Added Mark's code for OWL parser

tripal_chado/includes/loaders/OWLStanza.inc

@@ -0,0 +1,305 @@
+<?php
+/**
+ * @file
+ * OWL redesign using Classes (Objects)
+ */
+class OWLStanza {
+  // The XMLReader object.
+  private $owl = NULL;
+  // A boolean (TRUE or FALSE) indicating if children should be parsed.
+  private $parse_children = TRUE;
+  // The XML element tag name (e.g. ‘owl:ObjectProperty’,
+  // ‘owl:AnnotationProperty’, 'owl:Ontology').
+  private $tag_name = '';
+  // A key/value associative array of all of the attributes.
+  private $attributes = array ();
+  // An array of OWLStanza objects.
+  private $children = array ();
+  // The text value of a XML element.
+  private $value;
+  // Indicates if there is no more to read from the OWL XML file.
+  private $is_finished = FALSE;
+
+
+
+  /**
+   * Implements the constructor.
+   *
+   * @param $parse_children
+   * A boolean (TRUE or FALSE) indicating if children should be parsed.
+   * If FALSE only attributes will be parse.
+   */
+  public function __construct($owl, $parse_children = TRUE) {
+    $this->owl = $owl;
+    $this->parse_children = $parse_children;
+    $this->parse();
+  }
+
+  /**
+   * A wrapper for XMLReader::read() read function.
+   *
+   * This function calls read() on the $owl object and checks to see
+   * if we are at the end of the XML file. If so, it sets the $is_finished
+   * member variable to TRUE.
+   *
+   * @return
+   *   The value of XMLReader::read().
+   */
+  private function owl_read() {
+    $retval = $this->owl->read();
+
+    if ($this->owl->nodeType == XMLReader::END_ELEMENT and $this->owl->name == 'rdf:RDF') {
+      $this->is_finished = TRUE;
+    }
+    return $retval;
+  }
+
+  /**
+   *
+   * @param private
+   * This function is to parse each of the OWL Stanzas of the ro.owl file.
+   */
+
+    private function parse() {
+
+      // Make sure we are at the beginning of an element.
+      while ($this->owl->nodeType != XMLReader::ELEMENT) {
+        // In the event we've hit the end of the file, then return.
+        if ($this->is_finished) {
+          return;
+        }
+        $this->owl_read();
+       }
+
+      $this->tag_name = $this->owl->name;
+
+      $has_value = $this->owl->hasValue;
+      $is_empty = $this->owl->isEmptyElement;
+
+      // Get the attributes.
+      $num_attrs = $this->owl->attributeCount;
+      if ($num_attrs > 0) {
+        $this->owl->moveToFirstAttribute();
+        for ($i = 0; $i < $num_attrs; $i++) {
+          $this->attributes[$this->owl->name] = $this->owl->value;
+          $this->owl->moveToNextAttribute();
+        }
+      }
+
+      // If this element is empty then just return.
+      if ($is_empty) {
+        return;
+      }
+
+      // Determine if the element has a value. If so, then set the value for the class.
+      if ($this->owl->hasValue) {
+        $this->owl_read();
+        $this->value = $this->owl->value;
+      }
+
+      // Get the children that should be parsed within the Stanza.
+      if ($this->parse_children == TRUE) {
+        while ($this->owl_read()) {
+          if ($this->owl->nodeType == XMLReader::END_ELEMENT and $this->owl->name == $this->tag_name) {
+            return;
+          }
+          else if ($this->owl->nodeType == XMLReader::ELEMENT) {
+            $child = new OWLStanza($this->owl);
+            $this->children[] = $child;
+          }
+        }
+      }
+    }
+
+
+   /**
+    * Get the Value
+    *
+    * @ return The text value of a XML element.
+    */
+
+    public function getValue() {
+      return $this->value;
+    }
+
+  /**
+   * Gets the children array.
+   *
+   * @return An array of OWLStanza objects containing the children elements.
+   */
+  public function getChildren() {
+    return $this->children;
+  }
+  /**
+   * Sets the children array.
+   *
+   * @param $children
+   * An array of OWLStanza objects containing the children elements.
+   * @return FALSE if the array was not set, TRUE otherwise.
+   */
+  public function setChildren($children) {
+    // Makes sure the incoming argument is an array.
+    if (! is_array ( $children )) {
+      return FALSE;
+    }
+    // Make sure that all of the array elements are OWLStanza objects.
