from .arvcontainer import ArvadosContainer
from .pathmapper import ArvPathMapper
from .runner import make_builder
+from ._version import __version__
from functools import partial
from schema_salad.sourceline import SourceLine
from cwltool.errors import WorkflowException
runtimeContext.submit_runner_cluster not in arvrunner.api._rootDesc["remoteHosts"] and
runtimeContext.submit_runner_cluster != arvrunner.api._rootDesc["uuidPrefix"]):
raise WorkflowException("Unknown or invalid cluster id '%s' known remote clusters are %s" % (runtimeContext.submit_runner_cluster,
- ", ".join(list(arvrunner.api._rootDesc["remoteHosts"].keys()))))
+ ", ".join(list(arvrunner.api._rootDesc["remoteHosts"].keys()))))
+ if runtimeContext.project_uuid:
+ cluster_target = runtimeContext.submit_runner_cluster or arvrunner.api._rootDesc["uuidPrefix"]
+ if not runtimeContext.project_uuid.startswith(cluster_target):
+ raise WorkflowException("Project uuid '%s' should start with id of target cluster '%s'" % (runtimeContext.project_uuid, cluster_target))
+
+ try:
+ if runtimeContext.project_uuid[5:12] == '-tpzed-':
+ arvrunner.api.users().get(uuid=runtimeContext.project_uuid).execute()
+ else:
+ proj = arvrunner.api.groups().get(uuid=runtimeContext.project_uuid).execute()
+ if proj["group_class"] != "project":
+ raise Exception("not a project, group_class is '%s'" % (proj["group_class"]))
+ except Exception as e:
+ raise WorkflowException("Invalid project uuid '%s': %s" % (runtimeContext.project_uuid, e))
+
def set_cluster_target(tool, arvrunner, builder, runtimeContext):
cluster_target_req = None
for field in ("hints", "requirements"):
def __init__(self, arvrunner, toolpath_object, loadingContext):
super(ArvadosCommandTool, self).__init__(toolpath_object, loadingContext)
+
+ (docker_req, docker_is_req) = self.get_requirement("DockerRequirement")
+ if not docker_req:
+ self.hints.append({"class": "DockerRequirement",
+ "dockerPull": "arvados/jobs:"+__version__})
+
self.arvrunner = arvrunner
def make_job_runner(self, runtimeContext):
"/keep/%s/%s")
def job(self, joborder, output_callback, runtimeContext):
- builder = make_builder(joborder, self.hints, self.requirements, runtimeContext)
+ builder = make_builder(joborder, self.hints, self.requirements, runtimeContext, self.metadata)
runtimeContext = set_cluster_target(self.tool, self.arvrunner, builder, runtimeContext)
if runtimeContext.work_api == "containers":