t('Relationships'),
'description' => t('Relationships between records.'),
'default_widget' => 'chado_linker__relationship_widget',
'default_formatter' => 'chado_linker__relationship_formatter',
'settings' => array(),
'storage' => array(
'type' => 'field_chado_storage',
'module' => 'tripal_chado',
'active' => TRUE
),
);
}
/**
* @see TripalField::can_attach()
*/
protected function setCanAttach() {
$table_name = $this->details['chado_table'];
$type_table = $this->details['chado_type_table'];
$type_field = $this->details['chado_type_column'];
$cv_id = $this->details['chado_cv_id'];
$cvterm_id = $this->details['chado_cvterm_id'];
// If the linker table does not exists then we don't want to add attach.
$rel_table = $table_name . '_relationship';
if (chado_table_exists($rel_table)) {
$this->can_attach = TRUE;
return;
}
$this->can_attach = FALSE;
}
/**
* @see TripalField::setFieldName()
*/
protected function setFieldName() {
$table_name = $this->details['chado_table'];
$type_table = $this->details['chado_type_table'];
$type_field = $this->details['chado_type_column'];
$cv_id = $this->details['chado_cv_id'];
$cvterm_id = $this->details['chado_cvterm_id'];
$this->field_name = $table_name . '_relationship';
}
/**
* @see TripalField::create_info()
*/
function createInfo() {
if (!$this->can_attach) {
return;
}
$table_name = $this->details['chado_table'];
$type_table = $this->details['chado_type_table'];
$type_field = $this->details['chado_type_column'];
$cv_id = $this->details['chado_cv_id'];
$cvterm_id = $this->details['chado_cvterm_id'];
$rel_table = $table_name . '_relationship';
$schema = chado_get_schema($rel_table);
$pkey = $schema['primary key'][0];
return array(
'field_name' => $this->field_name,
'type' => 'chado_linker__relationship',
'cardinality' => FIELD_CARDINALITY_UNLIMITED,
'locked' => FALSE,
'storage' => array(
'type' => 'field_chado_storage',
),
'settings' => array(
'chado_table' => $rel_table,
'chado_column' => $pkey,
'base_table' => $table_name,
'semantic_web' => 'SBO:0000374',
),
);
}
/**
* @see TripalField::createInstanceInfo()
*/
function createInstanceInfo() {
if (!$this->can_attach) {
return;
}
$table_name = $this->details['chado_table'];
$type_table = $this->details['chado_type_table'];
$type_field = $this->details['chado_type_column'];
$cv_id = $this->details['chado_cv_id'];
$cvterm_id = $this->details['chado_cvterm_id'];
return array(
'field_name' => $this->field_name,
'entity_type' => $this->entity_type,
'bundle' => $this->bundle->name,
'label' => 'Relationships',
'description' => 'Other records with relationships to this record.',
'required' => FALSE,
'settings' => array(
'auto_attach' => FALSE,
),
'widget' => array(
'type' => 'chado_linker__relationship_widget',
'settings' => array(
'display_label' => 1,
),
),
'display' => array(
'default' => array(
'label' => 'above',
'type' => 'chado_linker__relationship_formatter',
'settings' => array(),
),
),
);
}
/**
* @see TripalField::widgetInfo()
*/
public static function widgetInfo() {
return array(
'chado_linker__relationship_widget' => array(
'label' => t('Relationship Settings'),
'field types' => array('chado_linker__relationship')
),
);
}
/**
* @see TripalField::formatterInfo()
*/
static function formatterInfo() {
return array(
'chado_linker__relationship_formatter' => array(
'label' => t('Relationships'),
'field types' => array('chado_linker__relationship'),
'settings' => array(
),
),
);
}
/**
* @see TripalField::formatterView()
*/
static function formatterView(&$element, $entity_type, $entity,
$field, $instance, $langcode, $items, $display) {
// Get the settings
$settings = $display['settings'];
$rows = array();
$headers = array('Subject' ,'Type', 'Object');
$headers = array('Relationship');
foreach ($items as $delta => $item) {
if (!$item['value']) {
continue;
}
$subject_name = $item['value']['subject']['name'];
$subject_type = $item['value']['subject']['type'];
$object_name = $item['value']['object']['name'];
$object_type = $item['value']['object']['type'];
$phrase = $item['value']['phrase'];
// Handle some special cases.
