tripal/tripal_cv/obo_loader.php

<?php

/**
 * @file
 * Tripal Ontology Loader
 *
 * @defgroup tripal_obo_loader Tripal Ontology Loader
 * @ingroup tripal_cv
 */

/**
 *
 * @ingroup tripal_obo_loader
 */
function tripal_cv_load_obo_v1_2_id($obo_id, $jobid = NULL) {

  // get the OBO reference
  $sql = "SELECT * FROM {tripal_cv_obo} WHERE obo_id = %d";
  $obo = db_fetch_object(db_query($sql, $obo_id));

  // if the reference is for a remote URL then run the URL processing function
  if (preg_match("/^http:\/\//", $obo->path) or preg_match("/^ftp:\/\//", $obo->path)) {
    tripal_cv_load_obo_v1_2_url($obo->name, $obo->path, $jobid, 0);
  }
  // if the reference is for a local file then run the file processing function
  else {
    // check to see if the file is located local to Drupal
    $dfile = $_SERVER['DOCUMENT_ROOT'] . base_path() . $obo->path;
    if (file_exists($dfile)) {
      tripal_cv_load_obo_v1_2_file($obo->name, $dfile , $jobid, 0);
    }
    // if not local to Drupal, the file must be someplace else, just use
    // the full path provided
    else {
      if (file_exists($obo->path)) {
        tripal_cv_load_obo_v1_2_file($obo->name, $obo->path, $jobid, 0);
      }
      else {
        print "ERROR: counld not find OBO file: '$obo->path'\n";
      }
    }
  }
}

/**
 *
 * @ingroup tripal_obo_loader
 */
function tripal_cv_load_obo_v1_2_file($obo_name, $file, $jobid = NULL, $is_new = TRUE) {
  $newcvs = array();

  tripal_cv_load_obo_v1_2($file, $jobid, $newcvs);
  if ($is_new) {
    tripal_cv_load_obo_add_ref($obo_name, $file);
  }

  // update the cvtermpath table
  tripal_cv_load_update_cvtermpath($newcvs, $jobid);
  print "Ontology Sucessfully loaded!\n";

}

/**
 *
 * @ingroup tripal_obo_loader
 */
function tripal_cv_load_obo_v1_2_url($obo_name, $url, $jobid = NULL, $is_new = TRUE) {

  $newcvs = array();

  // first download the OBO
  $temp = tempnam(sys_get_temp_dir(), 'obo_');
  print "Downloading URL $url, saving to $temp\n";
  $url_fh = fopen($url, "r");
  $obo_fh = fopen($temp, "w");
  if (!$url_fh) {
    tripal_cv_obo_quiterror("Unable to download the remote OBO file at $url. Could a firewall be blocking outgoing connections? ".
          " if you are unable to download the file you may manually downlod the OBO file and use the web interface to ".
          " specify the location of the file on your server.");

  }
  while (!feof($url_fh)) {
    fwrite($obo_fh, fread($url_fh, 255), 255);
  }
  fclose($url_fh);
  fclose($obo_fh);

  // second, parse the OBO
  tripal_cv_load_obo_v1_2($temp, $jobid, $newcvs);

  // now remove the temp file
  unlink($temp);

  if ($is_new) {
    tripal_cv_load_obo_add_ref($obo_name, $url);
  }

  // update the cvtermpath table
  tripal_cv_load_update_cvtermpath($newcvs, $jobid);

  print "Ontology Sucessfully loaded!\n";
}

/**
 *
 * @ingroup tripal_obo_loader
 */
function tripal_cv_load_update_cvtermpath($newcvs, $jobid) {

  print "\nUpdating cvtermpath table.  This may take a while...\n";
  foreach ($newcvs as $namespace => $cvid) {
    tripal_cv_update_cvtermpath($cvid, $jobid);
  }
}

/**
 *
 */
function tripal_cv_load_obo_add_ref($name, $path) {
  $isql = "INSERT INTO {tripal_cv_obo} (name,path) VALUES ('%s','%s')";
  db_query($isql, $name, $path);
}

/**
 *
 * @ingroup tripal_obo_loader
 */
function tripal_cv_load_obo_v1_2($file, $jobid = NULL, &$newcvs) {
  global $_tripal_cv_previous_db;

