# SPDX-License-Identifier: Apache-2.0
from cwltool.command_line_tool import CommandLineTool
+from cwltool.builder import Builder
from .arvjob import ArvadosJob
from .arvcontainer import ArvadosContainer
from .pathmapper import ArvPathMapper
from schema_salad.sourceline import SourceLine
from cwltool.errors import WorkflowException
+def validate_cluster_target(arvrunner, runtimeContext):
+ if (runtimeContext.submit_runner_cluster and
+ 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(arvrunner.api._rootDesc["remoteHosts"].keys())))
def set_cluster_target(tool, arvrunner, builder, runtimeContext):
cluster_target_req = None
for field in ("hints", "requirements"):
runtimeContext = runtimeContext.copy()
runtimeContext.submit_runner_cluster = builder.do_eval(cluster_target_req.get("cluster_id")) or runtimeContext.submit_runner_cluster
runtimeContext.project_uuid = builder.do_eval(cluster_target_req.get("project_uuid")) or runtimeContext.project_uuid
- if (runtimeContext.submit_runner_cluster and
- 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(arvrunner.api._rootDesc["remoteHosts"].keys())))
+ validate_cluster_target(arvrunner, runtimeContext)
+
return runtimeContext
+def make_builder(joborder, hints, requirements, runtimeContext):
+ return Builder(
+ job=joborder,
+ files=[], # type: List[Dict[Text, Text]]
+ bindings=[], # type: List[Dict[Text, Any]]
+ schemaDefs={}, # type: Dict[Text, Dict[Text, Any]]
+ names=None, # type: Names
+ requirements=requirements, # type: List[Dict[Text, Any]]
+ hints=hints, # type: List[Dict[Text, Any]]
+ resources={}, # type: Dict[str, int]
+ mutation_manager=None, # type: Optional[MutationManager]
+ formatgraph=None, # type: Optional[Graph]
+ make_fs_access=None, # type: Type[StdFsAccess]
+ fs_access=None, # type: StdFsAccess
+ job_script_provider=runtimeContext.job_script_provider, # type: Optional[Any]
+ timeout=runtimeContext.eval_timeout, # type: float
+ debug=runtimeContext.debug, # type: bool
+ js_console=runtimeContext.js_console, # type: bool
+ force_docker_pull=runtimeContext.force_docker_pull, # type: bool
+ loadListing="", # type: Text
+ outdir="", # type: Text
+ tmpdir="", # type: Text
+ stagedir="", # type: Text
+ )
+
class ArvadosCommandTool(CommandLineTool):
"""Wrap cwltool CommandLineTool to override selected methods."""
"$(task.keep)/%s/%s")
def job(self, joborder, output_callback, runtimeContext):
- builder = self._init_job(joborder, runtimeContext)
+ builder = make_builder(joborder, self.hints, self.requirements, runtimeContext)
runtimeContext = set_cluster_target(self.tool, self.arvrunner, builder, runtimeContext)
if runtimeContext.work_api == "containers":