satisfy php linter

jeffersoncasimir · Jan 27, 2025 · 8ae2722 · 8ae2722
1 parent 4e87ef7
commit 8ae2722
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Showing 11 changed files with 160 additions and 96 deletions.
diff --git a/modules/instrument_manager/php/instrument_data.class.inc b/modules/instrument_manager/php/instrument_data.class.inc
@@ -10,7 +10,13 @@ use LORIS\server_processes_manager as SP;
 /**
  * Upload instrument data
  *
- * @license http://www.gnu.org/licenses/gpl-3.0.txt GPLv3
+ * PHP Version 8
+ *
+ * @category Main
+ * @package  LORIS
+ * @author   Loris Team <[email protected]>
+ * @license  http://www.gnu.org/licenses/gpl-3.0.txt GPLv3
+ * @link     https://www.github.com/aces/Loris/
  */
 class Instrument_Data extends \NDB_Page
 {
@@ -109,27 +115,28 @@ class Instrument_Data extends \NDB_Page
         // Ensure the user is allowed to upload.
         if (!$request->getAttribute('user')->hasPermission(
             'instrument_manager_write'
-        )) {
+        )
+        ) {
             return new \LORIS\Http\Response\JSON\Forbidden();
         }
 
-        $requestBody  = (array) $request->getParsedBody();
+        $requestBody = (array) $request->getParsedBody();
 
         if (isset($requestBody['instrument'])) {
             $instrument = $requestBody['instrument'];
             if ($this->instrumentExists($instrument)) {
-                $dataFile     = $request->getUploadedFiles()['data_file'];
-                $userID = $request->getAttribute('user')->getUsername();
+                $dataFile = $request->getUploadedFiles()['data_file'];
+                $userID   = $request->getAttribute('user')->getUsername();
 
                 $uploadFolder = $this->loris
                     ->getConfiguration()->getSetting('instrumentDataPath');
                 $filePrefix   = $userID . '_' . time() . '_';
-                $fileLocation  = $uploadFolder . "/$filePrefix"
+                $fileLocation = $uploadFolder . "/$filePrefix"
                     . $dataFile->getClientFilename();
                 $dataFile->moveTo($fileLocation);
 
                 $fileInfo = new SplFileInfo($fileLocation);
-                $this->insertCSVFileEntry($fileInfo->getFilename());
+                $this->_insertCSVFileEntry($fileInfo->getFilename());
 
                 if ($fileInfo->getSize() > self::MAX_FILE_BYTES) {
                     // Run as background task
@@ -141,9 +148,10 @@ class Instrument_Data extends \NDB_Page
 
                     $result = [
                         'success' => true,
-                        'message' => "Due to the relatively large size of the uploaded file, " .
-                                     "the process has been sent to the background task queue. " .
-                                     "You will receive an email once completed."
+                        'message' => "Due to the relatively large size of the " .
+                            "uploaded file, the process has been sent to the " .
+                            "background task queue. You will receive an email " .
+                            "once completed."
 
                     ];
                     return new \LORIS\Http\Response\JSON\Created($result);
@@ -155,8 +163,8 @@ class Instrument_Data extends \NDB_Page
                         $instrument,
                         $fileInfo,
                     );
-                    $data      = $dataParser->parseCSV($this->loris);
-                    $validData = $dataParser->validateData(
+                    $data       = $dataParser->parseCSV($this->loris);
+                    $validData  = $dataParser->validateData(
                         $data,
                         [
                             'UserID'   => $userID,
@@ -213,11 +221,20 @@ class Instrument_Data extends \NDB_Page
         return $count > 0;
     }
 