  $header = array();
  $obo = array();

  print "Opening File $file\n";

  // set the search path
  $_tripal_cv_previous_db = tripal_db_set_active('chado');

  // make sure we have an 'internal' and a '_global' database
  if (!tripal_cv_obo_add_db('internal')) {
    tripal_cv_obo_quiterror("Cannot add 'internal' database");
  }
  if (!tripal_cv_obo_add_db('_global')) {
    tripal_cv_obo_quiterror("Cannot add '_global' database");
  }

  // parse the obo file
  tripal_cv_obo_parse($file, $obo, $header);

  // add the CV for this ontology to the database
  $defaultcv = tripal_cv_obo_add_cv($header['default-namespace'][0], '');
  if (!$defaultcv) {
    tripal_cv_obo_quiterror('Cannot add namespace ' . $header['default-namespace'][0]);
  }
  $newcvs[$header['default-namespace'][0]] = $defaultcv->cv_id;

  // add any typedefs to the vocabulary first
  $typedefs = $obo['Typedef'];
  foreach ($typedefs as $typedef) {
    tripal_cv_obo_process_term($typedef, $defaultcv, $obo, 1, $newcvs);
  }

  // next add terms to the vocabulary
  $terms = $obo['Term'];
  if (!tripal_cv_obo_process_terms($terms, $defaultcv, $obo, $jobid, $newcvs)) {
    tripal_cv_obo_quiterror('Cannot add terms from this ontology');
  }

  return tripal_cv_obo_loader_done();
}

/**
 *
 * @ingroup tripal_obo_loader
 */
function tripal_cv_obo_quiterror($message) {

  print "ERROR: $message\n";
  db_query("set search_path to public");
  exit;

}

/**
 *
 * @ingroup tripal_obo_loader
 */
function tripal_cv_obo_loader_done() {

  // return the search path to normal
  tripal_db_set_active($_tripal_cv_previous_db);
  db_query("set search_path to public");

  return '';
}

/**
 *
 * @ingroup tripal_obo_loader
 */
function tripal_cv_obo_process_terms($terms, $defaultcv, $obo, $jobid = NULL, &$newcvs) {

  $i = 0;
  $count = sizeof($terms);
  $interval = intval($count * 0.01);
  if ($interval > 1) {
    $interval = 1;
  }

  foreach ($terms as $term) {

    // update the job status every 1% terms
    if ($jobid and $i % $interval == 0) {
      tripal_job_set_progress($jobid, intval(($i / $count) * 50)); // we mulitply by 50 because parsing and loacing cvterms
                                                                   // is only the first half.  The other half is updating
    }                                                              // the cvtermpath table.

    if (!tripal_cv_obo_process_term($term, $defaultcv, $obo, 0, $newcvs)) {
      tripal_cv_obo_quiterror("Failed to process terms from the ontology");
    }

    $i++;
  }
  return 1;
}

/**
 *
 * @ingroup tripal_obo_loader
 */
function tripal_cv_obo_process_term($term, $defaultcv, $obo, $is_relationship = 0, &$newcvs) {

  // add the cvterm
  $cvterm = tripal_cv_obo_add_cvterm($term, $defaultcv, $is_relationship, 1);
  if (!$cvterm) {
    tripal_cv_obo_quiterror("Cannot add the term " . $term['id'][0]);
  }
  if ($term['namespace'][0]) {
    $newcvs[$term['namespace'][0]] = $cvterm->cv_id;
  }

  // now handle other properites
  if (isset($term['is_anonymous'])) {
    //print "WARNING: unhandled tag: is_anonymous\n";
  }
  if (isset($term['alt_id'])) {
    foreach ($term['alt_id'] as $alt_id) {
      if (!tripal_cv_obo_add_cvterm_dbxref($cvterm, $alt_id)) {
        tripal_cv_obo_quiterror("Cannot add alternate id $alt_id");
      }
    }
  }
  if (isset($term['subset'])) {
    //print "WARNING: unhandled tag: subset\n";
  }
  // add synonyms for this cvterm
  if (isset($term['synonym'])) {
    if (!tripal_cv_obo_add_synonyms($term, $cvterm)) {
      tripal_cv_obo_quiterror("Cannot add synonyms");
    }
  }

