tripal/tripal_feature/tripal_feature.module

<?php

require_once "admin.php";
require_once "syncFeatures.php";
require_once "indexFeatures.php";
require_once "fasta_loader.php";

require_once "tripal_feature.api.inc";

require_once "tripal_feature-secondary_tables.inc";
require_once "tripal_feature-properties.inc";
require_once "tripal_feature-relationships.inc";
require_once "tripal_feature-db_references.inc";


/*************************************************************************
*
*/
function tripal_feature_init(){

   // add the jGCharts JS and CSS
   drupal_add_js (drupal_get_path('theme', 'tripal').'/js/tripal_feature.js'); 
   drupal_add_js (drupal_get_path('theme', 'tripal').'/js/jgcharts/jgcharts.js'); 

   drupal_add_css(drupal_get_path('theme', 'tripal').
                                  '/css/tripal_feature.css');
}

/*************************************************************************
 * Implements hook_views_api()
 * Purpose: Essentially this hook tells drupal that there is views support for
 *  for this module which then includes tripal_db.views.inc where all the
 *  views integration code is
 */ 
function tripal_feature_views_api() {
   return array(
      'api' => 2.0,
   );
}

/************************************************************************
 * Display help and module information
 * @param path which path of the site we're displaying help
 * @param arg array that holds the current path as would be returned from arg() function
 * @return help text for the path
 */
function tripal_feature_help($path, $arg) {
   $output = '';
   switch ($path) {
      case "admin/help#tripal_feature":
         $output='<p>'.t("Displays links to nodes created on this date").'</p>';
         break;
   }
   return $output;
}

/************************************************************************
 *  Provide information to drupal about the node types that we're creating
 *  in this module
 */
function tripal_feature_node_info() {
   $nodes = array();

   $nodes['chado_feature'] = array(
      'name' => t('Feature'),
      'module' => 'chado_feature',
      'description' => t('A feature from the chado database'),
      'has_title' => FALSE,
      'title_label' => t('Feature'),
      'has_body' => FALSE,
      'body_label' => t('Feature Description'),
      'locked' => TRUE
   );
   return $nodes;
}

/************************************************************************
 *  Set the permission types that the chado module uses.  Essentially we
 *  want permissionis that protect creation, editing and deleting of chado
 *  data objects
 */
function tripal_feature_perm(){
   return array(
      'access chado_feature content',
      'create chado_feature content',
      'delete chado_feature content',
      'edit chado_feature content',
   );
}

/************************************************************************
 *  Set the permission types that the module uses.
 */
function chado_feature_access($op, $node, $account) {
   if ($op == 'create') {
      return user_access('create chado_feature content', $account);
   }

   if ($op == 'update') {
      if (user_access('edit chado_feature content', $account)) {
         return TRUE;
      }
   }
   if ($op == 'delete') {
      if (user_access('delete chado_feature content', $account)) {
         return TRUE;
      }
   }
   if ($op == 'view') {
      if (user_access('access chado_feature content', $account)) {
         return TRUE;
      }
   }
   return FALSE;
}
/************************************************************************
 *  Menu items are automatically added for the new node types created
 *  by this module to the 'Create Content' Navigation menu item.  This function
 *  adds more menu items needed for this module.
 */
function tripal_feature_menu() {
   $items = array();

   // the administative settings menu
   $items['admin/tripal/tripal_feature'] = array(
     'title' => 'Features',
     'description' => 'Settings for Chado Features',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_feature_admin'),
     'access arguments' => array('administer site configuration'),
     'type' => MENU_NORMAL_ITEM,
   );
   $items['admin/tripal/fasta_loader'] = array(
     'title' => 'Import a multi-FASTA file',
     'description' => 'Load sequences from a multi-FASTA file into Chado',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_feature_fasta_load_form'),
     'access arguments' => array('administer site configuration'),
     'type' => MENU_NORMAL_ITEM,
   );

 // Adding Secondary Properties-----------------
  $items['node/%tripal_feature_node/properties'] = array(       
    'title' => t('Add Properties & Synonyms'),                         
    'description' => t('Settings for Features'),
    'page callback' => 'tripal_feature_add_ALL_property_page',           
    'page arguments' => array(1), 
    'access arguments' => array('create chado_feature content'),
    'type' => MENU_CALLBACK
  ); 

  $items['node/%tripal_feature_node/db_references'] = array(                        
    'title' => t('Add Database References'),                   
    'description' => t('Settings for Features'),              
    'page callback' => 'tripal_feature_add_ALL_dbreferences_page',                         
    'page arguments' => array(1),
    'access arguments' => array('create chado_feature content'),
    'type' => MENU_CALLBACK
  ); 

  $items['node/%tripal_feature_node/relationships'] = array(                      
    'title' => t('Add Relationships'),                      
    'description' => t('Settings for Features'),               
    'page callback' => 'tripal_feature_add_ALL_relationships_page',                          
    'page arguments' => array(1),
    'access arguments' => array('create chado_feature content'),
    'type' => MENU_CALLBACK
  );
  //Edit/Deleting Secondary Properties-------------
  $items['node/%tripal_feature_node/edit_properties'] = array(
    'title' => t('Edit Properties'),
    'description' => t('Settings for Features'),
    'page callback' => 'tripal_feature_edit_ALL_properties_page',
    'page arguments' => array(1),
    'access arguments' => array('edit chado_feature content'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 8,
  );

    $items['node/%tripal_feature_node/edit_relationships'] = array(
    'title' => t('Edit Relationships'),
    'description' => t('Settings for Feature'), 
    'page callback' => 'tripal_feature_edit_ALL_relationships_page',
    'page arguments' => array(1),
    'access arguments' => array('edit chado_feature content'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 9,
  );

  $items['node/%tripal_feature_node/edit_db_references'] = array(
    'title' => t('Edit References'),
    'description' => t('Settings for Feature'),
    'page callback' => 'tripal_feature_edit_ALL_dbreferences_page',
    'page arguments' => array(1),
    'access arguments' => array('edit chado_feature content'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 10,
  );

   return $items;
}
/*************************************************************************
 * Implements Menu wildcard_load hook
 * Purpose: Allows the node ID of a chado stock to be dynamically 
 *   pulled from the path. The node is loaded from this node ID
 *   and supplied to the page as an arguement
 */
function tripal_feature_node_load($nid) {
  if (is_numeric($nid)) {
    $node = node_load($nid);
    if ($node->type == 'chado_feature') {
      return $node;
    }
  }

  return FALSE;
}
/************************************************************************
 *  When a new chado_feature node is created we also need to add information
 *  to our chado_feature table.  This function is called on insert of a new node
 *  of type 'chado_feature' and inserts the necessary information.
 */
function chado_feature_insert($node){
   // remove spaces, newlines from residues
   $residues = preg_replace("/[\n\r\s]/","",$node->residues);

   // If this feature already exists then don't recreate it in chado
   // TODO: the unique index in chado for this also includes the type_id. If the site
   // ever needs to have the same feature name for different types then this will break.
   $feature_sql = "SELECT * 
                   FROM {Feature} F
                     INNER JOIN {cvterm} CVT ON F.type_id = CVT.cvterm_id
                   WHERE uniquename = '%s' and organism_id = %d and CVT.name = '%s'";
   $previous_db = tripal_db_set_active('chado');
   $feature = db_fetch_object(db_query($feature_sql,$node->uniquename,$node->organism_id,$node->feature_type));
   tripal_db_set_active($previous_db);

