From 3be54840d57a19ee0df91e405840d99a9778d5ce Mon Sep 17 00:00:00 2001
From: Sara Sjunnebo <sara.sjunnebo@gmail.com>
Date: Mon, 16 Sep 2024 15:35:59 +0200
Subject: [PATCH] rename is_transferred function

---
 taca/analysis/analysis_element.py | 6 +++---
 taca/element/Element_Runs.py      | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/taca/analysis/analysis_element.py b/taca/analysis/analysis_element.py
index 0c0bf977..42fd3e00 100755
--- a/taca/analysis/analysis_element.py
+++ b/taca/analysis/analysis_element.py
@@ -72,7 +72,7 @@ def _process(run):
                 run.update_statusdb()
             return
         elif sequencing_done and demultiplexing_status == "finished":
-            if not run.is_transferred() and not run.transfer_ongoing() and not run.rsync_complete():
+            if not run.in_transfer_log() and not run.transfer_ongoing() and not run.rsync_complete():
                 run.aggregate_demux_results() # TODO: if multiple demux dirs, aggregate the results into Demultiplexing?
                 run.sync_metadata()
                 run.make_transfer_indicator()
@@ -87,7 +87,7 @@ def _process(run):
                     run.update_statusdb()
                 logger.info(f"{run} is being transferred. Skipping.")
                 return
-            elif run.rsync_complete() and not run.is_transferred():
+            elif run.rsync_complete() and not run.in_transfer_log():
                 if run.rsync_success():
                     run.remove_transfer_indicator()
                     run.update_transfer_log()
@@ -102,7 +102,7 @@ def _process(run):
                     run.status = "transfer failed"
                     logger.warning(f"An issue occurred while transfering {run} to the analysis cluster." )
                     # TODO: email warning to operator
-            elif run.is_transferred():
+            elif run.in_transfer_log():
                 logger.warning(
                     f"The run {run} has already been transferred but has not been archived. Please investigate"
                 )
diff --git a/taca/element/Element_Runs.py b/taca/element/Element_Runs.py
index 541bb319..6b8f03e5 100644
--- a/taca/element/Element_Runs.py
+++ b/taca/element/Element_Runs.py
@@ -198,7 +198,7 @@ def start_demux(self, run_manifest, demux_dir):
                 f"started for run {self} on {datetime.now()}"
             )
 
-    def is_transferred(self):
+    def in_transfer_log(self):
         with open(self.transfer_file, 'r') as transfer_file:
             for row in transfer_file.read():
                 if self.NGI_run_id in row: