Merge branch '7.x-3.x' into 7.x-3.x-dashboard

tripal/includes/TripalEntityController.inc

@@ -36,6 +36,7 @@ class TripalEntityController extends EntityAPIController {
     $values['title'] = '';
     $values['type'] = 'TripalEntity';
     $values['nid'] = '';
+    $values['status'] = 1;
 
     // Call the parent constructor.
     $entity = parent::create($values);
@@ -153,8 +154,8 @@ class TripalEntityController extends EntityAPIController {
       $alias = tripal_replace_entity_tokens($alias, $entity, $bundle_entity);
     }
 
-    // If there was no defaults supplied by the admins
-    // then we should gneerate our own using the term name and entity id.
+    // If there is still no alias supplied then we should generate one using
+    // the term name and entity id.
     if (!$alias) {
 
       // Load the term for this TripalEntity.
@@ -325,6 +326,26 @@ class TripalEntityController extends EntityAPIController {
     global $user;
     $pkeys = array();
 
+    // Get the author information.
+    $author = $user;
+    if (property_exists($entity, 'uid')) {
+      $author = user_load($entity->uid);
+    }
+
+    $changed_date = time();
+    $create_date = $changed_date;
+    if (property_exists($entity, 'created')) {
+      $temp = new DateTime($entity->created);
+      $create_date = $temp->getTimestamp();
+    }
+
+    $status = 1;
+    if (property_exists($entity, 'status')) {
+      if ($entity->status === 0 or $entity->status === 1) {
+        $status = $entity->status;
+      }
+    }
+
     $transaction  = db_transaction();
     try {
       // If our entity has no id, then we need to give it a
@@ -347,9 +368,10 @@ class TripalEntityController extends EntityAPIController {
         'type'      => $entity->type,
         'bundle'    => $entity->bundle,
         'title'     => $entity->title,
-        'uid'       => $user->uid,
-        'created'   => $entity->created,
-        'changed'   => time(),
+        'uid'       => $author->uid,
+        'created'   => $create_date,
+        'changed'   => $changed_date,
+        'status'    => $status,
       );
       if (property_exists($entity, 'nid') and $entity->nid) {
         $record['nid'] = $entity->nid;
@@ -383,6 +405,11 @@ class TripalEntityController extends EntityAPIController {
       module_invoke_all('entity_postsave', $entity, $entity->type);
       module_invoke_all($invocation, $entity, $entity->type);
 
+      // Clear any cache entries for this entity so it can be reloaded using
+      // the values that were just saved.
+      $cid = 'field:TripalEntity:' . $entity->id;
+      cache_clear_all($cid, 'cache_field', TRUE);
+
       return $entity;
     }
     catch (Exception $e) {
@@ -391,6 +418,8 @@ class TripalEntityController extends EntityAPIController {
       drupal_set_message("Could not save the entity: " . $e->getMessage(), "error");
       return FALSE;
     }
+
+
   }
 
   /**

tripal/includes/TripalEntityUIController.inc

@@ -119,6 +119,9 @@ function tripal_view_entity($entity, $view_mode = 'full') {
    $controller = entity_get_controller($entity->type);
    $content = $controller->view(array($entity->id => $entity));
    drupal_set_title($entity->title);
+   if ($entity->status == 0) {
+     drupal_set_message('This page is currently unpublished', 'warning');
+   }
    return $content;
  }
 
@@ -480,6 +483,81 @@ function tripal_view_entity($entity, $view_mode = 'full') {
        );
      }
    }
+   $form['additional_settings'] = array(
+     '#type' => 'vertical_tabs',
+     '#weight' => 99,
+   );
+
+   // Node author information for administrators
+   $form['author'] = array(
+     '#type' => 'fieldset',
+     '#access' => user_access('administer nodes'),
+     '#title' => t('Authoring information'),
+     '#collapsible' => TRUE,
+     '#collapsed' => TRUE,
+     '#group' => 'additional_settings',
+     '#attributes' => array(
+       'class' => array('TripalEntity-form-author'),
+     ),
+     '#attached' => array(
+       'js' => array(
+         drupal_get_path('module', 'node') . '/node.js',
+         array(
+           'type' => 'setting',
+           'data' => array('anonymous' => variable_get('anonymous', t('Anonymous'))),
+         ),
+       ),
+     ),
+
+     '#weight' => 90,
+   );
+
+   $account = user_load($entity->uid);
+   $form['author']['author_name'] = array(
+     '#type' => 'textfield',
+     '#title' => t('Authored by'),
+     '#maxlength' => 60,
+     '#autocomplete_path' => 'user/autocomplete',
+     '#default_value' => !empty($account->name) ? $account->name : '',
+     '#weight' => -1,
+     '#description' => t('Leave blank for %anonymous.', array('%anonymous' => variable_get('anonymous', t('Anonymous')))),
+   );
+   $form['author']['author_date'] = array(
+     '#type' => 'textfield',
+     '#title' => t('Authored on'),
+     '#maxlength' => 25,
+     '#description' => t('Format: %time. The date format is YYYY-MM-DD and ' .
+       '%timezone is the time zone offset from UTC. Leave blank to use the ' .
+       'time of form submission.',
+       array(
+         '%time' => !empty($entity->created) ? date('Y-m-d H:i:s O', $entity->created) : format_date($entity->created, 'custom', 'Y-m-d H:i:s O'),
+         '%timezone' => !empty($entity->created) ? date('O', $entity->created) : format_date($entity->created, 'custom', 'O'))
+       ),
+     '#default_value' => !empty($entity->created) ? date('Y-m-d H:i:s O', $entity->created) : '',
+   );
+   // Node options for administrators
+   $form['options'] = array(
+     '#type' => 'fieldset',
+     '#access' => user_access('administer nodes'),
+     '#title' => t('Publishing options'),
+     '#collapsible' => TRUE,
+     '#collapsed' => TRUE,
+     '#group' => 'additional_settings',
+     '#attributes' => array(
+       'class' => array('node-form-options'),
+     ),
+     '#attached' => array(
+       'js' => array(drupal_get_path('module', 'node') . '/node.js'),
+     ),
+     '#weight' => 95,
+   );
+   $form['options']['status'] = array(
+     '#type' => 'checkbox',
+     '#title' => t('Published'),
+     '#default_value' => $entity->status,
+   );
+
+
    $form['cancel_button'] = array(
      '#type' => 'submit',
      '#value' => t('Cancel'),
@@ -519,6 +597,19 @@ function tripal_entity_form_ajax_callback($form, $form_state) {
    // For adds and updates, perform validation.
    $entity = $form_state['TripalEntity'];
    field_attach_form_validate('TripalEntity', $entity, $form, $form_state);
+
+   $username = $form_state['values']['author_name'];
+   $user = user_load_by_name($username);
+   if (!$user) {
+     form_set_error('author_name', 'Please provide a valid author name.');
+   }
+
+   try {
+    $create_date = new DateTime($form_state['values']['author_date']);
+   }
+   catch (Exception $e) {
+     form_set_error('author_date', 'Please provide a valid authored on date.');
+   }
  }
 
