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@@ -0,0 +1,217 @@
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+<?php
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+
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+class chado_linker__phenotype extends TripalField {
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+
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+ /**
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+ * @see TripalField::field_info()
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+ */
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+ public function field_info() {
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+ return array(
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+ 'label' => t('Genotypes'),
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+ 'description' => t('Associates an indviddual or organization with
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+ this record.'),
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+ 'default_widget' => 'chado_linker__phenotype_widget',
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+ 'default_formatter' => 'chado_linker__phenotype_formatter',
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+ 'settings' => array(),
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+ 'storage' => array(
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+ 'type' => 'field_chado_storage',
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+ 'module' => 'tripal_chado',
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+ 'active' => TRUE
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+ ),
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+ );
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+ }
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+ /**
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+ * @see TripalField::widget_info()
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+ */
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+ function widget_info() {
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+ return array(
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+ 'label' => t('Genotypes'),
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+ 'field types' => array('chado_linker__phenotype'),
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+ );
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+ }
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+
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+ /**
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+ * @see TripalField::formatter_info()
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+ */
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+ public function formatter_info() {
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+ return array(
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+ 'label' => t('Genotypes'),
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+ 'field types' => array('chado_linker__phenotype'),
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+ 'settings' => array(
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+ ),
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+ );
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+ }
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+ /**
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+ * @see TripalField::attach_info()
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+ */
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+ public function attach_info($entity_type, $bundle, $settings) {
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+ $field_info = array();
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+
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+ $table_name = $settings['data_table'];
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+ $type_table = $settings['type_table'];
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+ $type_field = $settings['field'];
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+ $cv_id = $settings['cv_id'];
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+ $cvterm_id = $settings['cvterm_id'];
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+
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+ // If the linker table does not exists then we don't want to add attach.
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+ $phenotype_table = $table_name . '_phenotype';
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+ if (!chado_table_exists($phenotype_table)) {
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+ return $field_info;
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+ }
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+
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+ $schema = chado_get_schema($phenotype_table);
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+ $pkey = $schema['primary key'][0];
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+
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+ // Initialize the field array.
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+ $field_info = array(
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+ 'field_name' => $table_name . '__phenotype',
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+ 'field_type' => 'chado_linker__phenotype',
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+ 'widget_type' => 'chado_linker__phenotype_widget',
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+ 'widget_settings' => array('display_label' => 1),
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+ 'description' => '',
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+ 'label' => 'Genotypes',
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+ 'is_required' => 0,
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+ 'cardinality' => FIELD_CARDINALITY_UNLIMITED,
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+ 'storage' => 'field_chado_storage',
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+ 'field_settings' => array(
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+ 'chado_table' => $phenotype_table,
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+ 'chado_column' => $pkey,
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+ 'base_table' => $table_name,
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+ 'semantic_web' => array(
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+ 'name' => 'phenotype',
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+ 'accession' => 'phenotype',
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+ 'ns' => 'local',
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+ 'nsurl' => '',
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+ ),
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+ ),
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+ );
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+ return $field_info;
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+ }
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+
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+ /**
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+ * @see TripalField::formatter_view()
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+ */
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+ public function formatter_view(&$element, $entity_type, $entity,
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+ $field, $instance, $langcode, $items, $display) {
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+ // Get the settings
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+ $settings = $display['settings'];
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+ $record = $entity->chado_record;
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+
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+ $headers = array('Name', 'Value', 'Type');
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+ $rows = array();
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+
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+ foreach ($items as $delta => $item) {
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+ $phenotype = $item['value'];
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+ if (!$phenotype) {
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+ continue;
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+ }
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+
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+ // Get the field values
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+ $phenotype_name = $phenotype['name'];
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+ $value = $phenotype['value'];
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+ $type = $phenotype['type'];
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+
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+ // Add a link i there is an entity.
