sbo__database_cross_reference.inc
File
tripal_chado/includes/TripalFields/sbo__database_cross_reference/sbo__database_cross_reference.incView source
- <?php
-
- class sbo__database_cross_reference extends ChadoField {
-
-
- // --------------------------------------------------------------------------
- // EDITABLE STATIC CONSTANTS
- //
- // The following constants SHOULD be set for each descendent class. They are
- // used by the static functions to provide information to Drupal about
- // the field and it's default widget and formatter.
- // --------------------------------------------------------------------------
-
- // The default lable for this field.
- public static $default_label = 'Cross reference';
-
- // The default description for this field.
- public static $description = 'This record can be cross referenced with a record in
- another online database. This field is intended for one or more
- references. At a minimum, the database and accession must be provided.';
-
- // Provide a list of instance specific settings. These can be access within
- // the instanceSettingsForm. When the instanceSettingsForm is submitted
- // then Drupal with automatically change these settings for the instnace.
- // It is recommended to put settings at the instance level whenever possible.
- // If you override this variable in a child class be sure to replicate the
- // term_name, term_vocab, term_accession and term_fixed keys as these are
- // required for all TripalFields.
- public static $default_instance_settings = array(
- // The short name for the vocabulary (e.g. shcema, SO, GO, PATO, etc.).
- 'term_vocabulary' => 'SBO',
- // The name of the term.
- 'term_name' => 'Database Cross Reference',
- // The unique ID (i.e. accession) of the term.
- 'term_accession' => '0000554',
- // Set to TRUE if the site admin is allowed to change the term
- // type. This will create form elements when editing the field instance
- // to allow the site admin to change the term settings above.
- 'term_fixed' => FALSE,
- );
-
- // The default widget for this field.
- public static $default_widget = 'sbo__database_cross_reference_widget';
-
- // The default formatter for this field.
- public static $default_formatter = 'sbo__database_cross_reference_formatter';
-
- // --------------------------------------------------------------------------
- // PROTECTED CLASS MEMBERS -- DO NOT OVERRIDE
- // --------------------------------------------------------------------------
- // An array containing details about the field. The format of this array
- // is the same as that returned by field_info_fields()
- protected $field;
- // An array containing details about an instance of the field. A field does
- // not have to have an instance. But if dealing with an instance (such as
- // when using the widgetForm, formatterSettingsForm, etc.) it should be set.
- protected $instance;
-
-
- /**
- * @see TripalField::elementInfo()
- */
- public function elementInfo() {
-
- $field_term = $this->getFieldTermID();
- $dbname_term = chado_get_semweb_term('db', 'name');
- $accession_term = chado_get_semweb_term('dbxref', 'accession');
- $dburl_term = chado_get_semweb_term('db', 'url');
-
- return array(
- $field_term => array(
- 'operations' => array(),
- 'label' => 'Cross Reference',
- 'sortable' => FALSE,
- 'searchable' => FALSE,
- 'type' => 'xs:complexType',
- 'readonly' => FALSE,
- 'elements' => array(
- $dbname_term => array(
- 'searchable' => TRUE,
- 'label' => 'Cross Reference Database Name',
- 'help' => 'The name of the remote database that houses the cross reference.',
- 'sortable' => TRUE,
- 'type' => 'xs:string',
- 'readonly' => FALSE,
- 'required' => TRUE,
- ),
- $accession_term => array(
- 'searchable' => TRUE,
- 'label' => 'Cross Reference Database Accession',
- 'help' => 'The unique accession (identifier) in the database that houses the cross reference.',
- 'sortable' => TRUE,
- 'type' => 'xs:string',
- 'readonly' => FALSE,
- 'required' => TRUE,
- ),
- $dburl_term => array(
- 'searchable' => FALSE,
- 'label' => 'Cross Reference Database URL',
- 'help' => 'The URL of the database that houses the cross reference.',
- 'sortable' => FALSE,
- 'type' => 'xs:anyURI',
- 'readonly' => TRUE,
- 'required' => FALSE,
- ),
- ),
- ),
- );
- }
- /**
- *
- * @see TripalField::load()
- */
- public function load($entity) {
- $record = $entity->chado_record;
-
- $field_name = $this->field['field_name'];
- $field_type = $this->field['type'];
- $field_table = $this->instance['settings']['chado_table'];
- $field_column = $this->instance['settings']['chado_column'];
- $base_table = $record->tablename;
-
- $schema = chado_get_schema($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];
-
- $dbname_term = chado_get_semweb_term('db', 'name');
- $accession_term = chado_get_semweb_term('dbxref', 'accession');
- $dburl_term = chado_get_semweb_term('db', 'url');
-
- // Set some defaults for the empty record.
