Change miarka_destination to remote_destination

Author: ssjunnebo

README.md

@@ -98,7 +98,7 @@ statusdb:
 sequencers:
   NovaSeqXPlus:
     sequencing_path: /sequencing/NovaSeqXPlus
-    miarka_destination: /Illumina/NovaSeqXPlus
+    remote_destination: /Illumina/NovaSeqXPlus
     metadata_for_statusdb:
       - RunInfo.xml
       - RunParameters.xml

dataflow_transfer/run_classes/generic_runs.py

@@ -32,7 +32,7 @@ def __init__(self, run_dir, configuration):
         self.final_rsync_exitcode_file = os.path.join(
             self.run_dir, ".final_rsync_exitcode"
         )
-        self.miarka_destination = self.sequencer_config.get("miarka_destination")
+        self.remote_destination = self.sequencer_config.get("remote_destination")
         self.db = StatusdbSession(self.configuration.get("statusdb"))
 
     def confirm_run_type(self):
@@ -85,7 +85,7 @@ def generate_rsync_command(self, remote=False, with_exit_code_file=False):
                 + "@"
                 + self.transfer_details.get("host")
                 + ":"
-                + self.miarka_destination
+                + self.remote_destination
             )
             log_file_option = "--log-file=" + os.path.join(
                 self.run_dir, "rsync_remote_log.txt"
@@ -121,23 +121,23 @@ def start_transfer(self, final=False):
         transfer_command = self.generate_rsync_command(
             remote=True, with_exit_code_file=final
         )
-        if fs.rsync_is_running(src=self.run_dir, dst=self.miarka_destination):
+        if fs.rsync_is_running(src=self.run_dir, dst=self.remote_destination):
             logger.info(
-                f"Rsync is already running for {self.run_dir} to destination {self.miarka_destination}. Skipping background transfer initiation."
+                f"Rsync is already running for {self.run_dir} to destination {self.remote_destination}. Skipping background transfer initiation."
             )
             return
         try:
             fs.submit_background_process(transfer_command)
             logger.info(
-                f"{self.run_id}: Started rsync to {self.miarka_destination}"
+                f"{self.run_id}: Started rsync to {self.remote_destination}"
                 + f" with the following command: '{transfer_command}'"
             )
         except Exception as e:
             logger.error(f"Failed to start rsync for {self.run_id}: {e}")
             raise e
         rsync_info = {
             "command": transfer_command,
-            "destination_path": self.miarka_destination,
+            "destination_path": self.remote_destination,
         }
         if final:
             self.update_statusdb(

dataflow_transfer/tests/test_run_classes.py

@@ -21,7 +21,7 @@ def novaseqxplus_testobj(tmp_path):
         },
         "sequencers": {
             "NovaSeqXPlus": {
-                "miarka_destination": "/data/NovaSeqXPlus",
+                "remote_destination": "/data/NovaSeqXPlus",
                 "metadata_for_statusdb": ["RunInfo.xml", "RunParameters.xml"],
                 "ignore_folders": ["nosync"],
                 "remote_rsync_options": ["--chmod=Dg+s,g+rw"],
@@ -53,7 +53,7 @@ def nextseq_testobj(tmp_path):
         },
         "sequencers": {
             "NextSeq": {
-                "miarka_destination": "/data/NextSeq",
+                "remote_destination": "/data/NextSeq",
                 "metadata_for_statusdb": ["RunInfo.xml", "RunParameters.xml"],
                 "ignore_folders": ["nosync"],
                 "remote_rsync_options": ["--chmod=Dg+s,g+rw"],
@@ -85,7 +85,7 @@ def miseqseq_testobj(tmp_path):
         },
         "sequencers": {
             "MiSeq": {
-                "miarka_destination": "/data/MiSeq",
+                "remote_destination": "/data/MiSeq",
                 "metadata_for_statusdb": ["RunInfo.xml", "RunParameters.xml"],
                 "ignore_folders": ["nosync"],
                 "remote_rsync_options": ["--chmod=Dg+s,g+rw"],
@@ -117,7 +117,7 @@ def miseqseqi100_testobj(tmp_path):
         },
         "sequencers": {
             "MiSeqi100": {
-                "miarka_destination": "/data/MiSeqi100",
+                "remote_destination": "/data/MiSeqi100",
                 "metadata_for_statusdb": ["RunInfo.xml", "RunParameters.xml"],
                 "ignore_folders": ["nosync"],
                 "remote_rsync_options": ["--chmod=Dg+s,g+rw"],