Update analyses

Parameters

$node: The updated node object

Related topics

File

tripal_analysis/tripal_analysis.module, line 285

Contains all the main hook implementations for the tripal_analysis module

Code

function chado_analysis_update($node) {
  global $user;
  if ($node->revision) {
    // TODO -- decide what to do about revisions
  }
  // Create a timestamp so we can insert it into the chado database
  $time = $node->timeexecuted;
  $month = $time['month'];
  $day = $time['day'];
  $year = $time['year'];
  $timestamp = $month . '/' . $day . '/' . $year;

  // get the analysis_id for this node:
  $sql = "SELECT analysis_id " .
    "FROM {chado_analysis} " .
    "WHERE nid = %d";
  $analysis_id = db_fetch_object(db_query($sql, $node->nid))->analysis_id;

  $sql = "UPDATE {analysis} " .
    "SET name = '%s', " .
    "    description = '%s', " .
    "    program = '%s', " .
    "    programversion = '%s', " .
    "    algorithm = '%s', " .
    "    sourcename = '%s', " .
    "    sourceversion = '%s', " .
    "    sourceuri = '%s', " .
    "    timeexecuted = '%s' " .
    "WHERE analysis_id = %d ";

  chado_query($sql, $node->analysisname, $node->description, $node->program, 
  $node->programversion, $node->algorithm, $node->sourcename, 
  $node->sourceversion, $node->sourceuri, $timestamp, $analysis_id);

  // Create a title for the analysis node using the unique keys so when the
  // node is saved, it will have a title
  $record = new stdClass();
  // If the analysis has a name, use it as the node title. If not, construct
  // the title using program, programversion, and sourcename
  if ($node->analysisname) {
    $record->title = $node->analysisname;
  }
  else {
    //Construct node title as "program (version)
    $record->title = "$node->program ($node->programversion)";
  }

  $record->nid = $node->nid;
  drupal_write_record('node', $record, 'nid');
  drupal_write_record('node_revisions', $record, 'nid');

  // now update the properties
  $properties = array(); // stores all of the properties we need to add
  // get the list of properties for easy lookup (without doing lots of database queries
  $properties_list = array();
  $sql = "
      SELECT DISTINCT CVT.cvterm_id, CVT.name, CVT.definition
      FROM  {cvterm} CVT
      INNER JOIN {cv} ON CVT.cv_id = CV.cv_id
      WHERE
      CV.name = 'analysis_property' AND
      NOT CVT.is_obsolete = 1
      ORDER BY CVT.name ASC
      ";
  $prop_types = chado_query($sql);
  while ($prop = db_fetch_object($prop_types)) {
    $properties_list[$prop->cvterm_id] = $prop->name;
  }

  // get the properties that should be added. Properties are in one of three forms:
  //  1) prop_value-[type id]-[index]
  //  2) new_value-[type id]-[index]
  //  3) new_id, new_value
  //  dpm($node);
  foreach ($node as $key => $value) {
    if (preg_match('/^prop_value-(\d+)-(\d+)/', $key, $matches)) {
      $type_id = $matches[1];
      $index = $matches[2];
      $name = $properties_list[$type_id];
      $properties[$name][$index] = trim($value);
    }
    if (preg_match('/^new_value-(\d+)-(\d+)/', $key, $matches)) {
      $type_id = $matches[1];
      $index = $matches[2];
      $name = $properties_list[$type_id];
      $properties[$name][$index] = trim($value);
    }
  }
  if ($node->new_id and $node->new_value) {
    $type_id = $node->new_id;
    $name = $properties_list[$type_id];
    $index = count($properties[$name]);
    $properties[$name][$index] = trim($node->new_value);
  }

  // now add in the properties by first removing any the analysis
  // already has and adding the ones we have
  $sql = "
    DELETE FROM {analysisprop} WHERE analysis_id = %d AND type_id IN (
      SELECT CVT.cvterm_id
      FROM  {cvterm} CVT
        INNER JOIN {cv} ON CVT.cv_id = CV.cv_id
      WHERE CV.name = 'analysis_property')
  ";
  $success = chado_query($sql, $analysis_id);
  if (!$success) {
    drupal_set_message("Cannot update analysis properties", "error");
    watchdog('t_analysis', "Cannot update analysis properties.", array(), WATCHDOG_ERROR);
    return;
  }
  foreach ($properties as $property => $elements) {
    foreach ($elements as $rank => $value) {
      $status = tripal_analysis_insert_property($analysis_id, $property, $value, FALSE, 'analysis_property');
      if (!$status) {
        drupal_set_message("Error cannot add property: '$property'", "error");
        watchdog('t_analysis', "Error cannot add property: '%prop'", 
        array('%prop' => $property), WATCHDOG_ERROR);
      }
    }
  }
}