tripal/legacy/tripal_feature/includes/tripal_feature.chado_node.inc

<?php
/**
 * @file
 * Implementation of hooks to create a feature content type
 */

/**
 * Implements hook_node_info().
 *
 * Provide information to drupal about the node types that we're creating
 *  in this module
 *
 * @ingroup tripal_legacy_feature
 */
function tripal_feature_node_info() {
  $nodes = [];

  $nodes['chado_feature'] = [
    'name' => t('Feature (Tripal v2 legacy)'),
    'base' => 'chado_feature',
    'description' => t('A feature from the chado database'),
    'has_title' => TRUE,
    'locked' => TRUE,
    'chado_node_api' => [
      'base_table' => 'feature',
      'hook_prefix' => 'chado_feature',
      'record_type_title' => [
        'singular' => t('Feature'),
        'plural' => t('Features'),
      ],
      'sync_filters' => [
        'type_id' => TRUE,
        'organism_id' => TRUE,
      ],
    ],
  ];
  return $nodes;
}

/**
 * Implementation of hook_form().
 *
 * @ingroup tripal_legacy_feature
 */
function chado_feature_form($node, &$form_state) {

  $form = [];

  // Default values can come in the following ways:
  //
  // 1) as elements of the $node object.  This occurs when editing an existing feature
  // 2) in the $form_state['values'] array which occurs on a failed validation or
  //    ajax callbacks from non submit form elements
  // 3) in the $form_state['input'[ array which occurs on ajax callbacks from submit
  //    form elements and the form is being rebuilt
  //
  // set form field defaults
  $feature = NULL;
  $feature_id = NULL;
  $uniquename = '';
  $fname = '';
  $feature_type = '';
  $organism_id = '';
  $residues = '';
  $is_obsolete = '';
  $analyses = '';
  $references = '';
  $synonyms = '';

  // if we are editing an existing node then the feature is already part of the node
  if (property_exists($node, 'feature')) {
    $feature = $node->feature;
    $feature = chado_expand_var($feature, 'field', 'feature.residues');
    $feature_id = $feature->feature_id;
    $uniquename = $feature->uniquename;
    $fname = $feature->name;
    $feature_type = $feature->type_id->name;
    $organism_id = $feature->organism_id->organism_id;
    $residues = $feature->residues;
    $is_obsolete = $feature->is_obsolete;

    // get the synonyms from a previous post
    $synonyms = '';
    if (property_exists($node, 'synonyms')) {
      $synonyms = $node->synonyms;
    }

    // get synonyms from the database if we don't already have them
    if (!$synonyms) {
      $options = ['return_array' => 1];
      $feature = chado_expand_var($feature, 'table', 'feature_synonym', $options);
      $feature_synonyms = (isset($feature->feature_synonym)) ? $feature->feature_synonym : [];
      foreach ($feature_synonyms as $index => $synonym) {
        $synonyms .= $synonym->synonym_id->name . "\n";
      }
    }
    // keep track of the feature id
    $form['feature_id'] = [
      '#type' => 'value',
      '#value' => $feature_id,
    ];
  }
  // if we are re constructing the form from a failed validation or ajax callback
  // then use the $form_state['values'] values
  if (array_key_exists('values', $form_state) and isset($form_state['values']['uniquename'])) {
    $uniquename = $form_state['values']['uniquename'];
    $fname = $form_state['values']['fname'];
    $feature_type = $form_state['values']['feature_type'];
    $organism_id = $form_state['values']['organism_id'];
    $residues = $form_state['values']['residues'];
    $is_obsolete = $form_state['values']['is_obsolete'];
    $synonyms = $form_state['values']['synonyms'];
  }
  // if we are re building the form from after submission (from ajax call) then
  // the values are in the $form_state['input'] array
  if (array_key_exists('input', $form_state) and !empty($form_state['input'])) {
    $uniquename = $form_state['input']['uniquename'];
    $fname = $form_state['input']['fname'];
    $feature_type = $form_state['input']['feature_type'];
    $organism_id = $form_state['input']['organism_id'];
    $residues = $form_state['input']['residues'];
    $is_obsolete = array_key_exists('is_obsolete', $form_state['input']) ? $form_state['input']['is_obsolete'] : FALSE;
    $synonyms = $form_state['input']['synonyms'];
  }

