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 03b4e07c76f5849a97ae85b9bd179e897ec8fc33..ad11aa490fe4e9b9996560c8cf430619df608359 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -123,6 +123,8 @@ class ArvadosContainer(JobBase):
                 "kind": "collection",
                 "portable_data_hash": pdh
             }
+            if pdh in self.pathmapper.pdh_to_uuid:
+                mounts[targetdir]["uuid"] = self.pathmapper.pdh_to_uuid[pdh]
             if len(sp) == 2:
                 if tp == "Directory":
                     path = sp[1]
@@ -153,7 +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)] = {
@@ -329,8 +331,8 @@ class ArvadosContainer(JobBase):
             else:
                 processStatus = "permanentFail"
 
-            if processStatus == "permanentFail":
-                logc = arvados.collection.CollectionReader(container["log"],
+            if processStatus == "permanentFail" and record["log_uuid"]:
+                logc = arvados.collection.CollectionReader(record["log_uuid"],
                                                            api_client=self.arvrunner.api,
                                                            keep_client=self.arvrunner.keep_client,
                                                            num_retries=self.arvrunner.num_retries)
@@ -353,8 +355,8 @@ class ArvadosContainer(JobBase):
             if container["output"]:
                 outputs = done.done_outputs(self, container, "/tmp", self.outdir, "/keep")
         except WorkflowException as e:
-            # Only include a stack trace if in debug mode. 
-            # A stack trace may obfuscate more useful output about the workflow. 
+            # Only include a stack trace if in debug mode.
+            # A stack trace may obfuscate more useful output about the workflow.
             logger.error("%s unable to collect output from %s:\n%s",
                          self.arvrunner.label(self), container["output"], e, exc_info=(e if self.arvrunner.debug else False))
             processStatus = "permanentFail"
@@ -416,7 +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": {}
         }
 
@@ -525,6 +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")