renamed fieldInfo function of the TripalField class to fieldDefaults(). Fixed instanceSettingsForm on the relationship field

tripal/includes/TripalField.inc

@@ -147,7 +147,8 @@ class TripalField {
    * Provides default settings for the field.
    *
    * This is a static function and defines defaults for all fields of this
-   * type.
+   * type.  This function corresponds to the hook_field_info() of the Drupal
+   * Field API.
    *
    * @return
    *   An array whose keys are field type names and whose values are arrays
@@ -185,7 +186,7 @@ class TripalField {
    *     field_create_field() and field_create_instance(). Defaults to
    *     FALSE.
    */
-  public static function fieldInfo() {
+  public static function fieldDefaults() {
     return array(
     );
   }
@@ -196,7 +197,7 @@ class TripalField {
    *
    * These settings are global for every instance of the field.
    *
-   * he TripalField class allows a field to decide which bundles it would
+   * The TripalField class allows a field to decide which bundles it would
    * like to attach itself to. Therefore, the entity type, and bundle are
    * passed as arguments to allow the field to decide if it wants to be
    * attached.
@@ -622,7 +623,7 @@ class TripalField {
     $module = $field['module'];
     $element['#field'] = $field;
     $element['#instance'] = $instance;
-    $element['#element_validate'][] = $module . '_instance_settings_form_validate';
+    $element['#element_validate'][] = $module . '_field_instance_settings_form_validate';
 
     return $element;
   }

tripal/includes/fields/content_type.inc

@@ -19,9 +19,9 @@ class content_type extends TripalField {
     }
   }
   /**
-   * @see TripalField::fieldInfo()
+   * @see TripalField::fieldDefaults()
    */
-  static function fieldInfo() {
+  static function fieldDefaults() {
     return array(
       'label' => t('Record Type'),
       'description' => t('The content type.'),

tripal/includes/tripal.fields.inc

@@ -9,7 +9,7 @@ function tripal_field_info() {
 
   $field_types = tripal_get_field_types('tripal');
   foreach ($field_types as $field_type) {
-    $info[$field_type] = $field_type::fieldInfo();
+    $info[$field_type] = $field_type::fieldDefaults();
   }
   return $info;
 }

tripal_chado/includes/fields/chado_base__dbxref_id.inc

@@ -2,9 +2,9 @@
 
 class chado_base__dbxref_id extends TripalField {
   /**
-   * @see TripalField::fieldInfo()
+   * @see TripalField::fieldDefaults()
    */
-  static function fieldInfo() {
+  static function fieldDefaults() {
     return array(
       'label' => t('Accession'),
       'description' => t('This field specifies the unique stable accession (ID) for

tripal_chado/includes/fields/chado_base__organism_id.inc

@@ -5,7 +5,7 @@ class chado_base__organism_id extends TripalField {
   /**
    * @see TripalField::info()
    */
-  public static function fieldInfo() {
+  public static function fieldDefaults() {
     return array(
       'label' => t('Organism'),
       'description' => t('A field for specifying an organism.'),

tripal_chado/includes/fields/chado_feature__md5checksum.inc

@@ -3,9 +3,9 @@
 class chado_feature__md5checksum  extends TripalField {
 
   /**
-   * @see TripalField::fieldInfo()
+   * @see TripalField::fieldDefaults()
    */
-  static function fieldInfo() {
+  static function fieldDefaults() {
     return array(
       'label' => t('Sequence MD5 checksum'),
       'description' => t('A field for generating MD5 checksum for a sequence.'),

tripal_chado/includes/fields/chado_feature__residues.inc

@@ -3,9 +3,9 @@
 class chado_feature__residues extends TripalField {
 
   /**
-   * @see TripalField::fieldInfo()
+   * @see TripalField::fieldDefaults()
    */
-  static function fieldInfo() {
+  static function fieldDefaults() {
     return array(
       'label' => t('Sequences'),
       'description' => t('A field for managing nucleotide and protein residues.'),

tripal_chado/includes/fields/chado_feature__seqlen.inc

@@ -2,9 +2,9 @@
 
 class chado_feature__seqlen extends TripalField {
   /**
-   * @see TripalField::fieldInfo()
+   * @see TripalField::fieldDefaults()
    */
-  static function fieldInfo() {
+  static function fieldDefaults() {
     return array(
       'label' => t('Sequence length'),
       'description' => t('A field for calculating the length of a sequence.'),

