updates to blast, core, gff loader, etc... fixed several bugs

tripal_analysis/tripal_analysis.api.inc

@@ -76,14 +76,7 @@ function tripal_analysis_get_property($analysis_id,$property){
          'is_obsolete' => 0
       ),
    );
-   $columns = array('type_id','value');
-   $results = tripal_core_chado_select('analysisprop',$columns,$values);
-   // this next bit is a hack until we get the recursive add vars routine written
-   foreach($results as $prop){
-      $prop->type_id = new stdClass();
-      $prop->type_id->table_name = 'cvterm';
-      $prop->type_id->name = $property;
-   }
+   $results = tripal_core_generate_chado_var('analysisprop',$values);
    return $results;
 }
 /**
@@ -91,7 +84,17 @@ function tripal_analysis_get_property($analysis_id,$property){
 *
 * @ingroup tripal_api
 */
-function tripal_analysis_insert_property($analysis_id,$property,$value){
+function tripal_analysis_insert_property($analysis_id,$property,$value,$update_if_present = 0){
+   // first see if the property already exists, if so we can't 
+   $prop = tripal_analysis_get_property($analysis_id,$property);
+   if(count($prop)>0){
+      if($update_if_present){
+        return tripal_analysis_update_property($analysis_id,$property,$value) ;
+      } else {
+        return FALSE;
+      }
+   }
+
    // construct the array of values to be inserted  
    $values = array (
       'analysis_id' => $analysis_id,
@@ -112,7 +115,18 @@ function tripal_analysis_insert_property($analysis_id,$property,$value){
 *
 * @ingroup tripal_api
 */
-function tripal_analysis_update_property($analysis_id,$property,$value){
+function tripal_analysis_update_property($analysis_id,$property,$value,$insert_if_missing = 0){
+
+   // first see if the property is missing (we can't update a missing property
+   $prop = tripal_analysis_get_property($analysis_id,$property);
+   if(count($prop)==0){
+      if($insert_if_missing){
+        return tripal_analysis_insert_property($analysis_id,$property,$value);
+      } else {
+        return FALSE;
+      }
+   }
+
    // construct the array that will match the exact record to update
    $match = array (
       'analysis_id' => $analysis_id,
@@ -129,3 +143,23 @@ function tripal_analysis_update_property($analysis_id,$property,$value){
    );
    return tripal_core_chado_update('analysisprop',$match,$values);
 }
+/**
+* Adds a single property to an existing analysis record.
+*
+* @ingroup tripal_api
+*/
+function tripal_analysis_delete_property($analysis_id,$property){
+
+
+   // construct the array that will match the exact record to update
+   $match = array (
+      'analysis_id' => $analysis_id,
+      'type_id' => array ( 
+         'cv_id' => array (
+            'name' => 'tripal',
+         ),
+         'name' => $property,
+      ),
+   );
+   return tripal_core_chado_delete('analysisprop',$match);
+}

