Updated the tripal views file upload filter handler to work with D7 which included fixing the field_upload_combo form element

tripal_core/includes/form_elements.inc

@@ -8,28 +8,34 @@
 /**
  * Register form elements
  */
-function tripal_core_elements() {
+function tripal_core_element_info() {
+  $elements = array();
 
-  $type['file_upload_combo'] = array(
-    '#input'            => TRUE,
-    '#process'          => array('expand_file_upload_combo'),
-    '#element_validate' => array('file_upload_combo_validate'),
+  $elements['file_upload_combo'] = array(
+    '#input' => TRUE,
+    '#process' => array('expand_file_upload_combo'),
+    '#value_callback' =>'file_upload_combo_value_callback',
+    '#theme' => 'theme_file_upload_combo',
+    '#theme_wrappers' => array('form_element'),
   );
-  
-  $type['sequence_combo'] = array(
+
+  $elements['sequence_combo'] = array(
     '#input' => TRUE,
     '#process' => array('expand_sequence_combo'),
-    '#element_validate' => array('sequence_combo_validate'),
+    '#value_callback' => 'sequence_combo_value_callback',
+    '#theme' => 'theme_sequence_combo',
+    '#theme_wrappers' => array('form_element'),
+    '#tree' => TRUE,
   );
 
-  return $type;
+  return $elements;
 }
 
 /**
  * Upload File and keep track of previously uploaded files
  * Form element description
  */
-function expand_file_upload_combo($element, $edit, $form_state, $complete_form) {
+function expand_file_upload_combo($element, $form_state, $complete_form) {
 
   // set the default values for each field
   if (empty($element['#value'])) {
@@ -47,16 +53,16 @@ function expand_file_upload_combo($element, $edit, $form_state, $complete_form)
   $parents[] = 'items';
   $element['items'] = array(
     '#type' => 'textarea',
-    '#default_value' => $element['#value']['items'],
+    '#default_value' => (isset($element['#value']['items'])) ? $element['#value']['items'] : '',
   );
-  
+
   // add file upload element
   $parents = $element['#parents'];
   $parents[] = 'items_file';
   $element['items_file'] = array(
     '#type' => 'file',
     '#title' =>  'File upload',
-    '#default_value' => $element['#value']['items_file'],
+    '#default_value' => (isset($element['#value']['items_file'])) ? $element['#value']['items_file'] : '',
   );
 
   // add hidden elelment
@@ -64,7 +70,7 @@ function expand_file_upload_combo($element, $edit, $form_state, $complete_form)
   $parents[] = 'file_path';
   $element['file_path'] = array(
     '#type' => 'hidden',
-    '#default_value' => $element['#value']['file_path'],
+    '#default_value' => (isset($element['#value']['file_path'])) ? $element['#value']['file_path'] : '',
   );
 
   return $element;
@@ -74,20 +80,37 @@ function expand_file_upload_combo($element, $edit, $form_state, $complete_form)
 /**
  * Theme the file upload combo form element
  */
-function theme_file_upload_combo($element) {
-  return theme('form_element', $element, '<div class="container-inline">' . $element['#children'] . '</div>');
+function theme_file_upload_combo($variables) {
+  $element = $variables['element'];
+  $output = '';
+
+  $output .= drupal_render($element['items']);
+  $output .= " "; // This space forces our fields to have a little room in between.
+  $output .= drupal_render($element['items_file']);
+  $output .= " "; // This space forces our fields to have a little room in between.
+  $output .= drupal_render($element['file_path']);
+
+  return $output;
 }
 
 
 /**
  * Validate all content passed into the file upload combo form element
  */
-function file_upload_combo_validate($element, &$form) {
-  
+function file_upload_combo_value_callback($element, $input = FALSE, &$form_state) {
   $values = array();
-  
+
+  if ($input == FALSE) {
+    if (!empty($element['#default_value'])) {
+      return $element['#default_value'];
+    }
+    else {
+      return;
+    }
+  }
+
   // get the items in the textbox
-  $items =  $form['values'][$element['#name']]['items'];
+  $items =  $input['items'];
   if ($items) {
     // split on new line or comma
     $vals  = preg_split("/[\n,]+/", $items);
@@ -100,9 +123,9 @@ function file_upload_combo_validate($element, &$form) {
   // merge any items from the file upload
   $file = file_save_upload($element['#name'], array());
   if ($file) {
-    $file_path = $file->filepath;
-    
-    $form['values'][$element['#name']]['file_path'] = $file_path;
+    $file_path = $file->uri;
+
+    $input['file_path'] = $file_path;
     // we need to add our file path to the $_GET element as if it were
     // submitted along with the rest of the form
     $_GET[$element['#name']]['file_path'] = $file_path;
@@ -118,18 +141,20 @@ function file_upload_combo_validate($element, &$form) {
         $values[] = trim($value);
       }
     }
-    fclose($fh);       
+    fclose($fh);
   }
-  
-  // add a new 'items_array' element that contains the array of 
+
+  // add a new 'items_array' element that contains the array of
   // submitted items from both the textbox and the input file
-  $form['values'][$element['#name']]['items_array'] = $values;
+  $input['items_array'] = $values;
+  return $input;
 }
+
 /**
  * Form element description
  */
-function expand_sequence_combo($element, $edit, $form_state, $complete_form) {
- 
+function expand_sequence_combo($element, $form_state, $complete_form) {
+
   // set the default values for each field
   if (empty($element['#value'])) {
     $element['#value'] = array(
@@ -137,7 +162,7 @@ function expand_sequence_combo($element, $edit, $form_state, $complete_form) {
       'downstream' => '',
     );
   }
-  
+
   $element['#tree'] = TRUE;
 
