tripal/tripal_chado/includes/TripalFields/schema__publication/schema__publication.inc

<?php

class schema__publication 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 = 'Publication';

  // The default description for this field.
  public static $description = 'Associates a publication (e.g. journal article,
            conference proceedings, book chapter, etc.) with this record.';

  // 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' => 'schema',
    // The name of the term.
    'term_name' => 'publication',
    // The unique ID (i.e. accession) of the term.
    'term_accession' => 'publication',
    // 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 = 'schema__publication_widget';

  // The default formatter for this field.
  public static $default_formatter = 'schema__publication_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();
    return array(
      $field_term => array(
        'operations' => array(),
        'sortable' => FALSE,
        'searchable' => FALSE,
      ),
    );
  }
  /**
   *
   * @see TripalField::load()
   */
  public function load($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 = $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];

    // Set some defaults for the empty record.
    $entity->{$field_name}['und'][0] = array(
      'value' => array(),
      'chado-' . $field_table . '__' . $pkey => '',
      'chado-' . $field_table . '__' . $fkey_lcolumn => '',
      'chado-' . $field_table . '__' . 'pub_id' => '',
    );

    $linker_table = $base_table . '_pub';
    $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) {
        $pub = $linker->pub_id;
        $pub_details = tripal_get_minimal_pub_info($pub);

        $entity->{$field_name}['und'][$i]['value'] = $pub_details;
        $entity->{$field_name}['und'][$i]['chado-' . $field_table . '__' . $pkey] = $linker->$pkey;
        $entity->{$field_name}['und'][$i]['chado-' . $field_table . '__' . $fkey_lcolumn] = $linker->$fkey_lcolumn->$fkey_lcolumn;
        $entity->{$field_name}['und'][$i]['chado-' . $field_table . '__' . 'pub_id'] = $pub->pub_id;

        if (property_exists($pub, 'entity_id')) {
          $entity->{$field_name}['und'][$i]['value']['entity'] = 'TripalEntity:' . $pub->entity_id;
        }
        $i++;
      }
    }
  }

  /**
   * @see ChadoField::query()
   */
  public function query($query, $condition) {
    $pub_linker = $this->instance['settings']['chado_table'];
    $base_table = $this->instance['settings']['base_table'];
    $bschema = chado_get_schema($base_table);
    $bpkey = $bschema['primary key'][0];
    $alias = 'pub_linker';
    $operator = $condition['operator'];

    if ($condition['column'] == 'publication.database_cross_reference') {
      list($db_name, $accession) = explode(':', $condition['value']);

      $this->queryJoinOnce($query, $pub_linker, $alias, "base.$bpkey = $alias.$bpkey");
      $this->queryJoinOnce($query, 'pub_dbxref', 'PDBX', "PDBX.pub_id = $alias.pub_id");
      $this->queryJoinOnce($query, 'dbxref', 'DBX', "DBX.dbxref_id = PDBX.dbxref_id");
      $this->queryJoinOnce($query, 'db', 'DB', "DB.db_id = DBX.db_id");
      $query->condition("DB.name", $db_name);
      $query->condition("DBX.accession", $accession);
    }

    if ($condition['column'] == 'publication.title') {
      $this->queryJoinOnce($query, $pub_linker, $alias, "base.$bpkey = $alias.$bpkey");
      $this->queryJoinOnce($query, 'pub', 'PUB', "PUB.pub_id = $alias.pub_id");
      $query->condition('PUB.title', $condition['value'], $operator);
    }

    if ($condition['column'] == 'publication.citation') {

    }

    if ($condition['column'] == 'publication.authors') {

    }
    if ($condition['column'] == 'publication.abstract') {

    }
  }

}