Updated tripal_views_handler_filter_select_cvterm to not use deprecated views_handler_filter_chado_select_cvterm_name

tripal_views/tripal_views.views.inc

@@ -70,7 +70,7 @@ function tripal_views_views_handlers() {
         'parent' => 'views_handler_filter'
       ),
       'tripal_views_handler_filter_select_cvterm' => array(
-        'parent' => 'views_handler_filter_chado_select_cvterm_name',
+        'parent' => 'views_handler_filter_string',
       ),
       'tripal_views_handler_filter_select_string' => array(
         'parent' => 'chado_views_handler_filter_string',

tripal_views/views/handlers/tripal_views_handler_filter_select_cvterm.inc

@@ -10,7 +10,7 @@
  * @ingroup views_filter_handlers
  * @ingroup tripal_core
  */
-class tripal_views_handler_filter_select_cvterm extends views_handler_filter_chado_select_cvterm_name {
+class tripal_views_handler_filter_select_cvterm extends views_handler_filter_string {
 
  /**
   * Executed when the field is added
@@ -19,8 +19,64 @@ class tripal_views_handler_filter_select_cvterm extends views_handler_filter_cha
   function init(&$view, $options) {
 
     include_once('chado_wrapper_functions.inc');
+
     parent::init($view, $options);
 
+    if ($this->options['show_all']) {
+      $cv_id = variable_get('chado_' . $this->view->base_table . '_cv', NULL);
+      if ($cv_id) {
+        $results = tripal_core_chado_select('cvterm', array('cvterm_id', 'name'), array('cv_id' => $cv_id));
+        if (empty($results)) {
+          $results = array();
+        }
+        foreach ($results as $c) {
+          $cvterms[$c->cvterm_id] = $c->name;
+        }
+      }
+      else {
+        //get a list of cvs currently used
+        if ($this->view->base_table == 'cvterm') {
+          $sql = 'SELECT distinct(cv.cv_id) FROM ' . $this->view->base_table
+            .' LEFT JOIN cv cv ON cv.cv_id=cvterm.cv_id';
+        }
+        else {
+          $sql = 'SELECT distinct(cv.cv_id) FROM ' . $this->view->base_table
+            .' LEFT JOIN cvterm cvterm ON cvterm.cvterm_id=' . $this->view->base_table . '.type_id '
+            .'LEFT JOIN cv cv ON cv.cv_id=cvterm.cv_id';
+        }
+        $previous_db = tripal_db_set_active('chado');
+        $resource = db_query($sql);
+        tripal_db_set_active($previous_db);
+        $cvterms = array();
+        while ( $r = db_fetch_object($resource) ) {
+          $results = tripal_core_chado_select('cvterm', array('cvterm_id', 'name'), array('cv_id' => $r->cv_id));
+          if (empty($results)) {
+            $results = array();
+          }
+          foreach ($results as $c) {
+            $cvterms[$c->cvterm_id] = $c->name;
+          }
+        }
+      }// end of if variable not defined
+
+    }
+    else {
+      // @coder-ignore: non-drupal schema therefore table prefixing does not apply
+      $sql = "SELECT cvterm_id, name FROM cvterm WHERE cvterm_id IN (SELECT distinct(type_id) FROM %s)";
+      $previous_db = tripal_db_set_active('chado');
+      $resource = db_query($sql, $this->table);
+      tripal_db_set_active($previous_db);
+      $cvterms = array();
+      while ( $r = db_fetch_object($resource) ) {
+        $cvterms[$r->cvterm_id] = $r->name;
+      }
+    }
+    //sort cvterms by name (case insensitive)
+    natcasesort($cvterms);
+
+    //add to this handler
+    $this->cvterm_options = $cvterms;
+
   }
 
   /**
@@ -34,6 +90,36 @@ class tripal_views_handler_filter_select_cvterm extends views_handler_filter_cha
 
     parent::options_form($form, $form_state);
 
+    $form['values_form_type'] = array(
+      '#type' => 'radios',
+      '#title' => t('Filter Type'),
+      '#options' => array(
+        'textfield' => 'Text Field',
+        'select' => 'Drop-Down Box',
+      ),
+      '#default_value' => ($this->options['values_form_type']) ? $this->options['values_form_type'] : 'select',
+    );
+
+    $form['multiple'] = array(
+      '#type' => 'checkbox',
+      '#title' => t('Select Multiple'),
+      '#description' => t('Allows more then one option to be selected.'),
+      '#default_value' => (isset($this->options['multiple'])) ? $this->options['multiple'] : FALSE,
+    );
+
+    $form['optional'] = array(
+      '#type' => 'checkbox',
+      '#title' => t('Optional'),
+      '#description' => t('Adds --Any-- to the available options.'),
+      '#default_value' => (isset($this->options['optional'])) ? $this->options['optional'] : TRUE,
+    );
+
+    $form['show_all'] = array(
+      '#type' => 'checkbox',
+      '#title' => t('Show All Terms'),
+      '#description' => 'Otherwise only cvterms used in the base table will be used'
+    );
+
     $form['agg'] = array(
       '#type' => 'fieldset',
       '#title' => 'Apply to fields that are aggregated'
@@ -78,7 +164,36 @@ class tripal_views_handler_filter_select_cvterm extends views_handler_filter_cha
     }
 
