tripal/tripal_stock/includes/tripal_stock-db_references.inc

<?php
/**
 * @file
 * @todo Add file header description
 */

/**
 * Display the ADD Database References to Stock Page
 *
 * This page is displayed after the stock is created as part of a simulated multi-part form
 *
 * @param $node
 *   The stock node to add the database references to
 *
 * @return
 *   HTML formatted output
 *
 * @ingroup tripal_stock
 */
function tripal_stock_add_ALL_dbreferences_page($node) {
  $output = '';

  $output .= tripal_stock_add_chado_properties_progress('db_references') . '<br />';
  $output .= '<b>All Database References should strictly pertain to THE CURRENT Individual</b><br />';
  $output .= '<br />';
  $output .= theme('tripal_stock_references', $node);
  $output .= '<br /><br />';
  $output .= drupal_get_form('tripal_stock_add_ONE_dbreference_form', $node);
  $output .= '<br />';
  $output .= drupal_get_form('tripal_stock_add_chado_properties_navigate', 'db_references', $node->nid);
  return $output;
}


/**
 * Implements Hook_form(): Handles adding of Database References to Stocks
 *
 * @param $form_state
 *   An array describing the current state of the form
 * @param $node
 *   The stock node to add the database reference to
 *
 * @return
 *   An array describing the form to be rendered
 *
 * @ingroup tripal_stock
 */
function tripal_stock_add_ONE_dbreference_form($form_state, $node) {

  $stock_id = $node->stock->stock_id;

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

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

  $form['add_properties']['db_stock_id'] = array(
    '#type' => 'value',
    '#value' => $stock_id,
    '#required' => TRUE

  );

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

  $form['add_dbreference']['db_description'] = array(
    '#type' => 'textarea',
    '#title' => t('Description of Database 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']['database'] = array(
    '#type' => 'select',
    '#title' => t('Database'),
    '#options' => $db_options,
  );

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

  return $form;
}

/**
 * Implements hook_form_validate(): Validates the input from tripal_stock_add_ONE_dbreference_form()
 *
 * @param $form
 *   An array describing the form that was rendered
 * @param $form_state
 *   An array describing the current state of the form including user input
 *
 * @ingroup tripal_stock
 */
function tripal_stock_add_ONE_dbreference_form_validate($form, &$form_state) {

  // Only ensure db reference valid if adding
  if ($form_state['clicked_button']['#value'] == t('Add Database Reference') ) {
    //Do work of required validators
    if ($form_state['values']['accession'] == '') {
      form_set_error('accession', 'Accession field is Required.');
    }

    // Check database is valid db_id in chado
    if ( $form_state['values']['database'] > 0) {
      $sql = "SELECT count(*) as count FROM {db} WHERE db_id = :db_id";
      $tmp_obj = chado_query($sql, array(':db_id' => $form_state['values']['database']))->fetchObject();

      if ($tmp_obj->count != 1) {
        form_set_error('database', 'The database you selected is not valid. Please choose another one.');
      }
    }
    else {
      form_set_error('database', 'Please select a database');
    }

    // Check Accession is unique for database
    $sql =  "SELECT count(*) as count FROM {dbxref} WHERE accession = :accession";
    $tmp_obj = chado_query($sql, array(':accession' => $form_state['values']['accession']))->fetchObject();

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

  } //end of if adding

}

/**
 * Implements hoook_form_submit(): Actually adds the db reference to the stock
 *
 * @param $form
 *   An array describing the form that was rendered
 * @param $form_state
 *   An array describing the current state of the form including user input
 *
 * @ingroup tripal_stock
 */
function tripal_stock_add_ONE_dbreference_form_submit($form, &$form_state) {

  // FIX: Sometimes on programatic submission of form (drupal_execute) values in the form state get lost
  //     however, the post values always seem to be correct
  if (empty($form_state['values']['db_stock_id'])) {
  $form_state['values']['db_stock_id'] = $form_state['clicked_button']['#post']['db_stock_id']; }

  // Only Create if valid
  if ($form_state['values']['database'] > 0) {


    // create dbxref
    $sql = "
      INSERT INTO {dbxref} (db_id, accession, description) 
      VALUES (:db_id, :accession, :description)
    ";
    chado_query($sql, array(':db_id' => $form_state['values']['database'], 
      ':accession' => $form_state['values']['accession'], 
      ':description' => $form_state['values']['db_description']
    ));

    //create stock_dbxref
    $dbxref = tripal_db_get_dbxref_by_accession($form_state['values']['accession'], $form_state['values']['database']);
    if (!empty($dbxref->dbxref_id)) {
      $sl = "INSERT INTO {stock_dbxref} (stock_id, dbxref_id) VALUES (:stock_id, :dbxref_id)";
      chado_query($sql, array(':stock_id' => $form_state['values']['db_stock_id'],
        ':dbxref_id' => $dbxref->dbxref_id));

      drupal_set_message(t('Successfully Added Database Reference'));
    }
    else {
      drupal_set_message(t('Database reference NOT successfully created...'), 'error');
    } //end of if dbxref was created successfully
  } //end of if valid db reference

}

/**
 * Display the EDIT Database References to Stock Page
 *
 * This page is displayed as a tab on each stock details page (by default)
 *
 * @param $node
 *   The stock node to add the database references to
 *
 * @return
 *   HTML formatted output
 *
 * @ingroup tripal_stock
 */
function tripal_stock_edit_ALL_dbreferences_page($node) {
  $output = '';