   // if the feature doesn't exist then let's create it in chado.
   if(!$feature){
      $sql = "INSERT INTO {feature} (organism_id, name, uniquename, residues, seqlen,".
             "    is_obsolete, type_id)".
             " VALUES(%d,'%s','%s','%s',%d, %s, ".
             "   (SELECT cvterm_id ".
             "    FROM {CVTerm} CVT ".
             "    INNER JOIN CV ON CVT.cv_id = CV.cv_id ".
             "    WHERE CV.name = 'sequence' and CVT.name = '%s'))";
      $obsolete = 'FALSE';
      if($node->is_obsolete){
         $obsolete = 'TRUE';
      }

      // use chado database
      $previous_db = tripal_db_set_active('chado');
      db_query($sql,$node->organism_id,$node->name,$node->uniquename,
      $residues,strlen($residues),$obsolete,$node->feature_type);

      // now that we've added the feature, get the feature id for this feature
      $feature = db_fetch_object(db_query($feature_sql,$node->uniquename,$node->organism_id,$node->feature_type));

      // now use drupal database
      tripal_db_set_active($previous_db);
   }

   // add the genbank accession and synonyms
   chado_feature_add_synonyms($node->synonyms,$feature->feature_id);

   // make sure the entry for this feature doesn't already exist in the chado_feature table
   // if it doesn't exist then we want to add it.
   $node_check_sql = "SELECT * FROM {chado_feature} ".
                     "WHERE feature_id = '%s'";
   $node_check = db_fetch_object(db_query($node_check_sql,$feature->feature_id));
   if(!$node_check){
      // next add the item to the drupal table
      $sql = "INSERT INTO {chado_feature} (nid, vid, feature_id, sync_date) ".
             "VALUES (%d, %d, %d, " . time() . ")";
      db_query($sql,$node->nid,$node->vid,$feature->feature_id);
   }
}
/************************************************************************
 */
function chado_feature_delete($node){
   // get feature_id so we can remove it from chado database
   $sql_drupal = "SELECT feature_id ".
                 "FROM {chado_feature} ".
                 "WHERE nid = %d AND vid = %d";
   $feature_id = db_result(db_query($sql_drupal, $node->nid, $node->vid));

   // remove the drupal content  
   $sql_del = "DELETE FROM {chado_feature} ".
              "WHERE nid = %d ".
              "AND vid = %d";
   db_query($sql_del, $node->nid, $node->vid);
   $sql_del = "DELETE FROM {node} ".
              "WHERE nid = %d ".
              "AND vid = %d";
   db_query($sql_del, $node->nid, $node->vid);
   $sql_del = "DELETE FROM {node_revisions} ".
              "WHERE nid = %d ".
              "AND vid = %d";
   db_query($sql_del, $node->nid, $node->vid);


   // Remove data from feature tables of chado database.  This will
   // cause a cascade delete and remove all data in referencing tables
   // for this feature
   $previous_db = tripal_db_set_active('chado');
   db_query("DELETE FROM {feature} WHERE feature_id = %d", $feature_id);
   tripal_db_set_active($previous_db);
   
   drupal_set_message("The feature and all associated data were removed from ".
      "chado");

}
/************************************************************************
 */
function chado_feature_update($node){
   if($node->revision){
      // TODO -- decide what to do about revisions
   } else {
      // get the feature for this node:
      $sql = 'SELECT feature_id FROM {chado_feature} WHERE vid = %d';
      $feature = db_fetch_object(db_query($sql, $node->vid));

      // remove spaces, newlines from residues
      $residues = preg_replace("/[\n\r\s]/","",$node->residues);

      $sql = "UPDATE {feature} ".
             " SET residues = '%s', ".
             "   name = '%s', ".
             "   uniquename = '%s', ".
             "   seqlen = %d, ".
             "   organism_id = %d, ".
             "   is_obsolete = %s, ".
             "   type_id = (SELECT cvterm_id ".
             "              FROM {CVTerm} CVT ".
             "              INNER JOIN CV ON CVT.cv_id = CV.cv_id ".
             "              WHERE CV.name = 'sequence' and CVT.name = '%s') ".
             "WHERE feature_id = %d ";
      $obsolete = 'FALSE';
      if($node->is_obsolete){
         $obsolete = 'TRUE';
      }
      $previous_db = tripal_db_set_active('chado');  // use chado database
      db_query($sql,$residues,$node->name,$node->uniquename,
      strlen($residues),$node->organism_id,$obsolete,$node->feature_type,
      $feature->feature_id);
      tripal_db_set_active($previous_db);  // now use drupal database

      // add the genbank accession & synonyms
      // chado_feature_add_gbaccession($node->gbaccession,$feature->feature_id);
      chado_feature_add_synonyms($node->synonyms,$feature->feature_id);
   }
}
/************************************************************************
 *
 */
function chado_feature_add_synonyms($synonyms,$feature_id){

   // make sure we only have a single space between each synonym
   $synonyms = preg_replace("/[\s\n\r]+/"," ",$synonyms);
   // split the synonyms into an array based on a space as the delimieter
   $syn_array = array();
   $syn_array = explode(" ",$synonyms);

   // use the chado database
   $previous_db = tripal_db_set_active('chado');

   // remove any old synonyms
   $feature_syn_dsql = "DELETE FROM {feature_synonym} WHERE feature_id = %d";
   if(!db_query($feature_syn_dsql,$feature_id)){
      $error .= "Could not remove synonyms from feature. ";
   }

   // return if we don't have any synonmys to add
   if(!$synonyms){
      tripal_db_set_active($previous_db);
      return;
   }
   // iterate through each synonym and add it to the database
   foreach($syn_array as $syn){
      // skip this item if it's empty
      if(!$syn){ break; }

      // check to see if we have this accession number already in the database
      // if so then don't add it again. it messes up drupal if the insert fails.
      // It is possible for the accession number to be present and not the feature
      $synonym_sql = "SELECT synonym_id FROM {synonym} ".
                     "WHERE name = '%s'";
      $synonym = db_fetch_object(db_query($synonym_sql,$syn));
      if(!$synonym){
         $synonym_isql = "INSERT INTO {synonym} (name,synonym_sgml,type_id) ".
                         "VALUES ('%s','%s', ".
                         "   (SELECT cvterm_id ".
                         "    FROM {CVTerm} CVT ".
                         "    INNER JOIN CV ON CVT.cv_id = CV.cv_id ".
                         "    WHERE CV.name = 'feature_property' and CVT.name = 'synonym'))";
         if(!db_query($synonym_isql,$syn,$syn)){
            $error .= "Could not add synonym. ";
         }
         // now get the synonym we just added
         $synonym_sql = "SELECT synonym_id FROM {synonym} ".
                        "WHERE name = '%s'";
         $synonym = db_fetch_object(db_query($synonym_sql,$syn));
      }

      // now add in our new sysnonym
      $feature_syn_isql = "INSERT INTO {feature_synonym} (synonym_id,feature_id,pub_id) ".
                          "VALUES (%d,%d,1)";
      if(!db_query($feature_syn_isql,$synonym->synonym_id,$feature_id)){
         $error .= "Could not add synonyms to feature. ";
      }
   }

