Merge pull request #1559 from tripal/tv4g4-issue1557-obo-importer-php8

Tripal 4 php8 warning fix in OBO loader
tripal · Jul 6, 2023 · 1a23b43 · 1a23b43
2 parents 4cb1dbc + e01b302
commit 1a23b43
Showing 1 changed file with 14 additions and 4 deletions.
diff --git a/tripal_chado/src/Plugin/TripalImporter/OBOImporter.php b/tripal_chado/src/Plugin/TripalImporter/OBOImporter.php
@@ -2370,8 +2370,13 @@ private function parse($obo_file, &$header) {
               $stanza['namespace'][0] = 'EDAM';
             }
             $namespace = $stanza['namespace'][0];
-            $cv = $this->all_cvs[$namespace];
-            $this->obo_namespaces[$namespace] = $cv->cv_id;
+            if (array_key_exists($namespace, $this->all_cvs)) {
+              $cv = $this->all_cvs[$namespace];
+              $this->obo_namespaces[$namespace] = $cv->cv_id;
+            }
+            else {
+              $this->obo_namespaces[$namespace] = NULL;
+            }
           }
 
           // Before caching this stanza, check the term's name to
@@ -2430,8 +2435,13 @@ private function parse($obo_file, &$header) {
       // If this term has a namespace then we want to keep track of it.
       if (array_key_exists('namespace', $stanza)) {
         $namespace = $stanza['namespace'][0];
-        $cv = $this->all_cvs[$namespace];
-        $this->obo_namespaces[$namespace] = $cv->cv_id;
+        if (array_key_exists($namespace, $this->all_cvs)) {
+          $cv = $this->all_cvs[$namespace];
+          $this->obo_namespaces[$namespace] = $cv->cv_id;
+        }
+        else {
+          $this->obo_namespaces[$namespace] = NULL;
+        }
       }
       $this->cacheTermStanza($stanza, $type);
       $this->setItemsHandled($num_read);