+    foreach ( $children as $child ) {
+      if (get_class ( $child ) != 'OWLStanza') {
+        return FALSE;
+      }
+    }
+    // All is good, set the children.
+    $this->children = $children;
+  }
+
+  /**
+   * Gets the child($tag_name) array.
+   *
+   * @return
+   *  An OWLStanza object whos tag name matches the tag name provided.
+   *
+   *
+   */
+  public function getChild($tag_name) {
+    foreach ($this->children as $child) {
+      if ($child->getTagName() == $tag_name) {
+        return $child;
+      }
+    }
+    return NULL;
+  }
+
+  /**
+   * Gets the tag name.
+   *
+   * @return An XML element tag name (e.g. ‘owl:ObjectProperty’,
+   *         'owl:AnnotationProperty’, 'owl:Ontology').
+   */
+  public function getTagName() {
+    return $this->tag_name;
+  }
+  /**
+   * Sets the tag name.
+   *
+   * @param $tag_name The
+   *          XML element tag name
+   * @return value element tag name.
+   */
+  public function setTagName($tag_name) {
+    $this->tag_name = $tag_name;
+    return;
+  }
+
+  /**
+   * Gets the attributes array.
+   *
+   * @return An array containing a key/value associative array
+   *         of all of the attributes between the XML elements tag name.
+   */
+  public function getAttributes() {
+    return $this->attributes;
+  }
+
+  /**
+   * Sets the attributes array.
+   *
+   * @param $attributes An
+   *          array containing a key/value associative array of all of the attributes.
+   * @return FALSE if the array was not set, TRUE otherwise.
+   */
+  public function setAttributes($attributes) {
+    // Makes sure the incoming argument is an array.
+    if (! is_array ( $attributes )) {
+      return FALSE;
+    }
+    // Make sure that all of the array are key/values.
+    foreach ( $attributes as $attribute_name ) {
+      if (get_class ($attribute_name ) != 'OWLStanza') {
+        return FALSE;
+      }
+    }
+    // All is good, set the attributes.
+    $this->attributes = $attributes;
+  }
+
+  /**
+   *
+   * @param
+   *          $attribute_name
+   * @return An|NULL
+   */
+  public function getAttribute($attribute_name) {
+    foreach ($this->attributes as $aname => $value ) {
+      if ($aname == $attribute_name) {
+        return $value;
+      }
+    }
+    return NULL;
+
+  }
+
+  /**
+   * Checks if the OWL XML file has been completely parsed.
+   *
+   * @return
+   *   TRUE if parsing is completed, FALSE otherwise.
+   */
+  public function isFinished() {
+    return $this->is_finished;
+  }
+
+  /**
+   * Reconstructs the XML for the stanza.
+   *
+   * @return
+   *   A string containing XML for this stanza.
+   */
+  public function getXML() {
+
+    // Start the element with the tag name.
+    $xml = '<' . $this->tag_name;
+
+    // Iterate through the attributes and add them to our XML string.
+    if (count($this->attributes) > 0) {
+      foreach ($this->attributes as $aname => $value) {
+        $xml .=  " " . $aname . '="' . $value . '"';
+      }
+    }
+
+    // If this stanza has a value this implies there are no children,
+    // so close the element start, add the value and add the closing element
+    // tag.
+    if ($this->value) {
+      $xml .= '>' . $this->value . '</' . $this->tag_name . ">\n";
+      return $xml;
+    }
+
+    // If we're here, we do not have a value. This is therefore an empty
+    // element, or it has children.  If we have no children then we
+    // have an empty element and we can close it out and return.
+    if (count($this->children) == 0) {
+      $xml .= " />\n";
+      return $xml;
+    }
+
+    // Add in the children's XML recursively.
+    $childs = '';
+    foreach ($this->children as $child) {
+      // We want to add two character indentation to all lines returned by
+      // the child XML.
+      $childs .= preg_replace("/^/","  ", $child->getXML());
+    }
+    $xml .= ">\n";
+    $xml .= $childs;
+    $xml .= "</" . $this->tag_name . ">\n";
+    return $xml;
+  }
+}
+
+
+
+
+
+
+
+

tripal_chado/includes/loaders/tripal_cv.owl_loader.php

@@ -0,0 +1,513 @@
+<?php
+
+// This Tripal_cv.owl_loader.php and OWLStanza.inc(CLASS) file is being developed to read and parse through any scientific
+// ontology XML Owl file to have the vocabularies be inserted into the Chado database for the open source project
+// Tripal.info to be used.