tripal_analysis_blast/parse_blast_XML.inc

@@ -0,0 +1,864 @@
+<?php
+
+/*******************************************************************************
+ * Parse NCBI Blast results for indexing so that user can use blast results to
+ * find corresponding features
+ */
+function parse_NCBI_Blast_XML_index_version($xml_string,$db,$feature_id) {
+	// Get the parser using db_id
+	$sql = "SELECT * FROM {tripal_analysis_blast} WHERE db_id = %d";
+	$parser = db_fetch_object(db_query($sql, $db->db_id));
+	$db_name = $parser->displayname;
+	$is_genbank = $parser->genbank_style;
+	$regex_hit_id = $parser->regex_hit_id;
+	$regex_hit_def = $parser->regex_hit_def;
+	$regex_hit_accession = $parser->regex_hit_accession;
+
+	// set default if regular expressions have not been specified
+	if(!$regex_hit_id){
+		$regex_hit_id = '/^(.*?)\s.*$/';
+	} else {
+		$regex_hit_id = '/'.$regex_hit_id.'/';
+	}
+	if(!$regex_hit_def){
+		$regex_hit_def = '/^.*?\s(.*)$/';
+	} else {
+		$regex_hit_def = '/'.$regex_hit_def.'/';
+	}
+	if(!$regex_hit_accession){
+		$regex_hit_accession = '/^(.*?)\s.*$/';
+	} else {
+		$regex_hit_accession = '/'.$regex_hit_accession.'/';
+	}
+
+	$html_out .= "<h3>$db_name</h3>";
+
+	// Load the file.  This XML file should be an extract
+	// of the original XML file with only a single iteration.
+	// An iteration is essentially all the hits for a single
+	// query sequence.
+	$xml_output = simplexml_load_string($xml_string);
+	$iteration = '';
+	// new XML file parser has added the feature name within <Iteration_query-def> tags.
+	if ($xml_output->getName() == 'Iteration') {
+		foreach ($xml_output->children() as $xml_tag) {
+			if ($xml_tag->getName() == 'Iteration_query-def') {
+				// Here we show the feature name again to check if we pull the correct data
+				$html_out .= "Query: $xml_tag<br>";
+			} else if ($xml_tag->getName() == 'Iteration_hits') {
+				$iteration = $xml_tag;
+			}
+		}
+		// This is for the file parsed by the old parser
+	} else {
+		$iteration = $xml_output;
+	}
+
+	// now run through the blast hits/hsps of this iteration
+	// and generate the rows of the table
+	foreach($iteration->children() as $hits){
+		$best_evalue = 0;
+		foreach($hits->children() as $hit){
+			$best_evalue = 0;
+			$element_name = $hit->getName();
+			if($element_name == 'Hit_id'){
+				// if parsing "name, acc, desc" from three tags (1/3)
+				if ($is_genbank) {
+					$hit_name = $hit;
+				}
+			} else if($element_name == 'Hit_def'){
+				if($is_genbank){
+					$description = $hit;
+				} else {
+					$accession = preg_replace($regex_hit_accession,"$1",$hit);
+					$hit_name = preg_replace($regex_hit_id,"$1",$hit);
+					$description = preg_replace($regex_hit_def,"$1",$hit);
+				}
+			} else if($element_name == 'Hit_accession'){
+				// if parsing "name, acc, desc" from three tags (3/3)
+				if ($is_genbank){
+					$accession = $hit;
+				}
+				// now run through each HSP for this hit
+			}
+		}
+		$html_out .= "<p>$hit_name<br>";
+		$html_out .= "$accession<br>";
+		$html_out .= "<b>$description</b></br>";
+		$hsp_html_out = '';
+	}
+	return $html_out;
+}
+
+/*******************************************************************************
+ * Parse Blast XML Output file into analysisfeatureprop table
+ */
+function tripal_analysis_blast_parseXMLFile ($analysis_id, $blastdb, $blastfile, 
+   $no_parsed, $blastfile_ext, $query_re, $query_type, $query_uniquename,$job_id) {
+
+	// Prepare log
+	$filename = preg_replace("/.*\/(.*)/", "$1", $blastfile);
+	$logfile = file_directory_path() . "/tripal/tripal_analysis_blast/load_$filename.log";
+	$log = fopen($logfile, 'a'); // append parsing results to log file
+
+	// If user input a file (e.g. blast.xml)
+	if (is_file($blastfile)) {
+      tripal_analysis_blast_parseXML($analysis_id, $blastdb, $blastfile, 
+         $no_parsed, $blastfile_ext, $query_re, $query_type, $query_uniquename,
+         $job_id,1,$log);
+	} 
+   // Otherwise, $blastfile is a directory. Iterate through all xml files in it
+   else {
+      if(!$blastfile_ext){
+         $blastfile_ext = 'xml';
+      }
+
+		$dir_handle = @opendir($blastfile) or die("Unable to open $blastfile");
+		$pattern = sql_regcase($blastfile . "/*.$blastfile_ext");
+		$total_files = count(glob($pattern));
+		print "$total_files file(s) to be parsed.\n";
+		
+		$interval = intval($total_files * 0.01);
+		$no_file = 0;
+			
+		// Parsing all files in the directory
+		while ($file = readdir($dir_handle)) {
+			if(preg_match("/^.*\.$blastfile_ext/i",$file)){
+
+            tripal_analysis_blast_parseXML($analysis_id, $blastdb, "$blastfile/$file", 
+              $no_parsed, $blastfile_ext, $query_re, $query_type, $query_uniquename,
+              $job_id,0,$log);
+
+			   // Set job status
+			   if ($no_file % $interval == 0) {
+			      $percentage = (int) (($no_file / $total_files) * 100);
+				   tripal_job_set_progress($job_id, $percentage);
+				   print $percentage."% ";
+			   }				
+         }
+   	   $no_file ++;
+		}
+	}
+
+	print "Done.\nSuccessful and failed entries have been saved in the log file:\n $logfile\n";
+	fwrite($log, "\n");
+	fclose($log);
+	return;
+}
+/********************************************************************************
+ * 
+ */
+function tripal_analysis_blast_parseXML($analysis_id, $blastdb, $blastfile, 
+   $no_parsed, $blastfile_ext, $query_re, $query_type, $query_uniquename,
+  $job_id,$set_progress,$log){
+
+	// Parsing started
+	print "Parsing File:".$blastfile." ...\n";
+	fwrite($log, date("D M j G:i:s Y").". Loading $blastfile\n");
+	if ($no_parsed == 'all') {
+		print "Parsing all hits...\n";
+	} else {
+		print "Parsing top $no_parsed hits...\n";
+	}
+	
+	// Get cvterm_id for 'analysis_blast_output_iteration_hits' which is required
+	// for inserting into the analysisfeatureprop table
+	$previous_db = tripal_db_set_active('chado'); // use chado database
+	$sql = "SELECT CVT.cvterm_id FROM {cvterm} CVT ".
+       "INNER JOIN cv ON cv.cv_id = CVT.cv_id ".
+       "WHERE CVT.name = 'analysis_blast_output_iteration_hits' ".
+       "AND CV.name = 'tripal'";
+	$type_id = db_result(db_query($sql));
+
+	// Load the XML file.
+	$blastoutput = simplexml_load_file($blastfile);
+   if(!$blastoutput){
+      exit("Failed to open file '$blastfile'\n");
+   }
+	$no_iterations = 0;
+	foreach($blastoutput->children() as $tmp) {
+		if ($tmp->getName() == 'BlastOutput_iterations') {
+			foreach($tmp->children() as $itr) {
+				if ($itr->getName() == 'Iteration') {
+					$no_iterations ++;
+				}
+			}
+		}
+	}
+	print "$no_iterations iterations to be processed.\n";
+		
+	$interval = intval($no_iterations * 0.01);
+	$idx_iterations = 0;
+	foreach ($blastoutput->children() as $blastoutput_tags) {
+
+		if ($blastoutput_tags->getName() == 'BlastOutput_iterations') {
+			foreach($blastoutput_tags->children() as $iterations) {
+				if ($iterations->getName() == 'Iteration') {
+
+					// Set job status
+					$idx_iterations ++;
+					if ($set_progress and $idx_iterations % $interval == 0) {
+						$percentage = (int) (($idx_iterations / $no_iterations) * 100);
+						tripal_job_set_progress($job_id, $percentage);
+						print $percentage."% ";
+					}
+					// now run through the blast hits/hsps of this iteration
+					// and generate the rows of the table
+					$feature_id = 0;
+					foreach($iterations->children() as $iteration_tags) {
+
+
+
+
+						// Match chado feature uniquename with <Iteration_query-def>
+						// and get the feature_id
+						$featurenaem_xml = '';
+						if($iteration_tags->getName() == 'Iteration_query-def'){
+
+							// If the Iteration_query-def in the format provided by the 
+                     // user's regular expression 
+							if ($query_re and preg_match("/$query_re/", $iteration_tags, $matches)) {
+								$feature = $matches[1];
+								
+							} 
