update tests

src/jp2_remediator/main.py

@@ -50,7 +50,7 @@ def main():
         "--output-bucket", help="Name of the AWS S3 bucket to upload the modified file (optional)", required=True
     )
     s3_file_parser.add_argument(
-        "--output-key", help="Full key (path) for the uploaded file (overrides output-prefix)"
+        "--output-key", help="Full key (path) for the uploaded file"
     )
     s3_file_parser.set_defaults(
         func=lambda args: processor.process_s3_file(

src/jp2_remediator/tests/unit/test_box_reader.py

@@ -382,35 +382,52 @@ def test_process_trc_tag_size_mismatch(self):
             curv_trc_field_length}). Modifying the size..."""
         self.reader.logger.warning.assert_any_call(expected_warning)
 
-        # Test for process_trc_tag: when curv_trc_gamma_n != 1, in this case is 2
-        def test_process_trc_tag_sets_skip_remediation(self):
-            """
-            Ensure that if curv_trc_gamma_n != 1, skip_remediation is set to True.
-            """
-            # Prepare minimal file_contents with a single TRC tag
-            self.reader.file_contents = bytearray(
-                b"\x00" * 50 +
-                b"\x72\x54\x52\x43" +        # 'rTRC'
-                b"\x00\x00\x00\x64" +        # Some offset (100) in big-endian
-                b"\x00\x00\x00\x20" +        # Tag size (32) in big-endian
-                b"\x00" * 200                # Just extra space
-            )
+    # Test for process_trc_tag: when curv_trc_gamma_n != 1, in this case is 2
+    def test_process_trc_tag_sets_skip_remediation(self):
+        """
+        Ensure that if curv_trc_gamma_n != 1, skip_remediation is set to True.
+        """
+        # Prepare minimal file_contents with a single TRC tag
+        self.reader.file_contents = bytearray(
+            b"\x00" * 50 +
+            b"\x72\x54\x52\x43" +        # 'rTRC'
+            b"\x00\x00\x00\x64" +        # Some offset (100) in big-endian
+            b"\x00\x00\x00\x20" +        # Tag size (32) in big-endian
+            b"\x00" * 200                # Just extra space
+        )
+
+        # Force a header_offset_position that points to 'curv' data
+        header_offset_position = 50
 
-            # Force a header_offset_position that points to 'curv' data
-            header_offset_position = 50
+        # Insert a 'curv' signature + reserved + gamma_n != 1 at position (100 + header_offset_position)
+        curv_trc_position = 100 + header_offset_position
+        curv_data = b"curv" + (0).to_bytes(4, 'big') + (2).to_bytes(4, 'big')  # gamma_n = 2
+        self.reader.file_contents[curv_trc_position:curv_trc_position + 12] = curv_data
 
-            # Insert a 'curv' signature + reserved + gamma_n != 1 at position (100 + header_offset_position)
-            curv_trc_position = 100 + header_offset_position
-            curv_data = b"curv" + (0).to_bytes(4, 'big') + (2).to_bytes(4, 'big')  # gamma_n = 2
-            self.reader.file_contents[curv_trc_position:curv_trc_position + 12] = curv_data
+        new_contents = bytearray(self.reader.file_contents)
 
-            new_contents = bytearray(self.reader.file_contents)
+        # Call the method
+        self.reader.process_trc_tag(b"\x72\x54\x52\x43", "rTRC", new_contents, header_offset_position)
 
-            # Call the method
-            self.reader.process_trc_tag(b"\x72\x54\x52\x43", "rTRC", new_contents, header_offset_position)
+        # Assert skip_remediation is now True
+        self.assertTrue(self.reader.skip_remediation, "Expected skip_remediation to be True when gamma_n != 1.")
 
-            # Assert skip_remediation is now True
-            self.assertTrue(self.reader.skip_remediation, "Expected skip_remediation to be True when gamma_n != 1.")
+    def test_read_jp2_file_skip_remediation(self):
+        """
+        Ensure coverage for lines that handle skip_remediation in read_jp2_file().
+        """
+        self.reader.file_contents = b"SomeJP2Content"
+        self.reader.skip_remediation = True  # Force skipping
+
+        with patch.object(self.reader, 'write_modified_file') as mock_write:
+            self.reader.read_jp2_file()
+            # Because skip_remediation is True, we do not call write_modified_file
+            mock_write.assert_not_called()
+
+        # Check the log was called with that specific skip message
+        self.reader.logger.info.assert_any_call(
+            "Skipping 'write_modified_file' because gamma_n != 1 for at least one TRC channel."
+        )
 
 
 if __name__ == "__main__":

src/jp2_remediator/tests/unit/test_processor.py

@@ -110,7 +110,7 @@ def test_process_s3_file_file_does_not_exist(
         mock_s3_client.download_file.return_value = None
 
         mock_reader = MagicMock()
-        mock_reader.skip_remediation = False
+        mock_reader.skip_remediation = False  # Mock that skip_remediation is False, not testing this here
         mock_box_reader_factory.get_reader.return_value = mock_reader
 
