Fixed infrespecific taxon field

tripal/api/tripal.entities.api.inc

@@ -1056,7 +1056,9 @@ function tripal_replace_entity_tokens($string, &$entity, $bundle_entity = NULL)
       // Note: there is a memory leak in field_get_items() so we can't use it
       // here or bulk publising will slowly erode memory.
       //$field_value = field_get_items('TripalEntity', $entity, $field_name);
-      $value = $entity->{$field_name}['und'][0]['value'];
+      if (array_key_exists(0, $entity->{$field_name}['und'])) {
+        $value = $entity->{$field_name}['und'][0]['value'];
+      }
       // TODO: deal with the value when it is not a scalar.
     }
     // The TripalBundle__bundle_id is a special token for substituting the
@@ -1076,8 +1078,13 @@ function tripal_replace_entity_tokens($string, &$entity, $bundle_entity = NULL)
       $value = $entity->id;
     }
 
-    // Perform the replacement of the token with the value.
-    $string = str_replace($token, $value, $string);
+    // We can't support tokens that have multiple elements (i.e. in an array).
+    if (is_array($value)) {
+      $string = str_replace($token, '', $string);
+    }
+    else {
+      $string = str_replace($token, $value, $string);
+    }
   }
 
   return $string;

tripal_chado/includes/TripalFields/taxrank__infraspecific_taxon/taxrank__infraspecific_taxon.inc

@@ -59,15 +59,70 @@ class taxrank__infraspecific_taxon extends ChadoField {
    */
   public function elementInfo() {
     $field_term = $this->getFieldTermID();
+
+    $label_term = 'rdfs:label';
+    $infraspecific_name_term = tripal_get_chado_semweb_term('organism', 'infraspecific_name');
+    $infraspecific_type_term = tripal_get_chado_semweb_term('organism', 'type_id');
+
     return array(
       $field_term => array(
-        'operations' => array(),
-        'sortable' => FALSE,
-        'searchable' => FALSE,
+        'sortable' => TRUE,
+        'searchable' => TRUE,
+        'elements' => array(
+          $label_term => array(
+            'sortable' => TRUE,
+            'searchable' => TRUE,
+            'label' => 'Infraspecific Full Name',
+            'help' => 'The full infraspecific name including the rank and name.',
+          ),
+          $infraspecific_name_term => array(
+            'sortable' => TRUE,
+            'searchable' => TRUE,
+            'label' => 'Infrasepcies Name',
+            'help' => 'The infraspecific name of the organism below the rank of species.',
+          ),
+          $infraspecific_type_term => array(
+            'sortable' => TRUE,
+            'searchable' => TRUE,
+            'label' => 'Infraspecific Rank',
+            'help' => 'The infraspecific rank of the organism below the rank of species.',
+          ),
+        )
       ),
     );
   }
 
+  /**
+   * @see ChadoField::query()
+   */
+  public function query($query, $condition){
+    $alias = $this->field['field_name'];
+    $operator = $condition['operator'];
+
+    $field_term_id = $this->getFieldTermID();
+    $label_term = $field_term_id . ',' . 'rdfs:label';
+    $infraspecific_name_term = $field_term_id . ',' . tripal_get_chado_semweb_term('organism', 'infraspecific_name');
+    $infraspecific_type_term = $field_term_id . ',' . tripal_get_chado_semweb_term('organism', 'type_id');
+
+    if ($condition['column'] == $label_term or $condition['column'] == $field_term_id) {
+      $this->queryJoinOnce($query, 'cvterm', $alias . '_cvterm', $alias . "_cvterm.cvterm_id = base.type_id");
+      $query->where("CONCAT(" . $alias . "_cvterm.name, ' ', base.infraspecific_name) $operator :full_name",  array(':full_name' => $condition['value']));
+    }
+    if ($condition['column'] == $infraspecific_name_term) {
+      $query->condition('base.infraspecific_name', $condition['value'], $operator);
+    }
+    if ($condition['column'] == $infraspecific_type_term) {
+      $this->queryJoinOnce($query, 'cvterm', $alias . '_cvterm', $alias . "_cvterm.cvterm_id = base.type_id");
+      $query->condition($alias . '_cvterm.name', $condition['value'], $operator);
+    }
+  }
+  /**
+   * @see ChadoField::queryOrder()
+   */
+  public function queryOrder($query, $order) {
+
+  }
+
   /**
    *
    * @see TripalField::load()
@@ -81,15 +136,33 @@ class taxrank__infraspecific_taxon extends ChadoField {
     $field_table = $this->instance['settings']['chado_table'];
     $field_column = $this->instance['settings']['chado_column'];
 