  $form['fname'] = [
    '#type' => 'textfield',
    '#title' => t('Feature Name'),
    '#required' => TRUE,
    '#default_value' => $fname,
    '#description' => t('Enter the name used by humans to refer to this feature.'),
    '#maxlength' => 255,
  ];
  $form['uniquename'] = [
    '#type' => 'textfield',
    '#title' => t('Unique Feature Name'),
    '#required' => TRUE,
    '#default_value' => $uniquename,
    '#description' => t('Enter a unique name for this feature.  This name must be unique for the organism and feature type.'),
    '#maxlength' => 255,
  ];

  //$type_options = tripal_get_cvterm_default_select_options('feature', 'type_id', 'feature types');
  //$type_options[0] = 'Select a Type';
  $type_cv = tripal_get_default_cv('feature', 'type_id');
  $cv_id = $type_cv->cv_id;

  $form['feature_type'] = [
    '#title' => t('Feature Type'),
    '#type' => 'textfield',
    '#description' => t("Choose the feature type."),
    '#required' => TRUE,
    '#default_value' => $feature_type,
    '#autocomplete_path' => "aadmin/tripal/storage/chado/auto_name/cvterm/$cv_id",
  ];

  // get the list of organisms
  $sql = "SELECT * FROM {Organism} ORDER BY genus, species";
  $org_rset = chado_query($sql);
  $organisms = [];
  $organisms[''] = '';
  while ($organism = $org_rset->fetchObject()) {
    $organisms[$organism->organism_id] = "$organism->genus $organism->species ($organism->common_name)";
  }
  $form['organism_id'] = [
    '#title' => t('Organism'),
    '#type' => t('select'),
    '#description' => t("Choose the organism with which this feature is associated"),
    '#required' => TRUE,
    '#default_value' => $organism_id,
    '#options' => $organisms,
  ];

  // Get synonyms
  $syn_text = '';
  if ($synonyms) {
    if (is_array($synonyms)) {
      foreach ($synonyms as $synonym) {
        $syn_text .= "$synonym->name\n";
      }
    }
    else {
      $syn_text = $synonyms;
    }
  }
  $form['synonyms'] = [
    '#type' => 'textarea',
    '#title' => t('Synonyms'),
    '#required' => FALSE,
    '#default_value' => $syn_text,
    '#description' => t('Enter alternate names (synonmys) for this feature to help in searching and identification. You may enter as many alternate names as needed each on different lines.'),
  ];

  $form['residues'] = [
    '#type' => 'textarea',
    '#title' => t('Residues'),
    '#required' => FALSE,
    '#default_value' => $residues,
    '#description' => t('Enter the nucelotide sequences for this feature'),
  ];

  $checked = '';
  if ($is_obsolete == 't') {
    $checked = '1';
  }
  $form['is_obsolete'] = [
    '#type' => 'checkbox',
    '#title' => t('Is Obsolete'),
    '#required' => FALSE,
    '#default_value' => $checked,
    '#description' => t('Check this box if this sequence should be retired'),
  ];

  // PROPERTIES FORM
  //---------------------------------------------
  $prop_cv = tripal_get_default_cv('featureprop', 'type_id');
  $cv_id = $prop_cv ? $prop_cv->cv_id : NULL;
  $details = [
    'property_table' => 'featureprop',
    // the name of the prop table
    'chado_id' => $feature_id,
    // the value of feature_id for this record
    'cv_id' => $cv_id
    // the cv.cv_id of the cv governing featureprop.type_id
  ];
  chado_add_node_form_properties($form, $form_state, $details);

  // ADDITIONAL DBXREFS FORM
  //---------------------------------------------
  $details = [
    'linking_table' => 'feature_dbxref',
    // the name of the _dbxref table
    'base_foreign_key' => 'feature_id',
    // the name of the key in your base chado table
    'base_key_value' => $feature_id
    // the value of feature_id for this record
  ];
  chado_add_node_form_dbxrefs($form, $form_state, $details);

