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@@ -1,280 +1,338 @@
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<?php
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-/**
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- * Implements hook_info() for fields.
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- *
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- * This is a hook provided by the tripal_chado module for offloading the
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- * hook_field_info() hook for each field to specify.
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- */
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-function chado_linker__cvterm_info() {
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- return array(
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- 'label' => t('Annotations'),
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- 'description' => t('This record can be annotated with terms
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- from other vocabularies.'),
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- 'default_widget' => 'chado_linker__cvterm_widget',
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- 'default_formatter' => 'chado_linker__cvterm_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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- * Implements hook_attach_info().
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- *
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- * This is a hook provided by the tripal_Chado module. It allows the field
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- * to specify which bundles it will attach to and to specify thee settings.
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- *
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- * @param $entity_type
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- * @param $entity
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- * @param $term
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- *
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- * @return
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- * A field array
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- */
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-function chado_linker__cvterm_attach_info($entity_type, $bundle, $target) {
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- $field_info = array();
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- // This field is only attached by the chado_linker__cvterm_addr field.
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+class chado_linker__cvterm extends TripalField {
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+ /**
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+ * @see TripalField::field_info()
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+ */
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+ function field_info() {
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+ return array(
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+ 'label' => t('Annotations'),
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+ 'description' => t('This record can be annotated with terms
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+ from other vocabularies.'),
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+ 'default_widget' => 'chado_linker__cvterm_widget',
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+ 'default_formatter' => 'chado_linker__cvterm_formatter',
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+ 'settings' => array(),
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+ 'storage' => array(
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+ 'type' => 'field_chado_storage',
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+ 'module' => 'tripal_chado',
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+ 'active' => TRUE
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+ ),
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+ );
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+ }
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+ /**
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+ * @see TripalField::attach_info()
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+ */
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+ function attach_info($entity_type, $bundle, $target) {
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+ $field_info = array();
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- return $field_info;
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-}
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-/**
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- * Implements hook_widget_info.
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- *
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- * This is a hook provided by the tripal_chado module for offloading
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- * the hook_field_widget_info() hook for each field to specify.
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- */
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-function chado_linker__cvterm_widget_info() {
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- return array(
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- 'label' => t('Annotations'),
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- 'field types' => array('chado_linker__cvterm'),
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- 'description' => t('This record can be annotated with terms
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- from other vocabularies.'),
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- );
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-}
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-/**
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- * Implements hook_formatter_info.
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- *
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- * This is a hook provided by the tripal_chado module for
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- * offloading the hook_field_formatter_info() for each field
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- * to specify.
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- *
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- */
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-function chado_linker__cvterm_formatter_info() {
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- return array(
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- 'label' => t('Annotations'),
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- 'field types' => array('chado_linker__cvterm'),
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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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- *
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- * @param unknown $entity_type
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- * @param unknown $entity
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- * @param unknown $field
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- * @param unknown $instance
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- * @param unknown $langcode
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- * @param unknown $items
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- * @param unknown $display
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- */
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-function chado_linker__cvterm_formatter(&$element, $entity_type, $entity, $field,
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- $instance, $langcode, $items, $display) {
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-
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- $headers = array('Term', 'Definition', 'Is Not', 'Reference');
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- $rows = array();
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-
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- $chado_table = $field['settings']['chado_table'];
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- foreach ($items as $delta => $item) {
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- if ($item[$chado_table . '__cvterm_id']) {
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- $cvterm = chado_generate_var('cvterm', array('cvterm_id' => $item[$chado_table . '__cvterm_id']));
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- $dbxref = $cvterm->dbxref_id;
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-
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- // Build the accession.
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- $accession = $dbxref->db_id->name . ':' . $dbxref->accession;
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- if ($dbxref->db_id->urlprefix) {
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- $accession = l($accession, $dbxref->db_id->urlprefix . '/' . $dbxref->accession, array('attributes' => array('target' => '_blank')));
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- }
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+ // This field is only attached by the chado_linker__cvterm_addr field.
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- // Build the publication reference.