  /**
@@ -541,6 +632,17 @@ function tripal_entity_form_ajax_callback($form, $form_state) {
      $form_state['redirect'] = 'bio_data/' . $entity->id .'/delete';
      return;
    }
+
+   $username = $form_state['values']['author_name'];
+   $user = user_load_by_name($username);
+   $entity->uid = $user->uid;
+
+   $create_date = $form_state['values']['author_date'];
+   $entity->created = $create_date;
+
+   $published = $form_state['values']['status'];
+   $entity->status = $published;
+
    // Allow the fields to perform actions prior to submit.
    $instances = field_info_instances('TripalEntity', $entity->bundle);
    $langcode = 'und';

tripal/includes/TripalEntityViewsController.inc

@@ -31,7 +31,7 @@ class TripalEntityViewsController extends EntityDefaultViewsController {
     $data['tripal_entity']['uid']['help'] = 'The User\'s unique ID.';
 
     $data['tripal_entity']['status']['help'] = 'The publish status.';
-    $data['tripal_entity']['status']['field']['handler'] = 'tripal_views_handler_field_entity_status';
+    $data['tripal_entity']['status']['field']['handler'] = 'tripal_views_handler_field_boolean';
 
     // We want to use our own query plugin.
     $data['tripal_entity']['table']['base']['query class'] = 'tripal_views_query';

tripal/includes/TripalFields/TripalField.inc

@@ -284,7 +284,13 @@ class TripalField {
     $bundle_name = $this->instance['bundle'];
     $field_name = $this->field['field_name'];
 
-    $data[$bundle_name][$field_name] = array(
+    // Fields should be associated with the bundle's term identifier
+    // (i.e. [vocab]__[accession].
+    $bundle = tripal_load_bundle_entity(array('name' => $bundle_name));
+    $term = tripal_load_term_entity(array('term_id' => $bundle->term_id));
+    $table = $term->vocab->vocabulary . '__' . $term->accession;
+
+    $data[$table][$field_name] = array(
       'title' => $this->instance['label'],
       'help' => $this->instance['description'],
       'field' => array(
@@ -302,21 +308,6 @@ class TripalField {
     return $data;
   }
 
-  /**
-   * Allows the view data for this field to be altered.
-   *
-   * This function is the equivalent of the hook_field_views_data_alter()
-   * function of the Drupal Field API.  It provides the necessary details to
-   * allow views to integrate the field.
-   *
-   * @param $data
-   *   An array of views table data provided for a single field. This has the
-   *   same format as the return value of hook_views_data().
-   */
-  public function viewsDataAlter(&$data) {
-
-  }
-
   /**
    * Provides a form for the 'Field Settings' of an instance of this field.
    *

tripal/includes/tripal.fields.inc

@@ -104,32 +104,6 @@ function tripal_field_views_data($field) {
   return $data;
 }
 
-/**
- * Implements hook_field_views_data_alter();
- */
-function tripal_field_views_data_alter(&$result, $field, $module) {
-  // Skip fields that aren't TripalEntity fields.
-  if (!array_key_exists('TripalEntity', $field['bundles'])) {
-    return;
-  }
-
-  // Get the list of our Tripal field types for reference.
-  $tripal_field_types = tripal_get_field_types();
-
-  // Iterate through the bundles to which this field is attached and
-  // if it is a TripalField field then we'll call the viewsDataAlater function.
-  $bundles = $field['bundles']['TripalEntity'];
-  foreach ($bundles as $bundle_name) {
-
-    $field_type = $field['type'];
-    if (in_array($field_type, $tripal_field_types)) {
-      $instance = field_info_instance('TripalEntity', $field['field_name'], $bundle_name);
-      $tfield = new $field_type($field, $instance);
-      return $tfield->viewsDataAlter($result);
-    }
-  }
-}
-
 /**
  * Implements hook_field_formatter_info().
  */

tripal/tripal.info

@@ -11,10 +11,14 @@ scripts[]          = theme/js/tripal.js
 
 files[] = views_handlers/tripal_views_handler_field.inc
 files[] = views_handlers/tripal_views_handler_field_entity.inc
-files[] = views_handlers/tripal_views_handler_field_entity_status.inc
-files[] = views_handlers/tripal_views_handler_field_entity_default_formatter.inc
+files[] = views_handlers/tripal_views_handler_field_entity_link.inc
+files[] = views_handlers/tripal_views_handler_field_entity_link_edit.inc
+files[] = views_handlers/tripal_views_handler_field_entity_link_delete.inc
+files[] = views_handlers/tripal_views_handler_field_image.inc
+files[] = views_handlers/tripal_views_handler_field_boolean.inc
 files[] = views_handlers/tripal_views_handler_filter.inc
 files[] = views_handlers/tripal_views_handler_filter_string.inc
+files[] = views_handlers/tripal_views_handler_filter_boolean.inc
 files[] = views_handlers/tripal_views_handler_filter_entity_string.inc
 files[] = views_handlers/tripal_views_handler_filter_string_selectbox.inc
 files[] = views_handlers/tripal_views_handler_sort_entity_string.inc

tripal/tripal.views.inc

@@ -45,7 +45,7 @@ function tripal_views_data_fields(&$data) {
   $fields = field_info_fields();
   foreach ($fields as $field) {
 
-    // Skip fields that aren't attached to TripalEntity fields.
+    // Skip fields that aren't attached to TripalEntity entities.
     if (!array_key_exists('TripalEntity', $field['bundles'])) {
       continue;
     }
@@ -58,7 +58,7 @@ function tripal_views_data_fields(&$data) {
     // Set defaults for the field if no data array was returned.
     if (empty($result)) {
       // Iterate through the bundles to which this field is attached and
-      // if it is a TripalField field then we'll call the viewsDataAlater function.
+      // if it is a TripalField field then we'll call the viewsData function.
       $bundles = $field['bundles']['TripalEntity'];
       $result = array();
       foreach ($bundles as $bundle_name) {
@@ -89,14 +89,20 @@ function tripal_views_data_tripal_entity(&$data) {
   // Iterate through the bundles.
   while ($bundle = $bundles->fetchObject()) {
 