  // reformat the deprecated 'exact_synonym, narrow_synonym, and broad_synonym'
  // types to be of the v1.2 standard
  if (isset($term['exact_synonym']) or isset($term['narrow_synonym']) or isset($term['broad_synonym'])) {
    if (isset($term['exact_synonym'])) {
      foreach ($term['exact_synonym'] as $synonym) {
        $new = preg_replace('/^\s*(\".+?\")(.*?)$/', '$1 EXACT $2', $synonym);
        $term['synonym'][] = $new;
      }
    }
    if (isset($term['narrow_synonym'])) {
      foreach ($term['narrow_synonym'] as $synonym) {
        $new = preg_replace('/^\s*(\".+?\")(.*?)$/', '$1 NARROW $2', $synonym);
        $term['synonym'][] = $new;
      }
    }
    if (isset($term['broad_synonym'])) {
      foreach ($term['broad_synonym'] as $synonym) {
        $new = preg_replace('/^\s*(\".+?\")(.*?)$/', '$1 BROAD $2', $synonym);
        $term['synonym'][] = $new;
      }
    }

    if (!tripal_cv_obo_add_synonyms($term, $cvterm)) {
      tripal_cv_obo_quiterror("Cannot add/update synonyms");
    }
  }
  // add the comment to the cvtermprop table
  if (isset($term['comment'])) {
    $comments = $term['comment'];
    $j = 0;
    foreach ($comments as $comment) {
      if (!tripal_cv_obo_add_cvterm_prop($cvterm, 'comment', $comment, $j)) {
        tripal_cv_obo_quiterror("Cannot add/update cvterm property");
      }
      $j++;
    }
  }
  // add any other external dbxrefs
  if (isset($term['xref'])) {
    foreach ($term['xref'] as $xref) {
      if (!tripal_cv_obo_add_cvterm_dbxref($cvterm, $xref)) {
        tripal_cv_obo_quiterror("Cannot add/update cvterm database reference (dbxref).");
      }
    }
  }
  if (isset($term['xref_analog'])) {
    foreach ($term['xref_analog'] as $xref) {
      if (!tripal_cv_obo_add_cvterm_dbxref($cvterm, $xref)) {
        tripal_cv_obo_quiterror("Cannot add/update cvterm database reference (dbxref).");
      }
    }
  }
  if (isset($term['xref_unk'])) {
    foreach ($term['xref_unk'] as $xref) {
      if (!tripal_cv_obo_add_cvterm_dbxref($cvterm, $xref)) {
        tripal_cv_obo_quiterror("Cannot add/update cvterm database reference (dbxref).");
      }
    }
  }

  // add is_a relationships for this cvterm
  if (isset($term['is_a'])) {
    foreach ($term['is_a'] as $is_a) {
      if (!tripal_cv_obo_add_relationship($cvterm, $defaultcv, $obo, 'is_a', $is_a, $is_relationship)) {
        tripal_cv_obo_quiterror("Cannot add relationship is_a: $is_a");
      }
    }
  }
  if (isset($term['intersection_of'])) {
    //print "WARNING: unhandled tag: intersection_of\n";
  }
  if (isset($term['union_of'])) {
    //print "WARNING: unhandled tag: union_on\n";
  }
  if (isset($term['disjoint_from'])) {
    //print "WARNING: unhandled tag: disjoint_from\n";
  }
  if (isset($term['relationship'])) {
    foreach ($term['relationship'] as $value) {
      $rel = preg_replace('/^(.+?)\s.+?$/', '\1', $value);
      $object = preg_replace('/^.+?\s(.+?)$/', '\1', $value);
      if (!tripal_cv_obo_add_relationship($cvterm, $defaultcv, $obo, $rel, $object, $is_relationship)) {
        tripal_cv_obo_quiterror("Cannot add relationship $rel: $object");
      }
    }
  }
  if (isset($term['replaced_by'])) {
   //print "WARNING: unhandled tag: replaced_by\n";
  }
  if (isset($term['consider'])) {
    //print "WARNING: unhandled tag: consider\n";
  }
  if (isset($term['use_term'])) {
    //print "WARNING: unhandled tag: user_term\n";
  }
  if (isset($term['builtin'])) {
    //print "WARNING: unhandled tag: builtin\n";
  }
  return 1;
}