   // return to the drupal database
   tripal_db_set_active($previous_db);
   return $error;

}
/************************************************************************
 *
 */
function chado_feature_add_gbaccession($accession,$feature_id){

   // use chado database
   $previous_db = tripal_db_set_active('chado');

   // remove any old accession from genbank dbEST
   $fdbxref_dsql = "DELETE FROM {feature_dbxref} ".
                   "WHERE feature_id = %d and dbxref_id IN ".
                   "   (SELECT DBX.dbxref_id FROM {dbxref} DBX ".
                   "    INNER JOIN DB  ON DB.db_id = DBX.db_id ".
                   "    INNER JOIN feature_dbxref FDBX ON DBX.dbxref_id = FDBX.dbxref_id ".
                   "    WHERE DB.name = 'DB:Genbank' and FDBX.feature_id = %d)";
   if(!db_query($fdbxref_dsql,$feature_id,$feature_id)){
      $error .= "Could not remove accession from feature. ";
   }

   // if we don't have an accession number to add then just return
   if(!$accession){
      tripal_db_set_active($previous_db);
      return;
   }
   // get the db_id
   $db_sql = "SELECT db_id FROM {DB} ".
             "WHERE name = 'DB:Genbank_est'";
   $db = db_fetch_object(db_query($db_sql));

   // check to see if we have this accession number already in the database
   // if so then don't add it again. it messes up drupal if the insert fails.
   // It is possible for the accession number to be present and not the feature
   $dbxref_sql = "SELECT dbxref_id FROM {dbxref} ".
                 "WHERE db_id = %d and accession = '%s'";
   $dbxref = db_fetch_object(db_query($dbxref_sql,$db->db_id,$accession));
   if(!$dbxref){
      // add the accession number
      $dbxref_isql = "INSERT INTO {dbxref} (db_id,accession) ".
                     "  VALUES (%d, '%s') ";
      if(!db_query($dbxref_isql,$db->db_id,$accession)){
         $error .= 'Could not add accession as a database reference ';
      }
      // get the dbxref_id for the just added accession number
      $dbxref_sql = "SELECT dbxref_id FROM {dbxref} ".
                    "WHERE db_id = %d and accession = '%s'";
      $dbxref = db_fetch_object(db_query($dbxref_sql,$db->db_id,$accession));
   }


   // associate the accession number with the feature
   $feature_dbxref_isql = "INSERT INTO {feature_dbxref} (feature_id,dbxref_id) ".
                          "  VALUES (%d, %d) ";
   if(!db_query($feature_dbxref_isql,$feature_id,$dbxref->dbxref_id)){
      $error .= 'Could not add feature database reference. ';
   }

   tripal_db_set_active($previous_db);
   return $error;
}

/************************************************************************
 *
 */
function chado_feature_form ($node,$param){
   $type = node_get_types('type', $node);
   $form = array();
   $feature = $node->feature;
   $synonyms = $node->synonyms;
   $analyses = $node->analyses;
   $references = $node->references;

   // We need to pass above variables for preview to show
   $form['feature'] = array(
      '#type' => 'value',
      '#value' => $feature
   );
   // This field is read when previewing a node
   $form['synonyms'] = array(
      '#type' => 'value',
      '#value' => $synonyms
   );
   // This field is read when previewing a node
   $form['analyses'] = array(
      '#type' => 'value',
      '#value' => $analyses
   );
   // This field is read when previewing a node
   $form['references'] = array(
      '#type' => 'value',
      '#value' => $references
   );

   // keep track of the feature id if we have one.  If we do have one then
   // this would indicate an update as opposed to an insert.
   $form['feature_id'] = array(
      '#type' => 'value',
      '#value' => $feature->feature_id,
   );

   $form['title']= array(
      '#type' => 'textfield',
      '#title' => t('Title'),
      '#required' => TRUE,
      '#default_value' => $feature->featurename,
      '#description' => t('The title must be a unique identifier for this feature.  It is recommended to use a combination of uniquename, organism and feature type in the title as this is guranteed to be unique.'),
      '#weight' => 1,
      '#maxlength' => 255
   );

   $form['uniquename']= array(
      '#type' => 'textfield',
      '#title' => t('Unique Feature Name'),
      '#required' => TRUE,
      '#default_value' => $feature->featurename,
      '#description' => t('Enter a unique name for this feature.  This name must be unique for the organism and feature type.'),
      '#weight' => 1,
      '#maxlength' => 255
   );

   $form['name']= array(
      '#type' => 'textfield',
      '#title' => t('Feature Name'),
      '#required' => TRUE,
      '#default_value' => $feature->featurename,
      '#description' => t('Enter the name used by humans to refer to this feature.'),
      '#weight' => 1,
      '#maxlength' => 255
   );

   // get the list of supported feature types
   $ftypes = array();
   $ftypes[''] = '';
   $supported_ftypes = split("[ \n]",variable_get('chado_feature_types','EST contig'));
   foreach($supported_ftypes as $ftype){
      $ftypes["$ftype"] = $ftype;
   }

   $form['feature_type'] = array (
     '#title'       => t('Feature Type'),
     '#type'        => t('select'),
     '#description' => t("Choose the feature type."),
     '#required'    => TRUE,
     '#default_value' => $feature->cvname,
     '#options'     => $ftypes,
     '#weight'      => 2
   );
   // get the list of organisms
   $sql = "SELECT * FROM {Organism} ORDER BY genus, species";
   $previous_db = tripal_db_set_active('chado');  // use chado database
   $org_rset = db_query($sql);
   tripal_db_set_active($previous_db);  // now use drupal database

   //
   $organisms = array();
   $organisms[''] = '';
   while($organism = db_fetch_object($org_rset)){
      $organisms[$organism->organism_id] = "$organism->genus $organism->species ($organism->common_name)";
   }

   $form['organism_id'] = array (
     '#title'       => t('Organism'),
     '#type'        => t('select'),
     '#description' => t("Choose the organism with which this feature is associated "),
     '#required'    => TRUE,
     '#default_value' => $feature->organism_id,
     '#options'     => $organisms,
     '#weight'      => 3,
   );

   // Get synonyms
   if ($synonyms) {
      if (is_array($synonyms)) {
         foreach ($synonyms as $synonym){
            $syn_text .= "$synonym->name\n";
         }
      } else {
         $syn_text = $synonyms;
      }
   }
   $form['synonyms']= array(
      '#type' => 'textarea',
      '#title' => t('Synonyms'),
      '#required' => FALSE,
      '#default_value' => $syn_text,
      '#description' => t('Enter alternate names (synonmys) for this feature to help in searching and identification. You may enter as many alternate names as needed separated by spaces or on different lines.'),
      '#weight' => 5,
   );

   $form['residues']= array(
      '#type' => 'textarea',
      '#title' => t('Residues'),
      '#required' => FALSE,
      '#default_value' => $feature->residues,
      '#description' => t('Enter the nucelotide sequences for this feature'),
      '#weight' => 6
   );