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- $pub_ref = '';
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- $pub_id = $item[$chado_table . '__pub_id'];
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- if ($pub_id) {
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- $pub = chado_generate_var('pub', array('pub_id' => $pub_id));
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- $pub_ref = $pub->title;
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- }
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- $rows[] = array(
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- $accession,
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- $cvterm->definition,
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- $item[$chado_table . '__is_not'] ? 'Yes' : '',
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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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- // the $table array contains the headers and rows array as well as other
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- // options for controlling the display of the table. Additional
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- // documentation can be found here:
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- // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
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- $table = array(
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- 'header' => $headers,
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- 'rows' => $rows,
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- 'attributes' => array(
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- 'id' => "$chado_table-table-terms",
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- 'class' => 'tripal-data-table'
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- ),
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- 'caption' => '',
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- 'sticky' => FALSE,
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- 'colgroups' => array(),
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- 'empty' => 'There are no annotations of this type',
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- );
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-
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- $element[0] = array(
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- '#type' => 'markup',
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- '#markup' => theme_table($table),
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- );
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-}
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-/**
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- *
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- * @param unknown $field_name
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- * @param unknown $widget
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- * @param unknown $form
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- * @param unknown $form_state
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- * @param unknown $field
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- * @param unknown $instance
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- * @param unknown $langcode
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- * @param unknown $items
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- * @param unknown $delta
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- * @param unknown $element
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- */
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-function chado_linker__cvterm_widget(&$widget, $form, $form_state, $field,
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- $instance, $langcode, $items, $delta, $element) {
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-
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- $entity = $form['#entity'];
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- $field_name = $field['field_name'];
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-
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- $matches = array();
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- preg_match('/(.*?)__(\d+)/', $field_name, $matches);
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- // If the field name is not properly formatted then we can't tell what
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- // table and type this is. So just return.
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- if (count($matches) != 3) {
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- return $widget;
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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('Annotations'),
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+ 'field types' => array('chado_linker__cvterm'),
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+ 'description' => t('This record can be annotated with terms
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+ from other vocabularies.'),
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+ );
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}
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- $table_name = $matches[1];
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- $cv_id = $matches[2];
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-
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- // Get the FK column that links to the base table.
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- $chado_table = $field['settings']['chado_table'];
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- $base_table = $field['settings']['base_table'];
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- $schema = chado_get_schema($chado_table);
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- $pkey = $schema['primary key'][0];
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- $fkeys = array_values($schema['foreign keys'][$base_table]['columns']);
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- $fkey = $fkeys[0];
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-
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- // Get the field defaults.
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- $record_id = '';
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- $fkey_value = $element['#entity']->chado_record_id;
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- $cvterm_name = '';
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- $cvterm_id = '';
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- $is_not = '';
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- $cvterm = NULL;
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-
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- // If the field already has a value then it will come through the $items
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- // array. This happens when editing an existing record.
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- if (array_key_exists($delta, $items)) {
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- $record_id = $items[$delta]['value'];
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- $fkey_value = $items[$delta][$table_name . '__' . $fkey];
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- $cvterm_name = $items[$delta][$table_name . '--cvterm__name'];
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- $is_not = $items[$delta][$table_name . '__is_not'];
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- $cvterm_id = $items[$delta][$table_name . '__cvterm_id'];
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+ /**
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+ * @see TripalField::formatter_info()
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+ */
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+ function formatter_info() {
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+ return array(
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+ 'label' => t('Annotations'),
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+ 'field types' => array('chado_linker__cvterm'),
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+ 'settings' => array(
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+ ),
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+ );
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}
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+ /**
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+ * @see TripalField::formatter_view()
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+ */
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+ function formatter_view(&$element, $entity_type, $entity, $field,
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+ $instance, $langcode, $items, $display) {
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+
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+ $headers = array('Term', 'Definition', 'Is Not', 'Reference');
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+ $rows = array();
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+
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+ $chado_table = $field['settings']['chado_table'];
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+ foreach ($items as $delta => $item) {
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+ if ($item[$chado_table . '__cvterm_id']) {
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+ $cvterm = chado_generate_var('cvterm', array('cvterm_id' => $item[$chado_table . '__cvterm_id']));
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+ $dbxref = $cvterm->dbxref_id;
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+
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+ // Build the accession.