/**
 * Add a database record
 * @ingroup tripal_obo_loader
 */
function tripal_cv_obo_add_db($dbname) {

  $db_sql = "SELECT * FROM {db} WHERE name ='%s'";
  $db = db_fetch_object(db_query($db_sql, $dbname));
  if (!$db) {
    if (!db_query("INSERT INTO {db} (name) VALUES ('%s')", $dbname)) {
      tripal_cv_obo_quiterror("Cannot create '$dbname' db in Chado.");
    }
    $db = db_fetch_object(db_query($db_sql, $dbname));
  }

  return $db;
}

/**
 * Add a controlled vocab record
 * @ingroup tripal_obo_loader
 */
function tripal_cv_obo_add_cv($name, $comment) {

  // see if the CV (default-namespace) exists already in the database
  $vocab = $name;
  $remark = $comment;
  $cv_sql = "SELECT * FROM {cv} WHERE name = '%s'";
  $cv = db_fetch_object(db_query($cv_sql, $vocab));

  // if the CV exists then update it, otherwise insert
  if (!$cv) {
    $sql = "INSERT INTO {cv} (name,definition) VALUES ('%s','%s')";
    if (!db_query($sql, $vocab, $remark)) {
      tripal_cv_obo_quiterror("Failed to create the CV record");
    }
    $cv = db_fetch_object(db_query($cv_sql, $vocab));
  }
  else {
    $sql = "UPDATE {cv} SET definition = '%s' WHERE name ='%s'";
    if (!db_query($sql, $remark, $vocab)) {
      tripal_cv_obo_quiterror("Failed to update the CV record");
    }
    $cv = db_fetch_object(db_query($cv_sql, $vocab));
  }

  return $cv;
}

/**
 * Add a cvterm relationship
 *
 * @ingroup tripal_obo_loader
 */
function tripal_cv_obo_add_relationship($cvterm, $defaultcv, $obo, $rel, $objname, $object_is_relationship = 0) {

  // make sure the relationship cvterm exists
  $term = array(
    'name' => array($rel),
    'id' => array($rel),
    'definition' => array(''),
    'is_obsolete' => array(0),
  );
  $relcvterm = tripal_cv_obo_add_cvterm($term, $defaultcv, 1, 0);
  if (!$relcvterm) {
    tripal_cv_obo_quiterror("Cannot find or insert the relationship term: $rel\n");
  }

  // get the object term
  $objterm = tripal_cv_obo_get_term($obo, $objname);
  if (!$objterm) {
    tripal_cv_obo_quiterror("Could not find object term $objname\n");
  }
  $objcvterm = tripal_cv_obo_add_cvterm($objterm, $defaultcv, $object_is_relationship, 1);
  if (!$objcvterm) {
    tripal_cv_obo_quiterror("Cannot add/find cvterm");
  }

  // check to see if the cvterm_relationship already exists, if not add it
  $cvrsql = "SELECT * FROM {cvterm_relationship} WHERE type_id = %d and subject_id = %d and object_id = %d";
  if (!db_fetch_object(db_query($cvrsql, $relcvterm->cvterm_id, $cvterm->cvterm_id, $objcvterm->cvterm_id))) {
    $sql = "INSERT INTO {cvterm_relationship} ".
           "(type_id,subject_id,object_id) VALUES (%d,%d,%d)";
    if (!db_query($sql, $relcvterm->cvterm_id, $cvterm->cvterm_id, $objcvterm->cvterm_id)) {
      tripal_cv_obo_quiterror("Cannot add term relationship: '$cvterm->name' $rel '$objcvterm->name'");
    }
  }

  return TRUE;
}

/**
 *
 * @ingroup tripal_obo_loader
 */
function tripal_cv_obo_get_term($obo, $id) {
  foreach ($obo as $type) {
    foreach ($type as $term) {
      $accession = $term['id'][0];
      if (strcmp($accession, $id)==0) {
        return $term;
      }
    }
  }

  return FALSE;
}

/**
 *
 * @ingroup tripal_obo_loader
 */
function tripal_cv_obo_add_synonyms($term, $cvterm) {