   $checked = '';
   if($feature->is_obsolete == 't'){
      $checked = '1';
   }
   $form['is_obsolete']= array(
      '#type' => 'checkbox',
      '#title' => t('Is Obsolete'),
      '#required' => FALSE,
      '#default_value' => $checked,
      '#description' => t('Check this box if this sequence should be retired and no longer included in further analysis.'),
      '#weight' => 8
   );
   return $form;
}
/************************************************************************
 *
 */
function chado_feature_validate($node){
   $result = 0;

   // if this is an update, we want to make sure that a different feature for
   // the organism doesn't already have this uniquename. We don't want to give
   // two sequences the same uniquename
   if($node->feature_id){
      $sql = "SELECT * 
              FROM {Feature} F
                INNER JOIN {cvterm} CVT ON F.type_id = CVT.cvterm_id
              WHERE uniquename = '%s' 
               AND organism_id = %d AND CVT.name = '%s' AND NOT feature_id = %d";
      $previous_db = tripal_db_set_active('chado');
      $result = db_fetch_object(db_query($sql, $node->uniquename,$node->organism_id,$node->feature_type,$node->feature_id));
      tripal_db_set_active($previous_db);
      if($result){
         form_set_error('uniquename',t("Feature update cannot proceed. The feature name '$node->uniquename' is not unique for this organism. Please provide a unique name for this feature. "));
      }
   }

   // if this is an insert then we just need to make sure this name doesn't
   // already exist for this organism if it does then we need to throw an error
   else {
      $sql = "SELECT * 
              FROM {Feature} F
                INNER JOIN {cvterm} CVT ON F.type_id = CVT.cvterm_id
              WHERE uniquename = '%s' 
               AND organism_id = %d AND CVT.name = '%s'";
      $previous_db = tripal_db_set_active('chado');
      $result = db_fetch_object(db_query($sql, $node->uniquename,$node->organism_id,$node->feature_type));
      tripal_db_set_active($previous_db);
      if($result){
         form_set_error('uniquename',t("Feature insert cannot proceed. The feature name '$node->uniquename' already exists for this organism. Please provide a unique name for this feature. "));
      }
   }

   // we want to remove all characters except IUPAC nucleotide characters from the
   // the residues. however, residues are not required so if blank then we'll skip
   // this step
   if($node->residues){
      $residues = preg_replace("/[^\w]/",'',$node->residues);
      if(!preg_match("/^[ACTGURYMKSWBDHVN]+$/i",$residues)){
         form_set_error('residues',t("The residues in feature $node->name contains more than the nucleotide IUPAC characters. Only the following characters are allowed: A,C,T,G,U,R,Y,M,K,S,W,B,D,H,V,N: '" . $residues ."'"));
      }
   }

   // we don't allow a genbank accession number for a contig
   if($node->feature_type == 'contig' and $node->gbaccession){
      form_set_error('gbaccession',t("Contigs cannot have a genbank accession number.  Please change the feature type or remove the accession number"));
   }



}
/************************************************************************
 *  When a node is requested by the user this function is called to allow us
 *  to add auxiliary data to the node object.
 */
function chado_feature_load($node){
   // add the feature_id for this node:
   $sql = 'SELECT feature_id FROM {chado_feature} WHERE vid = %d';
   $map = db_fetch_object(db_query($sql, $node->vid));


   // get information about this feature and add it to the items in this node
   $sql = "SELECT F.feature_id, F.name as featurename, F.uniquename, ".
          "F.residues, F.seqlen, O.genus, O.species, O.common_name, ".
          "  CVT.name as cvname, O.organism_id, F.type_id, F.is_obsolete  ".
          "FROM {Feature} F ".
          "  INNER JOIN Organism O ON F.organism_id = O.organism_id ".
          "  INNER JOIN CVterm CVT ON F.type_id = CVT.cvterm_id ".
          "WHERE F.feature_id = %d";
   $previous_db = tripal_db_set_active('chado');  // use chado database
   $feature = db_fetch_object(db_query($sql,$map->feature_id));
   tripal_db_set_active($previous_db);  // now use drupal database
   $additions->feature = $feature;
   $additions->seqlen = $feature->seqlen;

   // add organism node nid
   $sql = "SELECT nid FROM {chado_organism} WHERE organism_id = %d";
   $org_nid = db_result(db_query($sql, $additions->feature->organism_id));
   $additions->org_nid = $org_nid;
   $additions->accession =  variable_get('chado_feature_accession_prefix','ID') . $feature->feature_id;

   // add organism details
   $sql = "SELECT * FROM {organism} WHERE organism_id = %d";
   $previous_db = tripal_db_set_active('chado');  // use chado database
   $organism = db_fetch_object(db_query($sql, $additions->feature->organism_id));
   tripal_db_set_active($previous_db);  // now use drupal database
   $additions->organism = $organism;
   
   // add the feature synonyms
   $sql = "SELECT S.name ".
          "FROM {Feature_Synonym} FS ".
          "  INNER JOIN Synonym S ".
          "    ON FS.synonym_id = S.Synonym_id ".
          "WHERE FS.feature_id = %d";
   $previous_db = tripal_db_set_active('chado');  // use chado database
   $results = db_query($sql,$map->feature_id);
   tripal_db_set_active($previous_db);  // now use drupal database
   $synonyms = array();
   $i=0;
   while($synonym = db_fetch_object($results)){
      $synonyms[$i++] = $synonym;
   }
   $additions->synonyms = $synonyms;

   // add feature references in external databases
   $sql = "SELECT F.uniquename,F.Feature_id,DBX.accession,DB.description as dbdesc, ".
          "   DB.db_id, DB.name as db_name, DB.urlprefix,DBX.dbxref_id ".
          "FROM {Feature} F ".
          "  INNER JOIN Feature_dbxref FDBX on F.feature_id = FDBX.feature_id ".
          "  INNER JOIN Dbxref DBX on DBX.dbxref_id = FDBX.dbxref_id ".
          "  INNER JOIN DB on DB.db_id = DBX.db_id ".
          "WHERE F.feature_id = %d";
   $previous_db = tripal_db_set_active('chado');  // use chado database
   $results = db_query($sql,$map->feature_id);
   tripal_db_set_active($previous_db);  // now use drupal database
   $references = array();
   $i=0;
   while($accession = db_fetch_object($results)){
      $references[$i++] = $accession;
   }
   $additions->references = $references;


   // add the feature relationsips
   $sql = "SELECT 
             FS.name as subject_name, 
             FS.uniquename as subject_uniquename, 
             FS.residues as subject_residues,
             CVTS.name as subject_type,
             FR.subject_id,          
             FR.type_id as relationship_type_id,
             CVT.name as rel_type,     
             FO.name as object_name, 
             FO.uniquename as object_uniquename, 
             CVTO.name as object_type,
             FR.object_id,
             FLS.name as src_name,
             FLS.uniquename as src_uniquename,
             FLS.feature_id as src_featureid,
             CVTR.name as src_cvname, 
             CVTR.cvterm_id as src_type_id,
             FL.fmin, 
             FL.fmax, 
             FL.is_fmin_partial, 
             FL.is_fmax_partial,
             FL.strand, 
             FL.phase, 
             FL.residue_info
           FROM {feature_relationship} FR
             INNER JOIN {cvterm} CVT ON FR.type_id = CVT.cvterm_id
             INNER JOIN {feature} FS ON FS.feature_id = FR.subject_id
             INNER JOIN {feature} FO ON FO.feature_id = FR.object_id
             INNER JOIN {cvterm} CVTO ON FO.type_id = CVTO.cvterm_id
             INNER JOIN {cvterm} CVTS ON FS.type_id = CVTS.cvterm_id
             LEFT JOIN {featureloc} FL on FL.feature_id = FS.feature_id 
             LEFT JOIN {feature} FLS on FLS.feature_id = FL.srcfeature_id
             LEFT JOIN {cvterm} CVTR on FLS.type_id = CVTR.cvterm_id
   ";
   $osql = "$sql  WHERE FR.object_id = %d ORDER BY FLS.name, FL.fmin ASC";
   $ssql = "$sql  WHERE FR.subject_id = %d ORDER BY FLS.name, FL.fmin ASC";

