tripal/tripal_feature/gff_loader.php

<?php


// TODO: The rank column on the feature_relationship table needs to be used to
//       make sure the ordering of CDS (exons) is correct.

// The entries in the GFF file are not in order so the order of the relationships
// is not put in correctly.
/*************************************************************************
*
*/
function tripal_core_gff3_load_form (){

   $form['gff_file']= array(
      '#type'          => 'textfield',
      '#title'         => t('GFF3 File'),
      '#description'   => t('Please enter the full system path for the GFF file, or a path within the Drupal
                             installation (e.g. /sites/default/files/xyz.obo).  The path must be accessible to the
                             server on which this Drupal instance is running.'),
      '#required' => TRUE,
      '#weight'        => 1
   );
   // 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 to which these sequences are associated "),
     '#required'    => TRUE,
     '#options'     => $organisms,
   );
   $form['import_options'] = array(
      '#type' => 'fieldset',
      '#title' => t('Import Options'),
      '#weight'=> 6,
      '#collapsed' => TRUE
   );
   $form['import_options']['add_only']= array(
      '#type' => 'checkbox',
      '#title' => t('Import only new features'),
      '#required' => FALSE,
      '#description' => t('The job will skip features in the GFF file that already
                           exist in the database and import only new features.'),
      '#weight' => 2
   );
   $form['import_options']['update']= array(
      '#type' => 'checkbox',
      '#title' => t('Import all and update'),
      '#required' => FALSE,
      '#default_value' => 'checked',
      '#description' => t('Existing features will be updated and new features will be added.  Attributes 
                           for a feature that are not present in the GFF but which are present in the 
                           database will not be altered.'),
      '#weight' => 3
   );
   $form['import_options']['refresh']= array(
      '#type' => 'checkbox',
      '#title' => t('Import all and replace'),
      '#required' => FALSE,
      '#description' => t('Existing features will be updated and feature properties not
                           present in the GFF file will be removed.'),
      '#weight' => 4
   );
   $form['import_options']['remove']= array(
      '#type' => 'checkbox',
      '#title' => t('Delete features'),
      '#required' => FALSE,
      '#description' => t('Features present in the GFF file that exist in the database
                           will be removed rather than imported'),
      '#weight' => 5
   );
   $form['button'] = array(
      '#type' => 'submit',
      '#value' => t('Import GFF3 file'),
      '#weight' => 10,
   );


   return $form;
}
/*************************************************************************
*
*/
function tripal_core_gff3_load_form_validate ($form, &$form_state){

   $gff_file = $form_state['values']['gff_file'];
   $organism_id = $form_state['values']['organism_id'];
   $add_only = $form_state['values']['add_only'];
   $update   = $form_state['values']['update'];
   $refresh  = $form_state['values']['refresh'];
   $remove   = $form_state['values']['remove'];

   // check to see if the file is located local to Drupal
   $dfile = $_SERVER['DOCUMENT_ROOT'] . base_path() . $gff_file; 
   if(!file_exists($dfile)){
      // if not local to Drupal, the file must be someplace else, just use
      // the full path provided
      $dfile = $gff_file;
   }
   if(!file_exists($dfile)){
      form_set_error('gff_file',t("Cannot find the file on the system. Check that the file exists or that the web server has permissions to read the file."));
   }

   if (($add_only and ($update or $refresh or $remove)) or 
       ($update   and ($add_only or $refresh or $remove)) or
       ($refresh and ($update or $add_only or $remove)) or
       ($remove and ($update or $refresh or $add_only))){
       form_set_error('add_only',t("Please select only one checkbox from the import options section"));
   }
}
/*************************************************************************
*
*/
function tripal_core_gff3_load_form_submit ($form, &$form_state){
   global $user;

   $gff_file = $form_state['values']['gff_file'];
   $organism_id = $form_state['values']['organism_id'];
   $add_only = $form_state['values']['add_only'];
   $update   = $form_state['values']['update'];
   $refresh  = $form_state['values']['refresh'];
   $remove   = $form_state['values']['remove'];