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+ $accession = $dbxref->db_id->name . ':' . $dbxref->accession;
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+ if ($dbxref->db_id->urlprefix) {
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+ $accession = l($accession, $dbxref->db_id->urlprefix . '/' . $dbxref->accession, array('attributes' => array('target' => '_blank')));
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+ }
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+
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+ // Build the publication reference.
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+ $pub_ref = '';
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+ $pub_id = $item[$chado_table . '__pub_id'];
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+ if ($pub_id) {
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+ $pub = chado_generate_var('pub', array('pub_id' => $pub_id));
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+ $pub_ref = $pub->title;
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+ }
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+ $rows[] = array(
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+ $accession,
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+ $cvterm->definition,
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+ $item[$chado_table . '__is_not'] ? 'Yes' : '',
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+ '',
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+ );
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+ }
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+ }
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+
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+ // the $table array contains the headers and rows array as well as other
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+ // options for controlling the display of the table. Additional
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+ // documentation can be found here:
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+ // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
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+ $table = array(
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+ 'header' => $headers,
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+ 'rows' => $rows,
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+ 'attributes' => array(
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+ 'id' => "$chado_table-table-terms",
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+ 'class' => 'tripal-data-table'
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+ ),
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+ 'caption' => '',
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+ 'sticky' => FALSE,
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+ 'colgroups' => array(),
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+ 'empty' => 'There are no annotations of this type',
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+ );
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- // Check $form_state['values'] to see if an AJAX call set the values.
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- if (array_key_exists('values', $form_state) and array_key_exists($delta, $form_state['values'])) {
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- $record_id = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name);
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- $fkey_value = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '__' . $fkey);
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- $is_not = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '__is_not');
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- $cvterm_name = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '--cvterm__name');
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+ $element[0] = array(
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+ '#type' => 'markup',
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+ '#markup' => theme_table($table),
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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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+ 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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+ $entity = $form['#entity'];
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+ $field_name = $field['field_name'];
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+
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+ $matches = array();
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+ preg_match('/(.*?)__(\d+)/', $field_name, $matches);
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+ // If the field name is not properly formatted then we can't tell what
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+ // table and type this is. So just return.
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+ if (count($matches) != 3) {
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+ return $widget;
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+ }
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+ $table_name = $matches[1];
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+ $cv_id = $matches[2];
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+
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+ // Get the FK column that links to the base table.
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+ $chado_table = $field['settings']['chado_table'];
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+ $base_table = $field['settings']['base_table'];
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+ $schema = chado_get_schema($chado_table);
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+ $pkey = $schema['primary key'][0];
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+ $fkeys = array_values($schema['foreign keys'][$base_table]['columns']);
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+ $fkey = $fkeys[0];
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+
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+ // Get the field defaults.
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+ $record_id = '';
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+ $fkey_value = $element['#entity']->chado_record_id;
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+ $cvterm_name = '';
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+ $cvterm_id = '';
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+ $is_not = '';
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+ $cvterm = NULL;
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+
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+ // If the field already has a value then it will come through the $items
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+ // array. This happens when editing an existing record.
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+ if (array_key_exists($delta, $items)) {
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+ $record_id = $items[$delta]['value'];
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+ $fkey_value = $items[$delta][$table_name . '__' . $fkey];
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+ $cvterm_name = $items[$delta][$table_name . '--cvterm__name'];
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+ $is_not = $items[$delta][$table_name . '__is_not'];
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+ $cvterm_id = $items[$delta][$table_name . '__cvterm_id'];
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+ }
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+
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+ // Check $form_state['values'] to see if an AJAX call set the values.