// For mRNA objects we don't want to show the CDS, exons, 5' UTR, etc.
// we want to show the parent gene and the protein.
if ($object_type == 'mRNA' and ($subject_type != 'polypeptide')) {
continue;
}
if ($subject_type == 'mRNA' and ($object_type != 'gene')) {
continue;
}
$phrase = preg_replace("/$subject_type/", "$subject_type", $phrase);
$phrase = preg_replace("/$object_type/", "$object_type", $phrase);
if (array_key_exists('entity', $item['value']['object'])) {
list($entity_type, $object_entity_id) = explode(':', $item['value']['object']['entity']);
if ($object_entity_id != $entity->id) {
$link = l($object_name, 'bio_data/' . $object_entity_id);
$phrase = preg_replace("/$object_name/", $link, $phrase);
}
}
if (array_key_exists('entity', $item['value']['subject'])) {
list($entity_type, $subject_entity_id) = explode(':', $item['value']['subject']['entity']);
if ($subject_entity_id != $entity->id) {
$link = l($subject_name, 'bio_data/' . $subject_entity_id);
$phrase = preg_replace("/$subject_name/", $link, $phrase);
}
}
$rows[] = array($phrase);
}
// the $table array contains the headers and rows array as well as other
// options for controlling the display of the table. Additional
// documentation can be found here:
// https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
$table = array(
'header' => $headers,
'rows' => $rows,
'attributes' => array(
'id' => 'chado-linker--relationship-table',
'class' => 'tripal-data-table'
),
'sticky' => FALSE,
'caption' => '',
'colgroups' => array(),
'empty' => 'There are no relationships',
);
// once we have our table array structure defined, we call Drupal's theme_table()
// function to generate the table.
if (count($items) > 0) {
$element[0] = array(
'#type' => 'markup',
'#markup' => theme_table($table),
);
}
}
/**
* @see TripalField::widgetForm()
*/
static function widgetForm(&$widget, &$form, &$form_state, $field, $instance,
$langcode, $items, $delta, $element) {
$field_name = $field['field_name'];
$field_type = $field['type'];
$field_table = $field['settings']['chado_table'];
$field_column = $field['settings']['chado_column'];
// Get the FK column that links to the base table.
$chado_table = $field['settings']['chado_table'];
$base_table = $field['settings']['base_table'];
$schema = chado_get_schema($chado_table);
$pkey = $schema['primary key'][0];
$fkeys = array_values($schema['foreign keys'][$base_table]['columns']);
$fkey = $fkeys[0];
// Get the field defaults.
$record_id = '';
$fkey_value = $element['#entity']->chado_record_id;
$subject_id = '';
$subject_uniquename = '';
$type_id = '';
$type = '';
$object_id = '';
$object_uniquename = '';
$value = '';
$rank = '';
// If the field already has a value then it will come through the $items
// array. This happens when editing an existing record.
