field['field_name'];
$field_type = $this->field['type'];
$field_table = $this->field['settings']['chado_table'];
$field_column = $this->field['settings']['chado_column'];
$base_table = $this->field['settings']['base_table'];
// Get the FK column that links to the base table.
$base_table = $this->field['settings']['base_table'];
$schema = chado_get_schema($field_table);
$pkey = $schema['primary key'][0];
$fkeys = array_values($schema['foreign keys'][$base_table]['columns']);
$fkey = $fkeys[0];
// Get the instance settings. There are three options for how this widget
// will be displayed. Those are controlled in the instance settings
// of the field.
// Option 1: relationship types are limited to a specific vocabulary.
// Option 2: relationship types are limited to a subset of one vocabulary.
// Option 3: relationship types are limited to a predefined set.
$instance = $this->instance;
$settings = '';
$option1_vocabs = '';
$option2_parent = '';
$option2_vocab = '';
$option3_rtypes = '';
if (array_key_exists('relationships', $instance)) {
$settings = $instance['settings']['relationships'];
$option1_vocabs = $settings['option1_vocabs'];
$option2_vocab = $settings['option2_vocab'];
$option2_parent = $settings['option2_parent'];
$option3_rtypes = $settings['relationship_types'];
}
// For testing if there are selected vocabs for option1 we'll copy the
// contents in a special variable for later.
$option1_test = $option1_vocabs;
// Get the field defaults.
$record_id = '';
$subject_id = '';
$object_id = '';
$type_id = '';
$value = '';
$rank = '';
$subject_uniquename = '';
$object_uniquename = '';
$type = '';
// Handle special cases
$subject_id_key = 'subject_id';
$object_id_key = 'object_id';
if ($field_table == 'nd_reagent_relationship') {
$subject_id_key = 'subject_reagent_id';
$object_id_key = 'object_reagent_id';
}
else if ($field_table == 'project_relationship') {
$subject_id_key = 'subject_project_id';
$object_id_key = 'object_project_id';
}
// If the field already has a value then it will come through the $items
// array. This happens when editing an existing record.
if (count($items) > 0 and array_key_exists($delta, $items)) {
// Check for element values that correspond to fields in the Chado table.
$record_id = tripal_get_field_item_keyval($items, $delta, 'chado-' . $field_table . '__' . $pkey, $record_id);
$subject_id = tripal_get_field_item_keyval($items, $delta, 'chado-' . $field_table . '__' . $subject_id_key, $subject_id);
$object_id = tripal_get_field_item_keyval($items, $delta, 'chado-' . $field_table . '__' . $object_id_key, $object_id);
$type_id = tripal_get_field_item_keyval($items, $delta, 'chado-' . $field_table . '__type_id', $type_id);
// Not all Chado tables have a value and rank. So we'll only get
// those if applicable.
if (array_key_exists('value', $schema['fields'])) {
$value = tripal_get_field_item_keyval($items, $delta, 'chado-' . $field_table . '__value', $value);
}
if (array_key_exists('rank', $schema['fields'])) {
$rank = tripal_get_field_item_keyval($items, $delta, 'chado-' . $field_table . '__rank', $rank);
}
// Get element values added to help support insert/updates.
$object_uniquename = tripal_get_field_item_keyval($items, $delta, 'object_name', $object_uniquename);
$subject_uniquename = tripal_get_field_item_keyval($items, $delta, 'subject_name', $subject_uniquename);
$type = tripal_get_field_item_keyval($items, $delta, 'type_name', $type);
}
// Check $form_state['values'] to see if an AJAX call set the values.