  $output .= drupal_get_form('tripal_stock_edit_ALL_db_references_form', $node);
  $output .= '<br />';
  $output .= drupal_get_form('tripal_stock_add_ONE_dbreference_form', $node);
  $output .= '<br />';
  $output .= drupal_get_form('tripal_stock_back_to_stock_button', $node->nid);

  return $output;
}

/**
 * Implements Hook_form(): Handles adding of Database References to Stocks
 *
 * Specifically this adds dbxrefs to a current stock using the stock_dbxref table
 *
 * @param $form_state
 *   An array describing the current state of the form
 * @param $node
 *   The stock node whose database references should be edited
 *
 * @return
 *   An array describing the form to be rendered
 *
 * @ingroup tripal_stock
 */
function tripal_stock_edit_ALL_db_references_form($form_state, $node) {
  $form = array();

  // Add database references to the node
  $node = tripal_core_expand_chado_vars($node, 'table', 'stock_dbxref');

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

  $i=0;
  if (!$node->stock->stock_dbxref) {
    $node->stock->stock_dbxref = array();
  }
  elseif (!is_array($node->stock->stock_dbxref)) {
    $node->stock->stock_dbxref = array($node->stock->stock_dbxref);
  }
  if (sizeof($node->stock->stock_dbxref) != 0) {
  foreach ($node->stock->stock_dbxref as $ref) {
    $i++;
    $form["num-$i"] = array(
      '#type' => 'item',
      '#value' => $i . '.'
    );

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

    $db_options = tripal_db_get_db_options();
    $db_options[0] = 'Select a Database';
    ksort($db_options);
    $form["database-$i"] = array(
      '#type' => 'select',
      //'#title' => t('Database'),
      '#options' => $db_options,
      '#default_value' => $ref->dbxref_id->db_id->db_id
    );


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

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

  }} //end of foreach db ref

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

  $form["submit-edits"] = array(
    '#type' => 'submit',
    '#value' => t('Update DB References')
  );

  return $form;
}

/**
 * Implements hook_form_submit(): Actually edits the database references
 *
 * @param $form
 *   An array representing the form
 * @param $form_state
 *   An array representing the current state of the form including user input
 *
 * @ingroup tripal_stock
 */
function tripal_stock_edit_ALL_db_references_form_submit($form, &$form_state) {

  if ($form_state['clicked_button']['#value'] == t('Update DB References') ) {

       //Update all
    for ($i=1; $i<=$form_state['values']['num_db_references']; $i++) {
      tripal_stock_update_db_reference(
        $form_state['values']["id-$i"],
        $form_state['values']["database-$i"],
        $form_state['values']["accession-$i"]
      );
    }
      drupal_set_message(t("Updated all Database References"));
      drupal_goto('node/' . $form_state['values']['nid']);

  }
  elseif ( preg_match('/Delete #(\d+)/', $form_state['clicked_button']['#value'], $matches) ) {

    $i = $matches[1];
    tripal_stock_delete_db_reference($form_state['values']["id-$i"]);
    drupal_set_message(t("Deleted Database Reference"));

  }
  else {
    drupal_set_message(t("Unrecognized Button Pressed"), 'error');

  }
}

/**
 * Updates a Database Reference
 *
 * @todo Make this function more generic ie: update all parts of the dbxref and db
 *
 * @param $dbxref_id
 *   The unique chado identifier of the database reference to be updated
 * @param $database_id
 *   The new database ID
 * @param $accession
 *   The new accession
 *
 * @ingroup tripal_stock
 */
function tripal_stock_update_db_reference($dbxref_id, $database_id, $accession) {
  $sql = "UPDATE {dbxref} SET db_id = :db_id, accession = :accession WHERE dbxref_id = :dbxref_id";
  chado_query($sql, array(':db_id' => $database_id, ':accession' => $accession, ':dbxref_id' =>  $dbxref_id));
}

/**
 * Deletes a given database reference
 *
 * @param $dbxref_id
 *   The chado unique idenfier for the database reference to be deleted
 *
 * @return
 *   TRUE on success; FALSE otherwise
 *
 * @ingroup tripal_stock
 */
function tripal_stock_delete_db_reference($dbxref_id) {
  chado_query("DELETE FROM {dbxref} WHERE dbxref_id = :dbxref_id", array(':dbxref_id' => $dbxref_id));
  chado_query("DELETE FROM {stock_dbxref} WHERE dbxref_id = :dbxref_id", array(':dbxref_id' => $dbxref_id));
}

/**
 * Themes the Edit All Database References for a stock form
 *
 * @param $form
 *   An array describing the form to be themed
 *
 * @return
 *   An HTML rendering of the form
 *
 * @ingroup tripal_stock
 */
function theme_tripal_stock_edit_ALL_db_references_form($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 stock 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;
}


/**
 *  List all database references for a given node
 *
 * @todo Make this function a theme function
 *
 * @param $db_references
 *   An array of database references to be listed
 *
 * @return
 *   HTML representation of the list
 *
 * @ingroup tripal_stock
 */
function tripal_stock_list_dbreferences_for_node($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 Stock';
  }

  return $output;
}