+    // This isn't really the table name, but because our bundle table
+    // names are unique on every Tripal site we must ust a more generic
+    // name.  Because we're using our own query class this should be fine.
+    $term = tripal_load_term_entity(array('term_id' => $bundle->term_id));
+    $table = $term->vocab->vocabulary . '__' . $term->accession;
+
     // Each bundle gets it's own "table".
-    $data[$bundle->name]['table']['group'] = t($bundle->label);
-    $data[$bundle->name]['table']['base'] = array(
+    $data[$table]['table']['group'] = t($bundle->label);
+    $data[$table]['table']['base'] = array(
       'query class' => 'tripal_views_query',
       'title' => t($bundle->label),
       'help' => t('Tripal ' . $bundle->label . ' pages'),
     );
-    $data[$bundle->name]['entity_id'] = array(
+    $data[$table]['entity_id'] = array(
       'title' => t('Entity ID'),
       'help' => t('The unique entity ID for this content type.'),
       'field' => array(
@@ -109,6 +115,65 @@ function tripal_views_data_tripal_entity(&$data) {
         'handler' => 'views_handler_sort',
       ),
     );
+    $data[$table]['link'] = array(
+      'title' => t('Link'),
+      'help' => t('Provide a simple link to the content.'),
+      'field' => array(
+        'handler' => 'tripal_views_handler_field_entity_link',
+      ),
+      'filter' => array(
+        'handler' => 'tripal_views_handler_filter',
+      ),
+      'sort' => array(
+        'handler' => 'views_handler_sort',
+      ),
+    );
+    $data[$table]['edit_link'] = array(
+      'title' => t('Edit Link'),
+      'help' => t('Provide a simple link to edit the content.'),
+      'field' => array(
+        'handler' => 'tripal_views_handler_field_entity_link_edit',
+      ),
+      'filter' => array(
+        'handler' => 'tripal_views_handler_filter',
+      ),
+      'sort' => array(
+        'handler' => 'views_handler_sort',
+      ),
+    );
+    $data[$table]['delete_link'] = array(
+      'title' => t('Delete Link'),
+      'help' => t('Provide a simple link to delete the content.'),
+      'field' => array(
+        'handler' => 'tripal_views_handler_field_entity_link_delete',
+      ),
+      'filter' => array(
+        'handler' => 'tripal_views_handler_filter',
+      ),
+      'sort' => array(
+        'handler' => 'views_handler_sort',
+      ),
+    );
+    $data[$table]['status'] = array(
+      'title' => t('Published'),
+      'help' => t('Whether or not the content is published.'),
+      'field' => array(
+        'handler' => 'tripal_views_handler_field_boolean',
+        'click sortable' => TRUE,
+        'output formats' => array(
+          'published-notpublished' => array(t('Published'), t('Not published')),
+        ),
+      ),
+      'filter' => array(
+        'handler' => 'views_handler_filter_boolean_operator',
+        'label' => t('Published'),
+        'type' => 'yes-no',
+        'use equal' => TRUE, // Use status = 1 instead of status <> 0 in WHERE statment
+      ),
+      'sort' => array(
+        'handler' => 'views_handler_sort',
+      ),
+    );
   }
 }
 

tripal/tripal_views_query.inc

@@ -39,6 +39,7 @@ class tripal_views_query extends views_plugin_query {
    *
    */
   public function init($base_table = 'tripal_entity', $base_field = 'id', $options) {
+
     parent::init($base_table, $base_field, $options);
 
     $this->fields = array();
@@ -47,9 +48,16 @@ class tripal_views_query extends views_plugin_query {
     // Creqte the TripalFieldQuery object.
     $this->query = new TripalFieldQuery();
 
-    // Make suer we only query on the entities for this bundle type.
+    // Convert the $base_table into the bundle table.  Because every
+    // tripal site will have different bundle tables we have to do the
+    // conversion for cross-site compatibility.
+    list($vocabulary, $accession) = explode('__', $base_table);
+    $term = tripal_load_term_entity(array('vocabulary' => $vocabulary, 'accession' => $accession));
+    $bundle = tripal_load_bundle_entity(array('term_id' => $term->id));
+
+    // Make sure we only query on the entities for this bundle type.
     $this->query->entityCondition('entity_type', 'TripalEntity');
-    $this->query->entityCondition('bundle', $base_table);
+    $this->query->entityCondition('bundle', $bundle->name);
   }
   /**
    *
@@ -107,35 +115,67 @@ class tripal_views_query extends views_plugin_query {
     $start = microtime(TRUE);
 
     // Execute the count query
+    // TODO: support paging.
     $cquery = clone $query;
     $cquery->count();
-    $num_records = $cquery->execute();
-    $views->total_rows = count($num_records['TripalEntity']);
+    //$views->total_rows = $cquery->execute();
 
+    // Get the IDs
     $results = $query->execute();
+    $entity_ids = array_keys($results['TripalEntity']);
+
+
+    // Get the fields to attach to the entity
+    $fields = array();
+    $field_ids = array();
+    foreach ($this->fields as $details) {
+      $field_name = $details['field_name'];
+      $field = field_info_field($field_name);
+      if ($field) {
+        $fields[$field_name] = $field;
+        $field_ids[] = $field['id'];
+      }
+    }
 
-    // Iterate through the entities that were returned and get the field
-    // values that are requested.  Those go in the view->result array.
+    $entities = tripal_load_entity('TripalEntity', $entity_ids, FALSE, $field_ids);
     $i = 0;
-    $view->result = array();
-    foreach ($results['TripalEntity'] as $entity_id => $stub) {
-      $entities = array($entity_id => $stub);
+    foreach ($entities as $entity_id => $entity) {
       $view->result[$i] = new stdClass();
-      $view->result[$i]->entity = $stub;
       foreach ($this->fields as $details) {
         $field_name = $details['field_name'];
-        $field = field_info_field($field_name);
-        module_invoke($field['storage']['module'], 'field_storage_load', 'TripalEntity',
-            $entities, FIELD_LOAD_CURRENT, array($field['id'] => array($entity_id)));
-        $view->result[$i]->$field_name = $entities[$entity_id]->$field_name['und'][0]['value'];
+        // The entity_id and link fields are not true fields. They are
+        // added by the tripal_views_data_tripal_entity() function to provide
+        // useful fields to reference entities. If we see these
+        // we need to support them here by giving them values.
+        if ($field_name == 'entity_id') {
+          $view->result[$i]->$field_name = $entity;
+          continue;
+        }
+        if ($field_name == 'link') {
+          $view->result[$i]->$field_name = $entity;
+          continue;
+        }
+        if ($field_name == 'edit_link') {
+          $view->result[$i]->$field_name = $entity;
+          continue;
+        }
+        if ($field_name == 'delete_link') {
+          $view->result[$i]->$field_name = $entity;
+          continue;
+        }
+        if ($field_name == 'status') {
+          $view->result[$i]->$field_name = $entity->status;
+          continue;
+        }
+        if (array_key_exists($field_name, $fields)) {
+          $items = field_get_items('TripalEntity', $entity, $field_name);
+          $view->result[$i]->$field_name = $items;
+        }
       }
-      $view->result[$i]->entity_id = $stub->id;
       $i++;
     }
     $view->execute_time = microtime(TRUE) - $start;
     $view->current_page = 0;
-    //dpm($view->query);
-    //dpm($view->result);
   }
 
 }

tripal/views_handlers/tripal_views_handler_field.inc

@@ -34,6 +34,7 @@ class tripal_views_handler_field extends views_handler_field {
    *   Optional name of the field where the value is stored.
    */
   function get_value($values, $field = NULL) {
+
     $alias = isset($field) ? $this->aliases[$field] : $this->field_alias;
 
