tripal/tripal_stock/includes/tripal_stock-administration.inc

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

/**
 * Purpose: Provide administration options for chado_stocks
 *
 * @return
 *   Form array (as described by the drupal form api)
 *
 * @ingroup tripal_stock
 */
function tripal_stock_admin() {
  $form = array();

  // before proceeding check to see if we have any
  // currently processing jobs. If so, we don't want
  // to give the opportunity to sync Stocks
  $active_jobs = FALSE;
  if (tripal_get_module_active_jobs('tripal_stock')) {
    $active_jobs = TRUE;
  }
  if ($active_jobs) {
    $form['notice'] = array(
       '#type' => 'fieldset',
       '#title' => t('Stock Management Temporarily Unavailable')
    );
    $form['notice']['message'] = array(
       '#value' => t("Currently, stock management jobs are waiting or ".
          "are running. Managemment features have been hidden until these ".
          "jobs complete.  Please check back later once these jobs have ".
          "finished.  You can view the status of pending jobs in the Tripal ".
          "jobs page."),
    );
  }
  else {

    // SET Vocabularies -----------------------------------------------------------------------------------------
    $form['set_cv'] = array(
      '#type' => 'fieldset',
      '#title' => t('Set Stock Controlled Vocabularies'),
      '#weight' => -10
    );

    $form['set_cv']['message'] = array(
         '#value' => t("This setting allows you to set which chado controlled vocabularies (cv)"
                ." are used. Cvs are used to control user input for the type of stock,"
          ." any properties they enter for a stock & the types of relationships"
          ." between stocks. Only cvs already loaded into chado can be selected here.")
    );

    // get the list of CVs for the next form element
    $sql = "SELECT * FROM {cv} ORDER BY name";
    $results = chado_query($sql);
    $cv_options = array();
    while ($r = db_fetch_object($results)) {
      $cv_options[$r->cv_id] = $r->name;
    }

    $form['set_cv']['stock_types_cv'] = array(
     '#type' => 'select',
     '#title' => t('Controlled Vocabulary governing Stock Types'),
     '#options' => $cv_options,
     '#default_value' => variable_get('chado_stock_types_cv', 0)
    );

    $form['set_cv']['stock_prop_types_cv'] = array(
     '#type' => 'select',
     '#title' => t('Controlled Vocabulary governing Types of Stock Properties'),
     '#description' => t("This cv must contain a cvterm entry where name='synonym'."),
     '#options' => $cv_options,
     '#default_value' => variable_get('chado_stock_prop_types_cv', 0)
    );

    $form['set_cv']['stock_relationship_cv'] = array(
     '#type' => 'select',
     '#title' => t('Controlled Vocabulary governing Types of Relationsips between Stocks'),
     '#options' => $cv_options,
     '#default_value' => variable_get('chado_stock_relationship_cv', 0)
    );

    $form['set_cv']['button'] = array(
      '#type' => 'submit',
      '#value' => t('Set Controlled Vacabularies')
    );

    // SYNC STOCKS-----------------------------------------------------------------------------------------------
    $form['sync'] = array(
      '#type' => 'fieldset',
      '#title' => t('Sync Stocks'),
      '#weight' => -10
    );

    $form['sync']['description'] = array(
      '#type' => 'item',
      '#value' => t("Click the 'Sync all Germplasm' button to create Drupal ".
         "content for stocks in chado. Depending on the ".
         "number of stocks in the chado database this may take a long ".
         "time to complete. ")
    );

    // get the list of organisms
    $sql = "SELECT * FROM {Organism} ORDER BY genus, species";
    $org_rset = chado_query($sql);
    $organisms = array();
    $organisms[''] = '';
    while ($organism = db_fetch_object($org_rset)) {
      $organisms[$organism->organism_id] = "$organism->genus $organism->species ($organism->common_name)";
    }
    $form['sync']['organisms'] = array(
      '#type' => 'checkboxes',
      '#title' => t('Organisms for which Stocks should be sync\'d'),
      '#description' => t('Only sync\'d Organisms are listed. Leaving an organism unchecked does not delete already sync\'d Stocks.'),
      '#options' => $organisms,
      '#required'    => FALSE,
      '#prefix'      => '<div id="lib_boxes">',
      '#suffix'      => '</div>'
    );

    $form['sync']['button'] = array(
      '#type' => 'submit',
      '#value' => t('Sync Stocks')
    );
    get_tripal_stock_admin_form_cleanup_set($form);
  }

  return system_settings_form($form);

}

/**
 * Implements hook_form_validate(): Validates user input
 *
 * @param $form
 *   An array describing the form that was rendered
 * @param $form_state
 *   An array describing the current state of the form including user input
 *
 * @ingroup tripal_stock
 */
function tripal_stock_admin_validate($form, &$form_state) {
  global $user;  // we need access to the user info
  $job_args = array();

  // Sync Stocks
  if ($form_state['values']['op'] == t('Sync Stocks')) {
    // Array organism_id => organims common_name
    //  which only includes those organisms which the user wants to select stocks for
    $organisms_2b_syncd = $form_state['values']['organisms'];

    //for each organism selected submit job (handled by tripal_stock_sync_stock_set)
    //  which syncs all stocks with an organism_id equal to the selelcted organism
    foreach ( $organisms_2b_syncd as $organism_id ) {
      if ($organism_id != 0) {
        $job_args[0] = $organism_id;
        tripal_add_job("Sync Stocks from Organism $organism_id", 'tripal_stock',
          'tripal_stock_sync_stock_set', $job_args, $user->uid);
      }
    }
  }

  if ($form_state['values']['op'] == t('Set Controlled Vacabularies')) {
    variable_set('chado_stock_types_cv', $form_state['values']['stock_types_cv']);
    variable_set('chado_stock_prop_types_cv', $form_state['values']['stock_prop_types_cv']);
    variable_set('chado_stock_relationship_cv', $form_state['values']['stock_relationship_cv']);
  }