  // RELATIONSHIPS FORM
  //---------------------------------------------
  $relationship_cv = tripal_get_default_cv('feature_relationship', 'type_id');
  $cv_id = $relationship_cv ? $relationship_cv->cv_id : NULL;
  $details = [
    'relationship_table' => 'feature_relationship',
    'base_table' => 'feature',
    'base_foreign_key' => 'feature_id',
    'base_key_value' => $feature_id,
    'nodetype' => 'feature',
    'cv_id' => $cv_id,
  ];
  chado_add_node_form_relationships($form, $form_state, $details);

  return $form;
}

/**
 * Implementation of hook_validate().
 *
 * This validation is being used for three activities:
 *   CASE A: Update a node that exists in both drupal and chado
 *   CASE B: Synchronizing a node from chado to drupal
 *   CASE C: Inserting a new node that exists in niether drupal nor chado
 *
 * @ingroup tripal_legacy_feature
 */
function chado_feature_validate($node, $form, &$form_state) {


  // We only want to validate when the node is saved.
  // Since this validate can be called on AJAX and Deletion of the node
  // we need to make this check to ensure queries are not executed
  // without the proper values.
  if (property_exists($node, "op") and $node->op != 'Save') {
    return;
  }

  // we are syncing if we do not have a node ID but we do have a feature_id. We don't
  // need to validate during syncing so just skip it.
  if (!property_exists($node, 'nid') and property_exists($node, 'feature_id') and $node->feature_id != 0) {
    return;
  }

  // remove surrounding white-space on submitted values
  $node->uniquename = property_exists($node, 'uniquename') ? trim($node->uniquename) : '';
  $node->fname = property_exists($node, 'fname') ? trim($node->fname) : '';
  $node->feature_type = property_exists($node, 'feature_type') ? trim($node->feature_type) : '';
  $node->residues = property_exists($node, 'residues') ? trim($node->residues) : '';

  // Validating for an update
  if (property_exists($node, 'nid')) {

    // make sure the feature type is a real sequence ontology term
    $type = tripal_get_cvterm([
      'name' => $node->feature_type,
      'cv_id' => ['name' => 'sequence'],
    ]);
    if (!$type) {
      form_set_error('feature_type', t("The feature type is not a valid name from the Sequence Ontology."));
    }

    // if this is an update, we want to make sure that a different feature for
    // the organism doesn't already have this uniquename. We don't want to give
    // two sequences the same uniquename
    if (property_exists($node, 'feature_id') and $node->feature_id != 0) {
      $sql = "
        SELECT *
        FROM {feature} F
          INNER JOIN {cvterm} CVT ON F.type_id = CVT.cvterm_id
        WHERE
          F.uniquename     = :uname AND
          F.organism_id    = :organism_id AND
          CVT.name         = :cvtname AND
          NOT f.feature_id = :feature_id
      ";
      $args = [
        ':uname' => $node->uniquename,
        ':organism_id' => $node->organism_id,
        ':cvtname' => $node->feature_type,
        ':feature_id' => $node->feature_id,
      ];
      $result = chado_query($sql, $args)->fetchObject();
      if ($result) {
        form_set_error('uniquename', t("Feature update cannot proceed. The feature name '$node->uniquename' is not unique for this organism. Please provide a unique name for this feature."));
      }
    }
  }
  // Validating for an insert
  else {

    // make sure the feature type is a real sequence ontology term
    $type = tripal_get_cvterm([
      'name' => $node->feature_type,
      'cv_id' => ['name' => 'sequence'],
    ]);
    if (!$type) {
      form_set_error('feature_type', t("The feature type is not a valid name from the Sequence Ontology."));
    }

    // if this is an insert then we just need to make sure this name doesn't
    // already exist for this organism if it does then we need to throw an error
    $sql = "
      SELECT *
      FROM {feature} F
        INNER JOIN {cvterm} CVT ON F.type_id = CVT.cvterm_id
      WHERE
        F.uniquename  = :name AND
        F.organism_id = :organism_id AND
        CVT.name      = :cvtname
    ";
    $args = [
      ':name' => $node->uniquename,
      ':organism_id' => $node->organism_id,
      ':cvtname' => $node->feature_type,
    ];

    $result = chado_query($sql, $args)->fetchObject();
    if ($result) {
      form_set_error('uniquename', t("Feature insert cannot proceed. The feature name '$node->uniquename' already exists for this organism. Please provide a unique name for this feature."));
    }
  }
}

