Merge branch 'master' into 9956-keepstore-config

[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 46850b388961924fb46b8fbc5f1e6c1fb703abaa..7ebb13f1bb48af456ce50f2c7d8629e03c975cb0 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -24,7 +24,7 @@ import arvados.config
 
 from .arvcontainer import ArvadosContainer, RunnerContainer
 from .arvjob import ArvadosJob, RunnerJob, RunnerTemplate
-from. runner import Runner
+from. runner import Runner, upload_instance
 from .arvtool import ArvadosCommandTool
 from .arvworkflow import ArvadosWorkflow, upload_workflow
 from .fsaccess import CollectionFsAccess
@@ -32,7 +32,7 @@ from .perf import Perf
 from .pathmapper import FinalOutputPathMapper
 
 from cwltool.pack import pack
-from cwltool.process import shortname, UnsupportedRequirement
+from cwltool.process import shortname, UnsupportedRequirement, getListing
 from cwltool.pathmapper import adjustFileObjs, adjustDirObjs
 from cwltool.draft2tool import compute_checksums
 from arvados.api import OrderedJsonModel
@@ -64,6 +64,8 @@ class ArvCwlRunner(object):
         self.pipeline = None
         self.final_output_collection = None
         self.output_name = output_name
+        self.project_uuid = None
+
         if keep_client is not None:
             self.keep_client = keep_client
         else:
@@ -266,6 +268,8 @@ class ArvCwlRunner(object):
             kwargs["docker_outdir"] = "$(task.outdir)"
             kwargs["tmpdir"] = "$(task.tmpdir)"
 
+        upload_instance(self, shortname(tool.tool["id"]), tool, job_order)
+
         runnerjob = None
         if kwargs.get("submit"):
             if self.work_api == "containers":
@@ -289,7 +293,7 @@ class ArvCwlRunner(object):
             logger.info("Pipeline instance %s", self.pipeline["uuid"])
 
         if runnerjob and not kwargs.get("wait"):
-            runnerjob.run()
+            runnerjob.run(wait=kwargs.get("wait"))
             return runnerjob.uuid
 
         self.poll_api = arvados.api('v1')
@@ -365,6 +369,7 @@ class ArvCwlRunner(object):
             self.make_output_collection(self.output_name, self.final_output)
 
         if kwargs.get("compute_checksum"):
+            adjustDirObjs(self.final_output, partial(getListing, self.fs_access))
             adjustFileObjs(self.final_output, partial(compute_checksums, self.fs_access))
 
         return self.final_output