         processor.process_s3_file(input_bucket, input_key, output_bucket, output_key=output_key)
@@ -120,3 +120,108 @@ def test_process_s3_file_file_does_not_exist(
         all_logger_msgs = [call.args[0] for call in processor.logger.info.mock_calls]
         assert any("not created" in msg for msg in all_logger_msgs), \
             "Expected 'not created' log message not found."
+
+    @patch("jp2_remediator.processor.os.path.exists", return_value=True)
+    @patch("jp2_remediator.processor.boto3.client", autospec=True)
+    def test_process_s3_file_no_output_key(
+        self, mock_boto3_client, mock_os_path_exists, processor, mock_box_reader_factory
+    ):
+        """
+        Test coverage for the branch where output_key is NOT provided.
+        """
+        mock_s3_client = MagicMock()
+        mock_boto3_client.return_value = mock_s3_client
+
+        input_bucket = "test-bucket"
+        input_key = "test-folder/no_output_key.jp2"
+        output_bucket = "output-bucket"
+
+        # Simulate everything existing
+        mock_s3_client.download_file.return_value = None
+        mock_s3_client.upload_file.return_value = None
+
+        # Provide a BoxReader whose skip_remediation remains False
+        mock_reader = MagicMock()
+        mock_reader.skip_remediation = False
+        mock_box_reader_factory.get_reader.return_value = mock_reader
+
+        # Call process_s3_file WITHOUT passing output_key
+        processor.process_s3_file(input_bucket, input_key, output_bucket)
+
+        # Now check that the method generated an output_key internally AND uploaded
+        mock_s3_client.upload_file.assert_called_once()
+
+        # Also check that we see the upload log
+        all_logger_msgs = [call.args[0] for call in processor.logger.info.mock_calls]
+        assert any("Uploading modified file to bucket: output-bucket, key:" in msg 
+                   for msg in all_logger_msgs), "Expected log about uploading file."
+
+    @patch("jp2_remediator.processor.boto3.client", autospec=True)
+    def test_process_s3_file_skip_remediation(
+        self, mock_boto3_client, processor, mock_box_reader_factory
+    ):
+        """
+        Covers lines where skip_remediation is True -> log + return (no upload).
+        """
+        mock_s3_client = MagicMock()
+        mock_boto3_client.return_value = mock_s3_client
+
+        input_bucket = "test-bucket"
+        input_key = "test-folder/skip_rem.jp2"
+        output_bucket = "output-bucket"
+
+        # Ensure the downloaded file "exists", so we skip for skip_remediation, not missing file
+        with patch("jp2_remediator.processor.os.path.exists", return_value=True):
+            mock_s3_client.download_file.return_value = None
+
+            # This time skip_remediation is True
+            mock_reader = MagicMock()
+            mock_reader.skip_remediation = True
+            mock_box_reader_factory.get_reader.return_value = mock_reader
+
+            processor.process_s3_file(input_bucket, input_key, output_bucket, output_key="some-output-file.jp2")
+
+        # Because skip_remediation is True, we never call upload_file
+        mock_s3_client.upload_file.assert_not_called()
+
+        # Also confirm we logged the skip message
+        all_logger_msgs = [call.args[0] for call in processor.logger.info.mock_calls]
+        assert any("Skipping upload for /tmp/skip_rem.jp2 because curv_trc_gamma_n" in msg
+                   for msg in all_logger_msgs), "Expected skip_remediation log message."
+
+    @patch("jp2_remediator.processor.os.path.exists", return_value=True)
+    @patch("jp2_remediator.processor.os.remove", autospec=True)
+    @patch("jp2_remediator.processor.boto3.client", autospec=True)
+    def test_process_s3_file_file_removed_successfully(
+        self, mock_boto3_client, mock_remove, mock_os_path_exists, processor, mock_box_reader_factory
+    ):
+        """
+        Covers the line where 'Deleted temporary file:' is logged after a successful os.remove().
+        """
+        mock_s3_client = MagicMock()
+        mock_boto3_client.return_value = mock_s3_client
+
+        input_bucket = "test-bucket"
+        input_key = "test-folder/file.jp2"
+        output_bucket = "output-bucket"
+        output_key = "output-folder/file_modified.jp2"
+
+        # Simulate successful S3 calls
+        mock_s3_client.download_file.return_value = None
+        mock_s3_client.upload_file.return_value = None
+
+        # Ensure skip_remediation is False so we don't exit early
+        mock_reader = MagicMock()
+        mock_reader.skip_remediation = False
+        mock_box_reader_factory.get_reader.return_value = mock_reader
+
+        # Run the method
+        processor.process_s3_file(input_bucket, input_key, output_bucket, output_key=output_key)
+
+        # Confirm remove was called
+        mock_remove.assert_called_once()
+
+        # Confirm we logged the 'Deleted temporary file:' message
+        all_logger_msgs = [call.args[0] for call in processor.logger.info.mock_calls]
+        assert any("Deleted temporary file:" in msg for msg in all_logger_msgs), \
+            "Expected 'Deleted temporary file:' log message not found."