class sio__annotation
Hierarchy
- class \TripalField
- class \ChadoField
- class \sio__annotation
- class \ChadoField
Expanded class hierarchy of sio__annotation
2 string references to 'sio__annotation'
- tripal_chado_bundle_fields_info_linker in tripal_chado/
includes/ tripal_chado.fields.inc - tripal_chado_bundle_instances_info_linker in tripal_chado/
includes/ tripal_chado.fields.inc
File
- tripal_chado/
includes/ TripalFields/ sio__annotation/ sio__annotation.inc, line 3
View source
class sio__annotation 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 = 'Annotations';
// The default description for this field.
public static $description = 'This record is annotated with controlled vocabulary terms.';
// 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' => 'SIO',
// The name of the term.
'term_name' => 'annotation',
// The unique ID (i.e. accession) of the term.
'term_accession' => '001166',
// 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 = 'chado_linker__cvterm_widget';
// The default formatter for this field.
public static $default_formatter = 'chado_linker__cvterm_formatter';
// A boolean specifying that users should not be allowed to create
// fields and instances of this field type through the UI. Such
// fields can only be created programmatically with field_create_field()
// and field_create_instance().
public static $no_ui = FALSE;
/**
* @see TripalField::validate()
*/
public function validate($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 = $this->field['field_name'];
foreach ($items as $delta => $item) {
// Get the term that matches.
$cvterm_name = $item['cvterm_name'];
$cv_id = $item['cv_id'];
if ($cvterm_name and $cv_id) {
$cvterm = chado_generate_var('cvterm', array(
'cv_id' => $cv_id,
'name' => $cvterm_name,
));
if (!$cvterm) {
$errors[$field_name][$langcode][$delta][] = array(
'message' => t("Cannot find a term that matches the term name and vocabulary."),
'error' => 'cvterm_name'
);
}
}
}
}
/**
* @see TripalField::elementInfo()
*/
public function elementInfo() {
$field_table = $this->instance['settings']['chado_table'];
$schema = chado_get_schema($field_table);
$vocabulary_term = chado_get_semweb_term('cvterm', 'cv_id');
$accession_term = chado_get_semweb_term('dbxref', 'accession');
$definition_term = chado_get_semweb_term('cvterm', 'definition');
$field_term = $this->getFieldTermID();
$info = array(
$field_term => array(
'operations' => array(),
'sortable' => FALSE,
'searchable' => FALSE,
'type' => 'xs:complexType',
'readonly' => FALSE,
'elements' => array(
$vocabulary_term => array(
'sortable' => TRUE,
'searchable' => TRUE,
'label' => 'Annotation Term Vocabulary',
'type' => 'xs:string',
'readonly' => FALSE,
'required' => TRUE,
),
$accession_term => array(
'sortable' => TRUE,
'searchable' => TRUE,
'label' => 'Annotation Term Accession',
'type' => 'xs:string',
'readonly' => FALSE,
'required' => TRUE,
),
$definition_term => array(
'sortable' => TRUE,
'searchable' => TRUE,
'label' => 'Annotation Term Description',
'type' => 'xs:string',
'readonly' => FALSE,
'required' => FALSE,
),
),
),
);
if (array_key_exists('is_not', $schema['fields'])) {
$negation_term = chado_get_semweb_term($field_table, 'is_not');
$info[$field_term]['elements'][$negation_term] = array(
'sortable' => FALSE,
'searchable' => FALSE,
'label' => 'Annotation Term Negates',
'type' => 'xs:boolean',
'readonly' => FALSE,
'required' => FALSE,
);
}
if (array_key_exists('rank', $schema['fields'])) {
$rank_term = chado_get_semweb_term($field_table, 'rank');
$info[$field_term]['elements'][$rank_term] = array(
'sortable' => FALSE,
'searchable' => FALSE,
'label' => 'Annotation Term Rank',
'type' => 'xs:integer',
'readonly' => FALSE,
'required' => FALSE,
);
}
if (array_key_exists('pub_id', $schema['fields'])) {
}
return $info;
}
/**
* @see ChadoField::query()
*/
public function query($query, $condition) {
$alias = $this->field['field_name'];
$operator = $condition['operator'];
$field_table = $this->instance['settings']['chado_table'];
$base_table = $this->instance['settings']['base_table'];
$schema = chado_get_schema($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];
$field_term_id = $this->getFieldTermID();
$vocabulary_term = $field_term_id . ',' . chado_get_semweb_term('cvterm', 'cv_id');
$accession_term = $field_term_id . ',' . chado_get_semweb_term('dbxref', 'accession');
$definition_term = $field_term_id . ',' . chado_get_semweb_term('cvterm', 'definition');
// Join to the xxx_cvterm table for this field.