if (array_key_exists($delta, $items)) {
$record_id = $items[$delta][$field_table . '__' . $pkey];
$subject_id = $items[$delta][$field_table . '__subject_id'];
$type_id = $items[$delta][$field_table . '__type_id'];
$object_id = $items[$delta][$field_table . '__object_id'];
if (array_key_exists('value', $schema['fields'])) {
$value = $items[$delta][$field_table . '__value'];
}
if (array_key_exists('rank', $schema['fields'])) {
$rank = $items[$delta][$field_table . '__rank'];
}
$object_uniquename = $items[$delta]['object_name'];
$subject_uniquename = $items[$delta]['subject_name'];
$type = $items[$delta]['type_name'];
}
// 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'])) {
$record_id = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_table . '__' . $pkey);
$subject_id = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_table . '__subject_id');
$subject_uniquename = tripal_chado_get_field_form_values($field_name, $form_state, $delta, 'subject_name');
$type_id = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_table . '__type_id');
$type = tripal_chado_get_field_form_values($field_name, $form_state, $delta, 'type_name');
$object_id = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_table . '__object_id');
$object_uniquename = tripal_chado_get_field_form_values($field_name, $form_state, $delta, 'object_name');
$value = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_table . '__value');
$rank = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_table . '__rank');
}
$widget['#table_name'] = $chado_table;
$widget['#fkeys'] = $schema['foreign keys'];
$widget['#base_table'] = $base_table;
$widget['#chado_record_id'] = $form['#entity']->chado_record_id;
//$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'] : '',
);
$widget[$field_table . '__' . $pkey] = array(
'#type' => 'value',
'#default_value' => $record_id,
);
$widget[$field_table . '__subject_id'] = array(
'#type' => 'value',
'#default_value' => $subject_id,
);
$widget[$field_table . '__type_id'] = array(
'#type' => 'value',
'#default_value' => $type_id,
);
$widget[$field_table . '__object_id'] = array(
'#type' => 'value',
'#default_value' => $object_id,
);
if (array_key_exists('value', $schema['fields'])) {
$widget[$field_table . '__value'] = array(
'#type' => 'value',
'#default_value' => $value,
);
}
if (array_key_exists('rank', $schema['fields'])) {
$widget[$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']) ? $schema['fields']['subject_id']['length'] : 255,
'#size' => 35,
'#autocomplete_path' => "admin/tripal/storage/chado/auto_name/$base_table",
);
$default_cv = tripal_get_default_cv($field_table, 'type_id');
$options = array();
if (!$default_cv) {
$msg = t('There is no default vocabulary set for the relationship types.');
if (module_exists('tripal_chado')) {
$msg .= t(' Please set the default vocabulary at Tripal > Data Storage > Chado > Vocabulary Defaults.', array('@url' => url('/admin/tripal/storage/chado/vocab')));
}
drupal_set_message($msg, 'warning');
}
else {
$options = tripal_get_cvterm_select_options($default_cv->cv_id, TRUE);
}
$widget['type_name'] = array(
'#type' => 'select',
'#title' => t('Type'),
'#options' => $options,
'#required' => $element['#required'],
'#default_value' => $type_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']) ? $schema['fields']['object_id']['length'] : 255,
'#size' => 35,
'#autocomplete_path' => "admin/tripal/storage/chado/auto_name/$base_table",
);
}
/**
* @see TripalField::validate()
*/
function validate($entity_type, $entity, $field, $instance, $langcode, $items, &$errors) {
$field_name = $field['field_name'];
$field_type = $field['type'];
$field_table = $field['settings']['chado_table'];
$field_column = $field['settings']['chado_column'];
$base_table = $field['settings']['base_table'];
$chado_record_id = $entity->chado_record_id;
$schema = chado_get_schema($field_table);
$fkeys = $schema['foreign keys'];
foreach ($items as $delta => $item) {
$subject_id = $item[$field_table . '__subject_id'];
$object_id = $item[ $field_table . '__object_id'];
$type_id = $item[$field_table . '__type_id'];
$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_name and !$subject_name and !$object_name) {
continue;
}
// Make sure we have values for all of the fields.
$form_error = FALSE;
if (!$type_name) {
$errors[$field['field_name']][$langcode][$delta][] = array(
'error' => 'chado_linker__relationship',
'message' => t("Please provide the type of relationship."),
);
}
if (!$subject_name) {
$errors[$field['field_name']][$langcode][$delta][] = array(
'error' => 'chado_linker__relationship',
'message' => t("Please provide the subject of the relationship."),
);
}
if (!$object_name) {
$errors[$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 values. There are two ways to get the value, 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'];
$matches = array();
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) {
$errors[$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) {
$errors[$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) {
$errors[$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'];
$matches = array();
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) {
$errors[$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) {
$errors[$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) {
$errors[$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 ($object_id != $chado_record_id and $subject_id != $chado_record_id) {
$errors[$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) {
$errors[$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 TripalField::submit()
*/
public function submit($entity_type, $entity, $field, $instance, $langcode,
&$items, $form, &$form_state) {
$field_name = $field['field_name'];
$field_type = $field['type'];
$field_table = $field['settings']['chado_table'];
$field_column = $field['settings']['chado_column'];
$base_table = $field['settings']['base_table'];
$chado_record_id = $entity->chado_record_id;
$schema = chado_get_schema($field_table);
$fkeys = $schema['foreign keys'];
foreach ($items as $delta => $item) {
$subject_id = $item[$field_table . '__subject_id'];
$object_id = $item[ $field_table . '__object_id'];
$type_id = $item[$field_table . '__type_id'];
$type_name = $item['type_name'];
$subject_name = $item['subject_name'];
$object_name = $item['object_name'];
// If the row is empty then skip this one, there's nothing to validate.
