14715: keepproxy.service checks for cluster config

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

diff --git a/sdk/cwl/arvados_cwl/arvjob.py b/sdk/cwl/arvados_cwl/arvjob.py
index 2e4ef55015157c4196c649797029b1e9912e00bb..11efc0c1c3965c25d26c0a615d3388db902efa36 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvjob.py
+++ b/sdk/cwl/arvados_cwl/arvjob.py
@@ -2,6 +2,10 @@
 #
 # SPDX-License-Identifier: Apache-2.0
 
+from past.builtins import basestring
+from builtins import object
+from future.utils import viewitems
+
 import logging
 import re
 import copy
@@ -67,7 +71,7 @@ class ArvadosJob(JobBase):
                                                     keep_client=self.arvrunner.keep_client,
                                                     num_retries=self.arvrunner.num_retries)
                 script_parameters["task.vwd"] = {}
-                generatemapper = VwdPathMapper([self.generatefiles], "", "",
+                generatemapper = VwdPathMapper(self.generatefiles["listing"], "", "",
                                                separateDirs=False)
 
                 with Perf(metrics, "createfiles %s" % self.name):
@@ -195,7 +199,7 @@ class ArvadosJob(JobBase):
                                     e)
             else:
                 logger.info("%s %s is %s", self.arvrunner.label(self), response["uuid"], response["state"])
-        except Exception as e:
+        except Exception:
             logger.exception("%s error" % (self.arvrunner.label(self)))
             self.output_callback({}, "permanentFail")
 
@@ -220,8 +224,8 @@ class ArvadosJob(JobBase):
                             body={
                                 "components": components
                             }).execute(num_retries=self.arvrunner.num_retries)
-                except Exception as e:
-                    logger.info("Error adding to components: %s", e)
+                except Exception:
+                    logger.exception("Error adding to components")
 
     def done(self, record):
         try:
@@ -232,8 +236,11 @@ class ArvadosJob(JobBase):
         try:
             if record["state"] == "Complete":
                 processStatus = "success"
+                # we don't have the real exit code so fake it.
+                record["exit_code"] = 0
             else:
                 processStatus = "permanentFail"
+                record["exit_code"] = 1
 
             outputs = {}
             try:
@@ -243,7 +250,7 @@ class ArvadosJob(JobBase):
                                                                    api_client=self.arvrunner.api,
                                                                    keep_client=self.arvrunner.keep_client,
                                                                    num_retries=self.arvrunner.num_retries)
-                        log = logc.open(logc.keys()[0])
+                        log = logc.open(list(logc.keys())[0])
                         dirs = {
                             "tmpdir": "/tmpdir",
                             "outdir": "/outdir",
@@ -268,10 +275,12 @@ class ArvadosJob(JobBase):
                         outputs = done.done(self, record, dirs["tmpdir"],
                                             dirs["outdir"], dirs["keep"])
             except WorkflowException as e:
+                # Only include a stack trace if in debug mode.
+                # This is most likely a user workflow error and a stack trace may obfuscate more useful output.
                 logger.error("%s unable to collect output from %s:\n%s",
                              self.arvrunner.label(self), record["output"], e, exc_info=(e if self.arvrunner.debug else False))
                 processStatus = "permanentFail"
-            except Exception as e:
+            except Exception:
                 logger.exception("Got unknown exception while collecting output for job %s:", self.name)
                 processStatus = "permanentFail"
 
@@ -343,7 +352,7 @@ class RunnerJob(Runner):
             find_or_create=self.enable_reuse
         ).execute(num_retries=self.arvrunner.num_retries)
 
-        for k,v in job_spec["script_parameters"].items():
+        for k,v in viewitems(job_spec["script_parameters"]):
             if v is False or v is None or isinstance(v, dict):
                 job_spec["script_parameters"][k] = {"value": v}