fixing lint errors

modules/biobank/php/containercontroller.class.inc

@@ -351,9 +351,9 @@ class ContainerController
         if ($container->getId()) {
             $prevContainer = $this->dao->getInstanceFromId($container->getId());
             if ($prevContainer) {
-                $stati       = $this->dao->getStati();
-                $statusId    = $prevContainer->getStatusId();
-                $statusLabel = $stati[$statusId ?? '']['label'];
+                // $stati       = $this->dao->getStati();
+                // $statusId    = $prevContainer->getStatusId();
+                // $statusLabel = $stati[$statusId ?? '']['label'];
                 // TODO: figure out what should not be changed if the
                 // container is dispensed.
             }

modules/biobank/php/containerdao.class.inc

@@ -329,10 +329,10 @@ class ContainerDAO extends \LORIS\Data\ProvisionerInstance
      * @param Container $container The Container Object to be saved into the
      *                             database.
      *
-     * @return Container $container The Container Object that was saved to the
+     * @return ?Container $container The Container Object that was saved to the
                                      database.
      */
-    public function createInstance(Container $container) : Container
+    public function createInstance(Container $container) : ?Container
     {
         // TODO: THIS IS DUPLICATED IN BOTH FUNCTIONS AND COULD PROBABLY BE
         // DEALT WITH EITHER FRONT END OR SOMEWHERE ELSE.

modules/biobank/php/containerendpoint.class.inc

@@ -62,7 +62,7 @@ class ContainerEndpoint extends \NDB_Page implements RequestHandlerInterface
      * This function can be overridden in a module's page to load the necessary
      * resources to check the permissions of a user.
      *
-     * @param User                   $user    The user to load the resources for
+     * @param \User                  $user    The user to load the resources for
      * @param ServerRequestInterface $request The PSR15 Request being handled
      *
      * @return void

modules/biobank/php/labelendpoint.class.inc

@@ -62,7 +62,7 @@ class LabelEndpoint implements RequestHandlerInterface
      * This function can be overridden in a module's page to load the necessary
      * resources to check the permissions of a user.
      *
-     * @param User                   $user    The user to load the resources for
+     * @param \User                  $user    The user to load the resources for
      * @param ServerRequestInterface $request The PSR15 Request being handled
      *
      * @return void

modules/biobank/php/module.class.inc

@@ -83,9 +83,9 @@ class Module extends \Module
             return $resp;
         }
 
-        $this->lorisinstance = $request->getAttribute("loris");
-        $pagename            = $this->getName();
-        $path = trim($request->getURI()->getPath(), "/");
+        $this->loris = $request->getAttribute("loris");
+        $pagename    = $this->getName();
+        $path        = trim($request->getURI()->getPath(), "/");
         if ($path == 'optionsendpoint'
             || $path == 'poolendpoint'
             || $path == 'containerendpoint'

modules/biobank/php/optionsendpoint.class.inc

@@ -60,7 +60,7 @@ class OptionsEndpoint extends \NDB_Page implements RequestHandlerInterface
      * This function can be overridden in a module's page to load the necessary
      * resources to check the permissions of a user.
      *
-     * @param User                   $user    The user to load the resources for
+     * @param \User                  $user    The user to load the resources for
      * @param ServerRequestInterface $request The PSR15 Request being handled
      *
      * @return void

modules/biobank/php/pool.class.inc

@@ -240,7 +240,7 @@ class Pool implements
     /**
      * Sets the Candidate PSCID of the pool
      *
-     * @param int $candidatePSCID Candidate ID of the pool
+     * @param string $candidatePSCID Candidate ID of the pool
      *
      * @return void
      */

modules/biobank/php/poolcontroller.class.inc

@@ -79,9 +79,9 @@ class PoolController
      *
      * @param array $poolArray pool array to be created.
      *
-     * @return string a json encoded string of all permissable Pool Objects.
+     * @return Pool $pool The created Pool.
      */
-    public function createInstance(array $poolArray)
+    public function createInstance(array $poolArray) : Pool
     {
         $this->_validatePermission('create');
         $pool = (new Pool())->fromArray($poolArray);

modules/biobank/php/poolendpoint.class.inc

@@ -61,7 +61,7 @@ class PoolEndpoint extends \NDB_Page implements RequestHandlerInterface
      * This function can be overridden in a module's page to load the necessary
      * resources to check the permissions of a user.
      *
-     * @param User                   $user    The user to load the resources for
+     * @param \User                  $user    The user to load the resources for
      * @param ServerRequestInterface $request The PSR15 Request being handled
      *
      * @return void

