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@@ -15,7 +15,7 @@ function tripal_entities_entity_form($form, &$form_state, $entity = NULL) {
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// Set defaults if an entity was provided.
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if ($entity) {
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- drupal_set_title('Edit ' .$entity->title);
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+ drupal_set_title('Edit ' . $entity->title);
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$id = $entity->id;
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$values = array('cvterm_id' => $entity->cvterm_id);
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$cvterm = chado_generate_var('cvterm', $values);
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@@ -123,7 +123,6 @@ function tripal_entities_entity_form($form, &$form_state, $entity = NULL) {
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'#weight' => -1000,
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);
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-
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if(!$do_sync) {
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tripal_entities_entity_form_add_new($bundle_id, $cvterm, $form, $form_state, $entity);
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}
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@@ -150,6 +149,12 @@ function tripal_entities_entity_form_add_sync($bundle_id, $cvterm, &$form, &$for
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*/
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function tripal_entities_entity_form_add_new($bundle_id, $cvterm, &$form, &$form_state, $entity) {
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+ // Add a vertical tabs element
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+ $form['entity_vetical_tabs'] = array(
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+ '#type' => 'vertical_tabs',
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+ '#weight' => 999,
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+ );
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+
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// If the entity doesn't exist then create one.
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if (!$entity) {
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$entity = entity_get_controller($cvterm->dbxref_id->db_id->name)->create(array('bundle' => $bundle_id));
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@@ -497,19 +502,58 @@ function tripal_entities_add_bundle($cvterm) {
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);
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$tripal_bundle = new TripalBundle($vals, $entity_type_name . '_bundle');
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$tripal_bundle->save();
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-
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- // Allow modules to now add fields to the bundle
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- module_invoke_all('add_bundle_fields', $entity_type_name, $bundle_name, $cvterm);
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}
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+
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+ // Allow modules to now add fields to the bundle
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+ module_invoke_all('add_bundle_fields', $entity_type_name, $bundle_name, $cvterm);
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+
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}
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/**
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+ * Implements hook_add_bundle_fields().
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*
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- * @param $table
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- * @param $entity_type
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+ * @param $entity_type_name
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* @param $bundle_name
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+ * @param $cvterm
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*/
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function tripal_entities_add_bundle_fields($entity_type_name, $bundle_name, $cvterm) {
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+ // Adds the fields for the base table to the entity.
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+ tripal_entities_add_bundle_base_fields($entity_type_name, $bundle_name, $cvterm);
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+
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+ // Check to see if there are any kv-property tables associated to this
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+ // base table. If so, add the fields for that type of table.
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+ tripal_entities_add_bundle_kv_property_fields($entity_type_name, $bundle_name, 'featureprop');
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+}
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+
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+/**
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+ * Adds the fields for a kv-property table fields
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+ *
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+ * @param $entity_type_name
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+ * @param $bundle_name
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+ * @param $kv_table
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+ */
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+function tripal_entities_add_bundle_kv_property_fields($entity_type_name, $bundle_name, $kv_table) {
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+ // First add a generic property field so that users can add new proeprty types.
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+ $field_name = $kv_table;
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+
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+ // Initialize the field array.
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+ $field_info = array(
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+ 'field_type' => 'kvproperty',
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+ 'widget_type' => 'tripal_fields_kvproperty_widget',
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+ 'field_settings' => array(),
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+ 'widget_settings' => array('display_label' => 1),
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+ 'description' => '',
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+ 'label' => 'Additional Properties',
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+ 'chado_table' => $kv_table,
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+ 'chado_column' => '',
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+ 'is_required' => 0,
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+ );
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+ tripal_entities_add_bundle_field($field_name, $field_info, $entity_type_name, $bundle_name);
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+}
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+/**
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+ * Adds the fields for the base table to the entity.
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+ */
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+function tripal_entities_add_bundle_base_fields($entity_type_name, $bundle_name, $cvterm) {
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// Get the list of tables where this cvterm is used.
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$match = array('cvterm_id' => $cvterm->cvterm_id);
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$term = chado_select_record('tripal_term', array('*'), $match);
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@@ -518,25 +562,24 @@ function tripal_entities_add_bundle_fields($entity_type_name, $bundle_name, $cvt
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// Iterate through the tables.