+    $entity->{$field_name}['und'][0]['value'] = '';
+
+    if (chado_get_version() < 1.3) {
+      return;
+    }
+
+    $label_term = 'rdfs:label';
+    $infraspecific_name_term = tripal_get_chado_semweb_term('organism', 'infraspecific_name');
+    $infraspecific_type_term = tripal_get_chado_semweb_term('organism', 'type_id');
+
     // Set some defaults for the empty record.
     $entity->{$field_name}['und'][0] = array(
-      'value' => '',
-      'organism__type_id' => '',
+      'value' => array(),
+      'chado-organism__infraspecific_name' => '',
+      'chado-organism__type_id' => '',
     );
 
+    if ($record->infraspecific_name) {
+      $label = $record->type_id->name . ' ' . $record->infraspecific_name;
+      $entity->{$field_name}['und'][0]['value'][$label_term] = $label;
+      $entity->{$field_name}['und'][0]['value'][$infraspecific_name_term] = $record->infraspecific_name;
+      $entity->{$field_name}['und'][0]['chado-organism__infraspecific_name'] = $record->infraspecific_name;
+    }
+
     if ($record->type_id) {
-      $entity->{$field_name}['und'][0]['value'] = $record->type_id->name;
-      $entity->{$field_name}['und'][0]['organism__type_id'] = $record->type_id->cvterm_id;
+      $entity->{$field_name}['und'][0]['value'][$infraspecific_type_term] = $record->type_id->name;
+      $entity->{$field_name}['und'][0]['chado-organism__type_id'] = $record->type_id->cvterm_id;
     }
   }
 }

tripal_chado/includes/TripalFields/taxrank__infraspecific_taxon/taxrank__infraspecific_taxon_formatter.inc

@@ -13,5 +13,22 @@ class taxrank__infraspecific_taxon_formatter extends ChadoFieldFormatter {
    */
   public function view(&$element, $entity_type, $entity, $langcode, $items, $display) {
 
+    dpm($items);
+    $label_term = 'rdfs:label';
+    $infraspecific_name_term = tripal_get_chado_semweb_term('organism', 'infraspecific_name');
+    $infraspecific_type_term = tripal_get_chado_semweb_term('organism', 'type_id');
+
+    if (is_array($items[0]['value']) and array_key_exists($infraspecific_name_term, $items[0]['value'])) {
+      $infraspecific_name = $items[0]['value'][$infraspecific_name_term];
+      $infraspecific_type = $items[0]['value'][$infraspecific_type_term];
+      $content = $items[0]['value'][$label_term];
+
+      // The cardinality of this field is 1 so we don't have to
+      // iterate through the items array, as there will never be more than 1.
+      $element[0] = array(
+        '#type' => 'markup',
+        '#markup' => $content,
+      );
+    }
   }
 }

tripal_chado/includes/TripalFields/taxrank__infraspecific_taxon/taxrank__infraspecific_taxon_widget.inc

@@ -7,50 +7,110 @@ class taxrank__infraspecific_taxon_widget extends ChadoFieldWidget {
   // The list of field types for which this formatter is appropriate.
   public static $field_types = array('taxrank__infraspecific_taxon');
 
+
   /**
    *
    * @see TripalFieldWidget::form()
    */
   public function form(&$widget, &$form, &$form_state, $langcode, $items, $delta, $element) {
     parent::form($widget, $form, $form_state, $langcode, $items, $delta, $element);
+
     $settings = $this->field['settings'];
     $field_name = $this->field['field_name'];
     $field_type = $this->field['type'];
     $field_table = $this->instance['settings']['chado_table'];
     $field_column = $this->instance['settings']['chado_column'];
 
+    $infra_name = '';
     $type_id = 0;
-    if (count($items) > 0 and array_key_exists('organism__type_id', $items[0])) {
-      $type_id = $items[0]['organism__type_id'];
+
+    if (count($items) > 0) {
+      $type_id = array_key_exists('chado-organism__type_id', $items[0]) ? $items[0]['chado-organism__type_id'] : $type_id;
+      $infra_name = array_key_exists('chado-organism__infraspecific_name', $items[0]) ? $items[0]['chado-organism__infraspecific_name'] : $infra_name;
     }
 