+                     // If not in above format then pull up to the first space
+                     else {
+								if (preg_match('/^(.*?)\s.*$/', $iteration_tags, $matches)) {
+   								$feature = $matches[1];
+                        } 
+                        // if no match up to the first space then just use the entire string
+                        else {
+                           $feature = $iteration_tags;
+                        }
+                     }
+                     // now find the feature in chado
+                     $select = array();
+                     if($query_uniquename){
+                        $select['uniquename'] = $feature;
+                     } else {
+                        $select['name'] = $feature;
+                     }
+                     if($query_type){
+                        $select['type_id'] = array(
+                          'cv_id' => array(
+                             'name' => 'sequence'
+                          ),
+                          'name' => $query_type,
+                        );
+                     }
+                     $feature_arr = tripal_core_chado_select('feature',array('feature_id'),$select);
+                     if(count($feature_arr) > 1){
+  							   fwrite($log, "Ambiguous: '$feature' matches more than one feature and is being skipped.\n");
+								continue;
+                     }
+                     if(count($feature_arr) < 1){
+								fwrite($log, "Failed: '$feature' cannot find a matching feature in the database.\n");
+                        continue;
+                     }
+                     $feature_id = $feature_arr[0]->feature_id;
+    						fwrite($log, "Matched: '$feature' => feature id:".$feature_id);
+							$featurename_xml = $iteration_tags->asXML();
+
+							
+						} 
+                  // Insert Iteration_hits into analysisfeatureprop and analysisfeature tables
+                  else if($iteration_tags->getName() == 'Iteration_hits'){
+							if ($feature_id) {
+
+								// Make sure this iteration doesn't exist in analysisfeatureprop. If it does, update but not insert
+								$sql = "SELECT analysisfeatureprop_id FROM {analysisfeatureprop} AFP ".
+                            "INNER JOIN analysisfeature AF ON AF.analysisfeature_id = AFP.analysisfeature_id ".       
+                            "WHERE feature_id=%d ".
+                            "AND analysis_id=%d ".
+                            "AND type_id=%d ";
+
+								$result = db_query($sql, $feature_id, $analysis_id, $type_id);
+								$analysisfeatureprop = db_fetch_object($result);
+								$xml_content =  "<Iteration>\n".$featurename_xml."\n";
+								// parse all hits
+								if ($no_parsed == 'all') {
+									$xml_content .= $iteration_tags->asXML();
+								
+								// parse only top hits
+								} else {
+									$counter = 0;
+									$xml_content .= "<Iteration_hits>\n";
+									foreach ($iteration_tags->children() As $hit) {
+										if ($counter < $no_parsed) {
+											$xml_content .= $hit->asXML();
+										} else {
+											break;
+										}
+										$counter ++;
+									}
+									$xml_content .= "</Iteration_hits>";
+								}
+								$xml_content .= "\n</Iteration>";
+
+								// If this Iteration_hits already exists, update it
+								if ($analysisfeatureprop) {
+									$sql = "UPDATE {analysisfeatureprop} ".
+                               "SET value = '%s' ".
+                               "WHERE analysisfeatureprop_id = %d ";
+										
+									db_query($sql, $xml_content, $analysisfeatureprop->analysisfeatureprop_id);
+									fwrite($log, " (Update)\n"); // write to log
+
+									// Otherwise, insert the Iteration_hits into analysisfeature and analysisfeatureprop tables
+								} else {
+									//------------------------------------------------------
+									// Insert into analysisfeature table
+									//------------------------------------------------------
+									$sql = "INSERT INTO {analysisfeature} (feature_id, analysis_id) ".
+                               "VALUES (%d, %d)";
+									db_query ($sql, $feature_id, $analysis_id);
+									// Get the newly inserted analysisfeature_id
+									$sql = "SELECT analysisfeature_id FROM {analysisfeature} WHERE feature_id = %d AND analysis_id = %d";
+									$analysisfeature_id = db_result(db_query($sql, $feature_id, $analysis_id));
+									//------------------------------------------------------
+									// Insert into analysisfeatureprop table
+									//------------------------------------------------------
+									$sql = "INSERT INTO {analysisfeatureprop} (analysisfeature_id, type_id, value, rank)".
+                               "VALUES (%d, %d, '%s', %d)";
+									db_query($sql, $analysisfeature_id, $type_id, $xml_content, '0');
+									fwrite($log, " (Insert)\n"); // write to log
+								}
+							}
+						}	
+					}
+				}
+			}
+		}
+	}
+	tripal_db_set_active ($previous_db); // Use drupal database
+}
+/********************************************************************************
+ * 
+ */
+function tripal_analysis_blast_get_result_object($xml_string,$db,$max,$feature_id, $analysis) {
+	$blast_object = new stdClass();
+	// Get the parser using db_id
+	$sql = "SELECT * FROM {tripal_analysis_blast} WHERE db_id = %d";
+	$parser = db_fetch_object(db_query($sql, $db->db_id));
+	$db_name = $parser->displayname;
+	$is_genbank = $parser->genbank_style;
+	$regex_hit_id = $parser->regex_hit_id;
+	$regex_hit_def = $parser->regex_hit_def;
+	$regex_hit_accession = $parser->regex_hit_accession;
+
+	// set default if regular expressions have not been specified
+	if(!$regex_hit_id){
+		$regex_hit_id = '/^(.*?)\s.*$/';
+	} else {
+		$regex_hit_id = '/'.$regex_hit_id.'/';
+	}
+	if(!$regex_hit_def){
+		$regex_hit_def = '/^.*?\s(.*)$/';
+	} else {
+		$regex_hit_def = '/'.$regex_hit_def.'/';
+	}
+	if(!$regex_hit_accession){
+		$regex_hit_accession = '/^(.*?)\s.*$/';
+	} else {
+		$regex_hit_accession = '/'.$regex_hit_accession.'/';
+	}
+
+	// Get analysis information
+	$blast_object->analysis = $analysis;
+	$blast_object->db = $db;
+	if (!$db_name) {
+		$blast_object->title = $analysis->name;
+	} else {
+		$blast_object->title = $db_name;
+	}
+
+	// Find node id for the analysis
+	$ana_nid = db_result(db_query("SELECT nid FROM {chado_analysis} WHERE analysis_id = %d", $analysis->aid));
+	$blast_object->ana_nid = $ana_nid;
+	$blast_object->ana_time = $analysis->time;
+	$blast_object->ana_name = $analysis->name;
+
+	// Load the file.  This XML file should be an extract
+	// of the original XML file with only a single iteration.
+	// An iteration is essentially all the hits for a single
+	// query sequence.
+	$xml_output = simplexml_load_string($xml_string);
+	$iteration = '';
+	// new XML file parser has added the feature name within <Iteration_query-def> tags.
+	if ($xml_output->getName() == 'Iteration') {
+		foreach ($xml_output->children() as $xml_tag) {
+			if ($xml_tag->getName() == 'Iteration_query-def') {
+				// Here we show the feature name again to check if we pull the correct data
+				$blast_object->xml_tag = $xml_tag;
+			} else if ($xml_tag->getName() == 'Iteration_hits') {
+				$iteration = $xml_tag;
+			}
+		}
+		// This is for the file parsed by the old parser
+	} else {
+		$iteration = $xml_output;
+	}
+
+	$number_hits = 0;
+	foreach($iteration->children() as $hits){
+		$number_hits ++;
+	}
+
+	// add the links for updating blast info using Ajax
+	$blast_object->max = $max;
+	$blast_object->number_hits = $number_hits;
+	$blast_object->feature_id = $feature_id;
+	
+	$hits_array = array();
+	$hit_count = 0;
+
+	foreach($iteration->children() as $hits){
+		$hsp_array = array();
+		$counter = 0;
+		foreach($hits->children() as $hit){
+			$best_evalue = 0;
+			$best_identity = 0;
+			$best_len = 0;
+			$element_name = $hit->getName();