- $entity->{$field_name}['und'][0] = array(
- 'value' => '',
- 'chado-' . $field_table . '__' . $pkey => '',
- 'chado-' . $field_table . '__' . $fkey_lcolumn => $record->$fkey_rcolumn,
- 'chado-' . $field_table . '__dbxref_id' => '',
- 'db_id' => '',
- 'accession' => '',
- );
-
- $linker_table = $base_table . '_dbxref';
- $options = array('return_array' => 1);
- $record = chado_expand_var($record, 'table', $linker_table, $options);
- if (count($record->$linker_table) > 0) {
- $i = 0;
- foreach ($record->$linker_table as $index => $linker) {
- $dbxref = $linker->dbxref_id;
-
- // Ignore the GFF_source database. This is a weird thing required by
- // GBrowse and is added by the GFF loader. We don't want to show it.
- if ($dbxref->db_id->name == 'GFF_source') {
- continue;
- }
-
- $URL = chado_get_dbxref_url($dbxref);
- $entity->{$field_name}['und'][$i] = array(
- 'value' => array(
- $dbname_term => $dbxref->db_id->name,
- $accession_term => $dbxref->accession,
- $dburl_term => $URL,
- ),
- 'chado-' . $field_table . '__' . $pkey => $linker->$pkey,
- 'chado-' . $field_table . '__' . $fkey_lcolumn => $linker->$fkey_lcolumn->$fkey_lcolumn,
- 'chado-' . $field_table . '__dbxref_id' => $dbxref->dbxref_id,
- 'db_id' => $dbxref->db_id->db_id,
- 'accession' => $dbxref->accession,
- );
- $i++;
- }
- }
- }
-
- /**
- * @see ChadoField::query()
- */
- public function query($query, $condition) {
- $dbxref_linker = $this->instance['settings']['chado_table'];
- $base_table = $this->instance['settings']['base_table'];
- $field_table = $this->instance['settings']['chado_table'];
-
- $bschema = chado_get_schema($base_table);
- $bpkey = $bschema['primary key'][0];
-
- $alias = $this->field['field_name'];
- $operator = $condition['operator'];
-
- $field_term_id = $this->getFieldTermID();
- $dbname_term = $field_term_id . ',' . chado_get_semweb_term('db', 'name');
- $accession_term = $field_term_id . ',' . chado_get_semweb_term('dbxref', 'accession');
- $dburl_term = $field_term_id . ',' . chado_get_semweb_term('db', 'url');
-
- $this->queryJoinOnce($query, $field_table, $alias, "base.$bpkey = $alias.$bpkey");
- $this->queryJoinOnce($query, 'dbxref', $alias . '_DBX', $alias . "_DBX.dbxref_id = $alias.dbxref_id");
-
- if ($condition['column'] == $dbname_term) {
- $this->queryJoinOnce($query, 'db', $alias . '_DB', $alias . "_DB.db_id = " . $alias . "_DBX.db_id");
- $query->condition($alias . "_DB.name", $condition['value'], $operator);
- }
- if ($condition['column'] == $accession_term) {
- $query->condition($alias . "_DBX.accession", $condition['value'], $operator);
- }
- }
-
- /**
- * @see ChadoField::queryOrder()
- */
- public function queryOrder($query, $order) {
- $dbxref_linker = $this->instance['settings']['chado_table'];
- $base_table = $this->instance['settings']['base_table'];
- $field_table = $this->instance['settings']['chado_table'];
-
- $bschema = chado_get_schema($base_table);
- $bpkey = $bschema['primary key'][0];
-
- $alias = $this->field['field_name'];
-
- $field_term_id = $this->getFieldTermID();
- $dbname_term = $field_term_id . ',' . chado_get_semweb_term('db', 'name');