     // For some reason the alias isn't being added to the $this->aliases
@@ -57,7 +58,13 @@ class tripal_views_handler_field extends views_handler_field {
    *   The values retrieved from the database.
    */
   function render($values) {
+
     $value = $this->get_value($values);
-    return $this->sanitize_value($value);
+    // Handle single value fields:
+    if (count($value == 1)) {
+      $value = $this->sanitize_value($value[0]['value'], 'xss');
+      return $value;
+    }
+    return '';
   }
-}
+}

tripal/views_handlers/tripal_views_handler_field_boolean.inc

@@ -0,0 +1,88 @@
+<?php
+class tripal_views_handler_field_boolean extends tripal_views_handler_field {
+  function option_definition() {
+    $options = parent::option_definition();
+    $options['type'] = array('default' => 'yes-no');
+    $options['type_custom_true'] = array('default' => '', 'translatable' => TRUE);
+    $options['type_custom_false'] = array('default' => '', 'translatable' => TRUE);
+    $options['not'] = array('definition bool' => 'reverse');
+
+    return $options;
+  }
+
+  function init(&$view, &$options) {
+    parent::init($view, $options);
+
+    $default_formats = array(
+      'yes-no' => array(t('Yes'), t('No')),
+      'true-false' => array(t('True'), t('False')),
+      'on-off' => array(t('On'), t('Off')),
+      'enabled-disabled' => array(t('Enabled'), t('Disabled')),
+      'boolean' => array(1, 0),
+      'unicode-yes-no' => array('✔', '✖'),
+    );
+    $output_formats = isset($this->definition['output formats']) ? $this->definition['output formats'] : array();
+    $custom_format = array('custom' => array(t('Custom')));
+    $this->formats = array_merge($default_formats, $output_formats, $custom_format);
+  }
+
+  function options_form(&$form, &$form_state) {
+    foreach ($this->formats as $key => $item) {
+      $options[$key] = implode('/', $item);
+    }
+
+    $form['type'] = array(
+      '#type' => 'select',
+      '#title' => t('Output format'),
+      '#options' => $options,
+      '#default_value' => $this->options['type'],
+    );
+
+    $form['type_custom_true'] = array(
+      '#type' => 'textfield',
+      '#title' => t('Custom output for TRUE'),
+      '#default_value' => $this->options['type_custom_true'],
+      '#states' => array(
+        'visible' => array(
+          'select[name="options[type]"]' => array('value' => 'custom'),
+        ),
+      ),
+    );
+
+    $form['type_custom_false'] = array(
+      '#type' => 'textfield',
+      '#title' => t('Custom output for FALSE'),
+      '#default_value' => $this->options['type_custom_false'],
+      '#states' => array(
+        'visible' => array(
+          'select[name="options[type]"]' => array('value' => 'custom'),
+        ),
+      ),
+    );
+
+    $form['not'] = array(
+      '#type' => 'checkbox',
+      '#title' => t('Reverse'),
+      '#description' => t('If checked, true will be displayed as false.'),
+      '#default_value' => $this->options['not'],
+    );
+    parent::options_form($form, $form_state);
+  }
+
+  function render($values) {
+    $value = $this->get_value($values);
+    if (!empty($this->options['not'])) {
+      $value = !$value;
+    }
+
+    if ($this->options['type'] == 'custom') {
+      return $value ? filter_xss_admin($this->options['type_custom_true']) : filter_xss_admin($this->options['type_custom_false']);
+    }
+    else if (isset($this->formats[$this->options['type']])) {
+      return $value ? $this->formats[$this->options['type']][0] : $this->formats[$this->options['type']][1];
+    }
+    else {
+      return $value ? $this->formats['yes-no'][0] : $this->formats['yes-no'][1];
+    }
+  }
+}

tripal/views_handlers/tripal_views_handler_field_entity.inc

@@ -45,6 +45,35 @@ class tripal_views_handler_field_entity extends tripal_views_handler_field {
     parent::options_form($form, $form_state);
   }
 
+  /**
+   * Get the value that's supposed to be rendered.
+   *
+   * This api exists so that other modules can easy set the values of the field
+   * without having the need to change the render method as well.
+   *
+   * @param $values
+   *   An object containing all retrieved values.
+   * @param $field
+   *   Optional name of the field where the value is stored.
+   */
+  function get_value($values, $field = NULL) {
+
+    $alias = isset($field) ? $this->aliases[$field] : $this->field_alias;
+
+    // For some reason the alias isn't being added to the $this->aliases
+    // variable when the user clicks the checkbox 'Link this field to the
+    // original piece of content'.  That may need to be investigated and is
+    // probably a side effect of using the  views_handler_field as a parent
+    // class that is expecting something more for SQL. We don't use aliases
+    // for fields so the following if statement will fix the problem.
+    if (!$alias) {
+      $alias = $this->field_alias;
+    }
+    if (isset($values->{$alias})) {
+      return $values->{$alias}->id;
+    }
+  }
+
   /**
    * Render whatever the data is as a link to the entity.
    *
@@ -53,16 +82,19 @@ class tripal_views_handler_field_entity extends tripal_views_handler_field {
   function render_link($data, $values) {
     if (!empty($this->options['link_to_entity']) && !empty($this->additional_fields['id'])) {
       if ($data !== NULL && $data !== '') {
-        $this->options['alter']['make_link'] = TRUE;
-        $this->options['alter']['path'] = "bio_data/" . $this->get_value($values, 'id');
-        if (isset($this->aliases['language'])) {
-          $languages = language_list();
-          $language = $this->get_value($values, 'language');
-          if (isset($languages[$language])) {
-            $this->options['alter']['language'] = $languages[$language];
-          }
-          else {
-            unset($this->options['alter']['language']);
+        $alias = $this->field_alias;
+        if (entity_access('view', 'TripalEntity', $values->{$alias})) {
+          $this->options['alter']['make_link'] = TRUE;
+          $this->options['alter']['path'] = "bio_data/" . $this->get_value($values, 'id');
+          if (isset($this->aliases['language'])) {
+            $languages = language_list();
+            $language = $this->get_value($values, 'language');
+            if (isset($languages[$language])) {
+              $this->options['alter']['language'] = $languages[$language];
+            }
+            else {
+              unset($this->options['alter']['language']);
+            }
           }
         }
       }

tripal/views_handlers/tripal_views_handler_field_entity_default_formatter.inc

@@ -1,27 +0,0 @@
-<?php
-/**
- * @file
-* Contains tripal_views_handler_field_entity_status Filter Handler
-*/
-
-/**
- * This Handler provides a generic select list for any chado field that is a string
-*  The select list includes all distinct values for that field.
-*
-* @ingroup tripal_views
-*/
-class tripal_views_handler_field_entity_default_formatter extends  views_handler_field {
-
-  function render($values) {
-
-    $field_name = $this->field;
-    $row_index = $this->view->row_index;
-    $result = $this->view->result[$row_index];
-    if (property_exists($result, entity)) {
-      $entity = $result->entity;
-      $format = field_view_field('TripalEntity', $entity, $field_name);
-      $format['#label_display'] = 'hidden';
-      return $format;
-    }
-  }
-}

tripal/views_handlers/tripal_views_handler_field_entity_link.inc

@@ -0,0 +1,40 @@
+<?php
+
+
+class tripal_views_handler_field_entity_link extends tripal_views_handler_field {
+
+  function option_definition() {
+    $options = parent::option_definition();
+    $options['text'] = array('default' => '', 'translatable' => TRUE);
+    return $options;
+  }
+
+  function options_form(&$form, &$form_state) {
+    $form['text'] = array(
+      '#type' => 'textfield',
+      '#title' => t('Text to display'),
+      '#default_value' => $this->options['text'],
+    );
+    parent::options_form($form, $form_state);
+
+    // The path is set by render_link function so don't allow to set it.
+    $form['alter']['path'] = array('#access' => FALSE);
+    $form['alter']['external'] = array('#access' => FALSE);
+  }
+
+  function render($values) {
+    if ($entity = $this->get_value($values)) {
+      return $this->render_link($entity, $values);
+    }
+  }
+
+  function render_link($entity, $values) {
+
+    if (entity_access('view', 'TripalEntity', $entity)) {
+      $this->options['alter']['make_link'] = TRUE;
+      $this->options['alter']['path'] = 'bio_data/' . $entity->id;
+      $text = !empty($this->options['text']) ? $this->options['text'] : t('view');
+      return $text;
+    }
+  }
+}