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+ if (array_key_exists('values', $form_state) and array_key_exists($delta, $form_state['values'])) {
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+ $record_id = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name);
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+ $fkey_value = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '__' . $fkey);
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+ $is_not = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '__is_not');
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+ $cvterm_name = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '--cvterm__name');
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+ }
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+
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+ if ($cvterm_name) {
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+ $cvterm = chado_generate_var('cvterm', array('cv_id' => $cv_id, 'name' => $cvterm_name));
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+ }
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+
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+ $schema = chado_get_schema('cvterm');
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+ $options = tripal_get_cv_select_options();
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+
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+ $widget['#table_name'] = $chado_table;
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+ $widget['#fkey_field'] = $fkey;
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+ $widget['#element_validate'] = array('chado_linker__cvterm_widget_validate');
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+ $widget['#theme'] = 'chado_linker__cvterm_widget';
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+ $widget['#prefix'] = "<span id='$table_name-$delta'>";
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+ $widget['#suffix'] = "</span>";
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+
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+ $widget['value'] = array(
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+ '#type' => 'value',
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+ '#value' => $items[$delta]['value'],
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+ );
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+
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+ $widget[$table_name . '__' . $pkey] = array(
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+ '#type' => 'value',
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+ '#default_value' => $record_id,
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|
+ );
|
|
|
+ $widget[$table_name . '--cvterm__cv_id--cv__cv_id'] = array(
|
|
|
+ '#type' => 'value',
|
|
|
+ '#default_value' => $cv_id,
|
|
|
+ );
|
|
|
+ $widget[$table_name . '__cvterm_id'] = array(
|
|
|
+ '#type' => 'value',
|
|
|
+ '#default_value' => $cvterm ? $cvterm->cvterm_id : '',
|
|
|
+ );
|
|
|
+ $widget[$table_name . '__' . $fkey] = array(
|
|
|
+ '#type' => 'value',
|
|
|
+ '#default_value' => $fkey_value,
|
|
|
+ );
|
|
|
+
|
|
|
+ $widget[$table_name . '--cvterm__name'] = array(
|
|
|
+ '#type' => 'textfield',
|
|
|
+ '#title' => t('Term Name'),
|
|
|
+ '#default_value' => $cvterm_name,
|
|
|
+ '#required' => $element['#required'],
|
|
|
+ '#maxlength' => array_key_exists('length', $schema['fields']['name']) ? $schema['fields']['name']['length'] : 255,
|
|
|
+ '#autocomplete_path' => 'admin/tripal/storage/chado/auto_name/cvterm/' . $cv_id,
|
|
|
+ '#ajax' => array(
|
|
|
+ 'callback' => "chado_linker__cvterm_widget_form_ajax_callback",
|
|
|
+ 'wrapper' => "$table_name-$delta",
|
|
|
+ 'effect' => 'fade',
|
|
|
+ 'method' => 'replace'
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ $widget[$table_name . '__is_not'] = array(
