Skip file transfer when the source file is absent

galaxyproject · Jul 16, 2023 · f549bf9 · f549bf9
1 parent 31d8a99
commit f549bf9
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Showing 2 changed files with 12 additions and 1 deletion.
diff --git a/pulsar/client/action_mapper.py b/pulsar/client/action_mapper.py
@@ -306,6 +306,9 @@ def __init__(self, source, file_lister=None):
     def path(self):
         return self.source.get("path")
 
+    def path_exists(self):
+        return exists(self.path)
+
     def unstructured_map(self, path_helper):
         unstructured_map = self.file_lister.unstructured_map(self.path)
         if self.staging_needed:

diff --git a/pulsar/managers/staging/post.py b/pulsar/managers/staging/post.py
@@ -79,7 +79,15 @@ def collect_output(self, results_collector, output_type, action, name):
 
         pulsar_path = self.job_directory.calculate_path(name, output_type)
         description = "staging out file {} via {}".format(pulsar_path, action)
-        self.action_executor.execute(lambda: action.write_from_path(pulsar_path), description)
+
+        if not action.path_exists():
+            log.warn(
+                f"Output not collectable. File does not exist: {pulsar_path}")
+        else:
+            self.action_executor.execute(
+                lambda: action.write_from_path(pulsar_path),
+                description,
+            )
 
 
 def __pulsar_outputs(job_directory):