+			if($element_name == 'Hit_id'){
+				// if parsing "name, acc, desc" from three tags (1/3)
+				if ($is_genbank) {
+					$hit_name = $hit;
+				}
+			} else if($element_name == 'Hit_def'){
+				if($is_genbank){
+					$description = $hit;
+				} else {
+					$accession = preg_replace($regex_hit_accession,"$1",$hit);
+					$hit_name = preg_replace($regex_hit_id,"$1",$hit);
+					$description = preg_replace($regex_hit_def,"$1",$hit);
+				}
+			} else if($element_name == 'Hit_accession'){
+				// if parsing "name, acc, desc" from three tags (3/3)
+				if ($is_genbank){
+					$accession = $hit;
+				}
+				// now run through each HSP for this hit
+			} else if($element_name == 'Hit_hsps'){		
+				foreach($hit->children() as $hsp){
+					foreach($hsp->children() as $hsp_info){
+						$element_name = $hsp_info->getName();
+						if($element_name == 'Hsp_num'){
+							$hsp_num = $hsp_info;
+						}
+						if($element_name == 'Hsp_bit-score'){
+							$hsp_bit_score = $hsp_info;
+						}
+						if($element_name == 'Hsp_score'){
+							$hsp_score = $hsp_info;
+						}
+						if($element_name == 'Hsp_evalue'){
+							$hsp_evalue = $hsp_info;
+							// use the first evalue for this set of HSPs
+							// as the best evalue. This get's shown as
+							// info for the overall match.
+							if(!$best_evalue){
+								$best_evalue = $hsp_evalue;
+							}
+						}
+						if($element_name == 'Hsp_query-from'){
+							$hsp_query_from = $hsp_info;
+						}
+						if($element_name == 'Hsp_query-to'){
+							$hsp_query_to = $hsp_info;
+						}
+						if($element_name == 'Hsp_hit-from'){
+							$hsp_hit_from = $hsp_info;
+						}
+						if($element_name == 'Hsp_hit-to'){
+							$hsp_hit_to = $hsp_info;
+						}
+						if($element_name == 'Hsp_query-frame'){
+							$hsp_query_frame = $hsp_info;
+						}
+						if($element_name == 'Hsp_identity'){
+							$hsp_identity = $hsp_info;
+							// use the first evalue for this set of HSPs
+							// as the best evalue. This get's shown as
+							// info for the overall match.
+							if(!$best_identity){
+								$best_identity = $hsp_identity;
+							}
+						}
+						if($element_name == 'Hsp_positive'){
+							$hsp_positive = $hsp_info;
+						}
+						if($element_name == 'Hsp_align-len'){
+							$hsp_align_len = $hsp_info;
+							// use the first evalue for this set of HSPs
+							// as the best evalue. This get's shown as
+							// info for the overall match.
+							if(!$best_len){
+								$best_len = $hsp_align_len;
+							}
+						}
+						if($element_name == 'Hsp_qseq'){
+							$hsp_qseq = $hsp_info;
+						}
+						if($element_name == 'Hsp_hseq'){
+							$hsp_hseq = $hsp_info;
+						}
+						if($element_name == 'Hsp_midline'){
+							$hsp_midline = $hsp_info;
+						}
+					}
+
+					$hsp_content = array();
+					$hsp_content['hsp_num'] = $hsp_num;
+					$hsp_content['bit_score'] = $hsp_bit_score;
+					$hsp_content['score'] = $hsp_score;
+					$hsp_content['evalue'] = $hsp_evalue;
+					$hsp_content['query_frame'] = $hsp_query_frame;
+					$hsp_content['qseq'] = $hsp_qseq;
+					$hsp_content['midline'] = $hsp_midline;
+					$hsp_content['hseq'] = $hsp_hseq;
+					$hsp_content['hit_from'] = $hsp_hit_from;
+					$hsp_content['hit_to'] = $hsp_hit_to;
+					$hsp_content['identity'] = $hsp_identity;
+					$hsp_content['align_len'] = $hsp_align_len;
+					$hsp_content['positive'] = $hsp_positive;
+					$hsp_content['query_from'] = $hsp_query_from;
+					$hsp_content['query_to'] = $hsp_query_to;
+					$hsp_array[$counter] = $hsp_content;
+					$counter ++;
+				}
+			}
+		}
+      $arrowr_url = url(drupal_get_path('theme', 'tripal')."/images/arrow_r.png");
+		$hits_array[$hit_count]['arrowr_url'] = $arrowr_url;
+		$hits_array[$hit_count]['accession'] = $accession;
+		$hits_array[$hit_count]['hit_name'] = $hit_name;
+		
+		if($accession && $db->urlprefix){
+			$hits_array[$hit_count]['hit_url'] = "$db->urlprefix$accession";
+		} else {
+			// Test if this is another feature in the database
+			$sql = "SELECT feature_id FROM {feature} WHERE uniquename = '%s'";
+			$previous_db = db_set_active('chado');
+			$hit_feature_id = db_result(db_query($sql, $hit_name));
+			db_set_active($previous_db);
+			// If it is, add link to that feature
+			if ($hit_feature_id) {
+				$hits_array[$hit_count]['hit_url'] = "ID$hit_feature_id";
+			}
+		}
+		
+		$hits_array[$hit_count]['best_evalue'] = $best_evalue;
+		$percent_identity = number_format($best_identity/$best_len*100, 2);
+		$hits_array[$hit_count]['percent_identity'] = $percent_identity;
+		$hits_array[$hit_count]['description'] = $description;
+		$hits_array[$hit_count]['hsp'] = $hsp_array;
+		$hit_count ++;
+		
+		// if we've hit the maximum number of hits then return
+		if($max > 0 && $hit_count >= $max){
+			break;
+		}
+	}
+	$blast_object->hits_array = $hits_array;
+	return $blast_object;
+}
+
+/********************************************************************************
+ * Parse the best hit to generate the best hit homology report 
+ */
+function tripal_analysis_blast_parse_best_hit ($analysis_id) {
+
+	// Select all features for this blast analysis, and save them to the 'featureSet' array
+	$sql = "SELECT feature_id
+	             FROM {analysisfeature} AF  
+	             WHERE analysis_id = %d";
+	$previous_db = tripal_db_set_active('chado');
+	$result = db_query($sql, $analysis_id);
+	$featureSet = array ();
+	$counter = 0;
+	while ($feature = db_fetch_object($result)) {
+		$featureSet [$counter] = $feature->feature_id;
+		$counter ++;
+	}
+
+	// Get analysis information including 'Time', 'Name', and 'DB Settings'
+	$sql = "SELECT value, name, to_char(timeexecuted, 'MM-DD-YYYY') AS time
+                FROM {analysis}  A
+                INNER JOIN {analysisprop} AP ON  A.analysis_id = AP.analysis_id 
+                WHERE A.analysis_id = %d
+                AND type_id= (SELECT cvterm_id 
+                                           FROM {cvterm} 
+                                           WHERE name = 'analysis_blast_settings')";
+	$analysis = db_fetch_object(db_query($sql, $analysis_id));
+	
+	// Parse the blast settings
+	$blastsettings = explode("|", $analysis->value);
+	$db_id = $blastsettings [0];
+	
+	// Get the xml description parser using db_id
+	tripal_db_set_active($previous_db);
+	$sql = "SELECT * FROM {tripal_analysis_blast} WHERE db_id = %d";
+	$parser = db_fetch_object(db_query($sql, $db_id));
+
+	$db_name = $parser->displayname;
+	$is_genbank = $parser->genbank_style;
+	$regex_hit_id = $parser->regex_hit_id;
+	$regex_hit_def = $parser->regex_hit_def;
+	$regex_hit_accession = $parser->regex_hit_accession;
+
+	// set default description parser  if regular expressions have not been specified
+	if(!$regex_hit_id){
+		$regex_hit_id = '/^(.*?)\s.*$/';
+	} else {
+		$regex_hit_id = '/'.$regex_hit_id.'/';
+	}
+	if(!$regex_hit_def){
+		$regex_hit_def = '/^.*?\s(.*)$/';
+	} else {
+		$regex_hit_def = '/'.$regex_hit_def.'/';
+	}
+	if(!$regex_hit_accession){
+		$regex_hit_accession = '/^(.*?)\s.*$/';
+	} else {
+		$regex_hit_accession = '/'.$regex_hit_accession.'/';
+	}
+	
+   $interval = intval($counter * 0.01);
+	for ($i = 0; $i < $counter; $i ++) {
+		
+		if ($i !=0 && $i % $interval == 0) {
+			$percentage = (int) ($i / $counter * 100);
+			tripal_job_set_progress($job_id, $percentage);	
+			print $percentage."% ";
+		}
+
+		$sql = "SELECT value
+		             FROM {analysisfeatureprop} AFP 
+		             INNER JOIN {analysisfeature} AF ON AFP.analysisfeature_id = AF.analysisfeature_id 
+		             WHERE analysis_id = %d 
+		             AND feature_id = %d
+		             AND type_id = (SELECT cvterm_id FROM cvterm WHERE name='analysis_blast_output_iteration_hits' AND cv_id = (SELECT cv_id FROM cv WHERE name='tripal'))";
+		$previous_db = tripal_db_set_active('chado');