  // make sure we have a 'synonym_type' vocabulary
  $sql = "SELECT * FROM {cv} WHERE name='synonym_type'";
  $syncv = db_fetch_object(db_query($sql));
  if (!$syncv) {
    $sql = "INSERT INTO {cv} (name,definition) VALUES ('synonym_type','')";
    if (!db_query($sql)) {
      tripal_cv_obo_quiterror("Failed to add the synonyms type vocabulary");
    }
    $syncv = db_fetch_object(db_query($sql));
  }

  // now add the synonyms
  if (isset($term['synonym'])) {
    foreach ($term['synonym'] as $synonym) {
      // separate out the synonym definition and the synonym type
      $def = preg_replace('/^\s*"(.*)"\s*.*$/', '\1', $synonym);
      $type = drupal_strtolower(preg_replace('/^.*"\s+(.*?)\s+.*$/', '\1', $synonym));

      // make sure the synonym type exists in the 'synonym_type' vocabulary
      $cvtsql = "
        SELECT *
        FROM {cvterm} CVT
           INNER JOIN {cv} CV ON CVT.cv_id = CV.cv_id
        WHERE CVT.name = '%s' and CV.name = '%s'
      ";
      $syntype = db_fetch_object(db_query($cvtsql, $type, 'synonym_type'));
      if (!$syntype) {
        // build a 'term' object so we can add the missing term
        $term = array(
           'name' => array($type),
           'id' => array("internal:$type"),
           'definition' => array(''),
           'is_obsolete' => array(0),
        );
        $syntype = tripal_cv_obo_add_cvterm($term, $syncv, 0, 1);
        if (!$syntype) {
          tripal_cv_obo_quiterror("Cannot add synonym type: internal:$type");
        }
      }

      // make sure the synonym doesn't already exists
      $sql = "
        SELECT *
        FROM {cvtermsynonym}
        WHERE cvterm_id = %d and synonym = '%s'
      ";
      $syn = db_fetch_object(db_query($sql, $cvterm->cvterm_id, $def));
      if (!$syn) {
        $sql = "INSERT INTO {cvtermsynonym} (cvterm_id,synonym,type_id)
                VALUES(%d,'%s',%d)";
        if (!db_query($sql, $cvterm->cvterm_id, $def, $syntype->cvterm_id)) {
          tripal_cv_obo_quiterror("Failed to insert the synonym for term: $name ($def)");
        }
      }

      // now add the dbxrefs for the synonym if we have a comma in the middle
      // of a description then this will cause problems when splitting os lets
      // just change it so it won't mess up our splitting and then set it back
      // later.
      /**
      $synonym = preg_replace('/(".*?),\s(.*?")/','$1,_$2',$synonym);
      $dbxrefs = preg_split("/, /",preg_replace('/^.*\[(.*?)\]$/','\1',$synonym));
      foreach ($dbxrefs as $dbxref) {
       $dbxref = preg_replace('/,_/',", ",$dbxref);
        if ($dbxref) {
          tripal_cv_obo_add_cvterm_dbxref($syn,$dbxref);
        }
      }
      */
    }
  }

  return TRUE;
}

/**
 * Actually parse the OBO file
 *
 * @ingroup tripal_obo_loader
 */
function tripal_cv_obo_parse($obo_file, &$obo, &$header) {
  $i = 0;
  $in_header = 1;
  $stanza = array();

  // iterate through the lines in the OBO file and parse the stanzas
  $fh = fopen($obo_file, 'r');
  while ($line = fgets($fh)) {
    $i++;

    // remove newlines
    $line = rtrim($line);

    // remove any special characters that may be hiding
    $line = preg_replace('/[^(\x20-\x7F)]*/', '', $line);

    // skip empty lines
    if (strcmp($line, '') == 0) {
      continue;
    }

    //remove comments from end of lines
    $line = preg_replace('/^(.*?)\!.*$/', '\1', $line);  // TODO: if the explamation is escaped

    if (preg_match('/^\s*\[/', $line)) {  // at the first stanza we're out of header
      $in_header = 0;
      // load the stanza we just finished reading
      if (sizeof($stanza) > 0) {
        if (!isset($obo[$type])) {
          $obo[$type] = array();
        }
        if (!isset($obo[$type][$stanza['id'][0]])) {
          $obo[$type][$stanza['id'][0]] = $stanza;
        }
        else {
          array_merge($obo[$type][$stanza['id'][0]], $stanza);
        }
      }
      // get the stanza type:  Term, Typedef or Instance
      $type = preg_replace('/^\s*\[\s*(.+?)\s*\]\s*$/', '\1', $line);