tripal/views_handlers/tripal_views_handler_field_entity_link_delete.inc

@@ -0,0 +1,40 @@
+<?php
+
+
+class tripal_views_handler_field_entity_link_delete extends tripal_views_handler_field {
+
+  function option_definition() {
+    $options = parent::option_definition();
+    $options['text'] = array('default' => '', 'translatable' => TRUE);
+    return $options;
+  }
+
+  function options_form(&$form, &$form_state) {
+    $form['text'] = array(
+      '#type' => 'textfield',
+      '#title' => t('Text to display'),
+      '#default_value' => $this->options['text'],
+    );
+    parent::options_form($form, $form_state);
+
+    // The path is set by render_link function so don't allow to set it.
+    $form['alter']['path'] = array('#access' => FALSE);
+    $form['alter']['external'] = array('#access' => FALSE);
+  }
+
+  function render($values) {
+    if ($entity = $this->get_value($values)) {
+      return $this->render_link($entity, $values);
+    }
+  }
+
+  function render_link($entity, $values) {
+
+    if (entity_access('delete', 'TripalEntity', $entity)) {
+      $this->options['alter']['make_link'] = TRUE;
+      $this->options['alter']['path'] = 'bio_data/' . $entity->id . '/delete';
+      $text = !empty($this->options['text']) ? $this->options['text'] : t('view');
+      return $text;
+    }
+  }
+}

tripal/views_handlers/tripal_views_handler_field_entity_link_edit.inc

@@ -0,0 +1,40 @@
+<?php
+
+
+class tripal_views_handler_field_entity_link_edit extends tripal_views_handler_field {
+
+  function option_definition() {
+    $options = parent::option_definition();
+    $options['text'] = array('default' => '', 'translatable' => TRUE);
+    return $options;
+  }
+
+  function options_form(&$form, &$form_state) {
+    $form['text'] = array(
+      '#type' => 'textfield',
+      '#title' => t('Text to display'),
+      '#default_value' => $this->options['text'],
+    );
+    parent::options_form($form, $form_state);
+
+    // The path is set by render_link function so don't allow to set it.
+    $form['alter']['path'] = array('#access' => FALSE);
+    $form['alter']['external'] = array('#access' => FALSE);
+  }
+
+  function render($values) {
+    if ($entity = $this->get_value($values)) {
+      return $this->render_link($entity, $values);
+    }
+  }
+
+  function render_link($entity, $values) {
+
+    if (entity_access('edit', 'TripalEntity', $entity)) {
+      $this->options['alter']['make_link'] = TRUE;
+      $this->options['alter']['path'] = 'bio_data/' . $entity->id . '/edit';
+      $text = !empty($this->options['text']) ? $this->options['text'] : t('view');
+      return $text;
+    }
+  }
+}

tripal/views_handlers/tripal_views_handler_field_entity_status.inc

@@ -1,24 +0,0 @@
-<?php
-/**
- * @file
-* Contains tripal_views_handler_field_entity_status Filter Handler
-*/
-
-/**
- * This Handler provides a generic select list for any chado field that is a string
-*  The select list includes all distinct values for that field.
-*
-* @ingroup tripal_views
-*/
-class tripal_views_handler_field_entity_status extends  views_handler_field {
-
-  function render($values) {
-    $value = $this->get_value($values);
-    if ($value == 1) {
-      return 'published';
-    }
-    else {
-      return 'unpublished';
-    }
-  }
-}

tripal/views_handlers/tripal_views_handler_field_image.inc

@@ -0,0 +1,71 @@
+<?php
+/**
+ * @file
+ *   Views field handler for basic TripalFields fields.
+ */
+
+/**
+ * Views field handler for basic TripalFields fields.
+ */
+class tripal_views_handler_field_image extends tripal_views_handler_field {
+
+  /**
+   * Overrides option_definition().
+   */
+  function option_definition() {
+    $options = parent::option_definition();
+    $options['image_width'] = array('default' => '');
+    $options['image_height'] = array('default' => '');
+
+    return $options;
+  }
+
+  /**
+   * Overrides options_form().
+   */
+  function options_form(&$form, &$form_state) {
+    parent::options_form($form, $form_state);
+    $form['image_width'] = array(
+      '#type' => 'textfield',
+      '#title' => t('Image Width'),
+      '#description' => t('Please provide the width for display of images. Leave blank to accept the width of the image.'),
+      '#size' => '10',
+      '#default_value' => $this->options['image_width'],
+    );
+    $form['image_height'] = array(
+      '#type' => 'textfield',
+      '#title' => t('Image Height'),
+      '#description' => t('Please provide the height for display of images. Leave blank to accept the width of the image.'),
+      '#size' => '10',
+      '#default_value' => $this->options['image_height'],
+    );
+  }
+  /**
+   * Render the field.
+   *
+   * @param $values
+   *   The values retrieved from the database.
+   */
+  function render($values) {
+    $value = $this->get_value($values);
+    // Handle single value fields:
+    if (count($value == 1)) {
+       $fid = $value[0]['fid'];
+       if ($fid) {
+         $file = file_load($fid);
+         $url = file_create_url($file->uri);
+         $width = '';
+         $height = '';
+         if ($this->options['image_width']) {
+           $width = ' width = "' . $this->options['image_width'] . '"';
+         }
+         if ($this->options['image_height']) {
+           $height = ' height = "' . $this->options['image_height'] . '"';
+         }
+         return '<img src="' . $url . '"'. $width . $height .' border="0">';
+
+       }
+    }
+    return '';
+  }
+}