   // first get the relationships where this feature is the object
   // then where it is the subject 
   $previous_db = tripal_db_set_active('chado');  // use chado database
   $oresults = db_query($osql, $map->feature_id);
   $sresults = db_query($ssql, $map->feature_id);
   tripal_db_set_active($previous_db);  // now use drupal database

   // identify the drupal node for each feature and add that to the 
   // relationship records
   $srelationships = array();
   $orelationships = array();
   $i=0;
   $nodesql = "SELECT nid FROM {chado_feature} WHERE feature_id = %d";
   $rel_locs;  // holds relationship locations
   $rel_loc;   // a single relationship location
   while($rel = db_fetch_object($oresults)){
     $node = db_fetch_object(db_query($nodesql,$rel->subject_id));
     if($node){
        $rel->subject_nid = $node->nid;
     }  
     $node = db_fetch_object(db_query($nodesql,$rel->object_id));
     if($node){
        $rel->object_nid = $node->nid;
     }  
     $orelationships[$i] = $rel; 
     if($rel->src_uniquename){
        $rel_loc = $rel->src_uniquename ."|".$rel->src_type_id;
        $rel_locs[$rel_loc]['uname'] = $rel->src_uniquename;
        $rel_locs[$rel_loc]['type'] = $rel->src_type_id;
        if(!$rel_locs[$rel_loc]['source_min']){
           $rel_locs[$rel_loc]['source_min'] = 99999999999;
        }
        if($rel->fmin < $rel_locs[$rel_loc]['source_min']){
           $rel_locs[$rel_loc]['source_min'] = $rel->fmin;
        }     
        if($rel->fmax > $rel_locs[$rel_loc]['source_max']){
           $rel_locs[$rel_loc]['source_max'] = $rel->fmax;
        }
     }
     $i++;
   }
   // build the parts array needed for coloring the relationsihps in the
   // reference sequence
   foreach($orelationships as $index => $rel){
      if($rel->src_uniquename){
         $rel_loc = $rel->src_uniquename ."|".$rel->src_type_id;
         $rel_locs[$rel_loc]['parts'][$index]['type'] = $rel->subject_type;
         $rel_locs[$rel_loc]['parts'][$index]['start'] = $rel->fmin - $rel_locs[$rel_loc]['source_min'];
         $rel_locs[$rel_loc]['parts'][$index]['end'] = $rel->fmax - $rel_locs[$rel_loc]['source_min'];
      }
   }
   $i=0;
   while($rel = db_fetch_object($sresults)){
     $node = db_fetch_object(db_query($nodesql,$rel->subject_id));
     if($node){
        $rel->subject_nid = $node->nid;
     }  
     $node = db_fetch_object(db_query($nodesql,$rel->object_id));
     if($node){
        $rel->object_nid = $node->nid;
     }  
     $srelationships[$i++] = $rel;      
   }
   $additions->object_relationships = $orelationships;
   $additions->subject_relationships = $srelationships;

   // now get the sequence from the reference for those feature as a 
   // subject relationship to this feature.
   $object_context = array();
   $i=0;
   foreach ($rel_locs as $rel_loc => $attrs){
      if($attrs['uname']){
         $sql = "SELECT residues 
                 FROM feature 
                 WHERE uniquename = '%s' AND organism_id = %d and type_id = %d";
         $context = db_fetch_object(db_query($sql,$attrs['uname'],$additions->feature->organism_id,$attrs['type']));
         $context->residues = substr($context->residues,$attrs['source_min'],$attrs['source_max'] - $attrs['source_min']);
         $context->source = $attrs['uname'];
         $context->fmin = $attrs['source_min'];
         $context->fmax = $attrs['source_max'];
         $context->residues = tripal_feature_color_sequence ($context->residues,$attrs['parts']);
      }
      $object_context[$i] = $context;
   }
   $additions->relationship_object_info = $object_context;

  // get the locations for this feature
   $sql = "SELECT F.name,F.feature_id, F.uniquename,CVT.name as cvname, CVT.cvterm_id,
             FL.fmin, FL.fmax, FL.is_fmin_partial, FL.is_fmax_partial,FL.strand, 
             FL.phase, FL.residue_info
           FROM featureloc FL
              INNER JOIN feature F on FL.srcfeature_id = F.feature_id
              INNER JOIN cvterm CVT on F.type_id = CVT.cvterm_id
           WHERE FL.feature_id = %d";
   $previous_db = tripal_db_set_active('chado');  // use chado database
   $flresults = db_query($sql, $map->feature_id);
   tripal_db_set_active($previous_db);  // now use drupal database 
   $i=0;
   $featurelocs = array();
   while($loc = db_fetch_object($flresults)){
      $featurelocs[$i++] = $loc;
   }
   $additions->featurelocs = $featurelocs;

   // get features that are aligned to this feature
   $sql = "SELECT F.name,F.feature_id, F.uniquename,CVT.name as cvname, CVT.cvterm_id,
             FL.fmin, FL.fmax, FL.is_fmin_partial, FL.is_fmax_partial,FL.strand, 
             FL.phase, FL.residue_info
           FROM featureloc FL
              INNER JOIN feature F on FL.feature_id = F.feature_id
              INNER JOIN cvterm CVT on F.type_id = CVT.cvterm_id
           WHERE FL.srcfeature_id = %d";
   $previous_db = tripal_db_set_active('chado');  // use chado database
   $flresults = db_query($sql, $map->feature_id);
   tripal_db_set_active($previous_db);  // now use drupal database 
   $i=0;
   $myfeaturelocs = array();
   while($loc = db_fetch_object($flresults)){
      $myfeaturelocs[$i++] = $loc;
   }
   $additions->myfeaturelocs = $myfeaturelocs;   

   return $additions;
}

/************************************************************************
 *  
 */
function tripal_feature_color_sequence ($sequence,$parts){

watchdog('tripal_feature',print_r($parts,1));
   $types = array();

   // first get the list of types so we can create a color legend
   foreach ($parts as $index => $child){ 
      $type = $child['type'];
      if(!in_array($type,$types)){
         $types[] = $type;
      }
   }
 
   $newseq .= "<div id=\"tripal_feature-sequence-legend\">Legend: ";
   foreach($types as $type){
      $newseq .= "<span class=\"tripal_feature-sequence-$type\">$type</span>";
   }
   $newseq .= "</div>";
   

