Bug fixes

SciLifeLab · Sep 25, 2024 · 23e9b64 · 23e9b64
1 parent 9e80a4f
commit 23e9b64
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Showing 2 changed files with 8 additions and 7 deletions.
diff --git a/taca/analysis/analysis_element.py b/taca/analysis/analysis_element.py
@@ -85,21 +85,21 @@ def _process(run):
             demux_results_dirs = glob.glob(
                 os.path.join(run.run_dir, "Delmultiplexing*")
             )
-            if len(demux_results_dirs > 1):
+            if len(demux_results_dirs) > 1:
                 run.aggregate_demux_results(demux_results_dirs)
             run.sync_metadata()
             run.make_transfer_indicator()
             run.status = "transferring"
             if run.status_changed:
                 run.update_statusdb()
                 # TODO: Also update statusdb with a timestamp of when the transfer started
-            run.transfer()  # I think this should be a detached command as well
+            run.transfer()
             return
         elif transfer_status == "ongoing":
             run.status = "transferring"
             if run.status_changed:
                 run.update_statusdb()
-            logger.info(f"{run} is being transferred. Skipping.")
+            logger.info(f"{run} is being transferred. Skipping.") # TODO: fix formatting, currently prints "ElementRun(20240910_AV242106_B2403418431) is being transferred"
             return
         elif transfer_status == "rsync done":
             if run.rsync_successful():

diff --git a/taca/element/Element_Runs.py b/taca/element/Element_Runs.py
@@ -441,7 +441,7 @@ def rsync_complete(self):
     def rsync_successful(self):
         with open(os.path.join(self.run_dir, ".rsync_exit_status")) as rsync_exit_file:
             rsync_exit_status = rsync_exit_file.readlines()
-        if rsync_exit_status[0].strip() == 0:
+        if rsync_exit_status[0].strip() == '0':
             return True
         else:
             return False
@@ -522,7 +522,7 @@ def make_transfer_indicator(self):
 
     def transfer(self):
         transfer_details = (
-            self.CONFIG.get("element_analysis").get(self.sequencer_type).get("transfer_details")
+            self.CONFIG.get("element_analysis").get("transfer_details")
         )  # TODO: Add section to taca.yaml
         command = (
             "rsync"
@@ -532,8 +532,8 @@ def transfer(self):
             + " --exclude BaseCalls"  # TODO: check that we actually want to exclude these
             + " --exclude Alignment"
             + f" {self.run_dir}"
-            + f" {transfer_details.get('user')@transfer_details.get('host')}:/aviti"
-            + "; echo $? > .rsync_exit_status"
+            + f" {transfer_details.get('user')}@{transfer_details.get('host')}:/aviti"
+            + f"; echo $? > {os.path.join(self.run_dir, ".rsync_exit_status")}"
         )  # TODO: any other options?
         try:
             p_handle = subprocess.Popen(command, stdout=subprocess.PIPE, shell=True)
@@ -568,3 +568,4 @@ def archive(self):
         src = self.run_dir
         dst = os.path.join(self.run_dir, os.pardir, "nosync")
         shutil.move(src, dst)
+        self.run_dir =