   $args = array($gff_file,$organism_id,$add_only,$update,$refresh,$remove);
   $type = '';
   if($add_only){
     $type = 'import only new features';
   }
   if($update){
     $type = 'import all and update';
   }
   if($refresh){
     $type = 'import all and replace';
   }
   if($remove){
     $type = 'delete features';
   }
   tripal_add_job("$type GFF3 file $dfile",'tripal_core',
      'tripal_core_load_gff3',$args,$user->uid);

   return '';
}
/*************************************************************************
*
*/
function tripal_core_load_gff3($gff_file, $organism_id,$add_only =0, 
   $update = 0, $refresh = 0, $remove = 0, $job = NULL)
{

   // this array is used to cache all of the features in the GFF file and
   // used to lookup parent and target relationships
   $gff_features = array();
 
   // check to see if the file is located local to Drupal
   $dfile = $_SERVER['DOCUMENT_ROOT'] . base_path() . $gff_file; 
   if(!file_exists($dfile)){
      // if not local to Drupal, the file must be someplace else, just use
      // the full path provided
      $dfile = $gff_file;
   }
   if(!file_exists($dfile)){
      print "ERROR: cannot find the file: $dfile\n";
      return 0;
   }

   $previous_db = tripal_db_set_active('chado');
   print "Opening $gff_file\n";
    
   $lines = file($dfile,FILE_SKIP_EMPTY_LINES);
   $i = 0;

   // get the controlled vocaubulary that we'll be using.  The
   // default is the 'sequence' ontology
   $sql = "SELECT * FROM cv WHERE name = '%s'";
   $cv = db_fetch_object(db_query($sql,'sequence'));
   if(!$cv){
      print "ERROR:  cannot find the 'sequence' ontology\n";
      return '';
   }

   // get the organism for which this GFF3 file belongs
   $sql = "SELECT * FROM organism WHERE organism_id = %d";
   $organism = db_fetch_object(db_query($sql,$organism_id));


   $num_lines = sizeof($lines);
   $interval = intval($num_lines * 0.01);
   foreach ($lines as $line_num => $line) {
      $i++;  // update the line count
      // update the job status every 1% features
      if($job and $i % $interval == 0){
         tripal_job_set_progress($job,intval(($i/$num_lines)*100));
      }

      // skip comments
      if(preg_match('/^#/',$line)){
         continue; 
      }
      // skip empty lines
      if(preg_match('/^\s*$/',$line)){
         continue; 
      }
      

      // TODO: remove URL encoding
  
      $cols = explode("\t",$line);
      if(sizeof($cols) != 9){
         print "ERROR: improper number of columns on line $i\n";
         return '';
      }
      // get the column values
      $landmark = $cols[0];
      $source = $cols[1];
      $type = $cols[2];
      $start = $cols[3];    
      $end = $cols[4];
      $score = $cols[5];
      $strand = $cols[6];
      $phase = $cols[7];
      $attrs = explode(";",$cols[8]);  // split by a semi-colon

      // ready the start and stop for chado
      $fmin = $start;
      $fmax = $end;
      if($end < $start){
         $fmin = $end;
         $fmax = $start;
      }
      // format the strand for chado
      if(strcmp($strand,'.')==0){
         $strand = 0;
      }
      elseif(strcmp($strand,'+')==0){
         $strand = 1;
      }
      elseif(strcmp($strand,'-')==0){
         $strand = -1;
      }
      if(strcmp($phase,'.')==0){
         $phase = '';
      }

      // get the type record
      $cvtermsql = "SELECT CVT.cvterm_id, CVT.cv_id, CVT.name, CVT.definition,
                       CVT.dbxref_id, CVT.is_obsolete, CVT.is_relationshiptype
                    FROM {cvterm} CVT
                       INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
                       LEFT JOIN {cvtermsynonym} CVTS on CVTS.cvterm_id = CVT.cvterm_id
                    WHERE CV.cv_id = %d and (CVT.name = '%s' or CVTS.synonym = '%s')";
      $cvterm = db_fetch_object(db_query($cvtermsql,$cv->cv_id,$type,$type));
      if(!$cvterm){
         print "ERROR: cannot find ontology term '$type' on line $i.\n";
         return '';
      }
      
