tripal_feature-db_references.inc

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tripal_feature/includes/tripal_feature-db_references.inc
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<?php

/**
 * @file
 * @todo Add file header description
 */

/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_feature_add_ALL_dbreferences_page($node) {
  $output = '';

  $output .= tripal_feature_implement_add_chado_properties_progress('db_references') . '<br />';
  $output .= '<b>All Database References should strictly pertain to THE CURRENT Individual</b><br />';
  $output .= '<br /><b>Current Database References</b><br />';
  $output .= list_dbreferences_for_node($node->db_references);
  $output .= '<br /><br />';
  $output .= drupal_get_form('tripal_feature_add_ONE_dbreference_form', $node);
  $output .= '<br />';
  $output .= drupal_get_form('tripal_feature_implement_add_chado_properties_navigate', 'db_references', $node->nid);
  return $output;
}

/**
 * Implements Hook_form()
 * Handles adding of Database References to features
 *
 * @ingroup tripal_feature
 */
function tripal_feature_add_ONE_dbreference_form($form_state, $node) {

  $form['nid'] = array(
    '#type' => 'hidden',
    '#value' => $node->nid
  );

  $form['feature_id'] = array(
    '#type' => 'hidden',
    '#value' => $node->feature->feature_id,
  );

  $form['add_dbreference'] = array(
    '#type' => 'fieldset',
    '#title' => t('Add Database References') . '<span class="form-optional" title="This field is optional">(optional)</span>',
  );

  $form['add_dbreference']['accession'] = array(
    '#type' => 'textfield',
    '#title' => t('Accession'),
    '#required' => TRUE,
  );

  $form['add_dbreference']['description'] = array(
    '#type' => 'textarea',
    '#title' => t('Description of Reference') . '<span class="form-optional" title="This field is optional">+</span>',
    '#description' => t('Optionally enter a description about the database accession.'),
  );

  $db_options = tripal_db_get_db_options();
  $db_options[0] = 'Select a Database';
  ksort($db_options);
  $form['add_dbreference']['db_id'] = array(
    '#type' => 'select',
    '#title' => t('Database'),
    '#options' => $db_options,
    '#required' => TRUE,
  );

  $form['add_dbreference']['submit'] = array(
    '#type' => 'submit',
    '#value' => t('Add Database Reference')
  );

  return $form;
}

/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_feature_add_ONE_dbreference_form_validate($form, &$form_state) {

  $db_id = $form_state['values']['db_id'];
  $accession = $form_state['values']['accession'];
  $description = $form_state['values']['description'];
  $feature_id = $form_state['values']['feature_id'];
  $nid = $form_state['values']['nid'];

  // Check database is valid db_id in chado
  $tmp_obj = db_fetch_object(chado_query("SELECT count(*) as count FROM {db} WHERE db_id=%d", $db_id));
  if ($tmp_obj->count != 1) {
    form_set_error('database', 'The database you selected is not valid. Please choose another one.');
  }

  // Check Accession is unique for database
  $sql = "SELECT count(*) as count FROM {dbxref} WHERE accession='%s' and db_id = %d";
  $tmp_obj = db_fetch_object(chado_query($sql, $accession, $db_id));

  if ($tmp_obj->count > 0) {
    form_set_error('accession', 'This accession has already been assigned to another feature in the selected database.');
  }

}

/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_feature_add_ONE_dbreference_form_submit($form, &$form_state) {

  $db_id = $form_state['values']['db_id'];
  $accession = $form_state['values']['accession'];
  $description = $form_state['values']['description'];
  $feature_id = $form_state['values']['feature_id'];
  $nid = $form_state['values']['nid'];

  // create dbxref
  $isql =  "INSERT INTO {dbxref} (db_id, accession, description) VALUES (%d, '%s', '%s')";
  chado_query($isql, $db_id, $accession, $description);

  //create feature_dbxref
  $dbxref = tripal_db_get_dbxref( array('db_id' => array('type' => 'INT', 'value' => $form_state['values']['db_id']),
                     'accession' => array('type' => 'STRING', 'exact' => TRUE, 'value' => $form_state['values']['accession']) ) );

  if (!empty($dbxref->dbxref_id)) {
      $isql = "INSERT INTO {feature_dbxref} (feature_id, dbxref_id) VALUES (%d, %d)";
      chado_query($isql, $feature_id, $dbxref->dbxref_id);
      drupal_set_message(t('Successfully Added Database Reference'));
      drupal_goto('node/' . $nid);
  }
  else {
    drupal_set_message(t('Database reference NOT successfully created...'), 'error');
  } //end of if dbxref was created successfully

}


/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_feature_edit_ALL_dbreferences_page($node) {
  $output = '';

  $output .= drupal_get_form('tripal_feature_edit_ALL_db_references_form', $node);
  $output .= '<br />';
  $output .= drupal_get_form('tripal_feature_add_ONE_dbreference_form', $node);
  $output .= '<br />';
  $output .= drupal_get_form('tripal_feature_implement_back_to_feature_button', $node->nid);

  return $output;
}

/**
 * Implements Hook_form()
 * Handles adding of DB References to Features
 *
 * @ingroup tripal_feature
 */
function tripal_feature_edit_ALL_db_references_form($form_state, $node) {
  $form = array();