if (!$type_name and !$subject_name and !$object_name) {
continue;
}
// 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.
$items[$delta][$field_table . '__subject_id'] = $subject_id;
$items[$delta][$field_table . '__object_id'] = $object_id;
$items[$delta][$field_table . '__type_id'] = $type_name;
$items[$delta][$field_table . '__rank'] = $item['_weight'];
}
}
/**
* @see TripalField::load()
*/
static function load($field, $entity, $details = array()) {
$settings = $field['settings'];
$record = $details['record'];
$field_name = $field['field_name'];
$field_type = $field['type'];
$field_table = $field['settings']['chado_table'];
$field_column = $field['settings']['chado_column'];
$base_table = $field['settings']['base_table'];
// Get the PKey for this table
$schema = chado_get_schema($field_table);
$pkey = $schema['primary key'][0];
// Get the Pkeys for the subject and object tables
$subject_fkey_table = '';
$object_fkey_table = '';
$fkeys = $schema['foreign keys'];
foreach ($fkeys as $fktable => $details) {
foreach ($details['columns'] as $fkey_lcolumn => $fkey_rcolumn) {
if ($fkey_lcolumn == 'subject_id') {
$subject_fkey_table = $fktable;
}
if ($fkey_lcolumn == 'object_id') {
$object_fkey_table = $fktable;
}
}
}
$subject_schema = chado_get_schema($subject_fkey_table);
$object_schema = chado_get_schema($object_fkey_table);
$subject_pkey = $subject_schema['primary key'][0];
$object_pkey = $object_schema['primary key'][0];
// Get the FK that links to the base record.
$schema = chado_get_schema($field_table);
$fkey_lcolumn = key($schema['foreign keys'][$base_table]['columns']);
$fkey_rcolumn = $schema['foreign keys'][$base_table]['columns'][$fkey_lcolumn];
// Set some defaults for the empty record.
// TODO: don't hardcode the uniquename as all tables won't have that.
$entity->{$field_name}['und'][0] = array(
'value' => array(),
$field_table . '__' . $pkey => '',
$field_table . '__subject_id' => '',
$field_table . '__object_id' => '',
$field_table . '__type_id' => '',
// These elements don't need to follow the naming scheme above
// becasue we don't need the chado_field_storage to try and
// save these values.
'object_name' => '',
'subject_name' => '',
'type_name' => '',
);
// If the table has rank and value fields then add those to the default
// value array.
if (array_key_exists('value', $schema['fields'])) {
$entity->{$field_name}['und'][0][$field_table . '__value'] = '';
}
if (array_key_exists('rank', $schema['fields'])) {
$entity->{$field_name}['und'][0][$field_table . '__rank'] = '';
}
// If we have no record then just return.
if (!$record) {
return;
}
// Expand the object to include the relationships.