   // set the background color of the rows based on the type
   $pos = 0;
   $newseq .= "<pre id=\"tripal_feature-sequence\">";
   foreach ($parts as $index => $child){
      $type = $child['type'];
      $start = $child['start'];
      $end = $child['end'];
      
      $class = "class=\"tripal_feature-sequence-$type\"";

      // iterate through the sequence up to the end of the child
      for ($i = $pos; $i < $end; $i++){ 
    
         // if we're at the beginning of the child sequence then set the
         // appropriate text color
         if($pos == $start){
            $newseq .= "<span $class>";
            $func = 'uc';  // nucleotides within the child should be uppercase
         }
         $newseq .= $sequence{$pos};
         $seqcount++;

         if($seqcount % 100 == 0){
            $newseq .= "\n";
         } 
         $pos++;  
         if($pos == $end){
            $newseq .= "</span>";
            $func = 'lc';
         }
      }
   }

   $newseq .= "</pre>";
   return $newseq;
}
/************************************************************************
 *  This function customizes the view of the chado_feature node.  It allows
 *  us to generate the markup.
 */
function chado_feature_view ($node, $teaser = FALSE, $page = FALSE) {

   if (!$teaser) {
      // use drupal's default node view:
      $node = node_prepare($node, $teaser);
            
      // if we're building the node for searching then
      // we want to handle this within the module and
      // not allow theme customization.  We don't want to
      // index all items (such as DNA sequence).
      if($node->build_mode == NODE_BUILD_SEARCH_INDEX){
         $node->content['index_version'] = array(
            '#value' => theme('tripal_feature_search_index',$node),
            '#weight' => 1,
         );
      }
      else if($node->build_mode == NODE_BUILD_SEARCH_RESULT){
         $node->content['index_version'] = array(
            '#value' => theme('tripal_feature_search_results',$node),
            '#weight' => 1,
         );
      }
      else {
         // do nothing here, let the theme derived template handle display
      }
   }

   return $node;
}

/*******************************************************************************
 * Display feature information for associated organisms. This function also
 * provides contents for indexing
 */
function tripal_feature_nodeapi(&$node, $op, $teaser, $page) {

   switch ($op) {
      // Note that this function only adds feature view to an organism node.
      // The view of a feature node is controled by the theme *.tpl file
      case 'view':
         // Set the node types for showing feature information
         $types_to_show = array('chado_organism', 'chado_library');

         // Abort if this node is not one of the types we should show.
         if (!in_array($node->type, $types_to_show, TRUE)) {
            break;
         }

         // Add feature to the content item if it's not a teaser
         if (!$teaser) {

            // Show feature browser
            $node->content['tripal_feature_browser'] = array(
               '#value' => theme('tripal_feature_browser', $node),
               '#weight' => 5
            );
            $node->content['tripal_feature_org_counts'] = array(
               '#value' => theme('tripal_feature_counts', $node),
               '#weight' => 4
            );
         }
   }
}
/************************************************************************
 *  We need to let drupal know about our theme functions and their arguments.
 *  We create theme functions to allow users of the module to customize the
 *  look and feel of the output generated in this module
 */
function tripal_feature_theme () {
   return array(
      'tripal_feature_search_index' => array (
         'arguments' => array('node'),
       ),
      'tripal_feature_search_results' => array (
         'arguments' => array('node'),
      ),
      'tripal_feature_browser' => array (
         'arguments' => array('node'),
      ),
      'tripal_feature_counts' => array (
         'arguments' => array('node'),
      )
   );
}
/*******************************************************************************
 *  create a list of features for the organism and pie chart
 */
function theme_tripal_feature_counts($node){

   // don't show the summary if the settings in the admin page is turned off
   $show_browser = variable_get('tripal_feature_summary_setting',array('show_feature_summary'));

   if(strcmp($show_browser[0],'show_feature_summary')!=0){
      return;
   }

   // get the feature counts.  This is dependent on a materialized view
   // installed with the organism module
   $content = '';
   if ($node->organism_id && $node->type == 'chado_organism') {
      $sql = "SELECT * FROM {organism_feature_count} ".
      		 "WHERE organism_id = %d AND NOT feature_type = 'EST_match' ".
             "ORDER BY num_features desc";
      $features = array();
      $previous_db = tripal_db_set_active('chado');  // use chado database
      $results = db_query($sql,$node->organism_id);
      tripal_db_set_active($previous_db);  // now use drupal database
      $feature = db_fetch_object($results); // retrieve the first result
      if ($feature) {
         $content .= "<div class=\"tripal_feature_summary-info-box\"><br>
                             <div class=\"tripal_expandableBox\">".
                     "<h3>Feature Summary</h3>".
                     "</div>";
         $content .= "<div class=\"tripal_expandableBoxContent\">";
         $content .= "<table class=\"tripal_table_horz\">";
         $content .= "  <tr>";
         $content .= "    <th class=\"dbfieldname\">Type</th>";
         $content .= "    <th class=\"dbfieldname\">Number</th>";
         $content .= "  </tr>";
         do {
            $content .= "<tr>";
            $content .= "  <td>$feature->feature_type</td>";
            $content .= "  <td>". number_format($feature->num_features) . "</td>";
            $content .= "</tr>";
         } while($feature = db_fetch_object($results));
         $content .= "</table>";
         $content .= "
            <img class=\"tripal_cv_chart\" id=\"tripal_feature_cv_chart_$node->organism_id\" src=\"\" border=\"0\">
         ";
         $content .= "</div></div>";
      }
   }
   return $content;
}
/************************************************************************
 *
 */
function tripal_feature_cv_chart($chart_id){

  // The CV module will create the JSON array necessary for buillding a
  // pie chart using jgChart and Google Charts.  We have to pass to it
  // a table that contains count information, tell it which column 
  // contains the cvterm_id and provide a filter for getting the
  // results we want from the table.
  $organism_id = preg_replace("/^tripal_feature_cv_chart_(\d+)$/","$1",$chart_id);
  $options = array(
     count_mview      => 'organism_feature_count',
     cvterm_id_column => 'cvterm_id',
     count_column     => 'num_features',
     size             => '650x200',
     filter           => "CNT.organism_id = $organism_id AND NOT feature_type = 'EST_match' ",
  );
  return $options;
}
/************************************************************************
 *
 */
function tripal_feature_cv_tree($tree_id){

  // The CV module will create the JSON array necessary for buillding a
  // pie chart using jgChart and Google Charts.  We have to pass to it
  // a table that contains count information, tell it which column 
  // contains the cvterm_id and provide a filter for getting the
  // results we want from the table.
  $organism_id = preg_replace("/^tripal_feature_cv_tree_(\d+)$/","$1",$tree_id);
  $options = array(
     cv_id            => tripal_cv_get_cv_id('sequence'),
     count_mview      => 'organism_feature_count',
     cvterm_id_column => 'cvterm_id',
     count_column     => 'num_features',
     filter           => "CNT.organism_id = $organism_id",
     label            => 'Features',
  );
  return $options;
}
/*******************************************************************************
 *  create a simple paged feature browser
 */
function theme_tripal_feature_browser($node){