  $form['nid'] = array(
    '#type' => 'hidden',
    '#value' => $node->nid
  );

  $i=0;

  $feature = $node->feature;
  $references = tripal_feature_load_references($feature->feature_id);

  // pre populate the database options
  $db_options = tripal_db_get_db_options();
  $db_options[0] = 'Select a Database';
  ksort($db_options);

  if (sizeof($references) != 0) {
    foreach ($references as $ref) {
      $i++;
      $form["num-$i"] = array(
        '#type' => 'fieldset',
        '#title' => t("Database Reference") . " $i"
      );

      $form["num-$i"]["accession-$i"] = array(
        '#type' => 'textfield',
        '#title' => t('Accession'),
        '#size' => 30,
        '#required' => TRUE,
        '#default_value' => $ref->accession
      );

      $form["num-$i"]["db_id-$i"] = array(
        '#type' => 'select',
        '#title' => t('Database'),
        '#options' => $db_options,
        '#required' => TRUE,
        '#default_value' => $ref->db_id
      );


      $form["num-$i"]["dbxref_id-$i"] = array(
        '#type' => 'hidden',
        '#value' => $ref->dbxref_id
      );

      $form["num-$i"]["delete-$i"] = array(
        '#type' => 'submit',
        '#value' => t("Delete"),
        '#name' => "delete-$i",
      );

      }

      $form['num_db_references'] = array(
        '#type' => 'hidden',
        '#value' => $i
      );

      $form["submit-edits"] = array(
        '#type' => 'submit',
        '#value' => t('Update All References')
      );
  } //end of foreach db ref
  return $form;
}

/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_feature_edit_ALL_db_references_form_submit($form, &$form_state) {

  $num_refs = $form_state['values']['num_db_references'];
  $action = $form_state['clicked_button']['#value'];
  $button = $form_state['clicked_button']['#name'];
  $nid = $form_state['values']['nid'];

  if (strcmp($action, 'Update All References')==0) {
    for ($i=1; $i<=$num_refs; $i++) {
    $dbxref_id = $form_state['values']["dbxref_id-$i"];
    $db_id = $form_state['values']["db_id-$i"];
    $accession = $form_state['values']["accession-$i"];
      tripal_feature_update_db_reference($dbxref_id, $db_id, $accession);
    }
    drupal_set_message(t("Updated all Database References"));
    drupal_goto('node/' . $nid);
  }
  elseif (strcmp($action, 'Delete')==0) {
    if (preg_match('/delete-(\d+)/', $button, $matches) ) {
      $i = $matches[1];
      $dbxref_id = $form_state['values']["dbxref_id-$i"];
      tripal_feature_delete_db_reference($dbxref_id);
      drupal_set_message(t("Deleted Database Reference"));
      drupal_goto('node/' . $nid);
    }
    else {
      drupal_set_message(t("Could not remove database reference:"), 'error');
    }
    }
  else {
    drupal_set_message(t("Unrecognized Button Pressed"), 'error');
  }

}

/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_feature_update_db_reference($dbxref_id, $db_id, $accession) {

  $sql =  "UPDATE {dbxref} SET db_id=%d, accession='%s' WHERE dbxref_id=%d";
  chado_query($sql, $db_id, $accession, $dbxref_id);

}

/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_feature_delete_db_reference($dbxref_id) {

  chado_query(
    "DELETE FROM {dbxref} WHERE dbxref_id=%d",
    $dbxref_id
  );

  chado_query(
    "DELETE FROM {feature_dbxref} WHERE dbxref_id=%d",
    $dbxref_id
  );
}

/**
 *
 *
 * @ingroup tripal_feature
 */
function theme_tripal_feature_edit_ALL_db_references_form($form) {
  $output = '';

  $output .= '<br /><fieldset>';
  $output .= '<legend>Edit Existing Database References<span class="form-optional" title="This field is optional">(optional)</span></legend>';
  $output .= '<p>Below is a list of already existing database references, one per line. When entering a database reference, the accession '
         .'is a unique identifier for this feature in the specified database.</p>';
  $output .= '<table>';
  $output .= '<tr><th>#</th><th>Database</th><th>Accession</th><th></th></tr>';

  for ($i=1; $i<=$form['num_db_references']['#value']; $i++) {
    $output .= '<tr><td>' . drupal_render($form["num-$i"]) . '</td><td>'
             . drupal_render($form["database-$i"]) . '</td><td>'
         . drupal_render($form["accession-$i"]) . '</td><td>'
         . drupal_render($form["submit-$i"]) . '</td></tr>';
  }

  $output .= '</table><br />';
  $output .= drupal_render($form);
  $output .= '</fieldset>';

  return $output;
}

/**
 *
 *
 * @ingroup tripal_feature
 */
function list_dbreferences_for_node($db_references) {

  if (!empty($db_references) ) {
    $output = '<table>';
    $output .= '<tr><th>Database</th><th>Accession</th></tr>';

    foreach ($db_references as $db) {
        $output .= '<tr><td>' . $db->db_name . '</td><td>' . $db->accession . '</td></tr>';
    } // end of foreach db reference

    $output .= '</table>';

  }
  else {
    $output = 'No Database References Added to the Current Feature';
  }

  return $output;
}