$options = array(
'return_array' => 1,
// we don't want to fully recurse we only need information about the
// relationship type and the object and subject
'include_fk' => array(
'type_id' => 1,
'object_id' => array(
'type_id' => 1,
),
'subject_id' => array(
'type_id' => 1,
),
),
);
$rel_table = $base_table . '_relationship';
$schema = chado_get_schema($rel_table);
if (array_key_exists('rank', $schema['fields'])) {
$options['order_by'] = array('rank' => 'ASC');
}
$record = chado_expand_var($record, 'table', $rel_table, $options);
if (!$record->$rel_table) {
return;
}
$srelationships = $record->$rel_table->subject_id;
$orelationships = $record->$rel_table->object_id;
$i = 0;
if ($orelationships) {
foreach ($orelationships as $relationship) {
$rel_acc = $relationship->type_id->dbxref_id->db_id->name . ':' . $relationship->type_id->dbxref_id->accession;
$rel_type = $relationship->type_id->name;
$verb = self::get_rel_verb($rel_type);
$subject_name = $relationship->subject_id->name;
$subject_type = $relationship->subject_id->type_id->name;
$object_name = $relationship->object_id->name;
$object_type = $relationship->object_id->type_id->name;
$entity->{$field_name}['und'][$i]['value'] = array(
'type' => $relationship->type_id->name,
'subject' => array(
'type' => $subject_type,
'name' => $subject_name,
),
'type' => $relationship->type_id->name,
'object' => array(
'type' => $object_type,
'name' => $object_name,
'entity' => 'TripalEntity:' . $entity->id,
)
);
if (property_exists($relationship->subject_id, 'uniquename')) {
$entity->{$field_name}['und'][$i]['value']['subject']['identifier'] = $relationship->subject_id->uniquename;;
}
if (property_exists($relationship->object_id, 'uniquename')) {
$entity->{$field_name}['und'][$i]['value']['object']['identifier'] = $relationship->object_id->uniquename;
}
if (property_exists($relationship->subject_id, 'entity_id')) {
$entity_id = $relationship->subject_id->entity_id;
$entity->{$field_name}['und'][$i]['value']['subject']['entity'] = 'TripalEntity:' . $entity_id;
}
$rel_type_clean = lcfirst(preg_replace('/_/', ' ', $rel_type));
$entity->{$field_name}['und'][$i]['value']['phrase'] = 'The ' . $subject_type . ', ' .
$subject_name . ', ' . $verb . ' ' . $rel_type_clean . ' this ' .
$object_type . '.';
$entity->{$field_name}['und'][$i]['semantic_web'] = array(
'type' => $rel_acc,
'subject' => $relationship->subject_id->type_id->dbxref_id->db_id->name . ':' . $relationship->subject_id->type_id->dbxref_id->accession,
'object' => $relationship->object_id->type_id->dbxref_id->db_id->name . ':' . $relationship->object_id->type_id->dbxref_id->accession,
);
$entity->{$field_name}['und'][$i][$field_table . '__' . $pkey] = $relationship->$pkey;
$entity->{$field_name}['und'][$i][$field_table . '__subject_id'] = $relationship->subject_id->$subject_pkey;
$entity->{$field_name}['und'][$i][$field_table . '__type_id'] = $relationship->type_id->cvterm_id;
$entity->{$field_name}['und'][$i][$field_table . '__object_id'] = $relationship->object_id->$object_pkey;
$entity->{$field_name}['und'][$i]['type_name'] = $relationship->type_id->name;
$entity->{$field_name}['und'][$i]['subject_name'] = $relationship->subject_id->name . ' [id: ' . $relationship->subject_id->$fkey_rcolumn . ']';
$entity->{$field_name}['und'][$i]['object_name'] = $relationship->object_id->name . ' [id: ' . $relationship->object_id->$fkey_rcolumn . ']';
if (array_key_exists('value', $schema['fields'])) {
$entity->{$field_name}['und'][$i][$field_table . '__value'] = $relationship->value;
}
if (array_key_exists('rank', $schema['fields'])) {
$entity->{$field_name}['und'][$i][$field_table . '__rank'] = $relationship->rank;
}
$i++;
}
}
if ($srelationships) {
foreach ($srelationships as $relationship) {
$rel_acc = $relationship->type_id->dbxref_id->db_id->name . ':' . $relationship->type_id->dbxref_id->accession;
$rel_type = $relationship->type_id->name;
$verb = self::get_rel_verb($rel_type);
$subject_name = $relationship->subject_id->name;
$subject_type = $relationship->subject_id->type_id->name;
$object_name = $relationship->object_id->name;
$object_type = $relationship->object_id->type_id->name;
$entity->{$field_name}['und'][$i]['value'] = array(
'@type' => $relationship->type_id->name,
'subject' => array(
'type' => $subject_type,
'name' => $subject_name,
'entity' => 'TripalEntity:' . $entity->id,
),
'type' => $relationship->type_id->name,
'object' => array(
'type' => $object_type,
'name' => $object_name,
)
);
if (property_exists($relationship->subject_id, 'uniquename')) {
$entity->{$field_name}['und'][$i]['value']['subject']['identifier'] = $relationship->subject_id->uniquename;
}
if (property_exists($relationship->object_id, 'uniquename')) {
$entity->{$field_name}['und'][$i]['value']['object']['identifier'] = $relationship->object_id->uniquename;
}
if (property_exists($relationship->object_id, 'entity_id')) {
$entity_id = $relationship->object_id->entity_id;
$entity->{$field_name}['und'][$i]['value']['object']['entity'] = 'TripalEntity:' . $entity_id;
}
$rel_type_clean = lcfirst(preg_replace('/_/', ' ', $rel_type));
$entity->{$field_name}['und'][$i]['value']['phrase'] = 'This ' .