      // start fresh with a new array
      $stanza = array();
      continue;
    }
    // break apart the line into the tag and value but ignore any escaped colons
    preg_replace("/\\:/", "|-|-|", $line); // temporarily replace escaped colons
    $pair = explode(":", $line, 2);
    $tag = $pair[0];
    $value = ltrim(rtrim($pair[1]));// remove surrounding spaces
    $tag = preg_replace("/\|-\|-\|/", "\:", $tag); // return the escaped colon
    $value = preg_replace("/\|-\|-\|/", "\:", $value);
    if ($in_header) {
      if (!isset($header[$tag])) {
        $header[$tag] = array();
      }
      $header[$tag][] = $value;
    }
    else {
      if (!isset($stanza[$tag])) {
        $stanza[$tag] = array();
      }
      $stanza[$tag][] = $value;
    }
  }
  // now add the last term in the file
  if (sizeof($stanza) > 0) {
    if (!isset($obo[$type])) {
      $obo[$type] = array();
    }
    if (!isset($obo[$type][$stanza['id'][0]])) {
      $obo[$type][$stanza['id'][0]] = $stanza;
    }
    else {
      array_merge($obo[$type][$stanza['id'][0]], $stanza);
    }
  }
}

/**
 * Add database reference to cvterm
 *
 * @ingroup tripal_obo_loader
 */
function tripal_cv_obo_add_cvterm_dbxref($cvterm, $xref) {

  $dbname = preg_replace('/^(.+?):.*$/', '$1', $xref);
  $accession = preg_replace('/^.+?:\s*(.*?)(\{.+$|\[.+$|\s.+$|\".+$|$)/', '$1', $xref);
  $description = preg_replace('/^.+?\"(.+?)\".*?$/', '$1', $xref);
  $dbxrefs = preg_replace('/^.+?\[(.+?)\].*?$/', '$1', $xref);

  if (!$accession) {
    tripal_cv_obo_quiterror();
    watchdog('tripal_cv', "Cannot add a dbxref without an accession: '$xref'", NULL, WATCHDOG_WARNING);
    return FALSE;
  }

  // if the xref is a database link, handle that specially
  if (strcmp($dbname, 'http') == 0) {
    $accession = $xref;
    $dbname = 'URL';
  }

  // check to see if the database exists
  $db = tripal_cv_obo_add_db($dbname);
  if (!$db) {
    tripal_cv_obo_quiterror("Cannot find database '$dbname' in Chado.");
  }

  // now add the dbxref
  $dbxref = tripal_cv_obo_add_dbxref($db->db_id, $accession, '', $description);
  if (!$dbxref) {
    tripal_cv_obo_quiterror("Cannot find or add the database reference (dbxref)");
  }

  // finally add the cvterm_dbxref but first check to make sure it exists
  $sql = "SELECT * from {cvterm_dbxref} WHERE cvterm_id = %d and dbxref_id = %d";
  if (!db_fetch_object(db_query($sql, $cvterm->cvterm_id, $dbxref->dbxref_id))) {
    $sql = "INSERT INTO {cvterm_dbxref} (cvterm_id,dbxref_id)".
           "VALUES (%d,%d)";
    if (!db_query($sql, $cvterm->cvterm_id, $dbxref->dbxref_id)) {
      tripal_cv_obo_quiterror("Cannot add cvterm_dbxref: $xref");
    }
  }

  return TRUE;
}

/**
 * Add property to CVterm
 * @ingroup tripal_obo_loader
 */
function tripal_cv_obo_add_cvterm_prop($cvterm, $property, $value, $rank) {

  // make sure the 'cvterm_property_type' CV exists
  $cv = tripal_cv_obo_add_cv('cvterm_property_type', '');
  if (!$cv) {
    tripal_cv_obo_quiterror("Cannot add/find cvterm_property_type cvterm");
  }

