Merge branch '15497-reuse-fix'

[arvados.git] / sdk / cwl / arvados_cwl / arvcontainer.py

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index b194f3dfcaa0be1cf676ea771e008cbcc9b0b2c0..ad11aa490fe4e9b9996560c8cf430619df608359 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -155,7 +155,7 @@ class ArvadosContainer(JobBase):
                                 vwd.mkdirs(p.target)
                             else:
                                 source, path = self.arvrunner.fs_access.get_collection(p.resolved)
-                                vwd.copy(path, p.target, source_collection=source)
+                                vwd.copy(path or ".", p.target, source_collection=source)
                         elif p.type == "CreateFile":
                             if self.arvrunner.secret_store.has_secret(p.resolved):
                                 secret_mounts["%s/%s" % (self.outdir, p.target)] = {
@@ -418,7 +418,7 @@ class RunnerContainer(Runner):
                 "ram": 1024*1024 * (math.ceil(self.submit_runner_ram) + math.ceil(self.collection_cache_size)),
                 "API": True
             },
-            "use_existing": self.enable_reuse,
+            "use_existing": False, # Never reuse the runner container - see #15497.
             "properties": {}
         }
 
@@ -527,6 +527,7 @@ class RunnerContainer(Runner):
             container = self.arvrunner.api.containers().get(
                 uuid=record["container_uuid"]
             ).execute(num_retries=self.arvrunner.num_retries)
+            container["log"] = record["log_uuid"]
         except Exception:
             logger.exception("%s while getting runner container", self.arvrunner.label(self))
             self.arvrunner.output_callback({}, "permanentFail")