+
+/**
+ * @file
+ * @add file from header
+ */
+require_once ('OWLStanza.inc');
+/**
+ * Parses an OWL XML file and imports the CV terms into Chado
+ *
+ * @param $filename The
+ *          full path to the OWL XML file.
+ *
+ * @return No return value.
+ *
+ * @throws Exception
+ */
+function tripal_cv_parse_owl($filename) {
+  // TODO: need to pass in the $db_name as the cv name into the function when you see the
+  // oboInOwl:default-namespace that is not the same as $db_name.
+  //
+  // TODO: this all should occur inside of a transaction.
+
+  // Opening the OWL file for parsing.
+  $owl = new XMLReader();
+  // This command will open and read the any Owl file.
+  if (!$owl->open($filename)) {
+    print "ERROR opening OWL file: '$filename'\n";
+    exit();
+  }
+
+  // Get the RDF stanza. We pass FALSE as the second parameter to prevent
+  // the object from reading the entire file into memory.
+  $rdf = new OWLStanza($owl, FALSE);
+
+  // Get the ontology stanza. It will contain the values for the database
+  // name for this ontology.
+  $ontology = new OWLStanza($owl);
+
+  // Look for the db name in using the 'oboInOwl:default-namespace term. If it's
+  // not present then we'll use the 'about' element to get the namespace.
+  $namespace = $ontology->getChild('oboInOwl:default-namespace');
+  if ($namespace) {
+    $db_name = $namespace->getValue();
+  }
+  else {
+    // Insert the database record into Chado using the owl:Ontology stanza of the owl file.
+    $about = $ontology->getAttribute('rdf:about');
+
+    // We wrote the regular expression on the rdf.about line to get the database name for any particular Owl file.
+    if (preg_match('/^.*\/(.*?)\..*$/', $about, $matches)) {
+      $db_name = strtoupper($matches[1]);
+    }
+  }
+
+  //
+  // Step 1: Make sure that all dependencies (database names) are met for each Owl ontology file.
+  //
+
+  // loop through each stanza, one at a time, and handle each one
+  // based on the tag name.
+  $stanza = new OWLStanza($owl);
+
+  // Set an empty array for the dependencies to go in.
+  $deps = array (
+    'db' => array (),
+    'dbxref' => array ()
+  );
+
+  // Start looping and parsing through the owl:Class stanza section of the Owl file.
+  while (!$stanza->isFinished()) {
+    // Use the tag name from OWLStanza.inc to identify which function should be called.
+    switch ($stanza->getTagName()) {
+      case 'owl:Class':
+        tripal_owl_check_class_depedencies($stanza, $vocab_db_name, $deps);
+        break;
+    }
+    // Get to the next stanza in the OWL file.
+    $stanza = new OWLStanza($owl);
+  }
+
+  if (count(array_keys($deps['db'])) > 0 or count(array_keys($deps['dbxref'])) > 0) {
+    // We have unmet dependencies. Print those out and return.
+    // The deps array will have DB’s, then terms' . "\n");
+    if (count($deps['db']) > 0) {
+      drupal_set_message('Cannot import ontology, "' . $db_name . '", as the following ' . 'dependent vocabularies must first be imported: ' . print_r(array_keys($deps['db']), TRUE) . '\n', 'error');
+    }
+    if (count($deps['dbxref']) > 0) {
+      drupal_set_message('Cannot import ontology, "' . $db_name . '", as the following ' . 'dependent terms must first be imported: ' . print_r(array_keys($deps['dbxref']), TRUE) . '\n', 'error');
+    }
+    return;
+  }
+
+  //
+  // Step 2: If we pass the dependency check in step 1 then we can insert
+  // the terms.
+  //
+
+  // Holds an array of CV and DB records that have already been
+  // inserted (reduces number of queires).
+  $vocabs = array (
+    'db' => array (),
+    'cv' => array (),
+    'this' => array ()
+  );
+
+  // Reload the ontology to reposition at the beginning of the OWl file for inserting the
+  // new terms into Chado.
+
+  $owl = new XMLReader();
+  if (!$owl->open($filename)) {
+    print "ERROR opening OWL file: '$filename'\n";
+    exit();
+  }
+  $rdf = new OWLStanza($owl, FALSE);
+  $ontology = new OWLStanza($owl);
+
+  // Insert the database record into Chado using the
+  // owl:Ontology stanza.