      // break apart each of the attributes
      $tags = array();
      $attr_name = '';
      $attr_uniquename = '';
      $attr_residue_info = '';
      $attr_locgroup = 0;
      $attr_fmin_partial = 'f';
      $attr_fmax_partial = 'f';
      $attr_is_obsolete = 'f';
      $attr_is_analysis = 'f';
      $attr_others = '';
      $residues = '';
      $generate_name = 0;
      foreach($attrs as $attr){
         $attr = rtrim($attr);
         $attr = ltrim($attr);
         if(strcmp($attr,'')==0){
            continue;
         }
         if(!preg_match('/^[^\=]+\=[^\=]+$/',$attr)){
            print "ERROR: attribute is not correctly formatted on line $i: $attr\n";
            return '';
         }

         // break apart each tag
         $tag = explode("=",$attr);  // split by equals sign
         // multiple instances of an attribute are separated by commas
         $tags[$tag[0]] = explode(",",$tag[1]);  // split by comma
         if(strcmp($tag[0],'ID')==0){
            $attr_uniquename = $tag[1];
         }
         elseif(strcmp($tag[0],'Name')==0){
            $attr_name = $tag[1];
         }
         // get the list of other attributes other than those reserved ones.
         elseif(strcmp($tag[0],'Alias')!=0        and strcmp($tag[0],'Parent')!=0 and 
                strcmp($tag[0],'Target')!=0       and strcmp($tag[0],'Gap')!=0 and
                strcmp($tag[0],'Derives_from')!=0 and strcmp($tag[0],'Note')!=0 and
                strcmp($tag[0],'Dbxref')!=0       and strcmp($tag[0],'Ontology_term')!=0 and
                strcmp($tag[0],'Is_circular')!=0){
            $attr_others[$tag[0]] = $tag[1];
         }
      }

      // if neither name nor uniquename are provided then generate one
      if(!$attr_uniquename and !$attr_name){
         $generate_name = 1;
      }

      // if a name is not specified then use the unique name
      if(strcmp($attr_name,'')==0){
         $attr_name = $attr_uniquename;
      }

      // if an ID attribute is not specified then use the attribute name and
      // hope for the best
      if(!$attr_uniquename){
         $attr_uniquename = $attr_name;
      }

      // make sure the landmark sequence exists in the database.  We don't
      // know the type of the landmark so we'll hope that it's unique across
      // all types. If not we'll error out.  This test is only necessary if
      // if the landmark and the uniquename are different.  If they are the same
      // then this is the information for the landmark
      if(strcmp($landmark,$attr_uniquename)!=0){
         $feature_sql = "SELECT count(*) as num_landmarks
                         FROM {feature} 
                         WHERE organism_id = %d and uniquename = '%s'";
         $count = db_fetch_object(db_query($feature_sql,$organism_id,$landmark));
         if(!$count or $count->num_landmarks == 0){
            print "ERROR: the landmark '$landmark' cannot be found for this organism. ". 
                  "Please add the landmark and then retry the import of this GFF3 ".
                  "file.\n";
            return '';

         }
         if($count->num_landmarks > 1){
            print "ERROR: the landmark '$landmark' is not unique for this organism. ".
                  "The features cannot be associated.\n";
            return '';
         }
      }

      
      // if the option is to remove or refresh then we want to remove
      // the feature from the database.
      if(!$generate_name and ($remove or $refresh)){
         print "Removing feature '$attr_uniquename'\n";
         $sql = "DELETE FROM {feature}
                 WHERE organism_id = %d and uniquename = '%s' and type_id = %d";
         $result = db_query($sql,$organism->organism_id,$attr_uniquename,$cvterm->cvterm_id); 
         if(!$result){
            print "ERROR: cannot delete feature $attr_uniquename\n";
         }
         $feature = 0; 
      }

      // add or update the feature and all properties
      if($update or $refresh or $add_only){
    

         // add/update the feature
         $feature = tripal_core_load_gff3_feature($organism,$cvterm,
            $attr_uniquename,$attr_name,$residues,$attr_is_analysis,
            $attr_is_obsolete, $add_only,$generate_name);