$this->queryJoinOnce($query, $field_table, $alias, "base.$fkey_rcolumn = $alias.$fkey_lcolumn");
if ($condition['column'] == $vocabulary_term) {
$this->queryJoinOnce($query, 'cvterm', $alias . '_cvterm', $alias . ".cvterm_id = " . $alias . "_cvterm.cvterm_id");
$this->queryJoinOnce($query, 'dbxref', $alias . '_dbxref', $alias . "_cvterm.dbxref_id = " . $alias . "_dbxref.dbxref_id");
$this->queryJoinOnce($query, 'db', $alias . '_db', $alias . "_db.db_id = " . $alias . "_dbxref.db_id");
$query->condition($alias . '_db.name', $condition['value'], $operator);
}
if ($condition['column'] == $accession_term) {
$this->queryJoinOnce($query, 'cvterm', $alias . '_cvterm', $alias . ".cvterm_id = " . $alias . "_cvterm.cvterm_id");
$this->queryJoinOnce($query, 'dbxref', $alias . '_dbxref', $alias . "_cvterm.dbxref_id = " . $alias . "_dbxref.dbxref_id");
$query->condition($alias . '_dbxref.accession', $condition['value'], $operator);
}
if ($condition['column'] == $definition_term) {
$this->queryJoinOnce($query, 'cvterm', $alias . '_cvterm', $alias . ".cvterm_id = " . $alias . "_cvterm.cvterm_id");
$query->condition($alias . '_cvterm.definition', $condition['value'], $operator);
}
}
/**
* @see ChadoField::queryOrder()
*/
public function queryOrder($query, $order) {
$alias = $this->field['field_name'];
$field_table = $this->instance['settings']['chado_table'];
$base_table = $this->instance['settings']['base_table'];
$schema = chado_get_schema($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];
$field_term_id = $this->getFieldTermID();
$vocabulary_term = $field_term_id . ',' . chado_get_semweb_term('cvterm', 'cv_id');
$accession_term = $field_term_id . ',' . chado_get_semweb_term('dbxref', 'accession');
$definition_term = $field_term_id . ',' . chado_get_semweb_term('cvterm', 'definition');
// Join to the xxx_cvterm table for this field.
$this->queryJoinOnce($query, $field_table, $alias, "base.$fkey_rcolumn = $alias.$fkey_lcolumn");
if ($order['column'] == $vocabulary_term) {
$this->queryJoinOnce($query, 'cvterm', $alias . '_cvterm', $alias . ".cvterm_id = " . $alias . "_cvterm.cvterm_id", "LEFT OUTER");
$this->queryJoinOnce($query, 'dbxref', $alias . '_dbxref', $alias . "_cvterm.dbxref_id = " . $alias . "_dbxref.dbxref_id", "LEFT OUTER");
$this->queryJoinOnce($query, 'db', $alias . '_db', $alias . "_db.db_id = " . $alias . "_dbxref.db_id", "LEFT OUTER");
$query->orderBy($alias . "_db.name", $order['direction']);
}
if ($order['column'] == $accession_term) {
$this->queryJoinOnce($query, 'cvterm', $alias . '_cvterm', $alias . ".cvterm_id = " . $alias . "_cvterm.cvterm_id", "LEFT OUTER");
$this->queryJoinOnce($query, 'dbxref', $alias . '_dbxref', $alias . "_cvterm.dbxref_id = " . $alias . "_dbxref.dbxref_id", "LEFT OUTER");
$query->orderBy($alias . "_dbxref.accession", $order['direction']);
}
if ($order['column'] == $definition_term) {
$this->queryJoinOnce($query, 'cvterm', $alias . '_cvterm', $alias . ".cvterm_id = " . $alias . "_cvterm.cvterm_id");
$query->orderBy($alias . "_cvterm.definition", $order['direction']);
}
}
/**
*
* @see TripalField::load()
*/
public function load($entity) {
$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 = $this->instance['settings']['base_table'];
// 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];
$vocabulary = chado_get_semweb_term('cvterm', 'cv_id');
$accession = chado_get_semweb_term('dbxref', 'accession');
$definition = chado_get_semweb_term('cvterm', 'definition');
if (array_key_exists('is_not', $schema['fields'])) {
$negation = chado_get_semweb_term($field_table, 'is_not');
}
if (array_key_exists('rank', $schema['fields'])) {
$rank_term = chado_get_semweb_term($field_table, 'rank');
}
// Set some defaults for the empty record.