|
|
|
+ '#type' => 'checkbox',
|
|
|
+ '#title' => t('Is Not'),
|
|
|
+ '#default_value' => $is_not,
|
|
|
+ '#required' => $element['#required'],
|
|
|
+ );
|
|
|
+
|
|
|
+ $widget[$table_name . '--cvterm__definition'] = array(
|
|
|
+ '#type' => 'item',
|
|
|
+ '#markup' => '',
|
|
|
+ );
|
|
|
|
|
|
- if ($cvterm_name) {
|
|
|
- $cvterm = chado_generate_var('cvterm', array('cv_id' => $cv_id, 'name' => $cvterm_name));
|
|
|
}
|
|
|
|
|
|
- $schema = chado_get_schema('cvterm');
|
|
|
- $options = tripal_get_cv_select_options();
|
|
|
-
|
|
|
- $widget['#table_name'] = $chado_table;
|
|
|
- $widget['#fkey_field'] = $fkey;
|
|
|
- $widget['#element_validate'] = array('chado_linker__cvterm_widget_validate');
|
|
|
- $widget['#theme'] = 'chado_linker__cvterm_widget';
|
|
|
- $widget['#prefix'] = "<span id='$table_name-$delta'>";
|
|
|
- $widget['#suffix'] = "</span>";
|
|
|
-
|
|
|
- $form['value'] = array(
|
|
|
- '#type' => 'value',
|
|
|
- '#value' => $items[$delta]['value'],
|
|
|
- );
|
|
|
-
|
|
|
- $widget[$table_name . '__' . $pkey] = array(
|
|
|
- '#type' => 'value',
|
|
|
- '#default_value' => $record_id,
|
|
|
- );
|
|
|
- $widget[$table_name . '--cvterm__cv_id--cv__cv_id'] = array(
|
|
|
- '#type' => 'value',
|
|
|
- '#default_value' => $cv_id,
|
|
|
- );
|
|
|
- $widget[$table_name . '__cvterm_id'] = array(
|
|
|
- '#type' => 'value',
|
|
|
- '#default_value' => $cvterm ? $cvterm->cvterm_id : '',
|
|
|
- );
|
|
|
- $widget[$table_name . '__' . $fkey] = array(
|
|
|
- '#type' => 'value',
|
|
|
- '#default_value' => $fkey_value,
|
|
|
- );
|
|
|
-
|
|
|
- $widget[$table_name . '--cvterm__name'] = array(
|
|
|
- '#type' => 'textfield',
|
|
|
- '#title' => t('Term Name'),
|
|
|
- '#default_value' => $cvterm_name,
|
|
|
- '#required' => $element['#required'],
|
|
|
- '#maxlength' => array_key_exists('length', $schema['fields']['name']) ? $schema['fields']['name']['length'] : 255,
|
|
|
- '#autocomplete_path' => 'admin/tripal/storage/chado/auto_name/cvterm/' . $cv_id,
|
|
|
- '#ajax' => array(
|
|
|
- 'callback' => "chado_linker__cvterm_widget_form_ajax_callback",
|
|
|
- 'wrapper' => "$table_name-$delta",
|
|
|
- 'effect' => 'fade',
|
|
|
- 'method' => 'replace'
|
|
|
- ),
|
|
|
- );
|
|
|
-
|
|
|
- $widget[$table_name . '__is_not'] = array(
|
|
|
- '#type' => 'checkbox',
|
|
|
- '#title' => t('Is Not'),
|
|
|
- '#default_value' => $is_not,
|
|
|
- '#required' => $element['#required'],
|
|
|
- );
|
|
|
-
|
|
|
- $widget[$table_name . '--cvterm__definition'] = array(
|
|
|
- '#type' => 'item',
|
|
|
- '#markup' => '',
|
|
|
- );
|
|
|
+ /**
|
|
|
+ * @see TripalField::load()
|
|
|
+ */
|
|
|
+ function load($field, $entity, $details) {
|
|
|
+
|
|
|
+ $record = $details['record'];
|
|
|
+
|
|
|
+ $field_name = $field['field_name'];
|
|
|
+ $field_type = $field['type'];
|
|
|
+ $field_table = $field['settings']['chado_table'];
|
|
|
+ $field_column = $field['settings']['chado_column'];
|
|
|
+
|
|
|
+ $matches = array();
|
|
|
+ preg_match('/(.*?)__(\d+)/', $field_name, $matches);
|
|
|
+ $table_name = $matches[1];
|
|
|
+ $cv_id = $matches[2];
|
|
|
+
|
|
|
+ // Get the FK that links to the base record.
|
|
|
+ $schema = chado_get_schema($field_table);
|
|
|
+ $pkey = $schema['primary key'][0];
|
|
|
+ $fkey_lcolumn = key($schema['foreign keys'][$base_table]['columns']);
|
|
|
+ $fkey_rcolumn = $schema['foreign keys'][$base_table]['columns'][$fkey_lcolumn];
|
|
|
+
|
|
|
+ // Set some defaults for the empty record.
|
|
|
+ $entity->{$field_name}['und'][0] = array(
|
|
|
+ 'value' => '',
|
|
|
+ $field_table . '__' . $fkey_lcolumn => '',
|
|
|
+ $field_table . '__' . 'cvterm_id' => '',
|
|
|
+ // The pub column is present in the cell_line_cvterm, feature_cvterm,
|
|
|
+ // library_cvterm, phenotype_comparision_cvterm, phenotype_cvterm,
|
|
|
+ // stock_cvterm, and stock_relationship_cvterm.