+  $url = '';
+  $homepage = $ontology->getChild('foaf:homepage');
+  if ($homepage) {
+    $url = $homepage->getValue();
+  }
+  $db = array (
+    'url' => $url,
+    'name' => $db_name
+  );
+
+  // Using the Tripal API function to insert the term into the Chado database.
+  $db = tripal_insert_db($db);
+
+  // Get the description for this vocabulary. This should be in the
+  // dc:description element. If that element is missing then the
+  // description should default to the empty string.
+  $cv_description = '';
+  $description = $ontology->getChild('dc:description');
+  if ($description) {
+    $cv_description = $description->getValue();
+  }
+
+  // Get the name for the CV. This should be in the 'dc:title' element. If the
+  // title is not present then the cv name should default to the database name.
+  $cv_name == $namespace = $ontology->getChild('oboInOwl:default-namespace');
+  if ($namespace) {
+    $cv_name = $namespace->getValue();
+  }
+
+  $title = $ontology->getChild('dc:title');
+  if ($title) {
+    $cv_name = preg_replace("/[^\w]/", "_", strtolower($title->getValue()));
+  }
+
+  // Insert the CV record into Chado.
+  $cv = tripal_insert_cv($cv_name, $cv_description);
+
+  // Add this CV and DB to our vocabs array so we can reuse it later.
+  $vocabs[$db_name]['cv'] = $namespace_cv;
+  $vocabs[$db_name]['db'] = $db;
+  $vocabs['this'] = $db_name;
+
+  // loop through each stanza of the owl file, one at a time, and handle each one
+  // based on the tag name from the OWLStanza.inc file.
+  $stanza = new OWLStanza($owl);
+  while (!$stanza->isFinished()) {
+
+    // Use the tag name to identify which function should be called.
+    switch ($stanza->getTagName()) {
+      case 'owl:AnnotationProperty':
+        // tripal_owl_handle_annotation_property($stanza, $vocabs);
+        break;
+      case 'rdf:Description':
+        // tripal_owl_handle_description($stanza, $vocabs);
+        break;
+      case 'owl:ObjectProperty':
+        // tripal_owl_handle_object_property($stanza, $vocabs);
+        break;
+      case 'owl:Class':
+        tripal_owl_handle_class($stanza, $vocabs);
+        break;
+      case 'owl:Axiom':
+        break;
+      case 'owl:Restriction':
+        break;
+      default:
+        throw new Exception("Unhandled stanza: " . $stanza->getTagName());
+        exit();
+        break;
+    }
+
+    // Get the next stanza in the OWL file.
+    $stanza = new OWLStanza($owl);
+  }
+
+  // Close the XMLReader $owl object.
+  $owl->close();
+}
+
+/**
+ * Checks for required vocabularies that are not loaded into Chado.
+ *
+ * Some vocabularies use terms from other ontologies. If this is happens
+ * we need to ensure that the dependent vocabularies are present in the
+ * database prior to loading this one. This function adds to the $deps
+ * array all of the database names and term accessions that are missing in
+ * Chado.
+ *
+ * @param $stanza The
+ *          OWLStanza object for the current stanza from the OWL file.
+ * @param $vocab_db_name The
+ *          name of the database for the vocabulary being loded.
+ * @param $deps The
+ *          dependencies array. The missing databases are provided in array
+ *          using a 'db' key, and missing terms are in a second array using a
+ *          'dbxref' key.
+ */
+function tripal_owl_check_class_depedencies(OWLStanza $stanza, $vocab_db_name, &$deps) {
+
+  // Initialize the variables.
+  $db_name = '';
+  $accession = '';
+  $db = null;
+
+  // Get the DB name and accession from the "rdf:about" attribute.
+  $about = $stanza->getAttribute('rdf:about');
+  if (!$about) {
+    // TODO: some owl:Class stanzas do not have an about. What are these?
+    // how should we handle them.
+    return;
+  }
+
+  // We wrote the regular expression on the rdf.about line to get the database
+  // name and accession term for any particular Owl file.
+  if (preg_match('/.*\/(.+)_(.+)/', $about, $matches)) {
+    $db_name = strtoupper($matches[1]);
+    $accession = $matches[2];
+  }
+  else {
+    throw new Exception("owl:Class stanza 'rdf:about' attribute is not formated as expected: '$about'. " . "This is necessary to determine the term's accession: \n\n" . $stanza->getXML());
+  }
+
+  // If the database name for this term is the same as the vocabulary
+  // we are trying to load, then don't include it in the $deps array.
