[ARVADOS] created: 1825696494802d264c74ed2af58cc39b6ff8c7f8

[Git user]

        at  1825696494802d264c74ed2af58cc39b6ff8c7f8 (commit)


commit 1825696494802d264c74ed2af58cc39b6ff8c7f8
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Thu Oct 13 21:13:58 2016 -0400

    10259: Add one level of indirection on dict parameters so that
    arv-run-pipeline-instance does not try to interpret the value.  Check pipeline
    state so that polling loop for cwl-runner job does not get stuck.

diff --git a/sdk/cwl/arvados_cwl/arvjob.py b/sdk/cwl/arvados_cwl/arvjob.py
index 5250410..8269eee 100644
--- a/sdk/cwl/arvados_cwl/arvjob.py
+++ b/sdk/cwl/arvados_cwl/arvjob.py
@@ -256,6 +256,10 @@ class RunnerJob(Runner):
     def run(self, *args, **kwargs):
         job_spec = self.arvados_job_spec(*args, **kwargs)
 
+        for k,v in job_spec["script_parameters"].items():
+            if isinstance(v, dict):
+                job_spec["script_parameters"][k] = {"value": v}
+
         self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().create(
             body={
                 "owner_uuid": self.arvrunner.project_uuid,
@@ -275,6 +279,8 @@ class RunnerJob(Runner):
                 uuid=self.arvrunner.pipeline["uuid"]).execute(
                     num_retries=self.arvrunner.num_retries)
             job = self.arvrunner.pipeline["components"]["cwl-runner"].get("job")
+            if not job and self.arvrunner.pipeline["state"] != "RunningOnServer":
+                raise WorkflowException("Submitted pipeline is %s" % (self.arvrunner.pipeline["state"]))
 
         self.uuid = job["uuid"]
         self.arvrunner.processes[self.uuid] = self
diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index f65a82b..d3bdf8f 100644
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -126,12 +126,12 @@ def stubs(func):
                 "cwl-runner": {
                     'runtime_constraints': {'docker_image': 'arvados/jobs'},
                     'script_parameters': {
-                        'y': {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'},
-                        'x': {'basename': 'blorp.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999994+99/blorp.txt'},
-                        'z': {'basename': 'anonymous', 'class': 'Directory',
+                        'y': {"value": {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'}},
+                        'x': {"value": {'basename': 'blorp.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999994+99/blorp.txt'}},
+                        'z': {"value": {'basename': 'anonymous', 'class': 'Directory',
                               'listing': [
                                   {'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt'}
-                              ]},
+                              ]}},
                         'cwl:tool': '99999999999999999999999999999991+99/wf/submit_wf.cwl'
                     },
                     'repository': 'arvados',

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