-    $form['value'] = array(
+    if (array_key_exists('values', $form_state) and
+        array_key_exists($field_name, $form_state['values'])) {
+      $type_id = $form_state['values'][$field_name][$langcode][$delta]['infraname']['specific_epithet'];
+      $infra_name = $form_state['values'][$field_name][$langcode][$delta]['infraname']['infrapsecific_epithet'];
+    }
+
+    $widget['value'] = array(
       '#type' => 'value',
       '#value' =>  array_key_exists($delta, $items) ? $items[$delta]['value'] : '',
     );
+    $widget['chado-organism__type_id'] = array(
+      '#type' => 'value',
+      '#value' =>  $type_id,
+    );
+    $widget['chado-organism__infraspecific_name'] = array(
+      '#type' => 'value',
+      '#value' =>  $infra_name,
+    );
 
-    $cv = tripal_get_default_cv($field_table, $field_column);
+    $cv = tripal_get_cv(array('name' => 'taxonomic_rank'));
+    $terms = tripal_get_cvterm_select_options($cv->cv_id);
+
+    // Unfortunately the taxonomic_rank vocabulary is not properly organized
+    // such that we an only include terms below 'species'. Therefore we will
+    // just list them here and hope we haven't missed one.
+    $valid_terms = array('cultivar', 'subspecies', 'varietas', 'subvariety', 'forma', 'subforma');
     $options = array();
-    if ($cv) {
-      $options = tripal_get_cvterm_select_options($cv->cv_id);
+    $options[] = '--Select a rank--';
+    foreach  ($terms as $cvterm_id => $name) {
+      if (in_array($name, $valid_terms)) {
+        $options[$cvterm_id] = $name;
+      }
     }
-    $widget['organism__type_id'] = array(
-      '#type' => 'select',
+
+    $widget['infraname'] = array(
+      '#type' => 'fieldset',
       '#title' => $element['#title'],
-      '#description' => $element['#description'],
+      '#collapsible' => FALSE,
+      '#collapsed' => FALSE,
+      '#description' => $element['#description']
+    );
+    $widget['infraname']['specific_epithet'] = array(
+      '#type' => 'select',
+      '#title' => 'Specific Epithet',
+      '#description' => 'The rank below species. This field may be left blank if not appropriate.',
       '#options' => $options,
       '#default_value' => $type_id,
+    );
+    $widget['infraname']['infrapsecific_epithet'] = array(
+      '#type' => 'textfield',
+      '#title' => 'Infrapsecific Epithet',
+      '#description' => 'The name below species.',
+      '#default_value' => $infra_name,
       '#required' => $element['#required'],
-      '#weight' => isset($element['#weight']) ? $element['#weight'] : 0,
-      '#delta' => $delta,
     );
   }
 
   /**
-   *
-   * @see TripalFieldWidget::submit()
+   * @see TripalFieldWidget::validate()
    */
-  public function submit($form, &$form_state, $entity_type, $entity, $langcode, $delta) {
+  public function validate($element, $form, &$form_state, $langcode, $delta) {
+    $field_name = $this->field['field_name'];
+    $field_table = $this->instance['settings']['chado_table'];
+    $field_column = $this->instance['settings']['chado_column'];
+
+    $type_id = $form_state['values'][$field_name]['und'][0]['infraname']['specific_epithet'];
+    $infra_name = $form_state['values'][$field_name]['und'][0]['infraname']['infrapsecific_epithet'];
+
+    if ($infra_name and $type_id) {
+      $form_state['values'][$field_name]['und'][0]['value'] = $infra_name;
+      $form_state['values'][$field_name]['und'][0]['chado-organism__type_id'] = $type_id;
+      $form_state['values'][$field_name]['und'][0]['chado-organism__infraspecific_name'] = $infra_name;
+    }
+    if ($infra_name and !$type_id) {
+      $form_state['values'][$field_name]['und'][0]['value'] = $infra_name;
+      $form_state['values'][$field_name]['und'][0]['chado-organism__type_id'] = '__NULL__';
+      $form_state['values'][$field_name]['und'][0]['chado-organism__infraspecific_name'] = $infra_name;
+    }
+    else {
+      $form_state['values'][$field_name]['und'][0]['chado-organism__type_id'] = '__NULL__';
+      $form_state['values'][$field_name]['und'][0]['chado-organism__infraspecific_name'] = '__NULL__';
+    }
 
   }
 }

tripal_chado/includes/tripal_chado.fields.inc

@@ -70,6 +70,13 @@ function tripal_chado_bundle_fields_info_base(&$info, $details, $entity_type, $b
       continue;
     }
 