   // add the upstream box
@@ -157,17 +182,19 @@ function expand_sequence_combo($element, $edit, $form_state, $complete_form) {
      '#prefix' => '<br>',
      '#title' => t('Get Downstream Bases'),
      '#description' => t('Specify the number of downstream bases to include in the sequnce'),
-     '#default_value' => $element['#value']['downstream'],     
+     '#default_value' => $element['#value']['downstream'],
   );
   return $element;
 }
+
 /**
  * Validate all content passed into the sequence combo form element
+ * D7 @todo: test/fix this callback
  */
-function sequence_combo_validate($element, &$form) {
+function sequence_combo_value_callback($element, $input = FALSE, &$form_state) {
   $upstream = $form['values'][$element['#name']]['upstream'];
   $downstream = $form['values'][$element['#name']]['downstream'];
-  
+
 
   if ($upstream < 0) {
     form_set_error($element['#name'], 'Please provide a positive number for upstream bases');
@@ -187,6 +214,13 @@ function sequence_combo_validate($element, &$form) {
 /**
  * Theme the file sequence form element
  */
-function theme_sequence_combo($element) {
-  return theme('form_element', $element, '<div class="container-inline">' . $element['#children'] . '</div>');
+function theme_sequence_combo($variables) {
+  $element = $variables['element'];
+  $output = '';
+
+  $output .= drupal_render($element['upstream']);
+  $output .= " "; // This space forces our fields to have a little room in between.
+  $output .= drupal_render($element['downstream']);
+
+  return $output;
 }

tripal_core/tripal_core.module

@@ -349,6 +349,12 @@ function tripal_core_theme() {
       'template' => 'tripal_core_customize',
       'path' => drupal_get_path('module', 'tripal_core') . '/theme'
     ),
+    'theme_file_upload_combo' => array(
+      'render element' => 'element',
+    ),
+    'theme_sequence_combo' => array(
+      'render element' => 'element',
+    ),
   );
 }
 

tripal_views/views/handlers/tripal_views_handler_filter_file_upload.inc

@@ -5,8 +5,6 @@
  * Purpose: This Handler provides a file upload field by extending the
  * views_handler_filter object.
  *
- * D7: still not compatible
- *
  * @ingroup tripal_views_integration
  */
 class tripal_views_handler_filter_file_upload extends views_handler_filter {
@@ -59,14 +57,7 @@ class tripal_views_handler_filter_file_upload extends views_handler_filter {
   }
 
   /**
-   *  Validates the input form
-   */
-  function exposed_validate(&$form, &$form_state) {
-     //dpm($form_state);
-  }
-
-  /**
-   *
+   * Add the where clause
    */
   function query() {
     $this->ensure_my_table();
@@ -76,18 +67,22 @@ class tripal_views_handler_filter_file_upload extends views_handler_filter {
     $value = $this->value[0];
     $values = $value['items_array'];
 
-    // iterate through all of the values and generate the corresponding
-    // sprintf style holders
-    for ($i = 0 ; $i < count($values); $i++) {
-      $values[$i] = trim($values[$i]);
-      $holders[] = "'%s'";
+    // trim all values supplied
+    foreach ($values as $k => $val) {
+      $values[$k] = trim($val);
+    }
+
+    // Determine the operator to use depending on # of items
+    if (sizeof($values)) {
+      $operator = 'IN';
+    }
+    else {
+      $operator = '=';
     }
 
-    // if we have any values supplied then update the where clause for
-    // the views query
-    if (count($holders) > 0) {
-      $where = "$field IN (" . implode(", ", $holders) . ")";
-      $this->query->add_where($this->options['group'], $where, $values);
+    // if we have any items then add the where
+    if (!empty($values)) {
+      $this->query->add_where($this->options['group'], $field, $values, $operator);
     }
   }
 }