         // store all of the features so far use later by parent and target
         // relationships
         $gff_features[$feature->uniquename]['type'] = $type;

         if($feature){
            if($generate_name){
               $attr_uniquename = $feature->uniquename;
            }
 
            // add/update the featureloc if the landmark and the ID are not the same
            // if they are the same then this entry in the GFF is probably a landmark identifier
            if(strcmp($landmark,$attr_uniquename)!=0){
               tripal_core_load_gff3_featureloc($feature,$organism,
                  $landmark,$fmin,$fmax,$strand,$phase,$attr_fmin_partial,
                  $attr_fmax_partial,$attr_residue_info,$attr_locgroup);
            }
            // add any aliases for this feature
            if(array_key_exists('Alias',$tags)){
               tripal_core_load_gff3_alias($feature,$tags['Alias']);
            }
            // add any aliases for this feature
            if(array_key_exists('Dbxref',$tags)){
               tripal_core_load_gff3_dbxref($feature,$tags['Dbxref']);
            }
            // add parent relationships
            if(array_key_exists('Parent',$tags)){
               tripal_core_load_gff3_parents($feature,$cvterm,$tags['Parent'],$gff_features,$organism_id);
            }
         }
      }
   }
   tripal_db_set_active($previous_db);
   return '';
}
/*************************************************************************
*
*/
function tripal_core_load_gff3_parents($feature,$cvterm,$parents,$gff_features,$organism_id){

   $uname = $feature->uniquename;
   $type = $cvterm->name;
   $rel_type = 'part_of';


   // create these SQL statements that will be used repeatedly below.
   $cvtermsql = "SELECT CVT.cvterm_id
                 FROM {cvterm} CVT
                    INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
                    LEFT JOIN {cvtermsynonym} CVTS on CVTS.cvterm_id = CVT.cvterm_id
                 WHERE cv.name = '%s' and (CVT.name = '%s' or CVTS.synonym = '%s')";

   $feature_sql = "SELECT * FROM {feature} 
                   WHERE organism_id = %d and uniquename = '%s' and type_id = %d";

   // iterate through the parents in the list
   foreach($parents as $parent){  
      $parent_type = $gff_features[$parent]['type'];

      $parentcvterm = db_fetch_object(db_query($cvtermsql,'sequence',$parent_type,$parent_type));
      $relcvterm = db_fetch_object(db_query($cvtermsql,'relationship',$rel_type,$rel_type));
      $parent_feature = db_fetch_object(db_query($feature_sql,$organism_id,$parent,$parentcvterm->cvterm_id));

      if($parent_feature){

         // check to see if the relationship already exists
         $sql = "SELECT * FROM {feature_relationship} WHERE subject_id = %d and object_id = %d and type_id = %d";
         $rel = db_fetch_object(db_query($sql,$feature->feature_id,$parent_feature->feature_id,$relcvterm->cvterm_id));
         if($rel){
            print "   Relationship already exists, skipping '$uname' ($type) $rel_type '$parent' ($parent_type)\n";
         } else {      
            $sql = "INSERT INTO {feature_relationship} (subject_id,object_id,type_id)
                    VALUES (%d,%d,%d)";
            $result = db_query($sql,$feature->feature_id,$parent_feature->feature_id,$relcvterm->cvterm_id);
            if(!$result){
               print "WARNING: failed to insert feature relationship '$uname' ($type) $rel_type '$parent' ($parent_type)\n";
            } else {
               print "   Inserted relationship relationship: '$uname' ($type) $rel_type '$parent' ($parent_type)\n";
            }
         } 
      }
      else {
         print "WARNING: cannot establish relationship '$uname' ($type) $rel_type '$parent' ($parent_type): Cannot find the parent\n";
      }
   }
}
/*************************************************************************
*
*/
function tripal_core_load_gff3_dbxref($feature,$dbxrefs){

   // iterate through each of the dbxrefs
   foreach($dbxrefs as $dbxref){

      // get the database name from the reference.  If it doesn't exist then create one.
      $ref = explode(":",$dbxref);
      $dbname = $ref[0];
      $accession = $ref[1];

