trying to fix lint after adjustements

modules/biobank/jsx/processForm.js

@@ -244,7 +244,7 @@ const SpecimenProcessForm = (props) => {
 
 // ProcessForm.propTypes
 SpecimenProcessForm.propTypes = {
-  edit: PropTypes.bool.isRequired,
+  edit: PropTypes.bool,
   process: PropTypes.shape({
     data: PropTypes.object,
     protocolId: PropTypes.number,
@@ -271,7 +271,7 @@ SpecimenProcessForm.propTypes = {
           label: PropTypes.string.isRequired,
         })
       ),
-      units: PropTypes.obj.isRequired,
+      units: PropTypes.obj,
       protocols: PropTypes.arrayOf(PropTypes.string),
       processes: PropTypes.arrayOf(PropTypes.string),
       protocolAttributes: PropTypes.arrayOf(
@@ -300,7 +300,7 @@ SpecimenProcessForm.propTypes = {
       typeId: PropTypes.string,
     }),
   }).isRequired,
-  hideProtocol: PropTypes.bool.isRequired,
+  hideProtocol: PropTypes.bool,
   increaseCoordinate: PropTypes.func.isRequired,
   createSpecimens: PropTypes.func.isRequired,
   printLabel: PropTypes.func.isRequired,

modules/biobank/php/barcodes.class.inc

@@ -4,8 +4,6 @@ namespace LORIS\biobank;
 
 define('MAX_BARCODES_PER_REQUEST', 1000); // Adjust this value as needed
 
-use Psr\Http\Message\ServerRequestInterface;
-
 /**
  * {@inheritDoc}
  *
@@ -85,7 +83,7 @@ class Barcodes extends Endpoint
                   FROM biobank_container
                     WHERE SUBSTRING(Barcode, 1, 2) = :year";
         $qparams         = [':year' => $currentYear];
-        $maxNumberResult = $this->loris->getDatabaseConnection()
+        $maxNumberResult = (array) $this->loris->getDatabaseConnection()
             ->pselectOne($query, $qparams);
 
         $maxNumber = $maxNumberResult['max_number'] ?? 0;

modules/biobank/php/condition.class.inc

@@ -0,0 +1,33 @@
+<?php declare(strict_types=1);
+
+namespace LORIS\biobank;
+
+/**
+ * Condition Class
+ *
+ * Defines a Condition object for modifying resource access.
+ * A Condition represents a filter or restriction applied to resource access
+ * in a query. It specifies the field to filter, the value to match, the
+ * comparison operator, and the logical operator for combining multiple conditions.
+ *
+ * @license https://www.gnu.org/licenses/gpl-3.0.html GNU General Public License
+ */
+class Condition
+{
+    /**
+     * Constructs a Condition instance.
+     *
+     * @param string           $field           The field to filter by
+     * @param ?string          $value           The value to compare against
+     * @param ?Operator        $operator        The comparison operator
+     * @param ?LogicalOperator $logicalOperator The logical operator for combining
+     *                                          with other conditions
+     */
+    public function __construct(
+        public string $field,
+        public ?string $value,
+        public ?Operator $operator = Operator::EQUALS,
+        public ?LogicalOperator $logicalOperator = LogicalOperator::AND,
+    ) {
+    }
+}

modules/biobank/php/endpoint.class.inc

@@ -52,6 +52,54 @@ abstract class Endpoint
      */
     abstract protected function getSubHandler(string $subpath): ?Endpoint;
 
