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File

tripal_stock/includes/tripal_stock.sync_stocks.inc, line 412

@todo Add file header description

Code

function tripal_stock_sync_stock($stock_id) {

  print "\tSyncing stock $stock_id\n";

  global $user;
  $create_node = 1; // set to 0 if the node exists and we just sync and not create

  // get the accession prefix
  $aprefix = variable_get('chado_stock_accession_prefix', 'SID');

  // if we don't have a stock_id then return
  if (!$stock_id) {
    drupal_set_message(t("Please provide a stock_id to sync"));
    return '';
  }

  // get information about this stock
  $fsql = "SELECT S.*, O.genus, O.species,CVT.name as cvname " .
    "FROM {stock} S " .
    "  INNER JOIN {cvterm} CVT ON S.type_id = CVT.cvterm_id " .
    "  INNER JOIN {organism} O ON S.organism_id = O.organism_ID " .
    "WHERE S.stock_id = %d";
  $stock = db_fetch_object(chado_query($fsql, $stock_id));

  /*
  // get the synonyms for this stock
  $synsql = "SELECT S.name ".
            "FROM {stock_synonym} SS ".
            "  INNER JOIN {synonym} S on SS.synonym_id = S.synonym_id ".
            "WHERE SS.stock_id = %d";
  $synonyms = chado_query($synsql, $stock_id);  
    
  // now add these synonyms to the stock object as a single string
  $synstring = '';
  while ($synonym = db_fetch_object($synonyms)) {
    $synstring .= "$synonym->name\n";
  }
  $stock->synonyms = $synstring;
  */

  // check to make sure that we don't have any nodes with this stock name as a title
  // but without a corresponding entry in the chado_stock table if so then we want to
  // clean up that node.  (If a node is found we don't know if it belongs to our stock or
  // not since stocks can have the same name/title.)
  $tsql = "SELECT * FROM {node} N " .
    "WHERE title = '%s'";
  $cnsql = "SELECT * FROM {chado_stock} " .
    "WHERE nid = %d";
  $nodes = db_query($tsql, $stock->name);
  // cycle through all nodes that may have this title
  while ($node = db_fetch_object($nodes)) {
    $stock_nid = db_fetch_object(db_query($cnsql, $node->nid));
    if (!$stock_nid) {
      drupal_set_message(t("%stock_id: A node is present but the chado_stock entry is missing... correcting", array('%stock_id' => $stock_id)));
      node_delete($node->nid);
    }
  }

  // check if this stock already exists in the chado_stock table.
  // if we have a chado stock, we want to check to see if we have a node
  $cfsql = "SELECT * FROM {chado_stock} " .
    "WHERE stock_id = %d";
  $nsql = "SELECT * FROM {node} N " .
    "WHERE nid = %d";
  $chado_stock = db_fetch_object(db_query($cfsql, $stock->stock_id));
  if ($chado_stock) {
    drupal_set_message(t("%stock_id: A chado_stock entry exists", array('%stock_id' => $stock_id)));
    $node = db_fetch_object(db_query($nsql, $chado_stock->nid));
    if (!$node) {
      // if we have a chado_stock but not a node then we have a problem and
      // need to cleanup
      drupal_set_message(t("%stock_id: The node is missing, but has a chado_stock entry... correcting", array('%stock_id' => $stock_id)));
      $df_sql = "DELETE FROM {chado_stock} WHERE stock_id = %d";
      db_query($df_sql, $stock_id);
    }
    else {
      drupal_set_message(t("%stock_id: A corresponding node exists", array('%stock_id' => $stock_id)));
      $create_node = 0;
    }
  }

  // if we've encountered an error then just return.
  if ($error_msg = db_error()) {
    //print "$error_msg\n";
    return '';
  }

  // if a drupal node does not exist for this stock then we want to
  // create one.  Note that the node_save call in this block
  // will call the hook_submit function which
  if ($create_node) {
    // get the organism for this stock
    $sql = "SELECT * FROM {organism} WHERE organism_id = %d";
    $organism = db_fetch_object(chado_query($sql, $stock->organism_id));

    drupal_set_message(t("%stock_id: Creating node $stock->name", array('%stock_id' => $stock_id)));
    $new_node = new stdClass();
    $new_node->type = 'chado_stock';
    $new_node->uid = $user->uid;
    $new_node->title = "$stock->name, $stock->uniquename ($stock->cvname) $organism->genus $organism->species";
    $new_node->sname = "$stock->name";
    $new_node->uniquename = "$stock->uniquename";
    $new_node->type_id = $stock->type_id;
    $new_node->organism_id = $stock->organism_id;
    $new_node->stock_id = $stock->stock_id;
    $new_node->chado_stock_exists = TRUE;

    // validate the node and if okay then submit
    node_validate($new_node);
    if ($errors = form_get_errors()) {
      print "Error encountered validating new node. Cannot sync: $msg\n";
      foreach ($errors as $key => $msg) {
        watchdog('trp-fsync', "%msg", array('%msg' => $msg), WATCHDOG_ERROR);
      }
      exit;
    }
    else {
      $node = node_submit($new_node);
      node_save($node);
    }
  }
  else {
    $node = $chado_stock;
  }

  return '';
}