Related topics

File

tripal_feature/includes/tripal_feature.admin.inc, line 456

@todo Add file header description

Code

function tripal_feature_set_taxonomy($node, $feature_id) {

  // iterate through the taxonomy classes that have been
  // selected by the admin user and make sure we only set those
  $tax_classes = variable_get('tax_classes', array());
  $do_ft = 0;
  $do_op = 0;
  $do_lb = 0;
  $do_an = 0;
  foreach ($tax_classes as $class) {
    if (strcmp($class, 'organism') == 0) {
      $do_op = 1;
    }
    if (strcmp($class, 'feature_type') == 0) {
      $do_ft = 1;
    }
    if (strcmp($class, 'library') == 0) {
      $do_lb = 1;
    }
    if (strcmp($class, 'analysis') == 0) {
      $do_an = 1;
    }
  }


  // get the list of vocabularies and find our two vocabularies of interest
  $vocabularies = taxonomy_get_vocabularies();
  $ft_vid = NULL;
  $op_vid = NULL;
  $lb_vid = NULL;
  $an_vid = NULL;
  foreach ($vocabularies as $vocab) {
    if ($vocab->name == 'Feature Type') {
      $ft_vid = $vocab->vid;
    }
    if ($vocab->name == 'Organism') {
      $op_vid = $vocab->vid;
    }
    if ($vocab->name == 'Library') {
      $lb_vid = $vocab->vid;
    }
    if ($vocab->name == 'Analysis') {
      $an_vid = $vocab->vid;
    }
  }

  // get the cvterm and the organism for this feature
  $sql = "SELECT CVT.name AS cvname, O.genus, O.species " .
    "FROM {CVTerm} CVT " .
    "  INNER JOIN {Feature} F on F.type_id = CVT.cvterm_id " .
    "  INNER JOIN {Organism} O ON F.organism_id = O.organism_id " .
    "WHERE F.feature_id = $feature_id";
  $feature = db_fetch_object(chado_query($sql));

  // Set the feature type for this feature
  if ($do_ft && $ft_vid) {
    $tags["$ft_vid"] = "$feature->cvname";
  }
  // Set the organism for this feature type
  if ($do_op && $op_vid) {
    $tags["$op_vid"] = "$feature->genus $feature->species";
  }

  // get the library that this feature may belong to and add it as taxonomy
  if ($do_lb && $lb_vid) {
    $sql = "SELECT L.name " .
      "FROM {Library} L " .
      "  INNER JOIN {Library_feature} LF ON LF.library_id = L.library_id " .
      "WHERE LF.feature_id = %d ";
    $library = db_fetch_object(chado_query($sql, $feature_id));
    $tags["$lb_vid"] = "$library->name";
  }

  // now add the taxonomy to the node
  $terms['tags'] = $tags;
  taxonomy_node_save($node, $terms);
  //   print "Setting $node->name: " . implode(", ",$tags) . "\n";

  // get the analysis that this feature may belong to and add it as taxonomy
  // We'll add each one individually since there may be more than one analysis
  if ($do_an && $an_vid) {
    $sql = "SELECT A.name " .
      "FROM {Analysis} A " .
      "  INNER JOIN {Analysisfeature} AF ON AF.analysis_id = A.analysis_id " .
      "WHERE AF.feature_id = $feature_id ";
    $results = chado_query($sql);
    $analysis_terms = array();
    while ($analysis = db_fetch_object($results)) {
      $tags2["$an_vid"] = "$analysis->name";
      $terms['tags'] = $tags2;
      taxonomy_node_save($node, $terms);
    }
  }

}