|
|
|
+ $field_table . '__' . 'pub_id' => '',
|
|
|
+ // The is_not column is present in feature_cvterm and stock_cvterm tables.
|
|
|
+ $field_table . '__' . 'is_not' => '',
|
|
|
+ // The rank column is present in the cell_line_cvterm, expression_cvterm,
|
|
|
+ // feature_cvterm, phenotype_comparision_cvterm, phenotype_cvterm,
|
|
|
+ // and stock_cvterm tables.
|
|
|
+ $field_table . '__' . 'rank' => '',
|
|
|
+ // The cvterm_type_id is present in the expression_cvterm table.
|
|
|
+ $field_table . '--' . 'cvterm_type_id' => '',
|
|
|
+ // The following field are to help link the cvterm.
|
|
|
+ $field_table . '--' . 'cvterm__cv_id--cv__cv_id' => '',
|
|
|
+ $field_table . '--' . 'cvterm__name' => '',
|
|
|
+ );
|
|
|
|
|
|
+ // Get the annotations associated with this base record for this fields type.
|
|
|
+ $columns = array('*');
|
|
|
+ $match = array(
|
|
|
+ $fkey_lcolumn => $record->$fkey_rcolumn,
|
|
|
+ 'cvterm_id' => array(
|
|
|
+ 'cv_id' => $cv_id,
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ $options = array(
|
|
|
+ 'return_array' => TRUE,
|
|
|
+ 'order_by' => array('rank' => 'ASC')
|
|
|
+ );
|
|
|
+ $fcvterms = chado_select_record($field_table, $columns, $match, $options);
|
|
|
+ for ($i = 0; $i < count($fcvterms); $i++) {
|
|
|
+ $linker = $fcvterms[$i];
|
|
|
+ $cvterm = chado_generate_var('cvterm', array('cvterm_id' => $linker->cvterm_id));
|
|
|
+ $entity->{$field_name}['und'][$i] = array(
|
|
|
+ 'value' => $linker->$pkey,
|
|
|
+ $field_table . '__' . $fkey_lcolumn => $linker->$fkey_lcolumn,
|
|
|
+ $field_table . '__' . 'cvterm_id' => $linker->cvterm_id,
|
|
|
+ $field_table . '__' . 'pub_id' => property_exists($linker, 'pub_id') ? $linker->pub_id : '',
|
|
|
+ $field_table . '__' . 'is_not' => property_exists($linker, 'is_not') ? $linker->is_not : '',
|
|
|
+ $field_table . '__' . 'rank' => property_exists($linker, 'rank') ? $linker->rank : '',
|
|
|
+ $field_table . '__' . 'cvterm_type_id' => property_exists($linker, 'cvterm_type_id') ? $linker->cvterm_type_id : '',
|
|
|
+ $field_table . '--' . 'cvterm__cv_id--cv__cv_id' => $cvterm->cv_id->cv_id,
|
|
|
+ $field_table . '--' . 'cvterm__name' => $cvterm->name,
|
|
|
+ );
|
|
|
+ }
|
|
|
+ }
|
|
|
}
|
|
|
+
|
|
|
/**
|
|
|
- * An Ajax callback for the dbxref widget.
|
|
|
+ * Theme function for the dbxref_id_widget.
|
|
|
+ *
|
|
|
+ * @param $variables
|
|
|
*/
|
|
|
-function chado_linker__cvterm_widget_form_ajax_callback($form, $form_state) {
|
|
|
+function theme_chado_linker__cvterm_widget($variables) {
|
|
|
+ $element = $variables['element'];
|
|
|
|
|
|
- $field_name = $form_state['triggering_element']['#parents'][0];
|
|
|
- $delta = $form_state['triggering_element']['#parents'][2];
|
|
|
+ // These two fields were added to the widget to help identify the fields
|
|
|
+ // for layout.
|
|
|
+ $table_name = $element['#table_name'];
|
|
|
+ $fkey = $element['#fkey_field'];
|
|
|
|
|
|
+ $layout = "
|
|
|
+ <div class=\"annotation-cvterm-widget\">
|
|
|
+ <div class=\"annotation-cvterm-widget-item\">" .