tripal/views_handlers/tripal_views_handler_filter_boolean.inc

@@ -0,0 +1,142 @@
+<?php
+class tripal_views_handler_filter_boolean_operator extends tripal_views_handler_filter {
+  // exposed filter options
+  var $always_multiple = TRUE;
+  // Don't display empty space where the operator would be.
+  var $no_operator = TRUE;
+  // Whether to accept NULL as a false value or not
+  var $accept_null = FALSE;
+
+  function construct() {
+    $this->value_value = t('True');
+    if (isset($this->definition['label'])) {
+      $this->value_value = $this->definition['label'];
+    }
+    if (isset($this->definition['accept null'])) {
+      $this->accept_null = (bool) $this->definition['accept null'];
+    }
+    else if (isset($this->definition['accept_null'])) {
+      $this->accept_null = (bool) $this->definition['accept_null'];
+    }
+    $this->value_options = NULL;
+    parent::construct();
+  }
+
+  /**
+   * Return the possible options for this filter.
+   *
+   * Child classes should override this function to set the possible values
+   * for the filter.  Since this is a boolean filter, the array should have
+   * two possible keys: 1 for "True" and 0 for "False", although the labels
+   * can be whatever makes sense for the filter.  These values are used for
+   * configuring the filter, when the filter is exposed, and in the admin
+   * summary of the filter.  Normally, this should be static data, but if it's
+   * dynamic for some reason, child classes should use a guard to reduce
+   * database hits as much as possible.
+   */
+  function get_value_options() {
+    if (isset($this->definition['type'])) {
+      if ($this->definition['type'] == 'yes-no') {
+        $this->value_options = array(1 => t('Yes'), 0 => t('No'));
+      }
+      if ($this->definition['type'] == 'on-off') {
+        $this->value_options = array(1 => t('On'), 0 => t('Off'));
+      }
+      if ($this->definition['type'] == 'enabled-disabled') {
+        $this->value_options = array(1 => t('Enabled'), 0 => t('Disabled'));
+      }
+    }
+
+    // Provide a fallback if the above didn't set anything.
+    if (!isset($this->value_options)) {
+      $this->value_options = array(1 => t('True'), 0 => t('False'));
+    }
+  }
+
+  function option_definition() {
+    $options = parent::option_definition();
+
+    $options['value']['default'] = FALSE;
+
+    return $options;
+  }
+
+  function operator_form(&$form, &$form_state) {
+    $form['operator'] = array();
+  }
+
+  function value_form(&$form, &$form_state) {
+    if (empty($this->value_options)) {
+      // Initialize the array of possible values for this filter.
+      $this->get_value_options();
+    }
+    if (!empty($form_state['exposed'])) {
+      // Exposed filter: use a select box to save space.
+      $filter_form_type = 'select';
+    }
+    else {
+      // Configuring a filter: use radios for clarity.
+      $filter_form_type = 'radios';
+    }
+    $form['value'] = array(
+      '#type' => $filter_form_type,
+      '#title' => $this->value_value,
+      '#options' => $this->value_options,
+      '#default_value' => $this->value,
+    );
+    if (!empty($this->options['exposed'])) {
+      $identifier = $this->options['expose']['identifier'];
+      if (!empty($form_state['exposed']) && !isset($form_state['input'][$identifier])) {
+        $form_state['input'][$identifier] = $this->value;
+      }
+      // If we're configuring an exposed filter, add an <Any> option.
+      if (empty($form_state['exposed']) || empty($this->options['expose']['required'])) {
+        $any_label = variable_get('views_exposed_filter_any_label', 'new_any') == 'old_any' ? '<Any>' : t('- Any -');
+        if ($form['value']['#type'] != 'select') {
+          $any_label = check_plain($any_label);
+        }
+        $form['value']['#options'] = array('All' => $any_label) + $form['value']['#options'];
+      }
+    }
+  }
+
+  function value_validate($form, &$form_state) {
+    if ($form_state['values']['options']['value'] == 'All' && !empty($form_state['values']['options']['expose']['required'])) {
+      form_set_error('value', t('You must select a value unless this is an non-required exposed filter.'));
+    }
+  }
+
+  function admin_summary() {
+    if ($this->is_a_group()) {
+      return t('grouped');
+    }
+    if (!empty($this->options['exposed'])) {
+      return t('exposed');
+    }
+    if (empty($this->value_options)) {
+      $this->get_value_options();
+    }
+    // Now that we have the valid options for this filter, just return the
+    // human-readable label based on the current value.  The value_options
+    // array is keyed with either 0 or 1, so if the current value is not
+    // empty, use the label for 1, and if it's empty, use the label for 0.
+    return $this->value_options[!empty($this->value)];
+  }
+
+  function expose_options() {
+    parent::expose_options();
+    $this->options['expose']['operator_id'] = '';
+    $this->options['expose']['label'] = $this->value_value;
+    $this->options['expose']['required'] = TRUE;
+  }
+
+  function query() {
+//     $this->ensure_my_table();
+//     $field = $this->real_field;
+
+//     $info = $this->operators();
+//     if (!empty($info[$this->operator]['method'])) {
+//       $this->{$info[$this->operator]['method']}($field);
+//     }
+  }
+}

tripal_chado/api/tripal_chado.variables.api.inc

@@ -312,24 +312,10 @@ function chado_generate_var($table, $values, $base_options = array()) {
       // Check to see if the current record maps to an entity.  Because
       // multiple bundles can map to the same table we have to check
       // all bundles for this table.
- /*
-      $bundles = db_select('chado_bundle', 'cb');
-      $bundles->fields('tb', array('name'));
-      $bundles->join('tripal_bundle', 'tb', 'tb.id = cb.bundle_id');
-      $bundles->condition('cb.data_table', $table);
-      $bundles->execute();
-      foreach ($bundles as $bundle) {
-        $cbundle_table = chado_get_bundle_entity_table($bundle);
-        $record = $db_select($cbundle_table, 'ce')
-          ->fields('ce', 'entity_id')
-          ->condition('record_id', $object->{$table_primary_key})
-          ->execute()
-          ->fetchObject();
-        if ($record) {
-          $object->entity_id = $record->entity_id;
-        }
+      $entity_id = chado_get_record_entity_by_table($table, $object->{$table_primary_key});
+      if ($entity_id) {
+        $object->entity_id = $entity_id;
       }
-*/
 
       // remove any fields where criteria needs to be evalulated---------------------------------------
       // The fields to be removed can be populated by implementing either

tripal_chado/includes/TripalFields/chado_linker__prop/chado_linker__prop_formatter.inc

@@ -59,6 +59,5 @@ class chado_linker__prop_formatter extends ChadoFieldFormatter {
         '#markup' => $content,
       );
     }
-
   }
 }

tripal_chado/includes/TripalFields/obi__organism/obi__organism.inc

@@ -114,9 +114,8 @@ class obi__organism extends ChadoField {
       $entity->{$field_name}['und'][0]['chado-' . $field_table . '__organism_id'] = $organism->organism_id;
 
       // Is there a published entity for this organism?
-      if (property_exists($entity->chado_record->$field_column, 'entity_id')) {
-        $fk_entity_id = $entity->chado_record->$field_column->entity_id;
-        $entity->{$field_name}['und'][0]['value']['entity'] = 'TripalEntity:' . $fk_entity_id;
+      if (property_exists($record->{$field_column}, 'entity_id')) {
+        $entity->{$field_name}['und'][0]['value']['entity'] = 'TripalEntity:' . $record->{$field_column}->entity_id;
       }
     }
   }

tripal_chado/includes/TripalFields/obi__organism/obi__organism_formatter.inc

@@ -14,6 +14,11 @@ class obi__organism_formatter extends ChadoFieldFormatter {
   public function view(&$element, $entity_type, $entity, $langcode, $items, $display) {
     if (count($items) > 0) {
       $content = $items[0]['value']['rdfs:label'];
+      $entity = isset($item['value']['entity']) ? $item['value']['entity'] : '';
+      if ($entity) {
+        list($entity_type, $entity_id) = explode(':', $entity);
+        $content = l(content, 'bio_data/' . $entity_id);
+      }
       if (array_key_exists('entity', $items[0]['value'])) {
         list($entity_type, $entity_id) = explode(':', $items[0]['value']['entity']);
         $content = l(strip_tags($items[0]['value']['rdfs:label']), 'bio_data/' . $entity_id);
@@ -27,4 +32,4 @@ class obi__organism_formatter extends ChadoFieldFormatter {
       );
     }
   }
-}
+}

tripal_chado/includes/TripalFields/ogi__location_on_map/ogi__location_on_map.inc

@@ -94,18 +94,18 @@ class ogi__location_on_map extends ChadoField {
         $value = array (
           // Map.
           'data:1274' => array(
-            'schema:name' => $featurmap->name,
+            'schema:name' => $featuremap->name,
             'schema:description' => $featuremap->description,
           ),
-          tripal_get_chado_semweb_term('featurepos', 'mappos') => $featurepos->mappos
+          'SIO:000056' => $featurepos->mappos
         );
         if (property_exists($featuremap, 'entity_id')) {
           $value['data:1274']['entity'] = 'TripalEntity:' . $featuremap->entity_id;
         }
-        $entity->{$field_name}['und'][$i]['value'][] = $value;
+        $entity->{$field_name}['und'][$i]['value'] = $value;
         $i++;
       }
     }
   }
 