     if (!$this->aggregated) {
-      parent::query();
+
+      if ($this->options['multiple']) {
+        // Remove any if it's there
+        unset($this->value['All']);
+
+        if (sizeof($this->value)) {
+          $holders = array();
+          foreach ($this->value as $v) {
+            if (preg_match('/^[\d\.]+$/', $v)) {
+              $holders[] = '%d';
+            }
+            else {
+              $holders[] = "'%s'";
+            }
+          }
+          $where = "cvterm.cvterm_id IN (" . implode(", ", $holders) . ")";
+        }
+      }
+      elseif ($this->value != 'All') {
+        if (preg_match('/^\d+$/', $this->value)) {
+          $where = 'cvterm.cvterm_id=%d';
+        }
+        else {
+          $where = "cvterm.name" . $this->operator . "'%s'";
+        }
+      }
+
+      if ($where) {
+        $this->query->add_where($this->options['group'], $where, $this->value);
+      }
     }
     else {
 
@@ -102,4 +217,115 @@ class tripal_views_handler_filter_select_cvterm extends views_handler_filter_cha
     }
 
   }
+
+ /**
+  * Defines the value field in both the views filter options form
+  *   and the exposed form
+  */
+  function value_form(&$form, &$form_state) {
+    parent::value_form($form, $form_state);
+
+    if (preg_match('/select/', $this->options['values_form_type'])) {
+      // Get Options
+      if ($this->options['optional']) {
+        $options['<select ' . $this->table . '>'] = '--None--';
+        $options['All'] = '--Any--';
+      }
+      $max_length = 40;
+      foreach ($this->cvterm_options as $cvterm_id => $cvterm_name) {
+        if (drupal_strlen($cvterm_name) > $max_length) {
+          $options[$cvterm_id] = drupal_substr($cvterm_name, 0, $max_length) . '...';
+        }
+        else {
+          $options[$cvterm_id] = $cvterm_name;
+        }
+      }
+
+      if (empty($options)) {
+        $options[0] = '';
+      }
+
+      //Select List
+      $form['value'] = array(
+          '#type' => 'select',
+          '#title' => t('%label', array('%label' => $this->options['label'])),
+          '#options' => $options,
+          '#default_value' => $this->value,
+      );
+
+      if ($this->options['multiple']) {
+        $form['value']['#multiple'] = TRUE;
+      }
+
+    }
+    else {
+      $form['value'] = array(
+        '#type' => 'textfield',
+        '#title' => t('%label', array('%label' => $this->options['label'])),
+        '#default_value' => $this->value,
+      );
+    }
+  }
+
+ /**
+  * Ensures the select list gets rendered when the filter is exposed
+  */
+  function exposed_form(&$form, &$form_state) {
+    if (empty($this->options['exposed'])) {
+      return;
+    }
+
+    $value = $this->options['expose']['identifier'];
+    $this->value_form($form, $form_state);
+    $form[$value] = $form['value'];
+
+    if (isset($form[$value]['#title']) && !empty($form[$value]['#type']) && $form[$value]['#type'] != 'checkbox') {
+      unset($form[$value]['#title']);
+    }
+
+    $this->exposed_translate($form[$value], 'value');
+
+    if (!empty($form['#type']) && ($form['#type'] == 'checkboxes' || ($form['#type'] == 'select' && !empty($form['#multiple'])))) {
+      unset($form[$value]['#default_value']);
+    }
+
+    if (!empty($form['#type']) && $form['#type'] == 'select' && empty($form['#multiple'])) {
+      $form[$value]['#default_value'] = 'All';
+    }
+
+    if ($value != 'value') {
+      unset($form['value']);
+    }
+
+  }
+
+  /**
+   * This kind of construct makes it relatively easy for a child class
+   * to add or remove functionality by overriding this function and
+   * adding/removing items from this array.
+   */
+  function operators() {
+    $operators = array(
+      '=' => array(
+        'title' => t('Is equal to'),
+        'short' => t('='),
+        'method' => 'op_equal',
+        'values' => 1,
+      ),
+      '!=' => array(
+        'title' => t('Is not equal to'),
+        'short' => t('!='),
+        'method' => 'op_equal',
+        'values' => 1,
+      ),
+      '~' => array(
+        'title' => t('Contains'),
+        'short' => t('contains'),
+        'method' => 'op_contains',
+        'values' => 1,
+      ),
+    );
+
+    return $operators;
+  }
 }