-    private function insertCSVFileEntry($filename)
+    /**
+     * Insert entry for CSV file
+     *
+     * @param string $filename The file name
+     *
+     * @return void
+     */
+    private function _insertCSVFileEntry($filename)
     {
-        // Create db entry for csv file
-        $this->loris->getDatabaseConnection()->insert('instrument_data_files', [
-            'FilePath' => $filename,
-        ]);
+        $this->loris->getDatabaseConnection()->insert(
+            'instrument_data_files',
+            [
+                'FilePath' => $filename,
+            ]
+        );
     }
 }
diff --git a/modules/server_processes_manager/php/abstractserverprocess.class.inc b/modules/server_processes_manager/php/abstractserverprocess.class.inc
@@ -582,21 +582,23 @@ abstract class AbstractServerProcess
     /**
      * Gets directory where all temporary files created by this task should go
      *
-     * @return string full path to the temporary directory
+     * @return   string full path to the temporary directory
      * @abstract
      */
     abstract public function getTmpDir();
 
     /**
      * Change file permissions
      *
+     * @return   void
      * @abstract
      */
     abstract public function changeFilePermissions();
 
     /**
      * Perform action once process is completed
      *
+     * @return   void
      * @abstract
      */
     abstract public function performPostAction();

diff --git a/modules/server_processes_manager/php/mriuploadserverprocess.class.inc b/modules/server_processes_manager/php/mriuploadserverprocess.class.inc
@@ -223,14 +223,20 @@ class MriUploadServerProcess extends AbstractServerProcess
     /**
      * Change file permissions
      *
+     * @return void
      */
-    public function changeFilePermissions() {}
+    public function changeFilePermissions()
+    {
+    }
 
     /**
      * Perform action once process is completed
      *
+     * @return void
      */
-    public function performPostAction() {}
+    public function performPostAction()
+    {
+    }
 }
 
 
diff --git a/modules/server_processes_manager/php/parseinstrumentdataserverprocess.class.inc b/modules/server_processes_manager/php/parseinstrumentdataserverprocess.class.inc
@@ -48,8 +48,9 @@ class ParseInstrumentDataServerProcess extends AbstractServerProcess
     /**
      * Builds a new ParseInstrumentDataServerProcess
      *
-     * @param string  $instrument  Instrument name
+     * @param string  $instrument   Instrument name
      * @param string  $fileLocation Location of the uploaded file
+     * @param ?int    $id           ID of the process in the database.
      * @param ?int    $pid          PID for this process
      * @param ?string $stdoutFile   full path of file used to store the process's
      *                              stdout
@@ -93,9 +94,11 @@ class ParseInstrumentDataServerProcess extends AbstractServerProcess
      */
     public function getShellCommand()
     {
-        $parseScript  = "php " . dirname(__DIR__, 3) . "/tools/parse_instrument_data.php ";
+        $parseScript  = "php " .
+            dirname(__DIR__, 3) .
+            "/tools/parse_instrument_data.php ";
         $parseScript .= "$this->_instrument $this->_fileLocation ";
-        $parseScript .= "{$this->getUserId()} {$this->getUserId()}";    // TODO: Examiner?
+        $parseScript .= "{$this->getUserId()} {$this->getUserId()}";
         return escapeshellarg($parseScript);
     }
 
@@ -127,7 +130,8 @@ class ParseInstrumentDataServerProcess extends AbstractServerProcess
         if (is_numeric($exitCode) && $exitCode == 0) {
             return "Instrument data parse completed without errors.\n\n$exitText";
         } else {
-            return "Instrument data parse failed with error code: $exitCode.\n\n$exitText";
+            return "Instrument data parse failed with error code: $exitCode." .
+                "\n\n$exitText";
         }
     }
 
@@ -173,8 +177,10 @@ class ParseInstrumentDataServerProcess extends AbstractServerProcess
     /**
      * Send email to user who triggered the process launch
      *
+     * @return void
      */
-    public function sendNotificationEmail() {
+    public function sendNotificationEmail()
+    {
         error_log("Sending email to {$this->getUserId()}");
 
         $user = \NDB_Factory::singleton()->database()->pselectRow(
@@ -183,32 +189,43 @@ class ParseInstrumentDataServerProcess extends AbstractServerProcess
         );
 
         $msg_data = [
-            'name' => $user['First_name'],
+            'name'    => $user['First_name'],
             'message' => $this->getExitText(),
         ];
-        \Email::send($user['Email'], 'notifier_instrument_data_upload.tpl', $msg_data);
+        \Email::send(
+            $user['Email'],
+            'notifier_instrument_data_upload.tpl',
+            $msg_data
+        );
     }
 