+  if ($db_name !== $vocab_db_name) {
+    return;
+  }
+
+  // Check if the db_name does not exist in the chado.db table. If it
+  // does not exist then add it to our $deps array. If the query fails then
+  // throw an exception.
+  $db = chado_select_record('db', array (
+    'db_id'
+  ), array (
+    'name' => $db_name
+  ));
+  if ($db === FALSE) {
+    throw new Exception("Failed to execute query to find vocabulary in chado.db table\n\n" . $stanza->getXML());
+  }
+  else if (count($db) == 0) {
+    $deps['db'][$db_name] = TRUE;
+
+    // Does this stanza provide the URL for the OWL file of this missing
+    // dependency. If so then add it to our deps array.
+    $imported_from = $stanza->getChild('obo:IAO_0000412');
+
+    if ($imported_from == NULL) {
+      return;
+    }
+    $url = $imported_from->getAttribute('rdf:resource');
+    if ($url) {
+      $deps['db'][$db_name] = $url;
+    }
+    return;
+  }
+
+  // If the db_name exists, then check if the accession exists in
+  // the chado.dbxref table. If it doesn't exist then add an entry to the
+  // $deps array. If the query fails then throw an exception.
+  $values = array (
+    'db_id' => $db[0]->db_id,
+    'accession' => $accession
+  );
+
+  $dbxref = chado_select_record('dbxref', array (
+    'dbxref_id',
+    'db_id'
+  ), $values);
+  if ($dbxref === FALSE) {
+    throw new Exception("Failed to execute query to find vocabulary term in chado.dbxref table\n\n" . $stanza->getXML());
+  }
+  elseif (count($accession) == 0) {
+    $deps['dbxref'][$db_name . ':' . $accesson] = TRUE;
+  }
+  return;
+}
+
+/**
+ *
+ * @param
+ *          $stanza
+ * @param
+ *          $vocabs
+ * @throws Exception
+ */
+function tripal_owl_handle_object_property($stanza, $vocabs) {
+}
+
+/**
+ *
+ * @param
+ *          $stanza
+ * @param
+ *          $vocabs
+ * @throws Exception
+ */
+function tripal_owl_handle_annotation_property($stanza, $vocabs) {
+
+// $matches = array();
+// $db_name = '';
+// $accession = '';
+// $about = $stanza->getAttribute('rdf:about');
+// // Get the DB name and accession from the about attribute using the preg match function.
+//   if (preg_match('/.*\/(.+)_(.+)/', $about, $matches)) {
+//     $db_name = ($matches[1]);
+//     $accession = $matches[2];
+//   }
+//   else {
+//         throw new Exception("owl:Class stanza 'rdf:about' attribute is not formated as expected: '$about'. " . "This is necessary to determine the term's accession: \n\n" . $stanza->getXML());
+//       }
+
+//   // Insert a DB Record
+// if (array_key_exists($db_name, $vocabs)) {
+//     $db = $vocabs[$db_name]['db'];
+//     $default_namespace_cv = $vocabs[$db_name]['cv'];
+//   }
+//   else {
+//     // Unfortunately, all we have is the name. The OWL format
+//     // doesn't provides us the URL, description, etc.
+//     $values = array(
+//       'name' => $db_name
+//     );
+//     $db = tripal_insert_db($values);
+// // Insert a dbxref record.
+//   $values = array(
+//     'db_id' => $db->db_id,
+//     'accession' => $accession
+//   );
+//   $dbxref = tripal_insert_dbxref($values);
+
+//   $imported_from = $stanza->getChild('obo:IAO_0000114');
+//     if ($imported_from == NULL) {
+//       return;
+//     }
+//     $url = $imported_from->getAttribute('rdf:resource');
+//     if ($url) {
+//       $vocabs['db'][$db_name] = $url;
+//     }
+//     return;
+//   }
+
+// // Insert a new cvterm record.
