adding the test for the id being a reference and handling appropriately

tripal_chado/includes/TripalImporter/OBOImporter.inc

@@ -409,18 +409,18 @@ class OBOImporter extends TripalImporter {
 
     // Update the cv_root_mview materiailzed view.
     $this->logMessage("Updating the cv_root_mview materialized view...");
-    $mview_id = chado_get_mview_id('cv_root_mview');
-    chado_populate_mview($mview_id);
+    $mview_id = tripal_get_mview_id('cv_root_mview');
+    tripal_populate_mview($mview_id);
 
     $this->logMessage("Updating the db2cv_mview materialized view...");
-    $mview_id = chado_get_mview_id('db2cv_mview');
-    chado_populate_mview($mview_id);
+    $mview_id = tripal_get_mview_id('db2cv_mview');
+    tripal_populate_mview($mview_id);
 
     // Upate the cvtermpath table for each newly added CV.
     $this->logMessage("Updating cvtermpath table.  This may take a while...");
     foreach ($this->newcvs as $namespace => $cvid) {
       $this->logMessage("- Loading paths for @vocab", array('@vocab' => $namespace));
-      chado_update_cvtermpath($cvid);
+      tripal_update_cvtermpath($cvid);
     }
   }
   /**
@@ -486,7 +486,7 @@ class OBOImporter extends TripalImporter {
    */
   private function loadOBO_v1_2_file($obo_name, $file, $is_new = TRUE) {
     if ($is_new) {
-      chado_insert_obo($obo_name, $file);
+      tripal_insert_obo($obo_name, $file);
     }
 
     $success = $this->loadOBO_v1_2($file, $obo_name);
@@ -528,7 +528,7 @@ class OBOImporter extends TripalImporter {
     fclose($obo_fh);
 
     if ($is_new) {
-      chado_insert_obo($obo_name, $url);
+      tripal_insert_obo($obo_name, $url);
     }
 
     // second, parse the OBO
@@ -568,7 +568,7 @@ class OBOImporter extends TripalImporter {
     // present for each stanza.  Some ontologies have adopted the v1.4 method
     // in their v1.2 files and not including it.
     if (array_key_exists('default-namespace', $header)) {
-      $defaultcv = chado_insert_cv($header['default-namespace'][0], '');
+      $defaultcv = tripal_insert_cv($header['default-namespace'][0], '');
       if (!$defaultcv) {
         throw new Exception('Cannot add namespace ' . $header['default-namespace'][0]);
       }
@@ -607,7 +607,7 @@ class OBOImporter extends TripalImporter {
         else {
           $results = $short_name;
         }
-        $defaultcv = chado_insert_cv(strtoupper($results), '');
+        $defaultcv = tripal_insert_cv(strtoupper($results), '');
         $this->newcvs[$defaultcv->name] = $defaultcv->cv_id;
       }
       catch (Exception $e) {
@@ -759,6 +759,42 @@ class OBOImporter extends TripalImporter {
       $t['is_obsolete'] = $term['is_obsolete'][0];
     }
 
+    // Check the id isn't a reference to another term.
+    if (strpos($t['id'], ':')) {
+      $pair = explode(":", $t['id']);
+      $ontology_id = $pair[0];
+      $accession_num = $pair[1];
+      if (is_numeric($accession_num)) {
+        $results = $this->oboEbiLookup($t['id'], 'query');
+        if (!empty($results)) {
+          if (array_key_exists('docs', $results)) {
+            if (!empty($results['docs'])) {
+              $t['id'] = $results['docs']['label'];
+            } else {
+              // The first search doesn't work, so let's try a broader one.
+              $results = $this->oboEbiLookup($t['id'], 'query-non-local');
+              if (!empty($results)) {
+                if (array_key_exists('docs', $results)) {
+                  if (!empty($results['docs'])) {
+                    $accession = $t['id'];
+                    $accession_underscore = str_replace(":", "_", $accession);
+                    foreach ($results['docs'] as $item) {
+                      if ($item['label'] != $accession && $item['label'] != $accession_underscore) {
+                        //Found the first place a label is other than the accession is used, so take
+                        // that info and then end the loop.
+                        $t['id'] = $item['label'];
+                        break;
+                      }
+                    }
+                  }
+                }
+              }
+            }
+          }
+        }
+      }
+    } 
+
     // Check that the default_cv is in the cv table.
     $sql =  "
       SELECT CV.name 
@@ -776,7 +812,7 @@ class OBOImporter extends TripalImporter {
         elseif (array_key_exists('namespace', $ontology_info['config'])) {
           $results = $ontology_info['config']['namespace'];
         }
-        $cv_returned = chado_insert_cv($results[0], '');
+        $cv_returned = tripal_insert_cv($results[0], '');
         // If name && definition are both empty then look up the term from the ontology you just loaded.
         if($cv_returned) {
           $defaultcv = $cv_returned;
@@ -790,7 +826,7 @@ class OBOImporter extends TripalImporter {
     $t['db_name'] = $default_db;
 