  // get the property type cvterm.  If it doesn't exist then we want to add it
  $sql = "
      SELECT *
      FROM {cvterm} CVT INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
      WHERE CVT.name = '%s' and CV.name = '%s'
  ";
  $cvproptype = db_fetch_object(db_query($sql, $property, 'cvterm_property_type'));
  if (!$cvproptype) {
    $term = array(
      'name' => array($property),
      'id' => array("internal:$property"),
      'definition' => array(''),
      'is_obsolete' => array(0),
    );
    $cvproptype = tripal_cv_obo_add_cvterm($term, $cv, 0, 0);
    if (!$cvproptype) {
      tripal_cv_obo_quiterror("Cannot add cvterm property: internal:$property");
    }
  }


  // remove any properties that currently exist for this term.  We'll reset them
  if ($rank == 0) {
    $sql = "DELETE FROM {cvtermprop} WHERE cvterm_id = %d";
    db_query($sql, $cvterm->cvterm_id);
  }

  // now add the property
  $sql = "INSERT INTO {cvtermprop} (cvterm_id,type_id,value,rank) ".
        "VALUES (%d, %d, '%s',%d)";
  if (!db_query($sql, $cvterm->cvterm_id, $cvproptype->cvterm_id, $value, $rank)) {
    tripal_cv_obo_quiterror("Could not add property $property for term\n");
  }

  return TRUE;

}

/**
 *
 * @ingroup tripal_obo_loader
 */
function tripal_cv_obo_add_cvterm($term, $defaultcv, $is_relationship = 0, $update = 1) {

  // get the term properties
  $id = $term['id'][0];
  $name = $term['name'][0];
  $cvname = $term['namespace'][0];
  $definition = preg_replace('/^\"(.*)\"/', '\1', $term['def'][0]);
  $is_obsolete = 0;
  if (isset($term['is_obsolete'][0]) and  strcmp($term['is_obsolete'][0], 'true') == 0) {
    $is_obsolete = 1;
  }
  if (!$cvname) {
    $cvname = $defaultcv->name;
  }

  // make sure the CV name exists
  $cv = tripal_cv_obo_add_cv($cvname, '');
  if (!$cv) {
    tripal_cv_obo_quiterror("Cannot find namespace '$cvname' when adding/updating $id");
  }

  // this SQL statement will be used a lot to find a cvterm so just set it
  // here for easy reference below.
  $cvtermsql = "SELECT CVT.name, CVT.cvterm_id, DB.name as dbname, DB.db_id
                FROM {cvterm} CVT
                  INNER JOIN {dbxref} DBX on CVT.dbxref_id = DBX.dbxref_id
                  INNER JOIN {db} DB on DBX.db_id = DB.db_id
                  INNER JOIN {cv} CV on CV.cv_id = CVT.cv_id
                WHERE CVT.name = '%s' and DB.name = '%s'";

  // get the accession and the database from the cvterm
  if (preg_match('/^.+?:.*$/', $id)) {
    $accession = preg_replace('/^.+?:(.*)$/', '\1', $id);
    $dbname = preg_replace('/^(.+?):.*$/', '\1', $id);
  }
  if ($is_relationship and !$dbname) {
    $accession = $id;
    // because this is a relationship cvterm first check to see if it
    // exists in the relationship ontology. If it does then return the cvterm.
    //  If not then set the dbname to _global and we'll add it or find it there
    $cvterm = db_fetch_object(db_query($cvtermsql, $name, 'OBO_REL'));
    if ($cvterm) {
      return $cvterm;
    }
    else {
      // next check if this term is in the _global ontology.  If it is then
      // return it no matter what the original CV
      $dbname = '_global';

      $cvterm = db_fetch_object(db_query($cvtermsql, $name, $dbname));
      if ($cvterm) {
        return $cvterm;
      }
    }
  }
  if (!$is_relationship and !$dbname) {
    tripal_cv_obo_quiterror("A database identifier is missing from the term: $id");
  }

  // check to see if the database exists.
  $db = tripal_cv_obo_add_db($dbname);
  if (!$db) {
    tripal_cv_obo_quiterror("Cannot find database '$dbname' in Chado.");
  }


  // if the cvterm doesn't exist then add it otherwise just update it
  $cvterm = db_fetch_object(db_query($cvtermsql, $name, $dbname));
  if (!$cvterm) {
    // check to see if the dbxref exists if not, add it
    $dbxref =  tripal_cv_obo_add_dbxref($db->db_id, $accession);
    if (!$dbxref) {
      tripal_cv_obo_quiterror("Failed to find or insert the dbxref record for cvterm, $name (id: $accession), for database $dbname");
    }