+		$xml_output = simplexml_load_string(db_result(db_query($sql, $analysis_id, $featureSet[$i])));
+		
+		$iteration = '';
+		// new XML file parser has added the feature name within <Iteration_query-def> tags.
+		if ($xml_output->getName() == 'Iteration') {
+			$query = "";
+			foreach ($xml_output->children() as $xml_tag) {
+				if ($xml_tag->getName() == 'Iteration_query-def') {
+					// Here we show the feature name again to check if we pull the correct data
+					$query = $xml_tag;
+				} else if ($xml_tag->getName() == 'Iteration_hits') {
+					$iteration = $xml_tag;
+				}
+			}
+	   // This is for the file parsed by the old parser
+		} else {
+			$iteration = $xml_output;
+		}
+
+		$number_hits = 0;
+		foreach($iteration->children() as $hits){
+			$number_hits ++;
+		}
+
+		$query = explode(" ", $query) ;
+		$query = $query [0];
+		if ($number_hits == 0) {
+			continue;
+		} 
+
+		// now run through the blast hits/hsps of this iteration
+		// and generate the rows of the table
+
+		foreach($iteration->children() as $hits){
+			$hit_count++;
+			foreach($hits->children() as $hit){
+				$best_evalue = 0;
+				$best_identity = 0;
+				$best_len = 0;
+				$element_name = $hit->getName();
+				if($element_name == 'Hit_id'){
+					// if parsing "name, acc, desc" from three tags (1/3)
+					if ($is_genbank) {
+						$hit_name = $hit;
+					}
+				} else if($element_name == 'Hit_def'){
+					if($is_genbank){
+						$description = $hit;
+					} else {
+						$accession = preg_replace($regex_hit_accession,"$1",$hit);
+						$hit_name = preg_replace($regex_hit_id,"$1",$hit);
+						$description = preg_replace($regex_hit_def,"$1",$hit);
+					}
+				} else if($element_name == 'Hit_accession'){
+					// if parsing "name, acc, desc" from three tags (3/3)
+					if ($is_genbank){
+						$accession = $hit;
+					}
+					// now run through each HSP for this hit
+				} else if($element_name == 'Hit_hsps'){
+					foreach($hit->children() as $hsp){
+						foreach($hsp->children() as $hsp_info){
+							$element_name = $hsp_info->getName();
+							if($element_name == 'Hsp_num'){
+								$hsp_num = $hsp_info;
+							}
+							if($element_name == 'Hsp_bit-score'){
+								$hsp_bit_score = $hsp_info;
+							}
+							if($element_name == 'Hsp_score'){
+								$hsp_score = $hsp_info;
+							}
+							if($element_name == 'Hsp_evalue'){
+								$hsp_evalue = $hsp_info;
+								// use the first evalue for this set of HSPs
+								// as the best evalue. This get's shown as
+								// info for the overall match.
+								if(!$best_evalue){
+									$best_evalue = $hsp_evalue;
+								}
+							}
+							if($element_name == 'Hsp_query-from'){
+								$hsp_query_from = $hsp_info;
+							}
+							if($element_name == 'Hsp_query-to'){
+								$hsp_query_to = $hsp_info;
+							}
+							if($element_name == 'Hsp_hit-from'){
+								$hsp_hit_from = $hsp_info;
+							}
+							if($element_name == 'Hsp_hit-to'){
+								$hsp_hit_to = $hsp_info;
+							}
+							if($element_name == 'Hsp_query-frame'){
+								$hsp_query_frame = $hsp_info;
+							}
+							if($element_name == 'Hsp_identity'){
+								$hsp_identity = $hsp_info;
+								// use the first evalue for this set of HSPs
+								// as the best evalue. This get's shown as
+								// info for the overall match.
+								if(!$best_identity){
+									$best_identity = $hsp_identity;
+								}
+							}
+							if($element_name == 'Hsp_positive'){
+								$hsp_positive = $hsp_info;
+							}
+							if($element_name == 'Hsp_align-len'){
+								$hsp_align_len = $hsp_info;
+								// use the first evalue for this set of HSPs
+								// as the best evalue. This get's shown as
+								// info for the overall match.
+								if(!$best_len){
+									$best_len = $hsp_align_len;
+								}
+							}
+							if($element_name == 'Hsp_qseq'){
+								$hsp_qseq = $hsp_info;
+							}
+							if($element_name == 'Hsp_hseq'){
+								$hsp_hseq = $hsp_info;
+							}
+							if($element_name == 'Hsp_midline'){
+								$hsp_midline = $hsp_info;
+							}
+						}
+					}
+				}
+			}
+			
+			// Get analysisfeature_id
+			$sql = "SELECT analysisfeature_id FROM {analysisfeature} WHERE analysis_id = %d AND feature_id = %d";
+			$af_id = db_result(db_query($sql, $analysis_id, $featureSet[$i]));
+			
+			// Get type_id
+			$sql = "SELECT cvterm_id FROM {cvterm} WHERE name = '%s' AND cv_id = (SELECT cv_id FROM {cv} WHERE name = 'tripal')"; 
+			$type_id = db_result(db_query($sql, 'analysis_blast_besthit_query'));
+			
+			$sql_test ="SELECT analysisfeatureprop_id FROM {analysisfeatureprop} WHERE analysisfeature_id = $af_id AND type_id = %d";
+			$test_afpid = db_result(db_query($sql_test, $type_id));
+			
+			//Insert only if this blast query not exists. 
+			if (!$test_afpid) {
+				$afp_sql = "INSERT INTO {analysisfeatureprop} (analysisfeature_id, type_id, value, rank) VALUES (%d, %d, '%s', 0)";
+				
+				//$query;
+				db_query($afp_sql, $af_id, $type_id, $query);
+
+				//$hit_name;
+				$type_id = db_result(db_query($sql, 'analysis_blast_besthit_match'));
+				db_query($afp_sql, $af_id, $type_id, $hit_name);
+					
+				//$description;
+				$type_id = db_result(db_query($sql, 'analysis_blast_besthit_description'));
+				db_query($afp_sql, $af_id, $type_id, $description);
+					
+				//$best_evalue;
+				$type_id = db_result(db_query($sql, 'analysis_blast_besthit_evalue'));
+				$e_digit = explode("e-", $best_evalue);
+				if (count($e_digit) == 2) {
+					$evalue_shown = number_format($e_digit [0],1);
+					$best_evalue = $evalue_shown."e-".$e_digit[1];
+				} 
+				db_query($afp_sql, $af_id, $type_id, $best_evalue);
+					
+				//$best_identity;
+				$type_id = db_result(db_query($sql, 'analysis_blast_besthit_identity'));
+				$percent_identity = number_format($best_identity/$best_len*100, 1);
+				db_query($afp_sql, $af_id, $type_id, $percent_identity);
+					
+				//$best_len;
+				$type_id = db_result(db_query($sql, 'analysis_blast_besthit_length'));
+				db_query($afp_sql, $af_id, $type_id, $best_len);
+				
+			// Otherwise, update all instead
+			} else {
+				$afp_sql = "UPDATE {analysisfeatureprop} SET analysisfeature_id = %d, type_id = %d, value = '%s', rank = 0 WHERE analysisfeatureprop_id = %d";
+
+				//$query;
+				db_query($afp_sql, $af_id, $type_id, $query, $test_afpid);
+				
+				//$hit_name;
+				$type_id = db_result(db_query($sql, 'analysis_blast_besthit_match'));
+				$test_afpid = db_result(db_query($sql_test, $type_id));
+				db_query($afp_sql, $af_id, $type_id, $hit_name, $test_afpid);
+
+				//$description;
+				$type_id = db_result(db_query($sql, 'analysis_blast_besthit_description'));
+				$test_afpid = db_result(db_query($sql_test, $type_id));
+				db_query($afp_sql, $af_id, $type_id, $description, $test_afpid);
+					
+				//$best_evalue;
+				$type_id = db_result(db_query($sql, 'analysis_blast_besthit_evalue'));
+				$test_afpid = db_result(db_query($sql_test, $type_id));
+				$e_digit = explode("e-", $best_evalue);
+				if (count($e_digit) == 2) {
+					$evalue_shown = number_format($e_digit [0],1);
+					$best_evalue = $evalue_shown."e-".$e_digit[1];
+				} 
+				db_query($afp_sql, $af_id, $type_id, $best_evalue, $test_afpid);
+					
+				//$best_identity;
+				$type_id = db_result(db_query($sql, 'analysis_blast_besthit_identity'));
+				$test_afpid = db_result(db_query($sql_test, $type_id));
+				$percent_identity = number_format($best_identity/$best_len*100, 1);
+				db_query($afp_sql, $af_id, $type_id, $percent_identity, $test_afpid);
+					
+				//$best_len;
+				$type_id = db_result(db_query($sql, 'analysis_blast_besthit_length'));
+				$test_afpid = db_result(db_query($sql_test, $type_id));
+				db_query($afp_sql, $af_id, $type_id, $best_len, $test_afpid);
+				
+			}
+			tripal_db_set_active($previous_db);
+			
+			break;
+		}
+	}
+   print "100%\n";
+	return;
+}

