add aureme and orthology stuff

templates/tripal_aureme_links.tpl.php

+<?php
+$feature = $variables['node']->feature;
+
+if ($feature->type_id->name == 'polypeptide') {
+    foreach ($feature->feature_relationship->subject_id as $rel) {
+        if ($rel->object_id->type_id->name == 'mRNA') {
+            $mrna_feat = chado_expand_var($rel->object_id, 'table', 'feature_relationship');
+
+            if (count($mrna_feat->feature_relationship->subject_id) == 0) {
+                // In some cases we might only have mRNA with no genes (brassica napus or transcriptomes
+                $target_id = $mrna_feat->uniquename;
+                echo '<a href="' . getenv('ENABLE_AUREME_LINKS') . $target_id . '">View data from metabolic model for ' . $feature->uniquename . '</a>';
+                break;
+            }
+            foreach ($mrna_feat->feature_relationship->subject_id as $rel_g) {
+                if ($rel_g->type_id->name == 'gene') {
+                    $target_id = $rel_g->uniquename;
+                    echo '<a href="' . getenv('ENABLE_AUREME_LINKS') . $target_id . '">View data from metabolic model for ' . $feature->uniquename . '</a>';
+                    break;
+                }
+            }
+        }
+    }
+}
+else if ($feature->type_id->name == 'mRNA') {
+    if (count($feature->feature_relationship->subject_id) == 0) {
+        // In some cases we might only have mRNA with no genes (brassica napus or transcriptomes
+        $target_id = $feature->uniquename;
+        echo '<a href="' . getenv('ENABLE_AUREME_LINKS') . $target_id . '">View data from metabolic model for ' . $feature->uniquename . '</a>';
+    }
+    foreach ($feature->feature_relationship->subject_id as $rel) {
+        if ($rel->object_id->type_id->name == 'gene') {
+            $target_id = $rel->object_id->uniquename;
+            echo '<a href="' . getenv('ENABLE_AUREME_LINKS') . $target_id . '">View data from metabolic model for ' . $feature->uniquename . '</a>';
+            break;
+        }
+    }
+}
+else if ($feature->type_id->name == 'gene') {
+    echo '<a href="' . getenv('ENABLE_AUREME_LINKS') . $feature->uniquename . '">View data from metabolic model for ' . $feature->uniquename . '</a>';
+}

templates/tripal_orthology_links.tpl.php

+<?php
+$feature = $variables['node']->feature;
+
+if ($feature->type_id->name == 'polypeptide') {
+    $target_id = $feature->uniquename;
+    echo '<a href="' . getenv('ENABLE_ORTHOLOGY_LINKS') . 'chado_gene_phylotree?gene_name=' . $target_id . '">View orthology data for ' . $feature->uniquename . '</a>';
+}
+else if ($feature->type_id->name == 'mRNA') {
+    foreach ($feature->feature_relationship->object_id as $rel) {
+        if ($rel->subject_id->type_id->name == 'polypeptide') {
+            $target_id = $rel->subject_id->uniquename;
+            echo '<a href="' . getenv('ENABLE_ORTHOLOGY_LINKS') . 'chado_gene_phylotree?gene_name=' . $target_id . '">View orthology data for ' . $feature->uniquename . '</a>';
+            break;
+        }
+    }
+}
+else if ($feature->type_id->name == 'gene') {
+    foreach ($feature->feature_relationship->object_id as $rel) {
+        if ($rel->subject_id->type_id->name == 'mRNA') {
+            $mrna_feat = chado_expand_var($rel->subject_id, 'table', 'feature_relationship');
+            foreach ($mrna_feat->feature_relationship->object_id as $rel_g) {
+                if ($rel_g->subject_id->type_id->name == 'polypeptide') {
+                    $target_id = $rel_g->subject_id->uniquename;
+                    echo '<p><a href="' . getenv('ENABLE_ORTHOLOGY_LINKS') . 'chado_gene_phylotree?gene_name=' . $target_id . '">View orthology data for ' . $rel_g->subject_id->uniquename . '</a></p>';
+                    break;
+                }
+            }
+        }
+    }
+}