   // don't show the browser if the settings in the admin page is turned off
   $show_browser = variable_get('tripal_feature_browse_setting',array('show_feature_browser'));

   if(strcmp($show_browser[0],'show_feature_browser')!=0){
      return;
   }
   if ($node->organism_id && $node->type == 'chado_organism') {
      # get the list of available sequence ontology terms for which
      # we will build drupal pages from features in chado.  If a feature
      # is not one of the specified typse we won't build a node for it.
      $allowed_types = variable_get('chado_feature_types','EST contig');
      $allowed_types = preg_replace("/[\s\n\r]+/"," ",$allowed_types);
      $so_terms = split(' ',$allowed_types);
      $where_cvt = "";
      foreach ($so_terms as $term){
         $where_cvt .= "CVT.name = '$term' OR ";
      }
      $where_cvt = substr($where_cvt,0,strlen($where_cvt)-3);  # strip trailing 'OR'

      // get the features for this organism
      $sql  = "SELECT F.name,F.feature_id,F.uniquename,CVT.name as cvname ".
              "FROM {feature} F ".
                 "  INNER JOIN {cvterm} CVT on F.type_id = CVT.cvterm_id ".
               "WHERE organism_id = $node->organism_id and ($where_cvt) ".
               "ORDER BY feature_id ASC";

      // the counting SQL
      $csql  = "SELECT count(*) ".
               "FROM {feature} F".
               "  INNER JOIN {cvterm} CVT on F.type_id = CVT.cvterm_id ".
               "WHERE organism_id = $node->organism_id and ($where_cvt) ".
               "GROUP BY organism_id ";

      $previous_db = tripal_db_set_active('chado');  // use chado database
      $features = pager_query($sql,10,0,$csql);
      tripal_db_set_active($previous_db);  // now use drupal database

      $content = "<br><div id=\"tripal_feature_box\" class=\"feature-info-box\">";
      $content .= "<div class=\"tripal_expandableBox\">".
                  "<h3>Browse Features</h3>".
                  "</div>";
      $content .= "<div class=\"tripal_expandableBoxContent\">";
      $content .= "Below are the features associated with this organism.\n";
      $content .= "<table class=\"tripal_table_horz\">";
      $content .= "  <tr>";
      $content .= "    <th>Feature Name</th>";
      $content .= "    <th>Type</th>";
      $content .= "  </tr>";

      // prepare the query that will lookup node ids
      $sql = "SELECT nid FROM {chado_feature} ".
              "WHERE feature_id = %d";
      while($feature = db_fetch_object($features)){
         $node = db_fetch_object(db_query($sql,$feature->feature_id));
         if($node){
            $name= "<a href=\"" . url("node/$node->nid") . "\">$feature->name</a>";
         } else {
            $name= "$feature->name";
         }
         $content .= "  <tr>";
         $content .= "    <td>$name</td>";
         $content .= "    <td>$feature->cvname</td>";
         $content .= "  </tr>";
      }
      $content .= "</table>";
      $content .= theme('pager');
      $content .= "</div></div>";
      return $content;
   }
}
/************************************************************************
 *  This function is an extension of the chado_feature_view by providing
 *  the markup for the feature object THAT WILL BE INDEXED.
 */
function theme_tripal_feature_search_index ($node) {
   $feature = $node->feature;
   $content = '';

   // get the accession prefix
   $aprefix = variable_get('chado_feature_accession_prefix','ID');

   $content .= "<h1>$feature->uniquename</h1>. ";
   $content .= "<strong>$aprefix$feature->feature_id.</strong> ";
   $content .= "$feature->cvname ";
   $content .= "$feature->common_name ";

   // add the synonyms of this feature to the text for searching
   $synonyms = $node->synonyms;
   if(count($synonyms) > 0){
      foreach ($synonyms as $result){
         $content .= "$result->name ";
      }
   }

   return $content;
}
/************************************************************************
 *  This function is an extension of the chado_feature_view by providing
 *  the markup for the feature object THAT WILL BE INDEXED.
 */
function theme_tripal_feature_search_results ($node) {
   $feature = $node->feature;
   $content = '';

   // get the accession prefix
   $aprefix = variable_get('chado_feature_accession_prefix','ID');

   $content .= "Feature Name: <h1>$feature->uniquename</h1>. ";
   $content .= "<strong>Accession: $aprefix$feature->feature_id.</strong>";
   $content .= "Type: $feature->cvname. ";
   $content .= "Organism: $feature->common_name. ";

   // add the synonyms of this feature to the text for searching
   $synonyms = $node->synonyms;
   if(count($synonyms) > 0){
      $content .= "Synonyms: ";
      foreach ($synonyms as $result){
         $content .= "$result->name, ";
      }
   }

   return $content;
}
/************************************************************************
 *
 */
function tripal_feature_set_vocabulary (){

   //include the file containing the required functions for adding taxonomy vocabs
   module_load_include('inc', 'taxonomy', 'taxonomy.admin');

   // get the vocabularies so that we make sure we don't recreate
   // the vocabs that already exist
   $vocabularies = taxonomy_get_vocabularies();
   $ft_vid = NULL;
   $op_vid = NULL;
   $lb_vid = NULL;
   $an_vid = NULL;

   // These taxonomic terms are hard coded because we
   // konw we have these relationships in the chado tables
   // through foreign key relationships.  The tripal
   // modules that correspond to these chado "modules" don't
   // need to be installed for the taxonomy to work.
   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;
      }
   }

   if(!$ft_vid){
      $form_state = array();
      $values = array(
         'name' => t('Feature Type'),
         'nodes' => array('chado_feature' => 'chado_feature'),
         'description' => t('The feature type (or SO cvterm for this feature).'),
         'help' => t('Select the term that matches the feature '),
         'tags' => 0,
         'hierarchy' => 1,
         'relations' => 1,
         'multiple' => 0,
         'required' => 0,
         'weight' => 1,
      );
      drupal_execute('taxonomy_form_vocabulary', $form_state,$values);
      drupal_execute('taxonomy_form_vocabulary', $form_state);
   }

   if(!$op_vid){
      $form_state = array();
      $values = array(
         'name' => t('Organism'),
         'nodes' => array('chado_feature' => 'chado_feature'),
         'description' => t('The organism to which this feature belongs.'),
         'help' => t('Select the term that matches the feature '),
         'tags' => 0,
         'hierarchy' => 1,
         'relations' => 1,
         'multiple' => 0,
         'required' => 0,
         'weight' => 2,
      );
      drupal_execute('taxonomy_form_vocabulary', $form_state,$values);
      drupal_execute('taxonomy_form_vocabulary', $form_state);
   }

   if(!$lb_vid){
      $form_state = array();
      $values = array(
         'name' => t('Library'),
         'nodes' => array('chado_feature' => 'chado_feature'),
         'description' => t('Chado features associated with a library are assigned the term associated with the library'),
         'help' => t('Select the term that matches the feature '),
         'tags' => 0,
         'hierarchy' => 1,
         'relations' => 1,
         'multiple' => 0,
         'required' => 0,
         'weight' => 3,
      );
      drupal_execute('taxonomy_form_vocabulary', $form_state, $values);
      drupal_execute('taxonomy_form_vocabulary', $form_state);
   }

   if(!$an_vid){
      $form_state = array();
      $values = array(
         'name' => t('Analysis'),
         'nodes' => array('chado_feature' => 'chado_feature'),
         'description' => t('Any analysis to which this feature belongs.'),
         'help' => t('Select the term that matches the feature '),
         'tags' => 0,
         'hierarchy' => 1,
         'relations' => 1,
         'multiple' => 1,
         'required' => 0,
         'weight' => 4,
      );
      drupal_execute('taxonomy_form_vocabulary', $form_state,$values);
      drupal_execute('taxonomy_form_vocabulary', $form_state);
   }
}
/************************************************************************
 *
 */
function tripal_feature_del_vocabulary(){
   //include the file containing the required functions for adding taxonomy vocabs
   module_load_include('inc', 'taxonomy', 'taxonomy.admin');

