-import arvados_cwl
+
import logging
import mock
import unittest
import os
+import functools
+import json
+
+import arvados_cwl
import cwltool.process
+from schema_salad.ref_resolver import Loader
if not os.getenv('ARVADOS_DEBUG'):
logging.getLogger('arvados.cwl-runner').setLevel(logging.WARN)
tool = {
"inputs": [],
"outputs": [],
- "baseCommand": "ls"
+ "baseCommand": "ls",
+ "arguments": [{"valueFrom": "$(runtime.outdir)"}]
}
- arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names, basedir="")
+ make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
+ arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names,
+ basedir="", make_fs_access=make_fs_access, loader=Loader({}))
arvtool.formatgraph = None
- for j in arvtool.job({}, mock.MagicMock(), basedir=""):
+ for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
j.run()
runner.api.jobs().create.assert_called_with(
body={
'runtime_constraints': {},
'script_parameters': {
'tasks': [{
- 'task.env': {'TMPDIR': '$(task.tmpdir)'},
- 'command': ['ls']
+ 'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
+ 'command': ['ls', '$(task.outdir)']
}],
},
'script_version': 'master',
}],
"baseCommand": "ls"
}
- arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names)
+ make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
+ arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names,
+ make_fs_access=make_fs_access, loader=Loader({}))
arvtool.formatgraph = None
- for j in arvtool.job({}, mock.MagicMock(), basedir=""):
+ for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
j.run()
runner.api.jobs().create.assert_called_with(
body={
'runtime_constraints': {},
'script_parameters': {
'tasks': [{
- 'task.env': {'TMPDIR': '$(task.tmpdir)'},
+ 'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
'command': ['ls']
}]
},
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)