[ARVADOS] updated: 0479c53c53a4a458b2759b067ae2cb928cbbf051
Git user
git at public.curoverse.com
Wed Dec 7 15:51:09 EST 2016
Summary of changes:
sdk/cwl/arvados_cwl/arvjob.py | 6 ------
sdk/cwl/arvados_cwl/runner.py | 6 ++++++
sdk/cwl/tests/test_submit.py | 43 ++++++++++++++++++++++++++++---------------
3 files changed, 34 insertions(+), 21 deletions(-)
via 0479c53c53a4a458b2759b067ae2cb928cbbf051 (commit)
from ed9be4cc10c12051bdb1a65210726ab1d688108c (commit)
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commit 0479c53c53a4a458b2759b067ae2cb928cbbf051
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Wed Dec 7 15:51:06 2016 -0500
10576: Fix tests for cwl.input.json part of container request record and not
placed in keep.
diff --git a/sdk/cwl/arvados_cwl/arvjob.py b/sdk/cwl/arvados_cwl/arvjob.py
index 93f84f8..3048bab 100644
--- a/sdk/cwl/arvados_cwl/arvjob.py
+++ b/sdk/cwl/arvados_cwl/arvjob.py
@@ -235,12 +235,6 @@ class RunnerJob(Runner):
workflowmapper = super(RunnerJob, self).arvados_job_spec(dry_run=dry_run, pull_image=pull_image, **kwargs)
- # Need to filter this out, gets added by cwltool when providing
- # parameters on the command line, and arv-run-pipeline-instance doesn't
- # like it.
- if "job_order" in self.job_order:
- del self.job_order["job_order"]
-
self.job_order["cwl:tool"] = workflowmapper.mapper(self.tool.tool["id"]).target[5:]
if self.output_name:
diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index d6497c4..490695a 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -185,6 +185,12 @@ class Runner(object):
def arvados_job_spec(self, *args, **kwargs):
self.name = os.path.basename(self.tool.tool["id"])
+
+ # Need to filter this out, gets added by cwltool when providing
+ # parameters on the command line.
+ if "job_order" in self.job_order:
+ del self.job_order["job_order"]
+
workflowmapper = upload_instance(self.arvrunner, self.name, self.tool, self.job_order)
adjustDirObjs(self.job_order, trim_listing)
return workflowmapper
diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index d489e69..8381548 100644
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -179,14 +179,21 @@ def stubs(func):
'path': '/var/spool/cwl/cwl.output.json',
'kind': 'file'
},
- '/var/lib/cwl/job/cwl.input.json': {
- 'portable_data_hash': 'd20d7cddd1984f105dd3702c7f125afb+60/cwl.input.json',
- 'kind': 'collection'
+ '/var/lib/cwl/cwl.input.json': {
+ 'kind': 'json',
+ 'content': {
+ 'y': {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'},
+ 'x': {'basename': u'blorp.txt', 'class': 'File', 'location': u'keep:99999999999999999999999999999994+99/blorp.txt'},
+ 'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [
+ {'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt'}
+ ]}
+ },
+ 'kind': 'json'
}
},
'state': 'Committed',
'owner_uuid': None,
- 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json'],
+ 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/cwl.input.json'],
'name': 'submit_wf.cwl',
'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
'output_path': '/var/spool/cwl',
@@ -417,7 +424,7 @@ class TestSubmit(unittest.TestCase):
except:
logging.exception("")
- stubs.expect_container_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--disable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json']
+ stubs.expect_container_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--disable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/cwl.input.json']
expect_container = copy.deepcopy(stubs.expect_container_spec)
stubs.api.container_requests().create.assert_called_with(
@@ -439,7 +446,7 @@ class TestSubmit(unittest.TestCase):
except:
logging.exception("")
- stubs.expect_container_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', "--output-name="+output_name, '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json']
+ stubs.expect_container_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', "--output-name="+output_name, '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/cwl.input.json']
expect_container = copy.deepcopy(stubs.expect_container_spec)
stubs.api.container_requests().create.assert_called_with(
@@ -461,7 +468,7 @@ class TestSubmit(unittest.TestCase):
except:
logging.exception("")
- stubs.expect_container_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', "--output-tags="+output_tags, '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json']
+ stubs.expect_container_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', "--output-tags="+output_tags, '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/cwl.input.json']
expect_container = copy.deepcopy(stubs.expect_container_spec)
stubs.api.container_requests().create.assert_called_with(
@@ -531,15 +538,18 @@ class TestSubmit(unittest.TestCase):
'portable_data_hash': '99999999999999999999999999999994+99',
'kind': 'collection'
},
- '/var/lib/cwl/job/cwl.input.json': {
- 'portable_data_hash': 'e5454f8ca7d5b181e21ecd45841e3373+58/cwl.input.json',
- 'kind': 'collection'}
+ '/var/lib/cwl/cwl.input.json': {
+ 'content': {
+ 'x': 'XxX'
+ },
+ 'kind': 'json'
+ }
}, 'state': 'Committed',
'owner_uuid': None,
'output_path': '/var/spool/cwl',
'name': 'expect_arvworkflow.cwl#main',
'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
- 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--enable-reuse', '/var/lib/cwl/workflow/expect_arvworkflow.cwl#main', '/var/lib/cwl/job/cwl.input.json'],
+ 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--enable-reuse', '/var/lib/cwl/workflow/expect_arvworkflow.cwl#main', '/var/lib/cwl/cwl.input.json'],
'cwd': '/var/spool/cwl',
'runtime_constraints': {
'API': True,
@@ -615,15 +625,18 @@ class TestSubmit(unittest.TestCase):
]
}
},
- '/var/lib/cwl/job/cwl.input.json': {
- 'portable_data_hash': 'e5454f8ca7d5b181e21ecd45841e3373+58/cwl.input.json',
- 'kind': 'collection'}
+ '/var/lib/cwl/cwl.input.json': {
+ 'content': {
+ 'x': 'XxX'
+ },
+ 'kind': 'json'
+ }
}, 'state': 'Committed',
'owner_uuid': None,
'output_path': '/var/spool/cwl',
'name': 'arvwf:962eh-7fd4e-gkbzl62qqtfig37#main',
'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
- 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--enable-reuse', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/job/cwl.input.json'],
+ 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--enable-reuse', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
'cwd': '/var/spool/cwl',
'runtime_constraints': {
'API': True,
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