|
|
|
+ drupal_render($element[$table_name . '--cvterm__cv_id--cv__cv_id']) . "
|
|
|
+ </div>
|
|
|
+ <div class=\"annotation-cvterm-widget-item\">" .
|
|
|
+ drupal_render($element[$table_name . '--cvterm__name']) . "
|
|
|
+ </div>
|
|
|
+ <div class=\"annotation-cvterm-widget-item\">" .
|
|
|
+ drupal_render($element[$table_name . '__is_not']) . "
|
|
|
+ </div>
|
|
|
+ </div>
|
|
|
+ ";
|
|
|
|
|
|
- return $form[$field_name]['und'][$delta];
|
|
|
+ return $layout;
|
|
|
}
|
|
|
-
|
|
|
/**
|
|
|
* Callback function for validating the chado_linker__cvterm_widget.
|
|
|
*/
|
|
|
@@ -325,115 +383,13 @@ function chado_linker__cvterm_widget_validate($element, &$form_state) {
|
|
|
|
|
|
}
|
|
|
/**
|
|
|
- * Theme function for the dbxref_id_widget.
|
|
|
- *
|
|
|
- * @param $variables
|
|
|
+ * An Ajax callback for the dbxref widget.
|
|
|
*/
|
|
|
-function theme_chado_linker__cvterm_widget($variables) {
|
|
|
- $element = $variables['element'];
|
|
|
-
|
|
|
- // These two fields were added to the widget to help identify the fields
|
|
|
- // for layout.
|
|
|
- $table_name = $element['#table_name'];
|
|
|
- $fkey = $element['#fkey_field'];
|
|
|
-
|
|
|
- $layout = "
|
|
|
- <div class=\"annotation-cvterm-widget\">
|
|
|
- <div class=\"annotation-cvterm-widget-item\">" .
|
|
|
- drupal_render($element[$table_name . '--cvterm__cv_id--cv__cv_id']) . "
|
|
|
- </div>
|
|
|
- <div class=\"annotation-cvterm-widget-item\">" .
|
|
|
- drupal_render($element[$table_name . '--cvterm__name']) . "
|
|
|
- </div>
|
|
|
- <div class=\"annotation-cvterm-widget-item\">" .
|
|
|
- drupal_render($element[$table_name . '__is_not']) . "
|
|
|
- </div>
|
|
|
- </div>
|
|
|
- ";
|
|
|
+function chado_linker__cvterm_widget_form_ajax_callback($form, $form_state) {
|
|
|
|
|
|
- return $layout;
|
|
|
-}
|
|
|
+ $field_name = $form_state['triggering_element']['#parents'][0];
|
|
|
+ $delta = $form_state['triggering_element']['#parents'][2];
|
|
|
|
|
|
-/**
|
|
|
- * Loads the field values with appropriate data.
|
|
|
- *
|
|
|
- * This function is called by the tripal_chado_field_storage_load() for
|
|
|
- * each property managed by the field_chado_storage storage type. This is
|
|
|
- * an optional hook function that is only needed if the field has
|
|
|
- * multiple form elements.
|
|
|
- *
|
|
|
- * @param $field
|
|
|
- * @param $entity
|
|
|
- * @param $base_table
|
|
|
- * @param $record
|
|
|
- */
|
|
|
-function chado_linker__cvterm_load($field, $entity, $base_table, $record) {
|
|
|
-
|
|
|
- $field_name = $field['field_name'];
|
|
|
- $field_type = $field['type'];
|
|
|
- $field_table = $field['settings']['chado_table'];
|
|
|
- $field_column = $field['settings']['chado_column'];
|
|
|
-
|
|
|
- $matches = array();
|
|
|
- preg_match('/(.*?)__(\d+)/', $field_name, $matches);
|
|
|
- $table_name = $matches[1];
|
|
|
- $cv_id = $matches[2];
|
|
|
-
|
|
|
- // Get the FK that links to the base record.