if (array_key_exists('values', $form_state) and array_key_exists($delta, $form_state['values'])) {
$record_id = $form_state['values'][$field_name]['und'][$delta]['chado-' . $field_table . '__' . $pkey];
$subject_id = $form_state['values'][$field_name]['und'][$delta]['chado-' . $field_table . '__' . $subject_id_key];
$object_id = $form_state['values'][$field_name]['und'][$delta]['chado-' . $field_table . '__' . $object_id_key];
$type_id = $form_state['values'][$field_name]['und'][$delta]['chado-' . $field_table . '__type_id'];
if (array_key_exists('value', $schema['fields'])) {
$value = $form_state['values'][$field_name]['und'][$delta]['chado-' . $field_table . '__value'];
}
if (array_key_exists('rank', $schema['fields'])) {
$rank = $form_state['values'][$field_name]['und'][$delta]['chado-' . $field_table . '__rank'];
}
$object_uniquename = $form_state['values'][$field_name]['und'][$delta]['object_name'];
$subject_uniquename = $form_state['values'][$field_name]['und'][$delta]['subject_name'];
$type = $form_state['values'][$field_name]['und'][$delta]['type_name'];
}
//$widget['#element_validate'] = array('chado_linker__relationship_validate');
$widget['#theme'] = 'chado_linker__relationship_widget';
$widget['#prefix'] = "";
$widget['#suffix'] = "";
$widget['value'] = array(
'#type' => 'value',
'#value' => array_key_exists($delta, $items) ? $items[$delta]['value'] : '',
);
$widget['chado-' . $field_table . '__' . $pkey] = array(
'#type' => 'value',
'#default_value' => $record_id,
);
$widget['chado-' . $field_table . '__' . $subject_id_key] = array(
'#type' => 'value',
'#default_value' => $subject_id,
);
$widget['chado-' . $field_table . '__type_id'] = array(
'#type' => 'value',
'#default_value' => $type_id,
);
$widget['chado-' . $field_table . '__' . $object_id_key] = array(
'#type' => 'value',
'#default_value' => $object_id,
);
if (array_key_exists('value', $schema['fields'])) {
$widget['chado-' . $field_table . '__value'] = array(
'#type' => 'value',
'#default_value' => $value,
);
}
if (array_key_exists('rank', $schema['fields'])) {
$widget['chado-' . $field_table . '__rank'] = array(
'#type' => 'value',
'#default_value' => $rank,
);
}
$widget['subject_name'] = array(
'#type' => 'textfield',
'#title' => t('Subject'),
'#default_value' => $subject_uniquename,
'#required' => $element['#required'],
'#maxlength' => array_key_exists('length', $schema['fields'][$subject_id_key]) ? $schema['fields'][$subject_id_key]['length'] : 255,
'#size' => 35,
'#autocomplete_path' => "admin/tripal/storage/chado/auto_name/$base_table",
);
// Getting default values for the relationship type element.
$default_voc = '';
if (isset($form_state['field'][$field_name]['und']['instance']['default_value'][0]['vocabulary'])) {
$default_voc = $form_state['field'][$field_name]['und']['instance']['default_value'][0]['vocabulary'];
}
$default_term = '';
if (isset($form_state['field'][$field_name]['und']['instance']['default_value'][0]['type_name'])) {
$default_term = $form_state['field'][$field_name]['und']['instance']['default_value'][0]['type_name'];
}
$default_type_id = $type_id;
if (!$type_id && isset($form_state['field'][$field_name]['und']['instance']['default_value'][0]['type_id'])) {
$default_type_id = $form_state['field'][$field_name]['und']['instance']['default_value'][0]['type_id'];
}
// Option 3: Custom list of Relationship Types
$rtype_options = array();
$rtype_options[] = 'Select a Type';
if ($option3_rtypes) {
$rtypes = explode(PHP_EOL, $option3_rtypes);
foreach($rtypes AS $rtype) {
// Ignore empty lines
if (trim($rtype) == '') {
continue;
}
$term = tripal_get_cvterm(array('name' => trim($rtype)));
// Try to get term with vocabulary specified
if (!$term) {
$tmp = explode('|', trim($rtype), 2);
$cv = tripal_get_cv(array('name' => trim($tmp[0])));
$rtype = trim($tmp[1]);
$term = tripal_get_cvterm(array('name' => $rtype, 'cv_id' => $cv->cv_id));
}
$rtype_options[$term->cvterm_id] = $term->name;
}
$widget['type_id'] = array(
'#type' => 'select',
'#title' => t('Relationship Type'),
'#options' => $rtype_options,
'#default_value' => $default_type_id,
);
if ($type_id && !key_exists($type_id, $rtype_options)) {
form_set_error($this->field['field_name'] . '[' . $langcode . '][' . $delta . '][type_id]', 'Illegal option detected for Relationship Type. Please contact site administrator to fix the problem');
}
}
// Option 2: Child terms of a selected cvterm
else if ($option2_vocab) {
$values = array(
'cv_id' => $option2_vocab,
'name' => $option2_parent
);
$parent_term = tripal_get_cvterm($values);
// If the term wasn't found then see if it's a synonym.
if(!$parent_term) {
$values = array(
'synonym' => array(
'name' => trim($option2_parent),
)
);
$synonym = tripal_get_cvterm($values);
if ($synonym && $synonym->cv_id->cv_id == $option2_vocab) {
$parent_term = $synonym;
}
}
// Get the child terms of the parent term found above.
$sql = "
SELECT subject_id,
(SELECT name from {cvterm} where cvterm_id = subject_id) AS name
FROM {cvtermpath}
WHERE
object_id = :parent_cvterm_id AND
cv_id = :parent_cv_id
ORDER BY name
";
$args = array(
':parent_cvterm_id' => $parent_term->cvterm_id,
':parent_cv_id' => $parent_term->cv_id->cv_id
);
$results = chado_query($sql, $args);
while($child = $results->fetchObject()) {
$rtype_options[$child->subject_id] = $child->name;
}
$widget['type_id'] = array(
'#type' => 'select',
'#title' => t('Relationship Type'),
'#options' => $rtype_options,
'#default_value' => $default_type_id,
);
if ($type_id && !key_exists($type_id, $rtype_options)) {
form_set_error($this->field['field_name'] . '[' . $langcode . '][' . $delta . '][type_id]', 'Illegal option detected for Relationship Type. Please contact site administrator to fix the problem');
}
}
// Option 1: All terms of selected vocabularies
else if ($option1_test && array_pop($option1_test)) {
$sql = "SELECT cvterm_id, name FROM {cvterm} WHERE cv_id IN (:cv_id) ORDER BY name";
$results = chado_query($sql, array(':cv_id' => $option1_vocabs));
while ($obj = $results->fetchObject()) {
$rtype_options[$obj->cvterm_id] = $obj->name;
}
$widget['type_id'] = array(
'#type' => 'select',
'#title' => t('Relationship Type'),
'#options' => $rtype_options,
'#default_value' => $default_type_id,
);
if ($type_id && !key_exists($type_id, $rtype_options)) {
form_set_error($this->field['field_name'] . '[' . $langcode . '][' . $delta . '][type_id]', 'Illegal option detected for Relationship Type. Please contact site administrator to fix the problem');
}
}
// Default option:
else {
// Set up available cvterms for selection
$vocs = array(0 => 'Select a vocabulary');
$vocs = tripal_get_cv_select_options();
$cv_id = isset($form_state['values'][$field_name]['und'][0]['vocabulary']) ? $form_state['values'][$field_name]['und'][0]['vocabulary'] : 0;
// Try getting the cv_id from cvterm for existing records
if (!$cv_id && $type_id) {
$cvterm = tripal_get_cvterm(array('cvterm_id' => $type_id));
if (isset($cvterm->cv_id->cv_id)) {
$cv_id = $cvterm->cv_id->cv_id;
$default_term = $cvterm->name;
}
}
if (!$cv_id) {
$cv_id = $default_voc;
}
$widget['vocabulary'] = array(
'#type' => 'select',
'#title' => t('Vocabulary'),
'#options' => $vocs,
'#required' => $element['#required'],
'#default_value' => $cv_id,
'#ajax' => array(
'callback' => "chado_linker__relationship_widget_form_ajax_callback",
'wrapper' => "$field_table-$delta",
'effect' => 'fade',
'method' => 'replace'
),
);
if ($cv_id) {
$options = array();
$widget['type_name'] = array(
'#type' => 'textfield',
'#title' => t('Relationship Type'),
'#size' => 15,
'#default_value' => $default_term,
'#autocomplete_path' => "admin/tripal/storage/chado/auto_name/cvterm/$cv_id"
);
}
}
$widget['object_name'] = array(
'#type' => 'textfield',
'#title' => t('Object'),
'#default_value' => $object_uniquename,
'#required' => $element['#required'],
'#maxlength' => array_key_exists('length', $schema['fields'][$object_id_key]) ? $schema['fields'][$object_id_key]['length'] : 255,
'#size' => 35,
'#autocomplete_path' => "admin/tripal/storage/chado/auto_name/$base_table",
);
}
/**
* Performs validation of the widgetForm.
*
* Use this validate to ensure that form values are entered correctly. Note
* this is different from the validate() function which ensures that the
* field data meets expectations.