-}
+}

tripal_chado/includes/TripalFields/ogi__location_on_map/ogi__location_on_map_formatter.inc

@@ -30,11 +30,11 @@ class ogi__location_on_map_formatter extends ChadoFieldFormatter {
       $val = $item['value'];
       $map_name = $item['value']['data:1274']['schema:name'];
       $map_desc = $item['value']['data:1274']['schema:description'];
-      $position = $item['value'][tripal_get_chado_semweb_term('featurepos', 'mappos')];
+      $position = $item['value']['SIO:000056'];
       $rows[] = array(
         $map_name,
-        $map_desc,
-        $position
+        $position,
+        $map_desc
       );
     }
     // the $table array contains the headers and rows array as well as other

tripal_chado/includes/TripalFields/sbo__phenotype/sbo__phenotype.inc

@@ -104,17 +104,18 @@ class sbo__phenotype extends ChadoField {
     if ($phenotype_linkers) {
       foreach ($phenotype_linkers as $i => $phenotype_linker) {
         $phenotype = $phenotype_linker->phenotype_id;
-        $entity->{$field_name}['und'][$i] = array(
-          'value' => array(
-            '@type' => $phenotype->attr_id->dbxref_id->db_id->name . ':' . $phenotype->attr_id->dbxref_id->accession,
-            'type' => $phenotype->attr_id->name,
-            'name' => $phenotype->name,
-            'value' => $phenotype->value,
-          ),
-          $field_table . '__' . $pkey => $phenotype_linker->$pkey,
-          $field_table . '__' . $fkey_lcolumn => $phenotype_linker->$fkey_lcolumn->$fkey_lcolumn,
-          $field_table . '__' . 'phenotype_id' => $phenotype->phenotype_id
-        );
+        $entity->{$field_name}['und'][$i]['value']['type'] =  $phenotype->attr_id->name;
+        $entity->{$field_name}['und'][$i]['value']['name'] =  $phenotype->name;
+        if ($phenotype->cvalue_id) {
+          $entity->{$field_name}['und'][$i]['value']['value'] =  $phenotype->cvalue_id->name;
+        }
+        else {
+          $entity->{$field_name}['und'][$i]['value']['value'] =  $phenotype->value;
+        }
+        
+        $entity->{$field_name}['und'][$i][$field_table . '__' . $pkey] = $phenotype_linker->$pkey;
+        $entity->{$field_name}['und'][$i][$field_table . '__' . $fkey_lcolumn] = $phenotype_linker->$fkey_lcolumn->$fkey_lcolumn;
+        $entity->{$field_name}['und'][$i][$field_table . '__' . 'phenotype_id'] = $phenotype->phenotype_id;
 
         if ($phenotype && property_exists($phenotype, 'entity_id')) {
           $entity->{$field_name}['und'][$i]['value']['entity'] = 'TripalEntity:' . $phenotype->entity_id;
@@ -123,4 +124,4 @@ class sbo__phenotype extends ChadoField {
     }
   }
 
-}
+}

tripal_chado/includes/TripalFields/sbo__phenotype/sbo__phenotype_formatter.inc

@@ -23,9 +23,14 @@ class sbo__phenotype_formatter extends ChadoFieldFormatter {
     // Get the settings
     $settings = $display['settings'];
 
-    $headers = array('Name', 'Value', 'Type');
+    $headers = array();
     $rows = array();
+    $has_type = FALSE;
+    $has_value = FALSE;
+    $has_name = FALSE;
 
+    // First iterate through the phenotypes to see if
+    // we have all of the data columns.
     foreach ($items as $delta => $item) {
       $phenotype = $item['value'];
       if (!$phenotype) {
@@ -33,16 +38,43 @@ class sbo__phenotype_formatter extends ChadoFieldFormatter {
       }
 
       // Get the field values
-      $phenotype_name = $phenotype['name'];
-      $value = $phenotype['value'];
-      $type = $phenotype['type'];
-
-      // Add a link i there is an entity.
-      if (array_key_exists('entity', $item['value']) and $item['value']['entity']) {
-        list($entity_type, $entity_id) = explode(':', $item['value']['entity']);
-        $phenotype_name = l($phenotype_name, "bio_data/" . $entity_id, array('attributes' => array('target' => "_blank")));
+      if ($phenotype['name']) {
+        $has_name = TRUE;
+      }
+      if ($phenotype['value']) {
+        $has_value = TRUE;
+      }
+      if ($phenotype['type']) {
+        $has_type = TRUE;
+      }
+    }
+    foreach ($items as $delta => $item) {
+      $row = array();
+      if ($has_type) {
+        $row[] = $phenotype['type'];
       }
-      $rows[] = array($phenotype_name, $value, $type);
+      if ($has_name) {
+        $phenotype_name = $phenotype['name'];
+        // Add a link i there is an entity.
+        if (array_key_exists('entity', $item['value']) and $item['value']['entity']) {
+          list($entity_type, $entity_id) = explode(':', $item['value']['entity']);
+          $phenotype_name = l($phenotype_name, "bio_data/" . $entity_id, array('attributes' => array('target' => "_blank")));
+        }
+        $row[] = $phenotype_name;
+      }
+      if ($has_value) {
+        $row[] = $phenotype['value'];
+      }
+      $rows[] = $row;
+    }
+    if ($has_type) {
+      $headers[] = 'Phenotype';
+    }
+    if ($has_name) {
+      $headers[] = 'Property';
+    }
+    if ($has_value) {
+      $headers[] = 'Value';
     }
     $table = array(
       'header' => $headers,

tripal_chado/includes/tripal_chado.field_storage.inc

@@ -37,7 +37,7 @@ function tripal_chado_field_storage_write($entity_type, $entity, $op, $fields) {
   $type_field = $entity->chado_column;
   $record     = $entity->chado_record;
   $record_id  = $entity->chado_record_id;
-  $linker     = $entity->chado_linker;
+  $linker     = property_exists($entity, 'chado_linker') ? $entity->chado_linker : '';
   $base_schema = chado_get_schema($base_table);
   $base_pkey = $base_schema['primary key'][0];
 

