DDL privileges (e.g. create/alter tables, routines, indexes, etc.).<br>
+							We recommend creating a backup of the database before applying any database patches.
+						</div>
+						<?php
+						if($curentVersion != '3.1'){
+							if(!is_writable($SERVER_ROOT . '/content/logsd/install/')){
+								?>
+								<div class="info-div">
+									<span style="color: orange">WARNING</span>: The log directory (e.g. /content/logs/schema/) is not writable by web user.
+									We strongly recommend that you adjust directory permissions as defined within the installation before running installation/update scripts.
+								</div>
+								<?php
+							}
+						}
+						?>
 						<form name="databaseMaintenanceForm" action="schemamanager.php" method="post">
 							<div class="form-section">
 								<label>Schema: </label>
@@ -99,7 +113,7 @@
 										foreach($schemaPatchArr as $schemaOption){
 											if($schemaOption > $curentVersion) echo '<option value="' . $schemaOption . '">Schema Patch ' . $schemaOption . '</option>';
 										}
-										echo '<option value="">Schema is Current - nothing to do</option>';
+										if($curentVersion == '3.1') echo '<option value="">Schema is Current - nothing to do</option>';
 									}
 									else{
 										echo '<option value="baseInstall">New Install (ver. 3.0)</option>';

diff --git a/classes/Manager.php b/classes/Manager.php
@@ -23,6 +23,7 @@ public function __construct($id=null, $conType='readonly', $connOverride = null)
 			$this->isConnInherited = true;
 		}
 		else $this->conn = MySQLiConnectionFactory::getCon($conType);
+		if($this->conn === null) exit;
  		if($id != null || is_numeric($id)){
 	 		$this->id = $id;
  		}

diff --git a/classes/ProfileManager.php b/classes/ProfileManager.php
@@ -315,7 +315,7 @@ public function register($postArr, $adminRegister = false){
 		$lastName = strip_tags($postArr['lastname']);
 		$pwd = $postArr['pwd'];
 		$email = filter_var($postArr['email'], FILTER_VALIDATE_EMAIL);
-		
+
 		$title = array_key_exists('title', $postArr) ? strip_tags($postArr['title']) : '';
 		$institution = array_key_exists('institution', $postArr) ? strip_tags($postArr['institution']) : '';
 		$city = array_key_exists('city', $postArr) ? strip_tags($postArr['city']) : '';
@@ -1032,70 +1032,51 @@ private function getTempPath(){
 		return $tPath;
 	}
 
-	//setter and getters
-	public function setRememberMe($test){
-		$this->rememberMe = $test;
-	}
-
-	public function getRememberMe(){
-		return $this->rememberMe;
-	}
-
-	public function setToken($token){
-		$this->token = $token;
-	}
-
-	public function setUid($uid){
-		if(is_numeric($uid)){
-			$this->uid = $uid;
-		}
-	}
-
-	public function setAccessibilityPreference($pref, $uid){
+	//Accessubility functions
+	private function setAccessibilityPreference($pref, $uid){
 		$status = false;
-		$currentDynamicProperties = $this->getDynamicProperties($uid) ? $this->getDynamicProperties($uid) : array();
+		$currentDynamicProperties = $this->getDynamicProperties($uid);
+		if(!$currentDynamicProperties) $currentDynamicProperties = array();
 		$currentDynamicProperties['accessibilityPref'] = $pref;
 		$status = $this->setDynamicProperties($uid, $currentDynamicProperties);
 		return $status;
 	}
 
-	public function setDynamicProperties($uid, $dynPropArr){
+	private function setDynamicProperties($uid, $dynPropArr){
 		$status = false;
 		if(!$uid) return $status;
 
 		$jsonDynProps = json_encode($dynPropArr);
 
-
 		$this->resetConnection(); // @TODO decided whether this is necessary
 		$sql = 'UPDATE users SET dynamicProperties = ? WHERE (uid = ?)';
 		if($stmt = $this->conn->prepare($sql)){
 			$stmt->bind_param('si', $jsonDynProps, $uid);
 			$stmt->execute();
-			if(!$stmt->error) $status = true; // note: removed $stmt->affected_rows && 
+			if(!$stmt->error) $status = true; // note: removed $stmt->affected_rows &&
 			$stmt->close();
 		}
 		return $status;
-
 	}
 
 	public function getAccessibilityPreference($uid){
+		if(!$uid){
+			return false;
+		}
 		$returnVal = false;
 		$dynPropArr = $this->getDynamicProperties($uid);
-		
+
 		if($dynPropArr && isset($dynPropArr['accessibilityPref'])){
 			$returnVal = ($dynPropArr['accessibilityPref'] === true) ? true : false;
 		}
 		return $returnVal;
 	}
 