    // check to see if the dbxref already has an entry in the cvterm table
    $sql = "SELECT * FROM {cvterm} WHERE dbxref_id = %d";
    $check = db_fetch_object(db_query($sql, $dbxref->dbxref_id));

    if (!$check) {
      // now add the cvterm
      $sql = "
          INSERT INTO {cvterm} (cv_id, name, definition, dbxref_id,
             is_obsolete, is_relationshiptype)
          VALUES (%d,'%s','%s',%d,%d,%d)
      ";
      if (!db_query($sql, $cv->cv_id, $name, $definition,
        $dbxref->dbxref_id, $is_obsolete, $is_relationship)) {
        if (!$is_relationship) {
          tripal_cv_obo_quiterror("Failed to insert the term: $name ($dbname)");
        }
        else {
          tripal_cv_obo_quiterror("Failed to insert the relationship term: $name (cv: " . $cvname . " db: $dbname)");
        }
      }
      if (!$is_relationship) {
        print "Added CV term: $name ($dbname)\n";
      }
      else {
        print "Added relationship CV term: $name ($dbname)\n";
      }
    }
    elseif ($check and strcmp($check->name, $name)!=0) {
      // this dbxref_id alrady exists in the database but the name is
      // different.  We will trust that the OBO is correct and that there
      // has been a name change for this dbxref, so we'll update
      $sql = "
          UPDATE {cvterm} SET name = '%s', definition = '%s',
             is_obsolete = %d, is_relationshiptype = %d
          WHERE dbxref_id = %d
      ";
      if (!db_query($sql, $name, $definition, $is_obsolete, $is_relationship, $dbxref->dbxref_id)) {
        if (!$is_relationship) {
          tripal_cv_obo_quiterror("Failed to update the term: $name ($dbname)");
        }
        else {
          tripal_cv_obo_quiterror("Failed to update the relationship term: $name (cv: " . $cvname . " db: $dbname)");
        }
      }
      if (!$is_relationship) {
        print "Updated CV term: $name ($dbname)\n";
      }
      else {
        print "Updated relationship CV term: $name ($dbname)\n";
      }
    }
    elseif ($check and strcmp($check->name, $name)==0) {
      // this entry already exists. We're good, so do nothing
    }
    $cvterm = db_fetch_object(db_query($cvtermsql, $name, $dbname));
  }
  elseif ($update) { // update the cvterm
    $sql = "
       UPDATE {cvterm} SET name='%s', definition='%s',
          is_obsolete = %d, is_relationshiptype = %d
       WHERE cvterm_id = %d
    ";
    if (!db_query($sql, $term['name'][0], $definition,
      $is_obsolete, $is_relationship, $cvterm->cvterm_id)) {
      tripal_cv_obo_quiterror("Failed to update the term: $name");
    }
    $cvterm = db_fetch_object(db_query($cvtermsql, $name, $dbname));
    if (!$is_relationship) {
      print "Updated CV term: $name ($dbname)\n";
    }
    else {
      print "Updated relationship CV term: $name ($dbname)\n";
    }
  }

  // return the cvterm
  return $cvterm;
}

/**
 * Add Database Reference
 * @ingroup tripal_obo_loader
 */
function tripal_cv_obo_add_dbxref($db_id, $accession, $version='', $description='') {

  // check to see if the dbxref exists if not, add it
  $dbxsql = "SELECT dbxref_id FROM {dbxref} WHERE db_id = %d and accession = '%s'";
  $dbxref = db_fetch_object(db_query($dbxsql, $db_id, $accession));
  if (!$dbxref) {
    $sql = "
       INSERT INTO {dbxref} (db_id, accession, version, description)
       VALUES (%d,'%s','%s','%s')
    ";
    if (!db_query($sql, $db_id, $accession, $version, $description)) {
      tripal_cv_obo_quiterror("Failed to insert the dbxref record $accession");
    }
    print "Added Dbxref accession: $accession\n";
    $dbxref = db_fetch_object(db_query($dbxsql, $db_id, $accession));
  }
  return $dbxref;

}