      // first look for the database name if it doesn't exist then create one.
      // first check for the fully qualified URI (e.g. DB:<dbname>. If that
      // can't be found then look for the name as is.  If it still can't be found
      // the create the database
      $db = tripal_core_chado_select('db',array('db_id'),array('name' => "DB:$dbname"));      
      if(sizeof($db) == 0){
         $db = tripal_core_chado_select('db',array('db_id'),array('name' => "$dbname"));      
      }        
      if(sizeof($db) == 0){
         $ret = tripal_core_chado_insert('db',array('name' => $dbname, 
           'description' => 'Added automatically by the GFF loader'));
         if($ret){ 
            print "Added new database: $dbname\n";
            $db = tripal_core_chado_select('db',array('db_id'),array('name' => "$dbname"));      
         } else {
            print "ERROR: cannot find or add the database $dbname\n";
            return 0;
         }
      } 
      $db = $db[0];
       
      // now check to see if the accession exists
      $dbxref = tripal_core_chado_select('dbxref',array('dbxref_id'),array(
         'accession' => $accession,'db_id' => $db->db_id));

      // if the accession doesn't exist then we want to add it
      if(sizeof($dbxref) == 0){
         $ret = tripal_core_chado_insert('dbxref',array('db_id' => $db->db_id,
            'accession' => $accession,'version' => ''));
         $dbxref = tripal_core_chado_select('dbxref',array('dbxref_id'),array(
            'accession' => $accession,'db_id' => $db->db_id));
      }
      $dbxref = $dbxref[0];

      // check to see if tihs feature dbxref already exists
      $fdbx = tripal_core_chado_select('feature_dbxref',array('feature_dbxref_id'),
         array('dbxref_id' => $dbxref->dbxref_id,'feature_id' => $feature->feature_id));

      // now associate this feature with the database reference if it doesn't
      // already exist
      if(sizeof($fdbx)==0){
         $ret = tripal_core_chado_insert('feature_dbxref',array(
            'feature_id' => $feature->feature_id,
            'dbxref_id' => $dbxref->dbxref_id));
         if($ret){
            print "Adding dbxref $dbname:$accession\n";
         } else {
            print "ERROR: failed to insert dbxref: $dbname:$accession\n";
            return 0;
         }
      } else {
         print "Dbxref already exists, skipping $dbname:$accession\n";
      }
   }
   return 1;
}

/*************************************************************************
*
*/
function tripal_core_load_gff3_alias($feature,$aliases){

   // 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)){
         print("ERROR: Failed to add the synonyms type vocabulary");
         return 0;
      }
      $syncv = db_fetch_object(db_query($sql));
   }

   // get the 'exact' cvterm, which is the type of synonym we're adding
   $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,'exact','synonym_type'));
   if(!$syntype){
      $term = array(
         'name' => array('exact'),
         'id' => array("internal:exact"),
         'definition' => array(''),
         'is_obsolete' => array(0),
      );
      $syntype = tripal_cv_obo_add_cv_term($term,$syncv,0,1);
      if(!$syntype){
         tripal_cv_obo_quiterror("Cannot add synonym type: internal:$type");
      }
   }

   // iterate through all of the aliases and add each one
   foreach($aliases as $alias){
      print "   Adding Alias $alias\n";

      // check to see if the alias already exists in the synonym table
      // if not, then add it
      $synsql = "SELECT * FROM {synonym}
                 WHERE name = '%s' and type_id = %d";
      $synonym = db_fetch_object(db_query($synsql,$alias,$syntype->cvterm_id));
      if(!$synonym){      
         $sql = "INSERT INTO {synonym}
                  (name,type_id,synonym_sgml)
                 VALUES ('%s',%d,'%s')";
         $result = db_query($sql,$alias,$syntype->cvterm_id,'');
         if(!$result){
            print "ERROR: cannot add alias $alias to synonym table\n";
         }
      }           
      $synonym = db_fetch_object(db_query($synsql,$alias,$syntype->cvterm_id));