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foreach ($tables as $table) {
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- $tablename = $table->data_table;
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+ $table_name = $table->data_table;
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$type_table = $table->type_table;
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$type_field = $table->field;
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// We only want to look at base tables.
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- if ($tablename == 'cvterm_dbxref' || $tablename == 'cvterm_relationship' ||
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- $tablename == 'cvtermpath' || $tablename == 'cvtermprop' || $tablename == 'chadoprop' ||
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- $tablename == 'cvtermsynonym' || preg_match('/_relationship$/', $tablename) ||
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- preg_match('/_cvterm$/', $tablename)) {
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+ if ($table_name == 'cvterm_dbxref' || $table_name == 'cvterm_relationship' ||
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+ $table_name == 'cvtermpath' || $table_name == 'cvtermprop' || $table_name == 'chadoprop' ||
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+ $table_name == 'cvtermsynonym' || preg_match('/_relationship$/', $table_name) ||
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+ preg_match('/_cvterm$/', $table_name)) {
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continue;
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}
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// Iterate through the columns of the table and see if fields have been
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// created for each one. If not, then create them.
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- $schema = chado_get_schema($tablename);
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+ $schema = chado_get_schema($table_name);
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$columns = $schema['fields'];
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foreach ($columns as $column_name => $details) {
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- $field_name = $tablename . '__' . $column_name;
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- $field = field_info_field($field_name);
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+ $field_name = $table_name . '__' . $column_name;
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// Skip the primary key field.
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if ($column_name == $schema['primary key'][0]) {
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@@ -544,95 +587,26 @@ function tripal_entities_add_bundle_fields($entity_type_name, $bundle_name, $cvt
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}
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// Skip the type field.
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- if ($tablename == $type_table and $column_name == $type_field) {
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+ if ($table_name == $type_table and $column_name == $type_field) {
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continue;
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}
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- // Determine if the field is required.
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- $is_required = 0;
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- if (array_key_exists('not null', $details) and $details['not null'] === TRUE) {
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- $is_required = array_key_exists('default', $details) ? 0 : 1;
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- }
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+ // Get the field defaults for this column.
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+ $field_info = tripal_entities_get_table_column_field_default($table_name, $schema, $column_name);
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- // Determine what type of field this should be.
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- // Drupal data types are: https://www.drupal.org/node/159605.
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- // Field types are here: https://www.drupal.org/node/1879542
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-
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- // Create an array with information about this field.
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- $field_info = array(
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- 'field_type' => '',
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- 'widget_type' => '',
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- 'field_settings' => array(),
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- 'widget_settings' => array('display_label' => 1),
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- 'description' => '',
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- 'label' => ucwords(preg_replace('/_/', ' ', $column_name)),
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- 'chado_table' => $tablename,
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- 'chado_column' => $column_name
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- );
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- // Alter the field info array dependiing on the column details.
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- switch($details['type']) {
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- case 'char':
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- $field_info['field_type'] = 'text';
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- $field_info['widget_type'] = 'text_textfield';
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- $field_info['field_settings']['max_length'] = $details['length'];
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- break;
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- case 'varchar':
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- $field_info['field_type'] = 'text';
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- $field_info['widget_type'] = 'text_textfield';
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- $field_info['field_settings']['max_length'] = $details['length'];
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- break;
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- case 'text':
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- $field_info['field_type'] = 'text';
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- $field_info['widget_type'] = 'text_textarea';
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- $field_info['field_settings']['max_length'] = 17179869184;
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- break;
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- case 'blob':
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- // not sure how to support a blob field.
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- continue;
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- break;
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- case 'int':
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- $field_info['field_type'] = 'number_integer';
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- $field_info['widget_type'] = 'number';
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- break;
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- case 'float':
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- $field_info['field_type'] = 'number_float';
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- $field_info['widget_type'] = 'number';
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- $field_info['field_settings']['precision'] = 10;
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- $field_info['field_settings']['scale'] = 2;
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- $field_info['field_settings']['decimal_separator'] = '.';
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- break;
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- case 'numeric':
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- $field_info['field_type'] = 'number_decimal';
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- $field_info['widget_type'] = 'number';
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- break;
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- case 'serial':
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- // Serial fields are most likely not needed as a field.