/**
 * Implement hook_node_access().
 *
 * This hook allows node modules to limit access to the node types they define.
 *
 * @param $node
 *  The node on which the operation is to be performed, or, if it does not yet
 *   exist, the type of node to be created
 *
 * @param $op
 *  The operation to be performed
 *
 * @param $account
 *  A user object representing the user for whom the operation is to be
 *   performed
 *
 * @return
 *  If the permission for the specified operation is not set then return FALSE.
 *   If the permission is set then return NULL as this allows other modules to
 *   disable access.  The only exception is when the $op == 'create'.  We will
 *   always return TRUE if the permission is set.
 *
 * @ingroup tripal_legacy_feature
 */
function tripal_feature_node_access($node, $op, $account) {
  $node_type = $node;
  if (is_object($node)) {
    $node_type = $node->type;
  }

  if ($node_type == 'chado_feature') {
    if ($op == 'create') {
      if (!user_access('create chado_feature content', $account)) {
        return NODE_ACCESS_DENY;
      }
      return NODE_ACCESS_ALLOW;
    }

    if ($op == 'update') {
      if (!user_access('edit chado_feature content', $account)) {
        return NODE_ACCESS_DENY;
      }
    }
    if ($op == 'delete') {
      if (!user_access('delete chado_feature content', $account)) {
        return NODE_ACCESS_DENY;
      }
    }
    if ($op == 'view') {
      if (!user_access('access chado_feature content', $account)) {
        return NODE_ACCESS_DENY;
      }
    }
  }
  return NODE_ACCESS_IGNORE;
}

/**
 * Implements hook_insert().
 *
 *  When a new chado_feature node is created we also need to add information
 *  to our chado_feature table.  This function is called on insert of a new node
 *  of type 'chado_feature' and inserts the necessary information.
 *
 * @ingroup tripal_legacy_feature
 */
function chado_feature_insert($node) {

  $feature_id = '';

  // if there is a feature_id in the $node object then this must be a sync so
  // we can skip adding the feature as it is already there, although
  // we do need to proceed with insertion into the chado/drupal linking table.
  if (!property_exists($node, 'feature_id')) {
    $node->uniquename = trim($node->uniquename);
    $node->fname = trim($node->fname);
    $node->feature_type = trim($node->feature_type);
    $node->residues = trim($node->residues);

    // remove spaces, newlines from residues
    $residues = preg_replace("/[\n\r\s]/", "", $node->residues);
    $obsolete = 'FALSE';
    if ($node->is_obsolete) {
      $obsolete = 'TRUE';
    }

    // get the feature type id
    $values = [
      'cv_id' => [
        'name' => 'sequence',
      ],
      'name' => $node->feature_type,
    ];
    $type = chado_select_record('cvterm', ['cvterm_id'], $values);

    $values = [
      'organism_id' => $node->organism_id,
      'name' => $node->fname,
      'uniquename' => $node->uniquename,
      'residues' => $residues,
      'seqlen' => drupal_strlen($residues),
      'is_obsolete' => $obsolete,
      'type_id' => $type[0]->cvterm_id,
      'md5checksum' => md5($residues),
    ];
    $feature = chado_insert_record('feature', $values);
    if (!$feature) {
      drupal_set_message(t('Unable to add feature.'), 'warning');
      tripal_report_error('tripal_feature', TRIPAL_WARNING, 'Insert feature: Unable to create feature where values: %values',
        ['%values' => print_r($values, TRUE)]);
      return;
    }
    $feature_id = $feature['feature_id'];

    // add the genbank accession and synonyms
    chado_feature_add_synonyms($node->synonyms, $feature_id);

    // * Properties Form *
    $details = [
      'property_table' => 'featureprop',
      // the name of the prop table
      'base_table' => 'feature',
      // the name of your chado base table
      'foreignkey_name' => 'feature_id',
      // the name of the key in your base table
      'foreignkey_value' => $feature_id
      // the value of the feature_id key
    ];
    chado_update_node_form_properties($node, $details);

    // * Additional DBxrefs Form *
    $details = [
      'linking_table' => 'feature_dbxref',
      // the name of your _dbxref table
      'foreignkey_name' => 'feature_id',
      // the name of the key in your base table
      'foreignkey_value' => $feature_id
      // the value of the feature_id key
    ];
    chado_update_node_form_dbxrefs($node, $details);

