X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/036c59ea6b19372e74f7ccacb5dcb2f522f99629..353eb4f4c4fb52e7f2a1c9aaad93e9d6bf0088f4:/sdk/cwl/arvados_cwl/arvjob.py

diff --git a/sdk/cwl/arvados_cwl/arvjob.py b/sdk/cwl/arvados_cwl/arvjob.py
index 7b318026d5..04a62953ba 100644
--- a/sdk/cwl/arvados_cwl/arvjob.py
+++ b/sdk/cwl/arvados_cwl/arvjob.py
@@ -18,8 +18,8 @@ import ruamel.yaml as yaml
 import arvados.collection
 
 from .arvdocker import arv_docker_get_image
-from .runner import Runner, arvados_jobs_image, packed_workflow, trim_listing
-from .pathmapper import InitialWorkDirPathMapper
+from .runner import Runner, arvados_jobs_image, packed_workflow, trim_listing, upload_workflow_collection
+from .pathmapper import VwdPathMapper
 from .perf import Perf
 from . import done
 from ._version import __version__
@@ -51,8 +51,8 @@ class ArvadosJob(object):
                                                     keep_client=self.arvrunner.keep_client,
                                                     num_retries=self.arvrunner.num_retries)
                 script_parameters["task.vwd"] = {}
-                generatemapper = InitialWorkDirPathMapper([self.generatefiles], "", "",
-                                                          separateDirs=False)
+                generatemapper = VwdPathMapper([self.generatefiles], "", "",
+                                               separateDirs=False)
 
                 with Perf(metrics, "createfiles %s" % self.name):
                     for f, p in generatemapper.items():
@@ -60,8 +60,9 @@ class ArvadosJob(object):
                             with vwd.open(p.target, "w") as n:
                                 n.write(p.resolved.encode("utf-8"))
 
-                with Perf(metrics, "generatefiles.save_new %s" % self.name):
-                    vwd.save_new()
+                if vwd:
+                    with Perf(metrics, "generatefiles.save_new %s" % self.name):
+                        vwd.save_new()
 
                 for f, p in generatemapper.items():
                     if p.type == "File":
@@ -141,11 +142,12 @@ class ArvadosJob(object):
 
             self.update_pipeline_component(response)
 
-            logger.info("%s %s is %s", self.arvrunner.label(self), response["uuid"], response["state"])
-
-            if response["state"] in ("Complete", "Failed", "Cancelled"):
+            if response["state"] == "Complete":
+                logger.info("%s reused job %s", self.arvrunner.label(self), response["uuid"])
                 with Perf(metrics, "done %s" % self.name):
                     self.done(response)
+            else:
+                logger.info("%s %s is %s", self.arvrunner.label(self), response["uuid"], response["state"])
         except Exception as e:
             logger.exception("%s error" % (self.arvrunner.label(self)))
             self.output_callback({}, "permanentFail")
@@ -236,30 +238,6 @@ class ArvadosJob(object):
 class RunnerJob(Runner):
     """Submit and manage a Crunch job that runs crunch_scripts/cwl-runner."""
 
-    def upload_workflow_collection(self, packed):
-        collection = arvados.collection.Collection(api_client=self.arvrunner.api,
-                                                   keep_client=self.arvrunner.keep_client,
-                                                   num_retries=self.arvrunner.num_retries)
-        with collection.open("workflow.cwl", "w") as f:
-            f.write(yaml.round_trip_dump(packed))
-
-        filters = [["portable_data_hash", "=", collection.portable_data_hash()],
-                   ["name", "like", self.name+"%"]]
-        if self.arvrunner.project_uuid:
-            filters.append(["owner_uuid", "=", self.arvrunner.project_uuid])
-        exists = self.arvrunner.api.collections().list(filters=filters).execute(num_retries=self.arvrunner.num_retries)
-
-        if exists["items"]:
-            logger.info("Using collection %s", exists["items"][0]["uuid"])
-        else:
-            collection.save_new(name=self.name,
-                                owner_uuid=self.arvrunner.project_uuid,
-                                ensure_unique_name=True,
-                                num_retries=self.arvrunner.num_retries)
-            logger.info("Uploaded to %s", collection.manifest_locator())
-
-        return collection.portable_data_hash()
-
     def arvados_job_spec(self, dry_run=False, pull_image=True, **kwargs):
         """Create an Arvados job specification for this workflow.
 
@@ -272,7 +250,7 @@ class RunnerJob(Runner):
             self.job_order["cwl:tool"] = self.tool.tool["id"][5:]
         else:
             packed = packed_workflow(self.arvrunner, self.tool)
-            wf_pdh = self.upload_workflow_collection(packed)
+            wf_pdh = upload_workflow_collection(self.arvrunner, self.name, packed)
             self.job_order["cwl:tool"] = "%s/workflow.cwl#main" % wf_pdh
 
         adjustDirObjs(self.job_order, trim_listing)