Working on field formatters

tripal/api/tripal.entities.api.inc

@@ -725,6 +725,7 @@ function tripal_get_tokens($entity, $options = array()) {
  */
 function tripal_replace_tokens($string, $entity, $bundle_entity = NULL) {
 
+
   // Determine which tokens were used in the format string
   if (preg_match_all('/\[\w+\]/', $string, $matches)) {
     $used_tokens = $matches[0];

tripal_chado/includes/fields/chado_base__organism_id.inc

@@ -1,18 +1,172 @@
 <?php
+/**
+ * Implements hook_formatter_info.
+ *
+ * This is a hook provided by the tripal_chado module for
+ * offloading the hook_field_formatter_info() for each field
+ * to specify.
+ *
+ */
+function chado_base__organism_id_formatter_info() {
+  return array(
+    'label' => t('Organism'),
+    'field types' => array('chado_base__organism_id'),
+    'settings' => array(
+      'field_display_teaser' => 0,
+      'field_display_string' => '<i>[organism__genus] [organism__species]</i>',
+    ),
+  );
+}
+/**
+ * Implements hook_formatter_settings_summary.
+ *
+ * This is a hook provided by the tripal_chado module for
+ * offloading the hook_field_formatter_settings_summary() for each field
+ * to specify.
+ *
+ */
+function chado_base__organism_id_formatter_settings_summary($field, $instance, $view_mode) {
+  $display = $instance['display'][$view_mode];
+  $settings = $display['settings'];
+  $summary = 'Settings summary: ';
+  if (array_key_exists('field_display_teaser', $settings) and
+      $settings['field_display_teaser'] == 1) {
+        $summary .= 'displays the organism teaser if published.';
+      }
+      else if (array_key_exists('field_display_string', $settings)) {
+        $summary .= 'uses the token string "' . $settings['field_display_string'] . '"';
+      }
+      else {
+        $summary .= "uses display defaults.";
+      }
+
+      return $summary;
+}
+
+/**
+ * Provides a settings form for the formatter.
+ *
+ * This is a hook provided by the tripal_chado module for
+ * offloading the hook_field_formatter_settings_form() for each field
+ * to specify.
+ */
+function chado_base__organism_id_formatter_settings_form($field, $instance,
+    $view_mode, $form, &$form_state) {
+
+  $display = $instance['display'][$view_mode];
+  $settings = $display['settings'];
+
+
+  $element = array();
+  $term = NULL;
+  $entity = NULL;
+
+  // Check to see if the organism bundle exists
+  $term = tripal_load_term_entity(array(
+    'namespace' => $field['settings']['semantic_web']['ns'],
+    'accession' => $field['settings']['semantic_web']['type']
+  ));
+  if ($term) {
+    $entity = tripal_load_bundle_entity(array('term_id' => $term->id));
+  }
+
+  $element['instructions'] = array(
+    '#type' => 'item',
+    '#markup' => 'Please provide the format for viewing the organism. You
+      can specify the format using tokens that correspond to each field'
+  );
+
+  $element['field_display_string'] = array(
+    '#type' => 'textfield',
+    '#title' => 'Display Format',
+    '#description' => t('Provide a mixture of text and/or tokens for the format.
+        For example: [organism__genus] [organism__species].  When displayed,
+        the tokens will be replaced with the actual value.'),
+    '#default_value' => $settings['field_display_string'],
+  );
+
+  $element['field_display_teaser'] = array(
+    '#type' => 'checkbox',
+    '#title' => 'Display teaser if available',
+    '#description' => t('If the organism that this field is associated with is
+        a published page then display the teaser rather use the display
+        format above.'),
+    '#default_value' => $settings['field_display_teaser'],
+  );
+
+  $element['tokens'] = array(
+    '#type' => 'fieldset',
+    '#collapsed' => TRUE,
+    '#collapsible' => TRUE,
+    '#title' => 'Available Tokens'
+  );
+  $headers = array('Token', 'Description');
+  $rows = array();
+  $tokens = tripal_get_tokens($entity);
+  foreach ($tokens as $token) {
+    $rows[] = array(
+      $token['token'],
+      $token['description'],
+    );
+  }
+
+  $table_vars = array(
+    'header'     => $headers,
+    'rows'       => $rows,
+    'attributes' => array(),
+    'sticky'     => FALSE,
+    'caption'    => '',
+    'colgroups'  => array(),
+    'empty'      => 'There are no tokens',
+  );
+  $project_details = theme('table', $table_vars);
+
+  $element['tokens']['list'] = array(
+    '#type' => 'item',
+    '#markup' => theme_table($table_vars),
+  );
+
+  $element['#element_validate'] = array('chado_base__organism_id_formatter_settings_form_validate');
+
+  return $element;
+
+}
+
+/**
+ * Validation function for the chado_base__organism_id_formatter_settings_form.
+ */
+function chado_base__organism_id_formatter_settings_form_validate(&$form, &$form_state) {
+
+  // Place here as an example for validating the settings form.
+}
 
 /**
  *
  */
-function chado_base__organism_id_formatter(&$element, $entity_type, $entity, $field,
-    $instance, $langcode, $items, $display) {
+function chado_base__organism_id_formatter(&$element, $entity_type, $entity,
+    $field, $instance, $langcode, $items, $display) {
+
+  // Get the settings
+  $settings = $display['settings'];
 
   foreach ($items as $delta => $item) {
     $organism = chado_select_record('organism', array('genus', 'species'), array('organism_id' => $item['value']));
-    $content = '<i>' . $organism[0]->genus .' ' . $organism[0]->species . '</i>';
-    $element[$delta] = array(
-      '#type' => 'markup',
-      '#markup' => $content,
-    );
+
+    if ($settings['field_display_teaser'] == 0) {
+      $field_name = $field['field_name'];
+      $string = $settings['field_display_string'];
+      $field_data = $entity->$field_name;
+      // TODO: add a way to get tokens from Chado records. this is
+      // needed in the case that a record is not published as an entity.
+      $content = tripal_replace_tokens($string, $field_data['und'][0]['entity']);
+      $element[$delta] = array(
+        '#type' => 'markup',
+        '#markup' => $content,
+      );
+    }
+    else {
+
+    }
   }
 }
 
@@ -100,100 +254,3 @@ function chado_base__organism_id_widget_validate($element, &$form_state) {
   }
 }
 
-/**
- * Provides a settings form for the formatter.
- *
- * This function is equiavlent to the hook_field_formatter_settings_form()
- * hook.
- *
- * @param $field
- *   The field structure being configured.
- * @param $instance
- *   The instance structure being configured.
- * @param $view_mode
- *   The view mode being configured.
- * @param $form
- *   The (entire) configuration form array, which will usually have no use here.
- * @param $form_state
- *   The form state of the (entire) configuration form.
- */
-function chado_base__organism_id_formatter_form($field, $instance,
-    $view_mode, $form, &$form_state) {
-
-  $display = $instance['display'][$view_mode];
-  $settings = $display['settings'];
-  $element = array();
-  $term = NULL;
-  $bundle = NULL;
-
-  // Check to see if the organism bundle exists
-  $term = tripal_load_term_entity(array(
-    'namespace' => $field['settings']['semantic_web']['ns'],
-    'accession' => $field['settings']['semantic_web']['type']
-  ));
-  if ($term) {
-    $bundle = tripal_load_bundle_entity(array('term_id' => $term->id));
-  }
-
-  $element['instructions'] = array(
-    '#type' => 'item',
-    '#markup' => 'Please provide the format for viewing the organism. You
-      can specify the format using tokens that correspond to each field'
-  );
-
-  $element['field_display'] = array(
-    '#type' => 'textfield',
-    '#title' => 'Display Format',
-    '#description' => t('Provide a mixture of text and/or tokens for the format.
-        For example: [organism__genus] [organism__species].  When displayed,
-        the tokens will be replaced with the actual value.'),
-    '#default_value' => '[organism__genus] [organism__species]',
-  );
-
-  $element['field_display_entity'] = array(
-    '#type' => 'checkbox',
-    '#title' => 'Display teaser if available',
-    '#description' => t('If the organism that this field is associated with is
-        a published page then display the teaser rather use the display
-        format above.'),
-  );
-
-  $element['tokens'] = array(
-    '#type' => 'fieldset',
-    '#collapsed' => TRUE,
-    '#collapsible' => TRUE,
-    '#title' => 'Available Tokens'
-  );
-  $headers = array('Token', 'Description');
-  $rows = array();
-  $tokens = tripal_get_tokens($bundle);
-  foreach ($tokens as $token) {
-    $rows[] = array(
-      $token['token'],
-      $token['description'],
-    );
-  }
-
-
-  $table_vars = array(
-    'header'     => $headers,
-    'rows'       => $rows,
-    'attributes' => array(),
-    'sticky'     => FALSE,
-    'caption'    => '',
-    'colgroups'  => array(),
-    'empty'      => 'There are no tokens',
-  );
-  $project_details = theme('table', $table_vars);
-
-  $element['tokens']['list'] = array(
-    '#type' => 'item',
-    '#markup' => theme_table($table_vars),
-  );
-
-  return $element;
-
-}
-
-
-

