[ARVADOS] created: 2.1.0-1044-ga1ee03455
Git user
git at public.arvados.org
Thu Jul 8 19:23:42 UTC 2021
at a1ee0345562ef5d36505828777a12cf2c2d2d415 (commit)
commit a1ee0345562ef5d36505828777a12cf2c2d2d415
Author: Peter Amstutz <peter.amstutz at curii.com>
Date: Thu Jul 8 15:20:51 2021 -0400
17879: Add test that acr doesn't fail on sbg fields
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>
diff --git a/sdk/cwl/tests/17879-ignore-sbg-fields-job.yml b/sdk/cwl/tests/17879-ignore-sbg-fields-job.yml
new file mode 100644
index 000000000..26e9d123a
--- /dev/null
+++ b/sdk/cwl/tests/17879-ignore-sbg-fields-job.yml
@@ -0,0 +1,5 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+sampleName: woble
diff --git a/sdk/cwl/tests/17879-ignore-sbg-fields.cwl b/sdk/cwl/tests/17879-ignore-sbg-fields.cwl
new file mode 100644
index 000000000..131fd0fd5
--- /dev/null
+++ b/sdk/cwl/tests/17879-ignore-sbg-fields.cwl
@@ -0,0 +1,37 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+$namespaces:
+ sbg: https://www.sevenbridges.com/
+class: "Workflow"
+cwlVersion: v1.1
+label: "check that sbg x/y fields are correctly ignored"
+inputs:
+ - id: sampleName
+ type: string
+ label: Sample name
+ 'sbg:x': -22
+ 'sbg:y': 33.4296875
+outputs:
+ - id: outstr
+ type: string
+ outputSource: step1/outstr
+steps:
+ step1:
+ in:
+ sampleName: sampleName
+ out: [outstr]
+ run:
+ class: CommandLineTool
+ inputs:
+ sampleName: string
+ stdout: out.txt
+ outputs:
+ outstr:
+ type: string
+ outputBinding:
+ glob: out.txt
+ loadContents: true
+ outputEval: $(self[0].contents)
+ arguments: [echo, "-n", "foo", $(inputs.sampleName), "bar"]
diff --git a/sdk/cwl/tests/arvados-tests.yml b/sdk/cwl/tests/arvados-tests.yml
index 717636cd3..ae22d65f4 100644
--- a/sdk/cwl/tests/arvados-tests.yml
+++ b/sdk/cwl/tests/arvados-tests.yml
@@ -433,3 +433,9 @@
"val": "keep:f225e6259bdd63bc7240599648dde9f1+97/hg19.fa"
tool: 17858-pack-visit-crash.cwl
doc: "Test issue 17858 - keep ref default inputs on ExpressionTool"
+
+- job: 17879-ignore-sbg-fields-job.yml
+ output:
+ "outstr": "foo woble bar"
+ tool: 17879-ignore-sbg-fields.cwl
+ doc: "Test issue 17879 - ignores sbg fields"
commit 8cb460d8c4693ba4031ded381b80e730939f000e
Author: Peter Amstutz <peter.amstutz at curii.com>
Date: Thu Jul 8 14:36:00 2021 -0400
17879: Default --thread-count=0, upgrade schema-salad
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>
diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 4bfe27278..04db611fb 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -201,7 +201,7 @@ def arg_parser(): # type: () -> argparse.ArgumentParser
help=argparse.SUPPRESS)
parser.add_argument("--thread-count", type=int,
- default=1, help="Number of threads to use for job submit and output collection.")
+ default=0, help="Number of threads to use for job submit and output collection.")
parser.add_argument("--http-timeout", type=int,
default=5*60, dest="http_timeout", help="API request timeout in seconds. Default is 300 seconds (5 minutes).")
diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index eb3d77892..1a701f258 100644
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -40,7 +40,7 @@ setup(name='arvados-cwl-runner',
# build.
install_requires=[
'cwltool==3.0.20210319143721',
- 'schema-salad==7.1.20210316164414',
+ 'schema-salad==7.1.20210611090601',
'arvados-python-client{}'.format(pysdk_dep),
'setuptools',
'ciso8601 >= 2.0.0'
diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index c448f218b..12daf6b67 100644
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -303,7 +303,7 @@ def stubs(func):
'state': 'Committed',
'command': ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate', '--disable-color',
- '--eval-timeout=20', '--thread-count=4',
+ '--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
'name': 'submit_wf.cwl',
@@ -414,7 +414,7 @@ class TestSubmit(unittest.TestCase):
expect_container["command"] = [
'arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate', '--disable-color',
- '--eval-timeout=20', '--thread-count=4',
+ '--eval-timeout=20', '--thread-count=0',
'--disable-reuse', "--collection-cache-size=256",
'--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
@@ -438,7 +438,7 @@ class TestSubmit(unittest.TestCase):
expect_container["command"] = [
'arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate', '--disable-color',
- '--eval-timeout=20', '--thread-count=4',
+ '--eval-timeout=20', '--thread-count=0',
'--disable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
expect_container["use_existing"] = False
@@ -470,7 +470,7 @@ class TestSubmit(unittest.TestCase):
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate', '--disable-color',
- '--eval-timeout=20', '--thread-count=4',
+ '--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=256",
'--debug', '--on-error=stop',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
@@ -493,7 +493,7 @@ class TestSubmit(unittest.TestCase):
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate', '--disable-color',
- '--eval-timeout=20', '--thread-count=4',
+ '--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=256",
"--output-name="+output_name, '--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
@@ -515,7 +515,7 @@ class TestSubmit(unittest.TestCase):
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate', '--disable-color',
- '--eval-timeout=20', '--thread-count=4',
+ '--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=256", "--debug",
"--storage-classes=foo", '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
@@ -578,7 +578,7 @@ class TestSubmit(unittest.TestCase):
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate', '--disable-color',
- '--eval-timeout=20', '--thread-count=4',
+ '--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=256", '--debug',
'--on-error=continue',
"--intermediate-output-ttl=3600",
@@ -601,7 +601,7 @@ class TestSubmit(unittest.TestCase):
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate', '--disable-color',
- '--eval-timeout=20', '--thread-count=4',
+ '--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=256",
'--debug', '--on-error=continue',
"--trash-intermediate",
@@ -625,7 +625,7 @@ class TestSubmit(unittest.TestCase):
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate', '--disable-color',
- '--eval-timeout=20', '--thread-count=4',
+ '--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=256",
"--output-tags="+output_tags, '--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
@@ -703,7 +703,7 @@ class TestSubmit(unittest.TestCase):
'container_image': '999999999999999999999999999999d3+99',
'command': ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate', '--disable-color',
- '--eval-timeout=20', '--thread-count=4',
+ '--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
'/var/lib/cwl/workflow/expect_arvworkflow.cwl#main', '/var/lib/cwl/cwl.input.json'],
'cwd': '/var/spool/cwl',
@@ -798,7 +798,7 @@ class TestSubmit(unittest.TestCase):
'container_image': "999999999999999999999999999999d3+99",
'command': ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate', '--disable-color',
- '--eval-timeout=20', '--thread-count=4',
+ '--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
'cwd': '/var/spool/cwl',
@@ -862,7 +862,7 @@ class TestSubmit(unittest.TestCase):
expect_container["owner_uuid"] = project_uuid
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate', '--disable-color',
- "--eval-timeout=20", "--thread-count=4",
+ "--eval-timeout=20", "--thread-count=0",
'--enable-reuse', "--collection-cache-size=256", '--debug',
'--on-error=continue',
'--project-uuid='+project_uuid,
@@ -884,7 +884,7 @@ class TestSubmit(unittest.TestCase):
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate', '--disable-color',
- '--eval-timeout=60.0', '--thread-count=4',
+ '--eval-timeout=60.0', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=256",
'--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
@@ -905,7 +905,7 @@ class TestSubmit(unittest.TestCase):
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate', '--disable-color',
- '--eval-timeout=20', '--thread-count=4',
+ '--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=500",
'--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
@@ -997,7 +997,7 @@ class TestSubmit(unittest.TestCase):
}
expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate', '--disable-color',
- '--eval-timeout=20', '--thread-count=4',
+ '--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=512", '--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
@@ -1063,7 +1063,7 @@ class TestSubmit(unittest.TestCase):
"--disable-validate",
"--disable-color",
"--eval-timeout=20",
- '--thread-count=4',
+ '--thread-count=0',
"--enable-reuse",
"--collection-cache-size=256",
'--debug',
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