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