import unittest
import os
import functools
+import threading
import cwltool.process
import cwltool.secrets
import cwltool.load_tool
"basedir": "",
"make_fs_access": make_fs_access,
"construct_tool_object": runner.arv_make_tool,
- "fetcher_constructor": functools.partial(arvados_cwl.CollectionFetcher, api_client=runner.api, fs_access=fs_access)
+ "fetcher_constructor": functools.partial(arvados_cwl.CollectionFetcher, api_client=runner.api, fs_access=fs_access),
+ "loader": Loader({}),
+ "metadata": cmap({"cwlVersion": INTERNAL_VERSION, "http://commonwl.org/cwltool#original_cwlVersion": "v1.0"})
})
runtimeContext = arvados_cwl.context.ArvRuntimeContext(
{"work_api": "containers",
"name": "test_run_"+str(enable_reuse),
"make_fs_access": make_fs_access,
"tmpdir": "/tmp",
+ "outdir": "/tmp",
"enable_reuse": enable_reuse,
"priority": 500,
- "project_uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
+ "project_uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
+ "workflow_eval_lock": threading.Condition(threading.RLock())
})
if isinstance(runner, mock.MagicMock):
"baseCommand": "echo",
"arguments": [],
"id": "",
- "cwlVersion": "v1.2",
- "class": "CommandLineTool"
+ "cwlVersion": "v1.0",
+ "class": "org.w3id.cwl.cwl.CommandLineTool"
})
loadingContext, runtimeContext = self.helper(runner, True)
- arvtool = cwltool.load_tool.load_tool(tool, loadingContext)
+ arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
arvtool.formatgraph = None
container_request = {
'name': 'test_run_True',
'runtime_constraints': {
'vcpus': 1,
- 'ram': 268435456
+ 'ram': 1073741824,
},
'use_existing': True,
'priority': 500,