tripal_analysis_blast/tripal_analysis_blast.install

@@ -159,7 +159,19 @@ function tripal_analysis_blast_update_6000(){
  */
 function tripal_analysis_blast_add_cvterms () {
 	
- // Add cvterm 'analysis_blast_output_iteration_hits' for inserting into featureprop table
+   // Add the cvterms for the anlysisprop table
+   tripal_add_cvterms('analysis_blast_settings', 'Settings of a blast analysis, '.
+      'including db_id, output file, and run parameters separated by a bar |');
+   tripal_add_cvterms('analysis_blast_blastdb','The database used for blasting');
+   tripal_add_cvterms('analysis_blast_blastfile','The input file or directory that contains the XML blast output');
+   tripal_add_cvterms('analysis_blast_blastparameters','The parameters used when performing blast.');
+   tripal_add_cvterms('analysis_blast_no_parsed','Indicates if the input file should be parsed to map results to features');
+   tripal_add_cvterms('analysis_blast_query_re','The regular expression for finding the feature name in the query definition line of the blast results');
+   tripal_add_cvterms('analysis_blast_query_type','The feature type (e.g. mRNA, polypeptide) of the query input file. This type is used to identify the query feature when multiple features have the same name');
+   tripal_add_cvterms('analysis_blast_query_uniquename','Indicates if the matched name in the query definition line of the blast results is feature uniquename');
+   tripal_add_cvterms('analysis_blast_blastfile_ext','Indicates the extension of the blast files. This is required if the blastfile setting is a directory.');
+
+   // Add cvterm 'analysis_blast_output_iteration_hits' for inserting into featureprop table
    tripal_add_cvterms('analysis_blast_output_iteration_hits', 'Hits of a blast '.
       'output iteration. Each iteration corresponds to a chado feature, and is '.
       'the content between <iteration> and </iteration> tags in the blast xml '.
@@ -183,7 +195,4 @@ function tripal_analysis_blast_add_cvterms () {
    tripal_add_cvterms('analysis_blast_besthit_length', 'length of the best hit 
    associated with a feature and a blast analysis ');
    