- $accession_term = $field_term_id . ',' . chado_get_semweb_term('dbxref', 'accession');
- $dburl_term = $field_term_id . ',' . chado_get_semweb_term('db', 'url');
-
- $this->queryJoinOnce($query, $field_table, $alias, "base.$bpkey = $alias.$bpkey", "LEFT OUTER");
- $this->queryJoinOnce($query, 'dbxref', $alias . '_DBX', $alias . "_DBX.dbxref_id = $alias.dbxref_id", "LEFT OUTER");
-
- if ($order['column'] == $dbname_term) {
- $this->queryJoinOnce($query, 'db', $alias . '_DB', $alias . "_DB.db_id = " . $alias . "_DBX.db_id", "LEFT OUTER");
- $query->orderBy($alias . "_DB.name", $order['direction']);
- }
- if ($order['column'] == $accession_term) {
- $query->orderBy($alias . "_DBX.accession", $order['direction']);
- }
- }
-
- /**
- * @see TripalField::validate()
- */
- public function validate($entity_type, $entity, $langcode, $items, &$errors) {
-
- // If we don't have an entity then we don't want to validate. The case
- // where this could happen is when a user is editing the field settings
- // and trying to set a default value. In that case there's no entity and
- // we don't want to validate. There will always be an entity for creation
- // and update operations of a content type.
- if (!$entity) {
- return;
- }
-
- $field_name = $this->field['field_name'];
- $field_type = $this->field['type'];
- $table_name = $this->instance['settings']['chado_table'];
- $field_table = $this->instance['settings']['chado_table'];
- $field_column = $this->instance['settings']['chado_column'];
- $base_table = $this->instance['settings']['base_table'];
- $schema = chado_get_schema($table_name);
- $pkey = $schema['primary key'][0];
- $fkeys = array_values($schema['foreign keys'][$base_table]['columns']);
- $fkey = $fkeys[0];
-
-
- // Get the field values.
- foreach ($items as $delta => $values) {
-
- // Get the field values.
- $dbxref_id = $values['chado-' . $field_table . '__dbxref_id'];
- $db_id = $values['db_id'];
- $accession = $values['accession'];
-
- // Make sure that if a database ID is provided that an accession is also
- // provided. Here we use the form_set_error function rather than the
- // form_error function because the form_error will add a red_highlight
- // around all of the fields in the fieldset which is confusing as it's not
- // clear to the user what field is required and which isn't. Therefore,
- // we borrow the code from the 'form_error' function and append the field
- // so that the proper field is highlighted on error.
- if (!$db_id) {
- $errors[$field_name][$delta]['und'][] = array(
- 'message' => t("A database must be provided for the cross reference."),
- 'error' => 'sbo__database_cross_reference',
- );
- }
- if ($db_id and !$accession) {
- $errors[$field_name][$delta]['und'][] = array(
- 'message' => t("A database and the accession must both be provided."),
- 'error' => 'sbo__database_cross_reference',
- );
- }
- if (!$db_id and !$accession) {
- $errors[$field_name][$delta]['und'][] = array(
- 'message' => t("A database and the accession must both be provided."),
- 'error' => 'sbo__database_cross_reference',
- );
- }
- }
- }
- }