+    /**
+     * //TODO: to be moved to a service layer.
+     * Handles getting multiple resources.
+     *
+     * @param QueryParams $params The number of requested barcodes
+     *
+     * @return array The data to be returned as JSON
+     */
+    abstract protected function get(QueryParams $params): array;
+
+    /**
+     * //TODO: to be moved to a service layer.
+     * Shows a specific resource.
+     *
+     * @param string $resourceId The resource identifier that is requested
+     *
+     * @return array
+     */
+    abstract protected function getOne(string $resourceId): array;
+
+    /**
+     * //TODO: to be moved to a service layer.
+     * Handles updating a specific resource.
+     *
+     * @param array $resource The resource to be updated
+     *
+     * @return array
+     */
+    abstract protected function update(string $resource): array;
+
+    /**
+     * //TODO: to be moved to a service layer.
+     * Handles file upload requests.
+     *
+     * @param array $uploadedFiles The files to be uploaded
+     *
+     * @return void
+     */
+    abstract protected function upload(array $uploadedFiles): void;
+
+    /**
+     * //TODO: to be moved to a service layer.
+     * Handles creating a new resource.
+     *
+     * @return array
+     */
+    abstract protected function create(): array;
+
     /**
      * Defines the allowed HTTP methods for this endpoint.
      *
@@ -77,7 +125,7 @@ abstract class Endpoint
     ) : void {
         if (!$user->hasPermission($this->getPermission($permission))) {
             throw new Forbidden(
-                get_called_class() . ": {$permission->name()} Permission Denied"
+                get_called_class() . ": {$permission->value} Permission Denied"
             );
         }
     }
@@ -100,7 +148,7 @@ abstract class Endpoint
         // Determine subendpoint handler based on the subpath
         if (count($pathparts) > 1) {
             $subpath    = $pathparts[1];
-            $subhandler = $this->getSubHandler($pathparts[1]);
+            $subhandler = $this->getSubHandler($subpath);
 
             if ($subhandler !== null) {
                 // Remove the handled part of the path and pass the remainder

modules/biobank/php/logicaloperator.class.inc

@@ -0,0 +1,16 @@
+<?php declare(strict_types=1);
+
+namespace LORIS\biobank;
+
+/**
+ * Enum LogicalOperator
+ *
+ * Defines the allowed LogicalOperators for chaining query conditions.
+ *
+ * @license https://www.gnu.org/licenses/gpl-3.0.html GNU General Public License
+ */
+enum LogicalOperator: string
+{
+    case AND = 'AND';
+    case OR  = 'OR';
+}

modules/biobank/php/operator.class.inc

@@ -0,0 +1,42 @@
+<?php declare(strict_types=1);
+
+namespace LORIS\biobank;
+
+/**
+ * Enum Operator
+ *
+ * Defines the allowed Operators for accessing resources.
+ *
+ * @license https://www.gnu.org/licenses/gpl-3.0.html GNU General Public License
+ */
+enum Operator: string
+{
+    case EQUALS       = 'eq';                    // Equals
+    case NOT_EQUALS   = 'neq';               // Not equals
+    case GREATER_THAN = 'gt';              // Greater than
+    case LESS_THAN    = 'lt';                 // Less than
+    case GREATER_THAN_OR_EQUALS = 'gte';   // Greater than or equals
+    case LESS_THAN_OR_EQUALS    = 'lte';      // Less than or equals
+    case LIKE = 'like';                    // Like (pattern match)
+    case IN   = 'in';                        // In (value in set)
+
+
+    /**
+     * Converts the Operator enum value to its corresponding SQL representation.
+     *
+     * @return string The SQL operator corresponding to the enum value.
+     */
+    public function toSql(): string
+    {
+        return match ($this) {
+            self::EQUALS => '=',
+            self::NOT_EQUALS => '!=',
+            self::GREATER_THAN => '>',
+            self::LESS_THAN => '<',
+            self::GREATER_THAN_OR_EQUALS => '>=',
+            self::LESS_THAN_OR_EQUALS => '<=',
+            self::LIKE => 'LIKE',
+            self::IN => 'IN',
+        };
+    }
+}

modules/biobank/php/queryparams.class.inc

@@ -66,19 +66,6 @@ class QueryParams
         return $this;
     }
 
-    /**
-     * Sets the group-by clause for the query.
-     *
-     * @param string $groupBy The field to group by.
-     *
-     * @return self
-     */
-    public function groupBy(string $groupBy): self
-    {
-        $this->groupBy = $groupBy;
-        return $this;
-    }
-
     /**
      * Sets the limit for the query results.
      *