-   // Add cveterm 'analysis_blast_settings' for inserting into analysisprop table   
-   tripal_add_cvterms('analysis_blast_settings', 'Settings of a blast analysis, '.
-      'including db_id, output file, and run parameters separated by a bar |');
-}
+}

tripal_analysis_unigene/tripal_analysis_unigene.module

@@ -132,6 +132,7 @@ function chado_analysis_unigene_insert($node){
    chado_analysis_insert($node);
 
    // add the unigene name as a property of the anslysis
+   tripal_analysis_insert_property($node->analysis->analysis_id,'analysis_type','tripal_analysis_unigene');	
    tripal_analysis_insert_property($node->analysis->analysis_id,'analysis_unigene_name',$node->unigene_name);	
    tripal_analysis_insert_property($node->analysis->analysis_id,'analysis_unigene_num_contigs',$node->num_contigs);	
    tripal_analysis_insert_property($node->analysis->analysis_id,'analysis_unigene_num_reads',$node->num_reads);	
@@ -144,47 +145,11 @@ function chado_analysis_unigene_insert($node){
 function chado_analysis_unigene_update($node){
    chado_analysis_update($node); 
 
-   // check to see if the property exists first if not then insert, if it does then update
-   $unigene_name = tripal_analysis_get_property($node->analysis_id,'analysis_unigene_name');
-   $num_contigs  = tripal_analysis_get_property($node->analysis_id,'analysis_unigene_num_contigs');
-   $num_reads    = tripal_analysis_get_property($node->analysis_id,'analysis_unigene_num_reads');
-   $num_clusters = tripal_analysis_get_property($node->analysis_id,'analysis_unigene_num_clusters');
-   $num_singlets = tripal_analysis_get_property($node->analysis_id,'analysis_unigene_num_singlets');
-
-
-   // update the unigene name as a property of the anslysis, but if for some
-   // reason it's missing then add it (do the same for all properties)
-   if(count($unigene_name)==0){
-      tripal_analysis_insert_property($node->analysis_id,'analysis_unigene_name',$node->unigene_name);	
-   } else {
-      tripal_analysis_update_property($node->analysis_id,'analysis_unigene_name',$node->unigene_name);	
-   }
-
-   if(count($num_contigs)==0){
-      tripal_analysis_insert_property($node->analysis_id,'analysis_unigene_num_contigs',$node->num_contigs);	
-   } else {
-      tripal_analysis_update_property($node->analysis_id,'analysis_unigene_num_contigs',$node->num_contigs);	
-   }
-
-   if(count($num_reads)==0){
-      tripal_analysis_insert_property($node->analysis_id,'analysis_unigene_num_reads',$node->num_reads);	
-   } else {
-      tripal_analysis_update_property($node->analysis_id,'analysis_unigene_num_reads',$node->num_reads);	
-   }
-
-   if(count($num_clusters)==0){
-      tripal_analysis_insert_property($node->analysis_id,'analysis_unigene_num_clusters',$node->num_clusters);	
-   } else {
-      tripal_analysis_update_property($node->analysis_id,'analysis_unigene_num_clusters',$node->num_clusters);	
-   }
-
-   if(count($num_singlets)==0){
-      tripal_analysis_insert_property($node->analysis_id,'analysis_unigene_num_singlets',$node->num_singlets);	
-   } else {
-      tripal_analysis_update_property($node->analysis_id,'analysis_unigene_num_singlets',$node->num_singlets);	
-   }
-
-   
+   tripal_analysis_update_property($node->analysis_id,'analysis_unigene_name',$node->unigene_name,1);
+   tripal_analysis_update_property($node->analysis_id,'analysis_unigene_num_contigs',$node->num_contigs,1);
+   tripal_analysis_update_property($node->analysis_id,'analysis_unigene_num_reads',$node->num_reads,1);
+   tripal_analysis_update_property($node->analysis_id,'analysis_unigene_num_clusters',$node->num_clusters,1);
+   tripal_analysis_update_property($node->analysis_id,'analysis_unigene_num_singlets',$node->num_singlets,1);   
 }
 /**
 *
@@ -222,11 +187,11 @@ function chado_analysis_unigene_load($node){
    $num_clusters = tripal_analysis_get_property($analysis_id,'analysis_unigene_num_clusters');
    $num_singlets = tripal_analysis_get_property($analysis_id,'analysis_unigene_num_singlets');
 
-   $analysis->tripal_analysis_unigene->unigene_name = $unigene_name[0]->value;
-   $analysis->tripal_analysis_unigene->num_contigs = $num_contigs[0]->value;
-   $analysis->tripal_analysis_unigene->num_reads = $num_reads[0]->value;
-   $analysis->tripal_analysis_unigene->num_clusters = $num_clusters[0]->value;
-   $analysis->tripal_analysis_unigene->num_singlets = $num_singlets[0]->value;
+   $analysis->tripal_analysis_unigene->unigene_name = $unigene_name->value;
+   $analysis->tripal_analysis_unigene->num_contigs = $num_contigs->value;
+   $analysis->tripal_analysis_unigene->num_reads = $num_reads->value;
+   $analysis->tripal_analysis_unigene->num_clusters = $num_clusters->value;
+   $analysis->tripal_analysis_unigene->num_singlets = $num_singlets->value;
 
    // add in organism information using the materialized view
    $sql = "SELECT * FROM {organism_unigene_mview} OUM ".
@@ -314,6 +279,7 @@ function tripal_analysis_unigene_theme () {
       ),
    );
 }
+
 /*******************************************************************************
  *  
  */
@@ -670,11 +636,11 @@ function tripal_analysis_unigene_load_organism_unigenes($organism){
       $num_clusters = tripal_analysis_get_property($analysis_id,'analysis_unigene_num_clusters');
       $num_singlets = tripal_analysis_get_property($analysis_id,'analysis_unigene_num_singlets');
       
-      $unigene->unigene_name = $unigene_name[0]->value;
-      $unigene->num_reads = $num_reads[0]->value;
-      $unigene->num_clusters = $num_clusters[0]->value;
-      $unigene->num_contigs = $num_contigs[0]->value;     
-      $unigene->num_singlets = $num_singlets[0]->value;
+      $unigene->unigene_name = $unigene_name->value;
+      $unigene->num_reads = $num_reads->value;
+      $unigene->num_clusters = $num_clusters->value;
+      $unigene->num_contigs = $num_contigs->value;     
+      $unigene->num_singlets = $num_singlets->value;
 
