From e401af2552c542a44f2eaf8352933ee9f8973adb Mon Sep 17 00:00:00 2001
From: Alex Skrenchuk <alexskr@stanford.edu>
Date: Wed, 22 Apr 2026 23:04:56 -0700
Subject: [PATCH] Fix nil @submission in OntologyProcessor when metadata
 extraction bails

SubmissionMetadataExtractor#extract_metadata used a bare `return` when the
submission failed validation, returning nil. OntologyProcessor assigned that
nil back over its own @submission, so the ensure-block call to
notify_submission_processed raised NoMethodError on nil.archived? -- which
its inner rescue logged as the misleading
"Email sending failed: undefined method `archived?' for nil:NilClass".

- submission_extract_metadata.rb: return @submission on the invalid path so
  the method has a consistent return value.
- submission_processor.rb: stop reassigning @submission from the
  extract_metadata return value; the extractor mutates the shared instance
  in place via @submission.save.
- submission_processor.rb: guard notify_submission_processed against a nil
  @submission so a missing submission can't surface as the misleading
  "Email sending failed" log line.
- Add regression test reproducing the full path.
---
 .../operations/submission_extract_metadata.rb |  2 +-
 .../submission_processor.rb                   |  4 +-
 test/services/test_submission_processor.rb    | 56 +++++++++++++++++++
 3 files changed, 60 insertions(+), 2 deletions(-)
 create mode 100644 test/services/test_submission_processor.rb

diff --git a/lib/ontologies_linked_data/services/submission_process/operations/submission_extract_metadata.rb b/lib/ontologies_linked_data/services/submission_process/operations/submission_extract_metadata.rb
index c7c57590..a029db5d 100644
--- a/lib/ontologies_linked_data/services/submission_process/operations/submission_extract_metadata.rb
+++ b/lib/ontologies_linked_data/services/submission_process/operations/submission_extract_metadata.rb
@@ -14,7 +14,7 @@ def extract_metadata(logger = nil, user_params, heavy_extraction: true)
 
         unless @submission.valid?
           logger.error("Cannot extract metadata from #{@submission.id} because the submission is invalid")
-          return
+          return @submission
         end
 
         ontology_iri = extract_ontology_iri
diff --git a/lib/ontologies_linked_data/services/submission_process/submission_processor.rb b/lib/ontologies_linked_data/services/submission_process/submission_processor.rb
index 1045aada..9edeb698 100644
--- a/lib/ontologies_linked_data/services/submission_process/submission_processor.rb
+++ b/lib/ontologies_linked_data/services/submission_process/submission_processor.rb
@@ -38,7 +38,7 @@ def process_submission(logger, options = {})
 
             parsed = @submission.ready?(status: %i[rdf])
 
-            @submission = @submission.extract_metadata(logger, user_params: options[:params], heavy_extraction: extract_metadata?(options))
+            @submission.extract_metadata(logger, user_params: options[:params], heavy_extraction: extract_metadata?(options))
 
             @submission.generate_missing_labels(logger) if generate_missing_labels?(options)
 
@@ -70,6 +70,8 @@ def process_submission(logger, options = {})
       end
 
       def notify_submission_processed(logger)
+        return if @submission.nil?
+
         LinkedData::Utils::Notifications.submission_processed(@submission) unless @submission.archived?
       rescue StandardError => e
         logger.error("Email sending failed: #{e.message}\n#{e.backtrace.join("\n\t")}"); logger.flush
diff --git a/test/services/test_submission_processor.rb b/test/services/test_submission_processor.rb
new file mode 100644
index 00000000..5a013aa5
--- /dev/null
+++ b/test/services/test_submission_processor.rb
@@ -0,0 +1,56 @@
+require_relative '../test_case'
+
+require 'logger'
+require 'mocha/minitest'
+require 'stringio'
+
+class TestSubmissionProcessor < LinkedData::TestCase
+
+  def self.before_suite
+    LinkedData::TestCase.backend_4s_delete
+    _count, _acronyms, onts = LinkedData::SampleData::Ontology.create_ontologies_and_submissions(
+      ont_count: 1, submission_count: 1, acronym: 'PROCTEST', process_submission: false
+    )
+    @@ont = onts.first
+  end
+
+  def self.after_suite
+    @@ont&.delete
+    LinkedData::TestCase.backend_4s_delete
+  end
+
+  # Regression test for:
+  #   "Email sending failed: undefined method `archived?' for nil:NilClass"
+  #
+  # When SubmissionMetadataExtractor#extract_metadata hit the `unless @submission.valid?`
+  # branch it used a bare `return` (returns nil). OntologyProcessor#process_submission
+  # reassigned @submission to that nil, and the ensure-block call to
+  # notify_submission_processed then raised NoMethodError on nil.archived?, which its
+  # inner rescue logged as the misleading "Email sending failed" line above.
+  def test_processor_survives_extract_metadata_returning_nil
+    log_io = StringIO.new
+    logger = Logger.new(log_io)
+
+    submission = @@ont.latest_submission(status: :any)
+    submission.bring_remaining
+
+    # Simulate the pre-fix extractor behavior on an invalid submission.
+    submission.stubs(:extract_metadata).returns(nil)
+
+    # Disable every other step so the test isolates the extract_metadata → notify path.
+    options = {
+      process_rdf: false, generate_missing_labels: false, generate_obsolete_classes: false,
+      index_search: false, index_properties: false, index_all_data: false,
+      run_metrics: false, diff: false, archive: false
+    }
+
+    begin
+      submission.process_submission(logger, options)
+    rescue NoMethodError => e
+      flunk "processor raised NoMethodError because @submission was overwritten with nil: #{e.message}"
+    end
+
+    refute_match(/Email sending failed/, log_io.string,
+                 'notify_submission_processed logged a misleading "Email sending failed" on a nil submission')
+  end
+end