*
* @param $form
* @param $form_state
*/
public function validate($form, &$form_state, $entity_type, $entity, $langcode, $delta) {
$field_name = $this->field['field_name'];
$field_type = $this->field['type'];
$field_table = $this->field['settings']['chado_table'];
$field_column = $this->field['settings']['chado_column'];
$base_table = $this->field['settings']['base_table'];
$schema = chado_get_schema($field_table);
$fkeys = $schema['foreign keys'];
// Handle special cases
$subject_id_key = 'subject_id';
$object_id_key = 'object_id';
if ($field_table == 'nd_reagent_relationship') {
$subject_id_key = 'subject_reagent_id';
$object_id_key = 'object_reagent_id';
}
else if ($field_table == 'project_relationship') {
$subject_id_key = 'subject_project_id';
$object_id_key = 'object_project_id';
}
foreach ($items as $delta => $item) {
$subject_id = $item['chado' . $field_table . '__' . $subject_id_key];
$object_id = $item['chado' . $field_table . '__' . $object_id_key];
$type_id = $item['chado' . $field_table . '__type_id'];
$type_id = isset($item['type_id']) ? $item['chado' . $field_table . '__type_id'] : $type_id;
$type_name = isset($item['type_name']) ? $item['type_name'] : '';
$subject_name = $item['subject_name'];
$object_name = $item['object_name'];
// If the row is empty then just continue, there's nothing to validate.
if (!$type_id and !$type_name and !$subject_name and !$object_name) {
continue;
}
// Make sure we have values for all of the fields.
$form_error = FALSE;
if (!$type_name && !$type_id) {
$errors[$this->field['field_name']][$langcode][$delta][] = array(
'error' => 'chado_linker__relationship',
'message' => t("Please provide the type of relationship."),
);
}
if ($entity and !$subject_name) {
$errors[$this->field['field_name']][$langcode][$delta][] = array(
'error' => 'chado_linker__relationship',
'message' => t("Please provide the subject of the relationship."),
);
}
if ($entity and !$object_name) {
$errors[$this->field['field_name']][$langcode][$delta][] = array(
'error' => 'chado_linker__relationship',
'message' => t("Please provide the object of the relationship."),
);
}
if ($form_error) {
continue;
}
// Before submitting this form we need to make sure that our subject_id and
// object_ids are real records. There are two ways to get the record, either
// just with the text value or with an [id: \d+] string embedded. If the
// later we will pull it out.
$subject_id = '';
$fkey_rcolumn = $fkeys[$base_table]['columns'][$subject_id_key];
$matches = array();
if ($entity) {
if(preg_match('/\[id: (\d+)\]/', $subject_name, $matches)) {
$subject_id = $matches[1];
$values = array($fkey_rcolumn => $subject_id);
$subject = chado_select_record($base_table, array($fkey_rcolumn), $values);
if (count($subject) == 0) {
$errors[$this->field['field_name']][$langcode][$delta][] = array(
'error' => 'chado_linker__relationship',
'message' => t("The subject record cannot be found using the specified id (e.g. [id: xx])."),
);
}
}
else {
$values = array('uniquename' => $subject_name);
$subject = chado_select_record($base_table, array($fkey_rcolumn), $values);
if (count($subject) == 0) {
$errors[$this->field['field_name']][$langcode][$delta][] = array(
'error' => 'chado_linker__relationship',
'message' => t("The subject record cannot be found. Please check spelling."),
);
}
elseif (count($subject) > 1) {
$errors[$this->field['field_name']][$langcode][$delta][] = array(
'error' => 'chado_linker__relationship',
'message' => t("The subject is not unique and therefore the relationship cannot be made."),
);
}
}
}
// Now check for a matching object.
$object_id = '';
$fkey_rcolumn = $fkeys[$base_table]['columns'][$object_id_key];
$matches = array();
if ($entity) {
if (preg_match('/\[id: (\d+)\]/', $object_name, $matches)) {
$object_id = $matches[1];
$values = array($fkey_rcolumn => $object_id);
$object = chado_select_record($base_table, array($fkey_rcolumn), $values);
if (count($subject) == 0) {
$errors[$this->field['field_name']][$langcode][$delta][] = array(
'error' => 'chado_linker__relationship',
'message' => t("The object record cannot be found using the specified id (e.g. [id: xx])."),
);
}
}
else {
$values = array('uniquename' => $object_name);
$object = chado_select_record($base_table, array($fkey_rcolumn), $values);
if (count($object) == 0) {
$errors[$this->field['field_name']][$langcode][$delta][] = array(
'error' => 'chado_linker__relationship',
'message' => t("The object record cannot be found. Please check spelling."),
);;
}
elseif (count($object) > 1) {
$errors[$this->field['field_name']][$langcode][$delta][] = array(
'error' => 'chado_linker__relationship',
'message' => t("The object is not unique and therefore the relationship cannot be made."),
);
}
}
}
// Make sure that either our object or our subject refers to the base record.
if ($entity) {
$chado_record_id = $entity->chado_record_id;
if ($object_id != $chado_record_id and $subject_id != $chado_record_id) {
$errors[$this->field['field_name']][$langcode][$delta][] = array(
'error' => 'chado_linker__relationship',
'message' => t("Either the subject or the object in the relationship must refer to this record."),
);
}
// Make sure that the object and subject are not both the same thing.