    // * Relationships Form *
    $details = [
      'relationship_table' => 'feature_relationship',
      'foreignkey_value' => $feature_id,
    ];
    chado_update_node_form_relationships($node, $details);

  }
  else {
    $feature_id = $node->feature_id;
  }

  // Make sure the entry for this feature doesn't already exist in the
  // chado_feature table if it doesn't exist then we want to add it.
  $check_org_id = chado_get_id_from_nid('feature', $node->nid);
  if (!$check_org_id) {
    $record = new stdClass();
    $record->nid = $node->nid;
    $record->vid = $node->vid;
    $record->feature_id = $feature_id;
    drupal_write_record('chado_feature', $record);
  }
}

/**
 * Implements hook_update().
 *
 * @ingroup tripal_legacy_feature
 */
function chado_feature_update($node) {

  $node->uniquename = trim($node->uniquename);
  $node->fname = trim($node->fname);
  $node->feature_type = trim($node->feature_type);
  $node->residues = trim($node->residues);


  $residues = preg_replace("/[\n\r\s]/", "", $node->residues);
  $obsolete = 'FALSE';
  if ($node->is_obsolete) {
    $obsolete = 'TRUE';
  }

  // get the feature type id
  $values = [
    'cv_id' => [
      'name' => 'sequence',
    ],
    'name' => $node->feature_type,
  ];
  $type = chado_select_record('cvterm', ['cvterm_id'], $values);

  $feature_id = chado_get_id_from_nid('feature', $node->nid);

  if (sizeof($type) > 0) {
    $match = [
      'feature_id' => $feature_id,
    ];
    $values = [
      'organism_id' => $node->organism_id,
      'name' => $node->fname,
      'uniquename' => $node->uniquename,
      'residues' => $residues,
      'seqlen' => drupal_strlen($residues),
      'is_obsolete' => $obsolete,
      'type_id' => $type[0]->cvterm_id,
      'md5checksum' => md5($residues),
    ];
    $options = ['return_record' => TRUE];
    $status = chado_update_record('feature', $match, $values, $options);

    // add the genbank synonyms
    chado_feature_add_synonyms($node->synonyms, $feature_id);

    // * Properties Form *
    $details = [
      'property_table' => 'featureprop',
      // the name of the prop table
      'base_table' => 'feature',
      // the name of your chado base table
      'foreignkey_name' => 'feature_id',
      // the name of the key in your base table
      'foreignkey_value' => $feature_id
      // the value of the feature_id key
    ];
    chado_update_node_form_properties($node, $details);

    // * Additional DBxrefs Form *
    $details = [
      'linking_table' => 'feature_dbxref',
      // the name of your _dbxref table
      'foreignkey_name' => 'feature_id',
      // the name of the key in your base table
      'foreignkey_value' => $feature_id
      // the value of the feature_id key
    ];
    chado_update_node_form_dbxrefs($node, $details);

    // * Relationships Form *
    $details = [
      'relationship_table' => 'feature_relationship',
      'foreignkey_value' => $feature_id,
    ];
    chado_update_node_form_relationships($node, $details);

  }
  else {
    drupal_set_message(t('Unable to update feature.'), 'warning');
    tripal_report_error('tripal_feature', TRIPAL_WARNING,
      'Update feature: Unable to update feature where values: %values',
      ['%values' => print_r($values, TRUE)]
    );
  }


}

/**
 * Implements hook_delete().
 *
 * @ingroup tripal_legacy_feature
 */
function chado_feature_delete($node) {

  $feature_id = chado_get_id_from_nid('feature', $node->nid);

  // If we don't have a feature id for this node then this isn't a node of
  // type chado_library or the entry in the chado_library table was lost.
  if (!$feature_id) {
    return;
  }

  // Remove the drupal content.
  $sql_del = "DELETE FROM {chado_feature} WHERE nid = :nid AND vid = :vid";
  db_query($sql_del, [':nid' => $node->nid, ':vid' => $node->vid]);
  $sql_del = "DELETE FROM {node} WHERE nid = :nid AND vid = :vid";
  db_query($sql_del, [':nid' => $node->nid, ':vid' => $node->vid]);
  $sql_del = "DELETE FROM {node_revision} WHERE nid = :nid AND vid = :vid";
  db_query($sql_del, [':nid' => $node->nid, ':vid' => $node->vid]);