   // get the vocabularies
   $vocabularies = taxonomy_get_vocabularies();

   // These taxonomic terms are hard coded because we
   // know we have these relationships in the chado tables
   // through foreign key relationships.  The tripal
   // modules that correspond to these chado "modules" don't
   // need to be installed for the taxonomy to work.
   foreach($vocabularies as $vocab){
      if($vocab->name == 'Feature Type'){
         taxonomy_del_vocabulary($vocab->vid);
      }
      if($vocab->name == 'Organism'){
         taxonomy_del_vocabulary($vocab->vid);
      }
      if($vocab->name == 'Library'){
         taxonomy_del_vocabulary($vocab->vid);
      }
      if($vocab->name == 'Analysis'){
         taxonomy_del_vocabulary($vocab->vid);
      }
   }

}
/************************************************************************
 *
 */
function tripal_features_set_taxonomy($max_sync = 0,$job_id = NULL){

   // make sure our vocabularies are cleaned and reset before proceeding
   tripal_feature_del_vocabulary();
   tripal_feature_set_vocabulary();

   // iterate through all drupal feature nodes and set the taxonomy
   $results = db_query("SELECT * FROM {chado_feature}");
   $nsql =  "SELECT * FROM {node} ".
            "WHERE nid = %d";
   $i = 0;

   // load into ids array
   $count = 0;
   $chado_features = array();
   while($chado_feature = db_fetch_object($results)){
      $chado_features[$count] = $chado_feature;
      $count++;
   }

   // Iterate through features that need to be synced
   $interval = intval($count * 0.01);
   foreach($chado_features as $chado_feature){

      // update the job status every 1% features
      if($job_id and $i % $interval == 0){
         tripal_job_set_progress($job_id,intval(($i/$count)*100));
      }
      $node = db_fetch_object(db_query($nsql,$chado_feature->nid));
      tripal_feature_set_taxonomy($node,$chado_feature->feature_id);

      $i++;
   }
}
/************************************************************************
 *
 */
function tripal_feature_set_taxonomy ($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', '');
   $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";
   $previous_db = tripal_db_set_active('chado');  // use chado database
   $feature = db_fetch_object(db_query($sql));
   tripal_db_set_active($previous_db);  // now use drupal database

   // 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 ";
      $previous_db = tripal_db_set_active('chado');  // use chado database
      $library = db_fetch_object(db_query($sql,$feature_id));
      tripal_db_set_active($previous_db);  // now use drupal database
      $tags["$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 ";
      $results = db_query($sql);
      $previous_db = tripal_db_set_active('chado');  // use chado database
      $analysis_terms = array();
      while($analysis=db_fetch_object($results)){
         $tags2["$an_vid"] = "$analysis->name";
         $terms['tags'] = $tags2;
         taxonomy_node_save($node,$terms);
      }
      tripal_db_set_active($previous_db);  // now use drupal database
   }

}
/************************************************************************
 *
 */
function tripal_features_cleanup($dummy = NULL, $job_id = NULL) {

   // build the SQL statments needed to check if nodes point to valid features
   $dsql = "SELECT * FROM {node} WHERE type = 'chado_feature' order by nid";
   $nsql = "SELECT * FROM {node} WHERE nid = %d";
   $csql = "SELECT * FROM {chado_feature} where nid = %d ";
   $cfsql= "SELECT * FROM {chado_feature}";
   $tsql = "SELECT * FROM {feature} F ".
          "  INNER JOIN CVTerm CVT ON F.type_id = CVT.cvterm_id ".
          "WHERE feature_id = %d  AND (";
   $supported_ftypes = split("[ \n]",variable_get('chado_feature_types','EST contig'));
   foreach($supported_ftypes as $ftype){
      $tsql .= " CVT.name = '$ftype' OR ";
   }
   $tsql .= " 0=1) ";  // add a 0=1 just as a filler so we don't have to remove a trailing 'OR'

   // load into nodes array
   $results = db_query($dsql);
   $count = 0;
   $nodes = array();
   while($node = db_fetch_object($results)){
      $nodes[$count] = $node;
      $count++;
   }

   // load the chado_features into an array
   $results = db_query($cfsql);
   $cnodes = array();
   while($node = db_fetch_object($results)){
      $cnodes[$count] = $node;
      $count++;
   }
   $interval = intval($count * 0.01);

   // iterate through all of the chado_feature nodes and delete those  that aren't valid
   foreach($nodes as $nid){

      // update the job status every 1% features
      if($job_id and $i % $interval == 0){
         tripal_job_set_progress($job_id,intval(($i/$count)*100));
      }

      // first check to see if the node has a corresponding entry
      // in the chado_feature table. If not then delete the node.
      $feature = db_fetch_object(db_query($csql,$nid->nid));
      if(!$feature){
         node_delete($nid->nid);
         $message = "Missing in chado_feature table.... DELETING: $nid->nid\n";
         watchdog('tripal_feature',$message,array(),WATCHDOG_WARNING);
         continue;
      }

      // second check to see if the node is for a feature of an allowed type.
      // if not, then delete the node.  This check will also take care of the
      // case when a node exists and an entry in the chado_feature table exists
      // but no feature with a matching feature_id exists
      $previous_db = tripal_db_set_active('chado');  // use chado database
      $ftype = db_fetch_object(db_query($tsql,$feature->feature_id));
      tripal_db_set_active($previous_db);  // now use drupal database

      if(!$ftype){
         node_delete($nid->nid);
         db_query("DELETE FROM {chado_feature} WHERE feature_id = $feature->feature_id");
         $message = "Node of the wrong feature type.... DELETING: $nid->nid\n";
         watchdog('tripal_feature',$message,array(),WATCHDOG_WARNING);
      }
      $i++;
   }

   // iterate through all of the chado_feature nodes and delete those  that aren't valid
   foreach($cnodes as $nid){
      // update the job status every 1% features
      if($job_id and $i % $interval == 0){
         tripal_job_set_progress($job_id,intval(($i/$count)*100));
      }
      $node = db_fetch_object(db_query($nsql,$nid->nid));
      if(!$node){
         db_query("DELETE FROM {chado_feature} WHERE nid = $nid->nid");
         $message = "chado_feature missing node.... DELETING: $nid->nid\n";
         watchdog('tripal_feature',$message,array(),WATCHDOG_WARNING);
      }

      $i++;
   }
   return '';
}
/************************************************************************
 *
 */
function tripal_feature_return_fasta($feature,$desc){   
   $fasta  = ">" . variable_get('chado_feature_accession_prefix','ID') . "$feature->feature_id|$feature->name";
   $fasta .= " $desc\n";
   $fasta .= wordwrap($feature->residues, 50, "\n", true);
   $fasta .= "\n\n";
   return $fasta;
}