Merge branch 'thehyve/fix-crunch-documentation' Fix a typo in Crunch Dispatch install...

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

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 12762118e62bc9fa1e2b8cc656056fbb60b01612..d509f400f1058396f2fc91e6ef320a2bbebe92e1 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -99,6 +99,11 @@ class ArvCwlRunner(object):
 
         self.collection_cache = CollectionCache(self.api, self.keep_client, self.num_retries)
 
+        self.fetcher_constructor = partial(CollectionFetcher,
+                                           api_client=self.api,
+                                           fs_access=CollectionFsAccess("", collection_cache=self.collection_cache),
+                                           num_retries=self.num_retries)
+
         self.work_api = None
         expected_api = ["jobs", "containers"]
         for api in expected_api:
@@ -119,10 +124,7 @@ class ArvCwlRunner(object):
 
     def arv_make_tool(self, toolpath_object, **kwargs):
         kwargs["work_api"] = self.work_api
-        kwargs["fetcher_constructor"] = partial(CollectionFetcher,
-                                                api_client=self.api,
-                                                fs_access=CollectionFsAccess("", collection_cache=self.collection_cache),
-                                                num_retries=self.num_retries)
+        kwargs["fetcher_constructor"] = self.fetcher_constructor
         kwargs["resolver"] = partial(collectionResolver, self.api, num_retries=self.num_retries)
         if "class" in toolpath_object and toolpath_object["class"] == "CommandLineTool":
             return ArvadosCommandTool(self, toolpath_object, **kwargs)
@@ -155,10 +157,12 @@ class ArvCwlRunner(object):
         with self.workflow_eval_lock:
             self.processes[container.uuid] = container
 
-    def process_done(self, uuid):
+    def process_done(self, uuid, record):
         with self.workflow_eval_lock:
-            if uuid in self.processes:
-                del self.processes[uuid]
+            j = self.processes[uuid]
+            logger.info("%s %s is %s", self.label(j), uuid, record["state"])
+            self.task_queue.add(partial(j.done, record))
+            del self.processes[uuid]
 
     def wrapped_callback(self, cb, obj, st):
         with self.workflow_eval_lock:
@@ -179,10 +183,7 @@ class ArvCwlRunner(object):
                         j.update_pipeline_component(event["properties"]["new_attributes"])
                         logger.info("%s %s is Running", self.label(j), uuid)
             elif event["properties"]["new_attributes"]["state"] in ("Complete", "Failed", "Cancelled", "Final"):
-                with self.workflow_eval_lock:
-                    j = self.processes[uuid]
-                self.task_queue.add(partial(j.done, event["properties"]["new_attributes"]))
-                logger.info("%s %s is %s", self.label(j), uuid, event["properties"]["new_attributes"]["state"])
+                self.process_done(uuid, event["properties"]["new_attributes"])
 
     def label(self, obj):
         return "[%s %s]" % (self.work_api[0:-1], obj.name)