X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/7a9e57f98e2d5bad3dec7d17cfb9c86e5c5c927c..c042cd8120be2c54f54ee2a6041adbc30e141190:/sdk/cwl/arvados_cwl/arvcontainer.py

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index af7c02a8f3..860bd954c6 100644
--- 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]
@@ -223,6 +225,10 @@ class ArvadosContainer(JobBase):
                                                                     runtimeContext.pull_image,
                                                                     runtimeContext.project_uuid)
 
+        network_req, _ = self.get_requirement("NetworkAccess")
+        if network_req:
+            runtime_constraints["API"] = network_req["networkAccess"]
+
         api_req, _ = self.get_requirement("http://arvados.org/cwl#APIRequirement")
         if api_req:
             runtime_constraints["API"] = True
@@ -304,8 +310,8 @@ class ArvadosContainer(JobBase):
                 logger.info("%s reused container %s", self.arvrunner.label(self), response["container_uuid"])
             else:
                 logger.info("%s %s state is %s", self.arvrunner.label(self), response["uuid"], response["state"])
-        except Exception as e:
-            logger.error("%s got error %s" % (self.arvrunner.label(self), str(e)))
+        except Exception:
+            logger.exception("%s got an error", self.arvrunner.label(self))
             self.output_callback({}, "permanentFail")
 
     def done(self, record):
@@ -329,8 +335,8 @@ 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)
@@ -342,7 +348,7 @@ class ArvadosContainer(JobBase):
             if record["output_uuid"]:
                 if self.arvrunner.trash_intermediate or self.arvrunner.intermediate_output_ttl:
                     # Compute the trash time to avoid requesting the collection record.
-                    trash_at = ciso8601.parse_datetime_unaware(record["modified_at"]) + datetime.timedelta(0, self.arvrunner.intermediate_output_ttl)
+                    trash_at = ciso8601.parse_datetime_as_naive(record["modified_at"]) + datetime.timedelta(0, self.arvrunner.intermediate_output_ttl)
                     aftertime = " at %s" % trash_at.strftime("%Y-%m-%d %H:%M:%S UTC") if self.arvrunner.intermediate_output_ttl else ""
                     orpart = ", or" if self.arvrunner.trash_intermediate and self.arvrunner.intermediate_output_ttl else ""
                     oncomplete = " upon successful completion of the workflow" if self.arvrunner.trash_intermediate else ""
@@ -353,11 +359,13 @@ 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.
             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"
-        except Exception as e:
-            logger.exception("%s while getting output object: %s", self.arvrunner.label(self), e)
+        except Exception:
+            logger.exception("%s while getting output object:", self.arvrunner.label(self))
             processStatus = "permanentFail"
         finally:
             self.output_callback(outputs, processStatus)
@@ -481,6 +489,9 @@ class RunnerContainer(Runner):
         if self.arvrunner.project_uuid:
             command.append("--project-uuid="+self.arvrunner.project_uuid)
 
+        if self.enable_dev:
+            command.append("--enable-dev")
+
         command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"])
 
         container_req["command"] = command
@@ -523,8 +534,9 @@ class RunnerContainer(Runner):
             container = self.arvrunner.api.containers().get(
                 uuid=record["container_uuid"]
             ).execute(num_retries=self.arvrunner.num_retries)
-        except Exception as e:
-            logger.exception("%s while getting runner container: %s", self.arvrunner.label(self), e)
+            container["log"] = record["log_uuid"]
+        except Exception:
+            logger.exception("%s while getting runner container", self.arvrunner.label(self))
             self.arvrunner.output_callback({}, "permanentFail")
         else:
             super(RunnerContainer, self).done(container)