Merge branch '14885-ciso-and-conda-packaging-pr'

refs #14885

Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>

diff --combined sdk/cwl/arvados_cwl/arvcontainer.py
index 9f93f0a6a6895780b2aca6e5ed235aca64d6aac9,461f5b66a563403fdad056073cebe56802818cb5..03b4e07c76f5849a97ae85b9bd179e897ec8fc33
--- 1/sdk/cwl/arvados_cwl/arvcontainer.py
--- 2/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@@ -304,8 -304,8 +304,8 @@@ 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):
@@@ -342,7 -342,7 +342,7 @@@
              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(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 ""
@@@ -353,13 -353,11 +353,13 @@@
              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)
@@@ -525,8 -523,8 +525,8 @@@ 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)
 +        except Exception:
 +            logger.exception("%s while getting runner container", self.arvrunner.label(self))
              self.arvrunner.output_callback({}, "permanentFail")
          else:
              super(RunnerContainer, self).done(container)