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- break;
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- case 'boolean':
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- $field_info['field_type'] = 'list_boolean';
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- $field_info['widget_type'] = 'options_onoff';
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- $field_info['field_settings']['allowed_values'] = array(0 => "No", 1 => "Yes");
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- break;
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- case 'datetime':
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- // Use the Drupal Date and Date API to create the field/widget
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- $field_info['field_type'] = 'datetime';
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- $field_info['widget_type'] = 'date_select';
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- $field_info['widget_settings']['increment'] = 1;
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- $field_info['widget_settings']['tz_handling'] = 'none';
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-
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- // TODO: Add settings so that the minutes increment by 1.
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- // And turn off the timezone, as the Chado field doesn't support it.
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- break;
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+ // Determine if the field is required.
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+ if (array_key_exists('not null', $details) and $details['not null'] === TRUE) {
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+ $field_info['is_required'] = array_key_exists('default', $details) ? 0 : 1;
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}
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// If we don't have a field type then we don't need to create a field.
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if (!$field_info['field_type']) {
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// If we don't have a field type but it is required and doesn't have
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// a default value then we are in trouble.
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- if ($is_required and !array_key_exists('default', $details)) {
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+ if ($field_info['is_required'] and !array_key_exists('default', $details)) {
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throw new Exception(t('The %table.%field type, %type, is not yet supported for Entity fields, but it is required,',
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- array('%table' => $tablename, '%field' => $column_name, '%type' => $details['type'])));
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+ array('%table' => $table_name, '%field' => $column_name, '%type' => $details['type'])));
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}
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continue;
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}
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@@ -648,39 +622,142 @@ function tripal_entities_add_bundle_fields($entity_type_name, $bundle_name, $cvt
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}
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}
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- // Allow other modules to alter the field information array.
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- drupal_alter('chado_field', $field_info);
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-
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- // If the field doesn't exist then create it.
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- if (!$field) {
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- $field = array(
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- 'field_name' => $field_name,
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- 'type' => $field_info['field_type'],
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- 'cardinality' => 1,
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- 'locked' => FALSE,
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- 'storage' => array(
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- 'type' => 'field_chado_storage'
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- ),
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- 'settings' => $field_info['field_settings'],
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- );
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- field_create_field($field);
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- }
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-
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- // Attach the field to the bundle.
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- $field_instance = array(
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- 'field_name' => $field_name,
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- 'label' => $field_info['label'],
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- 'description' => $field_info['description'],
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- 'widget' => array(
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- 'type' => $field_info['widget_type'],
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- 'settings' => $field_info['widget_settings'],
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- ),
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- 'entity_type' => $entity_type_name,
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- 'required' => $is_required,
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- 'settings' => $field_info['field_settings'],
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- 'bundle' => $bundle_name,
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- );
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- field_create_instance($field_instance);
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+ // Add the field to the bundle.
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+ tripal_entities_add_bundle_field($field_name, $field_info, $entity_type_name, $bundle_name);
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}
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}
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}
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+
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+/**
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+ * Returns a $field_info array for a field based on a databaes column.
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+ *
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+ */
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+function tripal_entities_get_table_column_field_default($table_name, $schema, $column_name) {
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+ $details = $schema['fields'][$column_name];
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+
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+ // Create an array with information about this field.
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+ $field_info = array(
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+ 'field_type' => '',
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+ 'widget_type' => '',
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+ 'field_settings' => array(),
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+ 'widget_settings' => array('display_label' => 1),
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+ 'description' => '',
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+ 'label' => ucwords(preg_replace('/_/', ' ', $column_name)),
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+ 'chado_table' => $table_name,
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+ 'chado_column' => $column_name,
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+ 'is_required' => 0,
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+ );
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+
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+ // Alter the field info array depending on the column details.
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+ switch($details['type']) {
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+ case 'char':
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+ $field_info['field_type'] = 'text';
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+ $field_info['widget_type'] = 'text_textfield';
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+ $field_info['field_settings']['max_length'] = $details['length'];
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+ break;
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+ case 'varchar':
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+ $field_info['field_type'] = 'text';
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+ $field_info['widget_type'] = 'text_textfield';
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+ $field_info['field_settings']['max_length'] = $details['length'];
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+ break;
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+ case 'text':
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+ $field_info['field_type'] = 'text';
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+ $field_info['widget_type'] = 'text_textarea';
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+ $field_info['field_settings']['max_length'] = 17179869184;
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+ break;
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+ case 'blob':
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+ // not sure how to support a blob field.