-	public function getDynamicProperties($uid){
-		if(! $uid){
-			return false;
-		}
+	private function getDynamicProperties($uid){
 		$returnVal = false;
 		$sql = 'SELECT dynamicProperties FROM users WHERE uid = ?';
 		$stmt = $this->conn->prepare($sql);
-		$stmt->bind_param("i", $uid);
+		$stmt->bind_param('i', $uid);
 		$stmt->execute();
 		$respns= $stmt->get_result();
 		if($fetchedObj = $respns->fetch_object()){
@@ -1133,4 +1114,23 @@ private function encodeArr(&$inArr,$cSet){
 			$inArr[$k] = $this->encodeString($v,$cSet);
 		}
 	}
+
+	//setter and getters
+	public function setRememberMe($test){
+		$this->rememberMe = $test;
+	}
+
+	public function getRememberMe(){
+		return $this->rememberMe;
+	}
+
+	public function setToken($token){
+		$this->token = $token;
+	}
+
+	public function setUid($uid){
+		if(is_numeric($uid)){
+			$this->uid = $uid;
+		}
+	}
 }
diff --git a/classes/SchemaManager.php b/classes/SchemaManager.php
@@ -58,7 +58,7 @@ public function installPatch(){
 								$this->logOrEcho($fragment, 1);
 							}
 							elseif(!$stmtType){
-								if(preg_match('/`([a-z]+)`/', $fragment, $m)){
+								if(preg_match('/`([a-zA-Z]+)`/', $fragment, $m)){
 									$targetTable = $m[1];
 								}
 								$stmtType = 'undefined';
@@ -67,10 +67,10 @@ public function installPatch(){
 									$this->setActiveTable($targetTable);
 								}
 								elseif(strpos($fragment, '/*!') === 0) $stmtType = 'Conditional statement';
-								elseif(preg_match('/^([A-Z\s]+)/', $fragment, $m)){
+								elseif(preg_match('/^([A-Z0-9_=\s]+)/', $fragment, $m)){
 									$stmtType = $m[1];
 								}
-								$this->logOrEcho('Type: ' . $stmtType . ($targetTable ? ' '.$targetTable : ''), 1);
+								$this->logOrEcho('Statement prefix: ' . $stmtType . ($targetTable ? ' '.$targetTable : ''), 1);
 								$sql = $fragment;
 							}
 							else{
@@ -115,7 +115,7 @@ public function installPatch(){
 								fwrite($this->amendmentFH, '# ERROR: '.$this->conn->error."\n\n");
 								fwrite($this->amendmentFH, $sql . "\n\n");
 								$this->logOrEcho('ERROR: ' . $this->conn->error, 2);
-								$this->logOrEcho('SQL: ' . $sql, 2);
+								//$this->logOrEcho('SQL: ' . $sql, 2);
 								//break;
 							}
 						}
@@ -209,8 +209,8 @@ private function setActiveTable($targetTable){
 				$rs->free();
 			}
 			catch(Exception $e){
-				$this->logOrEcho('ERROR: '.$this->conn->error, 2);
-				$this->logOrEcho($sql, 2);
+				//$this->logOrEcho('ERROR: '.$this->conn->error, 2);
+				//$this->logOrEcho($sql, 2);
 			}
 		}
 	}

diff --git a/classes/SiteMapManager.php b/classes/SiteMapManager.php
@@ -1,27 +1,25 @@
 <?php
-include_once($SERVER_ROOT.'/config/dbconnection.php');
+include_once('Manager.php');
 
-class SiteMapManager{
+class SiteMapManager extends Manager{
 
-	private $conn;
 	private $collArr = array();
 	private $obsArr = array();
 	private $genObsArr = array();
 
 	function __construct() {
-		$this->conn = MySQLiConnectionFactory::getCon("readonly");
+		parent::__construct();
 	}
 
 	function __destruct(){
- 		if(!($this->conn === false)) $this->conn->close();
+ 		parent::__destruct();
 	}
 