tripal_chado/includes/tripal_chado.fields.inc

@@ -2,6 +2,11 @@
 
 /**
  * Implements hook_field_info().
+ *
+ * TODO: move these array elements to a hook function that
+ * is implemented in the field file.  This will put all of the
+ * field info in a single place for each field.  See the formatter_info()
+ * function for an example.
  */
 function tripal_chado_field_info() {
   $fields = array(
@@ -183,6 +188,11 @@ function tripal_chado_field_info() {
 }
 /**
  * Implements hook_field_widget_info().
+ *
+ * TODO: move these array elements to a hook function that
+ * is implemented in the field file.  This will put all of the
+ * field info in a single place for each field.  See the formatter_info()
+ * function for an example.
  */
 function tripal_chado_field_widget_info() {
   return array(
@@ -266,76 +276,39 @@ function tripal_chado_field_widget_info() {
  * Implements hook_field_formatter_info().
  */
 function tripal_chado_field_formatter_info() {
-  return array(
-    'chado_base__organism_id_formatter' => array(
-      'label' => t('Organism'),
-      'field types' => array('chado_base__organism_id')
-    ),
-    'chado_base__dbxref_id_formatter' => array(
-      'label' => t('Cross reference'),
-      'field types' => array('chado_base__dbxref_id')
-    ),
-    'chado_linker__pub_formatter' => array(
-      'label' => t('Publications'),
-      'field types' => array('chado_linker__pub')
-    ),
-    'chado_linker__dbxref_formatter' => array(
-      'label' => t('Cross references'),
-      'field types' => array('chado_linker__dbxref')
-    ),
-    'chado_linker__cvterm_formatter' => array(
-      'label' => t('Annotations'),
-      'field types' => array('chado_linker__cvterm')
-    ),
-    'chado_linker__prop_formatter' => array(
-      'label' => t('Property'),
-      'field types' => array('chado_linker__prop')
-    ),
-    'chado_linker__synonym_formatter' => array(
-      'label' => t('Synonyms'),
-      'field types' => array('chado_linker__synonym')
-    ),
-    'chado_linker__cvterm_adder_formatter' => array(
-      'label' => t('Add an Annotation'),
-      'field types' => array('chado_linker__cvterm_adder')
-    ),
-    'chado_linker__prop_adder_formatter' => array(
-      'label' => t('Add a Property'),
-      'field types' => array('chado_linker__prop_adder')
-    ),
-    'chado_feature__md5checksum_formatter' => array(
-      'label' => t('MD5 checksum'),
-      'field types' => array('chado_feature__md5checksum')
-    ),
-    'chado_feature__residues_formatter' => array(
-      'label' => t('Residues'),
-      'field types' => array('chado_feature__residues')
-    ),
-    'chado_feature__seqlen_formatter' => array(
-      'label' => t('Sequence length'),
-      'field types' => array('chado_feature__seqlen')
-    ),
-  );
+  $formatters = array();
+
+  $fields = field_info_fields();
+  foreach ($fields as $field) {
+    $field_type = $field['type'];
+    if ($field['storage']['type'] == 'field_chado_storage') {
+      module_load_include('inc', 'tripal_chado', 'includes/fields/' . $field_type);
+      $function = $field_type . '_formatter_info';
+      if (function_exists($function)) {
+        $formatters[$field_type . '_formatter'] = $function();
+      }
+    }
+  }
+  return $formatters;
 }
 /**
- * Implements hook_field_formatter_settings_summary.
+ * Implements hook_field_formatter_settings_summary().
  */
 function tripal_chado_field_formatter_settings_summary($field, $instance, $view_mode) {
 
   $summary = '';
-  switch ($field['type']) {
-    case 'chado_base__organism_id':
-      $summary = 'Organisms can be displayed in vaious ways.';
-      break;
-    default:
-      $summary = '';
+  $field_type = $field['type'];
+  module_load_include('inc', 'tripal_chado', 'includes/fields/' . $field_type);
+  $function = $field_type . '_formatter_settings_summary';
+  if (function_exists($function)) {
+    $summary = $function($field, $instance, $view_mode);
   }
 
   return $summary;
 }
 
 /**
- * Implements hook_field_formatter_settings_form.
+ * Implements hook_field_formatter_settings_form().
  */
 function tripal_chado_field_formatter_settings_form($field, $instance, $view_mode, $form, &$form_state) {
   $element = array();
@@ -343,7 +316,7 @@ function tripal_chado_field_formatter_settings_form($field, $instance, $view_mod
   $field_type = $field['type'];
   form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/' . $field_type);
   module_load_include('inc', 'tripal_chado', 'includes/fields/' . $field_type);
-  $function = $field_type . '_formatter_form';
+  $function = $field_type . '_formatter_settings_form';
   if (function_exists($function)) {
     $element = $function($field, $instance, $view_mode, $form, $form_state);
   }
@@ -351,6 +324,8 @@ function tripal_chado_field_formatter_settings_form($field, $instance, $view_mod
   return $element;
 }
 
+
+
 /**
  * Implements hook_field_formatter_view().
  */