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+ if (array_key_exists('entity_id', $item) and $item['entity_id']) {
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+ $entity_id = $item['entity_id'];
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+ $phenotype_name = l($phenotype_name, "bio_data/" . $entity_id, array('attributes' => array('target' => "_blank")));
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+ }
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+ $rows[] = array($phenotype_name, $value, $type);
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+ }
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+ $table = array(
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+ 'header' => $headers,
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+ 'rows' => $rows,
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+ 'attributes' => array(
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+ 'id' => 'tripal_linker-table-phenotype-object',
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+ 'class' => 'tripal-data-table'
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+ ),
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+ 'sticky' => FALSE,
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+ 'caption' => "",
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+ 'colgroups' => array(),
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+ 'empty' => 'No phenotypes available',
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+ );
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+ $content = theme_table($table);
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+
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+ // once we have our table array structure defined, we call Drupal's theme_table()
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+ // function to generate the table.
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+ $element[$delta] = array(
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+ '#type' => 'markup',
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+ '#markup' => $content,
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+ );
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+ }
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+
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+
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+ /**
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+ * @see TripalField::widget_form()
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+ */
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+ public function widget_form(&$widget, $form, $form_state, $field, $instance,
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+ $langcode, $items, $delta, $element) {
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+
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+ }
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+
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+ /**
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+ * @see TripalField::load()
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+ */
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+ public function load($field, $entity, $details) {
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+ $record = $details['record'];
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+ $field_name = $field['field_name'];
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+ $field_type = $field['type'];
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+ $field_table = $field['settings']['chado_table'];
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+ $field_column = $field['settings']['chado_column'];
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+
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+ // Get the FK that links to the base record.
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+ $schema = chado_get_schema($field_table);
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+ $base_table = $details['record']->tablename;
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+ $pkey = $schema['primary key'][0];
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+ $fkey_lcolumn = key($schema['foreign keys'][$base_table]['columns']);
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+ $fkey_rcolumn = $schema['foreign keys'][$base_table]['columns'][$fkey_lcolumn];
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+
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+
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+ // Set some defaults for the empty record.
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+ $entity->{$field_name}['und'][0] = array(
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+ 'value' => array(),
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+ $field_table . '__' . $pkey => '',
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+ $field_table . '__' . $fkey_lcolumn => '',
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+ $field_table . '__' . 'phenotype_id' => '',
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+ // Ignore the synonym_sgml column for now.
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+ );
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+
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+ $linker_table = $base_table . '_phenotype';
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+ $options = array(
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+ 'return_array' => 1,
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+ 'include_fk' => array(
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+ 'phenotype_id' => array(
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+ 'attr_id' => array(
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+ 'dbxref_id' => array(
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+ 'db_id' => TRUE,
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+ ),
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+ ),
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+ ),
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+ $fkey_lcolumn => TRUE,
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+ ),
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+ );
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+ $record = chado_expand_var($record, 'table', $linker_table, $options);
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+ $phenotype_linkers = $record->$linker_table;
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+ if ($phenotype_linkers) {
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+ foreach ($phenotype_linkers as $i => $phenotype_linker) {
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+ $phenotype = $phenotype_linker->phenotype_id;
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+ $entity->{$field_name}['und'][$i] = array(
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+ 'value' => array(
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+ '@type' => $phenotype->attr_id->dbxref_id->db_id->name . ':' . $phenotype->attr_id->dbxref_id->accession,
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+ 'type' => $phenotype->attr_id->name,
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+ 'name' => $phenotype->name,
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+ 'value' => $phenotype->value,
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+ ),
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+ $field_table . '__' . $pkey => $phenotype_linker->$pkey,
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+ $field_table . '__' . $fkey_lcolumn => $phenotype_linker->$fkey_lcolumn->$fkey_lcolumn,
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+ $field_table . '__' . 'phenotype_id' => $phenotype->phenotype_id
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+ );
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+
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+ if ($phenotype && property_exists($phenotype, 'entity_id')) {
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+ $entity->{$field_name}['und'][$i]['entity_id'] = $phenotype->entity_id;
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+ $entity->{$field_name}['und'][$i]['entity_type'] = 'TripalEntity';
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+ }
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+ }
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+ }
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+ }
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+}
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Stephen Ficklin