 	public function setCollectionList(){
 		global $USER_RIGHTS, $IS_ADMIN;
 		$adminArr = array();
 		$editorArr = array();
-		$sql = 'SELECT c.collid, CONCAT_WS(":",c.institutioncode, c.collectioncode) AS ccode, c.collectionname, c.colltype '.
-			'FROM omcollections c ';
+		$sql = 'SELECT collid, CONCAT_WS(":", institutioncode, collectioncode) AS ccode, collectionname, colltype FROM omcollections ';
 		if(!$IS_ADMIN){
 			if(array_key_exists("CollAdmin",$USER_RIGHTS)){
 				$adminArr = $USER_RIGHTS['CollAdmin'];
@@ -30,14 +28,14 @@ public function setCollectionList(){
 				$editorArr = $USER_RIGHTS['CollEditor'];
 			}
 			if($adminArr || $editorArr){
-				$sql .= 'WHERE (c.collid IN('.implode(',',array_merge($adminArr,$editorArr)).')) ';
+				$sql .= 'WHERE (collid IN('.implode(',',array_merge($adminArr,$editorArr)).')) ';
 			}
 			else{
 				$sql = '';
 			}
 		}
 		if($sql){
-			$sql .= "ORDER BY c.collectionname";
+			$sql .= "ORDER BY collectionname";
 			//echo "<div>".$sql."</div>";
 			$rs = $this->conn->query($sql);
 			if($rs){
@@ -100,12 +98,11 @@ public function getChecklistList($clArr){
 
 	public function getProjectList($projArr = ""){
 		$returnArr = Array();
-		$sql = 'SELECT p.pid, p.projname, p.managers FROM fmprojects p '.
-			'WHERE p.ispublic = 1 ';
+		$sql = 'SELECT pid, projname, managers FROM fmprojects WHERE ispublic = 1 ';
 		if($projArr){
-			$sql .= 'AND (p.pid IN('.implode(',',$projArr).')) ';
+			$sql .= 'AND (pid IN('.implode(',',$projArr).')) ';
 		}
-		$sql .= 'ORDER BY p.projname';
+		$sql .= 'ORDER BY projname';
 		//echo '<div>'.$sql.'</div>';
 		$rs = $this->conn->query($sql);
 		if($rs){
@@ -134,17 +131,19 @@ public function hasGlossary(){
 	 * @return string representation of the most recently applied schema version
 	 */
 	public function getSchemaVersion() {
-		$result = "No Schema Version Found";
-		$sql = "select versionnumber, dateapplied from schemaversion order by dateapplied desc limit 1 ";
-		$statement = $this->conn->prepare($sql);
-		$statement->execute();
-		$statement->bind_result($version,$dateapplied);
-		while ($statement->fetch())  {
-			$result = $version;
+		$result = false;
+		$sql = 'SELECT versionnumber FROM schemaversion ORDER BY dateapplied DESC LIMIT 1 ';
+		try{
+			$statement = $this->conn->prepare($sql);
+			$statement->execute();
+			$statement->bind_result($result);
+			$statement->fetch();
+			$statement->close();
+		}
+		catch(Exception $e){
+			$this->errorMessage = $e->getMessage();
 		}
-		$statement->close();
 		return $result;
 	}
-
 }
 ?>
diff --git a/config/dbconnection_template.php b/config/dbconnection_template.php
@@ -27,16 +27,19 @@ public static function getCon($type) {
 		for ($i = 0, $n = count(MySQLiConnectionFactory::$SERVERS); $i < $n; $i++) {
 			$server = MySQLiConnectionFactory::$SERVERS[$i];
 			if($server['type'] == $type){
-				$connection = new mysqli($server['host'], $server['username'], $server['password'], $server['database'], $server['port']);
-				if(mysqli_connect_errno()){
-					throw new Exception('Could not connect to any databases! Please try again later.');
-				}
-				if(isset($server['charset']) && $server['charset']) {
-					if(!$connection->set_charset($server['charset'])){
-						throw new Exception('Error loading character set '.$server['charset'].': '.$connection->error);
+				try{
+					$connection = new mysqli($server['host'], $server['username'], $server['password'], $server['database'], $server['port']);
+					if(isset($server['charset']) && $server['charset']) {
+						if(!$connection->set_charset($server['charset'])){
+							throw new Exception('Error loading character set '.$server['charset'].': '.$connection->error);
+						}
 					}
+					return $connection;
+				}
+				catch(Exception $e){
+					echo $e->getMessage();
+					return null;
 				}
-				return $connection;
 			}
 		}
 	}

diff --git a/config/schema/3.0/db_schema-3.0.sql b/config/schema/3.0/db_schema-3.0.sql