       $unigenes[$i++] = $unigene;
    }

tripal_core/jobs.php

@@ -6,8 +6,7 @@
 * @ingroup tripal_core
 * @ingroup tripal_api
 */
-function tripal_add_job ($job_name,$modulename,$callback,$arguments,$uid,
-   $priority = 10){
+function tripal_add_job ($job_name,$modulename,$callback,$arguments,$uid,$priority = 10){
 
    # convert the arguments into a string for storage in the database
    $args = implode("::",$arguments);
@@ -23,9 +22,12 @@ function tripal_add_job ($job_name,$modulename,$callback,$arguments,$uid,
    if($args){
       $record->arguments = $args;
    }
-   drupal_write_record('tripal_jobs',$record);
-   $jobs_url = url("admin/tripal/tripal_jobs");
-   drupal_set_message(t("Job '$job_name' submitted.  Check the <a href='$jobs_url'>jobs page</a> for status"));
+   if(drupal_write_record('tripal_jobs',$record)){
+      $jobs_url = url("admin/tripal/tripal_jobs");
+      drupal_set_message(t("Job '$job_name' submitted.  Check the <a href='$jobs_url'>jobs page</a> for status"));
+   } else {
+      drupal_set_message("Failed to add job $job_name.");
+   }
 
    return 1;
 }

tripal_core/tripal_core.api.inc

@@ -219,6 +219,58 @@ function tripal_core_chado_insert($table,$values){
    return false;
 }
 /**
+*
+*/
+function tripal_core_chado_delete($table,$match){
+   $delete_matches = array();  // contains the values for the where clause
+   
+   // get the table description
+   $table_desc = module_invoke_all('chado_'.$table.'_schema');
+
+   // get the values needed for matching in the SQL statement
+   foreach ($match as $field => $value){
+      if(is_array($value)){
+         $results = tripal_core_chado_get_foreign_key($table_desc,$field,$value);
+         if (sizeof($results) > 1) {
+           watchdog('tripal_core', 'tripal_core_chado_delete: When trying to find record to delete, too many records match the criteria supplied for !foreign_key foreign key constraint (!criteria)', array('!foreign_key' => $field, '!criteria' => print_r($value,TRUE)), WATCHDOG_ERROR);         
+         } elseif (sizeof($results) < 1) {
+           watchdog('tripal_core', 'tripal_core_chado_delete: When trying to find record to delete, no record matches criteria supplied for !foreign_key foreign key constraint (!criteria)', array('!foreign_key' => $field, '!criteria' => print_r($value,TRUE)), WATCHDOG_ERROR);
+         } else {
+           $delete_matches[$field] = $results[0];
+         }
+      }
+      else {
+         $delete_matches[$field] = $value;
+      }
+   }
+   // now build the SQL statement
+   $sql = "DELETE FROM {$table} WHERE ";
+   $dargs = array();
+   foreach($delete_matches as $field => $value){
+      if(strcmp($fields[$field]['type'],'serial')==0 or 
+         strcmp($fields[$field]['type'],'int')==0){
+         $sql .= " $field = %d AND ";
+      } else {
+         $sql .= " $field = '%s' AND ";
+      }
+      array_push($dargs,$value);
+   }
+   $sql = substr($sql,0,-4);  // get rid of the trailing 'AND'
+   
+   // finally perform the delete.  If successful, return the updated record
+   $previous_db = tripal_db_set_active('chado');  // use chado database
+   $result = db_query($sql,$dargs);
+   tripal_db_set_active($previous_db);  // now use drupal database 
+   if($result){
+      return true;
+   } 
+   else {
+      watchdog('tripal_core',"Cannot delete record in $table table.  Match:" . print_r($match,1) . ". Values: ". print_r($values,1),array(),'WATCHDOG_ERROR');
+      return false;
+   }
+   return false;
+}
+/**
 * Provides a generic routine for updating into any Chado table
 *
 * Use this function to update a record in any Chado table.  The first
@@ -1107,4 +1159,4 @@ function tripal_core_exclude_type_by_default() {
  */
 function tripal_core_exclude_field_from_feature_by_default() {
   return array();
-}
+}

tripal_core/tripal_core_job_view.tpl.php

@@ -2,6 +2,7 @@
 $job = $variables['job'];
 
 $cancel_link = '';
+$return_link = url("admin/tripal/tripal_jobs/");
 if($job->start_time == 0 and $job->end_time == 0){
    $cancel_link = url("admin/tripal/tripal_jobs/cancel/".$job->job_id);
 }
@@ -12,7 +13,7 @@ $rerun_link = url("admin/tripal/tripal_jobs/rerun/".$job->job_id);
 <div id="tripal_core-job_view-box" class="tripal_core-info-box tripal-info-box">
   <div class="tripal_core-info-box-title tripal-info-box-title">Details for Job <?php print $job->job_id?></div>
   <div class="tripal_core-info-box-desc tripal-info-box-desc"></div>
-   <a href="<?php print url("admin/tripal/tripal_jobs/") ?>">Return to jobs list</a> | 
+   <a href="<?php print $return_link?>">Return to jobs list</a> | 
    <a href="<?php print $rerun_link?>">Re-run this job</a> | 
    <a href="<?php print $cancel_link?>">Cancel this Job</a><br>
    <table id="tripal_core-job_view-table" class="tripal_core-table tripal-table tripal-table-vert">

tripal_feature/gff_loader.php

@@ -746,7 +746,7 @@ function tripal_core_load_gff3_feature($organism,$analysis_id,$cvterm,$uniquenam
 
    // add the analysisfeature entry to the analysisfeature table if it doesn't already exist
    $af_values = array('analysis_id' => $analysis_id, 'feature_id' => $feature->feature_id);
-   if(tripal_core_chado_select('analysisfeature',array('analysisfeature_id'),$af_values,true)){
+   if(tripal_core_chado_select('analysisfeature',array('analysisfeature_id'),$af_values,array('has_record'))){
       if(!tripal_core_chado_insert('analysisfeature',$af_values)){
          print "ERROR: could not add analysisfeature record: $analysis_id, $feature->feature_id\n";
       } else {

tripal_feature/tripal_feature.module

@@ -2242,8 +2242,8 @@ function tripal_feature_job_describe_args($callback,$args){
 
       // add in the relationship arguments
       $new_args['Relationship Type'] = $args[8];
-      $new_args['Relationship Subject RE'] = $args[9];
-      $new_args['Relationship Parent RE'] = $args[10];
+      $new_args['Relationship Parent RE'] = $args[9];
+      $new_args['Relationship Parent Type'] = $args[10];
 
       // add in the database reference arguments
       $db = tripal_core_chado_select('db',array('name'),array('db_id' => $args[7]));