  // Remove data from feature tables of chado database.  This will
  // cause a cascade delete and remove all data in referencing tables
  // for this feature. However, we need t specifically delete from the
  // featureloc table because the box() PLSQL function calls another
  // function that does not reference the 'chado' schema and causes an error
  // the chado_query function can handle this problem so we specificall delete
  // from that table to prevent the error. The same problem exists for the
  // frange.featuregroup table
  $previous_db = chado_set_active('chado');
  db_query("DELETE FROM frange.featuregroup WHERE subject_id = :feature_id", [':feature_id' => $feature_id]);
  db_query("DELETE FROM frange.featuregroup WHERE object_id = :feature_id", [':feature_id' => $feature_id]);
  db_query("DELETE FROM frange.featuregroup WHERE group_id = :feature_id", [':feature_id' => $feature_id]);
  db_query("DELETE FROM frange.featuregroup WHERE srcfeature_id = :feature_id", [':feature_id' => $feature_id]);
  chado_set_active($previous_db);

  chado_query("DELETE FROM {featureloc} WHERE feature_id = :feature_id", [':feature_id' => $feature_id]);
  chado_query("DELETE FROM {featureloc} WHERE srcfeature_id = :feature_id", [':feature_id' => $feature_id]);
  chado_query("DELETE FROM {feature} WHERE feature_id = :feature_id", [':feature_id' => $feature_id]);

  drupal_set_message(t("The feature and all associated data were removed"));
}

/**
 * Add synonyms to a feature
 *
 * @param $synonyms
 *   A string containing synonyms separated by a return character
 * @param $feature_id
 *   The feature to attach the synonyms to
 *
 * @ingroup tripal_legacy_feature
 */
function chado_feature_add_synonyms($synonyms, $feature_id) {

  // separate synomys by carriage returns
  $synonyms = preg_replace("/[\n\r]+/", " ", $synonyms);
  // split the synonyms into an array based on a space as the delimieter
  $syn_array = [];
  $syn_array = explode(" ", $synonyms);


  // remove any old synonyms
  $feature_syn_dsql = "DELETE FROM {feature_synonym} WHERE feature_id = :feature_id";
  if (!chado_query($feature_syn_dsql, [':feature_id' => $feature_id])) {
    tripal_report_error('tripal_feature', TRIPAL_ERROR, "Could not remove synonyms from feature. ", []);
    return;
  }

  // return if we don't have any synonmys to add
  if (!$synonyms) {
    return;
  }
  // iterate through each synonym and add it to the database
  foreach ($syn_array as $syn) {
    // skip this item if it's empty
    if (!$syn) {
      break;
    }

    // check to see if we have this accession number already in the database
    // if so then don't add it again. it messes up drupal if the insert fails.
    // It is possible for the accession number to be present and not the feature
    $synonym_sql = "SELECT synonym_id FROM {synonym} WHERE name = :name";
    $synonym = chado_query($synonym_sql, [':name' => $syn])->fetchObject();
    if (!$synonym) {
      $synonym_isql = "
        INSERT INTO {synonym} (name, synonym_sgml, type_id)
        VALUES (:name, :synonym_sgml,
          (SELECT cvterm_id
           FROM {cvterm} CVT
             INNER JOIN {cv} ON CVT.cv_id = CV.cv_id
           WHERE CV.name = 'feature_property' and CVT.name = 'synonym')
          )
      ";
      if (!chado_query($synonym_isql, [
        ':name' => $syn,
        ':synonym_sgml' => $syn,
      ])) {
        tripal_report_error('tripal_feature', "Could not add synonym. ", [], TRIPAL_WARNING);
        return;
      }
      // now get the synonym we just added
      $synonym_sql = "SELECT synonym_id FROM {synonym} WHERE name = :name";
      $synonym = chado_query($synonym_sql, [':name' => $syn])->fetchObject();
    }