  // Submit the Cleanup Job if selected
  if ($form_state['values']['op'] == t('Clean up orphaned stocks')) {
    tripal_add_job('Cleanup orphaned stocks', 'tripal_stock',
       'tripal_stock_cleanup', $job_args, $user->uid);
  }
}

/**
 * Sync stocks associated with a given organism or sync all stocks
 *
 * Note: This is essentially an API function to make tripal stock sync act similar to other tripal modules
 *
 * @param $organism_id
 *   The ID of the organism to sync all stocks for
 * @param $job_id
 *   The ID of the tripal job
 */
function tripal_stock_sync_stocks($organism_id, $job_id) {

  if ($organism_id) {
    return tripal_stock_sync_stock_set($organism_id, $job_id);
  }
  else {
    //get a list of all organisms and sync all stocks for all organisms
    $organisms = tripal_core_chado_select('organism', array('organism_id','genus','species','common_name'), array());
    foreach ($organisms as $o) {
      print "Syncing stocks associated with $o->genus $o->species ($o->common_name)\n";
      tripal_stock_sync_stock_set($o->organism_id, $job_id);
    }
  }

}

/**
 * Syncs all Stocks associated with an organism
 *
 * Note: Handling of multiple organisms is done in tripal_stock_admin_validate()
 *
 * @param $organism_id
 *   The chado primary key of the organism for which stocks should be sync'd
 * @param $job_id
 *   The tripal job ID
 *
 * @return
 *   TRUE if successful; FALSE otherwise
 *
 * @ingroup tripal_stock
 */
function tripal_stock_sync_stock_set($organism_id, $job_id) {
  global $user;

  if (!$organism_id) {
    print '0 Stocks to Sync -No Organisms Selected.\n';
  }
  else {

  // Get list of stocks to sync
  $result = chado_query(
     "SELECT stock_id, uniquename, type_id, organism_id FROM {stock} WHERE organism_id=%d",
      $organism_id
  );

  $stocks_created_count = 0; //keeps track of total number of stocks successfully created
  $stocks_attempted = 0;
  // foreach stock to be sync'd -> create node & add stock_id
  while ( $r = db_fetch_object($result) ) {
    // $r is the current stock to be sync'd
    $stocks_attempted++;

    print 'Processing ' . $r->uniquename . "... ";

    // check not already in drupal
    $in_drupal_query = db_query(
      "SELECT * FROM {chado_stock} WHERE stock_id=%d",
      $r->stock_id
    );
    if ( !db_fetch_object($in_drupal_query) ) {

      //create new chado_stock node
      $new_node = new stdClass();
      $new_node->type = 'chado_stock';
      $new_node->uid = $user->uid;
      $new_node->title = $r->uniquename;
      $new_node->type_id = $r->type_id;
      $new_node->organism_id = $r->organism_id;
      $new_node->stock_id = $r->stock_id;
      $new_node->chado_stock_exists = TRUE;

      //print 'New Node:';
      //print_r($new_node);

      node_validate($new_node);

      if (!form_get_errors()) {
        //print 'Try to Create Node ';
        $node = node_submit($new_node);
        node_save($node);
        if ($node->nid) {
          $stocks_created_count++;

          //Add stock id to chado_stock table
          /**
           db_query(
             "INSERT INTO chado_stock (stock_id, nid, vid) VALUES (%d, %d, %d)",
             $r->stock_id,
             $node->nid,
             $node->vid
           );
           */
          }
        }
        else {
          print "Not completed due to errors:\nCreate Stock Form Errors: ";
          print_r(form_get_errors());
        }
        print "Nid=" . $node->nid . "\n";
      }
      else {
        print "Skipped $r->uniquename because it's already in drupal.\n";
      } //end of if not already in drupal
    } //end of while still stocks to be sync'd
  } //end of if organism_id not supplied

  if ($stocks_attempted == 0) {
    print "No stocks retrieved for organism (" . $organism_id . ")\n";
    return 1;
  }
  else {
    if ($stocks_created_count > 0) {
      print "$stocks_created_count Stocks Successfully Created\n";
      return 1;
    }
    else {
      return 0;
    }
  }
}

/**
 *
 *
 * @ingroup tripal_stock
 */
function get_tripal_stock_admin_form_cleanup_set(&$form) {
  $form['cleanup'] = array(
    '#type' => 'fieldset',
    '#title' => t('Clean Up')
  );
  $form['cleanup']['description'] = array(
     '#type' => 'item',
     '#value' => t("With Drupal and Chado residing in different databases ".
        "it is possible that nodes in Drupal and stocks in Chado become ".
        "\"orphaned\".  This can occur if an stock node in Drupal is ".
        "deleted but the corresponding chado stock is not and/or vice ".
        "versa. Click the button below to resolve these discrepancies."),
     '#weight' => 1,
  );
  $form['cleanup']['button'] = array(
    '#type' => 'submit',
    '#value' => t('Clean up orphaned stocks'),
    '#weight' => 2,
  );
}
/**
 * Remove orphaned drupal nodes
 *
 * @param $dummy
 *   Not Used -kept for backwards compatibility
 * @param $job_id
 *   The id of the tripal job executing this function
 *
 * @ingroup tripal_stock
 */
function tripal_stock_cleanup($dummy = NULL, $job_id = NULL) {

  return tripal_core_clean_orphaned_nodes('stock', $job_id);

}