      // check to see if we have a NULL publication in the pub table.  If not,
      // then add one.
      $pubsql = "SELECT * FROM {pub} WHERE uniquename = 'null'";
      $pub = db_fetch_object(db_query($pubsql));
      if(!$pub){
         $sql = "INSERT INTO pub (uniquename,type_id) VALUES ('%s',
                   (SELECT cvterm_id 
                    FROM cvterm CVT
                      INNER JOIN dbxref DBX on DBX.dbxref_id = CVT.dbxref_id
                      INNER JOIN db DB on DB.db_id = DBX.db_id
                    WHERE CVT.name = 'null' and DB.name = 'null')";
         $result = db_query($sql,'null');
         if(!$result){
            print "ERROR: cannot add null publication needed for setup of alias\n";
            return 0;
         }
      }
      $pub = db_fetch_object(db_query($pubsql));

      // check to see if the synonym exists in the feature_synonym table
      // if not, then add it.
      $synsql = "SELECT * FROM {feature_synonym}
                 WHERE synonym_id = %d and feature_id = %d and pub_id = %d";
      $fsyn = db_fetch_object(db_query($synsql,$synonym->synonym_id,$feature->feature_id,$pub->pub_id));
      if(!$fsyn){      
         $sql = "INSERT INTO {feature_synonym}
                  (synonym_id,feature_id,pub_id)
                 VALUES (%d,%d,%d)";
         $result = db_query($sql,$synonym->synonym_id,$feature->feature_id,$pub->pub_id);
         if(!$result){
            print "ERROR: cannot add alias $alias to feature synonym table\n";
            return 0;
         }
      } else {
         print "Synonym $alias already exists. Skipping\n";
      }
   }
   return 1;
}
/*************************************************************************
*
*/
function tripal_core_load_gff3_feature($organism,$cvterm,$uniquename,$name,
   $residues,$is_analysis='f',$is_obsolete='f',$add_only,$generate_name)  {

   if($generate_name){
      $uniquename = 'tripal_temp_loading_name' . rand(1,99999999);
   }

   // check to see if the feature already exists
   $feature_sql = "SELECT * FROM {feature} 
                   WHERE organism_id = %d and uniquename = '%s' and type_id = %d";
   $feature = db_fetch_object(db_query($feature_sql,$organism->organism_id,$uniquename,$cvterm->cvterm_id));

   if(strcmp($is_obsolete,'f')==0){
      $is_obsolete = 'false';
   }
   if(strcmp($is_analysis,'f')==0){
      $is_analysis = 'false';
   }


   // insert the feature if it does not exist otherwise perform an update
   if(!$feature){
      print "Adding feature '$uniquename' ($cvterm->name)\n";
      $isql = "INSERT INTO {feature} (organism_id, name, uniquename, residues, seqlen,
                  md5checksum, type_id,is_analysis,is_obsolete)
               VALUES(%d,'%s','%s','%s',%d, '%s', %d, %s, %s)";
      $result = db_query($isql,$organism->organism_id,$name,$uniquename,$residues,strlen($residues),
               md5($residues),$cvterm->cvterm_id,$is_analysis,$is_obsolete);
      if(!$result){
         print "ERROR: failed to insert feature '$uniquename' ($cvterm->name)\n";
         return 0;
      }
   } 
   elseif(!$add_only) {
      print "Updating feature '$uniquename' ($cvterm->name)\n";
      $usql = "UPDATE {feature} 
               SET name = '%s', residues = '%s', seqlen = '%s', md5checksum = '%s',
                  is_analysis = %s, is_obsolete = %s
               WHERE organism_id = %d and uniquename = '%s' and type_id = %d";
      $result = db_query($usql,$name,$residues,strlen($residues),md5($residues),$is_analysis,$is_obsolete,
                   $organism_id,$uniquename,$cvterm->cvterm_id);
      if(!$result){
         print "ERROR: failed to update feature '$uniquename' ($cvterm->name)\n";
         return 0;
      }
   }
   else {
      // the feature exists and we don't want to update it so return
      // a value of 0.  This will stop all downstream property additions
      print "Skipping existing feature: '$uniquename' ($cvterm->name).\n";
      return 0;
   }
   $feature = db_fetch_object(db_query($feature_sql,$organism->organism_id,$uniquename,$cvterm->cvterm_id));
   // now that we've added the feature let's reset it's uniquename to be
   // the feature id
   if($generate_name){
      $usql = "UPDATE {feature} 
               SET name = '%s', uniquename = '%s'
               WHERE feature_id = %d";
      print "   Renaming feature '$uniquename' => ";
      $uniquename = "$feature->feature_id";
      print "$uniquename\n";
      $result = db_query($usql,$uniquename,$uniquename,$feature_id);
      if(!$result){
         print "ERROR: failed to update unnamed feature '$uniquename' with generic name\n";
         return 0;
      }
      $feature->name = $uniquename;
      $feature->uniquename = $uniquename;
   }