tripal_chado/includes/fields/chado_gene__transcripts.inc

@@ -3,9 +3,9 @@
 class chado_gene__transcripts extends TripalField {
 
   /**
-   * @see TripalField::fieldInfo()
+   * @see TripalField::fieldDefaults()
    */
-  public static function fieldInfo() {
+  public static function fieldDefaults() {
     return array(
       'label' => t('Transcripts'),
       'description' => t('Transcripts of genes.'),

tripal_chado/includes/fields/chado_linker__contact.inc

@@ -3,9 +3,9 @@
 class chado_linker__contact extends TripalField {
 
   /**
-   * @see TripalField::fieldInfo()
+   * @see TripalField::fieldDefaults()
    */
-  public static function fieldInfo() {
+  public static function fieldDefaults() {
     return array(
       'label' => t('Contacts'),
       'description' => t('Associates an indviddual or organization with

tripal_chado/includes/fields/chado_linker__cvterm.inc

@@ -2,9 +2,9 @@
 
 class chado_linker__cvterm extends TripalField {
   /**
-   * @see TripalField::fieldInfo()
+   * @see TripalField::fieldDefaults()
    */
-  static function fieldInfo() {
+  static function fieldDefaults() {
     return array(
       'label' => t('Annotations'),
       'description' => t('This record can be annotated with terms

tripal_chado/includes/fields/chado_linker__cvterm_adder.inc

@@ -1,9 +1,9 @@
 <?php
 class chado_linker__cvterm_addr extends TripalField {
   /**
-   * @see TripalField::fieldInfo()
+   * @see TripalField::fieldDefaults()
    */
-  static function fieldInfo() {
+  static function fieldDefaults() {
     return array(
       'label' => t('Add an Annotation Type'),
       'description' => t('This record may have any number of types of

tripal_chado/includes/fields/chado_linker__dbxref.inc

@@ -16,7 +16,7 @@ class chado_linker__dbxref extends TripalField {
    * This is a hook provided by the tripal_chado module for offloading the
    * hook_fieldInfo() hook for each field to specify.
    */
-  static function fieldInfo() {
+  static function fieldDefaults() {
     return array(
       'label' => t('Cross references'),
       'description' => t('This record can be cross referenced with a record in

tripal_chado/includes/fields/chado_linker__expression.inc

@@ -3,9 +3,9 @@
 class chado_linker__expression extends TripalField {
 
   /**
-   * @see TripalField::fieldInfo()
+   * @see TripalField::fieldDefaults()
    */
-  public static function fieldInfo() {
+  public static function fieldDefaults() {
     return array(
       'label' => t('Expression'),
       'description' => t('Associates an expression with

tripal_chado/includes/fields/chado_linker__featureloc.inc

@@ -3,9 +3,9 @@
 class chado_linker__featureloc extends TripalField {
 
   /**
-   * @see TripalField::fieldInfo()
+   * @see TripalField::fieldDefaults()
    */
-  public static function fieldInfo() {
+  public static function fieldDefaults() {
     return array(
       'label' => t('Aligned Locations'),
       'description' => t('Locations on landmark sequences where the feature is aligned.'),

tripal_chado/includes/fields/chado_linker__genotype.inc

@@ -3,9 +3,9 @@
 class chado_linker__genotype extends TripalField {
 
   /**
-   * @see TripalField::fieldInfo()
+   * @see TripalField::fieldDefaults()
    */
-  public static function fieldInfo() {
+  public static function fieldDefaults() {
     return array(
       'label' => t('Genotypes'),
       'description' => t('Associates an indviddual or organization with

tripal_chado/includes/fields/chado_linker__phenotype.inc

@@ -3,9 +3,9 @@
 class chado_linker__phenotype extends TripalField {
 
   /**
-   * @see TripalField::fieldInfo()
+   * @see TripalField::fieldDefaults()
    */
-  public static function fieldInfo() {
+  public static function fieldDefaults() {
     return array(
       'label' => t('Phenotypes'),
       'description' => t('Associates an indviddual or organization with

tripal_chado/includes/fields/chado_linker__prop.inc

@@ -2,9 +2,9 @@
 
 class chado_linker__prop extends TripalField {
   /**
-   * @see TripalField::fieldInfo()
+   * @see TripalField::fieldDefaults()
    */
-  static function fieldInfo() {
+  static function fieldDefaults() {
     return array(
       'label' => t('Add a Property'),
       'description' => t('Add details about this property.'),