+// $cvterm_name = '';
+// $definition = '';
+
+// $cvterm_name = $stanza->getChild('rdfs:label');
+//   if ($cvterm_name) {
+//   $cvterm_name = $stanza->getValue();
+//   }
+//   $definition = $stanza->getChild('obo:IAO_0000115');
+//   if ($definition) {
+//   $definition = $stanza->getValue();
+//   }
+
+//   $term = array(
+//   	'id' => $db->name .':'. $dbxref->accession,
+//   	'name' => $cvterm_name,
+//   	'cv_name' => $cv->name,
+//   	'definition' => $definition,
+//   );
+//   $option =array();
+//   if ($vocabs['this'] != $db->name){
+//   	$option['update_existing'] = FALSE;
+//   }
+//   $cvterm = tripal_insert_cvterm($term, $option);
+// }
+}
+/**
+ *
+ * @param
+ *          $stanza
+ * @param
+ *          $vocabs
+ * @throws Exception
+ */
+function tripal_owl_handle_description($stanza, $vocabs) {
+}
+
+/**
+ *
+ * The function goes through owl:Class stanza to insert new vocabularies.
+ *
+ * @param $stanza The
+ *          OWLStanza object for the current stanza from the OWL file.
+ * @param
+ *          $vocabs
+ *
+ * @throws Exception
+ */
+function tripal_owl_handle_class(OWLStanza $stanza, $vocabs) {
+
+  // Initialize the database and cv variables.
+  $db_name = $vocabs['this'];
+  $accession = '';
+  $is_a = '';
+  $namespace_cv = $vocabs[$db_name]['cv'];
+  $db = $vocabs[$db_name]['db'];
+
+  // Insert the dbxref record into Chado using the owl:Class stanza of the owl file.
+  // Any oboInOwl:id supercedes what we find in the rdf:about in the owl file.
+  $obo_id = $stanza->getChild('oboInOwl:id');
+
+  if ($obo_id) {
+    if (preg_match('/.*>(.+):(.+)<.*/', $about, $matches)) {
+      $db_name = strtoupper($matches[1]);
+      $accession = $matches[2];
+    }
+    else {
+      $about = $stanza->getAttribute('rdf:about');
+      // We wrote the regular expression on the rdf.about line to get the
+      // db_name and accession for any particular Owl file.
+      if (preg_match('/.*\/(.+)_(.+)/', $about, $matches)) {
+        $db_name = strtoupper($matches[1]);
+        $accession = $matches[2];
+      }
+      else {
+        throw new Exception("owl:Class stanza 'rdf:about' attribute is not formated as expected: '$about'. " . "This is necessary to determine the term's accession: \n\n" . $stanza->getXML());
+      }
+    }
+  }
+
+  // If the database name for this term is the same as the vocabulary
+  // we are trying to load, then do include it in the $vocabs array.
+  if ($db_name == $vocabs['this']) {
+    return;
+  }
+
+  // insert dbxref
+  $values = array (
+    'db_id' => $db->db_id,
+    'accession' => $accession
+  );
+  print_r($values);
+  $dbxref = tripal_insert_dbxref($values);
+
+  $cvterm_name = $stanza->getChild('rdfs:label');
+  if ($cvterm_name) {
+  $cvterm_name = $stanza->getValue();
+  }
+  print_r($cvterm_name);
+
+  $definition = $stanza->getChild('obo:IAO_0000115');
+  if ($definition) {
+  $definition = $stanza->getValue();
+  }
+
+  $term = array (
+  'id' => $db->name . ':' . $dbxref->accession,
+  'name' => $db->name,
+  'cv_name' => $stanza->getValue(),
+  'definition' =>  $stanza->getValue(),
+  );
+  print_r($term);
+
+  $options = array ();
+  if ($vocabs['this'] != $db->name) {
+  $options['update_existing'] = FALSE;
+  }
+  $cvterm = tripal_insert_cvterm($term, $options);
+
+  // // Add a record to the chado relationship table if an ‘rdfs:subClassOf’ child exists.
+
+  // $cvterm_name = $stanza->getChild('rdfs:subClassOf');
+
+  // Insert a new cvterm record.
+  // $cvterm_name = '';
+  // $definition = '';
+  // $cvterm_name = $stanza->getChild('rdfs:label');
+  // if ($cvterm_name) {
+  // $cvterm_name = $stanza->getValue();
+  //}
+
+  // $definition = $stanza->getChild('obo:IAO_0000115');
+  // if ($definition) {
+  //$definition = $stanza->getValue();
+  //}
+
+
+  // $term = array (
+  // 'id' => $db->name . ':' . $dbxref->accession,
+  // 'name' => $cvterm_name,
+  // 'cv_name' => $cv->name,
+  // 'definition' => $definition
+  // );
+  // $option = array ();
+  // if ($vocabs['this'] != $db->name) {
+  // $option['update_existing'] = FALSE;
+  // }
+  // $cvterm = tripal_insert_cvterm($term, $option);
+  }