$subject_type . ' ' . $verb . ' ' . $rel_type_clean . ' the ' .
$object_type . ', ' . $object_name . '.';
$entity->{$field_name}['und'][$i]['semantic_web'] = array(
'type' => $rel_acc,
'subject' => $relationship->subject_id->type_id->dbxref_id->db_id->name . ':' . $relationship->subject_id->type_id->dbxref_id->accession,
'object' => $relationship->object_id->type_id->dbxref_id->db_id->name . ':' . $relationship->object_id->type_id->dbxref_id->accession,
);
$entity->{$field_name}['und'][$i][$field_table . '__' . $pkey] = $relationship->$pkey;
$entity->{$field_name}['und'][$i][$field_table . '__subject_id'] = $relationship->subject_id->$subject_pkey;
$entity->{$field_name}['und'][$i][$field_table . '__type_id'] = $relationship->type_id->cvterm_id;
$entity->{$field_name}['und'][$i][$field_table . '__object_id'] = $relationship->object_id->$object_pkey;
$entity->{$field_name}['und'][$i]['type_name'] = $relationship->type_id->name;
$entity->{$field_name}['und'][$i]['subject_name'] = $relationship->subject_id->name . ' [id: ' . $relationship->subject_id->$fkey_rcolumn . ']';
$entity->{$field_name}['und'][$i]['object_name'] = $relationship->object_id->name . ' [id: ' . $relationship->object_id->$fkey_rcolumn . ']';
if (array_key_exists('value', $schema['fields'])) {
$entity->{$field_name}['und'][$i][$field_table . '__value'] = $relationship->value;
}
if (array_key_exists('rank', $schema['fields'])) {
$entity->{$field_name}['und'][$i][$field_table . '__rank'] = $relationship->rank;
}
$i++;
}
}
}
/**
* A helper function to define English verbs for relationship types.
*
* @param $rel_type
* The vocabulary term name for the relationship.
*
* @return
* The verb to use when creating a sentence of the relationship.
*/
public static function get_rel_verb($rel_type) {
$rel_type_clean = lcfirst(preg_replace('/_/', ' ', $rel_type));
$verb = $rel_type_clean;
switch ($rel_type_clean) {
case 'integral part of':
case 'instance of':
$verb = 'is an';
break;
case 'proper part of':
case 'transformation of':
case 'genome of':
case 'part of':
$verb = 'is a';
case 'position of':
case 'sequence of':
case 'variant of':
$verb = 'is a';
break;
case 'derives from':
case 'connects on':
case 'contains':
case 'finishes':
case 'guides':
case 'has origin':
case 'has part':
case 'has quality':
case 'is consecutive sequence of':
case 'maximally overlaps':
case 'overlaps':
case 'starts':
break;
default:
$verb = 'is';
}
return $verb;
}
}
/**
* Theme function for the chado_linker__relationship_widget.
*/
function theme_chado_linker__relationship_widget($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;
}