Change remote to metadata_only

Author: ssjunnebo

dataflow_transfer/run_classes/generic_runs.py

@@ -58,7 +58,7 @@ def metadata_synced(self):
     def sync_metadata(self):
         """Start background rsync transfer for metadata files."""
         metadata_rsync_command = self.generate_rsync_command(
-            remote=False, with_exit_code_file=True
+            metadata_only=True, with_exit_code_file=True
         )
 
         if fs.rsync_is_running(src=self.run_dir, dst=self.metadata_destination):
@@ -76,9 +76,17 @@ def sync_metadata(self):
             logger.error(f"Failed to start metadata rsync for {self.run_id}: {e}")
             raise e
 
-    def generate_rsync_command(self, remote=False, with_exit_code_file=False):
+    def generate_rsync_command(self, metadata_only=False, with_exit_code_file=False):
         """Generate an rsync command string."""
-        if remote:
+        if metadata_only:
+            source = self.run_dir + "/"
+            destination = self.metadata_destination + "/"
+            log_file_option = "--log-file=" + os.path.join(
+                self.run_dir, "rsync_metadata_log.txt"
+            )
+            rsync_options = self.sequencer_config.get("metadata_rsync_options", [])
+            exit_code_file = self.metadata_rsync_exitcode_file
+        else:
             source = self.run_dir
             destination = (
                 self.transfer_details.get("user")
@@ -92,22 +100,15 @@ def generate_rsync_command(self, remote=False, with_exit_code_file=False):
             )
             rsync_options = self.sequencer_config.get("remote_rsync_options", [])
             exit_code_file = self.final_rsync_exitcode_file
-        else:
-            source = self.run_dir + "/"
-            destination = self.metadata_destination + "/"
-            log_file_option = "--log-file=" + os.path.join(
-                self.run_dir, "rsync_metadata_log.txt"
-            )
-            rsync_options = self.sequencer_config.get("metadata_rsync_options", [])
-            exit_code_file = self.metadata_rsync_exitcode_file
+
         run_one_bin = self.configuration.get("run_one_path", "run-one")
         command = [
             run_one_bin,
             "rsync",
             "-au",
             log_file_option,
             *(rsync_options),
-            "--exclude='*'" if not remote else "",
+            "--exclude='*'" if metadata_only else "",
             source,
             destination,
         ]
@@ -119,7 +120,7 @@ def generate_rsync_command(self, remote=False, with_exit_code_file=False):
     def start_transfer(self, final=False):
         """Start background rsync transfer to storage."""
         transfer_command = self.generate_rsync_command(
-            remote=True, with_exit_code_file=final
+            metadata_only=False, with_exit_code_file=final
         )
         if fs.rsync_is_running(src=self.run_dir, dst=self.remote_destination):
             logger.info(

dataflow_transfer/tests/test_run_classes.py

@@ -190,26 +190,28 @@ def test_sequencing_ongoing(run_fixture, request):
 
 
 @pytest.mark.parametrize(
-    "run_fixture, remote, with_exit_code_file",
+    "run_fixture, metadata_only, with_exit_code_file",
     [
         ("novaseqxplus_testobj", False, True),
-        ("novaseqxplus_testobj", True, False),
+        ("novaseqxplus_testobj", False, False),
         ("novaseqxplus_testobj", True, True),
         ("nextseq_testobj", False, True),
-        ("nextseq_testobj", True, False),
+        ("nextseq_testobj", False, False),
         ("nextseq_testobj", True, True),
         ("miseqseq_testobj", False, True),
-        ("miseqseq_testobj", True, False),
+        ("miseqseq_testobj", False, False),
         ("miseqseq_testobj", True, True),
         ("miseqseqi100_testobj", False, True),
-        ("miseqseqi100_testobj", True, False),
+        ("miseqseqi100_testobj", False, False),
         ("miseqseqi100_testobj", True, True),
     ],
 )
-def test_generate_rsync_command(run_fixture, remote, with_exit_code_file, request):
+def test_generate_rsync_command(
+    run_fixture, metadata_only, with_exit_code_file, request
+):
     run_obj = request.getfixturevalue(run_fixture)
     rsync_command = run_obj.generate_rsync_command(
-        remote=remote, with_exit_code_file=with_exit_code_file
+        metadata_only=metadata_only, with_exit_code_file=with_exit_code_file
     )
     assert "run-one rsync" in rsync_command
     assert "--log-file=" in rsync_command
@@ -337,7 +339,7 @@ def test_metadata_synced(run_fixture, sync_successful, request):
 def test_sync_metadata(run_fixture, request, monkeypatch):
     run_obj = request.getfixturevalue(run_fixture)
 
-    def mock_generate_rsync_command(remote, with_exit_code_file):
+    def mock_generate_rsync_command(metadata_only, with_exit_code_file):
         return "rsync command"
 
     def mock_rsync_is_running(src, dst):