X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/a355b779c5d8df691b726ba18dd88892097017ae..138fef8ee97f3cbd335434ad6acd26771fd0b762:/sdk/cwl/arvados_cwl/arvjob.py

diff --git a/sdk/cwl/arvados_cwl/arvjob.py b/sdk/cwl/arvados_cwl/arvjob.py
index 7fc62db951..e222152a16 100644
--- a/sdk/cwl/arvados_cwl/arvjob.py
+++ b/sdk/cwl/arvados_cwl/arvjob.py
@@ -10,7 +10,7 @@ import time
 
 from cwltool.process import get_feature, shortname, UnsupportedRequirement
 from cwltool.errors import WorkflowException
-from cwltool.draft2tool import revmap_file, CommandLineTool
+from cwltool.command_line_tool import revmap_file, CommandLineTool
 from cwltool.load_tool import fetch_document
 from cwltool.builder import Builder
 from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class
@@ -134,6 +134,8 @@ class ArvadosJob(object):
             if reuse_req:
                 enable_reuse = reuse_req["enableReuse"]
 
+        self.output_callback = self.arvrunner.get_wrapped_callback(self.output_callback)
+
         try:
             with Perf(metrics, "create %s" % self.name):
                 response = self.arvrunner.api.jobs().create(
@@ -150,7 +152,8 @@ class ArvadosJob(object):
                     find_or_create=enable_reuse
                 ).execute(num_retries=self.arvrunner.num_retries)
 
-            self.arvrunner.processes[response["uuid"]] = self
+            self.uuid = response["uuid"]
+            self.arvrunner.process_submitted(self)
 
             self.update_pipeline_component(response)
 
@@ -184,17 +187,19 @@ class ArvadosJob(object):
         if self.arvrunner.pipeline:
             self.arvrunner.pipeline["components"][self.name] = {"job": record}
             with Perf(metrics, "update_pipeline_component %s" % self.name):
-                self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().update(uuid=self.arvrunner.pipeline["uuid"],
-                                                                                 body={
-                                                                                    "components": self.arvrunner.pipeline["components"]
-                                                                                 }).execute(num_retries=self.arvrunner.num_retries)
+                self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().update(
+                    uuid=self.arvrunner.pipeline["uuid"],
+                    body={
+                        "components": self.arvrunner.pipeline["components"]
+                    }).execute(num_retries=self.arvrunner.num_retries)
         if self.arvrunner.uuid:
             try:
                 job = self.arvrunner.api.jobs().get(uuid=self.arvrunner.uuid).execute()
                 if job:
                     components = job["components"]
                     components[self.name] = record["uuid"]
-                    self.arvrunner.api.jobs().update(uuid=self.arvrunner.uuid,
+                    self.arvrunner.api.jobs().update(
+                        uuid=self.arvrunner.uuid,
                         body={
                             "components": components
                         }).execute(num_retries=self.arvrunner.num_retries)
@@ -261,8 +266,8 @@ class ArvadosJob(object):
                 processStatus = "permanentFail"
         finally:
             self.output_callback(outputs, processStatus)
-            if record["uuid"] in self.arvrunner.processes:
-                del self.arvrunner.processes[record["uuid"]]
+            self.arvrunner.process_done(record["uuid"])
+
 
 class RunnerJob(Runner):
     """Submit and manage a Crunch job that runs crunch_scripts/cwl-runner."""
@@ -278,7 +283,7 @@ class RunnerJob(Runner):
         if self.tool.tool["id"].startswith("keep:"):
             self.job_order["cwl:tool"] = self.tool.tool["id"][5:]
         else:
-            packed = packed_workflow(self.arvrunner, self.tool)
+            packed = packed_workflow(self.arvrunner, self.tool, self.merged_map)
             wf_pdh = upload_workflow_collection(self.arvrunner, self.name, packed)
             self.job_order["cwl:tool"] = "%s/workflow.cwl#main" % wf_pdh
 
@@ -312,8 +317,8 @@ class RunnerJob(Runner):
             }
         }
 
-    def run(self, *args, **kwargs):
-        job_spec = self.arvados_job_spec(*args, **kwargs)
+    def run(self, **kwargs):
+        job_spec = self.arvados_job_spec(**kwargs)
 
         job_spec.setdefault("owner_uuid", self.arvrunner.project_uuid)
 
@@ -328,12 +333,20 @@ class RunnerJob(Runner):
 
         del job_spec["owner_uuid"]
         job_spec["job"] = job
+
+        instance_spec = {
+            "owner_uuid": self.arvrunner.project_uuid,
+            "name": self.name,
+            "components": {
+                "cwl-runner": job_spec,
+            },
+            "state": "RunningOnServer",
+        }
+        if not self.enable_reuse:
+            instance_spec["properties"] = {"run_options": {"enable_job_reuse": False}}
+
         self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().create(
-            body={
-                "owner_uuid": self.arvrunner.project_uuid,
-                "name": self.name,
-                "components": {"cwl-runner": job_spec },
-                "state": "RunningOnServer"}).execute(num_retries=self.arvrunner.num_retries)
+            body=instance_spec).execute(num_retries=self.arvrunner.num_retries)
         logger.info("Created pipeline %s", self.arvrunner.pipeline["uuid"])
 
         if kwargs.get("wait") is False:
@@ -341,7 +354,7 @@ class RunnerJob(Runner):
             return
 
         self.uuid = job["uuid"]
-        self.arvrunner.processes[self.uuid] = self
+        self.arvrunner.process_submitted(self)
 
         if job["state"] in ("Complete", "Failed", "Cancelled"):
             self.done(job)
@@ -360,7 +373,7 @@ class RunnerTemplate(object):
     }
 
     def __init__(self, runner, tool, job_order, enable_reuse, uuid,
-                 submit_runner_ram=0, name=None):
+                 submit_runner_ram=0, name=None, merged_map=None):
         self.runner = runner
         self.tool = tool
         self.job = RunnerJob(
@@ -371,7 +384,8 @@ class RunnerTemplate(object):
             output_name=None,
             output_tags=None,
             submit_runner_ram=submit_runner_ram,
-            name=name)
+            name=name,
+            merged_map=merged_map)
         self.uuid = uuid
 
     def pipeline_component_spec(self):