|
|
|
- $schema = chado_get_schema($field_table);
|
|
|
- $pkey = $schema['primary key'][0];
|
|
|
- $fkey_lcolumn = key($schema['foreign keys'][$base_table]['columns']);
|
|
|
- $fkey_rcolumn = $schema['foreign keys'][$base_table]['columns'][$fkey_lcolumn];
|
|
|
-
|
|
|
- // Set some defaults for the empty record.
|
|
|
- $entity->{$field_name}['und'][0] = array(
|
|
|
- 'value' => '',
|
|
|
- $field_table . '__' . $fkey_lcolumn => '',
|
|
|
- $field_table . '__' . 'cvterm_id' => '',
|
|
|
- // The pub column is present in the cell_line_cvterm, feature_cvterm,
|
|
|
- // library_cvterm, phenotype_comparision_cvterm, phenotype_cvterm,
|
|
|
- // stock_cvterm, and stock_relationship_cvterm.
|
|
|
- $field_table . '__' . 'pub_id' => '',
|
|
|
- // The is_not column is present in feature_cvterm and stock_cvterm tables.
|
|
|
- $field_table . '__' . 'is_not' => '',
|
|
|
- // The rank column is present in the cell_line_cvterm, expression_cvterm,
|
|
|
- // feature_cvterm, phenotype_comparision_cvterm, phenotype_cvterm,
|
|
|
- // and stock_cvterm tables.
|
|
|
- $field_table . '__' . 'rank' => '',
|
|
|
- // The cvterm_type_id is present in the expression_cvterm table.
|
|
|
- $field_table . '--' . 'cvterm_type_id' => '',
|
|
|
- // The following field are to help link the cvterm.
|
|
|
- $field_table . '--' . 'cvterm__cv_id--cv__cv_id' => '',
|
|
|
- $field_table . '--' . 'cvterm__name' => '',
|
|
|
- );
|
|
|
-
|
|
|
- // Get the annotations associated with this base record for this fields type.
|
|
|
- $columns = array('*');
|
|
|
- $match = array(
|
|
|
- $fkey_lcolumn => $record->$fkey_rcolumn,
|
|
|
- 'cvterm_id' => array(
|
|
|
- 'cv_id' => $cv_id,
|
|
|
- ),
|
|
|
- );
|
|
|
- $options = array(
|
|
|
- 'return_array' => TRUE,
|
|
|
- 'order_by' => array('rank' => 'ASC')
|
|
|
- );
|
|
|
- $fcvterms = chado_select_record($field_table, $columns, $match, $options);
|
|
|
- for ($i = 0; $i < count($fcvterms); $i++) {
|
|
|
- $linker = $fcvterms[$i];
|
|
|
- $cvterm = chado_generate_var('cvterm', array('cvterm_id' => $linker->cvterm_id));
|
|
|
- $entity->{$field_name}['und'][$i] = array(
|
|
|
- 'value' => $linker->$pkey,
|
|
|
- $field_table . '__' . $fkey_lcolumn => $linker->$fkey_lcolumn,
|
|
|
- $field_table . '__' . 'cvterm_id' => $linker->cvterm_id,
|
|
|
- $field_table . '__' . 'pub_id' => property_exists($linker, 'pub_id') ? $linker->pub_id : '',
|
|
|
- $field_table . '__' . 'is_not' => property_exists($linker, 'is_not') ? $linker->is_not : '',
|
|
|
- $field_table . '__' . 'rank' => property_exists($linker, 'rank') ? $linker->rank : '',
|
|
|
- $field_table . '__' . 'cvterm_type_id' => property_exists($linker, 'cvterm_type_id') ? $linker->cvterm_type_id : '',
|
|
|
- $field_table . '--' . 'cvterm__cv_id--cv__cv_id' => $cvterm->cv_id->cv_id,
|
|
|
- $field_table . '--' . 'cvterm__name' => $cvterm->name,
|
|
|
- );
|
|
|
- }
|
|
|
-}
|
|
|
|
|
|
+ return $form[$field_name]['und'][$delta];
|
|
|
+}
|
Stephen Ficklin