modules/biobank/php/queryparamshandler.class.inc

@@ -6,7 +6,7 @@ namespace LORIS\biobank;
  * Class QueryParamsHandler
  *
  * Handles the parsing of query parameters into a `QueryParams` object.
- * This includes parsing fields, conditions, includes, limits, offsets, and
+ * This includes parsing fields, conditions, limits, offsets, and
  * count-only queries from the provided array of query parameters.
  *
  * @package    LORIS
@@ -44,7 +44,6 @@ final class QueryParamsHandler
         $queryParams = new QueryParams();
         $queryParams->select(...$this->parseFields())
             ->where(...$this->parseConditions())
-            ->include(...$this->parseIncludes()) // New include parsingi
             ->limit($this->parseLimit())
             ->offset($this->parseOffset())
             ->count($this->parseCount());  // Handle count
@@ -72,68 +71,6 @@ final class QueryParamsHandler
             [];
     }
 
-    /**
-     * Parses the 'include' query parameter for relationships.
-     *
-     * @return array The parsed includes as With objects.
-     */
-    protected function parseIncludes(): array
-    {
-        $includes = [];
-
-        if (isset($this->queryParams['include'])) {
-            $includes = $this->parseNestedIncludes(
-                explode(',', $this->queryParams['include'])
-            );
-        }
-
-        return $includes;
-    }
-
-    /**
-     * Recursively parses nested includes.
-     *
-     * @param array $includes The array of includes to process.
-     *
-     * @return array The parsed includes as With objects.
-     */
-    protected function parseNestedIncludes(array $includes): array
-    {
-        $result = [];
-
-        foreach ($includes as $include) {
-            $result[] = $this->createWithObject($include);
-        }
-
-        return $result;
-    }
-
-    /**
-     * Creates a With object representing an included relation.
-     *
-     * @param string $include The include string representing the relation.
-     *
-     * @return With The With object representing the relation.
-     */
-    protected function createWithObject(string $include): With
-    {
-        // Split the include string into parts
-        $parts = explode('.', $include);
-        $name  = array_shift($parts);
-
-        // Recursively build the nested With structure
-        $subIncludes = [];
-        if (!empty($parts)) {
-            $subIncludes[] = $this->createWithObject(implode('.', $parts));
-        }
-
-        // Parse conditions for the include, if any exist (this is a placeholder for
-        // actual logic)
-        $conditions = []; // This should be replaced with actual condition parsing
-
-        return new With($name, $conditions, $subIncludes);
-    }
-
     /**
      * Parses the 'conditions' query parameter.
      *

modules/biobank/php/specimendao.class.inc

@@ -606,11 +606,11 @@ class SpecimenDAO extends \LORIS\Data\ProvisionerInstance
     /**
      * Saves the Specimen Project to the database.
      *
-     * @param string $candId - The candidate for which to generate the sample number
+     * @param int $candId - The candidate for which to generate the sample number
      *
-     * @return string The sample number of the specimen
+     * @return int The sample number of the specimen
      */
-    private function _getSampleNumber($candId)
+    private function _getSampleNumber(int $candId)
     {
         // Query to get the maximum SampleNumber for the given candidate
         $query = "
@@ -622,7 +622,7 @@ class SpecimenDAO extends \LORIS\Data\ProvisionerInstance
 
         $sampleNumber = $this->db->pselectOneInt($query, ['candId' => $candId]);
 
-        return (string) $sampleNumber + 1;
+        return $sampleNumber + 1;
     }
 
     /**
@@ -646,9 +646,9 @@ class SpecimenDAO extends \LORIS\Data\ProvisionerInstance
             'SessionID'      => $specimen->getSessionId(),
         ];
 
-        // I'd prefere a better way of doing this, but for now this is the simplest
+        // I'd prefer a better way of doing this, but for now this is the simplest
         // way to ensure that the Sample Number does NOT get updated.
-        if (!$specimen->getId()) {
+        if ($specimen->getId() == null) {
             $sampleNumber = $this->_getSampleNumber($specimen->getCandidateId());
             $specimenData['SampleNumber'] = $sampleNumber;
         }