tripal_chado/includes/fields/chado_linker__prop_adder.inc

@@ -2,9 +2,9 @@
 
 class chado_linker__prop_adder extends TripalField {
   /**
-   * @see TripalField::fieldInfo()
+   * @see TripalField::fieldDefaults()
    */
-  static function fieldInfo() {
+  static function fieldDefaults() {
     return array(
       'label' => t('Add a Property Type'),
       'description' => t('This record may have any number of properties. Use

tripal_chado/includes/fields/chado_linker__pub.inc

@@ -2,9 +2,9 @@
 
 class chado_linker_pub extends TripalField {
   /**
-   * @see TripalField::fieldInfo()
+   * @see TripalField::fieldDefaults()
    */
-  static function fieldInfo() {
+  static function fieldDefaults() {
     return array(
       'label' => t('Publications'),
       'description' => t('Associates a publication (e.g. journal article,

tripal_chado/includes/fields/chado_linker__relationship.inc

@@ -2,9 +2,9 @@
 
 class chado_linker__relationship extends TripalField {
   /**
-   * @see TripalField::fieldInfo()
+   * @see TripalField::fieldDefaults()
    */
-  static function fieldInfo() {
+  static function fieldDefaults() {
     return array(
       'label' => t('Relationships'),
       'description' => t('Relationships between records.'),
@@ -860,8 +860,9 @@ class chado_linker__relationship extends TripalField {
    * @param unknown $instance
    * @param unknown $has_data
    */
-  public static function fieldSettingsForm($field, $instance, $has_data) {
-    $element = parent::fieldSettingsForm($field, $instance, $has_data);
+  public static function instanceSettingsForm($field, $instance) {
+
+    $element = parent::instanceSettingsForm($field, $instance);
     $element['instructions'] = array(
       '#type' => 'item',
       '#markup' => 'You may provide a list of terms that will be available in a select box
@@ -873,6 +874,7 @@ class chado_linker__relationship extends TripalField {
       '#type' => 'textarea',
       '#title' => 'Relationship Types',
       '#description' => 'Provide terms separated by a new line',
+      '#default_value' => $instance['settings']['relationship_types'],
     );
 
     return $element;
@@ -884,7 +886,7 @@ class chado_linker__relationship extends TripalField {
    * @param unknown $instance
    * @param unknown $has_data
    */
-  public static function fieldSettingsFormValidate($form, &$form_state) {
+  public static function instanceSettingsFormValidate($form, &$form_state) {
     //dpm($form);dpm($form_state);
   }
 }

tripal_chado/includes/fields/chado_linker__synonym.inc

@@ -3,9 +3,9 @@
 class chado_linker__synonym extends TripalField {
 
   /**
-   * @see TripalField::fieldInfo()
+   * @see TripalField::fieldDefaults()
    */
-  static function fieldInfo() {
+  static function fieldDefaults() {
     return array(
       'label' => t('Synonyms'),
       'description' => t('Adds an alternative name (synonym or alias) to this record.'),

tripal_chado/includes/fields/chado_organism__type_id.inc

@@ -3,9 +3,9 @@
 class chado_organism__type_id extends TripalField {
 
   /**
-   * @see TripalField::info()
+   * @see TripalField::fieldDefaults()
    */
-  public static function fieldInfo() {
+  public static function fieldDefaults() {
     return array(
       'label' => t('Infraspecific Type'),
       'description' => t('A field for specifying an infraspecific type.'),

tripal_chado/includes/tripal_chado.fields.inc

@@ -19,7 +19,7 @@ function tripal_chado_field_info() {
 
   $field_types = tripal_get_field_types('tripal_chado');
   foreach ($field_types as $field_type) {
-    $info[$field_type] = $field_type::fieldInfo();
+    $info[$field_type] = $field_type::fieldDefaults();
   }
   return $info;
 
@@ -533,7 +533,7 @@ function tripal_chado_field_settings_form($field, $instance, $has_data) {
 /**
  * Implements hook_instance_settings_form()
  */
-function tripal_chado_instance_settings_form($field, $instance) {
+function tripal_chado_field_instance_settings_form($field, $instance) {
   $form = array();
   $field_type = $field['type'];
   module_load_include('inc', 'tripal_chado', 'includes/fields/' . $field_type);
@@ -566,7 +566,7 @@ function tripal_chado_field_settings_form_validate($form, &$form_state) {
  * to alow the TripalField objects to have a instanceSettingsFormValidate()
  * member function.
  */
-function tripal_chado_instance_settings_form_validate($form, &$form_state) {
+function tripal_chado_field_instance_settings_form_validate($form, &$form_state) {
   $field = $form['#field'];
   $instance = $form['#instance'];
   $field_type = $field['type'];