     /**
      * Change file permissions
      *
+     * @return void
      */
-    public function changeFilePermissions() {
-        array_map(function($file){
-            chmod($file, 0775);
-        }, [
-            $this->getStdoutFile(),
-            $this->getStderrFile(),
-            $this->getExitCodeFile(),
-        ]);
+    public function changeFilePermissions()
+    {
+        array_map(
+            function ($file) {
+                chmod($file, 0775);
+            },
+            [
+                $this->getStdoutFile(),
+                $this->getStderrFile(),
+                $this->getExitCodeFile(),
+            ]
+        );
     }
 
 
     /**
      * Perform action once process is completed
      *
+     * @return void
      */
-    public function performPostAction() {
+    public function performPostAction()
+    {
         $this->sendNotificationEmail();
     }
 }

diff --git a/modules/server_processes_manager/php/serverprocessesmonitor.class.inc b/modules/server_processes_manager/php/serverprocessesmonitor.class.inc
@@ -141,7 +141,8 @@ class ServerProcessesMonitor
         $serverProcessFactory = new ServerProcessFactory();
         $savedProcesses       = [];
         foreach ($rows as $row) {
-            $savedProcesses[$row['id']] = $serverProcessFactory->getServerProcess($row);
+            $savedProcesses[$row['id']]
+                = $serverProcessFactory->getServerProcess($row);
 
         }
 
@@ -161,7 +162,6 @@ class ServerProcessesMonitor
             // Find process in the database with this id (null if none)
             $matchingProcess = $savedProcesses[$id] ?? null;
 
-
             if (is_null($matchingProcess)) {
                 // No process with this id. Unknown id = unknown state
                 $state    = 'UNKNOWN_ID';

diff --git a/modules/server_processes_manager/php/serverprocessfactory.class.inc b/modules/server_processes_manager/php/serverprocessfactory.class.inc
@@ -29,8 +29,10 @@ class ServerProcessFactory
     /**
      * Creates a server process based on the parameters passed as arguments.
      *
-     * @param array $dbRow  Process database row.
+     * @param array $dbRow Process database row.
+     *
      * @return AbstractServerProcess the server process created
+     *
      * @throws \InvalidArgumentException if the server process type is unknown
      */
     public function getServerProcess(array $dbRow): AbstractServerProcess
@@ -50,7 +52,7 @@ class ServerProcessFactory
                     $dbRow['start_time'],
                     $dbRow['end_time'],
                     $dbRow['exit_text']
-            ),
+                ),
             ParseInstrumentDataServerProcess::PROCESS_TYPE =>
                 new ParseInstrumentDataServerProcess(
                     '',
@@ -65,8 +67,10 @@ class ServerProcessFactory
                     $dbRow['start_time'],
                     $dbRow['end_time'],
                     $dbRow['exit_text']
-            ),
-            default => throw new \InvalidArgumentException("Unknown server process type: ${dbRow['type']}")
+                ),
+            default => throw new \InvalidArgumentException(
+                "Unknown server process type: ${dbRow['type']}"
+            )
         };
     }
 }

diff --git a/modules/server_processes_manager/php/serverprocesslauncher.class.inc b/modules/server_processes_manager/php/serverprocesslauncher.class.inc
@@ -161,18 +161,16 @@ class ServerProcessLauncher
     /**
      * Launch instrument data parse process
      *
-     * @param string $instrument    Instrument name
-     * @param string $fileLocation  File location
-     *
+     * @param string $instrument   Instrument name
+     * @param string $fileLocation File location
      *
      * @return ?int ID (in the database) of the launched process or null
      *             if the process could not be run
      */
     public function parseInstrumentData(
         string $instrument,
         string $fileLocation
-    ): ?int
-    {
+    ): ?int {
         $parseInstrumentDataProcess = new ParseInstrumentDataServerProcess(
             $instrument,
             $fileLocation