if ($object_id == $subject_id) {
$errors[$this->field['field_name']][$langcode][$delta][] = array(
'error' => 'chado_linker__relationship',
'message' => t("The subject and the object in the relationship cannot both refer to the same record."),
);
}
}
}
}
/**
*
* @see TripalFieldWidget::submit()
*/
public function submit($form, &$form_state, $entity_type, $entity, $langcode, $delta) {
$field_name = $this->field['field_name'];
$field_type = $this->field['type'];
$field_table = $this->field['settings']['chado_table'];
$field_column = $this->field['settings']['chado_column'];
$base_table = $this->field['settings']['base_table'];
$chado_record_id = $entity->chado_record_id;
$schema = chado_get_schema($field_table);
$fkeys = $schema['foreign keys'];
// Handle special cases
$subject_id_key = 'subject_id';
$object_id_key = 'object_id';
if ($field_table == 'nd_reagent_relationship') {
$subject_id_key = 'subject_reagent_id';
$object_id_key = 'object_reagent_id';
}
else if ($field_table == 'project_relationship') {
$subject_id_key = 'subject_project_id';
$object_id_key = 'object_project_id';
}
$type_name = array_key_exists('type_name', $item) ? $item['type_name'] : '';
$subject_id = $form_state['values'][$field_name][$langcode][$delta]['chado' . $field_table . '__' . $subject_id_key];
$object_id = $form_state['values'][$field_name][$langcode][$delta]['chado' . $field_table . '__' . $object_id_key];
$type_id = $form_state['values'][$field_name][$langcode][$delta]['chado' . $field_table . '__type_id'];
$subject_name = $form_state['values'][$field_name][$langcode][$delta]['subject_name'];
$object_name = $form_state['values'][$field_name][$langcode][$delta]['object_name'];
// If the row is empty then skip this one, there's nothing to validate.
if (!($type_id or !$type_name) and !$subject_name and !$object_name) {
return;
}
// Get the subject ID.
$subject_id = '';
$fkey_rcolumn = $fkeys[$base_table]['columns']['subject_id'];
$matches = array();
if (preg_match('/\[id: (\d+)\]/', $subject_name, $matches)) {
$subject_id = $matches[1];
}
else {
$values = array('uniquename' => $subject_name);
$subject = chado_select_record($base_table, array($fkey_rcolumn), $values);
$subject_id = $subject[0]->$fkey_rcolumn;
}
// Get the object ID.
$object_id = '';
$fkey_rcolumn = $fkeys[$base_table]['columns']['object_id'];
$matches = array();
if (preg_match('/\[id: (\d+)\]/', $object_name, $matches)) {
$object_id = $matches[1];
}
else {
$values = array('uniquename' => $object_name);
$object = chado_select_record($base_table, array($fkey_rcolumn), $values);
$object_id = $object[0]->$fkey_rcolumn;
}
// Set the IDs according to the values that were determined above.
$form_state['values'][$field_name][$langcode][$delta]['chado' . $field_table . '__' . $subject_id_key] = $subject_id;
$form_state['values'][$field_name][$langcode][$delta]['chado' . $field_table . '__' . $object_id_key] = $object_id;
$form_state['values'][$field_name][$langcode][$delta]['chado' . $field_table . '__type_id'] = $type_name;
$form_state['values'][$field_name][$langcode][$delta]['chado' . $field_table . '__rank'] = $item['_weight'];
}
}
/**
* Theme function for the chado_linker__relationship_widget.
*/
function theme_chado_linker__relationship_widget($variables) {
$element = $variables['element'];
$field_name = $element['#field_name'];
$field = field_info_field($field_name);
$field_type = $field['type'];
$field_table = $field['settings']['chado_table'];
$field_column = $field['settings']['chado_column'];
$layout = "
";
return $layout;
}
function theme_chado_linker__relationship_instance_settings ($variables) {
$element = $variables['element'];
$option1 = $element['option1'];
$option1_vocabs = $element['option1_vocabs'];
$option2 = $element['option2'];
$option2_vocab = $element['option2_vocab'];
$option2_parent = $element['option2_parent'];
$option3 = $element['option3'];
$rtype = $element['relationship_types'];
$layout = drupal_render($option1);
$layout .= drupal_render($option1_vocabs);
$layout .=
drupal_render($option2) .
"" .
"
" .
drupal_render($option2_vocab) .
"
" .
"
" .
drupal_render($option2_parent) .
"
" .
"