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+ continue;
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+ break;
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+ case 'int':
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+ $field_info['field_type'] = 'number_integer';
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+ $field_info['widget_type'] = 'number';
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+ break;
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+ case 'float':
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+ $field_info['field_type'] = 'number_float';
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+ $field_info['widget_type'] = 'number';
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+ $field_info['field_settings']['precision'] = 10;
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+ $field_info['field_settings']['scale'] = 2;
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+ $field_info['field_settings']['decimal_separator'] = '.';
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+ break;
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+ case 'numeric':
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+ $field_info['field_type'] = 'number_decimal';
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+ $field_info['widget_type'] = 'number';
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+ break;
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+ case 'serial':
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+ // Serial fields are most likely not needed as a field.
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+ break;
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+ case 'boolean':
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+ $field_info['field_type'] = 'list_boolean';
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+ $field_info['widget_type'] = 'options_onoff';
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+ $field_info['field_settings']['allowed_values'] = array(0 => "No", 1 => "Yes");
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+ break;
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+ case 'datetime':
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+ // Use the Drupal Date and Date API to create the field/widget
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+ $field_info['field_type'] = 'datetime';
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+ $field_info['widget_type'] = 'date_select';
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+ $field_info['widget_settings']['increment'] = 1;
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+ $field_info['widget_settings']['tz_handling'] = 'none';
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+
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+ // TODO: Add settings so that the minutes increment by 1.
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+ // And turn off the timezone, as the Chado field doesn't support it.
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+ break;
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+ }
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+
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+ return $field_info;
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+}
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+/**
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+ * Adds a field to a bundle.
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+ *
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+ * @param $field_name
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+ * The name of the field.
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+ * @param $field_info
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+ * An associative array containing the field information.
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+ */
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+function tripal_entities_add_bundle_field($field_name, $field_info,
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+ $entity_type_name, $bundle_name) {
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+
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+ $field = field_info_field($field_name);
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+
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+ // If the field exists and is attached to this bundle then just return,
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+ // there is nothing left to do.
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+ if ($field and array_key_exists('bundles', $field) and
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+ array_key_exists($entity_type_name, $field['bundles']) and
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|
+ in_array($bundle_name, $field['bundles'][$entity_type_name])) {
|
|
|
+ return;
|
|
|
+ }
|
|
|
+
|
|
|
+ // Allow other modules to alter the field information array.
|
|
|
+ drupal_alter('chado_field', $field_info);
|
|
|
+
|
|
|
+ // If the field doesn't exist then create it.
|
|
|
+ if (!$field) {
|
|
|
+ $field = array(
|
|
|
+ 'field_name' => $field_name,
|
|
|
+ 'type' => $field_info['field_type'],
|
|
|
+ 'cardinality' => 1,
|
|
|
+ 'locked' => FALSE,
|
|
|
+ 'storage' => array(
|
|
|
+ 'type' => 'field_chado_storage'
|
|
|
+ ),
|
|
|
+ 'settings' => $field_info['field_settings'],
|
|
|
+ );
|
|
|
+ field_create_field($field);
|
|
|
+ }
|
|
|
+
|
|
|
+ // Attach the field to the bundle.
|
|
|
+ $field_instance = array(
|
|
|
+ 'field_name' => $field_name,
|
|
|
+ 'label' => $field_info['label'],
|
|
|
+ 'description' => $field_info['description'],
|
|
|
+ 'widget' => array(
|
|
|
+ 'type' => $field_info['widget_type'],
|
|
|
+ 'settings' => $field_info['widget_settings'],
|
|
|
+ ),
|
|
|
+ 'entity_type' => $entity_type_name,
|
|
|
+ 'required' => $field_info['is_required'],
|
|
|
+ 'settings' => $field_info['field_settings'],
|
|
|
+ 'bundle' => $bundle_name,
|
|
|
+ );
|
|
|
+ field_create_instance($field_instance);
|
|
|
+}
|