   return $feature;
}
/*************************************************************************
*
*/
function tripal_core_load_gff3_featureloc($feature,$organism,$landmark,$fmin,
   $fmax,$strand,$phase,$is_fmin_partial,$is_fmax_partial,$residue_info,$locgroup)
{
 
   // get the source feature
   $sql = "SELECT * FROM {feature} 
           WHERE organism_id = %d and uniquename = '%s'";
   $srcfeature = db_fetch_object(db_query($sql,$organism->organism_id,$landmark));
   if(!$srcfeature){
      print "ERROR: cannot find landmark feature $landmark.  Cannot add the feature location record\n";
      return 0;
   }


   // TODO: create an attribute that recognizes the residue_info,locgroup, is_fmin_partial and is_fmax_partial, right now these are
   //       hardcoded to be false and 0 below.


   // check to see if this featureloc already exists, but also keep track of the
   // last rank value
   $rank = -1;  
   $exists = 0;  
   $featureloc_sql = "SELECT FL.featureloc_id,FL.fmin,FL.fmax, FL.is_fmin_partial,
                         FL.is_fmax_partial, FL.strand, FL.phase, FL.residue_info,
                         FL.locgroup, F.uniquename as srcname
                      FROM {featureloc} FL
                        INNER JOIN {feature} F on F.feature_id = FL.srcfeature_id
                      WHERE FL.feature_id = %d
                      ORDER BY rank ASC";
   $recs = db_query($featureloc_sql,$feature->feature_id);
   while ($featureloc = db_fetch_object($recs)){
      if(strcmp($featureloc->srcname,$landmark)==0 and
         $featureloc->fmin == $fmin and strcmp($featureloc->is_fmin_partial,$is_fmin_partial)==0 and
         $featureloc->fmax == $fmax and strcmp($featureloc->is_fmax_partial,$is_fmax_partial)==0 and
         $featureloc->phase == $phase and $featureloc->strand == $strand and
         strcmp($featureloc->residue_info,$residue_info)==0 and 
         $featureloc->locgroup == $locgroup){
         // this is the same featureloc, so do nothing... no need to update
         //TODO: need more checks here
         print "   No change to featureloc\n";
         $exists = 1;
      }
      $rank = $featureloc->rank;
   }
   if(!$exists){
      $rank++;
      // this feature location is new so add it
      if(!$phase){
          $phase = 'NULL';
      }
      if(strcmp($is_fmin_partial,'f')==0){
         $is_fmin_partial = 'false';
      }
      elseif(strcmp($is_fmin_partial,'t')==0){
         $is_fmin_partial = 'true';
      }
      if(strcmp($is_fmax_partial,'f')==0){
         $is_fmax_partial = 'false';
      }
      elseif(strcmp($is_fmax_partial,'t')==0){
         $is_fmax_partial = 'true';
      }
      print "   Adding featureloc $srcfeature->uniquename fmin: $fmin, fmax: $fmax, strand: $strand, phase: $phase, rank: $rank\n";
      $fl_isql = "INSERT INTO {featureloc} 
                    (feature_id, srcfeature_id, fmin, is_fmin_partial, fmax, is_fmax_partial,
                     strand, phase, residue_info, locgroup, rank) 
                 VALUES (%d,%d,%d,%s,%d,%s,%d,%s,'%s',%d,%d)";
      $result = db_query($fl_isql,$feature->feature_id,$srcfeature->feature_id,$fmin,$is_fmin_partial,$fmax,$is_fmax_partial,
               $strand,$phase,$residue_info,$locgroup,$rank);
      if(!$result){
         print "ERROR: failed to insert featureloc\n";
exit;
         return 0;
      }
   }
   return 1;
}
/*************************************************************************
*
*/