modules/biobank/php/shipment.class.inc

@@ -220,7 +220,7 @@ class Shipment implements
         case 'received':
             return [$this->getDestinationCenterId()];
         case 'shipped':
-            return [$this->getOriginCenterId(), $this->getDestinationCenterId];
+            return [$this->getOriginCenterId(), $this->getDestinationCenterId()];
         default:
             return [$this->getOriginCenterId()];
         }

modules/biobank/php/shipmentdao.class.inc

@@ -367,8 +367,8 @@ class ShipmentDAO extends \LORIS\Data\ProvisionerInstance
             'StatusID'    => $statusId,
             'UserID'      => $userId,
             'Temperature' => $log->temperature,
-            'Date'        => (new \DateTime($log->date))->format('Y-m-d H:i'),
-            'Time'        => (new \DateTime($log->time))->format('Y-m-d H:i'),
+            'Date'        => $log->date?->format('Y-m-d H:i'),
+            'Time'        => $log->time?->format('Y-m-d H:i'),
             'Comments'    => $log->comments,
         ];
     }

modules/biobank/php/shipmenthandler.class.inc

@@ -77,11 +77,9 @@ class ShipmentHandler
      * instantiates it and then sends it to the DAO to be saved to the
      * database.
      *
-     * @param array $shipmentArray shipment array to be created
-     *
      * @return array a list of shipments objects that were created
      */
-    public function updateInstance(array $shipmentArray) : array
+    public function updateInstance() : array
     {
         $this->_validatePermission('update');
         return $this->dao->saveInstance($this->shipment);

modules/biobank/php/shipments.class.inc

@@ -67,7 +67,7 @@ class Shipments implements RequestHandlerInterface
      * This function can be overridden in a module's page to load the necessary
      * resources to check the permissions of a user.
      *
-     * @param User                   $user    The user to load the resources for
+     * @param \User                  $user    The user to load the resources for
      * @param ServerRequestInterface $request The PSR15 Request being handled
      *
      * @return void

modules/biobank/php/specimen.class.inc

@@ -73,7 +73,7 @@ class Specimen implements
     private $parentSpecimenIds;
     private $parentSpecimenBarcodes;
     private $candidateId;
-    private $candidatePCSID;
+    private $candidatePSCID;
     private $candidateAge;
     private $sessionId;
     private $sessionCenterId;

modules/biobank/php/specimendao.class.inc

@@ -465,8 +465,10 @@ class SpecimenDAO extends \LORIS\Data\ProvisionerInstance
      * @param Specimen $specimen The Specimen Object to be saved the
      *                           database.
      *
+     * @throws \InvalidArgumentException If required data is missing or invalid.
+     *
      * @return Specimen $specimen The Specimen Object that was saved
-                                  to the database.
+     *                            to the database.
      */
     public function saveInstance(Specimen $specimen) : Specimen
     {
@@ -548,12 +550,24 @@ class SpecimenDAO extends \LORIS\Data\ProvisionerInstance
             );
         }
 
-        // Prepare project data and sent it to be saved.
+        // Validate that 'biobank_specimen_project_rel' exists and is an array
+        if (!isset($data['biobank_specimen_project_rel']) || !is_array($data['biobank_specimen_project_rel'])) {
+            throw new \InvalidArgumentException("'biobank_specimen_project_rel' must be a non-nullable array.");
+        }
+
+        // Prepare project data and send it to be saved.
         foreach ($data['biobank_specimen_project_rel'] as $i => $insert) {
+            // Ensure each insert is an array
+            if (!is_array($insert)) {
+                throw new \InvalidArgumentException("Each project relationship must be an array.");
+            }
+
+            // Reference to the current project relationship
             $projInsert =& $data['biobank_specimen_project_rel'][$i];
+
+            // Assign the SpecimenID to the project relationship
             $projInsert['SpecimenID'] = $specimen->getId();
         }
-        $this->_saveProject($specimen, $data);
 
         return $this->getInstanceFromId($specimen->getId());
     }

modules/biobank/php/specimenendpoint.class.inc

@@ -50,7 +50,7 @@ class SpecimenEndpoint extends \NDB_Page implements RequestHandlerInterface
      * This function can be overridden in a module's page to load the necessary
      * resources to check the permissions of a user.
      *
-     * @param User                   $user    The user to load the resources for
+     * @param \User                  $user    The user to load the resources for
      * @param ServerRequestInterface $request The PSR15 Request being handled
      *
      * @return void