     // add the cvterm
-    $cvterm = chado_insert_cvterm($t, array('update_existing' => TRUE));
+    $cvterm = tripal_insert_cvterm($t, array('update_existing' => TRUE));
     if (!$cvterm) {
       throw new Exception("Cannot add the term " . $term['id'][0]);
     }
@@ -1001,7 +1037,7 @@ class OBOImporter extends TripalImporter {
       'is_relationship' => TRUE,
       'db_name' => $default_db
     );
-    $relcvterm = chado_insert_cvterm($term, array('update_existing' => FALSE));
+    $relcvterm = tripal_insert_cvterm($term, array('update_existing' => FALSE));
 
     if (!$relcvterm) {
       // If the relationship term couldn't be found in the default_db provided
@@ -1015,7 +1051,7 @@ class OBOImporter extends TripalImporter {
         'is_relationship' => TRUE,
         'db_name' => 'OBO_REL'
       );
-      $relcvterm = chado_insert_cvterm($term, array('update_existing' => FALSE));
+      $relcvterm = tripal_insert_cvterm($term, array('update_existing' => FALSE));
       if (!$relcvterm) {
         throw new Exception("Cannot find the relationship term in the current ontology or in the relationship ontology: $rel\n");
       }
@@ -1047,7 +1083,7 @@ class OBOImporter extends TripalImporter {
     $objterm['is_relationship'] = $object_is_relationship;
     $objterm['db_name'] = $default_db;
 
-    $objcvterm = chado_insert_cvterm($objterm, array('update_existing' => TRUE));
+    $objcvterm = tripal_insert_cvterm($objterm, array('update_existing' => TRUE));
     if (!$objcvterm) {
       throw new Exception("Cannot add cvterm " . $oterm['name'][0]);
     }
@@ -1100,7 +1136,7 @@ class OBOImporter extends TripalImporter {
   private function addSynonym($term, $cvterm) {
 
     // make sure we have a 'synonym_type' vocabulary
-    $syncv = chado_insert_cv(
+    $syncv = tripal_insert_cv(
         'synonym_type',
         'A local vocabulary added for synonym types.'
     );
@@ -1124,7 +1160,7 @@ class OBOImporter extends TripalImporter {
             'name' => 'synonym_type',
           ),
         );
-        $syntype = chado_get_cvterm($values);
+        $syntype = tripal_get_cvterm($values);
 
         // if it doesn't exist then add it
         if (!$syntype) {
@@ -1137,7 +1173,7 @@ class OBOImporter extends TripalImporter {
             'cv_name' => $syncv->name,
             'is_relationship' => FALSE
           );
-          $syntype = chado_insert_cvterm($term, array('update_existing' => TRUE));
+          $syntype = tripal_insert_cvterm($term, array('update_existing' => TRUE));
           if (!$syntype) {
             throw new Exception("Cannot add synonym type: internal:$scope");
           }
@@ -1324,7 +1360,7 @@ class OBOImporter extends TripalImporter {
     }
 
     // add the database
-    $db = chado_insert_db(array('name' => $dbname));
+    $db = tripal_insert_db(array('name' => $dbname));
     if (!$db) {
       throw new Exception("Cannot find database '$dbname' in Chado.");
     }
@@ -1369,7 +1405,7 @@ class OBOImporter extends TripalImporter {
   private function addCvtermProp($cvterm, $property, $value, $rank) {
 
     // make sure the 'cvterm_property_type' CV exists
-    $cv = chado_insert_cv('cvterm_property_type', '');
+    $cv = tripal_insert_cv('cvterm_property_type', '');
     if (!$cv) {
       throw new Exception("Cannot add/find cvterm_property_type cvterm");
     }
@@ -1389,7 +1425,7 @@ class OBOImporter extends TripalImporter {
         'cv_name' => $cv->name,
         'is_relationship' => FALSE,
       );
-      $cvproptype = chado_insert_cvterm($term, array('update_existing' => FALSE));
+      $cvproptype = tripal_insert_cvterm($term, array('update_existing' => FALSE));
       if (!$cvproptype) {
         throw new Exception("Cannot add cvterm property: internal:$property");
       }