[ARVADOS] updated: 22773dcba5c8f59a01a08c1734dd5249517808c9
Git user
git at public.curoverse.com
Fri Sep 16 09:55:07 EDT 2016
Summary of changes:
sdk/cwl/arvados_cwl/arvjob.py | 3 +-
sdk/cwl/arvados_cwl/arvworkflow.py | 2 +-
sdk/cwl/tests/scatter2.cwl | 60 ++++++++++++++++++++++++++++++++++++++
sdk/cwl/tests/test_job.py | 56 +++++++++++++++++++++++++++++++++--
4 files changed, 116 insertions(+), 5 deletions(-)
create mode 100644 sdk/cwl/tests/scatter2.cwl
via 22773dcba5c8f59a01a08c1734dd5249517808c9 (commit)
from 64b05a6b4e2234a3a71d6978f0e1cf9d5f1b8c6e (commit)
Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.
commit 22773dcba5c8f59a01a08c1734dd5249517808c9
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Fri Sep 16 09:54:45 2016 -0400
10081: Add test for recursively calling cwltool when arv:RunInSingleContainer
is provided.
diff --git a/sdk/cwl/arvados_cwl/arvjob.py b/sdk/cwl/arvados_cwl/arvjob.py
index 7cde273..78bca6e 100644
--- a/sdk/cwl/arvados_cwl/arvjob.py
+++ b/sdk/cwl/arvados_cwl/arvjob.py
@@ -40,7 +40,6 @@ class ArvadosJob(object):
if self.generatefiles["listing"]:
vwd = arvados.collection.Collection()
script_parameters["task.vwd"] = {}
- logger.debug("generatefiles is %s", json.dumps(self.generatefiles, indent=4))
generatemapper = InitialWorkDirPathMapper([self.generatefiles], "", "",
separateDirs=False)
for f, p in generatemapper.items():
@@ -187,9 +186,11 @@ class ArvadosJob(object):
except WorkflowException as e:
logger.error("Error while collecting job outputs:\n%s", e, exc_info=(e if self.arvrunner.debug else False))
processStatus = "permanentFail"
+ outputs = None
except Exception as e:
logger.exception("Got unknown exception while collecting job outputs:")
processStatus = "permanentFail"
+ outputs = None
self.output_callback(outputs, processStatus)
finally:
diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index c20bffa..eed4711 100644
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -80,7 +80,7 @@ class ArvadosWorkflow(Workflow):
}]
}],
"hints": workflowobj["hints"],
- "arguments": ["workflow.json", "cwl.input.json"]
+ "arguments": ["--no-container", "--move-outputs", "workflow.json", "cwl.input.json"]
}
kwargs["loader"] = self.doc_loader
kwargs["avsc_names"] = self.doc_schema
diff --git a/sdk/cwl/tests/scatter2.cwl b/sdk/cwl/tests/scatter2.cwl
new file mode 100644
index 0000000..2952983
--- /dev/null
+++ b/sdk/cwl/tests/scatter2.cwl
@@ -0,0 +1,60 @@
+class: Workflow
+cwlVersion: v1.0
+$namespaces:
+ arv: "http://arvados.org/cwl#"
+inputs:
+ sleeptime:
+ type: int[]
+ default: [44, 29, 14]
+outputs: []
+requirements:
+ SubworkflowFeatureRequirement: {}
+ ScatterFeatureRequirement: {}
+ InlineJavascriptRequirement: {}
+ StepInputExpressionRequirement: {}
+steps:
+ scatterstep:
+ in:
+ sleeptime: sleeptime
+ out: []
+ scatter: sleeptime
+ hints:
+ - class: arv:RunInSingleContainer
+ run:
+ class: Workflow
+ id: mysub
+ inputs:
+ sleeptime: int
+ outputs: []
+ steps:
+ sleep1:
+ in:
+ sleeptime: sleeptime
+ out: [out]
+ run:
+ class: CommandLineTool
+ inputs:
+ sleeptime:
+ type: int
+ inputBinding: {position: 1}
+ outputs:
+ out:
+ type: string
+ outputBinding:
+ outputEval: "out"
+ baseCommand: sleep
+ sleep2:
+ in:
+ sleeptime:
+ source: sleeptime
+ valueFrom: $(self+1)
+ dep: sleep1/out
+ out: []
+ run:
+ class: CommandLineTool
+ inputs:
+ sleeptime:
+ type: int
+ inputBinding: {position: 1}
+ outputs: []
+ baseCommand: sleep
diff --git a/sdk/cwl/tests/test_job.py b/sdk/cwl/tests/test_job.py
index 6189a2d..324e2c3 100644
--- a/sdk/cwl/tests/test_job.py
+++ b/sdk/cwl/tests/test_job.py
@@ -1,12 +1,13 @@
-import arvados_cwl
+
import logging
import mock
import unittest
import os
import functools
-import cwltool.process
-from schema_salad.ref_resolver import Loader
+import json
+import arvados_cwl
+import cwltool.process
from schema_salad.ref_resolver import Loader
if not os.getenv('ARVADOS_DEBUG'):
@@ -193,3 +194,52 @@ class TestJob(unittest.TestCase):
mock.call().execute(num_retries=0)])
self.assertFalse(api.collections().create.called)
+
+
+class TestWorkflow(unittest.TestCase):
+ # The test passes no builder.resources
+ # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
+ def test_run(self):
+ runner = arvados_cwl.ArvCwlRunner(mock.MagicMock())
+ runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
+ runner.ignore_docker_for_reuse = False
+ document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
+
+ tool, metadata = document_loader.resolve_ref("tests/wf/scatter2.cwl")
+ metadata["cwlVersion"] = tool["cwlVersion"]
+
+ make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
+ arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, work_api="jobs", avsc_names=avsc_names,
+ basedir="", make_fs_access=make_fs_access, loader=document_loader,
+ makeTool=runner.arv_make_tool, metadata=metadata)
+ arvtool.formatgraph = None
+ for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
+ j.run()
+ runner.api.jobs().create.assert_called_with(
+ body={
+ 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
+ 'repository': 'arvados',
+ 'script_version': 'master',
+ 'script': 'crunchrunner',
+ 'script_parameters': {
+ 'tasks': [{'task.env': {
+ 'HOME': '$(task.outdir)',
+ 'TMPDIR': '$(task.tmpdir)'},
+ 'task.vwd': {
+ 'workflow.json': '$(task.keep)/f101400a398097d4398cdb3eb5d1a7ca+118/workflow.json',
+ 'cwl.input.json': '$(task.keep)/f101400a398097d4398cdb3eb5d1a7ca+118/cwl.input.json'
+ },
+ 'command': [u'cwltool', u'--no-container', u'--move-outputs', u'workflow.json', u'cwl.input.json'],
+ 'task.stdout': 'cwl.output.json'}]},
+ 'runtime_constraints': {
+ 'min_scratch_mb_per_node': 2048,
+ 'min_cores_per_node': 1,
+ 'docker_image': 'arvados/jobs',
+ 'min_ram_mb_per_node': 1024
+ },
+ 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'},
+ filters=[['repository', '=', 'arvados'],
+ ['script', '=', 'crunchrunner'],
+ ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
+ ['docker_image_locator', 'in docker', 'arvados/jobs']],
+ find_or_create=True)
-----------------------------------------------------------------------
hooks/post-receive
--
More information about the arvados-commits
mailing list