$chado_record = $entity->chado_record;
$entity->{$field_name}['und'][0] = array(
'value' => '',
'chado-' . $field_table . '__' . $pkey => '',
'chado-' . $field_table . '__' . $fkey_lcolumn => $chado_record->$fkey_rcolumn,
'chado-' . $field_table . '__cvterm_id' => '',
);
if (array_key_exists('is_not', $schema['fields'])) {
$entity->{$field_name}['und'][0]['chado-' . $field_table . '__is_not'] = '';
}
if (array_key_exists('rank', $schema['fields'])) {
$entity->{$field_name}['und'][0]['chado-' . $field_table . '__rank'] = '';
}
if (array_key_exists('pub_id', $schema['fields'])) {
$entity->{$field_name}['und'][0]['chado-' . $field_table . '__pub_id'] = '';
}
// Get the annotations associated with this base record for this fields type.
$columns = array('*');
$match = array(
$fkey_lcolumn => $chado_record->$fkey_rcolumn,
);
$order_by = array($pkey => 'ASC');
if (array_key_exists('rank', $schema['fields'])) {
$order_by = array('rank' => 'ASC');
}
$options = array(
'return_array' => TRUE,
'order_by' => $order_by
);
$fcvterms = chado_select_record($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' => array(
$vocabulary => $cvterm->dbxref_id->db_id->name,
$accession => $cvterm->dbxref_id->accession,
$definition => isset($cvterm->definition) ? $cvterm->definition : ''
),
'chado-' . $field_table . '__' . $pkey => $linker->$pkey,
'chado-' . $field_table . '__' . $fkey_lcolumn => $linker->$fkey_lcolumn,
'chado-' . $field_table . '__' . 'cvterm_id' => $linker->cvterm_id,
);
if (array_key_exists('is_not', $schema['fields'])) {
$entity->{$field_name}['und'][$i]['value'][$negation] = $linker->is_not;
$entity->{$field_name}['und'][$i]['chado-' . $field_table . '__is_not'] = $linker->is_not;
}
if (array_key_exists('rank', $schema['fields'])) {
$entity->{$field_name}['und'][$i]['value'][$rank_term] = $linker->rank;
$entity->{$field_name}['und'][$i]['chado-' . $field_table . '__rank'] = $linker->rank;
}
if (array_key_exists('pub_id', $schema['fields'])) {
$entity->{$field_name}['und'][$i]['chado-' . $field_table . '__pub_id'] = $linker->pub_id;
}
}
}
}
Members
Name | Modifiers | Type | Description |
---|---|---|---|
ChadoField:: |
public static | property |
Overrides TripalField:: |
ChadoField:: |
public static | property |
Overrides TripalField:: |
ChadoField:: |
public static | property |
Overrides TripalField:: |
ChadoField:: |
public static | property |
Overrides TripalField:: |
ChadoField:: |
public | function |
Overrides TripalField:: |
ChadoField:: |
protected | function | A convient way to join a table to a query without duplicates. |
sio__annotation:: |
public static | property |
Overrides TripalField:: |
sio__annotation:: |
public static | property |
Overrides ChadoField:: |
sio__annotation:: |
public static | property |
Overrides ChadoField:: |
sio__annotation:: |
public static | property |
Overrides TripalField:: |
sio__annotation:: |
public static | property | |
sio__annotation:: |
public static | property |
Overrides TripalField:: |
sio__annotation:: |
public | function |
Overrides TripalField:: |
sio__annotation:: |
public | function |
Overrides TripalField:: |
sio__annotation:: |
public | function |
Overrides ChadoField:: |
sio__annotation:: |
public | function |
Overrides ChadoField:: |
sio__annotation:: |
public | function |
Overrides TripalField:: |
TripalField:: |
protected | property | |
TripalField:: |
protected | property | |
TripalField:: |
public static | property | |
TripalField:: |
protected | property | |
TripalField:: |
public | function | After a field instance is created the following function is run. |
TripalField:: |
public | function | |
TripalField:: |
public | function | Retrives the name of this field. |
TripalField:: |
public | function | |
TripalField:: |
public | function | |
TripalField:: |
public | function | |
TripalField:: |
protected | function | When constructing a pager for use by a field, all pagers must have a unique ID |
TripalField:: |
public static | function | Provides default information about this field type |
TripalField:: |
public | function | Provides validation of the instance settings form. |
TripalField:: |
public | function | Provides a form for the 'Field Settings' of the field management page. |
TripalField:: |
public | function | _state |
TripalField:: |
public | function | Describes this field to Views. |
TripalField:: |
public | function | Describes this field to Tripal web services. |
TripalField:: |
protected | function | |
TripalField:: |
protected | function | |
TripalField:: |
public | function | Instantiates a new TripalField object. |