    // now add in our new sysnonym
    $feature_syn_isql = "
      INSERT INTO {feature_synonym} (synonym_id,feature_id,pub_id)
      VALUES (:synonym_id, :feature_id, :pub_id)";
    $args = [
      ':synonym_id' => $synonym->synonym_id,
      ':feature_id' => $feature_id,
      ':pub_id' => 1,
    ];
    if (!chado_query($feature_syn_isql, $args)) {
      tripal_report_error('tripal_feature', "Could not associate synonym with feature. ", [], TRIPAL_WARNING);
      return;
    }
  }
}

/**
 * Implements hook_load().
 *
 * When a node is requested by the user this function is called to allow us
 *  to add auxiliary data to the node object.
 *
 * @ingroup tripal_legacy_feature
 */
function chado_feature_load($nodes) {

  foreach ($nodes as $nid => $node) {
    // find the feature and add in the details
    $feature_id = chado_get_id_from_nid('feature', $nid);

    // if the nid does not have a matching record then skip this node.
    // this can happen with orphaned nodes.
    if (!$feature_id) {
      continue;
    }

    // build the feature variable
    $values = ['feature_id' => $feature_id];
    $feature = chado_generate_var('feature', $values);
    $nodes[$nid]->feature = $feature;

    // Now get the title
    $node->title = chado_get_node_title($node);
  }
}

/**
 * Implements hook_node_presave().
 * Acts on all content types.
 *
 * @ingroup tripal_legacy_feature
 */
function tripal_feature_node_presave($node) {

  // set the title to ensure it is always unique
  switch ($node->type) {
    // This step is for setting the title for the Drupal node.  This title
    // is permanent and thus is created to be unique.  Title changes provided
    // by tokens are generated on the fly dynamically, but the node title
    // seen in the content listing needs to be set here. Do not call
    // the chado_get_node_title() function here to set the title as the node
    // object isn't properly filled out and the function will fail.
    case 'chado_feature':
      // for a form submission the fields are part of the node object
      // but for a sync the fields are in an object of the node
      $name = '';
      $uname = '';
      $type = '';
      $organism_id = NULL;
      if (property_exists($node, 'uniquename')) {
        $organism_id = $node->organism_id;
        $name = $node->name;
        $uname = $node->uniquename;
        $type = $node->feature_type;
      }
      else {
        if (property_exists($node, 'feature')) {
          $organism_id = $node->feature->organism_id;
          $name = $node->feature->name;
          $uname = $node->feature->uniquename;
          $type = $node->feature->cvtname;
        }
      }

      $values = ['organism_id' => $organism_id];
      $organism = chado_select_record('organism', [
        'genus',
        'species',
      ], $values);
      $node->title = "$name, $uname ($type) " . $organism[0]->genus . ' ' . $organism[0]->species;

      break;
  }
}

/**
 * Implements hook_node_insert().
 * Acts on all content types.
 *
 * @ingroup tripal_legacy_feature
 */
function tripal_feature_node_insert($node) {
  // set the URL path after inserting.  We do it here because we do not
  // know the feature_id in the presave
  switch ($node->type) {
    case 'chado_feature':

      // We still don't have a fully loaded node object in this hook. Therefore,
      // we need to simulate one so that the right values are available for
      // the URL to be determined.
      $feature_id = chado_get_id_from_nid('feature', $node->nid);
      $node->feature = chado_generate_var('feature', ['feature_id' => $feature_id]);

      // Now use the API to set the path.
      chado_set_node_url($node);

      // Now get the title.
      $node->title = chado_get_node_title($node);
      break;
  }
}

/**
 * Implements hook_node_update().
 * Acts on all content types.
 *
 * @ingroup tripal_legacy_feature
 */
function tripal_feature_node_update($node) {

  // add items to other nodes, build index and search results
  switch ($node->type) {
    case 'chado_feature':

      // Now use the API to set the path.
      chado_set_node_url($node);

