Issue #72: Updating API to include 2.1 improvements: fb0379a

legacy/tripal_feature/tripal_feature.module

@@ -317,31 +317,38 @@ function tripal_feature_job_describe_args($callback, $args) {
   $new_args = array();
   if ($callback == 'tripal_feature_load_fasta') {
     $new_args['FASTA file'] = $args[0];
-    $organism = chado_select_record('organism', array('genus', 'species'), array('organism_id' => $args[1]));
-    $new_args['Organism'] = $organism[0]->genus . " " . $organism[0]->species;
-    $new_args['Sequence Type'] = $args[2];
-    $new_args['Name Match Type'] = $args[14];
-    $new_args['Name RE'] = $args[4];
-    $new_args['Unique Name RE'] = $args[5];
 
+    // Add in the organism.
+    if ($args[1] AND is_numeric($args[1])) {
+      $organism = chado_select_record('organism', array('genus', 'species'), array('organism_id' => $args[1]));
+      $new_args['Organism'] = $organism[0]->genus . " " . $organism[0]->species;
+    }
+    $new_args['Sequence Type'] = $args[2];
+    if (isset($args[14])) {
+      $new_args['Name Match Type'] = $args[14];
+      $new_args['Name RE'] = $args[4];
+      $new_args['Unique Name RE'] = $args[5];
+    }
     // add in the relationship arguments
-    $new_args['Relationship Type'] = $args[8];
-    $new_args['Relationship Parent RE'] = $args[9];
-    $new_args['Relationship Parent Type'] = $args[10];
+    if ($args[8]) {
+      $new_args['Relationship Type'] = $args[8];
+      $new_args['Relationship Parent RE'] = $args[9];
+      $new_args['Relationship Parent Type'] = $args[10];
+    }
 
     // add in the database reference arguments
-    if ($args[7]) {
+    if ($args[7] AND is_numeric($args[7])) {
       $db = chado_select_record('db', array('name'), array('db_id' => $args[7]));
+      $new_args['Database Reference'] = $db[0]->name;
+      $new_args['Accession RE'] = $args[6];
+      $new_args['Method'] = $args[11];
     }
-    $new_args['Database Reference'] = $db[0]->name;
-    $new_args['Accession RE'] = $args[6];
-    $new_args['Method'] = $args[11];
 
     // add in the analysis
-    if ($args[13]) {
-      $analysis = chado_select_record('analysis', array('name'), array('analysis_id' => $args[13]));
+    if ($args[12] AND is_numeric($args[12])) {
+      $analysis = chado_select_record('analysis', array('name'), array('analysis_id' => $args[12]));
+      $new_args['Analysis'] = $analysis[0]->name;
     }
-    $new_args['Analysis'] = $analysis[0]->name;
   }
   if ($callback == 'tripal_feature_delete_features') {
     if ($args[0]) {