from cwltool.process import shortname
from cwltool.workflow import Workflow, WorkflowException
from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class
+from cwltool.builder import Builder
import ruamel.yaml as yaml
dedup[r["class"]] = r
return [dedup[r] for r in sorted(dedup.keys())]
+def get_max_res_req(res_reqs):
+ """Take the max of a list of ResourceRequirement."""
+
+ total_res_req = {}
+ exception_msgs = []
+ for a in ("coresMin", "coresMax", "ramMin", "ramMax", "tmpdirMin", "tmpdirMax", "outdirMin", "outdirMax"):
+ total_res_req[a] = []
+ for res_req in res_reqs:
+ if a in res_req:
+ if isinstance(res_req[a], int): # integer check
+ total_res_req[a].append(res_req[a])
+ else:
+ msg = SourceLine(res_req).makeError(
+ "Non-top-level ResourceRequirement in single container cannot have expressions")
+ exception_msgs.append(msg)
+ if exception_msgs:
+ raise WorkflowException("\n".join(exception_msgs))
+ else:
+ max_res_req = {}
+ for a in total_res_req:
+ if total_res_req[a]:
+ max_res_req[a] = max(total_res_req[a])
+ if max_res_req:
+ max_res_req["class"] = "ResourceRequirement"
+ return cmap(max_res_req)
+
class ArvadosWorkflow(Workflow):
"""Wrap cwltool Workflow to override selected methods."""
packed = pack(document_loader, workflowobj, uri, self.metadata)
+ builder = Builder()
+ builder.job = joborder
+ builder.requirements = self.requirements
+ builder.hints = self.hints
+ builder.resources = {}
+
+ res_reqs = {"requirements": [], "hints": []}
+ for t in ("requirements", "hints"):
+ for item in packed["$graph"]:
+ if t in item:
+ if item["id"] == "#main": # evaluate potential expressions in the top-level requirements/hints
+ for req in item[t]:
+ if req["class"] == "ResourceRequirement":
+ eval_req = {"class": "ResourceRequirement"}
+ for a in ("coresMin", "coresMax", "ramMin", "ramMax", "tmpdirMin", "tmpdirMax", "outdirMin", "outdirMax"):
+ if a in req:
+ eval_req[a] = builder.do_eval(req[a])
+ res_reqs[t].append(eval_req)
+ else:
+ for req in item[t]:
+ if req["class"] == "ResourceRequirement":
+ res_reqs[t].append(req)
+ max_res_req = {"requirements": get_max_res_req(res_reqs["requirements"]),
+ "hints": get_max_res_req(res_reqs["hints"])}
+
+ new_spec = {"requirements": self.requirements, "hints": self.hints}
+ for t in ("requirements", "hints"):
+ for req in new_spec[t]:
+ if req["class"] == "ResourceRequirement":
+ new_spec[t].remove(req)
+ if max_res_req[t]:
+ new_spec[t].append(max_res_req[t])
+
upload_dependencies(self.arvrunner,
kwargs.get("name", ""),
document_loader,
"inputs": self.tool["inputs"],
"outputs": self.tool["outputs"],
"stdout": "cwl.output.json",
- "requirements": self.requirements+[
+ "requirements": new_spec["requirements"]+[
{
"class": "InitialWorkDirRequirement",
"listing": [{
"entry": json.dumps(joborder_keepmount, indent=2, sort_keys=True, separators=(',',': ')).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
}]
}],
- "hints": self.hints,
+ "hints": new_spec["hints"],
"arguments": ["--no-container", "--move-outputs", "--preserve-entire-environment", "workflow.cwl#main", "cwl.input.yml"],
"id": "#"
})
"sleeptime": 5
}''')])
+ # The test passes no builder.resources
+ # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
+ @mock.patch("arvados.collection.CollectionReader")
+ @mock.patch("arvados.collection.Collection")
+ @mock.patch('arvados.commands.keepdocker.list_images_in_arv')
+ def test_max_resource_singlecontainer(self, list_images_in_arv, mockcollection, mockcollectionreader):
+ arvados_cwl.add_arv_hints()
+
+ api = mock.MagicMock()
+ api._rootDesc = get_rootDesc()
+
+ runner = arvados_cwl.ArvCwlRunner(api)
+ self.assertEqual(runner.work_api, 'jobs')
+
+ list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
+ runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"}
+ runner.api.collections().list().execute.return_vaulue = {"items": [{"portable_data_hash": "99999999999999999999999999999993+99"}]}
+
+ runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
+ runner.ignore_docker_for_reuse = False
+ runner.num_retries = 0
+ document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
+
+ make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
+ collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
+ document_loader.fetcher_constructor = functools.partial(arvados_cwl.CollectionFetcher, api_client=api, fs_access=make_fs_access(""))
+ document_loader.fetcher = document_loader.fetcher_constructor(document_loader.cache, document_loader.session)
+ document_loader.fetch_text = document_loader.fetcher.fetch_text
+ document_loader.check_exists = document_loader.fetcher.check_exists
+
+ tool, metadata = document_loader.resolve_ref("tests/wf/echo-wf.cwl")
+ metadata["cwlVersion"] = tool["cwlVersion"]
+
+ mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118"
+
+ 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
+ it = arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access)
+ it.next().run()
+ it.next().run()
+
+ with open("tests/wf/echo-subwf.cwl") as f:
+ subwf = StripYAMLComments(f.read())
+
+ runner.api.jobs().create.assert_called_with(
+ body=JsonDiffMatcher({
+ 'minimum_script_version': 'a3f2cb186e437bfce0031b024b2157b73ed2717d',
+ 'repository': 'arvados',
+ 'script_version': 'master',
+ 'script': 'crunchrunner',
+ 'script_parameters': {
+ 'tasks': [{'task.env': {
+ 'HOME': '$(task.outdir)',
+ 'TMPDIR': '$(task.tmpdir)'},
+ 'task.vwd': {
+ 'workflow.cwl': '$(task.keep)/99999999999999999999999999999999+118/workflow.cwl',
+ 'cwl.input.yml': '$(task.keep)/99999999999999999999999999999999+118/cwl.input.yml'
+ },
+ 'command': [u'cwltool', u'--no-container', u'--move-outputs', u'--preserve-entire-environment', u'workflow.cwl#main', u'cwl.input.yml'],
+ 'task.stdout': 'cwl.output.json'}]},
+ 'runtime_constraints': {
+ 'min_scratch_mb_per_node': 2048,
+ 'min_cores_per_node': 3,
+ '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']],
+ find_or_create=True)
+
def test_default_work_api(self):
arvados_cwl.add_arv_hints()
projects / arvados.git / commitdiff