      // Now get the title
      $node->title = chado_get_node_title($node);

      break;
  }
}

/**
 * Implements hook_node_view().
 * Acts on all content types.
 *
 * @ingroup tripal_legacy_feature
 */
function tripal_feature_node_view($node, $view_mode, $langcode) {

  switch ($node->type) {
    case 'chado_feature':
      // Show feature browser and counts
      if ($view_mode == 'full') {
        $node->content['tripal_feature_alignments'] = [
          '#theme' => 'tripal_feature_alignments',
          '#node' => $node,
          '#tripal_toc_id' => 'alignments',
          '#tripal_toc_title' => 'Alignments',
        ];
        $node->content['tripal_feature_analyses'] = [
          '#theme' => 'tripal_feature_analyses',
          '#node' => $node,
          '#tripal_toc_id' => 'analyses',
          '#tripal_toc_title' => 'Analyses',
        ];
        $node->content['tripal_feature_base'] = [
          '#theme' => 'tripal_feature_base',
          '#node' => $node,
          '#tripal_toc_id' => 'base',
          '#tripal_toc_title' => 'Overview',
          '#weight' => -100,
        ];
        $node->content['tripal_feature_properties'] = [
          '#theme' => 'tripal_feature_properties',
          '#node' => $node,
          '#tripal_toc_id' => 'properties',
          '#tripal_toc_title' => 'Properties',
        ];
        $node->content['tripal_feature_publications'] = [
          '#theme' => 'tripal_feature_publications',
          '#node' => $node,
          '#tripal_toc_id' => 'publications',
          '#tripal_toc_title' => 'Publications',
        ];
        $node->content['tripal_feature_references'] = [
          '#theme' => 'tripal_feature_references',
          '#node' => $node,
          '#tripal_toc_id' => 'references',
          '#tripal_toc_title' => 'Cross References',
        ];
        $node->content['tripal_feature_relationships'] = [
          '#theme' => 'tripal_feature_relationships',
          '#node' => $node,
          '#tripal_toc_id' => 'relationships',
          '#tripal_toc_title' => 'Relationships',
        ];
        $node->content['tripal_feature_seqence'] = [
          '#theme' => 'tripal_feature_sequence',
          '#node' => $node,
          '#tripal_toc_id' => 'sequences',
          '#tripal_toc_title' => 'Sequences',
        ];
        $node->content['tripal_feature_synonyms'] = [
          '#theme' => 'tripal_feature_synonyms',
          '#node' => $node,
          '#tripal_toc_id' => 'synonyms',
          '#tripal_toc_title' => 'Synonyms',
        ];
        $node->content['tripal_feature_terms'] = [
          '#theme' => 'tripal_feature_terms',
          '#node' => $node,
          '#tripal_toc_id' => 'terms',
          '#tripal_toc_title' => 'Annotated Terms',
        ];
      }
      if ($view_mode == 'teaser') {
        $node->content['tripal_feature_teaser'] = [
          '#theme' => 'tripal_feature_teaser',
          '#node' => $node,
        ];
      }
      break;
    case 'chado_organism':
      // Show feature browser and counts
      if ($view_mode == 'full') {
        $node->content['tripal_organism_feature_counts'] = [
          '#theme' => 'tripal_organism_feature_counts',
          '#node' => $node,
          '#tripal_toc_id' => 'feature_counts',
          '#tripal_toc_title' => 'Feature Summary',
        ];
        $node->content['tripal_organism_feature_browser'] = [
          '#theme' => 'tripal_organism_feature_browser',
          '#node' => $node,
          '#tripal_toc_id' => 'feature_browser',
          '#tripal_toc_title' => 'Feature Browser',
        ];
      }
      break;
    // TODO: handle these node types. Should we also have a feature browser?
    case 'chado_library':
      break;
    case 'chado_stock':
      break;
    case 'chado_analysis':
      break;
  }
}

/**
 * Implements [content_type]_chado_node_default_title_format().
 *
 * Defines a default title format for the Chado Node API to set the titles on
 * Chado Feature nodes based on chado fields.
 */
function chado_feature_chado_node_default_title_format() {
  return '[feature.name], [feature.uniquename] ([feature.type_id>cvterm.name]) [feature.organism_id>organism.genus] [feature.organism_id>organism.species]';
}

/**
 * Implements hook_chado_node_default_url_format().
 *
 * Designates a default URL format for feature nodes.
 */
function chado_feature_chado_node_default_url_format() {
  return '/feature/[feature.organism_id>organism.genus]/[feature.organism_id>organism.species]/[feature.type_id>cvterm.name]/[feature.uniquename]';
}