import arvados_cwl
import cwltool.process
from schema_salad.ref_resolver import Loader
+from schema_salad.sourceline import cmap
from .mock_discovery import get_rootDesc
from .matcher import JsonDiffMatcher
list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"}
- tool = {
+ tool = cmap({
"inputs": [],
"outputs": [],
"baseCommand": "ls",
"arguments": [{"valueFrom": "$(runtime.outdir)"}]
- }
+ })
make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names,
basedir="", make_fs_access=make_fs_access, loader=Loader({}))
'repository': 'arvados',
'script': 'crunchrunner',
'runtime_constraints': {
- 'docker_image': 'arvados/jobs:'+arvados_cwl.__version__,
+ 'docker_image': 'arvados/jobs',
'min_cores_per_node': 1,
'min_ram_mb_per_node': 1024,
'min_scratch_mb_per_node': 2048 # tmpdirSize + outdirSize
filters=[['repository', '=', 'arvados'],
['script', '=', 'crunchrunner'],
['script_version', 'in git', 'a3f2cb186e437bfce0031b024b2157b73ed2717d'],
- ['docker_image_locator', 'in docker', 'arvados/jobs:'+arvados_cwl.__version__]]
+ ['docker_image_locator', 'in docker', 'arvados/jobs']]
)
# The test passes some fields in builder.resources
'repository': 'arvados',
'script': 'crunchrunner',
'runtime_constraints': {
- 'docker_image': 'arvados/jobs:'+arvados_cwl.__version__,
+ 'docker_image': 'arvados/jobs',
'min_cores_per_node': 3,
'min_ram_mb_per_node': 3000,
'min_scratch_mb_per_node': 5024, # tmpdirSize + outdirSize
filters=[['repository', '=', 'arvados'],
['script', '=', 'crunchrunner'],
['script_version', 'in git', 'a3f2cb186e437bfce0031b024b2157b73ed2717d'],
- ['docker_image_locator', 'in docker', 'arvados/jobs:'+arvados_cwl.__version__]])
+ ['docker_image_locator', 'in docker', 'arvados/jobs']])
@mock.patch("arvados.collection.CollectionReader")
def test_done(self, reader):
'runtime_constraints': {
'min_scratch_mb_per_node': 2048,
'min_cores_per_node': 1,
- 'docker_image': 'arvados/jobs:'+arvados_cwl.__version__,
+ 'docker_image': 'arvados/jobs',
'min_ram_mb_per_node': 1024
},
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'}),
filters=[['repository', '=', 'arvados'],
['script', '=', 'crunchrunner'],
['script_version', 'in git', 'a3f2cb186e437bfce0031b024b2157b73ed2717d'],
- ['docker_image_locator', 'in docker', 'arvados/jobs:'+arvados_cwl.__version__]],
+ ['docker_image_locator', 'in docker', 'arvados/jobs']],
find_or_create=True)
mockcollection().open().__enter__().write.assert_has_calls([mock.call(subwf)])
- mockcollection().open().__enter__().write.assert_has_calls([mock.call('{sleeptime: 5}')])
+ mockcollection().open().__enter__().write.assert_has_calls([mock.call(
+'''{
+ "sleeptime": 5
+}''')])
def test_default_work_api(self):
arvados_cwl.add_arv_hints()