tripal/tripal_chado/includes/TripalFields/so__cds/so__cds.inc

<?php

class so__cds 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 label for this field.
  public static $default_label = 'Coding Sequence';

  // The default description for this field.
  public static $description = 'A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.';

  // Provide a list of instance specific settings. These can be accessed within
  // the instanceSettingsForm.  When the instanceSettingsForm is submitted
  // then Drupal will automatically change these settings for the instance.
  // 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 = [
    // The short name for the vocabulary (e.g. schema, SO, GO, PATO, etc.).
    'term_vocabulary' => 'SO',
    // The name of the term.
    'term_name' => 'CDS',
    // The unique ID (i.e. accession) of the term.
    'term_accession' => '0000316',
    // 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 = 'so__cds_widget';

  // The default formatter for this field.
  public static $default_formatter = 'so__cds_formatter';


  /**
   * @see TripalField::elementInfo()
   */
  public function elementInfo() {
    $field_term = $this->getFieldTermID();
    return [
      $field_term => [
        'sortable' => FALSE,
        'searchable' => FALSE,
        'type' => 'xs:string',
        'readonly' => TRUE,
      ],
    ];
  }

  /**
   * @see TripalField::load()
   */
  public function load($entity) {
    $field_name = $this->field['field_name'];
    $feature = $entity->chado_record;
    $num_seqs = 0;

    // Set some defauls for the empty record
    $entity->{$field_name}['und'][0] = [
      'value' => '',
    ];

    // Get the featureloc records that this feature is aligned to. We use
    // this SQL rather than the chado_expand_var function because we don't
    // want the residues included from the srcfeature_id which may be huge
    // and overrun memory.
    $featurelocs_sql = "
      SELECT FL.featureloc_id, FL.srcfeature_id
      FROM {featureloc} FL
      WHERE FL.feature_id = :feature_id
      ORDER BY rank ASC
    ";
    $aligned = chado_query($featurelocs_sql, [':feature_id' => $feature->feature_id]);
    $index = 0;
    while ($featureloc = $aligned->fetchObject()) {
      // Generate a CDS sequence if one exsits for this feature alignment.
      $cds_sequence = chado_get_feature_sequences(
        [
          'feature_id' => $feature->feature_id,
          'parent_id' => $featureloc->srcfeature_id,
          'name' => $feature->name,
          'featureloc_id' => $featureloc->featureloc_id,
        ],
        [
          // CDS are in parent-child relationships so we want to use the
          // sequence from the parent
          'derive_from_parent' => 1,
          // we want to combine all CDS for this feature into a single sequence
          'aggregate' => 1,
          // we're looking for CDS features
          'sub_feature_types' => ['CDS'],
          'is_html' => 0,
        ]
      );

      if (count($cds_sequence) > 0) {
        // the chado_get_feature_sequences() function can return multiple sequences
        // if a feature is aligned to multiple places. In the case of CDSs we expect
        // that one mRNA is only aligned to a single location on the assembly so we
        // can access the CDS sequence with index 0.
        if ($cds_sequence[0]['residues']) {
          $entity->{$field_name}['und'][$num_seqs++] = [
            'value' => $cds_sequence[0]['residues'],
            // This field was incorrelctly listed as a field in the featureprop
            // table, but really it is a derived field. So, we have to do this
            // hacky fix to get around the problem.
            'chado-featureprop__featureprop_id' => NULL,
            'chado-featureprop__feature_id' => NULL,
            'chado-featureprop__value' => NULL,
            'chado-featureprop__type_id' => NULL,
            'chado-featureprop__rank' => NULL
          ];
        }
      }
    }
  }
}