Merge pull request #130 from TripalCultivate/g4.110-repairValidDataFile

Revises valid data file validator

trpcultivate_phenotypes/src/Plugin/TripalImporter/TripalCultivatePhenotypesTraitsImporter.php

@@ -459,7 +459,7 @@ public function formValidate($form, &$form_state) {
         // Set failures for this validator name to an empty array to signal that
         // this validator has been run.
         $failures[$validator_name] = [];
-        $result = $validator->validateFile('', $file_id);
+        $result = $validator->validateFile($file_id);
 
         // Check if validation failed and save the results if it did.
         if (array_key_exists('valid', $result) && $result['valid'] === FALSE) {

trpcultivate_phenotypes/src/Plugin/Validators/ValidDataFile.php

@@ -74,16 +74,14 @@ public static function create(ContainerInterface $container, array $configuratio
    * Validate that the input file is a valid file.
    *
    * Checks include:
-   * - Parameter filename or file id is valid.
+   * - File ID parameter is positive non-zero integer, and cannot be null.
    * - Has Drupal File Id number assigned and can be loaded.
    * - File extension and mime type are configured by the importer.
    * - File exists and is not empty.
    * - File can be opened.
    *
-   * @param string $filename
-   *   The full path to a file within the file system (Absolute file path).
    * @param int $fid
-   *   [OPTIONAL] The unique identifier (fid) of a file that is managed by
+   *   The unique identifier (fid) of a file that is managed by
    *   Drupal File System.
    *
    * @return array
@@ -96,84 +94,37 @@ public static function create(ContainerInterface $container, array $configuratio
    *     - 'fid': The fid of the provided file.
    *     - 'mime': The mime type of the input file if it is not supported.
    *     - 'extension': The extension of the input file if not supported.
-   *
-   * @throws \Exception
-   *   - If parameters $filename and $fid are both provided, but do not point to
-   *     the same file object.
    */
-  public function validateFile(string $filename, int|null $fid = NULL) {
+  public function validateFile(int|null $fid) {
 
-    // Parameter check, verify that the filename/file path is valid.
-    if (empty($filename) && is_null($fid)) {
+    // Parameter check, verify the file id number is not null, 0 or
+    // a negative value.
+    if (is_null($fid) || $fid <= 0) {
       return [
-        'case' => 'Filename is empty string',
+        'case' => 'Invalid file id number',
         'valid' => FALSE,
         'failedItems' => [
-          'filename' => '',
           'fid' => $fid,
         ],
       ];
     }
 
-    // Parameter check, verify the file id number is not 0 or a negative value.
-    if (!is_null($fid) && $fid <= 0) {
+    // Load the file object by fid number.
+    $file_object = $this->service_EntityTypeManager
+      ->getStorage('file')
+      ->load($fid);
+
+    // Check that the file input provided returned a file object.
+    if (!$file_object) {
       return [
-        'case' => 'Invalid file id number',
+        'case' => 'File id failed to load a file object',
         'valid' => FALSE,
         'failedItems' => [
-          'filename' => $filename,
           'fid' => $fid,
         ],
       ];
     }
 
-    // Holds the file object when file is a managed file.
-    $file_object = NULL;
-
-    // Load file object.
-    if (is_numeric($fid) && $fid > 0) {
-      // Load the file object by fid number.
-      $file_object = $this->service_EntityTypeManager
-        ->getStorage('file')
-        ->load($fid);
-
-      // Verify that the filename (if provided) matches the filename in the file
-      // object returned by the file id.
-      if (!empty($filename) && $file_object->getFileName() != pathinfo($filename, PATHINFO_FILENAME)) {
-        throw new \Exception('The filename provided does not match the filename set in the file object.');
-      }
-    }
-    elseif ($filename) {
-      // Locate the file entity by uri and load the file object using the
-      // returned file id number that matched.
-      $file_object = $this->service_EntityTypeManager
-        ->getStorage('file')
-        ->loadByProperties(['uri' => $filename]);
-      $file_object = reset($file_object);
-    }
-
-    // Check that the file input provided returned a file object.
-    if (!$file_object) {
-      if (is_null($fid)) {
-        return [
-          'case' => 'Filename failed to load a file object',
-          'valid' => FALSE,
-          'failedItems' => [
-            'filename' => $filename,
-          ],
-        ];
-      }
-      else {
-        return [
-          'case' => 'File id failed to load a file object',
-          'valid' => FALSE,
-          'failedItems' => [
-            'fid' => $fid,
-          ],
-        ];
-      }
-    }
-
     // File object loaded successfully. Any subsequent failed checks will
     // reference the filename and file id from the established file object.
     $file_filename = $file_object->getFileName();

trpcultivate_phenotypes/src/TripalCultivateValidator/TripalCultivatePhenotypesValidatorBase.php

@@ -89,7 +89,7 @@ public function validateMetadata(array $form_values) {
   /**
    * {@inheritdoc}
    */
-  public function validateFile(string $filename, int $fid) {
+  public function validateFile(int|null $fid) {
     $plugin_name = $this->getValidatorName();
     throw new \Exception("Method validateFile() from base class called for $plugin_name. If this plugin wants to support this type of validation then they need to override it.");
   }

trpcultivate_phenotypes/src/TripalCultivateValidator/TripalCultivatePhenotypesValidatorInterface.php

@@ -69,8 +69,6 @@ public function validateMetadata(array $form_values);
    * This should validate the file object (e.g. it exists, is readable) but
    * should not validate the contents in any way.
    *
-   * @param array $filename
-   *   The full path and filename with extension of the file to validate.
    * @param int $fid
    *   The file ID of the file object.
    *
@@ -86,7 +84,7 @@ public function validateMetadata(array $form_values);
    *     then this array should contain a key indicating what failed, and the
    *     resulting value from checking its mime-type/extension.
    */
-  public function validateFile(string $filename, int $fid);
+  public function validateFile(int|null $fid);
 
   /**
    * Validates rows within the data file submitted to an importer.

trpcultivate_phenotypes/tests/src/Kernel/Validators/ValidatorBaseTest.php

@@ -285,9 +285,8 @@ public function testValidatorValidateMethods() {
     $exception_caught = NULL;
     $exception_message = NULL;
     try {
-      $filename = 'public://does_not_exist.txt';
       $fid = 123;
-      $instance->validateFile($filename, $fid);
+      $instance->validateFile($fid);
     }
     catch (\Exception $e) {
       $exception_caught = TRUE;