tripal_chado/includes/tripal_chado.fields.inc

@@ -2148,3 +2148,23 @@ function tripal_chado_form_tripalbundle_form_alter(&$form, $form_state) {
     '#weight' => 0,
   );
 }
+
+/**
+ * Implements hook_field_views_data_alter();
+ */
+function tripal_chado_field_views_data_alter(&$result, $field, $module) {
+
+  // This module creates the data__image field for managing images on
+  // bio_data content types. But we want it to render correctly
+  // so we need to set some handlers.
+  if ($field['field_name'] == 'data__image') {
+    foreach ($result as $key => $fields) {
+      // It's not clear how to identify our bundle types, but they do have
+      // a double underscore in their name to separate the vocabulary from
+      // the accession, so we'll use that to find them.
+      if (preg_match('/__/', $key)) {
+        $result[$key]['data__image']['field']['handler'] = 'tripal_views_handler_field_image';
+      }
+    }
+  }
+}

tripal_chado/tripal_chado.install

@@ -306,6 +306,9 @@ function tripal_chado_upgrade_v2_v3_pre_enable() {
     if (db_query("SELECT 1 FROM pg_indexes WHERE indexname = 'tripal_cv_obo_obo_id_idx'")->fetchField()) {
       $sql = "ALTER INDEX tripal_cv_obo_obo_id_idx RENAME TO tripal_cv_obo_obo_id_idx2";
     }
+    else if (db_query("SELECT 1 FROM pg_indexes WHERE indexname = 'tripal_cv_obo_tripal_cv_obo_idx1_idx'")->fetchField()) {
+      $sql = "ALTER INDEX tripal_cv_obo_tripal_cv_obo_idx1_idx RENAME TO tripal_cv_obo_obo_id_idx2";
+    }
     else {
       $sql = "CREATE INDEX tripal_cv_obo_obo_id_idx2 ON tripal_cv_obo2 USING btree (obo_id)";
     }
@@ -313,9 +316,6 @@ function tripal_chado_upgrade_v2_v3_pre_enable() {
     if (db_query("SELECT 1 FROM pg_indexes WHERE indexname = 'tripal_cv_obo_pkey'")->fetchField()) {
       $sql = "ALTER INDEX tripal_cv_obo_pkey RENAME TO tripal_cv_obo_pkey2";
     }
-    else if (db_query("SELECT 1 FROM pg_indexes WHERE indexname = 'tripal_cv_obo_tripal_cv_obo_idx1_idx'")->fetchField()) {
-      $sql = "ALTER INDEX tripal_cv_obo_tripal_cv_obo_idx1_idx RENAME TO tripal_cv_obo_tripal_cv_obo_idx1_idx2";
-    }
     else {
       $sql = "CREATE UNIQUE INDEX tripal_cv_obo_pkey2 ON tripal_cv_obo2 USING btree (obo_id)";
     }
@@ -389,9 +389,6 @@ function tripal_chado_upgrade_v2_v3_enable() {
     if (db_query("SELECT 1 FROM pg_indexes WHERE indexname = 'tripal_cv_obo_pkey2'")->fetchField()) {
       $sql = "ALTER INDEX tripal_cv_obo_pkey2 RENAME TO tripal_cv_obo_pkey";
     }
-    else {
-      $sql = "ALTER INDEX tripal_cv_obo_tripal_cv_obo_idx1_idx2 RENAME TO tripal_cv_obo_tripal_cv_obo_idx1_idx";
-    }
     db_query($sql);
   }
 
@@ -1031,4 +1028,4 @@ function tripal_chado_update_7307() {
     $error = $e->getMessage();
     throw new DrupalUpdateException('Could not perform update: '. $error);
   }
-}
+}

tripal_ds/includes/tripal_ds.ds.inc

@@ -133,11 +133,15 @@ function _ds_layout_settings_info($bundle_name, $instances) {
 
     // Build one large multidimensional array of all instances to sort in alpha
     // order to display fields in label alpha order.
+    $right_fields = array();
     $all_field_groups = field_group_info_groups('TripalEntity', $bundle_name);
-    foreach ($all_field_groups['default'] as $key => $field_name) {
-      $right_fields[$key] = $field_name;
+    if (is_array($all_field_groups)) {
+      if (!isset($all_field_groups['default'])) { $all_field_groups['default'] = array(); }
+      foreach ($all_field_groups['default'] as $key => $field_name) {
+        $right_fields[$key] = $field_name;
+      }
+      usort($right_fields, sort_object('label'));
     }
-    usort($right_fields, sort_object('label'));
 
     // Now build the $region_right array and the fields array.
     $i = 0;

tripal_ds/theme/css/tripal_ds.css

@@ -15,7 +15,7 @@
 }
 
 .hideTripalPane {
-	display: none;
+	display: none!important;
 }
 .showTripalPane {
 	display: inherit;

tripal_ds/theme/js/tripal_ds.js

@@ -16,7 +16,7 @@
       });
 
       // Hide the pane when the close button is clicked
-      $('#tripal-pane-close-button').each(function (i) {
+      $('#tripal-pane-close-button .fa-lg').each(function (i) {
         $(this).click(function () {
           var fs = $(this).parents('div.tripal_pane');
           if($(fs).hasClass('showTripalPane'))  {
@@ -33,23 +33,20 @@
         $(this).click(function() {
           var id = '.tripal_pane-fieldset-' + $(this).attr('id');
           var prevObj = $(id).prev().attr('class');
-            // If the user clicks on other TOC item, move its fieldset to the top 
-            $(id + ' fieldset').removeClass('collapsed');
-            $(id + ' fieldset .fieldset-wrapper').show();
 
             // Highlight the fieldset instead of moving if it's already at the top
             if (prevObj.indexOf('group-tripal-pane-content-top') == 0) {
-              $(id + ' fieldset').fadeTo(10, 0.3, function() {});
-              $(id + ' fieldset').fadeTo(200, 1, function() {});
+              $(id).fadeTo(10, 0.3, function() {});
+              $(id).fadeTo(200, 1, function() {});
             }
             if ($(id).hasClass('hideTripalPane')) {
               $(id).removeClass('hideTripalPane');
               $(id).addClass('showTripalPane');
             }
-            $(id + ' fieldset .fieldset-wrapper').hide();
+            $(id).hide();
             var obj = $(id).detach();
             $('.group-tripal-pane-content-top').after(obj);
-            $(id + ' fieldset .fieldset-wrapper').show(300);
+            $(id).show(300);
           return false;
         });
       });

tripal_ds/tripal_ds.module

@@ -434,10 +434,10 @@ function tripal_ds_field_display_alter(&$display, $context){
           $parent_field_info = tripal_ds_find_field_group_parent($field_name, 'TripalEntity', $bundle, $context);
           if (!empty($parent_field_info)) {
             foreach ($parent_field_info as $parent_key => $parent_field){
-              // Stop the right rail element from rendering.
-              drupal_add_css('.' . $parent_field_info[$parent_key] . ' {display:none;}', 'inline');
-              // Hide any associated menu links.
-              drupal_add_css('#' . $parent_field_info[$parent_key] . ' {display:none;}', 'inline');
+               // We want to use JavaScript to remove the fields rather than
+               // CSS to hide them so that when users theme the table of
+               // contents using CSS they aren't theming empty rows.
+               drupal_add_js('jQuery(document).ready(function () { jQuery("#' . $parent_field_info[$parent_key] . '").parents(".views-row").remove() });', 'inline');
             }
           }
         }
@@ -445,9 +445,9 @@ function tripal_ds_field_display_alter(&$display, $context){
     }
   }
 }
-/*
 
-*/
+
+
 /**
  * Identifies field_group parents to find tripal_panes and return that
  * information to the function that calls it.