+    // Skip the infraspecific type_id and name from the organism table as we
+    // have a special field for those.
+    if ($table_name == 'organism' and ($column_name == 'type_id' or
+        $column_name == 'infraspecific_name')) {
+      continue;
+    }
+
     // Skip the cvterm.is_relationshptype.
     if ($table_name == 'cvterm' and $column_name == 'is_relationshiptype') {
       continue;
@@ -342,21 +349,19 @@ function tripal_chado_bundle_fields_info_custom(&$info, $details, $entity_type,
   }
 
   // ORGANISM TYPE_ID
-//   if ($table_name == 'organism' and array_key_exists('type_id', $schema['fields'])) {
-//     $field_name = 'taxarank__infraspecific_taxon';
-//     $field_type = 'taxarank__infraspecific_taxon';
-//     $info[$field_name] = array(
-//       'field_name' => $field_name,
-//       'type' => $field_type,
-//       'cardinality' => 1,
-//       'locked' => FALSE,
-//       'storage' => array(
-//         'type' => 'field_chado_storage',
-//       ),
-//       'settings' => array(
-//       ),
-//     );
-//   }
+  if ($table_name == 'organism' and array_key_exists('type_id', $schema['fields'])) {
+    $field_name = 'taxrank__infraspecific_taxon';
+    $field_type = 'taxrank__infraspecific_taxon';
+    $info[$field_name] = array(
+      'field_name' => $field_name,
+      'type' => $field_type,
+      'cardinality' => 1,
+      'locked' => FALSE,
+      'storage' => array(
+        'type' => 'field_chado_storage',
+      ),
+    );
+  }
 
   // FEATUREMAP UNITTYPE_ID
   if ($table_name == 'featuremap') {
@@ -723,6 +728,13 @@ function tripal_chado_bundle_instances_info_base(&$info, $entity_type, $bundle,
       continue;
     }
 
+    // Skip the infraspecific type_id and name from the organism table as we
+    // have a special field for those.
+    if ($table_name == 'organism' and ($column_name == 'type_id' or
+        $column_name == 'infraspecific_name')) {
+          continue;
+        }
+
     // Don't create base fields for the primary key and the type_id field.
     if ($column_name == $pkey or $column_name == $type_column) {
       continue;
@@ -1267,36 +1279,36 @@ function tripal_chado_bundle_instances_info_custom(&$info, $entity_type, $bundle
   }
 
   // ORGANISM TYPE_ID
-//   if ($table_name == 'organism' and array_key_exists('type_id', $schema['fields'])) {
-//     $field_name = 'taxarank__infraspecific_taxon';
-//     $info[$field_name] = array(
-//       'field_name' => $field_name,
-//       'entity_type' => $entity_type,
-//       'bundle' => $bundle->name,
-//       'label' => 'Infraspecific Taxon',
-//       'description' => 'The Infraspecific Taxon.',
-//       'required' => FALSE,
-//       'settings' => array(
-//         'auto_attach' => TRUE,
-//         'chado_table' => 'organism',
-//         'chado_column' => 'type_id',
-//         'base_table' => 'organism',
-//       ),
-//       'widget' => array(
-//         'type' => 'taxarank__infraspecific_taxon_widget',
-//         'settings' => array(
-//           'display_label' => 1,
-//         ),
-//       ),
-//       'display' => array(
-//         'default' => array(
-//           'label' => 'inline',
-//           'type' => 'taxarank__infraspecific_taxon_formatter',
-//           'settings' => array(),
-//         ),
-//       ),
-//     );
-//   }
+  if ($table_name == 'organism' and array_key_exists('type_id', $schema['fields'])) {
+    $field_name = 'taxrank__infraspecific_taxon';
+    $info[$field_name] = array(
+      'field_name' => $field_name,
+      'entity_type' => $entity_type,
+      'bundle' => $bundle->name,
+      'label' => 'Infraspecific Taxon',
+      'description' => 'The Infraspecific Taxon.',
+      'required' => FALSE,
+      'settings' => array(
+        'auto_attach' => TRUE,
+        'chado_table' => 'organism',
+        'chado_column' => 'type_id',
+        'base_table' => 'organism',
+      ),
+      'widget' => array(
+        'type' => 'taxrank__infraspecific_taxon_widget',
+        'settings' => array(
+          'display_label' => 1,
+        ),
+      ),
+      'display' => array(
+        'default' => array(
+          'label' => 'inline',
+          'type' => 'taxrank__infraspecific_taxon_formatter',
+          'settings' => array(),
+        ),
+      ),
+    );
+  }
 
 
   // FEATURE SEQLEN